Locus 190

Sequence ID 2R_DroMel_CAF1
Location 1,445,616 – 1,446,046
Length 430
Max. P 0.999980
window427 window428 window429 window430 window431 window432 window433 window434 window435 window436 window437 window438

overview

Window 7

Location 1,445,616 – 1,445,724
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.19
Mean single sequence MFE -37.96
Consensus MFE -35.60
Energy contribution -35.80
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.48
Structure conservation index 0.94
SVM decision value 1.35
SVM RNA-class probability 0.945593
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1445616 108 - 20766785
AUGAAUUGCAGCUGUUGCGUAGACACUGCAGCAGC------------AACAAGCGAGAGGAAUGCUUGGCCCGGAUUUGCAAUUCAUUGGCGUGUAUAUCCUGCCAGUGUGUGAGCCUGC
(((((((((((((((((((.......)))))))))------------..((((((.......)))))).........)))))))))).(((...((((..(.....)..)))).)))... ( -37.80)
>DroSec_CAF1 63677 108 - 1
AUGAAUUGCAGCUGUUGCGUAGACACUGCAGCAGC------------AACAAGCGCGAGGAAUGCUUGGCCCGGAUUUGCAAUUCAUUGGCGUGUAUAUCCUGCCAGUGUGUGAGCCUGC
(((((((((((((((((((.......)))))))))------------..((((((.......)))))).........)))))))))).(((...((((..(.....)..)))).)))... ( -38.10)
>DroSim_CAF1 62297 108 - 1
AUGAAUUGCAGCUGUUGCGUAGACACUGCAGCAGC------------AACAAGCGCGAGGAAUGCUUGGCCCGGAUUUGCAAUUCAUUGGCGUGUAUAUCCUGCCAGUGUGUGAGCCUGC
(((((((((((((((((((.......)))))))))------------..((((((.......)))))).........)))))))))).(((...((((..(.....)..)))).)))... ( -38.10)
>DroEre_CAF1 73176 114 - 1
AUGAAUUGCAGCUGUUGCGUAGACACUGCAGCAGCAAC------UGCAACAAGCGAGGAAAAUGCUUGGCCCGGAUUUGCAAUUCAUUGGCGUGUAUAUCCCGGCAGUGUGUGAGCCUGU
(((((((((((((((((((.......)))))))))..(------((...((((((.......))))))...)))...)))))))))).(((...((((..(.....)..)))).)))... ( -39.50)
>DroYak_CAF1 70311 120 - 1
AUGAAUUGCAGCUGUUGCGUAUACACUGCAGCAGCAACAACAUCAGCAACAAGCGAGAGGAAUACUUGGCCCGGAUUUGCAAUUCAUUGGCGUGUAUAUCCUGCCAGUGUGUGAGCCUGU
.(((.(((..(((((((((.......)))))))))..)))..)))((.....))...(((.(((((((((..((((.((((..(.....)..)))).)))).))))).))))...))).. ( -36.30)
>consensus
AUGAAUUGCAGCUGUUGCGUAGACACUGCAGCAGC____________AACAAGCGAGAGGAAUGCUUGGCCCGGAUUUGCAAUUCAUUGGCGUGUAUAUCCUGCCAGUGUGUGAGCCUGC
(((((((((((((((((((.......)))))))))..............((((((.......)))))).........)))))))))).(((...((((..(.....)..)))).)))... (-35.60 = -35.80 +   0.20) 

alignment

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secondary structure

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Window 8

Location 1,445,656 – 1,445,764
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.84
Mean single sequence MFE -37.80
Consensus MFE -33.10
Energy contribution -32.78
Covariance contribution -0.32
Combinations/Pair 1.07
Mean z-score -2.01
Structure conservation index 0.88
SVM decision value 2.26
SVM RNA-class probability 0.991293
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1445656 108 + 20766785
GCAAAUCCGGGCCAAGCAUUCCUCUCGCUUGUU------------GCUGCUGCAGUGUCUACGCAACAGCUGCAAUUCAUUAUAAAUGUGAUUUUCCCGCGAGCAGCAAAGGGCGUGGAA
.....((((.(((........(((((((..(((------------((.((((..(((....)))..)))).)))))((((.......)))).......))))).)).....))).)))). ( -35.12)
>DroSec_CAF1 63717 108 + 1
GCAAAUCCGGGCCAAGCAUUCCUCGCGCUUGUU------------GCUGCUGCAGUGUCUACGCAACAGCUGCAAUUCAUUAUAAAUGUGAUUUUCCCGCGAGCAGCAAAGGGCGUGGAA
.....((((.(((..((....((((((...(((------------((.((((..(((....)))..)))).)))))((((.......))))......))))))..))....))).)))). ( -37.70)
>DroSim_CAF1 62337 108 + 1
GCAAAUCCGGGCCAAGCAUUCCUCGCGCUUGUU------------GCUGCUGCAGUGUCUACGCAACAGCUGCAAUUCAUUAUAAAUGUGAUUUUCCCGCGAGCAGCAAAGGGCGUGGAA
.....((((.(((..((....((((((...(((------------((.((((..(((....)))..)))).)))))((((.......))))......))))))..))....))).)))). ( -37.70)
>DroEre_CAF1 73216 114 + 1
GCAAAUCCGGGCCAAGCAUUUUCCUCGCUUGUUGCA------GUUGCUGCUGCAGUGUCUACGCAACAGCUGCAAUUCAUUAUAAAUGUGAUUUCCACGCGAGCAGCAAAGGGCGUGGAA
.....((((.(((((((.........))))((((((------(((((.((((..(((....)))..)))).))))))..........(((.....)))....)))))....))).)))). ( -38.60)
>DroYak_CAF1 70351 120 + 1
GCAAAUCCGGGCCAAGUAUUCCUCUCGCUUGUUGCUGAUGUUGUUGCUGCUGCAGUGUAUACGCAACAGCUGCAAUUCAUUAUAAAUGUGAUUUCCCCACGAGCAGCAAAAGGCGUGGAA
.....((((.(((((((.........))))((((((((((..(((((.((((..(((....)))..)))).))))).)))).....((((.......))))))))))....))).)))). ( -39.90)
>consensus
GCAAAUCCGGGCCAAGCAUUCCUCUCGCUUGUU____________GCUGCUGCAGUGUCUACGCAACAGCUGCAAUUCAUUAUAAAUGUGAUUUUCCCGCGAGCAGCAAAGGGCGUGGAA
.....((((.(((((((.........))))...............(((((((((((((.......))).)))).............((((.......))))))))))....))).)))). (-33.10 = -32.78 +  -0.32) 

alignment

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secondary structure

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Window 9

Location 1,445,689 – 1,445,804
Length 115
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.74
Mean single sequence MFE -39.32
Consensus MFE -38.16
Energy contribution -38.00
Covariance contribution -0.16
Combinations/Pair 1.03
Mean z-score -2.76
Structure conservation index 0.97
SVM decision value 5.23
SVM RNA-class probability 0.999980
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1445689 115 + 20766785
-----GCUGCUGCAGUGUCUACGCAACAGCUGCAAUUCAUUAUAAAUGUGAUUUUCCCGCGAGCAGCAAAGGGCGUGGAAAACUUGCUGAAAUUUUCCGCGCUAUUUUCGAGCUCGUUGU
-----((.((((..(((....)))..)))).))...((((.......)))).......((((((.(.(((.(((((((((((.((....)).))))))))))).))).)..))))))... ( -37.70)
>DroSec_CAF1 63750 115 + 1
-----GCUGCUGCAGUGUCUACGCAACAGCUGCAAUUCAUUAUAAAUGUGAUUUUCCCGCGAGCAGCAAAGGGCGUGGAAAACUUGCUGAAAUUUUCCGCGCUAUUUUCGAGCUCGUUGU
-----((.((((..(((....)))..)))).))...((((.......)))).......((((((.(.(((.(((((((((((.((....)).))))))))))).))).)..))))))... ( -37.70)
>DroSim_CAF1 62370 115 + 1
-----GCUGCUGCAGUGUCUACGCAACAGCUGCAAUUCAUUAUAAAUGUGAUUUUCCCGCGAGCAGCAAAGGGCGUGGAAAACUUGCUGAAAUUUUCCGCGCUAUUUUCGAGCUCGUUGU
-----((.((((..(((....)))..)))).))...((((.......)))).......((((((.(.(((.(((((((((((.((....)).))))))))))).))).)..))))))... ( -37.70)
>DroEre_CAF1 73252 118 + 1
--GUUGCUGCUGCAGUGUCUACGCAACAGCUGCAAUUCAUUAUAAAUGUGAUUUCCACGCGAGCAGCAAAGGGCGUGGAAAAGUUGCUAAAAUUUUCCGCGCUAUUUUCGCGCUCGUUGU
--(((((.((((..(((....)))..)))).)))))...........(((.....)))((((((.(((((((((((((((((.((....)).))))))))))).)))).))))))))... ( -42.90)
>DroYak_CAF1 70391 120 + 1
UUGUUGCUGCUGCAGUGUAUACGCAACAGCUGCAAUUCAUUAUAAAUGUGAUUUCCCCACGAGCAGCAAAAGGCGUGGAAAACUUGCUAAAAUUUUCCGCGCUAUUUUCGAGCUCGUUGU
..(((((.((((..(((....)))..)))).)))))((((.......)))).......((((((.(.(((.(((((((((((.((....)).))))))))))).))).)..))))))... ( -40.60)
>consensus
_____GCUGCUGCAGUGUCUACGCAACAGCUGCAAUUCAUUAUAAAUGUGAUUUUCCCGCGAGCAGCAAAGGGCGUGGAAAACUUGCUGAAAUUUUCCGCGCUAUUUUCGAGCUCGUUGU
.....((.((((..(((....)))..)))).))...((((.......)))).......((((((.(.(((.(((((((((((.((....)).))))))))))).))).)..))))))... (-38.16 = -38.00 +  -0.16) 

alignment

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secondary structure

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Window 0

Location 1,445,689 – 1,445,804
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.74
Mean single sequence MFE -36.58
Consensus MFE -34.14
Energy contribution -34.34
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.66
Structure conservation index 0.93
SVM decision value 4.58
SVM RNA-class probability 0.999923
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1445689 115 - 20766785
ACAACGAGCUCGAAAAUAGCGCGGAAAAUUUCAGCAAGUUUUCCACGCCCUUUGCUGCUCGCGGGAAAAUCACAUUUAUAAUGAAUUGCAGCUGUUGCGUAGACACUGCAGCAGC-----
.(..(((((....(((..(((.(((((((((....))))))))).)))..)))...)))))..)..........................(((((((((.......)))))))))----- ( -35.60)
>DroSec_CAF1 63750 115 - 1
ACAACGAGCUCGAAAAUAGCGCGGAAAAUUUCAGCAAGUUUUCCACGCCCUUUGCUGCUCGCGGGAAAAUCACAUUUAUAAUGAAUUGCAGCUGUUGCGUAGACACUGCAGCAGC-----
.(..(((((....(((..(((.(((((((((....))))))))).)))..)))...)))))..)..........................(((((((((.......)))))))))----- ( -35.60)
>DroSim_CAF1 62370 115 - 1
ACAACGAGCUCGAAAAUAGCGCGGAAAAUUUCAGCAAGUUUUCCACGCCCUUUGCUGCUCGCGGGAAAAUCACAUUUAUAAUGAAUUGCAGCUGUUGCGUAGACACUGCAGCAGC-----
.(..(((((....(((..(((.(((((((((....))))))))).)))..)))...)))))..)..........................(((((((((.......)))))))))----- ( -35.60)
>DroEre_CAF1 73252 118 - 1
ACAACGAGCGCGAAAAUAGCGCGGAAAAUUUUAGCAACUUUUCCACGCCCUUUGCUGCUCGCGUGGAAAUCACAUUUAUAAUGAAUUGCAGCUGUUGCGUAGACACUGCAGCAGCAAC--
....((((((((((....(((.((((((..........)))))).)))..))))).))))).(((.....))).................(((((((((.......)))))))))...-- ( -37.30)
>DroYak_CAF1 70391 120 - 1
ACAACGAGCUCGAAAAUAGCGCGGAAAAUUUUAGCAAGUUUUCCACGCCUUUUGCUGCUCGUGGGGAAAUCACAUUUAUAAUGAAUUGCAGCUGUUGCGUAUACACUGCAGCAGCAACAA
.(.((((((.(((((...(((.(((((((((....))))))))).))).)))))..)))))).)(.((.(((.........))).)).).(((((((((.......)))))))))..... ( -38.80)
>consensus
ACAACGAGCUCGAAAAUAGCGCGGAAAAUUUCAGCAAGUUUUCCACGCCCUUUGCUGCUCGCGGGAAAAUCACAUUUAUAAUGAAUUGCAGCUGUUGCGUAGACACUGCAGCAGC_____
....(((((....(((..(((.(((((((((....))))))))).)))..)))...))))).............................(((((((((.......)))))))))..... (-34.14 = -34.34 +   0.20) 

alignment

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secondary structure

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Window 1

Location 1,445,724 – 1,445,835
Length 111
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.72
Mean single sequence MFE -38.22
Consensus MFE -35.48
Energy contribution -35.08
Covariance contribution -0.40
Combinations/Pair 1.05
Mean z-score -2.94
Structure conservation index 0.93
SVM decision value 4.97
SVM RNA-class probability 0.999966
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1445724 111 + 20766785
UAUAAAUGUGAUUUUCCCGCGAGCAGCAAAGGGCGUGGAAAACUUGCUGAAAUUUUCCGCGCUAUUUUCGAGCUCGUUGUCUG---------UGCCAAGCAAUCCGGAGCCACAUUUAAC
..((((((((...((((.((((((.(.(((.(((((((((((.((....)).))))))))))).))).)..))))))......---------(((...)))....)))).)))))))).. ( -36.10)
>DroSec_CAF1 63785 111 + 1
UAUAAAUGUGAUUUUCCCGCGAGCAGCAAAGGGCGUGGAAAACUUGCUGAAAUUUUCCGCGCUAUUUUCGAGCUCGUUGUCUG---------UGCCAAGCAAUCCGGAGCCACAUUUAAC
..((((((((...((((.((((((.(.(((.(((((((((((.((....)).))))))))))).))).)..))))))......---------(((...)))....)))).)))))))).. ( -36.10)
>DroSim_CAF1 62405 111 + 1
UAUAAAUGUGAUUUUCCCGCGAGCAGCAAAGGGCGUGGAAAACUUGCUGAAAUUUUCCGCGCUAUUUUCGAGCUCGUUGUCCG---------UGCCAAGCAAUCCGGAGCCACAUUUAAC
..((((((((........((((((.(.(((.(((((((((((.((....)).))))))))))).))).)..))))))..((((---------(((...)))...))))..)))))))).. ( -37.90)
>DroEre_CAF1 73290 120 + 1
UAUAAAUGUGAUUUCCACGCGAGCAGCAAAGGGCGUGGAAAAGUUGCUAAAAUUUUCCGCGCUAUUUUCGCGCUCGUUGUCUGUGCUGUGUGUGCCAAGCAAUCCGGAGCCACAUUUAAC
..((((((((..((((..((((((.(((((((((((((((((.((....)).))))))))))).)))).))))))))((..((.((.......))))..))....)))).)))))))).. ( -44.10)
>DroYak_CAF1 70431 111 + 1
UAUAAAUGUGAUUUCCCCACGAGCAGCAAAAGGCGUGGAAAACUUGCUAAAAUUUUCCGCGCUAUUUUCGAGCUCGUUGUCUG---------UGCCAAGCAAUCCGGAGCCACAUUUAAC
..((((((((..((((..((((((.(.(((.(((((((((((.((....)).))))))))))).))).)..))))))......---------(((...)))....)))).)))))))).. ( -36.90)
>consensus
UAUAAAUGUGAUUUUCCCGCGAGCAGCAAAGGGCGUGGAAAACUUGCUGAAAUUUUCCGCGCUAUUUUCGAGCUCGUUGUCUG_________UGCCAAGCAAUCCGGAGCCACAUUUAAC
..((((((((..((((..((((((.(.(((.(((((((((((.((....)).))))))))))).))).)..))))))...............(((...)))....)))).)))))))).. (-35.48 = -35.08 +  -0.40) 

alignment

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secondary structure

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dotplot

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Window 2

Location 1,445,724 – 1,445,835
Length 111
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.72
Mean single sequence MFE -35.56
Consensus MFE -31.40
Energy contribution -31.40
Covariance contribution 0.00
Combinations/Pair 1.06
Mean z-score -2.21
Structure conservation index 0.88
SVM decision value 2.99
SVM RNA-class probability 0.998045
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1445724 111 - 20766785
GUUAAAUGUGGCUCCGGAUUGCUUGGCA---------CAGACAACGAGCUCGAAAAUAGCGCGGAAAAUUUCAGCAAGUUUUCCACGCCCUUUGCUGCUCGCGGGAAAAUCACAUUUAUA
..(((((((((.(((.(..(((...)))---------.......(((((....(((..(((.(((((((((....))))))))).)))..)))...)))))).)))...))))))))).. ( -33.90)
>DroSec_CAF1 63785 111 - 1
GUUAAAUGUGGCUCCGGAUUGCUUGGCA---------CAGACAACGAGCUCGAAAAUAGCGCGGAAAAUUUCAGCAAGUUUUCCACGCCCUUUGCUGCUCGCGGGAAAAUCACAUUUAUA
..(((((((((.(((.(..(((...)))---------.......(((((....(((..(((.(((((((((....))))))))).)))..)))...)))))).)))...))))))))).. ( -33.90)
>DroSim_CAF1 62405 111 - 1
GUUAAAUGUGGCUCCGGAUUGCUUGGCA---------CGGACAACGAGCUCGAAAAUAGCGCGGAAAAUUUCAGCAAGUUUUCCACGCCCUUUGCUGCUCGCGGGAAAAUCACAUUUAUA
..(((((((((.((((...(((...)))---------))))(..(((((....(((..(((.(((((((((....))))))))).)))..)))...)))))..).....))))))))).. ( -35.80)
>DroEre_CAF1 73290 120 - 1
GUUAAAUGUGGCUCCGGAUUGCUUGGCACACACAGCACAGACAACGAGCGCGAAAAUAGCGCGGAAAAUUUUAGCAACUUUUCCACGCCCUUUGCUGCUCGCGUGGAAAUCACAUUUAUA
..(((((((((.((((...((((((.....)).)))).......((((((((((....(((.((((((..........)))))).)))..))))).)))))..))))..))))))))).. ( -36.90)
>DroYak_CAF1 70431 111 - 1
GUUAAAUGUGGCUCCGGAUUGCUUGGCA---------CAGACAACGAGCUCGAAAAUAGCGCGGAAAAUUUUAGCAAGUUUUCCACGCCUUUUGCUGCUCGUGGGGAAAUCACAUUUAUA
..(((((((((((((....(((...)))---------......((((((.(((((...(((.(((((((((....))))))))).))).)))))..))))))))))...))))))))).. ( -37.30)
>consensus
GUUAAAUGUGGCUCCGGAUUGCUUGGCA_________CAGACAACGAGCUCGAAAAUAGCGCGGAAAAUUUCAGCAAGUUUUCCACGCCCUUUGCUGCUCGCGGGAAAAUCACAUUUAUA
..(((((((((.(((.(..(((...)))................(((((....(((..(((.(((((((((....))))))))).)))..)))...)))))).)))...))))))))).. (-31.40 = -31.40 +   0.00) 

alignment

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secondary structure

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Window 3

Location 1,445,835 – 1,445,937
Length 102
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.89
Mean single sequence MFE -42.64
Consensus MFE -32.89
Energy contribution -33.62
Covariance contribution 0.73
Combinations/Pair 1.06
Mean z-score -2.54
Structure conservation index 0.77
SVM decision value 1.74
SVM RNA-class probability 0.974748
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1445835 102 + 20766785
ACAACGUAGCACAGC------------------GAACCGAACCAAGGGAGAACAAGUUUUCCCAUUUUCACGGGCCGCAGUGUGUGCUCGGCAUACCUUUGGUUUGCUGUGGCACACAGC
........((...((------------------(..(((......(((((((....))))))).......)))..)))..(((((((((((((.(((...))).))))).)))))))))) ( -41.22)
>DroSec_CAF1 63896 120 + 1
ACAACGCAGCACAGCGCGGCGCAGGAGCGACCCGAACCGAACCAAGGGAGAACAAGUUUUCCCAUUUUCACGGGCCGCAGUGUGUGCUCGGCAUACCUUUGGUUUGCUGUGGCACACAGC
.....((......))(((((.(.((..((........))..))..(((((((....)))))))........).)))))..(((((((((((((.(((...))).))))).)))))))).. ( -49.80)
>DroSim_CAF1 62516 120 + 1
ACAACGCAGCACAGCGCGGCGCAGGAGCGACCCGAACCGAACCAAGGGAGAACAAGUUUUCCCAUUUUCACGGGCCGCAGUGUGUGCUCGGCAUACCUUUGGUUUGCUGUGGCACACAGC
.....((......))(((((.(.((..((........))..))..(((((((....)))))))........).)))))..(((((((((((((.(((...))).))))).)))))))).. ( -49.80)
>DroEre_CAF1 73410 100 + 1
ACAACGCAGCGCAG--------------------ACCCGAACCAAGGGAGAACAAGUUUUCCCAUUUUCACGGGCCGCAGUGUGUGCUCGGCAUACCUUUGGCUUGCUGUGGCACACAGC
.....((...((.(--------------------.((((......(((((((....))))))).......))))).))..(((((((((((((..((...))..))))).)))))))))) ( -39.22)
>DroYak_CAF1 70542 100 + 1
ACAACGCAGAACAG--------------------ACCCCAACCAAGGGAGAACAAGUUUUCCCAUUUUCACGGGCCGCAGUGUGUGCUCGGCAUACCUUUGGUUUGCUGUGGCACAUAGC
.....((......(--------------------.(((.......(((((((....)))))))........))).)....(((((((((((((.(((...))).))))).)))))))))) ( -33.16)
>consensus
ACAACGCAGCACAGC__________________GAACCGAACCAAGGGAGAACAAGUUUUCCCAUUUUCACGGGCCGCAGUGUGUGCUCGGCAUACCUUUGGUUUGCUGUGGCACACAGC
.....((.((.........(((....))).......(((......(((((((....))))))).......))))).))..(((((((((((((.(((...))).))))).)))))))).. (-32.89 = -33.62 +   0.73) 

alignment

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secondary structure

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dotplot

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Window 4

Location 1,445,857 – 1,445,977
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 99.33
Mean single sequence MFE -37.56
Consensus MFE -37.34
Energy contribution -37.38
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -2.32
Structure conservation index 0.99
SVM decision value 3.22
SVM RNA-class probability 0.998761
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1445857 120 + 20766785
ACCAAGGGAGAACAAGUUUUCCCAUUUUCACGGGCCGCAGUGUGUGCUCGGCAUACCUUUGGUUUGCUGUGGCACACAGCACAUCUUGAGUGCUUUAUUGUUAUGUUUUAAAAUUCAAUG
.....(((((((....)))))))......(((....(((((((((((((((((.(((...))).))))).)))))))(((((.......)))))..)))))..))).............. ( -38.30)
>DroSec_CAF1 63936 120 + 1
ACCAAGGGAGAACAAGUUUUCCCAUUUUCACGGGCCGCAGUGUGUGCUCGGCAUACCUUUGGUUUGCUGUGGCACACAGCACAUCUUGAGUGCUUUAUUGUUAUGUUUUAAAAUUCAAUG
.....(((((((....)))))))......(((....(((((((((((((((((.(((...))).))))).)))))))(((((.......)))))..)))))..))).............. ( -38.30)
>DroSim_CAF1 62556 120 + 1
ACCAAGGGAGAACAAGUUUUCCCAUUUUCACGGGCCGCAGUGUGUGCUCGGCAUACCUUUGGUUUGCUGUGGCACACAGCACAUCUUGAGUGCUUUAUUGUUAUGUUUUAAAAUUCAAUG
.....(((((((....)))))))......(((....(((((((((((((((((.(((...))).))))).)))))))(((((.......)))))..)))))..))).............. ( -38.30)
>DroEre_CAF1 73430 120 + 1
ACCAAGGGAGAACAAGUUUUCCCAUUUUCACGGGCCGCAGUGUGUGCUCGGCAUACCUUUGGCUUGCUGUGGCACACAGCACAUCUUGAGUGCUUUAUUGUUAUGUUUUAAAAUUCAAUG
.....(((((((....)))))))......(((....(((((((((((((((((..((...))..))))).)))))))(((((.......)))))..)))))..))).............. ( -36.80)
>DroYak_CAF1 70562 120 + 1
ACCAAGGGAGAACAAGUUUUCCCAUUUUCACGGGCCGCAGUGUGUGCUCGGCAUACCUUUGGUUUGCUGUGGCACAUAGCACAUCUUGAGUGCUUUAUUGUUAUGUUUUAAAAUUCAAUG
.....(((((((....)))))))......(((....(((((((((((((((((.(((...))).))))).)))))))(((((.......)))))..)))))..))).............. ( -36.10)
>consensus
ACCAAGGGAGAACAAGUUUUCCCAUUUUCACGGGCCGCAGUGUGUGCUCGGCAUACCUUUGGUUUGCUGUGGCACACAGCACAUCUUGAGUGCUUUAUUGUUAUGUUUUAAAAUUCAAUG
.....(((((((....)))))))......(((....(((((((((((((((((.(((...))).))))).)))))))(((((.......)))))..)))))..))).............. (-37.34 = -37.38 +   0.04) 

alignment

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secondary structure

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dotplot

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Window 5

Location 1,445,857 – 1,445,977
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 99.33
Mean single sequence MFE -29.69
Consensus MFE -29.44
Energy contribution -29.48
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -1.31
Structure conservation index 0.99
SVM decision value 0.42
SVM RNA-class probability 0.728107
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1445857 120 - 20766785
CAUUGAAUUUUAAAACAUAACAAUAAAGCACUCAAGAUGUGCUGUGUGCCACAGCAAACCAAAGGUAUGCCGAGCACACACUGCGGCCCGUGAAAAUGGGAAAACUUGUUCUCCCUUGGU
..................(((((...(((((.......)))))((((((..(.(((.(((...))).))).).)))))).......(((((....))))).....))))).......... ( -30.30)
>DroSec_CAF1 63936 120 - 1
CAUUGAAUUUUAAAACAUAACAAUAAAGCACUCAAGAUGUGCUGUGUGCCACAGCAAACCAAAGGUAUGCCGAGCACACACUGCGGCCCGUGAAAAUGGGAAAACUUGUUCUCCCUUGGU
..................(((((...(((((.......)))))((((((..(.(((.(((...))).))).).)))))).......(((((....))))).....))))).......... ( -30.30)
>DroSim_CAF1 62556 120 - 1
CAUUGAAUUUUAAAACAUAACAAUAAAGCACUCAAGAUGUGCUGUGUGCCACAGCAAACCAAAGGUAUGCCGAGCACACACUGCGGCCCGUGAAAAUGGGAAAACUUGUUCUCCCUUGGU
..................(((((...(((((.......)))))((((((..(.(((.(((...))).))).).)))))).......(((((....))))).....))))).......... ( -30.30)
>DroEre_CAF1 73430 120 - 1
CAUUGAAUUUUAAAACAUAACAAUAAAGCACUCAAGAUGUGCUGUGUGCCACAGCAAGCCAAAGGUAUGCCGAGCACACACUGCGGCCCGUGAAAAUGGGAAAACUUGUUCUCCCUUGGU
..................(((((...(((((.......)))))((((((..(.(((.(((...))).))).).)))))).......(((((....))))).....))))).......... ( -30.60)
>DroYak_CAF1 70562 120 - 1
CAUUGAAUUUUAAAACAUAACAAUAAAGCACUCAAGAUGUGCUAUGUGCCACAGCAAACCAAAGGUAUGCCGAGCACACACUGCGGCCCGUGAAAAUGGGAAAACUUGUUCUCCCUUGGU
......................(((.(((((.......))))).)))((((..(((.(((...))).))).(((.(((........(((((....)))))......))).)))...)))) ( -26.94)
>consensus
CAUUGAAUUUUAAAACAUAACAAUAAAGCACUCAAGAUGUGCUGUGUGCCACAGCAAACCAAAGGUAUGCCGAGCACACACUGCGGCCCGUGAAAAUGGGAAAACUUGUUCUCCCUUGGU
..................(((((...(((((.......)))))((((((..(.(((.(((...))).))).).)))))).......(((((....))))).....))))).......... (-29.44 = -29.48 +   0.04) 

alignment

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secondary structure

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dotplot

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Window 6

Location 1,445,897 – 1,446,017
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.58
Mean single sequence MFE -33.14
Consensus MFE -30.20
Energy contribution -30.44
Covariance contribution 0.24
Combinations/Pair 1.02
Mean z-score -2.73
Structure conservation index 0.91
SVM decision value 3.92
SVM RNA-class probability 0.999708
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1445897 120 + 20766785
UGUGUGCUCGGCAUACCUUUGGUUUGCUGUGGCACACAGCACAUCUUGAGUGCUUUAUUGUUAUGUUUUAAAAUUCAAUGAAUUCUAAAAAUGUACCACCCUGUCCCAGGUCCCAGGUAU
(((((((((((((.(((...))).))))).))))))))((((.......))))(((((((..((........)).)))))))..........(((((..((((...)))).....))))) ( -34.60)
>DroSec_CAF1 63976 115 + 1
UGUGUGCUCGGCAUACCUUUGGUUUGCUGUGGCACACAGCACAUCUUGAGUGCUUUAUUGUUAUGUUUUAAAAUUCAAUGAAUUCUAAAAAUGUACCACCCUGU-----GUCCCAGGUAU
(((((((((((((.(((...))).))))).))))))))((((.......)))).....((.((((((((..(((((...)))))...)))))))).)).((((.-----....))))... ( -33.60)
>DroSim_CAF1 62596 115 + 1
UGUGUGCUCGGCAUACCUUUGGUUUGCUGUGGCACACAGCACAUCUUGAGUGCUUUAUUGUUAUGUUUUAAAAUUCAAUGAAUUCUAAAAAUGUACCACCCUGU-----GUCCCAGGUAU
(((((((((((((.(((...))).))))).))))))))((((.......)))).....((.((((((((..(((((...)))))...)))))))).)).((((.-----....))))... ( -33.60)
>DroEre_CAF1 73470 115 + 1
UGUGUGCUCGGCAUACCUUUGGCUUGCUGUGGCACACAGCACAUCUUGAGUGCUUUAUUGUUAUGUUUUAAAAUUCAAUGAAUUCUAAAAUUGUACCACCCAGC-----GUCCCAGGUAU
(((((((((((((..((...))..))))).))))))))....((((.(..((((.....((...((((((.(((((...))))).))))))...)).....)))-----)..).)))).. ( -32.20)
>DroYak_CAF1 70602 115 + 1
UGUGUGCUCGGCAUACCUUUGGUUUGCUGUGGCACAUAGCACAUCUUGAGUGCUUUAUUGUUAUGUUUUAAAAUUCAAUGAAUUCUAAAAAUGUACCACCCUGU-----GUCCCAGGUAU
(((((((((((((.(((...))).))))).))))))))((((.......)))).....((.((((((((..(((((...)))))...)))))))).)).((((.-----....))))... ( -31.70)
>consensus
UGUGUGCUCGGCAUACCUUUGGUUUGCUGUGGCACACAGCACAUCUUGAGUGCUUUAUUGUUAUGUUUUAAAAUUCAAUGAAUUCUAAAAAUGUACCACCCUGU_____GUCCCAGGUAU
(((((((((((((.(((...))).))))).))))))))((((.......)))).....((.(((((((((.(((((...))))).))))).)))).)).((((..........))))... (-30.20 = -30.44 +   0.24) 

alignment

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secondary structure

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Window 7

Location 1,445,897 – 1,446,017
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.58
Mean single sequence MFE -36.44
Consensus MFE -34.12
Energy contribution -34.24
Covariance contribution 0.12
Combinations/Pair 1.06
Mean z-score -4.31
Structure conservation index 0.94
SVM decision value 4.41
SVM RNA-class probability 0.999892
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1445897 120 - 20766785
AUACCUGGGACCUGGGACAGGGUGGUACAUUUUUAGAAUUCAUUGAAUUUUAAAACAUAACAAUAAAGCACUCAAGAUGUGCUGUGUGCCACAGCAAACCAAAGGUAUGCCGAGCACACA
((((((.((.((((...))))((((((((((((((((((((...)))))))))))...........(((((.......))))))))))))))......))..))))))............ ( -37.40)
>DroSec_CAF1 63976 115 - 1
AUACCUGGGAC-----ACAGGGUGGUACAUUUUUAGAAUUCAUUGAAUUUUAAAACAUAACAAUAAAGCACUCAAGAUGUGCUGUGUGCCACAGCAAACCAAAGGUAUGCCGAGCACACA
...((((....-----.))))((((((((((((((((((((...)))))))))))...........(((((.......)))))))))))))).(((.(((...))).))).......... ( -36.50)
>DroSim_CAF1 62596 115 - 1
AUACCUGGGAC-----ACAGGGUGGUACAUUUUUAGAAUUCAUUGAAUUUUAAAACAUAACAAUAAAGCACUCAAGAUGUGCUGUGUGCCACAGCAAACCAAAGGUAUGCCGAGCACACA
...((((....-----.))))((((((((((((((((((((...)))))))))))...........(((((.......)))))))))))))).(((.(((...))).))).......... ( -36.50)
>DroEre_CAF1 73470 115 - 1
AUACCUGGGAC-----GCUGGGUGGUACAAUUUUAGAAUUCAUUGAAUUUUAAAACAUAACAAUAAAGCACUCAAGAUGUGCUGUGUGCCACAGCAAGCCAAAGGUAUGCCGAGCACACA
...........-----(((.(((((((((.(((((((((((...)))))))))))...........(((((.......))))).)))))))).(((.(((...))).)))).)))..... ( -35.60)
>DroYak_CAF1 70602 115 - 1
AUACCUGGGAC-----ACAGGGUGGUACAUUUUUAGAAUUCAUUGAAUUUUAAAACAUAACAAUAAAGCACUCAAGAUGUGCUAUGUGCCACAGCAAACCAAAGGUAUGCCGAGCACACA
...((((....-----.))))((((((((((((((((((((...)))))))))))...........(((((.......)))))))))))))).(((.(((...))).))).......... ( -36.20)
>consensus
AUACCUGGGAC_____ACAGGGUGGUACAUUUUUAGAAUUCAUUGAAUUUUAAAACAUAACAAUAAAGCACUCAAGAUGUGCUGUGUGCCACAGCAAACCAAAGGUAUGCCGAGCACACA
...((((..........))))((((((((((((((((((((...)))))))))))...........(((((.......)))))))))))))).(((.(((...))).))).......... (-34.12 = -34.24 +   0.12) 

alignment

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secondary structure

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dotplot

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Window 8

Location 1,445,937 – 1,446,046
Length 109
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.98
Mean single sequence MFE -25.90
Consensus MFE -20.50
Energy contribution -20.34
Covariance contribution -0.16
Combinations/Pair 1.04
Mean z-score -1.46
Structure conservation index 0.79
SVM decision value 0.09
SVM RNA-class probability 0.579903
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1445937 109 - 20766785
-----------GUCGUUGUCGCUGGCAACCAGACAACCAGAUACCUGGGACCUGGGACAGGGUGGUACAUUUUUAGAAUUCAUUGAAUUUUAAAACAUAACAAUAAAGCACUCAAGAUGU
-----------(((.((((.....))))((((....((((....))))...))))))).(((((......(((((((((((...))))))))))).....(......))))))....... ( -25.70)
>DroSec_CAF1 64016 104 - 1
-----------GUCGUUGUCGCUGGCAACCAGACAACCAGAUACCUGGGAC-----ACAGGGUGGUACAUUUUUAGAAUUCAUUGAAUUUUAAAACAUAACAAUAAAGCACUCAAGAUGU
-----------(((.(((((...(....)..)))))((((....)))))))-----...(((((......(((((((((((...))))))))))).....(......))))))....... ( -23.90)
>DroSim_CAF1 62636 104 - 1
-----------GUCGUUGUCGCUGGCAACCAGACAACGAGAUACCUGGGAC-----ACAGGGUGGUACAUUUUUAGAAUUCAUUGAAUUUUAAAACAUAACAAUAAAGCACUCAAGAUGU
-----------(((((((((...(....)..))))))(((...((((....-----.)))).........(((((((((((...)))))))))))...............)))..))).. ( -26.50)
>DroEre_CAF1 73510 115 - 1
UCGUUGUCGUUGUCGUUGUCGCUGGCAACCAGACAACCAGAUACCUGGGAC-----GCUGGGUGGUACAAUUUUAGAAUUCAUUGAAUUUUAAAACAUAACAAUAAAGCACUCAAGAUGU
.(((((((.((((((((((.....)))))..)))))((((....)))))))-----(((..((.((....(((((((((((...)))))))))))....)).))..)))......)))). ( -29.20)
>DroYak_CAF1 70642 106 - 1
---------CUAUCGUUGUCGCUGGCAACCAGACAACCAGAUACCUGGGAC-----ACAGGGUGGUACAUUUUUAGAAUUCAUUGAAUUUUAAAACAUAACAAUAAAGCACUCAAGAUGU
---------.((((((.((((((((...)))).)..((((....)))))))-----)).(((((......(((((((((((...))))))))))).....(......))))))..)))). ( -24.20)
>consensus
___________GUCGUUGUCGCUGGCAACCAGACAACCAGAUACCUGGGAC_____ACAGGGUGGUACAUUUUUAGAAUUCAUUGAAUUUUAAAACAUAACAAUAAAGCACUCAAGAUGU
...........(((((((((...(....)..))))))..((((((..(.........)..))))......(((((((((((...)))))))))))................))..))).. (-20.50 = -20.34 +  -0.16) 

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:31:55 2006