Locus 2453

Sequence ID	2L_DroMel_CAF1
Location	6,712,483 – 6,712,638
Length	155
Max. P	0.958306

overview

Window 5

Location	6,712,483 – 6,712,573
Length	90
Sequences	6
Columns	98
Reading direction	forward
Mean pairwise identity	83.81
Mean single sequence MFE	-35.72
Consensus MFE	-28.54
Energy contribution	-29.10
Covariance contribution	0.56
Combinations/Pair	1.18
Mean z-score	-1.85
Structure conservation index	0.80
SVM decision value	0.36
SVM RNA-class probability	0.705669
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6712483 90 + 22407834
--UGCAGCUGAGCCAUUGCCAUUGGCAGUGCC------UUUAAGGCUGACCACAUUGGCCAACUUAGUGGUGGCUGAAACCGCGGCUGCCAUCACCUG
--.(((((((((.(((((((...))))))).)------))...(((..(.....)..)))......(((((.......)))))))))))......... ( -32.80)
>DroSec_CAF1 25107 90 + 1
--UGCAGCUGAGCCAUUGCCAUUGGCAGUGCC------UUUGAGGCCGACCACAUUGGCCAACUUUGUGGUGGCCGAGACCGCGGCUGCCAUCACCUG
--.(((((((((.(((((((...))))))).)------)....((((.((((((..(.....)..)))))))))).......)))))))......... ( -39.70)
>DroSim_CAF1 24973 90 + 1
--UGCAGCUGAGCCAUUGCCAUUGGCAGUGCC------UUUGAGGCCGACCACAUUGGCCAACUUUGUGGUGGCCGAGACCGCGGCUGCCAUCACCUG
--.(((((((((.(((((((...))))))).)------)....((((.((((((..(.....)..)))))))))).......)))))))......... ( -39.70)
>DroEre_CAF1 26340 90 + 1
--UGCAGCUGAGCCGUUGGAAUUGGCAGUGCC------UUUGAGGCCGACCACAUUGGCCAAUUUUGUGGUGGCCGAUACCGCGGCUGCCAUCACCUG
--.(((((((.((((.......))))......------.....((((.((((((...........)))))))))).......)))))))......... ( -33.80)
>DroWil_CAF1 43693 92 + 1
UCACCAGCAGCGCCAU------UUGCAGUGCUAUUUGACUUUAGGCGCACCACACGGGCCAACUUUGUUGUGGCCGCCACGGCAGCGGCCAUGACAUU
......((.(((((..------..((((......))).)....))))).((....))))......(((..(((((((.......)))))))..))).. ( -33.40)
>DroYak_CAF1 26614 90 + 1
--UGCAGCUGAGCCAUUGGAAUUGGCAGUGCC------UUUGAGGCCGACCACAUUGGCCAAUUUUGUGGUGGCCGAGACCGCGGCUGCCAUCACCUG
--.((((((..((((.......))))...((.------.((..((((.((((((...........))))))))))..))..))))))))......... ( -34.90)
>consensus
__UGCAGCUGAGCCAUUGCCAUUGGCAGUGCC______UUUGAGGCCGACCACAUUGGCCAACUUUGUGGUGGCCGAGACCGCGGCUGCCAUCACCUG
...(((((((.((((.......)))).................((((.((((((..(.....)..)))))))))).......)))))))......... (-28.54 = -29.10 +   0.56)

alignment

secondary structure

dotplot

Window 6

Location	6,712,502 – 6,712,603
Length	101
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	71.68
Mean single sequence MFE	-39.65
Consensus MFE	-21.57
Energy contribution	-22.65
Covariance contribution	1.08
Combinations/Pair	1.21
Mean z-score	-1.97
Structure conservation index	0.54
SVM decision value	1.49
SVM RNA-class probability	0.958306
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6712502 101 + 22407834
UUGGCAGUGCC------UUUAAGGCUGACCACAUUGGCCAACUUAGUGGUGGCUGAAACCGCGGCUGCCAUCACCUGGCCUCUUCCAUUCAGCAGCGAGUUGUUGGU-
.(((((..(((------.....))))).)))....(((((.....((((..((((......))))..))))....)))))........(((((((....))))))).- ( -35.40)
>DroVir_CAF1 41015 106 + 1
CCGGCAGCACCAUUUGUCUUAAGGCGCACCACAUGCGCCAGCUUUGUGGUGGCCGCAACUGCAGCAGCCAUCACAUUGCCAUUGUUAUUGGGCAACGUGUUGAUGG--
(((.((((((...((((((...((((((.....)))))).((..(((((((((.((.......)).)))))))))..))..........)))))).)))))).)))-- ( -46.00)
>DroPse_CAF1 42628 99 + 1
CC---GUUGCU------CUUGAGGCCCACAACAUGGGCCAACUUUGUUGUGGCCGCCACCGCAGCGGCCAUCACAGUGCCAUGUCUAUUGGCCAGAGAAUUGUUGUUG
.(---(...((------((...((((((.....)))))).....(((.((((((((.......)))))))).)))(.((((.......)))))))))...))...... ( -37.60)
>DroWil_CAF1 43709 105 + 1
-UUGCAGUGCUAUUUGACUUUAGGCGCACCACACGGGCCAACUUUGUUGUGGCCGCCACGGCAGCGGCCAUGACAUUGCCAUGACCGUUGGGUAAGGCAUUGUUGA--
-..(((((((((((..((.((((((((.((....))))......(((..(((((((.......)))))))..)))..))).)))..))..)))..))))))))...-- ( -41.90)
>DroYak_CAF1 26633 101 + 1
UUGGCAGUGCC------UUUGAGGCCGACCACAUUGGCCAAUUUUGUGGUGGCCGAGACCGCGGCUGCCAUCACCUGGCCACGUCCAUUGAGCAGCGAGUUGUUGGU-
..(((...)))------......((((((.((..((((((.....((((..((((......))))..))))....))))))(((..........))).)).))))))- ( -37.70)
>DroPer_CAF1 42021 100 + 1
CCG--GUUGCU------CUUGAGGCCCACAACAUGGGCCAACUUCGUUGUGGCCGCCACCGCAGCGGCCAUCACAGUGCCAUGUCUAUUGGCCAGAGAAUUGUUGUUG
.((--(((.((------((...((((((.....))))))......((.((((((((.......)))))))).)).(.((((.......))))))))))))))...... ( -39.30)
>consensus
CCGGCAGUGCC______CUUGAGGCCCACCACAUGGGCCAACUUUGUGGUGGCCGCCACCGCAGCGGCCAUCACAUUGCCAUGUCCAUUGGGCAGCGAAUUGUUGGU_
..(((.................((((((.....))))))......((((((((.((.......)).))))))))...)))............................ (-21.57 = -22.65 +   1.08)

alignment

secondary structure

dotplot

Window 7

Location	6,712,502 – 6,712,603
Length	101
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	71.68
Mean single sequence MFE	-37.24
Consensus MFE	-21.01
Energy contribution	-21.68
Covariance contribution	0.67
Combinations/Pair	1.33
Mean z-score	-1.82
Structure conservation index	0.56
SVM decision value	1.27
SVM RNA-class probability	0.938607
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6712502 101 - 22407834
-ACCAACAACUCGCUGCUGAAUGGAAGAGGCCAGGUGAUGGCAGCCGCGGUUUCAGCCACCACUAAGUUGGCCAAUGUGGUCAGCCUUAAA------GGCACUGCCAA
-....................(((.((..(((.((((.(((((((....)))...)))).))))..(((((((.....)))))))......------))).)).))). ( -30.90)
>DroVir_CAF1 41015 106 - 1
--CCAUCAACACGUUGCCCAAUAACAAUGGCAAUGUGAUGGCUGCUGCAGUUGCGGCCACCACAAAGCUGGCGCAUGUGGUGCGCCUUAAGACAAAUGGUGCUGCCGG
--((.....(((((((((..........)))))))))..(((.(((((....)))))(((((.....(((((((((...)))))))...)).....)))))..))))) ( -42.20)
>DroPse_CAF1 42628 99 - 1
CAACAACAAUUCUCUGGCCAAUAGACAUGGCACUGUGAUGGCCGCUGCGGUGGCGGCCACAACAAAGUUGGCCCAUGUUGUGGGCCUCAAG------AGCAAC---GG
...........((((((((....(((((((((((.((.((((((((.....))))))))))....)))..).)))))))...))))...))------))....---.. ( -38.00)
>DroWil_CAF1 43709 105 - 1
--UCAACAAUGCCUUACCCAACGGUCAUGGCAAUGUCAUGGCCGCUGCCGUGGCGGCCACAACAAAGUUGGCCCGUGUGGUGCGCCUAAAGUCAAAUAGCACUGCAA-
--(((((..((((..(((....)))...)))).(((..((((((((.....))))))))..)))..)))))....((..((((...............))))..)).- ( -39.76)
>DroYak_CAF1 26633 101 - 1
-ACCAACAACUCGCUGCUCAAUGGACGUGGCCAGGUGAUGGCAGCCGCGGUCUCGGCCACCACAAAAUUGGCCAAUGUGGUCGGCCUCAAA------GGCACUGCCAA
-.....((.((.((..(((....)).)..)).)).)).((((((.....((((.((((((((((...........)))))).))))....)------))).)))))). ( -34.60)
>DroPer_CAF1 42021 100 - 1
CAACAACAAUUCUCUGGCCAAUAGACAUGGCACUGUGAUGGCCGCUGCGGUGGCGGCCACAACGAAGUUGGCCCAUGUUGUGGGCCUCAAG------AGCAAC--CGG
...........((((((((....(((((((((((.((.((((((((.....))))))))))....)))..).)))))))...))))...))------))....--... ( -38.00)
>consensus
_ACCAACAACUCGCUGCCCAAUAGACAUGGCAAUGUGAUGGCCGCUGCGGUGGCGGCCACAACAAAGUUGGCCCAUGUGGUGGGCCUCAAG______AGCACUGCCAG
.............................((..(((..(((((((.......)))))))..))).....((((((.....))))))............))........ (-21.01 = -21.68 +   0.67)

alignment

secondary structure

dotplot

Window 8

Location	6,712,533 – 6,712,638
Length	105
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	73.51
Mean single sequence MFE	-41.47
Consensus MFE	-17.57
Energy contribution	-19.35
Covariance contribution	1.78
Combinations/Pair	1.15
Mean z-score	-2.30
Structure conservation index	0.42
SVM decision value	1.36
SVM RNA-class probability	0.946270
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6712533 105 + 22407834
CCAACUUAGUGGUGGCUGAAACCGCGGCUGCCAUCACCUGGCCUCUUCCAUUCAGCAGCG---AGUUGUUGGU------CAACUGCUUUUGCAUCAGCUGAUUGGAGGAGUCCA
........((((..((((......))))..)))).....((.((((((((.(((((....---(((((.....------)))))((....))....))))).)))))))).)). ( -44.90)
>DroVir_CAF1 41052 99 + 1
CCAGCUUUGUGGUGGCCGCAACUGCAGCAGCCAUCACAUUGCCAUUGUUAUUGGGCAACG---UGUUGAUGG------------GCUUCUGCAGCAGCUGAUUGGAGGAGUCCA
.((((..(((((((((.((.......)).)))))))))(((((..........)))))..---.)))).(((------------((((((.((((....).))).))))))))) ( -39.90)
>DroPse_CAF1 42656 111 + 1
CCAACUUUGUUGUGGCCGCCACCGCAGCGGCCAUCACAGUGCCAUGUCUAUUGGCCAGAG---AAUUGUUGUUGGCCGCAGCCGGCUUCUGCAUGAGUUGAUUGGAAGAGUCCA
.(((((((((...(((((.....((.(((((((.((((((((((.......)))).....---.)))).)).))))))).)))))))...))).))))))..((((....)))) ( -41.70)
>DroWil_CAF1 43745 102 + 1
CCAACUUUGUUGUGGCCGCCACGGCAGCGGCCAUGACAUUGCCAUGACCGUUGGGUAAGG---CAUUGUUGA---------CUGGCUUCUGAAGCAGCUGAUUGGAUGAGUCCA
.((((..(((..(((((((.......)))))))..))).((((...(((....)))..))---))..)))).---------..((((.(....).))))...((((....)))) ( -37.50)
>DroMoj_CAF1 41136 99 + 1
CCAGCUUUGUGGUGGCAGCCACAGCAGCAGCCACCACAUUGCCAUUGCCAUUGGGCAGCG---UGUUGAUGG------------GCUUCUGCAGUAAUUGAUUGGAGGAGUCCA
...((..(((((((((.((.......)).)))))))))..))..(((((....)))))..---......(((------------((((((.((((.....)))).))))))))) ( -44.20)
>DroAna_CAF1 29692 108 + 1
CCAACUUCGUUGUGGCUGCCACAGCCGCAGCCAUCACCUGGCCAUGUCCGUUAGCCAUCGAGGAGUUAUUGGC------AGGCGGCUUUUGCACCAGCUGGUUGGAGGAGUCCA
...(((((((((((((((...))))))))))......(..((((.(.((((..((((............))))------..)))))....((....))))))..).)))))... ( -40.60)
>consensus
CCAACUUUGUGGUGGCCGCCACAGCAGCAGCCAUCACAUUGCCAUGUCCAUUGGGCAGCG___AGUUGUUGG__________CGGCUUCUGCAGCAGCUGAUUGGAGGAGUCCA
(((((...((((((((.((.......)).))))))))...(((..........)))...........)))))............((((((.((.........)).))))))... (-17.57 = -19.35 +   1.78)

alignment

secondary structure

dotplot

Window 9

Location	6,712,533 – 6,712,638
Length	105
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	73.51
Mean single sequence MFE	-37.47
Consensus MFE	-19.13
Energy contribution	-19.22
Covariance contribution	0.09
Combinations/Pair	1.32
Mean z-score	-2.09
Structure conservation index	0.51
SVM decision value	1.38
SVM RNA-class probability	0.948316
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6712533 105 - 22407834
UGGACUCCUCCAAUCAGCUGAUGCAAAAGCAGUUG------ACCAACAACU---CGCUGCUGAAUGGAAGAGGCCAGGUGAUGGCAGCCGCGGUUUCAGCCACCACUAAGUUGG
(((.(((.((((.(((((.........((((((((------.....)))))---.)))))))).)))).))).)))((((.(((((((....)))...)))).))))....... ( -37.40)
>DroVir_CAF1 41052 99 - 1
UGGACUCCUCCAAUCAGCUGCUGCAGAAGC------------CCAUCAACA---CGUUGCCCAAUAACAAUGGCAAUGUGAUGGCUGCUGCAGUUGCGGCCACCACAAAGCUGG
((((....))))..((((((((((((.(((------------(.(((...(---(((((((..........))))))))))))))).)))))))((.((...)).)).))))). ( -39.20)
>DroPse_CAF1 42656 111 - 1
UGGACUCUUCCAAUCAACUCAUGCAGAAGCCGGCUGCGGCCAACAACAAUU---CUCUGGCCAAUAGACAUGGCACUGUGAUGGCCGCUGCGGUGGCGGCCACAACAAAGUUGG
((((....))))..(((((.........((((.(((.(((((.........---...)))))..)))...))))..(((..((((((((.....))))))))..))).))))). ( -39.70)
>DroWil_CAF1 43745 102 - 1
UGGACUCAUCCAAUCAGCUGCUUCAGAAGCCAG---------UCAACAAUG---CCUUACCCAACGGUCAUGGCAAUGUCAUGGCCGCUGCCGUGGCGGCCACAACAAAGUUGG
((((....))))....((((((.....)).)))---------)((((..((---((..(((....)))...)))).(((..((((((((.....))))))))..)))..)))). ( -35.30)
>DroMoj_CAF1 41136 99 - 1
UGGACUCCUCCAAUCAAUUACUGCAGAAGC------------CCAUCAACA---CGCUGCCCAAUGGCAAUGGCAAUGUGGUGGCUGCUGCUGUGGCUGCCACCACAAAGCUGG
((((....))))..........((....))------------(((......---((.((((....)))).))((..(((((((((.(((.....))).)))))))))..))))) ( -33.10)
>DroAna_CAF1 29692 108 - 1
UGGACUCCUCCAACCAGCUGGUGCAAAAGCCGCCU------GCCAAUAACUCCUCGAUGGCUAACGGACAUGGCCAGGUGAUGGCUGCGGCUGUGGCAGCCACAACGAAGUUGG
((((....)))).(((((((((((...((((((..------((((...(((......((((((.......)))))))))..)))).))))))...))).)).......)))))) ( -40.11)
>consensus
UGGACUCCUCCAAUCAGCUGCUGCAGAAGCCG__________CCAACAACU___CGCUGCCCAAUGGAAAUGGCAAUGUGAUGGCUGCUGCGGUGGCGGCCACAACAAAGUUGG
((((....)))).((((((...((....))..............................................(((..(((((((.......)))))))..))).)))))) (-19.13 = -19.22 +   0.09)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:28:20 2006