Locus 4962

Sequence ID X_DroMel_CAF1
Location 12,953,535 – 12,953,748
Length 213
Max. P 0.928643
window8086 window8087 window8088 window8089 window8090 window8091 window8092

overview

Window 6

Location 12,953,535 – 12,953,640
Length 105
Sequences 3
Columns 106
Reading direction forward
Mean pairwise identity 83.60
Mean single sequence MFE -28.23
Consensus MFE -19.72
Energy contribution -19.83
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -1.72
Structure conservation index 0.70
SVM decision value -0.04
SVM RNA-class probability 0.515186
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12953535 105 + 22224390
UAAUUGGCAAAGUGUUUGUCAAUCUAUCCAGUCAACGGCAUUGCCACAAUGAUAUACCAUUGUCUG-GCCGUCAACGCUGCGUAUACGUAAUUUGUGUUGCACGUA
..((((((((.....))))))))....((((.....(((...)))((((((......)))))))))-).(((((((((((((....))))....)))))).))).. ( -28.50)
>DroSec_CAF1 19786 94 + 1
UAAUUGGCAAAAAGUUUGUCAAUCUGUCCAGUC------------ACAAUGAUAUACCAUUGUCUGGGCCGUCAACGCUGCGUAUACGUAAUGUGUGUUGCACGUA
..((((((((.....))))))))..((((((..------------((((((......))))))))))))(((((((((((((....))))....)))))).))).. ( -30.50)
>DroEre_CAF1 11092 105 + 1
UAAUUGGCGAAAUAUUUGUCAAUCCGUCCAGUCGACCGCAUGGACACAAUGAUAGACCAUUGUCUG-GCCAUCAACGCUGCGUAUACGUAAUGUGUGUUGCACGAC
..((((((((.....))))))))(((((((((.....)).)))))((((((......))))))..)-)....((((((((((....))))....))))))...... ( -25.70)
>consensus
UAAUUGGCAAAAUGUUUGUCAAUCUGUCCAGUC_AC_GCAU_G_CACAAUGAUAUACCAUUGUCUG_GCCGUCAACGCUGCGUAUACGUAAUGUGUGUUGCACGUA
..((((((((.....))))))))......................((((((......))))))......(((((((((((((....))))....)))))).))).. (-19.72 = -19.83 +   0.11)

alignment

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secondary structure

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dotplot

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Window 7

Location 12,953,575 – 12,953,680
Length 105
Sequences 3
Columns 106
Reading direction forward
Mean pairwise identity 91.14
Mean single sequence MFE -39.62
Consensus MFE -32.20
Energy contribution -32.53
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.52
Structure conservation index 0.81
SVM decision value 0.58
SVM RNA-class probability 0.789835
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12953575 105 + 22224390
UUGCCACAAUGAUAUACCAUUGUCUG-GCCGUCAACGCUGCGUAUACGUAAUUUGUGUUGCACGUAUACGCCCUGUUUGGCUGCCAGUUAAUGGCUGGGCGUGGCC
..(((((.........((((((.(((-((.(((((((..(((((((((((((....)))..))))))))))..)).))))).))))).))))))......))))). ( -42.36)
>DroSec_CAF1 19819 100 + 1
-----ACAAUGAUAUACCAUUGUCUGGGCCGUCAACGCUGCGUAUACGUAAUGUGUGUUGCACGUAUACGCCCUGU-UGGCUGCCAGUUAAUGGCUGGGCGUGGCC
-----((((((......))))))...(((((((((((..((((((((((...((.....))))))))))))..)))-))))..(((((.....)))))....)))) ( -40.40)
>DroEre_CAF1 11132 104 + 1
UGGACACAAUGAUAGACCAUUGUCUG-GCCAUCAACGCUGCGUAUACGUAAUGUGUGUUGCACGACUACGCCCUGU-UGGCUGCCAGCUAAUGGCUGGGCGUGGCC
.(((((..(((......))))))))(-(((..((((((((((....))))....)))))).......((((((.((-((((.....))))))....)))))))))) ( -36.10)
>consensus
U_G_CACAAUGAUAUACCAUUGUCUG_GCCGUCAACGCUGCGUAUACGUAAUGUGUGUUGCACGUAUACGCCCUGU_UGGCUGCCAGUUAAUGGCUGGGCGUGGCC
.....((((((......))))))....(((((((((((((((....))))....)))))).))....((((((.........((((.....)))).))))))))). (-32.20 = -32.53 +   0.33)

alignment

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secondary structure

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dotplot

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Window 8

Location 12,953,575 – 12,953,680
Length 105
Sequences 3
Columns 106
Reading direction reverse
Mean pairwise identity 91.14
Mean single sequence MFE -38.23
Consensus MFE -31.57
Energy contribution -32.23
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -3.19
Structure conservation index 0.83
SVM decision value 1.19
SVM RNA-class probability 0.928643
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12953575 105 - 22224390
GGCCACGCCCAGCCAUUAACUGGCAGCCAAACAGGGCGUAUACGUGCAACACAAAUUACGUAUACGCAGCGUUGACGGC-CAGACAAUGGUAUAUCAUUGUGGCAA
.((((((....((((((..(((((.(.(((.....(((((((((((..........)))))))))))....))).).))-)))..)))))).......)))))).. ( -41.30)
>DroSec_CAF1 19819 100 - 1
GGCCACGCCCAGCCAUUAACUGGCAGCCA-ACAGGGCGUAUACGUGCAACACACAUUACGUAUACGCAGCGUUGACGGCCCAGACAAUGGUAUAUCAUUGU-----
((((.......((((.....)))).(.((-((...(((((((((((..........)))))))))))...)))).)))))...(((((((....)))))))----- ( -37.10)
>DroEre_CAF1 11132 104 - 1
GGCCACGCCCAGCCAUUAGCUGGCAGCCA-ACAGGGCGUAGUCGUGCAACACACAUUACGUAUACGCAGCGUUGAUGGC-CAGACAAUGGUCUAUCAUUGUGUCCA
(((...(((.(((.....)))))).))).-...(((((((((.(((.....))))))))))..((((((...(((((((-((.....))).)))))))))))))). ( -36.30)
>consensus
GGCCACGCCCAGCCAUUAACUGGCAGCCA_ACAGGGCGUAUACGUGCAACACACAUUACGUAUACGCAGCGUUGACGGC_CAGACAAUGGUAUAUCAUUGUG_C_A
((((((((...((((.....))))..((.....))(((((((((((..........))))))))))).))))....))).)..(((((((....)))))))..... (-31.57 = -32.23 +   0.67)

alignment

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secondary structure

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dotplot

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Window 9

Location 12,953,614 – 12,953,720
Length 106
Sequences 3
Columns 106
Reading direction forward
Mean pairwise identity 93.69
Mean single sequence MFE -39.77
Consensus MFE -36.38
Energy contribution -36.17
Covariance contribution -0.21
Combinations/Pair 1.12
Mean z-score -2.28
Structure conservation index 0.91
SVM decision value 1.01
SVM RNA-class probability 0.899196
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12953614 106 + 22224390
CGUAUACGUAAUUUGUGUUGCACGUAUACGCCCUGUUUGGCUGCCAGUUAAUGGCUGGGCGUGGCCAGUUCUUGGCUAGGUCUUGGCCUGAUGCAAUGCAUGACUU
.(((((((((((....)))..))))))))((..(((..((((((((.....)))).((((.(((((((...))))))).)))).))))....)))..))....... ( -37.50)
>DroSec_CAF1 19854 105 + 1
CGUAUACGUAAUGUGUGUUGCACGUAUACGCCCUGU-UGGCUGCCAGUUAAUGGCUGGGCGUGGCCAGUUCUUGGCUAGGUCUUGGCCUGAUGCAAUACAUGACUU
.......((...((((((((((....(((((((...-.....((((.....)))).)))))))(((((...)))))(((((....))))).)))))))))).)).. ( -38.90)
>DroEre_CAF1 11171 105 + 1
CGUAUACGUAAUGUGUGUUGCACGACUACGCCCUGU-UGGCUGCCAGCUAAUGGCUGGGCGUGGCCGAUUCUUGGCCAGCUCUUGGCCUGAUGCAAUGCAUGACUU
.......((...((((((((((((.((((((((.((-((((.....))))))....)))))))).))..((..((((((...)))))).)))))))))))).)).. ( -42.90)
>consensus
CGUAUACGUAAUGUGUGUUGCACGUAUACGCCCUGU_UGGCUGCCAGUUAAUGGCUGGGCGUGGCCAGUUCUUGGCUAGGUCUUGGCCUGAUGCAAUGCAUGACUU
.......((...((((((((((....(((((((.........((((.....)))).)))))))(((((...)))))(((((....))))).)))))))))).)).. (-36.38 = -36.17 +  -0.21)

alignment

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secondary structure

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dotplot

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Window 0

Location 12,953,614 – 12,953,720
Length 106
Sequences 3
Columns 106
Reading direction reverse
Mean pairwise identity 93.69
Mean single sequence MFE -32.77
Consensus MFE -28.70
Energy contribution -29.03
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.33
Structure conservation index 0.88
SVM decision value 0.72
SVM RNA-class probability 0.833794
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12953614 106 - 22224390
AAGUCAUGCAUUGCAUCAGGCCAAGACCUAGCCAAGAACUGGCCACGCCCAGCCAUUAACUGGCAGCCAAACAGGGCGUAUACGUGCAACACAAAUUACGUAUACG
.....((((...))))..(((((.(..((.....))..))))))..((((.((((.....)))).(.....).))))(((((((((..........))))))))). ( -30.40)
>DroSec_CAF1 19854 105 - 1
AAGUCAUGUAUUGCAUCAGGCCAAGACCUAGCCAAGAACUGGCCACGCCCAGCCAUUAACUGGCAGCCA-ACAGGGCGUAUACGUGCAACACACAUUACGUAUACG
..((.((((.((((((..(((((.(..((.....))..))))))((((((.((((.....)))).(...-.).))))))....))))))...)))).))....... ( -32.20)
>DroEre_CAF1 11171 105 - 1
AAGUCAUGCAUUGCAUCAGGCCAAGAGCUGGCCAAGAAUCGGCCACGCCCAGCCAUUAGCUGGCAGCCA-ACAGGGCGUAGUCGUGCAACACACAUUACGUAUACG
..((.(((..(((((...(((((.....)))))......((((.((((((.((((.....)))).(...-.).)))))).)))))))))....))).))....... ( -35.70)
>consensus
AAGUCAUGCAUUGCAUCAGGCCAAGACCUAGCCAAGAACUGGCCACGCCCAGCCAUUAACUGGCAGCCA_ACAGGGCGUAUACGUGCAACACACAUUACGUAUACG
......((..((((((..(((((....((.....))...)))))((((((.((((.....)))).(.....).))))))....))))))..))............. (-28.70 = -29.03 +   0.33)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,953,640 – 12,953,748
Length 108
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 85.76
Mean single sequence MFE -39.52
Consensus MFE -29.75
Energy contribution -30.25
Covariance contribution 0.50
Combinations/Pair 1.10
Mean z-score -1.95
Structure conservation index 0.75
SVM decision value 0.75
SVM RNA-class probability 0.840967
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12953640 108 + 22224390
UACGCCCUGUUUGGCUGCCAGUUAAUGGCUGGGCGUGGCCAGUUCUUGGCUAGGUCUUGGCCUGAUGCAAUGCAUGACUUAAAUUUGACUGGGCU---AAGU---------AUAAAGUAG
(((....((((((((..((((((((.(((..(((.(((((((...))))))).).))..)))..((((...)))).........)))))))))))---))))---------)....))). ( -37.30)
>DroSec_CAF1 19880 107 + 1
UACGCCCUGU-UGGCUGCCAGUUAAUGGCUGGGCGUGGCCAGUUCUUGGCUAGGUCUUGGCCUGAUGCAAUACAUGACUUAAAUUUAACUGGGCG---AAGU---------AUAAAGUGG
..(((((.((-(((((((((.....)))).((((.(((((((...))))))).)))).))))..(((.....)))...........))).)))))---....---------......... ( -36.30)
>DroEre_CAF1 11197 107 + 1
UACGCCCUGU-UGGCUGCCAGCUAAUGGCUGGGCGUGGCCGAUUCUUGGCCAGCUCUUGGCCUGAUGCAAUGCAUGACUUCAAUUUGACUGGGCG---AAGU---------ACAAAGUAU
..(((((.((-(((((((((.....)))).((((.(((((((...)))))))))))..))))..((((...))))...........))).)))))---....---------......... ( -40.80)
>DroYak_CAF1 11601 119 + 1
UACGCCCCGU-UGACUGCCAGUUAAUGGCUGGGCGUGGCCGAUUCUUGGCCAGCUCUUGCCCUGAUGCAAUACAUGACUUCCAUUCAACUGGGCGGCAAAGUAUUGCGGCUAUAAAGUAG
..(((((.((-(((.((..((((...(((.((((.(((((((...)))))))))))..)))...(((.....)))))))..)).))))).)))))((((....)))).(((....))).. ( -43.70)
>consensus
UACGCCCUGU_UGGCUGCCAGUUAAUGGCUGGGCGUGGCCAAUUCUUGGCCAGCUCUUGGCCUGAUGCAAUACAUGACUUAAAUUUAACUGGGCG___AAGU_________AUAAAGUAG
..(((((.((..((((((((.....)))).((((.(((((((...))))))).)))).))))..(((.....)))............)).)))))......................... (-29.75 = -30.25 +   0.50)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,953,640 – 12,953,748
Length 108
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 85.76
Mean single sequence MFE -32.02
Consensus MFE -24.35
Energy contribution -24.60
Covariance contribution 0.25
Combinations/Pair 1.08
Mean z-score -1.58
Structure conservation index 0.76
SVM decision value 0.22
SVM RNA-class probability 0.639883
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12953640 108 - 22224390
CUACUUUAU---------ACUU---AGCCCAGUCAAAUUUAAGUCAUGCAUUGCAUCAGGCCAAGACCUAGCCAAGAACUGGCCACGCCCAGCCAUUAACUGGCAGCCAAACAGGGCGUA
.........---------....---.(.((((((...........((((...))))..(((.........)))..).))))).)((((((.((((.....)))).(.....).)))))). ( -26.30)
>DroSec_CAF1 19880 107 - 1
CCACUUUAU---------ACUU---CGCCCAGUUAAAUUUAAGUCAUGUAUUGCAUCAGGCCAAGACCUAGCCAAGAACUGGCCACGCCCAGCCAUUAACUGGCAGCCA-ACAGGGCGUA
.........---------....---.(.((((((....(((.(((.((..(((...)))..)).))).))).....)))))).)((((((.((((.....)))).(...-.).)))))). ( -26.90)
>DroEre_CAF1 11197 107 - 1
AUACUUUGU---------ACUU---CGCCCAGUCAAAUUGAAGUCAUGCAUUGCAUCAGGCCAAGAGCUGGCCAAGAAUCGGCCACGCCCAGCCAUUAGCUGGCAGCCA-ACAGGGCGUA
.........---------....---(((((........(((.(.((.....))).)))(((.....(((((((.......))))).))(((((.....)))))..))).-...))))).. ( -33.90)
>DroYak_CAF1 11601 119 - 1
CUACUUUAUAGCCGCAAUACUUUGCCGCCCAGUUGAAUGGAAGUCAUGUAUUGCAUCAGGGCAAGAGCUGGCCAAGAAUCGGCCACGCCCAGCCAUUAACUGGCAGUCA-ACGGGGCGUA
.............((((....))))(((((.(((((.(((..........((((......))))..(((((((.......))))).)))))((((.....))))..)))-)).))))).. ( -41.00)
>consensus
CUACUUUAU_________ACUU___CGCCCAGUCAAAUUGAAGUCAUGCAUUGCAUCAGGCCAAGACCUAGCCAAGAACCGGCCACGCCCAGCCAUUAACUGGCAGCCA_ACAGGGCGUA
..........................(((...((...........((((...))))..(((((.....)))))..))...))).((((((.((((.....)))).(.....).)))))). (-24.35 = -24.60 +   0.25)

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 11:37:04 2006