Locus 4224

Sequence ID X_DroMel_CAF1
Location 11,064,328 – 11,064,463
Length 135
Max. P 0.999257
window6940 window6941 window6942 window6943

overview

Window 0

Location 11,064,328 – 11,064,437
Length 109
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.12
Mean single sequence MFE -29.07
Consensus MFE -16.74
Energy contribution -17.93
Covariance contribution 1.20
Combinations/Pair 1.18
Mean z-score -1.94
Structure conservation index 0.58
SVM decision value 0.31
SVM RNA-class probability 0.683738
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11064328 109 + 22224390
AUCGGCAUACAA-AU-----GCGCCCACUGCGAUUCCAUUAGUCGCUCGGCUGCAUUCCGCAUGCAUCGGCUAAC-----UUUUCCACUUCAACUUGGCCAGUUGGAUCACUUUGGCCAA
....((((.(.(-((-----(((((....((((((.....))))))..))).)))))..).))))...((((((.-----...((((((((.....))..)).)))).....)))))).. ( -31.10)
>DroSec_CAF1 16516 109 + 1
AUCGGCAUACAA-AU-----GCGCCCACUGCGAUUCCAUUAGCCGCUCGGCUGCAUUCCGCAUGCAUCGGCUAAC-----UUUUCCACUUCAACUUGGCCAGUUGGACCACUUUGGCCAA
...(((......-..-----.(((.....)))......(((((((....(((((.....))).))..))))))).-----..........(((..(((((....)).)))..)))))).. ( -29.30)
>DroSim_CAF1 18181 109 + 1
AUCGGCAUACAA-AU-----GCGCCCACUGCGAUUCCAUUAGCCGCUCGGCUGCAUUCCGCAUGCAUCGGCUAAC-----UUUUCCACUUCAACUUGGCCAGUUGGACCACUUUGGCCAA
...(((......-..-----.(((.....)))......(((((((....(((((.....))).))..))))))).-----..........(((..(((((....)).)))..)))))).. ( -29.30)
>DroEre_CAF1 19808 109 + 1
AUCGGCAUACAA-AU-----GCGCCCAUUGCGAUUCCAUUAGCCGCUCGGCUGCAUUCUGCAUGCAUCGGCUAAC-----UUUUCCACUUCAACUUGGCCAGUUGGACCACAUUAGCCGU
....((((.(((-((-----(((((....(((...........)))..))).))))).)).))))..(((((((.-----........(((((((.....))))))).....))))))). ( -30.04)
>DroYak_CAF1 17098 114 + 1
AUCGGCAUACAA-AUGCAAUGCGGCCAUUGCGAUUCCAUUAGCCGCUCGGCUGCAUUCUGCAUGCAUCGGCUAAC-----UUUUCCACUUCAACUUGGCCAGUUGCAGCACUUUAGCCAU
...(((......-(((((((((((((...(((...........)))..))))))))..)))))(((..((((((.-----..............))))))...))).........))).. ( -36.16)
>DroPer_CAF1 46054 101 + 1
AUCCGCUGGCAAAAU-----AUGCU--CUUCCAAUCCAUUUACCGCUCUGGUGCACUCUGAAUUCC-AGGCACACACAUAUUUUGCAAC---------CCAUUUCGGCCACU--AUCCGA
........(((((((-----(((..--.....((.....))...((.((((..(.....)....))-)))).....))))))))))...---------.....((((.....--..)))) ( -18.50)
>consensus
AUCGGCAUACAA_AU_____GCGCCCACUGCGAUUCCAUUAGCCGCUCGGCUGCAUUCCGCAUGCAUCGGCUAAC_____UUUUCCACUUCAACUUGGCCAGUUGGACCACUUUAGCCAA
...(((................................(((((((....(((((.....))).))..)))))))..............(((((((.....)))))))........))).. (-16.74 = -17.93 +   1.20)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,064,328 – 11,064,437
Length 109
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.12
Mean single sequence MFE -37.37
Consensus MFE -18.72
Energy contribution -20.60
Covariance contribution 1.88
Combinations/Pair 1.19
Mean z-score -2.17
Structure conservation index 0.50
SVM decision value 0.09
SVM RNA-class probability 0.577880
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11064328 109 - 22224390
UUGGCCAAAGUGAUCCAACUGGCCAAGUUGAAGUGGAAAA-----GUUAGCCGAUGCAUGCGGAAUGCAGCCGAGCGACUAAUGGAAUCGCAGUGGGCGC-----AU-UUGUAUGCCGAU
(((((((..((......)))))))))(((((..(....).-----.)))))((..(((((((.(((((.(((.(((((.........))))..).)))))-----))-)))))))))).. ( -36.10)
>DroSec_CAF1 16516 109 - 1
UUGGCCAAAGUGGUCCAACUGGCCAAGUUGAAGUGGAAAA-----GUUAGCCGAUGCAUGCGGAAUGCAGCCGAGCGGCUAAUGGAAUCGCAGUGGGCGC-----AU-UUGUAUGCCGAU
(((((..((((((((((.(((.(((........)))....-----((((((((.(((((.....)))))......)))))))).......)))))))).)-----))-))....))))). ( -38.30)
>DroSim_CAF1 18181 109 - 1
UUGGCCAAAGUGGUCCAACUGGCCAAGUUGAAGUGGAAAA-----GUUAGCCGAUGCAUGCGGAAUGCAGCCGAGCGGCUAAUGGAAUCGCAGUGGGCGC-----AU-UUGUAUGCCGAU
(((((..((((((((((.(((.(((........)))....-----((((((((.(((((.....)))))......)))))))).......)))))))).)-----))-))....))))). ( -38.30)
>DroEre_CAF1 19808 109 - 1
ACGGCUAAUGUGGUCCAACUGGCCAAGUUGAAGUGGAAAA-----GUUAGCCGAUGCAUGCAGAAUGCAGCCGAGCGGCUAAUGGAAUCGCAAUGGGCGC-----AU-UUGUAUGCCGAU
.((((((((....((((.((...........))))))...-----))))))))..(((((((((.(((.(((.((((..(.....)..)))..).)))))-----))-)))))))).... ( -39.90)
>DroYak_CAF1 17098 114 - 1
AUGGCUAAAGUGCUGCAACUGGCCAAGUUGAAGUGGAAAA-----GUUAGCCGAUGCAUGCAGAAUGCAGCCGAGCGGCUAAUGGAAUCGCAAUGGCCGCAUUGCAU-UUGUAUGCCGAU
.(((((((...(((.(((((.....))))).)))......-----.)))))))..(((((((((.(((((....(((((((.((......)).))))))).))))))-)))))))).... ( -43.20)
>DroPer_CAF1 46054 101 - 1
UCGGAU--AGUGGCCGAAAUGG---------GUUGCAAAAUAUGUGUGUGCCU-GGAAUUCAGAGUGCACCAGAGCGGUAAAUGGAUUGGAAG--AGCAU-----AUUUUGCCAGCGGAU
((((..--.....)))).....---------(((((((((((((((((..(((-(.....))).)..))).....((((......))))....--.))))-----)))))).)))).... ( -28.40)
>consensus
UUGGCCAAAGUGGUCCAACUGGCCAAGUUGAAGUGGAAAA_____GUUAGCCGAUGCAUGCAGAAUGCAGCCGAGCGGCUAAUGGAAUCGCAGUGGGCGC_____AU_UUGUAUGCCGAU
..(.(((..(((((.(((((.....)))))...............((((((((.(((((.....)))))......))))))))...)))))..))).)...................... (-18.72 = -20.60 +   1.88)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,064,362 – 11,064,463
Length 101
Sequences 5
Columns 101
Reading direction forward
Mean pairwise identity 93.66
Mean single sequence MFE -31.25
Consensus MFE -28.56
Energy contribution -28.92
Covariance contribution 0.36
Combinations/Pair 1.13
Mean z-score -2.21
Structure conservation index 0.91
SVM decision value 3.47
SVM RNA-class probability 0.999257
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11064362 101 + 22224390
AGUCGCUCGGCUGCAUUCCGCAUGCAUCGGCUAACUUUUCCACUUCAACUUGGCCAGUUGGAUCACUUUGGCCAACCGGAAACCUACAAAAGUUGGCUGCA
((((....))))((((.....))))..((((((((((((....(((...((((((((..(.....).))))))))...)))......)))))))))))).. ( -31.20)
>DroSec_CAF1 16550 101 + 1
AGCCGCUCGGCUGCAUUCCGCAUGCAUCGGCUAACUUUUCCACUUCAACUUGGCCAGUUGGACCACUUUGGCCAACCGGAAACCUACAAAAGUUGGCUGCU
((((....))))((((.....))))..(((((((((((((((........)))((.(((((.((.....))))))).))........)))))))))))).. ( -34.20)
>DroSim_CAF1 18215 101 + 1
AGCCGCUCGGCUGCAUUCCGCAUGCAUCGGCUAACUUUUCCACUUCAACUUGGCCAGUUGGACCACUUUGGCCAACCGGAAACCUACAAAAGUUGGCUGCU
((((....))))((((.....))))..(((((((((((((((........)))((.(((((.((.....))))))).))........)))))))))))).. ( -34.20)
>DroEre_CAF1 19842 101 + 1
AGCCGCUCGGCUGCAUUCUGCAUGCAUCGGCUAACUUUUCCACUUCAACUUGGCCAGUUGGACCACAUUAGCCGUCCGGAAACCCACGAAAGUUGGCUGCC
..(((..(((((((((.....))))...((((((((...(((........)))..)))))).)).....)))))..)))...((.((....)).))..... ( -31.70)
>DroYak_CAF1 17137 101 + 1
AGCCGCUCGGCUGCAUUCUGCAUGCAUCGGCUAACUUUUCCACUUCAACUUGGCCAGUUGCAGCACUUUAGCCAUCCGGAAACCUACAAAAGUUGCUUGCU
(((.(((.(((((.....(((.((((..((((((...............))))))...)))))))...)))))....(....).......))).))).... ( -24.96)
>consensus
AGCCGCUCGGCUGCAUUCCGCAUGCAUCGGCUAACUUUUCCACUUCAACUUGGCCAGUUGGACCACUUUGGCCAACCGGAAACCUACAAAAGUUGGCUGCU
((((....))))((((.....))))..((((((((((((....(((...((((((((..........))))))))...)))......)))))))))))).. (-28.56 = -28.92 +   0.36)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,064,362 – 11,064,463
Length 101
Sequences 5
Columns 101
Reading direction reverse
Mean pairwise identity 93.66
Mean single sequence MFE -33.84
Consensus MFE -28.00
Energy contribution -29.00
Covariance contribution 1.00
Combinations/Pair 1.06
Mean z-score -1.31
Structure conservation index 0.83
SVM decision value -0.01
SVM RNA-class probability 0.530274
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11064362 101 - 22224390
UGCAGCCAACUUUUGUAGGUUUCCGGUUGGCCAAAGUGAUCCAACUGGCCAAGUUGAAGUGGAAAAGUUAGCCGAUGCAUGCGGAAUGCAGCCGAGCGACU
.((.((.(((((((.((..((((.(.(((((((..((......))))))))).).)))))).))))))).))((.(((((.....)))))..)).)).... ( -31.30)
>DroSec_CAF1 16550 101 - 1
AGCAGCCAACUUUUGUAGGUUUCCGGUUGGCCAAAGUGGUCCAACUGGCCAAGUUGAAGUGGAAAAGUUAGCCGAUGCAUGCGGAAUGCAGCCGAGCGGCU
...(((((((((((........((((((((((.....)).))))))))(((........)))))))))).((((.(((((.....)))))..)).)))))) ( -37.00)
>DroSim_CAF1 18215 101 - 1
AGCAGCCAACUUUUGUAGGUUUCCGGUUGGCCAAAGUGGUCCAACUGGCCAAGUUGAAGUGGAAAAGUUAGCCGAUGCAUGCGGAAUGCAGCCGAGCGGCU
...(((((((((((........((((((((((.....)).))))))))(((........)))))))))).((((.(((((.....)))))..)).)))))) ( -37.00)
>DroEre_CAF1 19842 101 - 1
GGCAGCCAACUUUCGUGGGUUUCCGGACGGCUAAUGUGGUCCAACUGGCCAAGUUGAAGUGGAAAAGUUAGCCGAUGCAUGCAGAAUGCAGCCGAGCGGCU
((.((((.((....)).)))).))...((((((((....((((.((...........))))))...)))))))).(((((.....)))))(((....))). ( -34.40)
>DroYak_CAF1 17137 101 - 1
AGCAAGCAACUUUUGUAGGUUUCCGGAUGGCUAAAGUGCUGCAACUGGCCAAGUUGAAGUGGAAAAGUUAGCCGAUGCAUGCAGAAUGCAGCCGAGCGGCU
.....(((..(((((((.((...(((.(((((.....(((.(((((.....))))).))).....))))).)))..)).))))))))))((((....)))) ( -29.50)
>consensus
AGCAGCCAACUUUUGUAGGUUUCCGGUUGGCCAAAGUGGUCCAACUGGCCAAGUUGAAGUGGAAAAGUUAGCCGAUGCAUGCGGAAUGCAGCCGAGCGGCU
...(((((((((((.((..((((.(.(((((((..((......))))))))).).)))))).))))))).((((.(((((.....)))))..)).)))))) (-28.00 = -29.00 +   1.00)

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 11:19:38 2006