Locus 6528

Sequence ID X_DroMel_CAF1
Location 16,351,576 – 16,351,734
Length 158
Max. P 0.999889
window10658 window10659 window10660

overview

Window 8

Location 16,351,576 – 16,351,681
Length 105
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 71.58
Mean single sequence MFE -34.72
Consensus MFE -12.31
Energy contribution -13.47
Covariance contribution 1.16
Combinations/Pair 1.21
Mean z-score -2.93
Structure conservation index 0.35
SVM decision value 3.62
SVM RNA-class probability 0.999458
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16351576 105 + 22224390
UUCUUAGCCACUCGAGGCACUCAGUCAUUUCGGG--------------GACUCCACCUUGAUAAGUAAUU-GAAGCCCCCGGGCAGUGUCAAUAACUAUGGCAAUGCCAAAUGGCAAGCG
......(((......))).....(((((((((((--------------(.((.((..............)-).)).)))))((((.(((((.......))))).)))))))))))..... ( -32.04)
>DroPse_CAF1 14456 115 + 1
GCCUUAGCCA----GGGCACUCAGUCAUAUUGAGUGUACUCCCAGCUGGGAGCCACCUUGAUAAGUAAUU-AAAGCCCGCAGGCAAUGCCAAUAGCUAUGGCAAUGACAAAUGCCAAAUA
(((.((((((----(((((((((((...))))))))..(((((....)))))...)))))..........-...(((....)))..........)))).))).................. ( -36.00)
>DroSec_CAF1 18975 105 + 1
UCCUUAGCCACUCGAGGCACUCAGUCAUUUCGGG--------------GGCUCCACCUUGAUAAGUAAUU-GAAGCCCCCGAGCAGUGUCAAUAACUAUGGCAAUGCCAAAUGGCAAGCG
......(((......))).....(((((((((((--------------((((.((..............)-).)))))))))(((.(((((.......))))).)))..))))))..... ( -35.74)
>DroEre_CAF1 13092 90 + 1
UCCUUAGCCA---------------CAUUUCGGG--------------GGCUCCACCUCGAUAAGUAAUU-GAAGCCCCCAGGCAGUGUCAAUAACUAUGACAAUGCCAAAUGGCAAGCG
..(((.((((---------------......(((--------------((((.....(((((.....)))-))))))))).((((.(((((.......))))).))))...))))))).. ( -35.50)
>DroPer_CAF1 14636 116 + 1
GCCUUAGCCA----GGGCACUCAGUCAUAUUGAGUGUACUCCCAGCUGGGAGCCACCUUGAUAAGUAAAUAAAAGCCCGCAGGCAAUGCCAAUAACUAUGGCAAUGANNNNNNNNNNNNN
((((..((..----(((((((((((...)))))))...(((((....)))))......................))))))))))..(((((.......)))))................. ( -34.30)
>consensus
UCCUUAGCCA____AGGCACUCAGUCAUUUCGGG______________GGCUCCACCUUGAUAAGUAAUU_GAAGCCCCCAGGCAGUGUCAAUAACUAUGGCAAUGCCAAAUGGCAAGCG
..(((((((......)))...........(((((......................))))))))).........(((....((((.(((((.......))))).))))....)))..... (-12.31 = -13.47 +   1.16)

alignment

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secondary structure

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Window 9

Location 16,351,576 – 16,351,681
Length 105
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 71.58
Mean single sequence MFE -40.46
Consensus MFE -13.62
Energy contribution -14.55
Covariance contribution 0.93
Combinations/Pair 1.26
Mean z-score -3.52
Structure conservation index 0.34
SVM decision value 4.40
SVM RNA-class probability 0.999889
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16351576 105 - 22224390
CGCUUGCCAUUUGGCAUUGCCAUAGUUAUUGACACUGCCCGGGGGCUUC-AAUUACUUAUCAAGGUGGAGUC--------------CCCGAAAUGACUGAGUGCCUCGAGUGGCUAAGAA
..((((((((((((((((....((((((((.........((((((((((-(....((.....)).)))))))--------------)))).))))))))))))))..))))))).))).. ( -40.40)
>DroPse_CAF1 14456 115 - 1
UAUUUGGCAUUUGUCAUUGCCAUAGCUAUUGGCAUUGCCUGCGGGCUUU-AAUUACUUAUCAAGGUGGCUCCCAGCUGGGAGUACACUCAAUAUGACUGAGUGCCC----UGGCUAAGGC
....((((....))))..(((.((((((..(((...(((....)))...-....((((((((.((((((((((....)))))).)))).....))).)))))))).----)))))).))) ( -40.30)
>DroSec_CAF1 18975 105 - 1
CGCUUGCCAUUUGGCAUUGCCAUAGUUAUUGACACUGCUCGGGGGCUUC-AAUUACUUAUCAAGGUGGAGCC--------------CCCGAAAUGACUGAGUGCCUCGAGUGGCUAAGGA
..((((((((((((((((....((((((((........(((((((((((-(....((.....)).)))))))--------------)))))))))))))))))))..))))))).))).. ( -45.10)
>DroEre_CAF1 13092 90 - 1
CGCUUGCCAUUUGGCAUUGUCAUAGUUAUUGACACUGCCUGGGGGCUUC-AAUUACUUAUCGAGGUGGAGCC--------------CCCGAAAUG---------------UGGCUAAGGA
..((((((((..((((.(((((.......))))).))))((((((((((-(....(((...))).)))))))--------------))))....)---------------)))).))).. ( -41.30)
>DroPer_CAF1 14636 116 - 1
NNNNNNNNNNNNNUCAUUGCCAUAGUUAUUGGCAUUGCCUGCGGGCUUUUAUUUACUUAUCAAGGUGGCUCCCAGCUGGGAGUACACUCAAUAUGACUGAGUGCCC----UGGCUAAGGC
..................(((.((((((..(((...(((....)))........((((((((.((((((((((....)))))).)))).....))).)))))))).----)))))).))) ( -35.20)
>consensus
CGCUUGCCAUUUGGCAUUGCCAUAGUUAUUGACACUGCCUGGGGGCUUC_AAUUACUUAUCAAGGUGGAGCC______________CCCGAAAUGACUGAGUGCCC____UGGCUAAGGA
....((((....))))...((.((((((........(((....))).......(((((((((...(((...................)))...))).)))))).......)))))).)). (-13.62 = -14.55 +   0.93)

alignment

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secondary structure

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dotplot

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Window 0

Location 16,351,641 – 16,351,734
Length 93
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 64.96
Mean single sequence MFE -22.88
Consensus MFE -9.21
Energy contribution -11.21
Covariance contribution 2.00
Combinations/Pair 1.35
Mean z-score -1.76
Structure conservation index 0.40
SVM decision value 0.07
SVM RNA-class probability 0.571010
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16351641 93 + 22224390
GGGCAGUGUCAAUAACUAUGGCAAUGCCAAAUGGCAAGCGGCGAACGACAAAGGGAUAUAUACACA--------------UGUAUCCUGAAGCGGUAUAUUUA-ACAG
.((((.(((((.......))))).))))..((.((..(((.....)).)...(((((((((....)--------------))))))))...)).)).......-.... ( -24.60)
>DroPse_CAF1 14531 106 + 1
AGGCAAUGCCAAUAGCUAUGGCAAUGACAAAUGCCAAAUAACAAAGGACAGAGGACGAAGGACAAAGGCUCUUUGUGCCCCAAAAGCUUUGGCUUUAAAUU-G-AUAG
.......(((((.((((.(((((........)))))..............(.((((((((..(....)..)))))).)).)...)))))))))........-.-.... ( -26.40)
>DroSec_CAF1 19040 94 + 1
GAGCAGUGUCAAUAACUAUGGCAAUGCCAAAUGGCAAGCGGCGAACGACAAAGGGAUAUAUACACA--------------UGUAUCCUGAAGCGGUAUAUUUAUACAG
..((..(((((.......))))).((((....)))).))......((.....(((((((((....)--------------))))))))....))((((....)))).. ( -23.70)
>DroEre_CAF1 13142 93 + 1
AGGCAGUGUCAAUAACUAUGACAAUGCCAAAUGGCAAGCGGCGAAAGACAAAGGGAUAUGUACACG--------------UGUAUCCUGAAGCGGUAUAUAUA-ACAG
.((((.(((((.......))))).))))..((.((....(.(....).)...((((((..(....)--------------..))))))...)).)).......-.... ( -24.50)
>DroAna_CAF1 15485 77 + 1
CGGCUG------------CGGCAAUGCCACACA-CAAG-----GAUCACAAAAGGAUAUUUACGCA------------CUCAUAUCCUUUGGCGUUAUAUUUC-AAAG
..((..------------..))((((((.....-...(-----.....).(((((((((.......------------...))))))))))))))).......-.... ( -15.20)
>consensus
AGGCAGUGUCAAUAACUAUGGCAAUGCCAAAUGGCAAGCGGCGAACGACAAAGGGAUAUAUACACA______________UGUAUCCUGAAGCGGUAUAUUUA_ACAG
.((((.(((((.......))))).))))........................((((((((....................)))))))).................... ( -9.21 = -11.21 +   2.00)

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 12:16:03 2006