Locus 6430

Sequence ID X_DroMel_CAF1
Location 16,122,931 – 16,123,117
Length 186
Max. P 0.890918
window10497 window10498 window10499

overview

Window 7

Location 16,122,931 – 16,123,021
Length 90
Sequences 6
Columns 94
Reading direction reverse
Mean pairwise identity 79.94
Mean single sequence MFE -25.08
Consensus MFE -14.12
Energy contribution -16.07
Covariance contribution 1.95
Combinations/Pair 1.23
Mean z-score -1.88
Structure conservation index 0.56
SVM decision value 0.18
SVM RNA-class probability 0.619323
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16122931 90 - 22224390
GGUGGGGGGACAGCGAAAUUAUUAUAUCCCUGUCCCGAACCACCACCAUAACCGCCACCUAGAGUGCACAUAUUUCAUCGUUUUCAA----UUC
(((((.(((((((.((.((....)).)).)))))))...))))).........((.((.....))))....................----... ( -24.20)
>DroSim_CAF1 2401 94 - 1
GGUGGGGGGACAGCGAAAUUAUUAUAUCCCUGUCCCGAACCACCACCAUAACCGCCACCUAGAGUGCACAUAUUUCAGCGUUUUCAAUGUAUUC
(((((.(((((((.((.((....)).)).)))))))...))))).................(((((((...................))))))) ( -26.01)
>DroEre_CAF1 2371 94 - 1
GGUGGGGGGACAGCGAAAUUAUUAUAACCCUGUCCGGCACCACCACCAUAACCGCCACCUAGAGUGCACAUAUUUCAGUGUUUUCAGUGUAUUC
(((((((((((((.(.............)))))))((.....)).......)).)))))..((((((((.................)))))))) ( -27.75)
>DroWil_CAF1 1843 88 - 1
GGUGGAGGAACAGCAAAGUUGUUGUAUCCCUGUCCGGCACCACCACCGUAACCGCCACCUAAGG---ACAUCAUUAUGUACUU---AUGCAUUU
(((((.(((((((((....)))))).))).....(((........)))...)))))...((((.---((((....)))).)))---)....... ( -22.50)
>DroYak_CAF1 2323 94 - 1
GGUGGGGGGACAGCGAAAUUGUUAUAUCCCUGUCCGGCACCACCACCAUAACCGCCACCUAGAGUGCACAUAUUUCAGUGUUUUCAGUGUAUUC
(((((((((((((.((.((....)).)).))))))((.....)).......)).)))))..((((((((.................)))))))) ( -30.03)
>DroPer_CAF1 2077 86 - 1
GGUGGAGGGACAUUAAAAUUAUUAAAGCCCUGGCCG---CCGCCACCAUAACCUCCACCUAAAGCACAAAUAUUUCGAUGUUUUUUU----UU-
((((((((....((((.....)))).....((((..---..))))......)))))))).(((((((.........).))))))...----..- ( -20.00)
>consensus
GGUGGGGGGACAGCGAAAUUAUUAUAUCCCUGUCCGGCACCACCACCAUAACCGCCACCUAGAGUGCACAUAUUUCAGUGUUUUCAAUGUAUUC
(((((..((((((.((.((....)).)).))))))....))))).................(((.((((........)))).)))......... (-14.12 = -16.07 +   1.95)

alignment

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secondary structure

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Window 8

Location 16,122,965 – 16,123,061
Length 96
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 84.58
Mean single sequence MFE -30.00
Consensus MFE -21.26
Energy contribution -20.71
Covariance contribution -0.55
Combinations/Pair 1.29
Mean z-score -2.52
Structure conservation index 0.71
SVM decision value 0.22
SVM RNA-class probability 0.638767
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16122965 96 + 22224390
GGCGGUUAUGGUGGUGG---------UUCGGGACAGGGAUAUAAUAAUUUCGCUGUCCCCCCACCAAAUUACCAGCAAAUGCCAAAUAAAACGGGUAACUACAAC
.(((((.....((((((---------...(((((((.((..........)).))))))).))))))....))).))...((((..........))))........ ( -33.40)
>DroVir_CAF1 2 101 + 1
-GCGGUUAUGGUGGCGGUGGCGGUGGUGCCGGACAG---UACAAUAAUUUUGCUGUUCCUCCGCCAAAUUACCAACAAAUGCCAAACAAAACUGGUAAUUAUAAU
-..(((.....((((((.(((((.....)))(((((---((.........))))))))).))))))....)))......(((((........)))))........ ( -32.20)
>DroEre_CAF1 2409 96 + 1
GGCGGUUAUGGUGGUGG---------UGCCGGACAGGGUUAUAAUAAUUUCGCUGUCCCCCCACCAAACUACCAACAAAUGCCAAAUAAAACGGGUAACUACAAC
((((....(((((((((---------((..((((((.(..((....))..).))))))...))))..))))))).....))))...................... ( -31.00)
>DroWil_CAF1 1875 96 + 1
GGCGGUUACGGUGGUGG---------UGCCGGACAGGGAUACAACAACUUUGCUGUUCCUCCACCAAAUUACCAACAAAUGCCAAAUAAAAGUGGUAACUACAAU
...(((.....((((((---------....((((((.((..........)).))))))..))))))....)))......(((((........)))))........ ( -26.00)
>DroYak_CAF1 2361 96 + 1
GGCGGUUAUGGUGGUGG---------UGCCGGACAGGGAUAUAACAAUUUCGCUGUCCCCCCACCAAACUACCAACAAAUGCCAAAUAAAACGGGUAACUACAAC
((((....(((((((((---------((..((((((.((..........)).))))))...))))..))))))).....))))...................... ( -32.30)
>DroAna_CAF1 1 96 + 1
GGCGGUUAUGGUGGUGG---------UGCCGGGCAAGGCUACAACAAUUUUGCUGUUCCCCCGCCAAACUAUCAACAAAUGCCAAAUAAAUCUGGAAACUAUAAU
((((....(((((((((---------((..(((...(((............)))...))).))))..))))))).....))))..........(....)...... ( -25.10)
>consensus
GGCGGUUAUGGUGGUGG_________UGCCGGACAGGGAUACAACAAUUUCGCUGUCCCCCCACCAAACUACCAACAAAUGCCAAAUAAAACGGGUAACUACAAC
((..(((.((((((.((.............((((((.(............).)))))))))))))))))..))......((((..........))))........ (-21.26 = -20.71 +  -0.55)

alignment

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secondary structure

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dotplot

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Window 9

Location 16,123,021 – 16,123,117
Length 96
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 75.11
Mean single sequence MFE -19.10
Consensus MFE -12.08
Energy contribution -12.36
Covariance contribution 0.28
Combinations/Pair 1.08
Mean z-score -1.63
Structure conservation index 0.63
SVM decision value 0.96
SVM RNA-class probability 0.890918
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16123021 96 + 22224390
AAAUUACCAGCAAAUGCCAAAUAAAACGGGUAACUACAACGAGCCACCUCCGAACUACGGCAAACAAGGCGGUGGUAAGGCGUGCAUGCGAACU-----------UU
.........(((.(((((........((...........)).((((((.((...(....).......)).))))))..)))))...))).....-----------.. ( -23.50)
>DroVir_CAF1 63 106 + 1
AAAUUACCAACAAAUGCCAAACAAAACUGGUAAUUAUAAUGAGCCCCCUCCAAAUUAUAACAAACCAGGCGGUGGUAAGUCCAAUU-GUAAAUCAAACAGAAACUGU
...((((((.....((((.........((((..((((((((((....)))...)))))))...)))))))).))))))........-.........((((...)))) ( -16.90)
>DroSim_CAF1 2495 96 + 1
AAACUACCAGCAAAUGCCAAAUAAAACGGGUAACUACAACGAGCCACCUCCGAACUACGGCAAACAAGGCGGUGGUAAGGCGUGCAUGCAAAUU-----------UC
.........(((.(((((........((...........)).((((((.((...(....).......)).))))))..)))))...))).....-----------.. ( -23.50)
>DroEre_CAF1 2465 96 + 1
AAACUACCAACAAAUGCCAAAUAAAACGGGUAACUACAACGAACCACCUCCAAACUACGGCAAACAAGGCGGUGGUAAGGCGUGCAUGUGAACU-----------CC
.........(((.(((((........((...........)).((((((.((................)).))))))..)))))...))).....-----------.. ( -19.79)
>DroMoj_CAF1 78 107 + 1
AAAUUACCAGCAAAUGCCAAAUAAAACUGGUAACUAUAACGAGCCCCCUCCAAACUAUAACAAGCCAGGCGGAGGUAAGUACUAUCCAGAAAUUCAAUCCAAAUAGC
...(((((((................))))))).....((..(((.((.((...((......))...)).)).)))..))........................... ( -15.29)
>DroAna_CAF1 57 91 + 1
AAACUAUCAACAAAUGCCAAAUAAAUCUGGAAACUAUAAUGAACCACCUCCAAACUACAGCAAGCAAGGUGGUGGUAAG-----CACUUAAAUU-----------UU
..............(((...........(....)........((((((.((...((......))...)).))))))..)-----))........-----------.. ( -15.60)
>consensus
AAACUACCAACAAAUGCCAAAUAAAACGGGUAACUACAACGAGCCACCUCCAAACUACAGCAAACAAGGCGGUGGUAAGGCGUGCAUGUAAAUU___________UC
..............((((..........))))..........((((((.((................)).))))))............................... (-12.08 = -12.36 +   0.28)

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 12:13:33 2006