Locus 9713

Sequence ID 3R_DroMel_CAF1
Location 25,688,476 – 25,688,608
Length 132
Max. P 0.858398
window15512 window15513 window15514

overview

Window 2

Location 25,688,476 – 25,688,568
Length 92
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 81.97
Mean single sequence MFE -28.84
Consensus MFE -22.99
Energy contribution -23.02
Covariance contribution 0.03
Combinations/Pair 1.11
Mean z-score -1.56
Structure conservation index 0.80
SVM decision value 0.37
SVM RNA-class probability 0.706917
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25688476 92 + 27905053
-CCGGACUAACUCUUGAACUCAUUU------UUUCAGCUUGGCUCCGGCCGCGUGCACAAGGUGCGCACCCGUGGUGGAAACACCAAGCUCCGUGCUCU
-(((((((((...(((((.......------.))))).)))).)))))..(((..(.....)..))).....(((((....)))))(((.....))).. ( -31.00)
>DroSec_CAF1 4305 98 + 1
-UCGGACUAACUCUUGAACUUAUUUUUUUUUUUUCAGCUUGGCUCCGGACGCGUGCACAAGGUGCGCACCCGUGGUGGAAACACCAAGCUCCGUGCUCU
-..(((((((...(((((..............))))).)))).)))(((.((((((((...)))))).....(((((....))))).)))))....... ( -29.94)
>DroSim_CAF1 4281 95 + 1
-ACGGACUAACUCUUGAACUUAUUUU---UUUUUCAGCUUGGCUCCGGACGCGUGCACAAGGUGCGCACCCGUGGUGGAAACACCAAGCUCCGUGCUCU
-(((((........((((........---...))))(((((((..(((..(((..(.....)..)))..)))..)((....)))))))))))))..... ( -30.60)
>DroEre_CAF1 4847 93 + 1
-CCGGACUAAC-CAAGAACUCUUUU----UCUUUCAGCUUGGCUCCGGUCGCGUGCACAAGGUGCGCACUCGUGGUGGAAACACCAAGCUCCGUGCUCU
-(((((((((.-((((((......)----))))...).)))).)))))..(((..(.....)..))).....(((((....)))))(((.....))).. ( -31.00)
>DroWil_CAF1 4762 99 + 1
ACUUGACUCAUUUAUUAUCUUUUUCUUUUGUUUUUAGCUUGGUGGUGCCCGCGUGCACAAAGUCCGCACUCGUGGUGGUAACACCAAGUUGCGCGCUCU
.............................((.(.((((((((((.((((((.((((.........)))).))....)))).)))))))))).).))... ( -24.40)
>DroYak_CAF1 4780 97 + 1
-CCCGACUAAC-CAAAAACUCUUUUUUCUUCUUUUAGCUUGGCUCCGGACGCGUGCACUCUGUGCGCACUCGUGGUGGAAACACCAAACUCCGUGCUCU
-..........-............................(((..((((.(((..(.....)..))).....(((((....)))))...)))).))).. ( -26.10)
>consensus
_CCGGACUAACUCAUGAACUCAUUUU___UUUUUCAGCUUGGCUCCGGACGCGUGCACAAGGUGCGCACCCGUGGUGGAAACACCAAGCUCCGUGCUCU
...................................(((.(((...(((..(((..(.....)..)))..)))(((((....)))))....))).))).. (-22.99 = -23.02 +   0.03)

alignment

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secondary structure

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Window 3

Location 25,688,476 – 25,688,568
Length 92
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 81.97
Mean single sequence MFE -30.74
Consensus MFE -23.46
Energy contribution -24.02
Covariance contribution 0.56
Combinations/Pair 1.11
Mean z-score -1.58
Structure conservation index 0.76
SVM decision value 0.33
SVM RNA-class probability 0.690955
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25688476 92 - 27905053
AGAGCACGGAGCUUGGUGUUUCCACCACGGGUGCGCACCUUGUGCACGCGGCCGGAGCCAAGCUGAAA------AAAUGAGUUCAAGAGUUAGUCCGG-
......(((((((((((...(((....((.((((((.....)))))).))...))))))))))((((.------.......))))........)))).- ( -33.80)
>DroSec_CAF1 4305 98 - 1
AGAGCACGGAGCUUGGUGUUUCCACCACGGGUGCGCACCUUGUGCACGCGUCCGGAGCCAAGCUGAAAAAAAAAAAAUAAGUUCAAGAGUUAGUCCGA-
......(((((((((((...(((...(((.((((((.....)))))).)))..))))))))))((((..............))))........)))).- ( -33.14)
>DroSim_CAF1 4281 95 - 1
AGAGCACGGAGCUUGGUGUUUCCACCACGGGUGCGCACCUUGUGCACGCGUCCGGAGCCAAGCUGAAAAA---AAAAUAAGUUCAAGAGUUAGUCCGU-
.....((((((((((((...(((...(((.((((((.....)))))).)))..))))))))))((((...---........))))........)))))- ( -33.80)
>DroEre_CAF1 4847 93 - 1
AGAGCACGGAGCUUGGUGUUUCCACCACGAGUGCGCACCUUGUGCACGCGACCGGAGCCAAGCUGAAAGA----AAAAGAGUUCUUG-GUUAGUCCGG-
......(((((((((((...(((....((.((((((.....)))))).))...))))))))))...((((----(......))))).-.....)))).- ( -32.30)
>DroWil_CAF1 4762 99 - 1
AGAGCGCGCAACUUGGUGUUACCACCACGAGUGCGGACUUUGUGCACGCGGGCACCACCAAGCUAAAAACAAAAGAAAAAGAUAAUAAAUGAGUCAAGU
...((.(((..(.(((((....))))).).(((((.......)))))))).)).............................................. ( -21.20)
>DroYak_CAF1 4780 97 - 1
AGAGCACGGAGUUUGGUGUUUCCACCACGAGUGCGCACAGAGUGCACGCGUCCGGAGCCAAGCUAAAAGAAGAAAAAAGAGUUUUUG-GUUAGUCGGG-
......((((...(((((....)))))((.((((((.....)))))).))))))...((..(((((..(((((........))))).-.)))))..))- ( -30.20)
>consensus
AGAGCACGGAGCUUGGUGUUUCCACCACGAGUGCGCACCUUGUGCACGCGUCCGGAGCCAAGCUGAAAAA___AAAAAAAGUUCAAGAGUUAGUCCGG_
.........((((((((...(((....((.((((((.....)))))).))...)))))))))))................................... (-23.46 = -24.02 +   0.56)

alignment

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secondary structure

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Window 4

Location 25,688,497 – 25,688,608
Length 111
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.47
Mean single sequence MFE -46.98
Consensus MFE -31.31
Energy contribution -32.53
Covariance contribution 1.23
Combinations/Pair 1.26
Mean z-score -1.85
Structure conservation index 0.67
SVM decision value 0.82
SVM RNA-class probability 0.858398
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25688497 111 + 27905053
UUU---------UUUCAGCUUGGCUCCGGCCGCGUGCACAAGGUGCGCACCCGUGGUGGAAACACCAAGCUCCGUGCUCUGCGCCUGGAAACCGGAAACUUCGCCUGGGCCUCCGAGGGA
.((---------((((.(...(((((.(((.(((..(.....)..)))..((((((((....)))))...((((.((.....)).))))...))).......))).))))).).)))))) ( -43.20)
>DroVir_CAF1 3946 120 + 1
GUUUAUAAAUAUUUGCAGCUUGGCGGUGCCCGCGUGCACAAGGUGCGCACCCGUGGUGGCAACACCAAAUUGCGCGCCCUGCGACUGGAGACAGGCAAUUUCGCCUGGGCUUCAGAGGGU
............((((((....((((...))))........((((((((....(((((....)))))...))))))))))))))((((((.(((((......)))))..))))))..... ( -54.50)
>DroGri_CAF1 4024 112 + 1
GUG--------CUUACAGCUUGGAGGUGCACGCGUUCACUCUGUACGCACCCGAGGUGGCAACACCAAAUUGCGCGCUCUGCGCCUGGAAACCGGCAAUUUUGCAUGGGCUUCAGAGGGU
..(--------(.(((((..((((.((....)).))))..))))).))((((..((((....)))).....((((.....))))(((((..((((((....))).)))..))))).)))) ( -45.50)
>DroWil_CAF1 4784 117 + 1
UUCUUU---UGUUUUUAGCUUGGUGGUGCCCGCGUGCACAAAGUCCGCACUCGUGGUGGUAACACCAAGUUGCGCGCUCUGCGUCUGGAAACCGGCAAUUUUGCAUGGGCUUCCGAAGGU
......---........((((..(((.((((..(((((((.(((.((((....(((((....)))))...)))).))).)).(((.(....).))).....)))))))))..))).)))) ( -39.50)
>DroMoj_CAF1 3888 118 + 1
GUGUAU--GUAUUUACAGCUUGGCGGAUCCCGCGUGCACAAGGUGCGCACCCGUGGUGGUAACAUCAAAUUGCGCGCUCUGCGUUUGGAAACCGGCAAUUUCGCCUGGGCUUCAGAGGGU
((((((--((....))......((((...)))))))))).(((((((((....(((((....)))))...))))))).)).(.((((((..(((((......))).))..)))))).).. ( -42.90)
>DroAna_CAF1 2678 114 + 1
UCA------AUCUUUCAGCUUGGCUCCAGCCGCGUGCACAAGGUGCGCACUCGUGGUGGAAACACCAAACUGCGCGCUCUGCGCCUGGAAACCGGCAACUUCGCCUGGGCCUCUGAGGGU
...------..(((((((...(((.((((..(((.(((...((((((((....(((((....)))))...)))))))).)))(((.(....).))).....)))))))))).))))))). ( -56.30)
>consensus
GUG______U_UUUUCAGCUUGGCGGUGCCCGCGUGCACAAGGUGCGCACCCGUGGUGGAAACACCAAAUUGCGCGCUCUGCGCCUGGAAACCGGCAAUUUCGCCUGGGCUUCAGAGGGU
.................((((......(((((((.(((...((((((((....(((((....)))))...)))))))).)))(((.(....).))).....)))..))))......)))) (-31.31 = -32.53 +   1.23)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:40:25 2006