Locus 265

Sequence ID 2R_DroMel_CAF1
Location 1,659,954 – 1,660,109
Length 155
Max. P 0.984128
window563 window564 window565

overview

Window 3

Location 1,659,954 – 1,660,069
Length 115
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 83.46
Mean single sequence MFE -31.15
Consensus MFE -30.67
Energy contribution -30.67
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.11
Structure conservation index 0.98
SVM decision value 1.96
SVM RNA-class probability 0.984128
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1659954 115 + 20766785
----AAAAAAUUCAGUAAAAUUGCAUCAAAAUAA-AAAAGUCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCUUCUA
----..........(((....)))..........-...((..(((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).)))..)). ( -31.60)
>DroPse_CAF1 75350 112 + 1
UAACAAGAAGA----AAAAAAUG----UAAAAAAAUUGUGCCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCCGUUG
...........----........----............((.(((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).))).)).. ( -31.20)
>DroSec_CAF1 45566 108 + 1
----AAAA--------AAAAUUGCGUCUAAAAAAUCAAAUUCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCUCGUA
----....--------..........................(((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).)))..... ( -30.80)
>DroSim_CAF1 42478 109 + 1
----AAAAA-------AAAAUUGCAUCUAAAAAAGUAAAUUCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCUUAUG
----.....-------..........................(((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).)))..... ( -30.80)
>DroEre_CAF1 49963 112 + 1
----AAGUAGU----AAAAAUUGGAUCAAAAAAUUGUUUUUCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCUGACA
----.......----...................((((....(((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).))).)))) ( -31.30)
>DroPer_CAF1 69326 112 + 1
UAACAAGAAGA----AAAAAAUG----UAAAAAAGUUGUGCCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCCGUUG
...........----........----............((.(((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).))).)).. ( -31.20)
>consensus
____AAAAAG_____AAAAAUUGCAUCUAAAAAAGUAAAGUCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCUGAUA
..........................................(((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).)))..... (-30.67 = -30.67 +   0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 1,659,954 – 1,660,069
Length 115
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 83.46
Mean single sequence MFE -37.50
Consensus MFE -37.03
Energy contribution -37.03
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.75
Structure conservation index 0.99
SVM decision value 1.38
SVM RNA-class probability 0.948489
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1659954 115 - 20766785
UAGAAGCCUCCGUGGCGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCGACUUUU-UUAUUUUGAUGCAAUUUUACUGAAUUUUUU----
.((..(((((((.(((((.........)))).((((((..((((((....))))))..).)))))....).)))))))..))...-..............................---- ( -37.30)
>DroPse_CAF1 75350 112 - 1
CAACGGCCUCCGUGGCGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCGGCACAAUUUUUUUA----CAUUUUUU----UCUUCUUGUUA
...(.(((((((.(((((.........)))).((((((..((((((....))))))..).)))))....).))))))).).............----........----........... ( -37.50)
>DroSec_CAF1 45566 108 - 1
UACGAGCCUCCGUGGCGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCGAAUUUGAUUUUUUAGACGCAAUUUU--------UUUU----
.....(((((((.(((((.........)))).((((((..((((((....))))))..).)))))....).)))))))(..(((((....)))))..)......--------....---- ( -38.30)
>DroSim_CAF1 42478 109 - 1
CAUAAGCCUCCGUGGCGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCGAAUUUACUUUUUUAGAUGCAAUUUU-------UUUUU----
.....(((((((.(((((.........)))).((((((..((((((....))))))..).)))))....).)))))))..........................-------.....---- ( -37.10)
>DroEre_CAF1 49963 112 - 1
UGUCAGCCUCCGUGGCGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCGAAAAACAAUUUUUUGAUCCAAUUUUU----ACUACUU----
.(((((((((((.(((((.........)))).((((((..((((((....))))))..).)))))....).)))))))(((((....))))))))).........----.......---- ( -37.30)
>DroPer_CAF1 69326 112 - 1
CAACGGCCUCCGUGGCGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCGGCACAACUUUUUUA----CAUUUUUU----UCUUCUUGUUA
...(.(((((((.(((((.........)))).((((((..((((((....))))))..).)))))....).))))))).).............----........----........... ( -37.50)
>consensus
CAACAGCCUCCGUGGCGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGUCCACCCGGGGGCGAAAUAAAUUUUUUAGAUGCAAUUUUU_____CUUCUU____
.....(((((((.(((((.........)))).((((((..((((((....))))))..).)))))....).))))))).......................................... (-37.03 = -37.03 +   0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,659,989 – 1,660,109
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 83.71
Mean single sequence MFE -38.49
Consensus MFE -30.68
Energy contribution -30.85
Covariance contribution 0.17
Combinations/Pair 1.04
Mean z-score -2.02
Structure conservation index 0.80
SVM decision value 0.52
SVM RNA-class probability 0.769035
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1659989 120 + 20766785
UCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCUUCUACAUUUUGAUGGACUAAUGUCGAUUGUCAGCCAAGCCAAAA
..(((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).)))...........(((.(((....))).)))................ ( -35.60)
>DroPse_CAF1 75382 113 + 1
CCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCCGUUGCCGCUUUCACUUCAAAUGGCGAUUAAAAGAGAA-------
..(((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).))).(((((((.(((......))))))))))..........------- ( -36.60)
>DroSec_CAF1 45594 120 + 1
UCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCUCGUACAUUCUGUUAGACUAAUGUCGAGUGUAAGCCAAGCCAAAA
..((..((((((((.......))))).....((((((.....)))))).((((.........))))..))).((((..(((((((.....(((....))))))))))))))..))..... ( -39.10)
>DroSim_CAF1 42507 120 + 1
UCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCUUAUGCAUUUCAUUCGACUAAUGUCGAGUGUAAGCCAAGCCAAAA
......((((((((.......))))).....((((((.....)))))).((((.........))))..))).(((((..((.((.((((((((....)))))))).)))).))))).... ( -44.30)
>DroEre_CAF1 49995 120 + 1
UCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCUGACAUAAGUUCUUGGUCUAAUGUCAAGGGUAAGCCAAGCCAAAA
..(((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).)))((((((.((........)).))))))..(((.......))).... ( -39.50)
>DroPer_CAF1 69358 113 + 1
CCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCCGUUGCCGCUUUCACUUCAUAUGGCGAUUAAAAGAGAA-------
..(((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).))).(((((((.............)))))))..........------- ( -35.82)
>consensus
UCGCCCCCGGGUGGACUCGAACCACCAACCUUUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCUGAUACAUUUUGUUCGACUAAUGUCGAGUGUAAGCCAAGCCAAAA
..(((.((((((((.......))))).....((((((.....)))))).((((.........))))..))).)))...............(((....))).................... (-30.68 = -30.85 +   0.17)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:34:02 2006