Locus 4072

Sequence ID X_DroMel_CAF1
Location 10,773,588 – 10,773,710
Length 122
Max. P 0.766825
window6697 window6698 window6699

overview

Window 7

Location 10,773,588 – 10,773,683
Length 95
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 82.41
Mean single sequence MFE -31.87
Consensus MFE -24.23
Energy contribution -24.15
Covariance contribution -0.08
Combinations/Pair 1.30
Mean z-score -1.90
Structure conservation index 0.76
SVM decision value 0.52
SVM RNA-class probability 0.766825
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10773588 95 + 22224390
UCGCCAACGCCU---ACACCGGGAUCUCCUUCGGCUUGGCAAUCACCGUUGCCAACGCCCCAGCAUCCUGUGCAUCCGCCCACUAAGGCUACUUCGGC--
..(((.......---.(((.(((((...((..(((((((((((....)))))))).)))..)).)))))))).....(((......)))......)))-- ( -30.00)
>DroVir_CAF1 27436 97 + 1
---CCAACGCCAAGCACGCCAACAUCGCCAUCCGCGUGGCAGGCGCCUUUGCCGACGCCUGUGCAUCCAGCUGUGCCGGCUGUUAAGCCAGCUCCGGCAG
---.....(((..((((((((....(((.....)))))))(((((.(......).)))))))))..........((.((((....)))).))...))).. ( -36.70)
>DroSec_CAF1 22968 95 + 1
UCGCCAACGCCC---ACACCGGGAUCUCCUUCGGCUUGGCAAUCGCCGUUGCCAACGCCCCAGCAUCCUGUGCAUCCGCCAACCAAGGCUACUUCGGC--
..(((.......---.(((.(((((...((..(((((((((((....)))))))).)))..)).)))))))).....(((......)))......)))-- ( -30.50)
>DroSim_CAF1 21518 95 + 1
UCGCCAACGCCC---ACACCGGGAUCUCCUUCGGCUUGGCAAUCGCCGUUGCCAACGCCCCAGCAUCCUGUGCAUCCGCCCACGAAGGCUACAUCGGC--
..(((....(((---.....)))....((((((((((((((((....)))))))).)))...((((...))))..........))))).......)))-- ( -32.10)
>DroEre_CAF1 20657 95 + 1
UCGCCAACGCCC---ACACCGGGAUCUCCUUCGGCUUGGCAAUCGCCGUUGCCAACGCCCCAGCAUCCCGUGCAUCCUCCCACCAAGGCUACAUCAGC--
..(((.......---.....(((((...((..(((((((((((....)))))))).)))..)).)))))(((........)))...))).........-- ( -28.20)
>DroYak_CAF1 22497 95 + 1
UCGCCUACGCCC---ACGCCGGGCUCUCCAUCGGCUUGGCAAUCGCCGUUGCCAACGCCCCAGCAUCCUGUGCAUCCGCCCACCAAGGCUACGUCGGC--
..(((.(((...---..(((((((........(((((((((((....)))))))).)))...((((...))))....)))).....)))..))).)))-- ( -33.70)
>consensus
UCGCCAACGCCC___ACACCGGGAUCUCCUUCGGCUUGGCAAUCGCCGUUGCCAACGCCCCAGCAUCCUGUGCAUCCGCCCACCAAGGCUACUUCGGC__
........(((.....(((.(((((((.....(((((((((((....)))))))).)))..)).)))))))).....(((......)))......))).. (-24.23 = -24.15 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 8

Location 10,773,588 – 10,773,683
Length 95
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 82.41
Mean single sequence MFE -40.98
Consensus MFE -30.52
Energy contribution -31.38
Covariance contribution 0.87
Combinations/Pair 1.23
Mean z-score -1.53
Structure conservation index 0.74
SVM decision value 0.16
SVM RNA-class probability 0.613744
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10773588 95 - 22224390
--GCCGAAGUAGCCUUAGUGGGCGGAUGCACAGGAUGCUGGGGCGUUGGCAACGGUGAUUGCCAAGCCGAAGGAGAUCCCGGUGU---AGGCGUUGGCGA
--(((((.((.((((....))))...(((((.((((.((..(((.(((((((......))))))))))...))..))))..))))---).)).))))).. ( -39.00)
>DroVir_CAF1 27436 97 - 1
CUGCCGGAGCUGGCUUAACAGCCGGCACAGCUGGAUGCACAGGCGUCGGCAAAGGCGCCUGCCACGCGGAUGGCGAUGUUGGCGUGCUUGGCGUUGG---
..(((((.(((((((....)))))))..........(((((((((((......)))))))(((((((.....)))....))))))))))))).....--- ( -45.20)
>DroSec_CAF1 22968 95 - 1
--GCCGAAGUAGCCUUGGUUGGCGGAUGCACAGGAUGCUGGGGCGUUGGCAACGGCGAUUGCCAAGCCGAAGGAGAUCCCGGUGU---GGGCGUUGGCGA
--(((((....((((..((((((....)).))....))..)))).)))))..((.((((.(((..((((..((....))))))..---.))))))).)). ( -38.90)
>DroSim_CAF1 21518 95 - 1
--GCCGAUGUAGCCUUCGUGGGCGGAUGCACAGGAUGCUGGGGCGUUGGCAACGGCGAUUGCCAAGCCGAAGGAGAUCCCGGUGU---GGGCGUUGGCGA
--((((((((.((((....))))....((((.((((.((..(((.(((((((......))))))))))...))..))))..))))---..)))))))).. ( -41.70)
>DroEre_CAF1 20657 95 - 1
--GCUGAUGUAGCCUUGGUGGGAGGAUGCACGGGAUGCUGGGGCGUUGGCAACGGCGAUUGCCAAGCCGAAGGAGAUCCCGGUGU---GGGCGUUGGCGA
--((..((((..((((.....))))((((.((((((.((..(((.(((((((......))))))))))...))..))))))))))---..))))..)).. ( -39.80)
>DroYak_CAF1 22497 95 - 1
--GCCGACGUAGCCUUGGUGGGCGGAUGCACAGGAUGCUGGGGCGUUGGCAACGGCGAUUGCCAAGCCGAUGGAGAGCCCGGCGU---GGGCGUAGGCGA
--(((.((((.((((....))))...........((((((((.(((((((...(((....)))..))))))).....))))))))---..)))).))).. ( -41.30)
>consensus
__GCCGAAGUAGCCUUGGUGGGCGGAUGCACAGGAUGCUGGGGCGUUGGCAACGGCGAUUGCCAAGCCGAAGGAGAUCCCGGUGU___GGGCGUUGGCGA
..(((......((((....)))).(((((.....((((((((((.(((((...(((....)))..)))))....).))))))))).....)))))))).. (-30.52 = -31.38 +   0.87)

alignment

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secondary structure

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dotplot

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Window 9

Location 10,773,611 – 10,773,710
Length 99
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 81.33
Mean single sequence MFE -32.28
Consensus MFE -21.10
Energy contribution -20.92
Covariance contribution -0.19
Combinations/Pair 1.30
Mean z-score -1.66
Structure conservation index 0.65
SVM decision value 0.20
SVM RNA-class probability 0.632053
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10773611 99 + 22224390
UCCUUCGGCUUGGCAAUCACCGUUGCCAACGCCCCAGCAUCCUGUGCAUCCGCCCACUAAGGCUACUUCGGC---GGCCACGCCUACCCCGACACCAACGCC
......(((((((((((....)))))))).)))...((.....((((....(((......)))......(((---(....))))......).)))....)). ( -28.70)
>DroVir_CAF1 27459 102 + 1
GCCAUCCGCGUGGCAGGCGCCUUUGCCGACGCCUGUGCAUCCAGCUGUGCCGGCUGUUAAGCCAGCUCCGGCAGCUGUUACGCCCGGCACGCCAGCUGGCAG
(((....((((((((((((.(......).))))))).....(((((((((.((((....)))).))....))))))).)))))..)))..(((....))).. ( -45.90)
>DroSec_CAF1 22991 99 + 1
UCCUUCGGCUUGGCAAUCGCCGUUGCCAACGCCCCAGCAUCCUGUGCAUCCGCCAACCAAGGCUACUUCGGC---GGCCACGCCUACCCCGACACCAACGCC
......(((((((((((....)))))))).)))...((.....((((....(((......)))......(((---(....))))......).)))....)). ( -29.20)
>DroSim_CAF1 21541 99 + 1
UCCUUCGGCUUGGCAAUCGCCGUUGCCAACGCCCCAGCAUCCUGUGCAUCCGCCCACGAAGGCUACAUCGGC---GGCCACGCCUACCCCGACACCAACGCC
.((((((((((((((((....)))))))).)))...((((...))))..........))))).......(((---(....)))).................. ( -31.30)
>DroEre_CAF1 20680 99 + 1
UCCUUCGGCUUGGCAAUCGCCGUUGCCAACGCCCCAGCAUCCCGUGCAUCCUCCCACCAAGGCUACAUCAGC---GGCCACGCCUACGCCCACACCAUCGCC
......(((((((((((....)))))))).)))...((((...)))).............(((.......((---(....)))....)))............ ( -23.50)
>DroYak_CAF1 22520 99 + 1
UCCAUCGGCUUGGCAAUCGCCGUUGCCAACGCCCCAGCAUCCUGUGCAUCCGCCCACCAAGGCUACGUCGGC---GGCCACGCCUACGCCGACACCAACGCC
......(((((((((((....)))))))).)))...((((...))))....(((......)))...((((((---(..........)))))))......... ( -35.10)
>consensus
UCCUUCGGCUUGGCAAUCGCCGUUGCCAACGCCCCAGCAUCCUGUGCAUCCGCCCACCAAGGCUACUUCGGC___GGCCACGCCUACCCCGACACCAACGCC
......(((((((((((....)))))))).)))............((....(((......)))....((((....(((...)))....)))).......)). (-21.10 = -20.92 +  -0.19)

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 11:15:45 2006