Locus 6542

Sequence ID 2R_DroMel_CAF1
Location 20,456,225 – 20,456,347
Length 122
Max. P 0.938006
window10417 window10418 window10419

overview

Window 7

Location 20,456,225 – 20,456,327
Length 102
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 69.55
Mean single sequence MFE -27.02
Consensus MFE -12.13
Energy contribution -11.69
Covariance contribution -0.44
Combinations/Pair 1.38
Mean z-score -1.56
Structure conservation index 0.45
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20456225 102 + 20766785
UACG-----------UAACUGCGCAUCCCGUCAUUAGCUUUUUUACUUUCGACGGCGACGGACGUUUCUUUUCAUCCGUGUCCGCGCAUCCUUAGUUGACUAAAUUCUGCCGC
...(-----------((..(((((.(((((((...((........))...))))).)).(((((..............))))))))))...((((....))))....)))... ( -23.24)
>DroVir_CAF1 23506 101 + 1
ACAGUUGCGAUUUGGUGGCUGCGCAUUCCGUUAGUUGCUUUUUUCACUUCGGCGGCGGCAGUCGUUUCCUCU-------CGCCGCGCAGCGAACGCC-----AUUUUAGCCGC
...((.((((..((((((((((((...(((..(((..........))).))).(((((.((.......)).)-------)))))))))))...))))-----)..)).)).)) ( -33.80)
>DroSec_CAF1 19723 98 + 1
UACG-----------UAACUGCGCAUUCCGUCAAUAGCUUUUUUACUUUUGACGACGACGGAUGUUUCCUUU----CGUGUCCGCGCAUCCUUAGUUCACUAAAUUCUGCCGC
...(-----------((..(((((....((((((.((........)).))))))((((.(((....)))..)----)))....)))))...((((....))))....)))... ( -23.60)
>DroEre_CAF1 26490 102 + 1
UACG-----------UAACUGCGCAUUCCGCCAUUAGCUUUUUUACUUUCAACGGCGACGGAUGUUUCUUUUCAUUCGUGUCCGCGCAUCCUUAGUUCACUAAAUUCUGCGGC
..((-----------((..(((((....((((.....................))))(((((((........)))))))....)))))...((((....))))....)))).. ( -25.20)
>DroYak_CAF1 19674 102 + 1
UACG-----------UAACUGCGCAUUCCGCCAUUAGCUUUUCUACUUUCGACGGCGACGGAUGUUUCUUUUCAUUCGUGUCCGCGCAUCCUUAGUUCACUAAAUUCUGCCGC
...(-----------((..(((((....((((.....................))))(((((((........)))))))....)))))...((((....))))....)))... ( -22.10)
>DroMoj_CAF1 25931 101 + 1
UUCCUUACGAUUUGGUGGCUGCGCAUUCCGUUAGUUGCUUUUUUCACUUCAGCGGCGGCAGUCGCUCUCUUU-------CGCCGCGCAGCAAACGCC-----AUUUCAGCCGC
........((..(((((((((((((..........))).............(((((((.((.......)).)-------)))))))))))...))))-----)..))...... ( -34.20)
>consensus
UACG___________UAACUGCGCAUUCCGUCAUUAGCUUUUUUACUUUCGACGGCGACGGACGUUUCCUUU____CGUGUCCGCGCAUCCUUAGUUCACUAAAUUCUGCCGC
...................(((((....((((.....................))))..((((................)))))))))......................... (-12.13 = -11.69 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 8

Location 20,456,225 – 20,456,327
Length 102
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 69.55
Mean single sequence MFE -29.73
Consensus MFE -13.74
Energy contribution -15.42
Covariance contribution 1.67
Combinations/Pair 1.38
Mean z-score -1.91
Structure conservation index 0.46
SVM decision value 1.07
SVM RNA-class probability 0.909458
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20456225 102 - 20766785
GCGGCAGAAUUUAGUCAACUAAGGAUGCGCGGACACGGAUGAAAAGAAACGUCCGUCGCCGUCGAAAGUAAAAAAGCUAAUGACGGGAUGCGCAGUUA-----------CGUA
((((((...(((((....)))))..)))(((...(((((((........)))))))..((((((..(((......)))..))))))....))).....-----------))). ( -32.50)
>DroVir_CAF1 23506 101 - 1
GCGGCUAAAAU-----GGCGUUCGCUGCGCGGCG-------AGAGGAAACGACUGCCGCCGCCGAAGUGAAAAAAGCAACUAACGGAAUGCGCAGCCACCAAAUCGCAACUGU
((((......(-----(((.((((((..((((((-------.(.(....).....)))))))...))))))....(((.(....)...)))...)))).....))))...... ( -33.80)
>DroSec_CAF1 19723 98 - 1
GCGGCAGAAUUUAGUGAACUAAGGAUGCGCGGACACG----AAAGGAAACAUCCGUCGUCGUCAAAAGUAAAAAAGCUAUUGACGGAAUGCGCAGUUA-----------CGUA
((((((...(((((....)))))..)))(((((((((----...(....)...))).)))(((((.(((......))).)))))......))).....-----------))). ( -30.00)
>DroEre_CAF1 26490 102 - 1
GCCGCAGAAUUUAGUGAACUAAGGAUGCGCGGACACGAAUGAAAAGAAACAUCCGUCGCCGUUGAAAGUAAAAAAGCUAAUGGCGGAAUGCGCAGUUA-----------CGUA
...(((...(((((....)))))..)))(((...(((.(((........))).)))(((((((...(((......)))))))))).....))).....-----------.... ( -25.20)
>DroYak_CAF1 19674 102 - 1
GCGGCAGAAUUUAGUGAACUAAGGAUGCGCGGACACGAAUGAAAAGAAACAUCCGUCGCCGUCGAAAGUAGAAAAGCUAAUGGCGGAAUGCGCAGUUA-----------CGUA
((((((...(((((....)))))..)))(((...(((.(((........))).)))..((((((..(((......)))..))))))....))).....-----------))). ( -26.80)
>DroMoj_CAF1 25931 101 - 1
GCGGCUGAAAU-----GGCGUUUGCUGCGCGGCG-------AAAGAGAGCGACUGCCGCCGCUGAAGUGAAAAAAGCAACUAACGGAAUGCGCAGCCACCAAAUCGUAAGGAA
..(((((....-----....((..((..((((((-------..((.......))..))))))...))..))....(((.(....)...))).)))))......((....)).. ( -30.10)
>consensus
GCGGCAGAAUUUAGUGAACUAAGGAUGCGCGGACACG____AAAAGAAACAUCCGUCGCCGUCGAAAGUAAAAAAGCUAAUGACGGAAUGCGCAGUUA___________CGUA
..(((....(((((....)))))..(((((((....................))....((((((..(((......)))..))))))...))))))))................ (-13.74 = -15.42 +   1.67)

alignment

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secondary structure

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dotplot

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Window 9

Location 20,456,254 – 20,456,347
Length 93
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 67.75
Mean single sequence MFE -25.82
Consensus MFE -11.36
Energy contribution -11.95
Covariance contribution 0.59
Combinations/Pair 1.33
Mean z-score -1.99
Structure conservation index 0.44
SVM decision value 1.29
SVM RNA-class probability 0.938006
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20456254 93 - 20766785
-----------GGUGGUAGUGAGAAAAGCAUGCGGCAGAAUUUAGUCAACUAAGGAUGCGCGGACACGGAUGAAAAGAAACGUCCGUCGCCGUCGAAAGUAAAA
-----------((((............(..((((.((...(((((....)))))..))))))..)(((((((........)))))))))))..(....)..... ( -24.40)
>DroVir_CAF1 23546 91 - 1
UUUUAUUUUUUGGUGGUAGCAAUA-AUGCGUGCGGCUAAAAU-----GGCGUUCGCUGCGCGGCG-------AGAGGAAACGACUGCCGCCGCCGAAGUGAAAA
((((((..(((((((((.(((...-.)))(((((((......-----.......)))))))((((-------...(....)...))))))))))))))))))). ( -35.32)
>DroSec_CAF1 19752 89 - 1
-----------GGUGGUAGUGAGAAAAGCAUGCGGCAGAAUUUAGUGAACUAAGGAUGCGCGGACACG----AAAGGAAACAUCCGUCGUCGUCAAAAGUAAAA
-----------................((.((((.((...(((((....)))))..))))))((((((----(..(((....))).)))).)))....)).... ( -20.50)
>DroEre_CAF1 26519 93 - 1
-----------GGUGGUAGUGAGAGAAGCAUGCCGCAGAAUUUAGUGAACUAAGGAUGCGCGGACACGAAUGAAAAGAAACAUCCGUCGCCGUUGAAAGUAAAA
-----------...((((((.......)).))))(((...(((((....)))))..)))((((..(((.(((........))).)))..))))........... ( -21.50)
>DroYak_CAF1 19703 93 - 1
-----------GGUGGUACUGAGAAAAGCAUGCGGCAGAAUUUAGUGAACUAAGGAUGCGCGGACACGAAUGAAAAGAAACAUCCGUCGCCGUCGAAAGUAGAA
-----------.....((((..((...((.....(((...(((((....)))))..)))(((((......(....)......))))).))..))...))))... ( -19.80)
>DroMoj_CAF1 25971 91 - 1
UUUUAUUUUUUGGUGGUAGCAAUA-AUAUGUGCGGCUGAAAU-----GGCGUUUGCUGCGCGGCG-------AAAGAGAGCGACUGCCGCCGCUGAAGUGAAAA
(((((((((.((((((((((....-...((((((((......-----.......))))))))((.-------.......))).)))))))))..))))))))). ( -33.42)
>consensus
___________GGUGGUAGUGAGAAAAGCAUGCGGCAGAAUUUAGUGAACUAAGGAUGCGCGGACACG____AAAAGAAACAUCCGUCGCCGUCGAAAGUAAAA
...........((((((.................(((...(((((....)))))..)))((((....................)))).)))))).......... (-11.36 = -11.95 +   0.59)

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 12:13:25 2006