Locus 4508

Sequence ID X_DroMel_CAF1
Location 11,899,433 – 11,899,568
Length 135
Max. P 0.999281
window7413 window7414 window7415 window7416

overview

Window 3

Location 11,899,433 – 11,899,538
Length 105
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 71.03
Mean single sequence MFE -32.58
Consensus MFE -14.10
Energy contribution -17.29
Covariance contribution 3.19
Combinations/Pair 1.27
Mean z-score -2.81
Structure conservation index 0.43
SVM decision value 3.48
SVM RNA-class probability 0.999281
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11899433 105 + 22224390
UAAACAGGAGCAAAAAA-GCGCUGAGG-GGAAAGUGCAUUGGGCUGGCUCCAGUGGAGGCCAAAAGGCAGAUAUAGCUGA--------AGCUGGAGCCGGAACUGGAGUCCCUGA
....((((..(......-(((((....-....)))))...(..(((((((((((....(((....)))((......))..--------.)))))))))))..)....)..)))). ( -42.00)
>DroVir_CAF1 1536 86 + 1
UAAACACAAGCAAA-AA-GCGUUAAG--GGAAAGUGCAUUGGA-UGAC--AGGGUGCUGG-AAAAAGCAC----AGACCG------------GCAGCAGGACAUGGAGUG-----
....(((..((...-..-))......--.....(((..(((..-((..--.(((((((..-....)))))----...)).------------.)).)))..)))...)))----- ( -15.70)
>DroSec_CAF1 10305 102 + 1
UAAACAGAAGCAAAAAACGCGUUGAGG-GGAAAGUGCAUUGGGCUGGCUCCGGUUGAGGCCAGAAGGCAGAUAUAGCCGA------------GGAGCCGGAACUGGAGUUCCUGA
.........(((.....(.(.....).-).....))).(..((..((((((((((..((((....(((.......)))..------------.).)))..))))))))))))..) ( -33.00)
>DroEre_CAF1 7760 85 + 1
UAAACAGGAGCAAA-AC-GCGCUGAGG-GGAAAGUGCAUUGGGCUGGCUCCGGUUGAGGCCAGAAGGCAGUUAUAG---------------------------UGGAGUCCCUGA
....(((((((..(-(.-(((((....-....))))).))..)))(((((((.((((.(((....)))..))).).---------------------------))))))))))). ( -31.80)
>DroYak_CAF1 10009 114 + 1
UAAACAGGAGCAAAAAA-GCAAUGAGGGGGAAAGUGCAUUGGGCUGGCUCCAGUUGAGGCCAGAAGGCAGAUAUAGCCGAGGAGCAGGAGCCAAAGCCGGAACUGGAGCCCCUGA
....(((((((...((.-(((.............))).))..)))((((((((((..(((.....(((.......)))..((........))...)))..)))))))))))))). ( -40.42)
>consensus
UAAACAGGAGCAAAAAA_GCGCUGAGG_GGAAAGUGCAUUGGGCUGGCUCCGGUUGAGGCCAGAAGGCAGAUAUAGCCGA____________GGAGCCGGAACUGGAGUCCCUGA
....(((((((....((.(((((.........))))).))..)))((((((((((...(((....)))........(((..................))))))))))))))))). (-14.10 = -17.29 +   3.19)

alignment

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secondary structure

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dotplot

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Window 4

Location 11,899,433 – 11,899,538
Length 105
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 71.03
Mean single sequence MFE -25.89
Consensus MFE -6.74
Energy contribution -8.18
Covariance contribution 1.44
Combinations/Pair 1.19
Mean z-score -2.60
Structure conservation index 0.26
SVM decision value 2.62
SVM RNA-class probability 0.995865
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11899433 105 - 22224390
UCAGGGACUCCAGUUCCGGCUCCAGCU--------UCAGCUAUAUCUGCCUUUUGGCCUCCACUGGAGCCAGCCCAAUGCACUUUCC-CCUCAGCGC-UUUUUUGCUCCUGUUUA
...(((((....)))))(((((((((.--------...)))......(((....))).......)))))).((.....)).......-...(((.((-......))..))).... ( -29.40)
>DroVir_CAF1 1536 86 - 1
-----CACUCCAUGUCCUGCUGC------------CGGUCU----GUGCUUUUU-CCAGCACCCU--GUCA-UCCAAUGCACUUUCC--CUUAACGC-UU-UUUGCUUGUGUUUA
-----(((....(((..((.((.------------(((...----(((((....-..))))).))--).))-..))..)))......--......((-..-...))..))).... ( -11.80)
>DroSec_CAF1 10305 102 - 1
UCAGGAACUCCAGUUCCGGCUCC------------UCGGCUAUAUCUGCCUUCUGGCCUCAACCGGAGCCAGCCCAAUGCACUUUCC-CCUCAACGCGUUUUUUGCUUCUGUUUA
...(((((....)))))((((((------------..(((.......)))....((......))))))))(((..(((((.......-.......)))))....)))........ ( -28.64)
>DroEre_CAF1 7760 85 - 1
UCAGGGACUCCA---------------------------CUAUAACUGCCUUCUGGCCUCAACCGGAGCCAGCCCAAUGCACUUUCC-CCUCAGCGC-GU-UUUGCUCCUGUUUA
.(((((.((((.---------------------------........(((....))).......))))))(((..(((((.((....-....)).))-))-)..))).))).... ( -20.79)
>DroYak_CAF1 10009 114 - 1
UCAGGGGCUCCAGUUCCGGCUUUGGCUCCUGCUCCUCGGCUAUAUCUGCCUUCUGGCCUCAACUGGAGCCAGCCCAAUGCACUUUCCCCCUCAUUGC-UUUUUUGCUCCUGUUUA
.((((((((((((((..((((..(((....(((....))).......)))....))))..))))))))))(((.....(((.............)))-......))))))).... ( -38.82)
>consensus
UCAGGGACUCCAGUUCCGGCUCC____________UCGGCUAUAUCUGCCUUCUGGCCUCAACCGGAGCCAGCCCAAUGCACUUUCC_CCUCAACGC_UUUUUUGCUCCUGUUUA
.(((((........................................(((...(((((..(....)..)))))......)))..............((.......))))))).... ( -6.74 =  -8.18 +   1.44)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,899,466 – 11,899,568
Length 102
Sequences 4
Columns 110
Reading direction forward
Mean pairwise identity 77.50
Mean single sequence MFE -36.59
Consensus MFE -24.44
Energy contribution -24.82
Covariance contribution 0.38
Combinations/Pair 1.15
Mean z-score -1.91
Structure conservation index 0.67
SVM decision value 0.94
SVM RNA-class probability 0.886287
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11899466 102 + 22224390
GCAUUGGGCUGGCUCCAGUGGAGGCCAAAAGGCAGAUAUAGCUGA--------AGCUGGAGCCGGAACUGGAGUCCCUGACCCCCAACUACGGGAUACCAGAUCCAGUAA
..(((((((((((((((((....(((....)))((......))..--------.)))))))))))..((((.(((((..............))))).)))).)))))).. ( -42.74)
>DroSec_CAF1 10339 98 + 1
GCAUUGGGCUGGCUCCGGUUGAGGCCAGAAGGCAGAUAUAGCCGA------------GGAGCCGGAACUGGAGUUCCUGACCCCCAACUACGGGAUACCAGAUCCAGAAA
...((((((((((((((((....)))....(((.......)))..------------))))))))..((((...(((((...........)))))..)))).)))))... ( -37.90)
>DroEre_CAF1 7792 79 + 1
GCAUUGGGCUGGCUCCGGUUGAGGCCAGAAGGCAGUUAUAG---------------------------UGGAGUCCCUGACCCCCAACUGCAGGAUACCGGAUCCA----
(((((((((((((..(....)..)))))..(((((..((..---------------------------....))..))).))))))).))).((((.....)))).---- ( -27.20)
>DroYak_CAF1 10043 109 + 1
GCAUUGGGCUGGCUCCAGUUGAGGCCAGAAGGCAGAUAUAGCCGAGGAGCAGGAGCCAAAGCCGGAACUGGAGCCCCUGACCCCCAACUACAGGACACCAGAUCCAU-AU
......((((((((((.(((...(((....))).)))...((......)).))))))..))))(((.((((.(..((((...........)))).).)))).)))..-.. ( -38.50)
>consensus
GCAUUGGGCUGGCUCCAGUUGAGGCCAGAAGGCAGAUAUAGCCGA____________GGAGCCGGAACUGGAGUCCCUGACCCCCAACUACAGGAUACCAGAUCCAG_AA
....((((((((((((((((...(((....)))........(((..................)))))))))))..((((...........))))...)))).)))).... (-24.44 = -24.82 +   0.38)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,899,466 – 11,899,568
Length 102
Sequences 4
Columns 110
Reading direction reverse
Mean pairwise identity 77.50
Mean single sequence MFE -39.15
Consensus MFE -25.15
Energy contribution -25.34
Covariance contribution 0.19
Combinations/Pair 1.21
Mean z-score -2.54
Structure conservation index 0.64
SVM decision value 2.43
SVM RNA-class probability 0.993825
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11899466 102 - 22224390
UUACUGGAUCUGGUAUCCCGUAGUUGGGGGUCAGGGACUCCAGUUCCGGCUCCAGCU--------UCAGCUAUAUCUGCCUUUUGGCCUCCACUGGAGCCAGCCCAAUGC
....(((..(((((.(((...(((.(((((((((((((....)))))(((...(((.--------...)))......)))...))))))))))))))))))).))).... ( -39.40)
>DroSec_CAF1 10339 98 - 1
UUUCUGGAUCUGGUAUCCCGUAGUUGGGGGUCAGGAACUCCAGUUCCGGCUCC------------UCGGCUAUAUCUGCCUUCUGGCCUCAACCGGAGCCAGCCCAAUGC
...((((.((((((.....(((((((((((((.(((((....)))))))).))------------))))))))....(((....)))....)))))).))))........ ( -41.70)
>DroEre_CAF1 7792 79 - 1
----UGGAUCCGGUAUCCUGCAGUUGGGGGUCAGGGACUCCA---------------------------CUAUAACUGCCUUCUGGCCUCAACCGGAGCCAGCCCAAUGC
----(((.((((((..((.(((((((((((((...)))))).---------------------------...))))))).....)).....)))))).)))......... ( -27.20)
>DroYak_CAF1 10043 109 - 1
AU-AUGGAUCUGGUGUCCUGUAGUUGGGGGUCAGGGGCUCCAGUUCCGGCUUUGGCUCCUGCUCCUCGGCUAUAUCUGCCUUCUGGCCUCAACUGGAGCCAGCCCAAUGC
..-.(((..(((((.((((((((((((((..((((((((..(((....)))..))))))))..)))))))))))...(((....))).......)))))))).))).... ( -48.30)
>consensus
UU_CUGGAUCUGGUAUCCCGUAGUUGGGGGUCAGGGACUCCAGUUCCGGCUCC____________UCGGCUAUAUCUGCCUUCUGGCCUCAACCGGAGCCAGCCCAAUGC
...((((.((((((..((((....))))((((((((....(((....((((................))))....)))..))))))))...)))))).))))........ (-25.15 = -25.34 +   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 11:26:53 2006