Locus 1478

Sequence ID X_DroMel_CAF1
Location 4,413,647 – 4,413,837
Length 190
Max. P 0.892493
window2366 window2367

overview

Window 6

Location 4,413,647 – 4,413,757
Length 110
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.60
Mean single sequence MFE -32.26
Consensus MFE -25.60
Energy contribution -25.56
Covariance contribution -0.04
Combinations/Pair 1.03
Mean z-score -1.48
Structure conservation index 0.79
SVM decision value 0.03
SVM RNA-class probability 0.547105
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4413647 110 - 22224390
UUCCGGAUCAAAUUGUAAUACGCAUGUUGACCGCUCCGAAAACGGGAUGACCAAGAUCUCGGU---------GAACUGGUCAGCUAAAUGAAAUAUGAGUUCAAAGGGGCUUG-GAAUGG
((((((.((((..(((.....)))..))))))(((((.....((((((.......)))))).(---------(((((.((((......)))....).))))))..)))))..)-)))... ( -31.40)
>DroSec_CAF1 16060 110 - 1
UUCCGGAUCAAAUUGUAAUACGCAUGUUGACCGCUCCGAAAACGGGAUGACCAAGAUCUCGGU---------GAACUGGUCAGCUAAAUGAAAUAUGAGUUCAAAGGGGCCAG-GAAUGG
((((((.((((..(((.....)))..))))))(((((.....((((((.......)))))).(---------(((((.((((......)))....).))))))..)))))..)-)))... ( -31.20)
>DroSim_CAF1 17507 109 - 1
UUCCGGAUCAAAUUGUAAUACGCAUGUUGACCGCUCCGAAAACGGGAUGACCAAGAUCUCGGU---------GAACUGGUCAGCUAAAUGAAAUAUGAGUUCAAAG-GGCCAG-GAAUGG
((((((.((((..(((.....)))..))))))((.((.....((((((.......)))))).(---------(((((.((((......)))....).))))))..)-)))..)-)))... ( -27.10)
>DroEre_CAF1 17081 120 - 1
UUCCGGAUCAAAUUGUAAUACGCAUGUUGACCGCUCCGAAAACGGGAUGACCAAGAUCUCGGUGGACUCGGUGGACUGGUCAGCCAAAUGAAAUAUGAGUUCAAAGGGGCUAGGGAAUGA
((((((.((((..(((.....)))..))))))(((((.....((((((.......)))))).((((((((.(((.((....))))).........))))))))..)))))...))))... ( -36.70)
>DroYak_CAF1 16803 110 - 1
UUCCGGAUCAAAUUGUAAUACGCAUGUUGACCGCUCCGAAAACGGGAUGACCAAGAUCUCGGU---------GGACUGGUCAGCUAAAUGAAAUAUGAGUUCAAAGGGGCUCG-GAAUGA
((((...(((...(((.....))).((((((((.((((....((((((.......)))))).)---------))).))))))))....))).....((((((....)))))))-)))... ( -34.90)
>consensus
UUCCGGAUCAAAUUGUAAUACGCAUGUUGACCGCUCCGAAAACGGGAUGACCAAGAUCUCGGU_________GAACUGGUCAGCUAAAUGAAAUAUGAGUUCAAAGGGGCUAG_GAAUGG
((((((.((((..(((.....)))..))))))(((((.....((((((.......))))))...........(((((.((((......)))....).)))))...)))))..).)))... (-25.60 = -25.56 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,413,717 – 4,413,837
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.74
Mean single sequence MFE -26.79
Consensus MFE -24.58
Energy contribution -25.38
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -1.39
Structure conservation index 0.92
SVM decision value 0.97
SVM RNA-class probability 0.892493
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4413717 120 - 22224390
GGUCGCCAAAAGCCAGGAGCAGUAAGGAGAAGGGAAUAAAAGAAGUGACUGCGUCAUAAAACAAAUUCCUAAUCAAGGGAUUCCGGAUCAAAUUGUAAUACGCAUGUUGACCGCUCCGAA
(((........))).(((((.....((((..((((((.......(((((...))))).......))))))..((....))))))((.((((..(((.....)))..)))))))))))... ( -30.04)
>DroSec_CAF1 16130 116 - 1
GGUCGCCAAAAGCCAGGAGCAGUAAUGUGAAG----UAAAAAAAGUGACUGCGUCAUAAAACAAAUUCCUAAUCAAGGGAUUCCGGAUCAAAUUGUAAUACGCAUGUUGACCGCUCCGAA
(((........))).(((((.((..(((((.(----((...........))).)))))..)).(((((((.....)))))))..((.((((..(((.....)))..)))))))))))... ( -27.90)
>DroSim_CAF1 17576 116 - 1
GGUCGCCAAAAGCCAGGAGCAGUAAGGAGAAG----UAAAAAAAGUGACUGCGUCAUAAAACAAAUUCCUAAUCAAGGGAUUCCGGAUCAAAUUGUAAUACGCAUGUUGACCGCUCCGAA
(((........))).(((((.....((((...----........(((((...)))))........(((((.....)))))))))((.((((..(((.....)))..)))))))))))... ( -29.40)
>DroEre_CAF1 17161 115 - 1
GGUCGCCAAAAGCCAGAAGCAAUAAGGAGAAA----UAAA-AAAGUGACUGCGUCAUAAAACAAAUUCCUAAUCAAGGGAUUCCGGAUCAAAUUGUAAUACGCAUGUUGACCGCUCCGAA
(((........)))...........((((...----....-...(((((...)))))......(((((((.....))))))).(((.((((..(((.....)))..)))))))))))... ( -23.30)
>DroYak_CAF1 16873 115 - 1
GGUCGCCAAAAGCCAGAAGCAAUAAGGAGAAG----UAAA-AAAGUGACUGCGUCAUAAAACAAAUUCCUAAUCAAGGGAUUCCGGAUCAAAUUGUAAUACGCAUGUUGACCGCUCCGAA
(((........)))...........((((...----....-...(((((...)))))......(((((((.....))))))).(((.((((..(((.....)))..)))))))))))... ( -23.30)
>consensus
GGUCGCCAAAAGCCAGGAGCAGUAAGGAGAAG____UAAAAAAAGUGACUGCGUCAUAAAACAAAUUCCUAAUCAAGGGAUUCCGGAUCAAAUUGUAAUACGCAUGUUGACCGCUCCGAA
(((........))).(((((.....((((...............(((((...)))))........(((((.....)))))))))((.((((..(((.....)))..)))))))))))... (-24.58 = -25.38 +   0.80)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:10:31 2006