Locus 2321

Sequence ID X_DroMel_CAF1
Location 6,251,878 – 6,251,985
Length 107
Max. P 0.999793
window3763 window3764

overview

Window 3

Location 6,251,878 – 6,251,985
Length 107
Sequences 3
Columns 107
Reading direction forward
Mean pairwise identity 72.38
Mean single sequence MFE -37.39
Consensus MFE -20.66
Energy contribution -24.89
Covariance contribution 4.23
Combinations/Pair 1.15
Mean z-score -1.88
Structure conservation index 0.55
SVM decision value 0.75
SVM RNA-class probability 0.840846
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6251878 107 + 22224390
UUGGUAUUGGUGCUGGUGUGCGGCUGCCAAAAUUCGAAUGCCCCGCCGUGCUCCGAAAGGCCGGGAAUGGGGCAUCCAUUUUCUUGUCCAACGCUUCCUGGUCAGUU
......((((.(((((((.(.(((...............))))))))).)).))))..(((((((((..(((((..........))))).....))))))))).... ( -37.96)
>DroSec_CAF1 18578 100 + 1
UUGGU------GUUGGUGUGCGGCUGCCAAAAUUCGGAUGCCCC-CGCUGCUCCGAAAGUCCGGGAAAGGGGCAUCCAUUUUCUUGGCCGCCGCUUCCUGGCCAGUU
(((((------...((...(((((.(((((.....(((((((((-.....(.(((......))))...)))))))))......))))).)))))..))..))))).. ( -48.00)
>DroYak_CAF1 25762 83 + 1
UUGGU------GGCG--GUGCGGCUGCCAAAAUUCGGAUUCCCUCC---GCUCCAAAAGGCC------------UCCA-UUUUUAAGCCGCUGCUACCUGGUCAGUU
..(((------((((--..((((((...(((((..(((.....)))---(((......))).------------...)-))))..)))))))))))))......... ( -26.20)
>consensus
UUGGU______GCUGGUGUGCGGCUGCCAAAAUUCGGAUGCCCC_C__UGCUCCGAAAGGCCGGGAA_GGGGCAUCCAUUUUCUUGGCCGCCGCUUCCUGGUCAGUU
...........(((((...(((((.(((((.....(((((((((........((....))........)))))))))......))))).)))))...)))))..... (-20.66 = -24.89 +   4.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 6,251,878 – 6,251,985
Length 107
Sequences 3
Columns 107
Reading direction reverse
Mean pairwise identity 72.38
Mean single sequence MFE -36.63
Consensus MFE -23.77
Energy contribution -26.56
Covariance contribution 2.79
Combinations/Pair 1.17
Mean z-score -2.46
Structure conservation index 0.65
SVM decision value 4.09
SVM RNA-class probability 0.999793
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6251878 107 - 22224390
AACUGACCAGGAAGCGUUGGACAAGAAAAUGGAUGCCCCAUUCCCGGCCUUUCGGAGCACGGCGGGGCAUUCGAAUUUUGGCAGCCGCACACCAGCACCAAUACCAA
...............(((((.(((((...((((((((((....((((((.....).)).))).))))))))))..)))))((....))...)))))........... ( -33.20)
>DroSec_CAF1 18578 100 - 1
AACUGGCCAGGAAGCGGCGGCCAAGAAAAUGGAUGCCCCUUUCCCGGACUUUCGGAGCAGCG-GGGGCAUCCGAAUUUUGGCAGCCGCACACCAAC------ACCAA
...(((...((..(((((.(((((((...(((((((((((..(((((....)))).)....)-))))))))))..))))))).)))))...))...------.))). ( -47.50)
>DroYak_CAF1 25762 83 - 1
AACUGACCAGGUAGCAGCGGCUUAAAAA-UGGA------------GGCCUUUUGGAGC---GGAGGGAAUCCGAAUUUUGGCAGCCGCAC--CGCC------ACCAA
.........(((.((.((((((..((((-((((------------..(((((((...)---))))))..)))..)))))...))))))..--.)).------))).. ( -29.20)
>consensus
AACUGACCAGGAAGCGGCGGCCAAGAAAAUGGAUGCCCC_UUCCCGGCCUUUCGGAGCA__G_GGGGCAUCCGAAUUUUGGCAGCCGCACACCAAC______ACCAA
.............(((((.(((((((...((((((((((........((....))........))))))))))..))))))).)))))................... (-23.77 = -26.56 +   2.79)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:31:32 2006