Locus 1291

Sequence ID X_DroMel_CAF1
Location 3,852,672 – 3,852,771
Length 99
Max. P 0.912728
window2065 window2066

overview

Window 5

Location 3,852,672 – 3,852,771
Length 99
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 82.74
Mean single sequence MFE -33.00
Consensus MFE -22.26
Energy contribution -23.70
Covariance contribution 1.44
Combinations/Pair 1.17
Mean z-score -2.15
Structure conservation index 0.67
SVM decision value 0.83
SVM RNA-class probability 0.862508
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3852672 99 + 22224390
-----AAAGGGAUGGUGGGCUGGGGUUCUCU------GGCCACAACCAAAGUUAAAUGCAGCAUAAAUAAUG-UGCGUGAGCCCGCCCGGCCAAAAGGUCAGGCCCCAAAA
-----...(((.((((.(((..((....)).------.)))...))))..(((..(((((.(((.....)))-))))).)))..(((.((((....)))).)))))).... ( -36.10)
>DroSec_CAF1 35928 98 + 1
-----AAAGGGAUGGCAGGCUGGGGCUCUCU------GGCCACAACCAAAGUUAAAUGCAGCAUAAAUAAUG-UGCGUGAGCCCGCCCGGCCAAAAGGUCAGGCCCCAA-A
-----...(((..(((.(((..((....)).------.)))..............(((((.(((.....)))-)))))..))).(((.((((....)))).))))))..-. ( -35.80)
>DroEre_CAF1 34518 97 + 1
-----A-UGGGAUGGCAGGCUGGGGUUCUUU------GGCCACAACCAAAGUUAAAUGCAGCAUAAAUAAUG-UGCGUGAGUCCGCCCGGCCAAAAGGUCAGGCCCCAA-A
-----.-((((.((((.(((((((...((((------((......))))))....(((((.(((.....)))-))))).......))))))).....))))...)))).-. ( -34.90)
>DroYak_CAF1 30927 97 + 1
-----A-UGGGAAGGCAGGCUGGGGUUCUUU------GGCCACAACCAAAGUUAAAUGCAGCAUAAAUAAUG-UGCGUGAGCCCGCCCGGCCAAAAGGUCAGGCCCCAA-A
-----.-((((...........(((((((((------((......))))).....(((((.(((.....)))-)))))))))))(((.((((....)))).))))))).-. ( -35.70)
>DroAna_CAF1 34518 105 + 1
UGGUUAGUGGGAUGGG--GGAGAGGUUGUUCCCAAAAAGCCAAAACCAAAGUUAAAUGCAGCAUAAAUAAUUUUGCGUGUGCCCGGUCG---AGAAGGUCAGAGCCAAA-U
(((((...(((....(--((((......)))))...........((((((((((.............)))))))).))...)))(..(.---....)..)..)))))..-. ( -22.52)
>consensus
_____A_UGGGAUGGCAGGCUGGGGUUCUUU______GGCCACAACCAAAGUUAAAUGCAGCAUAAAUAAUG_UGCGUGAGCCCGCCCGGCCAAAAGGUCAGGCCCCAA_A
........(((..(((.((.((.((((..........)))).)).))........(((((.(((.....))).)))))..))).(((.((((....)))).)))))).... (-22.26 = -23.70 +   1.44)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,852,672 – 3,852,771
Length 99
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 82.74
Mean single sequence MFE -32.88
Consensus MFE -20.38
Energy contribution -22.58
Covariance contribution 2.20
Combinations/Pair 1.00
Mean z-score -2.49
Structure conservation index 0.62
SVM decision value 1.08
SVM RNA-class probability 0.912728
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3852672 99 - 22224390
UUUUGGGGCCUGACCUUUUGGCCGGGCGGGCUCACGCA-CAUUAUUUAUGCUGCAUUUAACUUUGGUUGUGGCC------AGAGAACCCCAGCCCACCAUCCCUUU-----
....((((((((.((....)).)))))(((((...(((-(((.....))).)))......(((((((....)))------))))......))))).....)))...----- ( -38.00)
>DroSec_CAF1 35928 98 - 1
U-UUGGGGCCUGACCUUUUGGCCGGGCGGGCUCACGCA-CAUUAUUUAUGCUGCAUUUAACUUUGGUUGUGGCC------AGAGAGCCCCAGCCUGCCAUCCCUUU-----
.-..((((((((.((....)).)))))((((((..(((-(((.....))).))).......((((((....)))------)))))))))...........)))...----- ( -38.20)
>DroEre_CAF1 34518 97 - 1
U-UUGGGGCCUGACCUUUUGGCCGGGCGGACUCACGCA-CAUUAUUUAUGCUGCAUUUAACUUUGGUUGUGGCC------AAAGAACCCCAGCCUGCCAUCCCA-U-----
.-.(((((((((.((....)).)))))((......(((-(((.....))).)))......(((((((....)))------))))....))..........))))-.----- ( -31.80)
>DroYak_CAF1 30927 97 - 1
U-UUGGGGCCUGACCUUUUGGCCGGGCGGGCUCACGCA-CAUUAUUUAUGCUGCAUUUAACUUUGGUUGUGGCC------AAAGAACCCCAGCCUGCCUUCCCA-U-----
.-.(((((((.........))))(((((((((...(((-(((.....))).)))......(((((((....)))------))))......)))))))))..)))-.----- ( -39.00)
>DroAna_CAF1 34518 105 - 1
A-UUUGGCUCUGACCUUCU---CGACCGGGCACACGCAAAAUUAUUUAUGCUGCAUUUAACUUUGGUUUUGGCUUUUUGGGAACAACCUCUCC--CCCAUCCCACUAACCA
.-.((((.((.((.....)---)))))))(((...(((.((....)).)))))).........(((((.(((......((((........)))--).....)))..))))) ( -17.40)
>consensus
U_UUGGGGCCUGACCUUUUGGCCGGGCGGGCUCACGCA_CAUUAUUUAUGCUGCAUUUAACUUUGGUUGUGGCC______AAAGAACCCCAGCCUGCCAUCCCA_U_____
....((((((((.((....)).)))))((......(((.(((.....))).)))..........(((((.((..............)).)))))..))..)))........ (-20.38 = -22.58 +   2.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:05:52 2006