Locus 3375

Sequence ID 3L_DroMel_CAF1
Location 9,873,122 – 9,873,221
Length 99
Max. P 0.694852
window5274 window5275

overview

Window 4

Location 9,873,122 – 9,873,221
Length 99
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 81.33
Mean single sequence MFE -35.01
Consensus MFE -17.59
Energy contribution -19.76
Covariance contribution 2.17
Combinations/Pair 1.00
Mean z-score -2.62
Structure conservation index 0.50
SVM decision value 0.34
SVM RNA-class probability 0.694852
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9873122 99 + 23771897
AUAACAACUG--UUGACCAGGGCUGGAAACGGCAAAUGCCCAUCUAUUGGCCAACACUGGCAACCCAAG-CCA-GGGUUGGCUUGUGCGUUUUUGGAGUAGUG
.((((....)--))).((((.((((....))))((((((.((......(((((((.(((((.......)-)))-).))))))))).))))))))))....... ( -37.00)
>DroVir_CAF1 31574 91 + 1
GUAUCGACUGUAUUGCACAGGGCUGGUUG--CCA------CGCGUACUUUACAACACUGCG---CCAGGGCUACAGGUUGGUUUGUGCAU-UUUGGAGUAGUG
((((((.((((.....))))(((.....)--)).------)).)))).......((((((.---((((.((.(((((....)))))))..-.)))).)))))) ( -27.00)
>DroSec_CAF1 34094 99 + 1
AUAACAACUG--UUGACCAGGGCUGGUAAAACCAAAUGCCCAACAGUUAGCCAACACUGGCAACCCAAG-CCA-GGGUUGGCUAGUGCGUUUUUGGAGUAGUG
...((.(((.--(.((((((((((((.....)))...)))).....(((((((((.(((((.......)-)))-).))))))))))).)))...).))).)). ( -36.80)
>DroSim_CAF1 35995 99 + 1
AUAUCAACUG--UUGACCAGGGCUGGUAAAACCAAAUGCCCAGCUAUUAGCCAACACUGGCAACCCAAG-CCA-GGGUUGGCUAGUGCGUUUUUGGAGUAGUG
......((((--....((((((((((.....)))...)))).((.((((((((((.(((((.......)-)))-).)))))))))))).....)))..)))). ( -40.30)
>DroEre_CAF1 36132 99 + 1
AUAACAACUG--UUGGCCAGGGCUGUCAAAGCCAAAUGCCCAGUUAUUAUCCAACACUGGCUACCCAAG-CCA-GGGUUGGCUAGUGCGUUUUUGGAGUAGUG
.(((.(((((--..(((...((((.....))))....)))))))).)))(((((((((((((((((...-...-))).))))))))).....)))))...... ( -37.00)
>DroYak_CAF1 35082 99 + 1
AUAUCAACUG--UUGACCAGGGCUGUCAAAAUCAAAUGCCCGGCUAUUACUCAACACUGGCAACCCAAG-CCA-GGGUUGGCUAGUGCGUUUUUGGAGUAGUG
..........--....((.((((..............)))))).((((((((..((((((((((((...-...-))))).)))))))((....)))))))))) ( -31.94)
>consensus
AUAACAACUG__UUGACCAGGGCUGGUAAAACCAAAUGCCCAGCUAUUAGCCAACACUGGCAACCCAAG_CCA_GGGUUGGCUAGUGCGUUUUUGGAGUAGUG
......((((......(((((((..............)))).............((((((((((((........))))).)))))))......)))..)))). (-17.59 = -19.76 +   2.17)

alignment

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secondary structure

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dotplot

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Window 5

Location 9,873,122 – 9,873,221
Length 99
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 81.33
Mean single sequence MFE -31.81
Consensus MFE -15.29
Energy contribution -16.73
Covariance contribution 1.45
Combinations/Pair 1.26
Mean z-score -2.47
Structure conservation index 0.48
SVM decision value -0.01
SVM RNA-class probability 0.528960
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9873122 99 - 23771897
CACUACUCCAAAAACGCACAAGCCAACCC-UGG-CUUGGGUUGCCAGUGUUGGCCAAUAGAUGGGCAUUUGCCGUUUCCAGCCCUGGUCAA--CAGUUGUUAU
............(((((.(((((((....-)))-)))).((((((((.(((((.....((((((.(....)))))))))))).)))).)))--).).)))).. ( -32.90)
>DroVir_CAF1 31574 91 - 1
CACUACUCCAAA-AUGCACAAACCAACCUGUAGCCCUGG---CGCAGUGUUGUAAAGUACGCG------UGG--CAACCAGCCCUGUGCAAUACAGUCGAUAC
............-.((((((...((((((((.((....)---))))).))))..........(------.((--(.....))))))))))............. ( -22.50)
>DroSec_CAF1 34094 99 - 1
CACUACUCCAAAAACGCACUAGCCAACCC-UGG-CUUGGGUUGCCAGUGUUGGCUAACUGUUGGGCAUUUGGUUUUACCAGCCCUGGUCAA--CAGUUGUUAU
............(((.....(((((((.(-(((-(.......))))).)))))))(((((((((.((.((((.....))))...)).))))--)))))))).. ( -37.30)
>DroSim_CAF1 35995 99 - 1
CACUACUCCAAAAACGCACUAGCCAACCC-UGG-CUUGGGUUGCCAGUGUUGGCUAAUAGCUGGGCAUUUGGUUUUACCAGCCCUGGUCAA--CAGUUGAUAU
.(((...(((.....((..((((((((.(-(((-(.......))))).))))))))...)).((((...(((.....))))))))))....--.)))...... ( -35.00)
>DroEre_CAF1 36132 99 - 1
CACUACUCCAAAAACGCACUAGCCAACCC-UGG-CUUGGGUAGCCAGUGUUGGAUAAUAACUGGGCAUUUGGCUUUGACAGCCCUGGCCAA--CAGUUGUUAU
......................(((((.(-(((-((.....)))))).)))))(((((((((((((....((((.....))))...)))..--)))))))))) ( -36.00)
>DroYak_CAF1 35082 99 - 1
CACUACUCCAAAAACGCACUAGCCAACCC-UGG-CUUGGGUUGCCAGUGUUGAGUAAUAGCCGGGCAUUUGAUUUUGACAGCCCUGGUCAA--CAGUUGAUAU
...(((((.......(((((.((.(((((-...-...))))))).))))).)))))...(((((((..............)))).)))...--.......... ( -27.14)
>consensus
CACUACUCCAAAAACGCACUAGCCAACCC_UGG_CUUGGGUUGCCAGUGUUGGCUAAUAGCUGGGCAUUUGGUUUUACCAGCCCUGGUCAA__CAGUUGAUAU
............((((((((.((.(((((........))))))).)))))((((((......((((...((.......)))))))))))).....)))..... (-15.29 = -16.73 +   1.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:56:35 2006