Locus 827

Sequence ID X_DroMel_CAF1
Location 2,310,779 – 2,310,875
Length 96
Max. P 0.943946
window1338 window1339

overview

Window 8

Location 2,310,779 – 2,310,875
Length 96
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 80.38
Mean single sequence MFE -26.10
Consensus MFE -18.28
Energy contribution -18.52
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -1.89
Structure conservation index 0.70
SVM decision value 0.76
SVM RNA-class probability 0.842535
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2310779 96 + 22224390
AAAUGACAAGCACUUU--AGACAGUGCAUGUGUUUAUA----------------------UUAAUCUAAAGAUGAUCUUCUUCUGAAUUAGCAAUGUUGAUUAAGUCGUUCGCCUCCUUG
.((((((..(((((..--....)))))...........----------------------....((..((((......))))..))((((((...))))))...)))))).......... ( -15.60)
>DroSec_CAF1 8723 95 + 1
AAAUGACAAGCACUUU--GGACAGUGCACGUGUUUAUA----------------------UUAAUCCAAAGCUGAUCU-CUUCUGAAUCAGCAAUGUUGAUUAAGUCGUUCGCCUCCUUG
.((((((..(((((..--....)))))...........----------------------((((((((..((((((.(-(....))))))))..))..)))))))))))).......... ( -23.40)
>DroSim_CAF1 9544 94 + 1
AAAUGACAAGCACUUU--GGACAGUGCACGUGUUUAUA----------------------UUAAUCCAAAGCUGAUCU-C-UCUGAAUCAGCAAUGUUGAUUAAGUCGUUCGCCUCCUUG
.((((((..(((((..--....)))))...........----------------------((((((((..(((((((.-.-...).))))))..))..)))))))))))).......... ( -22.50)
>DroEre_CAF1 10013 117 + 1
AAAUGACAAACACUUU--AGACAGUGCGAGUGUUUGUAUGUAUGUAUAUACAUACUCGUAUUAAUCUAAAGCUGAUCU-CUUCUGAAUCAGCAAGGCUGAUUAAGUCGUUCGCCUGCUUG
.((((((...((((((--(((.(((((((((((.((((((....)))))).)))))))))))..))))))).))....-......(((((((...)))))))..)))))).......... ( -36.30)
>DroYak_CAF1 9726 119 + 1
AAAUGACAAGCACUUUGGAGACAGUGCCAGUGUUUAUAUGCUUGUAUAUUCAUACUCGUCUUAAUCUAAAGCUGAUCU-CUUCUGAAUCAGCAAUGCUGAUUAAGUCGUUCGCCUGUCUG
..................((((((.((.(((((..(((((....)))))..)))))((.(((((((....((((((.(-(....))))))))......))))))).))...)))))))). ( -32.70)
>consensus
AAAUGACAAGCACUUU__AGACAGUGCAAGUGUUUAUA______________________UUAAUCUAAAGCUGAUCU_CUUCUGAAUCAGCAAUGUUGAUUAAGUCGUUCGCCUCCUUG
.((((((..(((((........))))).................................((((((....(((((((.......).))))))......)))))))))))).......... (-18.28 = -18.52 +   0.24)

alignment

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secondary structure

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dotplot

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Window 9

Location 2,310,779 – 2,310,875
Length 96
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 80.38
Mean single sequence MFE -26.00
Consensus MFE -19.66
Energy contribution -19.90
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -2.10
Structure conservation index 0.76
SVM decision value 1.34
SVM RNA-class probability 0.943946
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2310779 96 - 22224390
CAAGGAGGCGAACGACUUAAUCAACAUUGCUAAUUCAGAAGAAGAUCAUCUUUAGAUUAA----------------------UAUAAACACAUGCACUGUCU--AAAGUGCUUGUCAUUU
......(((((.....((((((.....((......))(((((......))))).))))))----------------------...........(((((....--..)))))))))).... ( -15.30)
>DroSec_CAF1 8723 95 - 1
CAAGGAGGCGAACGACUUAAUCAACAUUGCUGAUUCAGAAG-AGAUCAGCUUUGGAUUAA----------------------UAUAAACACGUGCACUGUCC--AAAGUGCUUGUCAUUU
......(((((.....((((((..((..(((((((......-.)))))))..))))))))----------------------...........(((((....--..)))))))))).... ( -24.10)
>DroSim_CAF1 9544 94 - 1
CAAGGAGGCGAACGACUUAAUCAACAUUGCUGAUUCAGA-G-AGAUCAGCUUUGGAUUAA----------------------UAUAAACACGUGCACUGUCC--AAAGUGCUUGUCAUUU
......(((((.....((((((..((..(((((((....-.-.)))))))..))))))))----------------------...........(((((....--..)))))))))).... ( -24.60)
>DroEre_CAF1 10013 117 - 1
CAAGCAGGCGAACGACUUAAUCAGCCUUGCUGAUUCAGAAG-AGAUCAGCUUUAGAUUAAUACGAGUAUGUAUAUACAUACAUACAAACACUCGCACUGUCU--AAAGUGUUUGUCAUUU
......(((((((..((.(((((((...))))))).))...-......(((((((((.....(((((.(((((........)))))...)))))....))))--)))))))))))).... ( -34.70)
>DroYak_CAF1 9726 119 - 1
CAGACAGGCGAACGACUUAAUCAGCAUUGCUGAUUCAGAAG-AGAUCAGCUUUAGAUUAAGACGAGUAUGAAUAUACAAGCAUAUAAACACUGGCACUGUCUCCAAAGUGCUUGUCAUUU
..((((.((...((.(((((((......(((((((......-.)))))))....))))))).)).((((....))))..))...........((((((........)))))))))).... ( -31.30)
>consensus
CAAGGAGGCGAACGACUUAAUCAACAUUGCUGAUUCAGAAG_AGAUCAGCUUUAGAUUAA______________________UAUAAACACGUGCACUGUCU__AAAGUGCUUGUCAUUU
......(((((.....((((((......(((((((........)))))))....)))))).................................(((((........)))))))))).... (-19.66 = -19.90 +   0.24)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:54:46 2006