Locus 1799

Sequence ID 3R_DroMel_CAF1
Location 5,142,658 – 5,142,786
Length 128
Max. P 0.985419
window2964 window2965

overview

Window 4

Location 5,142,658 – 5,142,749
Length 91
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 76.88
Mean single sequence MFE -28.99
Consensus MFE -10.40
Energy contribution -11.30
Covariance contribution 0.90
Combinations/Pair 1.17
Mean z-score -2.57
Structure conservation index 0.36
SVM decision value 0.64
SVM RNA-class probability 0.808422
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5142658 91 - 27905053
GUAU--------CCUGCUAUCCUGGCGACCAGAUGCUGGUCCUUUUGGAUG-CGAAUU-GGUCGUAAUAAAACGCAUAAAAAGGAUACCGG-CAAAUGGGGA
...(--------((((((.....)))).(((..(((((((((((((..(((-((..((-(.......)))..))))).)))))))..))))-))..)))))) ( -31.40)
>DroSec_CAF1 17022 91 - 1
GUAU--------CCUGCUAUCCUGGCGACCAGAUGCUGGUCCUUUUGGAUG-CGAAUU-GGUCGUAAUAAAACGCAUAAAAAGGAUACCGG-CAAAUGGGGA
...(--------((((((.....)))).(((..(((((((((((((..(((-((..((-(.......)))..))))).)))))))..))))-))..)))))) ( -31.40)
>DroSim_CAF1 14046 92 - 1
GUAU--------CCUGCUAUCCUGGCGACCAGAUGCUGGUCCUUUUGGAUG-CGAAUU-GGUCGUAAUAAAACGCAUAAAAAGGAUACCGGGGAAAUGGGGA
...(--------((((.((((((.((((((((.(((..((((....)))))-))..))-))))))................)))))).)))))......... ( -29.33)
>DroEre_CAF1 15294 88 - 1
-----------UCCUGUUAUCCUGGGGGCCAGAUGCUGGUCCUUUUGGAUG-GCAAUU-GUACGUAAUAAAACGCAUAAAAUGGAUCCCGG-CAAAUGGGAA
-----------(((((((((((.(((((((((...)))))))))..)))))-))).((-((.(((......))).))))...)))(((((.-....))))). ( -34.20)
>DroYak_CAF1 14374 99 - 1
GUAUGCUGUUAUCCUAUUGUCCUGGGGGCCAGAUGCUGGUCCUU-UGGAUGUGGAAUU-GCACGUAAUAAAACGCAUAAAAAGGAUCCAGG-CAAAUGGGGA
...........(((((((..((((((.(((((...)))))((((-(..(((((..(((-(....))))....)))))..))))).))))))-..))))))). ( -32.30)
>DroAna_CAF1 36975 81 - 1
GAA------------------AUAAAGGCCACAUGGUGGUCGGAGAAGAUG-GCUCUUAGCCCAUAAUAAAACGCAUAAAAAGGAUCUGUG-AAAAUG-GGA
...------------------.....((((((...))))))((((......-.))))...(((((.......((((...........))))-...)))-)). ( -15.30)
>consensus
GUAU________CCUGCUAUCCUGGCGACCAGAUGCUGGUCCUUUUGGAUG_CGAAUU_GGUCGUAAUAAAACGCAUAAAAAGGAUACCGG_CAAAUGGGGA
............(((...((((.((.((((((...))))))))...))))............(((......))).......................))).. (-10.40 = -11.30 +   0.90)

alignment

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secondary structure

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dotplot

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Window 5

Location 5,142,687 – 5,142,786
Length 99
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 75.41
Mean single sequence MFE -31.23
Consensus MFE -13.44
Energy contribution -13.97
Covariance contribution 0.53
Combinations/Pair 1.17
Mean z-score -2.77
Structure conservation index 0.43
SVM decision value 2.01
SVM RNA-class probability 0.985419
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5142687 99 - 27905053
UA-AACGAAGCCAUCGCCUUCGACAUUGGAAGUCAUUCGUAU--------CCUGCUAUCCUGGCGACCAGAUGCUGGUCCUUUUGGAUG-CGAAUU-GGUCGUAAUAAAA
..-.(((..((((..(.((((.......)))).)((((((((--------((.(((.....)))((((((...)))))).....)))))-))))))-))))))....... ( -31.30)
>DroSec_CAF1 17051 99 - 1
UA-AACGAAGCCAUCGCCAUCGACAUUGGCAGUCAUUCGUAU--------CCUGCUAUCCUGGCGACCAGAUGCUGGUCCUUUUGGAUG-CGAAUU-GGUCGUAAUAAAA
..-.(((..((((..((((.......))))....((((((((--------((.(((.....)))((((((...)))))).....)))))-))))))-))))))....... ( -34.60)
>DroSim_CAF1 14076 99 - 1
UA-AACGAAGCCAUCGCCAUCGACAUUGGCAGUCAUUCGUAU--------CCUGCUAUCCUGGCGACCAGAUGCUGGUCCUUUUGGAUG-CGAAUU-GGUCGUAAUAAAA
..-.(((..((((..((((.......))))....((((((((--------((.(((.....)))((((((...)))))).....)))))-))))))-))))))....... ( -34.60)
>DroEre_CAF1 15323 87 - 1
UA-AACGAAGCCA------UCGACAUUGGCAGUCA--------------UCCUGUUAUCCUGGGGGCCAGAUGCUGGUCCUUUUGGAUG-GCAAUU-GUACGUAAUAAAA
..-.(((..((((------.......)))).....--------------...((((((((.(((((((((...)))))))))..)))))-)))...-...)))....... ( -31.00)
>DroYak_CAF1 14403 101 - 1
UA-AACGAAGCCA------UCGACAUUGGCAGUCAUUCGUAUGCUGUUAUCCUAUUGUCCUGGGGGCCAGAUGCUGGUCCUU-UGGAUGUGGAAUU-GCACGUAAUAAAA
..-.(((((((((------.......)))).....))))).((((((..(((...(((((..((((((((...)))))))).-.))))).)))...-))).)))...... ( -33.40)
>DroAna_CAF1 37003 85 - 1
CACAACGAAGCCA------UCGACGUUGUAAGUCAUUUGAA------------------AUAAAGGCCACAUGGUGGUCGGAGAAGAUG-GCUCUUAGCCCAUAAUAAAA
......((.((((------(((((.......))).......------------------.....((((((...))))))......))))-))))................ ( -22.50)
>consensus
UA_AACGAAGCCA______UCGACAUUGGCAGUCAUUCGUAU________CCUGCUAUCCUGGCGACCAGAUGCUGGUCCUUUUGGAUG_CGAAUU_GGUCGUAAUAAAA
....(((..............(((.......)))......................((((.((.((((((...))))))))...))))............)))....... (-13.44 = -13.97 +   0.53)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:19:50 2006