Locus 6634

Sequence ID 3R_DroMel_CAF1
Location 17,441,953 – 17,442,056
Length 103
Max. P 0.990023
window10801 window10802

overview

Window 1

Location 17,441,953 – 17,442,056
Length 103
Sequences 5
Columns 104
Reading direction forward
Mean pairwise identity 88.31
Mean single sequence MFE -24.28
Consensus MFE -16.61
Energy contribution -16.85
Covariance contribution 0.24
Combinations/Pair 1.05
Mean z-score -2.17
Structure conservation index 0.68
SVM decision value 0.25
SVM RNA-class probability 0.651179
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17441953 103 + 27905053
AGAGGGUGGAGAGG-GAAAAGAAGCAAACGCAGCUGAAAAAAGUGCACACAAAAUUGUUUGGCUGUGUGAAUGUGUGUGUGUGUGUGCUGUUUCGCAGCGAAAA
............(.-((((...((((.((((.(((......)))(((((((...(..(........)..)...))))))))))).)))).)))).)........ ( -25.10)
>DroSec_CAF1 43468 89 + 1
AGCGGGUGGAGAGG-GAAAAGAAGCAAACGCAGCUGAAAAAAGUGCACACAAAAUUGUUUGGCUGUG--------------UGUGUGCUGUUUCGCAGCGAAAA
.((..((((((...-.......((((.(((((((..((.....((....))......))..))))))--------------)...)))).)))))).))..... ( -26.50)
>DroSim_CAF1 40636 103 + 1
AGCGGGUGGAGAGG-GAAAAGAAGCAAACGCAGCUGAAAAAAGUGCACACAAAAUUGUUUGGCUGUGUGAAUGUGUGUGAGUGUGUGCUGUUUCGCAGCGAAAA
.((..((((((...-.......((((.((((.(((......))).((((((...(..(........)..)...)))))).)))).)))).)))))).))..... ( -25.20)
>DroEre_CAF1 42879 95 + 1
-----GUGGAGAGGGGAAAAGAAGCAAACGCAGCUGAAAAAAGUGCACACAAAAUUAUUUGGUUGUGUGAAUGUGUG----UGUGUGCUCUUUCGCAGCGAAAA
-----..................((....)).((((...((((.(((((((....(((((........)))))....----))))))).))))..))))..... ( -24.60)
>DroYak_CAF1 43377 95 + 1
----GGUGGAGAGG-GAAAAGAAGCAAACGCAGCUGAAAAAAGUGCACAGAAAAUUGUUUGGCUAUGUGAAUGUGUG----UGUGUGCUGUUUCGCAGCGAAAA
----........(.-((((...((((.((((((((......)))((.((((......))))))............))----))).)))).)))).)........ ( -20.00)
>consensus
AG_GGGUGGAGAGG_GAAAAGAAGCAAACGCAGCUGAAAAAAGUGCACACAAAAUUGUUUGGCUGUGUGAAUGUGUG____UGUGUGCUGUUUCGCAGCGAAAA
..........(..(.((((...((((.(((((((..((...(((.........))).))..))))))).................)))).)))).)..)..... (-16.61 = -16.85 +   0.24)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 2

Location 17,441,953 – 17,442,056
Length 103
Sequences 5
Columns 104
Reading direction reverse
Mean pairwise identity 88.31
Mean single sequence MFE -15.54
Consensus MFE -13.63
Energy contribution -13.83
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.13
Structure conservation index 0.88
SVM decision value 2.19
SVM RNA-class probability 0.990023
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17441953 103 - 27905053
UUUUCGCUGCGAAACAGCACACACACACACACAUUCACACAGCCAAACAAUUUUGUGUGCACUUUUUUCAGCUGCGUUUGCUUCUUUUC-CCUCUCCACCCUCU
.....((((.((((..(((((((..............................)))))))...)))).)))).((....))........-.............. ( -14.81)
>DroSec_CAF1 43468 89 - 1
UUUUCGCUGCGAAACAGCACACA--------------CACAGCCAAACAAUUUUGUGUGCACUUUUUUCAGCUGCGUUUGCUUCUUUUC-CCUCUCCACCCGCU
.....((((.((((..(((((((--------------................)))))))...)))).)))).(((..((.........-......))..))). ( -17.65)
>DroSim_CAF1 40636 103 - 1
UUUUCGCUGCGAAACAGCACACACUCACACACAUUCACACAGCCAAACAAUUUUGUGUGCACUUUUUUCAGCUGCGUUUGCUUCUUUUC-CCUCUCCACCCGCU
.....((((.((((..(((((((..............................)))))))...)))).)))).(((..((.........-......))..))). ( -16.97)
>DroEre_CAF1 42879 95 - 1
UUUUCGCUGCGAAAGAGCACACA----CACACAUUCACACAACCAAAUAAUUUUGUGUGCACUUUUUUCAGCUGCGUUUGCUUCUUUUCCCCUCUCCAC-----
.....((((.(((((.(((((((----..........................))))))).)))))..)))).((....))..................----- ( -17.77)
>DroYak_CAF1 43377 95 - 1
UUUUCGCUGCGAAACAGCACACA----CACACAUUCACAUAGCCAAACAAUUUUCUGUGCACUUUUUUCAGCUGCGUUUGCUUCUUUUC-CCUCUCCACC----
.....((((.((((..(((((..----............................)))))...)))).)))).((....))........-..........---- ( -10.51)
>consensus
UUUUCGCUGCGAAACAGCACACA____CACACAUUCACACAGCCAAACAAUUUUGUGUGCACUUUUUUCAGCUGCGUUUGCUUCUUUUC_CCUCUCCACCC_CU
.....((((.((((..(((((((..............................)))))))...)))).)))).((....))....................... (-13.63 = -13.83 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:26:27 2006