Locus 1387

Sequence ID 2L_DroMel_CAF1
Location 3,688,556 – 3,688,702
Length 146
Max. P 0.946673
window2264 window2265

overview

Window 4

Location 3,688,556 – 3,688,665
Length 109
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 69.52
Mean single sequence MFE -26.69
Consensus MFE -8.82
Energy contribution -9.77
Covariance contribution 0.95
Combinations/Pair 1.36
Mean z-score -2.33
Structure conservation index 0.33
SVM decision value 1.36
SVM RNA-class probability 0.946673
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3688556 109 + 22407834
AUAUUUUAGCUAGUCCCCAAAA-----AAAGCAGAG----CGAAAGAGAGAGGCUUAUCUGGCAAAGAGAGAUGGGGCUGCCAGG-GUUAAAAGGGGGCGGCAACGUGGGGGGAAAAAG-
........(((.((((((....-----.((((....----(....)......)))).(((((((..............)))))))-.......))))))))).................- ( -30.14)
>DroSec_CAF1 150900 112 + 1
AUAUUUUAGCUAGUGCCCAAAAA---AAAAGAAGAG----CGAAAGAGAGAGGCUUAUCUGGCAAAGAGAGAUGGGGCUGCCAGGGGUUAAAAAGAGGCGGCAACGUGGGGCGAAAAAG-
.............(((((.....---...(((.(((----(...........)))).)))...........(((..((((((..............))))))..))).)))))......- ( -27.34)
>DroSim_CAF1 159921 113 + 1
AUAUUUUAGCUAGUGCCCAAAAA--AAAAAGCAAAG----CGAAAGAGAGAGGCUUAUCUGGCUAAGAGAGAUGGGGCUGCCAGGGGUUAAAAAGAGGCGGCAACGUGGGGCAAAAAAG-
.............(((((.....--...((((....----(....)......)))).(((.....)))...(((..((((((..............))))))..))).)))))......- ( -28.64)
>DroEre_CAF1 155945 109 + 1
AUAUUUCAGCUAGUGCCCAAAA-----AAAGCAGAG----CGAAAGAGAGGGGCUUAGCUGGCAAAGCGAGAUGGGAAUACCGGGCAUGA-AA-GGGGCGGAAACGUGGGGCGAGCAAGG
........(((.((((((....-----.((((....----(....)......)))).(((.....))).....((.....))))))))..-..-...(((....)))..)))........ ( -29.90)
>DroYak_CAF1 161353 89 + 1
AUAUUUCAGCUAGUCCCCAAAAA---AAAAGCAGAG----CGAAAGAGAGAGGCUUAGCUGGCAAAGCGAGAUGGGUAUAGCGGGAUUUA-AA-GGGG----------------------
.((..((.((((...((((....---..((((....----(....)......)))).(((.....)))....))))..))))..))..))-..-....---------------------- ( -21.30)
>DroAna_CAF1 167514 106 + 1
AUAUUUUUGCCAGAACCCCCAAAACCGGAGGGAUAGGGAUAGACAGAGAGGGGACUAUUUGGA-----GAGAA-----UGAGAGG---UAUAAAGAGUGGGUAGCUGGGGGUCUACUAA-
.((((((..(((((.(((((......)).)))................((....)).))))).-----.))))-----)).....---...........((((((.....).)))))..- ( -22.80)
>consensus
AUAUUUUAGCUAGUGCCCAAAAA___AAAAGCAGAG____CGAAAGAGAGAGGCUUAUCUGGCAAAGAGAGAUGGGGCUGCCAGG_GUUAAAAAGAGGCGGCAACGUGGGGCGAAAAAG_
..............((((...................................(((((((.........))))))).....................(((....))).))))........ ( -8.82 =  -9.77 +   0.95)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,688,587 – 3,688,702
Length 115
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 74.64
Mean single sequence MFE -31.64
Consensus MFE -18.62
Energy contribution -18.74
Covariance contribution 0.12
Combinations/Pair 1.32
Mean z-score -1.71
Structure conservation index 0.59
SVM decision value 0.46
SVM RNA-class probability 0.745558
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3688587 115 + 22407834
CGAAAGAGAGAGGCUUAUCUGGCAAAGAGAGAUGGGGCUGCCAGG-GUUAAAAGGGGGCGGCAACGUGGGGGGAAAAAG---GACAGAGCUAUUCUAGAACGAAGCCCCGAGCUUCAGA
(....)...(((((((.(((((((..............)))))))-........((((((....)((....((((...(---(......)).))))...))...))))))))))))... ( -34.34)
>DroSec_CAF1 150933 116 + 1
CGAAAGAGAGAGGCUUAUCUGGCAAAGAGAGAUGGGGCUGCCAGGGGUUAAAAAGAGGCGGCAACGUGGGGCGAAAAAG---GAGAGAGCUAUUCUAGAACGAAGCCCCGAGCUGCAGA
(....)...(.(((((.(((.....)))...(((..((((((..............))))))..)))(((((.......---.((((.....))))........)))))))))).)... ( -32.83)
>DroSim_CAF1 159955 116 + 1
CGAAAGAGAGAGGCUUAUCUGGCUAAGAGAGAUGGGGCUGCCAGGGGUUAAAAAGAGGCGGCAACGUGGGGCAAAAAAG---GAGAGAGCUAUUCUAGAACGAAGCCCCGAGCUGCAGA
(....)...(.(((((.(((.....)))...(((..((((((..............))))))..)))(((((.......---.((((.....))))........)))))))))).)... ( -31.73)
>DroEre_CAF1 155976 117 + 1
CGAAAGAGAGGGGCUUAGCUGGCAAAGCGAGAUGGGAAUACCGGGCAUGA-AA-GGGGCGGAAACGUGGGGCGAGCAAGGGAGAGAGAGCUAUUCUAGAGCGAAGCCCCAAGCUUCUGA
(....)..((((((((.(((.....)))(...(((.....)))..)....-..-...(((....)))(((((..((...((((((....)).))))...))...))))))))))))).. ( -37.30)
>DroAna_CAF1 167554 98 + 1
AGACAGAGAGGGGACUAUUUGGA-----GAGAA-----UGAGAGG---UAUAAAGAGUGGGUAGCUGGGGGUCUACUAA---GGGAGGAUGGUUCUAGAACGCCGCCCCAAGCU-----
...((((.((....)).))))..-----.....-----.......---..............((((((((((((.(...---..).))))(((........))).)))).))))----- ( -22.00)
>consensus
CGAAAGAGAGAGGCUUAUCUGGCAAAGAGAGAUGGGGCUGCCAGG_GUUAAAAAGAGGCGGCAACGUGGGGCGAAAAAG___GAGAGAGCUAUUCUAGAACGAAGCCCCGAGCUGCAGA
...........(((((..(((((................))))).............(((....)))(((((...........((((.....))))........))))))))))..... (-18.62 = -18.74 +   0.12)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:01:20 2006