Locus 3989

Sequence ID 2L_DroMel_CAF1
Location 11,617,214 – 11,617,340
Length 126
Max. P 0.997184
window6291 window6292

overview

Window 1

Location 11,617,214 – 11,617,320
Length 106
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 78.59
Mean single sequence MFE -32.97
Consensus MFE -19.24
Energy contribution -20.00
Covariance contribution 0.76
Combinations/Pair 1.38
Mean z-score -1.71
Structure conservation index 0.58
SVM decision value 0.28
SVM RNA-class probability 0.667524
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11617214 106 - 22407834
AGAAGAGCCA--GGACUUUUGGGUUCGUUAAGCUCUGCGGGCUGCAAUAUGGGUGUGUUGCGGCGAGAUAAAGAGUCCAUGGACAGAGUUGGU------AAUUCCGCAGCAUAA
...(((((..--(((((....))))).....)))))((((((((((((((....))))))))))..........(((....))).........------....))))....... ( -35.30)
>DroSec_CAF1 70512 106 - 1
AGAAGAGCCA--GGACUUUUGGGUUCGUUAAGCUCUGCGGGCUGCAAUAUGGGUGUGUGGCGGCGAGAUAAAGAGUCCAUGGACAGAGUUGGU------AAUUCCGCAGCAUAA
...(((((..--(((((....))))).....)))))(((((((((.((((....)))).)))))..........(((....))).........------....))))....... ( -31.20)
>DroSim_CAF1 74297 106 - 1
AGAAGAGCCA--GGACUUUUGGGUUCGUUAAGCUCAGCGGGCUGCAAUAUGGGUGUGUUGUGGCGAGAUAAAGAGUCCAUGGACAGAGUUGGU------AAUGCCGCAGCAUAA
......((((--((((((((...((((((.((((.....))))(((((((....)))))))))))))...)))))))).))).).........------.((((....)))).. ( -32.50)
>DroEre_CAF1 100990 104 - 1
AGCAGAGCCA--GGACUUUUGGGUUCGUUAAGCUCUGCGGGCUGCAA--UGGGUGUGUUGCGGGGAGAUGCAGAGUCCAUGGACAAAUUUGCU------GAUUCCGCAGCAUAA
.(((((((..--(((((....))))).....))))))).........--....((((((((((((....((((((((....)))...))))).------..)))))))))))). ( -41.10)
>DroYak_CAF1 73720 106 - 1
AGAAGAGCCA--GGACUUUUGGGUUCGUUAAGCUCUGCGGGCUGCAAUAUGGCUGUGUGGCGGGGAGAUAAAGAGUCCAUGGAGAGAUUUGUU------AAUUCCACGGCAUAA
......(((.--((((((((...(((.(...(((..((((.(........).))))..))).).)))...)))))))).(((((..(.....)------..))))).))).... ( -31.80)
>DroAna_CAF1 83667 107 - 1
AAAAGUGGCUGUGGGGCUUUGGGUUCGUUAAGCUUUGCGGGUUAAAAUGAAAGAUAUUUAUAAAGAUUUAGUGAGUCC-----CAGAGGUAACCAAGUGAAUUUUGC--CAGGA
.....((((..(((..(((((((((((((((((((((..(((.............)))..))))).))))))))).))-----)))))....)))..........))--))... ( -25.92)
>consensus
AGAAGAGCCA__GGACUUUUGGGUUCGUUAAGCUCUGCGGGCUGCAAUAUGGGUGUGUUGCGGCGAGAUAAAGAGUCCAUGGACAGAGUUGGU______AAUUCCGCAGCAUAA
...(((((....(((((....))))).....)))))((((.(((((((((....)))))))))...........(((....)))...................))))....... (-19.24 = -20.00 +   0.76)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,617,242 – 11,617,340
Length 98
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 93.56
Mean single sequence MFE -28.28
Consensus MFE -24.40
Energy contribution -25.84
Covariance contribution 1.44
Combinations/Pair 1.03
Mean z-score -2.29
Structure conservation index 0.86
SVM decision value 2.81
SVM RNA-class probability 0.997184
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11617242 98 - 22407834
AUAUUUAU--AUAAAAGUAAAUAGAAGAGCCAGGACUUUUGGGUUCGUUAAGCUCUGCGGGCUGCAAUAUGGGUGUGUUGCGGCGAGAUAAAGAGUCCAU
.(((((((--......))))))).........((((((((...((((((.((((.....))))(((((((....)))))))))))))...)))))))).. ( -31.60)
>DroSec_CAF1 70540 100 - 1
AUAUUUAUAUAUAAAAGUAAAUAGAAGAGCCAGGACUUUUGGGUUCGUUAAGCUCUGCGGGCUGCAAUAUGGGUGUGUGGCGGCGAGAUAAAGAGUCCAU
.(((((((........))))))).........((((((((...((((((.((((.....))))((.((((....)))).))))))))...)))))))).. ( -27.30)
>DroSim_CAF1 74325 100 - 1
AUAUUUAUAUAUAAAAGUAAAUAGAAGAGCCAGGACUUUUGGGUUCGUUAAGCUCAGCGGGCUGCAAUAUGGGUGUGUUGUGGCGAGAUAAAGAGUCCAU
.(((((((........))))))).........((((((((...((((((.((((.....))))(((((((....)))))))))))))...)))))))).. ( -29.10)
>DroEre_CAF1 101018 96 - 1
AUAUUUAU--AUAAAAGUAAAUAGCAGAGCCAGGACUUUUGGGUUCGUUAAGCUCUGCGGGCUGCAA--UGGGUGUGUUGCGGGGAGAUGCAGAGUCCAU
.(((((((--......)))))))(((((((..(((((....))))).....)))))))((((((((.--....))).(((((......)))))))))).. ( -30.10)
>DroYak_CAF1 73748 98 - 1
AUAUUCAU--GUAAAAGUAAAUAGAAGAGCCAGGACUUUUGGGUUCGUUAAGCUCUGCGGGCUGCAAUAUGGCUGUGUGGCGGGGAGAUAAAGAGUCCAU
........--......................((((((((...(((.(...(((..((((.(........).))))..))).).)))...)))))))).. ( -23.30)
>consensus
AUAUUUAU__AUAAAAGUAAAUAGAAGAGCCAGGACUUUUGGGUUCGUUAAGCUCUGCGGGCUGCAAUAUGGGUGUGUUGCGGCGAGAUAAAGAGUCCAU
.(((((((........))))))).........((((((((...((((((.((((.....))))(((((((....)))))))))))))...)))))))).. (-24.40 = -25.84 +   1.44)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:06:35 2006