Locus 7570

Sequence ID 3R_DroMel_CAF1
Location 20,298,172 – 20,298,263
Length 91
Max. P 0.611890
window12221 window12222

overview

Window 1

Location 20,298,172 – 20,298,263
Length 91
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 79.21
Mean single sequence MFE -16.79
Consensus MFE -12.35
Energy contribution -12.68
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.11
Structure conservation index 0.74
SVM decision value 0.16
SVM RNA-class probability 0.611890
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20298172 91 + 27905053
GCGGCCAAACAGCCGAAAAGUAGGCAACAUUGCGACUUUGCCAACUGCAUAGCCAUCUUUUAUCCCAAUACCC-----CUUAC-----CCAUAGGCAUAGA----
(((((......)))....(((.(((((..........))))).)))))...(((...................-----.....-----.....))).....---- ( -16.05)
>DroSec_CAF1 107039 83 + 1
GCGGCCAAACAGCCGAAAAGUAGGCAACAUUGCGACUUUGCCAACUGCAUAGCCAUCUUUUAUACCAAUACCC-----CUUAC-----CCAUA------------
.((((......))))(((((..(((.....((((...........))))..)))..)))))............-----.....-----.....------------ ( -13.70)
>DroSim_CAF1 115378 83 + 1
GCGGCCAAACAGCCGAAAAGUAGGCAACAUUGCGACUUUGCCAACUGCAUAGCCAUCUUUUAUACCAAUACCC-----CUUAC-----CCACA------------
.((((......))))(((((..(((.....((((...........))))..)))..)))))............-----.....-----.....------------ ( -13.70)
>DroEre_CAF1 110052 91 + 1
GCGGGCAAACAGCCGAAAAGUAGGCAACAUUGCGACUUUCCCAACUGCAUAGCCUUCUUUUAUCCCCAUACCU-----UAUAG-----CCAUCGCCAUAGC----
((((((.....))).(((((.((((.....((((...........))))..)))).)))))............-----.....-----....)))......---- ( -17.90)
>DroYak_CAF1 112539 95 + 1
GCGGCCAAACAGCCGAAAAGUAGGCAACAUUGCGACUUUCGCAACUGCCAAGCCAUCUUUUAUCCCCAUACCU-----UAUAG-----CCAUAGCCAUAGCCAUA
.((((......))))(((((..(((..(((((((.....))))).))....)))..)))))...........(-----(((.(-----(....)).))))..... ( -19.10)
>DroAna_CAF1 110526 105 + 1
GCGGCUAAGCAGCCGAAAAGUAGGCAACAUUGCGACUUUCCCAACUGCAUAGCCAUCUUUUAUUCCCGCUCCCAUCGUUACACUCGCACCAACCCCCCACCCCUA
(((((((.((((..(.(((((..(((....))).))))).)...)))).)))))............((.......))........)).................. ( -20.30)
>consensus
GCGGCCAAACAGCCGAAAAGUAGGCAACAUUGCGACUUUCCCAACUGCAUAGCCAUCUUUUAUCCCAAUACCC_____CAUAC_____CCAUAGCCAUAGC____
.((((......))))(((((..(((.....((((...........))))..)))..)))))............................................ (-12.35 = -12.68 +   0.33)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,298,172 – 20,298,263
Length 91
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 79.21
Mean single sequence MFE -27.07
Consensus MFE -21.76
Energy contribution -21.98
Covariance contribution 0.22
Combinations/Pair 1.10
Mean z-score -1.03
Structure conservation index 0.80
SVM decision value 0.15
SVM RNA-class probability 0.606800
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20298172 91 - 27905053
----UCUAUGCCUAUGG-----GUAAG-----GGGUAUUGGGAUAAAAGAUGGCUAUGCAGUUGGCAAAGUCGCAAUGUUGCCUACUUUUCGGCUGUUUGGCCGC
----(((((((((....-----.....-----))))).)))).........(((((.((((((((.(((((.(((....)))..))))))))))))).))))).. ( -28.50)
>DroSec_CAF1 107039 83 - 1
------------UAUGG-----GUAAG-----GGGUAUUGGUAUAAAAGAUGGCUAUGCAGUUGGCAAAGUCGCAAUGUUGCCUACUUUUCGGCUGUUUGGCCGC
------------(((.(-----(((..-----...)))).)))........(((((.((((((((.(((((.(((....)))..))))))))))))).))))).. ( -24.30)
>DroSim_CAF1 115378 83 - 1
------------UGUGG-----GUAAG-----GGGUAUUGGUAUAAAAGAUGGCUAUGCAGUUGGCAAAGUCGCAAUGUUGCCUACUUUUCGGCUGUUUGGCCGC
------------.((((-----((((.-----(.(((....)))....(.(((((.(((.....))).))))))..).))))))))....(((((....))))). ( -23.40)
>DroEre_CAF1 110052 91 - 1
----GCUAUGGCGAUGG-----CUAUA-----AGGUAUGGGGAUAAAAGAAGGCUAUGCAGUUGGGAAAGUCGCAAUGUUGCCUACUUUUCGGCUGUUUGCCCGC
----((((((((....)-----)))))-----.((((.(.((..(((((.((((...(((.(((.(.....).)))))).)))).)))))...)).).)))).)) ( -25.90)
>DroYak_CAF1 112539 95 - 1
UAUGGCUAUGGCUAUGG-----CUAUA-----AGGUAUGGGGAUAAAAGAUGGCUUGGCAGUUGCGAAAGUCGCAAUGUUGCCUACUUUUCGGCUGUUUGGCCGC
(((((((((....))))-----)))))-----...................((((..(((((((.((((((.(((....)))..)))))))))))))..)))).. ( -31.00)
>DroAna_CAF1 110526 105 - 1
UAGGGGUGGGGGGUUGGUGCGAGUGUAACGAUGGGAGCGGGAAUAAAAGAUGGCUAUGCAGUUGGGAAAGUCGCAAUGUUGCCUACUUUUCGGCUGCUUAGCCGC
.(((((((((.((....(((((.(.(..((((...(((.(..........).))).....))))..).).)))))...)).)))))))))(((((....))))). ( -29.30)
>consensus
____GCUAUGGCUAUGG_____GUAAA_____GGGUAUGGGGAUAAAAGAUGGCUAUGCAGUUGGCAAAGUCGCAAUGUUGCCUACUUUUCGGCUGUUUGGCCGC
...................................................(((((.((((((((.(((((.(((....)))..))))))))))))).))))).. (-21.76 = -21.98 +   0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:49:11 2006