Locus 3577

Sequence ID 3R_DroMel_CAF1
Location 9,673,730 – 9,673,850
Length 120
Max. P 0.671699
window5759 window5760

overview

Window 9

Location 9,673,730 – 9,673,850
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.58
Mean single sequence MFE -42.60
Consensus MFE -30.18
Energy contribution -32.50
Covariance contribution 2.32
Combinations/Pair 1.11
Mean z-score -2.04
Structure conservation index 0.71
SVM decision value 0.24
SVM RNA-class probability 0.646764
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9673730 120 + 27905053
GGCAAUUAAUUAAUCCUGCACUCCGUGGCCAACUUAGUUGGGCCGGCUAACUAACUAGACAGCGACUAGCAGGUUGCCGGUUGCACGUUGCAGGUUGCCGGUUGCAUAUUGCCGGGUCCA
(((...........((((((...((((.(((((...)))))((((((.((((..((((.......))))..))))))))))..)))).))))))...(((((........)))))))).. ( -45.50)
>DroSec_CAF1 65419 120 + 1
GGCAAUUAAUUAAUCCUGCACUCCGUGGCCAACUUAGUUGGACCGGCUAACUAACUAGACAGCGACUAGCAGGUUGCCGGUUGAACGUUGCACGUUGCCGGUUGCAUAUUGCCGGGUCCA
((((((....(((.((.(((...((((..((((...(((.(((((((.((((..((((.......))))..))))))))))).))))))))))).))).)))))...))))))....... ( -42.00)
>DroSim_CAF1 68357 120 + 1
GGCAAUUAAUUAAUCCUGCACUCCGUGGCCAACUUAGUUGGACCGGCUAACUAACUAGACAGCGACUAGCAGGUUGCCGGUUGCACGUUGCAGGUUGCCGGUUGCAUAUUGCCGGGUCCA
(((...........((((((...((((.(((((...)))))((((((.((((..((((.......))))..))))))))))..)))).))))))...(((((........)))))))).. ( -45.00)
>DroEre_CAF1 66653 107 + 1
GGCAAUUAAUUAAUCCUGCACUCCGCGGCCAACUUAGUUGGCCCGGCUAACUAACUAGACAGCGACUAGCAGGUUGCUG-------GUUGCAGGUUGCCUAUU------UGCAGGGUCCA
............((((((((....((((((...(((((((((...))))))))).......(((((((((.....))))-------))))).)))))).....------))))))))... ( -43.90)
>DroYak_CAF1 70485 120 + 1
GGCAAUUAAUUAAUCCUGCACUACGCGGCCAACUCACUUGGCCCGGCUAACUAACUAGACAGCGACUAGCAGGUUGCAGGCUUCGAGUUGCACGUUGCCUAUUGCCUAUUGCCGGGUCCA
((((((........(((((....((.((((((.....))))))))(((..((....))..))).....)))))....((((....((..((.....))))...))))))))))....... ( -36.60)
>consensus
GGCAAUUAAUUAAUCCUGCACUCCGUGGCCAACUUAGUUGGACCGGCUAACUAACUAGACAGCGACUAGCAGGUUGCCGGUUGCACGUUGCAGGUUGCCGGUUGCAUAUUGCCGGGUCCA
(((...........((((((...((((.(((((...)))))((((((.((((..((((.......))))..))))))))))..)))).))))))...(((((........)))))))).. (-30.18 = -32.50 +   2.32)

alignment

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secondary structure

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dotplot

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Window 0

Location 9,673,730 – 9,673,850
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.58
Mean single sequence MFE -41.66
Consensus MFE -30.00
Energy contribution -32.96
Covariance contribution 2.96
Combinations/Pair 1.03
Mean z-score -1.97
Structure conservation index 0.72
SVM decision value 0.29
SVM RNA-class probability 0.671699
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9673730 120 - 27905053
UGGACCCGGCAAUAUGCAACCGGCAACCUGCAACGUGCAACCGGCAACCUGCUAGUCGCUGUCUAGUUAGUUAGCCGGCCCAACUAAGUUGGCCACGGAGUGCAGGAUUAAUUAAUUGCC
.......((((((.(((.....))).((((((.((((...((((((((..(((((.......)))))..))).))))).(((((...))))).))))...))))))........)))))) ( -45.80)
>DroSec_CAF1 65419 120 - 1
UGGACCCGGCAAUAUGCAACCGGCAACGUGCAACGUUCAACCGGCAACCUGCUAGUCGCUGUCUAGUUAGUUAGCCGGUCCAACUAAGUUGGCCACGGAGUGCAGGAUUAAUUAAUUGCC
.......((((((.(((.....))).(.((((.(((...(((((((((..(((((.......)))))..))).))))))(((((...)))))..)))...)))).)........)))))) ( -39.50)
>DroSim_CAF1 68357 120 - 1
UGGACCCGGCAAUAUGCAACCGGCAACCUGCAACGUGCAACCGGCAACCUGCUAGUCGCUGUCUAGUUAGUUAGCCGGUCCAACUAAGUUGGCCACGGAGUGCAGGAUUAAUUAAUUGCC
.......((((((.(((.....))).((((((.((((..(((((((((..(((((.......)))))..))).))))))(((((...))))).))))...))))))........)))))) ( -46.80)
>DroEre_CAF1 66653 107 - 1
UGGACCCUGCA------AAUAGGCAACCUGCAAC-------CAGCAACCUGCUAGUCGCUGUCUAGUUAGUUAGCCGGGCCAACUAAGUUGGCCGCGGAGUGCAGGAUUAAUUAAUUGCC
.....((((((------..((((((....((.((-------.(((.....))).)).)))))))).........((((((((((...))))))).)))..)))))).............. ( -37.40)
>DroYak_CAF1 70485 120 - 1
UGGACCCGGCAAUAGGCAAUAGGCAACGUGCAACUCGAAGCCUGCAACCUGCUAGUCGCUGUCUAGUUAGUUAGCCGGGCCAAGUGAGUUGGCCGCGUAGUGCAGGAUUAAUUAAUUGCC
.......((((((..(((...(....).))).........((((((...(((.....((((.((....)).))))..((((((.....)))))))))...))))))........)))))) ( -38.80)
>consensus
UGGACCCGGCAAUAUGCAACCGGCAACCUGCAACGUGCAACCGGCAACCUGCUAGUCGCUGUCUAGUUAGUUAGCCGGGCCAACUAAGUUGGCCACGGAGUGCAGGAUUAAUUAAUUGCC
.......((((((..((.....))..((((((.((((...((((((((..(((((.......)))))..))).))))).(((((...))))).))))...))))))........)))))) (-30.00 = -32.96 +   2.96)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:04:51 2006