Locus 682

Sequence ID 3R_DroMel_CAF1
Location 2,457,637 – 2,457,797
Length 160
Max. P 0.982062
window1080 window1081 window1082

overview

Window 0

Location 2,457,637 – 2,457,757
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.97
Mean single sequence MFE -39.06
Consensus MFE -36.88
Energy contribution -38.45
Covariance contribution 1.56
Combinations/Pair 1.03
Mean z-score -2.57
Structure conservation index 0.94
SVM decision value 1.85
SVM RNA-class probability 0.979924
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2457637 120 + 27905053
UAACCUCGAAAUCGAGAGCGCAGAACUGAAAGUUGGCCAUCAAGUUGUGUGUGGGGCAAUCAGAGAGAUGCCAGAAAUCGGAUUGCUUGGCACAACAAUUUGGUGACCCAGAGUCAUUGA
....((((....))))..........(((...((((.(((((((((((((((.((((((((.....(((.......))).)))))))).)))).)))))))))))..))))..))).... ( -42.20)
>DroSec_CAF1 16647 120 + 1
UAACCUCGAAAUCGAGAGCGCAGAACUGAAAGUUGGCCAUCAUGUUGUGUGUGGGGCAAUCAGAGAAAUGCCAGAAAUCGGAUUGCCUGGCACAACAAUUUGGGGACCCAGAGUCAUUGA
....((((....))))..........(((...((((((.(((.(((((((((.((((((((.((.............)).)))))))).)))).))))).)))))..))))..))).... ( -38.42)
>DroSim_CAF1 13372 120 + 1
UAACCUCGAAAUCGAGAGCGCAGAACUGAAAGUUGGCCAUCAUGUUGUGUGUGGGGCAAUCAGAGAAAUGCCAGAAAUCGGAUUGCCUGGCACAACAAUUUGGUGACCCAGAGUCAUUGA
....((((....))))..........(((...((((.(((((.(((((((((.((((((((.((.............)).)))))))).)))).))))).)))))..))))..))).... ( -40.92)
>DroEre_CAF1 18139 117 + 1
CAACCUCGAAAUCGAGAGCGCAGAACU-AAAGUUGGCCAUCAAGUUGU--GUGGGGCAAUCAGAGAGAUGCCAGAAAUCGGAUUGCCUGGAACAACAAUUUGGUGACCCAGAGUCAUUGA
....((((....))))...........-....((((.(((((((((((--.(.((((((((.....(((.......))).)))))))).)....)))))))))))..))))......... ( -34.70)
>consensus
UAACCUCGAAAUCGAGAGCGCAGAACUGAAAGUUGGCCAUCAAGUUGUGUGUGGGGCAAUCAGAGAAAUGCCAGAAAUCGGAUUGCCUGGCACAACAAUUUGGUGACCCAGAGUCAUUGA
....((((....))))..........(((...((((.(((((((((((((((.((((((((.((.............)).)))))))).)))).)))))))))))..))))..))).... (-36.88 = -38.45 +   1.56)

alignment

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secondary structure

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dotplot

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Window 1

Location 2,457,677 – 2,457,797
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 96.39
Mean single sequence MFE -47.66
Consensus MFE -45.18
Energy contribution -45.74
Covariance contribution 0.56
Combinations/Pair 1.02
Mean z-score -3.77
Structure conservation index 0.95
SVM decision value 1.90
SVM RNA-class probability 0.982062
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2457677 120 + 27905053
CAAGUUGUGUGUGGGGCAAUCAGAGAGAUGCCAGAAAUCGGAUUGCUUGGCACAACAAUUUGGUGACCCAGAGUCAUUGACACGCCUCGUUUUCGGGGCAUUGGCUGGGCAUUAAAUUCA
((((((((((((.((((((((.....(((.......))).)))))))).)))).))))))))(((.(((((.(((...)))..((((((....)))))).....))))))))........ ( -48.70)
>DroSec_CAF1 16687 120 + 1
CAUGUUGUGUGUGGGGCAAUCAGAGAAAUGCCAGAAAUCGGAUUGCCUGGCACAACAAUUUGGGGACCCAGAGUCAUUGACACGCCUCGUUUUCGGGGCAUUGGCUGGGCAUUAAAUUCA
((.(((((((((.((((((((.((.............)).)))))))).)))).))))).))..(.(((((.(((...)))..((((((....)))))).....)))))).......... ( -45.62)
>DroSim_CAF1 13412 120 + 1
CAUGUUGUGUGUGGGGCAAUCAGAGAAAUGCCAGAAAUCGGAUUGCCUGGCACAACAAUUUGGUGACCCAGAGUCAUUGACACGCCUCGUUGUCGGGGCAUUGGCUGGGCAUUAAAUUCA
.......(((((.((((((((.((.............)).)))))))).)))))..(((((((((.(((((.(((...)))..((((((....)))))).....)))))))))))))).. ( -48.62)
>DroEre_CAF1 18178 118 + 1
CAAGUUGU--GUGGGGCAAUCAGAGAGAUGCCAGAAAUCGGAUUGCCUGGAACAACAAUUUGGUGACCCAGAGUCAUUGACACGCCUCGUUUUCGGGGCAUUGGCUGGGCAUUAAAUUCA
...(((((--.(.((((((((.....(((.......))).)))))))).).)))))(((((((((.(((((.(((...)))..((((((....)))))).....)))))))))))))).. ( -47.70)
>consensus
CAAGUUGUGUGUGGGGCAAUCAGAGAAAUGCCAGAAAUCGGAUUGCCUGGCACAACAAUUUGGUGACCCAGAGUCAUUGACACGCCUCGUUUUCGGGGCAUUGGCUGGGCAUUAAAUUCA
...(((((((...((((((((.((.............)).)))))))).)))))))(((((((((.(((((.(((...)))..((((((....)))))).....)))))))))))))).. (-45.18 = -45.74 +   0.56)

alignment

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secondary structure

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dotplot

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Window 2

Location 2,457,677 – 2,457,797
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 96.39
Mean single sequence MFE -32.89
Consensus MFE -31.27
Energy contribution -31.77
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.54
Structure conservation index 0.95
SVM decision value 0.19
SVM RNA-class probability 0.627127
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2457677 120 - 27905053
UGAAUUUAAUGCCCAGCCAAUGCCCCGAAAACGAGGCGUGUCAAUGACUCUGGGUCACCAAAUUGUUGUGCCAAGCAAUCCGAUUUCUGGCAUCUCUCUGAUUGCCCCACACACAACUUG
..(((((..(((((((...(((((.((....)).)))))(((...))).))))).))..)))))((((((....((((((.((.............)).))))))......))))))... ( -30.62)
>DroSec_CAF1 16687 120 - 1
UGAAUUUAAUGCCCAGCCAAUGCCCCGAAAACGAGGCGUGUCAAUGACUCUGGGUCCCCAAAUUGUUGUGCCAGGCAAUCCGAUUUCUGGCAUUUCUCUGAUUGCCCCACACACAACAUG
..........((((((...(((((.((....)).)))))(((...))).))))))........(((((((...(((((((.((.............)).))))))).....))))))).. ( -34.02)
>DroSim_CAF1 13412 120 - 1
UGAAUUUAAUGCCCAGCCAAUGCCCCGACAACGAGGCGUGUCAAUGACUCUGGGUCACCAAAUUGUUGUGCCAGGCAAUCCGAUUUCUGGCAUUUCUCUGAUUGCCCCACACACAACAUG
..(((((..(((((((...(((((.((....)).)))))(((...))).))))).))..)))))((((((...(((((((.((.............)).))))))).....))))))... ( -34.62)
>DroEre_CAF1 18178 118 - 1
UGAAUUUAAUGCCCAGCCAAUGCCCCGAAAACGAGGCGUGUCAAUGACUCUGGGUCACCAAAUUGUUGUUCCAGGCAAUCCGAUUUCUGGCAUCUCUCUGAUUGCCCCAC--ACAACUUG
..(((((..(((((((...(((((.((....)).)))))(((...))).))))).))..)))))(((((....(((((((.((.............)).)))))))....--)))))... ( -32.32)
>consensus
UGAAUUUAAUGCCCAGCCAAUGCCCCGAAAACGAGGCGUGUCAAUGACUCUGGGUCACCAAAUUGUUGUGCCAGGCAAUCCGAUUUCUGGCAUCUCUCUGAUUGCCCCACACACAACAUG
..(((((...((((((...(((((.((....)).)))))(((...))).))))))....)))))((((((...(((((((.((.............)).))))))).....))))))... (-31.27 = -31.77 +   0.50)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:49:15 2006