Locus 2959

Sequence ID 2R_DroMel_CAF1
Location 10,205,012 – 10,205,142
Length 130
Max. P 0.877587
window4891 window4892 window4893

overview

Window 1

Location 10,205,012 – 10,205,122
Length 110
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 80.30
Mean single sequence MFE -28.74
Consensus MFE -17.24
Energy contribution -19.80
Covariance contribution 2.56
Combinations/Pair 1.26
Mean z-score -2.05
Structure conservation index 0.60
SVM decision value 0.56
SVM RNA-class probability 0.781903
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10205012 110 - 20766785
AAG-AUUGGAGGAU-AAUACCCCCAGGUGUUGAAUUCAGGGAAUUGUUAGGUGUAUGCAGUCUAACAAGCAGUCUAAAUAGGUA-UUAGGGA-UACCAGUAAAAUCAAUACUUG----
...-...((.((..-....))))((((((((((......(((.((((((((((....)).))))))))....))).....((((-((...))-)))).......))))))))))---- ( -28.50)
>DroSec_CAF1 34587 99 - 1
AAG-AUUGGGGGAU-AAUACCCCCAGGUGUUGAAUUCAGGGAAUU-----------GCCGCCUAACAAGCAGUCUAAAUAGGCA-UUAGGGA-UACCAGUAAAAUCAAUACUUG----
...-...(((((..-....)))))(((((((((.....((.....-----------.))(((((...((....))...))))).-...((..-..)).......))))))))).---- ( -28.30)
>DroSim_CAF1 34508 110 - 1
AAG-AUUGGGGGAU-AAUACCCCCAGGUGUUGAAUUCAGGGAAUUGUUAGGUGUAUGCCGCCUAACAAGCAGUCUAAAUAGGCA-UUAGGGA-UACCAGUAAAAUCAAUACUUG----
...-...(((((..-....)))))(((((((((..........((((((((((.....))))))))))((.((((....)))).-...((..-..)).))....))))))))).---- ( -37.70)
>DroEre_CAF1 37686 115 - 1
AAGAUUUGGGGAAU-AAUGCUCCCAGGUGUUGAAUUCAGGGAAUUGUUAGGUGUAUGCCGUCUAACAAGCAGUCUAAAUAGGCA-UUAGGAA-UACCAGUAAAAUCAAUACUUGGCUG
.......((((...-....))))((((((((((......((..(((((((..(.....)..)))))))...((((....)))).-.......-..)).......)))))))))).... ( -27.72)
>DroYak_CAF1 34053 112 - 1
AAGGAUUGGGGGAU-AAUACCCCUAGGUGUUGAAUUCAGGGAAUUGUUAGGUGUAUGCCGUCUAACAAGCAGUCUAAAUAGGCA-UUAGGGAUUACCAGUAAAAUCAAUACUUG----
......((((((..-....))))))((((((((..........(((((((..(.....)..)))))))((.((((....)))).-...((.....)).))....))))))))..---- ( -30.30)
>DroAna_CAF1 39160 93 - 1
--------ACGGAUAAAUGUCCUUAGGUGUUGUAUUCACAGAAUUG---------UGCAACUUAACAAGCAGGCUAAACAGUCAAUGAGGGC-UUCCUGCAAAAUCAUU---GG----
--------..(((.....(((((((...(((((((..........)---------))))))..........((((....))))..)))))))-.)))............---..---- ( -19.90)
>consensus
AAG_AUUGGGGGAU_AAUACCCCCAGGUGUUGAAUUCAGGGAAUUGUUAGGUGUAUGCCGCCUAACAAGCAGUCUAAAUAGGCA_UUAGGGA_UACCAGUAAAAUCAAUACUUG____
.......(((((.......)))))(((((((((..........(((((((((.......)))))))))((.((((....)))).....((.....)).))....)))))))))..... (-17.24 = -19.80 +   2.56)

alignment

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secondary structure

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Window 2

Location 10,205,046 – 10,205,142
Length 96
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 89.14
Mean single sequence MFE -18.84
Consensus MFE -13.60
Energy contribution -13.32
Covariance contribution -0.28
Combinations/Pair 1.24
Mean z-score -2.46
Structure conservation index 0.72
SVM decision value 0.90
SVM RNA-class probability 0.877587
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10205046 96 + 20766785
UUUAGACUGCUUGUUAGACUGCAUACACCUAACAAUUCCCUGAAUUCAACACCUGGGGGUAUUAUCCUCCAAU-CUUUGCCCCUCUUAACAAUUUUC
(((((.....(((((((...........)))))))....)))))..........(((((((............-...)))))))............. ( -15.66)
>DroSec_CAF1 34621 85 + 1
UUUAGACUGCUUGUUAGGCGGC-----------AAUUCCCUGAAUUCAACACCUGGGGGUAUUAUCCCCCAAU-CUUUGUCCCUCUUAACAAUUUUC
..........((((((((.(((-----------((.....((....)).....((((((......))))))..-..)))))...))))))))..... ( -21.10)
>DroSim_CAF1 34542 96 + 1
UUUAGACUGCUUGUUAGGCGGCAUACACCUAACAAUUCCCUGAAUUCAACACCUGGGGGUAUUAUCCCCCAAU-CUUUGCCCCUCUUAACAAUUUUC
(((((.....((((((((.(.....).))))))))....))))).........((((((......))))))..-....................... ( -23.60)
>DroEre_CAF1 37724 97 + 1
UUUAGACUGCUUGUUAGACGGCAUACACCUAACAAUUCCCUGAAUUCAACACCUGGGAGCAUUAUUCCCCAAAUCUUUGCCCCUCUUGGCAAUUUUC
.......((((((((((..(.....)..))))))).((((..............)))))))...............(((((......)))))..... ( -17.94)
>DroYak_CAF1 34088 97 + 1
UUUAGACUGCUUGUUAGACGGCAUACACCUAACAAUUCCCUGAAUUCAACACCUAGGGGUAUUAUCCCCCAAUCCUUGCCCCCUCUUAACAAUUUUC
..........((((((((.((((..........(((((...))))).........((((......)))).......))))...)).))))))..... ( -15.90)
>consensus
UUUAGACUGCUUGUUAGACGGCAUACACCUAACAAUUCCCUGAAUUCAACACCUGGGGGUAUUAUCCCCCAAU_CUUUGCCCCUCUUAACAAUUUUC
..........((((((((.((............(((((...))))).......((((((......)))))).........)).)).))))))..... (-13.60 = -13.32 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 3

Location 10,205,046 – 10,205,142
Length 96
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 89.14
Mean single sequence MFE -26.20
Consensus MFE -18.04
Energy contribution -20.04
Covariance contribution 2.00
Combinations/Pair 1.14
Mean z-score -2.56
Structure conservation index 0.69
SVM decision value 0.54
SVM RNA-class probability 0.775139
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10205046 96 - 20766785
GAAAAUUGUUAAGAGGGGCAAAG-AUUGGAGGAUAAUACCCCCAGGUGUUGAAUUCAGGGAAUUGUUAGGUGUAUGCAGUCUAACAAGCAGUCUAAA
.....(((((......)))))((-(((((((..(((((((....)))))))..)))......((((((((((....)).)))))))).))))))... ( -24.10)
>DroSec_CAF1 34621 85 - 1
GAAAAUUGUUAAGAGGGACAAAG-AUUGGGGGAUAAUACCCCCAGGUGUUGAAUUCAGGGAAUU-----------GCCGCCUAACAAGCAGUCUAAA
((...((((((.(.((((((...-.(((((((......))))))).)))).(((((...)))))-----------.)).).))))))....)).... ( -23.80)
>DroSim_CAF1 34542 96 - 1
GAAAAUUGUUAAGAGGGGCAAAG-AUUGGGGGAUAAUACCCCCAGGUGUUGAAUUCAGGGAAUUGUUAGGUGUAUGCCGCCUAACAAGCAGUCUAAA
....((((((..(((...(((..-.(((((((......)))))))...)))..))).......(((((((((.....)))))))))))))))..... ( -32.20)
>DroEre_CAF1 37724 97 - 1
GAAAAUUGCCAAGAGGGGCAAAGAUUUGGGGAAUAAUGCUCCCAGGUGUUGAAUUCAGGGAAUUGUUAGGUGUAUGCCGUCUAACAAGCAGUCUAAA
(((...((((......))))((.((((((((........)))))))).))...)))..(((.(((((((..(.....)..)))))))....)))... ( -25.60)
>DroYak_CAF1 34088 97 - 1
GAAAAUUGUUAAGAGGGGGCAAGGAUUGGGGGAUAAUACCCCUAGGUGUUGAAUUCAGGGAAUUGUUAGGUGUAUGCCGUCUAACAAGCAGUCUAAA
....((((((....(((..(((.(.(((((((......))))))).).)))..))).......((((((..(.....)..))))))))))))..... ( -25.30)
>consensus
GAAAAUUGUUAAGAGGGGCAAAG_AUUGGGGGAUAAUACCCCCAGGUGUUGAAUUCAGGGAAUUGUUAGGUGUAUGCCGUCUAACAAGCAGUCUAAA
....(((((...(((...(((....(((((((......)))))))...)))..)))......((((((((((.....)))))))))))))))..... (-18.04 = -20.04 +   2.00)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:44:00 2006