Locus 4456

Sequence ID X_DroMel_CAF1
Location 11,789,518 – 11,789,661
Length 143
Max. P 0.999920
window7319 window7320 window7321 window7322

overview

Window 9

Location 11,789,518 – 11,789,621
Length 103
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 90.95
Mean single sequence MFE -40.80
Consensus MFE -35.68
Energy contribution -36.96
Covariance contribution 1.28
Combinations/Pair 1.06
Mean z-score -3.97
Structure conservation index 0.87
SVM decision value 4.56
SVM RNA-class probability 0.999920
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11789518 103 + 22224390
AA--CCCGGUAUGCGUCCGAUCAUGCGCGAUG--UGAAUGUGGCAUUAAGUGGCAGUUAAAAU-GUAACCGCCACAUCAACCGCUGAUUUAAGGACGCAUACCGCCUC
..--..(((((((((((((((((.((((.((.--.....)).)).....(((((.((((....-.)))).))))).......)))))))...)))))))))))).... ( -43.80)
>DroSec_CAF1 19129 103 + 1
AA--CCAGGGUUGCGUCCGAUCAUGCGCGAUG--UGAAUGUGGCAUUAAGUGGCGGUUAAAAU-GUAACCGCCACAUCAACCGCUGAUUUAAGGACGCAUACCGCCUC
..--...((..((((((((((((.((((.((.--.....)).)).....((((((((((....-.)))))))))).......)))))))...)))))))..))..... ( -43.30)
>DroSim_CAF1 19313 103 + 1
AU--CCCGGUAUGCGUCCGAUCAUGCGCGAUG--UGAAUGUGGCAUUAAGUGGCGGUUAAAAU-GUAACCGCCACAUCAACCGCUGAUUUAAGGACGCAUACCGCCUC
..--..(((((((((((((((((.((((.((.--.....)).)).....((((((((((....-.)))))))))).......)))))))...)))))))))))).... ( -49.90)
>DroEre_CAF1 18921 103 + 1
AA--CCCGGUUUGCGUCCGAUCAUGCGCGAUG--UGAAUGUGGUAUUAUGUGCCUGUUAAAUU-UUAAUCGACACAUCAACCGCUGAUUUAUGGACGCAUACCGCCUC
..--..((((.((((((((((((.(((.((((--((.....(((((...))))).((((....-.))))...))))))...))))))))...))))))).)))).... ( -35.70)
>DroYak_CAF1 19569 108 + 1
AAUCCCCGCUUUGCGACCGAUCAUGCGCGAUGUGUGAAUGUGGCAUUAAGUGGCGGUUAAAUUGUUAACCGACACUUCAACCGCUGAUUUAAGGACGCAUACCGCCUC
.......((..((((.(((((((.((((.((((....)))).))...(((((.(((((((....))))))).))))).....)))))))...)).))))....))... ( -31.30)
>consensus
AA__CCCGGUUUGCGUCCGAUCAUGCGCGAUG__UGAAUGUGGCAUUAAGUGGCGGUUAAAAU_GUAACCGCCACAUCAACCGCUGAUUUAAGGACGCAUACCGCCUC
......((((.((((((((((((.((((.((........)).)).....((((((((((......)))))))))).......)))))))...))))))).)))).... (-35.68 = -36.96 +   1.28)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,789,518 – 11,789,621
Length 103
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 90.95
Mean single sequence MFE -39.18
Consensus MFE -33.38
Energy contribution -34.26
Covariance contribution 0.88
Combinations/Pair 1.10
Mean z-score -3.26
Structure conservation index 0.85
SVM decision value 3.93
SVM RNA-class probability 0.999712
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11789518 103 - 22224390
GAGGCGGUAUGCGUCCUUAAAUCAGCGGUUGAUGUGGCGGUUAC-AUUUUAACUGCCACUUAAUGCCACAUUCA--CAUCGCGCAUGAUCGGACGCAUACCGGG--UU
....((((((((((((....((((((.(((((.((((((((((.-....)))))))))))))))((........--....)))).)))).))))))))))))..--.. ( -44.60)
>DroSec_CAF1 19129 103 - 1
GAGGCGGUAUGCGUCCUUAAAUCAGCGGUUGAUGUGGCGGUUAC-AUUUUAACCGCCACUUAAUGCCACAUUCA--CAUCGCGCAUGAUCGGACGCAACCCUGG--UU
..((.(((.(((((((....((((((.(((((.((((((((((.-....)))))))))))))))((........--....)))).)))).))))))))))))..--.. ( -39.70)
>DroSim_CAF1 19313 103 - 1
GAGGCGGUAUGCGUCCUUAAAUCAGCGGUUGAUGUGGCGGUUAC-AUUUUAACCGCCACUUAAUGCCACAUUCA--CAUCGCGCAUGAUCGGACGCAUACCGGG--AU
....((((((((((((....((((((.(((((.((((((((((.-....)))))))))))))))((........--....)))).)))).))))))))))))..--.. ( -46.80)
>DroEre_CAF1 18921 103 - 1
GAGGCGGUAUGCGUCCAUAAAUCAGCGGUUGAUGUGUCGAUUAA-AAUUUAACAGGCACAUAAUACCACAUUCA--CAUCGCGCAUGAUCGGACGCAAACCGGG--UU
....((((.(((((((....(((((((((..(((((((..(((.-....)))..)))))))...))).....(.--....).)).)))).))))))).))))..--.. ( -33.80)
>DroYak_CAF1 19569 108 - 1
GAGGCGGUAUGCGUCCUUAAAUCAGCGGUUGAAGUGUCGGUUAACAAUUUAACCGCCACUUAAUGCCACAUUCACACAUCGCGCAUGAUCGGUCGCAAAGCGGGGAUU
....((.(.((((.((....(((((((((..(((((.(((((((....))))))).)))))...))).......(.....).)).)))).)).)))).).))...... ( -31.00)
>consensus
GAGGCGGUAUGCGUCCUUAAAUCAGCGGUUGAUGUGGCGGUUAC_AUUUUAACCGCCACUUAAUGCCACAUUCA__CAUCGCGCAUGAUCGGACGCAAACCGGG__UU
....((((.(((((((....(((((((((....((((((((((......)))))))))).....))).....(.......).)).)))).))))))).))))...... (-33.38 = -34.26 +   0.88)

alignment

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secondary structure

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Window 1

Location 11,789,551 – 11,789,661
Length 110
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 91.76
Mean single sequence MFE -31.16
Consensus MFE -26.74
Energy contribution -27.42
Covariance contribution 0.68
Combinations/Pair 1.07
Mean z-score -1.73
Structure conservation index 0.86
SVM decision value 1.43
SVM RNA-class probability 0.952779
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11789551 110 + 22224390
AUGUGGCAUUAAGUGGCAGUUAAAAU-GUAACCGCCACAUCAACCGCUGAUUUAAGGACGCAUACCGCCUCACCGUGGAAUCUGCAUUGAUAAAUCACAUUCGACUCGACA
((((((......(((((.((((....-.)))).)))))(((((..((.(((((..((..((.....))....))...))))).)).)))))...))))))........... ( -27.90)
>DroSec_CAF1 19162 110 + 1
AUGUGGCAUUAAGUGGCGGUUAAAAU-GUAACCGCCACAUCAACCGCUGAUUUAAGGACGCAUACCGCCUCACCGUAGGAUCUGCAUUGAUAAAUCACAUUCGACUCGACA
((((((......((((((((((....-.))))))))))(((((..((.(((((..((..((.....))....))...))))).)).)))))...))))))........... ( -32.50)
>DroSim_CAF1 19346 110 + 1
AUGUGGCAUUAAGUGGCGGUUAAAAU-GUAACCGCCACAUCAACCGCUGAUUUAAGGACGCAUACCGCCUCACCGUGGGAUCUGCAUUGAUAAAUCACAUUCGACUCGACA
..((((......((((((((((....-.)))))))))).....))))(((((((..((.(((..((((......))))....))).))..))))))).............. ( -33.60)
>DroEre_CAF1 18954 110 + 1
AUGUGGUAUUAUGUGCCUGUUAAAUU-UUAAUCGACACAUCAACCGCUGAUUUAUGGACGCAUACCGCCUCACCGUGGGAUCUGCAUUGAUAAAUCGCACUCGACUCGGCG
..(((((...(((((.(.((((....-.)))).).)))))..))))).(((((((.((.(((..((((......))))....))).)).)))))))((.(.......))). ( -27.20)
>DroYak_CAF1 19606 111 + 1
AUGUGGCAUUAAGUGGCGGUUAAAUUGUUAACCGACACUUCAACCGCUGAUUUAAGGACGCAUACCGCCUCACCGUGGGUUCUGCAUUGUUAAAUCACGUUCGACUCGACG
..((((....(((((.(((((((....))))))).)))))...))))((((((((.((.(((..((((......))))....))).)).))))))))((((......)))) ( -34.60)
>consensus
AUGUGGCAUUAAGUGGCGGUUAAAAU_GUAACCGCCACAUCAACCGCUGAUUUAAGGACGCAUACCGCCUCACCGUGGGAUCUGCAUUGAUAAAUCACAUUCGACUCGACA
..((((......((((((((((......)))))))))).....))))(((((((..((.(((..((((......))))....))).))..))))))).............. (-26.74 = -27.42 +   0.68)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,789,551 – 11,789,661
Length 110
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 91.76
Mean single sequence MFE -33.94
Consensus MFE -30.76
Energy contribution -30.76
Covariance contribution -0.00
Combinations/Pair 1.18
Mean z-score -1.67
Structure conservation index 0.91
SVM decision value 1.79
SVM RNA-class probability 0.977438
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11789551 110 - 22224390
UGUCGAGUCGAAUGUGAUUUAUCAAUGCAGAUUCCACGGUGAGGCGGUAUGCGUCCUUAAAUCAGCGGUUGAUGUGGCGGUUAC-AUUUUAACUGCCACUUAAUGCCACAU
.((.(((((.....(((....))).....))))).))(((((((((.....)).)))).........(((((.((((((((((.-....)))))))))))))))))).... ( -33.30)
>DroSec_CAF1 19162 110 - 1
UGUCGAGUCGAAUGUGAUUUAUCAAUGCAGAUCCUACGGUGAGGCGGUAUGCGUCCUUAAAUCAGCGGUUGAUGUGGCGGUUAC-AUUUUAACCGCCACUUAAUGCCACAU
.(((((.(((....(((((((...(((((...((..(.....)..))..)))))...))))))).))))))))((((((((((.-....))))))))))............ ( -35.00)
>DroSim_CAF1 19346 110 - 1
UGUCGAGUCGAAUGUGAUUUAUCAAUGCAGAUCCCACGGUGAGGCGGUAUGCGUCCUUAAAUCAGCGGUUGAUGUGGCGGUUAC-AUUUUAACCGCCACUUAAUGCCACAU
.(((((.(((....(((((((...(((((.(((((.......)).))).)))))...))))))).))))))))((((((((((.-....))))))))))............ ( -36.30)
>DroEre_CAF1 18954 110 - 1
CGCCGAGUCGAGUGCGAUUUAUCAAUGCAGAUCCCACGGUGAGGCGGUAUGCGUCCAUAAAUCAGCGGUUGAUGUGUCGAUUAA-AAUUUAACAGGCACAUAAUACCACAU
.(((..(((((.((((((((((..(((((.(((((.......)).))).)))))..))))))).))).))))).(((..(....-...)..)))))).............. ( -30.60)
>DroYak_CAF1 19606 111 - 1
CGUCGAGUCGAACGUGAUUUAACAAUGCAGAACCCACGGUGAGGCGGUAUGCGUCCUUAAAUCAGCGGUUGAAGUGUCGGUUAACAAUUUAACCGCCACUUAAUGCCACAU
(((((...)).)))((((((((..(((((..(((..(.....)..))).)))))..))))))))(.(((..(((((.(((((((....))))))).)))))...))).).. ( -34.50)
>consensus
UGUCGAGUCGAAUGUGAUUUAUCAAUGCAGAUCCCACGGUGAGGCGGUAUGCGUCCUUAAAUCAGCGGUUGAUGUGGCGGUUAC_AUUUUAACCGCCACUUAAUGCCACAU
......(((((.(((((((((...(((((.(((((.......)).))).)))))...)))))).))).)))))((((((((((......))))))))))............ (-30.76 = -30.76 +  -0.00)

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 11:25:30 2006