Locus 5341

Sequence ID X_DroMel_CAF1
Location 13,928,952 – 13,929,073
Length 121
Max. P 0.999924
window8652 window8653 window8654 window8655

overview

Window 2

Location 13,928,952 – 13,929,046
Length 94
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 75.08
Mean single sequence MFE -43.43
Consensus MFE -25.92
Energy contribution -26.86
Covariance contribution 0.94
Combinations/Pair 1.17
Mean z-score -3.25
Structure conservation index 0.60
SVM decision value 4.18
SVM RNA-class probability 0.999826
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13928952 94 + 22224390
AUAG---GUGAA-GGGGGG-----AGGGAG------GGG----GUUCCGUCCUUUUGUAUGGUGUGGUCCAAAGAAGCUGCAGGAGUUUCUUAUUUUCUUCUUUGUUCUGCAC
....---.....-((((((-----(.((((------...----.)))).))))))).....(((..(..((((((((....(((.....))).....))))))))..)..))) ( -28.20)
>DroSec_CAF1 9038 103 + 1
AUAG---GUGAAAGGGGGG-----AGGGGGCAAA--GGGGCCAGGGCCGCCCUUUUGUAUGGUGUGGUCCAAAGAAGCUGCAGGAAUUUCUUGUUCGCUUCUUUGUUCUGCAC
....---(..((((((.((-----....(((...--...)))....)).))))))..)...(((..(..(((((((((.(((((.....)))))..)))))))))..)..))) ( -46.70)
>DroEre_CAF1 10783 113 + 1
AUAGGUGCUGAAAGGGGGCGCCAAAGGGUGCGGGGGGGUGUCGGUGGCGCCCCUUUGUACGGUGCGGUCCAAAGAAGCUGCAGGAAUUUCUGGUUCGCUUCUUUGUUCCGCAC
...((((((.......)))))).....((((((((((((((.....)))))))))))))).((((((..(((((((((.((.((.....)).))..)))))))))..)))))) ( -59.70)
>DroYak_CAF1 11024 103 + 1
AUAA---CUGAAUGGCGGGGGGGAGGGGGUCAAA--GGAGCAAGGGGCGCCCCUUUG-----UGUGGUCCAAAGAAGCUGCAGGAAUUUCUUGUUCGCUUCUUUGUUCUGCAC
....---(((.....)))...((((((((((...--.........))).)))))))(-----((..(..(((((((((.(((((.....)))))..)))))))))..)..))) ( -39.10)
>consensus
AUAG___CUGAAAGGGGGG_____AGGGGGCAAA__GGGGCCAGGGCCGCCCCUUUGUAUGGUGUGGUCCAAAGAAGCUGCAGGAAUUUCUUGUUCGCUUCUUUGUUCUGCAC
..........(((((((((...........................)).))))))).....((((((..(((((((((.(((((.....)))))..)))))))))..)))))) (-25.92 = -26.86 +   0.94)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,928,952 – 13,929,046
Length 94
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 75.08
Mean single sequence MFE -30.73
Consensus MFE -15.12
Energy contribution -15.00
Covariance contribution -0.12
Combinations/Pair 1.17
Mean z-score -3.28
Structure conservation index 0.49
SVM decision value 2.91
SVM RNA-class probability 0.997711
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13928952 94 - 22224390
GUGCAGAACAAAGAAGAAAAUAAGAAACUCCUGCAGCUUCUUUGGACCACACCAUACAAAAGGACGGAAC----CCC------CUCCCU-----CCCCCC-UUCAC---CUAU
(((.((..((((((((......((......))....)))))))).................(((.(((..----...------.))).)-----))...)-).)))---.... ( -18.70)
>DroSec_CAF1 9038 103 - 1
GUGCAGAACAAAGAAGCGAACAAGAAAUUCCUGCAGCUUCUUUGGACCACACCAUACAAAAGGGCGGCCCUGGCCCC--UUUGCCCCCU-----CCCCCCUUUCAC---CUAU
(((..(..(((((((((.....((......))...)))))))))..)..)))......((((((.((....(((...--...)))....-----)).))))))...---.... ( -28.80)
>DroEre_CAF1 10783 113 - 1
GUGCGGAACAAAGAAGCGAACCAGAAAUUCCUGCAGCUUCUUUGGACCGCACCGUACAAAGGGGCGCCACCGACACCCCCCCGCACCCUUUGGCGCCCCCUUUCAGCACCUAU
((((((..(((((((((....(((......)))..)))))))))..)))))).((..((((((((((((.....................))))).)))))))..))...... ( -46.50)
>DroYak_CAF1 11024 103 - 1
GUGCAGAACAAAGAAGCGAACAAGAAAUUCCUGCAGCUUCUUUGGACCACA-----CAAAGGGGCGCCCCUUGCUCC--UUUGACCCCCUCCCCCCCGCCAUUCAG---UUAU
(((.....(((((((((.....((......))...)))))))))...))).-----((((((((((.....))))))--)))).......................---.... ( -28.90)
>consensus
GUGCAGAACAAAGAAGCGAACAAGAAAUUCCUGCAGCUUCUUUGGACCACACCAUACAAAAGGGCGCCACUGGCCCC__UUUGCCCCCU_____CCCCCCUUUCAC___CUAU
(((.....(((((((((.....((......))...)))))))))...)))..........((((.....................))))........................ (-15.12 = -15.00 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 4

Location 13,928,973 – 13,929,073
Length 100
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 78.25
Mean single sequence MFE -47.12
Consensus MFE -32.57
Energy contribution -36.20
Covariance contribution 3.63
Combinations/Pair 1.14
Mean z-score -4.10
Structure conservation index 0.69
SVM decision value 4.58
SVM RNA-class probability 0.999924
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13928973 100 + 22224390
---GGG----GUUCCGUCCUUUUGUAUGGUGUGGUCCAAAGAAGCUGCAGGAGUUUCUUAUUUUCUUCUUUGUUCUGCACUCC-CAAAGG------------GAGGCCUUGGAUUUAUUA
---(((----(((...((((((((...((((..(..((((((((....(((.....))).....))))))))..)..))))..-))))))------------)))))))).......... ( -32.70)
>DroSec_CAF1 9063 106 + 1
A--GGGGCCAGGGCCGCCCUUUUGUAUGGUGUGGUCCAAAGAAGCUGCAGGAAUUUCUUGUUCGCUUCUUUGUUCUGCACUCCCCAAAGG------------CAGGCCUUGGAUUUAUUA
.--....(((((((((((..((((...((((..(..(((((((((.(((((.....)))))..)))))))))..)..))))...))))))------------).))))))))........ ( -50.20)
>DroEre_CAF1 10816 119 + 1
GGGGGUGUCGGUGGCGCCCCUUUGUACGGUGCGGUCCAAAGAAGCUGCAGGAAUUUCUGGUUCGCUUCUUUGUUCCGCACUCC-CAAAGGGGACGACCCGGUGAGGCCUUGGAUAUAUUA
.(((((.(((.(((((((((((((...(((((((..(((((((((.((.((.....)).))..)))))))))..)))))))..-)))))))).))..))).))).))))).......... ( -58.90)
>DroYak_CAF1 11054 112 + 1
A--GGAGCAAGGGGCGCCCCUUUG-----UGUGGUCCAAAGAAGCUGCAGGAAUUUCUUGUUCGCUUCUUUGUUCUGCACUCC-CAAAGGGGGCGAAAUGGCGAGGCCUUGGAUUUAUUA
(--((.((......((((((((((-----((..(..(((((((((.(((((.....)))))..)))))))))..)..)))...-..))))))))).....))....)))........... ( -46.70)
>consensus
A__GGGGCCAGGGCCGCCCCUUUGUAUGGUGUGGUCCAAAGAAGCUGCAGGAAUUUCUUGUUCGCUUCUUUGUUCUGCACUCC_CAAAGG____________GAGGCCUUGGAUUUAUUA
.......((((((((.((((((((...(((((((..(((((((((.(((((.....)))))..)))))))))..)))))))...))))))))............))))))))........ (-32.57 = -36.20 +   3.63)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,928,973 – 13,929,073
Length 100
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 78.25
Mean single sequence MFE -36.23
Consensus MFE -18.99
Energy contribution -21.05
Covariance contribution 2.06
Combinations/Pair 1.04
Mean z-score -3.12
Structure conservation index 0.52
SVM decision value 2.21
SVM RNA-class probability 0.990400
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13928973 100 - 22224390
UAAUAAAUCCAAGGCCUC------------CCUUUG-GGAGUGCAGAACAAAGAAGAAAAUAAGAAACUCCUGCAGCUUCUUUGGACCACACCAUACAAAAGGACGGAAC----CCC---
.......(((...(((((------------((...)-)))).))....((((((((......((......))....)))))))).......((........))..)))..----...--- ( -23.50)
>DroSec_CAF1 9063 106 - 1
UAAUAAAUCCAAGGCCUG------------CCUUUGGGGAGUGCAGAACAAAGAAGCGAACAAGAAAUUCCUGCAGCUUCUUUGGACCACACCAUACAAAAGGGCGGCCCUGGCCCC--U
........(((.((((.(------------(((((..((.(((.....(((((((((.....((......))...)))))))))...))).))......)))))))))).)))....--. ( -37.10)
>DroEre_CAF1 10816 119 - 1
UAAUAUAUCCAAGGCCUCACCGGGUCGUCCCCUUUG-GGAGUGCGGAACAAAGAAGCGAACCAGAAAUUCCUGCAGCUUCUUUGGACCGCACCGUACAAAGGGGCGCCACCGACACCCCC
............((..((....((.((.((((((((-...((((((..(((((((((....(((......)))..)))))))))..))))))....))))))))))))...))..))... ( -49.80)
>DroYak_CAF1 11054 112 - 1
UAAUAAAUCCAAGGCCUCGCCAUUUCGCCCCCUUUG-GGAGUGCAGAACAAAGAAGCGAACAAGAAAUUCCUGCAGCUUCUUUGGACCACA-----CAAAGGGGCGCCCCUUGCUCC--U
............(((...))).....((((((((((-...(((.....(((((((((.....((......))...)))))))))...))).-----)))))))).))..........--. ( -34.50)
>consensus
UAAUAAAUCCAAGGCCUC____________CCUUUG_GGAGUGCAGAACAAAGAAGCGAACAAGAAAUUCCUGCAGCUUCUUUGGACCACACCAUACAAAAGGGCGCCACUGGCCCC__U
............................((((((((.((.(((.....(((((((((.....((......))...)))))))))...))).))...))))))))................ (-18.99 = -21.05 +   2.06)

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 11:45:28 2006