Locus 4052

Sequence ID 2L_DroMel_CAF1
Location 11,732,572 – 11,732,726
Length 154
Max. P 0.996848
window6382 window6383 window6384 window6385

overview

Window 2

Location 11,732,572 – 11,732,663
Length 91
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 76.78
Mean single sequence MFE -20.93
Consensus MFE -14.95
Energy contribution -15.99
Covariance contribution 1.04
Combinations/Pair 1.05
Mean z-score -2.58
Structure conservation index 0.71
SVM decision value 2.76
SVM RNA-class probability 0.996848
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11732572 91 + 22407834
GCAGAGGCAUCCUUUUCCCACGCCUUACAGCACGCUCUUACCAAAACACAUGCAUACAAACACAAAGGCGUCGGAAAAUGGA-----------GAAAAGCCA
.....(((.(((((((((.(((((((..((....))..............((....))......))))))).)))))).)))-----------.....))). ( -23.50)
>DroSec_CAF1 192518 89 + 1
GCAGAGGCAUCCUUUUCCCACGCCU-------------UACCAACACACAUACAUACAAACACAAAGGCGUCGGAAAAUGGAAAUGGAAAAUGGAAAAGCCA
.....(((.(((((((((.((((((-------------(.........................))))))).)))))).)))..(....)........))). ( -23.01)
>DroSim_CAF1 184760 78 + 1
GCAGAGGCAUCCUUUUCCCACGCCU-------------UACCAACACACACACAUACAAACACAAAGGCGUCGGAAAAUGGA-----------GAAAAGCCA
.....(((.(((((((((.((((((-------------(.........................))))))).)))))).)))-----------.....))). ( -23.61)
>DroEre_CAF1 210470 89 + 1
GCAGAGGCAUCCUUUUCCUACGACUUUCAGUACAUUCUUGCCAGUACAC--ACACACAAACACAAAGGCGACGGAAAAUGGA-----------GAAAAGCCA
.....(((.((((((((((((........))).....(((((.......--...............))))).)))))).)))-----------.....))). ( -18.15)
>DroYak_CAF1 184873 89 + 1
GCACUGGUAUCCUUUUCCUACGACUUUCGGCACGUUCUUGUCCAUACAC--AAAUACAAACAUAAAGGCGACGGAAAAUGGA-----------GAAAAGCCA
.....(((.(((((((((..((.((((......((..((((......))--))..))......)))).))..)))))).)))-----------.....))). ( -16.40)
>consensus
GCAGAGGCAUCCUUUUCCCACGCCUU_C_G_AC__UCUUACCAACACACA_ACAUACAAACACAAAGGCGUCGGAAAAUGGA___________GAAAAGCCA
.....(((.(((((((((.(((((((......................................))))))).)))))).)))................))). (-14.95 = -15.99 +   1.04)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,732,572 – 11,732,663
Length 91
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 76.78
Mean single sequence MFE -25.45
Consensus MFE -16.09
Energy contribution -16.81
Covariance contribution 0.72
Combinations/Pair 1.19
Mean z-score -1.55
Structure conservation index 0.63
SVM decision value 0.08
SVM RNA-class probability 0.575227
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11732572 91 - 22407834
UGGCUUUUC-----------UCCAUUUUCCGACGCCUUUGUGUUUGUAUGCAUGUGUUUUGGUAAGAGCGUGCUGUAAGGCGUGGGAAAAGGAUGCCUCUGC
.(((.....-----------(((.((((((.(((((((...........((((((.(((....))).))))))...))))))).))))))))).)))..... ( -32.24)
>DroSec_CAF1 192518 89 - 1
UGGCUUUUCCAUUUUCCAUUUCCAUUUUCCGACGCCUUUGUGUUUGUAUGUAUGUGUGUUGGUA-------------AGGCGUGGGAAAAGGAUGCCUCUGC
.(((...(((.((((((((..((.....(((((((...((..(....)..))...)))))))..-------------.)).)))))))).))).)))..... ( -28.00)
>DroSim_CAF1 184760 78 - 1
UGGCUUUUC-----------UCCAUUUUCCGACGCCUUUGUGUUUGUAUGUGUGUGUGUUGGUA-------------AGGCGUGGGAAAAGGAUGCCUCUGC
.(((.....-----------(((.((((((.(((((((......(..((....))..).....)-------------)))))).))))))))).)))..... ( -25.30)
>DroEre_CAF1 210470 89 - 1
UGGCUUUUC-----------UCCAUUUUCCGUCGCCUUUGUGUUUGUGUGU--GUGUACUGGCAAGAAUGUACUGAAAGUCGUAGGAAAAGGAUGCCUCUGC
.(((.....-----------(((.((((((..((.((((......(((..(--.(((....)))...)..)))..)))).))..))))))))).)))..... ( -20.00)
>DroYak_CAF1 184873 89 - 1
UGGCUUUUC-----------UCCAUUUUCCGUCGCCUUUAUGUUUGUAUUU--GUGUAUGGACAAGAACGUGCCGAAAGUCGUAGGAAAAGGAUACCAGUGC
(((((((((-----------((.((((((.(.(((.(((.((((..(((..--..)))..)))).))).)))).)))))).)..)))))))....))).... ( -21.70)
>consensus
UGGCUUUUC___________UCCAUUUUCCGACGCCUUUGUGUUUGUAUGU_UGUGUAUUGGUAAGA__GU_C_G_AAGGCGUGGGAAAAGGAUGCCUCUGC
.(((................(((.((((((.(((((((..(((..((((......))))..)))............))))))).))))))))).)))..... (-16.09 = -16.81 +   0.72)

alignment

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secondary structure

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dotplot

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Window 4

Location 11,732,634 – 11,732,726
Length 92
Sequences 3
Columns 94
Reading direction forward
Mean pairwise identity 87.81
Mean single sequence MFE -20.95
Consensus MFE -18.52
Energy contribution -19.30
Covariance contribution 0.79
Combinations/Pair 1.17
Mean z-score -2.00
Structure conservation index 0.88
SVM decision value 0.73
SVM RNA-class probability 0.834473
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11732634 92 + 22407834
CAAAGGCGUCGGAAAAUGGAGAAAAGCCAAGCUUUGAGCUCAGUUCUGGCUACAAAAA--AUGCAGGGAAAAAAAGGUAAAGCAUCAAAGCUGG
....(((.((..........))...))).(((((((((((...((((.((........--..))..))))..........))).)))))))).. ( -20.32)
>DroEre_CAF1 210530 90 + 1
CAAAGGCGACGGAAAAUGGAGAAAAGCCAGGCUUCGAGCUGAGUUCUUUCAACAAAAA--AUGUAGGGA-A-AAAGGUAAAGCAUCAAAGCUGG
....(((..................))).(((((.(((((...((((((((.......--.)).)))))-)-........))).)).))))).. ( -15.37)
>DroYak_CAF1 184933 93 + 1
UAAAGGCGACGGAAAAUGGAGAAAAGCCAGGCUUUGAGCUGAGUCCUUGCAACAACAAGGAUGUUGCGAAA-AAAGGUAAAGCAUCAAAGCUGG
....(((..................))).(((((((((((....((((((((((.......))))))....-.))))...))).)))))))).. ( -27.17)
>consensus
CAAAGGCGACGGAAAAUGGAGAAAAGCCAGGCUUUGAGCUGAGUUCUUGCAACAAAAA__AUGUAGGGAAA_AAAGGUAAAGCAUCAAAGCUGG
....(((..................))).(((((((((((....((((((((((.......))))))......))))...))).)))))))).. (-18.52 = -19.30 +   0.79)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,732,634 – 11,732,726
Length 92
Sequences 3
Columns 94
Reading direction reverse
Mean pairwise identity 87.81
Mean single sequence MFE -20.62
Consensus MFE -15.01
Energy contribution -14.47
Covariance contribution -0.55
Combinations/Pair 1.19
Mean z-score -2.95
Structure conservation index 0.73
SVM decision value 0.82
SVM RNA-class probability 0.858159
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11732634 92 - 22407834
CCAGCUUUGAUGCUUUACCUUUUUUUCCCUGCAU--UUUUUGUAGCCAGAACUGAGCUCAAAGCUUGGCUUUUCUCCAUUUUCCGACGCCUUUG
..((((((((.((((.......((((..(((((.--....)))))..))))..)))))))))))).(((..................))).... ( -19.57)
>DroEre_CAF1 210530 90 - 1
CCAGCUUUGAUGCUUUACCUUU-U-UCCCUACAU--UUUUUGUUGAAAGAACUCAGCUCGAAGCCUGGCUUUUCUCCAUUUUCCGUCGCCUUUG
((((((((((.(((.....(((-(-((...(((.--....))).))))))....))))))))).)))).......................... ( -18.30)
>DroYak_CAF1 184933 93 - 1
CCAGCUUUGAUGCUUUACCUUU-UUUCGCAACAUCCUUGUUGUUGCAAGGACUCAGCUCAAAGCCUGGCUUUUCUCCAUUUUCCGUCGCCUUUA
((((((((((.(((...((((.-....((((((.......))))))))))....))))))))).)))).......................... ( -24.00)
>consensus
CCAGCUUUGAUGCUUUACCUUU_UUUCCCUACAU__UUUUUGUUGCAAGAACUCAGCUCAAAGCCUGGCUUUUCUCCAUUUUCCGUCGCCUUUG
((((((((((.(((.....(((......(((((.......)))))...)))...)))))))))).))).......................... (-15.01 = -14.47 +  -0.55)

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 11:08:06 2006