Locus 1324

Sequence ID 3R_DroMel_CAF1
Location 3,897,529 – 3,897,669
Length 140
Max. P 0.999910
window2166 window2167 window2168 window2169

overview

Window 6

Location 3,897,529 – 3,897,635
Length 106
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 98.49
Mean single sequence MFE -30.81
Consensus MFE -30.13
Energy contribution -30.33
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -3.41
Structure conservation index 0.98
SVM decision value 4.50
SVM RNA-class probability 0.999910
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3897529 106 + 27905053
CUUCCGCUACCCCUUGUUCCAGAUCCCAUUCGCUUUUCUGUUCUGCUUUGCACUCGGCUUGUUCAGCAUCUGUUUUUGAUGCUGCACAUAAAGCGGCGGAAGAACA
((((((((...........((((.............))))....(((((((.....)).(((.(((((((.......))))))).))).))))))))))))).... ( -33.42)
>DroSec_CAF1 20734 106 + 1
CUUCCGCUACCCCUUGUUCCAGAUCCCAUCCGCUUUUCUUUUCUGCUUUGCACUCUGCUUGUUCAGCAUCUGUUUUUGAUGCUGCACAUAAAGCGGCGGAAGAACA
((((((((......(((..((((..................))))....)))....((((((.(((((((.......))))))).)))...))))))))))).... ( -31.47)
>DroSim_CAF1 21177 106 + 1
CUUCCGCUACCCCUUGUUCCAGAUCCCAUCCGCUUUUCUUUUCUGCUUUGCACUCGGCUUGUUCAGCAUCUGUUUUUGAUGCUGCACAUAAAGCGGCGGAAGAACA
((((((((......(((..((((..................))))....)))....((((((.(((((((.......))))))).)))...))))))))))).... ( -31.47)
>DroEre_CAF1 19572 106 + 1
CUUCCGCUACCCCUUGUUCCAGAUCCCAUCCGCUUUUCUUUUCUGCUUUGCACUCGGCUUGUUCAGCAUCUGUUUUUGAUGCUGCACAUAAAGCGGCGAAAGAACA
...................................((((((((((((((((.....)).(((.(((((((.......))))))).))).))))))).))))))).. ( -26.20)
>DroYak_CAF1 22272 106 + 1
CUUCCGCUACCCCUUGUUCCAGAUCCCAUCCGCUUUUCUUUUCUGCUUUGCACUCGGCUUGUUCAGCAUCUGUUUUUGAUGCUGCACAUAAAGCGGCGGAAGAACA
((((((((......(((..((((..................))))....)))....((((((.(((((((.......))))))).)))...))))))))))).... ( -31.47)
>consensus
CUUCCGCUACCCCUUGUUCCAGAUCCCAUCCGCUUUUCUUUUCUGCUUUGCACUCGGCUUGUUCAGCAUCUGUUUUUGAUGCUGCACAUAAAGCGGCGGAAGAACA
((((((((......(((..((((..................))))....)))....((((((.(((((((.......))))))).)))...))))))))))).... (-30.13 = -30.33 +   0.20)

alignment

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secondary structure

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dotplot

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Window 7

Location 3,897,529 – 3,897,635
Length 106
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 98.49
Mean single sequence MFE -32.28
Consensus MFE -31.34
Energy contribution -31.18
Covariance contribution -0.16
Combinations/Pair 1.03
Mean z-score -2.56
Structure conservation index 0.97
SVM decision value 3.82
SVM RNA-class probability 0.999637
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3897529 106 - 27905053
UGUUCUUCCGCCGCUUUAUGUGCAGCAUCAAAAACAGAUGCUGAACAAGCCGAGUGCAAAGCAGAACAGAAAAGCGAAUGGGAUCUGGAACAAGGGGUAGCGGAAG
....(((((((..(((..(((.(((((((.......)))))))......(((..(((....(......)....)))..)))........)))..)))..))))))) ( -32.80)
>DroSec_CAF1 20734 106 - 1
UGUUCUUCCGCCGCUUUAUGUGCAGCAUCAAAAACAGAUGCUGAACAAGCAGAGUGCAAAGCAGAAAAGAAAAGCGGAUGGGAUCUGGAACAAGGGGUAGCGGAAG
....(((((((..(((..(((.(((((((.......)))))))......((((.(.((..((...........))...)).).))))..)))..)))..))))))) ( -34.30)
>DroSim_CAF1 21177 106 - 1
UGUUCUUCCGCCGCUUUAUGUGCAGCAUCAAAAACAGAUGCUGAACAAGCCGAGUGCAAAGCAGAAAAGAAAAGCGGAUGGGAUCUGGAACAAGGGGUAGCGGAAG
....(((((((..(((..(((.(((((((.......)))))))......(((..(.(...((...........)).....).)..))).)))..)))..))))))) ( -32.40)
>DroEre_CAF1 19572 106 - 1
UGUUCUUUCGCCGCUUUAUGUGCAGCAUCAAAAACAGAUGCUGAACAAGCCGAGUGCAAAGCAGAAAAGAAAAGCGGAUGGGAUCUGGAACAAGGGGUAGCGGAAG
(((((((((((((((((.(((.(((((((.......))))))).))).((.....)).............))))))).))))....)))))).............. ( -29.50)
>DroYak_CAF1 22272 106 - 1
UGUUCUUCCGCCGCUUUAUGUGCAGCAUCAAAAACAGAUGCUGAACAAGCCGAGUGCAAAGCAGAAAAGAAAAGCGGAUGGGAUCUGGAACAAGGGGUAGCGGAAG
....(((((((..(((..(((.(((((((.......)))))))......(((..(.(...((...........)).....).)..))).)))..)))..))))))) ( -32.40)
>consensus
UGUUCUUCCGCCGCUUUAUGUGCAGCAUCAAAAACAGAUGCUGAACAAGCCGAGUGCAAAGCAGAAAAGAAAAGCGGAUGGGAUCUGGAACAAGGGGUAGCGGAAG
....(((((((((((((.(((.(((((((.......))))))).))).((.....)).............))))))......((((........)))).))))))) (-31.34 = -31.18 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,897,555 – 3,897,669
Length 114
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 95.50
Mean single sequence MFE -31.19
Consensus MFE -28.26
Energy contribution -28.82
Covariance contribution 0.56
Combinations/Pair 1.06
Mean z-score -2.51
Structure conservation index 0.91
SVM decision value 3.14
SVM RNA-class probability 0.998548
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3897555 114 + 27905053
CAUUCGCUUUUCUGUUCUGCUUUGCACUCGGCUUGUUCAGCAUCUGUUUUUGAUGCUGCACAUAAAGCGGCGGAAGAACAUUCAACAUUUUUACUGUUUACAUCUGUGGAGAGU
.....(.(((((((..(((((((((.....)).(((.(((((((.......))))))).))).)))))))))))))).).............(((.(((((....))))).))) ( -32.20)
>DroSec_CAF1 20760 114 + 1
CAUCCGCUUUUCUUUUCUGCUUUGCACUCUGCUUGUUCAGCAUCUGUUUUUGAUGCUGCACAUAAAGCGGCGGAAGAACAUUCAACAUUUUUACUGUUUACAUCAGUGGAGAGU
.........((((((((((((((((.....)).(((.(((((((.......))))))).))).))))))).))))))).........(((((((((.......))))))))).. ( -33.50)
>DroSim_CAF1 21203 114 + 1
CAUCCGCUUUUCUUUUCUGCUUUGCACUCGGCUUGUUCAGCAUCUGUUUUUGAUGCUGCACAUAAAGCGGCGGAAGAACAUUCAACAUUUUUACUGUUUACAUCUGUGGAGAGU
..(((((..((((((((((((((((.....)).(((.(((((((.......))))))).))).))))))).))))))).....((((.......)))).......))))).... ( -32.10)
>DroEre_CAF1 19598 114 + 1
CAUCCGCUUUUCUUUUCUGCUUUGCACUCGGCUUGUUCAGCAUCUGUUUUUGAUGCUGCACAUAAAGCGGCGAAAGAACAUUCAACAUUUUUACUGUUUACAUCUGUGGAGAGU
..(((((..((((((((((((((((.....)).(((.(((((((.......))))))).))).))))))).))))))).....((((.......)))).......))))).... ( -32.50)
>DroYak_CAF1 22298 114 + 1
CAUCCGCUUUUCUUUUCUGCUUUGCACUCGGCUUGUUCAGCAUCUGUUUUUGAUGCUGCACAUAAAGCGGCGGAAGAACAUUCAACAUUUUUACUGUUUACAUCUGUUGAGAGU
.....((((((((((((((((((((.....)).(((.(((((((.......))))))).))).))))))).)))))))...((((((.................)))))))))) ( -30.23)
>DroAna_CAF1 22436 114 + 1
UUGCCACUUUUCUGUUGUGUUUUGCACUCAGCUUGUUCAGCAUCUGUUUUUGAUGCAGCACAUAAAGCGACGGAAGAACAUUCAACAUUUUUACUGUUUACAUCUGUGGAGAGU
.......((((((((((((.....)))...((((((.(.(((((.......))))).).)))...))))))))))))...............(((.(((((....))))).))) ( -26.60)
>consensus
CAUCCGCUUUUCUUUUCUGCUUUGCACUCGGCUUGUUCAGCAUCUGUUUUUGAUGCUGCACAUAAAGCGGCGGAAGAACAUUCAACAUUUUUACUGUUUACAUCUGUGGAGAGU
.........((((((((((((((((.....)).(((.(((((((.......))))))).))).))))))).)))))))..............(((.(((((....))))).))) (-28.26 = -28.82 +   0.56)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,897,555 – 3,897,669
Length 114
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 95.50
Mean single sequence MFE -25.82
Consensus MFE -22.82
Energy contribution -22.90
Covariance contribution 0.08
Combinations/Pair 1.07
Mean z-score -1.43
Structure conservation index 0.88
SVM decision value 0.50
SVM RNA-class probability 0.761463
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3897555 114 - 27905053
ACUCUCCACAGAUGUAAACAGUAAAAAUGUUGAAUGUUCUUCCGCCGCUUUAUGUGCAGCAUCAAAAACAGAUGCUGAACAAGCCGAGUGCAAAGCAGAACAGAAAAGCGAAUG
...........................((((...((((((......(((((.(((.(((((((.......))))))).))).((.....)))))))))))))....)))).... ( -24.30)
>DroSec_CAF1 20760 114 - 1
ACUCUCCACUGAUGUAAACAGUAAAAAUGUUGAAUGUUCUUCCGCCGCUUUAUGUGCAGCAUCAAAAACAGAUGCUGAACAAGCAGAGUGCAAAGCAGAAAAGAAAAGCGGAUG
....(((((((.......))))......(((.....(((((...(.(((((.(((.(((((((.......))))))).))).((.....))))))).)..))))).)))))).. ( -28.30)
>DroSim_CAF1 21203 114 - 1
ACUCUCCACAGAUGUAAACAGUAAAAAUGUUGAAUGUUCUUCCGCCGCUUUAUGUGCAGCAUCAAAAACAGAUGCUGAACAAGCCGAGUGCAAAGCAGAAAAGAAAAGCGGAUG
....(((.(.......((((.......)))).....(((((...(.(((((.(((.(((((((.......))))))).))).((.....))))))).)..)))))..).))).. ( -25.30)
>DroEre_CAF1 19598 114 - 1
ACUCUCCACAGAUGUAAACAGUAAAAAUGUUGAAUGUUCUUUCGCCGCUUUAUGUGCAGCAUCAAAAACAGAUGCUGAACAAGCCGAGUGCAAAGCAGAAAAGAAAAGCGGAUG
....(((.(.......((((.......)))).....((((((..(.(((((.(((.(((((((.......))))))).))).((.....))))))).).))))))..).))).. ( -25.70)
>DroYak_CAF1 22298 114 - 1
ACUCUCAACAGAUGUAAACAGUAAAAAUGUUGAAUGUUCUUCCGCCGCUUUAUGUGCAGCAUCAAAAACAGAUGCUGAACAAGCCGAGUGCAAAGCAGAAAAGAAAAGCGGAUG
((..((((((....((.....))....))))))..)).......(((((((.(((.(((((((.......))))))).))).((.....)).............)))))))... ( -28.30)
>DroAna_CAF1 22436 114 - 1
ACUCUCCACAGAUGUAAACAGUAAAAAUGUUGAAUGUUCUUCCGUCGCUUUAUGUGCUGCAUCAAAAACAGAUGCUGAACAAGCUGAGUGCAAAACACAACAGAAAAGUGGCAA
.....((((...((....)).......(((((..(((((....(.(((.....)))).(((((.......))))).))))).((.....))......))))).....))))... ( -23.00)
>consensus
ACUCUCCACAGAUGUAAACAGUAAAAAUGUUGAAUGUUCUUCCGCCGCUUUAUGUGCAGCAUCAAAAACAGAUGCUGAACAAGCCGAGUGCAAAGCAGAAAAGAAAAGCGGAUG
..........(((((.((((.......))))..)))))......(((((((.(((.(((((((.......))))))).))).((.....)).............)))))))... (-22.82 = -22.90 +   0.08)

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 10:06:49 2006