Locus 8473

Sequence ID X_DroMel_CAF1
Location 21,035,709 – 21,035,985
Length 276
Max. P 0.973978
window13917 window13918 window13919 window13920

overview

Window 7

Location 21,035,709 – 21,035,829
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.25
Mean single sequence MFE -30.62
Consensus MFE -27.32
Energy contribution -27.36
Covariance contribution 0.04
Combinations/Pair 1.10
Mean z-score -1.67
Structure conservation index 0.89
SVM decision value 1.72
SVM RNA-class probability 0.973978
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21035709 120 + 22224390
GCUCAACAUUUCUUCGUUAUUAAAUGGAUUUCUUCGCUGACUCGAAAUUGUAUGCAUACGUGCUCCAUUUGCACAUAUUUCUUAAUGGGUCAGCGCCCCGCGGAGUCCACUCCCCGCCCA
((..(((........)))......((((((((...(((((((((.....(((....)))((((.......))))...........)))))))))((...))))))))))......))... ( -31.00)
>DroSec_CAF1 6341 120 + 1
GCUCAACAUUUCUUCGUUAUUAAAUGGAUUUCUUCGCUGACUCGAAAUUGUAUGCAUACGUGCUCCAUUUGCACAUAUUUCUUAAUGGGUCAGCGCCCCGCGGAGUCCACUCCCCGCCCA
((..(((........)))......((((((((...(((((((((.....(((....)))((((.......))))...........)))))))))((...))))))))))......))... ( -31.00)
>DroSim_CAF1 6878 120 + 1
GCUCAACAUUUCUUCGUUAUUAAAUGGAUUUCUUCGCUGACUCGAAAUUGUAUGCAUACGUGCUCCAUUUGCACAUAUUUCUUAAUGGGUCAGCGCCCCGCGGAGUCCACUCCCCGCCCA
((..(((........)))......((((((((...(((((((((.....(((....)))((((.......))))...........)))))))))((...))))))))))......))... ( -31.00)
>DroEre_CAF1 6581 120 + 1
GCUUAGCUGUUCCUCGUUUCUAAAUGGAUUUCCUUGCUGACUCGGAAUUGUAUGCAUAUGUGCUCCAUUUGCACAUUUUUCUUAAUGGGUCAGCGCCCCGCGGAGUCCACUCCCCGCCCA
((...((...(((............))).......((((((((((((..((.((((.(((.....))).)))).))..))))....))))))))))...))((((....))))....... ( -32.30)
>DroYak_CAF1 7030 120 + 1
GCUUGACUGUUCGUCGUUUUUAAAUGGAUUUCUUCAGUGACUCGAAAUUGUAUGCAUAUGUGCUCCAUUUGCACAUAUUUCUUAAUGGGUCAGCGCCCCGCAGAGUCCACACCCCGCCCA
((..(((.....))).........(((((((......(((((((....((....))(((((((.......)))))))........)))))))(((...))).)))))))......))... ( -27.80)
>consensus
GCUCAACAUUUCUUCGUUAUUAAAUGGAUUUCUUCGCUGACUCGAAAUUGUAUGCAUACGUGCUCCAUUUGCACAUAUUUCUUAAUGGGUCAGCGCCCCGCGGAGUCCACUCCCCGCCCA
((..(((........)))......((((((((...(((((((((.....(((....)))((((.......))))...........)))))))))((...))))))))))......))... (-27.32 = -27.36 +   0.04)

alignment

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secondary structure

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dotplot

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Window 8

Location 21,035,709 – 21,035,829
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.25
Mean single sequence MFE -33.74
Consensus MFE -30.34
Energy contribution -30.58
Covariance contribution 0.24
Combinations/Pair 1.10
Mean z-score -1.23
Structure conservation index 0.90
SVM decision value 0.38
SVM RNA-class probability 0.711262
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21035709 120 - 22224390
UGGGCGGGGAGUGGACUCCGCGGGGCGCUGACCCAUUAAGAAAUAUGUGCAAAUGGAGCACGUAUGCAUACAAUUUCGAGUCAGCGAAGAAAUCCAUUUAAUAACGAAGAAAUGUUGAGC
...((((((......))))))(((.(((((((.......(((((.((((((.(((.....))).))))))..)))))..)))))))......)))......(((((......)))))... ( -34.60)
>DroSec_CAF1 6341 120 - 1
UGGGCGGGGAGUGGACUCCGCGGGGCGCUGACCCAUUAAGAAAUAUGUGCAAAUGGAGCACGUAUGCAUACAAUUUCGAGUCAGCGAAGAAAUCCAUUUAAUAACGAAGAAAUGUUGAGC
...((((((......))))))(((.(((((((.......(((((.((((((.(((.....))).))))))..)))))..)))))))......)))......(((((......)))))... ( -34.60)
>DroSim_CAF1 6878 120 - 1
UGGGCGGGGAGUGGACUCCGCGGGGCGCUGACCCAUUAAGAAAUAUGUGCAAAUGGAGCACGUAUGCAUACAAUUUCGAGUCAGCGAAGAAAUCCAUUUAAUAACGAAGAAAUGUUGAGC
...((((((......))))))(((.(((((((.......(((((.((((((.(((.....))).))))))..)))))..)))))))......)))......(((((......)))))... ( -34.60)
>DroEre_CAF1 6581 120 - 1
UGGGCGGGGAGUGGACUCCGCGGGGCGCUGACCCAUUAAGAAAAAUGUGCAAAUGGAGCACAUAUGCAUACAAUUCCGAGUCAGCAAGGAAAUCCAUUUAGAAACGAGGAACAGCUAAGC
...((((((......))))))..(((((((((.(.....(((...((((((.(((.....))).))))))...))).).))))))..((....))..................))).... ( -33.30)
>DroYak_CAF1 7030 120 - 1
UGGGCGGGGUGUGGACUCUGCGGGGCGCUGACCCAUUAAGAAAUAUGUGCAAAUGGAGCACAUAUGCAUACAAUUUCGAGUCACUGAAGAAAUCCAUUUAAAAACGACGAACAGUCAAGC
((((((((((....)))))))(((.......))).....(((((.((((((.(((.....))).))))))..)))))................))).........(((.....))).... ( -31.60)
>consensus
UGGGCGGGGAGUGGACUCCGCGGGGCGCUGACCCAUUAAGAAAUAUGUGCAAAUGGAGCACGUAUGCAUACAAUUUCGAGUCAGCGAAGAAAUCCAUUUAAUAACGAAGAAAUGUUGAGC
(((((((((......))))))....(((((((.......(((((.((((((.(((.....))).))))))..)))))..))))))).......)))........................ (-30.34 = -30.58 +   0.24)

alignment

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secondary structure

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dotplot

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Window 9

Location 21,035,749 – 21,035,869
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.33
Mean single sequence MFE -40.76
Consensus MFE -39.82
Energy contribution -39.82
Covariance contribution 0.00
Combinations/Pair 1.06
Mean z-score -1.34
Structure conservation index 0.98
SVM decision value 1.00
SVM RNA-class probability 0.898043
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21035749 120 - 22224390
CAGGCAGCCCCUUGACAACUGUCACUGGCAGGACAUUAUAUGGGCGGGGAGUGGACUCCGCGGGGCGCUGACCCAUUAAGAAAUAUGUGCAAAUGGAGCACGUAUGCAUACAAUUUCGAG
..((((((((((......((((.....))))............((((((......)))))))))).)))).))......(((((.((((((.(((.....))).))))))..)))))... ( -41.20)
>DroSec_CAF1 6381 120 - 1
CAGGCAGCCCCUUGACAACUGUCACCGGCAGGACAUUAUAUGGGCGGGGAGUGGACUCCGCGGGGCGCUGACCCAUUAAGAAAUAUGUGCAAAUGGAGCACGUAUGCAUACAAUUUCGAG
..((((((((((......((((.....))))............((((((......)))))))))).)))).))......(((((.((((((.(((.....))).))))))..)))))... ( -41.20)
>DroSim_CAF1 6918 120 - 1
CAGGCAGCCCCUUGACAACUGUCACCGGCAGGACAUUAUAUGGGCGGGGAGUGGACUCCGCGGGGCGCUGACCCAUUAAGAAAUAUGUGCAAAUGGAGCACGUAUGCAUACAAUUUCGAG
..((((((((((......((((.....))))............((((((......)))))))))).)))).))......(((((.((((((.(((.....))).))))))..)))))... ( -41.20)
>DroEre_CAF1 6621 120 - 1
CAGGCAGCCCCUUGACAACUGUCACUGGCAGGACAUUAUAUGGGCGGGGAGUGGACUCCGCGGGGCGCUGACCCAUUAAGAAAAAUGUGCAAAUGGAGCACAUAUGCAUACAAUUCCGAG
..((((((((((......((((.....))))............((((((......)))))))))).)))).))......(((...((((((.(((.....))).))))))...))).... ( -38.90)
>DroYak_CAF1 7070 120 - 1
CAGGCAGCCCCUCGACAACUGUCACUGGCAGGACAUUAUAUGGGCGGGGUGUGGACUCUGCGGGGCGCUGACCCAUUAAGAAAUAUGUGCAAAUGGAGCACAUAUGCAUACAAUUUCGAG
..((((((.((((.....((((.....))))............(((((((....))))))))))).)))).))......(((((.((((((.(((.....))).))))))..)))))... ( -41.30)
>consensus
CAGGCAGCCCCUUGACAACUGUCACUGGCAGGACAUUAUAUGGGCGGGGAGUGGACUCCGCGGGGCGCUGACCCAUUAAGAAAUAUGUGCAAAUGGAGCACGUAUGCAUACAAUUUCGAG
..((((((((((......((((.....))))............((((((......)))))))))).)))).))......(((((.((((((.(((.....))).))))))..)))))... (-39.82 = -39.82 +   0.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 21,035,869 – 21,035,985
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.23
Mean single sequence MFE -15.68
Consensus MFE -13.50
Energy contribution -13.34
Covariance contribution -0.16
Combinations/Pair 1.06
Mean z-score -1.38
Structure conservation index 0.86
SVM decision value 0.46
SVM RNA-class probability 0.744657
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21035869 116 + 22224390
AUUAAGAACUUAGUUAAAUGGAAAUCCGCAAAAAAAAAAAACAGGGAAAUAACAACAGCAAAUUCAAAUGGAAGCGGAGCAAAGAGUAAAGAAUUUAAUUUGCACAAAAUGGCACA----
............((((........(((((..............(........).........(((.....))))))))(((((...(((.....))).)))))......))))...---- ( -13.90)
>DroSec_CAF1 6501 110 + 1
AUUAAGAACUUAGUUAAAUAGAAAUCCGCAAAAAA------GAGAGAAAUAACAACAGCAAAUUCAAAUGGAAGCGGAGCAAAGAGCAAAGAAUUUAAUUUGCACAAAAUGGCACA----
............((((....(...(((((......------(..(....)..).........(((.....)))))))).).....(((((........)))))......))))...---- ( -14.10)
>DroSim_CAF1 7038 110 + 1
AUUAAGAACUUAGUUAAAUGGAAAUCCGCAAAAAA------GAGAGAAAUAACAACAGCAAAUUCAAAUGGAAGCGGAGCAAAGAGCAAAGAAUUUAAUUUGCACAAAAUGGCACA----
............((((........(((((......------(..(....)..).........(((.....)))))))).......(((((........)))))......))))...---- ( -14.00)
>DroEre_CAF1 6741 110 + 1
AUUAAGAACUUAGUUAAAUGGAAAUCCGCAAAAAAA------CGGGGAGUAACAACAACAAAUUCAAAUGGAAGCGGAGCAAAGAGCAAAGAAUUUAAUUUGCAGAACAUGGCACA----
............((...(((....(((((......(------(.....))............(((.....)))))))).......(((((........)))))....)))...)).---- ( -15.30)
>DroYak_CAF1 7190 117 + 1
AUUAAGAACUUAGUUAAAUGGAAAUCCGCAAAAAAUC---CGCGAGGAAUAACAACAACAAAUUCAAAUGGAAGCGGAGCAAAGAGCAAAGAAUUUAAUUUGCACAAAAUGGCACACACA
............((((........(((((......((---(....)))..............(((.....)))))))).......(((((........)))))......))))....... ( -21.10)
>consensus
AUUAAGAACUUAGUUAAAUGGAAAUCCGCAAAAAA______GAGAGAAAUAACAACAGCAAAUUCAAAUGGAAGCGGAGCAAAGAGCAAAGAAUUUAAUUUGCACAAAAUGGCACA____
............((((........(((((................(......).........(((.....)))))))).......(((((........)))))......))))....... (-13.50 = -13.34 +  -0.16)

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 13:04:52 2006