Locus 2860

Sequence ID 2R_DroMel_CAF1
Location 9,874,685 – 9,874,845
Length 160
Max. P 0.990026
window4730 window4731 window4732

overview

Window 0

Location 9,874,685 – 9,874,805
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.25
Mean single sequence MFE -43.72
Consensus MFE -33.88
Energy contribution -34.92
Covariance contribution 1.04
Combinations/Pair 1.07
Mean z-score -1.51
Structure conservation index 0.77
SVM decision value 0.10
SVM RNA-class probability 0.585152
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9874685 120 - 20766785
UCGCUGCUGUUCUACGGUAUGGCCAGCACCUGGUGGCAAGGCGUCCGCAAGGAGGCCACCACGUGGAAGGAAGCCAUCGCUCUCAUCCGCGAACACUUCUCGCCCACCAAGCCCGCCUAC
..((((((((.(....).)))).))))...(((((((..(((.(((....))).)))....((((((.(..(((....)))..).))))))..........).))))))........... ( -49.70)
>DroSec_CAF1 7309 120 - 1
UCACUGCUGUUCUACGGUAUGGCCAGCACCUGGUGGCAAGGCGUCCGCAAGGAGGCCACCACGUGGAAGGAAGCCAUCGCCCUCAUCCGCGAACACUUCUCGCCCACCAAGCCCUCCUAC
....(((((..(........)..)))))..(((((((..(((.(((....))).)))....(((((((((..((....)))))..))))))..........).))))))........... ( -44.10)
>DroSim_CAF1 7239 120 - 1
UCUCUGCUGUUCUACGGUAUGGCCAGCACCUGGUGGCAAGGCGUCCGCAAGGAGGCCACCACGUGGAAGGAAGCCAUCGCCCUCAUCCGCGAACACUUCUCGCCCACCAAGCCCGCCUAC
....(((((.....))))).(((..((...(((((((..(((.(((....))).)))....(((((((((..((....)))))..))))))..........).)))))).))..)))... ( -46.00)
>DroYak_CAF1 7221 120 - 1
UCACUGCUGUUCUACGGAAUGGCCAGCACCUGGUGGCAGGGCGUUCGUAAGGAGGCCGUGACGUGGAAAGAUGCCAUCGAUCUCAUCCGCGACCACUUCUCGCCCACCAAGCCCGCCUAC
.....(((((((....)))))))..((...(((((((..(((.(((....))).)))(((.((((((.((((.......))))..))))))..))).....).)))))).))........ ( -43.60)
>DroAna_CAF1 6975 120 - 1
UCGCUCCUUUUCUACGGACUUGCCUCUAUCUGGUGGCAGGGCGUUCGCAAGGAGGCCAACACCUGGAAUGAUGCCAUUGAUCUCAUCCGGGAGCACUUCUCGCCCACAAAGCCCGCCUAC
..((((((.(((((.((..(((((.((....)).)))))(((.(((....))).)))....))))))).((((..........)))).)))))).......................... ( -35.20)
>consensus
UCACUGCUGUUCUACGGUAUGGCCAGCACCUGGUGGCAAGGCGUCCGCAAGGAGGCCACCACGUGGAAGGAAGCCAUCGCUCUCAUCCGCGAACACUUCUCGCCCACCAAGCCCGCCUAC
....(((((..(........)..)))))..(((((((..(((.(((....))).)))....((((((.....((....)).....))))))..........).))))))........... (-33.88 = -34.92 +   1.04)

alignment

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secondary structure

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dotplot

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Window 1

Location 9,874,725 – 9,874,845
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.75
Mean single sequence MFE -48.04
Consensus MFE -34.44
Energy contribution -36.12
Covariance contribution 1.68
Combinations/Pair 1.15
Mean z-score -2.26
Structure conservation index 0.72
SVM decision value 0.83
SVM RNA-class probability 0.861502
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9874725 120 + 20766785
GCGAUGGCUUCCUUCCACGUGGUGGCCUCCUUGCGGACGCCUUGCCACCAGGUGCUGGCCAUACCGUAGAACAGCAGCGAGAUGCCCUUCAGGGCGUUCUCGUCGCUGAUACCUUCUACA
...((((((......(((.(((((((((((....))).)....))))))).)))..))))))...((((((((((.(((((((((((....))))).)))))).)))).....)))))). ( -56.00)
>DroSec_CAF1 7349 120 + 1
GCGAUGGCUUCCUUCCACGUGGUGGCCUCCUUGCGGACGCCUUGCCACCAGGUGCUGGCCAUACCGUAGAACAGCAGUGAGAUGCCCUUCAGGGCGUUCUCGUCGCUGAUCCCCUCCACA
(((((((((......(((.(((((((((((....))).)....))))))).)))..))))))..))).((.((((..((((((((((....))))).)))))..)))).))......... ( -50.70)
>DroSim_CAF1 7279 120 + 1
GCGAUGGCUUCCUUCCACGUGGUGGCCUCCUUGCGGACGCCUUGCCACCAGGUGCUGGCCAUACCGUAGAACAGCAGAGAGAUGCCCUUCAGGGCGUUCUCGUCGCUGAUCCCCUCCACA
(((((((((......(((.(((((((((((....))).)....))))))).)))..))))))..))).((.((((.(((((((((((....))))).)))).)))))).))......... ( -48.60)
>DroYak_CAF1 7261 120 + 1
UCGAUGGCAUCUUUCCACGUCACGGCCUCCUUACGAACGCCCUGCCACCAGGUGCUGGCCAUUCCGUAGAACAGCAGUGAGAUGCCCUUCAGGGCAUUCUCGUCGCUGAUCCCCUCCAGC
....(((.....(((.(((..(.((((((.....))..((((((....)))).)).)))).)..))).)))((((..((((((((((....))))).)))))..)))).......))).. ( -41.60)
>DroAna_CAF1 7015 120 + 1
UCAAUGGCAUCAUUCCAGGUGUUGGCCUCCUUGCGAACGCCCUGCCACCAGAUAGAGGCAAGUCCGUAGAAAAGGAGCGAGAGCCCCUUGAGGGCGUUCUCGUCGGUGAUGUUCUCCAGC
.....(((((((((((.((((((.((......)).)))))).((((.(......).)))).............)))(((((((((((....))).))))))))..))))))))....... ( -43.30)
>consensus
GCGAUGGCUUCCUUCCACGUGGUGGCCUCCUUGCGGACGCCUUGCCACCAGGUGCUGGCCAUACCGUAGAACAGCAGCGAGAUGCCCUUCAGGGCGUUCUCGUCGCUGAUCCCCUCCACA
....(((.....(((.(((..(((((((((....))).((((((....)))).)).))))))..))).)))((((.(((((((((((....))))).)))))).)))).......))).. (-34.44 = -36.12 +   1.68)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,874,725 – 9,874,845
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.75
Mean single sequence MFE -53.24
Consensus MFE -42.18
Energy contribution -43.22
Covariance contribution 1.04
Combinations/Pair 1.09
Mean z-score -2.69
Structure conservation index 0.79
SVM decision value 2.19
SVM RNA-class probability 0.990026
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9874725 120 - 20766785
UGUAGAAGGUAUCAGCGACGAGAACGCCCUGAAGGGCAUCUCGCUGCUGUUCUACGGUAUGGCCAGCACCUGGUGGCAAGGCGUCCGCAAGGAGGCCACCACGUGGAAGGAAGCCAUCGC
....((.(((..(((((.(((((..((((....)))).))))).)))))(((((((.....((((.(....).))))..(((.(((....))).)))....)))))))....))).)).. ( -57.20)
>DroSec_CAF1 7349 120 - 1
UGUGGAGGGGAUCAGCGACGAGAACGCCCUGAAGGGCAUCUCACUGCUGUUCUACGGUAUGGCCAGCACCUGGUGGCAAGGCGUCCGCAAGGAGGCCACCACGUGGAAGGAAGCCAUCGC
.(((..((....(((((..((((..((((....)))).))))..)))))(((((((.....((((.(....).))))..(((.(((....))).)))....))))))).....))..))) ( -53.40)
>DroSim_CAF1 7279 120 - 1
UGUGGAGGGGAUCAGCGACGAGAACGCCCUGAAGGGCAUCUCUCUGCUGUUCUACGGUAUGGCCAGCACCUGGUGGCAAGGCGUCCGCAAGGAGGCCACCACGUGGAAGGAAGCCAUCGC
.(((..((....(((((..((((..((((....)))).))))..)))))(((((((.....((((.(....).))))..(((.(((....))).)))....))))))).....))..))) ( -53.70)
>DroYak_CAF1 7261 120 - 1
GCUGGAGGGGAUCAGCGACGAGAAUGCCCUGAAGGGCAUCUCACUGCUGUUCUACGGAAUGGCCAGCACCUGGUGGCAGGGCGUUCGUAAGGAGGCCGUGACGUGGAAAGAUGCCAUCGA
....((.((.(((((((..((((.(((((....)))))))))..)))).(((((((..((((((.((.((((....)))))).(((....)))))))))..))))))).))).)).)).. ( -58.20)
>DroAna_CAF1 7015 120 - 1
GCUGGAGAACAUCACCGACGAGAACGCCCUCAAGGGGCUCUCGCUCCUUUUCUACGGACUUGCCUCUAUCUGGUGGCAGGGCGUUCGCAAGGAGGCCAACACCUGGAAUGAUGCCAUUGA
..(((....(((((..(((((((..((((.....))))))))).))...(((((.((..(((((.((....)).)))))(((.(((....))).)))....))))))))))))))).... ( -43.70)
>consensus
UGUGGAGGGGAUCAGCGACGAGAACGCCCUGAAGGGCAUCUCACUGCUGUUCUACGGUAUGGCCAGCACCUGGUGGCAAGGCGUCCGCAAGGAGGCCACCACGUGGAAGGAAGCCAUCGC
....((.((...(((((..((((..((((....)))).))))..)))))(((((((.....((((.(....).))))..(((.(((....))).)))....))))))).....)).)).. (-42.18 = -43.22 +   1.04)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:41:23 2006