Locus 6333

Sequence ID 2R_DroMel_CAF1
Location 19,848,765 – 19,848,855
Length 90
Max. P 0.650435
window10120 window10121

overview

Window 0

Location 19,848,765 – 19,848,855
Length 90
Sequences 6
Columns 94
Reading direction forward
Mean pairwise identity 81.38
Mean single sequence MFE -34.27
Consensus MFE -20.24
Energy contribution -21.83
Covariance contribution 1.60
Combinations/Pair 1.16
Mean z-score -1.75
Structure conservation index 0.59
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19848765 90 + 20766785
GAAGCCAAGAGUUCUCCUCCAGACAGGCUGACGAUUGCCUAGAAAGACAGCCGCACUGGAGCCAGCGGACUCCU----ACUGCCGGUGGAGGAG
.............(((((((....((((........)))).........((((((..((((((...)).)))).----..)).))))))))))) ( -31.60)
>DroSec_CAF1 90811 90 + 1
GAAGCCAAGAGUUCUCCUCCAGACAGGCUGACGAUCGCCUAGAAAGACAGCCGCACUGGAGCCAGCGGACUCCU----GCUGGCGGCGGAGGAG
...........(((((((((((...(((((.(..((.....))..).)))))...)))))((((((((....))----))))))...)))))). ( -41.10)
>DroSim_CAF1 67037 90 + 1
GAAGCCAAGAGUUCUCCUCCAGACAGGCUGACGAUCGCCUAGAAAGACAGCCGCACUGGAGCCAGCGGACUCCU----GCUGGCGGCGGAGGAG
...........(((((((((((...(((((.(..((.....))..).)))))...)))))((((((((....))----))))))...)))))). ( -41.10)
>DroEre_CAF1 92438 88 + 1
--AGCCAAGAGUUCUCCUCCAGACAGGCUGACGAUCGCCUAGAAAGACAGCCGCACUGGAGCCGGCGGACUCCA----CCAGGCGGCGGAGGAG
--...........(((((((....((((........)))).........(((((..(((((((...)).)))))----....)))))))))))) ( -37.10)
>DroYak_CAF1 90382 92 + 1
--GGCCAACAGUUCUCCUCCAGACAGGCUGACGAUCGCCUAGAAAGACAGCCGCACUGGAGCCACCGGACUGCGGACUGCCGACUGUGGAGGAG
--...........((((((((.(.((((........)))).....(.((((((((((((.....))))..))))).))).)...).)))))))) ( -34.30)
>DroAna_CAF1 87680 69 + 1
---GCCAAGG-------CCCAGACAAUCUGACGUUCGCCUAGAAAGACAGCCGCUCUGGAGCCAGCGAA---------------AGAGUCGGAG
---.((..((-------((((((....(((...(((.....)))...)))....))))).)))..(...---------------.)....)).. ( -20.40)
>consensus
__AGCCAAGAGUUCUCCUCCAGACAGGCUGACGAUCGCCUAGAAAGACAGCCGCACUGGAGCCAGCGGACUCCU____GCUGGCGGCGGAGGAG
....((..((((((..((((((...(((((.(..((.....))..).)))))...)))))).....)))))).......(((....))).)).. (-20.24 = -21.83 +   1.60)

alignment

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secondary structure

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dotplot

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Window 1

Location 19,848,765 – 19,848,855
Length 90
Sequences 6
Columns 94
Reading direction reverse
Mean pairwise identity 81.38
Mean single sequence MFE -35.97
Consensus MFE -23.03
Energy contribution -24.58
Covariance contribution 1.56
Combinations/Pair 1.10
Mean z-score -1.78
Structure conservation index 0.64
SVM decision value 0.24
SVM RNA-class probability 0.650435
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19848765 90 - 20766785
CUCCUCCACCGGCAGU----AGGAGUCCGCUGGCUCCAGUGCGGCUGUCUUUCUAGGCAAUCGUCAGCCUGUCUGGAGGAGAACUCUUGGCUUC
((((((((..(((((.----.((((((....))))))...(((..(((((....)))))..)))....)))))))))))))............. ( -37.80)
>DroSec_CAF1 90811 90 - 1
CUCCUCCGCCGCCAGC----AGGAGUCCGCUGGCUCCAGUGCGGCUGUCUUUCUAGGCGAUCGUCAGCCUGUCUGGAGGAGAACUCUUGGCUUC
((((((((((((..((----.((((((....)))))).)))))))........(((((........)))))...)))))))............. ( -39.50)
>DroSim_CAF1 67037 90 - 1
CUCCUCCGCCGCCAGC----AGGAGUCCGCUGGCUCCAGUGCGGCUGUCUUUCUAGGCGAUCGUCAGCCUGUCUGGAGGAGAACUCUUGGCUUC
((((((((((((..((----.((((((....)))))).)))))))........(((((........)))))...)))))))............. ( -39.50)
>DroEre_CAF1 92438 88 - 1
CUCCUCCGCCGCCUGG----UGGAGUCCGCCGGCUCCAGUGCGGCUGUCUUUCUAGGCGAUCGUCAGCCUGUCUGGAGGAGAACUCUUGGCU--
((((((((((((..(.----(((((((....))))))).))))))........(((((........)))))...)))))))...........-- ( -40.70)
>DroYak_CAF1 90382 92 - 1
CUCCUCCACAGUCGGCAGUCCGCAGUCCGGUGGCUCCAGUGCGGCUGUCUUUCUAGGCGAUCGUCAGCCUGUCUGGAGGAGAACUGUUGGCC--
((((((((.....(((((.(((((.(..((.....))).))))))))))....(((((........)))))..))))))))...........-- ( -37.70)
>DroAna_CAF1 87680 69 - 1
CUCCGACUCU---------------UUCGCUGGCUCCAGAGCGGCUGUCUUUCUAGGCGAACGUCAGAUUGUCUGGG-------CCUUGGC---
..........---------------...((((((.((((((((..(((((....)))))..))).......))))))-------))..)))--- ( -20.61)
>consensus
CUCCUCCGCCGCCAGC____AGGAGUCCGCUGGCUCCAGUGCGGCUGUCUUUCUAGGCGAUCGUCAGCCUGUCUGGAGGAGAACUCUUGGCU__
(((((((..............((((((....))))))...(((..(((((....)))))..)))..........)))))))............. (-23.03 = -24.58 +   1.56)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:08:31 2006