Locus 9481

Sequence ID 3R_DroMel_CAF1
Location 25,090,473 – 25,090,600
Length 127
Max. P 0.862256
window15183 window15184

overview

Window 3

Location 25,090,473 – 25,090,564
Length 91
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 88.68
Mean single sequence MFE -40.88
Consensus MFE -29.51
Energy contribution -30.36
Covariance contribution 0.85
Combinations/Pair 1.00
Mean z-score -2.36
Structure conservation index 0.72
SVM decision value 0.83
SVM RNA-class probability 0.862256
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25090473 91 + 27905053
UGUAUGCGCCAGCAGAUCCUUUUGUCAGGCCAAAUGCGCGAAAG-UGUGGCGCAGGCGCAGCAGGAUCCUGGAUUUGGAUCAGCU----U-------------CAGCUA
(((.((((((.((.(((......)))..(((....((((....)-)))))))).))))))))).(((((.......)))))(((.----.-------------..))). ( -35.70)
>DroSec_CAF1 19534 105 + 1
UGUAUGCGCCAGCAGUUCCUUUGGUCAGCCCAAAUGCGCGAAAGAUGUGGCGCAGGCGCAGCAGGAUCCUGGAUAUGGAUCAGCU----UCAGGCCCGGGAUUCAGCUA
.....(((((.........(((((.....)))))(((((.(......).))))))))))(((.(((((((((...((((.....)----)))...))))))))).))). ( -41.40)
>DroSim_CAF1 19924 104 + 1
UGUAUGCGCCAGCAGAUCCUUUUGUCAGCCCAAAUGCGCGAAAG-UGUGGCGCAGGCGCAGCAGGAUCCUGGAUUUGGAUCAGCU----UCAGGCUCGGGAUUCAGCUA
.....(((((.((.(((......))).(((.....((((....)-)))))))).)))))(((.((((((((..((((((.....)----)))))..)))))))).))). ( -43.90)
>DroEre_CAF1 19920 107 + 1
UGUAUGCGCCAGCAGAUCCUUUUGUCAGCCCAAAUGCGCGAAAG-UGUGGCGCAGGCGCAGCAGGAUCCUGGAUUUGGAUCAGCUCGCUUCCAACUCG-GAUUCAACUG
(((.((((((.((.(((......))).(((.....((((....)-)))))))).)))))))))((((((..((.(((((..((....))))))).)))-)))))..... ( -39.60)
>DroYak_CAF1 20179 107 + 1
UGUAUGCGCCAGCAGAUCCUUUUGUCAGCCCAAAUGCGCGAAAG-UGUGGCGCAGGCGCAGCAGGAUCCUGGAUUUGGAUCAGCUCGGUUCAAACUCG-GAUUCAGCUA
.....(((((.((.(((......))).(((.....((((....)-)))))))).)))))(((.((((((.(..((((((((.....))))))))..))-))))).))). ( -43.80)
>consensus
UGUAUGCGCCAGCAGAUCCUUUUGUCAGCCCAAAUGCGCGAAAG_UGUGGCGCAGGCGCAGCAGGAUCCUGGAUUUGGAUCAGCU____UCAAACUCG_GAUUCAGCUA
(((.((((((.(((((....))))).........(((((.(......).)))))))))))))).(((((.......)))))((((....((........))...)))). (-29.51 = -30.36 +   0.85)

alignment

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secondary structure

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dotplot

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Window 4

Location 25,090,508 – 25,090,600
Length 92
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 84.97
Mean single sequence MFE -39.86
Consensus MFE -30.07
Energy contribution -31.76
Covariance contribution 1.69
Combinations/Pair 1.03
Mean z-score -1.84
Structure conservation index 0.75
SVM decision value 0.50
SVM RNA-class probability 0.760623
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25090508 92 + 27905053
GCGCGAAAG-UGUGGCGCAGGCGCAGCAGGAUCCUGGAUUUGGAUCAGCU----U-------------CAGCUACAAAAUCAGGACACUGCGCACGUGCGUUGGG---AAG-UC
((((....)-)))((((((.(.((.((((..((((((.((((....(((.----.-------------..))).)))).))))))..)))))).).))))))...---...-.. ( -40.90)
>DroSec_CAF1 19569 106 + 1
GCGCGAAAGAUGUGGCGCAGGCGCAGCAGGAUCCUGGAUAUGGAUCAGCU----UCAGGCCCGGGAUUCAGCUACAAAAUCAGGACACUGCGCACGUGCGUUGGG---AAG-UC
((((....).)))((((((.(.(((((.(((((((((...((((.....)----)))...))))))))).))).......(((....))).)).).))))))...---...-.. ( -36.70)
>DroSim_CAF1 19959 105 + 1
GCGCGAAAG-UGUGGCGCAGGCGCAGCAGGAUCCUGGAUUUGGAUCAGCU----UCAGGCUCGGGAUUCAGCUACAAAAUCAGGACACUGCGCACGUGCGUUGGG---AAG-UC
((((....)-)))((((((.(.((.((((..((((((.((((((......----)).((((........)))).)))).))))))..)))))).).))))))...---...-.. ( -41.80)
>DroEre_CAF1 19955 102 + 1
GCGCGAAAG-UGUGGCGCAGGCGCAGCAGGAUCCUGGAUUUGGAUCAGCUCGCUUCCAACUCG-GAUUCAACUGCGAAAUCAGGAC-------ACGUGCGUUGGG---AAGUUU
((((....)-)))((((((.((((((..((((((..((.(((((..((....))))))).)))-)))))..)))))..........-------.).))))))...---...... ( -33.70)
>DroYak_CAF1 20214 112 + 1
GCGCGAAAG-UGUGGCGCAGGCGCAGCAGGAUCCUGGAUUUGGAUCAGCUCGGUUCAAACUCG-GAUUCAGCUACAAAAUCAGGACACUGCGCACGUGCGUUGGGAGGAAGUUU
((((....)-)))((((((.(.((.((((..((((((.((((....((((..((((......)-)))..)))).)))).))))))..)))))).).))))))............ ( -46.20)
>consensus
GCGCGAAAG_UGUGGCGCAGGCGCAGCAGGAUCCUGGAUUUGGAUCAGCU____UCAAACUCG_GAUUCAGCUACAAAAUCAGGACACUGCGCACGUGCGUUGGG___AAG_UC
((((....).)))((((((.(.((.((((..((((((.((((....((((....((........))...)))).)))).))))))..)))))).).))))))............ (-30.07 = -31.76 +   1.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:35:39 2006