Locus 3537

Sequence ID 3L_DroMel_CAF1
Location 10,368,334 – 10,368,485
Length 151
Max. P 0.956447
window5519 window5520 window5521

overview

Window 9

Location 10,368,334 – 10,368,431
Length 97
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 94.79
Mean single sequence MFE -30.35
Consensus MFE -28.77
Energy contribution -28.77
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.32
Structure conservation index 0.95
SVM decision value 1.47
SVM RNA-class probability 0.956447
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10368334 97 + 23771897
UUGCCCGGCACUUUUGGUAACCGGCAAUCAA-AGAGUG------GCUCGCUCGAAUGCCAAAUACCAAAUCGGUAAAGUGGCAAAGUGGCAGCCUGAUUGCA---GC
.....(((.((.....))..)))(((((((.-.....(------(((.(((....(((((..((((.....))))...)))))....)))))))))))))).---.. ( -31.30)
>DroSec_CAF1 242082 100 + 1
UUGCCCGGCACUUUUGGUAACCGGCAAUCAA-AGAGUG------GCUCGCUCGAAUGCCAAAUACCAAAUCAGUAAAGUGGCAAAGUGGCAGCCUGAUUGCAGCAGC
((((((.((...(((((((...((((.((..-.(((((------...))))))).))))...)))))))...))...).))))).((.((((.....)))).))... ( -29.70)
>DroSim_CAF1 252768 100 + 1
UUGCCCGGCACUUUUGGUAACCGGCAAUCAA-AGAGUG------GCUCGCUCGAAUGCCAAAUACCAAAUCAGUAAAGUGGCAAAGUGGCAGUCUGAUUGCAGCAGC
((((((.((...(((((((...((((.((..-.(((((------...))))))).))))...)))))))...))...).))))).((.(((((...))))).))... ( -30.40)
>DroEre_CAF1 256762 97 + 1
UUGCCCGGCACUUUUGGUAACCGGCAAUCAA-AGAGUG------GCUCGCUCGAAUGCCAAAUACCAAAUCAGUAAAGUGGCAAAGUGGCAGCCUGAUUGCA---GC
((((((.((...(((((((...((((.((..-.(((((------...))))))).))))...)))))))...))...).)))))....((((.....)))).---.. ( -28.10)
>DroYak_CAF1 254548 97 + 1
UUGCCCGGCACUUUUGGUAACCGGCAAUCAA-AGAGUG------GCUCGCUCGAAUGCCAAAUACCAAAUCAGUAAAGUGGCAAAGUGGCAGCCUGAUUGCA---GC
((((((.((...(((((((...((((.((..-.(((((------...))))))).))))...)))))))...))...).)))))....((((.....)))).---.. ( -28.10)
>DroAna_CAF1 248505 104 + 1
UUGCCCGGCACUUUUGGUAACCGGCAAUCAAAAGAGUGGCUUUGGCUCGCUCGAAUGCCAAAUACCAAAUCAGUAAAGUGGCAAAGUGGCAGCCCGAUUGCG---GC
((((((.((...(((((((...((((.((....(((((((....)).))))))).))))...)))))))...))...).))))).((.((((.....)))).---)) ( -34.50)
>consensus
UUGCCCGGCACUUUUGGUAACCGGCAAUCAA_AGAGUG______GCUCGCUCGAAUGCCAAAUACCAAAUCAGUAAAGUGGCAAAGUGGCAGCCUGAUUGCA___GC
((((((.((...(((((((...((((.((....((((.......))))....)).))))...)))))))...))...).)))))....((((.....))))...... (-28.77 = -28.77 +   0.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 10,368,334 – 10,368,431
Length 97
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 94.79
Mean single sequence MFE -33.72
Consensus MFE -28.73
Energy contribution -28.90
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -2.18
Structure conservation index 0.85
SVM decision value 1.18
SVM RNA-class probability 0.926753
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10368334 97 - 23771897
GC---UGCAAUCAGGCUGCCACUUUGCCACUUUACCGAUUUGGUAUUUGGCAUUCGAGCGAGC------CACUCU-UUGAUUGCCGGUUACCAAAAGUGCCGGGCAA
((---((((((((((((((.....(((((...((((.....))))..))))).....)).)))------).....-.)))))))((((.((.....))))))))).. ( -33.90)
>DroSec_CAF1 242082 100 - 1
GCUGCUGCAAUCAGGCUGCCACUUUGCCACUUUACUGAUUUGGUAUUUGGCAUUCGAGCGAGC------CACUCU-UUGAUUGCCGGUUACCAAAAGUGCCGGGCAA
((.(((.......))).))....(((((.(..((((..(((((((.((((((.(((((.(((.------..))))-)))).)))))).)))))))))))..)))))) ( -34.10)
>DroSim_CAF1 252768 100 - 1
GCUGCUGCAAUCAGACUGCCACUUUGCCACUUUACUGAUUUGGUAUUUGGCAUUCGAGCGAGC------CACUCU-UUGAUUGCCGGUUACCAAAAGUGCCGGGCAA
((..(((....)))...))....(((((.(..((((..(((((((.((((((.(((((.(((.------..))))-)))).)))))).)))))))))))..)))))) ( -32.70)
>DroEre_CAF1 256762 97 - 1
GC---UGCAAUCAGGCUGCCACUUUGCCACUUUACUGAUUUGGUAUUUGGCAUUCGAGCGAGC------CACUCU-UUGAUUGCCGGUUACCAAAAGUGCCGGGCAA
((---.((......)).))....(((((.(..((((..(((((((.((((((.(((((.(((.------..))))-)))).)))))).)))))))))))..)))))) ( -33.10)
>DroYak_CAF1 254548 97 - 1
GC---UGCAAUCAGGCUGCCACUUUGCCACUUUACUGAUUUGGUAUUUGGCAUUCGAGCGAGC------CACUCU-UUGAUUGCCGGUUACCAAAAGUGCCGGGCAA
((---.((......)).))....(((((.(..((((..(((((((.((((((.(((((.(((.------..))))-)))).)))))).)))))))))))..)))))) ( -33.10)
>DroAna_CAF1 248505 104 - 1
GC---CGCAAUCGGGCUGCCACUUUGCCACUUUACUGAUUUGGUAUUUGGCAUUCGAGCGAGCCAAAGCCACUCUUUUGAUUGCCGGUUACCAAAAGUGCCGGGCAA
((---((((((((((((((.....(((((...((((.....))))..))))).....)).))))((((.....)))))))))))((((.((.....))))))))).. ( -35.40)
>consensus
GC___UGCAAUCAGGCUGCCACUUUGCCACUUUACUGAUUUGGUAUUUGGCAUUCGAGCGAGC______CACUCU_UUGAUUGCCGGUUACCAAAAGUGCCGGGCAA
......(((.......)))....(((((.(..((((..(((((((.((((((.((((..(((.........)))..)))).)))))).)))))))))))..)))))) (-28.73 = -28.90 +   0.17)

alignment

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secondary structure

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dotplot

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Window 1

Location 10,368,394 – 10,368,485
Length 91
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 73.60
Mean single sequence MFE -28.57
Consensus MFE -8.68
Energy contribution -10.27
Covariance contribution 1.59
Combinations/Pair 1.25
Mean z-score -2.30
Structure conservation index 0.30
SVM decision value 0.44
SVM RNA-class probability 0.735941
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10368394 91 + 23771897
AAUCGGUAAAGUGGCAAAGUGGCAGCCUGAUUGCA---GCAAGUAUGCUGGAUUCUCGUUGCUG---------CUGC---UGUUGCUUUUCUAUCAU---UUCCAUCGA
....((.((((..(((.((..(((((..((.(.((---(((....))))).).))..)))))..---------))..---)))..)))).)).....---......... ( -32.90)
>DroGri_CAF1 261641 83 + 1
---UAGCCAACUGGCAGAUUGCUGGUCUGCUUUCA------UGAUUGCUCGAUU-----G---G---------CUGCUGUUGCCGCAUUUCAAUCCUUGAUUUCCUCAA
---.(((..((..((.....))..))..))).(((------.(((((...((((-----(---(---------(.......)))).))).)))))..)))......... ( -19.60)
>DroSec_CAF1 242142 94 + 1
AAUCAGUAAAGUGGCAAAGUGGCAGCCUGAUUGCAGCAGCAAGUAUGCUGGAUUCUCGUUGCUG---------UUGC---UGUUGCUUUUCUAUCAU---UUCCAUCGA
....((.((((..(((.((..(((((..((.(.(((((.......))))).).))..)))))..---------))..---)))..)))).)).....---......... ( -30.60)
>DroSim_CAF1 252828 94 + 1
AAUCAGUAAAGUGGCAAAGUGGCAGUCUGAUUGCAGCAGCAAGUAUGCUGGAUUCUCGUUGCUG---------UUGC---UGUUGCUUUUCUAUCAU---UUCCAUCGA
....((.((((..(((..(..(((((..((.(.(((((.......))))).).)).....))))---------)..)---)))..)))).)).....---......... ( -27.10)
>DroYak_CAF1 254608 100 + 1
AAUCAGUAAAGUGGCAAAGUGGCAGCCUGAUUGCA---GCAAGUAUGCUGGAUUCUCGUGGCUGCUGCUGCUGCUGU---UGUUGCUUUUCUAUCAU---UUCCAUCGA
....(((((((..(((.((..((((((.((.(.((---(((....))))).).))....))))))..))..)))..)---).)))))..........---......... ( -36.10)
>DroAna_CAF1 248572 82 + 1
AAUCAGUAAAGUGGCAAAGUGGCAGCCCGAUUGCG---GCAAGUACACUGGAUUCUCGCUGC---------------------CGCUUUUCUAUCAU---UUUCAUCGA
..........((((.(((((((((((..((.(.((---(........))).).))..)))))---------------------)))))).))))...---......... ( -25.10)
>consensus
AAUCAGUAAAGUGGCAAAGUGGCAGCCUGAUUGCA___GCAAGUAUGCUGGAUUCUCGUUGCUG_________CUGC___UGUUGCUUUUCUAUCAU___UUCCAUCGA
....((.(((((((((......((((....((((....))))....))))(.....).......................))))))))).))................. ( -8.68 = -10.27 +   1.59)

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 11:00:31 2006