Locus 6335

Sequence ID 2L_DroMel_CAF1
Location 17,681,393 – 17,681,483
Length 90
Max. P 0.777672
window10126 window10127

overview

Window 6

Location 17,681,393 – 17,681,483
Length 90
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 79.93
Mean single sequence MFE -29.78
Consensus MFE -17.35
Energy contribution -18.52
Covariance contribution 1.17
Combinations/Pair 1.21
Mean z-score -1.94
Structure conservation index 0.58
SVM decision value 0.40
SVM RNA-class probability 0.720772
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17681393 90 + 22407834
AACCAAAGCGAAGCACUUAAAUGCAGCCAUCAAAGGCACAGGACCCUGUGGCUGCC---------CCGCAU-CCUGAUAGAGAUAUU--U-----UGGCUGCUUUGA
........(((((((((.((((((.(((......))).(((((...(((((.....---------))))))-)))).....).))))--)-----.)).))))))). ( -27.60)
>DroSec_CAF1 76895 90 + 1
AACCAAAGCGGAGCACUUAAAUGCAGCCAUCAAAGGCACAGGACCUCGUGGCUGCC---------CCGCAU-CCUGAUAGAGAUAUU--U-----UGGCUGCUUUGG
..(((((((((...........((((((((...((((....).))).)))))))).---------......-((.((((....))))--.-----.))))))))))) ( -29.70)
>DroSim_CAF1 59430 90 + 1
AACCAAAGCGGAGCACUUAAAUGCAGCCAUCAAAGGCACAGGACCCCGUGGCUGUC---------CCGCAU-CCUGAUAGAGAUAUU--U-----UGGCUGCUUUGG
..(((((((((.(((......))).(((......))).(((((....((((.....---------)))).)-))))...........--.-----...))))))))) ( -29.60)
>DroEre_CAF1 64077 81 + 1
AACCAAAGCGAAGCACUUAAAUGCAGCCAUCAAAGGCACAGGACCCUGUGGCU-------------------CCUGAUAGAGAUAUU--U-----CGGCUGCCUUGG
..((((.((...(((......)))((((((((.((.(((((....))))).))-------------------..))))...((....--)-----))))))).)))) ( -27.70)
>DroYak_CAF1 80604 90 + 1
AACCAAAGCGAAGCACUUAAAUGCAGCCAUCAAAGGCACAGGACCCUGUGGCUGCC---------CCGCAU-CCUGAUAGAGAUAUU--U-----UGGCUGCUUUGG
..(((((((..(((....((((((.(((......))).(((((...(((((.....---------))))))-)))).....).))))--)-----..)))))))))) ( -29.80)
>DroAna_CAF1 58134 107 + 1
AACCAAAGGCGGACACUUAAACGCAGCUAUCAAAGGCACAGAGUCCCGUGGCUGCCGUUUCUGCCCUGCCUGCCCCAUUGCCAUGCCACUCGCCGCUGAUGCUGCGG
..((......)).........((((((.((((..(((...((((..((((((..........((...))..........))))))..)))))))..)))))))))). ( -34.25)
>consensus
AACCAAAGCGAAGCACUUAAAUGCAGCCAUCAAAGGCACAGGACCCCGUGGCUGCC_________CCGCAU_CCUGAUAGAGAUAUU__U_____UGGCUGCUUUGG
..(((((((..(((........((((((((....((.......))..))))))))....................((((....))))..........)))))))))) (-17.35 = -18.52 +   1.17)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,681,393 – 17,681,483
Length 90
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 79.93
Mean single sequence MFE -32.00
Consensus MFE -20.72
Energy contribution -20.17
Covariance contribution -0.55
Combinations/Pair 1.36
Mean z-score -1.77
Structure conservation index 0.65
SVM decision value 0.55
SVM RNA-class probability 0.777672
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17681393 90 - 22407834
UCAAAGCAGCCA-----A--AAUAUCUCUAUCAGG-AUGCGG---------GGCAGCCACAGGGUCCUGUGCCUUUGAUGGCUGCAUUUAAGUGCUUCGCUUUGGUU
(((((((.(((.-----.--..(((((......))-)))...---------)))(((((((((((.....))).))).)))))((((....))))...))))))).. ( -29.80)
>DroSec_CAF1 76895 90 - 1
CCAAAGCAGCCA-----A--AAUAUCUCUAUCAGG-AUGCGG---------GGCAGCCACGAGGUCCUGUGCCUUUGAUGGCUGCAUUUAAGUGCUCCGCUUUGGUU
(((((((.(((.-----.--..(((((......))-)))...---------)))(((((((((((.....))).))).)))))((((....))))...))))))).. ( -32.10)
>DroSim_CAF1 59430 90 - 1
CCAAAGCAGCCA-----A--AAUAUCUCUAUCAGG-AUGCGG---------GACAGCCACGGGGUCCUGUGCCUUUGAUGGCUGCAUUUAAGUGCUCCGCUUUGGUU
((((((((((((-----.--......((....(((-.(((((---------(((..(....).)))))))))))..)))))))((((....))))...))))))).. ( -33.21)
>DroEre_CAF1 64077 81 - 1
CCAAGGCAGCCG-----A--AAUAUCUCUAUCAGG-------------------AGCCACAGGGUCCUGUGCCUUUGAUGGCUGCAUUUAAGUGCUUCGCUUUGGUU
((((((((((((-----(--......)).(((((.-------------------((.(((((....))))).)))))))))))((((....))))...))))))).. ( -30.50)
>DroYak_CAF1 80604 90 - 1
CCAAAGCAGCCA-----A--AAUAUCUCUAUCAGG-AUGCGG---------GGCAGCCACAGGGUCCUGUGCCUUUGAUGGCUGCAUUUAAGUGCUUCGCUUUGGUU
(((((((.(((.-----.--..(((((......))-)))...---------)))(((((((((((.....))).))).)))))((((....))))...))))))).. ( -32.10)
>DroAna_CAF1 58134 107 - 1
CCGCAGCAUCAGCGGCGAGUGGCAUGGCAAUGGGGCAGGCAGGGCAGAAACGGCAGCCACGGGACUCUGUGCCUUUGAUAGCUGCGUUUAAGUGUCCGCCUUUGGUU
.(((.((....)).))).((..(((....)))..))((((.(((((.(((((.((((((.(((.(.....)))).))...)))))))))...)))))))))...... ( -34.30)
>consensus
CCAAAGCAGCCA_____A__AAUAUCUCUAUCAGG_AUGCGG_________GGCAGCCACAGGGUCCUGUGCCUUUGAUGGCUGCAUUUAAGUGCUCCGCUUUGGUU
(((((((...............................................(((((((((((.....))).))).)))))((((....))))...))))))).. (-20.72 = -20.17 +  -0.55)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:08:37 2006