Locus 1576

Sequence ID 2R_DroMel_CAF1
Location 5,933,158 – 5,933,248
Length 90
Max. P 0.744307
window2640 window2641

overview

Window 0

Location 5,933,158 – 5,933,248
Length 90
Sequences 4
Columns 108
Reading direction forward
Mean pairwise identity 61.78
Mean single sequence MFE -18.23
Consensus MFE -8.25
Energy contribution -9.50
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -1.69
Structure conservation index 0.45
SVM decision value 0.46
SVM RNA-class probability 0.744307
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5933158 90 + 20766785
UUU--------------CAAAUAAGCCAG--AAUUGGUGGCUAAUUUCCAAAGUUGUGCAUGCAAUCCAAACAGCUGAUCCAA--CAGCUGAUCAUUUUCCAAAGAGU
.((--------------(((((.(((((.--......))))).)))).....(((((....))))).....((((((......--)))))).............))). ( -17.50)
>DroSec_CAF1 75617 90 + 1
UUU--------------CAAAUAAGCCAG--AAUUGCUGGCUAAUUUCAAAAGUUGUCCAUGUAAACCAAACAGCUGACCCAA--CAGCUGAUCACUUUCCAAAGAGU
(((--------------.((((.((((((--.....)))))).)))).)))....................((((((......--))))))...((((......)))) ( -20.00)
>DroSim_CAF1 74164 100 + 1
UUUGCUUUAAACUUGAUCAAAUAACCCAAUCAGUCCCGAACCAAUUCCUUUAGG---AUCUGGUAUCAAAACAGCUGAUCCGAUUCAGCCGG-----CUUCAAACAUA
...............................((((..((((((..(((....))---)..)))).))......(((((......))))).))-----))......... ( -18.60)
>DroYak_CAF1 78280 83 + 1
UU---------------CCAGUAAGCCUG--AAUUAGUGGCUAUUUUGAACAGCUUCACAU------CAAACAGCUGAUCCAU--CAGCUGAUUACUUUCCAAAGAGU
..---------------..((((((((..--.......))))...................------....(((((((....)--))))))..))))........... ( -16.80)
>consensus
UUU______________CAAAUAAGCCAG__AAUUGCUGGCUAAUUUCAAAAGUUGUACAUG_AAUCCAAACAGCUGAUCCAA__CAGCUGAUCACUUUCCAAAGAGU
.......................((((...........)))).............................((((((........))))))................. ( -8.25 =  -9.50 +   1.25)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 1

Location 5,933,158 – 5,933,248
Length 90
Sequences 4
Columns 108
Reading direction reverse
Mean pairwise identity 61.78
Mean single sequence MFE -23.90
Consensus MFE -9.89
Energy contribution -10.95
Covariance contribution 1.06
Combinations/Pair 1.38
Mean z-score -1.78
Structure conservation index 0.41
SVM decision value -0.02
SVM RNA-class probability 0.522106
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5933158 90 - 20766785
ACUCUUUGGAAAAUGAUCAGCUG--UUGGAUCAGCUGUUUGGAUUGCAUGCACAACUUUGGAAAUUAGCCACCAAUU--CUGGCUUAUUUG--------------AAA
......((.((..(((.((((((--......)))))).)))..)).))........((..((....(((((......--.)))))..))..--------------)). ( -17.70)
>DroSec_CAF1 75617 90 - 1
ACUCUUUGGAAAGUGAUCAGCUG--UUGGGUCAGCUGUUUGGUUUACAUGGACAACUUUUGAAAUUAGCCAGCAAUU--CUGGCUUAUUUG--------------AAA
..(((.((.(((.(((.((((((--......)))))).))).))).)).))).....(((.((((.((((((.....--)))))).)))).--------------))) ( -24.90)
>DroSim_CAF1 74164 100 - 1
UAUGUUUGAAG-----CCGGCUGAAUCGGAUCAGCUGUUUUGAUACCAGAU---CCUAAAGGAAUUGGUUCGGGACUGAUUGGGUUAUUUGAUCAAGUUUAAAGCAAA
..(((((.(((-----(.((((((......))))))(((((((.(((((.(---((....))).))))))))))))((((..(.....)..)))).)))).))))).. ( -30.70)
>DroYak_CAF1 78280 83 - 1
ACUCUUUGGAAAGUAAUCAGCUG--AUGGAUCAGCUGUUUG------AUGUGAAGCUGUUCAAAAUAGCCACUAAUU--CAGGCUUACUGG---------------AA
....((..(.((((...((((((--(....))))))).(((------(.(((..(((((.....))))))))....)--))))))).)..)---------------). ( -22.30)
>consensus
ACUCUUUGGAAAGUGAUCAGCUG__UUGGAUCAGCUGUUUGGAUU_CAUGUACAACUUUUGAAAUUAGCCACCAAUU__CUGGCUUAUUUG______________AAA
.................((((((........))))))........................((((.((((((.......)))))).)))).................. ( -9.89 = -10.95 +   1.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:54 2006