Locus 4689

Sequence ID X_DroMel_CAF1
Location 12,214,422 – 12,214,528
Length 106
Max. P 0.964866
window7695 window7696

overview

Window 5

Location 12,214,422 – 12,214,528
Length 106
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 84.69
Mean single sequence MFE -32.00
Consensus MFE -23.52
Energy contribution -23.90
Covariance contribution 0.38
Combinations/Pair 1.09
Mean z-score -2.48
Structure conservation index 0.74
SVM decision value 1.50
SVM RNA-class probability 0.959560
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12214422 106 + 22224390
UUUCUUUAUUUUCUCCAGGGGACAGCGGCAAUUGAGGCGGCUAUU--CCCCACCUAGAUCCACUGACUCUGGAUUAUCCGAACUCUUGGGGUUUGG----UUUUUUUUUUUU
.............(((((((..(((.((..(((.(((.((.....--..)).))).))))).))).)))))))....(((((((.....)))))))----............ ( -29.90)
>DroSec_CAF1 41144 97 + 1
UUUCUUUAUUUUCUCCAGGGGACAGCGGCAAUUGAUGCGGCUAUU--CCCCACCGAGAUCCACUGACUCCGGAUUAUCCGAACCCUUGAGGUUUGG----UUU---------
.............(((.(((((.(((.(((.....))).)))..)--))))...(((.((....))))).)))....(((((((.....)))))))----...--------- ( -31.00)
>DroEre_CAF1 38657 101 + 1
UUUCUUUAUUUUCUCCGGGGGACAGCGGCAAUCGAGGCGGCUAUU--CCCCGCCUAGAUCCACUGCCUCUGGAUUAUCCGGACCCAUGGGGUUUGGUUUCUUU---------
.............((((((((.(((.((..(((.((((((.....--..)))))).))))).)))))))))))....((((((((...)))))))).......--------- ( -42.50)
>DroYak_CAF1 26058 99 + 1
UUUCUUUAUUUUCUCCAGGGGACAGCGGCAAUUGAGGCGGCUACUCUCCCCACCAAGAUCCACUGACUCUGGAUUAUCCGAACCCAUGGGCUUUUG----CAU---------
..............((((((((.(((.((.......)).)))....))))).....((((((.......))))))...........)))((....)----)..--------- ( -24.60)
>consensus
UUUCUUUAUUUUCUCCAGGGGACAGCGGCAAUUGAGGCGGCUAUU__CCCCACCUAGAUCCACUGACUCUGGAUUAUCCGAACCCAUGGGGUUUGG____UUU_________
.................((((..(((.((.......)).))).....)))).....((((((.......))))))..(((((((.....)))))))................ (-23.52 = -23.90 +   0.38)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 6

Location 12,214,422 – 12,214,528
Length 106
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 84.69
Mean single sequence MFE -31.55
Consensus MFE -23.67
Energy contribution -25.18
Covariance contribution 1.50
Combinations/Pair 1.12
Mean z-score -2.48
Structure conservation index 0.75
SVM decision value 1.57
SVM RNA-class probability 0.964866
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12214422 106 - 22224390
AAAAAAAAAAAA----CCAAACCCCAAGAGUUCGGAUAAUCCAGAGUCAGUGGAUCUAGGUGGGG--AAUAGCCGCCUCAAUUGCCGCUGUCCCCUGGAGAAAAUAAAGAAA
............----((.(((.......))).))....(((((.(.((((((....((((((..--.....))))))......)))))).)..)))))............. ( -27.90)
>DroSec_CAF1 41144 97 - 1
---------AAA----CCAAACCUCAAGGGUUCGGAUAAUCCGGAGUCAGUGGAUCUCGGUGGGG--AAUAGCCGCAUCAAUUGCCGCUGUCCCCUGGAGAAAAUAAAGAAA
---------...----.....((....((.(((((.....))))).))...)).((((.(.((((--(.((((.(((.....))).)))))))))).))))........... ( -33.60)
>DroEre_CAF1 38657 101 - 1
---------AAAGAAACCAAACCCCAUGGGUCCGGAUAAUCCAGAGGCAGUGGAUCUAGGCGGGG--AAUAGCCGCCUCGAUUGCCGCUGUCCCCCGGAGAAAAUAAAGAAA
---------.......((..((((...))))..))....(((.(.(((((((((((.((((((..--.....)))))).)))..)))))).)).).)))............. ( -35.10)
>DroYak_CAF1 26058 99 - 1
---------AUG----CAAAAGCCCAUGGGUUCGGAUAAUCCAGAGUCAGUGGAUCUUGGUGGGGAGAGUAGCCGCCUCAAUUGCCGCUGUCCCCUGGAGAAAAUAAAGAAA
---------..(----(....))((((.(..((((.....)).))..).)))).((((.(.(((((.((..((..........))..)).)))))).))))........... ( -29.60)
>consensus
_________AAA____CCAAACCCCAAGGGUUCGGAUAAUCCAGAGUCAGUGGAUCUAGGUGGGG__AAUAGCCGCCUCAAUUGCCGCUGUCCCCUGGAGAAAAUAAAGAAA
................((.(((((...))))).))....(((((.(.((((((....((((((.........))))))......)))))).)..)))))............. (-23.67 = -25.18 +   1.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:31:05 2006