Locus 3392

Sequence ID	X_DroMel_CAF1
Location	9,071,468 – 9,071,598
Length	130
Max. P	0.874997

overview

Window 2

Location	9,071,468 – 9,071,558
Length	90
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	78.75
Mean single sequence MFE	-35.02
Consensus MFE	-15.36
Energy contribution	-16.20
Covariance contribution	0.84
Combinations/Pair	1.17
Mean z-score	-1.91
Structure conservation index	0.44
SVM decision value	-0.04
SVM RNA-class probability	0.510904
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9071468 90 + 22224390
CUCGAAGCUCCGCAGGAAUC------CUCCUUCGGAUACGAUUACUCGCGACCC----UCGGC-----CGGAAGUAGCACUGACUUCCGGCCAUCCGUCCAGGUG
.(((....((((.((((...------.)))).))))..))).(((..(.(((..----..(((-----(((((((.......))))))))))....))))..))) ( -34.80)
>DroSec_CAF1 4637 90 + 1
CUCGAAGCUCCGCAGGAGUC------CUCCUUCGGAUACGAUUACUCCCGACCC----UCGGC-----CGGAAGUAGCACUGACUUCCGGCCAUCAGUACAGGUG
.(((....((((.((((...------.)))).))))..)))......((.((..----..(((-----(((((((.......))))))))))....))...)).. ( -32.60)
>DroSim_CAF1 5045 90 + 1
CUGGAGGCUCCACAGGAAUC------CUCCUUCGGAUACGAAUACUCGCGACCC----UCGGC-----CGGAAGUAGCACUGACUUCCGGCCAUCCGUACAGGUG
..(((((.(((...)))..)------))))..(((((.(((....)))......----..(((-----(((((((.......)))))))))))))))........ ( -35.70)
>DroYak_CAF1 5109 90 + 1
CUCGAAGCUCCGCAAGAAUC------CUCCUUUGGAUACGAUUACUCGCGUCCC----UCGGC-----CGGAAGUAGCACUGACUUCCGGCCAUCUGUUCAGGUG
..........(((..((((.------.......(((..(((....)))..))).----..(((-----(((((((.......))))))))))....))))..))) ( -30.30)
>DroPer_CAF1 8887 105 + 1
CUGGAGGCCCCCGAGGAGUCGUCGUCCGCCUACGGCUAUGACUACUCCAGGCCGAGCAGCAGCAGUAGUGGAAGCAGCUCGGGCUUCCGACCAUCUCCACAGCUG
.(((((((((((..(((((.(((((..(((...))).))))).))))).))..((((.((.((....))....)).)))))))))))))................ ( -41.70)
>consensus
CUCGAAGCUCCGCAGGAAUC______CUCCUUCGGAUACGAUUACUCGCGACCC____UCGGC_____CGGAAGUAGCACUGACUUCCGGCCAUCCGUACAGGUG
........((((.((((..........)))).))))........................(((.....(((((((.......))))))))))............. (-15.36 = -16.20 +   0.84)

alignment

secondary structure

dotplot

Window 3

Location	9,071,468 – 9,071,558
Length	90
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	78.75
Mean single sequence MFE	-40.32
Consensus MFE	-20.80
Energy contribution	-21.12
Covariance contribution	0.32
Combinations/Pair	1.30
Mean z-score	-2.18
Structure conservation index	0.52
SVM decision value	0.89
SVM RNA-class probability	0.874997
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9071468 90 - 22224390
CACCUGGACGGAUGGCCGGAAGUCAGUGCUACUUCCG-----GCCGA----GGGUCGCGAGUAAUCGUAUCCGAAGGAG------GAUUCCUGCGGAGCUUCGAG
..((.....))..((((((((((.......)))))))-----)))((----((...((((....)))).((((.(((..------....))).)))).))))... ( -38.30)
>DroSec_CAF1 4637 90 - 1
CACCUGUACUGAUGGCCGGAAGUCAGUGCUACUUCCG-----GCCGA----GGGUCGGGAGUAAUCGUAUCCGAAGGAG------GACUCCUGCGGAGCUUCGAG
..((((.(((..(((((((((((.......)))))))-----)))).----.))))))).....(((..((((.((((.------...)))).))))....))). ( -41.90)
>DroSim_CAF1 5045 90 - 1
CACCUGUACGGAUGGCCGGAAGUCAGUGCUACUUCCG-----GCCGA----GGGUCGCGAGUAUUCGUAUCCGAAGGAG------GAUUCCUGUGGAGCCUCCAG
........(((((((((((((((.......)))))))-----)))..----(((((....).))))..)))))..((((------(.((((...))))))))).. ( -41.00)
>DroYak_CAF1 5109 90 - 1
CACCUGAACAGAUGGCCGGAAGUCAGUGCUACUUCCG-----GCCGA----GGGACGCGAGUAAUCGUAUCCAAAGGAG------GAUUCUUGCGGAGCUUCGAG
.............((((((((((.......)))))))-----)))((----((..((((((.((((...(((...))).------))))))))))...))))... ( -36.30)
>DroPer_CAF1 8887 105 - 1
CAGCUGUGGAGAUGGUCGGAAGCCCGAGCUGCUUCCACUACUGCUGCUGCUCGGCCUGGAGUAGUCAUAGCCGUAGGCGGACGACGACUCCUCGGGGGCCUCCAG
((((.((((((..((((((....)))).))..))))))....))))(((...((((((((((.(((....(((....)))..))).)))))....)))))..))) ( -44.10)
>consensus
CACCUGUACAGAUGGCCGGAAGUCAGUGCUACUUCCG_____GCCGA____GGGUCGCGAGUAAUCGUAUCCGAAGGAG______GAUUCCUGCGGAGCUUCGAG
............(((((((((((.......))))))).....))))......(((.((((....)))).((((.(((((........))))).)))))))..... (-20.80 = -21.12 +   0.32)

alignment

secondary structure

dotplot

Window 4

Location	9,071,502 – 9,071,598
Length	96
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	80.02
Mean single sequence MFE	-41.08
Consensus MFE	-22.32
Energy contribution	-22.04
Covariance contribution	-0.28
Combinations/Pair	1.37
Mean z-score	-1.97
Structure conservation index	0.54
SVM decision value	0.28
SVM RNA-class probability	0.665609
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9071502 96 + 22224390
AUUACUCGCGACCC----UCGGC-----CGGAAGUAGCACUGACUUCCGGCCAUCCGUCCAGGUGCCAUCCAGUGACCCGUACGGCGAGGAGGAACCGGCGGACA
..............----..(((-----(((((((.......)))))))))).((((.((.(((.((.(((..((.((.....)))).))))).))))))))).. ( -38.80)
>DroSec_CAF1 4671 96 + 1
AUUACUCCCGACCC----UCGGC-----CGGAAGUAGCACUGACUUCCGGCCAUCAGUACAGGUGUCAUCCAGUGACCCGUACGGCGAGGAGGAACCGGCGGACA
....((((((.((.----..(((-----(((((((.......))))))))))....((((.((.(((((...))))))))))))))).))))............. ( -41.80)
>DroSim_CAF1 5079 96 + 1
AAUACUCGCGACCC----UCGGC-----CGGAAGUAGCACUGACUUCCGGCCAUCCGUACAGGUGCCAUCCAGUGACCCGUACGGCGAGGAGGAACCGGCGGACA
.....((((...((----(((((-----(((((((.......))))))))))..((((((.(((((......)).))).)))))).)))).(....).))))... ( -42.90)
>DroYak_CAF1 5143 96 + 1
AUUACUCGCGUCCC----UCGGC-----CGGAAGUAGCACUGACUUCCGGCCAUCUGUUCAGGUGCCAUCCAGUGACCCGUACGGCGAGGAGGAACCGGCGGACA
.........((((.----(((((-----(((((((.......)))))))))).........(((.((.(((..((.((.....)))).))))).))))).)))). ( -38.50)
>DroPer_CAF1 8927 105 + 1
ACUACUCCAGGCCGAGCAGCAGCAGUAGUGGAAGCAGCUCGGGCUUCCGACCAUCUCCACAGCUGCCCAGCGGCAGCGAAGGCUACGAGGAUGAGGUGGCGGACA
........((.((((((.((.((....))....)).)))))).))((((.(((((((....(((((...)))))(((....)))........))))))))))).. ( -43.40)
>consensus
AUUACUCGCGACCC____UCGGC_____CGGAAGUAGCACUGACUUCCGGCCAUCCGUACAGGUGCCAUCCAGUGACCCGUACGGCGAGGAGGAACCGGCGGACA
....................(((.....(((((((.......)))))))))).(((((...(((.((.(((..((.((.....)))).))))).))).))))).. (-22.32 = -22.04 +  -0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:58:16 2006