Locus 6233

Sequence ID	3L_DroMel_CAF1
Location	16,579,366 – 16,579,474
Length	108
Max. P	0.945611

overview

Window 8

Location	16,579,366 – 16,579,474
Length	108
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	80.72
Mean single sequence MFE	-45.63
Consensus MFE	-24.85
Energy contribution	-28.52
Covariance contribution	3.67
Combinations/Pair	1.00
Mean z-score	-3.22
Structure conservation index	0.54
SVM decision value	1.35
SVM RNA-class probability	0.945611
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16579366 108 + 23771897
GCUGGAGUU------------GGAGCUGAAGUUGGAGCCGAGGUGGAGGUCCAACUAAGCCUCGGGCAGCGGCUUCAGCUCCUUUAUCUGCUUGAUCAGAUAGGCCUUCUCGUCGUUGAA
((.(((...------------(((((((((((((..((((((((..((......))..))))).)))..)))))))))))))....)))))....((((...(((......))).)))). ( -47.30)
>DroPse_CAF1 3191 89 + 1
A------------------------------UU-GACCAUCCGUCGAUGGUCAACUAGGCCUCGGGCAGCGGUUUCAGCUCCUUUAUCUGCUUAAUCAGAUAGGCCUUCUCGUCGUUGAA
.------------------------------((-(((((((....)))))))))..(((((..(((.(((.......)))))).((((((......)))))))))))............. ( -31.10)
>DroSec_CAF1 3308 102 + 1
G------------------UUGGAGGUGAAGUUGGAGCCGAGGUGGAGGUCCAACUAAGCCUCGGGCAGCGGCUUCAGCUCCUUUAUCUGCUUGAUCAGAUAGGCCUUCUCGUCGUUGAA
.------------------..((((.((((((((..((((((((..((......))..))))).)))..)))))))).))))..((((((......))))))(((......)))...... ( -40.90)
>DroSim_CAF1 3324 120 + 1
GCUGGAGUUGGAGCUGGAGCUGGAGGUGAAGUUGGAGCCGAGGUGGAGGUCCAACUAAGCCUCGGGCAACGGCUUCAGCUCCUUUAUCUGCUUGAUCAGAUAGGCCUUCUCGUCGUUGAA
((((((((((((((((..(((.(((((..(((((((.((........)))))))))..))))).)))..)))))))))))))..((((((......)))))))))............... ( -59.50)
>DroEre_CAF1 3374 120 + 1
GCUGGAGUUGGAGCUGAAGUCGGAGCUGAAGUUGGAGCCGAGGUGGAGGUCCAACUAAGCCUCGGGCAGCGGCUUAAGCUCCUUUAUCUGCUUGAUCAGAUAGGCCUUCUCGUCGUUAAA
(((((((((.((((((..(((.(((((..(((((((.((........))))))))).)).))).)))..)))))).))))))..((((((......)))))))))............... ( -47.50)
>DroYak_CAF1 3401 108 + 1
GCUGGAGUUGGAGCU------------GAAGUUGGAGCCGAGGUGGAGGUCCAACUAAGCCUCGGGCAGCGGCUUCAGCUCCUUUAUCUGCUUGAUCAGAUAGGCCUUCUCAUCGUUGAA
...((((..((((((------------(((((((..((((((((..((......))..))))).)))..)))))))))))))((((((((......)))))))).))))(((....))). ( -47.50)
>consensus
GCUGGAGUU____________GGAG_UGAAGUUGGAGCCGAGGUGGAGGUCCAACUAAGCCUCGGGCAGCGGCUUCAGCUCCUUUAUCUGCUUGAUCAGAUAGGCCUUCUCGUCGUUGAA
.....................((((.((((((((..((((((((..((......))..))))).)))..)))))))).))))((((((((......))))))))................ (-24.85 = -28.52 +   3.67)

alignment

secondary structure

dotplot

Window 9

Location	16,579,366 – 16,579,474
Length	108
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.72
Mean single sequence MFE	-36.77
Consensus MFE	-23.15
Energy contribution	-23.43
Covariance contribution	0.28
Combinations/Pair	1.12
Mean z-score	-2.82
Structure conservation index	0.63
SVM decision value	1.24
SVM RNA-class probability	0.934762
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16579366 108 - 23771897
UUCAACGACGAGAAGGCCUAUCUGAUCAAGCAGAUAAAGGAGCUGAAGCCGCUGCCCGAGGCUUAGUUGGACCUCCACCUCGGCUCCAACUUCAGCUCC------------AACUCCAGC
.........(((......((((((......))))))..((((((((((..(..(((.((((......(((....))))))))))..)..))))))))))------------..))).... ( -38.90)
>DroPse_CAF1 3191 89 - 1
UUCAACGACGAGAAGGCCUAUCUGAUUAAGCAGAUAAAGGAGCUGAAACCGCUGCCCGAGGCCUAGUUGACCAUCGACGGAUGGUC-AA------------------------------U
.............(((((((((((......)))))...(((((.......))).))..)))))).((((((((((....)))))))-))------------------------------) ( -32.30)
>DroSec_CAF1 3308 102 - 1
UUCAACGACGAGAAGGCCUAUCUGAUCAAGCAGAUAAAGGAGCUGAAGCCGCUGCCCGAGGCUUAGUUGGACCUCCACCUCGGCUCCAACUUCACCUCCAA------------------C
......((.(.((((...((((((......))))))..((((((((((((.(.....).)))))((.(((....))).)))))))))..)))).).))...------------------. ( -32.00)
>DroSim_CAF1 3324 120 - 1
UUCAACGACGAGAAGGCCUAUCUGAUCAAGCAGAUAAAGGAGCUGAAGCCGUUGCCCGAGGCUUAGUUGGACCUCCACCUCGGCUCCAACUUCACCUCCAGCUCCAGCUCCAACUCCAGC
.........(((......((((((......))))))..(((((((.(((.(......((((...(((((((((........)).)))))))...))))).))).)))))))..))).... ( -41.10)
>DroEre_CAF1 3374 120 - 1
UUUAACGACGAGAAGGCCUAUCUGAUCAAGCAGAUAAAGGAGCUUAAGCCGCUGCCCGAGGCUUAGUUGGACCUCCACCUCGGCUCCAACUUCAGCUCCGACUUCAGCUCCAACUCCAGC
...........((((...((((((......))))))..((((((((((((.(.....).))))))((((((((........)).))))))...))))))..)))).(((........))) ( -37.70)
>DroYak_CAF1 3401 108 - 1
UUCAACGAUGAGAAGGCCUAUCUGAUCAAGCAGAUAAAGGAGCUGAAGCCGCUGCCCGAGGCUUAGUUGGACCUCCACCUCGGCUCCAACUUC------------AGCUCCAACUCCAGC
.........(((......((((((......))))))..((((((((((..(..(((.((((......(((....))))))))))..)..))))------------))))))..))).... ( -38.60)
>consensus
UUCAACGACGAGAAGGCCUAUCUGAUCAAGCAGAUAAAGGAGCUGAAGCCGCUGCCCGAGGCUUAGUUGGACCUCCACCUCGGCUCCAACUUCA_CUCC____________AACUCCAGC
.............(((((((((((......)))))...(((((.......))).))..))))))(((((((((........)).)))))))............................. (-23.15 = -23.43 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:13:21 2006