Locus 724

Sequence ID	X_DroMel_CAF1
Location	1,986,408 – 1,986,528
Length	120
Max. P	0.967192

overview

Window 4

Location	1,986,408 – 1,986,528
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.22
Mean single sequence MFE	-48.03
Consensus MFE	-40.53
Energy contribution	-40.77
Covariance contribution	0.25
Combinations/Pair	1.09
Mean z-score	-1.82
Structure conservation index	0.84
SVM decision value	0.66
SVM RNA-class probability	0.814506
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1986408 120 + 22224390
UUGCUGAACCUGCUGCACCUGCUGGGUCUGUGUUGACCCAGUAGAUCCAGGACCCGUCGCCGCCUGGACCGCGCUACUGGUGGUAGUCACUUUCUGAACCACUUUCUGGGCCAGCUUGCC
..((((..((.((.((..((((((((((......)))))))))).((((((.(........)))))))..))))....((((((..(((.....)))))))))....))..))))..... ( -47.90)
>DroSec_CAF1 19946 120 + 1
UUGCUGAACCUGCUGCACCUGCUGGGUCUGUGUGGACCCAGCGGAUCCAGGACCCGUCGCCGCCUGGACCGCGCUACUGGUGGUAGUCACCUUCUGAACCACUUUCUGGGCCAGCUUGCC
..((((..((.((.((....(((((((((....)))))))))((.((((((.(........)))))))))))))....((((((..(((.....)))))))))....))..))))..... ( -50.00)
>DroEre_CAF1 9538 120 + 1
UUGCUGAACCUGCUGCACCUGCUGGGUCUGUGUAGACCCAGUGGAUCCAGGACCCGUCGCCGCCUGGACUGCGCUACUGGUGGUGGUCACCUUCUGAACCACUUUCUGGGCCAGCUUGCC
..((((..((.((.(((.(..((((((((....))))))))..).((((((.(........))))))).)))))....((.((((((((.....)).)))))).)).))..))))..... ( -48.20)
>DroYak_CAF1 20269 111 + 1
UUGCUGAACCU---------GCUGGGUCUGUGUCGACCCAGUGGAUCCAGGACCCGUCGCCGCCUGUACUGCGCUACUGGUGGUGGUCACCUUCUGAACCACUUUCUGGGUCAGCUUGCC
..(((((..(.---------.(((((((......)))))))..).(((((((......((((((.(((......))).))))))(((((.....)).)))...))))))))))))..... ( -46.00)
>consensus
UUGCUGAACCUGCUGCACCUGCUGGGUCUGUGUAGACCCAGUGGAUCCAGGACCCGUCGCCGCCUGGACCGCGCUACUGGUGGUAGUCACCUUCUGAACCACUUUCUGGGCCAGCUUGCC
..((((............((((((((((......)))))))))).((((((.(........)))))))..((.(....((((((..(((.....)))))))))....).))))))..... (-40.53 = -40.77 +   0.25)

alignment

secondary structure

dotplot

Window 5

Location	1,986,408 – 1,986,528
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	92.22
Mean single sequence MFE	-51.40
Consensus MFE	-42.96
Energy contribution	-45.02
Covariance contribution	2.06
Combinations/Pair	1.03
Mean z-score	-2.73
Structure conservation index	0.84
SVM decision value	1.61
SVM RNA-class probability	0.967192
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1986408 120 - 22224390
GGCAAGCUGGCCCAGAAAGUGGUUCAGAAAGUGACUACCACCAGUAGCGCGGUCCAGGCGGCGACGGGUCCUGGAUCUACUGGGUCAACACAGACCCAGCAGGUGCAGCAGGUUCAGCAA
.....((((..((.....((((((((.....)))..)))))..((.((((((((((((((....))...))))))))..(((((((......)))))))...)))).)).))..)))).. ( -52.90)
>DroSec_CAF1 19946 120 - 1
GGCAAGCUGGCCCAGAAAGUGGUUCAGAAGGUGACUACCACCAGUAGCGCGGUCCAGGCGGCGACGGGUCCUGGAUCCGCUGGGUCCACACAGACCCAGCAGGUGCAGCAGGUUCAGCAA
.....((((..((.....(((((.....((....)))))))..((.((((((((((((((....))...)))))))).((((((((......))))))))..)))).)).))..)))).. ( -58.10)
>DroEre_CAF1 9538 120 - 1
GGCAAGCUGGCCCAGAAAGUGGUUCAGAAGGUGACCACCACCAGUAGCGCAGUCCAGGCGGCGACGGGUCCUGGAUCCACUGGGUCUACACAGACCCAGCAGGUGCAGCAGGUUCAGCAA
.....((((..((.....((((((........)))))).....((.((((.(((((((((....))...)))))))...((((((((....))))))))...)))).)).))..)))).. ( -50.90)
>DroYak_CAF1 20269 111 - 1
GGCAAGCUGACCCAGAAAGUGGUUCAGAAGGUGACCACCACCAGUAGCGCAGUACAGGCGGCGACGGGUCCUGGAUCCACUGGGUCGACACAGACCCAGC---------AGGUUCAGCAA
.....(((((.((....((((((((((..(((....)))(((.....(((.((....)).)))...))).))))).)))))(((((......)))))...---------.)).))))).. ( -43.70)
>consensus
GGCAAGCUGGCCCAGAAAGUGGUUCAGAAGGUGACCACCACCAGUAGCGCAGUCCAGGCGGCGACGGGUCCUGGAUCCACUGGGUCAACACAGACCCAGCAGGUGCAGCAGGUUCAGCAA
.....(((((.((.....((((((((.....)))..)))))..((.((((((((((((((....))...))))))))..(((((((......)))))))...)))).)).)).))))).. (-42.96 = -45.02 +   2.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:52:07 2006