Locus 35

Sequence ID	X_DroMel_CAF1
Location	135,335 – 135,466
Length	131
Max. P	0.929147

overview

Window 2

Location	135,335 – 135,430
Length	95
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	91.93
Mean single sequence MFE	-23.32
Consensus MFE	-18.62
Energy contribution	-18.90
Covariance contribution	0.28
Combinations/Pair	1.10
Mean z-score	-1.41
Structure conservation index	0.80
SVM decision value	0.04
SVM RNA-class probability	0.553408
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 135335 95 + 22224390
UUGUAGGCUGGCCGUUGCCCUGUUCCAAUUGGAACUGUACUUUUAUAGCCCACCCCAAUACA----ACCUAUAACAGUGGCGUCCUUCACUAUUGGAAC
..((.(((((((....)))..(((((....)))))...........)))).)).(((((...----.........(((((......))))))))))... ( -20.80)
>DroSec_CAF1 7500 95 + 1
UUGUAGGCUGGCCGUUGCCCUGUUCCAAUUGGAACUGUACUUUUAUAGCCCACCCCAAUACA----ACCUAUAACAGUGGCGUCUUUCACUAUUGGAAC
..((.(((((((....)))..(((((....)))))...........)))).)).(((((...----.........(((((......))))))))))... ( -20.80)
>DroSim_CAF1 7279 95 + 1
UUGUAGGCUGGCCGUUGCCCUGUUCCAAUUGGAACUGUACUUUUAUAGCCCACCCCAAUAUA----ACCUAUAACAGUGGCGUCUUUCACUAUUGGAAC
..((.(((((((....)))..(((((....)))))...........)))).)).(((((...----.........(((((......))))))))))... ( -20.80)
>DroEre_CAF1 6545 95 + 1
AUGUAGGGUGGCCCUUGCCCUGUUCCAAUUGGAACUGUACUUUUAUAGUCCACCCCAAUAAA----ACCUAUCACAGUGGCGUCCUUCACCAUUGGAAC
.....((((((..........(((((....)))))...(((.....))))))))).......----.....((.((((((.(.....).)))))))).. ( -24.90)
>DroYak_CAF1 6797 98 + 1
AUGUAGGGUGGCCCUUGUCCUGUUCCAAUUGGAACUGUACUUUCAUAG-CCACCCCAAUAGAACGAACCCAUCACAGUGGCGUCCUUCACUAUUGGAAC
.....(((((((....((.(.(((((....))))).).)).......)-))))))((((((...(.((((((....)))).)).)....)))))).... ( -29.30)
>consensus
UUGUAGGCUGGCCGUUGCCCUGUUCCAAUUGGAACUGUACUUUUAUAGCCCACCCCAAUACA____ACCUAUAACAGUGGCGUCCUUCACUAUUGGAAC
.((((((..(((....)))..(((((....)))))................................)))))).((((((.(.....).)))))).... (-18.62 = -18.90 +   0.28)

alignment

secondary structure

dotplot

Window 3

Location	135,335 – 135,430
Length	95
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	91.93
Mean single sequence MFE	-30.68
Consensus MFE	-23.56
Energy contribution	-24.40
Covariance contribution	0.84
Combinations/Pair	1.04
Mean z-score	-2.31
Structure conservation index	0.77
SVM decision value	1.20
SVM RNA-class probability	0.929147
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 135335 95 - 22224390
GUUCCAAUAGUGAAGGACGCCACUGUUAUAGGU----UGUAUUGGGGUGGGCUAUAAAAGUACAGUUCCAAUUGGAACAGGGCAACGGCCAGCCUACAA
..(((((((((.....))(((.........)))----..)))))))(((((((...........(((((....)))))..(((....)))))))))).. ( -29.40)
>DroSec_CAF1 7500 95 - 1
GUUCCAAUAGUGAAAGACGCCACUGUUAUAGGU----UGUAUUGGGGUGGGCUAUAAAAGUACAGUUCCAAUUGGAACAGGGCAACGGCCAGCCUACAA
..(((((((((.....))(((.........)))----..)))))))(((((((...........(((((....)))))..(((....)))))))))).. ( -29.40)
>DroSim_CAF1 7279 95 - 1
GUUCCAAUAGUGAAAGACGCCACUGUUAUAGGU----UAUAUUGGGGUGGGCUAUAAAAGUACAGUUCCAAUUGGAACAGGGCAACGGCCAGCCUACAA
..(((((((((.....))(((.........)))----..)))))))(((((((...........(((((....)))))..(((....)))))))))).. ( -29.50)
>DroEre_CAF1 6545 95 - 1
GUUCCAAUGGUGAAGGACGCCACUGUGAUAGGU----UUUAUUGGGGUGGACUAUAAAAGUACAGUUCCAAUUGGAACAGGGCAAGGGCCACCCUACAU
((..((.(((((.....))))).))..))....----.....((((((((.((......((...(((((....)))))...))...))))))))))... ( -29.30)
>DroYak_CAF1 6797 98 - 1
GUUCCAAUAGUGAAGGACGCCACUGUGAUGGGUUCGUUCUAUUGGGGUGG-CUAUGAAAGUACAGUUCCAAUUGGAACAGGACAAGGGCCACCCUACAU
....((((((....((((.(((......)))))))...))))))((((((-((......((...(((((....)))))...))...))))))))..... ( -35.80)
>consensus
GUUCCAAUAGUGAAGGACGCCACUGUUAUAGGU____UGUAUUGGGGUGGGCUAUAAAAGUACAGUUCCAAUUGGAACAGGGCAACGGCCAGCCUACAA
..(((((((.........(((.........)))......)))))))(((((((...........(((((....)))))..(((....)))))))))).. (-23.56 = -24.40 +   0.84)

alignment

secondary structure

dotplot

Window 4

Location	135,375 – 135,466
Length	91
Sequences	5
Columns	97
Reading direction	reverse
Mean pairwise identity	91.43
Mean single sequence MFE	-28.26
Consensus MFE	-21.46
Energy contribution	-21.22
Covariance contribution	-0.24
Combinations/Pair	1.11
Mean z-score	-1.92
Structure conservation index	0.76
SVM decision value	0.55
SVM RNA-class probability	0.778950
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 135375 91 - 22224390
UGGCUAGCUCACAGCAACCUUCAUUGGGUUU--UUCCAGUUCCAAUAGUGAAGGACGCCACUGUUAUAGGU----UGUAUUGGGGUGGGCUAUAAAA
(((((.((((.(((((((((..((((((...--.))))))...(((((((........)))))))..))))----)))..)))))).)))))..... ( -29.60)
>DroSec_CAF1 7540 91 - 1
UGGCUAGCUCACAGCAACCUUCAUUGGGUUU--UUCCAGUUCCAAUAGUGAAAGACGCCACUGUUAUAGGU----UGUAUUGGGGUGGGCUAUAAAA
(((((.((((.(((((((((..((((((...--.))))))...(((((((........)))))))..))))----)))..)))))).)))))..... ( -29.60)
>DroSim_CAF1 7319 91 - 1
UGGCUAGCUCACAGCAACCUUCAUUGGGUUU--UUCCAGUUCCAAUAGUGAAAGACGCCACUGUUAUAGGU----UAUAUUGGGGUGGGCUAUAAAA
....((((((((...(((((.....))))).--.((((((.(((((((((........)))))))...)).----...))))))))))))))..... ( -27.60)
>DroEre_CAF1 6585 93 - 1
UGGCUAGCUCGCAGCAACCUUCAUUGGGUUUUUUUUCAGUUCCAAUGGUGAAGGACGCCACUGUGAUAGGU----UUUAUUGGGGUGGACUAUAAAA
((((((.((((....(((((((((((((((((((.(((.......))).))))))).)))..)))).))))----)....)))).))).)))..... ( -24.70)
>DroYak_CAF1 6837 94 - 1
UGGCUAGCUCGCAGCAACCUUCAAUGGGUUU--UUUCAGUUCCAAUAGUGAAGGACGCCACUGUGAUGGGUUCGUUCUAUUGGGGUGG-CUAUGAAA
..(((.(....))))..((((((.((((...--.......))))....))))))..((((((.(((((((.....))))))).)))))-)....... ( -29.80)
>consensus
UGGCUAGCUCACAGCAACCUUCAUUGGGUUU__UUCCAGUUCCAAUAGUGAAGGACGCCACUGUUAUAGGU____UGUAUUGGGGUGGGCUAUAAAA
....((((((((...(((((.....)))))....((((((.((.((((((........))))))....))........))))))))))))))..... (-21.46 = -21.22 +  -0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:31:57 2006