Locus 7014

Sequence ID	3R_DroMel_CAF1
Location	18,477,627 – 18,477,764
Length	137
Max. P	0.915417

overview

Window 7

Location	18,477,627 – 18,477,724
Length	97
Sequences	4
Columns	107
Reading direction	forward
Mean pairwise identity	78.53
Mean single sequence MFE	-33.07
Consensus MFE	-20.08
Energy contribution	-22.20
Covariance contribution	2.12
Combinations/Pair	1.03
Mean z-score	-1.75
Structure conservation index	0.61
SVM decision value	0.05
SVM RNA-class probability	0.556327
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18477627 97 + 27905053
UGAAUGCUUACGCGUCGUAUGCGUAAUGUCGACGAAGUGGAUAUUCCGCUUUCGGUGGCACGGG----------GGUUGGUUUGAAAGUGCUGCUGCGACAAGUAAG
....(((((((((((...))))))).(((((..(((((((.....)))))))(((..((((...----------.............))))..)))))))))))).. ( -33.49)
>DroSec_CAF1 32792 106 + 1
UGAAUGCUUACGCGUCGUAUCCGUAAUGUCGACGAAGUGGAUAUUCCGCUUUGGAUGGCGGGGGUUGGAUGGGUGGCUG-GUUGAAAGUGCUGCUGCGACAAGUAAG
......(((((..((((((((((...(((((.((((((((.....))))))))..))))).....))))).((..((..-.........))..)))))))..))))) ( -37.40)
>DroSim_CAF1 32506 107 + 1
UGAAUGCUUACGCGUCGUAUGCGUAAUGUCGACGAAGUGGAUAUUCCGCUUUGGGUGGCAGGGGUUGGAUGGGUGGUUGGGUUGAAAGUGCUGCUGCGACAAGUAAG
....(((((((((((...))))))).((((..((((((((.....)))))))).(..((((.(.((.(((..(....)..)))..)).).))))..))))))))).. ( -34.20)
>DroEre_CAF1 33329 90 + 1
UGAAUGCUUACGCGGCGUAUGCGUAAUGUCGACGAACUGGAUAUGCCGUUUGGCAUG-----AA---AGUGGGUGAA---------GGCGGUGCUGCGACAAGUAAG
....(((((.(((((((....(((....((.((..(((...((((((....))))))-----..---)))..)))).---------.))).)))))))..))))).. ( -27.20)
>consensus
UGAAUGCUUACGCGUCGUAUGCGUAAUGUCGACGAAGUGGAUAUUCCGCUUUGGAUGGCAGGGG___GAUGGGUGGUUG_GUUGAAAGUGCUGCUGCGACAAGUAAG
....((((((((((.....)))))).(((((.((((((((.....))))))))..................((((((............)))))).))))))))).. (-20.08 = -22.20 +   2.12)

alignment

secondary structure

dotplot

Window 8

Location	18,477,667 – 18,477,764
Length	97
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	75.31
Mean single sequence MFE	-22.87
Consensus MFE	-15.88
Energy contribution	-16.08
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.70
Structure conservation index	0.69
SVM decision value	1.10
SVM RNA-class probability	0.915417
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18477667 97 - 27905053
UGUCUGUACAAUUGCGUGCCAAGGAGCAAAUAACAUUUUGCUUACUUGUCGCAGCAGCACU-----UUCAAACCAACC------------CC--CGUGCCACCGAAAG----CGGAAUAU
..(((((.....((((((.(((((((((((......))))))).)))).))).)))((((.-----............------------..--.))))........)----)))).... ( -25.19)
>DroSec_CAF1 32832 106 - 1
UGUCUGUACAAUUGCGUGCCAAGGAGCAAAUAUCAUUUUGCUUACUUGUCGCAGCAGCACU-----UUCAAC-CAGCCACCCAUCCAA--CC--CCCGCCAUCCAAAG----CGGAAUAU
.((((((.....((((...(((((((((((......))))))).)))).)))))))).)).-----......-...............--..--.((((........)----)))..... ( -24.70)
>DroSim_CAF1 32546 107 - 1
UGUCUGUACAAUUGCGUGCCAAGGAGCAAAUAACAUUUUGCUUACUUGUCGCAGCAGCACU-----UUCAACCCAACCACCCAUCCAA--CC--CCUGCCACCCAAAG----CGGAAUAU
.((((((.....((((...(((((((((((......))))))).)))).)))))))).)).-----......................--..--.((((........)----)))..... ( -22.50)
>DroEre_CAF1 33369 90 - 1
UGUCGGUACAAUUGCGUGCCAAGGAGCAAAUAGCAUUUUGCUUACUUGUCGCAGCACCGCC--------------UUCACCCACU-----UU-------CAUGCCAAA----CGGCAUAU
.(.((((....(((((...(((((((((((......))))))).)))).))))).)))).)--------------..........-----..-------.(((((...----.))))).. ( -26.00)
>DroYak_CAF1 34116 120 - 1
UGUCUGUACAAUUGCGUGCCAAGGAGCAAAUAACAUUUUACUUACUUGUCGCAGCACCGCACCACUUUCACCACAUUCACCCACCCAACCUGCCUGCACCACCCCAAAACAGCGGAAUAU
..(((((.....((((...(((((((.(((......))).))).)))).))))(((..(((.............................))).)))..............))))).... ( -15.95)
>consensus
UGUCUGUACAAUUGCGUGCCAAGGAGCAAAUAACAUUUUGCUUACUUGUCGCAGCAGCACU_____UUCAAC_CAACCACCCACCCAA__CC__CCCGCCACCCAAAG____CGGAAUAU
............((((((.(((((((((((......))))))).)))).))).)))................................................................ (-15.88 = -16.08 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:35:32 2006