Locus 6679

Sequence ID	3R_DroMel_CAF1
Location	17,563,287 – 17,563,398
Length	111
Max. P	0.992574

overview

Window 0

Location	17,563,287 – 17,563,398
Length	111
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.25
Mean single sequence MFE	-44.78
Consensus MFE	-40.58
Energy contribution	-41.38
Covariance contribution	0.80
Combinations/Pair	1.11
Mean z-score	-1.46
Structure conservation index	0.91
SVM decision value	1.15
SVM RNA-class probability	0.923477
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17563287 111 + 27905053
GGCAGCCACCAUGUUUCGAUAGUCGGCUACUCCGCGAAACAGGCUGAGAAACAUGUUGGUGAACAUGGUAACCUCAUCCUGGUUGAGAGGAUUAAGCUGCUGCUGCAGUGG---------
..((((((...(((((((..(((.....)))...)))))))((.((((...((((((....)))))).....)))).))))))))..........(((((....)))))..--------- ( -34.20)
>DroSec_CAF1 2509 120 + 1
GGCAGCCACCAUGUUUCGAUAGUCGGCUACUCCGCGGAACAGGCUGAGAAACAUGUUGGUGAACAUGGUAACCUCGUCCUGGUUGAGAGGAUUAUGCUGCUGCUGCAGCGGUGGCUUGGA
...(((((((.(.(((((((..((.((......)).)).((((.((((...((((((....)))))).....)))).))))))))))).).....(((((....)))))))))))).... ( -47.30)
>DroSim_CAF1 2525 120 + 1
GGCAGCCACCAUGUUUCGAUAGUCGGCUACUCCGCGGAACAGGCUGAGAAACAUGUUGGUGAACAUGGUAACCUCAUCCUGAUUGAGAGGAUUCAGCUGCUGCUGCAGCGGUGGCUUAGA
...(((((((.(.(((((((..((.((......)).)).((((.((((...((((((....)))))).....)))).))))))))))).).....(((((....)))))))))))).... ( -47.70)
>DroEre_CAF1 5297 120 + 1
GGCGGCCACCAUGUUUCGAUAGUCGGCUACUCCGCGGAACAGGCUGAGGAACAUGUUGGUGAACAUGGUGACCUCGUCCUGGUUGAGCGGAUUCAGCUGCUGCUGCAGCGGCGGCUUGGA
.(..(((((.((......)).)).)))..)(((((....((((.(((((..((((((....))))))....))))).)))).....)))))((((((((((((....)))))))).)))) ( -49.80)
>DroYak_CAF1 5460 120 + 1
GGCGGCCACCAUGUUUCGAUAGUCGGCUACUCCGCGGAACAGGCUGAGAAACAUGUUGGUGAACAUGGUUACCUCGUCCUGGUUGAGAGGAUUCAGCUGCUGCUGCAGUGGUGGCUUGGA
...(((((((.(.(((((((..((.((......)).)).((((.((((...((((((....)))))).....)))).))))))))))).).....(((((....)))))))))))).... ( -44.90)
>consensus
GGCAGCCACCAUGUUUCGAUAGUCGGCUACUCCGCGGAACAGGCUGAGAAACAUGUUGGUGAACAUGGUAACCUCGUCCUGGUUGAGAGGAUUCAGCUGCUGCUGCAGCGGUGGCUUGGA
...(((((((.(.(((((((..((.((......)).)).((((.((((...((((((....)))))).....)))).))))))))))).).....(((((....)))))))))))).... (-40.58 = -41.38 +   0.80)

alignment

secondary structure

dotplot

Window 1

Location	17,563,287 – 17,563,398
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.25
Mean single sequence MFE	-40.32
Consensus MFE	-33.42
Energy contribution	-34.06
Covariance contribution	0.64
Combinations/Pair	1.03
Mean z-score	-2.35
Structure conservation index	0.83
SVM decision value	2.34
SVM RNA-class probability	0.992574
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17563287 111 - 27905053
---------CCACUGCAGCAGCAGCUUAAUCCUCUCAACCAGGAUGAGGUUACCAUGUUCACCAACAUGUUUCUCAGCCUGUUUCGCGGAGUAGCCGACUAUCGAAACAUGGUGGCUGCC
---------...(((((((....))).............((((.(((((....((((((....))))))..))))).))))....)))).((((((.(((((......))))))))))). ( -35.20)
>DroSec_CAF1 2509 120 - 1
UCCAAGCCACCGCUGCAGCAGCAGCAUAAUCCUCUCAACCAGGACGAGGUUACCAUGUUCACCAACAUGUUUCUCAGCCUGUUCCGCGGAGUAGCCGACUAUCGAAACAUGGUGGCUGCC
....((((((((((((....))))).........((...((((..((((....((((((....))))))..))))..)))).....(((.....)))......)).....)))))))... ( -39.60)
>DroSim_CAF1 2525 120 - 1
UCUAAGCCACCGCUGCAGCAGCAGCUGAAUCCUCUCAAUCAGGAUGAGGUUACCAUGUUCACCAACAUGUUUCUCAGCCUGUUCCGCGGAGUAGCCGACUAUCGAAACAUGGUGGCUGCC
....(((((((((((((((....)))...(((.(.....((((.(((((....((((((....))))))..))))).))))....).))))))))((.....))......)))))))... ( -42.10)
>DroEre_CAF1 5297 120 - 1
UCCAAGCCGCCGCUGCAGCAGCAGCUGAAUCCGCUCAACCAGGACGAGGUCACCAUGUUCACCAACAUGUUCCUCAGCCUGUUCCGCGGAGUAGCCGACUAUCGAAACAUGGUGGCCGCC
.....((((((((((((((....)))...(((((..(((.(((..((((....((((((....))))))..))))..))))))..))))))))))((.....))......)))))).... ( -46.30)
>DroYak_CAF1 5460 120 - 1
UCCAAGCCACCACUGCAGCAGCAGCUGAAUCCUCUCAACCAGGACGAGGUAACCAUGUUCACCAACAUGUUUCUCAGCCUGUUCCGCGGAGUAGCCGACUAUCGAAACAUGGUGGCCGCC
.....(((((((((((.(.(((((((((..((((((......)).))))....((((((....))))))....)))).)))))).))))......((.....)).....))))))).... ( -38.40)
>consensus
UCCAAGCCACCGCUGCAGCAGCAGCUGAAUCCUCUCAACCAGGACGAGGUUACCAUGUUCACCAACAUGUUUCUCAGCCUGUUCCGCGGAGUAGCCGACUAUCGAAACAUGGUGGCUGCC
...........(((((....)))))....(((.(.....((((..((((....((((((....))))))..))))..))))....).)))((((((.(((((......))))))))))). (-33.42 = -34.06 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:27:25 2006