Locus 3189

Sequence ID	3R_DroMel_CAF1
Location	8,461,139 – 8,461,255
Length	116
Max. P	0.941549

overview

Window 8

Location	8,461,139 – 8,461,255
Length	116
Sequences	3
Columns	116
Reading direction	forward
Mean pairwise identity	98.85
Mean single sequence MFE	-45.03
Consensus MFE	-45.02
Energy contribution	-44.80
Covariance contribution	-0.22
Combinations/Pair	1.02
Mean z-score	-1.56
Structure conservation index	1.00
SVM decision value	0.36
SVM RNA-class probability	0.703069
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8461139 116 + 27905053
AGCGUUGCACUUCUUGGGUCACUCGCAGGGAUGCACCACGCUGGUGGUGCUCCUCAGCAUGCGACCGGAGUACAACAAGUUGGUCAAGACCGCAGUCCUAUUAGCUCCGGCUGUCU
.((((((.(((((...((((.(..((.((((.(((((((....)))))))))))..))..).))))))))).)))).....(((....)))))........((((....))))... ( -43.90)
>DroSec_CAF1 7040 116 + 1
AGCGUUGCACUUCUUGGGUCACUCGCAGGGAUGCACCACGCCGGUGGUGCUCCUCAGCAUGCGACCGGAGUACAACAAGUUGGUCAAGACCGCAGUCCUACUAGCUCCGGCUGUCU
(((((((.(((((...((((.(..((.((((.(((((((....)))))))))))..))..).))))))))).)))).(((((((...(((....)))..)))))))...))).... ( -45.60)
>DroSim_CAF1 7073 116 + 1
AGCGUUGCACUUCUUGGGUCACUCGCAGGGAUGCACCACGCUGGUGGUGCUCCUCAGCAUGCGACCGGAGUACAACAAGUUGGUCAAGACCGCAGUCCUACUAGCUCCGGCUGUCU
(((((((.(((((...((((.(..((.((((.(((((((....)))))))))))..))..).))))))))).)))).(((((((...(((....)))..)))))))...))).... ( -45.60)
>consensus
AGCGUUGCACUUCUUGGGUCACUCGCAGGGAUGCACCACGCUGGUGGUGCUCCUCAGCAUGCGACCGGAGUACAACAAGUUGGUCAAGACCGCAGUCCUACUAGCUCCGGCUGUCU
(((((((.(((((...((((.(..((.((((.(((((((....)))))))))))..))..).))))))))).)))).(((((((...(((....)))..)))))))...))).... (-45.02 = -44.80 +  -0.22)

alignment

secondary structure

dotplot

Window 9

Location	8,461,139 – 8,461,255
Length	116
Sequences	3
Columns	116
Reading direction	reverse
Mean pairwise identity	98.85
Mean single sequence MFE	-47.60
Consensus MFE	-47.60
Energy contribution	-47.60
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.17
Structure conservation index	1.00
SVM decision value	1.32
SVM RNA-class probability	0.941549
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8461139 116 - 27905053
AGACAGCCGGAGCUAAUAGGACUGCGGUCUUGACCAACUUGUUGUACUCCGGUCGCAUGCUGAGGAGCACCACCAGCGUGGUGCAUCCCUGCGAGUGACCCAAGAAGUGCAACGCU
.....((((.((((....)).)).))))............(((((((((.((((((.(((.(.((((((((((....))))))).)))).))).))))))...).))))))))... ( -47.60)
>DroSec_CAF1 7040 116 - 1
AGACAGCCGGAGCUAGUAGGACUGCGGUCUUGACCAACUUGUUGUACUCCGGUCGCAUGCUGAGGAGCACCACCGGCGUGGUGCAUCCCUGCGAGUGACCCAAGAAGUGCAACGCU
.....((((.((((....)).)).))))............(((((((((.((((((.(((.(.((((((((((....))))))).)))).))).))))))...).))))))))... ( -47.60)
>DroSim_CAF1 7073 116 - 1
AGACAGCCGGAGCUAGUAGGACUGCGGUCUUGACCAACUUGUUGUACUCCGGUCGCAUGCUGAGGAGCACCACCAGCGUGGUGCAUCCCUGCGAGUGACCCAAGAAGUGCAACGCU
.....((((.((((....)).)).))))............(((((((((.((((((.(((.(.((((((((((....))))))).)))).))).))))))...).))))))))... ( -47.60)
>consensus
AGACAGCCGGAGCUAGUAGGACUGCGGUCUUGACCAACUUGUUGUACUCCGGUCGCAUGCUGAGGAGCACCACCAGCGUGGUGCAUCCCUGCGAGUGACCCAAGAAGUGCAACGCU
.....((((.((((....)).)).))))............(((((((((.((((((.(((.(.((((((((((....))))))).)))).))).))))))...).))))))))... (-47.60 = -47.60 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:55:18 2006