Locus 1216

Sequence ID	3R_DroMel_CAF1
Location	3,665,261 – 3,665,373
Length	112
Max. P	0.949860

overview

Window 6

Location	3,665,261 – 3,665,373
Length	112
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	88.30
Mean single sequence MFE	-32.02
Consensus MFE	-23.12
Energy contribution	-25.56
Covariance contribution	2.44
Combinations/Pair	1.09
Mean z-score	-2.16
Structure conservation index	0.72
SVM decision value	0.64
SVM RNA-class probability	0.806889
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3665261 112 + 27905053
GCAUCAAUUAUGCAAGAUGAAGCUCGACUUCUGUUAAUUUCGCACCACACCACGCGGCGUAUACGUAAUGCGCAAUUCGAUCGACUGCCGUUCUCCCAUGCAAAUUGAGCAA
((.((((((.(((((((((.((.((((.............(((..........)))((((((.....)))))).......))))))..)).)))....)))))))))))).. ( -25.60)
>DroSec_CAF1 23937 112 + 1
GCAUCAAUUAUGCAAGAUGAAGCUCGACUUCUGUUAAUUUCGCAUCACACCACGCGGCGUAUACGUAAUGCGCAAUUCGAGCGACUGCCGAGUUCCCUUGCAAAUUGAGCAA
((.((((((.((((((.....((((((.............(((..........)))((((((.....))))))...))))))((((....))))..)))))))))))))).. ( -35.30)
>DroSim_CAF1 26171 112 + 1
GCAUCAAUUAUGCAAGAUGAAGCUCGACUUCUGUUAAUUUCGCAUCACACCACGCGGCGUAUACGUAAUGCGCAAUUCGAGCGACUGCCGAGUUCCCUUGCAAAUUGAGCAA
((.((((((.((((((.....((((((.............(((..........)))((((((.....))))))...))))))((((....))))..)))))))))))))).. ( -35.30)
>DroEre_CAF1 23092 105 + 1
GCAUCAAUUAUGCAAGAUGAAGCUCGACCUUUGUUAAUUUCGCACCAGACCACGCGGCGUAUGCUUAAUGCGCAAUUCGCGCGUCUGCCGAGCA-------AAUUUGAACAA
((((.....))))........(((((.....(((.......))).(((((..((((((((((.....))))))....)))).))))).))))).-------........... ( -28.80)
>DroYak_CAF1 15366 106 + 1
GCAUCAAUUAUGCAAGAUGAAGCUCGACUUCUGUUAAUUUUGCACAACACCACGCGGCGU------AAUGCGCAAUUCGAGCAUCUGCCGAGCUCCCUUGCAAAUUGAGCAA
((.((((((.((((((..((.(((((.(...((((....((((.((((.((....)).))------..)).))))....))))...).))))))).)))))))))))))).. ( -35.10)
>consensus
GCAUCAAUUAUGCAAGAUGAAGCUCGACUUCUGUUAAUUUCGCACCACACCACGCGGCGUAUACGUAAUGCGCAAUUCGAGCGACUGCCGAGCUCCCUUGCAAAUUGAGCAA
((.((((((.((((((....((((((.(...((((.....(((..........)))((((((.....))))))......))))...).))))))..)))))))))))))).. (-23.12 = -25.56 +   2.44)

alignment

secondary structure

dotplot

Window 7

Location	3,665,261 – 3,665,373
Length	112
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	88.30
Mean single sequence MFE	-37.78
Consensus MFE	-28.21
Energy contribution	-31.21
Covariance contribution	3.00
Combinations/Pair	1.05
Mean z-score	-2.53
Structure conservation index	0.75
SVM decision value	1.40
SVM RNA-class probability	0.949860
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3665261 112 - 27905053
UUGCUCAAUUUGCAUGGGAGAACGGCAGUCGAUCGAAUUGCGCAUUACGUAUACGCCGCGUGGUGUGGUGCGAAAUUAACAGAAGUCGAGCUUCAUCUUGCAUAAUUGAUGC
..((((((((((((..((((..((((..((.....((((.((((((((...((((...))))..)))))))).))))....)).))))..))))....)))).)))))).)) ( -34.50)
>DroSec_CAF1 23937 112 - 1
UUGCUCAAUUUGCAAGGGAACUCGGCAGUCGCUCGAAUUGCGCAUUACGUAUACGCCGCGUGGUGUGAUGCGAAAUUAACAGAAGUCGAGCUUCAUCUUGCAUAAUUGAUGC
..((((((((((((((((((((((((..((.....((((.((((((((...((((...))))..)))))))).))))....)).)))))).))).))))))).)))))).)) ( -41.10)
>DroSim_CAF1 26171 112 - 1
UUGCUCAAUUUGCAAGGGAACUCGGCAGUCGCUCGAAUUGCGCAUUACGUAUACGCCGCGUGGUGUGAUGCGAAAUUAACAGAAGUCGAGCUUCAUCUUGCAUAAUUGAUGC
..((((((((((((((((((((((((..((.....((((.((((((((...((((...))))..)))))))).))))....)).)))))).))).))))))).)))))).)) ( -41.10)
>DroEre_CAF1 23092 105 - 1
UUGUUCAAAUU-------UGCUCGGCAGACGCGCGAAUUGCGCAUUAAGCAUACGCCGCGUGGUCUGGUGCGAAAUUAACAAAGGUCGAGCUUCAUCUUGCAUAAUUGAUGC
...........-------.(((((((....((((.....)))).....((((..(((....)))...)))).............)))))))..((((..........)))). ( -28.40)
>DroYak_CAF1 15366 106 - 1
UUGCUCAAUUUGCAAGGGAGCUCGGCAGAUGCUCGAAUUGCGCAUU------ACGCCGCGUGGUGUUGUGCAAAAUUAACAGAAGUCGAGCUUCAUCUUGCAUAAUUGAUGC
..((((((((((((((((((((((((...((......(((((((..------(((((....))))))))))))......))...))))))))))..)))))).)))))).)) ( -43.80)
>consensus
UUGCUCAAUUUGCAAGGGAGCUCGGCAGUCGCUCGAAUUGCGCAUUACGUAUACGCCGCGUGGUGUGGUGCGAAAUUAACAGAAGUCGAGCUUCAUCUUGCAUAAUUGAUGC
..((((((((((((((((((((((((.........((((.(((((......((((((....))))))))))).)))).......))))))))))..)))))).)))))).)) (-28.21 = -31.21 +   3.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:03:50 2006