Locus 9643

Sequence ID	3R_DroMel_CAF1
Location	25,492,030 – 25,492,134
Length	104
Max. P	0.837736

overview

Window 7

Location	25,492,030 – 25,492,134
Length	104
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	74.95
Mean single sequence MFE	-22.11
Consensus MFE	-10.18
Energy contribution	-11.54
Covariance contribution	1.36
Combinations/Pair	1.32
Mean z-score	-2.07
Structure conservation index	0.46
SVM decision value	0.74
SVM RNA-class probability	0.837736
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25492030 104 + 27905053
CUUCACCAGCUGCAGUCAGCUGGUUUUCGACCGGGUUUUCACUACUACCACGCUUGAGUAAGUGAAUCCUAUGUGUGUAAUCCACUGCAAUUUCUUUAACAAUU
....((((((((....))))))))........(((..(((((((((..........))).)))))).))).((((((.....))).)))............... ( -24.10)
>DroSec_CAF1 173137 100 + 1
CUUCACCAGCUGCUCUCAGCUGGUUUUCGACCGGGUUUUCACCACUACCACUCUUGAGUAAGUGAAUCCUAUGUGUG-AAUACACUACAAUUUAU---ACAUUU
....((((((((....))))))))........(((..(((((...(((((....)).))).))))).)))(((((((-(((........))))))---)))).. ( -26.70)
>DroSim_CAF1 175176 101 + 1
CUUUACCAGCUGCACUCAGCUGGUUUUCGACCGGGUUUACACCACUACCACUCUUGAGUAAGUGAAUCCUAUGCG-A-AUUUCACUAUAAUUCCU-UAACAUUU
....((((((((....)))))))).((((...((((((((...(((..........)))..))))))))....))-)-)................-........ ( -23.40)
>DroEre_CAF1 180444 101 + 1
CUUCACCAGCUGCACUCAGCUGAUUUUCGACAGGGUGUUCACCACCACCACUUUGGAGUAAGUGAAUCCUAUGUGU--CACCCACUAAAAUUCUU-AAAAAUCU
......((((((....))))))..........(((((..(((......(((((......)))))........))).--)))))............-........ ( -22.84)
>DroYak_CAF1 188143 101 + 1
CUUUACCAGCUGCUCUCAGCUAGUUUUCGACCGGGUUUACACCACCACCACGCUAGAGUAAGUGCAUCCUUUGUGU--GACCCACUAAAUGUCUU-UAAAAUAU
....((.(((((....))))).))........(((((.((((........((((......))))........))))--)))))............-........ ( -19.39)
>DroAna_CAF1 182746 99 + 1
CUUCACCAGCUGUAAACAAUUGAUUUUUGAUAGAGUCUUCUCCAGCACGUCAAUAGAGUAAGG--AGCUUAUCCUU--AAACCUAUAAAAAUCUC-AAAAAUAA
......(((.((....)).)))((((((((..(((....)))..........((((..(((((--(.....)))))--)...)))).......))-)))))).. ( -16.20)
>consensus
CUUCACCAGCUGCACUCAGCUGGUUUUCGACCGGGUUUUCACCACCACCACUCUUGAGUAAGUGAAUCCUAUGUGU__AAUCCACUAAAAUUCUU_UAAAAUUU
....((((((((....))))))))........(((((..(((......(((..........)))........)))...)))))..................... (-10.18 = -11.54 +   1.36)

alignment

secondary structure

dotplot

Window 8

Location	25,492,030 – 25,492,134
Length	104
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	74.95
Mean single sequence MFE	-25.02
Consensus MFE	-16.42
Energy contribution	-16.03
Covariance contribution	-0.38
Combinations/Pair	1.41
Mean z-score	-1.18
Structure conservation index	0.66
SVM decision value	0.23
SVM RNA-class probability	0.642801
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25492030 104 - 27905053
AAUUGUUAAAGAAAUUGCAGUGGAUUACACACAUAGGAUUCACUUACUCAAGCGUGGUAGUAGUGAAAACCCGGUCGAAAACCAGCUGACUGCAGCUGGUGAAG
..........((.......(((.....))).....((.(((((((((.((....)))))..))))))...))..))....((((((((....)))))))).... ( -24.20)
>DroSec_CAF1 173137 100 - 1
AAAUGU---AUAAAUUGUAGUGUAUU-CACACAUAGGAUUCACUUACUCAAGAGUGGUAGUGGUGAAAACCCGGUCGAAAACCAGCUGAGAGCAGCUGGUGAAG
......---.....(((..(.((.((-(((.(((.....((((((......))))))..)))))))).)).)...)))..((((((((....)))))))).... ( -26.80)
>DroSim_CAF1 175176 101 - 1
AAAUGUUA-AGGAAUUAUAGUGAAAU-U-CGCAUAGGAUUCACUUACUCAAGAGUGGUAGUGGUGUAAACCCGGUCGAAAACCAGCUGAGUGCAGCUGGUAAAG
...((.((-(((((((.(((((....-.-))).)).))))).))))..)).((.(((..((.......))))).))....((((((((....)))))))).... ( -26.20)
>DroEre_CAF1 180444 101 - 1
AGAUUUUU-AAGAAUUUUAGUGGGUG--ACACAUAGGAUUCACUUACUCCAAAGUGGUGGUGGUGAACACCCUGUCGAAAAUCAGCUGAGUGCAGCUGGUGAAG
........-..(((((((((((....--.))).))))))))((((......))))((..(.(((....))))..))....((((((((....)))))))).... ( -28.00)
>DroYak_CAF1 188143 101 - 1
AUAUUUUA-AAGACAUUUAGUGGGUC--ACACAAAGGAUGCACUUACUCUAGCGUGGUGGUGGUGUAAACCCGGUCGAAAACUAGCUGAGAGCAGCUGGUAAAG
........-..(((.....(((.(((--........))).)))((((.(((.(.....).))).)))).....)))....((((((((....)))))))).... ( -25.80)
>DroAna_CAF1 182746 99 - 1
UUAUUUUU-GAGAUUUUUAUAGGUUU--AAGGAUAAGCU--CCUUACUCUAUUGACGUGCUGGAGAAGACUCUAUCAAAAAUCAAUUGUUUACAGCUGGUGAAG
........-..(((((((((((((((--(((((.....)--)))).(((((.........))))).)))).)))).))))))).....(((((.....))))). ( -19.10)
>consensus
AAAUGUUA_AAGAAUUUUAGUGGAUU__ACACAUAGGAUUCACUUACUCAAGAGUGGUAGUGGUGAAAACCCGGUCGAAAACCAGCUGAGUGCAGCUGGUGAAG
...................(((.......)))...((..(((((((((.......))))..)))))...)).........((((((((....)))))))).... (-16.42 = -16.03 +  -0.38)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:39:00 2006