Locus 530

Sequence ID	2R_DroMel_CAF1
Location	2,818,479 – 2,818,573
Length	94
Max. P	0.972567

overview

Window 4

Location	2,818,479 – 2,818,573
Length	94
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	78.14
Mean single sequence MFE	-21.48
Consensus MFE	-14.13
Energy contribution	-15.13
Covariance contribution	1.00
Combinations/Pair	1.21
Mean z-score	-2.25
Structure conservation index	0.66
SVM decision value	1.70
SVM RNA-class probability	0.972567
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2818479 94 + 20766785
AUGUAACCCCCUGAAGUCUCCUGACCCUGGCACCAUUUACCAUCAUUUCCUGUUCGC-CCACACACUUAAUAACCAAGUCAGGGGUCAGGCGACA
...............(((.((((((((((((........................))-).....((((.......))))..))))))))).))). ( -24.26)
>DroSec_CAF1 7591 94 + 1
AUGUAACCCCUUGGAGUCUCCUGACCCUGGCACCAUUUACCCUCAUUUCCUGUUCCC-CCACACACUUAAUAACCAAUUCAGAGGUCAGGUGACA
......((....)).(((.(((((((((((...........................-....................)))).))))))).))). ( -19.53)
>DroSim_CAF1 7246 92 + 1
A--UAACCCCUUCGAGUCUCCUGACCCUGGCACCAUUUACCCUCAUUUCCUGUUCCC-CCACACACUUAAUAACGAAGUCAGGGGUCAGGUGACA
.--............(((.((((((((((((...................(((....-..)))..(........)..)))).)))))))).))). ( -23.70)
>DroEre_CAF1 7335 94 + 1
AUGUA-GCCCCUAAAGUCCCCUGACCCUGGCACCAGCUACCCUCGAUGCCUGUUCCCUCCAGACACUUUAUAGCCAAACCGGGGGUCAGGAGUCA
.....-.........(.(.(((((((((.(.....((((.......((.(((.......))).)).....)))).....).))))))))).).). ( -24.30)
>DroYak_CAF1 7763 79 + 1
AUGUAAGCCCUUGAAGUCUCUUGAC----------------CUCAUUCCCUGUUCCCUCCACACACUUGAUAACCAAAUGAGAAGUCAGGAGUCA
...............(.((((((((----------------((((((....(((..(...........)..)))..))))))..)))))))).). ( -15.60)
>consensus
AUGUAACCCCUUGAAGUCUCCUGACCCUGGCACCAUUUACCCUCAUUUCCUGUUCCC_CCACACACUUAAUAACCAAAUCAGGGGUCAGGAGACA
...............(((.(((((((((((................................................)))).))))))).))). (-14.13 = -15.13 +   1.00)

alignment

secondary structure

dotplot

Window 5

Location	2,818,479 – 2,818,573
Length	94
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	78.14
Mean single sequence MFE	-29.72
Consensus MFE	-15.42
Energy contribution	-16.70
Covariance contribution	1.28
Combinations/Pair	1.05
Mean z-score	-1.84
Structure conservation index	0.52
SVM decision value	0.10
SVM RNA-class probability	0.582817
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2818479 94 - 20766785
UGUCGCCUGACCCCUGACUUGGUUAUUAAGUGUGUGG-GCGAACAGGAAAUGAUGGUAAAUGGUGCCAGGGUCAGGAGACUUCAGGGGGUUACAU
.(((.(((((((((((..(((.((((.......))))-.))).))).......(((((.....))))))))))))).)))............... ( -29.50)
>DroSec_CAF1 7591 94 - 1
UGUCACCUGACCUCUGAAUUGGUUAUUAAGUGUGUGG-GGGAACAGGAAAUGAGGGUAAAUGGUGCCAGGGUCAGGAGACUCCAAGGGGUUACAU
.....(((((((.(((.(((..(((((...(.(((..-....))).).......)))))..)))..)))))))))).(((((....))))).... ( -25.40)
>DroSim_CAF1 7246 92 - 1
UGUCACCUGACCCCUGACUUCGUUAUUAAGUGUGUGG-GGGAACAGGAAAUGAGGGUAAAUGGUGCCAGGGUCAGGAGACUCGAAGGGGUUA--U
.....(((((((((((..(((.((((.......))))-.))).)))........((((.....)))).)))))))).(((((....))))).--. ( -30.40)
>DroEre_CAF1 7335 94 - 1
UGACUCCUGACCCCCGGUUUGGCUAUAAAGUGUCUGGAGGGAACAGGCAUCGAGGGUAGCUGGUGCCAGGGUCAGGGGACUUUAGGGGC-UACAU
...((((((((((..((((..(((((...(((((((.......))))))).....)))))..).))).))))))))))...........-..... ( -41.00)
>DroYak_CAF1 7763 79 - 1
UGACUCCUGACUUCUCAUUUGGUUAUCAAGUGUGUGGAGGGAACAGGGAAUGAG----------------GUCAAGAGACUUCAAGGGCUUACAU
....(((((.(((((((((((.....))))))...)))))...)))))..((((----------------(((....)))))))........... ( -22.30)
>consensus
UGUCACCUGACCCCUGACUUGGUUAUUAAGUGUGUGG_GGGAACAGGAAAUGAGGGUAAAUGGUGCCAGGGUCAGGAGACUUCAAGGGGUUACAU
.(((.((((((((.................(.(((.......))).).......((((.....)))).)))))))).)))............... (-15.42 = -16.70 +   1.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:41:01 2006