Locus 6921

Sequence ID	3R_DroMel_CAF1
Location	18,265,476 – 18,265,572
Length	96
Max. P	0.904058

overview

Window 9

Location	18,265,476 – 18,265,572
Length	96
Sequences	6
Columns	102
Reading direction	forward
Mean pairwise identity	78.27
Mean single sequence MFE	-35.55
Consensus MFE	-20.23
Energy contribution	-20.59
Covariance contribution	0.36
Combinations/Pair	1.19
Mean z-score	-2.18
Structure conservation index	0.57
SVM decision value	1.03
SVM RNA-class probability	0.904058
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18265476 96 + 27905053
UAGGUGG-GUCUGGGGUCGCGAAAGAUGCAUGCACACCUUAUGGA----UGCUGGGUGG-GCAUCGGUGGACGCCCACUUGUGGUGCGUGUGAAAACGGAUU
......(-(((((...((.(....)..((((((((.((....)).----.((.((((((-((.((....)).)))))))))).))))))))))...)))))) ( -36.20)
>DroSec_CAF1 21675 100 + 1
UAGGUGG-GUCUGGGGUCGCGAAAGAUGCAUGCGCACCUUAUGGAUGGAUGCAGGGUGG-GCAUCGGUGGACGCCCACUUGUGGUGCGUGUGAAAACGGAUU
......(-(((((...((.(....)..((((((((.((....))......(((((.(((-((.((....)).)))))))))).))))))))))...)))))) ( -36.60)
>DroSim_CAF1 22459 100 + 1
UAGGUGG-GUCUGGGGUCGCGAAAGAUGCAUGCGCACCUUAUGGAUGGGUGCAGGGUGG-GCAUCGGUGGACGCCCACUUGUGGUGCGUGUGAAAACGGAUU
......(-(((((...((.(....)..((((((((((((.......)))))).((((((-((.((....)).)))))))).....))))))))...)))))) ( -40.60)
>DroEre_CAF1 22317 83 + 1
UAGGUGG-GUCUGGGGUCGC-------------GCACCCUAUAGAUGG----AGGGUGG-GCAUCCGUGAACGCCCACUUGUGGUGCGUGUGAAAACGGAUU
(((((((-((...((((.((-------------.((((((........----)))))).-))))))(....)))))))))).(((.(((......))).))) ( -34.80)
>DroYak_CAF1 22173 83 + 1
UAGGUGG-AUCUGGGGUCGC-------------GCACCCUAAAGAUGG----AGGGUGG-GCAUCGGUGAACGCCCACUUGUGGUGCGUGUGAAAACGGAUU
......(-(((((...((((-------------.((((((........----)))))).-))........(((((((....))).))))..))...)))))) ( -31.60)
>DroAna_CAF1 22801 90 + 1
UAGGUGGCGACUGGGGUCACA-------CAUGAA---CUCGAAGGGGGAUACAAGGCGCUGCA--GGGGAACACCCACUUGUGGUGCGUGUGAAAACCGAUU
...........(((..(((((-------(.....---(((....)))........((((..((--((((.....)).))))..))))))))))...)))... ( -33.50)
>consensus
UAGGUGG_GUCUGGGGUCGCG_______CAUGCGCACCUUAUAGAUGG_UGCAGGGUGG_GCAUCGGUGAACGCCCACUUGUGGUGCGUGUGAAAACGGAUU
........(((((...((((..............(((((..............)))))............(((((((....))).))))))))...))))). (-20.23 = -20.59 +   0.36)

alignment

secondary structure

dotplot

Window 0

Location	18,265,476 – 18,265,572
Length	96
Sequences	6
Columns	102
Reading direction	reverse
Mean pairwise identity	78.27
Mean single sequence MFE	-25.47
Consensus MFE	-12.50
Energy contribution	-13.25
Covariance contribution	0.75
Combinations/Pair	1.25
Mean z-score	-2.39
Structure conservation index	0.49
SVM decision value	0.89
SVM RNA-class probability	0.874579
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18265476 96 - 27905053
AAUCCGUUUUCACACGCACCACAAGUGGGCGUCCACCGAUGC-CCACCCAGCA----UCCAUAAGGUGUGCAUGCAUCUUUCGCGACCCCAGAC-CCACCUA
.....((((.....(((.......(((((((((....)))))-))))...(((----(.(((.....))).)))).......))).....))))-....... ( -26.80)
>DroSec_CAF1 21675 100 - 1
AAUCCGUUUUCACACGCACCACAAGUGGGCGUCCACCGAUGC-CCACCCUGCAUCCAUCCAUAAGGUGCGCAUGCAUCUUUCGCGACCCCAGAC-CCACCUA
.....((((.....(((.......(((((((((....)))))-))))..((((((((((.....)))).).)))))......))).....))))-....... ( -28.40)
>DroSim_CAF1 22459 100 - 1
AAUCCGUUUUCACACGCACCACAAGUGGGCGUCCACCGAUGC-CCACCCUGCACCCAUCCAUAAGGUGCGCAUGCAUCUUUCGCGACCCCAGAC-CCACCUA
.....((((.....(((.......(((((((((....)))))-))))...(((((.........))))).............))).....))))-....... ( -28.30)
>DroEre_CAF1 22317 83 - 1
AAUCCGUUUUCACACGCACCACAAGUGGGCGUUCACGGAUGC-CCACCCU----CCAUCUAUAGGGUGC-------------GCGACCCCAGAC-CCACCUA
.((((((......((((.(((....)))))))..))))))((-.((((((----........)))))).-------------))..........-....... ( -27.00)
>DroYak_CAF1 22173 83 - 1
AAUCCGUUUUCACACGCACCACAAGUGGGCGUUCACCGAUGC-CCACCCU----CCAUCUUUAGGGUGC-------------GCGACCCCAGAU-CCACCUA
............(.((((((....(((((((((....)))))-)))).((----........)))))))-------------).).........-....... ( -24.50)
>DroAna_CAF1 22801 90 - 1
AAUCGGUUUUCACACGCACCACAAGUGGGUGUUCCCC--UGCAGCGCCUUGUAUCCCCCUUCGAG---UUCAUG-------UGUGACCCCAGUCGCCACCUA
....((...((((((((.(....((.(((....))))--)...).))((((..........))))---.....)-------)))))..))............ ( -17.80)
>consensus
AAUCCGUUUUCACACGCACCACAAGUGGGCGUCCACCGAUGC_CCACCCUGCA_CCAUCCAUAAGGUGCGCAUG_______CGCGACCCCAGAC_CCACCUA
..............(((.......(((((((((....))))).))))........((((.....))))..............)))................. (-12.50 = -13.25 +   0.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:33:18 2006