Locus 3699

Sequence ID	3L_DroMel_CAF1
Location	10,765,640 – 10,765,879
Length	239
Max. P	0.958421

overview

Window 6

Location	10,765,640 – 10,765,746
Length	106
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.15
Mean single sequence MFE	-26.37
Consensus MFE	-19.10
Energy contribution	-19.78
Covariance contribution	0.68
Combinations/Pair	1.05
Mean z-score	-1.89
Structure conservation index	0.72
SVM decision value	0.34
SVM RNA-class probability	0.694659
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10765640 106 + 23771897
AGACUCUUUCUCCCUGAUAGCUU------------UGUCUCCAUCGCACUCUUUCGCCAGAUCUCUGAAGCU--AGAGAUCAGUGAGAAUAAGUCAAAUGCAUGGGCAAUAAUAAAUAGA
.((((..(((((.(((((.((..------------((....))..)).((((..(..(((....)))..)..--))))))))).)))))..))))...(((....)))............ ( -29.20)
>DroSec_CAF1 99330 108 + 1
AGACUCUUUCUCCCUGGUAGCUC------------CGUCUCCUUCGCACUCUUUCGCCAGAUCUCUGAAGCUAUAGAGAUCAGUGAGAAUAAGUCAAAUGCAUGGGCAAUAAUAAAUAGA
.((((..(((((.(((((.((..------------..........)).((((...(((((....)))..))...))))))))).)))))..))))...(((....)))............ ( -27.20)
>DroSim_CAF1 102194 108 + 1
AGACUCUUUCUCCCUGGUAGCUC------------CGUCUCCUUCGCACUCUUUCGCCAGAUCUCCGAAGCUAUAGAGAUCAGUGAGAAUAAGUCAAAUGCAUGGGCAAUAAUAAAUAGA
.((((..(((((.(((((..(((------------..(...(((((...(((......)))....)))))..)..)))))))).)))))..))))...(((....)))............ ( -26.00)
>DroEre_CAF1 104246 106 + 1
AGACUCUUUCUCCCAAGCAACUC------------CAUCUCCUUCGCACUCUUUCUCCAGAUCUCUGAAGCU--GGAGAUCAGUGAGAAUAAGUCAAAAGCAUGGGCAAUAAUAAAUAGA
...........((((.((.....------------...((..(((.((((...(((((((..........))--)))))..)))).)))..))......)).)))).............. ( -24.44)
>DroYak_CAF1 115363 118 + 1
AGACUCUUUCUCCCAAGUAACUCCAUUUCCAUCUCCAUCUCCCUCGCACUCUUUCUCCAGAUCUCUGCAGCU--AGAGAUCGGUGAGAAUAAGUCAAAUGCAUGGGCAAUAAUAAAUAGA
.((((..(((((((((((......))))...............................((((((((....)--))))))))).)))))..))))...(((....)))............ ( -25.00)
>consensus
AGACUCUUUCUCCCUGGUAGCUC____________CGUCUCCUUCGCACUCUUUCGCCAGAUCUCUGAAGCU__AGAGAUCAGUGAGAAUAAGUCAAAUGCAUGGGCAAUAAUAAAUAGA
.((((..(((((.(...............................((........))..(((((((........))))))).).)))))..))))...(((....)))............ (-19.10 = -19.78 +   0.68)

alignment

secondary structure

dotplot

Window 7

Location	10,765,668 – 10,765,783
Length	115
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	91.94
Mean single sequence MFE	-34.88
Consensus MFE	-26.76
Energy contribution	-27.48
Covariance contribution	0.72
Combinations/Pair	1.11
Mean z-score	-2.55
Structure conservation index	0.77
SVM decision value	1.49
SVM RNA-class probability	0.958421
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10765668 115 + 23771897
CCAUCGCACUCUUUCGCCAGAUCUCUGAAGCU--AGAGAUCAGUGAGAAUAAGUCAAAUGCAUGGGCAAUAAUAAAUAGAAGGGGAUCGGUGAACGAGGU--GCAGGCAAACUAGUAAC
.....((((((.((((((.(((((((....((--(..(((..((....))..)))...(((....)))........)))..))))))))))))).)).))--))............... ( -30.40)
>DroSec_CAF1 99358 119 + 1
CCUUCGCACUCUUUCGCCAGAUCUCUGAAGCUAUAGAGAUCAGUGAGAAUAAGUCAAAUGCAUGGGCAAUAAUAAAUAGAAGGGGAUCGGCGAACGAGGUGUGCAGGCAAACUAGUAAC
(((.(((((((.((((((.(((((((....((((...(((..((....))..)))...(((....))).......))))..))))))))))))).)).))))).)))............ ( -36.50)
>DroSim_CAF1 102222 119 + 1
CCUUCGCACUCUUUCGCCAGAUCUCCGAAGCUAUAGAGAUCAGUGAGAAUAAGUCAAAUGCAUGGGCAAUAAUAAAUAGAAGGGGAUCGGCGAAAGAGGUGUGCAGGCAAACUAGUAAC
(((.((((((((((((((.(((((((....((((...(((..((....))..)))...(((....))).......))))..)))))))))))))))).))))).)))............ ( -42.50)
>DroEre_CAF1 104274 115 + 1
CCUUCGCACUCUUUCUCCAGAUCUCUGAAGCU--GGAGAUCAGUGAGAAUAAGUCAAAAGCAUGGGCAAUAAUAAAUAGAAGGGGAUCGGUGAAAGAAGU--GCAGGCAAACUUGUAAC
.((((.((((...(((((.(((((((......--)))))))..................((....))..............)))))..))))...))))(--(((((....)))))).. ( -30.90)
>DroYak_CAF1 115403 115 + 1
CCCUCGCACUCUUUCUCCAGAUCUCUGCAGCU--AGAGAUCGGUGAGAAUAAGUCAAAUGCAUGGGCAAUAAUAAAUAGAAGGGGAUCGGAGAAAGAAGC--GCUGGAAAACUUGUAAC
.((.(((..(((((((((.(((((((....((--(..(((..((....))..)))...(((....)))........)))..)))))))))))))))).))--)..))............ ( -34.10)
>consensus
CCUUCGCACUCUUUCGCCAGAUCUCUGAAGCU__AGAGAUCAGUGAGAAUAAGUCAAAUGCAUGGGCAAUAAUAAAUAGAAGGGGAUCGGCGAAAGAGGU__GCAGGCAAACUAGUAAC
.....((.((((((((((.(((((((...........(((..((....))..)))...(((....))).............)))))))))))))))))....))............... (-26.76 = -27.48 +   0.72)

alignment

secondary structure

dotplot

Window 8

Location	10,765,746 – 10,765,849
Length	103
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	81.50
Mean single sequence MFE	-35.44
Consensus MFE	-23.71
Energy contribution	-24.11
Covariance contribution	0.40
Combinations/Pair	1.17
Mean z-score	-1.85
Structure conservation index	0.67
SVM decision value	0.43
SVM RNA-class probability	0.734387
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10765746 103 - 23771897
AGGGGUUUCUCAUACCAGAUGAAAAUCGAGGGGAGAUCGAGG----------GGUUGUUCCCUCGGCGUUCUCCUCGUUACUAGUUUGCCUGC--ACCUCGUUCACCGAUCCCCU
(((((..........(((((......(((((((((.((((((----------((....))))))))..)))))))))......))))).....--...(((.....))).))))) ( -38.20)
>DroSec_CAF1 99438 102 - 1
AGGGGUUCUUCAUACCAGAUGAAAAUCGAGGGGAGAUCAAGG----------GG---UUCCCUCGGCGUUCUCCUCGUUACUAGUUUGCCUGCACACCUCGUUCGCCGAUCCCCU
(((((.((.......(((((......(((((((((..(..((----------(.---...)))..)..)))))))))......)))))...((...........)).)).))))) ( -30.60)
>DroSim_CAF1 102302 102 - 1
AGGGGUUUUUCAUAGAAGAUGGAAAUCGAGGGGAGAUCGAGG----------GG---UUCCCUCGGCGUUCUCCUCGUUACUAGUUUGCCUGCACACCUCUUUCGCCGAUCCCCU
(((((....((...((((..((....(((((((((.((((((----------(.---..)))))))..)))))))))......((......))...))..))))...)).))))) ( -37.10)
>DroEre_CAF1 104352 110 - 1
AGGGGUUU-UCAUACCAGAUGAAAAUCGAGGGAAAAUCGGGGGAAAAUCGAGGGG--UACCCUCGGAGUUCUGCUCGUUACAAGUUUGCCUGC--ACUUCUUUCACCGAUCCCCU
(((((...-((......(((....)))(((((((...((((.(((...((((((.--..))))))(((.....)))........))).)))).--..)))))))...)).))))) ( -38.10)
>DroYak_CAF1 115481 95 - 1
AGGGGUUU-UC-----AGAUGAAAAUCGAGGGGAGAUUGAGG----------GGU--UACUCUUCGAGUUCUGCUCGUUACAAGUUUUCCAGC--GCUUCUUUCUCCGAUCCCCU
(((((...-((-----.(((....)))....(((((..((((----------.((--((((...((((.....)))).....))).....)))--.))))..))))))).))))) ( -33.20)
>consensus
AGGGGUUU_UCAUACCAGAUGAAAAUCGAGGGGAGAUCGAGG__________GG___UUCCCUCGGCGUUCUCCUCGUUACUAGUUUGCCUGC__ACCUCUUUCACCGAUCCCCU
(((((....((......(((....)))((((((((.((((((..................))))))..))))))))...............................)).))))) (-23.71 = -24.11 +   0.40)

alignment

secondary structure

dotplot

Window 9

Location	10,765,783 – 10,765,879
Length	96
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	80.95
Mean single sequence MFE	-31.96
Consensus MFE	-15.59
Energy contribution	-15.99
Covariance contribution	0.40
Combinations/Pair	1.21
Mean z-score	-2.76
Structure conservation index	0.49
SVM decision value	1.42
SVM RNA-class probability	0.952238
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10765783 96 - 23771897
GAAAGAUCGAAAUUUGGUGGGG-GGAUUACCAGGGGUUUCUCAUACCAGAUGAAAAUCGAGGGGAGAUCGAGG----------GGUUGUUCCCUCGGCGUUCUCCUC
....(((....(((((((((((-..(((......)))..))).))))))))....)))((((((((.((((((----------((....))))))))..)))))))) ( -40.50)
>DroSec_CAF1 99477 89 - 1
GAAAUAGCGAAAUG----GGGG-GGAUUACCAGGGGUUCUUCAUACCAGAUGAAAAUCGAGGGGAGAUCAAGG----------GG---UUCCCUCGGCGUUCUCCUC
.............(----((((-((((..((..(((..((((...((.(((....)))...))(....)..))----------))---..)))..)).))))))))) ( -27.90)
>DroSim_CAF1 102341 89 - 1
GAAAGAGCGAAAUU----GGGG-GGAUUACCAGGGGUUUUUCAUAGAAGAUGGAAAUCGAGGGGAGAUCGAGG----------GG---UUCCCUCGGCGUUCUCCUC
((((((.(....((----((..-......)))).).))))))......(((....)))((((((((.((((((----------(.---..)))))))..)))))))) ( -32.30)
>DroEre_CAF1 104389 100 - 1
GAAAGAGCGAAAUU----GGGGGGGCUUACCAGGGGUUU-UCAUACCAGAUGAAAAUCGAGGGAAAAUCGGGGGAAAAUCGAGGGG--UACCCUCGGAGUUCUGCUC
....(((((((.((----.(((((...((((...(((((-((...((.(((....)))((.......))))..)))))))....))--))))))).)).))).)))) ( -33.20)
>DroYak_CAF1 115518 84 - 1
GAAAGAGCGAAAUU----GGGG-GGAUUACCAGGGGUUU-UC-----AGAUGAAAAUCGAGGGGAGAUUGAGG----------GGU--UACUCUUCGAGUUCUGCUC
....(((((((.((----((((-((...(((...(((((-((-----.(((....)))....)))))))....----------)))--..)))))))).))).)))) ( -25.90)
>consensus
GAAAGAGCGAAAUU____GGGG_GGAUUACCAGGGGUUU_UCAUACCAGAUGAAAAUCGAGGGGAGAUCGAGG__________GG___UUCCCUCGGCGUUCUCCUC
...................((........)).................(((....)))((((((((.((((((..................))))))..)))))))) (-15.59 = -15.99 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:04:37 2006