Locus 1805

Sequence ID	3L_DroMel_CAF1
Location	5,081,020 – 5,081,136
Length	116
Max. P	0.830402

overview

Window 4

Location	5,081,020 – 5,081,136
Length	116
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.66
Mean single sequence MFE	-43.62
Consensus MFE	-34.81
Energy contribution	-34.69
Covariance contribution	-0.12
Combinations/Pair	1.09
Mean z-score	-1.61
Structure conservation index	0.80
SVM decision value	0.03
SVM RNA-class probability	0.548280
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5081020 116 + 23771897
UGACUAUGUGCAGUGCUAGUGUGUGUGUG----CUGAGUCCUUGUGUGGGUGCACUGGCAUGUUGUGAUUGCGGACUGUUGCUUCACUUGAGUGGCGGCAAGUCGGCGACCCAACAGCUA
.........((.(((((((((..(.((..----(.........)..)).)..)))))))))((((.(.((((.(((((((((..(((....)))))))).)))).)))).))))).)).. ( -44.70)
>DroSec_CAF1 287286 116 + 1
UACCUAUGUGCAGUGCAAAUGUGUGUGUG----CUGAGUCCUUGUGUGGGUGCACUGGCAUGUUGUGAUUGCGGACUGUUGCUUCACUUGAGUGGCGACAAGUCGGCGACCAAACGGCUA
((((((..(.(((..((........))..----))).......)..))))))...((((.((((.((.((((.(((((((((..(((....)))))))).)))).)))).)))))))))) ( -38.10)
>DroSim_CAF1 308630 116 + 1
UGCCUAUGUGCAGUGCAAAUGUGUGUGUG----CUGAGUCCUUGUGUGGGUGCACUGGCAUGUUGUGAUUGCGGACUGUUGCUUCACUUGAGUGGCGGCAAGUCGGCGACCCAACGGCUA
.(((.((((.(((((((...((......)----)....(((......))))))))))))))((((.(.((((.(((((((((..(((....)))))))).)))).)))).)))))))).. ( -42.40)
>DroYak_CAF1 298724 120 + 1
UGCCUAUGUACAGUGCCAGUGUGUGUGUGUGAGUUGAGUCCUUGUGUGGGUGCACUGGCAUGUUGUGAUUGCGGACUGUUGCUUCACUUCAGUGGCAGCAAGUCGGCGACCCAACAGCAA
(((.........(((((((((..(.((..((((.......))))..)).)..)))))))))((((.(.((((.(((((((((..(((....)))))))).)))).)))).))))).))). ( -49.30)
>consensus
UGCCUAUGUGCAGUGCAAAUGUGUGUGUG____CUGAGUCCUUGUGUGGGUGCACUGGCAUGUUGUGAUUGCGGACUGUUGCUUCACUUGAGUGGCGGCAAGUCGGCGACCCAACAGCUA
.....((((.(((((((.....................(((......))))))))))))))(((((..((((.(((((((((..(((....)))))))).)))).))))....))))).. (-34.81 = -34.69 +  -0.12)

alignment

secondary structure

dotplot

Window 5

Location	5,081,020 – 5,081,136
Length	116
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	92.66
Mean single sequence MFE	-32.24
Consensus MFE	-26.19
Energy contribution	-25.88
Covariance contribution	-0.31
Combinations/Pair	1.13
Mean z-score	-2.06
Structure conservation index	0.81
SVM decision value	0.71
SVM RNA-class probability	0.830402
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5081020 116 - 23771897
UAGCUGUUGGGUCGCCGACUUGCCGCCACUCAAGUGAAGCAACAGUCCGCAAUCACAACAUGCCAGUGCACCCACACAAGGACUCAG----CACACACACACUAGCACUGCACAUAGUCA
..((((((((((.((.(((((((...(((....)))..)))..)))).)).))).))))).))((((((..((......)).....(----......)......)))))).......... ( -29.10)
>DroSec_CAF1 287286 116 - 1
UAGCCGUUUGGUCGCCGACUUGUCGCCACUCAAGUGAAGCAACAGUCCGCAAUCACAACAUGCCAGUGCACCCACACAAGGACUCAG----CACACACACAUUUGCACUGCACAUAGGUA
..((((((((((.((.((((.((.(((((....)))..)).)))))).)).)))).))).(((.((((((.((......)).....(----......).....)))))))))....))). ( -29.80)
>DroSim_CAF1 308630 116 - 1
UAGCCGUUGGGUCGCCGACUUGCCGCCACUCAAGUGAAGCAACAGUCCGCAAUCACAACAUGCCAGUGCACCCACACAAGGACUCAG----CACACACACAUUUGCACUGCACAUAGGCA
..((((((((((.((.(((((((...(((....)))..)))..)))).)).))).)))).(((.((((((.((......)).....(----......).....)))))))))....))). ( -33.90)
>DroYak_CAF1 298724 120 - 1
UUGCUGUUGGGUCGCCGACUUGCUGCCACUGAAGUGAAGCAACAGUCCGCAAUCACAACAUGCCAGUGCACCCACACAAGGACUCAACUCACACACACACACUGGCACUGUACAUAGGCA
.(((((((((((.((.((((((((..(((....))).))))..)))).)).))).)))).((((((((..........((.......))..........)))))))).........)))) ( -36.15)
>consensus
UAGCCGUUGGGUCGCCGACUUGCCGCCACUCAAGUGAAGCAACAGUCCGCAAUCACAACAUGCCAGUGCACCCACACAAGGACUCAG____CACACACACACUUGCACUGCACAUAGGCA
..((((((((((.((.(((((((...(((....)))..)))..)))).)).))).)))).(((.(((((...................................))))))))....))). (-26.19 = -25.88 +  -0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:17:00 2006