Locus 4241

Sequence ID	2R_DroMel_CAF1
Location	14,013,577 – 14,013,697
Length	120
Max. P	0.999949

overview

Window 6

Location	14,013,577 – 14,013,697
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.33
Mean single sequence MFE	-38.74
Consensus MFE	-37.34
Energy contribution	-37.94
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-3.10
Structure conservation index	0.96
SVM decision value	4.78
SVM RNA-class probability	0.999949
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14013577 120 + 20766785
GAGCCUCUUUGGCGCCCGACGAGGUGACAAUUCCAUUUAAGAAUUGCGGGCAUAGCUUUGUUAUUGCCCAUGACCAUUCUAGCCAACCAUUCCGGCUAACAAUGGAAUAGUUAUCUCUUC
..(((.....)))....((.((((((((.((((((((..........(((((((((...)))).)))))..........(((((.........)))))..)))))))).)))))))).)) ( -40.20)
>DroSec_CAF1 44266 120 + 1
GAGCCUCUUUGGCGCCCGACGAGGUGUCAAUUCCAUUUAAGAAUUGCGGGCAUAGCUUUGUUAUUGCCCAUGACCAUUCUAGCCAACCAUUCCGGCUAACAAUGGAAUAGUUAUCUCUUC
..(((.....)))....((.((((((.(.((((((((..........(((((((((...)))).)))))..........(((((.........)))))..)))))))).).)))))).)) ( -35.60)
>DroSim_CAF1 43676 120 + 1
GAGCCUCUUUGGCGCCCGACGAGGUGACAAUUCCAUUUAAGAAUUGCGGGCAUAGCUUUGUUAUUGCCCAUGACCAUUCUAGCCAACCAUUCCGGCUAACAAUGGAAUAGUUAUCUCUUC
..(((.....)))....((.((((((((.((((((((..........(((((((((...)))).)))))..........(((((.........)))))..)))))))).)))))))).)) ( -40.20)
>DroEre_CAF1 44774 120 + 1
CAGCCUCUUUGGCGCCCGACGAGGUGACAAUUCCAUUUAAGAAUUGCGGGCAUAGCUUUGUUAUGGCCCAUGACCAUUCUAGCCCUCCAUUCCGGCUAACAAUGGCAUAGUUAUCUCUUC
..(((.....)))....((.(((((((((((((.......)))))..(((((((((...))))).))))(((.(((((.(((((.........)))))..)))))))).)))))))).)) ( -38.00)
>DroYak_CAF1 44480 120 + 1
GAGCCUCUUUGGCGCCCGACGAGGUGACUAUUCCAUUUAAGAAUUGCGGGCAUAGCUUUGUUAUUGCCCAUGACCAUUCUAGCCCACCAUUCCGGCUAACAAUGGCAUAGUUAUCUCUUC
..(((.....)))....((.(((((((((((.(((((..........(((((((((...)))).)))))..........(((((.........)))))..))))).))))))))))).)) ( -39.70)
>consensus
GAGCCUCUUUGGCGCCCGACGAGGUGACAAUUCCAUUUAAGAAUUGCGGGCAUAGCUUUGUUAUUGCCCAUGACCAUUCUAGCCAACCAUUCCGGCUAACAAUGGAAUAGUUAUCUCUUC
..(((.....)))....((.((((((((.((((((((..........(((((((((...))))).))))..........(((((.........)))))..)))))))).)))))))).)) (-37.34 = -37.94 +   0.60)

alignment

secondary structure

dotplot

Window 7

Location	14,013,577 – 14,013,697
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.33
Mean single sequence MFE	-36.62
Consensus MFE	-32.04
Energy contribution	-33.04
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.57
Structure conservation index	0.87
SVM decision value	0.72
SVM RNA-class probability	0.832000
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14013577 120 - 20766785
GAAGAGAUAACUAUUCCAUUGUUAGCCGGAAUGGUUGGCUAGAAUGGUCAUGGGCAAUAACAAAGCUAUGCCCGCAAUUCUUAAAUGGAAUUGUCACCUCGUCGGGCGCCAAAGAGGCUC
.......((((((((((..........))))))))))(((.((..(((...(((((............)))))((((((((.....)))))))).)))...)).)))(((.....))).. ( -37.20)
>DroSec_CAF1 44266 120 - 1
GAAGAGAUAACUAUUCCAUUGUUAGCCGGAAUGGUUGGCUAGAAUGGUCAUGGGCAAUAACAAAGCUAUGCCCGCAAUUCUUAAAUGGAAUUGACACCUCGUCGGGCGCCAAAGAGGCUC
.......((((((((((..........))))))))))(((.((..(((...(((((............)))))((((((((.....))))))).))))...)).)))(((.....))).. ( -36.40)
>DroSim_CAF1 43676 120 - 1
GAAGAGAUAACUAUUCCAUUGUUAGCCGGAAUGGUUGGCUAGAAUGGUCAUGGGCAAUAACAAAGCUAUGCCCGCAAUUCUUAAAUGGAAUUGUCACCUCGUCGGGCGCCAAAGAGGCUC
.......((((((((((..........))))))))))(((.((..(((...(((((............)))))((((((((.....)))))))).)))...)).)))(((.....))).. ( -37.20)
>DroEre_CAF1 44774 120 - 1
GAAGAGAUAACUAUGCCAUUGUUAGCCGGAAUGGAGGGCUAGAAUGGUCAUGGGCCAUAACAAAGCUAUGCCCGCAAUUCUUAAAUGGAAUUGUCACCUCGUCGGGCGCCAAAGAGGCUG
.......((((.........))))(((.((..((.(((((((.(((((.....))))).......))).))))((((((((.....))))))))..))...)).)))(((.....))).. ( -37.10)
>DroYak_CAF1 44480 120 - 1
GAAGAGAUAACUAUGCCAUUGUUAGCCGGAAUGGUGGGCUAGAAUGGUCAUGGGCAAUAACAAAGCUAUGCCCGCAAUUCUUAAAUGGAAUAGUCACCUCGUCGGGCGCCAAAGAGGCUC
((.(((...(((((.(((((.......(((((.((((((....(((((..((........))..))))))))))).)))))..))))).)))))...))).))....(((.....))).. ( -35.20)
>consensus
GAAGAGAUAACUAUUCCAUUGUUAGCCGGAAUGGUUGGCUAGAAUGGUCAUGGGCAAUAACAAAGCUAUGCCCGCAAUUCUUAAAUGGAAUUGUCACCUCGUCGGGCGCCAAAGAGGCUC
((.(((.........(((((.((((((((.....)))))))))))))....((((.(((.......)))))))((((((((.....))))))))...))).))....(((.....))).. (-32.04 = -33.04 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:15:02 2006