Locus 7226

Sequence ID	3R_DroMel_CAF1
Location	19,040,909 – 19,041,033
Length	124
Max. P	0.938598

overview

Window 3

Location	19,040,909 – 19,041,008
Length	99
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	89.17
Mean single sequence MFE	-19.28
Consensus MFE	-17.52
Energy contribution	-17.56
Covariance contribution	0.04
Combinations/Pair	1.17
Mean z-score	-1.63
Structure conservation index	0.91
SVM decision value	1.27
SVM RNA-class probability	0.938598
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19040909 99 - 27905053
AAAU----AACUCUUUCGACUGAGUCAUGGCAUCUCAGGUGUCGUGCCUCCGACUCUUGCUGUCCCUUUCGCUGUCUAUUAACAAUUUUCCAUUAUUAAGUCA-
....----.........(((((((.((((((((.....)))))))).))).(((....((..........)).)))......................)))).- ( -20.50)
>DroSec_CAF1 53533 99 - 1
AAAU----AUCUCUUUCGACUGAGUCACGGCAUCUCAGGUGUCGUGCCUCCGACUCACGCCGUCCCUUUCGCUCUCUAUUAACAAUUUUCCAUUAUUAAGUCA-
....----.........(((((((.((((((((.....)))))))).))).(((.......)))..................................)))).- ( -21.00)
>DroSim_CAF1 55219 99 - 1
AAAU----AUCUCUUUCGACUGAGUCACGGCAUCUCAGGUGUCGUGCCUCCGACUCUUGCCGUCCCUUUCGCUCUCUAUUAACAAUUUUCCAUUAUUAAGUCA-
....----.........(((((((.((((((((.....)))))))).))).(((.......)))..................................)))).- ( -21.00)
>DroEre_CAF1 56404 104 - 1
AAAUACGUAACUUUUUCGAUUGAGUCACGUUAUCUCAGGUGUCGUGCCUCCGACUCUCGCCGUCUCUCUCGCUCUCUAUGAGCAAUUUUCCAUUAUUAAGUCAC
.................(((((((.((((.(((.....))).)))).))).(((.......)))......((((.....))))...............)))).. ( -18.80)
>DroYak_CAF1 56723 104 - 1
AAAUAUGUAACUUUUUCGAUUGAGUCACGGCAUCUCAGUUGUCGUGCCUCCGACUCUCGCCAUCCCUUUCGCUCUCUAUUAACCAUUUUCCCUUAUUAAGUCAC
.................(((((((((..(((((..(....)..)))))...)))))..((.(......).))..........................)))).. ( -15.10)
>consensus
AAAU____AACUCUUUCGACUGAGUCACGGCAUCUCAGGUGUCGUGCCUCCGACUCUCGCCGUCCCUUUCGCUCUCUAUUAACAAUUUUCCAUUAUUAAGUCA_
.................(((((((.((((((((.....)))))))).))).(((.......)))..................................)))).. (-17.52 = -17.56 +   0.04)

alignment

secondary structure

dotplot

Window 4

Location	19,040,934 – 19,041,033
Length	99
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	78.12
Mean single sequence MFE	-32.20
Consensus MFE	-14.58
Energy contribution	-14.78
Covariance contribution	0.20
Combinations/Pair	1.09
Mean z-score	-2.02
Structure conservation index	0.45
SVM decision value	0.39
SVM RNA-class probability	0.718740
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19040934 99 + 27905053
UAGACAGCGAAAGGGACAGCAAGAGUCGGAGGCACGACACCUGAGAUGCCAUGACUCAGUCGAAAGAGUU----AUUUCAUUUCGAUA-------------AUUAUGCU-CUAAAAC-
((((...(....).....(((.((((((..(((((.........).)))).)))))).((((((((((..----..))).))))))).-------------....))))-)))....- ( -26.90)
>DroSec_CAF1 53558 100 + 1
UAGAGAGCGAAAGGGACGGCGUGAGUCGGAGGCACGACACCUGAGAUGCCGUGACUCAGUCGAAAGAGAU----AUUUAAUUUG---------UCUUU---GUUAUGCU-CUAAAAC-
...((((((.......((((.(((((((..(((((.........).)))).)))))))))))..((((((----(.......))---------)))))---....))))-)).....- ( -32.80)
>DroSim_CAF1 55244 109 + 1
UAGAGAGCGAAAGGGACGGCAAGAGUCGGAGGCACGACACCUGAGAUGCCGUGACUCAGUCGAAAGAGAU----AUUUCAUUUGGCUAAGCAGUCUUU---GUUAUGCU-CUAAAAC-
...((((((..((((((.((..((((((..(((((.........).)))).))))))(((((((.(((..----..))).)))))))..)).))))))---....))))-)).....- ( -37.40)
>DroEre_CAF1 56430 113 + 1
UAGAGAGCGAGAGAGACGGCGAGAGUCGGAGGCACGACACCUGAGAUAACGUGACUCAAUCGAAAAAGUUACGUAUUUCAUUUGGAAAGGCAGGCUUU---CGUAUGCU-CUACAUU-
(((((.(((((((...((((....))))...((....((..(((((((.(((((((..........))))))))))))))..)).....))...))))---)))...))-)))....- ( -36.80)
>DroYak_CAF1 56749 116 + 1
UAGAGAGCGAAAGGGAUGGCGAGAGUCGGAGGCACGACAACUGAGAUGCCGUGACUCAAUCGAAAAAGUUACAUAUUUCAUAUGGGUA--CAGUCGAUAAGUCUAUGCACCUGCAUUA
......((...(((....(((.((((((..(((((.........).)))).)))))).(((((....((..(((((...)))))...)--)..))))).......))).))))).... ( -27.10)
>consensus
UAGAGAGCGAAAGGGACGGCGAGAGUCGGAGGCACGACACCUGAGAUGCCGUGACUCAGUCGAAAGAGUU____AUUUCAUUUGGAUA__CAGUCUUU___GUUAUGCU_CUAAAAC_
(((....(....).....(((.((((((..(((((.........).)))).))))))....((((..........))))..........................)))..)))..... (-14.58 = -14.78 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:40:39 2006