Locus 1949

Sequence ID	2R_DroMel_CAF1
Location	7,366,215 – 7,366,404
Length	189
Max. P	0.970290

overview

Window 0

Location	7,366,215 – 7,366,330
Length	115
Sequences	3
Columns	115
Reading direction	reverse
Mean pairwise identity	97.68
Mean single sequence MFE	-40.87
Consensus MFE	-38.07
Energy contribution	-37.63
Covariance contribution	-0.44
Combinations/Pair	1.06
Mean z-score	-1.73
Structure conservation index	0.93
SVM decision value	0.19
SVM RNA-class probability	0.624144
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7366215 115 - 20766785
UCCCACCUGGCUGCUUGCUGGCAUAGUAGUUCAGGUGGUUCUUGGACUCCUCCAGGAACAGAUGCUCGAUAAACUUGUCGCUCAGCUCGUGGCCUGCACCCACAUCGCAGGUGUC
...((((((((((((((....)).))))).)))))))(((((((((....))))))))).((.((((((((....)))))...)))))...((((((.........))))))... ( -45.00)
>DroSim_CAF1 373 115 - 1
UCCCACCUGGCUGCUUGCUGGCAUAGUAGUUCAGGUGGUUCUUGGACUCCUCCAGGAACAGAUGCUCGAUAAACUUGUCGCUCAGCUCGUGGCCCGCACCCACAUCGCAGGUGUC
...((((((((((...((.((((.(((...((..((.(((((((((....)))))))))....))..))...))))))))).))))..((((.......))))....)))))).. ( -41.30)
>DroYak_CAF1 393 115 - 1
UCCCACCUGGCUGCUUACUGGCAUAGUAGUUCAGGUGGUUUUUGGACUCCUCCAGGAACAGAUGCUCGAUAAACUUGUCACUCAGCUCGUGGCCCGCACCCACAUCGCAGGUGUC
...((((((((((.....(((((.(((...((..((.(((((((((....)))))))))....))..))...))))))))..))))..((((.......))))....)))))).. ( -36.30)
>consensus
UCCCACCUGGCUGCUUGCUGGCAUAGUAGUUCAGGUGGUUCUUGGACUCCUCCAGGAACAGAUGCUCGAUAAACUUGUCGCUCAGCUCGUGGCCCGCACCCACAUCGCAGGUGUC
...((((((((((.....(((((.(((...((..((.(((((((((....)))))))))....))..))...))))))))..))))..((((.......))))....)))))).. (-38.07 = -37.63 +  -0.44)

alignment

secondary structure

dotplot

Window 1

Location	7,366,250 – 7,366,369
Length	119
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	90.81
Mean single sequence MFE	-36.53
Consensus MFE	-30.92
Energy contribution	-30.70
Covariance contribution	-0.22
Combinations/Pair	1.03
Mean z-score	-2.57
Structure conservation index	0.85
SVM decision value	0.90
SVM RNA-class probability	0.878534
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7366250 119 - 20766785
GGGAUUUAUUAUUUGGAGUUUUC-CUCGAUGAAAUAAUACUCCCACCUGGCUGCUUGCUGGCAUAGUAGUUCAGGUGGUUCUUGGACUCCUCCAGGAACAGAUGCUCGAUAAACUUGUCG
(((((((.......(((((((((-......))))....)))))((((((((((((((....)).))))).)))))))(((((((((....))))))))))))).)))((((....)))). ( -39.30)
>DroSim_CAF1 408 119 - 1
GGGCCUUAUUAUUUGAAAUUUUC-CUCGAUGAAAUAAUACUCCCACCUGGCUGCUUGCUGGCAUAGUAGUUCAGGUGGUUCUUGGACUCCUCCAGGAACAGAUGCUCGAUAAACUUGUCG
((((..((((((((...(((...-...))).))))))))....((((((((((((((....)).))))).)))))))(((((((((....)))))))))....))))((((....)))). ( -37.40)
>DroYak_CAF1 428 119 - 1
GGCAUUUAUUAUUUGUAAUUUUUUUUUAACGAAAU-AUAUUCCCACCUGGCUGCUUACUGGCAUAGUAGUUCAGGUGGUUUUUGGACUCCUCCAGGAACAGAUGCUCGAUAAACUUGUCA
(((((((............................-.......((((((((((((.........))))).)))))))(((((((((....)))))))))))))))).((((....)))). ( -32.90)
>consensus
GGGAUUUAUUAUUUGAAAUUUUC_CUCGAUGAAAUAAUACUCCCACCUGGCUGCUUGCUGGCAUAGUAGUUCAGGUGGUUCUUGGACUCCUCCAGGAACAGAUGCUCGAUAAACUUGUCG
.........((((((...........................(((((((((((((.........))))).))))))))((((((((....))))))))))))))...((((....)))). (-30.92 = -30.70 +  -0.22)

alignment

secondary structure

dotplot

Window 2

Location	7,366,290 – 7,366,404
Length	114
Sequences	3
Columns	115
Reading direction	forward
Mean pairwise identity	89.24
Mean single sequence MFE	-32.23
Consensus MFE	-30.09
Energy contribution	-30.43
Covariance contribution	0.34
Combinations/Pair	1.08
Mean z-score	-2.44
Structure conservation index	0.93
SVM decision value	1.66
SVM RNA-class probability	0.970290
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7366290 114 + 20766785
AACCACCUGAACUACUAUGCCAGCAAGCAGCCAGGUGGGAGUAUUAUUUCAUCGAG-GAAAACUCCAAAUAAUAAAUCCCAUUUGGUUACUUAGCCCAGGACAAGUCAGCGCAGG
.....((((..(((((.((((.(((((.((((((((((((.((((((((....(((-.....))).))))))))..)))))))))))).))).))...)).))))).))..)))) ( -38.70)
>DroSim_CAF1 448 114 + 1
AACCACCUGAACUACUAUGCCAGCAAGCAGCCAGGUGGGAGUAUUAUUUCAUCGAG-GAAAAUUUCAAAUAAUAAGGCCCAUUUGGUUACUUAGCCCAGGACAAGUCAGCGCAGG
.....((((..(((((.((((.(((((.(((((((((((..((((((((....(((-(....))))))))))))...))))))))))).))).))...)).))))).))..)))) ( -35.00)
>DroYak_CAF1 468 114 + 1
AACCACCUGAACUACUAUGCCAGUAAGCAGCCAGGUGGGAAUAU-AUUUCGUUAAAAAAAAAUUACAAAUAAUAAAUGCCUUUUGGCUCCUUAGCCCAGGACAAGUCGGCGCAGG
..(((((((........(((......)))..)))))))(((...-..)))...........................(((....))).(((..(((...((....)))))..))) ( -23.00)
>consensus
AACCACCUGAACUACUAUGCCAGCAAGCAGCCAGGUGGGAGUAUUAUUUCAUCGAG_GAAAAUUACAAAUAAUAAAUCCCAUUUGGUUACUUAGCCCAGGACAAGUCAGCGCAGG
.....((((..(((((.((((.(((((.(((((((((((..((((((((.................))))))))...))))))))))).))).))...)).))))).))..)))) (-30.09 = -30.43 +   0.34)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:17:06 2006