Locus 5760

Sequence ID	3L_DroMel_CAF1
Location	15,633,153 – 15,633,299
Length	146
Max. P	0.595477

overview

Window 3

Location	15,633,153 – 15,633,273
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	95.38
Mean single sequence MFE	-37.00
Consensus MFE	-30.30
Energy contribution	-31.18
Covariance contribution	0.88
Combinations/Pair	1.03
Mean z-score	-1.91
Structure conservation index	0.82
SVM decision value	0.12
SVM RNA-class probability	0.595477
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15633153 120 - 23771897
GAUUCCCGGACUCCUUGCUGUUUGUUUUUAAUAUAAAUGCAAAUUUCGCCAACGGCAUUCGCCCGGAGCCGUGCUCCAUAGUACAUAUGUGUGUAUGCGAGCCUGUUCCGGAGAUCUGUC
(((..(((((....((((.((((((.......))))))))))...........(((..((((..(((((...)))))...((((((....)))))))))))))...)))))..))).... ( -38.20)
>DroSec_CAF1 55424 118 - 1
GAUUCCCGGACUCCUUGCUGUUUGUUUUUAAUAUAAAUGCAAAUUUCGACAACGGCAUUCGCCAGGCGCCAUGCUCCCUAGUACAUAUGUGUG--UGCAAGCCUGUGCCGGAGAUCUGUC
......((((((((((((.((((((.......))))))))))...........((((.....(((((((...))......((((((....)))--)))..))))))))))))).)))).. ( -34.50)
>DroSim_CAF1 56381 118 - 1
GAUUCACGGACUCCUUGCUGUUUGUUUUUAAUAUAAAUGCAAAUUUCGCCAACGGCAUUCGCCAGGCGCCAUGCUCCAUAGUACAUAUGUGUG--UGCGAGCCUGUUCCGGAGAUCUGUC
.....(((((((((((((.((((((.......))))))))))....((((...(((....))).)))).((.((((((((.(((....)))))--)).)))).))....)))).))))). ( -35.90)
>DroYak_CAF1 60144 118 - 1
GAUUCCCGGACUCCUUGCUGUUUGUUUUUAAUAUAAAUGCAAAUUUCGCCAACGGCAUUCGCCAGGCGCCAUGCUCCACAGUACAUAUGUGUG--UGCGAGCCUGUUCCGGAGAUCUGUC
(((..(((((....((((.((((((.......))))))))))....((((...(((....))).)))).((.((((((((.(((....)))))--)).)))).)).)))))..))).... ( -39.40)
>consensus
GAUUCCCGGACUCCUUGCUGUUUGUUUUUAAUAUAAAUGCAAAUUUCGCCAACGGCAUUCGCCAGGCGCCAUGCUCCAUAGUACAUAUGUGUG__UGCGAGCCUGUUCCGGAGAUCUGUC
......((((((((((((.((((((.......))))))))))...........(((....))).(((((...((((((...((((....))))..)).))))..))))))))).)))).. (-30.30 = -31.18 +   0.88)

alignment

secondary structure

dotplot

Window 4

Location	15,633,193 – 15,633,299
Length	106
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	90.71
Mean single sequence MFE	-31.80
Consensus MFE	-25.01
Energy contribution	-25.08
Covariance contribution	0.06
Combinations/Pair	1.03
Mean z-score	-1.45
Structure conservation index	0.79
SVM decision value	-0.04
SVM RNA-class probability	0.515420
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15633193 106 - 23771897
GCUUCUGGUUUCUGGCUUCUG--------------GCCGAGAUUCCCGGACUCCUUGCUGUUUGUUUUUAAUAUAAAUGCAAAUUUCGCCAACGGCAUUCGCCCGGAGCCGUGCUCCAUA
((....((..((((((.....--------------))).)))..))(((.((((((((.((((((.......))))))))))...........(((....))).))))))).))...... ( -30.50)
>DroSec_CAF1 55462 106 - 1
GCUUCUGGUUUCUGGCUUCUG--------------GCCGAGAUUCCCGGACUCCUUGCUGUUUGUUUUUAAUAUAAAUGCAAAUUUCGACAACGGCAUUCGCCAGGCGCCAUGCUCCCUA
((...((((.((((((.....--------------((((((.((....))))).((((.((((((.......))))))))))...........)))....)))))).)))).))...... ( -29.10)
>DroSim_CAF1 56419 106 - 1
GCUUCUGGUUUCUGGCUUCUG--------------GCCGAGAUUCACGGACUCCUUGCUGUUUGUUUUUAAUAUAAAUGCAAAUUUCGCCAACGGCAUUCGCCAGGCGCCAUGCUCCAUA
.....(((....((((.((((--------------((.((((((...((...)).(((.((((((.......)))))))))))))))(((...)))....)))))).))))....))).. ( -29.70)
>DroYak_CAF1 60182 120 - 1
GCUUCUGGUUUCUGGCUUCUGGCUGCUGGAUGCUGGCCGAGAUUCCCGGACUCCUUGCUGUUUGUUUUUAAUAUAAAUGCAAAUUUCGCCAACGGCAUUCGCCAGGCGCCAUGCUCCACA
.....(((....((((.((((((....((((((((..(((((((...((...)).(((.((((((.......))))))))))))))))....)))))))))))))).))))....))).. ( -37.90)
>consensus
GCUUCUGGUUUCUGGCUUCUG______________GCCGAGAUUCCCGGACUCCUUGCUGUUUGUUUUUAAUAUAAAUGCAAAUUUCGCCAACGGCAUUCGCCAGGCGCCAUGCUCCAUA
((...((((.((((((....................(((.......)))......((((((((((.((((...)))).))).........)))))))...)))))).)))).))...... (-25.01 = -25.08 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:59:07 2006