Locus 4662

Sequence ID	2L_DroMel_CAF1
Location	13,363,101 – 13,363,288
Length	187
Max. P	0.731285

overview

Window 1

Location	13,363,101 – 13,363,221
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.89
Mean single sequence MFE	-29.00
Consensus MFE	-24.81
Energy contribution	-25.62
Covariance contribution	0.81
Combinations/Pair	1.03
Mean z-score	-1.67
Structure conservation index	0.86
SVM decision value	0.41
SVM RNA-class probability	0.725451
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13363101 120 + 22407834
AACUCUCUUAGCUGCAUAUUCCUCCCUUAAAUGCAGUUUUUUUUAGCUCAACUACCAAUUGAGUGAAUGUUAACGGAAUGUUAACUGCAAUCUCAAGACUCAAGCGCAGUUCUGAGUGAG
..(((.(((((((((................(((((((.......((((((.......)))))).((((((.....))))))))))))).((....)).......))))..))))).))) ( -26.00)
>DroSec_CAF1 3953 119 + 1
AACUCUCUUAGCUGCAUAUUCCUCUCUUAAAUGCAGUUUU-UUAAGCUCAACUUCCAAUUGAGUGAAUGUUUACGGAAUGUUAACUGCAGUCUCAAGACUCAAGCGCAGUUCUGAGUGAG
..(((.((((((((((((((((....(((((........)-))))((((((.......))))))..........))))))).....((((((....))))...))))))..))))).))) ( -29.70)
>DroSim_CAF1 3100 119 + 1
AACUCUCUUAGCUGCAUAUUCCUCUCUUAAAUGCAGUUUU-UUAAGCUCAACUUCCAAUUGAGUGAAUGUUUACGGAAUGUUAACUGCAGUCUCAAGACUCAAGCGCAGUUCUGAGUGAG
..(((.((((((((((((((((....(((((........)-))))((((((.......))))))..........))))))).....((((((....))))...))))))..))))).))) ( -29.70)
>DroYak_CAF1 3264 119 + 1
AACUCUCUUAGUUGCACAUUCCUCCCUUAAGUGCAGUCUA-UUAAGCUCGACUACCAUUGGAGUGAAUGUUUACAGAAUGUUAACUGCAAUCUCUAGACUCAAGCGCAGUUCUGAGUGAG
..(((.(((((((((.(((((((((....((((.((((..-........))))..)))))))).))))(((((.(((.(((.....))).))).)))))....).))))..))))).))) ( -30.60)
>consensus
AACUCUCUUAGCUGCAUAUUCCUCCCUUAAAUGCAGUUUU_UUAAGCUCAACUACCAAUUGAGUGAAUGUUUACGGAAUGUUAACUGCAAUCUCAAGACUCAAGCGCAGUUCUGAGUGAG
..(((.(((((((((................(((((((.......((((((.......)))))).((((((.....)))))))))))))(((....)))......))))..))))).))) (-24.81 = -25.62 +   0.81)

alignment

secondary structure

dotplot

Window 2

Location	13,363,181 – 13,363,288
Length	107
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	84.95
Mean single sequence MFE	-27.45
Consensus MFE	-20.38
Energy contribution	-20.38
Covariance contribution	0.00
Combinations/Pair	1.15
Mean z-score	-1.74
Structure conservation index	0.74
SVM decision value	0.42
SVM RNA-class probability	0.731285
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13363181 107 - 22407834
GAAU-------------CGUCAAAAUACUGCUCAUGACUCUUAUGAGCUUAGUCUGUUCCACUCAAAGCCACAUAUUUGACUCACUCAGAACUGCGCUUGAGUCUUGAGAUUGCAGUUAA
....-------------.........((((((((.(((((....((((.(((((((......(((((........)))))......))).)))).))))))))).)))....)))))... ( -26.80)
>DroSec_CAF1 4032 117 - 1
GAAUCC---AAUCCACUCGUCAAAAUCCUGCUCAUUUCUCUUAUGAGCUUGGUCUGUUCCACUCAAAGCUACUUAUUUGACUCACUCAGAACUGCGCUUGAGUCUUGAGACUGCAGUUAA
......---.........((((((.....((((((.......)))))).(((......)))..............))))))........((((((.....((((....)))))))))).. ( -24.50)
>DroSim_CAF1 3179 117 - 1
GAAUCC---AAUUCACUCGUCAAAAUUCUGCUCAUGGCUCUUAUGAGCUUGGUCUGUUCCACUCAAAGCUACUUAUUUGACUCACUCAGAACUGCGCUUGAGUCUUGAGACUGCAGUUAA
......---.........((((((.....(((...(((((....)))))(((......))).....)))......))))))........((((((.....((((....)))))))))).. ( -25.20)
>DroYak_CAF1 3343 120 - 1
GACUGCAAAAAUCCACUUGUCAAAAUGCAGCUCAUUGCACCAAUGAGCUUAGUCGGUUCCACUCAAAGCUACCAGUUAGACUCACUCAGAACUGCGCUUGAGUCUAGAGAUUGCAGUUAA
((((((((.((((.((((((......)))((((((((...))))))))..))).))))...(((...((.....))(((((((((.((....)).)..))))))))))).)))))))).. ( -33.30)
>consensus
GAAUCC___AAUCCACUCGUCAAAAUACUGCUCAUGGCUCUUAUGAGCUUAGUCUGUUCCACUCAAAGCUACUUAUUUGACUCACUCAGAACUGCGCUUGAGUCUUGAGACUGCAGUUAA
..................((((((.....((((((((...)))))))).......(((........)))......))))))........((((((.....((((....)))))))))).. (-20.38 = -20.38 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:00 2006