Locus 4010

Sequence ID	3L_DroMel_CAF1
Location	11,704,260 – 11,704,403
Length	143
Max. P	0.998577

overview

Window 6

Location	11,704,260 – 11,704,363
Length	103
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	70.38
Mean single sequence MFE	-29.27
Consensus MFE	-12.54
Energy contribution	-13.91
Covariance contribution	1.37
Combinations/Pair	1.37
Mean z-score	-3.02
Structure conservation index	0.43
SVM decision value	3.15
SVM RNA-class probability	0.998577
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11704260 103 + 23771897
UGUGAUGCUGAUGUAAGCU----AUAGGAGUAUUCUAAAA-----AAAUUGAAUACUUAUCUAUUACUU-CUAUUGCAGUUGCUUUUAAACUUGGAGAGCAGCUGUUUGGAGA
.((((((((......))).----....((((((((.....-----.....))))))))....)))))((-(((..((((((((((((.......)))))))))))).))))). ( -31.80)
>DroVir_CAF1 21493 106 + 1
CACAAGCCCAACGUGAGUUUGUCAUUAAUUUAAUC-ACAAGCUUGA------AAUGAAAUUGGUUUUUCUUUUUGGCAGCUGAUUUGUGCAUUGGAGAGACACUGCUUGAAUA
..(((((.((...(((((((((.((((...)))).-))))))))).------..)).....(((.(((((((...(((.(......))))...))))))).)))))))).... ( -25.10)
>DroSec_CAF1 17541 108 + 1
UGUGAUGCUGAGGUAAGCC----AUAAAAGUAUUCUAAAAGUUAUAUAUUGAAUACUUAUCUAGUAUUU-CUUGGGCAGUUGCUUUUAAACUUGGAGAGCAACUGUCUGGAUA
.(.(((((((.((....))----....((((((((...............))))))))...))))))).-)(..(((((((((((((.......)))))))))))))..)... ( -33.86)
>DroSim_CAF1 13012 108 + 1
UGUGAUGCUGAGGUAAGCU----AUUAAAGUAUUCUAAAAGCUAUAUAUUGAAUACUUAUCUAUUACUU-CUAUUCCAGUUGCUUUUAAACUUGGAGAGCAGCUGUCUGGAUA
.((((((((......))).----....((((((((...............))))))))....))))).(-(((...(((((((((((.......)))))))))))..)))).. ( -27.36)
>DroEre_CAF1 13527 107 + 1
UGUGAUGCUGAGGUAAACU----UUAACAGUAUAAUUAGAGUUAUCUAUUUAAUACUUAUUUACAACUU--UCUUGCAGUUGCUUUUAAACUUGGAGAGCAGCUGUCUGGAUA
(((((((.(((((....))----))).))((((((.((((....)))).)).))))....)))))...(--((..((((((((((((.......))))))))))))..))).. ( -27.50)
>DroYak_CAF1 13604 107 + 1
UGUGAUGCUGAUGUAAGCU----UUAACAGAGUUCUGAAAGUUAUAAAUUUGUUACUCAUUCAUUACUA--UCUUGCAGUUGCUUUUAAACUUGGAGAGCAGCUGUCUGGAUA
.((((((.(((.(((((((----((..(((....))))))))..........)))))))..))))))((--(((.((((((((((((.......))))))))))))..))))) ( -30.00)
>consensus
UGUGAUGCUGAGGUAAGCU____AUAAAAGUAUUCUAAAAGUUAUAUAUUGAAUACUUAUCUAUUACUU_CUAUUGCAGUUGCUUUUAAACUUGGAGAGCAGCUGUCUGGAUA
............................(((((((...............)))))))..................((((((((((((.......))))))))))))....... (-12.54 = -13.91 +   1.37)

alignment

secondary structure

dotplot

Window 7

Location	11,704,294 – 11,704,403
Length	109
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	73.75
Mean single sequence MFE	-25.98
Consensus MFE	-13.41
Energy contribution	-14.17
Covariance contribution	0.75
Combinations/Pair	1.25
Mean z-score	-1.61
Structure conservation index	0.52
SVM decision value	0.09
SVM RNA-class probability	0.579449
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11704294 109 + 23771897
AA-----AAAUUGAAUACUUAUCUAUUACUU-CUAUUGCAGUUGCUUUUAAACUUGGAGAGCAGCUGUUUGGAGAAUUUCCUAAACGAUGACACCAUUAUUGAGUCUGAGUUCCA
..-----.........(((((.((....(((-(....((((((((((((.......))))))))))))..))))...........((((((.....))))))))..))))).... ( -23.70)
>DroVir_CAF1 21530 109 + 1
AAGCUUGA------AAUGAAAUUGGUUUUUCUUUUUGGCAGCUGAUUUGUGCAUUGGAGAGACACUGCUUGAAUAUCUUCCUGGACGAUGAGACGCUUAGCGAGUCCGAAUACUC
..(((.((------((.((((......)))))))).))).(((((..(((.(((((..(((......))).....(((....))))))))..))).)))))((((......)))) ( -19.50)
>DroSec_CAF1 17575 114 + 1
AAGUUAUAUAUUGAAUACUUAUCUAGUAUUU-CUUGGGCAGUUGCUUUUAAACUUGGAGAGCAACUGUCUGGAUAAUUUUCUAAACGAUGACACGAUCAAUGAGUCUGAGUUCCA
(((((((.....(((((((.....)))))))-.(..(((((((((((((.......)))))))))))))..))))))))....(((...(((.((.....)).)))...)))... ( -29.00)
>DroSim_CAF1 13046 114 + 1
AAGCUAUAUAUUGAAUACUUAUCUAUUACUU-CUAUUCCAGUUGCUUUUAAACUUGGAGAGCAGCUGUCUGGAUAAUUUUCUAAACGAUGACACCAUCAAUGAGUCUGAAUUCCA
............((((((((((........(-(((...(((((((((((.......)))))))))))..)))).............((((....)))).))))))....)))).. ( -22.70)
>DroEre_CAF1 13561 113 + 1
GAGUUAUCUAUUUAAUACUUAUUUACAACUU--UCUUGCAGUUGCUUUUAAACUUGGAGAGCAGCUGUCUGGAUAAUUUUCUGAAUGAUGAUACCAUCAACGAGAAUGAGUACCA
...............(((((((((.(....(--((..((((((((((((.......))))))))))))..)))............(((((....)))))..).)))))))))... ( -29.50)
>DroYak_CAF1 13638 113 + 1
AAGUUAUAAAUUUGUUACUCAUUCAUUACUA--UCUUGCAGUUGCUUUUAAACUUGGAGAGCAGCUGUCUGGAUAAUUUCCUAAACGAUGACACCAUUGACGAGACUGAGUUUCA
............((..(((((.((.....((--(((.((((((((((((.......))))))))))))..)))))..........(((((....)))))....)).)))))..)) ( -31.50)
>consensus
AAGUUAUAUAUUGAAUACUUAUCUAUUACUU_CUAUUGCAGUUGCUUUUAAACUUGGAGAGCAGCUGUCUGGAUAAUUUCCUAAACGAUGACACCAUCAACGAGUCUGAGUUCCA
..................(((((..............((((((((((((.......))))))))))))..(((.....))).....)))))........................ (-13.41 = -14.17 +   0.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:12:20 2006