Locus 5437

Sequence ID	2R_DroMel_CAF1
Location	17,489,544 – 17,489,683
Length	139
Max. P	0.652124

overview

Window 4

Location	17,489,544 – 17,489,664
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	85.61
Mean single sequence MFE	-29.40
Consensus MFE	-20.46
Energy contribution	-21.40
Covariance contribution	0.94
Combinations/Pair	1.19
Mean z-score	-1.69
Structure conservation index	0.70
SVM decision value	0.25
SVM RNA-class probability	0.652124
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17489544 120 - 20766785
UUUAAAAGAGGAAAGCACUGAAGGGAAUCCUUUUUUUACUUGAAAUGUAAUUCUUCUUCUUGACUUGUGUUCAUAAUUUUCUGUUUACCCAACAGAGGAGGCAAUCUGGACGUUUUGCCA
.((((((((((((......(((((....)))))..((((.......)))))))))))).)))).............(((((((((.....)))))))))(((((..........))))). ( -25.10)
>DroSec_CAF1 17352 118 - 1
UUUAAAAGAGGAAAGCACUGAAGGGAAACCUU--UUUACUUGCAAUGUAAUUCCUUUUCUUGACUUGUGUUCAUAAUUUUCUGUUUACCCAACAGAGGAGGCAAUCUGGACGGUUUGCCA
.((((((((((((......(((((....))))--)((((.......)))))))))))).)))).............(((((((((.....)))))))))(((((.((....)).))))). ( -31.50)
>DroSim_CAF1 30213 118 - 1
UUUAAAAGAGGAAAGCACUGAAGGGAAACCUU--UUUACUUGCAAUGUAAUUCCUUUUCUUGACUCGUGGUCAUAAUUUUCUGUUUACCCAACAGAGGAGGCAAUCUGGACGGUUUGCCA
.....((((((((......(((((....))))--)((((.......))))))))))))..((((.....))))...(((((((((.....)))))))))(((((.((....)).))))). ( -34.10)
>DroYak_CAF1 26399 115 - 1
----AAUAAUGGAGGUACUUAAGGGAAUACUUC-UUUGCUGACAAUGUAAUUCUUUUCCUCGACUUGUUUUCAUAAAUCUCUGUUUACCCAACAGAGGAGCAAAUCUGAAUGGUUUGCCA
----....(((((..((.(..((((((......-.((((.......))))....))))))..)..))..)))))...((((((((.....)))))))).(((((((.....))))))).. ( -26.90)
>consensus
UUUAAAAGAGGAAAGCACUGAAGGGAAACCUU__UUUACUUGCAAUGUAAUUCCUUUUCUUGACUUGUGUUCAUAAUUUUCUGUUUACCCAACAGAGGAGGCAAUCUGGACGGUUUGCCA
.....((((((((.......((((....))))...((((.......))))))))))))..................(((((((((.....)))))))))(((((.((....)).))))). (-20.46 = -21.40 +   0.94)

alignment

secondary structure

dotplot

Window 5

Location	17,489,584 – 17,489,683
Length	99
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	83.24
Mean single sequence MFE	-21.47
Consensus MFE	-18.07
Energy contribution	-17.63
Covariance contribution	-0.44
Combinations/Pair	1.06
Mean z-score	-1.42
Structure conservation index	0.84
SVM decision value	0.13
SVM RNA-class probability	0.599205
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17489584 99 - 20766785
CCA---------------------AUAUAAAUUAGAUCAUUUUAAAAGAGGAAAGCACUGAAGGGAAUCCUUUUUUUACUUGAAAUGUAAUUCUUCUUCUUGACUUGUGUUCAUAAUUUU
...---------------------....((((((((.(((.....((((((((......(((((....)))))..((((.......))))...)))))))).....))).)).)))))). ( -17.00)
>DroSec_CAF1 17392 118 - 1
CCAAACCAAAUAGACGUUAUUAUAAUGUAAAUUAGAUCAUUUUAAAAGAGGAAAGCACUGAAGGGAAACCUU--UUUACUUGCAAUGUAAUUCCUUUUCUUGACUUGUGUUCAUAAUUUU
.............((((((...))))))((((((((.(((.((((((((((((......(((((....))))--)((((.......)))))))))))).))))...))).)).)))))). ( -22.10)
>DroSim_CAF1 30253 118 - 1
CCAAACCAAAUAGACGUUAUUAUAAUGUAAAUUAGAUCAUUUUAAAAGAGGAAAGCACUGAAGGGAAACCUU--UUUACUUGCAAUGUAAUUCCUUUUCUUGACUCGUGGUCAUAAUUUU
.............((((((...))))))((((((((((((.((((((((((((......(((((....))))--)((((.......)))))))))))).))))...)))))).)))))). ( -25.30)
>consensus
CCAAACCAAAUAGACGUUAUUAUAAUGUAAAUUAGAUCAUUUUAAAAGAGGAAAGCACUGAAGGGAAACCUU__UUUACUUGCAAUGUAAUUCCUUUUCUUGACUUGUGUUCAUAAUUUU
............................((((((((.(((.((((((((((((.......((((....))))...((((.......)))))))))))).))))...))).)).)))))). (-18.07 = -17.63 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:44:50 2006