Locus 5836

Sequence ID	2R_DroMel_CAF1
Location	18,491,685 – 18,491,805
Length	120
Max. P	0.944745

overview

Window 3

Location	18,491,685 – 18,491,805
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	86.39
Mean single sequence MFE	-39.89
Consensus MFE	-28.86
Energy contribution	-32.17
Covariance contribution	3.31
Combinations/Pair	1.13
Mean z-score	-2.45
Structure conservation index	0.72
SVM decision value	1.20
SVM RNA-class probability	0.930213
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18491685 120 + 20766785
UGAUGAUGGUGUCUGAUGUGAUGAUCGCCCCACUGCAUAUUGCUGUGCCAUCUAUUAUUACUUCCGCCUGGUACGGGGCAUCUUCAAUAUCCACAUCAUAACCUCCAAUGAUGCGGCUUU
.....(((((((..(((((((.(((.(((((...((.....)).((((((..................)))))))))))))).)).))))).)))))))..................... ( -32.77)
>DroSec_CAF1 10292 120 + 1
UGAGUAUGGUGUCUGAUGUGAUGAUGGCCCCACUGCAUAUAGCAGUGCCAUCUAUUAUCACUUCCGCCUGGUACGGGGCAUCUUCAAUGUCCGCAUCAUAUCCUCCAAUGAUGCGGCUUU
...((((((((...((.((((((((((...((((((.....))))))....)))))))))).))))))..)))).((((((.....))))))(((((((........)))))))...... ( -44.10)
>DroEre_CAF1 15755 120 + 1
UAAGGAUGGUAUGUGAUCCGAUGAUGGCCCCACUGCAAAUGGCAGUGUCAUCUAUUAUCACUUCCGCCUGGUAAGGGGCGUCUUCUAUGUCCACAACAUAGCCUCCAAUGAUGCGGGCUU
..(((.(((...(((((.....((((((...(((((.....)))))))))))....)))))..)))))).((...((((((.....))))))...))..(((((.((....)).))))). ( -38.00)
>DroYak_CAF1 17568 120 + 1
UGAGCACGGUUUGUGCUCCGAUGAUGGCUCCACUGCAGAUGGCAGUGCCAUCUAUUAUCACUUCCGCCUGGUAAGGCACAUCUUCUAUGUCCACAUCAUAGCCUCCAAUGAUGCGGGCUU
.((((((.....)))))).((((((((...((((((.....))))))....))))))))......((((....))))...........((((.((((((........)))))).)))).. ( -44.70)
>consensus
UGAGGAUGGUGUCUGAUCCGAUGAUGGCCCCACUGCAUAUGGCAGUGCCAUCUAUUAUCACUUCCGCCUGGUAAGGGGCAUCUUCAAUGUCCACAUCAUAGCCUCCAAUGAUGCGGCCUU
.((((((((...((((((....((((((...(((((.....)))))))))))...))))))..))((((......))))))))))...((((.((((((........)))))).)))).. (-28.86 = -32.17 +   3.31)

alignment

secondary structure

dotplot

Window 4

Location	18,491,685 – 18,491,805
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	86.39
Mean single sequence MFE	-39.67
Consensus MFE	-31.60
Energy contribution	-32.23
Covariance contribution	0.62
Combinations/Pair	1.08
Mean z-score	-2.28
Structure conservation index	0.80
SVM decision value	1.35
SVM RNA-class probability	0.944745
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18491685 120 - 20766785
AAAGCCGCAUCAUUGGAGGUUAUGAUGUGGAUAUUGAAGAUGCCCCGUACCAGGCGGAAGUAAUAAUAGAUGGCACAGCAAUAUGCAGUGGGGCGAUCAUCACAUCAGACACCAUCAUCA
....(((((((((........)))))))))....(((.((((((((((.(((.((....)).........))).)).((.....))...))))).))).))).................. ( -35.70)
>DroSec_CAF1 10292 120 - 1
AAAGCCGCAUCAUUGGAGGAUAUGAUGCGGACAUUGAAGAUGCCCCGUACCAGGCGGAAGUGAUAAUAGAUGGCACUGCUAUAUGCAGUGGGGCCAUCAUCACAUCAGACACCAUACUCA
...((((((((((........))))))))).)..(((..(((..((((.....))))..(((((....(((((((((((.....)))))...))))))))))).........)))..))) ( -41.50)
>DroEre_CAF1 15755 120 - 1
AAGCCCGCAUCAUUGGAGGCUAUGUUGUGGACAUAGAAGACGCCCCUUACCAGGCGGAAGUGAUAAUAGAUGACACUGCCAUUUGCAGUGGGGCCAUCAUCGGAUCACAUACCAUCCUUA
..((((.((((((((....(((((((...)))))))....((((........)))).......)))).)))).((((((.....)))))))))).......((((........))))... ( -35.50)
>DroYak_CAF1 17568 120 - 1
AAGCCCGCAUCAUUGGAGGCUAUGAUGUGGACAUAGAAGAUGUGCCUUACCAGGCGGAAGUGAUAAUAGAUGGCACUGCCAUCUGCAGUGGAGCCAUCAUCGGAGCACAAACCGUGCUCA
..(.(((((((((........))))))))).)...((.((((.((..(((...((....)).....((((((((...))))))))..)))..)))))).)).((((((.....)))))). ( -46.00)
>consensus
AAACCCGCAUCAUUGGAGGCUAUGAUGUGGACAUAGAAGAUGCCCCGUACCAGGCGGAAGUGAUAAUAGAUGGCACUGCCAUAUGCAGUGGGGCCAUCAUCACAUCACACACCAUCCUCA
....(((((((((........))))))))).....((.((((((((.......((....)).............(((((.....)))))))))).))).))................... (-31.60 = -32.23 +   0.62)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:55:45 2006