Locus 3330

Sequence ID	2R_DroMel_CAF1
Location	11,336,966 – 11,337,096
Length	130
Max. P	0.999624

overview

Window 5

Location	11,336,966 – 11,337,056
Length	90
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	81.82
Mean single sequence MFE	-29.78
Consensus MFE	-23.54
Energy contribution	-24.34
Covariance contribution	0.80
Combinations/Pair	1.20
Mean z-score	-2.62
Structure conservation index	0.79
SVM decision value	2.19
SVM RNA-class probability	0.990033
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11336966 90 - 20766785
CAUGGGCACGUGCCCGGCACUCCGGGCACAUCAUCCUUGUGUCCUUUGCCGCUCAUAACGGCAAUU---------CGUGUUGACAAGUGCAAACAUUAA
.(((.((((((((((((....))))))))..........((((..((((((.......))))))..---------......)))).))))...)))... ( -33.50)
>DroSec_CAF1 124719 71 - 1
CAUGGGCACGUGCCCGGCACUCCGGGCACAUCAUCCUUGUGUCCUUUGCCGCUCAUAACGGC----------------------------AAACAUUAA
...((((((((((((((....)))))))).........))))))(((((((.......))))----------------------------)))...... ( -31.20)
>DroSim_CAF1 130433 90 - 1
CAUGGGCACGUGCCAGGCACUCCGGGCACAUCAUCCUUGUGUCCUUUGCCGCUCAUAACGGCAAUU---------CGUGUUGACAAGUGCAAACAUUAA
.(((.((((.((...(((((...(((((((.......))))))).((((((.......))))))..---------.)))))..)).))))...)))... ( -31.60)
>DroEre_CAF1 128556 89 - 1
CAUGGGCACGUGCCCGGCUCUCUGGGUACAUCAUCCUUUCGUCCUUUGCCACUCAUAACGGUAAUU---------CGUGUUGACAAGUGCA-ACGGUAA
.....((((((((((((....)))))))).(((......((....(((((.........)))))..---------))...)))...)))).-....... ( -23.90)
>DroYak_CAF1 127709 98 - 1
CAUGGGCACGUGCCCGGCUCUCUGGGCACAUCAUCCUUUCGUCCUUUGCCGCUCAUAACGGUAAUUCGUGUAAUUCGUGUUGACAAGUGCA-ACAGUAA
.....((((((((((((....))))))))................((((((.......))))))...))))......(((((.(....)))-))).... ( -28.70)
>consensus
CAUGGGCACGUGCCCGGCACUCCGGGCACAUCAUCCUUGUGUCCUUUGCCGCUCAUAACGGCAAUU_________CGUGUUGACAAGUGCAAACAUUAA
..((.((((((((((((....))))))))................((((((.......))))))......................))))...)).... (-23.54 = -24.34 +   0.80)

alignment

secondary structure

dotplot

Window 6

Location	11,336,997 – 11,337,096
Length	99
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	94.44
Mean single sequence MFE	-28.20
Consensus MFE	-25.66
Energy contribution	-25.70
Covariance contribution	0.04
Combinations/Pair	1.21
Mean z-score	-2.41
Structure conservation index	0.91
SVM decision value	3.80
SVM RNA-class probability	0.999624
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11336997 99 - 20766785
UAAAUUGUCAAAUUGUUUGGCCCCCUUAUCACGAUGUCCUCAUGGGCACGUGCCCGGCACUCCGGGCACAUCAUCCUUGUGUCCUUUGCCGCUCAUAAC
.............((..((((........((((((((((....))))).((((((((....)))))))).......)))))......))))..)).... ( -32.14)
>DroSec_CAF1 124731 99 - 1
UAAAUUGUCAAAUUGUUUGGCCCCCUUAUCGCGAUGUCCUCAUGGGCACGUGCCCGGCACUCCGGGCACAUCAUCCUUGUGUCCUUUGCCGCUCAUAAC
.............((..((((........((((((((((....))))).((((((((....)))))))).......)))))......))))..)).... ( -31.74)
>DroSim_CAF1 130464 99 - 1
UAAAUUGUCAAAUUGUUUGGCCCCCUUAUCGCGAUGUCCUCAUGGGCACGUGCCAGGCACUCCGGGCACAUCAUCCUUGUGUCCUUUGCCGCUCAUAAC
.............((..((((..(((...((((.(((((....)))))))))..)))......(((((((.......)))))))...))))..)).... ( -29.90)
>DroEre_CAF1 128586 99 - 1
UAAAUUGUCAAAUUGUUUGUCCCUCUUAUCGCGAUGUCCUCAUGGGCACGUGCCCGGCUCUCUGGGUACAUCAUCCUUUCGUCCUUUGCCACUCAUAAC
..............................(((((((((....))))).((((((((....)))))))).........))))................. ( -21.70)
>DroYak_CAF1 127748 99 - 1
UAAACUGUCAAAUUGUUUGCCCCCCUUAUCGCGAUGUCCUCAUGGGCACGUGCCCGGCUCUCUGGGCACAUCAUCCUUUCGUCCUUUGCCGCUCAUAAC
(((((.........)))))...........(((.(((((....))))).((((((((....))))))))....................)))....... ( -25.50)
>consensus
UAAAUUGUCAAAUUGUUUGGCCCCCUUAUCGCGAUGUCCUCAUGGGCACGUGCCCGGCACUCCGGGCACAUCAUCCUUGUGUCCUUUGCCGCUCAUAAC
.............((..((((........((((((((((....))))).((((((((....)))))))).......)))))......))))..)).... (-25.66 = -25.70 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:52:51 2006