Locus 1559

Sequence ID	2R_DroMel_CAF1
Location	5,894,968 – 5,895,058
Length	90
Max. P	0.998106

overview

Window 7

Location	5,894,968 – 5,895,058
Length	90
Sequences	5
Columns	90
Reading direction	forward
Mean pairwise identity	95.89
Mean single sequence MFE	-28.64
Consensus MFE	-26.22
Energy contribution	-26.06
Covariance contribution	-0.16
Combinations/Pair	1.11
Mean z-score	-2.10
Structure conservation index	0.92
SVM decision value	3.01
SVM RNA-class probability	0.998106
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5894968 90 + 20766785
UGGGAAUGGGAUAGCCGAGAGUCCGCACGGCUAUUUCAAUUGCUGUCUGUAGUUGAUAUAAUCAACAUUAUGCGGACGUAUUUAUGCAGC
......((..(((((((.(......).)))))))..))...((((((((((((((((...))))))....)))))))(((....)))))) ( -28.60)
>DroSec_CAF1 31340 90 + 1
UGGGAAUGGGAUAGCCGAGAGUCCGCACGGCUAUUUCAAUUGCUGCCUGUAGUUGAUAUAAUCAACAUUAUGCGGACGUAUUUAUGCAGC
......((..(((((((.(......).)))))))..))...(((((.....((((((...))))))...((((....))))....))))) ( -27.70)
>DroSim_CAF1 30106 90 + 1
UGGGAAUGGGAUAGCCGAGAGUCCGCACGGCUAUUUCAAUUGCUGCCUGUAGUUGAUAUAAUCAACAUUAUGCGGACGUAUUUAUGCAGC
......((..(((((((.(......).)))))))..))...(((((.....((((((...))))))...((((....))))....))))) ( -27.70)
>DroEre_CAF1 29405 90 + 1
UGGGAAUGGGAGAGCCGAGCGUCUGCACGGCUACUUCAAUAGCUGUCUGUAGUUGAUAUAGUCAACAUUAUGCGGACGUAUUUAUGCAGC
........(((((((((.((....)).))))).))))....((((((((((((((((...))))))....)))))))(((....)))))) ( -28.70)
>DroYak_CAF1 29456 90 + 1
UGGGAAUGGGAUAGCCGAGUGUCCGCACGGCUAUUUCAAUUGCUGUCUGUAGUUGAUAUAAUCGACAUUAUGCGGACGUAUUUAUGCAGC
......((..(((((((.((....)).)))))))..))...((((((((((((((((...))))))....)))))))(((....)))))) ( -30.50)
>consensus
UGGGAAUGGGAUAGCCGAGAGUCCGCACGGCUAUUUCAAUUGCUGUCUGUAGUUGAUAUAAUCAACAUUAUGCGGACGUAUUUAUGCAGC
......(((((((((((.(......).)))))))))))...(((((.....((((((...))))))...((((....))))....))))) (-26.22 = -26.06 +  -0.16)

alignment

secondary structure

dotplot

Window 8

Location	5,894,968 – 5,895,058
Length	90
Sequences	5
Columns	90
Reading direction	reverse
Mean pairwise identity	95.89
Mean single sequence MFE	-20.11
Consensus MFE	-17.34
Energy contribution	-17.58
Covariance contribution	0.24
Combinations/Pair	1.05
Mean z-score	-1.28
Structure conservation index	0.86
SVM decision value	0.03
SVM RNA-class probability	0.550315
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5894968 90 - 20766785
GCUGCAUAAAUACGUCCGCAUAAUGUUGAUUAUAUCAACUACAGACAGCAAUUGAAAUAGCCGUGCGGACUCUCGGCUAUCCCAUUCCCA
((((.........((((((((...((((((...))))))........((..........)).))))))))...))))............. ( -18.60)
>DroSec_CAF1 31340 90 - 1
GCUGCAUAAAUACGUCCGCAUAAUGUUGAUUAUAUCAACUACAGGCAGCAAUUGAAAUAGCCGUGCGGACUCUCGGCUAUCCCAUUCCCA
((((.........((((((((...((((((...))))))....(((.............)))))))))))...))))............. ( -22.52)
>DroSim_CAF1 30106 90 - 1
GCUGCAUAAAUACGUCCGCAUAAUGUUGAUUAUAUCAACUACAGGCAGCAAUUGAAAUAGCCGUGCGGACUCUCGGCUAUCCCAUUCCCA
((((.........((((((((...((((((...))))))....(((.............)))))))))))...))))............. ( -22.52)
>DroEre_CAF1 29405 90 - 1
GCUGCAUAAAUACGUCCGCAUAAUGUUGACUAUAUCAACUACAGACAGCUAUUGAAGUAGCCGUGCAGACGCUCGGCUCUCCCAUUCCCA
((((........((((.((((...(((((.....)))))........(((((....))))).)))).))))..))))............. ( -19.50)
>DroYak_CAF1 29456 90 - 1
GCUGCAUAAAUACGUCCGCAUAAUGUCGAUUAUAUCAACUACAGACAGCAAUUGAAAUAGCCGUGCGGACACUCGGCUAUCCCAUUCCCA
((((.........((((((((..((((................))))((..........)).))))))))...))))............. ( -17.39)
>consensus
GCUGCAUAAAUACGUCCGCAUAAUGUUGAUUAUAUCAACUACAGACAGCAAUUGAAAUAGCCGUGCGGACUCUCGGCUAUCCCAUUCCCA
(((((........(....).....(((((.....)))))....).))))...((..(((((((.(......).)))))))..))...... (-17.34 = -17.58 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:31 2006