Locus 798

Sequence ID	2L_DroMel_CAF1
Location	2,280,784 – 2,280,946
Length	162
Max. P	0.804859

overview

Window 8

Location	2,280,784 – 2,280,890
Length	106
Sequences	4
Columns	110
Reading direction	reverse
Mean pairwise identity	86.73
Mean single sequence MFE	-40.50
Consensus MFE	-30.91
Energy contribution	-31.35
Covariance contribution	0.44
Combinations/Pair	1.14
Mean z-score	-1.62
Structure conservation index	0.76
SVM decision value	0.29
SVM RNA-class probability	0.669320
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2280784 106 - 22407834
AGCGGUGCCAGUGGUGCCAGUAGUACCGUUGGUGUCAGUGGGUCAGGCCC-UGGG---UGAGUGGGUGUUGCUAUAAUGGCAAAUCACUUUGCACCGCAAACAGAGUCCA
.(((((((.((((((((((((((((((((((....)))))).....((((-....---.....))))..))))))..)))))..)))))..)))))))............ ( -39.60)
>DroSec_CAF1 16974 106 - 1
GGCGGUGCCAGUGGUGCCGGUAGUACCGGUGGUGUCAGUGGGUCAGGCCC-UGGG---UGAGUGGGUGUUGCUAUAAUGGCAAAUCACUUUGCACCGCAAACAGAGUCCA
.(((((((.(((((((((((.....)))))..(((((...(((.(.((((-....---.....)))).).)))....))))).))))))..)))))))............ ( -43.70)
>DroSim_CAF1 17080 106 - 1
GGCGGUGCCAGUGGUGCCGGUAGUACCGGUGGUGUCAGUGGGUCAGGCCC-UGGG---UGAGUGGGUGUUGCUAUAAUGGCAAAUCACUUUGCACCGCAAACAGAGUCCA
.(((((((.(((((((((((.....)))))..(((((...(((.(.((((-....---.....)))).).)))....))))).))))))..)))))))............ ( -43.70)
>DroYak_CAF1 17383 95 - 1
GGCGGUGUUG---------------GCGGUGGUGUCAGUGGGUCAGGCCCCUGGGUACUGGAUGGGUGGUGCUAUAAUGGCAAAUCACUUUGCACCGCAAACAGAGUCCA
(((..((((.---------------(((((((..(((.(.(..((((((....))).)))..).).)))..))......(((((....)))))))))).))))..))).. ( -35.00)
>consensus
GGCGGUGCCAGUGGUGCCGGUAGUACCGGUGGUGUCAGUGGGUCAGGCCC_UGGG___UGAGUGGGUGUUGCUAUAAUGGCAAAUCACUUUGCACCGCAAACAGAGUCCA
.(((((((((.((((((.....)))))).)).(((((...(((.(.((((.(.........).)))).).)))....))))).........)))))))............ (-30.91 = -31.35 +   0.44)

alignment

secondary structure

dotplot

Window 9

Location	2,280,850 – 2,280,946
Length	96
Sequences	4
Columns	96
Reading direction	reverse
Mean pairwise identity	82.12
Mean single sequence MFE	-32.57
Consensus MFE	-23.02
Energy contribution	-25.40
Covariance contribution	2.38
Combinations/Pair	1.07
Mean z-score	-1.88
Structure conservation index	0.71
SVM decision value	0.63
SVM RNA-class probability	0.804859
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2280850 96 - 22407834
CAAAGUGCCAAAGACAGUGGUCCCGAGGGGCGGGAAAGUGGUAUGUCGAUGGUGUUAGCGGUGCCAGUGGUGCCAGUAGUACCGUUGGUGUCAGUG
...((..(((..((((....(((((.....)))))........))))..)))..))...((..((((((((((.....))))))))))..)).... ( -36.40)
>DroSec_CAF1 17040 96 - 1
CAAAGUGCCAAAGACAGUGGUCCCGAGGGGCGGGAAAGUGGUAUGUCGAUGGUGUUGGCGGUGCCAGUGGUGCCGGUAGUACCGGUGGUGUCAGUG
...((..(((..((((....(((((.....)))))........))))..)))..))...((..(((.((((((.....)))))).)))..)).... ( -37.50)
>DroSim_CAF1 17146 96 - 1
CAAAGUGCCAAAGACAGUGGUCCCGAGGGGCGGGAAAGUGGUAUGUCGAUGGUGUUGGCGGUGCCAGUGGUGCCGGUAGUACCGGUGGUGUCAGUG
...((..(((..((((....(((((.....)))))........))))..)))..))...((..(((.((((((.....)))))).)))..)).... ( -37.50)
>DroEre_CAF1 17169 72 - 1
CAAAGUGCCAAAGACAGUGGUCCCGGGGGGAAGUAAAGUGGUAUGUCGAUGGUGGUU------------------------CCGGUGGUGCCGGUG
..((.(((((..((((....((((...))))............))))..))))).))------------------------((((.....)))).. ( -18.89)
>consensus
CAAAGUGCCAAAGACAGUGGUCCCGAGGGGCGGGAAAGUGGUAUGUCGAUGGUGUUGGCGGUGCCAGUGGUGCCGGUAGUACCGGUGGUGUCAGUG
....(..(((..((((....(((((.....)))))........))))..((((((((.(((((((...))))))).)))))))).)))..)..... (-23.02 = -25.40 +   2.38)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:45:57 2006