Locus 1404

Sequence ID	2L_DroMel_CAF1
Location	3,746,574 – 3,746,710
Length	136
Max. P	0.981065

overview

Window 2

Location	3,746,574 – 3,746,680
Length	106
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	95.01
Mean single sequence MFE	-21.96
Consensus MFE	-19.84
Energy contribution	-20.56
Covariance contribution	0.72
Combinations/Pair	1.08
Mean z-score	-1.65
Structure conservation index	0.90
SVM decision value	1.74
SVM RNA-class probability	0.974814
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3746574 106 + 22407834
CCAAUAUAAAUGGCUGCUGUUAUAUGUACAAUCCCAUGCCACCCGCCCAUCAGAGCCACCAUCAGCAUGACCACCAUCAUGCGCAGCAGCACCACCCGGUGGCCCA
..........((((((..(((........)))..)).))))...........(.((((((....((((((......))))))((....)).......)))))).). ( -27.20)
>DroSec_CAF1 208671 103 + 1
CCAAUAUAAAUGGCUGCUGUUAUAUGUACAAUCCCAUGCCACCUGCCCAUCAGAGCCACUAUCAGCAUGACCACCAUCAGGCGCA---GCACCACCCGGUAGCCCA
...........((((((((...((((........))))....((((((......((........)).(((......))))).)))---).......)))))))).. ( -21.70)
>DroSim_CAF1 215805 103 + 1
CCAAUAUAAAUGGCUGCUGUUAUAUGUACAAUCCCAUGCCACCCGCCCAUCAGAGCCACCAUCAGCAUGACCACCAUCAUGCGCA---GCACCACCCGGUGGCCCA
....((((.(((((....))))).)))).........((((((.((.(....).))........((((((......))))))...---.........))))))... ( -23.20)
>DroEre_CAF1 223019 103 + 1
CAAAUUUAAAUGGCUGCUGUUAUAUGUACAAUCCCAUGCCACCCGCCCAUCAGAGCCACCAUCAGCAUGACCACCAUCAUACGCA---GCACCACCCAGUGGCCCA
...........(((((((((..((((........(((((.....((.(....).))........)))))........)))).)))---))).(((...)))))).. ( -18.21)
>DroYak_CAF1 226652 103 + 1
CCAAUUUAAAUGGCUGCUGUUAUAUGUACAAUCCCAUGCCACCCGCCCAUCAGAGUCACCAUCAGCAUGACCACCAUCAUACGCA---GCACCACCCGGUGGCCCA
...........(((((((((..((((........(((((.........................)))))........)))).)))---))(((....))))))).. ( -19.50)
>consensus
CCAAUAUAAAUGGCUGCUGUUAUAUGUACAAUCCCAUGCCACCCGCCCAUCAGAGCCACCAUCAGCAUGACCACCAUCAUGCGCA___GCACCACCCGGUGGCCCA
..........((((((..(((........)))..)).))))...........(.((((((....((((((......))))))((....)).......)))))).). (-19.84 = -20.56 +   0.72)

alignment

secondary structure

dotplot

Window 3

Location	3,746,609 – 3,746,710
Length	101
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	94.15
Mean single sequence MFE	-22.12
Consensus MFE	-21.46
Energy contribution	-22.58
Covariance contribution	1.12
Combinations/Pair	1.10
Mean z-score	-1.48
Structure conservation index	0.97
SVM decision value	1.88
SVM RNA-class probability	0.981065
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3746609 101 + 22407834
AUGCCACCCGCCCAUCAGAGCCACCAUCAGCAUGACCACCAUCAUGCGCAGCAGCACCACCCGGUGGCCCAGCAUCAGCACCACCCCCAUCAGUACGGGCC
.........((((....(.((((((....((((((......))))))((....)).......)))))).).((....)).................)))). ( -32.00)
>DroSec_CAF1 208706 98 + 1
AUGCCACCUGCCCAUCAGAGCCACUAUCAGCAUGACCACCAUCAGGCGCA---GCACCACCCGGUAGCCCAGCAUCAGCACCACCCCCACCAGUACGGCCC
..(((..((((((......((........)).(((......))))).)))---)........(((.((.........)))))..............))).. ( -17.60)
>DroSim_CAF1 215840 98 + 1
AUGCCACCCGCCCAUCAGAGCCACCAUCAGCAUGACCACCAUCAUGCGCA---GCACCACCCGGUGGCCCAGCAUCAGCACCACCCCCACCAGUACGGGCC
.........((((....(.((((((....((((((......))))))(..---....)....)))))).).((....)).................)))). ( -28.00)
>DroEre_CAF1 223054 98 + 1
AUGCCACCCGCCCAUCAGAGCCACCAUCAGCAUGACCACCAUCAUACGCA---GCACCACCCAGUGGCCCAGCAUCAGCACCACCCCCACCAGUACGGGCC
.........((((....(.(((((.....((((((......))))..)).---(.......).))))).).((....)).................)))). ( -17.70)
>DroYak_CAF1 226687 98 + 1
AUGCCACCCGCCCAUCAGAGUCACCAUCAGCAUGACCACCAUCAUACGCA---GCACCACCCGGUGGCCCAGCAUCAGCACCACCCCCACCAGUAUGCGCC
..((((((.........((.......)).((((((......))))..)).---.........))))))...((((..((.............))))))... ( -15.32)
>consensus
AUGCCACCCGCCCAUCAGAGCCACCAUCAGCAUGACCACCAUCAUGCGCA___GCACCACCCGGUGGCCCAGCAUCAGCACCACCCCCACCAGUACGGGCC
.........((((....(.((((((....((((((......))))))((....)).......)))))).).((....)).................)))). (-21.46 = -22.58 +   1.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:01:51 2006