Locus 5394

Sequence ID	X_DroMel_CAF1
Location	14,034,159 – 14,034,326
Length	167
Max. P	0.919515

overview

Window 2

Location	14,034,159 – 14,034,275
Length	116
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.43
Mean single sequence MFE	-34.33
Consensus MFE	-21.58
Energy contribution	-22.08
Covariance contribution	0.50
Combinations/Pair	1.20
Mean z-score	-1.56
Structure conservation index	0.63
SVM decision value	0.11
SVM RNA-class probability	0.588757
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14034159 116 - 22224390
GACGCUGGCAGCGAUCAACAGGUUGCGCACCAGCGACCAGCGAAGGGGCAAGCAACUGGCGGAGAUGCGAUAUUGCAUUCAGAUGCACUUUGCACGGUGAAAAGCAAAACAAUAAU----
..((((((..((((((....))))))...))))))(((.((((((..(((.((.....))...((((((....))))))....))).))))))..)))..................---- ( -37.70)
>DroVir_CAF1 21403 111 - 1
AGCGGCAGCAACAAGUAAUAAAUUGCGUGCGAGUAGCCAACGAGAGGGCACCGACCUUGCGUUUCUCAGAUAUUGCAUU-AAAUGCACUUUGCUCGGCCAAUC---AAACGUU-GC----
.(((((.(((....((((....)))).)))((...(((...(((((((((.......))).))))))......(((((.-..)))))........)))...))---....)))-))---- ( -27.80)
>DroSec_CAF1 3199 116 - 1
GACGCUGGCAGCGAUCAACAGGUUGCGCACCAGCGACCAGCGAAAGGGCAAGCAACUGGCAGAUAUGCGAUAUUGCAUUCAGAUGCACUUUGCACGGCUGAAAACAAAACAAUAAU----
..((((((..((((((....))))))...)))))).(((((....).(....)..))))(((...(((((...(((((....)))))..)))))...)))................---- ( -35.60)
>DroSim_CAF1 921 116 - 1
GACGCUGGCAGCGAUCAACAGGUUGCGCACCAGCGACCAGCGAAAGGGCAAGCAACUGGCGGAGAUGCGAUAUUGCAUUCAUAUGCACUUUGCACGGCUGAAAACAAAACAAUAAU----
..(((((((.((((((....))))))((....))).))))))....(((..((((...(((..((((((....))))))....)))...))))...))).................---- ( -35.20)
>DroEre_CAF1 3112 120 - 1
GACGCUGGCAGCGAUCAACAGGCUGCGCACCAGCGACCAGCGAAAGGGCAAGAACCUUGCACAGAUCCGAUAUUGCAUUCAGAUGCACUUUGCACGGCGGAAAUCAAGACAAUAAAUACG
..(((((((((.((((.....(((((((....)))..))))......(((((...)))))...))))......(((((....)))))..)))).)))))..................... ( -33.10)
>DroYak_CAF1 3099 118 - 1
GACGCUGGCAGCGAUCAACAGGUUGCGCACCAGCGACCAGCGAAAGGGCAAGAACCUUGCACAGAUCCGAUAUUGCAUUCAGAUGCACUUUGCACAGCGGAAAACAAGACAAUAAAUA--
..(((((((((.((((....((((((......))))))..(....).(((((...)))))...))))......(((((....)))))..)))).)))))...................-- ( -36.60)
>consensus
GACGCUGGCAGCGAUCAACAGGUUGCGCACCAGCGACCAGCGAAAGGGCAAGCAACUGGCAGAGAUCCGAUAUUGCAUUCAGAUGCACUUUGCACGGCGGAAAACAAAACAAUAAU____
..((((((..((((((....))))))...))))))....((.((((.((.........)).............(((((....)))))))))))........................... (-21.58 = -22.08 +   0.50)

alignment

secondary structure

dotplot

Window 3

Location	14,034,235 – 14,034,326
Length	91
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	76.26
Mean single sequence MFE	-42.20
Consensus MFE	-28.51
Energy contribution	-28.60
Covariance contribution	0.09
Combinations/Pair	1.33
Mean z-score	-1.65
Structure conservation index	0.68
SVM decision value	1.13
SVM RNA-class probability	0.919515
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14034235 91 - 22224390
------------------UUUGUGACUGC---UCGCUGUGGCGAAUGCCGGCGGGUUGGCGAUGGCGGUGGUGACGCUGGCAGCGAUCAACAGGUUGCGCACCAGCGACCAG
------------------.......(((.---((((((..(((...(((.....(((((((.((.(((((....))))).)).)).))))).)))..)))..)))))).))) ( -42.50)
>DroVir_CAF1 21474 94 - 1
------------------UGUGCAAGUGGUUGUGGUUGUGGCAAAGGCCGUGCGACUUGUGACAGCGGCAGUAGCGGCAGCAACAAGUAAUAAAUUGCGUGCGAGUAGCCAA
------------------...((((.((.((((.(((((.((.(..(((((.((.....))...)))))..).)).))))).)))).)).....))))(.((.....))).. ( -29.60)
>DroSec_CAF1 3275 91 - 1
------------------UUUGCGACUGC---UCGCUGCGGCGAAUGCCGGCGGGUUGGCGAUGGCGGUGGUGACGCUGGCAGCGAUCAACAGGUUGCGCACCAGCGACCAG
------------------.......(((.---((((((..(((...(((.....(((((((.((.(((((....))))).)).)).))))).)))..)))..)))))).))) ( -43.30)
>DroSim_CAF1 997 91 - 1
------------------UUUGCUACUGC---UCGCUGUGGCGAAUGCCGGCGGGUUGGCGAUGGCGGUGGUGACGCUGGCAGCGAUCAACAGGUUGCGCACCAGCGACCAG
------------------.(..(((((((---((((....)))).((((((....))))))...)))))))..)((((((..((((((....))))))...))))))..... ( -42.80)
>DroEre_CAF1 3192 109 - 1
CUGUGGCGACUGCUCGCUGUGGCGACUGC---UCGCUGUGGCGAAUGCCGGCGGAAUUGCGAUGGCGGUGGUGACGCUGGCAGCGAUCAACAGGCUGCGCACCAGCGACCAG
(((..((((....))))..)))...(((.---((((((..(((...(((.(..((.((((..((.(((((....))))).))))))))..).)))..)))..)))))).))) ( -50.10)
>DroYak_CAF1 3177 91 - 1
------------------UUCGCGACUGC---UCGCUGUGGCAAAUGCCGGCGGGACUGCGAUGGCGGUGGUGACGCUGGCAGCGAUCAACAGGUUGCGCACCAGCGACCAG
------------------.......(((.---((((((..((...((((((((..((..(.......)..))..))))))))((((((....))))))))..)))))).))) ( -44.90)
>consensus
__________________UUUGCGACUGC___UCGCUGUGGCGAAUGCCGGCGGGUUGGCGAUGGCGGUGGUGACGCUGGCAGCGAUCAACAGGUUGCGCACCAGCGACCAG
................................((((((((((....)))................(((((....))))))))))))......((((((......)))))).. (-28.51 = -28.60 +   0.09)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:54 2006