Locus 5138

Sequence ID	X_DroMel_CAF1
Location	13,410,718 – 13,410,838
Length	120
Max. P	0.929443

overview

Window 6

Location	13,410,718 – 13,410,838
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.89
Mean single sequence MFE	-40.72
Consensus MFE	-36.08
Energy contribution	-36.33
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-2.21
Structure conservation index	0.89
SVM decision value	1.20
SVM RNA-class probability	0.929443
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13410718 120 + 22224390
GUUAUGCUGCGUUGUUGUUGGCCAAGCCAACCGUUGUUGUUGCUGCUUCUGGCUGGCCAAAAAGGAGCAAACAAAAGGCGAGGCGAUGCAAAGCAAUCAACGUCAUAAGCAGGAGCAGCA
....((((((.(((((((((((...))))))((((((((((..(((.((.(.((.(((..................))).)).))).))).))))).))))).....)))))..)))))) ( -42.57)
>DroSec_CAF1 6562 115 + 1
GUUGUGCUGCGUU---GUUGGCCAAUCCGA--GUUGUUGUUGCUGCUUCUGGCUGGCCAAAAAGGAGCAAACAAAAGGCGAGGCGAUGCAAAGCAAUCAACGUCAUAAGCAGGAGCAGCA
(((((.((((..(---(((((((...((..--.(((((..((((.(((.(((....)))..))).)))))))))..))...)))..(((...)))..)))))......))))..))))). ( -37.20)
>DroSim_CAF1 6098 115 + 1
GUUGUGCUGCGUU---GUUGGCCAAGCCGA--GUUGUUGUUGCUGCUUCUGGCUGGCCAAAAAGGAGCAAACAAAAGGCGAGGCGAUGCAAAGCAAUCAACGUCAUAAGCAGGAGCAGCA
(((((.((((..(---(((((((..(((..--.(((((..((((.(((.(((....)))..))).)))))))))..)))..)))..(((...)))..)))))......))))..))))). ( -42.30)
>DroEre_CAF1 924 112 + 1
---GUGCUGCGUU---GUUGGCCAAGCCGC--GUUGUUGUUGCUGCUUCUGGCUGGCCAAAAAGGAGCAAACAAAAGGCGAGGCGAUGCAAAGCAAUCAACGUCAUAAGCAGGAGCAGCA
---.((((((.((---(((.(((..(((..--.(((((..((((.(((.(((....)))..))).)))))))))..)))..)))((((............))))...)))))..)))))) ( -40.80)
>consensus
GUUGUGCUGCGUU___GUUGGCCAAGCCGA__GUUGUUGUUGCUGCUUCUGGCUGGCCAAAAAGGAGCAAACAAAAGGCGAGGCGAUGCAAAGCAAUCAACGUCAUAAGCAGGAGCAGCA
....((((((......(((((((..(((.....(((((..((((.(((.(((....)))..))).)))))))))..)))..)))..(((...)))..))))((.....))....)))))) (-36.08 = -36.33 +   0.25)

alignment

secondary structure

dotplot

Window 7

Location	13,410,718 – 13,410,838
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.89
Mean single sequence MFE	-34.75
Consensus MFE	-31.27
Energy contribution	-31.53
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.96
Structure conservation index	0.90
SVM decision value	0.94
SVM RNA-class probability	0.886783
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13410718 120 - 22224390
UGCUGCUCCUGCUUAUGACGUUGAUUGCUUUGCAUCGCCUCGCCUUUUGUUUGCUCCUUUUUGGCCAGCCAGAAGCAGCAACAACAACGGUUGGCUUGGCCAACAACAACGCAGCAUAAC
((((((............(((((..(((...)))............(((((.(((.(((((.((....))))))).)))))))))))))((((((...))))))......)))))).... ( -36.80)
>DroSec_CAF1 6562 115 - 1
UGCUGCUCCUGCUUAUGACGUUGAUUGCUUUGCAUCGCCUCGCCUUUUGUUUGCUCCUUUUUGGCCAGCCAGAAGCAGCAACAACAAC--UCGGAUUGGCCAAC---AACGCAGCACAAC
((((((.....(....)..((((..(((...)))..(((...((..(((((((((.(((((.((....))))))).))))..))))).--..))...)))...)---))))))))).... ( -32.00)
>DroSim_CAF1 6098 115 - 1
UGCUGCUCCUGCUUAUGACGUUGAUUGCUUUGCAUCGCCUCGCCUUUUGUUUGCUCCUUUUUGGCCAGCCAGAAGCAGCAACAACAAC--UCGGCUUGGCCAAC---AACGCAGCACAAC
((((((.....(....)..((((..(((...)))..(((..(((..(((((((((.(((((.((....))))))).))))..))))).--..)))..)))...)---))))))))).... ( -35.10)
>DroEre_CAF1 924 112 - 1
UGCUGCUCCUGCUUAUGACGUUGAUUGCUUUGCAUCGCCUCGCCUUUUGUUUGCUCCUUUUUGGCCAGCCAGAAGCAGCAACAACAAC--GCGGCUUGGCCAAC---AACGCAGCAC---
((((((.....(....)..((((..(((...)))..(((..(((..(((((((((.(((((.((....))))))).))))..))))).--..)))..)))...)---))))))))).--- ( -35.10)
>consensus
UGCUGCUCCUGCUUAUGACGUUGAUUGCUUUGCAUCGCCUCGCCUUUUGUUUGCUCCUUUUUGGCCAGCCAGAAGCAGCAACAACAAC__UCGGCUUGGCCAAC___AACGCAGCACAAC
((((((................(((.((...)))))(((..(((..(((((((((.(((((.((....))))))).))))..))))).....)))..)))..........)))))).... (-31.27 = -31.53 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:40:54 2006