Locus 5410

Sequence ID	X_DroMel_CAF1
Location	14,093,731 – 14,093,920
Length	189
Max. P	0.910205

overview

Window 5

Location	14,093,731 – 14,093,824
Length	93
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	88.33
Mean single sequence MFE	-22.64
Consensus MFE	-18.74
Energy contribution	-19.62
Covariance contribution	0.88
Combinations/Pair	1.04
Mean z-score	-1.84
Structure conservation index	0.83
SVM decision value	1.07
SVM RNA-class probability	0.910205
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14093731 93 - 22224390
UCGAUUUGAAUAAUUGCAUAUGCAUAAGCGACUAUAGGAUAUAUCUGUAUCUGAACCCGAUCAACUAGAUCGGCUAGAUAAACUGGCCAAGC----------------A
..............(((....)))...((.......((((((....))))))......((((.....))))((((((.....))))))..))----------------. ( -21.10)
>DroSec_CAF1 4299 93 - 1
UCGAUUUGCAUAAUUGCAUAUGCAUAAGCGACUAUAGGAUAUAUCUGUAUCUGAACCCGAUCAACUAGAUCGGCUAGAUAAACUGGCCAAGC----------------A
(((...((((((......))))))....))).....((((((....))))))......((((.....))))((((((.....))))))....----------------. ( -25.00)
>DroSim_CAF1 3919 93 - 1
UCGAUUUGCAUAAUUGCAUAUGCAUAAGCGACUAUAGGAUAUAUCUGUAUCUGAACCCGAUCAACUAGAUCGGCUAGAUAAACUGGCCGAGC----------------A
(((...((((((......))))))....))).....((((((....))))))......((((.....))))((((((.....))))))....----------------. ( -25.00)
>DroEre_CAF1 4138 92 - 1
CCGAUUUGCAUAAUUGCAUAUGCAUAA-AGGCUAUAGGAUAUAUCUGUAUCUGAACCCGAUCAACUAGAUCAGCUAGCUAAACUGGCCAAGC----------------U
......((((((......))))))...-.((((...((((((....))))))......((((.....)))).(((((.....)))))..)))----------------) ( -20.70)
>DroYak_CAF1 4660 109 - 1
UCGAUUUGCAUAAUUGCAUAUGCAUAAGAUACUAUGGGAUAUAGCUGUAUCUGAACCCGAUCAACUAGAUCAGCUAGAUAAACUGGCCAAGCAGACCAACACACCACCA
((....((((((......))))))...)).....(((....((((((.(((((............)))))))))))......(((......))).)))........... ( -21.40)
>consensus
UCGAUUUGCAUAAUUGCAUAUGCAUAAGCGACUAUAGGAUAUAUCUGUAUCUGAACCCGAUCAACUAGAUCGGCUAGAUAAACUGGCCAAGC________________A
(((...((((((......))))))....))).....((((((....))))))......((((.....))))((((((.....))))))..................... (-18.74 = -19.62 +   0.88)

alignment

secondary structure

dotplot

Window 6

Location	14,093,824 – 14,093,920
Length	96
Sequences	5
Columns	96
Reading direction	reverse
Mean pairwise identity	93.12
Mean single sequence MFE	-22.13
Consensus MFE	-18.05
Energy contribution	-18.17
Covariance contribution	0.12
Combinations/Pair	1.12
Mean z-score	-1.47
Structure conservation index	0.82
SVM decision value	0.30
SVM RNA-class probability	0.678771
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14093824 96 - 22224390
CGGCGCAUUUAACAAUUAAUUCGAAAGUGUCCGCUAAAUGCACAUCUGGACAAACGUGGAAUGCACUGCGAUACCAAGUCCAUAGAUGUAAUCCCA
.((.(((((((..........(....).......)))))))((((((((((...((..(......)..)).......))))..))))))....)). ( -21.13)
>DroSec_CAF1 4392 96 - 1
CGGCGCAUUUAACAAUUAAUUAGAAAGUGCCCGCAAAAUGCACAUCUGGACAAACGUGGAAUGCACUGCGAUACCAAGUCCAUUGAUGUAAUCCCA
.((.((((((..............))))))))((.....))((((((((((...((..(......)..)).......)))))..)))))....... ( -21.44)
>DroSim_CAF1 4012 96 - 1
CGGCGCAUUUAACAAUUAAUUAGAAAGUGCCCGCAAAAUGCACAUCUGGACAAACGUGGAAUGCACUGCGAUGCCAAGUCCAUUGAUGUAAUCCCA
.((.((((((..............))))))))((.....))((((((((((.....(((..(((...)))...))).)))))..)))))....... ( -22.44)
>DroEre_CAF1 4230 96 - 1
CGGCGCGUUUUACAAUUAAUUAGAAAGUAUCCGUAAAAUGCACAUCUGGACAAACGUGGAAUGCACCGCGAUACCAAGUCCAUUGAUGUAAUCCCA
.((.(((((((((...................)))))))))((((((((((...(((((......))))).......)))))..)))))....)). ( -25.91)
>DroYak_CAF1 4769 94 - 1
CGGCGCAUUUUACAUUUAAUUAGAAAGUA--CGUAAAAUGCACAUCUGGACAAACGUGGAAUGCACUGCGACACCAAGUCCAUUGAUAUAAUCCCA
.((.(((((((((................--.)))))))))..((((((((....(((...(((...))).)))...)))))..)))......)). ( -19.73)
>consensus
CGGCGCAUUUAACAAUUAAUUAGAAAGUGCCCGCAAAAUGCACAUCUGGACAAACGUGGAAUGCACUGCGAUACCAAGUCCAUUGAUGUAAUCCCA
.((.(((((((.(...................).)))))))((((((((((...(((((......))))).......)))))..)))))....)). (-18.05 = -18.17 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:47:15 2006