Locus 5275

Sequence ID	3R_DroMel_CAF1
Location	13,763,623 – 13,763,750
Length	127
Max. P	0.994719

overview

Window 8

Location	13,763,623 – 13,763,723
Length	100
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	95.60
Mean single sequence MFE	-23.69
Consensus MFE	-21.72
Energy contribution	-21.84
Covariance contribution	0.12
Combinations/Pair	1.13
Mean z-score	-1.88
Structure conservation index	0.92
SVM decision value	2.50
SVM RNA-class probability	0.994719
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13763623 100 - 27905053
AAACCAUCAUAGUGAUUAAUGCUGUCACUGGCCAAAGAGUCAAUUAAACUUGGCACAGCUCGACUGAUUCGACUUGCGGUUUUCCAACUAUCAUCUAUCA
(((((....(((((((.......)))))))(((((..............))))).(((.((((.....)))).))).))))).................. ( -19.34)
>DroSec_CAF1 36136 100 - 1
AAUCCAUCAUAGUGAUUAAUGCUGUCACUGGCCAAAGAGCCAAUUAAACUUGGCUCAGCUCGACUGAUUCGACUUGCGGUUUUCCAACUAUCAUCUAUCA
.........(((((((.......)))))))(((...(((((((......))))))).((((((.....))))...))))).................... ( -24.30)
>DroSim_CAF1 35089 100 - 1
AAUCCAUCAUAGUGAUUAAUGCUGUCACUGGCCAAAGAGCCAAUUAAACUUGGCUCAGCUCGACUGAUUCGACUUGCGGUUUUCCAACUAUCAUCUAUCA
.........(((((((.......)))))))(((...(((((((......))))))).((((((.....))))...))))).................... ( -24.30)
>DroEre_CAF1 34860 100 - 1
AAUCCAUCAUAGUGAUUAAGGCUGUCACUGGCCAAAGAGCCAAUUAAACUUGGCUCAGCUCGAGUGAUUCGACUUGCGGCUUUCCAACUAUCAUCUAUCA
........((((((((...((((......))))...(((((((......)))))))(((((((((......))))).))))........)))).)))).. ( -27.70)
>DroYak_CAF1 37142 100 - 1
AAUCCAUCAGAGUGAUUAAUGCUGUCACUGGCCAAAGAGCCAAUUAAACUUGGCUCAGCUUGCCUGAAUCGACUUGCGGUUUUCCAACUAACAUCUAUCA
..........((((((.......))))))(((....(((((((......))))))).....))).((((((.....)))))).................. ( -22.80)
>consensus
AAUCCAUCAUAGUGAUUAAUGCUGUCACUGGCCAAAGAGCCAAUUAAACUUGGCUCAGCUCGACUGAUUCGACUUGCGGUUUUCCAACUAUCAUCUAUCA
.........(((((((.......)))))))(((...(((((((......))))))).((((((.....))))...))))).................... (-21.72 = -21.84 +   0.12)

alignment

secondary structure

dotplot

Window 9

Location	13,763,649 – 13,763,750
Length	101
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	88.49
Mean single sequence MFE	-24.31
Consensus MFE	-18.34
Energy contribution	-18.62
Covariance contribution	0.28
Combinations/Pair	1.10
Mean z-score	-1.90
Structure conservation index	0.75
SVM decision value	0.59
SVM RNA-class probability	0.791737
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13763649 101 - 27905053
AAUAAUAUCUGGAUUAUUGUAAU------GCGAAAACCAUCAUAGUGAUUAAUGCUGUCACUGGCCAAAGAGUCAAUUAAACUUGGCACAGCUCGACUGAUUCGACU
.........((((((((((....------((...........(((((((.......)))))))(((((..............)))))...)).))).)))))))... ( -18.54)
>DroSec_CAF1 36162 107 - 1
AAUAACAUCUGGAUUAUUGUAAUGCGAAUGCAAAAUCCAUCAUAGUGAUUAAUGCUGUCACUGGCCAAAGAGCCAAUUAAACUUGGCUCAGCUCGACUGAUUCGACU
.........((((((.(((((.......)))))))))))...(((((((.......)))))))......(((((((......)))))))((.((((.....)))))) ( -27.80)
>DroSim_CAF1 35115 101 - 1
AAUAACAUCUGGAUUAUUGUAAU------GCAAAAUCCAUCAUAGUGAUUAAUGCUGUCACUGGCCAAAGAGCCAAUUAAACUUGGCUCAGCUCGACUGAUUCGACU
.........((((((.(((....------.)))))))))...(((((((.......)))))))......(((((((......)))))))((.((((.....)))))) ( -26.50)
>DroEre_CAF1 34886 101 - 1
AAUAGCAUCUGGAUUACUGCAAU------GCAAAAUCCAUCAUAGUGAUUAAGGCUGUCACUGGCCAAAGAGCCAAUUAAACUUGGCUCAGCUCGAGUGAUUCGACU
.........(((((((((.(...------((...........(((((((.......)))))))......(((((((......))))))).))..))))))))))... ( -27.70)
>DroYak_CAF1 37168 92 - 1
AACAACAU---------UGUAAU------GCAAAAUCCAUCAGAGUGAUUAAUGCUGUCACUGGCCAAAGAGCCAAUUAAACUUGGCUCAGCUUGCCUGAAUCGACU
.......(---------((....------.)))......((((((((((.......))))))(((....(((((((......))))))).)))...))))....... ( -21.00)
>consensus
AAUAACAUCUGGAUUAUUGUAAU______GCAAAAUCCAUCAUAGUGAUUAAUGCUGUCACUGGCCAAAGAGCCAAUUAAACUUGGCUCAGCUCGACUGAUUCGACU
.............................((...........(((((((.......)))))))......(((((((......))))))).))((((.....)))).. (-18.34 = -18.62 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:50:51 2006