Locus 5699

Sequence ID	3L_DroMel_CAF1
Location	15,588,751 – 15,589,010
Length	259
Max. P	0.951486

overview

Window 9

Location	15,588,751 – 15,588,862
Length	111
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.21
Mean single sequence MFE	-17.15
Consensus MFE	-12.22
Energy contribution	-11.90
Covariance contribution	-0.32
Combinations/Pair	1.11
Mean z-score	-1.94
Structure conservation index	0.71
SVM decision value	-0.02
SVM RNA-class probability	0.523938
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15588751 111 + 23771897
GAAACUGAAAUUUCAUAUGAACCAAAUUGAAGUCCCA-AUCAAGGUUU---UUACGAAUAAUUUGUAAACAA----ACGCUCGACCA-AUUCAAUCUUAUCGAGCUUCAAUAUCAGCAAA
....((((...(((....)))....((((((......-......((((---((((((.....))))))..))----))((((((...-...........)))))))))))).)))).... ( -18.04)
>DroSec_CAF1 12097 117 + 1
GAAACUCAAAUUUCAUUUGAACCAAAUUGAAGUCCCAAAUCAAGGUUU---UUAUAAAAAAUUUGUAAACAAACAAAAGCUCGACCAAAUUCAAUCUUAUCGAGCUUCAAUAUCAGCAAA
((....(((((((.((..(((((...((((.........)))))))))---..))...)))))))...........((((((((...............)))))))).....))...... ( -15.56)
>DroSim_CAF1 12050 116 + 1
GAAACUCAAAUUUCAUUUGAACCAAAUUGAAGUCCCAAAUCAAGGUUU---UUAUAAAUAAUUUGUAAACAAACAAACGCUCGACCA-AUUCAAUCUUAUCGAGCUUCAAUAUCAGCAAA
((...((((((...)))))).....((((((.............((((---((((((.....))))))..))))....((((((...-...........)))))))))))).))...... ( -14.94)
>DroEre_CAF1 11987 114 + 1
GCAACUCAAAUUUCAUUUAAACCGAAUUGAAGUCUCA-AUCAAGGUUUUUUUUAUAAAUAAUUUGUAAACAA----ACGCUCGACCA-AUUCCAUCUUAUCGAGCUUCAAUAUCAGCAUA
((....((((((......(((((..(((((....)))-))...)))))...........)))))).......----..((((((...-...........))))))..........))... ( -17.67)
>DroYak_CAF1 13241 111 + 1
GCAACUCAAAUUUCAUUUAAACCGAAUUGAAGUCUCA-AUCAAGGUUU---UUAUAAAUAAUUUGUAAACAA----ACGCUCGACCA-AUUCAAUCUUAUCGAGCUUCAAUAUCAGCAAA
((....((((((..((..(((((..(((((....)))-))...)))))---..))....)))))).......----..((((((...-...........))))))..........))... ( -19.54)
>consensus
GAAACUCAAAUUUCAUUUGAACCAAAUUGAAGUCCCA_AUCAAGGUUU___UUAUAAAUAAUUUGUAAACAA____ACGCUCGACCA_AUUCAAUCUUAUCGAGCUUCAAUAUCAGCAAA
.........................((((((....................((((((.....))))))..........((((((...............))))))))))))......... (-12.22 = -11.90 +  -0.32)

alignment

secondary structure

dotplot

Window 0

Location	15,588,790 – 15,588,902
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.53
Mean single sequence MFE	-16.80
Consensus MFE	-15.30
Energy contribution	-15.14
Covariance contribution	-0.16
Combinations/Pair	1.05
Mean z-score	-1.27
Structure conservation index	0.91
SVM decision value	0.58
SVM RNA-class probability	0.788023
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15588790 112 + 23771897
CAAGGUUU---UUACGAAUAAUUUGUAAACAA----ACGCUCGACCA-AUUCAAUCUUAUCGAGCUUCAAUAUCAGCAAAACUUGAUAUUUAUAAACAAAUGCGCACACCGAUUCGAAUU
...(((..---...((....((((((......----..((((((...-...........))))))...((((((((......)))))))).....)))))).))...))).......... ( -18.74)
>DroSec_CAF1 12137 117 + 1
CAAGGUUU---UUAUAAAAAAUUUGUAAACAAACAAAAGCUCGACCAAAUUCAAUCUUAUCGAGCUUCAAUAUCAGCAAAACUUGAUAUUUAUAAACAAAUGCGCACACCGAUUCGAAUU
...(((..---.........((((((..........((((((((...............)))))))).((((((((......)))))))).....))))))......))).......... ( -17.59)
>DroSim_CAF1 12090 116 + 1
CAAGGUUU---UUAUAAAUAAUUUGUAAACAAACAAACGCUCGACCA-AUUCAAUCUUAUCGAGCUUCAAUAUCAGCAAAACUUGAUAUUUAUAAACAAAUGCGCACACCGAUUCGAAUU
...(((..---.........((((((............((((((...-...........))))))...((((((((......)))))))).....))))))......))).......... ( -16.27)
>DroEre_CAF1 12026 112 + 1
CAAGGUUUUUUUUAUAAAUAAUUUGUAAACAA----ACGCUCGACCA-AUUCCAUCUUAUCGAGCUUCAAUAUCAGCAUAACUUGAUAUUUAUAAACAAAUGCGCA---UGAUUCGAAUU
...(((((...((((.....((((((......----..((((((...-...........))))))...((((((((......)))))))).....))))))....)---)))...))))) ( -16.14)
>DroYak_CAF1 13280 112 + 1
CAAGGUUU---UUAUAAAUAAUUUGUAAACAA----ACGCUCGACCA-AUUCAAUCUUAUCGAGCUUCAAUAUCAGCAAAACUUGAUAUUUAUAAACAAGUGCGCACAACGAUUCGAAUU
........---.........((((((......----..((((((...-...........))))))...((((((((......)))))))).....))))))................... ( -15.24)
>consensus
CAAGGUUU___UUAUAAAUAAUUUGUAAACAA____ACGCUCGACCA_AUUCAAUCUUAUCGAGCUUCAAUAUCAGCAAAACUUGAUAUUUAUAAACAAAUGCGCACACCGAUUCGAAUU
....................((((((............((((((...............))))))...((((((((......)))))))).....))))))................... (-15.30 = -15.14 +  -0.16)

alignment

secondary structure

dotplot

Window 1

Location	15,588,902 – 15,589,010
Length	108
Sequences	4
Columns	116
Reading direction	forward
Mean pairwise identity	91.24
Mean single sequence MFE	-15.74
Consensus MFE	-13.57
Energy contribution	-14.70
Covariance contribution	1.13
Combinations/Pair	1.13
Mean z-score	-2.20
Structure conservation index	0.86
SVM decision value	1.41
SVM RNA-class probability	0.951486
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15588902 108 + 23771897
UGAUUUGCAAACAUAUUCCUUCCAUUCCCCCCGCAUUUAUAAUCCGAACAAGCUGAAGAAUAUUUCACAAUUCCAUUUAAUUUCACAGCAAACAUAAAAUCAAUUGCA--------
((((((((........................)).................((((..((((..................))))..)))).......))))))......-------- (  -7.23)
>DroSec_CAF1 12254 116 + 1
UGAUUUGCAAACAUAUUCCCUCCAUUCCCCCCGCAUUUAUAAUCCGAACAAGCUGAGAAAUAUUUCACAAUUUCAUUUAAUUUCACAGCAAACAUAAAAUCAAUUGCAAGUCAUUC
((((((((((.....................((.((.....)).)).....((((.(((((..................))))).))))..............))))))))))... ( -18.27)
>DroSim_CAF1 12206 116 + 1
UGAUUUGCAAACAUAUUCCCUCCAUUCCCCCCGCAUUUAUAGUCCGAACAAGCUGAGAAAUAUUUCACAAUUUCAUUUAAUUUCACAGCAAACAUAAAAUCAAUUGCAAGUCAUUU
((((((((((.....................((.((.....)).)).....((((.(((((..................))))).))))..............))))))))))... ( -18.87)
>DroEre_CAF1 12138 116 + 1
UGAUUUGCAAACAUAUUCCCUGCAUUCCCCCCGCAUUUAUAAUUUGAUCAAGCUGAAGAAUAUUUCACAAUUUCAUUUGAUUUCACAGCAAACAUAAAUUCAAUUGCAAGUCAUUU
((((((((((..........(((.........)))................((((..((.....)).(((......)))......))))..............))))))))))... ( -18.60)
>consensus
UGAUUUGCAAACAUAUUCCCUCCAUUCCCCCCGCAUUUAUAAUCCGAACAAGCUGAAAAAUAUUUCACAAUUUCAUUUAAUUUCACAGCAAACAUAAAAUCAAUUGCAAGUCAUUU
((((((((((.....................((.((.....)).)).....((((.(((((..................))))).))))..............))))))))))... (-13.57 = -14.70 +   1.13)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:56:55 2006