Locus 1981

Sequence ID	X_DroMel_CAF1
Location	5,431,748 – 5,431,904
Length	156
Max. P	0.975142

overview

Window 6

Location	5,431,748 – 5,431,864
Length	116
Sequences	3
Columns	116
Reading direction	forward
Mean pairwise identity	89.22
Mean single sequence MFE	-22.73
Consensus MFE	-22.02
Energy contribution	-21.80
Covariance contribution	-0.22
Combinations/Pair	1.04
Mean z-score	-1.88
Structure conservation index	0.97
SVM decision value	1.33
SVM RNA-class probability	0.943028
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5431748 116 + 22224390
UUUGCCCAGCAUCCUCUUAUUUUUUAGCGGCUCCUUUUUUCUUCUUUUUUUUUUUUGGGUAUCCUGAAGAGGUUCUGGGAAUCGAGAUCACUCAUCUACUUCCCAGCUACACGACA
.......(((..(((((......((((.((..(((.....................)))..)))))))))))...((((((...((((.....))))..)))))))))........ ( -21.80)
>DroSec_CAF1 38751 102 + 1
UUUGCCCAGCAUCCUCUUUUUUCUUAGCGGCUCCUUU--------------UUUUUAGGUAUCCUGAAGAGGUUCUGGGAAUCGAGAUCACUCAUCUACUUCCCAGCUACACUACA
.......(((..(((((......((((.((..(((..--------------.....)))..)))))))))))...((((((...((((.....))))..)))))))))........ ( -23.20)
>DroSim_CAF1 38445 102 + 1
UUUGCCCAGCAUCCUCUUUUUUCUUAGCGGCUCCUUU--------------UUUUUAGGUAUCCUGAAGAGGUUCUGGGAAUCGAGAUCACUCAUCUACUUCCCAGCUACACUACA
.......(((..(((((......((((.((..(((..--------------.....)))..)))))))))))...((((((...((((.....))))..)))))))))........ ( -23.20)
>consensus
UUUGCCCAGCAUCCUCUUUUUUCUUAGCGGCUCCUUU______________UUUUUAGGUAUCCUGAAGAGGUUCUGGGAAUCGAGAUCACUCAUCUACUUCCCAGCUACACUACA
.......(((..(((((......((((.((..(((.....................)))..)))))))))))...((((((...((((.....))))..)))))))))........ (-22.02 = -21.80 +  -0.22)

alignment

secondary structure

dotplot

Window 7

Location	5,431,748 – 5,431,864
Length	116
Sequences	3
Columns	116
Reading direction	reverse
Mean pairwise identity	89.22
Mean single sequence MFE	-28.40
Consensus MFE	-26.23
Energy contribution	-26.57
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.63
Structure conservation index	0.92
SVM decision value	1.74
SVM RNA-class probability	0.975142
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5431748 116 - 22224390
UGUCGUGUAGCUGGGAAGUAGAUGAGUGAUCUCGAUUCCCAGAACCUCUUCAGGAUACCCAAAAAAAAAAAAGAAGAAAAAAGGAGCCGCUAAAAAAUAAGAGGAUGCUGGGCAAA
....((.((((((((((...((.((....))))..))))))...((((((..((....))......................(....)..........))))))..)))).))... ( -27.60)
>DroSec_CAF1 38751 102 - 1
UGUAGUGUAGCUGGGAAGUAGAUGAGUGAUCUCGAUUCCCAGAACCUCUUCAGGAUACCUAAAAA--------------AAAGGAGCCGCUAAGAAAAAAGAGGAUGCUGGGCAAA
....((.((((((((((...((.((....))))..))))))...((((((..((...(((.....--------------..)))..))..........))))))..)))).))... ( -28.80)
>DroSim_CAF1 38445 102 - 1
UGUAGUGUAGCUGGGAAGUAGAUGAGUGAUCUCGAUUCCCAGAACCUCUUCAGGAUACCUAAAAA--------------AAAGGAGCCGCUAAGAAAAAAGAGGAUGCUGGGCAAA
....((.((((((((((...((.((....))))..))))))...((((((..((...(((.....--------------..)))..))..........))))))..)))).))... ( -28.80)
>consensus
UGUAGUGUAGCUGGGAAGUAGAUGAGUGAUCUCGAUUCCCAGAACCUCUUCAGGAUACCUAAAAA______________AAAGGAGCCGCUAAGAAAAAAGAGGAUGCUGGGCAAA
....((.((((((((((...((.((....))))..))))))...((((((..((...(((.....................)))..))..........))))))..)))).))... (-26.23 = -26.57 +   0.33)

alignment

secondary structure

dotplot

Window 8

Location	5,431,784 – 5,431,904
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	77.93
Mean single sequence MFE	-25.24
Consensus MFE	-17.08
Energy contribution	-19.42
Covariance contribution	2.34
Combinations/Pair	1.17
Mean z-score	-1.44
Structure conservation index	0.68
SVM decision value	-0.00
SVM RNA-class probability	0.531926
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5431784 120 + 22224390
UUUUCUUCUUUUUUUUUUUUGGGUAUCCUGAAGAGGUUCUGGGAAUCGAGAUCACUCAUCUACUUCCCAGCUACACGACAACUGGCGUGGGUUUGUCAUAAAUCAAUAGAAUCGCCAAGC
..............(((((..((...))..)))))((.(((((((...((((.....))))..)))))))..))........(((((.....(((........)))......)))))... ( -26.50)
>DroSec_CAF1 38787 106 + 1
U--------------UUUUUAGGUAUCCUGAAGAGGUUCUGGGAAUCGAGAUCACUCAUCUACUUCCCAGCUACACUACAACUGGCGUGGGUUCGCCAAAAAUCAAUAGAAUCGCCAAGC
.--------------((((((((...))))))))(((((((((((...((((.....))))..)))))..............(((((......))))).........))))))....... ( -28.10)
>DroSim_CAF1 38481 106 + 1
U--------------UUUUUAGGUAUCCUGAAGAGGUUCUGGGAAUCGAGAUCACUCAUCUACUUCCCAGCUACACUACAACUGGCGUGGGUUCGUCAAAAAUCAAUAGAAUCGCCAAGC
(--------------((((((((...)))))))))((.(((((((...((((.....))))..)))))))..))........(((((...((((..............)))))))))... ( -27.04)
>DroEre_CAF1 49379 91 + 1
-----------------UUCAGGUAUCCUGAAGAGGUUCUGGGAAUCCAGA------------UUCCCAGCUACAACAUAACUGGAGUAGGUUCGUCAAAAAUCAAUAGAAUCGCCAAGC
-----------------((((((...))))))(..((.((((((((....)------------)))))))..))..).....(((....(((((..............))))).)))... ( -24.44)
>DroYak_CAF1 40281 91 + 1
-----------------AUCAGGUAUCCUGCAGAGGUUCUGGGAAUCCACA------------UUCCCAACUACAACAUAACUGCUGUAGGUUCGUCAACAAUCAAUUAAAUCACCAAGC
-----------------....(((..(((((((.((((.(((((((....)------------))))))..........)))).)))))))...(....).............))).... ( -20.10)
>consensus
U______________UUUUUAGGUAUCCUGAAGAGGUUCUGGGAAUCGAGAUCACUCAUCUACUUCCCAGCUACACCACAACUGGCGUGGGUUCGUCAAAAAUCAAUAGAAUCGCCAAGC
...............((((((((...))))))))(((.(((((((...((((.....))))..)))))))((((.(((....))).)))).......................))).... (-17.08 = -19.42 +   2.34)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:27 2006