Locus 235

Sequence ID	3R_DroMel_CAF1
Location	931,568 – 931,742
Length	174
Max. P	0.998007

overview

Window 1

Location	931,568 – 931,668
Length	100
Sequences	4
Columns	112
Reading direction	forward
Mean pairwise identity	71.72
Mean single sequence MFE	-21.54
Consensus MFE	-11.71
Energy contribution	-11.02
Covariance contribution	-0.69
Combinations/Pair	1.53
Mean z-score	-1.98
Structure conservation index	0.54
SVM decision value	1.11
SVM RNA-class probability	0.916085
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 931568 100 + 27905053
AUAAUAUCAGGCUUUCAACGAUAAAAAAAGGGGGGCUACUUUAAUUAGUUGUAGCAGCUUUA------------AUGAACAACGAAAAAUGCAGGAAACUGCAAAAUGUUUA
......((.((((..(..............)..))))..........(((((..((......------------.)).)))))))....(((((....)))))......... ( -20.84)
>DroSec_CAF1 20597 99 + 1
GUAAUAUCAAGCUUUCAACGAUGAA-AAAGAGGGGCUACUUUAAUUAAUUGUAGCAGCCAUA------------AUGAACAGCGAAAAACGCAGGAAACUGCACAAUGUUUA
..........(((((((....(...-.)...((.(((((...........)))))..))...------------.)))).))).......((((....)))).......... ( -22.00)
>DroSim_CAF1 26510 97 + 1
--AAUAUCAAGCUUUCAACAAUGAA-AAAGAGGGGCUGCUUUAAUUAAUUGUAGCAGUUAUA------------AUGAACAACGAAAAACGCAGGAAACUGCAAAAUGUUUA
--....(((...(((((....))))-)......(((((((.(((....))).)))))))...------------.)))............((((....)))).......... ( -20.10)
>DroEre_CAF1 21614 100 + 1
GUAAUGCCAGGUUUGCAGCGGUAA--AAAGGGGAAUUACCUAAAUUAAUUGUAAUAGCUAUAGCGUUGUUGCUGAACAGCG----------CAGGAAAGUGCAGCAUUUUUA
..(((((...(((((((((((...--...(((......)))...............((....)).))))))).)))).(((----------(......)))).))))).... ( -23.20)
>consensus
GUAAUAUCAAGCUUUCAACGAUAAA_AAAGAGGGGCUACUUUAAUUAAUUGUAGCAGCUAUA____________AUGAACAACGAAAAACGCAGGAAACUGCAAAAUGUUUA
.........((((....(((((......((((......)))).....)))))...))))...............................((((....)))).......... (-11.71 = -11.02 +  -0.69)

alignment

secondary structure

dotplot

Window 2

Location	931,600 – 931,703
Length	103
Sequences	4
Columns	119
Reading direction	forward
Mean pairwise identity	70.35
Mean single sequence MFE	-24.92
Consensus MFE	-14.26
Energy contribution	-14.20
Covariance contribution	-0.06
Combinations/Pair	1.27
Mean z-score	-2.41
Structure conservation index	0.57
SVM decision value	2.98
SVM RNA-class probability	0.998007
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 931600 103 + 27905053
GGGCUACUUUAAUUAGUUGUAGCAGCUUUA------------AUGAACAACGAAAAAUGCAGGAAACUGCAAAAUGUUUACUACUCUUAAGUCUAAACUCAGACUCCAG---CU-UUUU
..(((((...........)))))((((...------------.((((((........(((((....)))))...)))))).........(((((......)))))..))---))-.... ( -23.30)
>DroSec_CAF1 20628 107 + 1
GGGCUACUUUAAUUAAUUGUAGCAGCCAUA------------AUGAACAGCGAAAAACGCAGGAAACUGCACAAUGUUUACAAGUCUUUAGUCUAAACACAGACUACAAAAACUGGCUA
..(((((...........)))))(((((..------------.((((((..(.....)((((....))))....))))))........((((((......)))))).......))))). ( -29.00)
>DroSim_CAF1 26539 107 + 1
GGGCUGCUUUAAUUAAUUGUAGCAGUUAUA------------AUGAACAACGAAAAACGCAGGAAACUGCAAAAUGUUUACUAGUCUUUAGUCUAAACGCAGACUACAAAAACUGGUUA
.(((((((.(((....))).)))))))...------------.((((((..(.....)((((....))))....))))))(((((.((((((((......))))))..)).)))))... ( -27.80)
>DroEre_CAF1 21644 106 + 1
GAAUUACCUAAAUUAAUUGUAAUAGCUAUAGCGUUGUUGCUGAACAGCG----------CAGGAAAGUGCAGCAUUUUUAUUACUCAUUAAUCUAUACUUAGACUGCAGAACCUGG---
......((......................((((((((....)))))))----------)(((....(((((.....(((........)))((((....)))))))))...)))))--- ( -19.60)
>consensus
GGGCUACUUUAAUUAAUUGUAGCAGCUAUA____________AUGAACAACGAAAAACGCAGGAAACUGCAAAAUGUUUACUACUCUUUAGUCUAAACUCAGACUACAAAAACUGGUUA
..(((((...........)))))...................................((((....))))..................((((((......))))))............. (-14.26 = -14.20 +  -0.06)

alignment

secondary structure

dotplot

Window 3

Location	931,630 – 931,742
Length	112
Sequences	3
Columns	116
Reading direction	forward
Mean pairwise identity	87.07
Mean single sequence MFE	-23.67
Consensus MFE	-16.51
Energy contribution	-16.40
Covariance contribution	-0.11
Combinations/Pair	1.09
Mean z-score	-2.37
Structure conservation index	0.70
SVM decision value	0.25
SVM RNA-class probability	0.653087
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 931630 112 + 27905053
AUGAACAACGAAAAAUGCAGGAAACUGCAAAAUGUUUACUACUCUUAAGUCUAAACUCAGACUCCAG---CU-UUUUCAUCAGUGGCUUAUCCAUUUCAAAGAAAUAAUAAGGUUU
..((((...(((((((((((....)))))..............((..(((((......)))))..))---.)-)))))........(((((..(((((...))))).))))))))) ( -22.20)
>DroSec_CAF1 20658 116 + 1
AUGAACAGCGAAAAACGCAGGAAACUGCACAAUGUUUACAAGUCUUUAGUCUAAACACAGACUACAAAAACUGGCUACAUGCAUGGCUUAUUCAUUUUAAAGAAAUAAUAAGGUUU
..((((.((.......((((....))))...((((.....(((.((((((((......))))))..)).)))....))))))....((((((.(((((...))))))))))))))) ( -24.40)
>DroSim_CAF1 26569 116 + 1
AUGAACAACGAAAAACGCAGGAAACUGCAAAAUGUUUACUAGUCUUUAGUCUAAACGCAGACUACAAAAACUGGUUACAUGCAUGGCAUAUUCAUUUUAAAGAAAUAAUAAGGUUU
(((((...........((((....))))...((((..((((((.((((((((......))))))..)).)))))).))))..........)))))..................... ( -24.40)
>consensus
AUGAACAACGAAAAACGCAGGAAACUGCAAAAUGUUUACUAGUCUUUAGUCUAAACACAGACUACAAAAACUGGUUACAUGCAUGGCUUAUUCAUUUUAAAGAAAUAAUAAGGUUU
..((((..........((((....))))..............((((((((((......)))))...................((((.....))))...))))).........)))) (-16.51 = -16.40 +  -0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:38:25 2006