Locus 2450

Sequence ID	3R_DroMel_CAF1
Location	6,779,018 – 6,779,175
Length	157
Max. P	0.999671

overview

Window 8

Location	6,779,018 – 6,779,135
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.22
Mean single sequence MFE	-26.35
Consensus MFE	-20.84
Energy contribution	-20.76
Covariance contribution	-0.08
Combinations/Pair	1.12
Mean z-score	-1.48
Structure conservation index	0.79
SVM decision value	0.15
SVM RNA-class probability	0.605461
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6779018 117 + 27905053
GGCAGCAUUUAUUCUCAAAAGCCUAGCUAACUUAUGCAAAAACUAUUUAUCUUUGACUGAAUAUACUUGCCCACUGAAUUUUUAUCGGUCGGUGGGUCGAGUG---GCAAUUUCAUUUAA
(((.................)))..((........))...............((((.((((..((((((((((((((...........)))))))).))))))---.....)))).)))) ( -25.43)
>DroSec_CAF1 43171 116 + 1
GACAGCAUUUAUUUUUAAAAGCCUAGCUAACUUAUGCAAAAACUAUUUAUCUUUGACUGAAUAUACUUGCCCACUGAAUUUUUAUU-GUCGGUGGGUCGAGUG---GCAAUUUCAUUUAA
....((.((((....)))).))...((........))...............((((.((((..((((((((((((((.........-.)))))))).))))))---.....)))).)))) ( -25.10)
>DroSim_CAF1 47190 116 + 1
GACAGCAUUUAUUCUUAAAAGCCUUGCUAACUUAUGCAAAAACUAUUUAUCUUUGACUGAAUAUACUUGCCCACUGAAUUUUUAUC-GUCGGUGGGUCGAGUG---GCAAUUUCAUUUAA
....((.((((....)))).)).((((........)))).............((((.((((..((((((((((((((.........-.)))))))).))))))---.....)))).)))) ( -26.60)
>DroEre_CAF1 28235 115 + 1
AACCGCAUUUAUUCGUAAAAGCCGAGCUAACUUAUGCAAAAACUAUCUGUUUUUGACUGAAUAUAC-UGCCCACUGAAUUUUUAUU-GCCGGUGGGCCGAGUG---GCAAUUUCAUUUAA
..((((...(((((.....(((...)))........(((((((.....)))))))...)))))..(-.((((((((..........-..)))))))).).)))---)............. ( -28.20)
>DroYak_CAF1 40548 119 + 1
GACAGCAGUUAUUCCUAAAAGCUACGCUAACUUAUGCAAAAACUAUUUAUCUUUAACUGAGUACACUUGCCCACUGAAUUUUUAUU-GCCGGUGGGCCGGGUGGCGGCAAUUUCAUUUAA
.....((((((....((((((....((........)).....)).))))....)))))).((.(((((((((((((..........-..))))))).))))))...))............ ( -26.40)
>consensus
GACAGCAUUUAUUCUUAAAAGCCUAGCUAACUUAUGCAAAAACUAUUUAUCUUUGACUGAAUAUACUUGCCCACUGAAUUUUUAUU_GUCGGUGGGUCGAGUG___GCAAUUUCAUUUAA
....((...................((........))..........................(((((((((((((.............))))))).))))))...))............ (-20.84 = -20.76 +  -0.08)

alignment

secondary structure

dotplot

Window 9

Location	6,779,058 – 6,779,175
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.01
Mean single sequence MFE	-32.30
Consensus MFE	-27.96
Energy contribution	-27.92
Covariance contribution	-0.04
Combinations/Pair	1.12
Mean z-score	-2.92
Structure conservation index	0.87
SVM decision value	3.87
SVM RNA-class probability	0.999671
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6779058 117 + 27905053
AACUAUUUAUCUUUGACUGAAUAUACUUGCCCACUGAAUUUUUAUCGGUCGGUGGGUCGAGUG---GCAAUUUCAUUUAAUUUUUAUUGCACUUUGCCGCUAAGGUCCUUUCAGUCUGCG
..............(((((((...(((((((((((((...........)))))))))..((((---((((...((............))....)))))))).))))...))))))).... ( -34.30)
>DroSec_CAF1 43211 115 + 1
AACUAUUUAUCUUUGACUGAAUAUACUUGCCCACUGAAUUUUUAUU-GUCGGUGGGUCGAGUG---GCAAUUUCAUUUAAUUUUUAUUGCACUUCGCCGCUAAGG-CCUUUCAGUCUGCG
..............(((((((..((((((((((((((.........-.)))))))).))))))---(((((..............))))).....(((.....))-)..))))))).... ( -34.94)
>DroSim_CAF1 47230 116 + 1
AACUAUUUAUCUUUGACUGAAUAUACUUGCCCACUGAAUUUUUAUC-GUCGGUGGGUCGAGUG---GCAAUUUCAUUUAAUUUUUAUUGCACUUCGCCGCUAAGGUCCUUUCAGUCUGCG
..............(((((((..((((((((((((((.........-.)))))))).))))))---(((((..............))))).....(((.....)))...))))))).... ( -32.84)
>DroEre_CAF1 28275 115 + 1
AACUAUCUGUUUUUGACUGAAUAUAC-UGCCCACUGAAUUUUUAUU-GCCGGUGGGCCGAGUG---GCAAUUUCAUUUAAUUUUUAUUGCACUUCUGCGCUAAGGUCCUUUCAGUCUGCC
..............(((((((...((-(((((((((..........-..)))))))).(((((---.((((..............))))))))).........)))...))))))).... ( -29.44)
>DroYak_CAF1 40588 119 + 1
AACUAUUUAUCUUUAACUGAGUACACUUGCCCACUGAAUUUUUAUU-GCCGGUGGGCCGGGUGGCGGCAAUUUCAUUUAAUUUUUAUUGCACUUCUGCGCCAAGGUCCUUUCAGUCUGCG
...............((((((..(((((((((((((..........-..))))))).))))))..(((((((......))))......(((....))))))........))))))..... ( -30.00)
>consensus
AACUAUUUAUCUUUGACUGAAUAUACUUGCCCACUGAAUUUUUAUU_GUCGGUGGGUCGAGUG___GCAAUUUCAUUUAAUUUUUAUUGCACUUCGCCGCUAAGGUCCUUUCAGUCUGCG
..............(((((((..(((((((((((((.............))))))).))))))...(((((..............)))))...................))))))).... (-27.96 = -27.92 +  -0.04)

alignment

secondary structure

dotplot

Window 0

Location	6,779,058 – 6,779,175
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.01
Mean single sequence MFE	-25.71
Consensus MFE	-19.54
Energy contribution	-19.74
Covariance contribution	0.20
Combinations/Pair	1.10
Mean z-score	-1.54
Structure conservation index	0.76
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6779058 117 - 27905053
CGCAGACUGAAAGGACCUUAGCGGCAAAGUGCAAUAAAAAUUAAAUGAAAUUGC---CACUCGACCCACCGACCGAUAAAAAUUCAGUGGGCAAGUAUAUUCAGUCAAAGAUAAAUAGUU
....(((((((...........(((((....((............))...))))---)(((.(.(((((.((...........)).)))))).)))...))))))).............. ( -24.90)
>DroSec_CAF1 43211 115 - 1
CGCAGACUGAAAGG-CCUUAGCGGCGAAGUGCAAUAAAAAUUAAAUGAAAUUGC---CACUCGACCCACCGAC-AAUAAAAAUUCAGUGGGCAAGUAUAUUCAGUCAAAGAUAAAUAGUU
....(((((((..(-((.....)))((.(((((((..............)))).---)))))(.(((((.((.-.........)).)))))).......))))))).............. ( -26.34)
>DroSim_CAF1 47230 116 - 1
CGCAGACUGAAAGGACCUUAGCGGCGAAGUGCAAUAAAAAUUAAAUGAAAUUGC---CACUCGACCCACCGAC-GAUAAAAAUUCAGUGGGCAAGUAUAUUCAGUCAAAGAUAAAUAGUU
....(((((((...........(((((....((............))...))))---)(((.(.(((((.((.-.........)).)))))).)))...))))))).............. ( -24.70)
>DroEre_CAF1 28275 115 - 1
GGCAGACUGAAAGGACCUUAGCGCAGAAGUGCAAUAAAAAUUAAAUGAAAUUGC---CACUCGGCCCACCGGC-AAUAAAAAUUCAGUGGGCA-GUAUAUUCAGUCAAAAACAGAUAGUU
....(((((((.((......((((....))))......((((......)))).)---).....((((((.((.-.........)).)))))).-.....))))))).............. ( -26.30)
>DroYak_CAF1 40588 119 - 1
CGCAGACUGAAAGGACCUUGGCGCAGAAGUGCAAUAAAAAUUAAAUGAAAUUGCCGCCACCCGGCCCACCGGC-AAUAAAAAUUCAGUGGGCAAGUGUACUCAGUUAAAGAUAAAUAGUU
....((((((....((((((((((....)))).............(((((((((((((....))).....)))-))).....)))).....)))).))..)))))).............. ( -26.30)
>consensus
CGCAGACUGAAAGGACCUUAGCGGCGAAGUGCAAUAAAAAUUAAAUGAAAUUGC___CACUCGACCCACCGAC_AAUAAAAAUUCAGUGGGCAAGUAUAUUCAGUCAAAGAUAAAUAGUU
....(((((((.........(((......)))..........................(((.(.(((((.((...........)).)))))).)))...))))))).............. (-19.54 = -19.74 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:36:34 2006