Locus 898

Sequence ID	2R_DroMel_CAF1
Location	4,045,492 – 4,045,691
Length	199
Max. P	0.997940

overview

Window 9

Location	4,045,492 – 4,045,611
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.14
Mean single sequence MFE	-29.80
Consensus MFE	-27.64
Energy contribution	-28.44
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-2.03
Structure conservation index	0.93
SVM decision value	2.73
SVM RNA-class probability	0.996698
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4045492 119 + 20766785
GCUGCAAAUGAAGUGCAAAAAAAUUGUUAAACGCUUUACGCACAAUUAGGCAGUCAGCCAGAAGACGUGUAAAGUGCGUGCCAAUGAGCACUAAAUAAAUAUUUGCACGAGAGCUUGA-A
(((.(....)..(((((((....(((((...((((((((((....((.(((.....))).))....)))))))))).((((......))))..)))))...)))))))...)))....-. ( -30.40)
>DroSec_CAF1 28139 118 + 1
GCUGCAAAUGAAGUGCAAA-AAAUUGUUAAACGCUUUACGCACAAUUAGGCAGUCAGCCAGAAGACGUGUAAAGUGCGUGCCAAUGAGCACUAAAUAAAUAUUUGCACGAGAGCUUGA-A
(((.(....)..(((((((-.(.(((((...((((((((((....((.(((.....))).))....)))))))))).((((......))))..))))).).)))))))...)))....-. ( -31.10)
>DroSim_CAF1 32807 118 + 1
GCUGCAAAUGAAGUGCAAA-AAAUUGUUAAACGCUUUACGCACAAUUAGGCAGUCAGCCAGAAGACGUGUAAAGUGCGUGCCAAUGAGCACUAAAUAAAUAUUUGCACGAGAGCUUGA-A
(((.(....)..(((((((-.(.(((((...((((((((((....((.(((.....))).))....)))))))))).((((......))))..))))).).)))))))...)))....-. ( -31.10)
>DroEre_CAF1 27433 118 + 1
GCUGCAAAUGAAGUGCAAC-AAAUUGUUAAACGCUUUACGCACAAUUAGGCAGUCAGCCAGAAGACGUGUAAAGUGCGUGCCAAUGAGCACUAAAUAAAUAUUUGCACGAGAGCUGGA-A
(((.(....)..((((((.-...(((((...((((((((((....((.(((.....))).))....)))))))))).((((......))))..)))))....))))))...)))....-. ( -29.90)
>DroYak_CAF1 31330 119 + 1
GCUGCAAAUGAAGUGCAAC-AAAUUGUUAAACGCUUAACGCACAAUUAGGCAGUCAGCCAUAAGACGUGUAAAGUGCGUGCCAAUGAGCACUAAAUAAAUAUUUGAACGAGCGCUUGAAA
........(.(((((((((-.....)))....(((((((((((..(((.((.(((........))))).))).)))))).....))))).....................)))))).).. ( -26.50)
>consensus
GCUGCAAAUGAAGUGCAAA_AAAUUGUUAAACGCUUUACGCACAAUUAGGCAGUCAGCCAGAAGACGUGUAAAGUGCGUGCCAAUGAGCACUAAAUAAAUAUUUGCACGAGAGCUUGA_A
............(((((((....(((((...((((((((((.......(((.....))).......)))))))))).((((......))))..)))))...)))))))............ (-27.64 = -28.44 +   0.80)

alignment

secondary structure

dotplot

Window 0

Location	4,045,492 – 4,045,611
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.14
Mean single sequence MFE	-27.40
Consensus MFE	-24.92
Energy contribution	-25.32
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.59
Structure conservation index	0.91
SVM decision value	1.29
SVM RNA-class probability	0.938594
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4045492 119 - 20766785
U-UCAAGCUCUCGUGCAAAUAUUUAUUUAGUGCUCAUUGGCACGCACUUUACACGUCUUCUGGCUGACUGCCUAAUUGUGCGUAAAGCGUUUAACAAUUUUUUUGCACUUCAUUUGCAGC
.-....((....(((((((..........(((((....)))))((.((((((.((......(((.....)))......)).)))))).))...........))))))).......))... ( -27.70)
>DroSec_CAF1 28139 118 - 1
U-UCAAGCUCUCGUGCAAAUAUUUAUUUAGUGCUCAUUGGCACGCACUUUACACGUCUUCUGGCUGACUGCCUAAUUGUGCGUAAAGCGUUUAACAAUUU-UUUGCACUUCAUUUGCAGC
.-....((....(((((((..........(((((....)))))((.((((((.((......(((.....)))......)).)))))).))..........-))))))).......))... ( -27.70)
>DroSim_CAF1 32807 118 - 1
U-UCAAGCUCUCGUGCAAAUAUUUAUUUAGUGCUCAUUGGCACGCACUUUACACGUCUUCUGGCUGACUGCCUAAUUGUGCGUAAAGCGUUUAACAAUUU-UUUGCACUUCAUUUGCAGC
.-....((....(((((((..........(((((....)))))((.((((((.((......(((.....)))......)).)))))).))..........-))))))).......))... ( -27.70)
>DroEre_CAF1 27433 118 - 1
U-UCCAGCUCUCGUGCAAAUAUUUAUUUAGUGCUCAUUGGCACGCACUUUACACGUCUUCUGGCUGACUGCCUAAUUGUGCGUAAAGCGUUUAACAAUUU-GUUGCACUUCAUUUGCAGC
.-....((....((((((...........(((((....)))))((.((((((.((......(((.....)))......)).)))))).))..........-.)))))).......))... ( -27.00)
>DroYak_CAF1 31330 119 - 1
UUUCAAGCGCUCGUUCAAAUAUUUAUUUAGUGCUCAUUGGCACGCACUUUACACGUCUUAUGGCUGACUGCCUAAUUGUGCGUUAAGCGUUUAACAAUUU-GUUGCACUUCAUUUGCAGC
....((((((((((.(((...........(((((....)))))..................(((.....)))...))).)))...)))))))........-((((((.......)))))) ( -26.90)
>consensus
U_UCAAGCUCUCGUGCAAAUAUUUAUUUAGUGCUCAUUGGCACGCACUUUACACGUCUUCUGGCUGACUGCCUAAUUGUGCGUAAAGCGUUUAACAAUUU_UUUGCACUUCAUUUGCAGC
......((....((((((...........(((((....)))))((.((((((.((......(((.....)))......)).)))))).))............)))))).......))... (-24.92 = -25.32 +   0.40)

alignment

secondary structure

dotplot

Window 1

Location	4,045,532 – 4,045,651
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.32
Mean single sequence MFE	-31.00
Consensus MFE	-28.80
Energy contribution	-29.04
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-2.14
Structure conservation index	0.93
SVM decision value	2.97
SVM RNA-class probability	0.997940
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4045532 119 + 20766785
CACAAUUAGGCAGUCAGCCAGAAGACGUGUAAAGUGCGUGCCAAUGAGCACUAAAUAAAUAUUUGCACGAGAGCUUGA-AAAAACAGCCCGAGUCCAAGAACAAGGACAAUCCGGGUAAG
.....((((((.(((........)))(((((((((((..........)))))..........))))))....))))))-.......(((((.((((........))))....)))))... ( -31.50)
>DroSec_CAF1 28178 119 + 1
CACAAUUAGGCAGUCAGCCAGAAGACGUGUAAAGUGCGUGCCAAUGAGCACUAAAUAAAUAUUUGCACGAGAGCUUGA-AAAAACAGCCCGAGUCCAAGAACAAGGACAAUCCGGGUAAG
.....((((((.(((........)))(((((((((((..........)))))..........))))))....))))))-.......(((((.((((........))))....)))))... ( -31.50)
>DroSim_CAF1 32846 119 + 1
CACAAUUAGGCAGUCAGCCAGAAGACGUGUAAAGUGCGUGCCAAUGAGCACUAAAUAAAUAUUUGCACGAGAGCUUGA-AAAAACAGCCCGAGUCCAAGAACAAGGACAAUCCGGGUAAG
.....((((((.(((........)))(((((((((((..........)))))..........))))))....))))))-.......(((((.((((........))))....)))))... ( -31.50)
>DroEre_CAF1 27472 119 + 1
CACAAUUAGGCAGUCAGCCAGAAGACGUGUAAAGUGCGUGCCAAUGAGCACUAAAUAAAUAUUUGCACGAGAGCUGGA-AAAAGCAGCCCGAGUCCAAGAACAAGGACAAUCCGGGUAAG
........(((.....)))......((((((((((((..........)))))..........)))))))...(((...-...))).(((((.((((........))))....)))))... ( -32.70)
>DroYak_CAF1 31369 120 + 1
CACAAUUAGGCAGUCAGCCAUAAGACGUGUAAAGUGCGUGCCAAUGAGCACUAAAUAAAUAUUUGAACGAGCGCUUGAAAAAAACAGCUCGAGUCCAAGAACAAGGACAAACCGGGUAAG
(((..((((((.....))).)))...)))...(((((..........))))).......((((((..(((((..((....))....))))).((((........))))....)))))).. ( -27.80)
>consensus
CACAAUUAGGCAGUCAGCCAGAAGACGUGUAAAGUGCGUGCCAAUGAGCACUAAAUAAAUAUUUGCACGAGAGCUUGA_AAAAACAGCCCGAGUCCAAGAACAAGGACAAUCCGGGUAAG
.....((((((.(((........)))(((((((((((..........)))))..........))))))....))))))........(((((.((((........))))....)))))... (-28.80 = -29.04 +   0.24)

alignment

secondary structure

dotplot

Window 2

Location	4,045,532 – 4,045,651
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.32
Mean single sequence MFE	-29.14
Consensus MFE	-26.72
Energy contribution	-27.16
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-1.19
Structure conservation index	0.92
SVM decision value	-0.01
SVM RNA-class probability	0.530799
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4045532 119 - 20766785
CUUACCCGGAUUGUCCUUGUUCUUGGACUCGGGCUGUUUUU-UCAAGCUCUCGUGCAAAUAUUUAUUUAGUGCUCAUUGGCACGCACUUUACACGUCUUCUGGCUGACUGCCUAAUUGUG
....(((((...((((........)))))))))........-..........((((((((....)))).(((((....)))))))))....((((......(((.....)))....)))) ( -29.50)
>DroSec_CAF1 28178 119 - 1
CUUACCCGGAUUGUCCUUGUUCUUGGACUCGGGCUGUUUUU-UCAAGCUCUCGUGCAAAUAUUUAUUUAGUGCUCAUUGGCACGCACUUUACACGUCUUCUGGCUGACUGCCUAAUUGUG
....(((((...((((........)))))))))........-..........((((((((....)))).(((((....)))))))))....((((......(((.....)))....)))) ( -29.50)
>DroSim_CAF1 32846 119 - 1
CUUACCCGGAUUGUCCUUGUUCUUGGACUCGGGCUGUUUUU-UCAAGCUCUCGUGCAAAUAUUUAUUUAGUGCUCAUUGGCACGCACUUUACACGUCUUCUGGCUGACUGCCUAAUUGUG
....(((((...((((........)))))))))........-..........((((((((....)))).(((((....)))))))))....((((......(((.....)))....)))) ( -29.50)
>DroEre_CAF1 27472 119 - 1
CUUACCCGGAUUGUCCUUGUUCUUGGACUCGGGCUGCUUUU-UCCAGCUCUCGUGCAAAUAUUUAUUUAGUGCUCAUUGGCACGCACUUUACACGUCUUCUGGCUGACUGCCUAAUUGUG
....(((((...((((........)))))))))..(((...-...)))....((((((((....)))).(((((....)))))))))....((((......(((.....)))....)))) ( -30.90)
>DroYak_CAF1 31369 120 - 1
CUUACCCGGUUUGUCCUUGUUCUUGGACUCGAGCUGUUUUUUUCAAGCGCUCGUUCAAAUAUUUAUUUAGUGCUCAUUGGCACGCACUUUACACGUCUUAUGGCUGACUGCCUAAUUGUG
............((((........)))).(((((.((((.....)))))))))................(((((....)))))........((((..(((.(((.....)))))).)))) ( -26.30)
>consensus
CUUACCCGGAUUGUCCUUGUUCUUGGACUCGGGCUGUUUUU_UCAAGCUCUCGUGCAAAUAUUUAUUUAGUGCUCAUUGGCACGCACUUUACACGUCUUCUGGCUGACUGCCUAAUUGUG
....(((((...((((........)))))))))..((((.....))))....((((((((....)))).(((((....)))))))))....((((......(((.....)))....)))) (-26.72 = -27.16 +   0.44)

alignment

secondary structure

dotplot

Window 3

Location	4,045,572 – 4,045,691
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.98
Mean single sequence MFE	-33.74
Consensus MFE	-31.72
Energy contribution	-32.00
Covariance contribution	0.28
Combinations/Pair	1.05
Mean z-score	-1.58
Structure conservation index	0.94
SVM decision value	1.62
SVM RNA-class probability	0.968269
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4045572 119 - 20766785
GGCGAAAAUGGCAAGCAAUGGUAUUAAAUGUUUAGCACGUCUUACCCGGAUUGUCCUUGUUCUUGGACUCGGGCUGUUUUU-UCAAGCUCUCGUGCAAAUAUUUAUUUAGUGCUCAUUGG
.((.......))...(((((((((((((((..(((((((.....(((((...((((........)))))))))..((((..-..))))...)))))...))..)))))))))).))))). ( -33.60)
>DroSec_CAF1 28218 119 - 1
GGCGAAAACGGCAAGCAAUGGUAUUAAAUGUUUAGCACGUCUUACCCGGAUUGUCCUUGUUCUUGGACUCGGGCUGUUUUU-UCAAGCUCUCGUGCAAAUAUUUAUUUAGUGCUCAUUGG
(.((....)).)...(((((((((((((((..(((((((.....(((((...((((........)))))))))..((((..-..))))...)))))...))..)))))))))).))))). ( -34.50)
>DroSim_CAF1 32886 119 - 1
GGCGAAAACGGCAAGCAAUGGUAUUAAAUGUUUAGCACGUCUUACCCGGAUUGUCCUUGUUCUUGGACUCGGGCUGUUUUU-UCAAGCUCUCGUGCAAAUAUUUAUUUAGUGCUCAUUGG
(.((....)).)...(((((((((((((((..(((((((.....(((((...((((........)))))))))..((((..-..))))...)))))...))..)))))))))).))))). ( -34.50)
>DroEre_CAF1 27512 119 - 1
GGCGAAAACGGCAAGCAAUGGUAUUAAAUGUUUAGCACGUCUUACCCGGAUUGUCCUUGUUCUUGGACUCGGGCUGCUUUU-UCCAGCUCUCGUGCAAAUAUUUAUUUAGUGCUCAUUGG
(.((....)).)...(((((((((((((((..(((((((.....(((((...((((........)))))))))..(((...-...)))...)))))...))..)))))))))).))))). ( -36.20)
>DroYak_CAF1 31409 120 - 1
GGCGAAAACGGCAAGCAAUGGUAUUAAAUGUUUAGUACGUCUUACCCGGUUUGUCCUUGUUCUUGGACUCGAGCUGUUUUUUUCAAGCGCUCGUUCAAAUAUUUAUUUAGUGCUCAUUGG
(.((....)).)...(((((((((((((((..((..................((((........)))).(((((.((((.....)))))))))......))..)))))))))).))))). ( -29.90)
>consensus
GGCGAAAACGGCAAGCAAUGGUAUUAAAUGUUUAGCACGUCUUACCCGGAUUGUCCUUGUUCUUGGACUCGGGCUGUUUUU_UCAAGCUCUCGUGCAAAUAUUUAUUUAGUGCUCAUUGG
(.((....)).)...(((((((((((((((..(((((((.....(((((...((((........)))))))))..((((.....))))...)))))...))..)))))))))).))))). (-31.72 = -32.00 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:50:32 2006