Locus 6927

Sequence ID	3R_DroMel_CAF1
Location	18,270,724 – 18,271,004
Length	280
Max. P	0.980631

overview

Window 6

Location	18,270,724 – 18,270,844
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	90.69
Mean single sequence MFE	-40.14
Consensus MFE	-30.15
Energy contribution	-32.02
Covariance contribution	1.87
Combinations/Pair	1.06
Mean z-score	-2.27
Structure conservation index	0.75
SVM decision value	0.67
SVM RNA-class probability	0.818361
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18270724 120 + 27905053
GCAUUAAUGAUUUGGGCGAGAAACGCCACAGCUAUGGGCAAAUCUUUCGGCUUGGUUUUGACCGGACUGAGCAGAGAGGAACAAUUCCUCACUGUAUUGCGUCCCAAGUCUGGACAAGCA
((......((((((((((......(((.((....))))).......((((..((((....))))..))))((((.(((((.....))))).))))....)).)))))))).......)). ( -40.12)
>DroSec_CAF1 26943 120 + 1
GCAUUAAUGAUUUGGGCGAGAAACAUCACAGCCUUGGGCAAAUCCGUCGACUUGGUUUUGACCGGACUGAGCAGUGAGGAACAAUUCCUCACUGUAUUGCGUCCCAAGUCUGGACAAGCA
((......((((((((((..........(((((..((.((((.(((......))).)))).)))).))).((((((((((.....))))))))))....)).)))))))).......)). ( -43.72)
>DroSim_CAF1 27930 120 + 1
GCAUUAAUGAUUUGGGCGAGAAACAUAACAGCCUUGGGCAAAUCCGUCGACUUGGUUUUGACCGGACUGAGCAGUGAGGAACAAUUCCUCACUGUAUUGCGUCCCAAGUCUGGACAAGCA
((......((((((((((..........(((((..((.((((.(((......))).)))).)))).))).((((((((((.....))))))))))....)).)))))))).......)). ( -43.72)
>DroYak_CAF1 27443 120 + 1
GCAUCAAUGAUUUGAGCCAGAAAAUUGAAAACCUUUGGCAAAUCCUCCGAUUUGGUUUUGAGCGGACUGAGCAGGGUGGAACAAUUCCUCACUGUAUUGCGUCCCAAGUCUGGACAAGCA
((.((((....))))((((((...(((((((((.((((........))))...))))))....(((((((((((.(.(((.....))).).)))).))).))))))).))))).)..)). ( -33.00)
>consensus
GCAUUAAUGAUUUGGGCGAGAAACAUCACAGCCUUGGGCAAAUCCGUCGACUUGGUUUUGACCGGACUGAGCAGUGAGGAACAAUUCCUCACUGUAUUGCGUCCCAAGUCUGGACAAGCA
((......((((((((((..........(((((..((.((((.((........)).)))).)))).))).((((((((((.....))))))))))....)).)))))))).......)). (-30.15 = -32.02 +   1.87)

alignment

secondary structure

dotplot

Window 7

Location	18,270,764 – 18,270,884
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.58
Mean single sequence MFE	-39.27
Consensus MFE	-35.28
Energy contribution	-35.77
Covariance contribution	0.50
Combinations/Pair	1.10
Mean z-score	-2.73
Structure conservation index	0.90
SVM decision value	1.87
SVM RNA-class probability	0.980631
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18270764 120 + 27905053
AAUCUUUCGGCUUGGUUUUGACCGGACUGAGCAGAGAGGAACAAUUCCUCACUGUAUUGCGUCCCAAGUCUGGACAAGCAGUUAGUGUUUGAAUAACCAAAUCCACUUUGCGCGGAUUAU
(((((.((((..((((....))))..))))((((((.(((.........(((((.(((((((((.......))))..))))))))))((((......))))))).))))))..))))).. ( -35.90)
>DroSec_CAF1 26983 120 + 1
AAUCCGUCGACUUGGUUUUGACCGGACUGAGCAGUGAGGAACAAUUCCUCACUGUAUUGCGUCCCAAGUCUGGACAAGCAGUUAGUGUUUUAAUAACCAAAUCCACUUUGCGCGGAUUAU
(((((((.((((((((....)))(((((((((((((((((.....)))))))))).))).)))).))))).......((((..((((..((........))..))))))))))))))).. ( -42.80)
>DroSim_CAF1 27970 120 + 1
AAUCCGUCGACUUGGUUUUGACCGGACUGAGCAGUGAGGAACAAUUCCUCACUGUAUUGCGUCCCAAGUCUGGACAAGCAGUUAGUGUUUUAAUAACCAAAUCCACUUUGCGCGGAUUAU
(((((((.((((((((....)))(((((((((((((((((.....)))))))))).))).)))).))))).......((((..((((..((........))..))))))))))))))).. ( -42.80)
>DroYak_CAF1 27483 120 + 1
AAUCCUCCGAUUUGGUUUUGAGCGGACUGAGCAGGGUGGAACAAUUCCUCACUGUAUUGCGUCCCAAGUCUGGACAAGCAGUUAGUGUUUUUAUGACCAAAUCCACUUUGCGCGGAUUUU
(((((((((.(((......)))))))....((((((((((.....((..(((((.(((((((((.......))))..)))))))))).......)).....))))))))))..))))).. ( -35.60)
>consensus
AAUCCGUCGACUUGGUUUUGACCGGACUGAGCAGUGAGGAACAAUUCCUCACUGUAUUGCGUCCCAAGUCUGGACAAGCAGUUAGUGUUUUAAUAACCAAAUCCACUUUGCGCGGAUUAU
((((((((((..(((.((((....(((((.((((((((((.....)))))))))).....((((.......))))...)))))...(((.....))))))).)))..))).))))))).. (-35.28 = -35.77 +   0.50)

alignment

secondary structure

dotplot

Window 8

Location	18,270,764 – 18,270,884
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.58
Mean single sequence MFE	-37.07
Consensus MFE	-30.14
Energy contribution	-31.45
Covariance contribution	1.31
Combinations/Pair	1.03
Mean z-score	-2.63
Structure conservation index	0.81
SVM decision value	0.85
SVM RNA-class probability	0.865529
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18270764 120 - 27905053
AUAAUCCGCGCAAAGUGGAUUUGGUUAUUCAAACACUAACUGCUUGUCCAGACUUGGGACGCAAUACAGUGAGGAAUUGUUCCUCUCUGCUCAGUCCGGUCAAAACCAAGCCGAAAGAUU
..(((((((.....))))))).(((((.........)))))(((((....((((..((((......(((.(((((.....))))).)))....)))))))).....)))))(....)... ( -34.50)
>DroSec_CAF1 26983 120 - 1
AUAAUCCGCGCAAAGUGGAUUUGGUUAUUAAAACACUAACUGCUUGUCCAGACUUGGGACGCAAUACAGUGAGGAAUUGUUCCUCACUGCUCAGUCCGGUCAAAACCAAGUCGACGGAUU
..(((((((......(((((..(((..(((......)))..))).)))))(((((.((((......(((((((((.....)))))))))....))))(((....))))))))).)))))) ( -42.10)
>DroSim_CAF1 27970 120 - 1
AUAAUCCGCGCAAAGUGGAUUUGGUUAUUAAAACACUAACUGCUUGUCCAGACUUGGGACGCAAUACAGUGAGGAAUUGUUCCUCACUGCUCAGUCCGGUCAAAACCAAGUCGACGGAUU
..(((((((......(((((..(((..(((......)))..))).)))))(((((.((((......(((((((((.....)))))))))....))))(((....))))))))).)))))) ( -42.10)
>DroYak_CAF1 27483 120 - 1
AAAAUCCGCGCAAAGUGGAUUUGGUCAUAAAAACACUAACUGCUUGUCCAGACUUGGGACGCAAUACAGUGAGGAAUUGUUCCACCCUGCUCAGUCCGCUCAAAACCAAAUCGGAGGAUU
..(((((......((((((((.(((........((((...(((..((((.......)))))))....)))).(((.....))).....))).)))))))).....((.....)).))))) ( -29.60)
>consensus
AUAAUCCGCGCAAAGUGGAUUUGGUUAUUAAAACACUAACUGCUUGUCCAGACUUGGGACGCAAUACAGUGAGGAAUUGUUCCUCACUGCUCAGUCCGGUCAAAACCAAGUCGAAGGAUU
..(((((.(((...)))(((((((((.............(((......))).....((((......(((((((((.....)))))))))....))))......)))))))))...))))) (-30.14 = -31.45 +   1.31)

alignment

secondary structure

dotplot

Window 9

Location	18,270,884 – 18,271,004
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	95.42
Mean single sequence MFE	-41.95
Consensus MFE	-38.29
Energy contribution	-38.10
Covariance contribution	-0.19
Combinations/Pair	1.05
Mean z-score	-1.62
Structure conservation index	0.91
SVM decision value	0.34
SVM RNA-class probability	0.694408
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18270884 120 + 27905053
CGUAGGGCUUGAAUAGAGAGCCAAGUAAUCUGCCCUGCAGUUUGUUUUGCUUUUGGCGGUAGUGCGUCAUCGCAUCAAAGCAGAUGCCGUGCUUGCGGGAAGUCAAAAGGACUAGCAGGA
.(((((((((.......))))).......))))(((((((((..(((.((((((.(((..((..((.((((((......)).)))).))..))))).)))))).)))..)))).))))). ( -44.91)
>DroSec_CAF1 27103 120 + 1
CGUAGGGCUUGAAUAGAGAGCCAAGUAAUCUGCCCUGCAGCUUGUUUUGCUUUUGGCGGUAGUGCGUCAUCGCAUCAAAGCAGAUGCCGUGCUUGCGGGAAGUCAGAAGGACCAGCAGGA
.(((((((((.......))))).......))))(((((.(.((.((((((((((.(((..((..((.((((((......)).)))).))..))))).))))).))))).)).).))))). ( -42.91)
>DroSim_CAF1 28090 120 + 1
CGUAGGGCUUGAAUAGAGAACCAAGUAAUCUGCCCUGCAGCUUGUUUUGCUUUUGGCGGUAGUGCGUCAUCGCAUCAAAGCAGAUGCCGUGCUUGCGGGAAGUCAGAAGGACCAGCAGAA
.(((((((.......................))))))).(((.(((((((((((.(((..((..((.((((((......)).)))).))..))))).))))))....))))).))).... ( -40.50)
>DroYak_CAF1 27603 120 + 1
UGUACGGCUUGUAUAGAGAGCCAAGUAAUCUGCCCUGCAGUUUGUUUUGCUUUUGGCGGUAGUGCGUCAUCGCAUCAAAGCAGAUGCCGUGCUUGCGGGAAGUAAGUAGGACCAGCAGUA
.....(((((.......)))))............((((.((((..(((((((((.(((..((..((.((((((......)).)))).))..))))).)))))))))..))))..)))).. ( -39.50)
>consensus
CGUAGGGCUUGAAUAGAGAGCCAAGUAAUCUGCCCUGCAGCUUGUUUUGCUUUUGGCGGUAGUGCGUCAUCGCAUCAAAGCAGAUGCCGUGCUUGCGGGAAGUCAGAAGGACCAGCAGGA
.(((((((......(((..((...))..)))))))))).(((.(((((((((((.(((..((..((.((((((......)).)))).))..))))).))))))....))))).))).... (-38.29 = -38.10 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:33:27 2006