Locus 5232

Sequence ID	3R_DroMel_CAF1
Location	13,682,361 – 13,682,608
Length	247
Max. P	0.999913

overview

Window 5

Location	13,682,361 – 13,682,467
Length	106
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	89.55
Mean single sequence MFE	-29.82
Consensus MFE	-25.28
Energy contribution	-25.56
Covariance contribution	0.28
Combinations/Pair	1.11
Mean z-score	-1.33
Structure conservation index	0.85
SVM decision value	0.07
SVM RNA-class probability	0.568181
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13682361 106 + 27905053
AGUUUUUUUAUUUUUAUUAGUGAAUAGAUUUUUUAAUAAUGGCC-CGGGCCCCAGGGAUGUGUACACCAAAUUGUCGGACAUGCAGUUGGACUGGUGUGCGGUCAAC
(((((.((((((......)))))).))))).........(((((-....((....))....((((((((....(((.(((.....))).)))))))))))))))).. ( -29.00)
>DroSec_CAF1 9689 100 + 1
AGUUU-------UUUAUUUGCGGAUAGAUUUUUUAAUAAUGGCCCCGGGCCCCAGGGACGUGUACACCAAAUUGUCCGACAUGCAGUUGGACUGGUGUGCGGUCAAC
.....-------((((((....))))))...........(((((.((..((....)).)).((((((((....(((((((.....)))))))))))))))))))).. ( -32.60)
>DroSim_CAF1 9740 102 + 1
AGUUUUU-----UUUAUUUGCGAAUAGAUUUUUUAAUAAUGGCCCCGGGCCCCAGGGACGUGUACACCAAAUUGUCCGACAUGCAGUUGGACUGGUGUGCGGUCAAC
.......-----((((((....))))))...........(((((.((..((....)).)).((((((((....(((((((.....)))))))))))))))))))).. ( -32.10)
>DroEre_CAF1 4168 99 + 1
CCUU--------UUUAUUUGUGGAUAGAUUUUUUAAUAAUGGCCCCGCGGCCCAGGGACGUGUACACCAAAUUGUUCGACAUGCAGUUGGACUGGUGUGCGGUCAAC
(((.--------((((((....))))))............((((....)))).)))(((.(((((((((....(((((((.....)))))))))))))))))))... ( -32.10)
>DroYak_CAF1 4367 99 + 1
CGUU--------UUUAUUUGUGGAUAGAUUUUUUAAUAAUGGCCCCAGGCGCAAAGGACGUGUACACCAAAUUGUCCGACAUGCAGUUGAACUGGUGUGCGGUCAAC
....--------((((((....))))))...........(((((...))).))...(((.(((((((((....((.((((.....)))).))))))))))))))... ( -23.30)
>consensus
AGUUU_______UUUAUUUGUGGAUAGAUUUUUUAAUAAUGGCCCCGGGCCCCAGGGACGUGUACACCAAAUUGUCCGACAUGCAGUUGGACUGGUGUGCGGUCAAC
............((((((....))))))............(((.....))).....(((.(((((((((....(((((((.....)))))))))))))))))))... (-25.28 = -25.56 +   0.28)

alignment

secondary structure

dotplot

Window 6

Location	13,682,400 – 13,682,492
Length	92
Sequences	5
Columns	93
Reading direction	forward
Mean pairwise identity	93.55
Mean single sequence MFE	-40.00
Consensus MFE	-36.56
Energy contribution	-36.72
Covariance contribution	0.16
Combinations/Pair	1.10
Mean z-score	-2.76
Structure conservation index	0.91
SVM decision value	4.52
SVM RNA-class probability	0.999913
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13682400 92 + 27905053
UGGCC-CGGGCCCCAGGGAUGUGUACACCAAAUUGUCGGACAUGCAGUUGGACUGGUGUGCGGUCAACCAAGGAUGUCGUCCCUUUUGGCCAG
.....-..((((..(((((((.((((((((....(((.(((.....))).)))))))))))((....))........)))))))...)))).. ( -38.30)
>DroSec_CAF1 9721 93 + 1
UGGCCCCGGGCCCCAGGGACGUGUACACCAAAUUGUCCGACAUGCAGUUGGACUGGUGUGCGGUCAACCAUGGAUAUCGUCCCUUUUGGCCAG
........((((..(((((((.((((((((....(((((((.....)))))))))))))))((....))........)))))))...)))).. ( -43.80)
>DroSim_CAF1 9774 93 + 1
UGGCCCCGGGCCCCAGGGACGUGUACACCAAAUUGUCCGACAUGCAGUUGGACUGGUGUGCGGUCAACCAUGGAUAUCGUCCCUUUUGGCCAG
........((((..(((((((.((((((((....(((((((.....)))))))))))))))((....))........)))))))...)))).. ( -43.80)
>DroEre_CAF1 4199 93 + 1
UGGCCCCGCGGCCCAGGGACGUGUACACCAAAUUGUUCGACAUGCAGUUGGACUGGUGUGCGGUCAACCAAGGAUGUCGUCCCUUUUGGCCAG
.........((((.(((((((.((((((((....(((((((.....)))))))))))))))((....))........)))))))...)))).. ( -40.80)
>DroYak_CAF1 4398 93 + 1
UGGCCCCAGGCGCAAAGGACGUGUACACCAAAUUGUCCGACAUGCAGUUGAACUGGUGUGCGGUCAACCAAGGAUAUUGUCCCUUUUGGCCAG
(((((..(((.((((..(((.(((((((((....((.((((.....)))).))))))))))))))..(....)...)))).)))...))))). ( -33.30)
>consensus
UGGCCCCGGGCCCCAGGGACGUGUACACCAAAUUGUCCGACAUGCAGUUGGACUGGUGUGCGGUCAACCAAGGAUAUCGUCCCUUUUGGCCAG
(((((.........(((((((.((((((((....(((((((.....)))))))))))))))((....))........)))))))...))))). (-36.56 = -36.72 +   0.16)

alignment

secondary structure

dotplot

Window 7

Location	13,682,400 – 13,682,492
Length	92
Sequences	5
Columns	93
Reading direction	reverse
Mean pairwise identity	93.55
Mean single sequence MFE	-33.66
Consensus MFE	-29.96
Energy contribution	-30.32
Covariance contribution	0.36
Combinations/Pair	1.11
Mean z-score	-1.62
Structure conservation index	0.89
SVM decision value	1.55
SVM RNA-class probability	0.963181
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13682400 92 - 27905053
CUGGCCAAAAGGGACGACAUCCUUGGUUGACCGCACACCAGUCCAACUGCAUGUCCGACAAUUUGGUGUACACAUCCCUGGGGCCCG-GGCCA
((((((...(((((((((.......))))...(.(((((((((..((.....))..)))....)))))).)...)))))..)).)))-).... ( -29.10)
>DroSec_CAF1 9721 93 - 1
CUGGCCAAAAGGGACGAUAUCCAUGGUUGACCGCACACCAGUCCAACUGCAUGUCGGACAAUUUGGUGUACACGUCCCUGGGGCCCGGGGCCA
((((((...(((((((........((....))(.((((((((((.((.....)).))))....)))))).).)))))))..)).))))..... ( -38.30)
>DroSim_CAF1 9774 93 - 1
CUGGCCAAAAGGGACGAUAUCCAUGGUUGACCGCACACCAGUCCAACUGCAUGUCGGACAAUUUGGUGUACACGUCCCUGGGGCCCGGGGCCA
((((((...(((((((........((....))(.((((((((((.((.....)).))))....)))))).).)))))))..)).))))..... ( -38.30)
>DroEre_CAF1 4199 93 - 1
CUGGCCAAAAGGGACGACAUCCUUGGUUGACCGCACACCAGUCCAACUGCAUGUCGAACAAUUUGGUGUACACGUCCCUGGGCCGCGGGGCCA
..((((...((((((((((((...(((((..((.(((.(((.....)))..)))))..))))).)))))...))))))).))))......... ( -33.50)
>DroYak_CAF1 4398 93 - 1
CUGGCCAAAAGGGACAAUAUCCUUGGUUGACCGCACACCAGUUCAACUGCAUGUCGGACAAUUUGGUGUACACGUCCUUUGCGCCUGGGGCCA
..((((..(((((((.........((....))(.((((((((((.((.....)).))))....)))))).)..)))))))........)))). ( -29.10)
>consensus
CUGGCCAAAAGGGACGAUAUCCUUGGUUGACCGCACACCAGUCCAACUGCAUGUCGGACAAUUUGGUGUACACGUCCCUGGGGCCCGGGGCCA
..((((...(((((((........((....))(.((((((((((.((.....)).))))....)))))).).))))))).(....)..)))). (-29.96 = -30.32 +   0.36)

alignment

secondary structure

dotplot

Window 8

Location	13,682,492 – 13,682,608
Length	116
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	91.03
Mean single sequence MFE	-23.00
Consensus MFE	-16.70
Energy contribution	-16.50
Covariance contribution	-0.20
Combinations/Pair	1.18
Mean z-score	-1.72
Structure conservation index	0.73
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13682492 116 - 27905053
AUAUCAAAUUUUCUCAAAGCGAGUGGCACCUACCAUAUUCACCGAAUAAAUUACUCAACAGUGAAUUUAUCAAAUGGAAUGGCAUUUCGCAUUUCAUAAUUGCCUGCAACAGGCGA
..................(((((((.((....((((((((...)))))..(((((....)))))..........)))..)).)).))))).........(((((((...))))))) ( -22.10)
>DroSec_CAF1 9814 116 - 1
AUAUCAAAUUUUCUCAAACCGAAUGGCACCUACCAUAUUCACUGAAUAAAUUACUCGACAGUGAAUCUAUCAAAUGGUAUGGCAUUUCGCAUUUCAUAAUUGCCUGCAACAGGCGA
...................((((..((.(.((((((((((((((..............)))))))).......)))))).)))..))))..........(((((((...))))))) ( -25.65)
>DroSim_CAF1 9867 116 - 1
AUAUCAAAUUUUCUCAAACCGAGUGGCACCUACCAUAUUCACUGAAUAAAUUACUCAAUAGUGAAUCUAUCAACUGGUUUGGCAUUUCGCAUUUCAUAAUCGCCUGCAACAGGCGA
..............(((((((.((((......))))((((((((..............))))))))........)))))))((.....)).........(((((((...))))))) ( -26.34)
>DroEre_CAF1 4292 114 - 1
AUAUCAAAUUUUCUCAAACCGAGUGGCAUCCACUA--CUCACUGAAUAAAUUACCCAACUGUGAAUCUAUCAAACGGAAUGGCAUUUCGCAUUUCAUAAUUGCCUGCAACAGGCGA
......(((((..(((....((((((......)))--)))..)))..))))).......((((((.((((........))))...))))))........(((((((...))))))) ( -22.10)
>DroYak_CAF1 4491 116 - 1
AUAUCAAAUUUUCUCAAACCAAGUGGCAUCAACUACACUCACUGAAUAAAUUACUCGACUGUGAAUCUAUAAAAUGGGAUGGCAUUUCGCAUUUCAUAAUUGCCUGCAACAGGCGA
......(((((..(((.....((((..........))))...)))..)))))....((.((((((.((((........))))...))))))..))....(((((((...))))))) ( -18.80)
>consensus
AUAUCAAAUUUUCUCAAACCGAGUGGCACCUACCAUAUUCACUGAAUAAAUUACUCAACAGUGAAUCUAUCAAAUGGAAUGGCAUUUCGCAUUUCAUAAUUGCCUGCAACAGGCGA
......(((((..(((......((((......))))......)))..)))))........(((((.((((........))))...))))).........(((((((...))))))) (-16.70 = -16.50 +  -0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:49:42 2006