Locus 6259

Sequence ID	3R_DroMel_CAF1
Location	16,329,527 – 16,329,658
Length	131
Max. P	0.867972

overview

Window 7

Location	16,329,527 – 16,329,618
Length	91
Sequences	6
Columns	91
Reading direction	forward
Mean pairwise identity	79.14
Mean single sequence MFE	-27.88
Consensus MFE	-12.00
Energy contribution	-13.37
Covariance contribution	1.36
Combinations/Pair	1.48
Mean z-score	-2.66
Structure conservation index	0.43
SVM decision value	0.65
SVM RNA-class probability	0.810570
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16329527 91 + 27905053
UUGCUCGCCAACUCGGUGCACACGAACUCCUCAUCAGCUUAUCAGCUGCCCACGUUGCGUAUACGUUGCGUAUACGCCGCGUAUCGUGACU
.(((..(((.....))))))(((((.........(((((....)))))...((((.(((((((((...))))))))).)))).)))))... ( -32.60)
>DroSec_CAF1 32745 91 + 1
UUGCUCGCCAACUCGGUGCACACGACCUCCUCAUCAGCUUAUCAGCUGCCCACGUUGCGUAUACGUUGCGUAUACGCCGCGUAUCGUGACU
.(((..(((.....))))))(((((.........(((((....)))))...((((.(((((((((...))))))))).)))).)))))... ( -32.30)
>DroSim_CAF1 34384 91 + 1
UUGCUCGCCAACUCGGCGCACACGACCUCCUCAUCAGCUUAUCAGCUGCCCACGUUGCGUAUACGUUGCGUAUACGCCGCGUAUCGUGACU
.....((((.....))))..(((((.........(((((....)))))...((((.(((((((((...))))))))).)))).)))))... ( -33.70)
>DroEre_CAF1 30977 80 + 1
UUGCUCGCCAACUCGCUGCACACGACCUUCUCAUCAGCUUAUCAGCUGCCCACGUUGC-----------GUAUACGCCGUGUAUCGUGACU
.(((..((......)).)))(((((.........(((((....)))))..((((..((-----------(....)))))))..)))))... ( -20.90)
>DroYak_CAF1 45877 80 + 1
UUGCUCGCCAACUCGCUGCACACGGCCUUCUCAUCAGCUCAUCAGCUGCCCACGUUGC-----------GUAUACGCCGCGUAUCGUGACU
.(((..((......)).)))(((((.........(((((....)))))...((((.((-----------(....))).)))).)))))... ( -21.70)
>DroAna_CAF1 26878 80 + 1
UCGCUUGCCAACUCGAUGCACACGUCUUUUCGAUUGGCUUAUCAAUCG-----------AAUGCGUUGCGUAUACGCCGUGCGGUAUGAGU
..........(((((.(((((((((...(((((((((....)))))))-----------)).)))).(((....))).)))))...))))) ( -26.10)
>consensus
UUGCUCGCCAACUCGGUGCACACGACCUCCUCAUCAGCUUAUCAGCUGCCCACGUUGC_UAUACGUUGCGUAUACGCCGCGUAUCGUGACU
..(((((......))).)).(((((.........(((((....))))).............(((((.(((....))).))))))))))... (-12.00 = -13.37 +   1.36)

alignment

secondary structure

dotplot

Window 8

Location	16,329,527 – 16,329,618
Length	91
Sequences	6
Columns	91
Reading direction	reverse
Mean pairwise identity	79.14
Mean single sequence MFE	-29.62
Consensus MFE	-15.80
Energy contribution	-16.37
Covariance contribution	0.57
Combinations/Pair	1.18
Mean z-score	-1.85
Structure conservation index	0.53
SVM decision value	0.04
SVM RNA-class probability	0.555094
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16329527 91 - 27905053
AGUCACGAUACGCGGCGUAUACGCAACGUAUACGCAACGUGGGCAGCUGAUAAGCUGAUGAGGAGUUCGUGUGCACCGAGUUGGCGAGCAA
..(((...((((..(((((((((...)))))))))..))))..(((((....))))).)))...((((((..((.....))..)))))).. ( -33.40)
>DroSec_CAF1 32745 91 - 1
AGUCACGAUACGCGGCGUAUACGCAACGUAUACGCAACGUGGGCAGCUGAUAAGCUGAUGAGGAGGUCGUGUGCACCGAGUUGGCGAGCAA
...(((((((((..(((((((((...)))))))))..)))...(((((....)))))........))))))(((.((.....))...))). ( -32.40)
>DroSim_CAF1 34384 91 - 1
AGUCACGAUACGCGGCGUAUACGCAACGUAUACGCAACGUGGGCAGCUGAUAAGCUGAUGAGGAGGUCGUGUGCGCCGAGUUGGCGAGCAA
...(((((((((..(((((((((...)))))))))..)))...(((((....)))))........))))))..((((.....))))..... ( -36.20)
>DroEre_CAF1 30977 80 - 1
AGUCACGAUACACGGCGUAUAC-----------GCAACGUGGGCAGCUGAUAAGCUGAUGAGAAGGUCGUGUGCAGCGAGUUGGCGAGCAA
...((((((.(((((((....)-----------))..))))..(((((....)))))........))))))(((.((......))..))). ( -26.40)
>DroYak_CAF1 45877 80 - 1
AGUCACGAUACGCGGCGUAUAC-----------GCAACGUGGGCAGCUGAUGAGCUGAUGAGAAGGCCGUGUGCAGCGAGUUGGCGAGCAA
.((((((.((((((((...(((-----------(...))))..(((((....)))))........))))))))...))...))))...... ( -24.30)
>DroAna_CAF1 26878 80 - 1
ACUCAUACCGCACGGCGUAUACGCAACGCAUU-----------CGAUUGAUAAGCCAAUCGAAAAGACGUGUGCAUCGAGUUGGCAAGCGA
((((....((((((((((.......)))).((-----------((((((......))))))))....))))))....)))).......... ( -25.00)
>consensus
AGUCACGAUACGCGGCGUAUACGCAACGUAUA_GCAACGUGGGCAGCUGAUAAGCUGAUGAGAAGGUCGUGUGCACCGAGUUGGCGAGCAA
.((((....((.(((.(((((((..........((.......))((((....))))...........))))))).))).))))))...... (-15.80 = -16.37 +   0.57)

alignment

secondary structure

dotplot

Window 9

Location	16,329,547 – 16,329,658
Length	111
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	90.17
Mean single sequence MFE	-26.78
Consensus MFE	-20.14
Energy contribution	-22.22
Covariance contribution	2.08
Combinations/Pair	1.08
Mean z-score	-1.69
Structure conservation index	0.75
SVM decision value	0.20
SVM RNA-class probability	0.632043
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16329547 111 + 27905053
CACGAACUCCUCAUCAGCUUAUCAGCUGCCCACGUUGCGUAUACGUUGCGUAUACGCCGCGUAUCGUGACUCAGCCCACAGCCCAGAAGCACACAAUAAAAAGCAUGAAAA
(((((.........(((((....)))))...((((.(((((((((...))))))))).)))).)))))............((......))..................... ( -28.90)
>DroSec_CAF1 32765 111 + 1
CACGACCUCCUCAUCAGCUUAUCAGCUGCCCACGUUGCGUAUACGUUGCGUAUACGCCGCGUAUCGUGACUCAGCCAACAGCCCAGAAGCACACAAUAAAAAGCAUGAAAA
.............(((((((....((((.....((..((.((((((.(((....))).))))))))..)).)))).....((......))..........)))).)))... ( -28.80)
>DroSim_CAF1 34404 111 + 1
CACGACCUCCUCAUCAGCUUAUCAGCUGCCCACGUUGCGUAUACGUUGCGUAUACGCCGCGUAUCGUGACUCAGCCAACAGCCCAGAAGCACACAAUAAAAAGCAUGAAAA
.............(((((((....((((.....((..((.((((((.(((....))).))))))))..)).)))).....((......))..........)))).)))... ( -28.80)
>DroEre_CAF1 30997 100 + 1
CACGACCUUCUCAUCAGCUUAUCAGCUGCCCACGUUGC-----------GUAUACGCCGUGUAUCGUGACUCAGCCGACAGCCCAGAAGCACACAAUAAAAAGCAUGAGAC
........((((((..((((.((.((((.....((..(-----------(.((((.....))))))..)).)))).))..((......))..........)))))))))). ( -23.30)
>DroYak_CAF1 45897 100 + 1
CACGGCCUUCUCAUCAGCUCAUCAGCUGCCCACGUUGC-----------GUAUACGCCGCGUAUCGUGACUCAGCCGACAGCCCAGAAGCACACAAUAAAAAGCGUGAAAA
..((((....(((((((((....)))))...((((.((-----------(....))).))))...))))....))))............(((.(........).))).... ( -24.10)
>consensus
CACGACCUCCUCAUCAGCUUAUCAGCUGCCCACGUUGCGUAUACGUUGCGUAUACGCCGCGUAUCGUGACUCAGCCAACAGCCCAGAAGCACACAAUAAAAAGCAUGAAAA
(((((.........(((((....)))))...((((.((((((((.....)))))))).)))).)))))............((......))..................... (-20.14 = -22.22 +   2.08)

alignment

secondary structure

dotplot

Window 0

Location	16,329,547 – 16,329,658
Length	111
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	90.17
Mean single sequence MFE	-37.24
Consensus MFE	-32.10
Energy contribution	-33.82
Covariance contribution	1.72
Combinations/Pair	1.12
Mean z-score	-1.56
Structure conservation index	0.86
SVM decision value	0.86
SVM RNA-class probability	0.867972
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16329547 111 - 27905053
UUUUCAUGCUUUUUAUUGUGUGCUUCUGGGCUGUGGGCUGAGUCACGAUACGCGGCGUAUACGCAACGUAUACGCAACGUGGGCAGCUGAUAAGCUGAUGAGGAGUUCGUG
.......((((((((((....((((.(.((((((.(((...)))....((((..(((((((((...)))))))))..)))).)))))).).)))).))))))))))..... ( -39.00)
>DroSec_CAF1 32765 111 - 1
UUUUCAUGCUUUUUAUUGUGUGCUUCUGGGCUGUUGGCUGAGUCACGAUACGCGGCGUAUACGCAACGUAUACGCAACGUGGGCAGCUGAUAAGCUGAUGAGGAGGUCGUG
....(((((((((((((....((((.(.((((((((((...)))....((((..(((((((((...)))))))))..))))))))))).).)))).)))))))))..)))) ( -39.40)
>DroSim_CAF1 34404 111 - 1
UUUUCAUGCUUUUUAUUGUGUGCUUCUGGGCUGUUGGCUGAGUCACGAUACGCGGCGUAUACGCAACGUAUACGCAACGUGGGCAGCUGAUAAGCUGAUGAGGAGGUCGUG
....(((((((((((((....((((.(.((((((((((...)))....((((..(((((((((...)))))))))..))))))))))).).)))).)))))))))..)))) ( -39.40)
>DroEre_CAF1 30997 100 - 1
GUCUCAUGCUUUUUAUUGUGUGCUUCUGGGCUGUCGGCUGAGUCACGAUACACGGCGUAUAC-----------GCAACGUGGGCAGCUGAUAAGCUGAUGAGAAGGUCGUG
....(((((((((((((....((((.(.((((((((((...)))......(((((((....)-----------))..))))))))))).).)))).)))))))))..)))) ( -32.50)
>DroYak_CAF1 45897 100 - 1
UUUUCACGCUUUUUAUUGUGUGCUUCUGGGCUGUCGGCUGAGUCACGAUACGCGGCGUAUAC-----------GCAACGUGGGCAGCUGAUGAGCUGAUGAGAAGGCCGUG
....(((((((((((((....((((.(.((((((((((...)))....((((..(((....)-----------))..))))))))))).).)))).)))))))))..)))) ( -35.90)
>consensus
UUUUCAUGCUUUUUAUUGUGUGCUUCUGGGCUGUCGGCUGAGUCACGAUACGCGGCGUAUACGCAACGUAUACGCAACGUGGGCAGCUGAUAAGCUGAUGAGGAGGUCGUG
....(((((((((((((....((((.(.((((((((((...)))......((((((((((((.....))))))))..))))))))))).).)))).)))))))))..)))) (-32.10 = -33.82 +   1.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:16:57 2006