Locus 6318

Sequence ID	3R_DroMel_CAF1
Location	16,502,692 – 16,502,862
Length	170
Max. P	0.904800

overview

Window 6

Location	16,502,692 – 16,502,788
Length	96
Sequences	6
Columns	96
Reading direction	forward
Mean pairwise identity	79.72
Mean single sequence MFE	-37.05
Consensus MFE	-25.68
Energy contribution	-26.93
Covariance contribution	1.25
Combinations/Pair	1.26
Mean z-score	-2.03
Structure conservation index	0.69
SVM decision value	1.04
SVM RNA-class probability	0.904800
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16502692 96 + 27905053
UUAGUUCCGGGUCCGAGUACUCUCCCUCCAGACCAGGCUGUGGCUGCCACGAGCCAUCUUCGGGGGGCGAAGGCGGCUUGUAGGAGCCAUCGUCUU
.........((((.(((........)))..))))((((.((((((.(((((((((..(((((.....)))))..))))))).)))))))).)))). ( -42.60)
>DroVir_CAF1 64266 89 + 1
-------GGACUCCACAUAUUCGCCCUCCAGGCCCGGCUGUGGUUUCCACAAACCAUCAUCUGCGUCAAUUGGCGGCUUAUAGCUGCCAUCAUCCU
-------(((..(((((.....(((.....))).....)))))..)))......................(((((((.....)))))))....... ( -27.30)
>DroSec_CAF1 58960 96 + 1
UUAAUUCCGGGUCCGAGUACUCUCCCUCCAGACCAGGCUGUGGCUGCCACGAGCCAUCUUCUGGUGGCGAAGGCGGCUUGUAGGAGCCAUCGUCUU
.........((((.(((........)))..))))((((.((((((.(((((((((..((((.......))))..))))))).)))))))).)))). ( -39.90)
>DroSim_CAF1 62986 96 + 1
UUAAUUCCGGGUCCGAGUACUCUCCCUCCAGACCAGGCUGUGGCUGCCACGAGCCAUCUUCUGGUGGCGAAGGCGGCUUGUAGGAGCCAUCGUCUU
.........((((.(((........)))..))))((((.((((((.(((((((((..((((.......))))..))))))).)))))))).)))). ( -39.90)
>DroEre_CAF1 60770 96 + 1
UUAAUUCAGGGUCGGAGUACUCUCCCUCCAGACCAGGCUGCGGCUGCCACGAGCCAUCUGCGGGGGGCAAAGGCGGCUUGUAGGAGCCAUCGUCUU
.........((((((((........)))).))))((((...((((.(((((((((..((((.....))..))..))))))).))))))...)))). ( -36.90)
>DroAna_CAF1 56438 96 + 1
UCAAUUCGGGGUCCACGUACUCUCCCUCCAAGCCCGGCUGGGGCUUCCAUAAGCCAUCCUCCGCACUCGAGGGUGGCUUGUACGAGCCAUCAUCGU
.......(((((...(((((.........((((((.....))))))....(((((((((((.......)))))))))))))))).))).))..... ( -35.70)
>consensus
UUAAUUCCGGGUCCGAGUACUCUCCCUCCAGACCAGGCUGUGGCUGCCACGAGCCAUCUUCUGGGGGCGAAGGCGGCUUGUAGGAGCCAUCGUCUU
.........((((.................))))((((.((((((.(.(((((((.(((((.......))))).))))))).).)))))).)))). (-25.68 = -26.93 +   1.25)

alignment

secondary structure

dotplot

Window 7

Location	16,502,692 – 16,502,788
Length	96
Sequences	6
Columns	96
Reading direction	reverse
Mean pairwise identity	79.72
Mean single sequence MFE	-36.12
Consensus MFE	-27.30
Energy contribution	-27.08
Covariance contribution	-0.22
Combinations/Pair	1.42
Mean z-score	-1.59
Structure conservation index	0.76
SVM decision value	0.74
SVM RNA-class probability	0.837169
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16502692 96 - 27905053
AAGACGAUGGCUCCUACAAGCCGCCUUCGCCCCCCGAAGAUGGCUCGUGGCAGCCACAGCCUGGUCUGGAGGGAGAGUACUCGGACCCGGAACUAA
.....(.(((((.((((.(((((.(((((.....))))).))))).)))).))))))..((.((((((.((........)))))))).))...... ( -39.50)
>DroVir_CAF1 64266 89 - 1
AGGAUGAUGGCAGCUAUAAGCCGCCAAUUGACGCAGAUGAUGGUUUGUGGAAACCACAGCCGGGCCUGGAGGGCGAAUAUGUGGAGUCC-------
.((((..((((.((.....)).)))).((..(((((((....)))))))..))(((((.....(((.....))).....))))).))))------- ( -29.50)
>DroSec_CAF1 58960 96 - 1
AAGACGAUGGCUCCUACAAGCCGCCUUCGCCACCAGAAGAUGGCUCGUGGCAGCCACAGCCUGGUCUGGAGGGAGAGUACUCGGACCCGGAAUUAA
.....(.(((((.((((.(((((.((((.......)))).))))).)))).))))))..((.((((((.((........)))))))).))...... ( -38.30)
>DroSim_CAF1 62986 96 - 1
AAGACGAUGGCUCCUACAAGCCGCCUUCGCCACCAGAAGAUGGCUCGUGGCAGCCACAGCCUGGUCUGGAGGGAGAGUACUCGGACCCGGAAUUAA
.....(.(((((.((((.(((((.((((.......)))).))))).)))).))))))..((.((((((.((........)))))))).))...... ( -38.30)
>DroEre_CAF1 60770 96 - 1
AAGACGAUGGCUCCUACAAGCCGCCUUUGCCCCCCGCAGAUGGCUCGUGGCAGCCGCAGCCUGGUCUGGAGGGAGAGUACUCCGACCCUGAAUUAA
........((((.((((.(((((..(((((.....)))))))))).)))).)))).(((...((((.((((........)))))))))))...... ( -36.10)
>DroAna_CAF1 56438 96 - 1
ACGAUGAUGGCUCGUACAAGCCACCCUCGAGUGCGGAGGAUGGCUUAUGGAAGCCCCAGCCGGGCUUGGAGGGAGAGUACGUGGACCCCGAAUUGA
.((((...(((((((((...(..((..(((((.(((..(..(((((....))))).)..))).)))))..))..).))))).)).))....)))). ( -35.00)
>consensus
AAGACGAUGGCUCCUACAAGCCGCCUUCGCCCCCAGAAGAUGGCUCGUGGCAGCCACAGCCUGGUCUGGAGGGAGAGUACUCGGACCCGGAAUUAA
.......(((((.((((.(((((.((((.......)))).))))).)))).)))))....((((..(.(((........))).)..))))...... (-27.30 = -27.08 +  -0.22)

alignment

secondary structure

dotplot

Window 8

Location	16,502,748 – 16,502,862
Length	114
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	73.30
Mean single sequence MFE	-44.47
Consensus MFE	-18.03
Energy contribution	-20.59
Covariance contribution	2.56
Combinations/Pair	1.37
Mean z-score	-2.06
Structure conservation index	0.41
SVM decision value	0.61
SVM RNA-class probability	0.800249
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16502748 114 + 27905053
UCUUCGGGGGGCGAAGGCGGCUUGUAGGAGCCAUCGUCUUCCGGCGGAGGAGGAGGUGGCUGGACUAGCAAGACAACGGGUG------GAGACAGCAGAUAGGUUCCGACUGCAGGAAGA
((((((..(.((....))..(((((((.(((((((.((((((......)))))))))))))...)).))))).)..)...((------....))((((...(....)..))))..))))) ( -42.00)
>DroGri_CAF1 75514 111 + 1
UCAUCCUCGCUGAUUGACGGCUUAUAGCUGCCAUCGUCCUCGGGCGCA---------GGCUGCACCAGCAGCAAAACUGGCGUAGCUGGCGCCAACAAAUAAGUGCCAGCCACUGGAAGA
((.(((..((((...((.(((........))).)).......(((((.---------((((((.((((........)))).)))))).))))).............))))....))).)) ( -42.30)
>DroSec_CAF1 59016 114 + 1
UCUUCUGGUGGCGAAGGCGGCUUGUAGGAGCCAUCGUCUUCCGGUGGAGGAGGAGGUGGCUGGACUAGCAAGACAACGGGUG------GAGACAGUAGAUAAGUUCCGACUGCUGGAAGG
.((((..(..(((....((.(((((((.(((((((.((((((......)))))))))))))...)).)))))....))(.((------....)).)..........)).)..)..)))). ( -44.20)
>DroSim_CAF1 63042 114 + 1
UCUUCUGGUGGCGAAGGCGGCUUGUAGGAGCCAUCGUCUUCCGGCGGAGGAGGAGGUGGCUGGACUAGCAAGACAACGGGUG------GAGACAGUAGAUAAGUUCCGACUGCUGGAAGG
.((((..(..(((....((.(((((((.(((((((.((((((......)))))))))))))...)).)))))....))(.((------....)).)..........)).)..)..)))). ( -44.20)
>DroEre_CAF1 60826 114 + 1
UCUGCGGGGGGCAAAGGCGGCUUGUAGGAGCCAUCGUCUUCCGGCGGAGGAGGAGGUGGUUGGACUAGCAGAACAACGGGUG------GAGACAGCAGAUAGGUUCCGACUGCAGGAAGG
((((((((((((....((.(((.((...(((((((.((((((......)))))))))))))..)).)))...........((------....))))......)))))..))))))).... ( -42.70)
>DroAna_CAF1 56494 120 + 1
UCCUCCGCACUCGAGGGUGGCUUGUACGAGCCAUCAUCGUCUGGAGGAGGCGGUGGUGUCUGGACGAGUAAAAGCACUGGUGCUGGCUGGGAAAUCAAGAAGGUUCCAGCCCCCGGCAAG
(((((((....(((.((((((((....)))))))).)))..)))))))(.(((.((.(.((((((.(((...((((....)))).))).)...(((.....)))))))))))))).)... ( -51.40)
>consensus
UCUUCCGGGGGCGAAGGCGGCUUGUAGGAGCCAUCGUCUUCCGGCGGAGGAGGAGGUGGCUGGACUAGCAAGACAACGGGUG______GAGACAGCAGAUAAGUUCCGACUGCUGGAAGG
(((((.......))))).(((((....)))))....(((((((((((....((((.(.((((..............................)))).....).))))..))))))))))) (-18.03 = -20.59 +   2.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:18:35 2006