Locus 500

Sequence ID 3R_DroMel_CAF1
Location 1,882,406 – 1,882,513
Length 107
Max. P 0.816213
window804 window805

overview

Window 4

Location 1,882,406 – 1,882,513
Length 107
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 81.97
Mean single sequence MFE -26.75
Consensus MFE -17.91
Energy contribution -19.13
Covariance contribution 1.22
Combinations/Pair 1.05
Mean z-score -2.35
Structure conservation index 0.67
SVM decision value 0.66
SVM RNA-class probability 0.816213
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1882406 107 + 27905053
CUCCUCGCCCUCGU------CCA------UUUCCGUAUCCGGCUCAUCGCUAGAUAUCUCCUCCUCGUCGGAUGACUCCGAGGAUAUAUCCUCUUCAGGCUCGCUCUCCAAGUGCUUAA
.((((((...((((------((.------.....(((((..((.....))..)))))...(.....)..))))))...))))))............((((.(.........).)))).. ( -24.60)
>DroPse_CAF1 31282 119 + 1
CUCUUCACCCUCGUCCUCGCCCAUAUCCUCUUCCGUAUCAGGUUCGUCGCUGGAUAUAGGUUCCUCCUCUGAUGACUCAGAGGAAACAUCUAUUUCCCCCUCGCUCAGAUCGUACUUGG
......................................(((((.((((((.(((.((((((...((((((((....))))))))...)))))).))).....))...)).)).))))). ( -26.40)
>DroSec_CAF1 40390 107 + 1
CUCCUCGCCCUCGU------CCA------UUUCCGUAUCCGGCUCAUCGCUGGAUAUCUCCUCCUCGUCCGAUGACUCCGAGGAUAUAUCCUCUUCAGGCUCGCUUUCCAAGUGCUUAA
......(((.....------...------.....(((((((((.....))))))))).(((((...(((....)))...))))).............))).((((.....))))..... ( -26.10)
>DroSim_CAF1 40998 107 + 1
CUCCUCGCCCUCGU------CCA------UUUCCGUAUCCGGCUCAUCGCUGGAUAUCUCCUCCUCGUCCGAUGACUCCGAGGAUAUAUCCUCUUCAGGCUCGCUUUCCAAGUGCUUAA
......(((.....------...------.....(((((((((.....))))))))).(((((...(((....)))...))))).............))).((((.....))))..... ( -26.10)
>DroEre_CAF1 41205 110 + 1
CUCCUCGCCCUCGUCC---UCCA------UAUCCGUAUCCGGCUCAUCGCUGGAUAUAUCCUCCUCGUCAGAUGACUCCGAGGUCACAUCCUCAUCAGGCUCGCUCUCCAAAUGCUUAA
......(((.......---....------.....(((((((((.....))))))))).........(((....)))...((((......))))....)))..((.........)).... ( -25.60)
>DroYak_CAF1 46382 110 + 1
CUCCUCGCCCUCGUCG---UCUA------UAUCCGUAUCCGGCUCAUCACUGGAUAUCUCCUCCUCGUCGGACGACUCCGAGGAUAUAUCCUCAUCGGGCUCGCUCUCUAAAUGCUUAA
......((((..((((---(((.------.....((((((((.......))))))))...(.....)..)))))))...(((((....)))))...))))..((.........)).... ( -31.70)
>consensus
CUCCUCGCCCUCGU______CCA______UUUCCGUAUCCGGCUCAUCGCUGGAUAUCUCCUCCUCGUCCGAUGACUCCGAGGAUAUAUCCUCUUCAGGCUCGCUCUCCAAGUGCUUAA
......(((.........................(((((((((.....)))))))))....((((((((....)))...))))).............)))................... (-17.91 = -19.13 +   1.22) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 1,882,406 – 1,882,513
Length 107
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 81.97
Mean single sequence MFE -31.73
Consensus MFE -23.05
Energy contribution -24.00
Covariance contribution 0.95
Combinations/Pair 1.22
Mean z-score -1.25
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 1882406 107 - 27905053
UUAAGCACUUGGAGAGCGAGCCUGAAGAGGAUAUAUCCUCGGAGUCAUCCGACGAGGAGGAGAUAUCUAGCGAUGAGCCGGAUACGGAAA------UGG------ACGAGGGCGAGGAG
....((.(.....).))..((((...(.((((((.(((((...(((....)))...))))).))))))..(.((...(((....)))..)------).)------.)..))))...... ( -29.60)
>DroPse_CAF1 31282 119 - 1
CCAAGUACGAUCUGAGCGAGGGGGAAAUAGAUGUUUCCUCUGAGUCAUCAGAGGAGGAACCUAUAUCCAGCGACGAACCUGAUACGGAAGAGGAUAUGGGCGAGGACGAGGGUGAAGAG
((..((.((.(((((((..(((((((((....)))))))))..))..))))).......(((((((((.....((....))...(....).)))))))))))...))..))........ ( -34.00)
>DroSec_CAF1 40390 107 - 1
UUAAGCACUUGGAAAGCGAGCCUGAAGAGGAUAUAUCCUCGGAGUCAUCGGACGAGGAGGAGAUAUCCAGCGAUGAGCCGGAUACGGAAA------UGG------ACGAGGGCGAGGAG
....((.........))..((((...(.((((((.(((((...(((....)))...))))).))))))..(.((...(((....)))..)------).)------.)..))))...... ( -31.50)
>DroSim_CAF1 40998 107 - 1
UUAAGCACUUGGAAAGCGAGCCUGAAGAGGAUAUAUCCUCGGAGUCAUCGGACGAGGAGGAGAUAUCCAGCGAUGAGCCGGAUACGGAAA------UGG------ACGAGGGCGAGGAG
....((.........))..((((...(.((((((.(((((...(((....)))...))))).))))))..(.((...(((....)))..)------).)------.)..))))...... ( -31.50)
>DroEre_CAF1 41205 110 - 1
UUAAGCAUUUGGAGAGCGAGCCUGAUGAGGAUGUGACCUCGGAGUCAUCUGACGAGGAGGAUAUAUCCAGCGAUGAGCCGGAUACGGAUA------UGGA---GGACGAGGGCGAGGAG
....((.........))..((((..((.(((((((.((((...(((....)))...)))).)))))))..(.(((..(((....))).))------).).---...)).))))...... ( -30.20)
>DroYak_CAF1 46382 110 - 1
UUAAGCAUUUAGAGAGCGAGCCCGAUGAGGAUAUAUCCUCGGAGUCGUCCGACGAGGAGGAGAUAUCCAGUGAUGAGCCGGAUACGGAUA------UAGA---CGACGAGGGCGAGGAG
....((.........))..((((.....((((((.(((((...(((....)))...))))).)))))).((......(((....)))...------...)---).....))))...... ( -33.60)
>consensus
UUAAGCACUUGGAGAGCGAGCCUGAAGAGGAUAUAUCCUCGGAGUCAUCCGACGAGGAGGAGAUAUCCAGCGAUGAGCCGGAUACGGAAA______UGG______ACGAGGGCGAGGAG
....((.........))..((((.....((((((.(((((...(((....)))...))))).)))))).........(((....)))......................))))...... (-23.05 = -24.00 +   0.95) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:44:41 2006