Locus 4290

Sequence ID	3R_DroMel_CAF1
Location	11,415,092 – 11,415,330
Length	238
Max. P	0.999592

overview

Window 9

Location	11,415,092 – 11,415,210
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	83.32
Mean single sequence MFE	-42.36
Consensus MFE	-31.40
Energy contribution	-33.56
Covariance contribution	2.16
Combinations/Pair	1.17
Mean z-score	-2.30
Structure conservation index	0.74
SVM decision value	1.31
SVM RNA-class probability	0.940656
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11415092 118 + 27905053
CUGUCU--UUUUUUGGGUUUAAAGUUCCGGCAGGUGGGCCAUCGGUCGGUGGACUACCUUCACUUUUUUCGGUGGCUCCUAAUUUUGGGUAGAACCCGAUCUGCACCGGAGCAGCUGCCC
......--......((((.....((((((((((((((((((((((..((((((.....))))))....)))))))))).......((((.....))))))))))..))))))....)))) ( -46.00)
>DroSec_CAF1 162672 120 + 1
CUGCCUUUUUUUUUGGGUUUAAAGUUCCGGCAGGUGGGCCAUCGGUCGGUGGACUACCUUCACUUUUUUCGGUGGCUCCUAAUUUUGGGUAGAACCCGAUCUGCACCGGAGCAGCUGCCC
..............((((.....((((((((((((((((((((((..((((((.....))))))....)))))))))).......((((.....))))))))))..))))))....)))) ( -46.00)
>DroSim_CAF1 155458 120 + 1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGUGGGCCAUCGGACGGUGGACUACCUUCACUUUUUUCCGUGGCUCCUAAUUUUGGGUAGAACCCGAUCUGCACCGGAGCAGCUGCCC
................................((.((((((.((((.((((((.....))))))....))))))))))))......((((((..((((........))).)...)))))) ( -32.20)
>DroEre_CAF1 150472 117 + 1
CUACCU--UUUUUUGGGUUAAAAGUUCCGGCAGGUGGGCCGUCGCUCUGUGGACUACCUUCACUUUU-UUGGUGGCUCCUAAUUUCGGGUAGAACCCGAUCUGCGCCGGAGCAGCUGCCC
......--......((((.....((((((((.((.(((((..((....(((((.....)))))....-.))..)))))))....(((((.....))))).....))))))))....)))) ( -44.50)
>DroYak_CAF1 154616 117 + 1
CUGCCU--UUUUUUGGGCUAAAAGUUCCGGCAGGUGGGCCAUCGGUCUGCUGACUACCUUCACUUUU-UCGGUGGCUCCUAAUUUUGGGUAGAACCCGAUCUGCACCGGAGCAGCUGGAC
..((((--......)))).....((((((((((((((((((((((.....(((......))).....-)))))))))).......((((.....))))))))))..))))))........ ( -43.10)
>consensus
CUGCCU__UUUUUUGGGUUAAAAGUUCCGGCAGGUGGGCCAUCGGUCGGUGGACUACCUUCACUUUUUUCGGUGGCUCCUAAUUUUGGGUAGAACCCGAUCUGCACCGGAGCAGCUGCCC
..((((........)))).....((((((((((((((((((((((..((((((.....))))))....)))))))))).......((((.....))))))))))..))))))........ (-31.40 = -33.56 +   2.16)

alignment

secondary structure

dotplot

Window 0

Location	11,415,210 – 11,415,330
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.92
Mean single sequence MFE	-28.55
Consensus MFE	-26.00
Energy contribution	-25.72
Covariance contribution	-0.28
Combinations/Pair	1.11
Mean z-score	-1.55
Structure conservation index	0.91
SVM decision value	1.23
SVM RNA-class probability	0.933805
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11415210 120 + 27905053
UGAAGAAGUAGCGCACCAGAAAACGCCUCUCAUUUUUCAACUCUGAUCAGCGAAGGUUGCCAUCUAAUUAAGUAAAUUGUCCGUUUUACAUAUGUUUCCUGGUGCCACUAAUUUUUAUGA
..(((((.(((.(((((((.(((((...................(((((((....))))..))).......(((((........)))))...))))).)))))))..))).))))).... ( -26.80)
>DroSec_CAF1 162792 120 + 1
UGGAGAAGUAGCGCACCAGAAAACGCCUCUUAUUUUUCAACUCUGAUCAGCGAGGGCUGCCAUCUAAUUAAGUAAAUUGUCCGUUUUACAUAUGUUUCCUGGUGCCACUAAUUUUUAUGA
..(((((.(((.(((((((.(((((((.((..((..(((....)))..))..)))))..............(((((........)))))....)))).)))))))..))).))))).... ( -30.50)
>DroSim_CAF1 155578 120 + 1
UGGAGAAGUAGCGCACCAGAAAACGCCUCUUAUUUUUCAACUCUGAUCAGCGAGGGCUACCAUCUAAUUAAGUAAAUUGUCCGUUUUACAUAUGUUUCCUGGUGCCACUAAUUUUUAUGA
..(((((.(((.(((((((.(((((((.((..((..(((....)))..))..)))))..............(((((........)))))....)))).)))))))..))).))))).... ( -30.50)
>DroEre_CAF1 150589 120 + 1
CGCAGAAGUAGCGCACCAGAAAACGCCUCUUAUUUUUCAACUCUGAUCAGCGAAGGCUGCCAUCUAAUUAAGUAAAUUGUCCGUUUUACAUAUGUUUCCUGGUGCCACUAAUUUUUAUGA
((.((((((((.(((((((.(((((...................(((((((....))))..))).......(((((........)))))...))))).)))))))..)).)))))).)). ( -28.40)
>DroYak_CAF1 154733 120 + 1
UGGAGAAGUAGCGCACCAGAAAACGCCUCUUAUUUUUCAACUCUGAUCAGCGAAGGCUGCCAUCUAAUUAAGUAAAUUGUGCGUUUUACAUAUGUUUCCCGGUGCCACUAAUUUUUAUGA
..(((((.(((.(((((..((((((((..((((((.........(((((((....))))..))).....))))))...).)))))))((....)).....)))))..))).))))).... ( -26.54)
>consensus
UGGAGAAGUAGCGCACCAGAAAACGCCUCUUAUUUUUCAACUCUGAUCAGCGAAGGCUGCCAUCUAAUUAAGUAAAUUGUCCGUUUUACAUAUGUUUCCUGGUGCCACUAAUUUUUAUGA
..(((((.(((.(((((((.((((((((.((.((..(((....)))..)).))))))..............(((((........)))))....)))).)))))))..))).))))).... (-26.00 = -25.72 +  -0.28)

alignment

secondary structure

dotplot

Window 1

Location	11,415,210 – 11,415,330
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.92
Mean single sequence MFE	-32.32
Consensus MFE	-31.10
Energy contribution	-30.98
Covariance contribution	-0.12
Combinations/Pair	1.06
Mean z-score	-2.26
Structure conservation index	0.96
SVM decision value	3.76
SVM RNA-class probability	0.999592
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11415210 120 - 27905053
UCAUAAAAAUUAGUGGCACCAGGAAACAUAUGUAAAACGGACAAUUUACUUAAUUAGAUGGCAACCUUCGCUGAUCAGAGUUGAAAAAUGAGAGGCGUUUUCUGGUGCGCUACUUCUUCA
..........(((((.(((((((((((....(((((........))))).......((.(....)..))(((..(((...........)))..)))))))))))))))))))........ ( -31.40)
>DroSec_CAF1 162792 120 - 1
UCAUAAAAAUUAGUGGCACCAGGAAACAUAUGUAAAACGGACAAUUUACUUAAUUAGAUGGCAGCCCUCGCUGAUCAGAGUUGAAAAAUAAGAGGCGUUUUCUGGUGCGCUACUUCUCCA
..........(((((.(((((((((((....(((((........)))))((((((...(((((((....)))).))).))))))............))))))))))))))))........ ( -33.20)
>DroSim_CAF1 155578 120 - 1
UCAUAAAAAUUAGUGGCACCAGGAAACAUAUGUAAAACGGACAAUUUACUUAAUUAGAUGGUAGCCCUCGCUGAUCAGAGUUGAAAAAUAAGAGGCGUUUUCUGGUGCGCUACUUCUCCA
..........(((((.(((((((((((....(((((........)))))((((((...(((((((....))).)))).))))))............))))))))))))))))........ ( -31.30)
>DroEre_CAF1 150589 120 - 1
UCAUAAAAAUUAGUGGCACCAGGAAACAUAUGUAAAACGGACAAUUUACUUAAUUAGAUGGCAGCCUUCGCUGAUCAGAGUUGAAAAAUAAGAGGCGUUUUCUGGUGCGCUACUUCUGCG
..........(((((.(((((((((((....(((((........)))))((((((...(((((((....)))).))).))))))............))))))))))))))))........ ( -33.20)
>DroYak_CAF1 154733 120 - 1
UCAUAAAAAUUAGUGGCACCGGGAAACAUAUGUAAAACGCACAAUUUACUUAAUUAGAUGGCAGCCUUCGCUGAUCAGAGUUGAAAAAUAAGAGGCGUUUUCUGGUGCGCUACUUCUCCA
..........(((((.(((((((((((....(((((........)))))((((((...(((((((....)))).))).))))))............))))))))))))))))........ ( -32.50)
>consensus
UCAUAAAAAUUAGUGGCACCAGGAAACAUAUGUAAAACGGACAAUUUACUUAAUUAGAUGGCAGCCUUCGCUGAUCAGAGUUGAAAAAUAAGAGGCGUUUUCUGGUGCGCUACUUCUCCA
..........(((((.(((((((((((....(((((........)))))((((((...(((((((....)))).))).))))))............))))))))))))))))........ (-31.10 = -30.98 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:52 2006