Locus 191

Sequence ID	3R_DroMel_CAF1
Location	849,617 – 849,777
Length	160
Max. P	0.725157

overview

Window 2

Location	849,617 – 849,737
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	83.19
Mean single sequence MFE	-38.25
Consensus MFE	-27.29
Energy contribution	-28.35
Covariance contribution	1.06
Combinations/Pair	1.03
Mean z-score	-1.55
Structure conservation index	0.71
SVM decision value	0.08
SVM RNA-class probability	0.571660
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 849617 120 + 27905053
GCUUUUUUUCAUUCUAUGUGCAACUUAUUGUUUUCCGUGUACCUUGGUGUCCGUCCGAGGAGGAACUUUCGAUUACCGAAAGGCACUUCAACCCGUUCUACGGGUCGAGGCCCCGCAGUC
((...............((((...........((((.....((((((.......)))))).))))((((((.....))))))))))(((.(((((.....))))).))).....)).... ( -35.10)
>DroSec_CAF1 25308 116 + 1
GCUGUUUUUUAUUCUAUGCGAAACUGAUUGUUUUCCGUGUAGCUUGGUGU----CCGAGGAGGAACUUUCGAGUACCGAAAGGCACUUCAACCCGUUCUCCGGGUCGAGGCCUCGCAGUC
(((((........(((((((((((.....))))..)))))))(((((...----)))))((((..((((((.....))))))...((((.(((((.....))))).))))))))))))). ( -38.70)
>DroSim_CAF1 24539 116 + 1
GCUGCUUUUUAUUCUAUGCGAAACUGAUUGUUUUCCGUGUAGCUUGGUGU----CCGAGGAGGAACUUUCGAGUACCGAAAGGCACUUCAACCCGUUCUCCGGGUAGAGGCCUCGCAGUC
(((((........(((((((((((.....))))..)))))))(((((...----)))))((((..((((((.....))))))...((((.(((((.....))))).))))))))))))). ( -41.20)
>DroEre_CAF1 26287 100 + 1
----------------UGUGCCGCCGAUUGUUCUCCGUGUAGAUUGGUGU----CCGCGGAGCAAUUUUCGAGUACCGAAAGGCACUUCAACCCGUUCUCCGGGUCGAGGACUCGCAGUC
----------------..(((....((..((((((((((..(((....))----)))))))).)))..))((((.((....))..((((.(((((.....))))).)))))))))))... ( -38.00)
>consensus
GCUGUUUUUUAUUCUAUGCGAAACUGAUUGUUUUCCGUGUAGCUUGGUGU____CCGAGGAGGAACUUUCGAGUACCGAAAGGCACUUCAACCCGUUCUCCGGGUCGAGGCCUCGCAGUC
.........................((((((...........(((((.......)))))((((..((((((.....))))))...((((.(((((.....))))).)))))))))))))) (-27.29 = -28.35 +   1.06)

alignment

secondary structure

dotplot

Window 3

Location	849,657 – 849,777
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.07
Mean single sequence MFE	-42.92
Consensus MFE	-36.59
Energy contribution	-37.40
Covariance contribution	0.81
Combinations/Pair	1.03
Mean z-score	-1.76
Structure conservation index	0.85
SVM decision value	0.41
SVM RNA-class probability	0.725157
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 849657 120 + 27905053
ACCUUGGUGUCCGUCCGAGGAGGAACUUUCGAUUACCGAAAGGCACUUCAACCCGUUCUACGGGUCGAGGCCCCGCAGUCCGGCUCAAACGCACACUCGGGCGUAUUCGAGUAAGACAAA
..(((((....((((((((..(((.((((((.....))))))((.((((.(((((.....))))).))))....))..))).((......))...))))))))...)))))......... ( -42.60)
>DroSec_CAF1 25348 116 + 1
AGCUUGGUGU----CCGAGGAGGAACUUUCGAGUACCGAAAGGCACUUCAACCCGUUCUCCGGGUCGAGGCCUCGCAGUCCGGCUCAAACGCACACUCGGGCGUAUUCGAGUAAGACAAA
.(((((((((----(((((((((..((((((.....))))))...((((.(((((.....))))).))))))))...((.((.......)).)).))))))))...))))))........ ( -43.90)
>DroSim_CAF1 24579 116 + 1
AGCUUGGUGU----CCGAGGAGGAACUUUCGAGUACCGAAAGGCACUUCAACCCGUUCUCCGGGUAGAGGCCUCGCAGUCCGGCUCAAACGCACACUCGGGCGUAUUCGAGUAAGACAAA
.(((((((((----(((((((((..((((((.....))))))...((((.(((((.....))))).))))))))...((.((.......)).)).))))))))...))))))........ ( -43.90)
>DroEre_CAF1 26311 116 + 1
AGAUUGGUGU----CCGCGGAGCAAUUUUCGAGUACCGAAAGGCACUUCAACCCGUUCUCCGGGUCGAGGACUCGCAGUCCGGCUCAAACGCACACUCGGGCGUAUUCGAGUAAGACAAA
.......(((----(.(((((((....(((((((.((....))..((((.(((((.....))))).))))))))).))....))))...)))..(((((((....)))))))..)))).. ( -41.30)
>consensus
AGCUUGGUGU____CCGAGGAGGAACUUUCGAGUACCGAAAGGCACUUCAACCCGUUCUCCGGGUCGAGGCCUCGCAGUCCGGCUCAAACGCACACUCGGGCGUAUUCGAGUAAGACAAA
..(((((.......)))))((((..((((((.....))))))...((((.(((((.....))))).))))))))...(((..((((((((((........)))).)).))))..)))... (-36.59 = -37.40 +   0.81)

alignment

secondary structure

dotplot

Window 4

Location	849,657 – 849,777
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.07
Mean single sequence MFE	-44.40
Consensus MFE	-36.62
Energy contribution	-37.50
Covariance contribution	0.88
Combinations/Pair	1.03
Mean z-score	-1.62
Structure conservation index	0.82
SVM decision value	0.01
SVM RNA-class probability	0.536092
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 849657 120 - 27905053
UUUGUCUUACUCGAAUACGCCCGAGUGUGCGUUUGAGCCGGACUGCGGGGCCUCGACCCGUAGAACGGGUUGAAGUGCCUUUCGGUAAUCGAAAGUUCCUCCUCGGACGGACACCAAGGU
..((((.((((((........))))))..((((((((..((((((..(((((((((((((.....))))))).)).))))..))))...(....)..))..))))))))))))....... ( -48.00)
>DroSec_CAF1 25348 116 - 1
UUUGUCUUACUCGAAUACGCCCGAGUGUGCGUUUGAGCCGGACUGCGAGGCCUCGACCCGGAGAACGGGUUGAAGUGCCUUUCGGUACUCGAAAGUUCCUCCUCGG----ACACCAAGCU
...((..((((((........)))))).))(((((((..((((((.((((((((((((((.....))))))).)).))))).))))...(....)..))..)))))----))........ ( -44.50)
>DroSim_CAF1 24579 116 - 1
UUUGUCUUACUCGAAUACGCCCGAGUGUGCGUUUGAGCCGGACUGCGAGGCCUCUACCCGGAGAACGGGUUGAAGUGCCUUUCGGUACUCGAAAGUUCCUCCUCGG----ACACCAAGCU
...((..((((((........)))))).))(((((((..((((((.((((((((.(((((.....))))).).)).))))).))))...(....)..))..)))))----))........ ( -40.70)
>DroEre_CAF1 26311 116 - 1
UUUGUCUUACUCGAAUACGCCCGAGUGUGCGUUUGAGCCGGACUGCGAGUCCUCGACCCGGAGAACGGGUUGAAGUGCCUUUCGGUACUCGAAAAUUGCUCCGCGG----ACACCAAUCU
..(((((((((((........)))))).(((...((((.((((.....))))((((((((.....))))))))((((((....))))))........)))))))))----)))....... ( -44.40)
>consensus
UUUGUCUUACUCGAAUACGCCCGAGUGUGCGUUUGAGCCGGACUGCGAGGCCUCGACCCGGAGAACGGGUUGAAGUGCCUUUCGGUACUCGAAAGUUCCUCCUCGG____ACACCAAGCU
...((((..((((((..(((......)))..))))))..))))..(((((..((((((((.....))))))))((((((....))))))...........)))))............... (-36.62 = -37.50 +   0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:36:47 2006