Locus 6886

Sequence ID	X_DroMel_CAF1
Location	17,217,060 – 17,217,188
Length	128
Max. P	0.665392

overview

Window 2

Location	17,217,060 – 17,217,161
Length	101
Sequences	4
Columns	115
Reading direction	reverse
Mean pairwise identity	84.07
Mean single sequence MFE	-18.04
Consensus MFE	-15.40
Energy contribution	-15.40
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.50
Structure conservation index	0.85
SVM decision value	0.20
SVM RNA-class probability	0.629630
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17217060 101 - 22224390
GCGCCAUCUCGCUUUAGCGCACAUUUCCGGCAUUUGGCCAAAGUCUGCUUCUUCU------CGGAACCCC-------CCAUCC-CCCCCCCCCCCCUUCCACUUUCUUGGCUAUC
..((((....((....))(((.((((..(((.....))).)))).))).......------.(((.....-------...)))-.......................)))).... ( -16.80)
>DroSec_CAF1 62872 90 - 1
GCGCCAUCUCGCUUUAGCGCACAUUUCCGGCAUUUGGCCAAAGUCUGCUUCUUCU------GGG-CCCCC-------ACAUUU-CCCC----------CCACUUUCUUGGCCAUC
..(((....(((....))).........)))...((((((((((..........(------((.-...))-------).....-....----------..)))...))))))).. ( -18.32)
>DroEre_CAF1 69917 88 - 1
GCGCCAUCUCGCUUUAGCGCACAUUUCCGGCAUUUGGCCAAAGUCUGCUUCUUCU-------GG-CCCCC-------ACAUUU--CCC----------CCACUUUCUUGGCCAUC
((((.(........).))))........(((....((((((((.......))).)-------))-))...-------......--...----------.((......)))))... ( -18.20)
>DroYak_CAF1 70718 104 - 1
GCGCCAUCUCGCUUUAGCGCACAUUUCCGGCAUUUGGCCAAAGUCUGCUUCUUCUUCUUCAGGG-CCCCCCCCCCCAACAUUUUCCCC----------CCACUUUCUUGGCCAUC
..(((....(((....))).........)))...(((((((((....)))...........(((-........)))............----------.........)))))).. ( -18.82)
>consensus
GCGCCAUCUCGCUUUAGCGCACAUUUCCGGCAUUUGGCCAAAGUCUGCUUCUUCU______GGG_CCCCC_______ACAUUU_CCCC__________CCACUUUCUUGGCCAUC
..((((....((....))(((.((((..(((.....))).)))).)))...........................................................)))).... (-15.40 = -15.40 +   0.00)

alignment

secondary structure

dotplot

Window 3

Location	17,217,097 – 17,217,188
Length	91
Sequences	6
Columns	102
Reading direction	forward
Mean pairwise identity	78.27
Mean single sequence MFE	-26.33
Consensus MFE	-16.74
Energy contribution	-18.38
Covariance contribution	1.64
Combinations/Pair	1.16
Mean z-score	-1.45
Structure conservation index	0.64
SVM decision value	0.28
SVM RNA-class probability	0.665392
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17217097 91 + 22224390
-----GGGGUUCCG------AGAAGAAGCAGACUUUGGCCAAAUGCCGGAAAUGUGCGCUAAAGCGAGAUGGCGCUCUCAUUGUUGGCGGUGGCAAAAAAAA
-----..(.(((..------....))).)........((((..((((((.((((.((((((........))))))...)))).)))))).))))........ ( -27.00)
>DroPse_CAF1 89385 76 + 1
-----GGGAG-AC-------AGUCAAA----GCCUUGGCCAAAUGCCGGAAACGUGCGCCAAAGCGAGAUGGCGUUCUCAUUGAAGGAGGUGA---------
-----(((((-..-------.((((..----((.(((((.....((((....)).))))))).))....)))).)))))..............--------- ( -23.70)
>DroSec_CAF1 62899 89 + 1
-----GGGGG-CCC------AGAAGAAGCAGACUUUGGCCAAAUGCCGGAAAUGUGCGCUAAAGCGAGAUGGCGCUCUCAUUGUUGGCGGUGGCAAAA-AAA
-----((...-.))------....((((....)))).((((..((((((.((((.((((((........))))))...)))).)))))).))))....-... ( -28.00)
>DroEre_CAF1 69943 88 + 1
-----GGGGG-CC-------AGAAGAAGCAGACUUUGGCCAAAUGCCGGAAAUGUGCGCUAAAGCGAGAUGGCGCUCUCAUUGUUCGUGGUGGCAAAAAAA-
-----...((-((-------(((..........)))))))...(((((((((((.((((((........))))))...)))..)))....)))))......- ( -24.80)
>DroYak_CAF1 70748 101 + 1
GGGGGGGGGG-CCCUGAAGAAGAAGAAGCAGACUUUGGCCAAAUGCCGGAAAUGUGCGCUAAAGCGAGAUGGCGCUCUCAUUGUUGGCGGUGGCAAAAAAAA
..((((....-)))).........((((....)))).((((..((((((.((((.((((((........))))))...)))).)))))).))))........ ( -30.80)
>DroPer_CAF1 83948 76 + 1
-----GGGAG-AC-------AGUCAAA----GCCUUGGCCAAAUGCCGGAAACGUGCGCCAAAGCGAGAUGGCGUUCUCAUUGAAGGAGGUGA---------
-----(((((-..-------.((((..----((.(((((.....((((....)).))))))).))....)))).)))))..............--------- ( -23.70)
>consensus
_____GGGGG_CC_______AGAAGAAGCAGACUUUGGCCAAAUGCCGGAAAUGUGCGCUAAAGCGAGAUGGCGCUCUCAUUGUUGGCGGUGGCAAAA_AA_
.....................................((((...(((((.((((.((((((........))))))...)))).)))))..))))........ (-16.74 = -18.38 +   1.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:25:09 2006