Locus 6344

Sequence ID	2L_DroMel_CAF1
Location	17,725,609 – 17,725,740
Length	131
Max. P	0.899530

overview

Window 2

Location	17,725,609 – 17,725,701
Length	92
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	82.24
Mean single sequence MFE	-31.91
Consensus MFE	-16.88
Energy contribution	-17.08
Covariance contribution	0.20
Combinations/Pair	1.11
Mean z-score	-2.25
Structure conservation index	0.53
SVM decision value	0.32
SVM RNA-class probability	0.689372
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17725609 92 + 22407834
AGGG-CGCCGAUAAAAUGGGAUGUGG--------------GGCUGGCAAGUGUCCAGAUCACACAACAACAUCUGGCAUGUUGUCAUUAAAGGCCAGGCCAAAUAAC
..((-((((.....((((...(((((--------------..(((((....).))))..).))))(((((((.....)))))))))))...)))...)))....... ( -25.60)
>DroSec_CAF1 25831 92 + 1
AGGG-CCCCCAUAUAAAGGGAUGUGG--------------GGCUGGCAAGUGUCCAGCUCACACAACAACAUCUGGCAUGUUGUCAUUAAAGGCCAGGCCAAAUUAC
..((-(((((.......))).(((((--------------(((((((....).))))))).))))........((((...(((....)))..))))))))....... ( -33.90)
>DroEre_CAF1 35675 92 + 1
AGGG-UCCUGAUAAAAAGGGAUGUGG--------------GGCUGGCAAGUGUCCAGAUCGCACAACAACAUCUGGCAUGUUGUCAUUAAAGGCCAGGCCAAAUGAC
.(.(-((((........))))).).(--------------(.(((((..((((.......)))).(((((((.....)))))))........))))).))....... ( -28.30)
>DroYak_CAF1 28089 93 + 1
AGAGACCCUGAUAAAAAGGGAUGUGG--------------GGCUGGCAAGUGUCCAGAUCGCACAACAACAUCUGGCAUGUUGUCAUUACAGGCCAGCCCAAAUGAC
.....((((.......)))).....(--------------(((((((..(((.((((((.(........)))))))))).((((....))))))))))))....... ( -33.70)
>DroAna_CAF1 35257 100 + 1
AGGG-CC------AAAAGGGGCGUGACCGGGUGGCUCGCUGGCUGGCAAGUGUCCAGAUCAGGCAACAACAUCUGGCAUGUUGUCAUUAAAGGGCAGCCAGACUGAC
.(((-((------(...((.......))...)))))).(((((((.(..(((.((((((..(....)...))))))))).............).)))))))...... ( -38.06)
>consensus
AGGG_CCCCGAUAAAAAGGGAUGUGG______________GGCUGGCAAGUGUCCAGAUCACACAACAACAUCUGGCAUGUUGUCAUUAAAGGCCAGGCCAAAUGAC
........................................(((((((..((((.......)))).(((((((.....)))))))........))))).))....... (-16.88 = -17.08 +   0.20)

alignment

secondary structure

dotplot

Window 3

Location	17,725,634 – 17,725,740
Length	106
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	81.63
Mean single sequence MFE	-32.57
Consensus MFE	-21.68
Energy contribution	-22.08
Covariance contribution	0.40
Combinations/Pair	1.09
Mean z-score	-2.19
Structure conservation index	0.67
SVM decision value	1.01
SVM RNA-class probability	0.899530
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17725634 106 + 22407834
GGCUGGCAAGUGUCCAGAUCACACAACAACAUCUGGCAUGUUGUCAUUAAAGGCCAGGCCAAAUAACCCCCCCAAA-AAACAGGGGAACUUUCAAGGGGAUGGCCUA
((((((((((((.((((((...........))))))))).)))))......))))((((((.....(((((((...-.....)))((....))..)))).)))))). ( -36.20)
>DroSec_CAF1 25856 107 + 1
GGCUGGCAAGUGUCCAGCUCACACAACAACAUCUGGCAUGUUGUCAUUAAAGGCCAGGCCAAAUUACCCCCCCAAAAAAACAGGGGAUCUUUCAAGUGGAUGGCCUA
(((((((....).))))))......(((((((.....)))))))......((((((..(((........((((.........))))..........))).)))))). ( -33.57)
>DroEre_CAF1 35700 106 + 1
GGCUGGCAAGUGUCCAGAUCGCACAACAACAUCUGGCAUGUUGUCAUUAAAGGCCAGGCCAAAUGACCCCCCCACA-AAACAGGGGAACUUUCAAGGGGAUAACCUG
(((((((..((((.......)))).(((((((.....)))))))........)))).)))......(((((((...-.....)))((....))..))))........ ( -31.30)
>DroYak_CAF1 28115 106 + 1
GGCUGGCAAGUGUCCAGAUCGCACAACAACAUCUGGCAUGUUGUCAUUACAGGCCAGCCCAAAUGACCCCCGAAAA-AAAGAGGGUAACUUUCAAGGGGACAGCCUG
...(((((((((.((((((.(........)))))))))).))))))...(((((...(((.....((((.(.....-...).))))..((....)))))...))))) ( -32.50)
>DroAna_CAF1 35290 90 + 1
GGCUGGCAAGUGUCCAGAUCAGGCAACAACAUCUGGCAUGUUGUCAUUAAAGGGCAGCCAGACUGACCCCCAGAACAGCAGAGGGGACA-----------C------
(((((((..(((.((((((..(....)...)))))))))..((((.......))))))))).))...((((...........))))...-----------.------ ( -29.30)
>consensus
GGCUGGCAAGUGUCCAGAUCACACAACAACAUCUGGCAUGUUGUCAUUAAAGGCCAGGCCAAAUGACCCCCCCAAA_AAACAGGGGAACUUUCAAGGGGAUAGCCUA
(((((((..((((.......)))).(((((((.....)))))))........))))).)).......((((...........))))..................... (-21.68 = -22.08 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:08:51 2006