Locus 750

Sequence ID	3L_DroMel_CAF1
Location	2,240,362 – 2,240,462
Length	100
Max. P	0.792017

overview

Window 5

Location	2,240,362 – 2,240,462
Length	100
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	78.50
Mean single sequence MFE	-32.11
Consensus MFE	-18.27
Energy contribution	-20.60
Covariance contribution	2.33
Combinations/Pair	1.00
Mean z-score	-1.67
Structure conservation index	0.57
SVM decision value	0.11
SVM RNA-class probability	0.590436
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2240362 100 + 23771897
GAAAAGCCGUGGAAAU-UCUGCACAGGCUGCGUGGGC-GUGAAAGCCCUAAAGCCCC--GCCCACUCUGCCGCACUUGGCCAUUUCAUUUGGCAUUUCCACGAG
.......(((((((((-..(((...(((.(.((((((-(.(...((......)).))--)))))).).))))))....((((.......))))))))))))).. ( -38.90)
>DroSec_CAF1 1265 88 + 1
CAAAAGCCGUGGAAAU-UCUGCACAGGCUGCGUGGGC-GUGAAAGCCCUAAAGCCCC--------------CCACCUUGCCCUUCCAUUGGGCAUUUCCACGAG
.......((((((((.-........((((....((((-......))))...))))..--------------......(((((.......))))))))))))).. ( -34.90)
>DroSim_CAF1 3510 88 + 1
GAAAAGCCGUGGAAAU-UCUGCACAGGCUGCGUGGGC-GUGAAAGCCCUAAAGCCCC--------------CCACUUUGCCCUUCCAUUGAGCAUUUCCACGAG
.......((((((((.-..(((...((((....((((-......))))...))))..--------------...(..((......))..).))))))))))).. ( -28.10)
>DroEre_CAF1 3987 100 + 1
GAAAAGCCGUGGAAAU-UCUGCACAGGCUGCGUGGGC-UUGAAAGCCCUAAAGCCCC--GCCCACUCCGCCGCACUUGGCCCUUCCAUUUGGCAUUUCCACGAG
.......(((((((((-...((...((((....((((-(....)))))...))))..--)).......((((....(((.....)))..))))))))))))).. ( -34.60)
>DroYak_CAF1 4161 100 + 1
GAAAAGCCGUGGAAAU-UCUGCACAGGCUGCGUGGGC-GUGAAAGCCCUAAAGCCCC--GCCCACUUCGCCGCACUUGGCCCUUCCAUUUGGCUUUUCCACGAG
((((((((((((((..-...((...((((....((((-......))))...))))..--)).......((((....))))..))))))..))))))))...... ( -37.00)
>DroAna_CAF1 6812 86 + 1
GAAAAGCGGUGAAAAUGUCUGCAAAGGCUGCGUAGGCGGUGAAAGCCCAGAAUCCCUCCGACCACCAC----CCCUUAGCCCGCACA--------------GAG
.....((((.......((((....)))).((..(((.((((........................)))----))))..))))))...--------------... ( -19.16)
>consensus
GAAAAGCCGUGGAAAU_UCUGCACAGGCUGCGUGGGC_GUGAAAGCCCUAAAGCCCC__GCCCACU_C___GCACUUGGCCCUUCCAUUUGGCAUUUCCACGAG
.......((((((((..........((((....((((.......))))...)))).......................(((.........))).)))))))).. (-18.27 = -20.60 +   2.33)

alignment

secondary structure

dotplot

Window 6

Location	2,240,362 – 2,240,462
Length	100
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	78.50
Mean single sequence MFE	-38.23
Consensus MFE	-20.47
Energy contribution	-22.55
Covariance contribution	2.08
Combinations/Pair	1.09
Mean z-score	-2.08
Structure conservation index	0.54
SVM decision value	0.59
SVM RNA-class probability	0.792017
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2240362 100 - 23771897
CUCGUGGAAAUGCCAAAUGAAAUGGCCAAGUGCGGCAGAGUGGGC--GGGGCUUUAGGGCUUUCAC-GCCCACGCAGCCUGUGCAGA-AUUUCCACGGCUUUUC
.((((((((((((((.......))))...(..((((...((((((--(.((((....))))....)-))))))...))).)..)...-))))))))))...... ( -44.40)
>DroSec_CAF1 1265 88 - 1
CUCGUGGAAAUGCCCAAUGGAAGGGCAAGGUGG--------------GGGGCUUUAGGGCUUUCAC-GCCCACGCAGCCUGUGCAGA-AUUUCCACGGCUUUUG
.((((((((((((((.......))))..(((((--------------..((((....))))..).)-)))...(((.....)))...-))))))))))...... ( -35.60)
>DroSim_CAF1 3510 88 - 1
CUCGUGGAAAUGCUCAAUGGAAGGGCAAAGUGG--------------GGGGCUUUAGGGCUUUCAC-GCCCACGCAGCCUGUGCAGA-AUUUCCACGGCUUUUC
.((((((((((.((........((((...(((.--------------.((.(.....).))..)))-))))..(((.....))))).-))))))))))...... ( -32.20)
>DroEre_CAF1 3987 100 - 1
CUCGUGGAAAUGCCAAAUGGAAGGGCCAAGUGCGGCGGAGUGGGC--GGGGCUUUAGGGCUUUCAA-GCCCACGCAGCCUGUGCAGA-AUUUCCACGGCUUUUC
.(((((((((((((.........)))...(..((((...((((((--.(((((....)))))....-))))))...))).)..)...-))))))))))...... ( -42.10)
>DroYak_CAF1 4161 100 - 1
CUCGUGGAAAAGCCAAAUGGAAGGGCCAAGUGCGGCGAAGUGGGC--GGGGCUUUAGGGCUUUCAC-GCCCACGCAGCCUGUGCAGA-AUUUCCACGGCUUUUC
......((((((((...((((((..(...(..((((...((((((--(.((((....))))....)-))))))...))).)..).).-.)))))).)))))))) ( -44.40)
>DroAna_CAF1 6812 86 - 1
CUC--------------UGUGCGGGCUAAGGG----GUGGUGGUCGGAGGGAUUCUGGGCUUUCACCGCCUACGCAGCCUUUGCAGACAUUUUCACCGCUUUUC
.((--------------((((.(((((...((----(((((((((((((...))))))....)))))))))....))))).))))))................. ( -30.70)
>consensus
CUCGUGGAAAUGCCAAAUGGAAGGGCCAAGUGC___G_AGUGGGC__GGGGCUUUAGGGCUUUCAC_GCCCACGCAGCCUGUGCAGA_AUUUCCACGGCUUUUC
.(((((((((((((.........)))......................(((((...((((.......))))....)))))........))))))))))...... (-20.47 = -22.55 +   2.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:50:15 2006