Locus 3778

Sequence ID	2R_DroMel_CAF1
Location	12,495,275 – 12,495,422
Length	147
Max. P	0.987726

overview

Window 9

Location	12,495,275 – 12,495,385
Length	110
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	81.65
Mean single sequence MFE	-32.28
Consensus MFE	-20.92
Energy contribution	-23.00
Covariance contribution	2.08
Combinations/Pair	1.03
Mean z-score	-2.88
Structure conservation index	0.65
SVM decision value	2.09
SVM RNA-class probability	0.987726
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12495275 110 + 20766785
UUUGUGGGUGGGAAAGCAUCGAGAAAAACCAUUAUGG-GAUACCGUAAUGGAUGGUGGAUAUGAUGGAUGUCUUGAGAUACCAUUGAUCCAUACAAGUGACCCAA------GAAAAA
(((.(((((.(.................(((((((((-....)))))))))...((((((.((((((.((((....)))))))))))))))).....).))))).------)))... ( -36.40)
>DroSec_CAF1 29864 108 + 1
UUUGUGGGUGGGAAAGCAUCGAGAAAAACCAUUAAGG-GA--------UGGAUGGUGGAUAUGAUGGAUGUCUUAAGAUACCAUUGAUCCAUUAAGGUGACCCAAGGUGAAGAAAAA
((..(...((((....((((........(((((....-))--------))).((((((((.((((((.((((....)))))))))))))))))).)))).))))..)..))...... ( -31.00)
>DroSim_CAF1 25177 115 + 1
UUGGUGGGUGGGAAAGCAUCGAGAAAAACCAUUAAGG-GAUGCCGUAAUGGAUGGUGGAUAUGAUGGAUGUCUUAAGAUACCAUUGAUCCAUUAGGGUGACCCAAGGUGG-GAAAAA
((((((..(....)..))))))......(((((..((-(.((((.((((((((........((((((.((((....)))))))))))))))))).)))).)))..)))))-...... ( -35.70)
>DroEre_CAF1 24985 114 + 1
UUUGUGGGUG-GAAAGCAUCGGGAA-AACCUUUAGGGCGCCACCGUAAUGGAUGCUGGAUAUGAUGGAUGCC-UGAGAUACCAUUGAUCCAUGAAAUUGACACAAGGUGUUCGGAAA
((((((((((-(...((...(((..-..))).....)).)))))...........(((((.((((((((...-....)).))))))))))).........))))))........... ( -27.50)
>DroYak_CAF1 25492 114 + 1
UUUGUGGGUG-GAAAGCGGGGAGAA-AUCCAUUAAGG-GAUUCUGUAAUGGAUGGCGGAUUUGAUGGAUGCCUUGAGAUACCAUUGAUCCAUGAAAGUGACCCAAGGUGCAAGGAGA
....((((((-(....(((((....-((((((((((.-...(((((........))))))))))))))).))))).....)).......(((....))))))))............. ( -30.80)
>consensus
UUUGUGGGUGGGAAAGCAUCGAGAAAAACCAUUAAGG_GAUACCGUAAUGGAUGGUGGAUAUGAUGGAUGUCUUGAGAUACCAUUGAUCCAUGAAAGUGACCCAAGGUG__GAAAAA
....(((((...................((((((.((.....)).))))))...((((((.((((((.((((....)))))))))))))))).......)))))............. (-20.92 = -23.00 +   2.08)

alignment

secondary structure

dotplot

Window 0

Location	12,495,275 – 12,495,385
Length	110
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	81.65
Mean single sequence MFE	-21.07
Consensus MFE	-15.58
Energy contribution	-16.78
Covariance contribution	1.20
Combinations/Pair	1.08
Mean z-score	-2.37
Structure conservation index	0.74
SVM decision value	1.61
SVM RNA-class probability	0.967668
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12495275 110 - 20766785
UUUUUC------UUGGGUCACUUGUAUGGAUCAAUGGUAUCUCAAGACAUCCAUCAUAUCCACCAUCCAUUACGGUAUC-CCAUAAUGGUUUUUCUCGAUGCUUUCCCACCCACAAA
......------.(((((.....((((((((..((((..((....))...))))...)))).....((((((.((....-)).)))))).........))))......))))).... ( -23.10)
>DroSec_CAF1 29864 108 - 1
UUUUUCUUCACCUUGGGUCACCUUAAUGGAUCAAUGGUAUCUUAAGACAUCCAUCAUAUCCACCAUCCA--------UC-CCUUAAUGGUUUUUCUCGAUGCUUUCCCACCCACAAA
.............(((((.(((((((.((((..(((((....((.((......)).))...)))))..)--------))-).)))).))).......((.....))..))))).... ( -18.20)
>DroSim_CAF1 25177 115 - 1
UUUUUC-CCACCUUGGGUCACCCUAAUGGAUCAAUGGUAUCUUAAGACAUCCAUCAUAUCCACCAUCCAUUACGGCAUC-CCUUAAUGGUUUUUCUCGAUGCUUUCCCACCCACCAA
......-......(((((........(((((..((((..((....))...))))...)))))....((((((.((....-)).))))))...................))))).... ( -21.30)
>DroEre_CAF1 24985 114 - 1
UUUCCGAACACCUUGUGUCAAUUUCAUGGAUCAAUGGUAUCUCA-GGCAUCCAUCAUAUCCAGCAUCCAUUACGGUGGCGCCCUAAAGGUU-UUCCCGAUGCUUUC-CACCCACAAA
.....(((.(((((((((((.....((((((...(((.......-((...)).......)))..)))))).....))))))....))))).-)))...........-.......... ( -22.54)
>DroYak_CAF1 25492 114 - 1
UCUCCUUGCACCUUGGGUCACUUUCAUGGAUCAAUGGUAUCUCAAGGCAUCCAUCAAAUCCGCCAUCCAUUACAGAAUC-CCUUAAUGGAU-UUCUCCCCGCUUUC-CACCCACAAA
.............(((((.........((((..((((..((....))...))))...))))...((((((((.((....-.))))))))))-..............-.))))).... ( -20.20)
>consensus
UUUUUC__CACCUUGGGUCACUUUAAUGGAUCAAUGGUAUCUCAAGACAUCCAUCAUAUCCACCAUCCAUUACGGUAUC_CCUUAAUGGUUUUUCUCGAUGCUUUCCCACCCACAAA
.............(((((........(((((..((((..((....))...))))...)))))....((((((.((.....)).))))))...................))))).... (-15.58 = -16.78 +   1.20)

alignment

secondary structure

dotplot

Window 1

Location	12,495,312 – 12,495,422
Length	110
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	78.04
Mean single sequence MFE	-29.99
Consensus MFE	-18.78
Energy contribution	-19.62
Covariance contribution	0.84
Combinations/Pair	1.17
Mean z-score	-1.85
Structure conservation index	0.63
SVM decision value	0.64
SVM RNA-class probability	0.808226
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12495312 110 + 20766785
-GAUACCGUAAUGGAUGGUGGAUAUGAUGGAUGUCUUGAGAUACCAUUGAUCCAUACAAGUGACCCAA------GAAAAAGAAAAAG--GCGUCCUU-CAUCAUUUAGGCCAUCAUUAAU
-(((.((......((((((((((.((((((.((((....))))))))))))))))..(((.(((((..------............)--).))))))-)))).....))..)))...... ( -27.14)
>DroSec_CAF1 29901 110 + 1
-GA--------UGGAUGGUGGAUAUGAUGGAUGUCUUAAGAUACCAUUGAUCCAUUAAGGUGACCCAAGGUGAAGAAAAAGAAAAAAAAGGGUACUU-CAUUAUUUAGGCCAUCAUUAAU
-((--------(((.((((((((.((((((.((((....))))))))))))))))))(((((.(((.......................))))))))-...........)))))...... ( -29.20)
>DroSim_CAF1 25214 115 + 1
-GAUGCCGUAAUGGAUGGUGGAUAUGAUGGAUGUCUUAAGAUACCAUUGAUCCAUUAGGGUGACCCAAGGUGG-GAAAAAGAAAAAA--AGGUCCUU-CAUCAUUUAGGCCCUCAUUAAU
-((.(((......(((((.((((..(((((.((((....)))))))))..((((((.((....))...)))))-)............--..)))).)-)))).....)))..))...... ( -32.60)
>DroEre_CAF1 25020 112 + 1
CGCCACCGUAAUGGAUGCUGGAUAUGAUGGAUGCC-UGAGAUACCAUUGAUCCAUGAAAUUGACACAAGGUGUUCGGAAAGCAAGAG--GAGCCCUU-CAUCAUUUAUGCUUUCA----U
((.(((((((.....)))(((((.((((((((...-....)).)))))))))))..............))))..))(((((((.(((--((......-..)).))).))))))).----. ( -24.60)
>DroYak_CAF1 25527 117 + 1
-GAUUCUGUAAUGGAUGGCGGAUUUGAUGGAUGCCUUGAGAUACCAUUGAUCCAUGAAAGUGACCCAAGGUGCAAGGAGACAAAGAG--GAGUCCUUCCAUCAUUUACGCUAUCAUUAAU
-.......(((((.((((((....(((((((..(((((...((((.(((...(((....)))...)))))))))))).(((......--..)))..)))))))....))))))))))).. ( -36.40)
>consensus
_GAUACCGUAAUGGAUGGUGGAUAUGAUGGAUGUCUUGAGAUACCAUUGAUCCAUGAAAGUGACCCAAGGUG__GAAAAAGAAAAAG__GAGUCCUU_CAUCAUUUAGGCCAUCAUUAAU
.............((((((((((.((((((.((((....))))))))))))))....((((((...((((.......................))))...))))))..))))))...... (-18.78 = -19.62 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:03:56 2006