Locus 78

Sequence ID	2L_DroMel_CAF1
Location	267,201 – 267,356
Length	155
Max. P	0.999915

overview

Window 8

Location	267,201 – 267,304
Length	103
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	95.77
Mean single sequence MFE	-36.92
Consensus MFE	-35.60
Energy contribution	-36.20
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.48
Structure conservation index	0.96
SVM decision value	4.53
SVM RNA-class probability	0.999915
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 267201 103 - 22407834
CCGCAAAAAGGGGGGUGGCGAACAUCCUGUUUUUCUGCGCCCGCUGCCAGAGUAACCACCCCCUCUCAGGGACGACAACAACAAAGUGGACUU--------AAGCGAAAAA
.(((.....(((((((((.((((.....))))(((((.((.....)))))))...)))))))))...(((..(.((.........)))..)))--------..)))..... ( -31.10)
>DroSec_CAF1 59001 111 - 1
CCGCAAAAAGGGGGGUGGCGAACAUCCUGUUUUUCUGCGCCCGCUGCCAGAGUAACCACCCCCUCUCAGGGACGACAACAACAAAGUGGGCUUGAGAAUAUAAGCGAAAAA
.(((......((((((((.((((.....))))(((((.((.....)))))))...))))))))(((((((..(.((.........)).).)))))))......)))..... ( -38.50)
>DroSim_CAF1 72187 111 - 1
CCGCAAAAAGGGGGGUGGCGAACAUCCUGUUUUUCUGCGCCCGCUGCCAGAGUAACCACCCCCUCUCAGGGACGACAACAACAAAGUGGACUUGAGAAUAUAAGCGAAAAA
.(((......((((((((.((((.....))))(((((.((.....)))))))...))))))))(((((((..(.((.........)))..)))))))......)))..... ( -39.20)
>DroEre_CAF1 65133 111 - 1
CCGCAAAAAGGGGGGUGGCGAACAUCCUGUUUUUCUGCGCCCGCUGCCAGAGUAACCACCCCCUCUCAGGGACGACAACAACAAAGUGGACUUGAGUAUAAAAGCGAAAAA
.(((.....(((((((((.((((.....))))(((((.((.....)))))))...)))))))))((((((..(.((.........)))..)))))).......)))..... ( -37.90)
>DroYak_CAF1 62957 111 - 1
CCGCAAAAAGGGGGGUGGCGAACAUCCUGUUUUUCUGCGCCCGCUGCCAGAGUAACCACCCCCUCUCAGGGACGACAACAACAAAGUGGACUUGAGUGUAAAAGCGAAAAA
.(((.....(((((((((.((((.....))))(((((.((.....)))))))...)))))))))((((((..(.((.........)))..)))))).......)))..... ( -37.90)
>consensus
CCGCAAAAAGGGGGGUGGCGAACAUCCUGUUUUUCUGCGCCCGCUGCCAGAGUAACCACCCCCUCUCAGGGACGACAACAACAAAGUGGACUUGAGAAUAAAAGCGAAAAA
.(((.....(((((((((.((((.....))))(((((.((.....)))))))...)))))))))((((((..(.((.........)))..)))))).......)))..... (-35.60 = -36.20 +   0.60)

alignment

secondary structure

dotplot

Window 9

Location	267,232 – 267,325
Length	93
Sequences	5
Columns	93
Reading direction	reverse
Mean pairwise identity	98.71
Mean single sequence MFE	-32.26
Consensus MFE	-29.90
Energy contribution	-30.30
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.63
Structure conservation index	0.93
SVM decision value	1.15
SVM RNA-class probability	0.922848
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 267232 93 - 22407834
GGAAAACCAUAGAGAGGAAUUCCGCAAAAAGGGGGGUGGCGAACAUCCUGUUUUUCUGCGCCCGCUGCCAGAGUAACCACCCCCUCUCAGGGA
......((...((((((....))........((((((((.((((.....))))(((((.((.....)))))))...))))))))))))..)). ( -32.50)
>DroSec_CAF1 59040 93 - 1
GGAAAACCAUAGAGAGGAAUUCCGCAAAAAGGGGGGUGGCGAACAUCCUGUUUUUCUGCGCCCGCUGCCAGAGUAACCACCCCCUCUCAGGGA
......((...((((((....))........((((((((.((((.....))))(((((.((.....)))))))...))))))))))))..)). ( -32.50)
>DroSim_CAF1 72226 93 - 1
GGAAAACCAUAGAGAGGAAUUCCGCAAAAAGGGGGGUGGCGAACAUCCUGUUUUUCUGCGCCCGCUGCCAGAGUAACCACCCCCUCUCAGGGA
......((...((((((....))........((((((((.((((.....))))(((((.((.....)))))))...))))))))))))..)). ( -32.50)
>DroEre_CAF1 65172 93 - 1
GGAAAACCAUAGAGAGGAAUUCCGCAAAAAGGGGGGUGGCGAACAUCCUGUUUUUCUGCGCCCGCUGCCAGAGUAACCACCCCCUCUCAGGGA
......((...((((((....))........((((((((.((((.....))))(((((.((.....)))))))...))))))))))))..)). ( -32.50)
>DroYak_CAF1 62996 92 - 1
GGAAAACCGUAGCGAG-AAUUCCGCAAAAAGGGGGGUGGCGAACAUCCUGUUUUUCUGCGCCCGCUGCCAGAGUAACCACCCCCUCUCAGGGA
......((...(((.(-....)))).....(((((((((.((((.....))))(((((.((.....)))))))...)))))))))....)).. ( -31.30)
>consensus
GGAAAACCAUAGAGAGGAAUUCCGCAAAAAGGGGGGUGGCGAACAUCCUGUUUUUCUGCGCCCGCUGCCAGAGUAACCACCCCCUCUCAGGGA
......((...((((((....))........((((((((.((((.....))))(((((.((.....)))))))...))))))))))))..)). (-29.90 = -30.30 +   0.40)

alignment

secondary structure

dotplot

Window 0

Location	267,265 – 267,356
Length	91
Sequences	5
Columns	91
Reading direction	reverse
Mean pairwise identity	98.24
Mean single sequence MFE	-22.38
Consensus MFE	-21.72
Energy contribution	-21.92
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.87
Structure conservation index	0.97
SVM decision value	2.42
SVM RNA-class probability	0.993762
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 267265 91 - 22407834
UGUGGGAGACAAACAAAUAGCAAAACGAGAAGGAAAACCAUAGAGAGGAAUUCCGCAAAAAGGGGGGUGGCGAACAUCCUGUUUUUCUGCG
(((.(....)..)))................((((..((.......))..))))((((((((.((((((.....)))))).))))).))). ( -22.70)
>DroSec_CAF1 59073 91 - 1
UGUGGGAGACAAACAAAUAGCAAAACGAGAAGGAAAACCAUAGAGAGGAAUUCCGCAAAAAGGGGGGUGGCGAACAUCCUGUUUUUCUGCG
(((.(....)..)))................((((..((.......))..))))((((((((.((((((.....)))))).))))).))). ( -22.70)
>DroSim_CAF1 72259 91 - 1
UGUGGGAGACAAACAAAUAGCAAAACGAGAAGGAAAACCAUAGAGAGGAAUUCCGCAAAAAGGGGGGUGGCGAACAUCCUGUUUUUCUGCG
(((.(....)..)))................((((..((.......))..))))((((((((.((((((.....)))))).))))).))). ( -22.70)
>DroEre_CAF1 65205 91 - 1
UGUGGGAGACAAACAAAUAGCAAAACGAAAAGGAAAACCAUAGAGAGGAAUUCCGCAAAAAGGGGGGUGGCGAACAUCCUGUUUUUCUGCG
(((.(....)..)))................((((..((.......))..))))((((((((.((((((.....)))))).))))).))). ( -22.70)
>DroYak_CAF1 63029 90 - 1
UGUGGGAGACAAACAAAUAGCAAAACGAGAAGGAAAACCGUAGCGAG-AAUUCCGCAAAAAGGGGGGUGGCGAACAUCCUGUUUUUCUGCG
(((.(....)..)))..........((...((((((((....(((.(-....)))).......((((((.....)))))))))))))).)) ( -21.10)
>consensus
UGUGGGAGACAAACAAAUAGCAAAACGAGAAGGAAAACCAUAGAGAGGAAUUCCGCAAAAAGGGGGGUGGCGAACAUCCUGUUUUUCUGCG
(((.(....)..)))................((((..((.......))..))))((((((((.((((((.....)))))).))))).))). (-21.72 = -21.92 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:25:11 2006