Locus 42

Sequence ID	2R_DroMel_CAF1
Location	1,258,950 – 1,259,083
Length	133
Max. P	0.999533

overview

Window 7

Location	1,258,950 – 1,259,043
Length	93
Sequences	5
Columns	96
Reading direction	reverse
Mean pairwise identity	96.82
Mean single sequence MFE	-36.02
Consensus MFE	-32.02
Energy contribution	-31.98
Covariance contribution	-0.04
Combinations/Pair	1.04
Mean z-score	-2.99
Structure conservation index	0.89
SVM decision value	3.69
SVM RNA-class probability	0.999533
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1258950 93 - 20766785
GCGGUUUUCGUUCGUAAACCAGAAUAUGAACGGAUUGAACUGG---CUGCCUGCGUUGAUCGCAGGGCGUUGAAAGCGCUGGAUAAGCCGCAGGAA
((((((((((((((((........)))))))))).....(..(---(..((((((.....))))))((.......))))..)...))))))..... ( -37.20)
>DroSec_CAF1 10503 93 - 1
GCGGUUUUCGUUCGUAAACCAGAAUAUGAACGGAUUGAACUGG---CUGCCUGCGUUGAUCGCAGGGCGUUGAAAGCGCUGGAUAAGCCGCAGGAA
((((((((((((((((........)))))))))).....(..(---(..((((((.....))))))((.......))))..)...))))))..... ( -37.20)
>DroSim_CAF1 16415 93 - 1
GCGGUUUUCGUUCGUAAACCAGAAUAUGAACGGAUUGAACUGG---CUGCCUGCGUUGAUCGCAGGGCGUUGAAAGCGCUGGAUAAGCCGCAGGAA
((((((((((((((((........)))))))))).....(..(---(..((((((.....))))))((.......))))..)...))))))..... ( -37.20)
>DroEre_CAF1 15183 93 - 1
GCGGUUUUUGUUCGUAAACCAGAAUAUGAACGGAUUGAACUGG---CUGCCUGCGUUGAACGCAGGGCGUUGAAAGCGCUGGAUAAGCCGCAGGAA
((((((((((((((((........)))))))))).....(..(---(..((((((.....))))))((.......))))..)...))))))..... ( -35.60)
>DroYak_CAF1 13632 96 - 1
GCGGUUUUUGUUCGUAAACCAGAAUAUGAACGGAUUAAACUGGCGGCUGCCUCCGUUGAUCGCAGGGCGUUGAAAGCGCUGGAUAAGCCGCAGGAA
.(((((((((((((((........))))))))))...)))))((((((.((..((((...(((...))).....))))..))...))))))..... ( -32.90)
>consensus
GCGGUUUUCGUUCGUAAACCAGAAUAUGAACGGAUUGAACUGG___CUGCCUGCGUUGAUCGCAGGGCGUUGAAAGCGCUGGAUAAGCCGCAGGAA
((((((((((((((((........))))))))))...............((((((.....))))))((((.....))))......))))))..... (-32.02 = -31.98 +  -0.04)

alignment

secondary structure

dotplot

Window 8

Location	1,258,990 – 1,259,083
Length	93
Sequences	5
Columns	96
Reading direction	reverse
Mean pairwise identity	93.62
Mean single sequence MFE	-29.56
Consensus MFE	-25.74
Energy contribution	-25.22
Covariance contribution	-0.52
Combinations/Pair	1.14
Mean z-score	-1.18
Structure conservation index	0.87
SVM decision value	-0.03
SVM RNA-class probability	0.519929
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1258990 93 - 20766785
AAAGGGGGCGUAGACCAUGAGUGAUGCUGCUGUGGCAGUUGCGGUUUUCGUUCGUAAACCAGAAUAUGAACGGAUUGAACUGG---CUGCCUGCGU
...((.(((((..((.....)).))))).))((((((((..(((((((((((((((........)))))))))...)))))))---))))).)).. ( -31.00)
>DroSec_CAF1 10543 93 - 1
AAAGAGGGCGUGGACCAUGAGUGAUGCUGCUGUGGCAGUUGCGGUUUUCGUUCGUAAACCAGAAUAUGAACGGAUUGAACUGG---CUGCCUGCGU
......(((((.(........).)))))((...((((((..(((((((((((((((........)))))))))...)))))))---))))).)).. ( -29.80)
>DroSim_CAF1 16455 93 - 1
AAAGAGGGCGUGGACCAUGAGUGAUGCUGCUGUGGCAGUUGCGGUUUUCGUUCGUAAACCAGAAUAUGAACGGAUUGAACUGG---CUGCCUGCGU
......(((((.(........).)))))((...((((((..(((((((((((((((........)))))))))...)))))))---))))).)).. ( -29.80)
>DroEre_CAF1 15223 91 - 1
AG--AGGGCGUGGACCAUGAGUGAUGCUGCUGUGGCAGUUGCGGUUUUUGUUCGUAAACCAGAAUAUGAACGGAUUGAACUGG---CUGCCUGCGU
..--..(((((.(........).)))))((...((((((..(((((((((((((((........)))))))))...)))))))---))))).)).. ( -27.80)
>DroYak_CAF1 13672 94 - 1
AG--AGAGUGUGGACCAUGAGUGAUGCUGCUGUGGCAGUUGCGGUUUUUGUUCGUAAACCAGAAUAUGAACGGAUUAAACUGGCGGCUGCCUCCGU
..--.......(((.....(((......)))..(((((((((((((((((((((((........))))))))))...)))).)))))))))))).. ( -29.40)
>consensus
AAAGAGGGCGUGGACCAUGAGUGAUGCUGCUGUGGCAGUUGCGGUUUUCGUUCGUAAACCAGAAUAUGAACGGAUUGAACUGG___CUGCCUGCGU
......(((((.(........).)))))((...(((((...(((((((((((((((........)))))))))...))))))....))))).)).. (-25.74 = -25.22 +  -0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:24:29 2006