Locus 8517

Sequence ID	3L_DroMel_CAF1
Location	22,306,669 – 22,306,798
Length	129
Max. P	0.987133

overview

Window 5

Location	22,306,669 – 22,306,788
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.00
Mean single sequence MFE	-35.28
Consensus MFE	-31.18
Energy contribution	-31.26
Covariance contribution	0.08
Combinations/Pair	1.15
Mean z-score	-1.86
Structure conservation index	0.88
SVM decision value	2.07
SVM RNA-class probability	0.987133
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22306669 119 + 23771897
AAGAUCGGGGGAUGGG-GGUUGUUCUGGUAGACAGAAAACCGGAUUUUGUAUUCUUCGCCAGUUUUCCUCUUUUUCUUGGUCGGGGGGAAUGCAAGAAAACACAUUUUUCUUAUGGAAAA
..(((((((..(.(((-((.....(((((.((.((((.((........)).)))))))))))....))))).)..)))))))(((..(((((..........)))))..)))........ ( -35.30)
>DroSec_CAF1 65287 120 + 1
AAGAUCGGGGGAUGGGGGGUUGUUCUGGUAGACAGAAAACCGGAUUUUGUAUUCUUCGCCAGUUUUCCUCUUUUUCUUGGUCGAGGGGAAUGCAAGAAAACACAUUUUUCUUAUGGAAAA
..(((((((..(.((((((.....(((((.((.((((.((........)).)))))))))))...)))))).)..)))))))(((..(((((..........)))))..)))........ ( -36.50)
>DroSim_CAF1 47322 120 + 1
AAGAUCGGAGGAUGGGGGGUUGUUCUGGUAGACAGAAAACCGGAUUUUGUAUUCUUCGCCAGUUUUCCUCUUUUUCUUGGUCGAGGGGAAUGCAAGAAAACACAUUUUUCUUAUGGAAAA
.....(((((((((.((((((.(((((.....))))).....)))))).)))))))))(((((.((((((((..(....)..)))))))).))(((((((.....))))))).))).... ( -33.90)
>DroEre_CAF1 63744 118 + 1
AAGGUCGGGGAU--GGAGGUUGUUCUGGUAGACAGAAAACCGGAUUUUGUAUUCUUCGCCAGUUUUCCUCUUUUUCUUGGUCGGGGGGAAUGCAACAAAACACAUUUUUCUUAUGGAAAA
..(..((((((.--(((((.....(((((.((.((((.((........)).)))))))))))....)))))..))))))..)(((..(((((..........)))))..)))........ ( -33.30)
>DroYak_CAF1 40909 120 + 1
AAGAUCUGGGAAUGGGAGGUUGUUCUGGUAGACAGAAAACCGGAUUUUGUAUUCUUCGCCAGUUUUCCUCUUUUUCUUGGUAGAGGGGAAUGCAAGAAAACACAUUUUCCUCAUGGAAAA
.....(..((((..(((((.....(((((.((.((((.((........)).)))))))))))....)))))..))))..)..((((..((((..........))))..))))........ ( -37.40)
>consensus
AAGAUCGGGGGAUGGGAGGUUGUUCUGGUAGACAGAAAACCGGAUUUUGUAUUCUUCGCCAGUUUUCCUCUUUUUCUUGGUCGAGGGGAAUGCAAGAAAACACAUUUUUCUUAUGGAAAA
..((((((((((.((((((.....(((((.((.((((.((........)).)))))))))))....))))))))))))))))((((((((((..........))))))))))........ (-31.18 = -31.26 +   0.08)

alignment

secondary structure

dotplot

Window 6

Location	22,306,708 – 22,306,798
Length	90
Sequences	4
Columns	101
Reading direction	forward
Mean pairwise identity	91.75
Mean single sequence MFE	-26.25
Consensus MFE	-22.15
Energy contribution	-21.96
Covariance contribution	-0.19
Combinations/Pair	1.03
Mean z-score	-1.78
Structure conservation index	0.84
SVM decision value	0.62
SVM RNA-class probability	0.803442
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22306708 90 + 23771897
CGGAUUUUGUAUUCUUCGCCAGUUUUCCUCUUUUUCUUGGUCGGGGGGAAUGCAAGAAAACACAUUUUUCUUAUGGAAAAUUGCGGCCAG-----------
.((.(((((((((((((.((.(....((..........)).))))))))))))))))...(.((.(((((.....))))).)).).))..----------- ( -22.20)
>DroSec_CAF1 65327 101 + 1
CGGAUUUUGUAUUCUUCGCCAGUUUUCCUCUUUUUCUUGGUCGAGGGGAAUGCAAGAAAACACAUUUUUCUUAUGGAAAAUUGCGGCCAGAAGAAUAAAUG
.........(((((((((((((((((((..(((..(((....)))..)))...(((((((.....)))))))..))))))))..)))..)))))))).... ( -27.30)
>DroSim_CAF1 47362 101 + 1
CGGAUUUUGUAUUCUUCGCCAGUUUUCCUCUUUUUCUUGGUCGAGGGGAAUGCAAGAAAACACAUUUUUCUUAUGGAAAAUUGCGGCCAGAAGAAUAAAUG
.........(((((((((((((((((((..(((..(((....)))..)))...(((((((.....)))))))..))))))))..)))..)))))))).... ( -27.30)
>DroYak_CAF1 40949 101 + 1
CGGAUUUUGUAUUCUUCGCCAGUUUUCCUCUUUUUCUUGGUAGAGGGGAAUGCAAGAAAACACAUUUUCCUCAUGGAAAAUUGCGGCCAAAAGAAUAGAUG
.......(.(((((((.(((.((.(((((((((........))))))))).)).......((.(((((((....))))))))).)))...))))))).).. ( -28.20)
>consensus
CGGAUUUUGUAUUCUUCGCCAGUUUUCCUCUUUUUCUUGGUCGAGGGGAAUGCAAGAAAACACAUUUUUCUUAUGGAAAAUUGCGGCCAGAAGAAUAAAUG
.((.((((((((((((((((((..............)))))...)))))))))))))...(.((((((((....)))))).)).).))............. (-22.15 = -21.96 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:17:44 2006