Locus 6540

Sequence ID	3L_DroMel_CAF1
Location	17,285,718 – 17,285,878
Length	160
Max. P	0.965453

overview

Window 4

Location	17,285,718 – 17,285,838
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	95.28
Mean single sequence MFE	-48.42
Consensus MFE	-43.01
Energy contribution	-42.83
Covariance contribution	-0.19
Combinations/Pair	1.12
Mean z-score	-1.87
Structure conservation index	0.89
SVM decision value	0.65
SVM RNA-class probability	0.810381
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17285718 120 + 23771897
UGGAUCUAUCUUGAUGGUCUCGGCCACGGCCUGAACGGCACUGAUCGAAAGCCAUCCCUGCUGCCGCUGGGCAAUAUCCAGUAGUGGCAGGAGUGCUCCCUUCCACUCCGCCUGCGGAUA
((((........((((((.(((..((..(((.....)))..))..)))..))))))(((((..(..(((((.....)))))..)..)))))..........)))).((((....)))).. ( -48.40)
>DroSec_CAF1 169422 120 + 1
CGGAUCUAUCUUGAUGUUCUCGGCCACGGCCUGAACGGCGCUGAUCGAAAGCCAUCCCUGCUGCCGCUGGGCAAUAUCCAGCAGUGGCAGGAGUGCUCCCUUCCACUCCGCCUGCGGAUA
.(((...........((((..(((....))).))))((((((((((....)..)))(((((..(.((((((.....)))))).)..)))))))))))....)))..((((....)))).. ( -49.20)
>DroSim_CAF1 165641 120 + 1
CGGAUCUAUCUUGAUGGUCUCGGCCACGGCCUGAACGGCGCUGAUCGAAAGCCAUCCCUGCUGCCGCUGGGCAAUAUCCAGCAGUGGCAGGAGUGCUCCCUUCCACUCCGCCUGCGGAUA
.(((........((((((.(((..((..(((.....)))..))..)))..))))))(((((..(.((((((.....)))))).)..)))))..........)))..((((....)))).. ( -49.00)
>DroYak_CAF1 177656 120 + 1
GGGAUCUAUCUUGAUGGUCUCCGCCACGGCCUGAACAGCGCUGAUCGAAAGCCAUCCCUGCUGCCGCUGGGCAAUGUCCAGGAGCGGCAGGAGUGCUCCCUUCCACUCCGCCCUCGGAUA
((((........(((((..(.((...((((((....)).))))..)).)..)))))((((((((..((((((...))))))..)))))))).....))))......((((....)))).. ( -47.10)
>consensus
CGGAUCUAUCUUGAUGGUCUCGGCCACGGCCUGAACGGCGCUGAUCGAAAGCCAUCCCUGCUGCCGCUGGGCAAUAUCCAGCAGUGGCAGGAGUGCUCCCUUCCACUCCGCCUGCGGAUA
.(((.................(((....))).....((((((((((....)..)))((((((((.((((((.....)))))).))))))))))))))....)))..((((....)))).. (-43.01 = -42.83 +  -0.19)

alignment

secondary structure

dotplot

Window 5

Location	17,285,758 – 17,285,878
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	95.97
Mean single sequence MFE	-48.64
Consensus MFE	-47.49
Energy contribution	-47.43
Covariance contribution	-0.06
Combinations/Pair	1.06
Mean z-score	-2.18
Structure conservation index	0.98
SVM decision value	1.58
SVM RNA-class probability	0.965453
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17285758 120 + 23771897
CUGAUCGAAAGCCAUCCCUGCUGCCGCUGGGCAAUAUCCAGUAGUGGCAGGAGUGCUCCCUUCCACUCCGCCUGCGGAUACCAGGCGAGCAGGGCCUUCACCCUCCGCUGGUUAUCCUUG
......((.((((...(((((..(..(((((.....)))))..)..)))))((((((((((.....((((....))))....))).))))((((......))))..))))))).)).... ( -47.90)
>DroSec_CAF1 169462 120 + 1
CUGAUCGAAAGCCAUCCCUGCUGCCGCUGGGCAAUAUCCAGCAGUGGCAGGAGUGCUCCCUUCCACUCCGCCUGCGGAUACCAGGCGAGCAGGGCCUUCACCCUCCGCUGGUUAUCCUUG
......((.((((...(((((..(.((((((.....)))))).)..)))))((((((((((.....((((....))))....))).))))((((......))))..))))))).)).... ( -49.00)
>DroSim_CAF1 165681 120 + 1
CUGAUCGAAAGCCAUCCCUGCUGCCGCUGGGCAAUAUCCAGCAGUGGCAGGAGUGCUCCCUUCCACUCCGCCUGCGGAUACCAGGCGAGCAGGGCCUUCACCCUCCGCUGGUUAUCCUUG
......((.((((...(((((..(.((((((.....)))))).)..)))))((((((((((.....((((....))))....))).))))((((......))))..))))))).)).... ( -49.00)
>DroYak_CAF1 177696 120 + 1
CUGAUCGAAAGCCAUCCCUGCUGCCGCUGGGCAAUGUCCAGGAGCGGCAGGAGUGCUCCCUUCCACUCCGCCCUCGGAUACCAGGCGAGCAGGGCCUUCACCCUUCGUUGGUUGUCCUUC
..((..((.(((((.((((((((((.((((((...))))))(((.(((.((((((........))))))))))))........))).)))))))..............))))).))..)) ( -48.66)
>consensus
CUGAUCGAAAGCCAUCCCUGCUGCCGCUGGGCAAUAUCCAGCAGUGGCAGGAGUGCUCCCUUCCACUCCGCCUGCGGAUACCAGGCGAGCAGGGCCUUCACCCUCCGCUGGUUAUCCUUG
......((.(((((..((((((((.((((((.....)))))).))))))))..((((((((.....((((....))))....))).)))))(((......))).....))))).)).... (-47.49 = -47.43 +  -0.06)

alignment

secondary structure

dotplot

Window 6

Location	17,285,758 – 17,285,878
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	95.97
Mean single sequence MFE	-51.27
Consensus MFE	-49.17
Energy contribution	-49.67
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.48
Structure conservation index	0.96
SVM decision value	0.17
SVM RNA-class probability	0.618709
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17285758 120 - 23771897
CAAGGAUAACCAGCGGAGGGUGAAGGCCCUGCUCGCCUGGUAUCCGCAGGCGGAGUGGAAGGGAGCACUCCUGCCACUACUGGAUAUUGCCCAGCGGCAGCAGGGAUGGCUUUCGAUCAG
....(((..(((..(.(((((....))))).)(((((((.......)))))))..)))..(..(((..((((((..(..((((.......))))..)..))))))...)))..).))).. ( -48.30)
>DroSec_CAF1 169462 120 - 1
CAAGGAUAACCAGCGGAGGGUGAAGGCCCUGCUCGCCUGGUAUCCGCAGGCGGAGUGGAAGGGAGCACUCCUGCCACUGCUGGAUAUUGCCCAGCGGCAGCAGGGAUGGCUUUCGAUCAG
....(((..(((..(.(((((....))))).)(((((((.......)))))))..)))..(..(((..((((((..(((((((.......)))))))..))))))...)))..).))).. ( -53.60)
>DroSim_CAF1 165681 120 - 1
CAAGGAUAACCAGCGGAGGGUGAAGGCCCUGCUCGCCUGGUAUCCGCAGGCGGAGUGGAAGGGAGCACUCCUGCCACUGCUGGAUAUUGCCCAGCGGCAGCAGGGAUGGCUUUCGAUCAG
....(((..(((..(.(((((....))))).)(((((((.......)))))))..)))..(..(((..((((((..(((((((.......)))))))..))))))...)))..).))).. ( -53.60)
>DroYak_CAF1 177696 120 - 1
GAAGGACAACCAACGAAGGGUGAAGGCCCUGCUCGCCUGGUAUCCGAGGGCGGAGUGGAAGGGAGCACUCCUGCCGCUCCUGGACAUUGCCCAGCGGCAGCAGGGAUGGCUUUCGAUCAG
...((....))......(..((((((((.(((((.(((....((((....)))).....)))))))).((((((.(((.((((.......)))).))).))))))..))))))))..).. ( -49.60)
>consensus
CAAGGAUAACCAGCGGAGGGUGAAGGCCCUGCUCGCCUGGUAUCCGCAGGCGGAGUGGAAGGGAGCACUCCUGCCACUGCUGGAUAUUGCCCAGCGGCAGCAGGGAUGGCUUUCGAUCAG
...((....))......(..((((((((.(((((.(((....((((....)))).....)))))))).((((((..(((((((.......)))))))..))))))..))))))))..).. (-49.17 = -49.67 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:23:40 2006