Locus 5838

Sequence ID	3L_DroMel_CAF1
Location	15,760,465 – 15,760,634
Length	169
Max. P	0.999407

overview

Window 1

Location	15,760,465 – 15,760,555
Length	90
Sequences	4
Columns	90
Reading direction	forward
Mean pairwise identity	95.37
Mean single sequence MFE	-24.31
Consensus MFE	-21.25
Energy contribution	-21.50
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.73
Structure conservation index	0.87
SVM decision value	0.31
SVM RNA-class probability	0.682337
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15760465 90 + 23771897
AUUUUCUUCUCGGGCUCUUGUGCAAUUUUCCUCUUUGGCAGUGUUUGCGAGUCGCUGGAGGAAAAUGGGAAAAACCCAUUUCCAUUAUAC
......(((((.(((.((((((((.....((.....))...)))..)))))..))).)))))(((((((.....)))))))......... ( -24.40)
>DroSec_CAF1 12063 90 + 1
AUUUUCUUCACGGGCUCUUGUGCAAUUUUCCUCUUUGGCAGUGUUUGCGAGUCGCUGGAGGAAAAUGGGAAAAACCCAUUUCCAUUAUAC
.(((((((((..(((((....((((..((((.....)).))...)))))))))..)))))))))(((((.....)))))........... ( -23.20)
>DroSim_CAF1 12349 90 + 1
AUUUUCUUCACGGGCUCUUGUGCAAUUUUCCUCUUUGGCAGUGUUUGCGAGUCGCUGGAGGAAAAUGGGAAAAACCCAUUUCCAUUAUAC
.(((((((((..(((((....((((..((((.....)).))...)))))))))..)))))))))(((((.....)))))........... ( -23.20)
>DroEre_CAF1 12328 86 + 1
AUUUUCUUCUCGGGCUCCAGUGCAAUUUUCCUCUUUGGCAGUGU----GAGUCGCUGGUGGAAAAUGGGAAAAACCCAUUUCCAUUAUAC
............(((((((.(((..............))).)).----)))))..(((((((((.((((.....)))))))))))))... ( -26.44)
>consensus
AUUUUCUUCACGGGCUCUUGUGCAAUUUUCCUCUUUGGCAGUGUUUGCGAGUCGCUGGAGGAAAAUGGGAAAAACCCAUUUCCAUUAUAC
(((((((((..((((((....(((.....((.....))...)))....))))).)..))))))))).(((((......)))))....... (-21.25 = -21.50 +   0.25)

alignment

secondary structure

dotplot

Window 2

Location	15,760,518 – 15,760,634
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.90
Mean single sequence MFE	-25.17
Consensus MFE	-21.68
Energy contribution	-22.16
Covariance contribution	0.48
Combinations/Pair	1.06
Mean z-score	-2.38
Structure conservation index	0.86
SVM decision value	2.80
SVM RNA-class probability	0.997122
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15760518 116 + 23771897
---GCUGGAGGAAAAUGGGAAAAACCCAUUUCCAUUAUACAAUGCCACAUUUCUCUUUUCCGGUUUAUACCGUUUAGAUCGAUUGCAUUUUAUAGUUUGUUUUAAUGUUU-UUUCUUCCU
---...(((((((((((((.....)))).....((((((.(((((...(((..(((....((((....))))...)))..))).))))).)))))).............)-)))))))). ( -27.80)
>DroSec_CAF1 12116 117 + 1
---GCUGGAGGAAAAUGGGAAAAACCCAUUUCCAUUAUACAAUGCCACAUUUCUCUUUUCCGGUUUAUACCGUUUAGAUCGAUUGCAUUUUAUAGUUUGUUUUAAUGUUUUUUUCUUCCU
---...(((((((((((((.....)))).....((((((.(((((...(((..(((....((((....))))...)))..))).))))).))))))..............))))))))). ( -27.80)
>DroSim_CAF1 12402 116 + 1
---GCUGGAGGAAAAUGGGAAAAACCCAUUUCCAUUAUACAAUGCCACAUUUCUCUUUUCCGGUUUAUACCGUUUAGAUCGAUUGCAUUUUAUAGUUUGUUUUAAUGUUU-UUUCUUCCU
---...(((((((((((((.....)))).....((((((.(((((...(((..(((....((((....))))...)))..))).))))).)))))).............)-)))))))). ( -27.80)
>DroEre_CAF1 12377 116 + 1
---GCUGGUGGAAAAUGGGAAAAACCCAUUUCCAUUAUACAAUGCCACAUUUCUCUUUUCCGGUUUAUACCGUUUAGAUCGAUUGCAUUUUAUAGUUUGUUUUAAUGUUU-UUUCUUCCU
---...((.(((((.((((.....)))))))))((((((.(((((...(((..(((....((((....))))...)))..))).))))).))))))..............-......)). ( -24.10)
>DroAna_CAF1 7081 118 + 1
CCUGCAGGACGAAA-AGAGAAAAACCCAUUUCCAUUAUACAAUGCCACAUUUCUCUCUUCCGGUUUAUACAGUUUAGAUCGAUUGCAUUUUAUAGUUUGUUUUAAUGUUU-UUUUUUCUG
((....))......-(((((((((..((((...((((((.(((((...............(((((((.......)))))))...))))).)))))).......))))..)-)))))))). ( -18.37)
>consensus
___GCUGGAGGAAAAUGGGAAAAACCCAUUUCCAUUAUACAAUGCCACAUUUCUCUUUUCCGGUUUAUACCGUUUAGAUCGAUUGCAUUUUAUAGUUUGUUUUAAUGUUU_UUUCUUCCU
......((((((((...(((((......)))))((((((.(((((...(((..(((....((((....))))...)))..))).))))).))))))...............)))))))). (-21.68 = -22.16 +   0.48)

alignment

secondary structure

dotplot

Window 3

Location	15,760,518 – 15,760,634
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.90
Mean single sequence MFE	-25.49
Consensus MFE	-22.26
Energy contribution	-23.10
Covariance contribution	0.84
Combinations/Pair	1.04
Mean z-score	-2.73
Structure conservation index	0.87
SVM decision value	3.58
SVM RNA-class probability	0.999407
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15760518 116 - 23771897
AGGAAGAAA-AAACAUUAAAACAAACUAUAAAAUGCAAUCGAUCUAAACGGUAUAAACCGGAAAAGAGAAAUGUGGCAUUGUAUAAUGGAAAUGGGUUUUUCCCAUUUUCCUCCAGC---
.(((.....-................((((.(((((......(((...((((....))))....)))........))))).))))..(((((((((.....))))))))).)))...--- ( -27.04)
>DroSec_CAF1 12116 117 - 1
AGGAAGAAAAAAACAUUAAAACAAACUAUAAAAUGCAAUCGAUCUAAACGGUAUAAACCGGAAAAGAGAAAUGUGGCAUUGUAUAAUGGAAAUGGGUUUUUCCCAUUUUCCUCCAGC---
.(((......................((((.(((((......(((...((((....))))....)))........))))).))))..(((((((((.....))))))))).)))...--- ( -27.04)
>DroSim_CAF1 12402 116 - 1
AGGAAGAAA-AAACAUUAAAACAAACUAUAAAAUGCAAUCGAUCUAAACGGUAUAAACCGGAAAAGAGAAAUGUGGCAUUGUAUAAUGGAAAUGGGUUUUUCCCAUUUUCCUCCAGC---
.(((.....-................((((.(((((......(((...((((....))))....)))........))))).))))..(((((((((.....))))))))).)))...--- ( -27.04)
>DroEre_CAF1 12377 116 - 1
AGGAAGAAA-AAACAUUAAAACAAACUAUAAAAUGCAAUCGAUCUAAACGGUAUAAACCGGAAAAGAGAAAUGUGGCAUUGUAUAAUGGAAAUGGGUUUUUCCCAUUUUCCACCAGC---
.((......-................((((.(((((......(((...((((....))))....)))........))))).)))).((((((((((.....)))).))))))))...--- ( -26.54)
>DroAna_CAF1 7081 118 - 1
CAGAAAAAA-AAACAUUAAAACAAACUAUAAAAUGCAAUCGAUCUAAACUGUAUAAACCGGAAGAGAGAAAUGUGGCAUUGUAUAAUGGAAAUGGGUUUUUCUCU-UUUCGUCCUGCAGG
.........-......................................(((((...((..((((((((((((.((.((((....))))....)).))))))))))-))..))..))))). ( -19.80)
>consensus
AGGAAGAAA_AAACAUUAAAACAAACUAUAAAAUGCAAUCGAUCUAAACGGUAUAAACCGGAAAAGAGAAAUGUGGCAUUGUAUAAUGGAAAUGGGUUUUUCCCAUUUUCCUCCAGC___
.(((......................((((.(((((......(((...((((....))))....)))........))))).))))..(((((((((.....))))))))).)))...... (-22.26 = -23.10 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:01:38 2006