Locus 1479

Sequence ID	2L_DroMel_CAF1
Location	3,955,830 – 3,955,933
Length	103
Max. P	0.929998

overview

Window 5

Location	3,955,830 – 3,955,933
Length	103
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	76.55
Mean single sequence MFE	-25.50
Consensus MFE	-12.92
Energy contribution	-12.50
Covariance contribution	-0.42
Combinations/Pair	1.14
Mean z-score	-2.27
Structure conservation index	0.51
SVM decision value	1.20
SVM RNA-class probability	0.929998
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3955830 103 + 22407834
---AAAGGGA--UGGGAAAA-CACAAGGGCAAACCAG-GCGGGCAAAAACCAAAUCCCGAAAGUGUACCCAAAUCACUUUUGAAACUAUCUUGCGCCUUGACACAGCCCC
---...(((.--(((.....-).(((((((((...((-..((.......))......((((((((.........))))))))...))...)))).)))))...)).))). ( -25.30)
>DroGri_CAF1 134438 86 + 1
---------------CACAG------CAGCA--GCUC-CAGGACAAAAACCAAAUCCCAAAAGUGUACCCAAAUCACUUUUGAAACUAUCUGGCGCCUUGACGCAGUCCC
---------------...((------(....--))).-..((((.............((((((((.........))))))))..........(((......))).)))). ( -18.40)
>DroSec_CAF1 88896 102 + 1
---A-AAGGA--UGGGAAAA-CACAAGGGCAACCCAG-GCGGGCAAAAACCAAAUCCCGAAAGUGUACCCAAAUCACUUUUGAAACUAUCUUGCGCCUUGACACAGCCCC
---.-.....--.(((....-..((((((((((((..-..)))..............((((((((.........))))))))........)))).)))))......))). ( -26.40)
>DroSim_CAF1 88108 103 + 1
---AAAAGGA--UGGGAAAA-CACAAGGGCAGCCCAG-GCGGGCAAAAACCAAAUCCCGAAAGUGUACCCAAAUCACUUUUGAAACUAUCUUGCGCCUUGACACAGCCCC
---.......--.(((....-..((((((((((((..-..)))).............((((((((.........)))))))).........))).)))))......))). ( -30.30)
>DroMoj_CAF1 152625 100 + 1
----ACAGCAGCUCCAGCAGCAC---CAGCA--GCAGCCAGGACAA-AACCAAAUCCCAAAAGUGUACCCAAAUCACUUUUGAAACUAUCUGGCGCCUUGACGCAGUCCG
----...((.((....)).((..---..)).--)).....((((..-..........((((((((.........))))))))..........(((......))).)))). ( -23.20)
>DroAna_CAF1 109377 99 + 1
GAGGAAAGGA--GGGGCAA-------GG-AGGUGCUU-UUGGGCAAAAACCAAGUCCCAAAAGUGUACCCAAAUCACUUUUGAAACUAUCUUGCGCCUUGACACAGACCC
........((--((.((((-------((-.(((((((-((((((.........).))))))))).....((((.....))))..))).)))))).))))........... ( -29.40)
>consensus
___AAAAGGA__UGGGAAAA_CA___GGGCA__CCAG_GCGGGCAAAAACCAAAUCCCAAAAGUGUACCCAAAUCACUUUUGAAACUAUCUUGCGCCUUGACACAGCCCC
........................................((((.............((((((((.........))))))))......((.........))....)))). (-12.92 = -12.50 +  -0.42)

alignment

secondary structure

dotplot

Window 6

Location	3,955,830 – 3,955,933
Length	103
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	76.55
Mean single sequence MFE	-30.73
Consensus MFE	-19.21
Energy contribution	-18.68
Covariance contribution	-0.53
Combinations/Pair	1.15
Mean z-score	-1.38
Structure conservation index	0.63
SVM decision value	0.25
SVM RNA-class probability	0.651769
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3955830 103 - 22407834
GGGGCUGUGUCAAGGCGCAAGAUAGUUUCAAAAGUGAUUUGGGUACACUUUCGGGAUUUGGUUUUUGCCCGC-CUGGUUUGCCCUUGUG-UUUUCCCA--UCCCUUU---
((((..(((..((((((((((..(((..(.((((((((....)).)))))).)..))).(((....(((...-..)))..)))))))))-))))..))--)))))..--- ( -29.90)
>DroGri_CAF1 134438 86 - 1
GGGACUGCGUCAAGGCGCCAGAUAGUUUCAAAAGUGAUUUGGGUACACUUUUGGGAUUUGGUUUUUGUCCUG-GAGC--UGCUG------CUGUG---------------
(((((.((((....)))).....(((..((((((((((....)).))))))))..)))........)))))(-.(((--....)------)).).--------------- ( -26.20)
>DroSec_CAF1 88896 102 - 1
GGGGCUGUGUCAAGGCGCAAGAUAGUUUCAAAAGUGAUUUGGGUACACUUUCGGGAUUUGGUUUUUGCCCGC-CUGGGUUGCCCUUGUG-UUUUCCCA--UCCUU-U---
((((..(((..((((((((((..(((..(.((((((((....)).)))))).)..))).(((....((((..-..)))).)))))))))-))))..))--)))))-.--- ( -30.40)
>DroSim_CAF1 88108 103 - 1
GGGGCUGUGUCAAGGCGCAAGAUAGUUUCAAAAGUGAUUUGGGUACACUUUCGGGAUUUGGUUUUUGCCCGC-CUGGGCUGCCCUUGUG-UUUUCCCA--UCCUUUU---
((((..(((..((((((((((..(((..(.((((((((....)).)))))).)..))).(((....((((..-..)))).)))))))))-))))..))--)))))..--- ( -32.00)
>DroMoj_CAF1 152625 100 - 1
CGGACUGCGUCAAGGCGCCAGAUAGUUUCAAAAGUGAUUUGGGUACACUUUUGGGAUUUGGUU-UUGUCCUGGCUGC--UGCUG---GUGCUGCUGGAGCUGCUGU----
(((...((..((.((((((((.((((..((((((((((....)).))))))))((((......-..)))).....))--)))))---)))))..))..))..))).---- ( -35.80)
>DroAna_CAF1 109377 99 - 1
GGGUCUGUGUCAAGGCGCAAGAUAGUUUCAAAAGUGAUUUGGGUACACUUUUGGGACUUGGUUUUUGCCCAA-AAGCACCU-CC-------UUGCCCC--UCCUUUCCUC
((((..((((...((.((((((.(((..((((((((((....)).))))))))..)))....))))))))..-..))))..-..-------..)))).--.......... ( -30.10)
>consensus
GGGGCUGUGUCAAGGCGCAAGAUAGUUUCAAAAGUGAUUUGGGUACACUUUCGGGAUUUGGUUUUUGCCCGC_CUGC__UGCCC___UG_UUUUCCCA__UCCUUUU___
.((((.((((....)))).....(((..(.((((((((....)).)))))).)..)))........))))........................................ (-19.21 = -18.68 +  -0.53)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:03:41 2006