Locus 8587

Sequence ID	3L_DroMel_CAF1
Location	22,371,560 – 22,371,724
Length	164
Max. P	0.705121

overview

Window 7

Location	22,371,560 – 22,371,660
Length	100
Sequences	4
Columns	106
Reading direction	reverse
Mean pairwise identity	80.66
Mean single sequence MFE	-38.23
Consensus MFE	-26.36
Energy contribution	-29.30
Covariance contribution	2.94
Combinations/Pair	1.16
Mean z-score	-1.54
Structure conservation index	0.69
SVM decision value	-0.03
SVM RNA-class probability	0.516999
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22371560 100 - 23771897
GGCAGUCACCUCUGCCCGCCGCAGUUUCCACUCCACA------UUAUGUUCCAUGUGGACUGGGAAGUACUGGGAUUGGAAAGGGGUAUGCCAAAUUUGGAUGGAA
((((...((((((..((.((.(((((((((.((((((------(........))))))).)))))...))))))...))..)))))).)))).............. ( -38.80)
>DroSec_CAF1 22701 106 - 1
GGCAGCCACCUCCGCCCACCGCAGUUUCCACUCCACGGAGUGGUUAUGGCCCAUGUGGGCUGGGAAGUACUGGAAUGGGAAAGGGGUAUGCCACAUUUGCAUGGAA
(((((((.(((...((((...((((..((((((....))))))....(((((....))))).......))))...))))..)))))).)))).............. ( -42.50)
>DroSim_CAF1 37096 106 - 1
GGCAGCCACCUCCGCCCACCGCAGUUUCCACUCCACGGAGUGGUUAUGGCCCAUGUGGGCUGGGAAGUACUGGGAUGGGAAAGGGGUAUGCCACAUUUCCAUGGAA
(((((((.(((...((((((.((((..((((((....))))))....(((((....))))).......)))))).))))..)))))).))))....(((....))) ( -46.70)
>DroYak_CAF1 31136 100 - 1
GACUGCUACCUCUGC------UACUUCGCUCUCCACGUAGUGGUUAUGGCCUAUGUGGGCUGGGAUGUACUAAGACUGGGAAGGGGUAUACAACAUUUGCAUGGAA
...((((((((((..------(((.((.(..((((((((..(((....)))))))))))..).)).)))(((....)))..)))))))..........)))..... ( -24.90)
>consensus
GGCAGCCACCUCCGCCCACCGCAGUUUCCACUCCACGGAGUGGUUAUGGCCCAUGUGGGCUGGGAAGUACUGGGAUGGGAAAGGGGUAUGCCACAUUUGCAUGGAA
((((...(((((..((((.(.(((((((((.((((((....(((....)))..)))))).)))))...)))).).))))...))))).)))).............. (-26.36 = -29.30 +   2.94)

alignment

secondary structure

dotplot

Window 8

Location	22,371,623 – 22,371,724
Length	101
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	77.83
Mean single sequence MFE	-35.52
Consensus MFE	-26.17
Energy contribution	-25.29
Covariance contribution	-0.88
Combinations/Pair	1.33
Mean z-score	-1.59
Structure conservation index	0.74
SVM decision value	0.36
SVM RNA-class probability	0.705121
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22371623 101 + 23771897
---UGUGGAGUGGAAACUGCGGCGGGCAGAGGUGACUGCC----------------AGCUGUUUACUCGUUUCUGCUGCGGCUGCACUUCACUUUGAUUUAUCAAUAAAAGCCAAAGUGU
---.((.(((..(((((.(((((.(((((......)))))----------------.)))))......)))))..)).).)).......(((((((..((........))..))))))). ( -33.50)
>DroSec_CAF1 22767 104 + 1
CUCCGUGGAGUGGAAACUGCGGUGGGCGGAGGUGGCUGCC----------------AGCUGUCUACUGGCUGCUGCUGCGGCUGCACUUCACUUUGAUUUAUUAAUAAAAGCCAAAGUUU
(.((((..(((....))))))).)((((((((..((((((----------------(((.(((....))).))))..)))))..).)))).......((((....)))).)))....... ( -37.60)
>DroSim_CAF1 37162 104 + 1
CUCCGUGGAGUGGAAACUGCGGUGGGCGGAGGUGGCUGCC----------------AGCUGUCUACUGGCUGCUGCUGCGGCUGCACUUCACUUUGAUUUAUCAAUAAAAGCCAAAGUUU
(.((((..(((....))))))).)((((((((..((((((----------------(((.(((....))).))))..)))))..).))))...((((....)))).....)))....... ( -39.60)
>DroYak_CAF1 31202 114 + 1
CUACGUGGAGAGCGAAGUA------GCAGAGGUAGCAGUCGCAGAGAUGGGAGAGAAGCUGACUACUGGCUGUUGCUGUGUAUGCACUUCACUUUGAUUUAUCAAUAAAAGACAAAGUUU
....((((((.(((.((((------((((.(((((((((..(............)..)))).)))))..)))))))).....))).)))))).((((....))))............... ( -31.40)
>consensus
CUCCGUGGAGUGGAAACUGCGGUGGGCAGAGGUGGCUGCC________________AGCUGUCUACUGGCUGCUGCUGCGGCUGCACUUCACUUUGAUUUAUCAAUAAAAGCCAAAGUUU
....((((((((.(..((((((((.((((.((((((.((..................)).).)))))..)))))))))))).).)))))))).((((....))))............... (-26.17 = -25.29 +  -0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:19:40 2006