Locus 7228

Sequence ID	3L_DroMel_CAF1
Location	19,376,356 – 19,376,495
Length	139
Max. P	0.916701

overview

Window 1

Location	19,376,356 – 19,376,455
Length	99
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.89
Mean single sequence MFE	-26.63
Consensus MFE	-14.11
Energy contribution	-13.92
Covariance contribution	-0.19
Combinations/Pair	1.19
Mean z-score	-3.04
Structure conservation index	0.53
SVM decision value	0.71
SVM RNA-class probability	0.829221
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19376356 99 - 23771897
GGCACU--UUGUUUGC-----UCU-ACGCAUUACGACAAAUAUUUGCCCAUCGGACAACAUAUUCU--UGUGUUGUC--------UUCUGGCGUGUUCUGCCGUAUUUUACUCUGCU---
((((.(--((((((((-----...-..)))....)))))).....(((((..((((((((((....--)))))))))--------)..))).))....))))...............--- ( -27.50)
>DroSec_CAF1 9257 99 - 1
GGCACU--UUGUUUGC-----UCU-ACGCAUUACGACAAAUAUUUGCCCAUCGGACAACAUAUUCU--UGUGUUGUC--------UUCUGGCUUGUUCUGCCGUAUUUUACUCUGCU---
((((.(--((((((((-----...-..)))....)))))).....(((....((((((((((....--)))))))))--------)...)))......))))...............--- ( -26.70)
>DroSim_CAF1 6635 102 - 1
GGCACU--UUGUUUGC-----UCU-ACGCAUUACGACAAAUAUUUGCCCAUCGGACAACAUAUUCU--UGUGUUGUC--------UUCUGGCUUGUUCUGCCGUAUUUUACUCUGCUCUG
((((.(--((((((((-----...-..)))....)))))).....(((....((((((((((....--)))))))))--------)...)))......)))).................. ( -26.70)
>DroEre_CAF1 13229 99 - 1
GGCACU--UUGUUUGC-----UCU-ACGCAUUACGACAAAUAUUUGCCCAUCGGACAACAUAUUCU--UGUGUUGUC--------UUCUGGGCUGUUCUGCCGUAUUUUACUCUGCU---
((((.(--((((((((-----...-..)))....)))))).....(((((..((((((((((....--)))))))))--------)..))))).....))))...............--- ( -33.00)
>DroWil_CAF1 30771 117 - 1
UGUAGUUGUUGUUUGCCUACUUCUAACGCAUUACGGCAAAUAUUUGCGCAAUGGACAACAUAUUCUCUUAGGUUGUAUGUCUGUGUACUUACUUAUCUUUCCGUUUUCUAUUCUGUU---
.((((....((((((((((...(....)...)).)))))))).))))(.((((((.(((.........(((((.((((......))))..))))).......))).)))))))....--- ( -19.59)
>DroAna_CAF1 15792 98 - 1
GGCACU--CUGUUUGC-----UUU-ACGCAUUACGACAAAUAUUUGCCCAUCGGACAACAUAUUCU--UGUGUUGUC--------UUCUGGGUUUUUUU-UUUUGGUUUAUUCGGUC---
(((...--.(((.(((-----...-..)))..))).((((.....(((((..((((((((((....--)))))))))--------)..)))))......-.)))).........)))--- ( -26.30)
>consensus
GGCACU__UUGUUUGC_____UCU_ACGCAUUACGACAAAUAUUUGCCCAUCGGACAACAUAUUCU__UGUGUUGUC________UUCUGGCUUGUUCUGCCGUAUUUUACUCUGCU___
((((....((((((((...........)))....))))).....)))).....(((((((((......)))))))))........................................... (-14.11 = -13.92 +  -0.19)

alignment

secondary structure

dotplot

Window 2

Location	19,376,388 – 19,376,495
Length	107
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	95.45
Mean single sequence MFE	-20.24
Consensus MFE	-18.55
Energy contribution	-18.72
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-1.40
Structure conservation index	0.92
SVM decision value	1.11
SVM RNA-class probability	0.916701
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19376388 107 - 23771897
CCGCUUCGAGACUUUCCCCAAAUAUAUUUCCAUCAUCAGAGGCACUUUGUUUGCUCUACGCAUUACGACAAAUAUUUGCCCAUCGGACAACAUAUUCUUGUGUUGUC
......(((.......................((....))((((.(((((((((.....)))....))))))....))))..)))(((((((((....))))))))) ( -20.10)
>DroSec_CAF1 9289 107 - 1
CCGUUUCGAGUCUUUCCCCAAAUAUAUUUCCAUCAUCAGAGGCACUUUGUUUGCUCUACGCAUUACGACAAAUAUUUGCCCAUCGGACAACAUAUUCUUGUGUUGUC
......(((.......................((....))((((.(((((((((.....)))....))))))....))))..)))(((((((((....))))))))) ( -20.10)
>DroSim_CAF1 6670 107 - 1
CCGCUUCGAGUCUUUCCCCAAAUAUAUUUCCAUCAUCAGAGGCACUUUGUUUGCUCUACGCAUUACGACAAAUAUUUGCCCAUCGGACAACAUAUUCUUGUGUUGUC
......(((.......................((....))((((.(((((((((.....)))....))))))....))))..)))(((((((((....))))))))) ( -20.10)
>DroEre_CAF1 13261 107 - 1
CCGCUUCGAGACUUUCCCCAAAUAUAUUUCCACCAUCAGAGGCACUUUGUUUGCUCUACGCAUUACGACAAAUAUUUGCCCAUCGGACAACAUAUUCUUGUGUUGUC
......(((...................((........))((((.(((((((((.....)))....))))))....))))..)))(((((((((....))))))))) ( -19.50)
>DroYak_CAF1 43598 107 - 1
CCGCUUCGAGACUUUCCCCAAAUAUAUUUCCAUCAUCAGAGGCACUUUGUUUGCUCUACGCAUUACGACAAAUAUUUGCCCAUCGGACAACAUAUUCUUGUGUUGUC
......(((.......................((....))((((.(((((((((.....)))....))))))....))))..)))(((((((((....))))))))) ( -20.10)
>DroAna_CAF1 15823 107 - 1
GCUCUCGGAGACUUUUCCCAAAUAUAUUCCCAUCAUCUCCGGCACUCUGUUUGCUUUACGCAUUACGACAAAUAUUUGCCCAUCGGACAACAUAUUCUUGUGUUGUC
......(((((........................)))))((((...(((((((.....)))....))))......)))).....(((((((((....))))))))) ( -21.56)
>consensus
CCGCUUCGAGACUUUCCCCAAAUAUAUUUCCAUCAUCAGAGGCACUUUGUUUGCUCUACGCAUUACGACAAAUAUUUGCCCAUCGGACAACAUAUUCUUGUGUUGUC
........................................((((.(((((((((.....)))....))))))....)))).....(((((((((....))))))))) (-18.55 = -18.72 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:41:36 2006