Locus 3597

Sequence ID	3L_DroMel_CAF1
Location	10,584,042 – 10,584,148
Length	106
Max. P	0.998977

overview

Window 8

Location	10,584,042 – 10,584,148
Length	106
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	69.91
Mean single sequence MFE	-22.53
Consensus MFE	-8.91
Energy contribution	-10.60
Covariance contribution	1.69
Combinations/Pair	1.23
Mean z-score	-2.18
Structure conservation index	0.40
SVM decision value	1.68
SVM RNA-class probability	0.971457
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10584042 106 + 23771897
AGCUUAAAGGAAAUUUUCAGGCUUGAUAACUUACGAUUUCGAUUUACGACACUAAAAUUAAGACGUCUUACUGCCACAGCAAA--AAAGCUGAG---UCCUGGAAUCAACU
(((((((((....)))).))))).................(((((..(((........((((....))))......((((...--...)))).)---))...))))).... ( -17.00)
>DroSec_CAF1 463506 106 + 1
GACUGAAAGGAAAUUUUCAGGCUUGAUAACUUCCGCUUUCGAUUUACGACACUAAAAUUAAGACAUUUUACUGUCAUAACAUA--AAAGCAGAG---UCUUAGAAUCAAGC
..(((((((....)))))))(((((((.((((..(((((....(((.((((.((((((......)))))).)))).)))....--))))).)))---)......))))))) ( -24.60)
>DroSim_CAF1 465875 106 + 1
AACUAAAAGGAAAUUUUCAGGCUUGAUAAUUUCCGAUUUCUAUUUACGACACUAAAAUUAACAUGUUUAACUGUUACAGCAAA--AAAGCGAAG---UCCUGGAAUCAAAC
........(((((((.((......)).)))))))((((((.......(((........(((((........)))))..((...--...))...)---))..)))))).... ( -18.40)
>DroEre_CAF1 472933 100 + 1
AGCUG-----AAAUUUGCAGGCUUAAUAACUUUC------GAUUUAUGACAAUAAAAUGAGGGCAUUUUGCUGUCACAACCAAAGAAAGCGGUGAUAUCUGCAAGUCAAGA
..((.-----..(((((((((....((..(((((------......(((((.(((((((....))))))).)))))........)))))..))....)))))))))..)). ( -25.44)
>DroYak_CAF1 474965 86 + 1
GACUGAAAGGAAAUUUUCAGGCUUGAUAACUUCCGAUGCCGAUUUACGGCAAUAAAAUUAAGGCAUUUUACUGCCAA-------------------------AAGUCAAGC
..(((((((....)))))))(((((((.........(((((.....)))))..........((((......))))..-------------------------..))))))) ( -27.20)
>consensus
AACUGAAAGGAAAUUUUCAGGCUUGAUAACUUCCGAUUUCGAUUUACGACACUAAAAUUAAGACAUUUUACUGUCACAACAAA__AAAGCGGAG___UCCUGGAAUCAAGC
..(((((((....)))))))(((((((......((....))......((((.((((((......)))))).)))).............................))))))) ( -8.91 = -10.60 +   1.69)

alignment

secondary structure

dotplot

Window 9

Location	10,584,042 – 10,584,148
Length	106
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	69.91
Mean single sequence MFE	-25.92
Consensus MFE	-12.16
Energy contribution	-13.20
Covariance contribution	1.04
Combinations/Pair	1.30
Mean z-score	-2.72
Structure conservation index	0.47
SVM decision value	3.31
SVM RNA-class probability	0.998977
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10584042 106 - 23771897
AGUUGAUUCCAGGA---CUCAGCUUU--UUUGCUGUGGCAGUAAGACGUCUUAAUUUUAGUGUCGUAAAUCGAAAUCGUAAGUUAUCAAGCCUGAAAAUUUCCUUUAAGCU
((..((((.((((.---((((((...--...)))).((((.(((((........))))).)))).......((...(....)...)).))))))..))))..))....... ( -18.70)
>DroSec_CAF1 463506 106 - 1
GCUUGAUUCUAAGA---CUCUGCUUU--UAUGUUAUGACAGUAAAAUGUCUUAAUUUUAGUGUCGUAAAUCGAAAGCGGAAGUUAUCAAGCCUGAAAAUUUCCUUUCAGUC
(((((((.....((---(((((((((--(...((((((((.((((((......)))))).))))))))...)))))))).)))))))))))((((((......)))))).. ( -39.40)
>DroSim_CAF1 465875 106 - 1
GUUUGAUUCCAGGA---CUUCGCUUU--UUUGCUGUAACAGUUAAACAUGUUAAUUUUAGUGUCGUAAAUAGAAAUCGGAAAUUAUCAAGCCUGAAAAUUUCCUUUUAGUU
((((((((((..((---(...((...--...))..(((((........)))))........))).......(....))))....)))))))((((((......)))))).. ( -16.40)
>DroEre_CAF1 472933 100 - 1
UCUUGACUUGCAGAUAUCACCGCUUUCUUUGGUUGUGACAGCAAAAUGCCCUCAUUUUAUUGUCAUAAAUC------GAAAGUUAUUAAGCCUGCAAAUUU-----CAGCU
..((((.((((((........((((((.....(((((((((.((((((....)))))).)))))))))...------))))))........))))))...)-----))).. ( -25.69)
>DroYak_CAF1 474965 86 - 1
GCUUGACUU-------------------------UUGGCAGUAAAAUGCCUUAAUUUUAUUGCCGUAAAUCGGCAUCGGAAGUUAUCAAGCCUGAAAAUUUCCUUUCAGUC
((((((...-------------------------..((((......)))).(((((((..(((((.....)))))...)))))))))))))((((((......)))))).. ( -29.40)
>consensus
GCUUGAUUCCAAGA___CUCCGCUUU__UUUGCUGUGACAGUAAAAUGUCUUAAUUUUAGUGUCGUAAAUCGAAAUCGGAAGUUAUCAAGCCUGAAAAUUUCCUUUCAGUU
.................................(((((((.((((((......)))))).)))))))..........(((((((.(((....))).)))))))........ (-12.16 = -13.20 +   1.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:01:53 2006