Locus 231

Sequence ID	3L_DroMel_CAF1
Location	633,445 – 633,591
Length	146
Max. P	0.905425

overview

Window 2

Location	633,445 – 633,553
Length	108
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	78.55
Mean single sequence MFE	-20.98
Consensus MFE	-12.78
Energy contribution	-13.94
Covariance contribution	1.16
Combinations/Pair	1.14
Mean z-score	-2.00
Structure conservation index	0.61
SVM decision value	0.86
SVM RNA-class probability	0.868306
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 633445 108 - 23771897
AAAAAAUUCCAC-CACAACAAAUACUGCUCA----AUCUAUUCAGUAAUCAGUGCGCGUAAGCACAAAGCUGUGUGCAUUUAUGGUUGAAUAAAAAUAUGAAA-------AAGUAUCAGC
............-........(((((..(((----...(((((((..((.(((((((...(((.....)))..))))))).))..)))))))......)))..-------.))))).... ( -20.80)
>DroSec_CAF1 752 117 - 1
AA--AAUUCCAC-CAUAACAAAUAUUGCUCAAUCAAUCUAUUCAGUAAUCAGUGCGCGUAAGCACAAAGCUGUGUGCACUUAUGGUUGAAUAAAAAUAUGGAAAACAUUAAAGUAUCAGC
..--.((((.((-((((......((((((.(((......))).)))))).(((((((...(((.....)))..))))))))))))).))))............................. ( -25.10)
>DroSim_CAF1 932 113 - 1
AA--AAUUCCAC-CACAACAAAUAUUACUCA----AUCUAUUCAGUAAUCAGUGCGCGUAAGCACAAAGCUGUGUGCACUUAUGGUUGAAUAAAAAUAUGGAAAACAUUAAAGUAUCAGC
..--..(((((.-..........(((....)----)).(((((((..((.(((((((...(((.....)))..))))))).))..)))))))......)))))................. ( -21.80)
>DroEre_CAF1 3621 101 - 1
AA--AAUUCCACAAAAAAC----AUUGCUCA----UCCUAUUCAGUAAUCAGUAGGCGUAAGCGCAGAGCUAUGAGCAUUUGGAGUUGAAUAAAAAUAUGAAAAACAUCAU---------
..--(((((((.......(----((.((((.----..(((((.(....).)))))(((....))).)))).)))......)))))))..........((((......))))--------- ( -21.12)
>DroYak_CAF1 936 114 - 1
AG--AAUUCAGUAGAAAACAAAUAUUGCUUA----UACUACUCAGUAAUCAGUACGCGUAAGCACAAAGCUAUGACCAUUUAGAGUUGAAUAGAAAUAUGAAAAACAUUCAAGUAUCAAC
..--.....................((((((----..(((((.(....).)))).)..))))))(((..(((........)))..)))....((.((.((((.....)))).)).))... ( -16.10)
>consensus
AA__AAUUCCAC_CAAAACAAAUAUUGCUCA____AUCUAUUCAGUAAUCAGUGCGCGUAAGCACAAAGCUGUGUGCAUUUAUGGUUGAAUAAAAAUAUGAAAAACAUUAAAGUAUCAGC
......................................(((((((..((.((((((((((.((.....)))))))))))).))..)))))))............................ (-12.78 = -13.94 +   1.16)

alignment

secondary structure

dotplot

Window 3

Location	633,478 – 633,591
Length	113
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	83.44
Mean single sequence MFE	-26.46
Consensus MFE	-19.29
Energy contribution	-19.09
Covariance contribution	-0.20
Combinations/Pair	1.14
Mean z-score	-2.18
Structure conservation index	0.73
SVM decision value	1.04
SVM RNA-class probability	0.905425
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 633478 113 - 23771897
UGUGUUCUUUAAAUAGCUGUUGAUAGUGCUGAUUAGGUAAAAAAUUCCAC-CACAACAAAUACUGCUCA----AUCUAUUCAGUAAUCAGUGCGCGUAAGCACAAAGCUGUGUGCAUU
.((((.......((((((.(((...(..(((((..(((..........))-)........(((((....----.......))))))))))..)((....)).)))))))))..)))). ( -25.60)
>DroSec_CAF1 792 114 - 1
AUUUUUUUAUAAAUAGCUGU-GAUAGUGCUGAUUAGGUAA--AAUUCCAC-CAUAACAAAUAUUGCUCAAUCAAUCUAUUCAGUAAUCAGUGCGCGUAAGCACAAAGCUGUGUGCACU
...............((((.-(((((...(((((..((((--.(((....-.......))).))))..)))))..)))))))))....(((((((...(((.....)))..))))))) ( -26.90)
>DroSim_CAF1 972 110 - 1
AGUUUUUUAUAAAUAGCUGU-GAUAGUGCUGAUUAGGUAA--AAUUCCAC-CACAACAAAUAUUACUCA----AUCUAUUCAGUAAUCAGUGCGCGUAAGCACAAAGCUGUGUGCACU
............((((((.(-(...(..((((((((((..--......))-).................----..((....)))))))))..)((....)).)).))))))....... ( -24.10)
>DroEre_CAF1 3652 107 - 1
AGCGAUUUAUAAAUAGCUGU-GAUAGUGCUGAUUAGGAAA--AAUUCCACAAAAAAC----AUUGCUCA----UCCUAUUCAGUAAUCAGUAGGCGUAAGCGCAGAGCUAUGAGCAUU
.((.........((((((.(-(....((((((.(((((..--...............----........----))))).))))))........((....)).)).))))))..))... ( -25.41)
>DroYak_CAF1 976 111 - 1
AGCGAUUUAUAAAUAGCUGU-GAUAGUGCUGAUUAGGUAG--AAUUCAGUAGAAAACAAAUAUUGCUUA----UACUACUCAGUAAUCAGUACGCGUAAGCACAAAGCUAUGACCAUU
............((((((.(-(...(((((((((((((((--.((.(((((.........)))))...)----).)))))...))))))))))((....)).)).))))))....... ( -30.30)
>consensus
AGUGUUUUAUAAAUAGCUGU_GAUAGUGCUGAUUAGGUAA__AAUUCCAC_CAAAACAAAUAUUGCUCA____AUCUAUUCAGUAAUCAGUGCGCGUAAGCACAAAGCUGUGUGCAUU
............((((((...(((..((((((.(((((...................................))))).))))))))).....((....))....))))))....... (-19.29 = -19.09 +  -0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:36:56 2006