Locus 1362

Sequence ID	2L_DroMel_CAF1
Location	3,609,705 – 3,609,797
Length	92
Max. P	0.940374

overview

Window 6

Location	3,609,705 – 3,609,797
Length	92
Sequences	6
Columns	96
Reading direction	forward
Mean pairwise identity	88.44
Mean single sequence MFE	-20.77
Consensus MFE	-15.91
Energy contribution	-16.92
Covariance contribution	1.00
Combinations/Pair	1.20
Mean z-score	-3.03
Structure conservation index	0.77
SVM decision value	0.47
SVM RNA-class probability	0.748793
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3609705 92 + 22407834
-UUUUGGUCUGCUC--UUUUUUUGGACCAUUGCCAUGCAUAUUUUAUGGUAUUU-UUUCGUGUUUCCACGAAUAAAAUUAGAUUUUUUAGAGCAGA
-......(((((((--(...(((((.....(((((((.......)))))))(((-.((((((....)))))).))).)))))......)))))))) ( -23.70)
>DroSec_CAF1 77522 93 + 1
UUCAUUGUCUGCUC--UUUUUUUGGACCAUUGCCAUGCAUAUUUUAUGGUAUUU-UUUCGUGUUUCCACGAAUAAAAUUAGAUUUUUUAGAGCAGA
.......(((((((--(...(((((.....(((((((.......)))))))(((-.((((((....)))))).))).)))))......)))))))) ( -23.70)
>DroSim_CAF1 82801 93 + 1
UUCAUUGUCUGCUC--UUUUUUUGGACCAUUGCCAUGCAUAUUUUAUGGUAUUU-UUUCGUGUUUCCACGAAUAAAAUUAGAUUUUUUAGAGCAGA
.......(((((((--(...(((((.....(((((((.......)))))))(((-.((((((....)))))).))).)))))......)))))))) ( -23.70)
>DroEre_CAF1 78885 92 + 1
CUCAUUGUCUGCUC---UUUUUUGGACCAUUGCCAUGCAUAUUUUAUGGCAUUU-UUUCGUUUUUCCACGAAUAAAAUUAGAUUUUUUAGAGCACA
.........(((((---(............(((((((.......)))))))(((-.(((((......))))).)))............)))))).. ( -18.50)
>DroYak_CAF1 81233 95 + 1
UUCAUUGUCUGCUCAUUUUUUUUGGACCAUUGCCGUGCAUAUUUUAUGGUAUUU-UUUCGUGUUUCCACGAAUAAAAUUAGAUUUUUUAGAGCAGA
.......(((((((................(((((((.......)))))))(((-.((((((....)))))).))).............))))))) ( -23.00)
>DroAna_CAF1 82320 83 + 1
UUCAAUUU-----U--UUUCUUCGGU------CCAUGCAUAUUUUAUGGUAUUUUUUUCGUGUUUCUACGAAAAAAAUUAGAUUUUUUAGAGCAAA
........-----.--.((((.....------(((((.......))))).((((((((((((....))))))))))))..........)))).... ( -12.00)
>consensus
UUCAUUGUCUGCUC__UUUUUUUGGACCAUUGCCAUGCAUAUUUUAUGGUAUUU_UUUCGUGUUUCCACGAAUAAAAUUAGAUUUUUUAGAGCAGA
.......(((((((................(((((((.......))))))).....((((((....)))))).................))))))) (-15.91 = -16.92 +   1.00)

alignment

secondary structure

dotplot

Window 7

Location	3,609,705 – 3,609,797
Length	92
Sequences	6
Columns	96
Reading direction	reverse
Mean pairwise identity	88.44
Mean single sequence MFE	-22.78
Consensus MFE	-14.57
Energy contribution	-16.23
Covariance contribution	1.67
Combinations/Pair	1.00
Mean z-score	-5.05
Structure conservation index	0.64
SVM decision value	1.31
SVM RNA-class probability	0.940374
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3609705 92 - 22407834
UCUGCUCUAAAAAAUCUAAUUUUAUUCGUGGAAACACGAAA-AAAUACCAUAAAAUAUGCAUGGCAAUGGUCCAAAAAAA--GAGCAGACCAAAA-
((((((((..........(((((.((((((....)))))))-))))(((((......(((...))))))))........)--)))))))......- ( -26.60)
>DroSec_CAF1 77522 93 - 1
UCUGCUCUAAAAAAUCUAAUUUUAUUCGUGGAAACACGAAA-AAAUACCAUAAAAUAUGCAUGGCAAUGGUCCAAAAAAA--GAGCAGACAAUGAA
((((((((..........(((((.((((((....)))))))-))))(((((......(((...))))))))........)--)))))))....... ( -26.60)
>DroSim_CAF1 82801 93 - 1
UCUGCUCUAAAAAAUCUAAUUUUAUUCGUGGAAACACGAAA-AAAUACCAUAAAAUAUGCAUGGCAAUGGUCCAAAAAAA--GAGCAGACAAUGAA
((((((((..........(((((.((((((....)))))))-))))(((((......(((...))))))))........)--)))))))....... ( -26.60)
>DroEre_CAF1 78885 92 - 1
UGUGCUCUAAAAAAUCUAAUUUUAUUCGUGGAAAAACGAAA-AAAUGCCAUAAAAUAUGCAUGGCAAUGGUCCAAAAAA---GAGCAGACAAUGAG
..((((((................(((((......))))).-...((((((.........))))))............)---)))))......... ( -19.50)
>DroYak_CAF1 81233 95 - 1
UCUGCUCUAAAAAAUCUAAUUUUAUUCGUGGAAACACGAAA-AAAUACCAUAAAAUAUGCACGGCAAUGGUCCAAAAAAAAUGAGCAGACAAUGAA
(((((((...........(((((.((((((....)))))))-))))(((((......(((...))))))))...........)))))))....... ( -25.20)
>DroAna_CAF1 82320 83 - 1
UUUGCUCUAAAAAAUCUAAUUUUUUUCGUAGAAACACGAAAAAAAUACCAUAAAAUAUGCAUGG------ACCGAAGAAA--A-----AAAUUGAA
((((.((((.........(((((((((((......)))))))))))..((((...))))..)))------).))))....--.-----........ ( -12.20)
>consensus
UCUGCUCUAAAAAAUCUAAUUUUAUUCGUGGAAACACGAAA_AAAUACCAUAAAAUAUGCAUGGCAAUGGUCCAAAAAAA__GAGCAGACAAUGAA
(((((((.................((((((....)))))).......((((.........))))..................)))))))....... (-14.57 = -16.23 +   1.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:00:40 2006