Locus 9829

Sequence ID	3R_DroMel_CAF1
Location	26,137,454 – 26,137,546
Length	92
Max. P	0.985003

overview

Window 8

Location	26,137,454 – 26,137,546
Length	92
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	81.22
Mean single sequence MFE	-14.82
Consensus MFE	-10.85
Energy contribution	-11.45
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.57
Structure conservation index	0.73
SVM decision value	1.99
SVM RNA-class probability	0.985003
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26137454 92 + 27905053
UUUUUCUUUUUUCAAAUUUGAAUAGAAAUAAAUAAAUGUU----CGUUGCC--UGUUUGCGAUCAUUU-UUUUUUCUAUUCGCCUUCCUAUUGCA-AACU
...................(((((((((.....(((((.(----(((....--.....)))).)))))-...)))))))))..............-.... ( -16.10)
>DroSec_CAF1 127853 87 + 1
UU----AUUUUUCAAAUUUGAAUAGAAAUAAAUAAAUGUU----CGUUGCC-CUGUUUGCGAUCAUUU----UUUCUAUUCGCCUUCCCAUUCCAAAACU
..----.............(((((((((.....(((((.(----(((....-......)))).)))))----)))))))))................... ( -14.30)
>DroSim_CAF1 133626 88 + 1
UU----AUUUUUCAAAUUUGAAUAGAAAUAAAUAAAUGUU----CGUUGCCGAUGUUUGCGAUCAUUU----UUUCUAUUCGCCUUCCCAUUCCAAAACU
..----.............(((((((((.....(((((.(----(((.((....))..)))).)))))----)))))))))................... ( -15.00)
>DroEre_CAF1 136632 78 + 1
---------UUUCAAAUUUGAAUAGAAAUAAAUAAACGUUCGUUCGCUGCC--UGUUUGCGAUCAUUUCUUUUUUCUAUUCGC----------CA-AACU
---------..........(((((((((.(((.(((.(.((((..((....--.))..)))).).))).))))))))))))..----------..-.... ( -14.90)
>DroYak_CAF1 135428 84 + 1
---------UUUCAAAUUUGAAUAGAAAUAAAUAAACGUACGUUCGUUGCC--UGUUUGCGAUCAUUU----UUUCUAUUCGCCUUUCUAUUCCA-AACU
---------..........(((((((((......((((......))))...--.....((((......----.......)))).)))))))))..-.... ( -13.82)
>consensus
UU_____UUUUUCAAAUUUGAAUAGAAAUAAAUAAAUGUU____CGUUGCC__UGUUUGCGAUCAUUU____UUUCUAUUCGCCUUCCCAUUCCA_AACU
...................(((((((((.....(((((.......(((((........))))))))))....)))))))))................... (-10.85 = -11.45 +   0.60)

alignment

secondary structure

dotplot

Window 9

Location	26,137,454 – 26,137,546
Length	92
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	81.22
Mean single sequence MFE	-15.44
Consensus MFE	-10.84
Energy contribution	-10.60
Covariance contribution	-0.24
Combinations/Pair	1.06
Mean z-score	-1.99
Structure conservation index	0.70
SVM decision value	0.84
SVM RNA-class probability	0.864040
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26137454 92 - 27905053
AGUU-UGCAAUAGGAAGGCGAAUAGAAAAAA-AAAUGAUCGCAAACA--GGCAACG----AACAUUUAUUUAUUUCUAUUCAAAUUUGAAAAAAGAAAAA
((((-((.((((((((.((((.((.......-...)).)))).....--(....).----............)))))))))))))).............. ( -14.20)
>DroSec_CAF1 127853 87 - 1
AGUUUUGGAAUGGGAAGGCGAAUAGAAA----AAAUGAUCGCAAACAG-GGCAACG----AACAUUUAUUUAUUUCUAUUCAAAUUUGAAAAAU----AA
.......(((((((((.((((.((....----...)).))))......-(....).----............))))))))).............----.. ( -14.30)
>DroSim_CAF1 133626 88 - 1
AGUUUUGGAAUGGGAAGGCGAAUAGAAA----AAAUGAUCGCAAACAUCGGCAACG----AACAUUUAUUUAUUUCUAUUCAAAUUUGAAAAAU----AA
.......(((((((((.((((.((....----...)).)))).....(((....))----)...........))))))))).............----.. ( -18.00)
>DroEre_CAF1 136632 78 - 1
AGUU-UG----------GCGAAUAGAAAAAAGAAAUGAUCGCAAACA--GGCAGCGAACGAACGUUUAUUUAUUUCUAUUCAAAUUUGAAA---------
....-..----------..(((((((((.((((((((.((((.....--....)))).....))))).))).)))))))))..........--------- ( -14.50)
>DroYak_CAF1 135428 84 - 1
AGUU-UGGAAUAGAAAGGCGAAUAGAAA----AAAUGAUCGCAAACA--GGCAACGAACGUACGUUUAUUUAUUUCUAUUCAAAUUUGAAA---------
....-..(((((((((.((((.((....----...)).)))).....--(....)((((....)))).....)))))))))..........--------- ( -16.20)
>consensus
AGUU_UGGAAUAGGAAGGCGAAUAGAAA____AAAUGAUCGCAAACA__GGCAACG____AACAUUUAUUUAUUUCUAUUCAAAUUUGAAAAA_____AA
...................(((((((((....(((((...(....)...(....).......))))).....)))))))))................... (-10.84 = -10.60 +  -0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:43:08 2006