Locus 121

Sequence ID	X_DroMel_CAF1
Location	492,868 – 493,013
Length	145
Max. P	0.999396

overview

Window 8

Location	492,868 – 492,974
Length	106
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	96.60
Mean single sequence MFE	-35.62
Consensus MFE	-34.90
Energy contribution	-34.90
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.88
Structure conservation index	0.98
SVM decision value	3.04
SVM RNA-class probability	0.998215
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 492868 106 + 22224390
ACGGGGCCCUCAGGCAGAGAAAGAGGGCGAAAGCAAGCUACAAGCGGGUGCGAGCGAGAGCGCGCGCUUGCCUCACGCACAUAUAUAUAAAUCUGUACAUACAUAU
(((((((((((...........))))))........((.....(((((((((.((....)).))))))))).....)).............))))).......... ( -36.50)
>DroSec_CAF1 5745 104 + 1
ACGGGGCCCUCAGGCAGAGAAA--GGGCGAAAGCAAGCUACAAGCGGGUGCGAGCGAGAGCGCGCGCUUGCCUCACGCAUAUAUAUAUAAAUCUGUACAUACAUAU
((((((((....))).(((...--..((....)).........(((((((((.((....)).)))))))))))).................))))).......... ( -35.30)
>DroSim_CAF1 5631 104 + 1
ACGGGGCCCUCAGGCAGAGAAA--GGGCGAAAGCAAGCUACAAGCGGGUGCGAGCGAGAGCGCGCGCUUGCCUCACGCAUAUAUAUAUAAAUCUGUACAUACAUAU
((((((((....))).(((...--..((....)).........(((((((((.((....)).)))))))))))).................))))).......... ( -35.30)
>DroEre_CAF1 6439 106 + 1
ACGGGGCCCGCAGGCAGAGAGAGAGGGCGAGAGCAAGCUACAAGCGGGUGCGAGCGAGAGCGCGCGCUUGCCUCACGCACAUAUAUAUAAAUCUGUACAUACAUAU
((((((((....)))...(((((...((....))...))....(((((((((.((....)).)))))))))))).................))))).......... ( -35.50)
>DroYak_CAF1 5895 106 + 1
ACGGGGCCCGCAGGCAGAGAGAGAGGGCGAGAGCAAGCUACAAGCGGGUGCGAGCGAGAGCGCGCGCUUGCCUCACGCACAUAUAUAUAAAUCUGUACAUACAUAU
((((((((....)))...(((((...((....))...))....(((((((((.((....)).)))))))))))).................))))).......... ( -35.50)
>consensus
ACGGGGCCCUCAGGCAGAGAAAGAGGGCGAAAGCAAGCUACAAGCGGGUGCGAGCGAGAGCGCGCGCUUGCCUCACGCACAUAUAUAUAAAUCUGUACAUACAUAU
((((((((....))).(((.......((....)).........(((((((((.((....)).)))))))))))).................))))).......... (-34.90 = -34.90 +  -0.00)

alignment

secondary structure

dotplot

Window 9

Location	492,868 – 492,974
Length	106
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	96.60
Mean single sequence MFE	-35.12
Consensus MFE	-32.86
Energy contribution	-32.38
Covariance contribution	-0.48
Combinations/Pair	1.06
Mean z-score	-1.92
Structure conservation index	0.94
SVM decision value	2.69
SVM RNA-class probability	0.996392
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 492868 106 - 22224390
AUAUGUAUGUACAGAUUUAUAUAUAUGUGCGUGAGGCAAGCGCGCGCUCUCGCUCGCACCCGCUUGUAGCUUGCUUUCGCCCUCUUUCUCUGCCUGAGGGCCCCGU
(((((((((((......)))))))))))(((.((((((((((((.((....)).)))((......)).))))))))).((((((...........))))))..))) ( -37.00)
>DroSec_CAF1 5745 104 - 1
AUAUGUAUGUACAGAUUUAUAUAUAUAUGCGUGAGGCAAGCGCGCGCUCUCGCUCGCACCCGCUUGUAGCUUGCUUUCGCCC--UUUCUCUGCCUGAGGGCCCCGU
(((((((((((......)))))))))))(((.((((((((((((.((....)).)))((......)).))))))))).((((--((.........))))))..))) ( -34.90)
>DroSim_CAF1 5631 104 - 1
AUAUGUAUGUACAGAUUUAUAUAUAUAUGCGUGAGGCAAGCGCGCGCUCUCGCUCGCACCCGCUUGUAGCUUGCUUUCGCCC--UUUCUCUGCCUGAGGGCCCCGU
(((((((((((......)))))))))))(((.((((((((((((.((....)).)))((......)).))))))))).((((--((.........))))))..))) ( -34.90)
>DroEre_CAF1 6439 106 - 1
AUAUGUAUGUACAGAUUUAUAUAUAUGUGCGUGAGGCAAGCGCGCGCUCUCGCUCGCACCCGCUUGUAGCUUGCUCUCGCCCUCUCUCUCUGCCUGCGGGCCCCGU
(((((((((((......)))))))))))(((.((((((((((((.((....)).)))((......)).)))))).)))((((.(...........).))))..))) ( -34.40)
>DroYak_CAF1 5895 106 - 1
AUAUGUAUGUACAGAUUUAUAUAUAUGUGCGUGAGGCAAGCGCGCGCUCUCGCUCGCACCCGCUUGUAGCUUGCUCUCGCCCUCUCUCUCUGCCUGCGGGCCCCGU
(((((((((((......)))))))))))(((.((((((((((((.((....)).)))((......)).)))))).)))((((.(...........).))))..))) ( -34.40)
>consensus
AUAUGUAUGUACAGAUUUAUAUAUAUGUGCGUGAGGCAAGCGCGCGCUCUCGCUCGCACCCGCUUGUAGCUUGCUUUCGCCCUCUUUCUCUGCCUGAGGGCCCCGU
(((((((((((......)))))))))))..((((((((((((((.((....)).)))((......)).)))))).)))))...........(((....)))..... (-32.86 = -32.38 +  -0.48)

alignment

secondary structure

dotplot

Window 0

Location	492,907 – 493,013
Length	106
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	95.46
Mean single sequence MFE	-27.60
Consensus MFE	-25.56
Energy contribution	-25.32
Covariance contribution	-0.24
Combinations/Pair	1.05
Mean z-score	-2.24
Structure conservation index	0.93
SVM decision value	3.57
SVM RNA-class probability	0.999396
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 492907 106 + 22224390
ACAAGCGGGUGCGAGCGAGAGCGCGCGCUUGCCUCACGCACAUAUAUAUAAAUCUGUACAUACAUAUAGUAUCAGAAGAAAAAACUAAAGCCGCUAUUCGAUUUAC
...((((((((((.((....)).))))).(((.....)))............(((((((.........))).))))..............)))))........... ( -26.40)
>DroSec_CAF1 5782 104 + 1
ACAAGCGGGUGCGAGCGAGAGCGCGCGCUUGCCUCACGCAUAUAUAUAUAAAUCUGUACAUACAUAUAGUAUCAGAA-AAAAGACUAAAGCCGCUAU-CGAUUUAC
...((((((((((.((....)).))))).(((.....)))............(((((((.........))).)))).-............)))))..-........ ( -26.50)
>DroSim_CAF1 5668 105 + 1
ACAAGCGGGUGCGAGCGAGAGCGCGCGCUUGCCUCACGCAUAUAUAUAUAAAUCUGUACAUACAUAUAGUAUCAGAA-AAAAGACUAAAGCCGCUAUUCGAAUAAC
...((((((((((.((....)).))))).(((.....)))............(((((((.........))).)))).-............)))))........... ( -26.50)
>DroEre_CAF1 6478 104 + 1
ACAAGCGGGUGCGAGCGAGAGCGCGCGCUUGCCUCACGCACAUAUAUAUAAAUCUGUACAUACAUAUAGUAUCAGAAAAAAAGACUAAAGUCGCUAUUCGAUUU--
....(((((((((.((....)).))))))))).....((.............(((((((.........))).))))......(((....)))))..........-- ( -29.30)
>DroYak_CAF1 5934 104 + 1
ACAAGCGGGUGCGAGCGAGAGCGCGCGCUUGCCUCACGCACAUAUAUAUAAAUCUGUACAUACAUAUAGUAUCAGAAAAAAAGACUAAAGUCGCUAUUCGAUUU--
....(((((((((.((....)).))))))))).....((.............(((((((.........))).))))......(((....)))))..........-- ( -29.30)
>consensus
ACAAGCGGGUGCGAGCGAGAGCGCGCGCUUGCCUCACGCACAUAUAUAUAAAUCUGUACAUACAUAUAGUAUCAGAA_AAAAGACUAAAGCCGCUAUUCGAUUUAC
...((((((((((.((....)).))))).(((.....)))............(((((((.........))).))))..............)))))........... (-25.56 = -25.32 +  -0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:34:48 2006