Locus 1626

Sequence ID	X_DroMel_CAF1
Location	4,638,282 – 4,638,420
Length	138
Max. P	0.997347

overview

Window 6

Location	4,638,282 – 4,638,380
Length	98
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	96.33
Mean single sequence MFE	-23.74
Consensus MFE	-19.98
Energy contribution	-20.42
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-1.47
Structure conservation index	0.84
SVM decision value	0.22
SVM RNA-class probability	0.638876
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4638282 98 - 22224390
UAUGUAUUCAUAUGCAAUGUCGAAAAUAAUCGUUAAUAUGCUGAUAAAACACGCCCCCUCAACAUUGUGGGCAUGUCGUUUGUCGACUGCGUAUAGUG
.........(((((((..(((((((((.(((((......)).)))...(((.((((.(........).)))).))).)))).)))))))))))).... ( -23.00)
>DroSec_CAF1 23992 98 - 1
UAUGUAUUCAUAUGCAAUGUCGAAAAUAAUCGUUAAUAUGCUGAUAAAACACGCCCCCUCAACAAUGUGGGCAUGUCGUGUGUCGACUGCGUAUAGUG
.........(((((((..(((((.....(((((......)).)))...((((((.(((.((....)).)))...).))))).)))))))))))).... ( -23.70)
>DroSim_CAF1 5623 98 - 1
UAUGUAUUCAUAUGCAAUGUCGAAAAUAAUCGUUAAUAUGCUGAUAAAACACGCCCCCUCAACAAUGUGGGCAUGUCGUGUGUCGACUGCGUAUAGUG
.........(((((((..(((((.....(((((......)).)))...((((((.(((.((....)).)))...).))))).)))))))))))).... ( -23.70)
>DroEre_CAF1 22082 98 - 1
UAUGUAUUCAUAUGCAAUGUCGAAAAUAAUCGUUAAUAUGCUGAUAAAACACGCCCCCUCAACAAUGUGGGCAUGUCGAAUGUCGAAUGCGUAUAGUG
(((((((((....(((((..(((......)))...)).))).((((..(((.((((.(........).)))).)))....)))))))))))))..... ( -24.10)
>DroYak_CAF1 23459 97 - 1
UAUGUAUUCAUAUGCAAUGUUGAAAAUAAUCGUUAAUAUGCUGAUAAAACACGCC-CCUCAACAAUGUGGGCAUGUCGAAUGUCGAAUGCGUAUAGUA
(((((((((....(((.((((((.........))))))))).((((..(((.(((-((........).)))).)))....)))))))))))))..... ( -24.20)
>consensus
UAUGUAUUCAUAUGCAAUGUCGAAAAUAAUCGUUAAUAUGCUGAUAAAACACGCCCCCUCAACAAUGUGGGCAUGUCGUAUGUCGACUGCGUAUAGUG
.........(((((((..(((((.....(((((......)).)))...(((.((((.(........).)))).)))......)))))))))))).... (-19.98 = -20.42 +   0.44)

alignment

secondary structure

dotplot

Window 7

Location	4,638,300 – 4,638,420
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	90.67
Mean single sequence MFE	-29.56
Consensus MFE	-24.83
Energy contribution	-26.92
Covariance contribution	2.09
Combinations/Pair	1.06
Mean z-score	-4.11
Structure conservation index	0.84
SVM decision value	2.84
SVM RNA-class probability	0.997347
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4638300 120 + 22224390
AACGACAUGCCCACAAUGUUGAGGGGGCGUGUUUUAUCAGCAUAUUAACGAUUAUUUUCGACAUUGCAUAUGAAUACAUAAAUAAACAAAAAUACGCCAUCAACAAAUAUAAAUGCAUGU
....((((((......((((((...((((((((((....(((......(((......)))....))).((((....))))........)))))))))).)))))).........)))))) ( -31.46)
>DroSec_CAF1 24010 120 + 1
CACGACAUGCCCACAUUGUUGAGGGGGCGUGUUUUAUCAGCAUAUUAACGAUUAUUUUCGACAUUGCAUAUGAAUACAUAAAUAAACAAAAAUACGCCAUCAACAAAUAUAAAUGCAUGU
....((((((.....(((((((...((((((((((....(((......(((......)))....))).((((....))))........)))))))))).)))))))........)))))) ( -32.52)
>DroSim_CAF1 5641 120 + 1
CACGACAUGCCCACAUUGUUGAGGGGGCGUGUUUUAUCAGCAUAUUAACGAUUAUUUUCGACAUUGCAUAUGAAUACAUAAAUAAACAAAAAUACGCCAUCAACAAAUAUAAAUGCAUGU
....((((((.....(((((((...((((((((((....(((......(((......)))....))).((((....))))........)))))))))).)))))))........)))))) ( -32.52)
>DroEre_CAF1 22100 120 + 1
UUCGACAUGCCCACAUUGUUGAGGGGGCGUGUUUUAUCAGCAUAUUAACGAUUAUUUUCGACAUUGCAUAUGAAUACAUAAAUAAACAAAAAUACGCCAUCAACAAAUAUAAAUGCAUGU
....((((((.....(((((((...((((((((((....(((......(((......)))....))).((((....))))........)))))))))).)))))))........)))))) ( -32.52)
>DroYak_CAF1 23477 119 + 1
UUCGACAUGCCCACAUUGUUGAGG-GGCGUGUUUUAUCAGCAUAUUAACGAUUAUUUUCAACAUUGCAUAUGAAUACAUAAAUAAACAAAAAUACGCCAUCAACAAAUAUAAAUGCAUGU
....((((((.....(((((((..-((((((((((....(((.......((......)).....))).((((....))))........)))))))))).)))))))........)))))) ( -29.92)
>DroMoj_CAF1 116009 103 + 1
CACAACAUG--------------UGGGCGUAUUUUAUCAGCAAAUUAAUGAUUAUU-GCGACAAUGCAUAUGAAUACAUAAAUAAACAAAAAUACGCCAUCAACAAAU--AAAUGCACAA
(((.....)--------------))((((((((((....((((...........))-)).........((((....))))........))))))))))..........--.......... ( -18.40)
>consensus
CACGACAUGCCCACAUUGUUGAGGGGGCGUGUUUUAUCAGCAUAUUAACGAUUAUUUUCGACAUUGCAUAUGAAUACAUAAAUAAACAAAAAUACGCCAUCAACAAAUAUAAAUGCAUGU
....((((((.....(((((((...((((((((((....(((......(((......)))....))).((((....))))........)))))))))).)))))))........)))))) (-24.83 = -26.92 +   2.09)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:15:05 2006