Locus 7125

Sequence ID	2L_DroMel_CAF1
Location	19,979,134 – 19,979,233
Length	99
Max. P	0.939226

overview

Window 2

Location	19,979,134 – 19,979,233
Length	99
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	89.00
Mean single sequence MFE	-17.56
Consensus MFE	-15.78
Energy contribution	-16.02
Covariance contribution	0.24
Combinations/Pair	1.06
Mean z-score	-1.67
Structure conservation index	0.90
SVM decision value	1.28
SVM RNA-class probability	0.939226
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19979134 99 + 22407834
AUACAUACAUAUAUUUUUGAUUGUCCGCCUCUCGGGCCAUUUGGCUUGAUUAUUUUAUUUAUAUUGCCAGGCAUUGUUUUUUGGGCACUGUUUAUUAUU
.....................(((((.....(((((((....)))))))...........(((.(((...))).))).....)))))............ ( -17.00)
>DroSec_CAF1 162037 90 + 1
A--------UAUAUUUUUGAUUGUCCGCCUCUCGGGCCAUUUGGCUUGAUUAUUUUAUUUAUAUUGCCAGGCAUUGUUU-UUGGCCACUGUUUAUUAUU
.--------.................(((..(((((((....)))))))...........(((.(((...))).)))..-..))).............. ( -14.70)
>DroSim_CAF1 164574 90 + 1
A--------UAUAUUUUUGAUUGUCCGCCUCUCGGGCCAUUUGGCUUGAUUAUUUUAUUUAUAUUGCCAGGCAUUGUUU-UUGGCCACUGUUUAUUAUU
.--------.................(((..(((((((....)))))))...........(((.(((...))).)))..-..))).............. ( -14.70)
>DroEre_CAF1 160170 90 + 1
A--------UAUACUUUUGAUUGUCCGCCUCUCGGGCCAUUUGGCCUGAUUAUAUUAUUUAUAUUGCCAGGCAUUGUUU-UUGGGCACUCUUUAUUAUU
.--------.........((.(((((((((.(((((((....))))))).((((.....)))).....)))).......-..))))).))......... ( -22.40)
>DroYak_CAF1 161084 86 + 1
A--------UAUACAUUUUACUGUCCGCUUCUCGGGCCAUUUGGCUUGAUUAUUUUAUUCAUAUUGCCAGGCAUUGUUU-UUGGGCAAU----GUUAUU
.--------.............(((((.....)))))....((((.(((.........)))....))))(((((((((.-...))))))----)))... ( -19.00)
>consensus
A________UAUAUUUUUGAUUGUCCGCCUCUCGGGCCAUUUGGCUUGAUUAUUUUAUUUAUAUUGCCAGGCAUUGUUU_UUGGGCACUGUUUAUUAUU
.....................(((((.....(((((((....)))))))...........(((.(((...))).))).....)))))............ (-15.78 = -16.02 +   0.24)

alignment

secondary structure

dotplot

Window 3

Location	19,979,134 – 19,979,233
Length	99
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	89.00
Mean single sequence MFE	-13.59
Consensus MFE	-10.63
Energy contribution	-10.83
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.47
Structure conservation index	0.78
SVM decision value	0.05
SVM RNA-class probability	0.559293
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19979134 99 - 22407834
AAUAAUAAACAGUGCCCAAAAAACAAUGCCUGGCAAUAUAAAUAAAAUAAUCAAGCCAAAUGGCCCGAGAGGCGGACAAUCAAAAAUAUAUGUAUGUAU
.........(((.((............)))))((((((((..............(((....)))(((.....))).............))))).))).. ( -12.80)
>DroSec_CAF1 162037 90 - 1
AAUAAUAAACAGUGGCCAA-AAACAAUGCCUGGCAAUAUAAAUAAAAUAAUCAAGCCAAAUGGCCCGAGAGGCGGACAAUCAAAAAUAUA--------U
............((.((..-.......(((((((....................))))...)))((....)).)).))............--------. ( -12.35)
>DroSim_CAF1 164574 90 - 1
AAUAAUAAACAGUGGCCAA-AAACAAUGCCUGGCAAUAUAAAUAAAAUAAUCAAGCCAAAUGGCCCGAGAGGCGGACAAUCAAAAAUAUA--------U
............((.((..-.......(((((((....................))))...)))((....)).)).))............--------. ( -12.35)
>DroEre_CAF1 160170 90 - 1
AAUAAUAAAGAGUGCCCAA-AAACAAUGCCUGGCAAUAUAAAUAAUAUAAUCAGGCCAAAUGGCCCGAGAGGCGGACAAUCAAAAGUAUA--------U
.........((.((.((..-.......((((((..((((.....))))..))))))......(((.....))))).)).)).........--------. ( -17.90)
>DroYak_CAF1 161084 86 - 1
AAUAAC----AUUGCCCAA-AAACAAUGCCUGGCAAUAUGAAUAAAAUAAUCAAGCCAAAUGGCCCGAGAAGCGGACAGUAAAAUGUAUA--------U
......----((((((...-...........)))))).................(((....)))(((.....)))(((......)))...--------. ( -12.54)
>consensus
AAUAAUAAACAGUGCCCAA_AAACAAUGCCUGGCAAUAUAAAUAAAAUAAUCAAGCCAAAUGGCCCGAGAGGCGGACAAUCAAAAAUAUA________U
............((.((..........(((((((....................))))...)))((....)).)).))..................... (-10.63 = -10.83 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:28:03 2006