Locus 6477

Sequence ID	X_DroMel_CAF1
Location	16,257,419 – 16,257,593
Length	174
Max. P	0.575055

overview

Window 3

Location	16,257,419 – 16,257,539
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.81
Mean single sequence MFE	-34.88
Consensus MFE	-31.54
Energy contribution	-31.58
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.14
Structure conservation index	0.90
SVM decision value	-0.02
SVM RNA-class probability	0.525121
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16257419 120 + 22224390
AAACAGCAACAGCGAACGGUCGGCGCGACAAAACUGCUGUCGCCUGUGCAUCGCCCCACAAACCGAAUGCAUCUCGAUCAUCAAUAGCUAUGCGGCCGACAAGGAGCCGCUGUCCACCAA
..(((((....((.....((((((((((((.......))))))...(((((.((.........(((.......)))..........)).))))))))))).....)).)))))....... ( -35.01)
>DroSec_CAF1 5748 120 + 1
ACACAGCAACAGCGAACGGUCGGCGCGACAAAACUGCUGUCGCCUGUGCAUCGCCCCACAAACCGAAUGCAUCUCGAUCAUCAAUAGCUAUGCGGCGGACAAGGAGCCGCUGUCCACCAA
.....(((..(((....((((((.((((((.......))))))..((((((((..........)).)))))).)))))).......))).)))((.(((((.(....)..))))).)).. ( -35.80)
>DroSim_CAF1 5631 120 + 1
ACACAGCAACAGCGAACGGUCGGCGCGACAAAACUGCUGUCGCCUGUGCAUCGCCCCACAAACCGAAUGCAUCUCGAUCAUCAAUAGCUAUGCGGCGGACAAGGAGCCGCUGUCCACCAA
.....(((..(((....((((((.((((((.......))))))..((((((((..........)).)))))).)))))).......))).)))((.(((((.(....)..))))).)).. ( -35.80)
>DroEre_CAF1 5778 114 + 1
A------AACAGCGAACGGUCGGCGCGACAAAACUGCUGUCGCCUAUGCAUCGCCCCACAAACCGAAUGCAUCUCGAUCAUCAAUAGCUAUGCGGCGGACAAGGAGCCGCUGUCCACCAA
.------...(((....((((((.((((((.......))))))..((((((((..........)).)))))).)))))).......)))....((.(((((.(....)..))))).)).. ( -32.30)
>DroYak_CAF1 5618 114 + 1
A------AACAGCGAAUGGUCGGCGCGACAAAACUGCUGUCGCCUGUGCAUCGCCCCACAAACCGAAUGCAUCUCGAUCAUCAAUAGCUAUGCGGCGGACAAGGAGCCGCUGUCCACCAA
.------...(((..((((((((.((((((.......))))))..((((((((..........)).)))))).)))))))).....)))....((.(((((.(....)..))))).)).. ( -35.50)
>consensus
A_ACAGCAACAGCGAACGGUCGGCGCGACAAAACUGCUGUCGCCUGUGCAUCGCCCCACAAACCGAAUGCAUCUCGAUCAUCAAUAGCUAUGCGGCGGACAAGGAGCCGCUGUCCACCAA
..........(((....((((((.((((((.......))))))..((((((((..........)).)))))).)))))).......)))....((.(((((.(....)..))))).)).. (-31.54 = -31.58 +   0.04)

alignment

secondary structure

dotplot

Window 4

Location	16,257,499 – 16,257,593
Length	94
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	84.89
Mean single sequence MFE	-26.62
Consensus MFE	-25.58
Energy contribution	-25.82
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.15
Structure conservation index	0.96
SVM decision value	0.08
SVM RNA-class probability	0.575055
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16257499 94 - 22224390
--------------------------CACCCAUACCCAUACCCAUAACCACUCACCUUGAUGCCGACGCAGUUGUGGAUCUUGGUGGACAGCGGCUCCUUGUCGGCCGCAUAGCUAUUGA
--------------------------...(((...(((...(((((((...((.....))(((....))))))))))....))))))...((((((.......))))))........... ( -24.00)
>DroSec_CAF1 5828 94 - 1
--------------------------CACCCAUACCCAUACCCAUAGCCACUCACCUUGAUGCCGACGCAGUUGAGGAUCUUGGUGGACAGCGGCUCCUUGUCCGCCGCAUAGCUAUUGA
--------------------------...............(.(((((......(((..((((....))).)..))).....(((((((((.(....)))))))))).....))))).). ( -27.70)
>DroSim_CAF1 5711 94 - 1
--------------------------CACCCAUACCCAUACCCAUAGCCACUCACCUUGAUGCCGACGCAGUUGAGGAUCUUGGUGGACAGCGGCUCCUUGUCCGCCGCAUAGCUAUUGA
--------------------------...............(.(((((......(((..((((....))).)..))).....(((((((((.(....)))))))))).....))))).). ( -27.70)
>DroEre_CAF1 5852 120 - 1
CAUACCCAUACCCAUACCCAUACCCAUACCCACACCUAUACCCAUAGCCACUCACCUUGAUGCCGACGCAGUUGUGGAUCUUGGUGGACAGCGGCUCCUUGUCCGCCGCAUAGCUAUUGA
.........................................(.(((((...(((((..(((.(((((...)))).).)))..)))))...(((((.........)))))...))))).). ( -27.10)
>consensus
__________________________CACCCAUACCCAUACCCAUAGCCACUCACCUUGAUGCCGACGCAGUUGAGGAUCUUGGUGGACAGCGGCUCCUUGUCCGCCGCAUAGCUAUUGA
.........................................(.(((((...(((((..(((.(((((...)))).).)))..)))))...(((((.........)))))...))))).). (-25.58 = -25.82 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:14:44 2006