Locus 3951

Sequence ID	3R_DroMel_CAF1
Location	10,681,280 – 10,681,437
Length	157
Max. P	0.978070

overview

Window 3

Location	10,681,280 – 10,681,397
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.05
Mean single sequence MFE	-33.50
Consensus MFE	-25.42
Energy contribution	-25.82
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.14
Structure conservation index	0.76
SVM decision value	0.09
SVM RNA-class probability	0.580464
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10681280 117 + 27905053
UCGCCCG---CCAGAUGAGCAGCGAUUCGCUGGCGUAGCCUAGCAGCAAGAUUAUAAUUAAAAGUAAUCAACGACAUUAUCAAGCCAAAUGCUAAGGCCAGAACGCGAAGCAUAAAGCCA
((((.((---((((.((((......))))))))))..((((((((((..((((((........))))))...((.....))..))....)))).))))......)))).((.....)).. ( -31.60)
>DroSec_CAF1 22554 120 + 1
UCGCCCGCCGCCAGAUGAGCAGCGAUUCGCUGGCGUAGCCUAGCAGCAAGAUUAUAAUUAAAAGUAAUCAACGACAUUAUGAAGGCAAAUGCUAAGGCCAGAACGCGGAGCAUAAAGCCA
..((((((((((((.((((......))))))))))..((((((((((..((((((........))))))..(..(.....)..)))...)))).))))......)))).))......... ( -36.30)
>DroSim_CAF1 24572 120 + 1
UCGCCCGCCGCCAGAUGAGCAGCGAUUCGCUGGCGUAGCCUAGCAGCAAGAUUAUAAUUAAAAGUAAUCAACGACAUUAUCAAGGCAAAUGCUAAGGCCAGAACGCGGAGCAUAAAGCCA
..((((((((((((.((((......))))))))))..((((((((((..((((((........))))))...((.....))...))...)))).))))......)))).))......... ( -37.00)
>DroEre_CAF1 19863 117 + 1
UCGCCCG---ACAGAUGAGCAGCGAUUCGCUGGCGUAGCCUAGCAGCCAGAUUAUAAUUAAAAGUAAUCAACGACAUUAUCAAGGCAAAUGCUAAGGCCAGAACGCAGAGCAUAAAGCCA
..((.(.---.........(((((...)))))((((.(((((((((((.((((((........))))))...((.....))..)))...)))).))))....)))).).))......... ( -30.90)
>DroYak_CAF1 14849 117 + 1
UCGCCCG---GCAGAUGAGCAGCGAUUCGCUGGCGUAGCCUAGCAGCAAGAUUAUAAUUAAAAGUAAUCAACGACAUUAUCAAGGCAAAUGCUAAGGCCAGAACGCAGAGCAUAAAGCCA
......(---((..(((..(((((...)))))((((.((((((((((..((((((........))))))...((.....))...))...)))).))))....))))....)))...))). ( -31.70)
>consensus
UCGCCCG___CCAGAUGAGCAGCGAUUCGCUGGCGUAGCCUAGCAGCAAGAUUAUAAUUAAAAGUAAUCAACGACAUUAUCAAGGCAAAUGCUAAGGCCAGAACGCGGAGCAUAAAGCCA
.............(((((....((....((((((...))).))).....((((((........))))))..))...)))))..(((..(((((...((......))..)))))...))). (-25.42 = -25.82 +   0.40)

alignment

secondary structure

dotplot

Window 4

Location	10,681,317 – 10,681,437
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.46
Mean single sequence MFE	-24.50
Consensus MFE	-20.82
Energy contribution	-21.22
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.92
Structure conservation index	0.85
SVM decision value	1.81
SVM RNA-class probability	0.978070
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10681317 120 + 27905053
UAGCAGCAAGAUUAUAAUUAAAAGUAAUCAACGACAUUAUCAAGCCAAAUGCUAAGGCCAGAACGCGAAGCAUAAAGCCAAGGCUAAGCAACGGCAAAAGGCGAAAAUCCAGAAAUUCUG
.....((..((((((........))))))..............(((..(((((...((......))..)))))..(((....))).......))).....)).......(((.....))) ( -21.70)
>DroSec_CAF1 22594 120 + 1
UAGCAGCAAGAUUAUAAUUAAAAGUAAUCAACGACAUUAUGAAGGCAAAUGCUAAGGCCAGAACGCGGAGCAUAAAGCCAAGGCUGAGCAACGGCAAAAGGCGAAAAUCCAGAAAUUCUG
...((((..((((((........))))))..............(((..(((((...((......))..)))))...)))...)))).....((.(....).))......(((.....))) ( -24.20)
>DroSim_CAF1 24612 120 + 1
UAGCAGCAAGAUUAUAAUUAAAAGUAAUCAACGACAUUAUCAAGGCAAAUGCUAAGGCCAGAACGCGGAGCAUAAAGCCAAGGCUGAGCAACGGCAAAAGGCGAAAAUCCAGAAAUUCUG
(((((((..((((((........))))))...((.....))...))...)))))....(((((..((((.......(((...((((.....))))....))).....))).)...))))) ( -24.30)
>DroEre_CAF1 19900 112 + 1
UAGCAGCCAGAUUAUAAUUAAAAGUAAUCAACGACAUUAUCAAGGCAAAUGCUAAGGCCAGAACGCAGAGCAUAAAGCCAAGGCUGAGCAAAGGCAA--------AAUCCAGAAAUUCUG
...(((((.((((((........))))))..............(((..(((((...((......))..)))))...)))..))))).((....))..--------....(((.....))) ( -27.90)
>DroYak_CAF1 14886 112 + 1
UAGCAGCAAGAUUAUAAUUAAAAGUAAUCAACGACAUUAUCAAGGCAAAUGCUAAGGCCAGAACGCAGAGCAUAAAGCCAAGGCUGAGCAACGGCAA--------AAUCCAGAAAUUCUG
...((((..((((((........))))))..............(((..(((((...((......))..)))))...)))...)))).((....))..--------....(((.....))) ( -24.40)
>consensus
UAGCAGCAAGAUUAUAAUUAAAAGUAAUCAACGACAUUAUCAAGGCAAAUGCUAAGGCCAGAACGCGGAGCAUAAAGCCAAGGCUGAGCAACGGCAAAAGGCGAAAAUCCAGAAAUUCUG
...((((..((((((........))))))..............(((..(((((...((......))..)))))...)))...)))).((....))..............(((.....))) (-20.82 = -21.22 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:14:18 2006