Locus 8714

Sequence ID	3R_DroMel_CAF1
Location	23,296,732 – 23,296,872
Length	140
Max. P	0.918305

overview

Window 4

Location	23,296,732 – 23,296,836
Length	104
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	79.42
Mean single sequence MFE	-33.49
Consensus MFE	-21.00
Energy contribution	-22.39
Covariance contribution	1.39
Combinations/Pair	1.10
Mean z-score	-2.25
Structure conservation index	0.63
SVM decision value	1.12
SVM RNA-class probability	0.918305
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23296732 104 - 27905053
UAAGUGGCUGCUAACUUGGCUUUCGAA-UGAGGCAGAGCAAUCGACUGGCGGCGAUCAAGCCCCAGUUGCAAAUAAUGCAAAAUUGCAAUGAAAUGCGGCCAGGU----
....(((((((....(((.(((.....-.))).))).(((((.((((((.(((......)))))))))(((.....)))...)))))........)))))))...---- ( -37.90)
>DroPse_CAF1 98439 91 - 1
CAAGUGGCUGCUAACUCGGCUUUC---------------AAUGGAUCGCCGA---CUCCGAUUCAGCUGCAAAUAAUGCAAAACUGCAAUGAAAUGCGGCCAGCUGUUG
..((..((((.....(((((..((---------------....))..)))))---..........((((((..((.((((....)))).))...))))))))))..)). ( -28.20)
>DroSim_CAF1 98286 104 - 1
CAAGUGGCUGCUAACUUGGCUUUCGAA-UGCUGCAGAGCAAUGGACUGGCGGCGAUCAAGCCCCAGUUGCAAAUAAUGCAAAAUUGCAAUGAAAUGCGGCCAGGG----
....(((((((......(((.......-.))).((..(((((.((((((.(((......)))))))))(((.....)))...)))))..))....)))))))...---- ( -37.60)
>DroEre_CAF1 99899 104 - 1
CAAGUGGCUGCUAACUUGGCUUUCGAA-UGCGGCAGAGCAAUGGACUGGCGGCGAUCAAGCCCCAGUUGCAAAUAAUGCAAAAUUGCAAUGAAAUGCGGCCAGCU----
....(((((((.......((.......-.))..((..(((((.((((((.(((......)))))))))(((.....)))...)))))..))....)))))))...---- ( -36.80)
>DroYak_CAF1 97213 105 - 1
CGAGUGGCUGCUAACUUGGCUUUCGAAUUGCGGCAGAGCAAUGGACUGGCGGCGAUCAAGCCCCAGUUGCAAAUAAUGCAAAAUUGCAAUGAAAUGCGGCCAGGU----
....(((((((.......((......(((((......))))).((((((.(((......)))))))))))......((((....)))).......)))))))...---- ( -36.80)
>DroPer_CAF1 98873 91 - 1
CAAGUGGCUGCUAACUCGGCUUUC---------------AAUGGAUCGCCGA---CUCCGAUUCAGCUGCAAAUAAUGCAAAACUGCAAUGAAAUGCGCCCAGCUGUCG
...(..((((.....(((((..((---------------....))..)))))---........))))..)......((((....))))..((...((.....))..)). ( -23.62)
>consensus
CAAGUGGCUGCUAACUUGGCUUUCGAA_UGCGGCAGAGCAAUGGACUGGCGGCGAUCAAGCCCCAGUUGCAAAUAAUGCAAAAUUGCAAUGAAAUGCGGCCAGCU____
....(((((((.......((.......................((((((.(((......)))))))))(((.....)))......))........)))))))....... (-21.00 = -22.39 +   1.39)

alignment

secondary structure

dotplot

Window 5

Location	23,296,761 – 23,296,872
Length	111
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	82.31
Mean single sequence MFE	-36.77
Consensus MFE	-23.82
Energy contribution	-24.77
Covariance contribution	0.95
Combinations/Pair	1.15
Mean z-score	-1.78
Structure conservation index	0.65
SVM decision value	0.09
SVM RNA-class probability	0.577145
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23296761 111 - 27905053
ACUCUUG----UUGGCCCGGCUAAUAGCAGAAAGCAAACUUAAGUGGCUGCUAACUUGGCUUUCGAA-UGAGGCAGAGCAAUCGACUGGCGGCGAUCAAGCCCCAGUUGCAAAUAA
.((((((----..((((.((....((((((...((........))..)))))).)).))))..))).-.)))((.((....))((((((.(((......)))))))))))...... ( -37.80)
>DroSec_CAF1 94347 111 - 1
ACUCAUG----UUGGCCCGGCUAAUAGCAGCAAGCAAACUCAAGUGGCUGCUAACUUGGCUUUCGAA-UGCGGCAGAGCAAUGGACUGGCGGCGAUCAAGCCCCAGUUGCAAAUAA
...((((----((.(((((((((((((((((..((........)).)))))))..))))))......-.).)))..))).)))((((((.(((......)))))))))........ ( -36.11)
>DroSim_CAF1 98315 111 - 1
ACUCAUG----UUGGCCCGGCUAAUAGCAGCAAGCAAACUCAAGUGGCUGCUAACUUGGCUUUCGAA-UGCUGCAGAGCAAUGGACUGGCGGCGAUCAAGCCCCAGUUGCAAAUAA
.(((.((----(((((...)))))))((((((..((((..(((((........)))))..))).)..-)))))).))).....((((((.(((......)))))))))........ ( -39.40)
>DroEre_CAF1 99928 111 - 1
GGCACUG----UUGGCCCGGCUAAUAGCGGCAAGCAAACUCAAGUGGCUGCUAACUUGGCUUUCGAA-UGCGGCAGAGCAAUGGACUGGCGGCGAUCAAGCCCCAGUUGCAAAUAA
.((.(((----(((.(..(((((((((((((..((........)).)))))))..))))))...)..-..)))))).))....((((((.(((......)))))))))........ ( -38.00)
>DroYak_CAF1 97242 112 - 1
ACUUCUG----UUGGCUUGGCUAAUAGCAGCAAGCAAACUCGAGUGGCUGCUAACUUGGCUUUCGAAUUGCGGCAGAGCAAUGGACUGGCGGCGAUCAAGCCCCAGUUGCAAAUAA
...((((----((((((((((.....))..)))))....(((((.((((........)))))))))....)))))))(((....(((((.(((......)))))))))))...... ( -38.40)
>DroPer_CAF1 98906 97 - 1
GCCUCUGCUACUGAGGAGGGCUAAUGGGAGCAAGCA-ACUCAAGUGGCUGCUAACUCGGCUUUC---------------AAUGGAUCGCCGA---CUCCGAUUCAGCUGCAAAUAA
.....(((..((((((((.......(..((((.((.-((....)).))))))..)(((((..((---------------....))..)))))---))))...))))..)))..... ( -30.90)
>consensus
ACUCCUG____UUGGCCCGGCUAAUAGCAGCAAGCAAACUCAAGUGGCUGCUAACUUGGCUUUCGAA_UGCGGCAGAGCAAUGGACUGGCGGCGAUCAAGCCCCAGUUGCAAAUAA
..............((..(((((((((((((..((........)).)))))))..))))))......................((((((.(((......)))))))))))...... (-23.82 = -24.77 +   0.95)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:17:55 2006