Locus 7948

Sequence ID dm3.chr3L
Location 18,854,076 – 18,854,130
Length 54
Max. P 0.970160
window10942 window10943

overview

Window 2

Location 18,854,076 – 18,854,130
Length 54
Sequences 14
Columns 57
Reading direction forward
Mean pairwise identity 83.10
Shannon entropy 0.39394
G+C content 0.35719
Mean single sequence MFE -9.52
Consensus MFE -8.26
Energy contribution -8.33
Covariance contribution 0.07
Combinations/Pair 1.00
Mean z-score -1.06
Structure conservation index 0.87
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.95
SVM RNA-class probability 0.859190
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3L 18854076 54 + 24543557
UAUAAUUUUGAUUGUUGCUCAGAAAGCCCUCA---UUGUUUACCAGUUGGCUUUCGA
.....................(((((((...(---(((.....)))).))))))).. ( -11.00, z-score =  -1.64, R)
>apiMel3.Group2 8429416 51 - 14465785
UAUGCUUUUGAUUGUUGCUCAGAAAGCCUUGA-----UUAUGAUA-UUGGCUUUCGG
.....................(((((((....-----........-..))))))).. ( -10.04, z-score =  -0.97, R)
>anoGam1.chrU 28635747 54 + 59568033
UAAAAUUUUGAUUGUUGCUCAGAAAGCCGUGU---CGAUUAAGCAAUUCGCUUUCGG
.....................((((((..(((---.......)))....)))))).. (  -7.90, z-score =   0.44, R)
>droGri2.scaffold_15110 429824 52 - 24565398
UAUAAUUUUGAUUGUUGCUCAGAAAGCCUUUC-----ACUUGACACUUGGCUUUCGA
.....................(((((((....-----...........))))))).. (  -9.96, z-score =  -1.58, R)
>droMoj3.scaffold_6680 1115545 55 - 24764193
UAUAAUUUUGAUUGUUGCUCAGAAAGCCCGUAAUUUAACUUAACA--UGGCUUUCGA
.....................(((((((..(((......)))...--.))))))).. (  -9.40, z-score =  -1.38, R)
>droVir3.scaffold_13049 7149499 52 - 25233164
UAUCAUUUUGAUUGUUGCUCAGAAAGCCCUGC-----AUUCAAUACUUGGCUUUCGA
.....................(((((((..(.-----........)..))))))).. (  -9.10, z-score =  -0.61, R)
>droWil1.scaffold_180955 104855 55 + 2875958
UAUAAUUUUGAUUGUUGCUCAGAAAGCCCUCA--UUACUUUAUCAGUUGGCUUUCGA
.....................(((((((..(.--...........)..))))))).. (  -9.50, z-score =  -1.12, R)
>droPer1.super_9 1244066 54 - 3637205
UCUAUUUUUGAUUGUUGCUCAGAAAGCCCUUA---UAAUUAACCAGUUGGCUUUCGA
.....................(((((((....---.............))))))).. (  -8.63, z-score =  -0.90, R)
>dp4.chrXR_group6 9210488 54 - 13314419
UCUAUUUUUGAUUGUUGCUCAGAAAGCCCUUA---UAAUUAACCAGUUGGCUUUCGA
.....................(((((((....---.............))))))).. (  -8.63, z-score =  -0.90, R)
>droAna3.scaffold_13337 4708353 54 - 23293914
UAUAAUUUUGAUUGUUGCUCAGAAAGCCCUUA---UAAAUUAUUAGCUGGCUUUCGA
.....................(((((((....---(((....)))...))))))).. (  -9.50, z-score =  -0.99, R)
>droEre2.scaffold_4784 18670615 53 + 25762168
UAUAAUUUUGAUUGUUGCUCAGAAAGCCCU-A---UUAUCUAACAGCUGGCUUUCGA
.....................(((((((..-.---.............))))))).. (  -8.69, z-score =  -0.57, R)
>droYak2.chr3L 2410521 54 - 24197627
UAUAAUUUUGAUUGUUGCUCAGAAAGCCCUUA---CUAUUUAACAGCUGGCUUUCGA
.....................(((((((....---.............))))))).. (  -8.63, z-score =  -0.67, R)
>droSec1.super_19 820247 52 + 1257711
UAUAAUUUUGAUUGUUGCUCAGAAAGCCCUUA---UUGU--ACCAGUUGGCUUUCGA
.....................(((((((...(---(((.--..)))).))))))).. ( -10.60, z-score =  -1.70, R)
>droSim1.chr3L 18159384 54 + 22553184
UAUAAUUUUGAUUGUUGCUCAGAAAGCCCUUA---UUGUUUACCAGUUGGCUUUCGA
.....................(((((((...(---(((.....)))).))))))).. ( -11.70, z-score =  -2.25, R)
>consensus
UAUAAUUUUGAUUGUUGCUCAGAAAGCCCUUA___UAAUUUAACAGUUGGCUUUCGA
.....................(((((((....................))))))).. ( -8.26 =  -8.33 +   0.07)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 18,854,076 – 18,854,130
Length 54
Sequences 14
Columns 57
Reading direction reverse
Mean pairwise identity 83.10
Shannon entropy 0.39394
G+C content 0.35719
Mean single sequence MFE -10.30
Consensus MFE -8.36
Energy contribution -8.43
Covariance contribution 0.07
Combinations/Pair 1.00
Mean z-score -1.76
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.83
SVM RNA-class probability 0.970160
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3L 18854076 54 - 24543557
UCGAAAGCCAACUGGUAAACAA---UGAGGGCUUUCUGAGCAACAAUCAAAAUUAUA
..(((((((.(.((.....)).---)...)))))))(((.......)))........ ( -10.60, z-score =  -1.77, R)
>apiMel3.Group2 8429416 51 + 14465785
CCGAAAGCCAA-UAUCAUAA-----UCAAGGCUUUCUGAGCAACAAUCAAAAGCAUA
..(((((((..-........-----....)))))))...((...........))... (  -9.34, z-score =  -2.54, R)
>anoGam1.chrU 28635747 54 - 59568033
CCGAAAGCGAAUUGCUUAAUCG---ACACGGCUUUCUGAGCAACAAUCAAAAUUUUA
.(((((((.....))))..)))---.....((((...))))................ (  -6.60, z-score =   0.11, R)
>droGri2.scaffold_15110 429824 52 + 24565398
UCGAAAGCCAAGUGUCAAGU-----GAAAGGCUUUCUGAGCAACAAUCAAAAUUAUA
..(((((((.....((....-----))..)))))))(((.......)))........ (  -9.90, z-score =  -1.56, R)
>droMoj3.scaffold_6680 1115545 55 + 24764193
UCGAAAGCCA--UGUUAAGUUAAAUUACGGGCUUUCUGAGCAACAAUCAAAAUUAUA
..(((((((.--(((...........))))))))))(((.......)))........ ( -10.70, z-score =  -2.16, R)
>droVir3.scaffold_13049 7149499 52 + 25233164
UCGAAAGCCAAGUAUUGAAU-----GCAGGGCUUUCUGAGCAACAAUCAAAAUGAUA
..(((((((..((((...))-----))..))))))).........(((.....))). ( -12.80, z-score =  -2.05, R)
>droWil1.scaffold_180955 104855 55 - 2875958
UCGAAAGCCAACUGAUAAAGUAA--UGAGGGCUUUCUGAGCAACAAUCAAAAUUAUA
..(((((((..((.((......)--).)))))))))(((.......)))........ ( -10.50, z-score =  -1.79, R)
>droPer1.super_9 1244066 54 + 3637205
UCGAAAGCCAACUGGUUAAUUA---UAAGGGCUUUCUGAGCAACAAUCAAAAAUAGA
..(((((((.....((.....)---)...)))))))(((.......)))........ (  -9.40, z-score =  -1.25, R)
>dp4.chrXR_group6 9210488 54 + 13314419
UCGAAAGCCAACUGGUUAAUUA---UAAGGGCUUUCUGAGCAACAAUCAAAAAUAGA
..(((((((.....((.....)---)...)))))))(((.......)))........ (  -9.40, z-score =  -1.25, R)
>droAna3.scaffold_13337 4708353 54 + 23293914
UCGAAAGCCAGCUAAUAAUUUA---UAAGGGCUUUCUGAGCAACAAUCAAAAUUAUA
..(((((((...(((....)))---....)))))))(((.......)))........ ( -10.00, z-score =  -1.81, R)
>droEre2.scaffold_4784 18670615 53 - 25762168
UCGAAAGCCAGCUGUUAGAUAA---U-AGGGCUUUCUGAGCAACAAUCAAAAUUAUA
..(((((((..(((((....))---)-)))))))))(((.......)))........ ( -12.10, z-score =  -2.04, R)
>droYak2.chr3L 2410521 54 + 24197627
UCGAAAGCCAGCUGUUAAAUAG---UAAGGGCUUUCUGAGCAACAAUCAAAAUUAUA
..(((((((.(((((...))))---)...)))))))(((.......)))........ ( -13.10, z-score =  -2.57, R)
>droSec1.super_19 820247 52 - 1257711
UCGAAAGCCAACUGGU--ACAA---UAAGGGCUUUCUGAGCAACAAUCAAAAUUAUA
..(((((((...((..--....---))..)))))))(((.......)))........ (  -9.20, z-score =  -1.57, R)
>droSim1.chr3L 18159384 54 - 22553184
UCGAAAGCCAACUGGUAAACAA---UAAGGGCUUUCUGAGCAACAAUCAAAAUUAUA
..(((((((...((.....)).---....)))))))(((.......)))........ ( -10.60, z-score =  -2.34, R)
>consensus
UCGAAAGCCAACUGUUAAAUAA___UAAGGGCUUUCUGAGCAACAAUCAAAAUUAUA
..(((((((....................)))))))(((.......)))........ ( -8.36 =  -8.43 +   0.07)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:36:34 2011