Locus 7201

Sequence ID dm3.chr3L
Location 12,945,640 – 12,945,695
Length 55
Max. P 0.995447
window9908 window9909

overview

Window 8

Location 12,945,640 – 12,945,695
Length 55
Sequences 13
Columns 56
Reading direction forward
Mean pairwise identity 90.26
Shannon entropy 0.24068
G+C content 0.37160
Mean single sequence MFE -15.11
Consensus MFE -10.73
Energy contribution -11.75
Covariance contribution 1.02
Combinations/Pair 1.16
Mean z-score -3.43
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.80
SVM RNA-class probability 0.995447
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 12945640 55 + 24543557
AAAGCAAAAUAAUUGGCGUAUCAGACAUUUUGUUACGCCC-AAUUUAAGUGCUUCC
.(((((....((((((((((.((((...)))).)))).))-))))....))))).. ( -17.10, z-score =  -4.60, R)
>droSim1.chr3L 12330849 55 + 22553184
AAAGCAAAAUAAUUGGCGUAUCAGACAUUUUGUUACGCCC-AAUUUAAGUGCUUCC
.(((((....((((((((((.((((...)))).)))).))-))))....))))).. ( -17.10, z-score =  -4.60, R)
>droSec1.super_0 5120765 55 + 21120651
AAAGCAAAAUAAUUGGCGUAUCAGACAUUUUGUUACGCCC-AAUUUAAGUGCUUCC
.(((((....((((((((((.((((...)))).)))).))-))))....))))).. ( -17.10, z-score =  -4.60, R)
>droYak2.chr3L 13025902 55 + 24197627
AAAGCAAAAUAAUUGGCGUGUCAGACAUUUUGUUACGCCC-AAUUUAAGUGCUUCC
.(((((....((((((((((.((((...)))).)))).))-))))....))))).. ( -16.70, z-score =  -3.92, R)
>droEre2.scaffold_4784 12955167 55 + 25762168
AAAGCAAAAUAAUUGGCGUGUCAGACAUUUUGUUACGCCC-AAUUUAAGUGCUUCC
.(((((....((((((((((.((((...)))).)))).))-))))....))))).. ( -16.70, z-score =  -3.92, R)
>droAna3.scaffold_13337 6487430 55 - 23293914
AAAGCAAAAUAAUUGGCGUGUCAGACAUUUUGUUACGCCC-AAUUUAAGUGCUUCC
.(((((....((((((((((.((((...)))).)))).))-))))....))))).. ( -16.70, z-score =  -3.92, R)
>dp4.chrXR_group6 4320979 55 + 13314419
AAAGCAAAAUAAUUGGCGUGUCAGACAUUUUGUUACGCCC-AAUUUAAGUGCUUCC
.(((((....((((((((((.((((...)))).)))).))-))))....))))).. ( -16.70, z-score =  -3.92, R)
>droPer1.super_9 2610366 55 + 3637205
AAAGCAAAAUAAUUGGCGUGUCAGACAUUUUGUUACGCCC-AAUUUAAGUGCUUCC
.(((((....((((((((((.((((...)))).)))).))-))))....))))).. ( -16.70, z-score =  -3.92, R)
>droWil1.scaffold_180698 5337738 55 + 11422946
AAACCAAAAUAAUUGGCGUGUCAGACAUUUUGUUAUGGCC-AAUUUAAGUGCUUCC
....((....((((((((((.((((...)))).))).)))-))))....))..... (  -9.30, z-score =  -0.41, R)
>droVir3.scaffold_13049 2666223 55 - 25233164
AAAGCAAAAUAAUUGGCGUGUCAGACAUUUUGUUACGCCC-AAUUUAAGUGCUUCC
.(((((....((((((((((.((((...)))).)))).))-))))....))))).. ( -16.70, z-score =  -3.92, R)
>droMoj3.scaffold_6680 7577140 55 - 24764193
AAAGCAAAAUAAUUGGCGUGUCAGACAUUUUGUUACGCCC-AAUUUAAGUGCUUCC
.(((((....((((((((((.((((...)))).)))).))-))))....))))).. ( -16.70, z-score =  -3.92, R)
>droGri2.scaffold_15121 8721 55 - 279557
AAAGCAAAAUAAUUGGCGUGUCAGACAUUUUGCUACGCCC-AAUUUAAGUGCUUCC
.(((((....((((((((((.((((...)))).)))).))-))))....))))).. ( -16.70, z-score =  -3.54, R)
>anoGam1.chr2R 18641077 56 - 62725911
GAAACAAGUUACAUGCAAUUUCAAACAUCGAAUCUUGAAGGAAUAUAUACACUAAC
......(((((.(((...((((((..........))))))...))).)).)))... (  -2.20, z-score =   0.57, R)
>consensus
AAAGCAAAAUAAUUGGCGUGUCAGACAUUUUGUUACGCCC_AAUUUAAGUGCUUCC
.(((((....((((((((((.((((...)))).))))))..))))....))))).. (-10.73 = -11.75 +   1.02)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 12,945,640 – 12,945,695
Length 55
Sequences 13
Columns 56
Reading direction reverse
Mean pairwise identity 90.26
Shannon entropy 0.24068
G+C content 0.37160
Mean single sequence MFE -12.63
Consensus MFE -8.82
Energy contribution -9.13
Covariance contribution 0.31
Combinations/Pair 1.35
Mean z-score -1.96
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.39
SVM RNA-class probability 0.676939
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 12945640 55 - 24543557
GGAAGCACUUAAAUU-GGGCGUAACAAAAUGUCUGAUACGCCAAUUAUUUUGCUUU
.((((((....((((-((.((((.((.......)).))))))))))....)))))) ( -15.40, z-score =  -3.21, R)
>droSim1.chr3L 12330849 55 - 22553184
GGAAGCACUUAAAUU-GGGCGUAACAAAAUGUCUGAUACGCCAAUUAUUUUGCUUU
.((((((....((((-((.((((.((.......)).))))))))))....)))))) ( -15.40, z-score =  -3.21, R)
>droSec1.super_0 5120765 55 - 21120651
GGAAGCACUUAAAUU-GGGCGUAACAAAAUGUCUGAUACGCCAAUUAUUUUGCUUU
.((((((....((((-((.((((.((.......)).))))))))))....)))))) ( -15.40, z-score =  -3.21, R)
>droYak2.chr3L 13025902 55 - 24197627
GGAAGCACUUAAAUU-GGGCGUAACAAAAUGUCUGACACGCCAAUUAUUUUGCUUU
.((((((....((((-((.(((..((.......))..)))))))))....)))))) ( -13.10, z-score =  -2.13, R)
>droEre2.scaffold_4784 12955167 55 - 25762168
GGAAGCACUUAAAUU-GGGCGUAACAAAAUGUCUGACACGCCAAUUAUUUUGCUUU
.((((((....((((-((.(((..((.......))..)))))))))....)))))) ( -13.10, z-score =  -2.13, R)
>droAna3.scaffold_13337 6487430 55 + 23293914
GGAAGCACUUAAAUU-GGGCGUAACAAAAUGUCUGACACGCCAAUUAUUUUGCUUU
.((((((....((((-((.(((..((.......))..)))))))))....)))))) ( -13.10, z-score =  -2.13, R)
>dp4.chrXR_group6 4320979 55 - 13314419
GGAAGCACUUAAAUU-GGGCGUAACAAAAUGUCUGACACGCCAAUUAUUUUGCUUU
.((((((....((((-((.(((..((.......))..)))))))))....)))))) ( -13.10, z-score =  -2.13, R)
>droPer1.super_9 2610366 55 - 3637205
GGAAGCACUUAAAUU-GGGCGUAACAAAAUGUCUGACACGCCAAUUAUUUUGCUUU
.((((((....((((-((.(((..((.......))..)))))))))....)))))) ( -13.10, z-score =  -2.13, R)
>droWil1.scaffold_180698 5337738 55 - 11422946
GGAAGCACUUAAAUU-GGCCAUAACAAAAUGUCUGACACGCCAAUUAUUUUGGUUU
.(((.((....((((-(((.....((.......))....)))))))....)).))) (  -7.00, z-score =   0.41, R)
>droVir3.scaffold_13049 2666223 55 + 25233164
GGAAGCACUUAAAUU-GGGCGUAACAAAAUGUCUGACACGCCAAUUAUUUUGCUUU
.((((((....((((-((.(((..((.......))..)))))))))....)))))) ( -13.10, z-score =  -2.13, R)
>droMoj3.scaffold_6680 7577140 55 + 24764193
GGAAGCACUUAAAUU-GGGCGUAACAAAAUGUCUGACACGCCAAUUAUUUUGCUUU
.((((((....((((-((.(((..((.......))..)))))))))....)))))) ( -13.10, z-score =  -2.13, R)
>droGri2.scaffold_15121 8721 55 + 279557
GGAAGCACUUAAAUU-GGGCGUAGCAAAAUGUCUGACACGCCAAUUAUUUUGCUUU
.((((((....((((-((.(((..((.......))..)))))))))....)))))) ( -14.50, z-score =  -2.04, R)
>anoGam1.chr2R 18641077 56 + 62725911
GUUAGUGUAUAUAUUCCUUCAAGAUUCGAUGUUUGAAAUUGCAUGUAACUUGUUUC
(((((((((........((((((........))))))..))))).))))....... (  -4.80, z-score =   0.62, R)
>consensus
GGAAGCACUUAAAUU_GGGCGUAACAAAAUGUCUGACACGCCAAUUAUUUUGCUUU
.((((((...((((...(((((..((.......))..)))))....)))))))))) ( -8.82 =  -9.13 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:22:20 2011