Locus 998

Sequence ID dm3.chr2L
Location 7,425,800 – 7,425,876
Length 76
Max. P 0.999527
window1363 window1364

overview

Window 3

Location 7,425,800 – 7,425,876
Length 76
Sequences 15
Columns 82
Reading direction forward
Mean pairwise identity 78.75
Shannon entropy 0.49212
G+C content 0.54450
Mean single sequence MFE -32.04
Consensus MFE -24.06
Energy contribution -24.18
Covariance contribution 0.12
Combinations/Pair 1.35
Mean z-score -3.21
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.98
SVM RNA-class probability 0.999527
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 7425800 76 + 23011544
GUC-UCCUACCUUGCGCGCUAAUCAGUGACCGGGGCUGGUU--UUUUAU---AUACAGUCAGGUACCUGAAGUAGCGCGCGU
...-.........((((((((.((((..(((..(((((...--......---...))))).)))..))))..)))))))).. ( -31.70, z-score =  -3.54, R)
>droSim1.chr2L 7217370 76 + 22036055
GUC-UCCUACCUUGCGCGCUAAUCAGUGACCGGGGCUGGUU--UUUUAU---AUACAGUCAGGUACCUGAAGUAGCGCGCGU
...-.........((((((((.((((..(((..(((((...--......---...))))).)))..))))..)))))))).. ( -31.70, z-score =  -3.54, R)
>droSec1.super_3 2941260 76 + 7220098
GUC-UCCUACCUUGCGCGCUAAUCAGUGACCGGGGCUUGUU--UUUUAU---AUACAGUCAGGUACCUGAAGUAGCGCGCGU
...-.........((((((((.((((..(((..((((.((.--......---..)))))).)))..))))..)))))))).. ( -28.80, z-score =  -3.03, R)
>droYak2.chr2L 16850578 76 - 22324452
GUC-UCCUACCUUGCGCGCUAAUCAGUGACCGGGGCUGGUU--UUUUAU---AUACAGUCAGGUACCUGAAGUAGCGCGCGU
...-.........((((((((.((((..(((..(((((...--......---...))))).)))..))))..)))))))).. ( -31.70, z-score =  -3.54, R)
>droEre2.scaffold_4929 16344526 76 + 26641161
GUC-UCCUACCUUGCGCGCUAAUCAGUGACCGGGGCUGGUU--UUUUAU---AUACAGUCAGGUACCUGAAGUAGCGCGCGU
...-.........((((((((.((((..(((..(((((...--......---...))))).)))..))))..)))))))).. ( -31.70, z-score =  -3.54, R)
>droAna3.scaffold_12916 15333995 74 + 16180835
GUC-UCCUACCUUGCGCGCUAAUCAGUGACCGGGGCUGGUUU-UUGCA------ACAGUCAGGUACCUGAAGUAGCGCGCGU
...-.........((((((((.((((..(((..(((((....-.....------.))))).)))..))))..)))))))).. ( -31.90, z-score =  -3.03, R)
>dp4.chr4_group1 4175740 76 + 5278887
GUC-UCCUACCAUGCGCGCUAAUCAGAGACCGGGGCUGGUUU-UUUCAC----UGCAGUCAGGUACCUGAAGUAGCGCGCGU
...-.......((((((((((.((((..(((..(((((....-......----..))))).)))..))))..)))))))))) ( -31.70, z-score =  -2.94, R)
>droPer1.super_5 5727157 76 - 6813705
GUC-UCCUACCAUGCGCGCUAAUCAGAGACCGGGGCUGGUUU-UUUCAC----UGCAGUCAGGUACCUGAAGUAGCGCGCGU
...-.......((((((((((.((((..(((..(((((....-......----..))))).)))..))))..)))))))))) ( -31.70, z-score =  -2.94, R)
>droWil1.scaffold_180772 3648555 81 - 8906247
GUC-UCUUACCUUGCGCGCUAAUCAGUGACCAGGGCUGAGUAAUUUUAUUCAAUACAGUCAGGUACCUGAAGUAGCGCGCGU
...-.........((((((((.((((..(((..(((((.((...........)).))))).)))..))))..)))))))).. ( -29.00, z-score =  -3.28, R)
>droMoj3.scaffold_6500 13952913 79 - 32352404
GUC-UUUUACCGUGCGCGCUAAUCAGUGACCGGGGCUGGUUUCGAUUAUCU--CACAGUCAGGUACCUGAAGUAGCGCGCGU
...-.........((((((((.((((..(((..(((((.............--..))))).)))..))))..)))))))).. ( -31.46, z-score =  -2.90, R)
>droVir3.scaffold_12963 4786196 79 - 20206255
GUC-UUUUACCGUGCGCGCUAAUCAGUGACCGGGGCUGGUUUUGGUUAUCC--CACAGUCAGGUACCUGAAGUAGCGCGCGU
...-.........((((((((.((((..(((..(((((....(((.....)--))))))).)))..))))..)))))))).. ( -32.70, z-score =  -2.90, R)
>droGri2.scaffold_15126 5008400 79 + 8399593
GUC-GUUUACCGCGCGCGCUAAUCAGUGACCGGGGCUGGUUUUGAUUAUCC--CACAGUCAGGUACCUGAAGUAGCGCGCGU
...-.......((((((((((.((((..(((..(((((.............--..))))).)))..))))..)))))))))) ( -34.46, z-score =  -3.31, R)
>anoGam1.chr3R 39066347 81 + 53272125
GCCGUCUAAUGACACGCGCUAAGCAGGAACCGGGACUUGGUACACAUUCGC-UAGCAGUCAGGUACCUGAAGUAGCGCGCGU
((.(((....)))..((((((..((((.(((..((((((((........))-))..)))).))).))))...)))))))).. ( -33.10, z-score =  -2.82, R)
>apiMel3.Group4 8490912 79 - 10796202
GUC-GUGCGCAACGCGCGUUACUCGGGUACUUUAGGCUGUGCCAAUUUCGA--AUCAGUCAGGUACCUGAAGUAGCGCGCGC
...-........((((((((((((((((((((..(((((...(......).--..)))))))))))))).))))))))))). ( -37.10, z-score =  -4.00, R)
>triCas2.ChLG9 5914742 75 - 15222296
GCC-UGUUGCUACGCGUGUUACCUCAGUACCU-AGGCUGGGGUU-UUUCGA--A--AGUCAGGUACCUGAAGUAGCGCGCGC
...-........((((((((((.(((((((((-.((((..((..-..))..--.--))))))))).)))).)))))))))). ( -31.90, z-score =  -2.83, R)
>consensus
GUC_UCCUACCUUGCGCGCUAAUCAGUGACCGGGGCUGGUUU_UUUUAU____UACAGUCAGGUACCUGAAGUAGCGCGCGU
............(((((((((.((((..(((..((((...................)))).)))..))))..))))))))). (-24.06 = -24.18 +   0.12)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 4

Location 7,425,800 – 7,425,876
Length 76
Sequences 15
Columns 82
Reading direction reverse
Mean pairwise identity 78.75
Shannon entropy 0.49212
G+C content 0.54450
Mean single sequence MFE -26.88
Consensus MFE -19.16
Energy contribution -19.51
Covariance contribution 0.35
Combinations/Pair 1.20
Mean z-score -2.30
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.98
SVM RNA-class probability 0.996786
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 7425800 76 - 23011544
ACGCGCGCUACUUCAGGUACCUGACUGUAU---AUAAAA--AACCAGCCCCGGUCACUGAUUAGCGCGCAAGGUAGGA-GAC
..((((((((..((((..(((.(.(((...---......--...)))..).)))..)))).)))))))).........-... ( -25.30, z-score =  -2.34, R)
>droSim1.chr2L 7217370 76 - 22036055
ACGCGCGCUACUUCAGGUACCUGACUGUAU---AUAAAA--AACCAGCCCCGGUCACUGAUUAGCGCGCAAGGUAGGA-GAC
..((((((((..((((..(((.(.(((...---......--...)))..).)))..)))).)))))))).........-... ( -25.30, z-score =  -2.34, R)
>droSec1.super_3 2941260 76 - 7220098
ACGCGCGCUACUUCAGGUACCUGACUGUAU---AUAAAA--AACAAGCCCCGGUCACUGAUUAGCGCGCAAGGUAGGA-GAC
..((((((((..((((..(((.(..(((..---......--.)))..)...)))..)))).)))))))).........-... ( -24.00, z-score =  -2.04, R)
>droYak2.chr2L 16850578 76 + 22324452
ACGCGCGCUACUUCAGGUACCUGACUGUAU---AUAAAA--AACCAGCCCCGGUCACUGAUUAGCGCGCAAGGUAGGA-GAC
..((((((((..((((..(((.(.(((...---......--...)))..).)))..)))).)))))))).........-... ( -25.30, z-score =  -2.34, R)
>droEre2.scaffold_4929 16344526 76 - 26641161
ACGCGCGCUACUUCAGGUACCUGACUGUAU---AUAAAA--AACCAGCCCCGGUCACUGAUUAGCGCGCAAGGUAGGA-GAC
..((((((((..((((..(((.(.(((...---......--...)))..).)))..)))).)))))))).........-... ( -25.30, z-score =  -2.34, R)
>droAna3.scaffold_12916 15333995 74 - 16180835
ACGCGCGCUACUUCAGGUACCUGACUGU------UGCAA-AAACCAGCCCCGGUCACUGAUUAGCGCGCAAGGUAGGA-GAC
..((((((((..((((.....((((((.------.((..-......))..)))))))))).)))))))).........-... ( -27.50, z-score =  -2.32, R)
>dp4.chr4_group1 4175740 76 - 5278887
ACGCGCGCUACUUCAGGUACCUGACUGCA----GUGAAA-AAACCAGCCCCGGUCUCUGAUUAGCGCGCAUGGUAGGA-GAC
..((((((((..((((..(((.(.(((..----.(....-)...)))..).)))..)))).)))))))).........-... ( -27.40, z-score =  -2.06, R)
>droPer1.super_5 5727157 76 + 6813705
ACGCGCGCUACUUCAGGUACCUGACUGCA----GUGAAA-AAACCAGCCCCGGUCUCUGAUUAGCGCGCAUGGUAGGA-GAC
..((((((((..((((..(((.(.(((..----.(....-)...)))..).)))..)))).)))))))).........-... ( -27.40, z-score =  -2.06, R)
>droWil1.scaffold_180772 3648555 81 + 8906247
ACGCGCGCUACUUCAGGUACCUGACUGUAUUGAAUAAAAUUACUCAGCCCUGGUCACUGAUUAGCGCGCAAGGUAAGA-GAC
..((((((((..((((..(((.(.(((.(((......)))....))).)..)))..)))).)))))))).........-... ( -26.80, z-score =  -2.91, R)
>droMoj3.scaffold_6500 13952913 79 + 32352404
ACGCGCGCUACUUCAGGUACCUGACUGUG--AGAUAAUCGAAACCAGCCCCGGUCACUGAUUAGCGCGCACGGUAAAA-GAC
..((((((((..((((..(((.(.(((((--(.....)))....)))..).)))..)))).)))))))).........-... ( -26.20, z-score =  -2.39, R)
>droVir3.scaffold_12963 4786196 79 + 20206255
ACGCGCGCUACUUCAGGUACCUGACUGUG--GGAUAACCAAAACCAGCCCCGGUCACUGAUUAGCGCGCACGGUAAAA-GAC
..((((((((..((((.....((((((.(--((..............))))))))))))).)))))))).........-... ( -30.44, z-score =  -3.37, R)
>droGri2.scaffold_15126 5008400 79 - 8399593
ACGCGCGCUACUUCAGGUACCUGACUGUG--GGAUAAUCAAAACCAGCCCCGGUCACUGAUUAGCGCGCGCGGUAAAC-GAC
.(((((((((..((((.....((((((.(--((..............))))))))))))).)))))))))((.....)-).. ( -32.24, z-score =  -3.42, R)
>anoGam1.chr3R 39066347 81 - 53272125
ACGCGCGCUACUUCAGGUACCUGACUGCUA-GCGAAUGUGUACCAAGUCCCGGUUCCUGCUUAGCGCGUGUCAUUAGACGGC
((((((((((...((((.(((.((((....-(((....)))....))))..))).))))..))))))))))........... ( -30.10, z-score =  -1.87, R)
>apiMel3.Group4 8490912 79 + 10796202
GCGCGCGCUACUUCAGGUACCUGACUGAU--UCGAAAUUGGCACAGCCUAAAGUACCCGAGUAACGCGCGUUGCGCAC-GAC
(((((((.(((((..(((((.(((.....--))).....(((...)))....))))).))))).))))))).......-... ( -25.30, z-score =  -1.10, R)
>triCas2.ChLG9 5914742 75 + 15222296
GCGCGCGCUACUUCAGGUACCUGACU--U--UCGAAA-AACCCCAGCCU-AGGUACUGAGGUAACACGCGUAGCAACA-GGC
(((((.(.((((((((.((((((...--.--......-..........)-))))))))))))).).))))).......-... ( -24.55, z-score =  -1.67, R)
>consensus
ACGCGCGCUACUUCAGGUACCUGACUGUA____AUAAAA_AAACCAGCCCCGGUCACUGAUUAGCGCGCAAGGUAGGA_GAC
..((((((((..((((..(((..............................)))..)))).))))))))............. (-19.16 = -19.51 +   0.35)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:23:41 2011