Locus 9077

Sequence ID dm3.chr3R
Location 3,966,447 – 3,966,523
Length 76
Max. P 0.997761
window12451 window12452

overview

Window 1

Location 3,966,447 – 3,966,523
Length 76
Sequences 13
Columns 88
Reading direction forward
Mean pairwise identity 68.63
Shannon entropy 0.63413
G+C content 0.58493
Mean single sequence MFE -27.02
Consensus MFE -24.23
Energy contribution -20.90
Covariance contribution -3.33
Combinations/Pair 1.85
Mean z-score -2.06
Structure conservation index 0.90
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.17
SVM RNA-class probability 0.997761
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 3966447 76 + 27905053
-CCGAUCCUGCCAGGAGUCGAACCUGGAAUCU---------UCUGAUCCGUAGUCAGACGCGUUAUCC-AUUGCGCCACAGGACCGA-
-.((.((((((((((.......))))).....---------((((((.....)))))).((((.....-...))))..))))).)).- ( -25.60, z-score =  -2.08, R)
>droSim1.chr3R 10225134 76 - 27517382
-CCGAUCCUGCCAGGAGUCGAACCUGGAAUCU---------UCUGAUCCGUAGUCAGACGCGUUAUCC-AUUGCGCCACAGGACCGA-
-.((.((((((((((.......))))).....---------((((((.....)))))).((((.....-...))))..))))).)).- ( -25.60, z-score =  -2.08, R)
>droSec1.super_20 605364 83 - 1148123
-UCGCAGCCGGUAGGAUUCGAACCUACGCUCCCAGAGGGAAUCUGAUUUCGAGUCAGACGCCUUAACC-ACUCGGCCACGACUGC---
-(((..(((((((((.......)))))........((((..((((((.....))))))..))))....-...))))..)))....--- ( -27.00, z-score =  -1.57, R)
>droYak2.chr3R 8038966 77 + 28832112
UGCGAUCCUGCCAGGAGUCGAACCUGGAAUCU---------UCUGAUCCGUAGUCAGACGCGUUAUCC-AUUGCGCCACAGGACCGA-
..((.((((((((((.......))))).....---------((((((.....)))))).((((.....-...))))..))))).)).- ( -25.50, z-score =  -1.70, R)
>droEre2.scaffold_4770 131891 76 - 17746568
-CCGAUCCUGCCAGGAGUCGAACCUGGAAUCU---------UCUGAUCCGUAGUCAGACGCGUUAUCC-AUUGCGCCACAGGACCGA-
-.((.((((((((((.......))))).....---------((((((.....)))))).((((.....-...))))..))))).)).- ( -25.60, z-score =  -2.08, R)
>droAna3.scaffold_13266 18744044 66 + 19884421
-UCGAUCCUGCCAGGAGUCGAACCUGGAAUCU---------UCUGAUCCGUAGUCAGACGCGUUAUCC-AUUGCGCC-----------
-..(((....(((((.......))))).))).---------((((((.....)))))).((((.....-...)))).----------- ( -17.90, z-score =  -0.84, R)
>dp4.chr2 7051452 76 - 30794189
-CUGUUUCCGCCCGGGAUUGAACCGGGGGCCU---------UCCGCGUGUUAGGCGGAUGUGAUAACC-ACUACACCACGGAAACUG-
-..((((((((((((.......)))))((...---------(((((.......))))).(((.....)-))....)).)))))))..- ( -30.10, z-score =  -2.16, R)
>droPer1.super_73 202111 76 - 267513
-CCGAUCCUGCCAGGAGUCGAACCUGGAAUCU---------UCUGAUCCGUAGUCAGACGCGUUAUCC-AUUGCGCCACAGGACCCG-
-....((((((((((.......))))).....---------((((((.....)))))).((((.....-...))))..)))))....- ( -23.20, z-score =  -1.66, R)
>droWil1.scaffold_180700 738705 75 - 6630534
--CGAUCCUGCCAGGAGUCGAACCUGGAAUCU---------UCUGAUCCGUAGUCAGACGCGUUAUCC-AUUGCGCCACAGGACCGU-
--((.((((((((((.......))))).....---------((((((.....)))))).((((.....-...))))..))))).)).- ( -24.80, z-score =  -1.82, R)
>droMoj3.scaffold_6496 25292866 77 + 26866924
-UCGCCCCCGGGUGGACUCGAACCACCAACCU---------UUCGGUUAACAGCCGAACGCGCUAACCGAUUGCGCCACGGAGGCCA-
-..(((.((((((((.......))))).....---------((((((.....)))))).((((.........))))..))).)))..- ( -30.40, z-score =  -2.55, R)
>droVir3.scaffold_12875 15833733 77 - 20611582
-UCGCCCCCGGGUGGACUCGAACCACCAACCU---------UUCGGUUAACAGCCGAACGCGCUAACCGAUUGCGCCACGGAGGCGG-
-.((((.((((((((.......))))).....---------((((((.....)))))).((((.........))))..))).)))).- ( -33.10, z-score =  -2.88, R)
>droGri2.scaffold_15245 208595 77 + 18325388
-UCGCCCCCGGGUGGACUCGAACCACCAACCU---------UUCGGUUAACAGCCGAACGCGCUAACCAAUUGCGCCACGGAGGCUG-
-..(((.((((((((.......))))).....---------((((((.....)))))).((((.........))))..))).)))..- ( -30.80, z-score =  -3.21, R)
>anoGam1.chr3R 13656675 77 + 53272125
-AUGUUUCCGCCCGGGAUCGAACCGGGGGCCU---------UCCGCGUGUUAGGCGGAUGUGAUAACC-ACUACACCACGGAAACAGA
-.(((((((((((((.......)))))((...---------(((((.......))))).(((.....)-))....)).)))))))).. ( -31.60, z-score =  -2.12, R)
>consensus
_CCGAUCCUGCCAGGAGUCGAACCUGGAAUCU_________UCUGAUCCGUAGUCAGACGCGUUAUCC_AUUGCGCCACAGGACCGA_
.....((((((((((.......)))))..............((((((.....)))))).((((.........))))..)))))..... (-24.23 = -20.90 +  -3.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 3,966,447 – 3,966,523
Length 76
Sequences 13
Columns 88
Reading direction reverse
Mean pairwise identity 68.63
Shannon entropy 0.63413
G+C content 0.58493
Mean single sequence MFE -30.09
Consensus MFE -27.53
Energy contribution -23.03
Covariance contribution -4.50
Combinations/Pair 2.00
Mean z-score -1.83
Structure conservation index 0.91
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.93
SVM RNA-class probability 0.996458
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 3966447 76 - 27905053
-UCGGUCCUGUGGCGCAAU-GGAUAACGCGUCUGACUACGGAUCAGA---------AGAUUCCAGGUUCGACUCCUGGCAGGAUCGG-
-.((((((((((((((...-.......))))).......(((((...---------.)))))((((.......))))))))))))).- ( -28.70, z-score =  -1.86, R)
>droSim1.chr3R 10225134 76 + 27517382
-UCGGUCCUGUGGCGCAAU-GGAUAACGCGUCUGACUACGGAUCAGA---------AGAUUCCAGGUUCGACUCCUGGCAGGAUCGG-
-.((((((((((((((...-.......))))).......(((((...---------.)))))((((.......))))))))))))).- ( -28.70, z-score =  -1.86, R)
>droSec1.super_20 605364 83 + 1148123
---GCAGUCGUGGCCGAGU-GGUUAAGGCGUCUGACUCGAAAUCAGAUUCCCUCUGGGAGCGUAGGUUCGAAUCCUACCGGCUGCGA-
---((((((((((((....-)))))..((((((((.......))))))((((...))))))(((((.......))))))))))))..- ( -31.20, z-score =  -1.27, R)
>droYak2.chr3R 8038966 77 - 28832112
-UCGGUCCUGUGGCGCAAU-GGAUAACGCGUCUGACUACGGAUCAGA---------AGAUUCCAGGUUCGACUCCUGGCAGGAUCGCA
-.((((((((((((((...-.......))))).......(((((...---------.)))))((((.......))))))))))))).. ( -27.80, z-score =  -1.44, R)
>droEre2.scaffold_4770 131891 76 + 17746568
-UCGGUCCUGUGGCGCAAU-GGAUAACGCGUCUGACUACGGAUCAGA---------AGAUUCCAGGUUCGACUCCUGGCAGGAUCGG-
-.((((((((((((((...-.......))))).......(((((...---------.)))))((((.......))))))))))))).- ( -28.70, z-score =  -1.86, R)
>droAna3.scaffold_13266 18744044 66 - 19884421
-----------GGCGCAAU-GGAUAACGCGUCUGACUACGGAUCAGA---------AGAUUCCAGGUUCGACUCCUGGCAGGAUCGA-
-----------.(((....-......))).((((((....).)))))---------.(((((((((.......)))))...))))..- ( -18.10, z-score =  -0.16, R)
>dp4.chr2 7051452 76 + 30794189
-CAGUUUCCGUGGUGUAGU-GGUUAUCACAUCCGCCUAACACGCGGA---------AGGCCCCCGGUUCAAUCCCGGGCGGAAACAG-
-..(((((((.(((.(.((-(.....))).(((((.......)))))---------).)))(((((.......))))))))))))..- ( -30.10, z-score =  -2.51, R)
>droPer1.super_73 202111 76 + 267513
-CGGGUCCUGUGGCGCAAU-GGAUAACGCGUCUGACUACGGAUCAGA---------AGAUUCCAGGUUCGACUCCUGGCAGGAUCGG-
-..(((((((((((((...-.......))))).......(((((...---------.)))))((((.......))))))))))))..- ( -26.60, z-score =  -1.09, R)
>droWil1.scaffold_180700 738705 75 + 6630534
-ACGGUCCUGUGGCGCAAU-GGAUAACGCGUCUGACUACGGAUCAGA---------AGAUUCCAGGUUCGACUCCUGGCAGGAUCG--
-.((((((((((((((...-.......))))).......(((((...---------.)))))((((.......)))))))))))))-- ( -27.80, z-score =  -1.89, R)
>droMoj3.scaffold_6496 25292866 77 - 26866924
-UGGCCUCCGUGGCGCAAUCGGUUAGCGCGUUCGGCUGUUAACCGAA---------AGGUUGGUGGUUCGAGUCCACCCGGGGGCGA-
-..(((((((.(((((.........)))).((((((..((((((...---------.))))))..).)))))....).)))))))..- ( -36.90, z-score =  -2.27, R)
>droVir3.scaffold_12875 15833733 77 + 20611582
-CCGCCUCCGUGGCGCAAUCGGUUAGCGCGUUCGGCUGUUAACCGAA---------AGGUUGGUGGUUCGAGUCCACCCGGGGGCGA-
-.((((((((.(((((.........)))).((((((..((((((...---------.))))))..).)))))....).)))))))).- ( -39.00, z-score =  -2.78, R)
>droGri2.scaffold_15245 208595 77 - 18325388
-CAGCCUCCGUGGCGCAAUUGGUUAGCGCGUUCGGCUGUUAACCGAA---------AGGUUGGUGGUUCGAGUCCACCCGGGGGCGA-
-..(((((((.(((((.........)))).((((((..((((((...---------.))))))..).)))))....).)))))))..- ( -37.10, z-score =  -2.89, R)
>anoGam1.chr3R 13656675 77 - 53272125
UCUGUUUCCGUGGUGUAGU-GGUUAUCACAUCCGCCUAACACGCGGA---------AGGCCCCCGGUUCGAUCCCGGGCGGAAACAU-
..((((((((.(((.(.((-(.....))).(((((.......)))))---------).)))(((((.......))))))))))))).- ( -30.50, z-score =  -1.87, R)
>consensus
_CCGGUCCCGUGGCGCAAU_GGAUAACGCGUCUGACUACGGAUCAGA_________AGAUUCCAGGUUCGACUCCUGGCAGGAUCGA_
...(((((((..(((...........))).(((((.......)))))..............(((((.......))))))))))))... (-27.53 = -23.03 +  -4.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:57:34 2011