Locus 2030

Sequence ID dm3.chr2L
Location 15,650,354 – 15,650,445
Length 91
Max. P 0.759276
window2789 window2790

overview

Window 9

Location 15,650,354 – 15,650,445
Length 91
Sequences 11
Columns 119
Reading direction forward
Mean pairwise identity 61.32
Shannon entropy 0.72189
G+C content 0.50178
Mean single sequence MFE -25.55
Consensus MFE -10.49
Energy contribution -10.65
Covariance contribution 0.17
Combinations/Pair 1.53
Mean z-score -0.94
Structure conservation index 0.41
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.44
SVM RNA-class probability 0.694817
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 15650354 91 + 23011544
-----GUUGGA--GCCACUGUGCAUG-UUGUGAUGUGGCU-GCGGCGACUUGGGUCGAACCUGAUUGAGGAAGAGGUUUUCCGUA-UAAGUAAUGUGGAAU------------------
-----((((.(--(((((...((...-..))...))))))-.))))(((....)))((((((...........))))))((((((-(.....)))))))..------------------ ( -26.80, z-score =  -1.53, R)
>droSec1.super_3 1905058 82 + 7220098
-----GUUGGA--GCCACUGUGCAUG-UUGUGAUGUGGCU-GCGGCGACUUGGGUCGAACCUGAUUGAGGAAAAGGUUUUCCGUAGUUAGU----------------------------
-----((((.(--(((((...((...-..))...))))))-.))))(((....)))....(((((((.(((((....))))).))))))).---------------------------- ( -29.10, z-score =  -2.59, R)
>droYak2.chr2L 2654299 91 - 22324452
-----GUUGGA--GCCACUGUGCAUG-UUGUGAUGUGGCU-GCGGCGACUUAGGUCGAACCUGAUUCAAGACGAGAUUUUUCGUA-UAAGUAAAGUAGCCA------------------
-----...(.(--(((((...((...-..))...))))))-.)(((((.(((((.....))))).))...(((((....))))).-...........))).------------------ ( -28.10, z-score =  -1.68, R)
>droEre2.scaffold_4929 7395769 91 + 26641161
-----GUUGGA--GCCACUGUGCAUG-UUGUGAUGUGGCU-GCGGCGACUUGGGUCGAACCUGAUGCGGGACAAAAUAUUUCACA-UAAGUAAAGUGGCCU------------------
-----...((.--((((((.(((.((-(.((((.(((((.-...))..((((.((((....)))).))))......))).)))))-)).))).))))))))------------------ ( -27.20, z-score =  -0.51, R)
>droAna3.scaffold_12916 15520855 86 - 16180835
-----GUUUGA--GCCACUGUGCAUG-UUGUGGUGUGGUU-GCGGUGACUUGGGUCGAACCUGUAUGAGAUCGGAGU------UGAUAAACAGAGAACCCC------------------
-----((((((--(((((..(((...-..)))..))))))-.....(((((.((((............)))).))))------)..)))))..........------------------ ( -20.00, z-score =   0.57, R)
>dp4.chr4_group4 4451227 87 + 6586962
-----GUUGGA--GCCACUGUGCAUG-UUGUGAUGUGGCU-GCGGCGACUUUGGUCGAACCUGAGGGAAGGAAA-----UCAAAGAUUAGUGGAGUGCCCA------------------
-----((((.(--(((((...((...-..))...))))))-.))))..(((((((....(((......)))..)-----)))))).....(((.....)))------------------ ( -26.10, z-score =  -0.56, R)
>droPer1.super_93 73461 87 + 177177
-----GUUGGA--GCCACUGUGCAUG-UUGUGAUGUGGCU-GCGGCGACUUUGGUCGAACCUGAGGAAAGGAAA-----UCAAAGAUUAGUGGAAUGCCCA------------------
-----((((.(--(((((...((...-..))...))))))-.))))..(((((((....(((......)))..)-----)))))).....(((.....)))------------------ ( -26.10, z-score =  -1.08, R)
>droWil1.scaffold_180772 6058748 81 + 8906247
-----AUUGGA--ACCACUGUGCAAG-CUAUGAUGUGGUU-GCGGUGACUUGGGUCGAACCUGAGUGAAAUUGA-------AAACGUCAGUGGAAUG----------------------
-----......--.(((((((((((.-(........).))-))).(.(((..((.....))..))).)......-------......))))))....---------------------- ( -23.50, z-score =  -2.21, R)
>anoGam1.chr3R 37573260 107 + 53272125
----GACCGGAAUGCCACCGUGC----CCGUGGUGUGGCU-GAGGUGAACGUGGACGCACCUGCAGGGGGGGAAAGGG---AGAGAAGAGUAGGGUGAAGCAACGAGAGAGAGAGAAGA
----.(((((....)).((.(.(----(.((((((((..(-.(.(....).).).)))))).)).)).).))......---............))).......(....).......... ( -23.60, z-score =   1.13, R)
>apiMel3.Group5 9631758 98 + 13386189
AGUAUAAUGGAUUGAUAUAUCGGAUACUUACGUUUCGAUUUGCGGUGAGUUUCAUUACCGGAAUUCGUAGCUGAAUAUUCCGGUGGCUGGGAGGGUUG---------------------
.................(((((((((.(((.(((.(((.((.((((((......)))))).)).))).)))))).)).))))))).............--------------------- ( -23.50, z-score =  -0.17, R)
>droSim1.chr2L 15403635 91 + 22036055
-----GUUGGA--GCCACUGUGCAUG-UUGUGAUGUGGCU-GCGGCGACUUGGGUCGAACCUGAUUGAGGAAAAGGUUUUCCGUA-UUAGUAAAGUGGAAU------------------
-----((((.(--(((((...((...-..))...))))))-.))))(((....)))....(((((...(((((....)))))..)-))))...........------------------ ( -27.10, z-score =  -1.72, R)
>consensus
_____GUUGGA__GCCACUGUGCAUG_UUGUGAUGUGGCU_GCGGCGACUUGGGUCGAACCUGAUUGAGGAAAAAGUUUUCCGUA_UUAGUAGAGUGGCC___________________
........((...(((((..((((....))))..)))))......((((....))))..)).......................................................... (-10.49 = -10.65 +   0.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 15,650,354 – 15,650,445
Length 91
Sequences 11
Columns 119
Reading direction reverse
Mean pairwise identity 61.32
Shannon entropy 0.72189
G+C content 0.50178
Mean single sequence MFE -18.03
Consensus MFE -5.88
Energy contribution -6.58
Covariance contribution 0.70
Combinations/Pair 1.27
Mean z-score -1.49
Structure conservation index 0.33
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.61
SVM RNA-class probability 0.759276
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 15650354 91 - 23011544
------------------AUUCCACAUUACUUA-UACGGAAAACCUCUUCCUCAAUCAGGUUCGACCCAAGUCGCCGC-AGCCACAUCACAA-CAUGCACAGUGGC--UCCAAC-----
------------------...............-...((((......)))).......((..((((....))))))(.-((((((.......-........)))))--).)...----- ( -16.56, z-score =  -2.09, R)
>droSec1.super_3 1905058 82 - 7220098
----------------------------ACUAACUACGGAAAACCUUUUCCUCAAUCAGGUUCGACCCAAGUCGCCGC-AGCCACAUCACAA-CAUGCACAGUGGC--UCCAAC-----
----------------------------.........(((((....))))).......((..((((....))))))(.-((((((.......-........)))))--).)...----- ( -17.06, z-score =  -2.03, R)
>droYak2.chr2L 2654299 91 + 22324452
------------------UGGCUACUUUACUUA-UACGAAAAAUCUCGUCUUGAAUCAGGUUCGACCUAAGUCGCCGC-AGCCACAUCACAA-CAUGCACAGUGGC--UCCAAC-----
------------------.(((.((((...(((-.((((......))))..)))...(((.....))))))).)))(.-((((((.......-........)))))--).)...----- ( -20.46, z-score =  -1.77, R)
>droEre2.scaffold_4929 7395769 91 - 26641161
------------------AGGCCACUUUACUUA-UGUGAAAUAUUUUGUCCCGCAUCAGGUUCGACCCAAGUCGCCGC-AGCCACAUCACAA-CAUGCACAGUGGC--UCCAAC-----
------------------.(((.(((((((...-.))))).....(((..((......))..))).....)).)))(.-((((((.......-........)))))--).)...----- ( -20.96, z-score =  -1.16, R)
>droAna3.scaffold_12916 15520855 86 + 16180835
------------------GGGGUUCUCUGUUUAUCA------ACUCCGAUCUCAUACAGGUUCGACCCAAGUCACCGC-AACCACACCACAA-CAUGCACAGUGGC--UCAAAC-----
------------------.(((((.(((((..(((.------.....))).....)))))...))))).((((((.((-(............-..)))...)))))--).....----- ( -17.34, z-score =  -0.83, R)
>dp4.chr4_group4 4451227 87 - 6586962
------------------UGGGCACUCCACUAAUCUUUGA-----UUUCCUUCCCUCAGGUUCGACCAAAGUCGCCGC-AGCCACAUCACAA-CAUGCACAGUGGC--UCCAAC-----
------------------..(((...............((-----...(((......))).))(((....))))))(.-((((((.......-........)))))--).)...----- ( -18.56, z-score =  -0.90, R)
>droPer1.super_93 73461 87 - 177177
------------------UGGGCAUUCCACUAAUCUUUGA-----UUUCCUUUCCUCAGGUUCGACCAAAGUCGCCGC-AGCCACAUCACAA-CAUGCACAGUGGC--UCCAAC-----
------------------..(((...............((-----...(((......))).))(((....))))))(.-((((((.......-........)))))--).)...----- ( -18.56, z-score =  -1.02, R)
>droWil1.scaffold_180772 6058748 81 - 8906247
----------------------CAUUCCACUGACGUUU-------UCAAUUUCACUCAGGUUCGACCCAAGUCACCGC-AACCACAUCAUAG-CUUGCACAGUGGU--UCCAAU-----
----------------------....((((((......-------.............(((..(((....))))))((-((.(........)-.)))).)))))).--......----- ( -16.80, z-score =  -2.71, R)
>anoGam1.chr3R 37573260 107 - 53272125
UCUUCUCUCUCUCUCGUUGCUUCACCCUACUCUUCUCU---CCCUUUCCCCCCCUGCAGGUGCGUCCACGUUCACCUC-AGCCACACCACGG----GCACGGUGGCAUUCCGGUC----
.............(((.(((..((((............---.............((.(((((((....))..))))))-)(((........)----))..)))))))...)))..---- ( -19.30, z-score =  -0.02, R)
>apiMel3.Group5 9631758 98 - 13386189
---------------------CAACCCUCCCAGCCACCGGAAUAUUCAGCUACGAAUUCCGGUAAUGAAACUCACCGCAAAUCGAAACGUAAGUAUCCGAUAUAUCAAUCCAUUAUACU
---------------------...........((.((((((((..((......))))))))))..((.....))..))..((((..((....))...)))).................. ( -15.70, z-score =  -1.68, R)
>droSim1.chr2L 15403635 91 - 22036055
------------------AUUCCACUUUACUAA-UACGGAAAACCUUUUCCUCAAUCAGGUUCGACCCAAGUCGCCGC-AGCCACAUCACAA-CAUGCACAGUGGC--UCCAAC-----
------------------...............-...(((((....))))).......((..((((....))))))(.-((((((.......-........)))))--).)...----- ( -17.06, z-score =  -2.21, R)
>consensus
___________________GGCCACUCUACUAA_CACGGAAAACCUUUUCCUCAAUCAGGUUCGACCCAAGUCGCCGC_AGCCACAUCACAA_CAUGCACAGUGGC__UCCAAC_____
..........................................................(((..(((....))))))....(((((................)))))............. ( -5.88 =  -6.58 +   0.70)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:43:23 2011