Locus 12277

Sequence ID dm3.chr3R
Location 27,043,283 – 27,043,383
Length 100
Max. P 0.960557
window16881 window16882

overview

Window 1

Location 27,043,283 – 27,043,383
Length 100
Sequences 14
Columns 116
Reading direction forward
Mean pairwise identity 72.82
Shannon entropy 0.58230
G+C content 0.49360
Mean single sequence MFE -27.71
Consensus MFE -18.44
Energy contribution -18.29
Covariance contribution -0.15
Combinations/Pair 1.24
Mean z-score -0.46
Structure conservation index 0.67
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.46
SVM RNA-class probability 0.702824
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 27043283 100 + 27905053
--------------AACAGC-UGGCUC-GGCCGAUUCUCAGACCUUCCCGGGGCAAUGGUUUGUGGAGUAAUCAGAUACUCGUUGUGUGGGCCCCAGAUGCUAGUUUGCAACUGAC
--------------..((((-(((...-((((.((.(.((((((.((....))....)))))).)(((((......))))).....)).)))))))).(((......))).))).. ( -29.30, z-score =   0.56, R)
>droAna3.scaffold_13340 14434699 99 + 23697760
--------------AACAACAUGGCUU-GGCCGAUUCUCAGACCUUCCCGGGGCAA--AAUAAGAGAGUAAUCAGAUACUCGUUGUGUGUGCCCCAGAUGCUGGAUUGUAACUGAC
--------------.((((..((((..-.))))..((.(((....((..((((((.--.((((..(((((......))))).))))...)))))).))..)))))))))....... ( -28.10, z-score =  -1.09, R)
>droEre2.scaffold_4820 9532348 100 - 10470090
--------------AACAGC-AUGCUC-GGCCAAUUCUCAGACCUUCCCGGGGCAAUGGUUCGUGGAGUAAUCAGAUACUCGUUGUGUGAGCCCCAGAUGCUAGUUUGCAACUGAC
--------------.(((((-...(.(-(((((..((((.(......).))))...))).))).)(((((......))))))))))........(((.(((......))).))).. ( -23.40, z-score =   1.42, R)
>droYak2.chr3R 27979653 100 + 28832112
--------------AACAGC-AGGCUC-GGCCAAUUCUCAGACCUUCCCGGGGCAAUGGUUUGUGGAGUAAUCAGAUACUCGUUGUGUGAGCCCCAGAUGCUAGUUUGCAACUGAC
--------------......-.(((((-(..((((.(.((((((.((....))....)))))).)(((((......)))))))))..)))))).(((.(((......))).))).. ( -30.40, z-score =  -0.39, R)
>droSec1.super_4 5861277 100 + 6179234
--------------AACAGC-UGGCUC-GGCCGAUUCUCAGACCUUCCCGGGGCAAUGGUUUGUGGAGUAAUCAGAUACUCGUUGUGUGGGCCCCAGAUGCUAGUUUGCAACUGAC
--------------..((((-(((...-((((.((.(.((((((.((....))....)))))).)(((((......))))).....)).)))))))).(((......))).))).. ( -29.30, z-score =   0.56, R)
>droSim1.chr3R 26686454 100 + 27517382
--------------AACAGC-UGGCUC-GGCCGAUUCUCAGACCUUCCCGGGGCAAUGGUUUGUGGAGUAAUCAGAUACUCGUUGUGUGGGCCCCAGAUGCUAGUUUGCAACUGAC
--------------..((((-(((...-((((.((.(.((((((.((....))....)))))).)(((((......))))).....)).)))))))).(((......))).))).. ( -29.30, z-score =   0.56, R)
>droPer1.super_7 1566407 109 - 4445127
AUGUUGU-AACAACA-CAAGGAGGCUU-GGCCAAAUCUCAGACCUUCCCGGGGCA----AAGUAAGAGUAAUCAGAUACUCGUUGUGUGUGCCCCAGAUGCUAGUUUGUAACUGAC
.....((-.((((.(-(..(((((..(-((.......)))..)))))..((((((----......(((((......)))))........))))))........)))))).)).... ( -28.14, z-score =  -0.17, R)
>dp4.chr2 30707174 109 - 30794189
AUGUUGU-AACAACA-CAAGGAGGCUU-GGCCAAAUCUCAGACCUUCCCGGGGCA----AAGUAAGAGUAAUCAGAUACUCGUUGUGUGUGCCCCAGAUGCUAGUUUGUAACUGAC
.....((-.((((.(-(..(((((..(-((.......)))..)))))..((((((----......(((((......)))))........))))))........)))))).)).... ( -28.14, z-score =  -0.17, R)
>droWil1.scaffold_181108 710415 107 + 4707319
AUGUUGUACA---AAACACACAAGCUUCGACCAAUUCUCAGACCUUCCCGGGGCA----A--AGAGAGUAAUCAGAUACUCGUUAUGUGUGCCCCAGAUGCUAGAUUGCAACUGAC
..........---...((((((.((((((...................)))))).----.--...(((((......)))))....))))))...(((.(((......))).))).. ( -25.11, z-score =  -0.84, R)
>droVir3.scaffold_12855 8932326 114 - 10161210
AUGUUGU-UACAGCAACAAGGGAGCUUUGACCAUAUCUCAGACCUUCCCGGGGCGUU-GUAAAAAGAGUAAUCAGAUACUCGUUGUGUGUGCCCCAGAUGCUAGAUUGUAACUGAC
.....((-(((((((.(..(((((.(((((.......))))).))))).((((((..-.......(((((......)))))........)))))).).))).....)))))).... ( -32.33, z-score =  -1.41, R)
>droMoj3.scaffold_6540 7172155 112 - 34148556
GCGUUGU-UACGGCAACAAGGGAGCUUUGACCAAAUCUCAGACCUUCCCGGGGCA---AUCAUAAGAGUAAUCAGAUACUCGUUGUGUGUGCCCCAGAUGCUAGAUUGUAACUGAC
..(((((-(((((((.(..(((((.(((((.......))))).))))).((((((---..((((((((((......))))).)))))..)))))).).)))).....))))).))) ( -38.40, z-score =  -3.01, R)
>droGri2.scaffold_14624 417492 112 - 4233967
UUGUUGUGCACACAAACAAGGGAGCUUUGACCAAUUCUCAGACCUUCCCGGGGCU----UUUAUAGAGUAAUCAGAUACUCGUUGUGUGUGCCCCAGAUGCUAGAUUGUAACUGAC
.....(..(((((((.(..(((((.(((((.......))))).)))))..)....----......(((((......))))).)))))))..)..(((.(((......))).))).. ( -32.00, z-score =  -1.39, R)
>anoGam1.chr2R 17983806 85 - 62725911
----------------------------UGCCUUAUCUCAGACCUUCCCGAAGCAA--ACAACCAGAGUAACCAGGUACUCG-UACGGGUGCUCCAAGUGCGAGAUUACCACUAGC
----------------------------(((((...(((.................--.......))).....)))))((((-(((.((....))..)))))))............ ( -15.86, z-score =   0.69, R)
>triCas2.ChLG3 160638 76 + 32080666
-----------------------------------UCUCAGACCUUCCCGGGGCU----UUACAAGUGUAA-CAAGUACACAGUAAGUAAGCCCCAAAUGCAAGAUUGUCACAGAC
-----------------------------------.....(((..((..((((((----((((..(((((.-....))))).)))...)))))))........))..)))...... ( -18.10, z-score =  -1.80, R)
>consensus
______________AACAAC_AGGCUU_GGCCAAUUCUCAGACCUUCCCGGGGCAA__GUUAGUAGAGUAAUCAGAUACUCGUUGUGUGUGCCCCAGAUGCUAGAUUGCAACUGAC
.....................................((((........(((((...........(((((......))))).........)))))...(((......))).)))). (-18.44 = -18.29 +  -0.15)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 27,043,283 – 27,043,383
Length 100
Sequences 14
Columns 116
Reading direction reverse
Mean pairwise identity 72.82
Shannon entropy 0.58230
G+C content 0.49360
Mean single sequence MFE -29.75
Consensus MFE -20.81
Energy contribution -20.07
Covariance contribution -0.74
Combinations/Pair 1.43
Mean z-score -1.05
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.68
SVM RNA-class probability 0.960557
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 27043283 100 - 27905053
GUCAGUUGCAAACUAGCAUCUGGGGCCCACACAACGAGUAUCUGAUUACUCCACAAACCAUUGCCCCGGGAAGGUCUGAGAAUCGGCC-GAGCCA-GCUGUU--------------
..(((((((.........((((((((.........(((((......)))))...........))))))))..((((........))))-..).))-))))..-------------- ( -30.35, z-score =  -0.86, R)
>droAna3.scaffold_13340 14434699 99 - 23697760
GUCAGUUACAAUCCAGCAUCUGGGGCACACACAACGAGUAUCUGAUUACUCUCUUAUU--UUGCCCCGGGAAGGUCUGAGAAUCGGCC-AAGCCAUGUUGUU--------------
.......(((((...((.(((((((((........(((((......))))).......--.)))))))))..((((........))))-..))...))))).-------------- ( -30.39, z-score =  -1.86, R)
>droEre2.scaffold_4820 9532348 100 + 10470090
GUCAGUUGCAAACUAGCAUCUGGGGCUCACACAACGAGUAUCUGAUUACUCCACGAACCAUUGCCCCGGGAAGGUCUGAGAAUUGGCC-GAGCAU-GCUGUU--------------
..(((((((.........((((((((.........(((((......)))))...........))))))))..((((........))))-..))).-))))..-------------- ( -31.65, z-score =  -1.16, R)
>droYak2.chr3R 27979653 100 - 28832112
GUCAGUUGCAAACUAGCAUCUGGGGCUCACACAACGAGUAUCUGAUUACUCCACAAACCAUUGCCCCGGGAAGGUCUGAGAAUUGGCC-GAGCCU-GCUGUU--------------
..((((.((.........((((((((.........(((((......)))))...........))))))))..((((........))))-..))..-))))..-------------- ( -30.65, z-score =  -0.91, R)
>droSec1.super_4 5861277 100 - 6179234
GUCAGUUGCAAACUAGCAUCUGGGGCCCACACAACGAGUAUCUGAUUACUCCACAAACCAUUGCCCCGGGAAGGUCUGAGAAUCGGCC-GAGCCA-GCUGUU--------------
..(((((((.........((((((((.........(((((......)))))...........))))))))..((((........))))-..).))-))))..-------------- ( -30.35, z-score =  -0.86, R)
>droSim1.chr3R 26686454 100 - 27517382
GUCAGUUGCAAACUAGCAUCUGGGGCCCACACAACGAGUAUCUGAUUACUCCACAAACCAUUGCCCCGGGAAGGUCUGAGAAUCGGCC-GAGCCA-GCUGUU--------------
..(((((((.........((((((((.........(((((......)))))...........))))))))..((((........))))-..).))-))))..-------------- ( -30.35, z-score =  -0.86, R)
>droPer1.super_7 1566407 109 + 4445127
GUCAGUUACAAACUAGCAUCUGGGGCACACACAACGAGUAUCUGAUUACUCUUACUU----UGCCCCGGGAAGGUCUGAGAUUUGGCC-AAGCCUCCUUG-UGUUGUU-ACAACAU
....((.((((....((((((((((((........(((((......)))))......----)))))))))..((((........))))-.........))-).)))).-))..... ( -31.04, z-score =  -1.28, R)
>dp4.chr2 30707174 109 + 30794189
GUCAGUUACAAACUAGCAUCUGGGGCACACACAACGAGUAUCUGAUUACUCUUACUU----UGCCCCGGGAAGGUCUGAGAUUUGGCC-AAGCCUCCUUG-UGUUGUU-ACAACAU
....((.((((....((((((((((((........(((((......)))))......----)))))))))..((((........))))-.........))-).)))).-))..... ( -31.04, z-score =  -1.28, R)
>droWil1.scaffold_181108 710415 107 - 4707319
GUCAGUUGCAAUCUAGCAUCUGGGGCACACAUAACGAGUAUCUGAUUACUCUCU--U----UGCCCCGGGAAGGUCUGAGAAUUGGUCGAAGCUUGUGUGUUU---UGUACAACAU
.((((.(((......)))(((((((((........(((((......)))))...--.----))))))))).....))))...(((..((((((......))))---))..)))... ( -30.70, z-score =  -0.95, R)
>droVir3.scaffold_12855 8932326 114 + 10161210
GUCAGUUACAAUCUAGCAUCUGGGGCACACACAACGAGUAUCUGAUUACUCUUUUUAC-AACGCCCCGGGAAGGUCUGAGAUAUGGUCAAAGCUCCCUUGUUGCUGUA-ACAACAU
..((((.((((...(((.((((((((.........(((((......))))).......-...))))))))..(..(........)..)...)))...)))).))))..-....... ( -31.61, z-score =  -1.65, R)
>droMoj3.scaffold_6540 7172155 112 + 34148556
GUCAGUUACAAUCUAGCAUCUGGGGCACACACAACGAGUAUCUGAUUACUCUUAUGAU---UGCCCCGGGAAGGUCUGAGAUUUGGUCAAAGCUCCCUUGUUGCCGUA-ACAACGC
....((((((((((.((.(((((((((..((.((.(((((......))))))).))..---)))))))))...))...))))).(((..(((....)))...))))))-))..... ( -33.80, z-score =  -1.74, R)
>droGri2.scaffold_14624 417492 112 + 4233967
GUCAGUUACAAUCUAGCAUCUGGGGCACACACAACGAGUAUCUGAUUACUCUAUAAA----AGCCCCGGGAAGGUCUGAGAAUUGGUCAAAGCUCCCUUGUUUGUGUGCACAACAA
....(((....(((((...)))))(((((((.((((((((......)))))......----......((((.(.(.(((.......))).).)))))..))))))))))..))).. ( -27.70, z-score =  -0.12, R)
>anoGam1.chr2R 17983806 85 + 62725911
GCUAGUGGUAAUCUCGCACUUGGAGCACCCGUA-CGAGUACCUGGUUACUCUGGUUGU--UUGCUUCGGGAAGGUCUGAGAUAAGGCA----------------------------
....((((.....)))).(((((((((..((..-((((((......))))).)..)).--.)))))))))...((((......)))).---------------------------- ( -23.20, z-score =   0.61, R)
>triCas2.ChLG3 160638 76 - 32080666
GUCUGUGACAAUCUUGCAUUUGGGGCUUACUUACUGUGUACUUG-UUACACUUGUAA----AGCCCCGGGAAGGUCUGAGA-----------------------------------
.(((..(((..(((......((((((((...(((.(((((....-.)))))..))))----))))))))))..)))..)))----------------------------------- ( -23.60, z-score =  -1.83, R)
>consensus
GUCAGUUACAAACUAGCAUCUGGGGCACACACAACGAGUAUCUGAUUACUCUACAAAC__UUGCCCCGGGAAGGUCUGAGAAUUGGCC_AAGCCU_GUUGUU______________
....((((.....)))).((((((((.........(((((......)))))...........))))))))..((((........))))............................ (-20.81 = -20.07 +  -0.74)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:59:08 2011