Locus 1281

Sequence ID dm3.chr2L
Location 9,769,030 – 9,769,125
Length 95
Max. P 0.748383
window1744 window1745

overview

Window 4

Location 9,769,030 – 9,769,120
Length 90
Sequences 12
Columns 110
Reading direction reverse
Mean pairwise identity 65.72
Shannon entropy 0.70744
G+C content 0.49504
Mean single sequence MFE -30.71
Consensus MFE -8.51
Energy contribution -8.84
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.76
Structure conservation index 0.28
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.40
SVM RNA-class probability 0.681396
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 9769030 90 - 23011544
CCAGGAGGGCGAAUAGAAGGCACUUGUUCAGCGACAUCGUUGUCGUUG-------GUUUGAGCCAACACUCGGCUAGCCACU-UCCUUUUAUAGGCCU------------
......((((..((((((((.........(((((((....)))))))(-------((...((((.......)))).)))...-.))))))))..))))------------ ( -30.40, z-score =  -1.85, R)
>droVir3.scaffold_12963 18358104 101 + 20206255
CCAACAGGGCAAAGAGAAGCAACUUAUUCAGCGACAUGGCGGUCGUUG-------GUAUAAACAAUACGAUUUCGCGUGGUU-GGUUUAUAUAGUCGAUGG-GGUUUUGG
((((....((........))..(((((((((((((......)))))))-------((((((((..((((......))))...-.))))))))....)))))-)...)))) ( -25.30, z-score =  -1.36, R)
>droGri2.scaffold_14978 474892 102 - 1124632
CCAACAGGGCUAACAGUAGCGACUUGUUCAGCGACAUGGUUGUCGUUG-------UUCUAAAUUAGACAAUCGUGUUAGAUU-GGCUUAUAUAGUCGAUGGCUGUUGAUA
.((((((.(((((((((....)).)))).)))((((((((((((....-------..........))))))))))))..(((-((((.....)))))))..))))))... ( -33.14, z-score =  -2.90, R)
>droMoj3.scaffold_6500 3543996 101 + 32352404
CAAACAGAGCGAAAAGAAGCGACUUGUUCAGCGACAUGGUUGUCGUGG-------UUAUUAGCCAUUUAAGGUCGCGUGGUU-GGUUUUUAUUGUCGCUAG-AGCUUAUA
.......(((((.(((((.(((((......((((((((((((......-------....))))))).....)))))..))))-).)))))....)))))..-........ ( -26.90, z-score =  -0.86, R)
>droWil1.scaffold_180772 1141548 108 + 8906247
CCAAAAGGGCCAAAACUAGAGACUUAUUCAGCGACAUGACUGCCGUUGGUAGUACGUAUGAGCUCUUAACGAACUUGUCAACAUGCUUUUAUACCAAUUUACUGCUCU--
.....(((((.......((((.(((((...(((.....((((((...)))))).))))))))))))....((.....))........................)))))-- ( -18.20, z-score =   0.81, R)
>droPer1.super_1 8405487 101 + 10282868
CCAGGAGGGCCAACAAAAGGGACUUGGUCAGCGACAUAGUUGUCGUUG----UUUGUAUGAGCUCCAAACGGGCGAGAUGGU-UGCUUUUAUAGGCCAGACCAAAA----
...((..((((...(((((.((((..((((((((((....)))))))(----(((((.((.....)).))))))..))))))-).)))))...))))...))....---- ( -33.30, z-score =  -1.90, R)
>dp4.chr4_group3 11290453 101 + 11692001
CCAGGAGGGCCAACAAAAGGGACUUGGUCAGCGACAUAGUUGUCGUCG----UUUGUAUGAGCUCCAAACGGGCGAGAUGGU-UGCUUUUAUAGGCCAGACCAAAA----
...((..((((...(((((.((((..(((..(((((....)))))(((----(((((.((.....)).))))))))))))))-).)))))...))))...))....---- ( -34.10, z-score =  -2.07, R)
>droAna3.scaffold_12943 1205135 90 - 5039921
CCAGGAGGGCUAGCAGCAGGCACUUGGUCAGCGACAUGGUUGUCGUUG-------GUUUGAACCUUCGCCUGGUUCACCCAC-CGCUUUUAUAGGCCA------------
...((.(((..(((..(((((....(((((((((((....))))))))-------......)))...))))))))..))).)-)((((....))))..------------ ( -31.80, z-score =  -0.89, R)
>droEre2.scaffold_4929 10381680 90 - 26641161
CCAGGAGGGCGAAUAGAAGGCACUUAGUCAGCGACAUGGUUGUCGUUG-------GUUUGAGCCAAGACCGGGUGAACCACU-UCCUUUUAUAGCCCU------------
.....(((((..((((((((((((..((((((((((....)))))))(-------((....)))..)))..)))).......-.)))))))).)))))------------ ( -36.00, z-score =  -3.43, R)
>droYak2.chr2L 12457791 90 - 22324452
CCAGGAGGGCGAAUAGAAGGCACUUGGUCAGCGACAUGGUUGUCGUUG-------GUUUGAGCCAACACCGGGCGAACCACU-UCCUUUUAUAGGCCC------------
......((((..((((((((....((((..((((((....))))((((-------((....)))))).....))..))))..-.))))))))..))))------------ ( -35.30, z-score =  -2.69, R)
>droSec1.super_3 5216234 90 - 7220098
CCAGGAGGGCGAAUAGAAGGCACUUGGUCAGCGACAUGGUUGUCGUUG-------GUUUGAGCCAACACUCGGCUAGCCACU-UCUUUAUAUAGGCCU------------
......((((..(((.((((....(((..(((((((....))))((((-------((....)))))).....)))..)))..-.)))).)))..))))------------ ( -28.90, z-score =  -1.07, R)
>droSim1.chr2L 9547978 90 - 22036055
CUAGGAGGGCGAAUAGAAGGCACUUGGUCAGCGACAUGGUUGUCGUUG-------GUUUGAGCCAACACUCGGCUAGCCACU-UCCUUUUAUAGGCCU------------
......((((..((((((((....(((..(((((((....))))((((-------((....)))))).....)))..)))..-.))))))))..))))------------ ( -35.20, z-score =  -2.88, R)
>consensus
CCAGGAGGGCGAAUAGAAGGCACUUGGUCAGCGACAUGGUUGUCGUUG_______GUUUGAGCCAACACCGGGCGAGCCACU_UGCUUUUAUAGGCCA____________
............................((((((((....)))))))).............................................................. ( -8.51 =  -8.84 +   0.33)

alignment

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secondary structure

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dotplot

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Window 5

Location 9,769,030 – 9,769,125
Length 95
Sequences 12
Columns 113
Reading direction reverse
Mean pairwise identity 67.13
Shannon entropy 0.67434
G+C content 0.50656
Mean single sequence MFE -32.97
Consensus MFE -9.45
Energy contribution -9.97
Covariance contribution 0.51
Combinations/Pair 1.09
Mean z-score -1.90
Structure conservation index 0.29
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.57
SVM RNA-class probability 0.748383
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 9769030 95 - 23011544
GAUGGCCAGGAGGGCGAAUAGAAGGCACUUGUUCAGCGACAUCGUUGUCGUUG-------GUUUGAGCCAACACUCGGCUAGCCACU-UCCUUUUAUAGGCCU----------
...((((((((((.(.....)..(((......(((((((((....))))))))-------)....((((.......)))).))).))-))))......)))).---------- ( -34.40, z-score =  -2.16, R)
>droVir3.scaffold_12963 18358109 101 + 20206255
UAGGCCCAACAGGGCAAAGAGAAGCAACUUAUUCAGCGACAUGGCGGUCGUUG-------GUAUAAACAAUACGAUUUCGCGUGGUU-GGUUUAUAUAGUCGAUGGGGU----
...((((....))))............(((((((((((((......)))))))-------((((((((..((((......))))...-.))))))))....))))))..---- ( -30.00, z-score =  -2.44, R)
>droGri2.scaffold_14978 474897 102 - 1124632
GAGGCCCAACAGGGCUAACAGUAGCGACUUGUUCAGCGACAUGGUUGUCGUUG-------UUCUAAAUUAGACAAUCGUGUUAGAUU-GGCUUAUAUAGUCGAUGGCUGU---
..(((((....))))).(((((..(((((.(..((((((((....))))))))-------..).........(((((......))))-)........)))))...)))))--- ( -37.30, z-score =  -3.71, R)
>droMoj3.scaffold_6500 3544001 101 + 32352404
AAGGACAAACAGAGCGAAAAGAAGCGACUUGUUCAGCGACAUGGUUGUCGUGG-------UUAUUAGCCAUUUAAGGUCGCGUGGUU-GGUUUUUAUUGUCGCUAGAGC----
.(((((((..(((((.((.....(((((((.....((((((....))))))((-------(.....))).....)))))))....))-.)))))..))))).)).....---- ( -30.90, z-score =  -2.13, R)
>droWil1.scaffold_180772 1141548 113 + 8906247
AAGACCCAAAAGGGCCAAAACUAGAGACUUAUUCAGCGACAUGACUGCCGUUGGUAGUACGUAUGAGCUCUUAACGAACUUGUCAACAUGCUUUUAUACCAAUUUACUGCUCU
..(.(((....))).)......(((((((...((((((.((....)).)))))).)))..((((((((..((.(((....))).))...))))..))))..........)))) ( -18.60, z-score =   0.95, R)
>droPer1.super_1 8405492 101 + 10282868
GACGGCCAGGAGGGCCAACAAAAGGGACUUGGUCAGCGACAUAGUUGUCGUUG----UUUGUAUGAGCUCCAAACGGGCGAGAUGGU-UGCUUUUAUAGGCCAGAC-------
...((((.((((((((((..........))))))(((((((....))))))).----..........))))....((((((.....)-))))).....))))....------- ( -33.00, z-score =  -1.56, R)
>dp4.chr4_group3 11290458 101 + 11692001
GACGGCCAGGAGGGCCAACAAAAGGGACUUGGUCAGCGACAUAGUUGUCGUCG----UUUGUAUGAGCUCCAAACGGGCGAGAUGGU-UGCUUUUAUAGGCCAGAC-------
...((((.((....))...(((((.((((..(((..(((((....)))))(((----(((((.((.....)).))))))))))))))-).)))))...))))....------- ( -33.50, z-score =  -1.58, R)
>droAna3.scaffold_12943 1205135 95 - 5039921
AACGGCCAGGAGGGCUAGCAGCAGGCACUUGGUCAGCGACAUGGUUGUCGUUG-------GUUUGAACCUUCGCCUGGUUCACCCAC-CGCUUUUAUAGGCCA----------
...((((..((((((..((.....))....(((((((((((....))))))))-------(..((((((.......))))))..)))-)))))))...)))).---------- ( -37.80, z-score =  -1.93, R)
>droEre2.scaffold_4929 10381680 95 - 26641161
GAUGGCCAGGAGGGCGAAUAGAAGGCACUUAGUCAGCGACAUGGUUGUCGUUG-------GUUUGAGCCAAGACCGGGUGAACCACU-UCCUUUUAUAGCCCU----------
..........(((((..((((((((((((..((((((((((....)))))))(-------((....)))..)))..)))).......-.)))))))).)))))---------- ( -36.00, z-score =  -2.61, R)
>droYak2.chr2L 12457791 95 - 22324452
GAUGGCCAGGAGGGCGAAUAGAAGGCACUUGGUCAGCGACAUGGUUGUCGUUG-------GUUUGAGCCAACACCGGGCGAACCACU-UCCUUUUAUAGGCCC----------
...........((((..((((((((....((((..((((((....))))((((-------((....)))))).....))..))))..-.))))))))..))))---------- ( -35.30, z-score =  -1.93, R)
>droSec1.super_3 5216234 95 - 7220098
GAUGGCCAGGAGGGCGAAUAGAAGGCACUUGGUCAGCGACAUGGUUGUCGUUG-------GUUUGAGCCAACACUCGGCUAGCCACU-UCUUUAUAUAGGCCU----------
...((((((((((((........(((.....)))(((((((....))))((((-------((....)))))).....))).))).))-))).......)))).---------- ( -33.61, z-score =  -1.70, R)
>droSim1.chr2L 9547978 95 - 22036055
GAUGGCUAGGAGGGCGAAUAGAAGGCACUUGGUCAGCGACAUGGUUGUCGUUG-------GUUUGAGCCAACACUCGGCUAGCCACU-UCCUUUUAUAGGCCU----------
...........((((..((((((((....(((..(((((((....))))((((-------((....)))))).....)))..)))..-.))))))))..))))---------- ( -35.20, z-score =  -2.06, R)
>consensus
GAUGGCCAGGAGGGCGAAUAGAAGGCACUUGGUCAGCGACAUGGUUGUCGUUG_______GUUUGAGCCAACACCGGGCGAGCCACU_UGCUUUUAUAGGCCA__________
...(.((....)).)..................((((((((....))))))))............................................................ ( -9.45 =  -9.97 +   0.51)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:28:55 2011