Locus 11788

Sequence ID dm3.chr3R
Location 23,825,539 – 23,825,645
Length 106
Max. P 0.873276
window16203 window16204

overview

Window 3

Location 23,825,539 – 23,825,641
Length 102
Sequences 12
Columns 115
Reading direction forward
Mean pairwise identity 86.98
Shannon entropy 0.26555
G+C content 0.36720
Mean single sequence MFE -27.28
Consensus MFE -16.71
Energy contribution -16.62
Covariance contribution -0.09
Combinations/Pair 1.18
Mean z-score -2.51
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.01
SVM RNA-class probability 0.873276
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 23825539 102 + 27905053
UUUGCC-UUUUGUUGCGCUCGACUUGAGCACAAAUACCGGAAAUUGUUGUCAAGAUAAUUAUUGUUAUUUGUUUUUC-AACAGGGGG-CACACAAAAUGA-AGCAA---------
..((((-((((((((.((((.....))))(((((((.(((.(((((((.....))))))).))).)))))))....)-)))))))))-))..........-.....--------- ( -30.60, z-score =  -3.12, R)
>droSim1.chr3R 23527480 102 + 27517382
UUUGCC-UUUUGUUGCGCUCGACUUGAGCACAAAUACCGGAAAUUGUUGUCAAGAUAAUUAUUGUUAUUUGUUUUUC-AACAGGGGG-CACACAAAAUGA-AGCAA---------
..((((-((((((((.((((.....))))(((((((.(((.(((((((.....))))))).))).)))))))....)-)))))))))-))..........-.....--------- ( -30.60, z-score =  -3.12, R)
>droSec1.super_22 448468 102 + 1066717
UUUGCC-UUUUGUUGCGCUCGACUUGAGCACAAAUACCGGAAAUUGUUGUCAAGAUAAUUAUUGUUAUUUGUUUUUC-AACAGGGGG-CACACAAAAUAA-AGCAA---------
..((((-((((((((.((((.....))))(((((((.(((.(((((((.....))))))).))).)))))))....)-)))))))))-))..........-.....--------- ( -30.60, z-score =  -3.46, R)
>droYak2.chr3R 6158299 102 - 28832112
UUUGCC-UUUUGUUGCGCUCGACUUGAGCACAAAUACCGGAAAUUGUUGUCAAGAUAAUUAUUGUUAUUUGUUUUUC-AACAGGGGG-CACACAAUAUGA-AGCAA---------
..((((-((((((((.((((.....))))(((((((.(((.(((((((.....))))))).))).)))))))....)-)))))))))-))..........-.....--------- ( -30.60, z-score =  -3.25, R)
>droEre2.scaffold_4820 6250688 101 - 10470090
UUUGCC-UUUUGUUGCGCUCGACUUGAGCACAAAUACCGGAAAUUGUUGUCAAGAUAAUUAUUGUUAUUUGUUUUUC-AACAGGGG--CACACAAAAUGA-AGCAA---------
..((((-(((.((((.((((.....))))(((((((.(((.(((((((.....))))))).))).)))))))....)-))))))))--))..........-.....--------- ( -26.30, z-score =  -1.94, R)
>droAna3.scaffold_13340 21964033 100 + 23697760
UUUGCC-UUUUGUUGCGCUCGACUUGAGCACAAAUACCGGAAAUUGUUGUCAAGAUAAUUAUUGUUAUUUGUUUUUC-AACAGGGA---GCACAAAAUGA-ACCAA---------
..(((.-.(((((((.((((.....))))(((((((.(((.(((((((.....))))))).))).)))))))....)-))))))..---)))........-.....--------- ( -24.20, z-score =  -1.69, R)
>dp4.chr2 22533399 103 - 30794189
UUUGCC-UUUUGUUGCGCUCGACUUGAGCACAAAUACCGGAAAUUGUUGUCAAGAUAAUUAUUGUUAUUUGUUUUUC-CACAGAGAGAGGCACAACAUAA-ACCAG---------
..((((-((((.(((.((((.....))))(((((((.(((.(((((((.....))))))).))).))))))).....-..))).))))))))........-.....--------- ( -26.30, z-score =  -2.71, R)
>droPer1.super_0 9726506 103 - 11822988
UUUGCC-UUUUGUUGCGCUCGACUUGAGCACAAAUACCGGAAAUUGUUGUCAAGAUAAUUAUUGUUAUUUGUUUUUC-CACAGAGAGAGGCACAACAUAA-ACCAG---------
..((((-((((.(((.((((.....))))(((((((.(((.(((((((.....))))))).))).))))))).....-..))).))))))))........-.....--------- ( -26.30, z-score =  -2.71, R)
>droWil1.scaffold_181108 1038058 100 + 4707319
UUUGCC-UUUUGUUGCGCUCGACUUGAGCACAAAUACCGGAAAUUGUUGUCAAGAUAAUUAUUGUUAUUUGUUUUUC-AACAGAGG--CACACAA-AUAA-AGCAA---------
..((((-(((.((((.((((.....))))(((((((.(((.(((((((.....))))))).))).)))))))....)-))))))))--)).....-....-.....--------- ( -27.10, z-score =  -2.85, R)
>droMoj3.scaffold_6540 14888571 114 - 34148556
UUUGCC-UCUCGUUGCGCUCGACUGAAGCGCAAAUACCGGAAAUUGUUGUCAAGAUAAUUAUUGUUAUUUGUUUUACCAACAAAGGCACAAAUAACGAAAGAACAACAACAACAA
..((((-(....(((((((.......)))))))..........((((((..(((((((.((....)).)))))))..))))))))))).......(....).............. ( -26.30, z-score =  -2.28, R)
>droGri2.scaffold_14830 4257610 112 + 6267026
UUUGCC-CUUCGUUGCGCUUGACUGAAGCGCAAAUACCGGAAAUUGUUGUCAAGAUAAUUAUUGUUAUUUGUUUUUCCAACAGAGGCACAAAUAAGGCAAAAACAAC--CAGCAA
((((((-.((((((((((((.....))))))))....))))..((((((..(((((((.((....)).)))))))..))))))............))))))......--...... ( -28.40, z-score =  -1.91, R)
>droVir3.scaffold_13047 3469978 100 - 19223366
UUUGCCAUUUUGUUACGCUCGACUAAAGCGCAAAUACCGGAAAUUGUUGUCAAGAUAAUUAUUGUUAUUUGUUUUUCCAACAGAGGCACAAAUAAAGCAA---------------
..((((..((((((..(((.......)))(((((((.(((.(((((((.....))))))).))).)))))))......))))))))))............--------------- ( -20.10, z-score =  -1.06, R)
>consensus
UUUGCC_UUUUGUUGCGCUCGACUUGAGCACAAAUACCGGAAAUUGUUGUCAAGAUAAUUAUUGUUAUUUGUUUUUC_AACAGAGGG_CACACAAAAUAA_AGCAA_________
.......(((((((..((((.....))))(((((((.(((.(((((((.....))))))).))).)))))))......))))))).............................. (-16.71 = -16.62 +  -0.09)

alignment

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secondary structure

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dotplot

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Window 4

Location 23,825,543 – 23,825,645
Length 102
Sequences 12
Columns 115
Reading direction forward
Mean pairwise identity 86.71
Shannon entropy 0.27466
G+C content 0.37845
Mean single sequence MFE -24.54
Consensus MFE -17.00
Energy contribution -17.16
Covariance contribution 0.15
Combinations/Pair 1.15
Mean z-score -1.91
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.52
SVM RNA-class probability 0.727045
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 23825543 102 + 27905053
-CCUUUUGUUGCGCUCGACUUGAGCACAAAUACCGGAAAUUGUUGUCAAGAUAAUUAUUGUUAUUUGUUUUUC-AACAGGGGG-CACACAAAAUGA-AGCAACAAC---------
-((((((((((.((((.....))))(((((((.(((.(((((((.....))))))).))).)))))))....)-)))))))))-............-.........--------- ( -25.30, z-score =  -1.81, R)
>droSim1.chr3R 23527484 102 + 27517382
-CCUUUUGUUGCGCUCGACUUGAGCACAAAUACCGGAAAUUGUUGUCAAGAUAAUUAUUGUUAUUUGUUUUUC-AACAGGGGG-CACACAAAAUGA-AGCAACAAC---------
-((((((((((.((((.....))))(((((((.(((.(((((((.....))))))).))).)))))))....)-)))))))))-............-.........--------- ( -25.30, z-score =  -1.81, R)
>droSec1.super_22 448472 102 + 1066717
-CCUUUUGUUGCGCUCGACUUGAGCACAAAUACCGGAAAUUGUUGUCAAGAUAAUUAUUGUUAUUUGUUUUUC-AACAGGGGG-CACACAAAAUAA-AGCAACAAC---------
-((((((((((.((((.....))))(((((((.(((.(((((((.....))))))).))).)))))))....)-)))))))))-............-.........--------- ( -25.30, z-score =  -2.18, R)
>droYak2.chr3R 6158303 102 - 28832112
-CCUUUUGUUGCGCUCGACUUGAGCACAAAUACCGGAAAUUGUUGUCAAGAUAAUUAUUGUUAUUUGUUUUUC-AACAGGGGG-CACACAAUAUGA-AGCAACAUC---------
-((((((((((.((((.....))))(((((((.(((.(((((((.....))))))).))).)))))))....)-)))))))))-............-.........--------- ( -25.30, z-score =  -1.88, R)
>droEre2.scaffold_4820 6250692 101 - 10470090
-CCUUUUGUUGCGCUCGACUUGAGCACAAAUACCGGAAAUUGUUGUCAAGAUAAUUAUUGUUAUUUGUUUUUC-AACAGGGG--CACACAAAAUGA-AGCAACAAC---------
-....(((((((((((...(((((.(((((((.(((.(((((((.....))))))).))).)))))))..)))-))...)))--).((.....)).-.))))))).--------- ( -25.30, z-score =  -2.06, R)
>droAna3.scaffold_13340 21964037 100 + 23697760
-CCUUUUGUUGCGCUCGACUUGAGCACAAAUACCGGAAAUUGUUGUCAAGAUAAUUAUUGUUAUUUGUUUUUC-AACAGGGA---GCACAAAAUGA-ACCAACAAC---------
-..((((((.((.(((...(((((.(((((((.(((.(((((((.....))))))).))).)))))))..)))-))..))).---))))))))...-.........--------- ( -22.40, z-score =  -1.45, R)
>dp4.chr2 22533403 103 - 30794189
-CCUUUUGUUGCGCUCGACUUGAGCACAAAUACCGGAAAUUGUUGUCAAGAUAAUUAUUGUUAUUUGUUUUUC-CACAGAGAGAGGCACAACAUAA-ACCAGCAAC---------
-......(((((((((.....)))).........((....((((((..(((((((....)))))))(((((((-......)))))))))))))...-.)).)))))--------- ( -26.60, z-score =  -2.86, R)
>droPer1.super_0 9726510 103 - 11822988
-CCUUUUGUUGCGCUCGACUUGAGCACAAAUACCGGAAAUUGUUGUCAAGAUAAUUAUUGUUAUUUGUUUUUC-CACAGAGAGAGGCACAACAUAA-ACCAGCAAC---------
-......(((((((((.....)))).........((....((((((..(((((((....)))))))(((((((-......)))))))))))))...-.)).)))))--------- ( -26.60, z-score =  -2.86, R)
>droWil1.scaffold_181108 1038062 100 + 4707319
-CCUUUUGUUGCGCUCGACUUGAGCACAAAUACCGGAAAUUGUUGUCAAGAUAAUUAUUGUUAUUUGUUUUUC-AACAGAGG--CACACAA-AUAA-AGCAAGAAC---------
-.(((((((((.((((.....))))(((((((.(((.(((((((.....))))))).))).)))))))....)-))))))))--.......-....-.........--------- ( -23.20, z-score =  -1.88, R)
>droMoj3.scaffold_6540 14888575 114 - 34148556
-CCUCUCGUUGCGCUCGACUGAAGCGCAAAUACCGGAAAUUGUUGUCAAGAUAAUUAUUGUUAUUUGUUUUACCAACAAAGGCACAAAUAACGAAAGAACAACAACAACAACAGC
-((.....(((((((.......))))))).....))...(((((((...........(((((((((((....((......)).)))))))))))..........))))))).... ( -26.10, z-score =  -2.46, R)
>droGri2.scaffold_14830 4257614 112 + 6267026
-CCCUUCGUUGCGCUUGACUGAAGCGCAAAUACCGGAAAUUGUUGUCAAGAUAAUUAUUGUUAUUUGUUUUUCCAACAGAGGCACAAAUAAGGCAAAAACAAC--CAGCAACAGU
-((.....((((((((.....)))))))).....))..((((((((..............((((((((.((((.....)))).))))))))((.........)--).)))))))) ( -26.50, z-score =  -1.61, R)
>droVir3.scaffold_13047 3469982 100 - 19223366
CCAUUUUGUUACGCUCGACUAAAGCGCAAAUACCGGAAAUUGUUGUCAAGAUAAUUAUUGUUAUUUGUUUUUCCAACAGAGG----CACAA-AUAA-AGCAACAGC---------
((..((((...((((.......))))))))....))...((((((((((........)))((((((((.((((.....))))----.))))-))))-.))))))).--------- ( -16.60, z-score =  -0.07, R)
>consensus
_CCUUUUGUUGCGCUCGACUUGAGCACAAAUACCGGAAAUUGUUGUCAAGAUAAUUAUUGUUAUUUGUUUUUC_AACAGAGGG_CACACAAAAUAA_AGCAACAAC_________
.....((((((.((((.....))))(((((((.(((.(((((((.....))))))).))).)))))))...............................)))))).......... (-17.00 = -17.16 +   0.15)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:49:42 2011