Locus 13315

Sequence ID dm3.chrX
Location 5,756,154 – 5,756,350
Length 196
Max. P 0.947493
window18325 window18326 window18327 window18328 window18329 window18330

overview

Window 5

Location 5,756,154 – 5,756,254
Length 100
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 82.27
Shannon entropy 0.29580
G+C content 0.28831
Mean single sequence MFE -23.68
Consensus MFE -15.55
Energy contribution -15.80
Covariance contribution 0.25
Combinations/Pair 1.15
Mean z-score -1.71
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.09
SVM RNA-class probability 0.540063
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5756154 100 - 22422827
UUCUUAUUUCUGAUUUCAUUA------------------AUAAUUGAUCAGCGUGACAUUUCUGAUCGAUUCCUAUCAAAUUUGCAGCUUUUGUAAUUGGAAUUAAGUAUGCAACAAA
..((((.(((..(........------------------..((((((((((.(......).))))))))))..........((((((...)))))))..))).))))........... ( -16.80, z-score =  -0.42, R)
>droYak2.chrX 19053833 117 + 21770863
UUCCUAGUUCUGAAUUUAUUAGUAAUUGUUGAAAUAUUUAUAAUUGGUCAACGUGACAUUUAUGGCCGAUUUCGAUUAAAGUUGCAGA-UUUGCAAUUGGAAUUAAAUAUGCAACAAA
...(((((.........)))))...((((((..((((((..(((((((((............)))))))))..((((..((((((...-...))))))..)))))))))).)))))). ( -23.50, z-score =  -1.24, R)
>droSec1.super_4 5177598 117 + 6179234
UUCUUAUUUCUGAUUAUAUUAACAAUUUGUUAGGUAUUCAUAAUUGGUCAGCGUGACAUUUCUGAUCGAUUCCUAUUAAAGUUGCAGC-UUUGUAAUUGGAAUUAAGUAUGCAACAAA
..((((.(((..((((((....((((((..((((.......((((((((((.(......).))))))))))))))...))))))....-..))))))..))).))))........... ( -27.21, z-score =  -2.59, R)
>droSim1.chrX 4499947 117 - 17042790
UUCUUAUUUCUGAUUAUAUUAACAAUUUGUUAGGUAUUCAUAAUUGGUCAGCGUGACAUUUCUGAUCGAUUCCUAUUAAAGUUGCAGC-UUUGUAAUUGGAAUUAAGUAUGCAACAAA
..((((.(((..((((((....((((((..((((.......((((((((((.(......).))))))))))))))...))))))....-..))))))..))).))))........... ( -27.21, z-score =  -2.59, R)
>consensus
UUCUUAUUUCUGAUUAUAUUAACAAUUUGUUAGGUAUUCAUAAUUGGUCAGCGUGACAUUUCUGAUCGAUUCCUAUUAAAGUUGCAGC_UUUGUAAUUGGAAUUAAGUAUGCAACAAA
..((((.((((..............................((((((((((.(......).))))))))))........((((((((...)))))))))))).))))........... (-15.55 = -15.80 +   0.25)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,756,192 – 5,756,293
Length 101
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 74.93
Shannon entropy 0.35820
G+C content 0.34010
Mean single sequence MFE -22.25
Consensus MFE -11.05
Energy contribution -11.83
Covariance contribution 0.78
Combinations/Pair 1.20
Mean z-score -1.98
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value -0.00
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>dm3.chrX 5756192 101 + 22422827
UUUGAUAGGAAUCGAUCAGAAAUGUCACGCUGAUCAAUUAU------------------UAAUGAAAUCAGAAAUAAGAACUAGA-UUUCUUGCCAUACACAAAUACAUGGCUCGAAUCG
(((((.(((((((((((((..........))))))..((((------------------(..((....))..)))))......))-))))).(((((..........))))))))))... ( -21.80, z-score =  -2.21, R)
>droYak2.chrX 19053870 118 - 21770863
UUUAAUCGAAAUCGGCCAUAAAUGUCACGUUGACCAAUUAUAAAUAUUUCAACAAUUACUAAUAAAUUCAGAACUAGGAACUGCACUUUCUGGCCGUACAUAA--ACAUGGCCGGAAUCG
......(((..((((((((..((((.(((((((...............)))))....................(((((((......)))))))..))))))..--..))))))))..))) ( -24.76, z-score =  -2.73, R)
>droSec1.super_4 5177635 119 - 6179234
UUUAAUAGGAAUCGAUCAGAAAUGUCACGCUGACCAAUUAUGAAUACCUAACAAAUUGUUAAUAUAAUCAGAAAUAAGAACUGGA-UUUCUGGCCAUACAUAAAUACAUGGCUCGAAUCG
........((.((((.((((((((((.....)))......(((.((..((((.....))))...)).)))..............)-))))))(((((..........))))))))).)). ( -20.20, z-score =  -1.02, R)
>consensus
UUUAAUAGGAAUCGAUCAGAAAUGUCACGCUGACCAAUUAU_AAUA__U_A__AAUU__UAAUAAAAUCAGAAAUAAGAACUGGA_UUUCUGGCCAUACAUAAAUACAUGGCUCGAAUCG
.............((((((..........))))))....................................................(((.((((((..........)))))).)))... (-11.05 = -11.83 +   0.78)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,756,192 – 5,756,293
Length 101
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 74.93
Shannon entropy 0.35820
G+C content 0.34010
Mean single sequence MFE -26.24
Consensus MFE -16.45
Energy contribution -16.23
Covariance contribution -0.22
Combinations/Pair 1.17
Mean z-score -1.83
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.71
SVM RNA-class probability 0.795629
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5756192 101 - 22422827
CGAUUCGAGCCAUGUAUUUGUGUAUGGCAAGAAA-UCUAGUUCUUAUUUCUGAUUUCAUUA------------------AUAAUUGAUCAGCGUGACAUUUCUGAUCGAUUCCUAUCAAA
.(((..((((((((........))))))..((((-((.((.........))))))))....------------------...(((((((((.(......).)))))))))))..)))... ( -23.10, z-score =  -1.69, R)
>droYak2.chrX 19053870 118 + 21770863
CGAUUCCGGCCAUGU--UUAUGUACGGCCAGAAAGUGCAGUUCCUAGUUCUGAAUUUAUUAGUAAUUGUUGAAAUAUUUAUAAUUGGUCAACGUGACAUUUAUGGCCGAUUUCGAUUAAA
(((...((((((((.--((((((..((((((.....((((((.(((((.........))))).))))))..............)))))).))))))....))))))))...)))...... ( -30.11, z-score =  -2.31, R)
>droSec1.super_4 5177635 119 + 6179234
CGAUUCGAGCCAUGUAUUUAUGUAUGGCCAGAAA-UCCAGUUCUUAUUUCUGAUUAUAUUAACAAUUUGUUAGGUAUUCAUAAUUGGUCAGCGUGACAUUUCUGAUCGAUUCCUAUUAAA
.((.((((((((((........))))))((((((-....(((..(((........)))..)))....(((((.((..(((....)))...)).))))))))))).)))).))........ ( -25.50, z-score =  -1.49, R)
>consensus
CGAUUCGAGCCAUGUAUUUAUGUAUGGCCAGAAA_UCCAGUUCUUAUUUCUGAUUUUAUUA__AAUU__U_A__UAUU_AUAAUUGGUCAGCGUGACAUUUCUGAUCGAUUCCUAUUAAA
...(((..((((((........))))))..)))....(((.........))).............................((((((((((.(......).))))))))))......... (-16.45 = -16.23 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,756,232 – 5,756,331
Length 99
Sequences 3
Columns 118
Reading direction forward
Mean pairwise identity 71.71
Shannon entropy 0.39753
G+C content 0.41282
Mean single sequence MFE -26.13
Consensus MFE -18.02
Energy contribution -18.47
Covariance contribution 0.45
Combinations/Pair 1.13
Mean z-score -1.88
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.53
SVM RNA-class probability 0.947493
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5756232 99 + 22422827
------------------UUAAUGAAAUCAGAAAUAAGAACUAGA-UUUCUUGCCAUACACAAAUACAUGGCUCGAAUCGAUAUCUUGGCCCAAAGGCCAUCGAUCUUGGUCCGGGCC
------------------.....((((((((.........)).))-))))...................((((((.(((((.(((.(((((....)))))..))).))))).)))))) ( -28.00, z-score =  -2.73, R)
>droYak2.chrX 19053910 112 - 21770863
UAAAUAUUUCAACAAUUACUAAUAAAUUCAGAACUAGGAACUGCACUUUCUGGCCGUACAUAAA--CAUGGCCGGAAUCGAUUUCGUGGCCCAAGAACCAUCGAUCUUGGCCUG----
....................................((((.((....((((((((((.......--.)))))))))).)).))))..((((.((((........))))))))..---- ( -25.90, z-score =  -2.11, R)
>droSec1.super_4 5177675 114 - 6179234
UGAAUACCUAACAAAUUGUUAAUAUAAUCAGAAAUAAGAACUGGA-UUUCUGGCCAUACAUAAAUACAUGGCUCGAAUCGAUUCCUUGGCCCAAAGGCCAUCGAUCUUGGCCCGG---
(((.((..((((.....))))...)).)))..........((((.-.(((.((((((..........)))))).)))..((((...(((((....)))))..)))).....))))--- ( -24.50, z-score =  -0.80, R)
>consensus
U_AAUA__U_A__AAUU_UUAAUAAAAUCAGAAAUAAGAACUGGA_UUUCUGGCCAUACAUAAAUACAUGGCUCGAAUCGAUUUCUUGGCCCAAAGGCCAUCGAUCUUGGCCCGG___
..................................(((((........(((.((((((..........)))))).)))((((.....(((((....))))))))))))))......... (-18.02 = -18.47 +   0.45)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,756,233 – 5,756,350
Length 117
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 78.29
Shannon entropy 0.37497
G+C content 0.45050
Mean single sequence MFE -30.92
Consensus MFE -14.83
Energy contribution -17.90
Covariance contribution 3.07
Combinations/Pair 1.08
Mean z-score -2.48
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.01
SVM RNA-class probability 0.873189
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5756233 117 + 22422827
UAAUGAAAUCAGAAAUAAGAACUAGA-UUUCUUGCCAUACACAAAUACAUGGCUCGAAUCGAUAUCUUGGCCCAAAGGCCAUCGAUCUUGGUCCGGGCCCCCCCCCAGUUCGAUUUAU
.....((((((....)..(((((.((-(((...(((((..........)))))..)))))........(((((...(((((.......))))).))))).......)))))))))).. ( -31.70, z-score =  -2.27, R)
>droEre2.scaffold_4690 3102354 111 + 18748788
UAAUAAAACCAGAACCAAUUUCUGGACUUUCUGGCCAUACAUAAA-AGAUGG-CCAAAUCGAUUUCAUGGCCCAAACACCAUCGAUCUUGGCCUGC-----CACCCAGUUCGAUUUAU
........((((((.....)))))).......((((((.(.....-.)))))-))(((((((.....((((((((............))))...))-----))......))))))).. ( -29.10, z-score =  -3.35, R)
>droYak2.chrX 19053929 111 - 21770863
UAAUAAAUUCAGAACUAGGAACUGCACUUUCUGGCCGUACAUAAA--CAUGGCCGGAAUCGAUUUCGUGGCCCAAGAACCAUCGAUCUUGGCCUGG-----CCCCCCAUUCGAUUUAU
..(((((((..((((((((.....(((.((((((((((.......--.))))))))))..(....))))..((((((........)))))))))))-----.......)))))))))) ( -28.51, z-score =  -1.13, R)
>droSec1.super_4 5177694 113 - 6179234
UAAUAUAAUCAGAAAUAAGAACUGGA-UUUCUGGCCAUACAUAAAUACAUGGCUCGAAUCGAUUCCUUGGCCCAAAGGCCAUCGAUCUUGGCCCGG----CCCCCCAGUUCGAUUUAU
..................(((((((.-.(((.((((((..........)))))).)))..........((((....(((((.......))))).))----))..)))))))....... ( -34.80, z-score =  -2.95, R)
>droSim1.chrX 4500043 95 + 17042790
UAAUAUAAUCAGAAAUAAGAACUGGA-UUUCUGGC------------------UCGAAUCGAUUCCUUGGCCCACAGGCCAUCGAUCUUGGCCCGG----CCCCCCAGUUCGAUUUAU
..................(((((((.-...((((.------------------.((((((((.....(((((....)))))))))).)))..))))----....)))))))....... ( -30.50, z-score =  -2.67, R)
>consensus
UAAUAAAAUCAGAAAUAAGAACUGGA_UUUCUGGCCAUACAUAAA_ACAUGGCUCGAAUCGAUUUCUUGGCCCAAAGGCCAUCGAUCUUGGCCCGG____CCCCCCAGUUCGAUUUAU
..................(((((((...(((.((((((..........)))))).)))((((.....(((((....)))))))))...................)))))))....... (-14.83 = -17.90 +   3.07)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,756,233 – 5,756,350
Length 117
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 78.29
Shannon entropy 0.37497
G+C content 0.45050
Mean single sequence MFE -34.90
Consensus MFE -21.90
Energy contribution -22.98
Covariance contribution 1.08
Combinations/Pair 1.21
Mean z-score -1.44
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.10
SVM RNA-class probability 0.544900
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5756233 117 - 22422827
AUAAAUCGAACUGGGGGGGGGCCCGGACCAAGAUCGAUGGCCUUUGGGCCAAGAUAUCGAUUCGAGCCAUGUAUUUGUGUAUGGCAAGAAA-UCUAGUUCUUAUUUCUGAUUUCAUUA
...((((((.(((((......)))))......(((..(((((....))))).))).))))))...((((((........))))))..((((-((.((.........)))))))).... ( -36.10, z-score =  -1.07, R)
>droEre2.scaffold_4690 3102354 111 - 18748788
AUAAAUCGAACUGGGUG-----GCAGGCCAAGAUCGAUGGUGUUUGGGCCAUGAAAUCGAUUUGG-CCAUCU-UUUAUGUAUGGCCAGAAAGUCCAGAAAUUGGUUCUGGUUUUAUUA
...(((.((((..(.((-----(....))).(((((((....(((((((..((....)).(((((-(((((.-.....).)))))))))..))))))).))))))))..)))).))). ( -33.50, z-score =  -1.51, R)
>droYak2.chrX 19053929 111 + 21770863
AUAAAUCGAAUGGGGGG-----CCAGGCCAAGAUCGAUGGUUCUUGGGCCACGAAAUCGAUUCCGGCCAUG--UUUAUGUACGGCCAGAAAGUGCAGUUCCUAGUUCUGAAUUUAUUA
(((((((((((.(((((-----(..((((..(((((((((((....))))).....))))))..))))...--....(((((.........))))))))))).)))).).)))))).. ( -34.70, z-score =  -1.16, R)
>droSec1.super_4 5177694 113 + 6179234
AUAAAUCGAACUGGGGGG----CCGGGCCAAGAUCGAUGGCCUUUGGGCCAAGGAAUCGAUUCGAGCCAUGUAUUUAUGUAUGGCCAGAAA-UCCAGUUCUUAUUUCUGAUUAUAUUA
.......((((((((.((----((.(((...(((((((((((....))))).....))))))...)))..((((....)))))))).....-)))))))).................. ( -38.90, z-score =  -2.18, R)
>droSim1.chrX 4500043 95 - 17042790
AUAAAUCGAACUGGGGGG----CCGGGCCAAGAUCGAUGGCCUGUGGGCCAAGGAAUCGAUUCGA------------------GCCAGAAA-UCCAGUUCUUAUUUCUGAUUAUAUUA
.......((((((((...----...(((...(((((((((((....))))).....))))))...------------------))).....-)))))))).................. ( -31.30, z-score =  -1.30, R)
>consensus
AUAAAUCGAACUGGGGGG____CCGGGCCAAGAUCGAUGGCCUUUGGGCCAAGAAAUCGAUUCGAGCCAUGU_UUUAUGUAUGGCCAGAAA_UCCAGUUCUUAUUUCUGAUUUUAUUA
.......(((((((((......)).((((..(((((((((((....))))).....)))))).....((((....))))...)))).......))))))).................. (-21.90 = -22.98 +   1.08)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:19:01 2011