Locus 12596

Sequence ID dm3.chrX
Location 1,100,272 – 1,100,386
Length 114
Max. P 0.999673
window17322 window17323 window17324 window17325

overview

Window 2

Location 1,100,272 – 1,100,381
Length 109
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 80.97
Shannon entropy 0.33160
G+C content 0.36572
Mean single sequence MFE -28.92
Consensus MFE -9.92
Energy contribution -11.44
Covariance contribution 1.52
Combinations/Pair 1.15
Mean z-score -3.73
Structure conservation index 0.34
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.69
SVM RNA-class probability 0.961253
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 1100272 109 + 22422827
GGGAAAACGUCUACACAGAAAAAAA----CAUUACGAUCUCUUGUGGCUACUGAACGCAAGAAAUUCAUGUUGAUUAUGACCAUGUUAUAGCAAUUUUUU-CUGUGCAGCACGG
.......(((((.(((((((((((.----......((..(((((((.........)))))))...))...(((.(((((((...))))))))))))))))-))))).)).))). ( -30.00, z-score =  -3.32, R)
>droSim1.chrX 879374 109 + 17042790
GGAAAACCGUCUACACAGAAAAAAA----CUUUACGAUCUCUUGCGGCUACUUUAUGCAAGAAAUUCAUGUUGAUUAUCACCAUGUUAUGUCAAUUUUUU-CUGUGCAGCACGG
......((((((.(((((((((((.----......(((.(((((((.........))))))).)))((((.((.....)).)))).........))))))-))))).)).)))) ( -30.30, z-score =  -4.13, R)
>droSec1.super_10 931837 109 + 3036183
GGAAAACCGUCUACACAGAAAAAAA----CUUUACGAUCUCUUGUGGCUAUUUAAUGCAAGAAAUUCAUGUUGAUUAUCACCAUGUUAUGUCAAUUUUUU-CUGUGCAGCACGG
......((((((.(((((((((((.----......(((.(((((((.........))))))).)))((((.((.....)).)))).........))))))-))))).)).)))) ( -27.70, z-score =  -3.10, R)
>droYak2.chrX 1014910 109 + 21770863
GGAAAACCGCCUACACAGAAAAAAA----CAUAACCAUCUCUUUUGGUUACUAAAUGGUAGAGAUUCAUGUUGAUUAUCACCACAUUAGAGCAUUUUUUUUCUGUGCAGCCAG-
((....))(.((.((((((((((((----..((((((.......))))))((((.((((.((...((.....))...))))))..)))).....)))))))))))).)).)..- ( -27.90, z-score =  -3.63, R)
>droEre2.scaffold_4644 1085271 111 + 2521924
GCAAAACAGCCUGCACAGAAAAAAAAAAACAUUAACAUGAAC-AUGCCUACUAAAUGAAAGAAAUUCAUGUUGAAUAUUACCAUAUUAUAGCAGUUUUUU-CCGUGCAGGCGG-
........((((((((.(((((((........((((((((((-((.........))).......)))))))))(((((....))))).......))))))-).))))))))..- ( -28.71, z-score =  -4.46, R)
>consensus
GGAAAACCGUCUACACAGAAAAAAA____CAUUACGAUCUCUUGUGGCUACUAAAUGCAAGAAAUUCAUGUUGAUUAUCACCAUGUUAUAGCAAUUUUUU_CUGUGCAGCACGG
..........((.(((((((((((...............(((((((.........)))))))....((((.((.....)).)))).........)))))).))))).))..... ( -9.92 = -11.44 +   1.52)

alignment

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secondary structure

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dotplot

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Window 3

Location 1,100,272 – 1,100,381
Length 109
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 80.97
Shannon entropy 0.33160
G+C content 0.36572
Mean single sequence MFE -35.22
Consensus MFE -18.80
Energy contribution -19.20
Covariance contribution 0.40
Combinations/Pair 1.23
Mean z-score -4.91
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.17
SVM RNA-class probability 0.999673
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 1100272 109 - 22422827
CCGUGCUGCACAG-AAAAAAUUGCUAUAACAUGGUCAUAAUCAACAUGAAUUUCUUGCGUUCAGUAGCCACAAGAGAUCGUAAUG----UUUUUUUCUGUGUAGACGUUUUCCC
.(((.((((((((-((((((((((.....((((...........)))).((((((((.((......))..)))))))).))))).----..))))))))))))))))....... ( -31.00, z-score =  -3.73, R)
>droSim1.chrX 879374 109 - 17042790
CCGUGCUGCACAG-AAAAAAUUGACAUAACAUGGUGAUAAUCAACAUGAAUUUCUUGCAUAAAGUAGCCGCAAGAGAUCGUAAAG----UUUUUUUCUGUGUAGACGGUUUUCC
((((.((((((((-((((((...((....((((.((.....)).)))).(((((((((...........))))))))).))....----.))))))))))))))))))...... ( -37.90, z-score =  -5.61, R)
>droSec1.super_10 931837 109 - 3036183
CCGUGCUGCACAG-AAAAAAUUGACAUAACAUGGUGAUAAUCAACAUGAAUUUCUUGCAUUAAAUAGCCACAAGAGAUCGUAAAG----UUUUUUUCUGUGUAGACGGUUUUCC
((((.((((((((-((((((...((....((((.((.....)).)))).((((((((.............)))))))).))....----.))))))))))))))))))...... ( -33.92, z-score =  -4.66, R)
>droYak2.chrX 1014910 109 - 21770863
-CUGGCUGCACAGAAAAAAAAUGCUCUAAUGUGGUGAUAAUCAACAUGAAUCUCUACCAUUUAGUAACCAAAAGAGAUGGUUAUG----UUUUUUUCUGUGUAGGCGGUUUUCC
-(((.(((((((((((((((.....((((.(((((((.(.((.....)).).)).)))))))))((((((.......))))))..----))))))))))))))).)))...... ( -35.20, z-score =  -4.65, R)
>droEre2.scaffold_4644 1085271 111 - 2521924
-CCGCCUGCACGG-AAAAAACUGCUAUAAUAUGGUAAUAUUCAACAUGAAUUUCUUUCAUUUAGUAGGCAU-GUUCAUGUUAAUGUUUUUUUUUUUCUGUGCAGGCUGUUUUGC
-..((((((((((-((((((.((((((...))))))(((((.(((((((((..(((.(.....).)))...-))))))))))))))....))))))))))))))))........ ( -38.10, z-score =  -5.90, R)
>consensus
CCGUGCUGCACAG_AAAAAAUUGCUAUAACAUGGUGAUAAUCAACAUGAAUUUCUUGCAUUAAGUAGCCACAAGAGAUCGUAAUG____UUUUUUUCUGUGUAGACGGUUUUCC
.....((((((((.((((((.........((((...........)))).((((((((.............))))))))...........)))))).)))))))).......... (-18.80 = -19.20 +   0.40)

alignment

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secondary structure

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dotplot

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Window 4

Location 1,100,277 – 1,100,386
Length 109
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 82.51
Shannon entropy 0.30472
G+C content 0.37302
Mean single sequence MFE -29.10
Consensus MFE -10.50
Energy contribution -13.02
Covariance contribution 2.52
Combinations/Pair 1.13
Mean z-score -3.31
Structure conservation index 0.36
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.91
SVM RNA-class probability 0.850767
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 1100277 109 + 22422827
AACGUCUACACAGAAAAAAA----CAUUACGAUCUCUUGUGGCUACUGAACGCAAGAAAUUCAUGUUGAUUAUGACCAUGUUAUAGCAAUUUUUU-CUGUGCAGCACGGCAGCU
..(((((.(((((((((((.----......((..(((((((.........)))))))...))...(((.(((((((...))))))))))))))))-))))).)).)))...... ( -30.00, z-score =  -2.80, R)
>droSim1.chrX 879379 109 + 17042790
ACCGUCUACACAGAAAAAAA----CUUUACGAUCUCUUGCGGCUACUUUAUGCAAGAAAUUCAUGUUGAUUAUCACCAUGUUAUGUCAAUUUUUU-CUGUGCAGCACGGCAGCU
.((((((.(((((((((((.----......(((.(((((((.........))))))).)))((((.((.....)).)))).........))))))-))))).)).))))..... ( -30.70, z-score =  -3.80, R)
>droSec1.super_10 931842 109 + 3036183
ACCGUCUACACAGAAAAAAA----CUUUACGAUCUCUUGUGGCUAUUUAAUGCAAGAAAUUCAUGUUGAUUAUCACCAUGUUAUGUCAAUUUUUU-CUGUGCAGCACGGCAGCU
.((((((.(((((((((((.----......(((.(((((((.........))))))).)))((((.((.....)).)))).........))))))-))))).)).))))..... ( -28.10, z-score =  -2.84, R)
>droYak2.chrX 1014915 109 + 21770863
ACCGCCUACACAGAAAAAAA----CAUAACCAUCUCUUUUGGUUACUAAAUGGUAGAGAUUCAUGUUGAUUAUCACCACAUUAGAGCAUUUUUUUUCUGUGCAGC-CAGCAGCU
...((((.((((((((((((----..((((((.......))))))((((.((((.((...((.....))...))))))..)))).....)))))))))))).)).-..)).... ( -28.00, z-score =  -3.46, R)
>droEre2.scaffold_4644 1085276 111 + 2521924
ACAGCCUGCACAGAAAAAAAAAAACAUUAACAUGAAC-AUGCCUACUAAAUGAAAGAAAUUCAUGUUGAAUAUUACCAUAUUAUAGCAGUUUUUU-CCGUGCAGG-CGGCAGCU
...((((((((.(((((((........((((((((((-((.........))).......)))))))))(((((....))))).......))))))-).)))))))-)....... ( -28.71, z-score =  -3.66, R)
>consensus
ACCGUCUACACAGAAAAAAA____CAUUACGAUCUCUUGUGGCUACUAAAUGCAAGAAAUUCAUGUUGAUUAUCACCAUGUUAUAGCAAUUUUUU_CUGUGCAGCACGGCAGCU
.((((((.(((((((((((...............(((((((.........)))))))....((((.((.....)).)))).........)))))).))))).)).))))..... (-10.50 = -13.02 +   2.52)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,100,277 – 1,100,386
Length 109
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 82.51
Shannon entropy 0.30472
G+C content 0.37302
Mean single sequence MFE -36.24
Consensus MFE -20.84
Energy contribution -21.92
Covariance contribution 1.08
Combinations/Pair 1.23
Mean z-score -4.42
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.77
SVM RNA-class probability 0.999295
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 1100277 109 - 22422827
AGCUGCCGUGCUGCACAG-AAAAAAUUGCUAUAACAUGGUCAUAAUCAACAUGAAUUUCUUGCGUUCAGUAGCCACAAGAGAUCGUAAUG----UUUUUUUCUGUGUAGACGUU
......(((.((((((((-((((((((((.....((((...........)))).((((((((.((......))..)))))))).))))).----..)))))))))))))))).. ( -31.00, z-score =  -2.51, R)
>droSim1.chrX 879379 109 - 17042790
AGCUGCCGUGCUGCACAG-AAAAAAUUGACAUAACAUGGUGAUAAUCAACAUGAAUUUCUUGCAUAAAGUAGCCGCAAGAGAUCGUAAAG----UUUUUUUCUGUGUAGACGGU
....(((((.((((((((-((((((...((....((((.((.....)).)))).(((((((((...........))))))))).))....----.))))))))))))))))))) ( -39.50, z-score =  -5.29, R)
>droSec1.super_10 931842 109 - 3036183
AGCUGCCGUGCUGCACAG-AAAAAAUUGACAUAACAUGGUGAUAAUCAACAUGAAUUUCUUGCAUUAAAUAGCCACAAGAGAUCGUAAAG----UUUUUUUCUGUGUAGACGGU
....(((((.((((((((-((((((...((....((((.((.....)).)))).((((((((.............)))))))).))....----.))))))))))))))))))) ( -35.52, z-score =  -4.46, R)
>droYak2.chrX 1014915 109 - 21770863
AGCUGCUG-GCUGCACAGAAAAAAAAUGCUCUAAUGUGGUGAUAAUCAACAUGAAUCUCUACCAUUUAGUAACCAAAAGAGAUGGUUAUG----UUUUUUUCUGUGUAGGCGGU
....((((-.(((((((((((((((.....((((.(((((((.(.((.....)).).)).)))))))))((((((.......))))))..----))))))))))))))).)))) ( -36.80, z-score =  -4.50, R)
>droEre2.scaffold_4644 1085276 111 - 2521924
AGCUGCCG-CCUGCACGG-AAAAAACUGCUAUAAUAUGGUAAUAUUCAACAUGAAUUUCUUUCAUUUAGUAGGCAU-GUUCAUGUUAAUGUUUUUUUUUUUCUGUGCAGGCUGU
....((.(-(((((((((-((((((.((((((...))))))(((((.(((((((((..(((.(.....).)))...-))))))))))))))....)))))))))))))))).)) ( -38.40, z-score =  -5.34, R)
>consensus
AGCUGCCGUGCUGCACAG_AAAAAAUUGCUAUAACAUGGUGAUAAUCAACAUGAAUUUCUUGCAUUAAGUAGCCACAAGAGAUCGUAAUG____UUUUUUUCUGUGUAGACGGU
....(((((.((((((((.((((((.........((((...........)))).((((((((.............))))))))...........)))))).))))))))))))) (-20.84 = -21.92 +   1.08)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:05:19 2011