Locus 14122

Sequence ID dm3.chrX
Location 11,304,955 – 11,305,126
Length 171
Max. P 0.967501
window19427 window19428 window19429 window19430

overview

Window 7

Location 11,304,955 – 11,305,066
Length 111
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 76.92
Shannon entropy 0.42148
G+C content 0.53925
Mean single sequence MFE -38.40
Consensus MFE -25.54
Energy contribution -26.10
Covariance contribution 0.56
Combinations/Pair 1.39
Mean z-score -1.11
Structure conservation index 0.67
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.19
SVM RNA-class probability 0.583868
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 11304955 111 - 22422827
AGGAUGCAGGCCAUCUAUGUCCAGUUUGGUCUGCAUCCUGGAGAUCCUUACAUCCUUCAC------CACCUUCGGGGGAUUCUCGUGACCGAAAUGGACCAGGGAAAUGGCCUUCUU
((((...(((((((((..(((((.(((((((.(.(((((((((...........))))).------..((....)))))).)....))))))).)))))...)))..)))))))))) ( -39.90, z-score =  -1.16, R)
>droSim1.chrX_random 3170745 108 - 5698898
AGGAUGCAGGCCAUCUAUGUCCAUCUUGGUCUGCAUCCUGGAGAUCCGUACAUCCUUCAC---------CUUGCAGGGCUCCUCGUGACCGAAAUGGACCAGGGAAAUGGCCUUCUU
((((...(((((((((..((((((.((((((.((.....((((.((((((..........---------..))).)))))))..)))))))).))))))...)))..)))))))))) ( -37.40, z-score =  -0.98, R)
>droSec1.super_36 28068 108 - 449511
AGGAUGCAGGCCAUCUAUGUCCAGCUUGGUCUGCAUCCUGGAGAUCCUUACAUCCUUCAC---------CUUGGAGGGCUCCUCGUAACCGAAAUGGACCAGGGAAAUGGCCUUCUU
(((((((((((((.((......))..)))))))))))))((((.(((((.((........---------..)))))))))))(((....)))...((.(((......)))))..... ( -39.20, z-score =  -1.36, R)
>droYak2.chrX 10922790 117 + 21770863
AGGAUGCAGGCCAUCGAUGUCCAGUUUGGUCUGCAUCCUGGAAAUCCUCACAUCCCUCACAUCCCUCACCUUCGAGUGCUCCUCGUGGCCGAAAUGGACCAGGGAAAUGGCCCUCUU
(((((((((((((.(........)..)))))))))))))((....))(((..(((((....(((.((.((..((((.....)))).))..))...)))..)))))..)))....... ( -39.10, z-score =  -1.02, R)
>droEre2.scaffold_4690 14898583 108 + 18748788
AGGAUGCAGGCCAUCUAUGUCCAGUUUGGUCUGCAUCCUGGAGAUCCUCACAUCCUUCACA---------UUGGCCUGCUCCUCGUGGCUGAAAUGGACCAGGGUGAUGGCCUUCUU
(((((((((((((.((......))..)))))))))))))((((..(.((((..((......---------..))((((.(((.............))).)))))))).)..)))).. ( -42.62, z-score =  -1.89, R)
>droAna3.scaffold_13248 1774529 108 - 4840945
CGGACGCAGGCCAUUCCACUCCAGCUUGUUGUUCAUUUUGGAGACCCUCAGGUCCCUGAA---------CUUGGUGGGUGCUCCCUUGUCGGCCAUUCCAUUGAUAAUCGCCCGUCU
.(((((..((((......((((((..((.....))..))))))((((((((((......)---------))))).))))...........))))........(.....)...))))) ( -32.20, z-score =  -0.28, R)
>consensus
AGGAUGCAGGCCAUCUAUGUCCAGCUUGGUCUGCAUCCUGGAGAUCCUCACAUCCUUCAC_________CUUGGAGGGCUCCUCGUGACCGAAAUGGACCAGGGAAAUGGCCUUCUU
(((((((((((((.............)))))))))))))(((..........)))..................(((((((.(((....((.....))....)))....))))))).. (-25.54 = -26.10 +   0.56)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,304,995 – 11,305,097
Length 102
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 73.28
Shannon entropy 0.46595
G+C content 0.54250
Mean single sequence MFE -38.54
Consensus MFE -24.54
Energy contribution -25.74
Covariance contribution 1.20
Combinations/Pair 1.22
Mean z-score -1.83
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.78
SVM RNA-class probability 0.967501
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 11304995 102 + 22422827
------CCCCGAAGGUGGUGAAGGAUGUAAGGAUCUCCAGGAUGCAGACCAAACUGGACAUAGAUGGCCUGCAUCCUUGCGGCAGCUCCAUUGAUUCCUUUGCCAACA---------
------.......(.(((..(((((..((((((.(((((((((((((.(((..(((....))).))).)))))))))...)).)).))).)))..)))))..))).).--------- ( -40.50, z-score =  -2.93, R)
>droSim1.chrX_random 3170785 99 + 5698898
---------CCUGCAAGGUGAAGGAUGUACGGAUCUCCAGGAUGCAGACCAAGAUGGACAUAGAUGGCCUGCAUCCUUGCGGCAGCUCUAUUGAUUCCUUCGCCAGCA---------
---------...((..(((((((((.....(((.(((((((((((((.(((..((....))...))).)))))))))...)).)).)))......))))))))).)).--------- ( -38.60, z-score =  -2.32, R)
>droSec1.super_36 28108 99 + 449511
---------CCUCCAAGGUGAAGGAUGUAAGGAUCUCCAGGAUGCAGACCAAGCUGGACAUAGAUGGCCUGCAUCCUUGCGGCAGCUCCAUUGAUUCCUUCGCCAGCA---------
---------.......(((((((((..((((((.(((((((((((((.(((..(((....))).))).)))))))))...)).)).))).)))..)))))))))....--------- ( -42.70, z-score =  -3.22, R)
>droYak2.chrX 10922830 108 - 21770863
ACUCGAAGGUGAGGGAUGUGAGGGAUGUGAGGAUUUCCAGGAUGCAGACCAAACUGGACAUCGAUGGCCUGCAUCCUUGCUGCGGCUCCGUUGAUUCCCUGGCCAGUG---------
.......(((.(((((..(((.(((.((..((....))(((((((((.(((.............))).))))))))).......))))).)))..))))).)))....--------- ( -40.22, z-score =  -1.06, R)
>droEre2.scaffold_4690 14898623 99 - 18748788
---------AGGCCAAUGUGAAGGAUGUGAGGAUCUCCAGGAUGCAGACCAAACUGGACAUAGAUGGCCUGCAUCCUUGCUGCAGCUCCAUUGAUUCCCUUGCCAUCA---------
---------.(((.((.(.(((.((((.(((...(..((((((((((.(((..(((....))).))).)))))))).))..)...)))))))..)))).)))))....--------- ( -30.50, z-score =  -0.08, R)
>droAna3.scaffold_13248 1774569 108 + 4840945
---------CCACCAAGUUCAGGGACCUGAGGGUCUCCAAAAUGAACAACAAGCUGGAGUGGAAUGGCCUGCGUCCGUGUCGCAAGAACACCGAUCCCUUCGGCGUGGAUCGCAUCA
---------((((...(((((((((((....)))))).....))))).....(((((((.(((..(((....))).(((((....).))))...))))))))))))))......... ( -38.70, z-score =  -1.35, R)
>consensus
_________CCACCAAGGUGAAGGAUGUAAGGAUCUCCAGGAUGCAGACCAAACUGGACAUAGAUGGCCUGCAUCCUUGCGGCAGCUCCAUUGAUUCCUUCGCCAGCA_________
................(((((((((.....((....))(((((((((.(((.............))).)))))))))..................)))))))))............. (-24.54 = -25.74 +   1.20)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,304,995 – 11,305,097
Length 102
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 73.28
Shannon entropy 0.46595
G+C content 0.54250
Mean single sequence MFE -38.40
Consensus MFE -23.75
Energy contribution -24.05
Covariance contribution 0.31
Combinations/Pair 1.25
Mean z-score -1.81
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.64
SVM RNA-class probability 0.957056
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 11304995 102 - 22422827
---------UGUUGGCAAAGGAAUCAAUGGAGCUGCCGCAAGGAUGCAGGCCAUCUAUGUCCAGUUUGGUCUGCAUCCUGGAGAUCCUUACAUCCUUCACCACCUUCGGGG------
---------...(((..(((((......(((.((.((...(((((((((((((.((......))..))))))))))))))))).))).....)))))..)))((....)).------ ( -42.00, z-score =  -3.04, R)
>droSim1.chrX_random 3170785 99 - 5698898
---------UGCUGGCGAAGGAAUCAAUAGAGCUGCCGCAAGGAUGCAGGCCAUCUAUGUCCAUCUUGGUCUGCAUCCUGGAGAUCCGUACAUCCUUCACCUUGCAGG---------
---------(((.((.((((((.........((....)).(((((((((((((.............)))))))))))))((....)).....)))))).))..)))..--------- ( -40.42, z-score =  -3.00, R)
>droSec1.super_36 28108 99 - 449511
---------UGCUGGCGAAGGAAUCAAUGGAGCUGCCGCAAGGAUGCAGGCCAUCUAUGUCCAGCUUGGUCUGCAUCCUGGAGAUCCUUACAUCCUUCACCUUGGAGG---------
---------....((.((((((......(((.((.((...(((((((((((((.((......))..))))))))))))))))).))).....)))))).)).......--------- ( -40.70, z-score =  -2.28, R)
>droYak2.chrX 10922830 108 + 21770863
---------CACUGGCCAGGGAAUCAACGGAGCCGCAGCAAGGAUGCAGGCCAUCGAUGUCCAGUUUGGUCUGCAUCCUGGAAAUCCUCACAUCCCUCACAUCCCUCACCUUCGAGU
---------....((..(((((......(((((....)).(((((((((((((.(........)..)))))))))))))((....)).....)))......)))))..))....... ( -36.40, z-score =  -1.44, R)
>droEre2.scaffold_4690 14898623 99 + 18748788
---------UGAUGGCAAGGGAAUCAAUGGAGCUGCAGCAAGGAUGCAGGCCAUCUAUGUCCAGUUUGGUCUGCAUCCUGGAGAUCCUCACAUCCUUCACAUUGGCCU---------
---------.((((...(((((......(((.((.((....((((((((((((.((......))..)))))))))))))).)).))).....)))))..)))).....--------- ( -34.90, z-score =  -0.68, R)
>droAna3.scaffold_13248 1774569 108 - 4840945
UGAUGCGAUCCACGCCGAAGGGAUCGGUGUUCUUGCGACACGGACGCAGGCCAUUCCACUCCAGCUUGUUGUUCAUUUUGGAGACCCUCAGGUCCCUGAACUUGGUGG---------
............(((((((((((((((....((((((.......)))))).....)).((((((..((.....))..)))))).......)))))))....)))))).--------- ( -36.00, z-score =  -0.41, R)
>consensus
_________UGCUGGCGAAGGAAUCAAUGGAGCUGCCGCAAGGAUGCAGGCCAUCUAUGUCCAGCUUGGUCUGCAUCCUGGAGAUCCUCACAUCCUUCACCUUGGUCG_________
.................(((((..................(((((((((((((.............)))))))))))))((....)).....))))).................... (-23.75 = -24.05 +   0.31)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,305,026 – 11,305,126
Length 100
Sequences 6
Columns 121
Reading direction reverse
Mean pairwise identity 70.53
Shannon entropy 0.51028
G+C content 0.55056
Mean single sequence MFE -39.17
Consensus MFE -23.25
Energy contribution -24.54
Covariance contribution 1.29
Combinations/Pair 1.47
Mean z-score -1.39
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.09
SVM RNA-class probability 0.888871
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 11305026 100 - 22422827
---------------------AUAGGCUUUGGAUGACUGCGGGCUGUCAGUGUUGGCAAAGGAAUCAAUGGAGCUGCCGCAAGGAUGCAGGCCAUCUAUGUCCAGUUUGGUCUGCAUCCUG
---------------------...((((((.(((..((((.(((.......))).))..))..)))...))))))......(((((((((((((.((......))..))))))))))))). ( -37.80, z-score =  -1.38, R)
>droSim1.chrX_random 3170813 100 - 5698898
---------------------GUAGGCUUUCUUGGACUGCGGGUUGUCAGUGCUGGCGAAGGAAUCAAUAGAGCUGCCGCAAGGAUGCAGGCCAUCUAUGUCCAUCUUGGUCUGCAUCCUG
---------------------...(((.((((..((.(.(...((((((....)))))).).).))...))))..)))...(((((((((((((.............))))))))))))). ( -38.12, z-score =  -1.57, R)
>droSec1.super_36 28136 100 - 449511
---------------------GUAGGCUUUGGAGGACGGCGGGUUGUCAGUGCUGGCGAAGGAAUCAAUGGAGCUGCCGCAAGGAUGCAGGCCAUCUAUGUCCAGCUUGGUCUGCAUCCUG
---------------------.............(.((((((.((((((....))))((.....))....)).))))))).(((((((((((((.((......))..))))))))))))). ( -38.10, z-score =  -0.68, R)
>droYak2.chrX 10922867 100 + 21770863
---------------------GUAGGCUUGGUAGGACUUUGGUUUCUUGCCACUGGCCAGGGAAUCAACGGAGCCGCAGCAAGGAUGCAGGCCAUCGAUGUCCAGUUUGGUCUGCAUCCUG
---------------------...(((((.((.......((((((((((((...)).)))))))))))).)))))......(((((((((((((.(........)..))))))))))))). ( -43.41, z-score =  -2.80, R)
>droEre2.scaffold_4690 14898651 100 + 18748788
---------------------GUAGGCUUGGGAGGACUGCGGCUUGCCACUGAUGGCAAGGGAAUCAAUGGAGCUGCAGCAAGGAUGCAGGCCAUCUAUGUCCAGUUUGGUCUGCAUCCUG
---------------------.............(.((((((((..(((.((((.........)))).)))))))))))).(((((((((((((.((......))..))))))))))))). ( -42.40, z-score =  -1.94, R)
>droAna3.scaffold_13248 1774597 120 - 4840945
AUCAGCAUGUGAUACAUCCGGGCACGGUCUACCGUAUCAUUGA-UGCGAUCCACGCCGAAGGGAUCGGUGUUCUUGCGACACGGACGCAGGCCAUUCCACUCCAGCUUGUUGUUCAUUUUG
....(((((((((((..(((....)))......)))))))..)-)))(((((.(......)))))).(((((.....)))))((((((((((............))))).)))))...... ( -35.20, z-score =   0.07, R)
>consensus
_____________________GUAGGCUUUGGAGGACUGCGGGUUGUCAGUGCUGGCGAAGGAAUCAAUGGAGCUGCCGCAAGGAUGCAGGCCAUCUAUGUCCAGCUUGGUCUGCAUCCUG
........................(((((((...((.(.(...((((((....)))))).).).))..)))))))......(((((((((((((.............))))))))))))). (-23.25 = -24.54 +   1.29)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:34:07 2011