Locus 14339

Sequence ID dm3.chrX
Location 12,764,449 – 12,764,662
Length 213
Max. P 0.997461
window19740 window19741 window19742 window19743 window19744

overview

Window 0

Location 12,764,449 – 12,764,548
Length 99
Sequences 3
Columns 100
Reading direction reverse
Mean pairwise identity 98.00
Shannon entropy 0.02755
G+C content 0.42135
Mean single sequence MFE -24.57
Consensus MFE -22.29
Energy contribution -22.73
Covariance contribution 0.45
Combinations/Pair 1.04
Mean z-score -1.61
Structure conservation index 0.91
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.28
SVM RNA-class probability 0.627982
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 12764449 99 - 22422827
GCAAUGCACUUUUUCCGGCCAUCUGGUU-GGAAUACUGGUCCAUAAAGUUUAAUGAUCCAUACACAACGAAGCUCCUAAAGUUAGAUUUCGGCAAAACUU
....(((.....((((((((....))))-))))...(((..(((........)))..))).......(((((...(((....))).))))))))...... ( -19.90, z-score =  -0.59, R)
>droSec1.super_21 514680 100 - 1102487
GCAAUGCACUUUUUCCGGCCAUCUGGCUGGGAAUACUGGUCCAUAAAGUUUAAUGAUCCAUACACAACGAAGCUCCUAAAGUGAGAUUUCGGCAAAACUU
....(((....(((((((((....)))))))))...(((..(((........)))..))).......(((((((((....).))).))))))))...... ( -26.90, z-score =  -2.12, R)
>droSim1.chrX 9732726 100 - 17042790
GCAAUGCACUUUUUCCGGCCAUCUGGCUGGGAAUACUGGUCCAUAAAGUUUAAUGAUCCAUACACAACGAAGCUCCUAAAGUGAGAUUUCGGCAAAACUU
....(((....(((((((((....)))))))))...(((..(((........)))..))).......(((((((((....).))).))))))))...... ( -26.90, z-score =  -2.12, R)
>consensus
GCAAUGCACUUUUUCCGGCCAUCUGGCUGGGAAUACUGGUCCAUAAAGUUUAAUGAUCCAUACACAACGAAGCUCCUAAAGUGAGAUUUCGGCAAAACUU
....(((....(((((((((....)))))))))...(((..(((........)))..))).......((((((((.......))).))))))))...... (-22.29 = -22.73 +   0.45)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,764,548 – 12,764,660
Length 112
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 67.66
Shannon entropy 0.56796
G+C content 0.35859
Mean single sequence MFE -23.14
Consensus MFE -8.24
Energy contribution -8.76
Covariance contribution 0.52
Combinations/Pair 1.47
Mean z-score -2.08
Structure conservation index 0.36
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.90
SVM RNA-class probability 0.848168
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 12764548 112 + 22422827
UGCAUGGA-----CUUUCCCAAACAAAAUCAUAUCAGAUGUCACGAUGUAAUUUGGAGUAUUUCUAUAGAAUAUCCUUUCUGACAUCCUAGACUUAAAAA-UACCGCUCUACCGAAAA
.((.(((.-----.....)))..................(((..(((((.....(((....(((....)))..)))......)))))...))).......-....))........... ( -15.90, z-score =  -0.22, R)
>droEre2.scaffold_4690 4660200 102 - 18748788
UGCAUGAU-----AUA--------GACAGGAUAUCAAAUGUCAUGAUGUCAUUUGGAGUAUUCCUAUAGAAUGUCCUUUUAGACAUUCUAGACUAGAAUAGCCCCCCUUUACUGA---
........-----...--------..((((((((((.......)))))))....((..(((((...(((((((((......))))))))).....)))))..)).......))).--- ( -25.40, z-score =  -2.28, R)
>droSec1.super_21 514780 110 + 1102487
UGCAUGGA-----CUUUCCCAAACAACAUCAUAUCAGAUGUCAUGAUGCCAUUUGGAGUAUUUCUAUAGAAUGUCCUUUCAGACAUUCUAGACUAGAAUA---CCGCUCUACCGAAAA
.((((((.-----.....)).....(((((......)))))....))))....((((((..((((((((((((((......)))))))))...)))))..---..))))))....... ( -27.50, z-score =  -3.04, R)
>droSim1.chrX 9732826 110 + 17042790
UGCACGGA-----CUUUCCCAAACAACAUCAUAUCAGAUGUCAUGAUGUCAUUUCGAGUAUUUCUAUAGAAUGUCCUUUCAGACAUUCUAGAAUAGAAUA---CCGCUCUACCGAAAA
....(((.-----............(((((((..(....)..)))))))......((((..((((((((((((((......)))))))))...)))))..---..))))..))).... ( -27.70, z-score =  -3.63, R)
>triCas2.chrUn_29 118726 113 + 145421
UACGUGAUUAUCGGUCCACCAUUUGAAAAAAUAACAGUUGGCUUCAUUAAGGCCCUAGACUUUCUAAUUAACCUUGUUUUUUACAAAAAUCAAUAAAAU-----CGCUACACGGAAAA
...((((((...((....)).(((((((((((((..((((((((.....))))).(((.....)))...))).))))))))).)))).........)))-----)))........... ( -19.20, z-score =  -1.26, R)
>consensus
UGCAUGGA_____CUUUCCCAAACAACAUCAUAUCAGAUGUCAUGAUGUCAUUUGGAGUAUUUCUAUAGAAUGUCCUUUCAGACAUUCUAGACUAGAAUA___CCGCUCUACCGAAAA
.................................(((((((.(.....).)))))))..........(((((((((......)))))))))............................ ( -8.24 =  -8.76 +   0.52)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,764,548 – 12,764,660
Length 112
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 67.66
Shannon entropy 0.56796
G+C content 0.35859
Mean single sequence MFE -30.14
Consensus MFE -15.96
Energy contribution -17.52
Covariance contribution 1.56
Combinations/Pair 1.50
Mean z-score -2.47
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.11
SVM RNA-class probability 0.997461
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 12764548 112 - 22422827
UUUUCGGUAGAGCGGUA-UUUUUAAGUCUAGGAUGUCAGAAAGGAUAUUCUAUAGAAAUACUCCAAAUUACAUCGUGACAUCUGAUAUGAUUUUGUUUGGGAAAG-----UCCAUGCA
......((((..(((((-((((((....(((((((((......)))))))))))))))))))((((((...((((((.(....).))))))...))))))....)-----..).))). ( -27.60, z-score =  -1.70, R)
>droEre2.scaffold_4690 4660200 102 + 18748788
---UCAGUAAAGGGGGGCUAUUCUAGUCUAGAAUGUCUAAAAGGACAUUCUAUAGGAAUACUCCAAAUGACAUCAUGACAUUUGAUAUCCUGUC--------UAU-----AUCAUGCA
---...((.....((((.((((((....((((((((((....))))))))))..)))))))))).....))..(((((.((..(((.....)))--------.))-----.))))).. ( -27.60, z-score =  -2.29, R)
>droSec1.super_21 514780 110 - 1102487
UUUUCGGUAGAGCGG---UAUUCUAGUCUAGAAUGUCUGAAAGGACAUUCUAUAGAAAUACUCCAAAUGGCAUCAUGACAUCUGAUAUGAUGUUGUUUGGGAAAG-----UCCAUGCA
......((((..(((---(((((((...((((((((((....))))))))))))).))))))(((((..((((((((.(....).))))))))..)))))....)-----..).))). ( -40.40, z-score =  -4.98, R)
>droSim1.chrX 9732826 110 - 17042790
UUUUCGGUAGAGCGG---UAUUCUAUUCUAGAAUGUCUGAAAGGACAUUCUAUAGAAAUACUCGAAAUGACAUCAUGACAUCUGAUAUGAUGUUGUUUGGGAAAG-----UCCGUGCA
.........(.((((---..(((((...((((((((((....)))))))))))))))...(((.(((..((((((((.(....).))))))))..))))))....-----.)))).). ( -36.90, z-score =  -4.12, R)
>triCas2.chrUn_29 118726 113 - 145421
UUUUCCGUGUAGCG-----AUUUUAUUGAUUUUUGUAAAAAACAAGGUUAAUUAGAAAGUCUAGGGCCUUAAUGAAGCCAACUGUUAUUUUUUCAAAUGGUGGACCGAUAAUCACGUA
.....((((...((-----.(((((((((...((((.....))))(((...((((.....)))).))))))))))))....(..((((((....))))))..)..)).....)))).. ( -18.20, z-score =   0.75, R)
>consensus
UUUUCGGUAGAGCGG___UAUUCUAGUCUAGAAUGUCUGAAAGGACAUUCUAUAGAAAUACUCCAAAUGACAUCAUGACAUCUGAUAUGAUGUUGUUUGGGAAAG_____UCCAUGCA
...........(((......(((((...((((((((((....))))))))))))))).......(((((((((((((.(....).)))))))))))))................))). (-15.96 = -17.52 +   1.56)

alignment

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secondary structure

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dotplot

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Window 3

Location 12,764,550 – 12,764,662
Length 112
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 65.76
Shannon entropy 0.59963
G+C content 0.35981
Mean single sequence MFE -22.60
Consensus MFE -8.24
Energy contribution -8.76
Covariance contribution 0.52
Combinations/Pair 1.47
Mean z-score -2.14
Structure conservation index 0.36
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.30
SVM RNA-class probability 0.923121
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 12764550 112 + 22422827
-----CAUGGACUUUCCCAAACA-AAAUCAUAUCAGAUGUCACGAUGUAAUUUGGAGUAUUUCUAUAGAAUAUCCUUUCUGACAUCCUAGACUUAAAAA-UACCGCUCUACCGAAAAAC
-----..(((.............-..(((......)))(((..(((((.....(((....(((....)))..)))......)))))...))).......-..........)))...... ( -14.20, z-score =   0.15, R)
>droEre2.scaffold_4690 4660202 100 - 18748788
--------------CAUGAUAUAGACAGGAUAUCAAAUGUCAUGAUGUCAUUUGGAGUAUUCCUAUAGAAUGUCCUUUUAGACAUUCUAGACUAGAAUAGCCCCCCUUUACUGA-----
--------------...........((((((((((.......)))))))....((..(((((...(((((((((......))))))))).....)))))..)).......))).----- ( -25.40, z-score =  -2.47, R)
>droSec1.super_21 514782 110 + 1102487
-----CAUGGACUUUCCCAAACA-ACAUCAUAUCAGAUGUCAUGAUGCCAUUUGGAGUAUUUCUAUAGAAUGUCCUUUCAGACAUUCUAGACUAGAAUA---CCGCUCUACCGAAAAAC
-----..(((......(((((..-.((((((..(....)..))))))...))))).(((((.((((((((((((......)))))))))...)))))))---).......)))...... ( -26.50, z-score =  -3.10, R)
>droSim1.chrX 9732828 110 + 17042790
-----CACGGACUUUCCCAAACA-ACAUCAUAUCAGAUGUCAUGAUGUCAUUUCGAGUAUUUCUAUAGAAUGUCCUUUCAGACAUUCUAGAAUAGAAUA---CCGCUCUACCGAAAAAC
-----..(((.............-(((((((..(....)..)))))))......((((..((((((((((((((......)))))))))...)))))..---..))))..)))...... ( -27.70, z-score =  -3.99, R)
>triCas2.chrUn_29 118728 113 + 145421
CGUGAUUAUCGGUCCACCAUUUG-AAAAAAUAACAGUUGGCUUCAUUAAGGCCCUAGACUUUCUAAUUAACCUUGUUUUUUACAAAAAUCAAUAAAAU-----CGCUACACGGAAAAAC
.((((((...((....)).((((-(((((((((..((((((((.....))))).(((.....)))...))).))))))))).)))).........)))-----)))............. ( -19.20, z-score =  -1.28, R)
>consensus
_____CAUGGACUUUCCCAAACA_ACAUCAUAUCAGAUGUCAUGAUGUCAUUUGGAGUAUUUCUAUAGAAUGUCCUUUCAGACAUUCUAGACUAGAAUA___CCGCUCUACCGAAAAAC
................................(((((((.(.....).)))))))..........(((((((((......))))))))).............................. ( -8.24 =  -8.76 +   0.52)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,764,550 – 12,764,662
Length 112
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 65.76
Shannon entropy 0.59963
G+C content 0.35981
Mean single sequence MFE -29.64
Consensus MFE -12.82
Energy contribution -12.90
Covariance contribution 0.08
Combinations/Pair 1.50
Mean z-score -2.45
Structure conservation index 0.43
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.58
SVM RNA-class probability 0.992984
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 12764550 112 - 22422827
GUUUUUCGGUAGAGCGGUA-UUUUUAAGUCUAGGAUGUCAGAAAGGAUAUUCUAUAGAAAUACUCCAAAUUACAUCGUGACAUCUGAUAUGAUUU-UGUUUGGGAAAGUCCAUG-----
..(((((........((((-((((((....(((((((((......)))))))))))))))))))((((((...((((((.(....).))))))..-.)))))))))))......----- ( -27.00, z-score =  -1.60, R)
>droEre2.scaffold_4690 4660202 100 + 18748788
-----UCAGUAAAGGGGGGCUAUUCUAGUCUAGAAUGUCUAAAAGGACAUUCUAUAGGAAUACUCCAAAUGACAUCAUGACAUUUGAUAUCCUGUCUAUAUCAUG--------------
-----...((.....((((.((((((....((((((((((....))))))))))..)))))))))).....))..(((((.((..(((.....))).)).)))))-------------- ( -27.20, z-score =  -2.39, R)
>droSec1.super_21 514782 110 - 1102487
GUUUUUCGGUAGAGCGG---UAUUCUAGUCUAGAAUGUCUGAAAGGACAUUCUAUAGAAAUACUCCAAAUGGCAUCAUGACAUCUGAUAUGAUGU-UGUUUGGGAAAGUCCAUG-----
..(((((........((---(((((((...((((((((((....))))))))))))).))))))(((((..((((((((.(....).))))))))-..))))))))))......----- ( -39.80, z-score =  -5.00, R)
>droSim1.chrX 9732828 110 - 17042790
GUUUUUCGGUAGAGCGG---UAUUCUAUUCUAGAAUGUCUGAAAGGACAUUCUAUAGAAAUACUCGAAAUGACAUCAUGACAUCUGAUAUGAUGU-UGUUUGGGAAAGUCCGUG-----
.............((((---..(((((...((((((((((....)))))))))))))))...(((.(((..((((((((.(....).))))))))-..)))))).....)))).----- ( -36.60, z-score =  -4.15, R)
>triCas2.chrUn_29 118728 113 - 145421
GUUUUUCCGUGUAGCG-----AUUUUAUUGAUUUUUGUAAAAAACAAGGUUAAUUAGAAAGUCUAGGGCCUUAAUGAAGCCAACUGUUAUUUUUU-CAAAUGGUGGACCGAUAAUCACG
.......((((...((-----.(((((((((...((((.....))))(((...((((.....)))).))))))))))))....(..((((((...-.))))))..)..)).....)))) ( -17.60, z-score =   0.90, R)
>consensus
GUUUUUCGGUAGAGCGG___UAUUCUAGUCUAGAAUGUCUGAAAGGACAUUCUAUAGAAAUACUCCAAAUGACAUCAUGACAUCUGAUAUGAUGU_UGUUUGGGAAAGUCCAUG_____
......................(((((...((((((((((....)))))))))))))))............((((((((.(....).))))))))........................ (-12.82 = -12.90 +   0.08)

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 01:38:22 2011