Locus 4744

Sequence ID dm3.chr2R
Location 15,446,440 – 15,446,572
Length 132
Max. P 0.993391
window6509 window6510 window6511

overview

Window 9

Location 15,446,440 – 15,446,541
Length 101
Sequences 7
Columns 115
Reading direction reverse
Mean pairwise identity 81.00
Shannon entropy 0.36140
G+C content 0.41154
Mean single sequence MFE -28.06
Consensus MFE -13.25
Energy contribution -13.55
Covariance contribution 0.29
Combinations/Pair 1.24
Mean z-score -2.14
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.10
SVM RNA-class probability 0.544489
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 15446440 101 - 21146708
UGAAACAUUUCUGGCC--AGAUAAUAAUUUUGCUUUAUUAUUUUUUGGCUU--CUGUCGUUCGGCCA-UUCUGUCC---------CAUCGAGUGCGAGUGGCCUUUGUUGAUGGU
............((((--(((.((((((........)))))).))))))).--((((((...(((((-(((.(..(---------......)..))))))))).....)))))). ( -28.60, z-score =  -2.29, R)
>droSim1.chr2R 14147772 101 - 19596830
UGAAACAUUUCUGGCC--AGAUAAUAAUUUUGCUUUAUUAUUUUCUGGCUU--CUGUCGUUCGGCCA-UUCUGUCC---------CAUCGAGUGCGAGUGGCCUUUGUUGAUGGU
............((((--(((.((((((........)))))).))))))).--((((((...(((((-(((.(..(---------......)..))))))))).....)))))). ( -31.20, z-score =  -3.09, R)
>droSec1.super_1 12965880 101 - 14215200
UGAAACAUUUCUGGCC--AGAUAAUAAUUUUGCUUUAUUAUUUUCUGGCUU--CUGUCGUUCGGCCA-UGCUGUCC---------CAUCGAGUGCGAGUGGCCUUUGUUGAUGGU
............((((--(((.((((((........)))))).))))))).--((((((...(((((-(..((..(---------......)..)).)))))).....)))))). ( -28.90, z-score =  -1.91, R)
>droYak2.chr2R 7411369 101 + 21139217
UGAAACAUUUCUGGCC--AGAUAAUAAUUUUGCUUUAUUAUUUUCGGGCUU--GUGUCGUACGGCCA-UUCAGUCG---------CAUCGAGUGCGAGUGGCCUUUGUUGAUGGU
....((((....((((--.((.((((((........)))))).)).)))).--)))).....(((((-(((.(.((---------(.....))))))))))))............ ( -28.10, z-score =  -1.07, R)
>droEre2.scaffold_4845 9645808 101 - 22589142
UGAAACAUUUCUGGCC--AGAUAAUAAUUUUGCUUUAUUAUUUUCUGGCUU--CUGUCGUUCGGCCA-UUCAGUCC---------CAUCGAGUGCGAGUGGCCUUUGUUGAUGGU
............((((--(((.((((((........)))))).))))))).--((((((...(((((-(((.(..(---------......)..))))))))).....)))))). ( -31.20, z-score =  -2.87, R)
>droAna3.scaffold_13266 10053266 113 + 19884421
UGAAACAUUUCUGGCC--AGAUAAUAAUUUUGCUUUAUUAUUUUCUGGCUUCAGAGUCGCUUGUCUGCCUCCAUCAUCUGCCUGCCACAAAGUGUGAGUGGCUUUUGUUGGUGCC
........((((((((--(((.((((((........)))))).))))))..)))))..........((..(((.((...(((.(((((.....))).)))))...)).))).)). ( -32.00, z-score =  -1.94, R)
>droWil1.scaffold_180701 1467015 94 - 3904529
GGAAACAUUUCUGGUCAGAGAUAAUAAUUUUGCUUUAUUA-UUUCUGUUUU--UUCUCUCUUUUUUUGCUCU-------------CAUUCUGUCAUAGUGG--UGUGUUCAU---
(((.((((..(((..((((((((((((.......))))))-))))))....--..............((...-------------......))..)))..)--))).)))..--- ( -16.40, z-score =  -1.84, R)
>consensus
UGAAACAUUUCUGGCC__AGAUAAUAAUUUUGCUUUAUUAUUUUCUGGCUU__CUGUCGUUCGGCCA_UUCUGUCC_________CAUCGAGUGCGAGUGGCCUUUGUUGAUGGU
...((((.....((((..(((((((((.......)))))))))...))))............(((((.(((........................))))))))..))))...... (-13.25 = -13.55 +   0.29)

alignment

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secondary structure

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dotplot

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Window 0

Location 15,446,475 – 15,446,572
Length 97
Sequences 7
Columns 108
Reading direction forward
Mean pairwise identity 79.19
Shannon entropy 0.37936
G+C content 0.39893
Mean single sequence MFE -22.43
Consensus MFE -13.32
Energy contribution -14.36
Covariance contribution 1.04
Combinations/Pair 1.00
Mean z-score -2.95
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.61
SVM RNA-class probability 0.993391
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 15446475 97 + 21146708
--------GAAUGGCCGAA--CGACAGAAGCCAAAAAAUAAUAAAGCAAAAUUAUUAUCUGGCCAGAAAUGUUUCAAUAACAACAGACAGUUGGGG-CCCCCAGAAAA
--------....((((((.--.((((...((((.(.((((((........)))))).).))))......)))))).....((((.....)))).))-))......... ( -19.10, z-score =  -1.48, R)
>droSim1.chr2R 14147807 97 + 19596830
--------GAAUGGCCGAA--CGACAGAAGCCAGAAAAUAAUAAAGCAAAAUUAUUAUCUGGCCAGAAAUGUUUCAAUAACAACAGACAGUUGGGG-CCCCCAGAAAA
--------....((((((.--.((((...((((((.((((((........)))))).))))))......)))))).....((((.....)))).))-))......... ( -25.30, z-score =  -3.67, R)
>droSec1.super_1 12965915 97 + 14215200
--------GCAUGGCCGAA--CGACAGAAGCCAGAAAAUAAUAAAGCAAAAUUAUUAUCUGGCCAGAAAUGUUUCAAUAACAACAGACAGUUGGGG-CCCCCAGAAAA
--------....((((((.--.((((...((((((.((((((........)))))).))))))......)))))).....((((.....)))).))-))......... ( -25.30, z-score =  -3.34, R)
>droYak2.chr2R 7411404 98 - 21139217
--------GAAUGGCCGUA--CGACACAAGCCCGAAAAUAAUAAAGCAAAAUUAUUAUCUGGCCAGAAAUGUUUCAAUAACAACAGACAGUUGGGGGCCCCCAGAAAA
--------....((((...--((((....(((.((.((((((........)))))).)).)))......((((.....)))).......))))..))))......... ( -21.00, z-score =  -1.15, R)
>droEre2.scaffold_4845 9645843 96 + 22589142
--------GAAUGGCCGAA--CGACAGAAGCCAGAAAAUAAUAAAGCAAAAUUAUUAUCUGGCCAGAAAUGUUUCAAUAACAACAGACAGUUGGG--CCCCCAGAAAA
--------....((((.((--(.......((((((.((((((........)))))).))))))......((((.....)))).......))).))--))......... ( -26.00, z-score =  -4.56, R)
>droAna3.scaffold_13266 10053303 91 - 19884421
GAUGAUGGAGGCAGACAAGCGACUCUGAAGCCAGAAAAUAAUAAAGCAAAAUUAUUAUCUGGCCAGAAAUGUUUCAAUAACAGGCGAAAGA-----------------
.......((((((..........((((..((((((.((((((........)))))).))))))))))..)))))).........(....).----------------- ( -20.30, z-score =  -2.21, R)
>droPer1.super_2 30744 80 - 9036312
--------GGAGAGACGACUCCGACUAAGGCCACAAAAUAAUAAAGCAAAAUUAUUAUCUGGCCAGAAAUGUUUCAAUACCAG-AGACA-------------------
--------((((......))))......(((((.(.((((((........)))))).).))))).....((((((.......)-)))))------------------- ( -20.00, z-score =  -4.24, R)
>consensus
________GAAUGGCCGAA__CGACAGAAGCCAGAAAAUAAUAAAGCAAAAUUAUUAUCUGGCCAGAAAUGUUUCAAUAACAACAGACAGUUGGGG_CCCCCAGAAAA
.............................((((((.((((((........)))))).))))))......((((.....))))........(((((....))))).... (-13.32 = -14.36 +   1.04)

alignment

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secondary structure

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dotplot

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Window 1

Location 15,446,475 – 15,446,572
Length 97
Sequences 7
Columns 108
Reading direction reverse
Mean pairwise identity 79.19
Shannon entropy 0.37936
G+C content 0.39893
Mean single sequence MFE -23.86
Consensus MFE -15.70
Energy contribution -16.27
Covariance contribution 0.57
Combinations/Pair 1.14
Mean z-score -2.32
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.97
SVM RNA-class probability 0.977343
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 15446475 97 - 21146708
UUUUCUGGGGG-CCCCAACUGUCUGUUGUUAUUGAAACAUUUCUGGCCAGAUAAUAAUUUUGCUUUAUUAUUUUUUGGCUUCUGUCG--UUCGGCCAUUC--------
.........((-((.((((.....)))).....(((........(((((((.((((((........)))))).))))))).......--)))))))....-------- ( -24.46, z-score =  -2.12, R)
>droSim1.chr2R 14147807 97 - 19596830
UUUUCUGGGGG-CCCCAACUGUCUGUUGUUAUUGAAACAUUUCUGGCCAGAUAAUAAUUUUGCUUUAUUAUUUUCUGGCUUCUGUCG--UUCGGCCAUUC--------
.........((-((.((((.....)))).....(((........(((((((.((((((........)))))).))))))).......--)))))))....-------- ( -27.06, z-score =  -3.10, R)
>droSec1.super_1 12965915 97 - 14215200
UUUUCUGGGGG-CCCCAACUGUCUGUUGUUAUUGAAACAUUUCUGGCCAGAUAAUAAUUUUGCUUUAUUAUUUUCUGGCUUCUGUCG--UUCGGCCAUGC--------
.........((-((.((((.....)))).....(((........(((((((.((((((........)))))).))))))).......--)))))))....-------- ( -27.06, z-score =  -2.64, R)
>droYak2.chr2R 7411404 98 + 21139217
UUUUCUGGGGGCCCCCAACUGUCUGUUGUUAUUGAAACAUUUCUGGCCAGAUAAUAAUUUUGCUUUAUUAUUUUCGGGCUUGUGUCG--UACGGCCAUUC--------
.........((((..((((.....))))....((..((((....((((.((.((((((........)))))).)).)))).))))..--)).))))....-------- ( -23.00, z-score =  -0.64, R)
>droEre2.scaffold_4845 9645843 96 - 22589142
UUUUCUGGGGG--CCCAACUGUCUGUUGUUAUUGAAACAUUUCUGGCCAGAUAAUAAUUUUGCUUUAUUAUUUUCUGGCUUCUGUCG--UUCGGCCAUUC--------
.........((--((((((.....)))).....(((........(((((((.((((((........)))))).))))))).......--)))))))....-------- ( -27.06, z-score =  -3.30, R)
>droAna3.scaffold_13266 10053303 91 + 19884421
-----------------UCUUUCGCCUGUUAUUGAAACAUUUCUGGCCAGAUAAUAAUUUUGCUUUAUUAUUUUCUGGCUUCAGAGUCGCUUGUCUGCCUCCAUCAUC
-----------------...............(((.....(((((((((((.((((((........)))))).))))))..)))))..((......)).....))).. ( -18.90, z-score =  -2.08, R)
>droPer1.super_2 30744 80 + 9036312
-------------------UGUCU-CUGGUAUUGAAACAUUUCUGGCCAGAUAAUAAUUUUGCUUUAUUAUUUUGUGGCCUUAGUCGGAGUCGUCUCUCC--------
-------------------.(.((-((((....(((....))).(((((.(.((((((........)))))).).)))))....)))))).)........-------- ( -19.50, z-score =  -2.37, R)
>consensus
UUUUCUGGGGG_CCCCAACUGUCUGUUGUUAUUGAAACAUUUCUGGCCAGAUAAUAAUUUUGCUUUAUUAUUUUCUGGCUUCUGUCG__UUCGGCCAUUC________
.....((((....))))...........................(((((((.((((((........)))))).)))))))...((((....))))............. (-15.70 = -16.27 +   0.57)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:35:07 2011