Locus 1079

Sequence ID dm3.chr2L
Location 8,115,870 – 8,116,062
Length 192
Max. P 0.987490
window1472 window1473 window1474 window1475

overview

Window 2

Location 8,115,870 – 8,115,965
Length 95
Sequences 7
Columns 96
Reading direction forward
Mean pairwise identity 78.39
Shannon entropy 0.44139
G+C content 0.30211
Mean single sequence MFE -16.15
Consensus MFE -8.21
Energy contribution -9.09
Covariance contribution 0.88
Combinations/Pair 1.18
Mean z-score -1.96
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.90
SVM RNA-class probability 0.848690
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 8115870 95 + 23011544
GCGGCUAUUUAUUAUUAAAAGUGAUUUAUAGGGCAGAGUUGAAAAGCAACUUUCAGCUAAUAUAGAUUAAUAACAAAUAAAGACCGAAAAACCAC-
.(((...((((((........(((((((((.((((((((((.....)))))))..)))..)))))))))......))))))..))).........- ( -18.94, z-score =  -2.94, R)
>anoGam1.chr3R 42862608 83 - 53272125
----------AUUGAUGGUGGCGAUGGAAAAAGCAAAACUAAGCAGCAAAGAGUAAAUAAUUUAGAGAAUUAAAAUAAAUAAAUCCAGAAUAU---
----------..............((((....((........)).............((((((...))))))...........))))......--- (  -5.50, z-score =   0.85, R)
>droAna3.scaffold_12916 11839311 89 - 16180835
GCGGCUAUUUAAUA----AAGUGAUUGAUAGGGCAGAGUUGAAAUCCAACUUUCAGCUAAUAUAGAUUAAUAAUAAAAUCUGAGAAAAAACCC---
...(((..(((((.----.....)))))...)))..((((((((......))))))))....((((((........))))))...........--- ( -14.80, z-score =  -1.07, R)
>droEre2.scaffold_4929 17021607 95 + 26641161
GCGGCUAUUUAUUAUUAAAAGUGAUUUAUAGGGCAGAGUUGAAAUGCAAAUUUCAGCUAAUUUAGAUUAAUAACAAAUAAAGACCGAAAAACCAC-
.(((((((..(((((.....)))))..)))).....(((((((((....))))))))).........................))).........- ( -17.00, z-score =  -1.88, R)
>droYak2.chr2L 10746730 95 + 22324452
GCGGCUAUUUAUUAUUAAAAGUGAUUUAUAGGGCAGAGUUGAAAAGCAACUUUCAGCUAAUAUAGAUUAAUAACAAAUAAAGACCGAAAAACCAC-
.(((...((((((........(((((((((.((((((((((.....)))))))..)))..)))))))))......))))))..))).........- ( -18.94, z-score =  -2.94, R)
>droSec1.super_3 3612245 96 + 7220098
GCGGCUAUUUAUUAUUAAAAGUGAUUUAUAGGGCAGAGUUGAAACGCAACUUUCAGCUAAUAUAGAUUAAUAACAAAUAAAGACCGAAAAACCACA
.(((...((((((........(((((((((.((((((((((.....)))))))..)))..)))))))))......))))))..))).......... ( -18.94, z-score =  -2.80, R)
>droSim1.chr2L 7895383 95 + 22036055
GCGGCUAUUUAUUAUUAAAAGUGAUUUAUAGGGCAGAGUUGAAAAGCAACUUUCAGCUAAUAUAGAUUAAUAACAAAUAAAGACCGAAAAACCAC-
.(((...((((((........(((((((((.((((((((((.....)))))))..)))..)))))))))......))))))..))).........- ( -18.94, z-score =  -2.94, R)
>consensus
GCGGCUAUUUAUUAUUAAAAGUGAUUUAUAGGGCAGAGUUGAAAAGCAACUUUCAGCUAAUAUAGAUUAAUAACAAAUAAAGACCGAAAAACCAC_
.....................(((((((((......((((((((......))))))))..)))))))))........................... ( -8.21 =  -9.09 +   0.88)

alignment

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secondary structure

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dotplot

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Window 3

Location 8,115,942 – 8,116,038
Length 96
Sequences 7
Columns 105
Reading direction forward
Mean pairwise identity 85.83
Shannon entropy 0.26317
G+C content 0.30800
Mean single sequence MFE -15.36
Consensus MFE -15.19
Energy contribution -15.21
Covariance contribution 0.02
Combinations/Pair 1.07
Mean z-score -1.80
Structure conservation index 0.99
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.14
SVM RNA-class probability 0.983478
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 8115942 96 + 23011544
ACAAAUAAAGACCGAAAAACC---ACAAAAAAAAA-----ACAAAUAUUUUAAA-GCAAGCGCUUGAAUUGUACAUUUUUACAAGGCAACUGUACAUUAAGCGCC
.....................---...........-----..............-....((((((((..((((((.........(....))))))))))))))). ( -15.60, z-score =  -2.20, R)
>droGri2.scaffold_15252 13739866 102 + 17193109
---UGUAACAUUUAAUAAAAACGGAAACAACAAAAAACCAAAAAAUAUUUUAAAAGCAAGCGCUUGAAUUGUACAUUUUUACAAGGCAACUGUACAUUUAGCGCC
---...................(....)...............................(((((.((((.(((((.........(....))))))))))))))). ( -14.70, z-score =  -0.42, R)
>droAna3.scaffold_12916 11839379 90 - 16180835
----AUAAAAUCUGAGAAAAA---ACCCAAAAAAAAA-------AUAUUUUAAA-GCAAGCGCUUGGAUUGUACAUUUUUACAAGGCAACUGUACAUUAAGCGCC
----.................---.............-------..........-....((((((((..((((((.........(....))))))))))))))). ( -14.80, z-score =  -1.15, R)
>droEre2.scaffold_4929 17021679 90 + 26641161
ACAAAUAAAGACCGAAAAACC---ACAAAAAAAA-----------UAUUUUAAA-GCAAGCGCUUGAAUUGUACAUUUUUACAAGGCAACUGUACAUUAAGCGCC
.....................---..........-----------.........-....((((((((..((((((.........(....))))))))))))))). ( -15.60, z-score =  -2.22, R)
>droYak2.chr2L 10746802 101 + 22324452
ACAAAUAAAGACCGAAAAACC---ACAAAAAAAAAAAUCAACAAAUAUUUUAAA-GCAAGCGCUUGAAUUGUACAUUUUUACAAGGCAACUGUACAUUAAGCGCC
.....................---..............................-....((((((((..((((((.........(....))))))))))))))). ( -15.60, z-score =  -2.18, R)
>droSec1.super_3 3612317 99 + 7220098
ACAAAUAAAGACCGAAAAACC---ACAAAAAAAAAAA--AACAAAUAUUUUAAA-GCAAGCGCUUGAAUUGUACAUUUUUACAAGGCAACUGUACAUUAAGCGCC
.....................---.............--...............-....((((((((..((((((.........(....))))))))))))))). ( -15.60, z-score =  -2.21, R)
>droSim1.chr2L 7895455 98 + 22036055
ACAAAUAAAGACCGAAAAACC---ACAAAAAAAAAAA---ACAAAUAUUUUAAA-GCAAGCGCUUGAAUUGUACAUUUUUACAAGGCAACUGUACAUUAAGCGCC
.....................---.............---..............-....((((((((..((((((.........(....))))))))))))))). ( -15.60, z-score =  -2.19, R)
>consensus
ACAAAUAAAGACCGAAAAACC___ACAAAAAAAAAAA___ACAAAUAUUUUAAA_GCAAGCGCUUGAAUUGUACAUUUUUACAAGGCAACUGUACAUUAAGCGCC
...........................................................((((((((..((((((.........(....))))))))))))))). (-15.19 = -15.21 +   0.02)

alignment

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secondary structure

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dotplot

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Window 4

Location 8,115,965 – 8,116,062
Length 97
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 91.73
Shannon entropy 0.14493
G+C content 0.29003
Mean single sequence MFE -18.35
Consensus MFE -18.31
Energy contribution -18.17
Covariance contribution -0.14
Combinations/Pair 1.05
Mean z-score -1.31
Structure conservation index 1.00
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.28
SVM RNA-class probability 0.920215
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 8115965 97 + 23011544
-----AAAAAAAAAACAAAUAUUUUAAAGCAAGCGCUUGAAUUGUACAUUUUUACAAGGCAACUGUACAUUAAGCGCCCACGGCAUUAAGUAAAAAAUAAAA-
-----.................(((((.((..((((((((..((((((.........(....))))))))))))))).....)).)))))............- ( -18.30, z-score =  -1.34, R)
>droAna3.scaffold_12916 11839400 94 - 16180835
---------AAAAAAAAAAUAUUUUAAAGCAAGCGCUUGGAUUGUACAUUUUUACAAGGCAACUGUACAUUAAGCGCCCACGGCAUUAAGUAAAAAAAAAAAA
---------.............(((((.((..((((((((..((((((.........(....))))))))))))))).....)).)))))............. ( -17.50, z-score =  -0.81, R)
>droEre2.scaffold_4929 17021702 91 + 26641161
-----------AAAAAAAAUAUUUUAAAGCAAGCGCUUGAAUUGUACAUUUUUACAAGGCAACUGUACAUUAAGCGCCCACGGCAUUAAGUAAAAAAUAAAA-
-----------...........(((((.((..((((((((..((((((.........(....))))))))))))))).....)).)))))............- ( -18.30, z-score =  -1.30, R)
>droYak2.chr2L 10746825 103 + 22324452
AAAAAAAAAAAUCAACAAAUAUUUUAAAGCAAGCGCUUGAAUUGUACAUUUUUACAAGGCAACUGUACAUUAAGCGCCCACGGCAUUAAGUAAAAAAAUGAAA
...........(((........(((((.((..((((((((..((((((.........(....))))))))))))))).....)).)))))........))).. ( -19.39, z-score =  -1.58, R)
>droSec1.super_3 3612341 99 + 7220098
---AAAAAAAAAAAACAAAUAUUUUAAAGCAAGCGCUUGAAUUGUACAUUUUUACAAGGCAACUGUACAUUAAGCGCCCACGGCAUUAAGUAAAAAAUAAAA-
---...................(((((.((..((((((((..((((((.........(....))))))))))))))).....)).)))))............- ( -18.30, z-score =  -1.41, R)
>droSim1.chr2L 7895478 99 + 22036055
---AAAAAAAAAAAACAAAUAUUUUAAAGCAAGCGCUUGAAUUGUACAUUUUUACAAGGCAACUGUACAUUAAGCGCCCACGGCAUUAAGUAAAAAAUAAAA-
---...................(((((.((..((((((((..((((((.........(....))))))))))))))).....)).)))))............- ( -18.30, z-score =  -1.41, R)
>consensus
_____AAAAAAAAAACAAAUAUUUUAAAGCAAGCGCUUGAAUUGUACAUUUUUACAAGGCAACUGUACAUUAAGCGCCCACGGCAUUAAGUAAAAAAUAAAA_
......................(((((.((..((((((((..((((((.........(....))))))))))))))).....)).)))))............. (-18.31 = -18.17 +  -0.14)

alignment

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secondary structure

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dotplot

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Window 5

Location 8,115,965 – 8,116,062
Length 97
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 91.73
Shannon entropy 0.14493
G+C content 0.29003
Mean single sequence MFE -22.08
Consensus MFE -22.00
Energy contribution -22.00
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.05
Structure conservation index 1.00
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.28
SVM RNA-class probability 0.987490
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 8115965 97 - 23011544
-UUUUAUUUUUUACUUAAUGCCGUGGGCGCUUAAUGUACAGUUGCCUUGUAAAAAUGUACAAUUCAAGCGCUUGCUUUAAAAUAUUUGUUUUUUUUUU-----
-.....................(..(((((((((((((((.((((...))))...))))).))).)))))))..).......................----- ( -22.10, z-score =  -1.99, R)
>droAna3.scaffold_12916 11839400 94 + 16180835
UUUUUUUUUUUUACUUAAUGCCGUGGGCGCUUAAUGUACAGUUGCCUUGUAAAAAUGUACAAUCCAAGCGCUUGCUUUAAAAUAUUUUUUUUUU---------
......................(..(((((((..((((((.((((...))))...))))))....)))))))..)...................--------- ( -22.00, z-score =  -2.26, R)
>droEre2.scaffold_4929 17021702 91 - 26641161
-UUUUAUUUUUUACUUAAUGCCGUGGGCGCUUAAUGUACAGUUGCCUUGUAAAAAUGUACAAUUCAAGCGCUUGCUUUAAAAUAUUUUUUUU-----------
-.....................(..(((((((((((((((.((((...))))...))))).))).)))))))..).................----------- ( -22.10, z-score =  -2.21, R)
>droYak2.chr2L 10746825 103 - 22324452
UUUCAUUUUUUUACUUAAUGCCGUGGGCGCUUAAUGUACAGUUGCCUUGUAAAAAUGUACAAUUCAAGCGCUUGCUUUAAAAUAUUUGUUGAUUUUUUUUUUU
......................(..(((((((((((((((.((((...))))...))))).))).)))))))..)............................ ( -22.10, z-score =  -1.70, R)
>droSec1.super_3 3612341 99 - 7220098
-UUUUAUUUUUUACUUAAUGCCGUGGGCGCUUAAUGUACAGUUGCCUUGUAAAAAUGUACAAUUCAAGCGCUUGCUUUAAAAUAUUUGUUUUUUUUUUUU---
-.....................(..(((((((((((((((.((((...))))...))))).))).)))))))..).........................--- ( -22.10, z-score =  -2.06, R)
>droSim1.chr2L 7895478 99 - 22036055
-UUUUAUUUUUUACUUAAUGCCGUGGGCGCUUAAUGUACAGUUGCCUUGUAAAAAUGUACAAUUCAAGCGCUUGCUUUAAAAUAUUUGUUUUUUUUUUUU---
-.....................(..(((((((((((((((.((((...))))...))))).))).)))))))..).........................--- ( -22.10, z-score =  -2.06, R)
>consensus
_UUUUAUUUUUUACUUAAUGCCGUGGGCGCUUAAUGUACAGUUGCCUUGUAAAAAUGUACAAUUCAAGCGCUUGCUUUAAAAUAUUUGUUUUUUUUUU_____
......................(..(((((((..((((((.((((...))))...))))))....)))))))..)............................ (-22.00 = -22.00 +   0.00)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:25:12 2011