Locus 13706

Sequence ID dm3.chrX
Location 8,563,422 – 8,563,567
Length 145
Max. P 0.998058
window18858 window18859 window18860 window18861

overview

Window 8

Location 8,563,422 – 8,563,521
Length 99
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 69.79
Shannon entropy 0.51149
G+C content 0.45685
Mean single sequence MFE -33.40
Consensus MFE -19.68
Energy contribution -19.72
Covariance contribution 0.04
Combinations/Pair 1.27
Mean z-score -2.66
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.25
SVM RNA-class probability 0.998058
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 8563422 99 + 22422827
------------------UUGGAGUUUGGAGUUUUGGGACUCGCAGGGGC-AUGCAGCGCUGGAAAAGCGGGGCACAUUAUUGUGACCCGUAAAUGAUACAAAAAUUGUGUGUCAUUA
------------------...((((((.((...)).))))))(((.....-.)))..((((.....))))(((((((....)))).)))...(((((((((.......))))))))). ( -32.00, z-score =  -2.45, R)
>droSim1.chrX 6810873 98 + 17042790
------------------UCGGAGUUUGGAGUUU-GGGGCUCGCAGGAGA-AUGCAGCGCUGGAAAAGCGGGGCACAUUAUUGUGACCCGUAAAUGAUACAAAAAUUGUGUGUCAUUA
------------------.............((.-.(.(((.(((.....-.)))))).)..))...(((((.((((....)))).))))).(((((((((.......))))))))). ( -33.60, z-score =  -3.07, R)
>droSec1.super_35 409939 98 + 471130
------------------UCGGAGUUUGAAGUUU-GGGGCUCGCAGGAGA-AUGCAGCGCUGGAAAAGCGGGGCACAUUAUUGUGACCCGUAAAUGAUACAAAAAUUGUGUGUCAUUA
------------------.............((.-.(.(((.(((.....-.)))))).)..))...(((((.((((....)))).))))).(((((((((.......))))))))). ( -33.60, z-score =  -3.18, R)
>droAna3.scaffold_13248 801180 107 - 4840945
-----------UCGGGAGGUGGAGAUCUGAUUUCGGAUGCCCAAAGUCCCCAAGAGGCGAUCGAAGAACGGGCCACAUUAUUGUGACCCGUAAAUGAUACAAAAAUUGUGUGUCAUUA
-----------..((((..(((..(((((....)))))..)))...)))).................(((((.((((....)))).))))).(((((((((.......))))))))). ( -36.50, z-score =  -2.83, R)
>droWil1.scaffold_181150 3925043 118 + 4952429
UCGGAGUCAGCUUGGUCAGCAGCUUAAAGAGCCAGAAUGCGCUUCUGUGCAACGCCACGAAAAGUUAACCGAAAACAUUAUUGUGACCCGUAAAUGAUACAAAAAUUGUGUGUCAUUA
.(((.(((...(((((.(((.((((...)))).....(((((....)))))............))).)))))..(((....)))))))))..(((((((((.......))))))))). ( -31.30, z-score =  -1.79, R)
>consensus
__________________UCGGAGUUUGGAGUUU_GGGGCUCGCAGGAGC_AUGCAGCGCUGGAAAAGCGGGGCACAUUAUUGUGACCCGUAAAUGAUACAAAAAUUGUGUGUCAUUA
........................((((((((......)))).))))....................(((((.((((....)))).))))).(((((((((.......))))))))). (-19.68 = -19.72 +   0.04)

alignment

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secondary structure

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dotplot

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Window 9

Location 8,563,422 – 8,563,521
Length 99
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 69.79
Shannon entropy 0.51149
G+C content 0.45685
Mean single sequence MFE -23.38
Consensus MFE -13.00
Energy contribution -12.36
Covariance contribution -0.64
Combinations/Pair 1.26
Mean z-score -1.48
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.06
SVM RNA-class probability 0.883708
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 8563422 99 - 22422827
UAAUGACACACAAUUUUUGUAUCAUUUACGGGUCACAAUAAUGUGCCCCGCUUUUCCAGCGCUGCAU-GCCCCUGCGAGUCCCAAAACUCCAAACUCCAA------------------
.(((((.(((.......))).)))))...(((.((((....)))))))((((.....))))..(((.-.....)))((((......))))..........------------------ ( -19.40, z-score =  -1.54, R)
>droSim1.chrX 6810873 98 - 17042790
UAAUGACACACAAUUUUUGUAUCAUUUACGGGUCACAAUAAUGUGCCCCGCUUUUCCAGCGCUGCAU-UCUCCUGCGAGCCCC-AAACUCCAAACUCCGA------------------
.(((((.(((.......))).)))))...(((.((((....)))).)))(((.....)))((((((.-.....))).)))...-................------------------ ( -19.80, z-score =  -1.81, R)
>droSec1.super_35 409939 98 - 471130
UAAUGACACACAAUUUUUGUAUCAUUUACGGGUCACAAUAAUGUGCCCCGCUUUUCCAGCGCUGCAU-UCUCCUGCGAGCCCC-AAACUUCAAACUCCGA------------------
.(((((.(((.......))).)))))...(((.((((....)))).)))(((.....)))((((((.-.....))).)))...-................------------------ ( -19.80, z-score =  -1.72, R)
>droAna3.scaffold_13248 801180 107 + 4840945
UAAUGACACACAAUUUUUGUAUCAUUUACGGGUCACAAUAAUGUGGCCCGUUCUUCGAUCGCCUCUUGGGGACUUUGGGCAUCCGAAAUCAGAUCUCCACCUCCCGA-----------
.(((((.(((.......))).))))).((((((((((....)))))))))).....((((((((...(....)...))))....(....).))))............----------- ( -31.10, z-score =  -2.02, R)
>droWil1.scaffold_181150 3925043 118 - 4952429
UAAUGACACACAAUUUUUGUAUCAUUUACGGGUCACAAUAAUGUUUUCGGUUAACUUUUCGUGGCGUUGCACAGAAGCGCAUUCUGGCUCUUUAAGCUGCUGACCAAGCUGACUCCGA
.(((((.(((.......))).)))))..((((((.....((((((..(((........))).))))))((.(((((.....)))))))......((((........))))))).))). ( -26.80, z-score =  -0.31, R)
>consensus
UAAUGACACACAAUUUUUGUAUCAUUUACGGGUCACAAUAAUGUGCCCCGCUUUUCCAGCGCUGCAU_GCUCCUGCGAGCCCC_AAACUCCAAACUCCGA__________________
.(((((.(((.......))).)))))..((((.((((....)))).))))..........(((..............)))...................................... (-13.00 = -12.36 +  -0.64)

alignment

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secondary structure

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dotplot

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Window 0

Location 8,563,453 – 8,563,558
Length 105
Sequences 11
Columns 119
Reading direction forward
Mean pairwise identity 71.67
Shannon entropy 0.58242
G+C content 0.46789
Mean single sequence MFE -30.05
Consensus MFE -15.29
Energy contribution -14.80
Covariance contribution -0.49
Combinations/Pair 1.14
Mean z-score -2.17
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.61
SVM RNA-class probability 0.993359
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 8563453 105 + 22422827
------------CAUGCAGCGCUGGAAAAGCGGGGCACAUUAUUGUGACCCGUAAAUGAUACAAAAAUUGUGUGUCAUUAAUAAACGGCACAGCAUGGCAUCCGGCAGAAGGGGCGG--
------------(((((.(.((((.....(((((.((((....)))).))))).(((((((((.......)))))))))......)))).).)))))((.(((.......)))))..-- ( -39.50, z-score =  -3.81, R)
>droSim1.chrX 6810903 104 + 17042790
------------AAUGCAGCGCUGGAAAAGCGGGGCACAUUAUUGUGACCCGUAAAUGAUACAAAAAUUGUGUGUCAUUAAUAAACGGCACAGCAUGGCAUCCGGCAGA-GGGGCGG--
------------.((((.(.((((.....(((((.((((....)))).))))).(((((((((.......)))))))))......)))).).)))).((.(((......-)))))..-- ( -37.10, z-score =  -3.12, R)
>droSec1.super_35 409969 104 + 471130
------------AAUGCAGCGCUGGAAAAGCGGGGCACAUUAUUGUGACCCGUAAAUGAUACAAAAAUUGUGUGUCAUUAAUAAACGGCACAGCAUGGCAUCCGGCAGA-GGGGCGG--
------------.((((.(.((((.....(((((.((((....)))).))))).(((((((((.......)))))))))......)))).).)))).((.(((......-)))))..-- ( -37.10, z-score =  -3.12, R)
>droYak2.chrX 9022525 104 - 21770863
------------AACGUGGCGAUCGAAAAGCGGGGCACAUUAUUGUGACCCGUAAAUGAUACAAAAAUUGUGUGUCAUUAAUAAACGGCACAGCGUGGCAUCCACCAGGGGGGGGC---
------------...(((.((........(((((.((((....)))).))))).(((((((((.......)))))))))......)).)))......((..((.(....)))..))--- ( -33.50, z-score =  -1.82, R)
>droEre2.scaffold_4690 12197893 101 - 18748788
------------AACGCAGCAAUCGAAAAGCGGGGCACAUUAUUGUGACCCGUAAAUGAUACAAAAGUUGUGUGUCAUUAAUAAACGGCACAGCGUGGCAUCCU-CAGG-GGGGC----
------------.((((.((.........(((((.((((....)))).))))).(((((((((.......)))))))))........))...)))).((..((.-...)-)..))---- ( -31.40, z-score =  -2.03, R)
>droAna3.scaffold_13248 801216 108 - 4840945
---------CCCCAAGAGGCGAUCGAAGAACGGGCCACAUUAUUGUGACCCGUAAAUGAUACAAAAAUUGUGUGUCAUUAAUAAGCAGCACAGCGUGGCAUUUAUGAGGAGGGAAAG--
---------.(((..(..((.........(((((.((((....)))).))))).(((((((((.......))))))))).....))..).(..((((.....))))..).)))....-- ( -30.40, z-score =  -2.44, R)
>dp4.chrXL_group1e 7800830 86 + 12523060
-----------------------------UGGGGCAACAUUAUUGUGACCCGUAAAUGAUACAAAAAUUGUGUGUCAUUAAUAAGCGGCACAGCAUGG----CCUCCACAGAGAGCCAG
-----------------------------..(((..(((....)))..)))...(((((((((.......))))))))).....((......)).(((----((((....))).)))). ( -26.30, z-score =  -2.26, R)
>droPer1.super_13 1541034 86 - 2293547
-----------------------------UGGGGCAACAUUAUUGUGACCCGUAAAUGAUACAAAAAUUGUGUGUCAUUAAUAAGCGGCACAGCAUGG----CCUCCACAGAGAGCGAG
-----------------------------((((((..(((..(((((..((((.(((((((((.......))))))))).....))))))))).))))----)).)))........... ( -22.60, z-score =  -1.19, R)
>droWil1.scaffold_181150 3925081 119 + 4952429
GCGCUUCUGUGCAACGCCACGAAAAGUUAACCGAAAACAUUAUUGUGACCCGUAAAUGAUACAAAAAUUGUGUGUCAUUAAUAAGCGGCACAGCAUGGUAUCCCGCCACAGAGAGAGAG
.(.(((((((((..((((((((.(((((.......))).)).))))).......(((((((((.......))))))))).....)))))))))..((((.....))))..))).).... ( -26.50, z-score =  -0.80, R)
>droVir3.scaffold_12970 5324717 80 - 11907090
--------------------AGCUUU---GCAGCGAACAUUAUUGUGACCCGUAAAUGAUACAAAAAUUGUGUGUCAUUAAUAAGCGGCACAGCGUGGCAUCC----------------
--------------------.(((.(---((.((..(((....)))........(((((((((.......))))))))).....)).))).))).........---------------- ( -19.90, z-score =  -0.76, R)
>droGri2.scaffold_14853 5914353 88 + 10151454
------------AGGUCCGCAGCCGCA--GCAGAACAUAUUAUUGUGACCCGUAAAUGAUACAAAAAUUGUGUGUCAUUAAUAAGCGGCACAGCGUG-CAUCC----------------
------------..(..(((.(((((.--......((((....)))).......(((((((((.......))))))))).....)))))...)))..-)....---------------- ( -26.20, z-score =  -2.48, R)
>consensus
____________AA_GCAGCGAUCGAAAAGCGGGGCACAUUAUUGUGACCCGUAAAUGAUACAAAAAUUGUGUGUCAUUAAUAAGCGGCACAGCAUGGCAUCCCGCAGA_GGGGC_G__
.....................................(((..(((((..((((.(((((((((.......))))))))).....))))))))).)))...................... (-15.29 = -14.80 +  -0.49)

alignment

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secondary structure

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dotplot

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Window 1

Location 8,563,459 – 8,563,567
Length 108
Sequences 7
Columns 108
Reading direction forward
Mean pairwise identity 81.36
Shannon entropy 0.38392
G+C content 0.49261
Mean single sequence MFE -30.84
Consensus MFE -20.83
Energy contribution -21.16
Covariance contribution 0.33
Combinations/Pair 1.10
Mean z-score -1.92
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.43
SVM RNA-class probability 0.939395
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 8563459 108 + 22422827
GCGCUGGAAAAGCGGGGCACAUUAUUGUGACCCGUAAAUGAUACAAAAAUUGUGUGUCAUUAAUAAACGGCACAGCAUGGCAUCCGGCAGAAGGGGCGGGGGGGUGAG
..((((.....(((((.((((....)))).))))).(((((((((.......)))))))))...........)))).(.((.((((.(......).))))...)).). ( -36.00, z-score =  -2.65, R)
>droSim1.chrX 6810909 104 + 17042790
GCGCUGGAAAAGCGGGGCACAUUAUUGUGACCCGUAAAUGAUACAAAAAUUGUGUGUCAUUAAUAAACGGCACAGCAUGGCAUCCGGCAGAGGGGCGGGGGGAG----
..((((.....(((((.((((....)))).))))).(((((((((.......)))))))))...........))))......(((.((......)).)))....---- ( -34.60, z-score =  -2.68, R)
>droSec1.super_35 409975 104 + 471130
GCGCUGGAAAAGCGGGGCACAUUAUUGUGACCCGUAAAUGAUACAAAAAUUGUGUGUCAUUAAUAAACGGCACAGCAUGGCAUCCGGCAGAGGGGCGGGGGGAG----
..((((.....(((((.((((....)))).))))).(((((((((.......)))))))))...........))))......(((.((......)).)))....---- ( -34.60, z-score =  -2.68, R)
>droYak2.chrX 9022531 104 - 21770863
GCGAUCGAAAAGCGGGGCACAUUAUUGUGACCCGUAAAUGAUACAAAAAUUGUGUGUCAUUAAUAAACGGCACAGCGUGGCAUCCACCAGGGGGGGGCGGGGAA----
((.........(((((.((((....)))).))))).(((((((((.......)))))))))........))....(.(.((..((.(....)))..)).).)..---- ( -31.20, z-score =  -1.12, R)
>droEre2.scaffold_4690 12197899 101 - 18748788
GCAAUCGAAAAGCGGGGCACAUUAUUGUGACCCGUAAAUGAUACAAAAGUUGUGUGUCAUUAAUAAACGGCACAGCGUGGCAUCCU-CAGGGGGGCGGGGUA------
((.........(((((.((((....)))).))))).(((((((((.......)))))))))........))...((.(.((..((.-...))..)).).)).------ ( -32.30, z-score =  -1.98, R)
>droAna3.scaffold_13248 801225 105 - 4840945
GCGAUCGAAGAACGGGCCACAUUAUUGUGACCCGUAAAUGAUACAAAAAUUGUGUGUCAUUAAUAAGCAGCACAGCGUGGCAUUUAUGAGGAGGGAAAGGGGCUA---
((..((.....(((((.((((....)))).))))).(((((((((.......))))))))).....((.((.....)).)).................)).))..--- ( -25.30, z-score =  -0.58, R)
>droGri2.scaffold_14853 5914359 82 + 10151454
--GCAGCCGCAGCAGAACAUAUUAUUGUGACCCGUAAAUGAUACAAAAAUUGUGUGUCAUUAAUAAGCGGCACAGCGUG-CAUCC-----------------------
--((.(((((.......((((....)))).......(((((((((.......))))))))).....)))))...))...-.....----------------------- ( -21.90, z-score =  -1.76, R)
>consensus
GCGCUGGAAAAGCGGGGCACAUUAUUGUGACCCGUAAAUGAUACAAAAAUUGUGUGUCAUUAAUAAACGGCACAGCGUGGCAUCCGGCAGAGGGGCGGGGGGAG____
((.........(((((.((((....)))).))))).(((((((((.......))))))))).............))................................ (-20.83 = -21.16 +   0.33)

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 01:26:19 2011