Locus 1564

Sequence ID dm3.chr2L
Location 12,102,916 – 12,103,050
Length 134
Max. P 0.554806
window2140 window2141

overview

Window 0

Location 12,102,916 – 12,103,018
Length 102
Sequences 13
Columns 115
Reading direction forward
Mean pairwise identity 71.81
Shannon entropy 0.58362
G+C content 0.60682
Mean single sequence MFE -44.94
Consensus MFE -8.36
Energy contribution -8.12
Covariance contribution -0.24
Combinations/Pair 1.85
Mean z-score -2.69
Structure conservation index 0.19
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.12
SVM RNA-class probability 0.554806
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 12102916 102 + 23011544
------CGGUCGAUGAUCCAAAUGGAUGUC---GUCGGCGUGGGCAUGGCCAUCCUCCUCCGCGACGACCAUGUUGCAGGAGG---AGGAGGCGGUUAGGGGCAACGCCCACAC-
------..(((((((((((....)))..))---))))))((((((((.(((.((((((((((((((......))))).)))))---))))))).))....(....)))))))..- ( -59.70, z-score =  -5.84, R)
>droSim1.chr2L 11900560 102 + 22036055
------CGGUCGAUGAUCCAAAUGGAUGUC---GUCGGCGUGGGCAUGGCCAUCCUCCUCCGCGACGACCAUGUUGCAGGAGG---AGGAGGCGGUUAGGGGCAACGCCCACAC-
------..(((((((((((....)))..))---))))))((((((((.(((.((((((((((((((......))))).)))))---))))))).))....(....)))))))..- ( -59.70, z-score =  -5.84, R)
>droSec1.super_16 291141 102 + 1878335
------CGGUCGAUGAUCCAAAUGGAUGUC---GUCGGCGUGGGCAUGGCCAUCCUCCUCCGCGACGACCAUGUUGCAGGAGG---AGGAGGCGGUUAGGGGCAACGCCCACAC-
------..(((((((((((....)))..))---))))))((((((((.(((.((((((((((((((......))))).)))))---))))))).))....(....)))))))..- ( -59.70, z-score =  -5.84, R)
>droYak2.chr2L 8520308 102 + 22324452
------UGGUCGGUGAUCCAAAUGGAUGUC---GUCGGCGUGGGCAUGGCCAUCCUCCUCCGCGACGACCAUGUUGCAGGAGG---AGGAGGCGGUUAGGGGCAACGCCCACAC-
------..((((..(((((....)))..))---..))))((((((((.(((.((((((((((((((......))))).)))))---))))))).))....(....)))))))..- ( -56.90, z-score =  -4.84, R)
>droEre2.scaffold_4929 13330372 102 - 26641161
------UGGUCGGUGAUCCAAAUGGAUGUC---GUCGGCGUGGGCAUGGCCAUCCUCCUCCGCGACGACCAUGUUGCAGGAGG---AGGAGGCGGUUAGGGGCAACGCCCACAC-
------..((((..(((((....)))..))---..))))((((((((.(((.((((((((((((((......))))).)))))---))))))).))....(....)))))))..- ( -56.90, z-score =  -4.84, R)
>droAna3.scaffold_12943 2507840 102 - 5039921
------CGGUCGAUGGUCGAGAUGAAUCUC---AUCCGCGUGGGCAUGGCCAUCCUCCUCUGCCACUACCAUGUUGCAUGAGG---AGGAGGCUGUCAGGGGCAGCGCCCAUAC-
------.....(.(((..((((....))))---..))))((((((.......(((((((((((.((......)).))).))))---)))).(((((.....)))))))))))..- ( -46.40, z-score =  -2.30, R)
>dp4.chr4_group3 911660 96 + 11692001
------CGGGCGAUGGUCGAUAUCUAUGUC---CUCGGCAUGGGCAUGCUCCUCCGCCACC------ACCAUAUUGCAUGAUG---AGGAUGCCGUCAGGGGAAGCGCCCACAC-
------.(((((((((.......)))).((---((((((...(((((.(((.((.((....------........))..)).)---)).)))))))).)))))..)))))....- ( -32.70, z-score =   0.41, R)
>droPer1.super_1 2391411 96 + 10282868
------CGGGCGAUGGUCGAUAUCUAUGUC---CUCGGCAUGGGCAUGCUCCUCCGCCACC------ACCAUAUUGCAUGAUG---AGGAUGCCGUCAGGGGAAGCGCCCACAC-
------.(((((((((.......)))).((---((((((...(((((.(((.((.((....------........))..)).)---)).)))))))).)))))..)))))....- ( -32.70, z-score =   0.41, R)
>droWil1.scaffold_181038 47012 95 + 637489
-------------CCAUCGAGAGCCCCGUC---AUCUGGGUGAUCAUGAUGACCAUCCUCUUCG---ACCAUAUUGCAAGAUGCAGACGAGGCUGUCAGGGGCAGCGCCCAUAU-
-------------.....((.((((.((((---....(((((.((.....)).)))))......---.......(((.....))))))).)))).))..((((...))))....- ( -32.80, z-score =  -1.04, R)
>droVir3.scaffold_12963 15929650 96 + 20206255
------CGGACGAUGAUCGAUGUCAAUGUCAAUGUCCGCAUGGGCGUGACCAUCCUCCUCC---------AUGUUGCAUGACG---AGGAGGCCGUCAGGGGCAGCGCCCAAAC-
------((((((.((((..........)))).))))))..(((((((..((..((((((((---------(((...))))..)---))))))((....))))..)))))))...- ( -41.30, z-score =  -2.39, R)
>droMoj3.scaffold_6500 2910690 96 + 32352404
------GGCUCGAUGAUCAAUGUCGAUGUCAAUGUCAGCAUGAGCAUGACCGUCUUCCUCC---------AUGUUGCAUGACG---AAGAGGCCGUCAGGGGCAGCGCCCAUAC-
------(((..((((.(((.(((..((((........))))..)))))).)))).......---------..(((((.(((((---.......)))))...)))))))).....- ( -28.80, z-score =   0.36, R)
>droGri2.scaffold_15252 13357862 96 + 17193109
------GGGCCGAUGAUCGAUGUCGAUAUCGAUGUCGGCAUGUGCAUGGCCAUCUUCUUCC---------AUGUUGCAAGACG---AGGAGGCCGUUAGGGGCAGCGCCCAAAC-
------((((((((.(((((((....)))))))))))))..((((...(((.....(((((---------.((((....))))---.)))))((....))))).))))))....- ( -38.50, z-score =  -1.84, R)
>anoGam1.chr3R 21441117 105 + 53272125
CUAUCCUUCUCCUGCGUCGGCGUCUUCGCCU-CCUCCGGAUGGUGUGGAUGAUCACUCUCCUCGGUCACCAUGUUGCAUGAUG---------CCGUCAGGGGCAGUGCCCACACC
.........(((.(.(..((((....)))).-.).).))).(((((((.....((((((((((((.((.((((...)))).))---------)))..))))).)))).))))))) ( -38.10, z-score =  -1.41, R)
>consensus
______CGGUCGAUGAUCGAAAUCGAUGUC___GUCGGCGUGGGCAUGGCCAUCCUCCUCCGCG___ACCAUGUUGCAUGAGG___AGGAGGCCGUCAGGGGCAGCGCCCACAC_
.......((((.(((.((.......................)).)))))))................................................((((...))))..... ( -8.36 =  -8.12 +  -0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 12,102,946 – 12,103,050
Length 104
Sequences 14
Columns 117
Reading direction reverse
Mean pairwise identity 74.58
Shannon entropy 0.52644
G+C content 0.64917
Mean single sequence MFE -49.15
Consensus MFE -13.86
Energy contribution -14.15
Covariance contribution 0.29
Combinations/Pair 1.42
Mean z-score -2.32
Structure conservation index 0.28
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.06
SVM RNA-class probability 0.524426
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 12102946 104 - 23011544
AGGUGCAUCCAAGUCC---GGGGGCGGCG---CGCAGUGUGUGGGCGUUGCCCCUAACCGCCUCCU---CCUCCUGCAACAUGGUCGUCGCGGAGGAGGAUGGCCAUGCCCAC----
.((.((((........---((((((((((---(.((.....)).)))))))))))....(((((((---(((((.((.((......)).))))))))))).))).))))))..---- ( -57.70, z-score =  -3.31, R)
>droSim1.chr2L 11900590 104 - 22036055
AGGUGCAUCCAAGUCC---GGGGGCGGCG---CGCAGUGUGUGGGCGUUGCCCCUAACCGCCUCCU---CCUCCUGCAACAUGGUCGUCGCGGAGGAGGAUGGCCAUGCCCAC----
.((.((((........---((((((((((---(.((.....)).)))))))))))....(((((((---(((((.((.((......)).))))))))))).))).))))))..---- ( -57.70, z-score =  -3.31, R)
>droSec1.super_16 291171 104 - 1878335
AGGUGCAUCCAAGUCC---GGGGGCGGCG---CGCAGUGUGUGGGCGUUGCCCCUAACCGCCUCCU---CCUCCUGCAACAUGGUCGUCGCGGAGGAGGAUGGCCAUGCCCAC----
.((.((((........---((((((((((---(.((.....)).)))))))))))....(((((((---(((((.((.((......)).))))))))))).))).))))))..---- ( -57.70, z-score =  -3.31, R)
>droYak2.chr2L 8520338 104 - 22324452
AGGUGCAUCCAAGUCC---GGGGGCGGCG---CGCAGUGUGUGGGCGUUGCCCCUAACCGCCUCCU---CCUCCUGCAACAUGGUCGUCGCGGAGGAGGAUGGCCAUGCCCAC----
.((.((((........---((((((((((---(.((.....)).)))))))))))....(((((((---(((((.((.((......)).))))))))))).))).))))))..---- ( -57.70, z-score =  -3.31, R)
>droEre2.scaffold_4929 13330402 104 + 26641161
AGGUGCAUCCAAGUCC---GGGGGCGGCG---CGUAGUGUGUGGGCGUUGCCCCUAACCGCCUCCU---CCUCCUGCAACAUGGUCGUCGCGGAGGAGGAUGGCCAUGCCCAC----
.((.((((........---((((((((((---(.((.....)).)))))))))))....(((((((---(((((.((.((......)).))))))))))).))).))))))..---- ( -55.90, z-score =  -3.13, R)
>droAna3.scaffold_12943 2507870 104 + 5039921
AGGUGCACCCGAGUCC---GGGGGCAGCG---CGCAGUGUAUGGGCGCUGCCCCUGACAGCCUCCU---CCUCAUGCAACAUGGUAGUGGCAGAGGAGGAUGGCCAUGCCCAC----
.((.(((.....(((.---((((((((((---(.((.....)).)))))))))))))).(((((((---((((.(((.((......)).))))))))))).)))..)))))..---- ( -63.10, z-score =  -4.89, R)
>dp4.chr4_group3 911690 98 - 11692001
AGAUUCACCCCAGCCC---GGGGGCGGCG---CGGAGUGUGUGGGCGCUUCCCCUGACGGCAUCCU---CAUCAUGCAAUAUGGU------GGUGGCGGAGGAGCAUGCCCAU----
.(.(((.(((((((((---(((((.((((---(...........))))).))))))..)))....(---(((((((...))))))------))))).)).))).)........---- ( -36.40, z-score =   1.68, R)
>droPer1.super_1 2391441 98 - 10282868
AGAUUCACCCCAGCCC---GGGGGCGGCG---CGGAGUGUGUGGGCGCUUCCCCUGACGGCAUCCU---CAUCAUGCAAUAUGGU------GGUGGCGGAGGAGCAUGCCCAU----
.(.(((.(((((((((---(((((.((((---(...........))))).))))))..)))....(---(((((((...))))))------))))).)).))).)........---- ( -36.40, z-score =   1.68, R)
>droWil1.scaffold_181038 47035 110 - 637489
AAGUGCAUCCUAGUCCCGGGGGGGCGGCGGCCCGUAGCAUAUGGGCGCUGCCCCUGACAGCCUCGUCUGCAUCUUGCAAUAUGGUCG---AAGAGGAUGGUCAUCAUGAUCAC----
..(((((((((..(((((.((((((((((.((((((...))))))))))))))))(((......)))(((.....)))...)))..)---)..))))))(((.....))))))---- ( -45.70, z-score =  -1.17, R)
>droVir3.scaffold_12963 15929683 95 - 20206255
AGGUACACCCCAGUCC---GGGGGCAGCG---CGCAGCGUUUGGGCGCUGCCCCUGACGGCCUCCU---CGUCAUGCAACAUG---------GAGGAGGAUGGUCACGCCCAU----
.(((........(((.---((((((((((---(.(((...))).))))))))))))))((((((((---(.(((((...))))---------)..))))).))))..)))...---- ( -51.10, z-score =  -3.15, R)
>droMoj3.scaffold_6500 2910723 95 - 32352404
AGGUACACCCCAGCCC---AGGGGCAGCG---CGCAGUGUAUGGGCGCUGCCCCUGACGGCCUCUU---CGUCAUGCAACAUG---------GAGGAAGACGGUCAUGCUCAU----
.((......))(((.(---((((((((((---(.((.....)).))))))))))))..((((((((---(.(((((...))))---------)..))))).))))..)))...---- ( -48.90, z-score =  -3.53, R)
>droGri2.scaffold_15252 13357895 95 - 17193109
AGGUACACCCCAGUCC---GGGGGCAGCG---CGCAGUGUUUGGGCGCUGCCCCUAACGGCCUCCU---CGUCUUGCAACAUG---------GAAGAAGAUGGCCAUGCACAU----
.((.((......))))---((((((((((---(.(((...))).)))))))))))...((((...(---(.((((.(.....)---------.)))).)).))))........---- ( -42.80, z-score =  -2.08, R)
>anoGam1.chr3R 21441154 100 - 53272125
--GUGCAUCCGAGUCCU--GGUAGUGCUCGCACUUUG-GUGUGGGCACUGCCCCUGACGG---------CAUCAUGCAACAUGGUGA---CCGAGGAGAGUGAUCAUCCACACCAUC
--(((..(((..(((..--((((((((((((((....-))))))))))))))...)))((---------(((((((...))))))).---))..)))((....))...)))...... ( -45.30, z-score =  -2.93, R)
>triCas2.ChLG4 1461532 92 + 13894384
AAGUGUUUCCAAGUCC---GGGCACUGCC---CGAAGCGUGUGGGCUUUGCCCCAAA------------CCUCCUGCAACAUGGUCG---CAGACACCGACCAUCCUGCCACC----
..(((...........---(((((..(((---((.......)))))..)))))....------------......(((..(((((((---.......)))))))..)))))).---- ( -31.70, z-score =  -1.70, R)
>consensus
AGGUGCAUCCAAGUCC___GGGGGCGGCG___CGCAGUGUGUGGGCGCUGCCCCUAACGGCCUCCU___CCUCAUGCAACAUGGUCG___CGGAGGAGGAUGGCCAUGCCCAC____
...................((((((((((...((.......))..)))))))))).............................................................. (-13.86 = -14.15 +   0.29)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:34:25 2011