Locus 4507

Sequence ID	dm3.chr2R
Location	13,561,634 – 13,561,724
Length	90
Max. P	0.999387

overview

Window 6

Location	13,561,634 – 13,561,724
Length	90
Sequences	11
Columns	103
Reading direction	forward
Mean pairwise identity	60.34
Shannon entropy	0.82165
G+C content	0.50789
Mean single sequence MFE	-29.33
Consensus MFE	-6.32
Energy contribution	-5.61
Covariance contribution	-0.71
Combinations/Pair	1.83
Mean z-score	-1.76
Structure conservation index	0.22
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.34
SVM RNA-class probability	0.650243
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13561634 90 + 21146708
----GACGCAACAGCU-CUGCUUCCUAUCUUUCGGAUGCGUUUCAAACGCAUCC--GAGACUGUCGUUUACAUUAUUCGCAAAUUG-GGUG-GGGGGUU----
----((.((....)))-).((((((((((((((((((((((.....))))))))--)))).((.((..((...))..)))).....-))))-)))))).---- ( -31.50, z-score =  -3.39, R)
>droGri2.scaffold_15245 14697625 79 - 18325388
----AGCACAACAGUUUCGG----AUGUACC-AAGACACGUUUCAAACGCAUC-GAAAAACUGUUG--------AUUUGUCCAAACGGG---GUGGGUUC---
----....(((((((((..(----((((...-..((......))....)))))-...)))))))))--------(((..(((.....))---)..)))..--- ( -18.70, z-score =  -0.26, R)
>droVir3.scaffold_12875 10103717 82 - 20611582
----AGCACAACAGUUACGU----AUGCGCC-GAGACACGUUUCAAACGCGUCAGAAAAACUGCUG--------AUACGUCAAGUCGGGCG-GGGGGUUU---
----.(((..((......))----.)))(((-..(((.(((.....))).))).......((((((--------((.......))).))))-)..)))..--- ( -17.90, z-score =   1.17, R)
>droWil1.scaffold_180701 1112998 103 - 3904529
ACGCAAAACUGUUGCCAUGUCCAUAUAUAUGGGUGGCGGGACCGGUAAUCGACUCGACUUCUGCUUGAGUCCGGGUUUAAUUAAUUGAUUGUAUUGGUUUGUU
..(((...((((..((((((......)))).))..))))((((((((...((((((((((......)))).))))))(((((....)))))))))))))))). ( -26.80, z-score =  -0.48, R)
>droPer1.super_4 1185299 95 - 7162766
----GGUGCAACAGCUUCUGCGCCGUACUCUUGAGAUGCGUUUCAAACGCAUCCCCGAAGCUGUUGUCUGUUCCGUUCGAGGGAUGUGGUG-GGGGGGUU---
----........(((((((.(((((((((((((((((((((.....)))))))..((.(((........))).)).))))))).)))))))-.)))))))--- ( -34.50, z-score =  -0.95, R)
>dp4.chr3 9131211 95 - 19779522
----GGUGCAACAGCUUCUGCGCCGUACUCUUGAGACGCGUUUCAAACGCAUCCCCGAAGCUGUUGUCUGUUCCGUUCGAGGGAUGUGGUG-GGGGGGUU---
----((((((........))))))..((((((((((....))))...((((((((((((((........))....)))).))))))))...-.)))))).--- ( -32.80, z-score =  -0.17, R)
>droAna3.scaffold_13266 9262863 86 - 19884421
----AAUAUUACAACGGCUG-----UGCUCUUCAAGCGCGUUUCAAACGCGUGC--GCAACUGUUGAAUGUUUUCUUCGCGGGAUG-GGUG-GGGGGUU----
----((((((.((((((.((-----(((.......((((((.....))))))))--))).))))))))))))((((((((......-.)))-)))))..---- ( -29.01, z-score =  -2.03, R)
>droEre2.scaffold_4845 7791083 91 + 22589142
----GAUGCAACAGCUUUUGCUCCCUAUCUUUCGGAUGCGUUUCAAACGCAUCC--GACACUGUCGUUUACAUUACUUGCGGAUUG-GGUG-GGGGGUU----
----...((....))....(((((((((((.((((((((((.....))))))))--))..((((.((.......))..))))...)-))))-)))))).---- ( -34.60, z-score =  -4.00, R)
>droYak2.chr2R 5517020 91 - 21139217
----GAUGCAACAGCUUCGGCUCCCUAUCUUUCGAAUGCGUUUCAAACGCAUCC--GACACUGUCGUUUACAUUAUUUGCGGAUUG-GGUG-GGGGGUU----
----((.((....)).))(((((((((((..(((.((((((.....)))))).)--))((...((((...........))))..))-))))-)))))))---- ( -29.60, z-score =  -2.19, R)
>droSec1.super_1 11060867 91 + 14215200
----GACGCAACAGCUUCUGCUCCCUAUCUUUCAGAUGCGUUUCAAACGCAUCC--GACACUGUCGUUUACAUUAUUCGCGGAUUG-GGUG-GGGGGUU----
----((.((....)).)).(((((((((((.((.(((((((.....)))))))(--(((...))))...............))..)-))))-)))))).---- ( -30.70, z-score =  -2.79, R)
>droSim1.chr2R 12298378 91 + 19596830
----GACGCAACAGCUUCUGCUCCCUAUCUUUCGGAUGCGUUUCAAACGCAUCC--GACACUGUCGUUUACAAUAUUCGCGGAUCG-GGUG-GGGGGUU----
----((.((....)).)).(((((((((((.((((((((((.....))))))))--))..(((.((..((...))..)))))...)-))))-)))))).---- ( -36.50, z-score =  -4.25, R)
>consensus
____GACGCAACAGCUUCUGCUCCCUAUCUUUCAGAUGCGUUUCAAACGCAUCC__GAAACUGUUGUUUACAUUAUUCGCGGAAUG_GGUG_GGGGGUU____
....(((((....))...................(((((((.....))))))).........)))...................................... ( -6.32 =  -5.61 +  -0.71)

alignment

secondary structure

dotplot

Window 7

Location	13,561,634 – 13,561,724
Length	90
Sequences	11
Columns	103
Reading direction	reverse
Mean pairwise identity	60.34
Shannon entropy	0.82165
G+C content	0.50789
Mean single sequence MFE	-24.45
Consensus MFE	-12.64
Energy contribution	-12.34
Covariance contribution	-0.30
Combinations/Pair	1.88
Mean z-score	-1.91
Structure conservation index	0.52
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	3.84
SVM RNA-class probability	0.999387
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13561634 90 - 21146708
----AACCCCC-CACC-CAAUUUGCGAAUAAUGUAAACGACAGUCUC--GGAUGCGUUUGAAACGCAUCCGAAAGAUAGGAAGCAG-AGCUGUUGCGUC----
----.......-....-...((((((.....))))))((((((.(((--((((((((.....))))))))........(....).)-))))))))....---- ( -25.40, z-score =  -2.77, R)
>droGri2.scaffold_15245 14697625 79 + 18325388
---GAACCCAC---CCCGUUUGGACAAAU--------CAACAGUUUUUC-GAUGCGUUUGAAACGUGUCUU-GGUACAU----CCGAAACUGUUGUGCU----
---....(((.---......)))......--------((((((((((..-(((((((.....)))))))..-((.....----))))))))))))....---- ( -19.50, z-score =  -1.12, R)
>droVir3.scaffold_12875 10103717 82 + 20611582
---AAACCCCC-CGCCCGACUUGACGUAU--------CAGCAGUUUUUCUGACGCGUUUGAAACGUGUCUC-GGCGCAU----ACGUAACUGUUGUGCU----
---........-.((.((((...((((((--------..((((.....))(((((((.....)))))))..-.))..))----))))....)))).)).---- ( -22.90, z-score =  -1.63, R)
>droWil1.scaffold_180701 1112998 103 + 3904529
AACAAACCAAUACAAUCAAUUAAUUAAACCCGGACUCAAGCAGAAGUCGAGUCGAUUACCGGUCCCGCCACCCAUAUAUAUGGACAUGGCAACAGUUUUGCGU
.....(((((.((................((((..((.....))(((((...))))).))))....((((.((((....))))...))))....)).))).)) ( -18.50, z-score =  -0.50, R)
>droPer1.super_4 1185299 95 + 7162766
---AACCCCCC-CACCACAUCCCUCGAACGGAACAGACAACAGCUUCGGGGAUGCGUUUGAAACGCAUCUCAAGAGUACGGCGCAGAAGCUGUUGCACC----
---........-.......(((.......)))...(.((((((((((.(((((((((.....)))))))))....((.....)).)))))))))))...---- ( -31.00, z-score =  -2.63, R)
>dp4.chr3 9131211 95 + 19779522
---AACCCCCC-CACCACAUCCCUCGAACGGAACAGACAACAGCUUCGGGGAUGCGUUUGAAACGCGUCUCAAGAGUACGGCGCAGAAGCUGUUGCACC----
---........-.......(((.......)))...(.((((((((((.(((((((((.....)))))))))....((.....)).)))))))))))...---- ( -30.60, z-score =  -1.92, R)
>droAna3.scaffold_13266 9262863 86 + 19884421
----AACCCCC-CACC-CAUCCCGCGAAGAAAACAUUCAACAGUUGC--GCACGCGUUUGAAACGCGCUUGAAGAGCA-----CAGCCGUUGUAAUAUU----
----.......-....-.................(((((((.((((.--((.(((((.....)))))(.....).)).-----)))).)))).)))...---- ( -15.60, z-score =  -0.67, R)
>droEre2.scaffold_4845 7791083 91 - 22589142
----AACCCCC-CACC-CAAUCCGCAAGUAAUGUAAACGACAGUGUC--GGAUGCGUUUGAAACGCAUCCGAAAGAUAGGGAGCAAAAGCUGUUGCAUC----
----.......-..((-(.((((....).................((--((((((((.....))))))))))..))).))).((((......))))...---- ( -27.60, z-score =  -3.32, R)
>droYak2.chr2R 5517020 91 + 21139217
----AACCCCC-CACC-CAAUCCGCAAAUAAUGUAAACGACAGUGUC--GGAUGCGUUUGAAACGCAUUCGAAAGAUAGGGAGCCGAAGCUGUUGCAUC----
----.......-....-....................(((((((.((--((((((((.....))))))((....)).......)))).)))))))....---- ( -23.80, z-score =  -1.81, R)
>droSec1.super_1 11060867 91 - 14215200
----AACCCCC-CACC-CAAUCCGCGAAUAAUGUAAACGACAGUGUC--GGAUGCGUUUGAAACGCAUCUGAAAGAUAGGGAGCAGAAGCUGUUGCGUC----
----.......-..((-(.((((((.................)))((--((((((((.....))))))))))..))).))).((((......))))...---- ( -24.53, z-score =  -1.66, R)
>droSim1.chr2R 12298378 91 - 19596830
----AACCCCC-CACC-CGAUCCGCGAAUAUUGUAAACGACAGUGUC--GGAUGCGUUUGAAACGCAUCCGAAAGAUAGGGAGCAGAAGCUGUUGCGUC----
----.......-..((-(.(((......((((((.....))))))((--((((((((.....))))))))))..))).))).((((......))))...---- ( -29.50, z-score =  -2.98, R)
>consensus
____AACCCCC_CACC_CAAUCCGCGAAUAAUGUAAACAACAGUUUC__GGAUGCGUUUGAAACGCAUCUGAAAGAUAGGGAGCAGAAGCUGUUGCAUC____
.....................................(((((((.((..((((((((.....))))))))...............)).)))))))........ (-12.64 = -12.34 +  -0.30)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:30:22 2011