Locus 4529

Sequence ID dm3.chr2R
Location 13,791,780 – 13,791,877
Length 97
Max. P 0.994383
window6204 window6205

overview

Window 4

Location 13,791,780 – 13,791,877
Length 97
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 75.78
Shannon entropy 0.43633
G+C content 0.46137
Mean single sequence MFE -34.82
Consensus MFE -23.61
Energy contribution -25.15
Covariance contribution 1.54
Combinations/Pair 1.31
Mean z-score -2.44
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.70
SVM RNA-class probability 0.994383
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13791780 97 + 21146708
CUCGGCCAGAAAUAUUCCUA-UAAAGUUUUGCGGAACUUUUGGUUUCGCUUGCUCAUGGCAGAGAGA------G--UUUUUGGUUAGC------UUUCUGGCCGAGAUGGCG---
((((((((((((..(..(((-.(((.(((((((((((.....)))))))((((.....)))).))))------.--))).)))..)..------))))))))))))......--- ( -38.90, z-score =  -4.09, R)
>droAna3.scaffold_13266 9484690 92 - 19884421
CCUGGGUUGACACAUUUUCAAUUAAGUUUUGCGAAACUCUGAGUCUUUAACGUGGUCGGAAGCAGUGC-----GAGGUUUUGGUUAGU-----UUUUUCGAC-------------
.((..(((((.......)))))..)).....(((((..((((..((..(((.(.(((....)....))-----.).)))..)))))).-----..)))))..------------- ( -14.20, z-score =   2.18, R)
>droEre2.scaffold_4845 8019360 99 + 22589142
CUCCGCCAGAAAUAUUCCUA-UAAAGUUUUGCGGAACUUUUGGUUUCGCUUGCUCCUGGCAGAGAGA------GAGUUUUCGGUUAGC------UUUCUGGCCGAGAAGCUG---
(((.(((((...(((....)-)).(((...(((((((.....)))))))..))).))))).)))...------.(((((((((((((.------...))))))))).)))).--- ( -34.90, z-score =  -2.21, R)
>droYak2.chr2R 5748802 114 - 21139217
CUCGGCCAGAAAUAUUCCUA-UAAAGUUUUGCGGAACUUUUGGUUUCGCUUGCUUCUGGCACAGAGACAGACAGAGUUUUUGGUUAGCGUUGGCUUUCUGGCCAAGAAGAAGCUG
((.(((((((((....((..-..((((...(((((((.....)))))))..))))(((((.(((((((.......))))))))))))....)).))))))))).))......... ( -37.90, z-score =  -1.93, R)
>droSec1.super_1 11286928 99 + 14215200
CUCGGCCAGAAAUAUUCCUA-UAAAGUUUUGCGGAACUUUUGGUUUCGCUUGCUGCUGGCAGAGAGA------GAGUUUUUGGUUAGC------UUUCUGGCCGAGAUGCCG---
((((((((((((........-...(((...(((((((.....)))))))..)))((((((.(((((.------...))))).))))))------))))))))))))......--- ( -41.50, z-score =  -4.28, R)
>droSim1.chr2R 12534479 99 + 19596830
CUCGGCCAGAAAUAUUCCUA-UAAAGUUUUGCGGAACUUUUGGUUUCGCUUGCUGCUGGCAGAGAGA------GAGUUUUUGGUUAGC------UUUCUGGCCGAGAUGCCG---
((((((((((((........-...(((...(((((((.....)))))))..)))((((((.(((((.------...))))).))))))------))))))))))))......--- ( -41.50, z-score =  -4.28, R)
>consensus
CUCGGCCAGAAAUAUUCCUA_UAAAGUUUUGCGGAACUUUUGGUUUCGCUUGCUGCUGGCAGAGAGA______GAGUUUUUGGUUAGC______UUUCUGGCCGAGAUGCCG___
((((((((((((............(((...(((((((.....)))))))..))).(((((.(((((..........))))).))))).......))))))))))))......... (-23.61 = -25.15 +   1.54)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 13,791,780 – 13,791,877
Length 97
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 75.78
Shannon entropy 0.43633
G+C content 0.46137
Mean single sequence MFE -26.42
Consensus MFE -17.14
Energy contribution -19.25
Covariance contribution 2.11
Combinations/Pair 1.14
Mean z-score -2.46
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.61
SVM RNA-class probability 0.993383
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13791780 97 - 21146708
---CGCCAUCUCGGCCAGAAA------GCUAACCAAAAA--C------UCUCUCUGCCAUGAGCAAGCGAAACCAAAAGUUCCGCAAAACUUUA-UAGGAAUAUUUCUGGCCGAG
---......((((((((((((------.....((.....--.------...(((......)))...(((.(((.....))).))).........-..))....)))))))))))) ( -30.20, z-score =  -4.53, R)
>droAna3.scaffold_13266 9484690 92 + 19884421
-------------GUCGAAAAA-----ACUAACCAAAACCUC-----GCACUGCUUCCGACCACGUUAAAGACUCAGAGUUUCGCAAAACUUAAUUGAAAAUGUGUCAACCCAGG
-------------.........-----...............-----...(((.....(((.(((((...((....((((((....))))))..))...))))))))....))). (  -8.50, z-score =   1.36, R)
>droEre2.scaffold_4845 8019360 99 - 22589142
---CAGCUUCUCGGCCAGAAA------GCUAACCGAAAACUC------UCUCUCUGCCAGGAGCAAGCGAAACCAAAAGUUCCGCAAAACUUUA-UAGGAAUAUUUCUGGCGGAG
---.(((((.((.....))))------)))............------...((((((((((((...(((.(((.....))).)))....((...-.)).....)))))))))))) ( -27.40, z-score =  -1.65, R)
>droYak2.chr2R 5748802 114 + 21139217
CAGCUUCUUCUUGGCCAGAAAGCCAACGCUAACCAAAAACUCUGUCUGUCUCUGUGCCAGAAGCAAGCGAAACCAAAAGUUCCGCAAAACUUUA-UAGGAAUAUUUCUGGCCGAG
.........((((((((((((.((..((((...((.......))..((..((((...))))..))))))......((((((......)))))).-..))....)))))))))))) ( -32.00, z-score =  -2.67, R)
>droSec1.super_1 11286928 99 - 14215200
---CGGCAUCUCGGCCAGAAA------GCUAACCAAAAACUC------UCUCUCUGCCAGCAGCAAGCGAAACCAAAAGUUCCGCAAAACUUUA-UAGGAAUAUUUCUGGCCGAG
---......((((((((((((------.....((......((------.((..(((....)))..)).)).....((((((......)))))).-..))....)))))))))))) ( -30.20, z-score =  -3.64, R)
>droSim1.chr2R 12534479 99 - 19596830
---CGGCAUCUCGGCCAGAAA------GCUAACCAAAAACUC------UCUCUCUGCCAGCAGCAAGCGAAACCAAAAGUUCCGCAAAACUUUA-UAGGAAUAUUUCUGGCCGAG
---......((((((((((((------.....((......((------.((..(((....)))..)).)).....((((((......)))))).-..))....)))))))))))) ( -30.20, z-score =  -3.64, R)
>consensus
___CGGCAUCUCGGCCAGAAA______GCUAACCAAAAACUC______UCUCUCUGCCAGCAGCAAGCGAAACCAAAAGUUCCGCAAAACUUUA_UAGGAAUAUUUCUGGCCGAG
.........((((((((((((.................................(((.....))).(((.(((.....))).)))..................)))))))))))) (-17.14 = -19.25 +   2.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:30:53 2011