Locus 4291

Sequence ID dm3.chr2R
Location 11,978,665 – 11,978,729
Length 64
Max. P 0.986967
window5880 window5881

overview

Window 0

Location 11,978,665 – 11,978,729
Length 64
Sequences 8
Columns 70
Reading direction forward
Mean pairwise identity 68.85
Shannon entropy 0.58578
G+C content 0.54966
Mean single sequence MFE -16.78
Consensus MFE -8.49
Energy contribution -8.49
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.57
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.55
SVM RNA-class probability 0.949778
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 11978665 64 + 21146708
UGGCCCAAGUGUCAAGCGGCGGCAAUAUGCCACCGAUACAGA-CCUCUUGUCCUCUCCCUGCCAA-----
((((.((((.(((...(((.(((.....))).))).....))-)..))))..........)))).----- ( -18.80, z-score =  -1.64, R)
>droSim1.chr2R 10714193 64 + 19596830
UGGCCCAAGUGUCAAGCGGCGGCAAUGUGCCACCGAUACAGA-CCUCUUGUCCUCUCCCUGCCAA-----
((((.((((.(((...(((.(((.....))).))).....))-)..))))..........)))).----- ( -18.80, z-score =  -1.16, R)
>droSec1.super_1 9474482 64 + 14215200
UGGCCCAAGUGUCAAGCGGCGGCAAUAUGCCACCGAUACAGA-CCUCUUGUCCUCUCCCUGCCAA-----
((((.((((.(((...(((.(((.....))).))).....))-)..))))..........)))).----- ( -18.80, z-score =  -1.64, R)
>droYak2.chr2R 4133846 63 - 21139217
--GCCCAAGUGUCAAGCGGCGGCAAUAUGCCACCGAUACAGAACCUCUGUUCCUCUCCCAACCAA-----
--......(((((....((.(((.....))).))))))).((((....)))).............----- ( -13.60, z-score =  -1.46, R)
>droEre2.scaffold_4845 8710003 64 - 22589142
UGGCCCAAGUGUCAAGCGGCGGCAAUAUGCCACCGAUACAGA-CCUCUGUUCCUCUCCCGGCCAA-----
(((((...........(((.(((.....))).)))..((((.-...)))).........))))).----- ( -21.90, z-score =  -2.19, R)
>droAna3.scaffold_13266 4460056 64 - 19884421
UGGCCAAGCGGUGUCGGGGCGGCAAUAUGCCACCGAUACAGA-CUGCUCCUCCACUCCACACCAC-----
(((...(((((((((((((((......)))).)))))....)-)))))...)))...........----- ( -21.90, z-score =  -1.39, R)
>dp4.chr3 16412226 62 + 19779522
-----AAAAAGUGUCA-GGCGGCAAUAUGCCACCAAUACAUAUUUGUCUCUCUCUC--GCUCUCUGUCUA
-----.....((((..-((.(((.....))).)).)))).................--............ ( -10.20, z-score =  -1.47, R)
>droPer1.super_4 6812660 64 - 7162766
-----AAAAAGUGUCA-GGCGGCAAUAUGCCACCAAUACAUAUUUGUCUCUCUCUCUCGCUCUCUGUCUA
-----.....((((..-((.(((.....))).)).))))............................... ( -10.20, z-score =  -1.63, R)
>consensus
UGGCCCAAGUGUCAAGCGGCGGCAAUAUGCCACCGAUACAGA_CCUCUUCUCCUCUCCCCGCCAA_____
.................((.(((.....))).)).................................... ( -8.49 =  -8.49 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 11,978,665 – 11,978,729
Length 64
Sequences 8
Columns 70
Reading direction reverse
Mean pairwise identity 68.85
Shannon entropy 0.58578
G+C content 0.54966
Mean single sequence MFE -22.09
Consensus MFE -11.49
Energy contribution -11.49
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.91
Structure conservation index 0.52
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.26
SVM RNA-class probability 0.986967
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 11978665 64 - 21146708
-----UUGGCAGGGAGAGGACAAGAGG-UCUGUAUCGGUGGCAUAUUGCCGCCGCUUGACACUUGGGCCA
-----.((((...(((.((((.....)-)))((..(((((((.....)))))))....)).)))..)))) ( -23.80, z-score =  -1.54, R)
>droSim1.chr2R 10714193 64 - 19596830
-----UUGGCAGGGAGAGGACAAGAGG-UCUGUAUCGGUGGCACAUUGCCGCCGCUUGACACUUGGGCCA
-----.((((...(((.((((.....)-)))((..(((((((.....)))))))....)).)))..)))) ( -23.80, z-score =  -1.29, R)
>droSec1.super_1 9474482 64 - 14215200
-----UUGGCAGGGAGAGGACAAGAGG-UCUGUAUCGGUGGCAUAUUGCCGCCGCUUGACACUUGGGCCA
-----.((((...(((.((((.....)-)))((..(((((((.....)))))))....)).)))..)))) ( -23.80, z-score =  -1.54, R)
>droYak2.chr2R 4133846 63 + 21139217
-----UUGGUUGGGAGAGGAACAGAGGUUCUGUAUCGGUGGCAUAUUGCCGCCGCUUGACACUUGGGC--
-----...((..((...(((((....)))))....(((((((.....)))))))))..))........-- ( -22.50, z-score =  -2.18, R)
>droEre2.scaffold_4845 8710003 64 + 22589142
-----UUGGCCGGGAGAGGAACAGAGG-UCUGUAUCGGUGGCAUAUUGCCGCCGCUUGACACUUGGGCCA
-----.(((((.(..(((..((((...-.))))..(((((((.....))))))))))..).....))))) ( -26.50, z-score =  -2.07, R)
>droAna3.scaffold_13266 4460056 64 + 19884421
-----GUGGUGUGGAGUGGAGGAGCAG-UCUGUAUCGGUGGCAUAUUGCCGCCCCGACACCGCUUGGCCA
-----(((((((((.(((.(((.....-))).))).((((((.....)))))))).)))))))....... ( -25.50, z-score =  -0.92, R)
>dp4.chr3 16412226 62 - 19779522
UAGACAGAGAGC--GAGAGAGAGACAAAUAUGUAUUGGUGGCAUAUUGCCGCC-UGACACUUUUU-----
.....(((((((--....)...........(((...((((((.....))))))-..)))))))))----- ( -15.40, z-score =  -2.90, R)
>droPer1.super_4 6812660 64 + 7162766
UAGACAGAGAGCGAGAGAGAGAGACAAAUAUGUAUUGGUGGCAUAUUGCCGCC-UGACACUUUUU-----
.....(((((((....).............(((...((((((.....))))))-..)))))))))----- ( -15.40, z-score =  -2.87, R)
>consensus
_____UUGGCAGGGAGAGGACAAGAGG_UCUGUAUCGGUGGCAUAUUGCCGCCGCUUGACACUUGGGCCA
....................................((((((.....))))))................. (-11.49 = -11.49 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:26:21 2011