Locus 3615

Sequence ID	dm3.chr2R
Location	6,683,181 – 6,683,294
Length	113
Max. P	0.959384

overview

Window 8

Location	6,683,181 – 6,683,294
Length	113
Sequences	7
Columns	113
Reading direction	forward
Mean pairwise identity	76.67
Shannon entropy	0.44351
G+C content	0.54514
Mean single sequence MFE	-40.01
Consensus MFE	-27.63
Energy contribution	-27.18
Covariance contribution	-0.45
Combinations/Pair	1.44
Mean z-score	-1.36
Structure conservation index	0.69
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.00
SVM RNA-class probability	0.870508
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 6683181 113 + 21146708
GGCCGCUCCGCCCUCUGUUUGUGUCCCUGGAGAAAAGGGCUCGAUUAGGGGACGAUGUGAGGGGGCGUGUACUAUCAGCUGUUUCCCAUUAUGACUACAGCGGAAAUACACAA
(.((.(((((.((((((.(((.(.((((.......))))).))).)))))).))....))).)).)(((((...((.(((((.((.......))..))))).))..))))).. ( -39.20, z-score =  -0.91, R)
>droSim1.chr2R 5273681 113 + 19596830
GGCCGUUCCGCCCCCUGUUUGUGUCCCUGGAGAAAAGGGCUCGAUUUGGGGGCGAUGGGCGGGGGCUUGUACUAUCAGCUGUUUCCCAUUAUGACUUCAGCGGAAAUACACAA
..(((((..((((((...(((.(.((((.......))))).)))...))))))((((((..(.((((.(......))))).)..))))))........))))).......... ( -43.40, z-score =  -1.07, R)
>droSec1.super_1 4270538 112 + 14215200
GGCCGUUCCGCCCCCUGUUUGUGUCCCUGGAGAAAAGGGCUCGAUU-AGGGGCGAUGGGCGGGGGCGUGUACUAUCAGCUGUUUCCCAUUAUGACUUCAGCGGAAAUACACAA
.....((((((((((((.(((.(.((((.......))))).))).)-))))).((((((..(.(((.((......))))).)..)))))).........))))))........ ( -42.00, z-score =  -0.82, R)
>droEre2.scaffold_4845 3496882 112 - 22589142
GGCCGCCCCGCCCCCUUUCUGUGUCCCUGGAGAAA-GGGCUCGAUUAGGGGGCGGUGGGAGGGGGCGUGUACUAUCAGCUGUUUCCCAUUAUGACUUCAGCGGAAAUACACAA
..((((.(((((((((...((.(.((((......)-)))).))...)))))))))(((((((.(((.((......))))).)))))))...........)))).......... ( -50.30, z-score =  -2.07, R)
>droYak2.chr2R 18691761 112 - 21139217
GGCUGCCCCGCCCCCUGUUUGUGUCCCCAGAGAAA-AGGCUCGAUUAGGGGGCAGUGGAAGGGGGCGUGUACUAUCAGCUGUUUUCCAUUAUGACUUCAGCGGAAAUACACAA
((.....))(((((((.....(((((((.(((...-...))).....))))))).....)))))))(((((...((.((((...((......))...)))).))..))))).. ( -43.00, z-score =  -1.59, R)
>dp4.chr3 3811565 98 - 19779522
---AGCCCCGUUUCC-GCCUCUCUCUCUCUCGAAG-------AAUAAAGAGGUUGUGG--GGGGGCGUGUGUUAUCAGCUGUUGCCCAUUAUGACUUCAGCGGAAAUAUAU--
---......((((((-((.(((.((......))))-------).....(((((..(((--..(((((...((.....))...))))).)))..))))).))))))))....-- ( -31.60, z-score =  -1.40, R)
>droPer1.super_4 794959 90 + 7162766
---AGCCCCGUUCCC-GCCUCUCUCUC-------G-------AAGAAAGAGGUUGUGG--GGGG-CGUGUGUUAUCAGCUGUUGCCCAUUAUGACUUCAGCGGAAAUAUAU--
---.(((((.(..(.-((((((.((..-------.-------..)).)))))).)..)--))))-)(((((((.((.((((................)))).)))))))))-- ( -30.59, z-score =  -1.63, R)
>consensus
GGCCGCCCCGCCCCCUGUUUGUGUCCCUGGAGAAA_GGGCUCGAUUAGGGGGCGGUGGGAGGGGGCGUGUACUAUCAGCUGUUUCCCAUUAUGACUUCAGCGGAAAUACACAA
.........((((((......(((((((.(((.......))).....)))))))......))))))(((((...((.((((................)))).))..))))).. (-27.63 = -27.18 +  -0.45)

alignment

secondary structure

dotplot

Window 9

Location	6,683,181 – 6,683,294
Length	113
Sequences	7
Columns	113
Reading direction	reverse
Mean pairwise identity	76.67
Shannon entropy	0.44351
G+C content	0.54514
Mean single sequence MFE	-37.82
Consensus MFE	-20.73
Energy contribution	-21.57
Covariance contribution	0.84
Combinations/Pair	1.12
Mean z-score	-2.19
Structure conservation index	0.55
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.67
SVM RNA-class probability	0.959384
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 6683181 113 - 21146708
UUGUGUAUUUCCGCUGUAGUCAUAAUGGGAAACAGCUGAUAGUACACGCCCCCUCACAUCGUCCCCUAAUCGAGCCCUUUUCUCCAGGGACACAAACAGAGGGCGGAGCGGCC
..(((((((((.(((((..((......))..))))).)).)))))))((((((.....(((.........)))((((((((((....))).......))))))))).).))). ( -34.81, z-score =  -1.22, R)
>droSim1.chr2R 5273681 113 - 19596830
UUGUGUAUUUCCGCUGAAGUCAUAAUGGGAAACAGCUGAUAGUACAAGCCCCCGCCCAUCGCCCCCAAAUCGAGCCCUUUUCUCCAGGGACACAAACAGGGGGCGGAACGGCC
...((((((((.((((...((.......))..)))).)).)))))).......(((..((((((((........((((.......)))).........))))))))...))). ( -36.53, z-score =  -1.01, R)
>droSec1.super_1 4270538 112 - 14215200
UUGUGUAUUUCCGCUGAAGUCAUAAUGGGAAACAGCUGAUAGUACACGCCCCCGCCCAUCGCCCCU-AAUCGAGCCCUUUUCUCCAGGGACACAAACAGGGGGCGGAACGGCC
..(((((((((.((((...((.......))..)))).)).)))))))......(((..((((((((-.......((((.......)))).........))))))))...))). ( -37.59, z-score =  -1.26, R)
>droEre2.scaffold_4845 3496882 112 + 22589142
UUGUGUAUUUCCGCUGAAGUCAUAAUGGGAAACAGCUGAUAGUACACGCCCCCUCCCACCGCCCCCUAAUCGAGCCC-UUUCUCCAGGGACACAGAAAGGGGGCGGGGCGGCC
..(((((((((.((((...((.......))..)))).)).)))))))(((.((.....(((((((((..((...(((-(......)))).....)).))))))))))).))). ( -46.00, z-score =  -2.41, R)
>droYak2.chr2R 18691761 112 + 21139217
UUGUGUAUUUCCGCUGAAGUCAUAAUGGAAAACAGCUGAUAGUACACGCCCCCUUCCACUGCCCCCUAAUCGAGCCU-UUUCUCUGGGGACACAAACAGGGGGCGGGGCAGCC
..(((((((((.((((...((......))...)))).)).)))))))(((((........(((((((....(((...-...)))((....)).....)))))))))))).... ( -43.30, z-score =  -2.64, R)
>dp4.chr3 3811565 98 + 19779522
--AUAUAUUUCCGCUGAAGUCAUAAUGGGCAACAGCUGAUAACACACGCCCCC--CCACAACCUCUUUAUU-------CUUCGAGAGAGAGAGAGGC-GGAAACGGGGCU---
--.......((.((((..(((......)))..)))).))........(((((.--......(((((((.((-------(((...)))))))))))).-(....)))))).--- ( -32.90, z-score =  -3.19, R)
>droPer1.super_4 794959 90 - 7162766
--AUAUAUUUCCGCUGAAGUCAUAAUGGGCAACAGCUGAUAACACACG-CCCC--CCACAACCUCUUUCUU-------C-------GAGAGAGAGGC-GGGAACGGGGCU---
--.......((.((((..(((......)))..)))).))........(-((((--...(..((((((((..-------.-------..)))))))).-.)....))))).--- ( -33.60, z-score =  -3.60, R)
>consensus
UUGUGUAUUUCCGCUGAAGUCAUAAUGGGAAACAGCUGAUAGUACACGCCCCCUCCCACCGCCCCCUAAUCGAGCCC_UUUCUCCAGGGACACAAACAGGGGGCGGGGCGGCC
...((((((((.((((...((......))...)))).)).))))))(((((((.........(((.....................))).........)))))))........ (-20.73 = -21.57 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:13:31 2011