Locus 8333

Sequence ID	dm3.chr3L
Location	22,097,986 – 22,098,082
Length	96
Max. P	0.880208

overview

Window 7

Location	22,097,986 – 22,098,082
Length	96
Sequences	4
Columns	101
Reading direction	forward
Mean pairwise identity	51.27
Shannon entropy	0.82382
G+C content	0.48829
Mean single sequence MFE	-27.38
Consensus MFE	-10.48
Energy contribution	-13.10
Covariance contribution	2.62
Combinations/Pair	1.68
Mean z-score	-0.80
Structure conservation index	0.38
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.42
SVM RNA-class probability	0.687824
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 22097986 96 + 24543557
---GAAGGGAUUUCUUGGCACUUUAUACCCCCGUCUGCUCCACAUUUCGGAGGGAUGUGGGAAGCUGGAGUUCGCUCAAUUAAACUCCAUAU--GAAACGA
---(..(((....)))..)..(((((((((.(((((.((((.......))))))))).)))....(((((((..........))))))))))--))).... ( -25.80, z-score =  -0.27, R)
>droYak2.chrU 23565886 88 + 28119190
AAAGCGGAUGCGAAUUUGCG-UUCACACUCCCUCGGGCUCCGCACAUGGGCGGACUAUGGGAGGCAGGUGUGAAAACUGCAAAGCACCU------------
...(((((((((....))))-)))...(((((...((.(((((......)))))))..)))))))((((((............))))))------------ ( -35.30, z-score =  -2.49, R)
>apiMel3.GroupUn 219586076 96 - 399230636
---GAAAGCAUUGAUUGGUGAUUUAUACCACCAUAUGCAUCACAUUUCGGUGGCUUAUGGGAAAGCACUGUUAAAUCGGCUAAAUGACACAU--AUUACGU
---....((((....(((((........))))).))))...........(((((((......)))).(((......)))........)))..--....... ( -17.70, z-score =   0.35, R)
>triCas2.chrUn_298 5931 98 - 21235
---GAACGUCUUCGGUGGCAUUGAAACCCCCCAUCAGCCCCUCACUUUGGAGGGAUUUGGGAGGCCGGCAUUAAGUCGGUCAAAACCCAUUUUUACAUCGU
---.........(((((............((((.....(((((......)))))...)))).(((((((.....)))))))..............))))). ( -30.70, z-score =  -0.80, R)
>consensus
___GAAGGUAUUAAUUGGCA_UUUAUACCCCCAUCUGCUCCACACUUCGGAGGGAUAUGGGAAGCCGGUGUUAAAUCGGCUAAACACCAUAU__A_AACGU
..............(((((..(((((((((((((((..(((((......)))))))))))).....))))))))....))))).................. (-10.48 = -13.10 +   2.62)

alignment

secondary structure

dotplot

Window 8

Location	22,097,986 – 22,098,082
Length	96
Sequences	4
Columns	101
Reading direction	reverse
Mean pairwise identity	51.27
Shannon entropy	0.82382
G+C content	0.48829
Mean single sequence MFE	-27.48
Consensus MFE	-9.61
Energy contribution	-10.68
Covariance contribution	1.06
Combinations/Pair	1.63
Mean z-score	-1.27
Structure conservation index	0.35
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.04
SVM RNA-class probability	0.880208
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 22097986 96 - 24543557
UCGUUUC--AUAUGGAGUUUAAUUGAGCGAACUCCAGCUUCCCACAUCCCUCCGAAAUGUGGAGCAGACGGGGGUAUAAAGUGCCAAGAAAUCCCUUC---
.(((((.--...((((((((........))))))))(((..((((((.........))))))))))))))(((((...............)))))...--- ( -25.76, z-score =  -1.05, R)
>droYak2.chrU 23565886 88 - 28119190
------------AGGUGCUUUGCAGUUUUCACACCUGCCUCCCAUAGUCCGCCCAUGUGCGGAGCCCGAGGGAGUGUGAA-CGCAAAUUCGCAUCCGCUUU
------------.((((((((((.((..((((((.(.((((......(((((......)))))....)))).))))))))-))))))...)))))...... ( -30.80, z-score =  -1.98, R)
>apiMel3.GroupUn 219586076 96 + 399230636
ACGUAAU--AUGUGUCAUUUAGCCGAUUUAACAGUGCUUUCCCAUAAGCCACCGAAAUGUGAUGCAUAUGGUGGUAUAAAUCACCAAUCAAUGCUUUC---
..(((((--(((((((((.....((........((((((......))).)))))....)))))))))))((((((....))))))......)))....--- ( -20.80, z-score =  -1.12, R)
>triCas2.chrUn_298 5931 98 + 21235
ACGAUGUAAAAAUGGGUUUUGACCGACUUAAUGCCGGCCUCCCAAAUCCCUCCAAAGUGAGGGGCUGAUGGGGGGUUUCAAUGCCACCGAAGACGUUC---
..(((((.......(((.(((((((.(.....).)))(((((((..((((((......))))))....)))))))..)))).))).......))))).--- ( -32.54, z-score =  -0.93, R)
>consensus
ACGUU_U__AUAUGGAGUUUAACCGAUUUAACACCGGCCUCCCAUAUCCCUCCGAAAUGUGGAGCAGAUGGGGGUAUAAA_CGCCAAUAAAUACCUUC___
............(((((((..........)))))))..(((((((..(((((......)))))....)))))))........................... ( -9.61 = -10.68 +   1.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:43:41 2011