Locus 1165

Sequence ID	dm3.chr2L
Location	8,759,027 – 8,759,090
Length	63
Max. P	0.684202

overview

Window 6

Location	8,759,027 – 8,759,090
Length	63
Sequences	12
Columns	67
Reading direction	forward
Mean pairwise identity	88.56
Shannon entropy	0.24292
G+C content	0.36423
Mean single sequence MFE	-15.45
Consensus MFE	-11.54
Energy contribution	-11.69
Covariance contribution	0.15
Combinations/Pair	1.12
Mean z-score	-1.76
Structure conservation index	0.75
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.41
SVM RNA-class probability	0.684202
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 8759027 63 + 23011544
---UUGUCCAUUAGCCAAAAUGGAGCAGACUAUUUUU-GAUCUAAUGAGCCAUGCUCAAAUGGUUUU
---.....((((((..(((((((......))))))).-...))))))((((((......)))))).. ( -13.40, z-score =  -0.95, R)
>droSim1.chr2L 8537884 63 + 22036055
---UUGUCCAUUAGCCAAAAUGGAGCAGACUAUUUUU-GAUCUAAUGAGCCAUGCUCUAAUGGUUUU
---.....((((((..(((((((......))))))).-...))))))((((((......)))))).. ( -13.40, z-score =  -0.99, R)
>droSec1.super_3 4232485 63 + 7220098
---UUGUCCAUUAGCCAAAAUGGAGCAGACUAUUUUU-GAUCUAAUGAGCCGUGCUCUAAUGGUUUU
---.....((((((..(((((((......))))))).-...))))))((((((......)))))).. ( -13.00, z-score =  -0.84, R)
>droYak2.chr2L 11401854 63 + 22324452
---UUGUCCAUUAGCCAAAAUGGAGUAGACUAUUUUU-GAUUUAAUGAGCCGUGUUCUAAUGGUUUU
---...((((((......)))))).............-........(((((((......))))))). ( -11.70, z-score =  -1.19, R)
>droEre2.scaffold_4929 9345971 62 + 26641161
---UUGUCCAUUAGCCAAAAUGGAGCAGACUAUUUU--GAUUUAAUGAGCCAUGGUCUAAUGGUUGU
---.....((((((.((((((((......)))))))--)..))))))((((((......)))))).. ( -15.30, z-score =  -1.58, R)
>droAna3.scaffold_12916 10398938 64 + 16180835
---UUGUCCAUUAGCCAAAAUGGAGUAGGCCAUUUUUCCAUUUAAUGAGCCCUCAAAUAAUGGAUUU
---..((((((((.((.....)).(..(((((((.........)))).)))..)...)))))))).. ( -15.90, z-score =  -2.12, R)
>dp4.chr4_group5 1544021 63 - 2436548
---UUGUCCAUUAGCCAAAAUGGAGCAGGCUAUUUUU-GAUUUAAUGAGCCAUGGUCUAAUGGAUUU
---..((((((((((((...(((..((....(((...-)))....))..)))))).))))))))).. ( -18.30, z-score =  -2.24, R)
>droPer1.super_5 1512994 63 - 6813705
---UUGUCCAUUAGCCAAAAUGGAGCAGGCUAUUUUU-GAUUUAAUGAGCCAUGGUCUAAUGGAUUU
---..((((((((((((...(((..((....(((...-)))....))..)))))).))))))))).. ( -18.30, z-score =  -2.24, R)
>droWil1.scaffold_180772 48724 62 + 8906247
---UUGUCCAUUAGU-AAAAUGGAGCAGGCUAUUUUU-GAUUUAAUGAGCCAUGGACUAAUGGAUUU
---..((((((((((-...((((..((....(((...-)))....))..))))..)))))))))).. ( -19.30, z-score =  -3.76, R)
>droVir3.scaffold_12723 4753220 61 + 5802038
----UGUCCAUUAGC-AAAAUGGAGCAGGCUAUUUCU-GAUUUAAUGAGCCAGAGACUAAUGGAUUU
----.(((((((((.-....(((..((....(((...-)))....))..)))....))))))))).. ( -15.00, z-score =  -1.62, R)
>droMoj3.scaffold_6500 10721235 65 + 32352404
CGGCUGUCCAUUAGC-GAAAUGGAGCAGGCUAUUUUU-GAUUUAAUGAGCCAUAGUCUAAUGGAUUU
.....((((((((((-...((((..((....(((...-)))....))..)))).).))))))))).. ( -15.90, z-score =  -1.11, R)
>droGri2.scaffold_15126 7754172 60 + 8399593
----UGUCCAUUAGC--AAAUGGAGCAGGCUAUUUUU-GAUUUAAUGAGCCAUAGACUAAUGGAUUU
----.(((((((((.--..((((..((....(((...-)))....))..))))...))))))))).. ( -15.90, z-score =  -2.47, R)
>consensus
___UUGUCCAUUAGCCAAAAUGGAGCAGGCUAUUUUU_GAUUUAAUGAGCCAUGGUCUAAUGGAUUU
.......(((((((.....((((..((....(((....)))....))..))))...))))))).... (-11.54 = -11.69 +   0.15)

alignment

secondary structure

dotplot

Window 7

Location	8,759,027 – 8,759,090
Length	63
Sequences	12
Columns	67
Reading direction	reverse
Mean pairwise identity	88.56
Shannon entropy	0.24292
G+C content	0.36423
Mean single sequence MFE	-14.19
Consensus MFE	-8.16
Energy contribution	-8.01
Covariance contribution	-0.15
Combinations/Pair	1.14
Mean z-score	-2.32
Structure conservation index	0.58
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.20
SVM RNA-class probability	0.592227
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 8759027 63 - 23011544
AAAACCAUUUGAGCAUGGCUCAUUAGAUC-AAAAAUAGUCUGCUCCAUUUUGGCUAAUGGACAA---
....(((((.(((((.((((.(((.....-...))))))))))))..........)))))....--- ( -12.20, z-score =  -0.67, R)
>droSim1.chr2L 8537884 63 - 22036055
AAAACCAUUAGAGCAUGGCUCAUUAGAUC-AAAAAUAGUCUGCUCCAUUUUGGCUAAUGGACAA---
....(((((((((((.((((.(((.....-...)))))))))))((.....)))))))))....--- ( -15.50, z-score =  -2.12, R)
>droSec1.super_3 4232485 63 - 7220098
AAAACCAUUAGAGCACGGCUCAUUAGAUC-AAAAAUAGUCUGCUCCAUUUUGGCUAAUGGACAA---
....(((((((((((.((((.(((.....-...)))))))))))((.....)))))))))....--- ( -15.50, z-score =  -2.51, R)
>droYak2.chr2L 11401854 63 - 22324452
AAAACCAUUAGAACACGGCUCAUUAAAUC-AAAAAUAGUCUACUCCAUUUUGGCUAAUGGACAA---
....(((((((.....((((.(((.....-...)))))))....((.....)))))))))....--- ( -11.10, z-score =  -2.59, R)
>droEre2.scaffold_4929 9345971 62 - 26641161
ACAACCAUUAGACCAUGGCUCAUUAAAUC--AAAAUAGUCUGCUCCAUUUUGGCUAAUGGACAA---
....(((((((.(((.(((..((((....--....))))..)))......))))))))))....--- ( -14.30, z-score =  -2.46, R)
>droAna3.scaffold_12916 10398938 64 - 16180835
AAAUCCAUUAUUUGAGGGCUCAUUAAAUGGAAAAAUGGCCUACUCCAUUUUGGCUAAUGGACAA---
...(((((((.....((((.((((.........))))))))...((.....)).)))))))...--- ( -14.00, z-score =  -0.94, R)
>dp4.chr4_group5 1544021 63 + 2436548
AAAUCCAUUAGACCAUGGCUCAUUAAAUC-AAAAAUAGCCUGCUCCAUUUUGGCUAAUGGACAA---
...((((((((.(((.((((.(((.....-...)))))))..........)))))))))))...--- ( -16.80, z-score =  -3.11, R)
>droPer1.super_5 1512994 63 + 6813705
AAAUCCAUUAGACCAUGGCUCAUUAAAUC-AAAAAUAGCCUGCUCCAUUUUGGCUAAUGGACAA---
...((((((((.(((.((((.(((.....-...)))))))..........)))))))))))...--- ( -16.80, z-score =  -3.11, R)
>droWil1.scaffold_180772 48724 62 - 8906247
AAAUCCAUUAGUCCAUGGCUCAUUAAAUC-AAAAAUAGCCUGCUCCAUUUU-ACUAAUGGACAA---
...(((((((((.((.((((.(((.....-...))))))))).........-)))))))))...--- ( -13.10, z-score =  -3.15, R)
>droVir3.scaffold_12723 4753220 61 - 5802038
AAAUCCAUUAGUCUCUGGCUCAUUAAAUC-AGAAAUAGCCUGCUCCAUUUU-GCUAAUGGACA----
...(((((((((....((((.(((.....-...)))))))...........-)))))))))..---- ( -13.26, z-score =  -1.90, R)
>droMoj3.scaffold_6500 10721235 65 - 32352404
AAAUCCAUUAGACUAUGGCUCAUUAAAUC-AAAAAUAGCCUGCUCCAUUUC-GCUAAUGGACAGCCG
...((((((((...((((..((.......-..........))..))))...-.))))))))...... ( -12.63, z-score =  -1.96, R)
>droGri2.scaffold_15126 7754172 60 - 8399593
AAAUCCAUUAGUCUAUGGCUCAUUAAAUC-AAAAAUAGCCUGCUCCAUUU--GCUAAUGGACA----
...(((((((((..((((..((.......-..........))..))))..--)))))))))..---- ( -15.13, z-score =  -3.31, R)
>consensus
AAAUCCAUUAGACCAUGGCUCAUUAAAUC_AAAAAUAGCCUGCUCCAUUUUGGCUAAUGGACAA___
....(((((((.....((((.(((.........))))))).............)))))))....... ( -8.16 =  -8.01 +  -0.15)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:26:53 2011