Locus 6037

Sequence ID	dm3.chr3L
Location	3,251,024 – 3,251,104
Length	80
Max. P	0.999242

overview

Window 3

Location	3,251,024 – 3,251,104
Length	80
Sequences	13
Columns	82
Reading direction	forward
Mean pairwise identity	88.54
Shannon entropy	0.27652
G+C content	0.42021
Mean single sequence MFE	-34.82
Consensus MFE	-32.89
Energy contribution	-32.82
Covariance contribution	-0.07
Combinations/Pair	1.04
Mean z-score	-6.36
Structure conservation index	0.94
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.87
SVM RNA-class probability	0.995982
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 3251024 80 + 24543557
UUCCUUCUAAAUCUAGCCUCUACUAGGCUUUGUCUGUGCA-UUCGAAAGCC-GAUCAGACAUAGCCUAUAAGAGGUUAGGUG
..........(((((((((((..((((((.((((((....-.(((.....)-)).)))))).))))))..))))))))))). ( -35.70, z-score =  -6.46, R)
>droGri2.scaffold_15110 607073 82 + 24565398
UUCCUUAUAAAUCUAGCCUCUACUAGGCUUUGUCUGUGCACUUUUUCAAUUCAAUCAGACAUAGCCUAUGAGAGGUUAGGUG
..........(((((((((((..((((((.((((((...................)))))).))))))..))))))))))). ( -33.31, z-score =  -6.50, R)
>droMoj3.scaffold_6680 22800806 80 - 24764193
UUCCUUAUAAAUCUAGCCUCUACUAGGCUUUGUCUGUGCA-UUUGAUAUAA-GAUCAGACAUAGCCUAUGAGAGGUUAGGUG
..........(((((((((((..((((((.((((((...(-(((......)-))))))))).))))))..))))))))))). ( -34.30, z-score =  -5.92, R)
>droVir3.scaffold_12758 61327 80 - 972128
UUCCUUAUAAAUCUAGCCUCUACUAGGCUUUGUCUGUGCA-UUCGAUAUAC-GGUCAGACAUAGCCUAUGAGAGGUUAGGUG
..........(((((((((((..((((((.((((((....-.(((.....)-)).)))))).))))))..))))))))))). ( -35.10, z-score =  -5.90, R)
>droWil1.scaffold_181136 1999691 75 + 2313701
AUCCUUAUAAAUCUAGCCUCUACUAGGCUUUGUCUGUGCA-UUUGG------AUUCAGACAUAGCCUAUGAGAGGUUAGGUG
..........(((((((((((..((((((.((((((..(.-....)------...)))))).))))))..))))))))))). ( -34.30, z-score =  -6.04, R)
>droPer1.super_65 293396 81 - 397436
UGCCUUAUAAAUCUAGCCUCUACUAGGCUUUGUCUGUGCA-UUUGAAAACCCGAUCAGACAUAGCCUAUAAGAGGUUAGGUG
..........(((((((((((..((((((.((((((....-.(((......))).)))))).))))))..))))))))))). ( -33.80, z-score =  -6.19, R)
>dp4.chrXR_group8 5912838 81 - 9212921
UGCCUUAUAAAUCUAGCCUCUACUAGGCUUUGUCUGUGCA-UUUGAAAACCCGAUCAGACAUAGCCUAUAAGAGGUUAGGUG
..........(((((((((((..((((((.((((((....-.(((......))).)))))).))))))..))))))))))). ( -33.80, z-score =  -6.19, R)
>droAna3.scaffold_13337 7556609 80 + 23293914
UUCCUUAUAGAUCUAGCCUCUACUAGGCUUUGUCUGUGCA-UUCGAAAGUC-GAUCAGACAUAGCCUAUAAGAGGUUAGGUG
..........(((((((((((..((((((.((((((....-.(((.....)-)).)))))).))))))..))))))))))). ( -36.40, z-score =  -6.38, R)
>droEre2.scaffold_4784 5933725 80 + 25762168
UUCCUUAUAAAUCUAGCCUCUACUAGGCUUUGUCUGUGCA-UUCAAAAGCC-GAUCAGACAUAGCCUAUAAGAGGUUAGGUG
..........(((((((((((..((((((.((((((.((.-.......)).-...)))))).))))))..))))))))))). ( -35.00, z-score =  -6.79, R)
>droYak2.chr3L 3795941 80 + 24197627
UUCCUUAUAAAUCUAGCCUCUACUAGGCUUUGUCUGUGCA-UACGAAAGCC-GAUCAGACAUAGCCUAUAAGAGGUUAGGUG
..........(((((((((((..((((((.((((((....-..(....)..-...)))))).))))))..))))))))))). ( -35.50, z-score =  -6.50, R)
>droSec1.super_2 3244762 80 + 7591821
UUCCUUUUAAAUCUAGCCUCUACUAGGCUUUGUCUGUGCA-UUCGAAAGCC-GAUCAGACAUAGCCUAUAAGAGGUUAGGUG
..........(((((((((((..((((((.((((((....-.(((.....)-)).)))))).))))))..))))))))))). ( -35.70, z-score =  -6.66, R)
>droSim1.chr3L 2784398 80 + 22553184
UUCCUUUUAAAUCUAGCCUCUACUAGGCUUUGUCUGUGCA-UUCGAAAGCC-GAUCAGACAUAGCCUAUAAGAGGUUAGGUG
..........(((((((((((..((((((.((((((....-.(((.....)-)).)))))).))))))..))))))))))). ( -35.70, z-score =  -6.66, R)
>anoGam1.chr2L 31868088 70 - 48795086
---------AAUCUAGCCUCUUCUAGGCUUUGUCUGUACAGUUUCUG---CAAACCAGACAUAGCCUGUCAGAGGUUAGGUG
---------.(((((((((((..((((((.((((((....((....)---)....)))))).))))))..))))))))))). ( -34.00, z-score =  -6.45, R)
>consensus
UUCCUUAUAAAUCUAGCCUCUACUAGGCUUUGUCUGUGCA_UUCGAAAGCC_GAUCAGACAUAGCCUAUAAGAGGUUAGGUG
..........(((((((((((..((((((.((((((...................)))))).))))))..))))))))))). (-32.89 = -32.82 +  -0.07)

alignment

secondary structure

dotplot

Window 4

Location	3,251,024 – 3,251,104
Length	80
Sequences	13
Columns	82
Reading direction	reverse
Mean pairwise identity	88.54
Shannon entropy	0.27652
G+C content	0.42021
Mean single sequence MFE	-29.04
Consensus MFE	-26.36
Energy contribution	-26.43
Covariance contribution	0.08
Combinations/Pair	1.00
Mean z-score	-4.58
Structure conservation index	0.91
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	3.73
SVM RNA-class probability	0.999242
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 3251024 80 - 24543557
CACCUAACCUCUUAUAGGCUAUGUCUGAUC-GGCUUUCGAA-UGCACAGACAAAGCCUAGUAGAGGCUAGAUUUAGAAGGAA
...(((.(((((..((((((.((((((...-.((.......-.)).)))))).))))))..))))).)))............ ( -30.10, z-score =  -4.31, R)
>droGri2.scaffold_15110 607073 82 - 24565398
CACCUAACCUCUCAUAGGCUAUGUCUGAUUGAAUUGAAAAAGUGCACAGACAAAGCCUAGUAGAGGCUAGAUUUAUAAGGAA
...(((.(((((..((((((.((((((..((..((....))...)))))))).))))))..))))).)))............ ( -29.00, z-score =  -4.87, R)
>droMoj3.scaffold_6680 22800806 80 + 24764193
CACCUAACCUCUCAUAGGCUAUGUCUGAUC-UUAUAUCAAA-UGCACAGACAAAGCCUAGUAGAGGCUAGAUUUAUAAGGAA
...(((.(((((..((((((.((((((...-..........-....)))))).))))))..))))).)))............ ( -26.83, z-score =  -4.32, R)
>droVir3.scaffold_12758 61327 80 + 972128
CACCUAACCUCUCAUAGGCUAUGUCUGACC-GUAUAUCGAA-UGCACAGACAAAGCCUAGUAGAGGCUAGAUUUAUAAGGAA
...(((.(((((..((((((.((((((...-((((.....)-))).)))))).))))))..))))).)))............ ( -29.60, z-score =  -5.08, R)
>droWil1.scaffold_181136 1999691 75 - 2313701
CACCUAACCUCUCAUAGGCUAUGUCUGAAU------CCAAA-UGCACAGACAAAGCCUAGUAGAGGCUAGAUUUAUAAGGAU
...(((.(((((..((((((.((((((...------.....-....)))))).))))))..))))).)))............ ( -27.20, z-score =  -4.87, R)
>droPer1.super_65 293396 81 + 397436
CACCUAACCUCUUAUAGGCUAUGUCUGAUCGGGUUUUCAAA-UGCACAGACAAAGCCUAGUAGAGGCUAGAUUUAUAAGGCA
...(((.(((((..((((((.((((((...(.(((....))-).).)))))).))))))..))))).)))............ ( -27.80, z-score =  -3.78, R)
>dp4.chrXR_group8 5912838 81 + 9212921
CACCUAACCUCUUAUAGGCUAUGUCUGAUCGGGUUUUCAAA-UGCACAGACAAAGCCUAGUAGAGGCUAGAUUUAUAAGGCA
...(((.(((((..((((((.((((((...(.(((....))-).).)))))).))))))..))))).)))............ ( -27.80, z-score =  -3.78, R)
>droAna3.scaffold_13337 7556609 80 - 23293914
CACCUAACCUCUUAUAGGCUAUGUCUGAUC-GACUUUCGAA-UGCACAGACAAAGCCUAGUAGAGGCUAGAUCUAUAAGGAA
...(((.(((((..((((((.((((((.((-(.....))).-....)))))).))))))..))))).)))............ ( -29.10, z-score =  -4.62, R)
>droEre2.scaffold_4784 5933725 80 - 25762168
CACCUAACCUCUUAUAGGCUAUGUCUGAUC-GGCUUUUGAA-UGCACAGACAAAGCCUAGUAGAGGCUAGAUUUAUAAGGAA
...(((.(((((..((((((.((((((...-.((.......-.)).)))))).))))))..))))).)))............ ( -30.10, z-score =  -4.69, R)
>droYak2.chr3L 3795941 80 - 24197627
CACCUAACCUCUUAUAGGCUAUGUCUGAUC-GGCUUUCGUA-UGCACAGACAAAGCCUAGUAGAGGCUAGAUUUAUAAGGAA
...(((.(((((..((((((.((((((...-.((.......-.)).)))))).))))))..))))).)))............ ( -30.10, z-score =  -4.41, R)
>droSec1.super_2 3244762 80 - 7591821
CACCUAACCUCUUAUAGGCUAUGUCUGAUC-GGCUUUCGAA-UGCACAGACAAAGCCUAGUAGAGGCUAGAUUUAAAAGGAA
...(((.(((((..((((((.((((((...-.((.......-.)).)))))).))))))..))))).)))............ ( -30.10, z-score =  -4.74, R)
>droSim1.chr3L 2784398 80 - 22553184
CACCUAACCUCUUAUAGGCUAUGUCUGAUC-GGCUUUCGAA-UGCACAGACAAAGCCUAGUAGAGGCUAGAUUUAAAAGGAA
...(((.(((((..((((((.((((((...-.((.......-.)).)))))).))))))..))))).)))............ ( -30.10, z-score =  -4.74, R)
>anoGam1.chr2L 31868088 70 + 48795086
CACCUAACCUCUGACAGGCUAUGUCUGGUUUG---CAGAAACUGUACAGACAAAGCCUAGAAGAGGCUAGAUU---------
...(((.(((((...(((((.((((((...((---(((...))))))))))).)))))...))))).)))...--------- ( -29.70, z-score =  -5.26, R)
>consensus
CACCUAACCUCUUAUAGGCUAUGUCUGAUC_GGCUUUCGAA_UGCACAGACAAAGCCUAGUAGAGGCUAGAUUUAUAAGGAA
...(((.(((((..((((((.((((((...................)))))).))))))..))))).)))............ (-26.36 = -26.43 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:00:10 2011