Locus 10820

Sequence ID dm3.chr3R
Location 16,716,412 – 16,716,492
Length 80
Max. P 0.993881
window14867 window14868

overview

Window 7

Location 16,716,412 – 16,716,492
Length 80
Sequences 12
Columns 82
Reading direction forward
Mean pairwise identity 90.31
Shannon entropy 0.21949
G+C content 0.53328
Mean single sequence MFE -26.75
Consensus MFE -25.29
Energy contribution -25.24
Covariance contribution -0.05
Combinations/Pair 1.14
Mean z-score -2.08
Structure conservation index 0.95
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.16
SVM RNA-class probability 0.984252
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 16716412 80 + 27905053
AAACGUAGCCUCUUUAGCUCAGUGG--UAGAGCGUUGGUCUCGUAAACCAAAGGCCGUGAGUUCAACCCUCACAGGAGGCAA
.......(((((((..((((.....--..))))...(((((..........)))))(((((.......)))))))))))).. ( -26.80, z-score =  -2.32, R)
>droEre2.scaffold_4770 12805069 80 - 17746568
GAACAUAGCCUCUUUAGCUCAGUGG--UAGAGCGUUGGUCUCGUAAACCAAAGGCCGUGAGUUCAACCCUCACAGGAGGCAG
.......(((((((..((((.....--..))))...(((((..........)))))(((((.......)))))))))))).. ( -26.80, z-score =  -2.36, R)
>droYak2.chr3R 5519529 80 + 28832112
GAACGUAGCCUCUUUAGCUCAGUGG--UAGAGCGUUGGUCUCGUAAACCAAAGGCCGUGAGUUCAACCCUCACAGGAGGCAG
.......(((((((..((((.....--..))))...(((((..........)))))(((((.......)))))))))))).. ( -26.80, z-score =  -2.05, R)
>droSec1.super_27 781363 80 - 799419
GAACGUAGCCUCUUUAGCUCAGUGG--UAGAGCGUUGGUCUCGUAAACCAAAGGCCGUGAGUUCAACCCUCACAGGAGGCAA
.......(((((((..((((.....--..))))...(((((..........)))))(((((.......)))))))))))).. ( -26.80, z-score =  -2.05, R)
>droSim1.chr3R 22773074 80 - 27517382
GAACGUAGCCUCUUUAGCUCAGUGG--UAGAGCGUUGGUCUCGUAAACCAAAGGCCGUGAGUUCAACCCUCACAGGAGGCAA
.......(((((((..((((.....--..))))...(((((..........)))))(((((.......)))))))))))).. ( -26.80, z-score =  -2.05, R)
>dp4.chr2 18068658 80 - 30794189
CCACGAAGCCUCUUUAGCUCAGUGG--UAGAGCGUUGGUCUCGUAAACCAAAGGCCGUGAGUUCAACCCUCACAGGAGGCAA
.......(((((((..((((.....--..))))...(((((..........)))))(((((.......)))))))))))).. ( -26.80, z-score =  -2.04, R)
>droPer1.super_0 7732505 80 + 11822988
CCACGAAGCCUCUUUAGCUCAGUGG--UAGAGCGUUGGUCUCGUAAACCAAAGGCCGUGAGUUCAACCCUCACAGGAGGCAA
.......(((((((..((((.....--..))))...(((((..........)))))(((((.......)))))))))))).. ( -26.80, z-score =  -2.04, R)
>droAna3.scaffold_13340 7979136 80 + 23697760
CGUCGAAGCCUCUUUAGCUCAGUGG--UAGAGCGUUGGUCUCGUAAACCAAAGGCCGUGAGUUCAACCCUCACAGGAGGCAA
.......(((((((..((((.....--..))))...(((((..........)))))(((((.......)))))))))))).. ( -26.80, z-score =  -2.03, R)
>droVir3.scaffold_12822 447802 80 + 4096053
UCUCAUCGCCUCUUUAGCUCAGUGG--UAGAGCGUUGGUCUCGUAAACCAAAGGCCGUGAGUUCAACCCUCACAGGAGGCAG
.......(((((((..((((.....--..))))...(((((..........)))))(((((.......)))))))))))).. ( -26.90, z-score =  -2.53, R)
>droMoj3.scaffold_6540 33090018 80 + 34148556
ACGCAUCGCCUCUUUAGCUCAGUGG--UAGAGCGUUGGUCUCGUAAACCAAAGGCCGUGAGUUCAACCCUCACAGGAGGCAG
.......(((((((..((((.....--..))))...(((((..........)))))(((((.......)))))))))))).. ( -26.90, z-score =  -2.08, R)
>droGri2.scaffold_15074 4392423 80 - 7742996
UCGCAUCGCCUCUUUAGCUCAGUGG--UAGAGCGUUGGUCUCGUAAACCAAAGGCCGUGAGUUCAACCCUCACAGGAGGCAG
.......(((((((..((((.....--..))))...(((((..........)))))(((((.......)))))))))))).. ( -26.90, z-score =  -2.24, R)
>anoGam1.chr2R 13947725 82 - 62725911
AACUAUAGGCCCCAUAGCUCAGCUGGUUAGAGCGUCGUGCUAAUAACGCGAAGGUCGUGAGUUCGAUCCUCUCUGGAGCCAA
.......(((.(((((((...))))...((((.((((.(((....((((....).))).))).)))).)))).))).))).. ( -25.90, z-score =  -1.16, R)
>consensus
GAACGUAGCCUCUUUAGCUCAGUGG__UAGAGCGUUGGUCUCGUAAACCAAAGGCCGUGAGUUCAACCCUCACAGGAGGCAA
.......(((((((..((((.........))))...(((((..........)))))(((((.......)))))))))))).. (-25.29 = -25.24 +  -0.05)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 16,716,412 – 16,716,492
Length 80
Sequences 12
Columns 82
Reading direction reverse
Mean pairwise identity 90.31
Shannon entropy 0.21949
G+C content 0.53328
Mean single sequence MFE -28.32
Consensus MFE -27.17
Energy contribution -26.97
Covariance contribution -0.20
Combinations/Pair 1.18
Mean z-score -2.46
Structure conservation index 0.96
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.65
SVM RNA-class probability 0.993881
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 16716412 80 - 27905053
UUGCCUCCUGUGAGGGUUGAACUCACGGCCUUUGGUUUACGAGACCAACGCUCUA--CCACUGAGCUAAAGAGGCUACGUUU
..((((((((((((.......)))))))...((((((.....)))))).((((..--.....))))....)))))....... ( -28.40, z-score =  -2.76, R)
>droEre2.scaffold_4770 12805069 80 + 17746568
CUGCCUCCUGUGAGGGUUGAACUCACGGCCUUUGGUUUACGAGACCAACGCUCUA--CCACUGAGCUAAAGAGGCUAUGUUC
..((((((((((((.......)))))))...((((((.....)))))).((((..--.....))))....)))))....... ( -28.40, z-score =  -2.72, R)
>droYak2.chr3R 5519529 80 - 28832112
CUGCCUCCUGUGAGGGUUGAACUCACGGCCUUUGGUUUACGAGACCAACGCUCUA--CCACUGAGCUAAAGAGGCUACGUUC
..((((((((((((.......)))))))...((((((.....)))))).((((..--.....))))....)))))....... ( -28.40, z-score =  -2.54, R)
>droSec1.super_27 781363 80 + 799419
UUGCCUCCUGUGAGGGUUGAACUCACGGCCUUUGGUUUACGAGACCAACGCUCUA--CCACUGAGCUAAAGAGGCUACGUUC
..((((((((((((.......)))))))...((((((.....)))))).((((..--.....))))....)))))....... ( -28.40, z-score =  -2.63, R)
>droSim1.chr3R 22773074 80 + 27517382
UUGCCUCCUGUGAGGGUUGAACUCACGGCCUUUGGUUUACGAGACCAACGCUCUA--CCACUGAGCUAAAGAGGCUACGUUC
..((((((((((((.......)))))))...((((((.....)))))).((((..--.....))))....)))))....... ( -28.40, z-score =  -2.63, R)
>dp4.chr2 18068658 80 + 30794189
UUGCCUCCUGUGAGGGUUGAACUCACGGCCUUUGGUUUACGAGACCAACGCUCUA--CCACUGAGCUAAAGAGGCUUCGUGG
..((((((((((((.......)))))))...((((((.....)))))).((((..--.....))))....)))))....... ( -28.40, z-score =  -2.13, R)
>droPer1.super_0 7732505 80 - 11822988
UUGCCUCCUGUGAGGGUUGAACUCACGGCCUUUGGUUUACGAGACCAACGCUCUA--CCACUGAGCUAAAGAGGCUUCGUGG
..((((((((((((.......)))))))...((((((.....)))))).((((..--.....))))....)))))....... ( -28.40, z-score =  -2.13, R)
>droAna3.scaffold_13340 7979136 80 - 23697760
UUGCCUCCUGUGAGGGUUGAACUCACGGCCUUUGGUUUACGAGACCAACGCUCUA--CCACUGAGCUAAAGAGGCUUCGACG
..((((((((((((.......)))))))...((((((.....)))))).((((..--.....))))....)))))....... ( -28.40, z-score =  -2.74, R)
>droVir3.scaffold_12822 447802 80 - 4096053
CUGCCUCCUGUGAGGGUUGAACUCACGGCCUUUGGUUUACGAGACCAACGCUCUA--CCACUGAGCUAAAGAGGCGAUGAGA
.(((((((((((((.......)))))))...((((((.....)))))).((((..--.....))))....))))))...... ( -29.00, z-score =  -2.78, R)
>droMoj3.scaffold_6540 33090018 80 - 34148556
CUGCCUCCUGUGAGGGUUGAACUCACGGCCUUUGGUUUACGAGACCAACGCUCUA--CCACUGAGCUAAAGAGGCGAUGCGU
.(((((((((((((.......)))))))...((((((.....)))))).((((..--.....))))....))))))...... ( -29.00, z-score =  -2.46, R)
>droGri2.scaffold_15074 4392423 80 + 7742996
CUGCCUCCUGUGAGGGUUGAACUCACGGCCUUUGGUUUACGAGACCAACGCUCUA--CCACUGAGCUAAAGAGGCGAUGCGA
.(((((((((((((.......)))))))...((((((.....)))))).((((..--.....))))....))))))...... ( -29.00, z-score =  -2.65, R)
>anoGam1.chr2R 13947725 82 + 62725911
UUGGCUCCAGAGAGGAUCGAACUCACGACCUUCGCGUUAUUAGCACGACGCUCUAACCAGCUGAGCUAUGGGGCCUAUAGUU
..(((((((..((((.(((......))).))))((.......)).....((((.........))))..)))))))....... ( -25.60, z-score =  -1.38, R)
>consensus
UUGCCUCCUGUGAGGGUUGAACUCACGGCCUUUGGUUUACGAGACCAACGCUCUA__CCACUGAGCUAAAGAGGCUACGUUC
..((((((((((((.......)))))))...((((((.....)))))).((((.........))))....)))))....... (-27.17 = -26.97 +  -0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:31:04 2011