Locus 6843

Sequence ID dm3.chr3L
Location 10,217,130 – 10,217,281
Length 151
Max. P 0.896756
window9407 window9408 window9409 window9410

overview

Window 7

Location 10,217,130 – 10,217,241
Length 111
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 69.82
Shannon entropy 0.55172
G+C content 0.64021
Mean single sequence MFE -47.44
Consensus MFE -21.96
Energy contribution -24.20
Covariance contribution 2.24
Combinations/Pair 1.33
Mean z-score -1.23
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.09
SVM RNA-class probability 0.536519
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 10217130 111 + 24543557
CGGUGGUGCUCCUCCUCCGUAGUGUGGCUGUCCACCAGGACCACCUACAUAAGGUGGCUGUCCGCCUGGACCACCCGCAUAAGGUGGCUGACCACCUGGACCACCCAUGUA
.((((((.(............((((((..(((((...(((((((((.....))))))...)))...)))))...)))))).((((((....))))))).))))))...... ( -48.00, z-score =  -1.82, R)
>droSim1.chr3L 9606247 111 + 22553184
UGGUGGUGCUCCUCCUCCGUAGGGCGGCUGUCCACCAGGACCACCCACAUAAGGUGGCUGUCCGCCUGGACCACCCGCAUACGGGGGCUGACCACCUGGUCCACCCAUGUA
.((((((.(....((((((((..((((..(((((...((((...((((.....))))..))))...)))))...)))).))))))))..)))))))(((.....))).... ( -50.70, z-score =  -0.97, R)
>droSec1.super_0 2432437 111 + 21120651
UGGUGGUGCUCCUCCUCCGUAGGGCGGCUGUCCACCAGGACCACCCACAUAAGGUGGCUGUCCGCCUGGACCACCCGCAUACGGGGGCUGACCACCUGGACCACCCAUGUA
.((((((..((..((((((((..((((..(((((...((((...((((.....))))..))))...)))))...)))).))))))))..))((....))))))))...... ( -51.40, z-score =  -1.27, R)
>droEre2.scaffold_4784 10205976 99 + 25762168
AGGUGGUGCUCCUCCUCCGUAGGGUGGCUGUCCACCGGGACCACCUCCAUAAGGUGG------------AGCACCCGCAUAAGGUGGCUGGCCACCUGGACCACCCACGUA
.(((((((((((.(((.....((((((...(((....))))))))).....))).))------------))))))......((((((....))))))..)))......... ( -45.90, z-score =  -1.08, R)
>droGri2.scaffold_15110 11899280 102 - 24565398
CGGCUGAGGUCCUGGUCCAUAUGCUUGCGGCGGACCAGCUGGUCCUGGCGGAUACUCAAAUGAAUGUGGAGCACCACUACCAGC--GCCAGC-GCCUGCGCCAAA------
.(((..((((..((((((...((....))..))))))((((((.((((.......((....))..((((....))))..)))).--))))))-))))..)))...------ ( -41.20, z-score =  -1.02, R)
>consensus
CGGUGGUGCUCCUCCUCCGUAGGGUGGCUGUCCACCAGGACCACCUACAUAAGGUGGCUGUCCGCCUGGACCACCCGCAUAAGGGGGCUGACCACCUGGACCACCCAUGUA
.((((((...((.(((.....((((((..((((....))))..........((((((....))))))...)))))).....))).))...))))))............... (-21.96 = -24.20 +   2.24)

alignment

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secondary structure

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dotplot

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Window 8

Location 10,217,130 – 10,217,241
Length 111
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 69.82
Shannon entropy 0.55172
G+C content 0.64021
Mean single sequence MFE -49.80
Consensus MFE -28.84
Energy contribution -31.56
Covariance contribution 2.72
Combinations/Pair 1.26
Mean z-score -1.24
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.13
SVM RNA-class probability 0.896756
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 10217130 111 - 24543557
UACAUGGGUGGUCCAGGUGGUCAGCCACCUUAUGCGGGUGGUCCAGGCGGACAGCCACCUUAUGUAGGUGGUCCUGGUGGACAGCCACACUACGGAGGAGGAGCACCACCG
......((((((..((((((....))))))...((.(((.((((....)))).))).((((.((((((((((((....))...))))).)))))...)))).)))))))). ( -51.20, z-score =  -1.69, R)
>droSim1.chr3L 9606247 111 - 22553184
UACAUGGGUGGACCAGGUGGUCAGCCCCCGUAUGCGGGUGGUCCAGGCGGACAGCCACCUUAUGUGGGUGGUCCUGGUGGACAGCCGCCCUACGGAGGAGGAGCACCACCA
((((((((((((((((((.....)))((((....)))))))))))(((.....)))..))))))))((((.(((((((((....)))))(....)...)))).)))).... ( -53.30, z-score =  -0.83, R)
>droSec1.super_0 2432437 111 - 21120651
UACAUGGGUGGUCCAGGUGGUCAGCCCCCGUAUGCGGGUGGUCCAGGCGGACAGCCACCUUAUGUGGGUGGUCCUGGUGGACAGCCGCCCUACGGAGGAGGAGCACCACCA
......((((.(((.(((.(((.(((((((....)))).)))(((((......(((((((.....))))))))))))..))).))).(((....).)).))).)))).... ( -52.50, z-score =  -0.52, R)
>droEre2.scaffold_4784 10205976 99 - 25762168
UACGUGGGUGGUCCAGGUGGCCAGCCACCUUAUGCGGGUGCU------------CCACCUUAUGGAGGUGGUCCCGGUGGACAGCCACCCUACGGAGGAGGAGCACCACCU
...((((.(((((.....))))).)))).....(..((((((------------((.((((.(((.((((((((....))...)))))))))..)))).))))))))..). ( -48.90, z-score =  -1.59, R)
>droGri2.scaffold_15110 11899280 102 + 24565398
------UUUGGCGCAGGC-GCUGGC--GCUGGUAGUGGUGCUCCACAUUCAUUUGAGUAUCCGCCAGGACCAGCUGGUCCGCCGCAAGCAUAUGGACCAGGACCUCAGCCG
------...(((..((((-((((((--.(((((.((((....))))((((....))))....)))))).)))))(((((((.(....)....))))))).).)))..))). ( -43.10, z-score =  -1.58, R)
>consensus
UACAUGGGUGGUCCAGGUGGUCAGCCACCUUAUGCGGGUGGUCCAGGCGGACAGCCACCUUAUGUAGGUGGUCCUGGUGGACAGCCACCCUACGGAGGAGGAGCACCACCA
....(((.....)))((((((...((.((((....((((((((((((......(((((((.....))))))))))))......)))))))....)))).))...)))))). (-28.84 = -31.56 +   2.72)

alignment

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secondary structure

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dotplot

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Window 9

Location 10,217,170 – 10,217,281
Length 111
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 69.73
Shannon entropy 0.55283
G+C content 0.62015
Mean single sequence MFE -42.92
Consensus MFE -22.36
Energy contribution -26.20
Covariance contribution 3.84
Combinations/Pair 1.31
Mean z-score -1.09
Structure conservation index 0.52
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.37
SVM RNA-class probability 0.664502
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 10217170 111 + 24543557
CCACCUACAUAAGGUGGCUGUCCGCCUGGACCACCCGCAUAAGGUGGCUGACCACCUGGACCACCCAUGUAAGGUGGUUGUCCGGCUCCGUAGGGCGGAGCUUCUCCGUAU
...(((((...((((((....))))))(((((.........((((((....)))))).(((((((.......)))))))....)).))))))))((((((...)))))).. ( -49.30, z-score =  -2.15, R)
>droSim1.chr3L 9606287 111 + 22553184
CCACCCACAUAAGGUGGCUGUCCGCCUGGACCACCCGCAUACGGGGGCUGACCACCUGGUCCACCCAUGUAAGGUGGUUGUCCGGCCCCGUAGGGCGGAGCUUCUCCGUAC
(((((.......)))))...(((((((((.....))...(((((((.((((((((((((....))......)))))))))...).))))))))))))))............ ( -46.30, z-score =  -0.10, R)
>droSec1.super_0 2432477 111 + 21120651
CCACCCACAUAAGGUGGCUGUCCGCCUGGACCACCCGCAUACGGGGGCUGACCACCUGGACCACCCAUGUAAGGUGGUUGUCCGGCUCCGUAGGGCGGAGCUUCUCCGUAC
(((((.......)))))..((((....))))........(((((((((.((((((((..((.......)).))))))))))))(((((((.....)))))))...))))). ( -47.40, z-score =  -0.69, R)
>droEre2.scaffold_4784 10206016 99 + 25762168
CCACCUCCAUAAGGU------------GGAGCACCCGCAUAAGGUGGCUGGCCACCUGGACCACCCACGUAAGGUGGUUGUCCGGCUCCGUAGGGCUGAGCUUCUCCGUAC
((((((.....))))------------))(((.((..(...((((((....))))))((((.(((..(....)..))).))))......)..))))).............. ( -39.40, z-score =  -0.71, R)
>droGri2.scaffold_15110 11899320 99 - 24565398
--GGUCCUGGCGGAUACUCAAAUGAAUGUGGAGCACCACUACCAGCGCCAGC-GCCUGCGCCA------AAAGGUGCUGAUCCACCGCCAUAA---UAGACAUCUCCGUAA
--.(((.((((((..............((((....))))...(((((((.((-(....)))..------...))))))).....))))))...---..))).......... ( -32.20, z-score =  -1.79, R)
>consensus
CCACCCACAUAAGGUGGCUGUCCGCCUGGACCACCCGCAUACGGGGGCUGACCACCUGGACCACCCAUGUAAGGUGGUUGUCCGGCUCCGUAGGGCGGAGCUUCUCCGUAC
((((((.....))))))...(((((((((.....)).......((((((((((((((..............)))))))....)))))))...)))))))............ (-22.36 = -26.20 +   3.84)

alignment

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secondary structure

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dotplot

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Window 0

Location 10,217,170 – 10,217,281
Length 111
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 69.73
Shannon entropy 0.55283
G+C content 0.62015
Mean single sequence MFE -46.20
Consensus MFE -21.12
Energy contribution -23.64
Covariance contribution 2.52
Combinations/Pair 1.33
Mean z-score -1.24
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.12
SVM RNA-class probability 0.551746
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 10217170 111 - 24543557
AUACGGAGAAGCUCCGCCCUACGGAGCCGGACAACCACCUUACAUGGGUGGUCCAGGUGGUCAGCCACCUUAUGCGGGUGGUCCAGGCGGACAGCCACCUUAUGUAGGUGG
..........((((((.....)))))).......((((((.(((((((((((((((((((....)))))).....))...((((....)))).)))))).))))))))))) ( -49.80, z-score =  -1.98, R)
>droSim1.chr3L 9606287 111 - 22553184
GUACGGAGAAGCUCCGCCCUACGGGGCCGGACAACCACCUUACAUGGGUGGACCAGGUGGUCAGCCCCCGUAUGCGGGUGGUCCAGGCGGACAGCCACCUUAUGUGGGUGG
((.(((((...))))((((....)))).).))..((((((.(((((((((((((((((.....)))((((....)))))))))))(((.....)))..))))))))))))) ( -55.60, z-score =  -1.84, R)
>droSec1.super_0 2432477 111 - 21120651
GUACGGAGAAGCUCCGCCCUACGGAGCCGGACAACCACCUUACAUGGGUGGUCCAGGUGGUCAGCCCCCGUAUGCGGGUGGUCCAGGCGGACAGCCACCUUAUGUGGGUGG
((.((.....((((((.....)))))))).))..((((((.(((((((((((((...(((...(((((((....)))).))))))...))...)))))).))))))))))) ( -48.60, z-score =  -0.51, R)
>droEre2.scaffold_4784 10206016 99 - 25762168
GUACGGAGAAGCUCAGCCCUACGGAGCCGGACAACCACCUUACGUGGGUGGUCCAGGUGGCCAGCCACCUUAUGCGGGUGCUCC------------ACCUUAUGGAGGUGG
(((((((...(..(.((.(....).)).)..)..((((((.....)))))))))((((((....)))))).......)))).((------------(((((...))))))) ( -39.60, z-score =  -0.42, R)
>droGri2.scaffold_15110 11899320 99 + 24565398
UUACGGAGAUGUCUA---UUAUGGCGGUGGAUCAGCACCUUU------UGGCGCAGGC-GCUGGCGCUGGUAGUGGUGCUCCACAUUCAUUUGAGUAUCCGCCAGGACC--
..........((((.---...((((((((((...(((((..(------..((((....-....))))..)....))))))))))((((....))))...))))))))).-- ( -37.40, z-score =  -1.47, R)
>consensus
GUACGGAGAAGCUCCGCCCUACGGAGCCGGACAACCACCUUACAUGGGUGGUCCAGGUGGUCAGCCCCCGUAUGCGGGUGGUCCAGGCGGACAGCCACCUUAUGUGGGUGG
((((((....((((((.....)))))).(((...((((((.....))))))))).(((.....))).))))))..(((...)))..........((((((.....)))))) (-21.12 = -23.64 +   2.52)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:15:27 2011