Locus 6861

Sequence ID dm3.chr3L
Location 10,310,284 – 10,310,417
Length 133
Max. P 0.986492
window9436 window9437 window9438 window9439

overview

Window 6

Location 10,310,284 – 10,310,382
Length 98
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 84.15
Shannon entropy 0.27998
G+C content 0.45065
Mean single sequence MFE -22.57
Consensus MFE -12.35
Energy contribution -13.02
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.39
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.47
SVM RNA-class probability 0.707372
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 10310284 98 + 24543557
AUCCAUCAUCCCAUCCAGUUUUUCAGU--------GCCAAUUCCAGUUUUCUGGCCCAAUGUGGGCAGUUCUUCCUCAGUA---AAACUGGCACAGAAGAAAAAAAAAG
..................((((((.((--------((((....(((....)))((((.....))))...............---....)))))).))))))........ ( -24.00, z-score =  -2.78, R)
>droSim1.chr3L 9700329 93 + 22553184
AUCCAUCAUCCCAUCCAGUUUUUCAGU--------GCCAGUUCCAGUUUUCUGUCCCAAUGUGGGCAGUUCUUCCUCAGUA---AAACUAGCAAAGAAAAAAAG-----
..................((((((..(--------((.((((........((((((......)))))).............---.)))).)))..))))))...----- ( -15.85, z-score =  -2.61, R)
>droSec1.super_0 2524158 95 + 21120651
AUCCAUCAUCCCAUCCAGUUUUACAGU--------GCCAGUUCCAGUUUUCUGGCCCAAUGUGGGCAGUUCUUCCUCAGUU---AAACUGGCACAGAAAAAAAACG---
.................(((((...((--------(((((((.(((....)))((((.....))))...............---.)))))))))......))))).--- ( -25.40, z-score =  -3.47, R)
>droYak2.chr3L 10299511 103 + 24197627
AUCCAUCAUCCCGUCCAGUUUUUCAGUUUUUCAGUGCCAGUUCCAGUUUUCUGGCCCAAUGUGGGCAGUUCUUCCUCAGUA---AAAGUGGCACAGGAAAAAACAG---
..........................((((((.((((((.((.(((....)))((((.....))))...............---.)).)))))).)))))).....--- ( -24.20, z-score =  -2.36, R)
>droEre2.scaffold_4784 10303524 93 + 25762168
AUCCAUCAUCCCGUCCAGUUUUUCAGU--------GCCAGUACCAGUUUUCUGGCCCAAUGUGGGCAGUUCUUCCUCAGUG---AAACUGGCACAGGAAAAAAG-----
..................((((((.((--------((((((..(((....)))((((.....))))...............---..)))))))).))))))...----- ( -27.80, z-score =  -2.94, R)
>droAna3.scaffold_13337 15231051 95 + 23293914
AUCCAUCAUCCCGUCCAGUUUCAGAGU--------UCCAGUUCCAGUUU-CUGGCCCGAUGUGGGCAGAACUUCCUCACCAUAAAAAAUGGCACAAAAAAAUGG-----
..((((.................(((.--------...((((((((...-)))((((.....)))).)))))..))).((((.....)))).........))))----- ( -18.20, z-score =  -0.17, R)
>consensus
AUCCAUCAUCCCAUCCAGUUUUUCAGU________GCCAGUUCCAGUUUUCUGGCCCAAUGUGGGCAGUUCUUCCUCAGUA___AAACUGGCACAGAAAAAAAG_____
..............(((((((......................(((....)))((((.....))))..................))))))).................. (-12.35 = -13.02 +   0.67)

alignment

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secondary structure

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dotplot

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Window 7

Location 10,310,284 – 10,310,382
Length 98
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 84.15
Shannon entropy 0.27998
G+C content 0.45065
Mean single sequence MFE -27.13
Consensus MFE -18.72
Energy contribution -18.72
Covariance contribution 0.00
Combinations/Pair 1.20
Mean z-score -2.00
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.74
SVM RNA-class probability 0.802319
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 10310284 98 - 24543557
CUUUUUUUUUCUUCUGUGCCAGUUU---UACUGAGGAAGAACUGCCCACAUUGGGCCAGAAAACUGGAAUUGGC--------ACUGAAAAACUGGAUGGGAUGAUGGAU
.....((((((....((((((((((---(((((((......))((((.....))))))).....))))))))))--------)).)))))).................. ( -26.30, z-score =  -1.39, R)
>droSim1.chr3L 9700329 93 - 22553184
-----CUUUUUUUCUUUGCUAGUUU---UACUGAGGAAGAACUGCCCACAUUGGGACAGAAAACUGGAACUGGC--------ACUGAAAAACUGGAUGGGAUGAUGGAU
-----(..((((((..(((((((((---((((.....))..((((((.....))).))).....))))))))))--------)..))))))..)............... ( -25.30, z-score =  -3.25, R)
>droSec1.super_0 2524158 95 - 21120651
---CGUUUUUUUUCUGUGCCAGUUU---AACUGAGGAAGAACUGCCCACAUUGGGCCAGAAAACUGGAACUGGC--------ACUGUAAAACUGGAUGGGAUGAUGGAU
---(((((.(((((.((((((((((---...............((((.....))))(((....)))))))))))--------)).).))))..)))))........... ( -27.90, z-score =  -2.00, R)
>droYak2.chr3L 10299511 103 - 24197627
---CUGUUUUUUCCUGUGCCACUUU---UACUGAGGAAGAACUGCCCACAUUGGGCCAGAAAACUGGAACUGGCACUGAAAAACUGAAAAACUGGACGGGAUGAUGGAU
---(((((...((((((.(((.(((---(..((.((........))))..(..((((((..........))))).)..)........)))).))))))))).))))).. ( -25.00, z-score =  -1.49, R)
>droEre2.scaffold_4784 10303524 93 - 25762168
-----CUUUUUUCCUGUGCCAGUUU---CACUGAGGAAGAACUGCCCACAUUGGGCCAGAAAACUGGUACUGGC--------ACUGAAAAACUGGACGGGAUGAUGGAU
-----((.((.((((((.(((((((---((.((....((.((.((((.....))))(((....))))).))..)--------).)))..)))))))))))).)).)).. ( -29.40, z-score =  -2.14, R)
>droAna3.scaffold_13337 15231051 95 - 23293914
-----CCAUUUUUUUGUGCCAUUUUUUAUGGUGAGGAAGUUCUGCCCACAUCGGGCCAG-AAACUGGAACUGGA--------ACUCUGAAACUGGACGGGAUGAUGGAU
-----(((((.(((((((((((.....)))))(((..(((((.((((.....))))(((-...))))))))...--------.))).........)))))).))))).. ( -28.90, z-score =  -1.74, R)
>consensus
_____CUUUUUUUCUGUGCCAGUUU___UACUGAGGAAGAACUGCCCACAUUGGGCCAGAAAACUGGAACUGGC________ACUGAAAAACUGGACGGGAUGAUGGAU
...........((((((.(((((((..................((((.....))))(((....)))......................)))))))))))))........ (-18.72 = -18.72 +   0.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 10,310,315 – 10,310,417
Length 102
Sequences 7
Columns 105
Reading direction forward
Mean pairwise identity 76.75
Shannon entropy 0.46522
G+C content 0.45132
Mean single sequence MFE -26.42
Consensus MFE -14.65
Energy contribution -16.83
Covariance contribution 2.19
Combinations/Pair 1.21
Mean z-score -1.46
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.47
SVM RNA-class probability 0.709930
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 10310315 102 + 24543557
AUUCCAGUUUUCUGGCCCAAUGUGGGCAGUUCUUCCUCAGUA---AAACUGGCACAGAAGAAAAAAAAAGCCAAUGGAAACUGGACAAAUGAGCGACAAAACUGG
..((((((((((..((((.....))))..((((((.((((..---...))))....)))))).............)))))))))).................... ( -28.60, z-score =  -1.83, R)
>droSim1.chr3L 9700360 97 + 22553184
GUUCCAGUUUUCUGUCCCAAUGUGGGCAGUUCUUCCUCAGUA---AAACUAGCAAAG-----AAAAAAAGGCAAAGGAAACUGGACAAAUGAGCGACAAAACUGG
...((((((((((((((......))))))....((((((...---......((....-----........))..((....)).......)))).)).)))))))) ( -22.50, z-score =  -0.77, R)
>droSec1.super_0 2524189 99 + 21120651
GUUCCAGUUUUCUGGCCCAAUGUGGGCAGUUCUUCCUCAGUU---AAACUGGCACAG---AAAAAAAACGCCAAAGGAAACUGGACAAAUGAGCGACAAAACUGG
...((((((((...((((.....)))).((((.(((......---....((((....---.........)))).((....))))).....))))...)))))))) ( -27.72, z-score =  -1.48, R)
>droYak2.chr3L 10299550 99 + 24197627
GUUCCAGUUUUCUGGCCCAAUGUGGGCAGUUCUUCCUCAGUA---AAAGUGGCACAG---GAAAAAACAGCCAAAGGAAACUGGACAAAUGAGCGACAAAACUGG
...((((((((...((((.....)))).((((.(((......---....((((....---.........)))).((....))))).....))))...)))))))) ( -27.82, z-score =  -1.06, R)
>droEre2.scaffold_4784 10303555 97 + 25762168
GUACCAGUUUUCUGGCCCAAUGUGGGCAGUUCUUCCUCAGUG---AAACUGGCACAG-----GAAAAAAGCCAAAGGAAACUGGACAAAUGAGCGACAAAACUGG
...((((((((...((((.....)))).((((((((((((..---...)))....))-----)))....((((..(....)))).)....))))...)))))))) ( -29.00, z-score =  -1.48, R)
>droAna3.scaffold_13337 15231082 99 + 23293914
GUUCCAGUUU-CUGGCCCGAUGUGGGCAGAACUUCCUCACCAUAAAAAAUGGCACAA-----AAAAAUGGUUAAAGGAAACUGGACAAAUUGGCCAUAAAACUGG
...(((((((-.(((((.(((.((..(((...(((((.(((((..............-----....)))))...))))).)))..)).))))))))..))))))) ( -28.47, z-score =  -2.15, R)
>droGri2.scaffold_15110 11990408 80 - 24565398
-UUGCAGUCGCCUG--CCAAAGCCAGUAAG-----CUCAUCA----AAAUGGCAAAC------------GGCAAGCAACUGCCUACAAAUGAGCUACAAACGAG-
-..(((((.((.((--((...((((.....-----.......----...))))....------------)))).)).)))))......................- ( -20.86, z-score =  -1.42, R)
>consensus
GUUCCAGUUUUCUGGCCCAAUGUGGGCAGUUCUUCCUCAGUA___AAACUGGCACAG_____AAAAAAAGCCAAAGGAAACUGGACAAAUGAGCGACAAAACUGG
..(((((((((((.((((.....))))......................((((................)))).))))))))))).................... (-14.65 = -16.83 +   2.19)

alignment

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secondary structure

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dotplot

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Window 9

Location 10,310,315 – 10,310,417
Length 102
Sequences 7
Columns 105
Reading direction reverse
Mean pairwise identity 76.75
Shannon entropy 0.46522
G+C content 0.45132
Mean single sequence MFE -30.57
Consensus MFE -16.27
Energy contribution -18.30
Covariance contribution 2.03
Combinations/Pair 1.31
Mean z-score -2.48
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.24
SVM RNA-class probability 0.986492
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 10310315 102 - 24543557
CCAGUUUUGUCGCUCAUUUGUCCAGUUUCCAUUGGCUUUUUUUUUCUUCUGUGCCAGUUU---UACUGAGGAAGAACUGCCCACAUUGGGCCAGAAAACUGGAAU
((((((((.(.(((((..((..((((((((((((((................))))))..---......)))..)))))..))...))))).).))))))))... ( -30.79, z-score =  -2.28, R)
>droSim1.chr3L 9700360 97 - 22553184
CCAGUUUUGUCGCUCAUUUGUCCAGUUUCCUUUGCCUUUUUUU-----CUUUGCUAGUUU---UACUGAGGAAGAACUGCCCACAUUGGGACAGAAAACUGGAAC
....................((((((((.............((-----((((..(((...---..)))..))))))((((((.....))).))).)))))))).. ( -23.10, z-score =  -0.77, R)
>droSec1.super_0 2524189 99 - 21120651
CCAGUUUUGUCGCUCAUUUGUCCAGUUUCCUUUGGCGUUUUUUUU---CUGUGCCAGUUU---AACUGAGGAAGAACUGCCCACAUUGGGCCAGAAAACUGGAAC
((((((((.(.(((((..((..(((((((((((((((........---...)))))....---....)))))..)))))..))...))))).).))))))))... ( -31.90, z-score =  -2.52, R)
>droYak2.chr3L 10299550 99 - 24197627
CCAGUUUUGUCGCUCAUUUGUCCAGUUUCCUUUGGCUGUUUUUUC---CUGUGCCACUUU---UACUGAGGAAGAACUGCCCACAUUGGGCCAGAAAACUGGAAC
((((((((.(.(((((..((..((((((((((((((.........---....))))....---....)))))..)))))..))...))))).).))))))))... ( -31.92, z-score =  -2.66, R)
>droEre2.scaffold_4784 10303555 97 - 25762168
CCAGUUUUGUCGCUCAUUUGUCCAGUUUCCUUUGGCUUUUUUC-----CUGUGCCAGUUU---CACUGAGGAAGAACUGCCCACAUUGGGCCAGAAAACUGGUAC
((((((((.(.(((((..((..((((((((((((((.......-----....))))....---....)))))..)))))..))...))))).).))))))))... ( -31.60, z-score =  -2.53, R)
>droAna3.scaffold_13337 15231082 99 - 23293914
CCAGUUUUAUGGCCAAUUUGUCCAGUUUCCUUUAACCAUUUUU-----UUGUGCCAUUUUUUAUGGUGAGGAAGUUCUGCCCACAUCGGGCCAG-AAACUGGAAC
((((((((.(((((....((..((((((((((..(((((....-----..............))))))))))))..)))..)).....))))))-)))))))... ( -32.47, z-score =  -3.47, R)
>droGri2.scaffold_15110 11990408 80 + 24565398
-CUCGUUUGUAGCUCAUUUGUAGGCAGUUGCUUGCC------------GUUUGCCAUUU----UGAUGAG-----CUUACUGGCUUUGG--CAGGCGACUGCAA-
-((((..((.....))..)).))(((((((((((((------------(...((((.(.----.(.....-----)..).))))..)))--)))))))))))..- ( -32.20, z-score =  -3.13, R)
>consensus
CCAGUUUUGUCGCUCAUUUGUCCAGUUUCCUUUGGCUUUUUUU_____CUGUGCCAGUUU___UACUGAGGAAGAACUGCCCACAUUGGGCCAGAAAACUGGAAC
((((((((.(.(((((..((..(((((((((.......................((((......)))))))))..))))..))...))))).).))))))))... (-16.27 = -18.30 +   2.03)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:15:50 2011