Locus 1601

Sequence ID dm3.chr2L
Location 12,373,986 – 12,374,123
Length 137
Max. P 0.921710
window2189 window2190 window2191

overview

Window 9

Location 12,373,986 – 12,374,085
Length 99
Sequences 11
Columns 120
Reading direction forward
Mean pairwise identity 76.11
Shannon entropy 0.44205
G+C content 0.57747
Mean single sequence MFE -26.42
Consensus MFE -13.15
Energy contribution -12.79
Covariance contribution -0.36
Combinations/Pair 1.19
Mean z-score -1.56
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.01
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>dm3.chr2L 12373986 99 + 23011544
---------------------CAACCACCCACUCCAGCCGUCCUCCAUGUCCACAAACAUGGCCACAAAUGGCCAUCAGUUGUAUCCGGCGAUAACGGCAACGUAUUGGCUCCCGCCGCC
---------------------...............(((((..(((......((((..(((((((....)))))))...)))).....).))..)))))........(((....)))... ( -27.00, z-score =  -1.53, R)
>droSim1.chr2L 12177352 99 + 22036055
---------------------CAACCAUCCACUCCAGCCGUCCUCCAUGUCCACAAACAUGGCCACAAAUGGCCAUCAGUUGUAUCCGGCGAUAACGGCAACGUAUUGGCUCCCGCCGCC
---------------------...............(((((..(((......((((..(((((((....)))))))...)))).....).))..)))))........(((....)))... ( -27.00, z-score =  -1.65, R)
>droSec1.super_16 565014 99 + 1878335
---------------------CAACCAUCCACUCCAGCCGUCCUCCAUGUCCACAAACAUGGCCACAAAUGGCCAUCAGUUGUAUCCGGCGAUAACGGCAACGUAUUGGCUCCCGCCGCC
---------------------...............(((((..(((......((((..(((((((....)))))))...)))).....).))..)))))........(((....)))... ( -27.00, z-score =  -1.65, R)
>droYak2.chr2L 8809458 99 + 22324452
---------------------CAACCACCCACUCCAGCCGUCCUCCAUGUCCACAAACAUGGCCACAAAUGGCCAUCAGUUGUAUCCGGCGAUAACGGCAACGUAUUGGCUCCCGCCGCC
---------------------...............(((((..(((......((((..(((((((....)))))))...)))).....).))..)))))........(((....)))... ( -27.00, z-score =  -1.53, R)
>droEre2.scaffold_4929 13598891 99 - 26641161
---------------------CAACCACCCACUCCAGCCGUCCUCCAUGUCCACAAACAUGGCCACAAAUGGCCAUCAGUUGUAUCCGGCGAUAACGGCAACGUAUUGGCUCCCGCCGCC
---------------------...............(((((..(((......((((..(((((((....)))))))...)))).....).))..)))))........(((....)))... ( -27.00, z-score =  -1.53, R)
>dp4.chr4_group3 5968277 120 - 11692001
CCAUCAGAGCCCGAACCCCAACCAAAACCAGCAGCACCCGCCAACGAUGUCCACAAACAUGACCACAAAUGGCCAUCAGUUGUAUCCGGCGAUAACGGCAACGUAUUGGCUGCCGCCACC
..............................(((((..(((.((((((((.(((................))).)))).))))....)))(((((.((....))))))))))))....... ( -26.39, z-score =  -0.52, R)
>droPer1.super_1 3067872 120 - 10282868
CCAUCAGAGCCCGAACCCCAACCAAAACCAGCAGCACCCGCCAACGAUGUCCACAAACAUGACCACAAAUGGCCAUCAGUUGUAUCCGGCGAUAACGGCAACGUAUUGGCUGCCGCCACC
..............................(((((..(((.((((((((.(((................))).)))).))))....)))(((((.((....))))))))))))....... ( -26.39, z-score =  -0.52, R)
>droWil1.scaffold_180708 10106489 95 + 12563649
-------------------------CCCCCUCCGACGCCCUCAUCGAUGUCCGCAAACAUGACCACAAAUGGCCAUCAGUUGUAUCCGGCGAUAACAGCGACCUAUUGGCUACCCCCACC
-------------------------...........(((......((((.(((................))).)))).((((((((....))).)))))........))).......... ( -14.99, z-score =   0.84, R)
>droVir3.scaffold_12963 17478211 78 + 20206255
----------------------------------------GCAGCA--GCCCACAAACAUGGCCACAAAUGGCCAUCAGUCGUAUCCGGCGAUAACGGCAACGUAUUGGCUGCCGCCACC
----------------------------------------((.(((--(((.......(((((((....)))))))..(((((.....))))).(((....)))...)))))).)).... ( -32.20, z-score =  -3.62, R)
>droMoj3.scaffold_6500 22524188 78 + 32352404
----------------------------------------GCAGCA--GCCCACUAACAUGGCCACAAAUGGCCAUCAGUCGUAUCCGGCGAUAACGGCAACGUAUUGGCUGCCGCCACC
----------------------------------------((.(((--(((.......(((((((....)))))))..(((((.....))))).(((....)))...)))))).)).... ( -32.20, z-score =  -3.55, R)
>droGri2.scaffold_15252 14912655 78 + 17193109
----------------------------------------GCAACA--GUCCACAAACAUGGCCACAAAUGGCCAUCAGUCGUAUCCGGCGAUAACGGCAACGUAUUGGCUACCGCCACC
----------------------------------------......--(((.......(((((((....)))))))..((((....))))))).(((....)))..((((....)))).. ( -23.40, z-score =  -1.92, R)
>consensus
_____________________CAACCACCCACUCCAGCCGUCAUCCAUGUCCACAAACAUGGCCACAAAUGGCCAUCAGUUGUAUCCGGCGAUAACGGCAACGUAUUGGCUCCCGCCACC
................................................(((.........))).......(((((...(((((.....))))).(((....)))..)))))......... (-13.15 = -12.79 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 0

Location 12,373,986 – 12,374,085
Length 99
Sequences 11
Columns 120
Reading direction reverse
Mean pairwise identity 76.11
Shannon entropy 0.44205
G+C content 0.57747
Mean single sequence MFE -37.00
Consensus MFE -26.38
Energy contribution -26.08
Covariance contribution -0.30
Combinations/Pair 1.17
Mean z-score -1.47
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.29
SVM RNA-class probability 0.921710
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 12373986 99 - 23011544
GGCGGCGGGAGCCAAUACGUUGCCGUUAUCGCCGGAUACAACUGAUGGCCAUUUGUGGCCAUGUUUGUGGACAUGGAGGACGGCUGGAGUGGGUGGUUG---------------------
((((((....)))..(((...((((((....(((..(((((...(((((((....)))))))..)))))....)))..))))))....)))....))).--------------------- ( -36.40, z-score =  -0.99, R)
>droSim1.chr2L 12177352 99 - 22036055
GGCGGCGGGAGCCAAUACGUUGCCGUUAUCGCCGGAUACAACUGAUGGCCAUUUGUGGCCAUGUUUGUGGACAUGGAGGACGGCUGGAGUGGAUGGUUG---------------------
((((((....)))..(((...((((((....(((..(((((...(((((((....)))))))..)))))....)))..))))))....)))....))).--------------------- ( -36.40, z-score =  -1.34, R)
>droSec1.super_16 565014 99 - 1878335
GGCGGCGGGAGCCAAUACGUUGCCGUUAUCGCCGGAUACAACUGAUGGCCAUUUGUGGCCAUGUUUGUGGACAUGGAGGACGGCUGGAGUGGAUGGUUG---------------------
((((((....)))..(((...((((((....(((..(((((...(((((((....)))))))..)))))....)))..))))))....)))....))).--------------------- ( -36.40, z-score =  -1.34, R)
>droYak2.chr2L 8809458 99 - 22324452
GGCGGCGGGAGCCAAUACGUUGCCGUUAUCGCCGGAUACAACUGAUGGCCAUUUGUGGCCAUGUUUGUGGACAUGGAGGACGGCUGGAGUGGGUGGUUG---------------------
((((((....)))..(((...((((((....(((..(((((...(((((((....)))))))..)))))....)))..))))))....)))....))).--------------------- ( -36.40, z-score =  -0.99, R)
>droEre2.scaffold_4929 13598891 99 + 26641161
GGCGGCGGGAGCCAAUACGUUGCCGUUAUCGCCGGAUACAACUGAUGGCCAUUUGUGGCCAUGUUUGUGGACAUGGAGGACGGCUGGAGUGGGUGGUUG---------------------
((((((....)))..(((...((((((....(((..(((((...(((((((....)))))))..)))))....)))..))))))....)))....))).--------------------- ( -36.40, z-score =  -0.99, R)
>dp4.chr4_group3 5968277 120 + 11692001
GGUGGCGGCAGCCAAUACGUUGCCGUUAUCGCCGGAUACAACUGAUGGCCAUUUGUGGUCAUGUUUGUGGACAUCGUUGGCGGGUGCUGCUGGUUUUGGUUGGGGUUCGGGCUCUGAUGG
((((((((((((......)))))))))))).((((((.(((((.(((((((....)))))))....(..(.((((.......)))))..).......)))))..)))))).......... ( -45.80, z-score =  -1.36, R)
>droPer1.super_1 3067872 120 + 10282868
GGUGGCGGCAGCCAAUACGUUGCCGUUAUCGCCGGAUACAACUGAUGGCCAUUUGUGGUCAUGUUUGUGGACAUCGUUGGCGGGUGCUGCUGGUUUUGGUUGGGGUUCGGGCUCUGAUGG
((((((((((((......)))))))))))).((((((.(((((.(((((((....)))))))....(..(.((((.......)))))..).......)))))..)))))).......... ( -45.80, z-score =  -1.36, R)
>droWil1.scaffold_180708 10106489 95 - 12563649
GGUGGGGGUAGCCAAUAGGUCGCUGUUAUCGCCGGAUACAACUGAUGGCCAUUUGUGGUCAUGUUUGCGGACAUCGAUGAGGGCGUCGGAGGGGG-------------------------
(((((.((..(((....)))..)).)))))((((.(.(((.....((((((....))))))))).).))).).((((((....))))))......------------------------- ( -29.80, z-score =  -0.14, R)
>droVir3.scaffold_12963 17478211 78 - 20206255
GGUGGCGGCAGCCAAUACGUUGCCGUUAUCGCCGGAUACGACUGAUGGCCAUUUGUGGCCAUGUUUGUGGGC--UGCUGC----------------------------------------
((((((((((((......))))))))))))(((...(((((...(((((((....)))))))..))))))))--......---------------------------------------- ( -35.40, z-score =  -2.45, R)
>droMoj3.scaffold_6500 22524188 78 - 32352404
GGUGGCGGCAGCCAAUACGUUGCCGUUAUCGCCGGAUACGACUGAUGGCCAUUUGUGGCCAUGUUAGUGGGC--UGCUGC----------------------------------------
....(((((((((....(((..(((.......)))..)))(((((((((((....))))))..))))).)))--))))))---------------------------------------- ( -36.20, z-score =  -2.69, R)
>droGri2.scaffold_15252 14912655 78 - 17193109
GGUGGCGGUAGCCAAUACGUUGCCGUUAUCGCCGGAUACGACUGAUGGCCAUUUGUGGCCAUGUUUGUGGAC--UGUUGC----------------------------------------
((((((((((((......))))))))))))((.(..(((((...(((((((....)))))))..)))))..)--.))...---------------------------------------- ( -32.00, z-score =  -2.49, R)
>consensus
GGUGGCGGGAGCCAAUACGUUGCCGUUAUCGCCGGAUACAACUGAUGGCCAUUUGUGGCCAUGUUUGUGGACAUGGAUGACGGCUGGAGUGGGUGGUUG_____________________
((((((((.(((......))).))))...))))(..(((((...(((((((....)))))))..)))))..)................................................ (-26.38 = -26.08 +  -0.30)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,374,005 – 12,374,123
Length 118
Sequences 12
Columns 120
Reading direction reverse
Mean pairwise identity 92.27
Shannon entropy 0.16701
G+C content 0.50941
Mean single sequence MFE -40.45
Consensus MFE -33.97
Energy contribution -33.36
Covariance contribution -0.62
Combinations/Pair 1.15
Mean z-score -1.64
Structure conservation index 0.84
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.40
SVM RNA-class probability 0.680338
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 12374005 118 - 23011544
AAC--ACUAAUUACCUGGAACUAAAUAUGGCGCCGGAUUCGGCGGCGGGAGCCAAUACGUUGCCGUUAUCGCCGGAUACAACUGAUGGCCAUUUGUGGCCAUGUUUGUGGACAUGGAGGA
...--........(((((........(((((((((....))))(((....)))........))))).....))(..(((((...(((((((....)))))))..)))))..)....))). ( -40.82, z-score =  -1.45, R)
>droSim1.chr2L 12177371 118 - 22036055
AAC--ACUAAUUACCUGGAACUAAAUAUGGCGCCGGAUUCGGCGGCGGGAGCCAAUACGUUGCCGUUAUCGCCGGAUACAACUGAUGGCCAUUUGUGGCCAUGUUUGUGGACAUGGAGGA
...--........(((((........(((((((((....))))(((....)))........))))).....))(..(((((...(((((((....)))))))..)))))..)....))). ( -40.82, z-score =  -1.45, R)
>droSec1.super_16 565033 118 - 1878335
AAC--ACUAAUUACCUGGAACUAAAUAUGGCGCCGGAUUCGGCGGCGGGAGCCAAUACGUUGCCGUUAUCGCCGGAUACAACUGAUGGCCAUUUGUGGCCAUGUUUGUGGACAUGGAGGA
...--........(((((........(((((((((....))))(((....)))........))))).....))(..(((((...(((((((....)))))))..)))))..)....))). ( -40.82, z-score =  -1.45, R)
>droYak2.chr2L 8809477 118 - 22324452
AAC--ACUAAUUACCUGGAACUAAAUAUGGCGCCGGAUUCGGCGGCGGGAGCCAAUACGUUGCCGUUAUCGCCGGAUACAACUGAUGGCCAUUUGUGGCCAUGUUUGUGGACAUGGAGGA
...--........(((((........(((((((((....))))(((....)))........))))).....))(..(((((...(((((((....)))))))..)))))..)....))). ( -40.82, z-score =  -1.45, R)
>droEre2.scaffold_4929 13598910 118 + 26641161
AAC--ACUAAUUACCUGGAACUAAAUAUGGCGCCGGAUUCGGCGGCGGGAGCCAAUACGUUGCCGUUAUCGCCGGAUACAACUGAUGGCCAUUUGUGGCCAUGUUUGUGGACAUGGAGGA
...--........(((((........(((((((((....))))(((....)))........))))).....))(..(((((...(((((((....)))))))..)))))..)....))). ( -40.82, z-score =  -1.45, R)
>droAna3.scaffold_12916 3157813 118 + 16180835
AAC--ACUAAUUACCUGGAACUAAAUAUGGCGCCGGAUUCGGUGGCGGCAGCCAAUACGUUGCCGUUAUCGCCGGAUACGACUGAUGGCCAUUUGUGGUCAUGCUUGUGGACACUGGCGA
...--.........((((..(((....)))..))))....((((((((((((......))))))))))))(((((.(((((...(((((((....)))))))..)))))....))))).. ( -43.90, z-score =  -2.28, R)
>dp4.chr4_group3 5968317 118 + 11692001
AAC--ACUAAUUACCUGGAACUAAAUAUGGCGCCGGAUUUGGUGGCGGCAGCCAAUACGUUGCCGUUAUCGCCGGAUACAACUGAUGGCCAUUUGUGGUCAUGUUUGUGGACAUCGUUGG
...--.(((((....((..((.(((((((((.((((....((((((((((((......)))))))))))).)))).(((((.((.....)).))))))))))))))))...))..))))) ( -39.70, z-score =  -1.50, R)
>droPer1.super_1 3067912 118 + 10282868
AAC--ACUAAUUACCUGGAACUAAAUAUGGCGCCGGAUUUGGUGGCGGCAGCCAAUACGUUGCCGUUAUCGCCGGAUACAACUGAUGGCCAUUUGUGGUCAUGUUUGUGGACAUCGUUGG
...--.(((((....((..((.(((((((((.((((....((((((((((((......)))))))))))).)))).(((((.((.....)).))))))))))))))))...))..))))) ( -39.70, z-score =  -1.50, R)
>droWil1.scaffold_180708 10106504 120 - 12563649
AACUAACUAAUUACCUGGAACUAAAUAUGGCGCCGGAUUCGGUGGGGGUAGCCAAUAGGUCGCUGUUAUCGCCGGAUACAACUGAUGGCCAUUUGUGGUCAUGUUUGCGGACAUCGAUGA
.............((..((((......((...((((...((((((.((..(((....)))..)).))))))))))...))....(((((((....)))))))))))..)).......... ( -33.30, z-score =   0.20, R)
>droVir3.scaffold_12963 17478217 110 - 20206255
AAC--ACUAAUUACCUGGAACUAAAUAUGGCGCCGGAUUUGGUGGCGGCAGCCAAUACGUUGCCGUUAUCGCCGGAUACGACUGAUGGCCAUUUGUGGCCAUGUUUGUGGGC--------
...--........(((...((.(((((((((.((((....((((((((((((......)))))))))))).)))).(((((.((.....)).))))))))))))))))))).-------- ( -41.40, z-score =  -2.16, R)
>droMoj3.scaffold_6500 22524194 110 - 32352404
AAC--ACUAAUUACCUGGAACUAAAUAUGGCGCCGGAUUUGGUGGCGGCAGCCAAUACGUUGCCGUUAUCGCCGGAUACGACUGAUGGCCAUUUGUGGCCAUGUUAGUGGGC--------
..(--((((((...((((..(((....)))..))))((((((((((((((((......))))))))...)))))))).......(((((((....))))))))))))))...-------- ( -44.30, z-score =  -3.00, R)
>droGri2.scaffold_15252 14912661 110 - 17193109
AAC--ACUAAUUACCUGGAACUAAAUAUGGCGCCGGAUUUGGUGGCGGUAGCCAAUACGUUGCCGUUAUCGCCGGAUACGACUGAUGGCCAUUUGUGGCCAUGUUUGUGGAC--------
...--........((..((((......((...((((....((((((((((((......)))))))))))).))))...))....(((((((....)))))))))))..))..-------- ( -39.00, z-score =  -2.19, R)
>consensus
AAC__ACUAAUUACCUGGAACUAAAUAUGGCGCCGGAUUCGGUGGCGGCAGCCAAUACGUUGCCGUUAUCGCCGGAUACAACUGAUGGCCAUUUGUGGCCAUGUUUGUGGACAUGGAGGA
..............((((..(((....)))..))))((((((((((((.(((......))).))))...))))))))((((...(((((((....)))))))..))))............ (-33.97 = -33.36 +  -0.62)

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 21:35:06 2011