Locus 1731

Sequence ID dm3.chr2L
Location 13,354,394 – 13,354,486
Length 92
Max. P 0.996867
window2372 window2373

overview

Window 2

Location 13,354,394 – 13,354,486
Length 92
Sequences 12
Columns 111
Reading direction forward
Mean pairwise identity 70.10
Shannon entropy 0.59375
G+C content 0.62050
Mean single sequence MFE -39.45
Consensus MFE -23.35
Energy contribution -23.35
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -0.97
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.07
SVM RNA-class probability 0.885295
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 13354394 92 + 23011544
----CGGAGCCCCCCGGG------GAUUGCUGCUUGUACUGGGGGGGGCUCCGGCUAUUCAGCAUGUUGGAGUGCAGGGAGC-GGGGGAU-UAGAUUUCGGUCU-------
----(((((((((((..(------(..(((.....)))))..)))))))))))((..(((((....)))))..))..(((.(-(..(...-....)..)).)))------- ( -40.00, z-score =  -1.24, R)
>droGri2.scaffold_15126 56577 88 + 8399593
----CGGAGCCCCCCGUUCCCGUUGCGAGUUGUUUGUACGAUGGGGGGCUCCUGCUGCCUAACAUGGCGGUGUGC----------AGGAG-GGUGGGUGAGUU--------
----.((((((((((((...(((.(((((...)))))))))))))))))))).((((((......))))))....----------.....-............-------- ( -39.40, z-score =  -1.70, R)
>droMoj3.scaffold_6500 6372101 98 + 32352404
----CGGAGCCCCCCGAUCCCGAUGCGAGCGGCUUGUAAGCUGGGGGGCUCCUGCUGCCUAACAUGACGGAGUGCAGGUGGGUGGUGGGC-GGUGGGUGAGUG--------
----.(((((((((((.(..(((.((.....)))))..)..))))))))))).((((((((.(((..(........)....))).)))))-))).........-------- ( -41.10, z-score =   0.06, R)
>droVir3.scaffold_12723 2393604 97 - 5802038
----CGGAGCCCCCCGUUCCGGUUGUCAGUGGCUUGUACGCUGGGGGGCUCCUGCUGCCUAACAUGGCGGAGAAC-GGUAGGGUUUGGGU-GGUGGGUCAGUU--------
----.((((((((((((.(.((((......)))).)...)).)))))))))).((..((((((.((.((.....)-).))..).))))).-.)).........-------- ( -39.90, z-score =  -0.12, R)
>droWil1.scaffold_180708 7131544 91 - 12563649
----CGGAGCCCCCCGUU------GCUAGUUUCUUAUAUUGUGGGGGGCUCCGACUGUUCAGCAUGACGCGGUGUGGGGAA--GGGGGAU-UGGAUGUAGAUUA-------
----((((((((((((..------..((((.......)))))))))))))))).((.(((.((((......))))...)))--.))....-.............------- ( -33.20, z-score =  -1.15, R)
>droPer1.super_5 3013992 93 + 6813705
----CGGAGCCCCCCCUU------GCCUGCUGCUUGUACUGAGGGGGGCUCCGGCUAUUCAGCAUGUCGGAGUGCAGGGAGCAGGGGGAU-UAGUUUUCAGCGU-------
----(((((((((((.((------...(((.....)))..)))))))))))))(((.....((((......)))).(..(((..(....)-..)))..))))..------- ( -38.10, z-score =   0.00, R)
>dp4.chr4_group1 3043228 93 - 5278887
----CGGAGCCCCCCCUU------GCCUGCUGCUUGUACUGAGGGGGGCUCCGGCUAUUCAGCAUGUCGGAGUGCAGGGAGCAGGGGGAU-UAGUUUUCAGCGU-------
----(((((((((((.((------...(((.....)))..)))))))))))))(((.....((((......)))).(..(((..(....)-..)))..))))..------- ( -38.10, z-score =   0.00, R)
>droAna3.scaffold_12943 2005140 101 + 5039921
----CGGAGCCCCCCGUG------GAUUGCUGCUUAUUUCGAGGGGGGCUCCGGCUAUAUGGCAUGGUUGGGAGGAAGGGGUGCAGGGAUCUCAAAAUUAGUUUCUUGACU
----(((((((((((.((------((...........)))).)))))))))))(((....)))..(((..(((((..(((((......)))))........)))))..))) ( -40.30, z-score =  -1.59, R)
>droEre2.scaffold_4929 14554403 96 - 26641161
CCAGCGGAGCCCCCCGGG------GAUUGCAGCUUGUACUGGGGGGGGCUCCGGCUAUUCAGCAUGUUGGAGUGCAGGGAGC-GGGGGAU-UAGAUUUCGGUCU-------
(((((((((((((((..(------(..(((.....)))))..)))))))))).(((....)))..))))).......(((.(-(..(...-....)..)).)))------- ( -42.00, z-score =  -1.16, R)
>droYak2.chr2L 9792868 92 + 22324452
----CGGAGCCCCCCGGG------GAUUGCUGCUUGUACUGUGGGGGGCUCCGGCUAUUCAGCAUGUUGGAGUGCAGGGAGC-GGGGGAU-UAGAUUUCUGAAU-------
----((((((((((((.(------(..(((.....))))).))))))))))))(((.(((.((((......)))).))))))-......(-(((....))))..------- ( -41.30, z-score =  -2.36, R)
>droSec1.super_16 1512834 92 + 1878335
----CGGAGCCCCCCGGG------GAUUGCUGCUUGUACUGGGGGGGGCUCCGGCUAUUCAGCAUGUUGGAGUGCAGGGAGC-GGGGGAU-UAGAUUUCGGUCU-------
----(((((((((((..(------(..(((.....)))))..)))))))))))((..(((((....)))))..))..(((.(-(..(...-....)..)).)))------- ( -40.00, z-score =  -1.24, R)
>droSim1.chr2L 13142595 92 + 22036055
----CGGAGCCCCCCGGC------GAUUGCUGCUUGUACUGGGGGGGGCUCCGGCUAUUCAGCAUGUUGGAGUGCAGGGAGC-GGGGGAU-UAGAUUUCGGUCU-------
----((((((((((((((------....))).((......)))))))))))))((..(((((....)))))..))..(((.(-(..(...-....)..)).)))------- ( -40.00, z-score =  -1.16, R)
>consensus
____CGGAGCCCCCCGUU______GAUUGCUGCUUGUACUGUGGGGGGCUCCGGCUAUUCAGCAUGUCGGAGUGCAGGGAGC_GGGGGAU_UAGAUUUCAGUCU_______
.....((((((((((...........................))))))))))........................................................... (-23.35 = -23.35 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 13,354,394 – 13,354,486
Length 92
Sequences 12
Columns 111
Reading direction reverse
Mean pairwise identity 70.10
Shannon entropy 0.59375
G+C content 0.62050
Mean single sequence MFE -30.11
Consensus MFE -23.91
Energy contribution -23.73
Covariance contribution -0.18
Combinations/Pair 1.15
Mean z-score -1.78
Structure conservation index 0.79
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.00
SVM RNA-class probability 0.996867
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 13354394 92 - 23011544
-------AGACCGAAAUCUA-AUCCCCC-GCUCCCUGCACUCCAACAUGCUGAAUAGCCGGAGCCCCCCCCAGUACAAGCAGCAAUC------CCCGGGGGGCUCCG----
-------.............-.......-(((....(((........))).....)))(((((((((((..................------...)))))))))))---- ( -27.70, z-score =  -1.82, R)
>droGri2.scaffold_15126 56577 88 - 8399593
--------AACUCACCCACC-CUCCU----------GCACACCGCCAUGUUAGGCAGCAGGAGCCCCCCAUCGUACAAACAACUCGCAACGGGAACGGGGGGCUCCG----
--------............-.....----------.......(((......)))....((((((((((...((....))..((((...))))...)))))))))).---- ( -32.80, z-score =  -2.64, R)
>droMoj3.scaffold_6500 6372101 98 - 32352404
--------CACUCACCCACC-GCCCACCACCCACCUGCACUCCGUCAUGUUAGGCAGCAGGAGCCCCCCAGCUUACAAGCCGCUCGCAUCGGGAUCGGGGGGCUCCG----
--------............-............((((.((........)))))).....((((((((((.(((....)))..((((...))))...)))))))))).---- ( -33.20, z-score =  -1.02, R)
>droVir3.scaffold_12723 2393604 97 + 5802038
--------AACUGACCCACC-ACCCAAACCCUACC-GUUCUCCGCCAUGUUAGGCAGCAGGAGCCCCCCAGCGUACAAGCCACUGACAACCGGAACGGGGGGCUCCG----
--------............-..............-.......(((......)))....((((((((((.((......))..(((.....)))...)))))))))).---- ( -34.00, z-score =  -2.15, R)
>droWil1.scaffold_180708 7131544 91 + 12563649
-------UAAUCUACAUCCA-AUCCCCC--UUCCCCACACCGCGUCAUGCUGAACAGUCGGAGCCCCCCACAAUAUAAGAAACUAGC------AACGGGGGGCUCCG----
-------.............-.......--...........((.....))........(((((((((((..................------...)))))))))))---- ( -24.80, z-score =  -2.46, R)
>droPer1.super_5 3013992 93 - 6813705
-------ACGCUGAAAACUA-AUCCCCCUGCUCCCUGCACUCCGACAUGCUGAAUAGCCGGAGCCCCCCUCAGUACAAGCAGCAGGC------AAGGGGGGGCUCCG----
-------..((((.......-.......(((.....)))...............))))((((((((((((..((...........))------..))))))))))))---- ( -31.35, z-score =  -0.52, R)
>dp4.chr4_group1 3043228 93 + 5278887
-------ACGCUGAAAACUA-AUCCCCCUGCUCCCUGCACUCCGACAUGCUGAAUAGCCGGAGCCCCCCUCAGUACAAGCAGCAGGC------AAGGGGGGGCUCCG----
-------..((((.......-.......(((.....)))...............))))((((((((((((..((...........))------..))))))))))))---- ( -31.35, z-score =  -0.52, R)
>droAna3.scaffold_12943 2005140 101 - 5039921
AGUCAAGAAACUAAUUUUGAGAUCCCUGCACCCCUUCCUCCCAACCAUGCCAUAUAGCCGGAGCCCCCCUCGAAAUAAGCAGCAAUC------CACGGGGGGCUCCG----
..((((((......))))))......................................(((((((((((..................------...)))))))))))---- ( -27.20, z-score =  -1.70, R)
>droEre2.scaffold_4929 14554403 96 + 26641161
-------AGACCGAAAUCUA-AUCCCCC-GCUCCCUGCACUCCAACAUGCUGAAUAGCCGGAGCCCCCCCCAGUACAAGCUGCAAUC------CCCGGGGGGCUCCGCUGG
-------...(((.......-.......-(((....(((........))).....)))(((((((((((.((((....)))).....------...))))))))))).))) ( -31.70, z-score =  -1.82, R)
>droYak2.chr2L 9792868 92 - 22324452
-------AUUCAGAAAUCUA-AUCCCCC-GCUCCCUGCACUCCAACAUGCUGAAUAGCCGGAGCCCCCCACAGUACAAGCAGCAAUC------CCCGGGGGGCUCCG----
-------((((((.......-.......-((.....))...........))))))...(((((((((((..................------...)))))))))))---- ( -29.31, z-score =  -2.68, R)
>droSec1.super_16 1512834 92 - 1878335
-------AGACCGAAAUCUA-AUCCCCC-GCUCCCUGCACUCCAACAUGCUGAAUAGCCGGAGCCCCCCCCAGUACAAGCAGCAAUC------CCCGGGGGGCUCCG----
-------.............-.......-(((....(((........))).....)))(((((((((((..................------...)))))))))))---- ( -27.70, z-score =  -1.82, R)
>droSim1.chr2L 13142595 92 - 22036055
-------AGACCGAAAUCUA-AUCCCCC-GCUCCCUGCACUCCAACAUGCUGAAUAGCCGGAGCCCCCCCCAGUACAAGCAGCAAUC------GCCGGGGGGCUCCG----
-------.............-.......-(((....(((........))).....)))(((((((((((...((....)).((....------)).)))))))))))---- ( -30.20, z-score =  -2.22, R)
>consensus
_______AAACUGAAAUCUA_AUCCCCC_GCUCCCUGCACUCCAACAUGCUGAAUAGCCGGAGCCCCCCACAGUACAAGCAGCAAUC______AACGGGGGGCUCCG____
................................................(((....))).((((((((((...........................))))))))))..... (-23.91 = -23.73 +  -0.18)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:37:39 2011