Locus 2156

Sequence ID dm3.chr2L
Location 16,638,589 – 16,638,715
Length 126
Max. P 0.989093
window2971 window2972 window2973

overview

Window 1

Location 16,638,589 – 16,638,687
Length 98
Sequences 7
Columns 106
Reading direction reverse
Mean pairwise identity 77.47
Shannon entropy 0.40789
G+C content 0.56228
Mean single sequence MFE -20.88
Consensus MFE -16.19
Energy contribution -16.43
Covariance contribution 0.24
Combinations/Pair 1.06
Mean z-score -1.81
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.89
SVM RNA-class probability 0.973416
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 16638589 98 - 23011544
----GUGUAUCUAAUAGAUACAUUUCGCAUGCCGUGACUGCCACGCCCUCCUUGCGCCCUC-UUGCCCCU---CACCGCACAUCGCUUUGCUUUUCGCAUGCAGGC
----(((((((.....)))))))...((((((((((.....))))........(((.....-.(((....---....)))...)))..........)))))).... ( -23.30, z-score =  -1.34, R)
>droSim1.chr2L 16337092 97 - 22036055
----GUGUAUCUAAUAGAUACAUUUCGCAUGCCGUGACUGCCACGCCCUCC-UGCGCCCUC-UUGCCCCU---CACCGCACUUCACUUUGCUUUUCGCAUGCAGGC
----(((((((.....)))))))...((((((.((((..((..(((.....-.))).....-..))...)---))).(((........))).....)))))).... ( -22.90, z-score =  -1.92, R)
>droSec1.super_7 285639 97 - 3727775
----GUGUAUCUAAUAGAUACAUUUCGCAUGCCGUGACUGCCACGCCCUCC-UGCGCCCUC-UUGCCCCU---CACCGCACUUCACUUUGCUUUUCGCAUGCAGGC
----(((((((.....)))))))...((((((.((((..((..(((.....-.))).....-..))...)---))).(((........))).....)))))).... ( -22.90, z-score =  -1.92, R)
>droYak2.chr2R 16674037 99 + 21139217
----GGGUAUCUAAUAGAUACAUUUCGCAUGCCGUGACUGCCACGCCCUCU-UGCGCCCC--UCGCCUCCUCGCCCCAUACCGCACUUCACUUUUCGCAUGCAGGC
----..(((((.....))))).....((((((((((.....))))......-((((....--..((......)).......))))...........)))))).... ( -22.42, z-score =  -0.68, R)
>droEre2.scaffold_4845 19709006 101 - 22589142
----GUGUAUCUAAUAGAUACAUUUCGCAUGCCGUGACUGCCACGCCCUCU-UGCGCCCCCUUCACCCCUUCACCCCUCACCGCACUUCACUUUUCGCAUGCAGGC
----(((((((.....)))))))...((((((((((.....))))......-((((.........................))))...........)))))).... ( -21.41, z-score =  -2.86, R)
>dp4.chr4_group3 8378197 81 - 11692001
ACACUCGUAUCUAAUAGAUACAUUUCGCAUGCCGUGACUGCCACGCCC-------------------------CUCCCCACUCAGCCCCACUUUUCGCAUGCAGGC
......(((((.....))))).....((((((.(((.....)))((..-------------------------...........))..........)))))).... ( -16.62, z-score =  -1.97, R)
>droPer1.super_1 9827958 81 - 10282868
ACACUCGUAUCUAAUAGAUACAUUUCGCAUGCCGUGACUGCCACGCCC-------------------------CUCCCCACUCAGCCCCACUUUUCGCAUGCAGGC
......(((((.....))))).....((((((.(((.....)))((..-------------------------...........))..........)))))).... ( -16.62, z-score =  -1.97, R)
>consensus
____GUGUAUCUAAUAGAUACAUUUCGCAUGCCGUGACUGCCACGCCCUCC_UGCGCCCUC_UUGCCCCU___CACCGCACUUCACUUCACUUUUCGCAUGCAGGC
......(((((.....))))).....((((((((((.....))))........(((.......)))..............................)))))).... (-16.19 = -16.43 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 16,638,622 – 16,638,715
Length 93
Sequences 9
Columns 121
Reading direction forward
Mean pairwise identity 72.00
Shannon entropy 0.48786
G+C content 0.53356
Mean single sequence MFE -30.96
Consensus MFE -16.12
Energy contribution -16.53
Covariance contribution 0.41
Combinations/Pair 1.17
Mean z-score -1.96
Structure conservation index 0.52
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.45
SVM RNA-class probability 0.938384
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 16638622 93 + 23011544
--------AGGGGCAA-GAGGGCGCAAGGAG-GGCGUGGCAGUCACGGCAUGCGAAAUGUAUCUAUUAGAUACA-------------CGCCUGCGAAA-UGCGGUUAACUGCAUUGG----
--------..((((..-.....((((.....-(.((((.....)))).).))))...((((((.....))))))-------------.))))....((-(((((....)))))))..---- ( -30.10, z-score =  -1.44, R)
>droSim1.chr2L 16337125 92 + 22036055
--------AGGGGCAA-GAGGGCGCA-GGAG-GGCGUGGCAGUCACGGCAUGCGAAAUGUAUCUAUUAGAUACA-------------CGCCUGCGAAA-UGCGGUUAACUGCAUUGG----
--------........-.....((((-((.(-.(((((.(......).)))))....((((((.....))))))-------------).)))))).((-(((((....)))))))..---- ( -33.40, z-score =  -2.64, R)
>droSec1.super_7 285672 92 + 3727775
--------AGGGGCAA-GAGGGCGCA-GGAG-GGCGUGGCAGUCACGGCAUGCGAAAUGUAUCUAUUAGAUACA-------------CGCCUGCGAAA-UGCGGUUAACUGCAUUGG----
--------........-.....((((-((.(-.(((((.(......).)))))....((((((.....))))))-------------).)))))).((-(((((....)))))))..---- ( -33.40, z-score =  -2.64, R)
>droYak2.chr2R 16674065 99 - 21139217
UGGGGCGAGGAGGCGA--GGGGCGCA-AGAG-GGCGUGGCAGUCACGGCAUGCGAAAUGUAUCUAUUAGAUACC-------------CGCCUGCGAAA-UGCGGUUAACUGCAUUGG----
........(.(((((.--((..((((-....-(.((((.....)))).).)))).....((((.....))))))-------------))))).)..((-(((((....)))))))..---- ( -33.70, z-score =  -0.70, R)
>droEre2.scaffold_4845 19709034 101 + 22589142
AGGGGUGAAGGGGUGAAGGGGGCGCA-AGAG-GGCGUGGCAGUCACGGCAUGCGAAAUGUAUCUAUUAGAUACA-------------CGCCUGCGAAA-UGCGGUUAACUGCAUUGG----
............((((..(..((((.-....-.))))..)..)))).(((.(((...((((((.....))))))-------------))).)))..((-(((((....)))))))..---- ( -33.00, z-score =  -2.13, R)
>droAna3.scaffold_12916 257583 96 - 16180835
--------------------AGUGGAGAAGGCGGCGUGGCAGUCACGGCAUGCGAAAUGUAUCUAUUAGAUACGCAAGUGUGCGAAGUGACUGCGAAA-UGCGGUUAACUGCAUUGG----
--------------------((((.((..(((.((((.((((((((.((((((....((((((.....))))))...))))))...))))))))...)-))).)))..)).))))..---- ( -39.80, z-score =  -4.47, R)
>dp4.chr4_group3 8378219 93 + 11692001
------------------UGAGUGGGGAGGG--GCGUGGCAGUCACGGCAUGCGAAAUGUAUCUAUUAGAUACG--AGUGUGCGA-GUGCAUGCGAAA-UGCGGUUAACAGCAUUGG----
------------------.............--(((((.((.((...((((((....((((((.....))))))--.))))))))-.)))))))..((-(((........)))))..---- ( -26.60, z-score =  -0.85, R)
>droPer1.super_1 9827980 93 + 10282868
------------------UGAGUGGGGAGGG--GCGUGGCAGUCACGGCAUGCGAAAUGUAUCUAUUAGAUACG--AGUGUGCGA-GUGCAUGCGAAA-UGCGGUUAACAGCAUUGG----
------------------.............--(((((.((.((...((((((....((((((.....))))))--.))))))))-.)))))))..((-(((........)))))..---- ( -26.60, z-score =  -0.85, R)
>droWil1.scaffold_181132 92290 84 - 1035393
---------------------------GGCACGAAGGGGUAGAUAGGUGUGGCCAAAUGUAUCUAUUAGAUACA----------AAAUGCACGCAAAAAUGCGGUUAACUGCAUUUGACGG
---------------------------.((((....)((((((((.((........)).)))))))).......----------...))).((...((((((((....))))))))..)). ( -22.00, z-score =  -1.96, R)
>consensus
_________G_GG__A__AGGGCGCA_AGAG_GGCGUGGCAGUCACGGCAUGCGAAAUGUAUCUAUUAGAUACA_____________CGCCUGCGAAA_UGCGGUUAACUGCAUUGG____
.....................((..........(((((.(......).))))).....(((((.....)))))...................)).....(((((....)))))........ (-16.12 = -16.53 +   0.41)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 16,638,622 – 16,638,715
Length 93
Sequences 9
Columns 121
Reading direction reverse
Mean pairwise identity 72.00
Shannon entropy 0.48786
G+C content 0.53356
Mean single sequence MFE -22.44
Consensus MFE -12.98
Energy contribution -13.32
Covariance contribution 0.35
Combinations/Pair 1.07
Mean z-score -2.24
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.35
SVM RNA-class probability 0.989093
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 16638622 93 - 23011544
----CCAAUGCAGUUAACCGCA-UUUCGCAGGCG-------------UGUAUCUAAUAGAUACAUUUCGCAUGCCGUGACUGCCACGCC-CUCCUUGCGCCCUC-UUGCCCCU--------
----.....(((((((...(((-(...((.((.(-------------((((((.....))))))).))))))))..)))))))..(((.-......))).....-........-------- ( -23.90, z-score =  -1.99, R)
>droSim1.chr2L 16337125 92 - 22036055
----CCAAUGCAGUUAACCGCA-UUUCGCAGGCG-------------UGUAUCUAAUAGAUACAUUUCGCAUGCCGUGACUGCCACGCC-CUCC-UGCGCCCUC-UUGCCCCU--------
----.....(((((((...(((-(...((.((.(-------------((((((.....))))))).))))))))..)))))))..(((.-....-.))).....-........-------- ( -24.40, z-score =  -2.17, R)
>droSec1.super_7 285672 92 - 3727775
----CCAAUGCAGUUAACCGCA-UUUCGCAGGCG-------------UGUAUCUAAUAGAUACAUUUCGCAUGCCGUGACUGCCACGCC-CUCC-UGCGCCCUC-UUGCCCCU--------
----.....(((((((...(((-(...((.((.(-------------((((((.....))))))).))))))))..)))))))..(((.-....-.))).....-........-------- ( -24.40, z-score =  -2.17, R)
>droYak2.chr2R 16674065 99 + 21139217
----CCAAUGCAGUUAACCGCA-UUUCGCAGGCG-------------GGUAUCUAAUAGAUACAUUUCGCAUGCCGUGACUGCCACGCC-CUCU-UGCGCCCC--UCGCCUCCUCGCCCCA
----..(((((........)))-))..(.(((((-------------((((((.....)))))....((((.(.((((.....)))).)-....-))))....--)))))).)........ ( -24.30, z-score =  -0.48, R)
>droEre2.scaffold_4845 19709034 101 - 22589142
----CCAAUGCAGUUAACCGCA-UUUCGCAGGCG-------------UGUAUCUAAUAGAUACAUUUCGCAUGCCGUGACUGCCACGCC-CUCU-UGCGCCCCCUUCACCCCUUCACCCCU
----.....(((((((...(((-(...((.((.(-------------((((((.....))))))).))))))))..)))))))..(((.-....-.)))...................... ( -24.40, z-score =  -3.13, R)
>droAna3.scaffold_12916 257583 96 + 16180835
----CCAAUGCAGUUAACCGCA-UUUCGCAGUCACUUCGCACACUUGCGUAUCUAAUAGAUACAUUUCGCAUGCCGUGACUGCCACGCCGCCUUCUCCACU--------------------
----..(((((........)))-))..((((((((...(((....)))(((((.....)))))............))))))))..................-------------------- ( -25.00, z-score =  -3.25, R)
>dp4.chr4_group3 8378219 93 - 11692001
----CCAAUGCUGUUAACCGCA-UUUCGCAUGCAC-UCGCACACU--CGUAUCUAAUAGAUACAUUUCGCAUGCCGUGACUGCCACGC--CCCUCCCCACUCA------------------
----..(((((.(....).)))-))..((((((..-..(......--)(((((.....))))).....))))))((((.....)))).--.............------------------ ( -19.40, z-score =  -2.49, R)
>droPer1.super_1 9827980 93 - 10282868
----CCAAUGCUGUUAACCGCA-UUUCGCAUGCAC-UCGCACACU--CGUAUCUAAUAGAUACAUUUCGCAUGCCGUGACUGCCACGC--CCCUCCCCACUCA------------------
----..(((((.(....).)))-))..((((((..-..(......--)(((((.....))))).....))))))((((.....)))).--.............------------------ ( -19.40, z-score =  -2.49, R)
>droWil1.scaffold_181132 92290 84 + 1035393
CCGUCAAAUGCAGUUAACCGCAUUUUUGCGUGCAUUU----------UGUAUCUAAUAGAUACAUUUGGCCACACCUAUCUACCCCUUCGUGCC---------------------------
..((((((((((......((((....))))))))...----------((((((.....))))))))))))........................--------------------------- ( -16.80, z-score =  -1.98, R)
>consensus
____CCAAUGCAGUUAACCGCA_UUUCGCAGGCG_____________UGUAUCUAAUAGAUACAUUUCGCAUGCCGUGACUGCCACGCC_CUCU_UGCGCCCU__U__CC_C_________
.........(((((((...((......))...................(((((.....))))).............)))))))...................................... (-12.98 = -13.32 +   0.35)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:45:54 2011