Locus 1018

Sequence ID dm3.chr2L
Location 7,602,474 – 7,602,594
Length 120
Max. P 0.808059
window1386 window1387 window1388

overview

Window 6

Location 7,602,474 – 7,602,574
Length 100
Sequences 9
Columns 109
Reading direction forward
Mean pairwise identity 66.25
Shannon entropy 0.66141
G+C content 0.40943
Mean single sequence MFE -23.97
Consensus MFE -7.22
Energy contribution -7.03
Covariance contribution -0.18
Combinations/Pair 1.36
Mean z-score -1.67
Structure conservation index 0.30
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.13
SVM RNA-class probability 0.556474
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 7602474 100 + 23011544
UUCAAUUGGACGCGAAAU--GCGGUAAGAUA-UUUAUCGCACGACAGCGAUACCCUUUAAUUUG-AAGGGAGUCUUAAGCUGUU---AUUUUGAUUGGAUAAUCAAA--
((((((..((.......(--((((((((...-))))))))).(((((((((.((((((.....)-))))).)))....))))))---..))..))))))........-- ( -31.00, z-score =  -4.00, R)
>droSim1.chr2L 7399209 100 + 22036055
CUCAAUUGGACGCGAAAU--GCGGCAAGAUA-UUUAUCGCACGACAGCGAUACCCUUUAAUUUG-AAGGGAAUUUCAAGCUGUU---AUAUUGAUUGGAUAAUCAAA--
.(((((..(.(((.....--)))((......-..((((((......))))))((((((.....)-)))))........))....---...)..))))).........-- ( -24.20, z-score =  -1.83, R)
>droSec1.super_3 3116028 100 + 7220098
UUCAAUUGGACGCGAAAU--GCGGCAAGAUA-UUUAUCGCACGACAGCGAUACCCUUUAAUUUG-AAGGGAAUUUCAAGCUGUU---AUUUUGAUUGGAUAAUCAGA--
((((((..((........--(((((......-..((((((......))))))((((((.....)-)))))........))))).---..))..))))))........-- ( -26.40, z-score =  -2.46, R)
>droYak2.chr2L 17031266 100 - 22324452
UUCAAUUGGACGCGAAAU--GCGCCAAGAUA-UUUAUCGCACAACAGCGAUACCCUUCAAGAUG-UAGGGAACUUCAAGCUGUU---AUUUUAACUGGAUAAUCGAA--
.....((((.(((.....--)))))))....-..((((((......))))))((((.(.....)-.)))).........(.(((---((((.....))))))).)..-- ( -22.00, z-score =  -1.19, R)
>droEre2.scaffold_4929 16521748 100 + 26641161
UUAAAUUGGACGCGAAAU--GCGGUAAGAUA-UUUAUCGCGCCACAGCGAUACCCUGCAAUUUG-CAGGGAGUUUCAAGCUGUU---AUUUCAAUUGAAUCCGCAAG--
.......(((..(((...--((((((((...-))))))))...((((((((.((((((.....)-))))).)))....))))).---.......)))..))).....-- ( -30.20, z-score =  -2.59, R)
>droAna3.scaffold_12916 15533023 108 + 16180835
UUCAAUUGAACGCGAAAAAAGCGACAAAAUA-UUUAUCGCACGACAGCGAUACCCUUCAAUUUACAAGGGAAUUUCGAGCCAAUUGUGUUUUAAUUGAGGCAGUGAAUG
(((((((((((((((......(((.......-..((((((......))))))(((((........)))))....)))......))))).)))))))))).......... ( -27.20, z-score =  -2.65, R)
>dp4.chr4_group3 1490040 84 + 11692001
UUCAAUUGAACGCGAAAA--GCGAAAAGUU--UUUAUCGCACGAUACGGCUACCCUG--GCAGCCAGGGGGUAUAUUGGGCAUA---AUGGAA----------------
((((.......(((((((--((.....)))--))..)))).(((((..(((.(((((--(...))))))))).)))))......---.)))).---------------- ( -23.60, z-score =  -1.50, R)
>droPer1.super_1 2958430 84 + 10282868
UUCAAUUGAACGCGAAAA--GCGAAAAGUU--UUUAUCGCACGAUACGGCUACCCUG--GCAGCCAAGGGGUAUAUUGGGCAUA---AUGGAA----------------
((((..((..((((((((--((.....)))--))..)))).......((((.(....--).))))............)..))..---.)))).---------------- ( -18.20, z-score =   0.19, R)
>droWil1.scaffold_180772 3425700 91 + 8906247
UUCAAUUGAACGCGAAAAU-GUGCAAAAUCAGUUUAUCGCACGAAAUGGUUACCCUACCACAAGGAACGGGCAUAUCCCCUAAG---AAGUCACA--------------
(((..(((...((((((((-...........)))).))))......((((......))))))).....(((......)))...)---))......-------------- ( -12.90, z-score =   1.00, R)
>consensus
UUCAAUUGGACGCGAAAU__GCGGCAAGAUA_UUUAUCGCACGACAGCGAUACCCUUCAAUUUG_AAGGGAAUUUCAAGCUGUU___AUUUUAAUUGGAUAAUCAAA__
....................((((.(((....))).))))............((((..........))))....................................... ( -7.22 =  -7.03 +  -0.18)

alignment

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secondary structure

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dotplot

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Window 7

Location 7,602,474 – 7,602,574
Length 100
Sequences 9
Columns 109
Reading direction reverse
Mean pairwise identity 66.25
Shannon entropy 0.66141
G+C content 0.40943
Mean single sequence MFE -21.97
Consensus MFE -8.33
Energy contribution -8.12
Covariance contribution -0.21
Combinations/Pair 1.43
Mean z-score -1.49
Structure conservation index 0.38
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.75
SVM RNA-class probability 0.808059
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 7602474 100 - 23011544
--UUUGAUUAUCCAAUCAAAAU---AACAGCUUAAGACUCCCUU-CAAAUUAAAGGGUAUCGCUGUCGUGCGAUAAA-UAUCUUACCGC--AUUUCGCGUCCAAUUGAA
--(((((((....)))))))..---.......(((((..(((((-.......)))))((((((......))))))..-..))))).(((--.....))).......... ( -20.80, z-score =  -2.38, R)
>droSim1.chr2L 7399209 100 - 22036055
--UUUGAUUAUCCAAUCAAUAU---AACAGCUUGAAAUUCCCUU-CAAAUUAAAGGGUAUCGCUGUCGUGCGAUAAA-UAUCUUGCCGC--AUUUCGCGUCCAAUUGAG
--.............(((((..---....((..((....(((((-.......)))))((((((......))))))..-..))..))(((--.....)))....))))). ( -21.10, z-score =  -1.80, R)
>droSec1.super_3 3116028 100 - 7220098
--UCUGAUUAUCCAAUCAAAAU---AACAGCUUGAAAUUCCCUU-CAAAUUAAAGGGUAUCGCUGUCGUGCGAUAAA-UAUCUUGCCGC--AUUUCGCGUCCAAUUGAA
--.............((((...---....((..((....(((((-.......)))))((((((......))))))..-..))..))(((--.....))).....)))). ( -20.10, z-score =  -1.65, R)
>droYak2.chr2L 17031266 100 + 22324452
--UUCGAUUAUCCAGUUAAAAU---AACAGCUUGAAGUUCCCUA-CAUCUUGAAGGGUAUCGCUGUUGUGCGAUAAA-UAUCUUGGCGC--AUUUCGCGUCCAAUUGAA
--.((((((.....(((...((---((((((..((....((((.-(.....).))))..))))))))))..)))...-......(((((--.....))))).)))))). ( -24.10, z-score =  -1.44, R)
>droEre2.scaffold_4929 16521748 100 - 26641161
--CUUGCGGAUUCAAUUGAAAU---AACAGCUUGAAACUCCCUG-CAAAUUGCAGGGUAUCGCUGUGGCGCGAUAAA-UAUCUUACCGC--AUUUCGCGUCCAAUUUAA
--..(((((.((((((((....---..))).)))))...(((((-(.....))))))((((((......))))))..-.......))))--)................. ( -29.20, z-score =  -2.54, R)
>droAna3.scaffold_12916 15533023 108 - 16180835
CAUUCACUGCCUCAAUUAAAACACAAUUGGCUCGAAAUUCCCUUGUAAAUUGAAGGGUAUCGCUGUCGUGCGAUAAA-UAUUUUGUCGCUUUUUUCGCGUUCAAUUGAA
.......................((((((((.(((((..(((((........)))))((((((......))))))..-..............))))).).))))))).. ( -24.30, z-score =  -1.72, R)
>dp4.chr4_group3 1490040 84 - 11692001
----------------UUCCAU---UAUGCCCAAUAUACCCCCUGGCUGC--CAGGGUAGCCGUAUCGUGCGAUAAA--AACUUUUCGC--UUUUCGCGUUCAAUUGAA
----------------.((.((---(((((..............((((((--....)))))).......((((....--......))))--.....))))..))).)). ( -18.00, z-score =  -0.72, R)
>droPer1.super_1 2958430 84 - 10282868
----------------UUCCAU---UAUGCCCAAUAUACCCCUUGGCUGC--CAGGGUAGCCGUAUCGUGCGAUAAA--AACUUUUCGC--UUUUCGCGUUCAAUUGAA
----------------.((.((---(((((..............((((((--....)))))).......((((....--......))))--.....))))..))).)). ( -18.00, z-score =  -0.67, R)
>droWil1.scaffold_180772 3425700 91 - 8906247
--------------UGUGACUU---CUUAGGGGAUAUGCCCGUUCCUUGUGGUAGGGUAACCAUUUCGUGCGAUAAACUGAUUUUGCAC-AUUUUCGCGUUCAAUUGAA
--------------.((((...---.....(..((.(((((...((....))..)))))...))..)((((((..........))))))-....))))........... ( -22.10, z-score =  -0.48, R)
>consensus
__UUUGAUUAUCCAAUUAAAAU___AACAGCUUGAAAUUCCCUU_CAAAUUGAAGGGUAUCGCUGUCGUGCGAUAAA_UAUCUUGCCGC__AUUUCGCGUCCAAUUGAA
..........................(((((........((((..........))))....)))))..(((((.....................))))).......... ( -8.33 =  -8.12 +  -0.21)

alignment

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secondary structure

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dotplot

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Window 8

Location 7,602,494 – 7,602,594
Length 100
Sequences 9
Columns 108
Reading direction reverse
Mean pairwise identity 56.58
Shannon entropy 0.86713
G+C content 0.41049
Mean single sequence MFE -20.24
Consensus MFE -4.37
Energy contribution -4.26
Covariance contribution -0.11
Combinations/Pair 1.56
Mean z-score -1.50
Structure conservation index 0.22
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.03
SVM RNA-class probability 0.508830
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 7602494 100 - 23011544
AAAAGCUAACCCGUCA--UUUGUUUGAUUAUCCAAUCAAAAU---AACAGCUUAAGACUCCCUU-CAAAUUAAAGGGUAUCGCUGUCGUGCGAUAAA--UAUCUUACC
..(((((....((...--..))(((((((....)))))))..---...)))))((((..(((((-.......)))))((((((......))))))..--..))))... ( -20.00, z-score =  -2.94, R)
>droSim1.chr2L 7399229 100 - 22036055
AAAAGCUAACCCUUUA--UUUGUUUGAUUAUCCAAUCAAUAU---AACAGCUUGAAAUUCCCUU-CAAAUUAAAGGGUAUCGCUGUCGUGCGAUAAA--UAUCUUGCC
....((..((((((((--.((((((((((....)))))).))---))....(((((......))-)))..))))))))(((((......)))))...--......)). ( -22.00, z-score =  -3.38, R)
>droSec1.super_3 3116048 100 - 7220098
AAAAGCUAACCCUGCA--UUUGUCUGAUUAUCCAAUCAAAAU---AACAGCUUGAAAUUCCCUU-CAAAUUAAAGGGUAUCGCUGUCGUGCGAUAAA--UAUCUUGCC
....((..(((((((.--.((((.(((((....)))))..))---))..))(((((......))-))).....)))))(((((......)))))...--......)). ( -19.40, z-score =  -2.22, R)
>droYak2.chr2L 17031286 100 + 22324452
AAUAGCUAAGCCGACA--UCUGUUCGAUUAUCCAGUUAAAAU---AACAGCUUGAAGUUCCCUA-CAUCUUGAAGGGUAUCGCUGUUGUGCGAUAAA--UAUCUUGGC
....((((((.((((.--...).))).(((((..((....((---((((((..((....((((.-(.....).))))..))))))))))))))))).--...)))))) ( -21.30, z-score =  -0.65, R)
>droEre2.scaffold_4929 16521768 100 - 26641161
AACUGCCAACCUGUCA--UCUGCUUGCGGAUUCAAUUGAAAU---AACAGCUUGAAACUCCCUG-CAAAUUGCAGGGUAUCGCUGUGGCGCGAUAAA--UAUCUUACC
....(((....((..(--((((....))))).))........---.(((((..((....(((((-(.....))))))..))))))))))........--......... ( -26.60, z-score =  -2.14, R)
>droAna3.scaffold_12916 15533045 106 - 16180835
AAAAGUUAAUUGAUCAAGUGCAUUCACUGCCUCAAUUAAAACACAAUUGGCUCGAAAUUCCCUUGUAAAUUGAAGGGUAUCGCUGUCGUGCGAUAAA--UAUUUUGUC
.....((((((((...((((....))))...)))))))).............((((((.(((((........)))))((((((......))))))..--.)))))).. ( -23.70, z-score =  -1.94, R)
>dp4.chr4_group3 1490060 79 - 11692001
----------------------CGGACCUAUCC-UCCCUUCCAU-UAUGCCCAAUAUACCCCCUGGCUGC--CAGGGUAGCCGUAUCGUGCGAUAAA--AACUUUUC-
----------------------.(((....)))-..........-...................((((((--....)))))).((((....))))..--........- ( -14.70, z-score =  -0.04, R)
>droPer1.super_1 2958450 79 - 10282868
----------------------UGGACUUAUCC-UCUCUUCCAU-UAUGCCCAAUAUACCCCUUGGCUGC--CAGGGUAGCCGUAUCGUGCGAUAAA--AACUUUUC-
----------------------.(((....)))-..........-...................((((((--....)))))).((((....))))..--........- ( -14.40, z-score =  -0.10, R)
>droWil1.scaffold_180772 3425720 91 - 8906247
----------------AAAUUCCUGCCUCAUCUAUAUGUGACUU-CUUAGGGGAUAUGCCCGUUCCUUGUGGUAGGGUAACCAUUUCGUGCGAUAAACUGAUUUUGCA
----------------....(((((((((((......))))...-..((((((((......)))))))).)))))))...........(((((..........))))) ( -20.10, z-score =  -0.10, R)
>consensus
AAAAGCUAACCC_UCA__UUUGUUUGCUUAUCCAAUUAAAAU___AACAGCUUGAAAUUCCCUU_CAAAUUGAAGGGUAUCGCUGUCGUGCGAUAAA__UAUCUUGCC
..............................................(((((........((((..........))))....)))))...................... ( -4.37 =  -4.26 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:24:00 2011