Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020798.1 Corchorus olitorius cultivar O-4 contig20831, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 60919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:20794 original size:27 final size:27
Alignment explanation
Indices: 20764--20824 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
20754 CATATAAATT
* *
20764 TATAAATTTAGGTTCAGCGCCACATCA
1 TATAAATTTAGCTCCAGCGCCACATCA
* * *
20791 TATAGACTTAGCTCCAGTGCCACATCA
1 TATAAATTTAGCTCCAGCGCCACATCA
20818 TATAAAT
1 TATAAAT
20825 CATATAGACT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.30
Consensus pattern (27 bp):
TATAAATTTAGCTCCAGCGCCACATCA
Found at i:20834 original size:36 final size:36
Alignment explanation
Indices: 20785--22262 Score: 553
Period size: 36 Copynumber: 47.0 Consensus size: 36
20775 GTTCAGCGCC
*
20785 ACATCATATAGACTTAGCTCCAGTGCCACATCATAT
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
* *
20821 AAATCATATAGACTTAGACT-CAGTGCCACATCATAT
1 ACATCATATAGACTTAG-CTCCAGCGCCACATCATAT
*
20857 ACATCATATAGACTTAGACT-CAGCGCCACATCACAT
1 ACATCATATAGACTTAG-CTCCAGCGCCACATCATAT
* *
20893 ACATCATATAGACTTAGGTCCAGTGCCACATCATAT
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
*
20929 A-GTC-T-TAG-----G-TCCAGCGCCACATCATAT
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
*
20956 A-GTC-T-TAG-----G-TCCAGCGCCACATCATAT
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
*
20983 A-GTC-T-TAG-----G-TCCAGCGCCACATCATAT
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
* *
21010 ACATCATATAGACTTAGACT-CAACGCCACATCATAA
1 ACATCATATAGACTTAG-CTCCAGCGCCACATCATAT
* * * **
21046 ACATCATATACAATTAGGCT-CAGTGGTACATCATAT
1 ACATCATATAGACTTA-GCTCCAGCGCCACATCATAT
* *
21082 ACATCATATAGACTAAGGCT-CAGTGCCACATCATAT
1 ACATCATATAGACTTA-GCTCCAGCGCCACATCATAT
*
21118 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
*
21154 ACATCATATAGACTTAGGTCCAGCG---C--C----
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
*
21181 ACATCATATAGACTTAGGTCCAGCG-C-CA-C----
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
*
21210 --ATCATATAGACTTAGGT-CAGCGCCACATC--AT
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
*
21241 -------ATAGACTTAGGT-CAGCGCCACATC--AT
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
*
21267 -------ATAGACTTAGGT-CAGCGCCACATC--AT
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
*
21293 -------ATAGACTTAGGTCC-GCGCCACATCATAT
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
* *
21321 ATATCATATAGACTTAGGTCCAGCGCCACATCATAT
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
*
21357 A-GTC-T-TAG-----G-TCCAGCGCCACATCATAT
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
*
21384 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
*
21420 A-GTC-T-TAG-----G-TCCAGCG-C-CA-C----
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
*
21440 --ATCATATAGACTTAGGTCCAGCG-C-CA-C----
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
*
21467 --ATCATATAGACTTAGGTCCAGCG-C-CA-C----
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
*
21494 --ATCATATAGACTTAGGTCCAGCGCCACATCATAT
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
* *
21528 A-GTC-T-TAG-----G-TCCAGCACCACATCATAT
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
*
21555 A-GTC-T-TAG-----G-TCCAGCGCCACATCATAT
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
* * * *
21582 ACATTATATAGTCTTAGGTCCAGTGCCACATCATAT
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
*
21618 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
* *
21654 GCATCATATAGACTTAGGTCCAGCG---C--C----
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
*
21681 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
* *
21717 A-GTC-T-TAG-----G-TCCAACGCCACATCATAT
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
* * * *
21744 ACATTATATAGTCTTAGGTCCAGTGCCACATCATAT
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
* * * *
21780 ACATTATATAGTCTTAGGTCCAGTGCCACATCATAT
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
*
21816 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
* *
21852 GCATCATATAGACTTAG-GCCAGCG---C--C----
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
*
21878 ACATCATATAGACTTAGGTCCAGCG-C-CA-C----
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
* *
21907 --ATCATATAGACTTAGGTCCAGTGCCACATC--A-
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
* *
21938 ------TATAGACTTAGGTCCAGCGCCACATTATAT
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
* * *
21968 ACATCATATAGACTTAGGTCCAACGCCACATCATAA
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
* *
22004 ACATCATATAGAATTAGACT-CAGCG---------GT
1 ACATCATATAGACTTAG-CTCCAGCGCCACATCATAT
*
22031 ACATCATATAGACTTAGACT-CAGCCCCACATCATAT
1 ACATCATATAGACTTAG-CTCCAGCGCCACATCATAT
* * * * * *
22067 CCATGATATAGATTTAGGCT-CAGTGTCGCATCATAT
1 ACATCATATAGACTTA-GCTCCAGCGCCACATCATAT
*
22103 ACATCATATAGAACTAAGCT-CAGCGCCACATCATAT
1 ACATCATATAG-ACTTAGCTCCAGCGCCACATCATAT
*
22139 AGA-C---TAG-----GCT-CAGCGCCACATC--AT
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
* * *
22163 -------ATAGGCTTATCT-CAGCGCCATATCATAT
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
22191 ACATCATATAGACTTAGACT-CAGCGCCACATCATAT
1 ACATCATATAGACTTAG-CTCCAGCGCCACATCATAT
* * *
22227 ACATCATATTGACTTAGCT-CAGTGCCATATCATAT
1 ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
22262 A
1 A
22263 GGCTTATCTC
Statistics
Matches: 1222, Mismatches: 92, Indels: 257
0.78 0.06 0.16
Matches are distributed among these distances:
19 2 0.00
20 1 0.00
21 6 0.00
24 3 0.00
25 2 0.00
26 125 0.10
27 364 0.30
28 21 0.02
29 12 0.01
30 16 0.01
31 2 0.00
32 5 0.00
33 17 0.01
34 5 0.00
35 63 0.05
36 569 0.47
37 9 0.01
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.26
Consensus pattern (36 bp):
ACATCATATAGACTTAGCTCCAGCGCCACATCATAT
Found at i:20852 original size:63 final size:62
Alignment explanation
Indices: 20771--22227 Score: 827
Period size: 63 Copynumber: 23.4 Consensus size: 62
20761 ATTTATAAAT
* * *
20771 TTAGGTTCAGCGCCACATCATATAGACTTAGCTCCAGTGCCACATCATATAAATCATATAGAC
1 TTAGG-TCAGCGCCACATCATATAGACTTAGGTCCAGCGCCACATCATATACATCATATAGAC
* * * * *
20834 TTAGACTCAGTGCCACATCATATACATCATATAGACTTAGACTCAGCGCCACATCACATACATCA
1 TTAG-GTCAGCGCCACATCATATAGA-C-T-TAG-----GTC-CAGCGCCACATCATATACATCA
20899 TATAGAC
56 TATAGAC
* * *
20906 TTAGGTCCAGTGCCACATCATATAGTCTTAGGTCCAGCG---C--C----ACATCATATAGTC
1 TTAGGT-CAGCGCCACATCATATAGACTTAGGTCCAGCGCCACATCATATACATCATATAGAC
*
20960 TTAGGTCCAGCGCCACATCATATAGTCTTAGGTCCAGCGCCACATCATATACATCATATAGAC
1 TTAGGT-CAGCGCCACATCATATAGACTTAGGTCCAGCGCCACATCATATACATCATATAGAC
* * * * **
21023 TTAGACTCAACGCCACATCATAAACATCATATACAATTAGG-CTCAGTGGTACATCATATACATC
1 TTAG-GTCAGCG-C-CA-CAT---CAT-ATAGAC--TTAGGTC-CAGCGCCACATCATATACATC
21087 ATATAGAC
55 ATATAGAC
* *
21095 TAAGGCTCAGTGCCACATCATATACATCATATAGACTTAGGTCCAGCGCCACATCATATACATCA
1 TTAGG-TCA--G-CGC--C----ACATCATATAGACTTAGGTCCAGCGCCACATCATATACATCA
21160 TATAGAC
56 TATAGAC
21167 TTAGGTCCAGCGCCACATCATATAGACTTAGGTCCAGCG---C--C----ACATCATATAGAC
1 TTAGGT-CAGCGCCACATCATATAGACTTAGGTCCAGCGCCACATCATATACATCATATAGAC
21221 TTAGGTCAGCGCCACATCATATAGACTTAGGT-CAGCG---C--C----ACATCATATAGAC
1 TTAGGTCAGCGCCACATCATATAGACTTAGGTCCAGCGCCACATCATATACATCATATAGAC
*
21273 TTAGGTCAGCGCCACATCATATAGACTTAGGTCC-GCGCCACATCATATATATCATATAGAC
1 TTAGGTCAGCGCCACATCATATAGACTTAGGTCCAGCGCCACATCATATACATCATATAGAC
*
21334 TTAGGTCCAGCGCCACATCATATAGTCTTAGGTCCAGCGCCACATCATATACATCATATAGAC
1 TTAGGT-CAGCGCCACATCATATAGACTTAGGTCCAGCGCCACATCATATACATCATATAGAC
*
21397 TTAGGTCCAGCGCCACATCATATAGTCTTAGGTCCAGCG---C--C----ACATCATATAGAC
1 TTAGGT-CAGCGCCACATCATATAGACTTAGGTCCAGCGCCACATCATATACATCATATAGAC
21451 TTAGGTCCAGCGCCACATCATATAGACTTAGGTCCAGCG---C--C----ACATCATATAGAC
1 TTAGGT-CAGCGCCACATCATATAGACTTAGGTCCAGCGCCACATCATATACATCATATAGAC
* * * *
21505 TTAGGTCCAGCGCCACATCATATAGTCTTAGGTCCAGCACCACATCATATA-GTC-T-TAG-G
1 TTAGGT-CAGCGCCACATCATATAGACTTAGGTCCAGCGCCACATCATATACATCATATAGAC
* * * * * * *
21564 TCCAGCGCCA-CATCATATACATTATATAGTCTTAGGTCCAGTGCCACATCATATACATCATATA
1 T-TAG-GTCAGC-GC---CACATCATATAGACTTAGGTCCAGCGCCACATCATATACATCATATA
21628 GAC
60 GAC
* * * * ***
21631 TTAGGTCCAGCGCCACATCATAT-GCATCATATA-GACTTAG-GTC-CAGC-GCCACATCATATA
1 TTAGGT-CAGCGCCACATCATATAG-A-C-T-TAGGTC-CAGCGCCACATCATATACATCATATA
21691 GAC
60 GAC
* * * *
21694 TTAGGTCCAGCGCCACATCATATAGTCTTAGGTCCAACGCCACATCATATACATTATATAGTC
1 TTAGGT-CAGCGCCACATCATATAGACTTAGGTCCAGCGCCACATCATATACATCATATAGAC
* * *
21757 TTAGGTCCAGTGCCACATCATATACATTATATAGTCTTAGGTCCAGTGCCACATCATATACATCA
1 TTAGGT-CAGCG-C-CA-C--AT-C---ATATAGACTTAGGTCCAGCGCCACATCATATACATCA
21822 TATAGAC
56 TATAGAC
* * * *
21829 TTAGGTCCAGCGCCACATCATAT-GCATCATATA-GACTTAG-GCCAGC-GC---CACATCATAT
1 TTAGGT-CAGCGCCACATCATATAG-A-C-T-TAGGTC-CAGCGCCA-CATCATATACATCATAT
21887 AGAC
59 AGAC
* * *
21891 TTAGGTCCAGCGCCACATCATATAGACTTAGGTCCAGTGCCACATCATATAGA-C-T-TAG-G
1 TTAGGT-CAGCGCCACATCATATAGACTTAGGTCCAGCGCCACATCATATACATCATATAGAC
* * *** * *
21950 TCCAGCGCCA-CATTATATACATCATATAGACTTAGGTCCAACGCCACATCATAAACATCATATA
1 T-TAG-GTCAGC----GCCACATCATATAGACTTAGGTCCAGCGCCACATCATATACATCATATA
*
22014 GAA
60 GAC
* ** * * * * *
22017 TTAGACTCAGCGGTACATCATATAGACTTA-GACTCAGCCCCACATCATATCCATGATATAGAT
1 TTAG-GTCAGCGCCACATCATATAGACTTAGGTC-CAGCGCCACATCATATACATCATATAGAC
* * * * ** * * * * ***
22080 TTAGGCTCAGTGTCGCATCATATACATCATATAGAACTA-AG-CTCAGC-GCCACATCATATAGA
1 TTAGG-TCAGCGCCACATCATATAGA-C-T-TAGGTCCAGCGCCACATCATATACATCATATAGA
22142 C
62 C
* *
22143 -TAGGCTCAGCGCCACATCATATAGGCTTA--TCTCAGCGCCATATCATATACATCATATAGAC
1 TTAGG-TCAGCGCCACATCATATAGACTTAGGTC-CAGCGCCACATCATATACATCATATAGAC
*
22204 TTAGACTCAGCGCCACATCATATA
1 TTAG-GTCAGCGCCACATCATATA
22228 CATCATATTG
Statistics
Matches: 1117, Mismatches: 147, Indels: 261
0.73 0.10 0.17
Matches are distributed among these distances:
52 55 0.05
53 27 0.02
54 172 0.15
55 1 0.00
57 4 0.00
58 4 0.00
59 14 0.01
60 33 0.03
61 42 0.04
62 116 0.10
63 349 0.31
64 20 0.02
65 22 0.02
66 35 0.03
67 9 0.01
68 2 0.00
69 10 0.01
70 8 0.01
71 6 0.01
72 172 0.15
73 1 0.00
74 6 0.01
75 5 0.00
78 3 0.00
79 1 0.00
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.26
Consensus pattern (62 bp):
TTAGGTCAGCGCCACATCATATAGACTTAGGTCCAGCGCCACATCATATACATCATATAGAC
Found at i:20925 original size:27 final size:27
Alignment explanation
Indices: 20893--21968 Score: 616
Period size: 27 Copynumber: 35.4 Consensus size: 27
20883 CACATCACAT
* *
20893 ACATCATATAGACTTAGGTCCAGTGCC
1 ACATCATATAGTCTTAGGTCCAGCGCC
20920 ACATCATATAGTCTTAGGTCCAGCGCC
1 ACATCATATAGTCTTAGGTCCAGCGCC
20947 ACATCATATAGTCTTAGGTCCAGCGCC
1 ACATCATATAGTCTTAGGTCCAGCGCC
20974 ACATCATATAGTCTTAGGTCCAGCGCC
1 ACATCATATAGTCTTAGGTCCAGCGCC
* * *
21001 ACATCATATACATCATATAGACTTAGACTCAACGCC
1 ACATCATATA-GTC-T-TAG-----GTC-CAGCGCC
* * **
21037 ACATCATAAACATCATATACAATTAGG-CTCAGTGGT
1 ACATCAT----AT-A-GT-C--TTAGGTC-CAGCGCC
* * *
21073 ACATCATATACATCATATAGACTAAGGCTCAGTGCC
1 ACATCATATA-GTC-T-TAG-----GTC-CAGCGCC
*
21109 ACATCATATACATCATATAGACTTAGGTCCAGCGCC
1 A---------CATCATATAGTCTTAGGTCCAGCGCC
*
21145 ACATCATATACATCATATAGACTTAGGTCCAGCGCC
1 ACATCATATA-GTC--------TTAGGTCCAGCGCC
*
21181 ACATCATATAGACTTAGGTCCAGCGCC
1 ACATCATATAGTCTTAGGTCCAGCGCC
*
21208 ACATCATATAGACTTAGGT-CAGCGCC
1 ACATCATATAGTCTTAGGTCCAGCGCC
*
21234 ACATCATATAGACTTAGGT-CAGCGCC
1 ACATCATATAGTCTTAGGTCCAGCGCC
*
21260 ACATCATATAGACTTAGGT-CAGCGCC
1 ACATCATATAGTCTTAGGTCCAGCGCC
*
21286 ACATCATATAGACTTAGGTCC-GCGCCAC
1 ACATCATATAGTCTTAGGTCCAGCG-C-C
*
21314 ATCATATATATCATATAGACTTAGGTCCAGCGCC
1 A-C------ATCATATAGTCTTAGGTCCAGCGCC
21348 ACATCATATAGTCTTAGGTCCAGCGCCACATC
1 ACATCATATAGTCTTAGGTCCAGCG---C--C
*
21380 ATATACATCATATAGACTTAGGTCCAGCGCC
1 ----ACATCATATAGTCTTAGGTCCAGCGCC
21411 ACATCATATAGTCTTAGGTCCAGCGCC
1 ACATCATATAGTCTTAGGTCCAGCGCC
*
21438 ACATCATATAGACTTAGGTCCAGCGCC
1 ACATCATATAGTCTTAGGTCCAGCGCC
*
21465 ACATCATATAGACTTAGGTCCAGCGCC
1 ACATCATATAGTCTTAGGTCCAGCGCC
*
21492 ACATCATATAGACTTAGGTCCAGCGCC
1 ACATCATATAGTCTTAGGTCCAGCGCC
*
21519 ACATCATATAGTCTTAGGTCCAGCACC
1 ACATCATATAGTCTTAGGTCCAGCGCC
21546 ACATCATATAGTCTTAGGTCCAGCGCCAC
1 ACATCATATAGTCTTAGGTCCAGCG-C-C
*
21575 ATCATATACATTATATAGTCTTAGGTCCAGTGCCACATC
1 A-C--AT-C---ATATAGTCTTAGGTCCA--G-CGC--C
*
21614 ATATACATCATATAGACTTAGGTCCAGCGCCACATC
1 ----ACATCATATAGTCTTAGGTCCAGCGC-----C
*
21650 ATATGCATCATATAGACTTAGGTCCAGCGCC
1 --A--CATCATATAGTCTTAGGTCCAGCGCC
*
21681 ACATCATATAGACTTAGGTCCAGCGCC
1 ACATCATATAGTCTTAGGTCCAGCGCC
*
21708 ACATCATATAGTCTTAGGTCCAACGCCAC
1 ACATCATATAGTCTTAGGTCCAGCG-C-C
*
21737 ATCATATACATTATATAGTCTTAGGTCCAGTGCCAC
1 A-C--AT-C---ATATAGTCTTAGGTCCAGCG-C-C
*
21773 ATCATATACATTATATAGTCTTAGGTCCAGTGCCACATC
1 A-C--AT-C---ATATAGTCTTAGGTCCA--G-CGC--C
*
21812 ATATACATCATATAGACTTAGGTCCAGCGCC
1 ----ACATCATATAGTCTTAGGTCCAGCGCC
*
21843 ACATCATAT-GCATCATATAGACTTAGGCCAGCGCC
1 ACATCATATAG--TC-T-TAG-----GTCCAGCGCC
*
21878 ACATCATATAGACTTAGGTCCAGCGCC
1 ACATCATATAGTCTTAGGTCCAGCGCC
* *
21905 ACATCATATAGACTTAGGTCCAGTGCC
1 ACATCATATAGTCTTAGGTCCAGCGCC
*
21932 ACATCATATAGACTTAGGTCCAGCGCC
1 ACATCATATAGTCTTAGGTCCAGCGCC
*
21959 ACATTATATA
1 ACATCATATA
21969 CATCATATAG
Statistics
Matches: 891, Mismatches: 48, Indels: 220
0.77 0.04 0.19
Matches are distributed among these distances:
26 82 0.09
27 438 0.49
28 8 0.01
29 10 0.01
30 13 0.01
31 6 0.01
32 10 0.01
33 9 0.01
34 8 0.01
35 42 0.05
36 220 0.25
37 3 0.00
38 4 0.00
39 5 0.01
40 6 0.01
41 3 0.00
42 9 0.01
43 5 0.01
44 1 0.00
45 9 0.01
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (27 bp):
ACATCATATAGTCTTAGGTCCAGCGCC
Found at i:20975 original size:54 final size:54
Alignment explanation
Indices: 20893--21968 Score: 708
Period size: 54 Copynumber: 17.7 Consensus size: 54
20883 CACATCACAT
*
20893 ACATCATATAGACTTAGGTCCAGTGCCACATCATATAGTCTTAGGTCCAGCGCC
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATATAGTCTTAGGTCCAGCGCC
*
20947 ACATCATATAGTCTTAGGTCCAGCGCCACATCATATAGTCTTAGGTCCAGCGCC
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATATAGTCTTAGGTCCAGCGCC
* * * *
21001 ACATCATATACATCATATAGACTTAGACTCAACGCCACATCATAAACATCATATACAATTAGG-C
1 ACATCATATAGA-C-T-TAG-----GTC-CAGCGCCACATCAT----AT-A-GT-C--TTAGGTC
* *
21065 TCAGTGGTAC
48 -CAG-CG-CC
* * *
21075 ATCATATACATCATATAGACTAAGG-CTCAGTGCCACATCATATACATCATATAGACTTAGGTCC
1 A-------CATCATATAGACTTAGGTC-CA--G-CGC--C----ACATCATATAGTCTTAGGTCC
21139 AGCGCCAC
49 AGCG-C-C
*
21147 ATCATATACATCATATAGACTTAGGTCCAGCGCCACATCATATAGACTTAGGTCCAGCGCC
1 A-C--AT-CAT-A--TAGACTTAGGTCCAGCGCCACATCATATAGTCTTAGGTCCAGCGCC
*
21208 ACATCATATAGACTTAGGT-CAGCGCCACATCATATAGACTTAGGT-CAGCGCC
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATATAGTCTTAGGTCCAGCGCC
*
21260 ACATCATATAGACTTAGGT-CAGCGCCACATCATATAGACTTAGGTCC-GCGCCAC
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATATAGTCTTAGGTCCAGCG-C-C
21314 ATCATATATATCATATAGACTTAGGTCCAGCGCCACATCATATAGTCTTAGGTCCAGCGCCACAT
1 A-C------ATCATATAGACTTAGGTCCAGCGCCACATCATATAGTCTTAGGTCCAGCG---C--
21379 C
54 C
21380 ATATACATCATATAGACTTAGGTCCAGCGCCACATCATATAGTCTTAGGTCCAGCGCC
1 ----ACATCATATAGACTTAGGTCCAGCGCCACATCATATAGTCTTAGGTCCAGCGCC
*
21438 ACATCATATAGACTTAGGTCCAGCGCCACATCATATAGACTTAGGTCCAGCGCC
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATATAGTCTTAGGTCCAGCGCC
*
21492 ACATCATATAGACTTAGGTCCAGCGCCACATCATATAGTCTTAGGTCCAGCACC
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATATAGTCTTAGGTCCAGCGCC
* *
21546 ACATCATATAGTCTTAGGTCCAGCGCCACATCATATACATTATATAGTCTTAGGTCCAGTGCCAC
1 ACATCATATAGACTTAGGTCCAGCG-C-CA-C--AT-C---ATATAGTCTTAGGTCCA--G-CGC
21611 ATC
54 --C
*
21614 ATATACATCATATAGACTTAGGTCCAGCGCCACATCATATGCATCATATAGACTTAGGTCCAGCG
1 ----ACATCATATAGACTTAGGTCCAGCG---C--C--A--CATCATATAGTCTTAGGTCCAGCG
21679 CC
53 CC
*
21681 ACATCATATAGACTTAGGTCCAGCGCCACATCATATAGTCTTAGGTCCAACGCCAC
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATATAGTCTTAGGTCCAGCG-C-C
* *
21737 ATCATATACATTATATAGTCTTAGGTCCAGTGCCACATCATATACATTATATAGTCTTAGGTCCA
1 A-C--AT-C---ATATAGACTTAGGTCCAGCG-C-CA-C--AT-C---ATATAGTCTTAGGTCCA
*
21802 GTGCCACATC
50 --G-CGC--C
*
21812 ATATACATCATATAGACTTAGGTCCAGCGCCACATCATAT-GCATCATATAGACTTAGGCCAGCG
1 ----ACATCATATAGACTTAGGTCCAGCGCCACATCATATAG--TC-T-TAG-----GTCCAGCG
21876 CC
53 CC
* *
21878 ACATCATATAGACTTAGGTCCAGCGCCACATCATATAGACTTAGGTCCAGTGCC
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATATAGTCTTAGGTCCAGCGCC
*
21932 ACATCATATAGACTTAGGTCCAGCGCCACATTATATA
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATATA
21969 CATCATATAG
Statistics
Matches: 848, Mismatches: 49, Indels: 250
0.74 0.04 0.22
Matches are distributed among these distances:
52 55 0.06
53 28 0.03
54 270 0.32
55 4 0.00
56 7 0.01
57 8 0.01
58 4 0.00
59 7 0.01
60 6 0.01
61 20 0.02
62 67 0.08
63 156 0.18
64 3 0.00
65 5 0.01
66 11 0.01
67 6 0.01
68 8 0.01
69 12 0.01
70 7 0.01
71 7 0.01
72 108 0.13
73 4 0.00
74 5 0.01
75 7 0.01
76 5 0.01
77 4 0.00
78 4 0.00
79 2 0.00
80 1 0.00
81 17 0.02
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (54 bp):
ACATCATATAGACTTAGGTCCAGCGCCACATCATATAGTCTTAGGTCCAGCGCC
Found at i:20980 original size:162 final size:160
Alignment explanation
Indices: 20771--22139 Score: 972
Period size: 162 Copynumber: 8.8 Consensus size: 160
20761 ATTTATAAAT
* * * *
20771 TTAGGTTCAGCGCCACATCATATAGACTTAGCTCCAGTGCCACATCATATAAATCATATAGACTT
1 TTAGGTCCAGCGCCACATCATATAGACTTAGGTCCAGCGCCACATCATATACATCATATAGACTT
* * *
20836 AGACTCAGTGCCACATCATATACATCATATAGACTTAGACTCAGCGCCACATCACATACATCATA
66 AG-GTCAGCGCCACATCATATACATCATATAGACTTAG-CTCAGCGCCACATCATATACATCATA
* *
20901 TAGACTTAGGTCCAGTGCCACATCATATAGTC
129 TAGACTTAGGTCCAGCGCCACATCATATAGAC
* *
20933 TTAGGTCCAGCGCCACATCATATAGTCTTAGGTCCAGCG---C--C----ACATCATATAGTCTT
1 TTAGGTCCAGCGCCACATCATATAGACTTAGGTCCAGCGCCACATCATATACATCATATAGACTT
* *
20989 AGGTCCAGCGCCACATCATATACATCATATAGACTTAGACTCAACGCCACATCATAAACATCATA
66 AGGT-CAGCGCCACATCATATACATCATATAGACTTAG-CTCAGCGCCACATCATATACATCATA
* * *
21054 TACAATTAGG-CTCAGTGGTACATCATATACATCATATAGAC
129 TAGACTTAGGTC-CAG-CG--C--C----ACATCATATAGAC
* *
21095 TAAGG-CTCAGTGCCACATCATATACATCATATAGACTTAGGTCCAGCGCCACATCATATACATC
1 TTAGGTC-CA--G-CGC--C----ACATCATATAGACTTAGGTCCAGCGCCACATCATATACATC
* *
21159 ATATAGACTTAGGTCCAGCGCCACATCATATAGA-C-T-TAG--GT--C-CAGCG---C--C---
56 ATATAGACTTAGGT-CAGCGCCACATCATATACATCATATAGACTTAGCTCAGCGCCACATCATA
21208 -ACATCATATAGACTTAGGT-CAGCGCCACATCATATAGAC
120 TACATCATATAGACTTAGGTCCAGCGCCACATCATATAGAC
21247 TTAGGT-CAGCGCCACATCATATAGACTTAGGT-CAGCG---C--C----ACATCATATAGACTT
1 TTAGGTCCAGCGCCACATCATATAGACTTAGGTCCAGCGCCACATCATATACATCATATAGACTT
* * * *
21301 AGGTCCGCGCCACATCATATATATCATATAGACTTAGGTCCAGCGCCACATCATATA-GTC-T-T
66 AGGTCAGCGCCACATCATATACATCATATAGACTTAGCT-CAGCGCCACATCATATACATCATAT
* * * * ***
21363 AG-GTCCAGCGCCACATCATATACATCATATAGAC
130 AGACT-TAG-GTC-CAGC-GCCACATCATATAGAC
*
21397 TTAGGTCCAGCGCCACATCATATAGTCTTAGGTCCAGCG---C--C----ACATCATATAGACTT
1 TTAGGTCCAGCGCCACATCATATAGACTTAGGTCCAGCGCCACATCATATACATCATATAGACTT
* *
21453 AGGTCCAGCGCCACATCATATAGA-C-T-TAG--GT--C-CAGCG---C--C----ACATCATAT
66 AGGT-CAGCGCCACATCATATACATCATATAGACTTAGCTCAGCGCCACATCATATACATCATAT
*
21501 AGACTTAGGTCCAGCGCCACATCATATAGTC
130 AGACTTAGGTCCAGCGCCACATCATATAGAC
* * * *
21532 TTAGGTCCAGCACCACATCATATAGTCTTAGGTCCAGCGCCACATCATATACATTATATAGTCTT
1 TTAGGTCCAGCGCCACATCATATAGACTTAGGTCCAGCGCCACATCATATACATCATATAGACTT
* * *
21597 AGGTCCAGTGCCACATCATATACATCATATAGACTTAGGTCCAGCGCCACATCATATGCATCATA
66 AGGT-CAGCGCCACATCATATACATCATATAGACTTAGCT-CAGCGCCACATCATATACATCATA
21662 TAGACTTAGGTCCAGCGCCACATCATATAGAC
129 TAGACTTAGGTCCAGCGCCACATCATATAGAC
* * * *
21694 TTAGGTCCAGCGCCACATCATATAGTCTTAGGTCCAACGCCACATCATATACATTATATAGTCTT
1 TTAGGTCCAGCGCCACATCATATAGACTTAGGTCCAGCGCCACATCATATACATCATATAGACTT
* * * * *
21759 AGGTCCAGTGCCACATCATATACATTATATAGTCTTAGGTCCAGTGCCACATCATATACATCATA
66 AGGT-CAGCGCCACATCATATACATCATATAGACTTAGCT-CAGCGCCACATCATATACATCATA
21824 TAGACTTAGGTCCAGCGCCACATCATATGCATCATATAGAC
129 TAGACTTAGGTCCAGCG---C--C--A--CATCATATAGAC
21865 TTAGG-CCAGCGCCACATCATATAGACTTAGGTCCAGCG---C--C----ACATCATATAGACTT
1 TTAGGTCCAGCGCCACATCATATAGACTTAGGTCCAGCGCCACATCATATACATCATATAGACTT
* * * *
21920 AGGTCCAGTGCCACATCATATAGA-C-T-TAG--GT--C-CAGCGCCACATTATATACATCATAT
66 AGGT-CAGCGCCACATCATATACATCATATAGACTTAGCTCAGCGCCACATCATATACATCATAT
* * *
21977 AGACTTAGGTCCAACGCCACATCATAAACATC
130 AGACTTAGGTCCAGCGCCACATCATATAGA-C
* ** * * * *
22009 ATATAGAATTAGACTCAGCGGTACATCATATAGACTTA-GACTCAGCCCCACATCATATCCATGA
1 -T-TAG-----GTC-CAGCGCCACATCATATAGACTTAGGTC-CAGCGCCACATCATATACATCA
* * * * *
22073 TATAGATTTAGGCTCAGTGTCGCATCATATACATCATATAGAACTAAGCTCAGCGCCACATCATA
57 TATAGACTTAGG-TCAGCGCCACATCATATACATCATATAG-ACTTAGCTCAGCGCCACATCATA
22138 TA
120 TA
22140 GACTAGGCTC
Statistics
Matches: 985, Mismatches: 94, Indels: 247
0.74 0.07 0.19
Matches are distributed among these distances:
131 17 0.02
132 20 0.02
133 1 0.00
134 3 0.00
135 51 0.05
136 7 0.01
137 3 0.00
138 7 0.01
139 2 0.00
140 6 0.01
141 6 0.01
142 19 0.02
143 10 0.01
144 41 0.04
145 5 0.01
146 10 0.01
147 6 0.01
148 5 0.01
149 7 0.01
150 22 0.02
151 29 0.03
152 87 0.09
153 129 0.13
154 1 0.00
156 5 0.01
157 1 0.00
158 7 0.01
159 2 0.00
160 1 0.00
161 40 0.04
162 279 0.28
163 2 0.00
164 2 0.00
165 7 0.01
166 1 0.00
167 3 0.00
168 1 0.00
169 1 0.00
170 32 0.03
171 61 0.06
172 1 0.00
174 1 0.00
175 1 0.00
176 1 0.00
177 3 0.00
178 1 0.00
179 1 0.00
180 37 0.04
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.26
Consensus pattern (160 bp):
TTAGGTCCAGCGCCACATCATATAGACTTAGGTCCAGCGCCACATCATATACATCATATAGACTT
AGGTCAGCGCCACATCATATACATCATATAGACTTAGCTCAGCGCCACATCATATACATCATATA
GACTTAGGTCCAGCGCCACATCATATAGAC
Found at i:22061 original size:27 final size:27
Alignment explanation
Indices: 22004--22066 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
21994 CACATCATAA
***
22004 ACATCATATAGAATTAGACTCAGCGGT
1 ACATCATATAGAATTAGACTCAGCCCC
*
22031 ACATCATATAGACTTAGACTCAGCCCC
1 ACATCATATAGAATTAGACTCAGCCCC
22058 ACATCATAT
1 ACATCATAT
22067 CCATGATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (27 bp):
ACATCATATAGAATTAGACTCAGCCCC
Found at i:22076 original size:99 final size:98
Alignment explanation
Indices: 21905--22165 Score: 287
Period size: 99 Copynumber: 2.6 Consensus size: 98
21895 GTCCAGCGCC
* * * * *
21905 ACATCATATAG-ACTTAGGTCCAGTGCCACATCATATAGACTTAGGTCCAGCGCCACATTATATA
1 ACATCATATAGAACTAAGCT-CAGCGCCACATCATATAGACTTAGCT-CAGCGCCACATCATATA
21969 CATCATATAGACTTAGG-TCCAACGCCACATCATAA
64 CATCATATAGACTTAGGCT-CAACGCCACATCATAA
* ** * *
22004 ACATCATATAGAA-TTAGACTCAGCGGTACATCATATAGACTTAGACTCAGCCCCACATCATATC
1 ACATCATATAGAACTAAG-CTCAGCGCCACATCATATAGACTTAG-CTCAGCGCCACATCATATA
* * ** * * *
22068 CATGATATAGATTTAGGCTCAGTGTCGCATCATAT
64 CATCATATAGACTTAGGCTCAACGCCACATCATAA
22103 ACATCATATAGAACTAAGCTCAGCGCCACATCATATAGAC-TAGGCTCAGCGCCACATCATATA
1 ACATCATATAGAACTAAGCTCAGCGCCACATCATATAGACTTA-GCTCAGCGCCACATCATATA
22166 GGCTTATCTC
Statistics
Matches: 136, Mismatches: 20, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
98 19 0.14
99 110 0.81
100 7 0.05
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (98 bp):
ACATCATATAGAACTAAGCTCAGCGCCACATCATATAGACTTAGCTCAGCGCCACATCATATACA
TCATATAGACTTAGGCTCAACGCCACATCATAA
Found at i:22141 original size:27 final size:26
Alignment explanation
Indices: 22103--22191 Score: 117
Period size: 26 Copynumber: 3.4 Consensus size: 26
22093 CGCATCATAT
*
22103 ACATCATATAGAACTAAGCTCAGCGCC
1 ACATCATATAG-ACTTAGCTCAGCGCC
22130 ACATCATATAGAC-TAGGCTCAGCGCC
1 ACATCATATAGACTTA-GCTCAGCGCC
* *
22156 ACATCATATAGGCTTATCTCAGCGCC
1 ACATCATATAGACTTAGCTCAGCGCC
*
22182 ATATCATATA
1 ACATCATATA
22192 CATCATATAG
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
25 1 0.02
26 42 0.75
27 13 0.23
ACGTcount: A:0.34, C:0.28, G:0.15, T:0.24
Consensus pattern (26 bp):
ACATCATATAGACTTAGCTCAGCGCC
Found at i:22190 original size:88 final size:92
Alignment explanation
Indices: 22095--22288 Score: 254
Period size: 97 Copynumber: 2.1 Consensus size: 92
22085 CTCAGTGTCG
*
22095 CATCATATACATCATATAGAACTAAG-CTCAGCGCCACATCATATAGA-C-TA-G-GCTCAGCGC
1 CATCATATACATCATATAG-ACTAAGACTCAGCGCCACATCATATACATCATATGAGCTCAGCGC
22155 CACATCATATAGGCTTATCTCAGCGCCA
65 CACATCATATAGGCTTATCTCAGCGCCA
* *
22183 TATCATATACATCATATAGACTTAGACTCAGCGCCACATCATATACATCATATTGACTTAGCTCA
1 CATCATATACATCATATAGACTAAGACTCAGCGCCACATCATATACATCATA-TG----AGCTCA
* *
22248 GTGCCATATCATATAGGCTTATCTCAGCGCCA
61 GCGCCACATCATATAGGCTTATCTCAGCGCCA
22280 CATCATATA
1 CATCATATA
22289 GACTTAGGCT
Statistics
Matches: 90, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
87 5 0.06
88 38 0.42
89 1 0.01
90 2 0.02
92 1 0.01
97 43 0.48
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (92 bp):
CATCATATACATCATATAGACTAAGACTCAGCGCCACATCATATACATCATATGAGCTCAGCGCC
ACATCATATAGGCTTATCTCAGCGCCA
Found at i:22311 original size:27 final size:27
Alignment explanation
Indices: 22227--22513 Score: 283
Period size: 27 Copynumber: 10.4 Consensus size: 27
22217 CACATCATAT
* *
22227 ACATCATATTGACTTA-GCTCAGTGCC
1 ACATCATATAGACTTAGGCTCAGCGCC
* * *
22253 ATATCATATAGGCTTA-TCTCAGCGCC
1 ACATCATATAGACTTAGGCTCAGCGCC
22279 ACATCATATAGACTTAGGCTCAGCGCC
1 ACATCATATAGACTTAGGCTCAGCGCC
* * * *
22306 ATATCATATGGACTTAGACTCAACGCC
1 ACATCATATAGACTTAGGCTCAGCGCC
* * *
22333 ACATCATATATATCATATATACTTAGCTCAGTGCC
1 ACATCATATAGA-C---T-TA---GGCTCAGCGCC
22368 ACATCATATAGACTTAGGCTCAGCGCC
1 ACATCATATAGACTTAGGCTCAGCGCC
* *
22395 ACATCATATAGACTTTGTCTCAGCGCC
1 ACATCATATAGACTTAGGCTCAGCGCC
* *
22422 ATATCATATAAACTTAGGCTCAGCGCC
1 ACATCATATAGACTTAGGCTCAGCGCC
* *
22449 ACATCATATAGTCTTAGG-TCTAGCACC
1 ACATCATATAGACTTAGGCTC-AGCGCC
* * *
22476 ACATCATATAGACCTAGACCCAGCGCC
1 ACATCATATAGACTTAGGCTCAGCGCC
22503 ACATCATATAG
1 ACATCATATAG
22514 GTTTATGCAT
Statistics
Matches: 213, Mismatches: 37, Indels: 21
0.79 0.14 0.08
Matches are distributed among these distances:
26 37 0.17
27 149 0.70
28 2 0.01
30 2 0.01
31 2 0.01
32 2 0.01
34 1 0.00
35 18 0.08
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
ACATCATATAGACTTAGGCTCAGCGCC
Found at i:22376 original size:35 final size:36
Alignment explanation
Indices: 22306--22377 Score: 101
Period size: 35 Copynumber: 2.0 Consensus size: 36
22296 GCTCAGCGCC
*
22306 ATATCATATGGACTTAGACTCAACGCCACATCATAT
1 ATATCATATAGACTTAGACTCAACGCCACATCATAT
* **
22342 ATATCATATATACTTAG-CTCAGTGCCACATCATAT
1 ATATCATATAGACTTAGACTCAACGCCACATCATAT
22377 A
1 A
22378 GACTTAGGCT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 17 0.53
36 15 0.47
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.31
Consensus pattern (36 bp):
ATATCATATAGACTTAGACTCAACGCCACATCATAT
Found at i:22383 original size:89 final size:89
Alignment explanation
Indices: 22253--22512 Score: 297
Period size: 89 Copynumber: 3.0 Consensus size: 89
22243 GCTCAGTGCC
** * * *
22253 ATATCATATAGGCTTATCTCAGCGCCACATCATATAGACTTAGGCTCAGCGCCATATCATATGGA
1 ATATCATATAAACTTAGCTCAGCGCCACATCATATAGACTTAGGCTCAGCGCCACATCATATAGA
22318 CTTAGACTCAACGCCACATCATAT
66 CTTAGACTCAACGCCACATCATAT
* *
22342 ATATCATATATACTTAGCTCAGTGCCACATCATATAGACTTAGGCTCAGCGCCACATCATATAGA
1 ATATCATATAAACTTAGCTCAGCGCCACATCATATAGACTTAGGCTCAGCGCCACATCATATAGA
* * *
22407 CTTTGTCTC-A-G-CGC--C----
66 CTTAGACTCAACGCCACATCATAT
* *
22422 ATATCATATAAACTTAGGCTCAGCGCCACATCATATAGTCTTAGG-TCTAGCACCACATCATATA
1 ATATCATATAAACTTA-GCTCAGCGCCACATCATATAGACTTAGGCTC-AGCGCCACATCATATA
* * *
22486 GACCTAGACCCAGCGCCACATCATAT
64 GACTTAGACTCAACGCCACATCATAT
22512 A
1 A
22513 GGTTTATGCA
Statistics
Matches: 141, Mismatches: 19, Indels: 21
0.78 0.10 0.12
Matches are distributed among these distances:
80 17 0.12
81 48 0.34
83 1 0.01
84 3 0.02
86 3 0.02
87 1 0.01
88 1 0.01
89 66 0.47
90 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.27
Consensus pattern (89 bp):
ATATCATATAAACTTAGCTCAGCGCCACATCATATAGACTTAGGCTCAGCGCCACATCATATAGA
CTTAGACTCAACGCCACATCATAT
Found at i:22803 original size:37 final size:37
Alignment explanation
Indices: 22762--22840 Score: 151
Period size: 37 Copynumber: 2.2 Consensus size: 37
22752 GTGTAAATGT
22762 TGTTTGCTATTGATGTTTGAATGTTGATATATTTGTA
1 TGTTTGCTATTGATGTTTGAATGTTGATATATTTGTA
22799 TGTTTGCTATTGATGTTTGAATGTTGATATATTTGTA
1 TGTTTGCTATTGATGTTTGAATGTTGATATATTTGTA
22836 T-TTTG
1 TGTTTG
22841 AATTGCTCGT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 4 0.10
37 38 0.90
ACGTcount: A:0.20, C:0.03, G:0.22, T:0.56
Consensus pattern (37 bp):
TGTTTGCTATTGATGTTTGAATGTTGATATATTTGTA
Found at i:23138 original size:26 final size:26
Alignment explanation
Indices: 23102--23156 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
23092 TGTTTTATTC
23102 CTTATGGTGGTGTGTTTGATTGAAAT
1 CTTATGGTGGTGTGTTTGATTGAAAT
23128 CTTATGGTGGTGTGTTTGATTGAAAT
1 CTTATGGTGGTGTGTTTGATTGAAAT
23154 CTT
1 CTT
23157 TGATTTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.18, C:0.05, G:0.29, T:0.47
Consensus pattern (26 bp):
CTTATGGTGGTGTGTTTGATTGAAAT
Found at i:23678 original size:29 final size:31
Alignment explanation
Indices: 23646--23712 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
23636 ACGCAATTTG
23646 GGATATAACGTTA-CAAAA-CAAGCAATTAA
1 GGATATAACGTTATCAAAAGCAAGCAATTAA
* *
23675 GGATATAACGTTATGAAAAGCGAGCAATTAA
1 GGATATAACGTTATCAAAAGCAAGCAATTAA
23706 GGATATA
1 GGATATA
23713 GTCAGCTAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 13 0.38
30 4 0.12
31 17 0.50
ACGTcount: A:0.48, C:0.10, G:0.19, T:0.22
Consensus pattern (31 bp):
GGATATAACGTTATCAAAAGCAAGCAATTAA
Found at i:23901 original size:32 final size:31
Alignment explanation
Indices: 23832--23908 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
23822 CCTATCTGAT
* **
23832 TATATCCTTAATCGCTTGAAATCGAAAACAA
1 TATATCCTTAATTGCTTGAAATAAAAAACAA
**
23863 TATATCCTTAATTGCTTGAAATAAAAAAACGT
1 TATATCCTTAATTGCTTGAAAT-AAAAAACAA
*
23895 TTTATCCTTAATTG
1 TATATCCTTAATTG
23909 TTTGCTTTGT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 21 0.54
32 18 0.46
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (31 bp):
TATATCCTTAATTGCTTGAAATAAAAAACAA
Found at i:24038 original size:19 final size:19
Alignment explanation
Indices: 24008--24045 Score: 60
Period size: 18 Copynumber: 2.0 Consensus size: 19
23998 AGAAAAGAAA
24008 ATAATTTGAATA-TTATTT
1 ATAATTTGAATATTTATTT
24026 ATAATTATGAATATTTATTT
1 ATAATT-TGAATATTTATTT
24046 TGATTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 6 0.33
20 6 0.33
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
ATAATTTGAATATTTATTT
Found at i:24786 original size:31 final size:31
Alignment explanation
Indices: 24748--24846 Score: 126
Period size: 31 Copynumber: 3.2 Consensus size: 31
24738 TTTAGGATAT
* * **
24748 ATATAACGTTTGCTATCGCAAGCAATTAAGG
1 ATATAACGTTTTCAATTTCAAGCAATTAAGG
* * *
24779 ATATAACGTTTTCGATTTTAAGAAATTAAGG
1 ATATAACGTTTTCAATTTCAAGCAATTAAGG
*
24810 ATATAACGTTTTCAATTTCAAGCAATTAATG
1 ATATAACGTTTTCAATTTCAAGCAATTAAGG
24841 ATATAA
1 ATATAA
24847 TCAGTTAGGG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 58 1.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.35
Consensus pattern (31 bp):
ATATAACGTTTTCAATTTCAAGCAATTAAGG
Found at i:25086 original size:24 final size:25
Alignment explanation
Indices: 25059--25114 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 25
25049 CCTGAATTGA
*
25059 TTATTTAGCCTTTTTATT-GC-TTCG
1 TTATTTAGACTTTTT-TTGGCTTTCG
*
25083 TTATTTTGACTTTTTTTGGGCTTTCG
1 TTATTTAGACTTTTTTT-GGCTTTCG
25109 TTATTT
1 TTATTT
25115 TTCGTTATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 2 0.07
24 13 0.48
25 2 0.07
26 10 0.37
ACGTcount: A:0.11, C:0.12, G:0.14, T:0.62
Consensus pattern (25 bp):
TTATTTAGACTTTTTTTGGCTTTCG
Found at i:25812 original size:6 final size:6
Alignment explanation
Indices: 25802--25846 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
25792 TGTTTATTCA
* *
25802 AAAAAA AAAAAC -AAAAC AAAAAC AAAAAC AAAAAC TAAAAC AAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAA
25847 GCGAAACGGC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
5 5 0.14
6 30 0.86
ACGTcount: A:0.84, C:0.13, G:0.00, T:0.02
Consensus pattern (6 bp):
AAAAAC
Found at i:31028 original size:2 final size:2
Alignment explanation
Indices: 31021--31056 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
31011 AGGAAAATTG
31021 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31057 TACATTTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32532 original size:334 final size:321
Alignment explanation
Indices: 31736--32564 Score: 972
Period size: 322 Copynumber: 2.5 Consensus size: 321
31726 TTTTGGCAAA
* * * * *
31736 AATACTCATAAAATATATATAAGTCAAGGCCAAAAAGATTG-GAGGACTTTTCACGCTTTTAATA
1 AATACTCAGAAAA-ATATATAATTCAACGCCAAAAAGATTGACAGG-CTTTTCACGCTTCTAATA
* * *
31800 TCGTTTTTCATATTTTTTTA-GAATTAATTTCTAATTAAATCGAAACAAGATTCATATGCACATA
64 TCGTTTTTC-CATTTTTTTACGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATA
31864 AAAATAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATACAAATATTTCAAGGAGT
128 AAAATAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATACAAATATTTCAAGGAGT
* * * *
31929 CTCAGCGCCAAAAATCATGCAAAACAGAGCCGTGGCCTCGGAACGCGTTTTTAGTCAAAAATCGT
193 CTCAGCGCCAAAAATCATGCAAAACAGAGCCGGGGCCTCGGAACACGTTTTTAGCCAAAAACCGT
* * * *
31994 AATGTTATTACACTATTTCGCCTAAAAACTGTCCCGAAACGTTTTTTTCTCAATTTTTTGCCAC
258 AATGTTAGTACACGATTTCGCCTAAAAACTGTCCCGAAAAGTTTTTTGCTCAATTTTTTGCCAC
32058 AATACTCAGAAAAATATATAATTCAACGCCAAAAAGATTGACAGGCTTTTCACGCTTCTAATATC
1 AATACTCAGAAAAATATATAATTCAACGCCAAAAAGATTGACAGGCTTTTCACGCTTCTAATATC
* *
32123 GTTTTTCCCATTTTTTT-CTGAATTAATTTCTAATTAAATCGAAACAAAATTTAGATGCTCATAA
66 GTTTTT-CCATTTTTTTAC-GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAA
* * * * * * * *
32187 AAACAAATCCTTATATCCAATGTGGATGACATTTGGTTCGATGGATATAGATATTTCAAGGAGTC
129 AAATAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATACAAATATTTCAAGGAGTC
** * **** *
32252 TTTGCGTCAAAAATCATGCAAATTTTAGCTGGGG-CTCCGGAACACGTTTTTA-CCAAGAAACCG
194 TCAGCGCCAAAAATCATGCAAAACAGAGCCGGGGCCT-CGGAACACGTTTTTAGCCAA-AAACCG
* * **
32315 TGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATAAACCCGAAAAG-TTTTTGCTCAA
257 TAAT-GTTAGTACACGATTTCGCCTAAAA-ACTG------T---CCCGAAAAGTTTTTTGCTCAA
32379 TTTTTTGCCAC
311 TTTTTTGCCAC
* * * *
32390 AGTATTCAGAAAAAATATATAATTCAACGCCAAAAA-ATTTGA-ATGGTTTTTTCAGGCTTCTAA
1 AATACTCAG-AAAAATATATAATTCAACGCCAAAAAGA-TTGACA-GG-CTTTTCACGCTTCTAA
* * *
32453 TATCGTTTTTCCATTTTTTTACCGCATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG
62 TATCGTTTTTCCATTTTTTTA-CGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCA
* *
32518 TAAAAATAAATCCTTAAATCCATTGTGGCTGAGATTTAGTTAGATGA
126 TAAAAATAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGA
32565 CTTTTGAAGG
Statistics
Matches: 429, Mismatches: 55, Indels: 34
0.83 0.11 0.07
Matches are distributed among these distances:
321 63 0.15
322 161 0.38
323 21 0.05
324 2 0.00
330 1 0.00
332 30 0.07
333 50 0.12
334 100 0.23
335 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (321 bp):
AATACTCAGAAAAATATATAATTCAACGCCAAAAAGATTGACAGGCTTTTCACGCTTCTAATATC
GTTTTTCCATTTTTTTACGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAA
ATAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATACAAATATTTCAAGGAGTCTC
AGCGCCAAAAATCATGCAAAACAGAGCCGGGGCCTCGGAACACGTTTTTAGCCAAAAACCGTAAT
GTTAGTACACGATTTCGCCTAAAAACTGTCCCGAAAAGTTTTTTGCTCAATTTTTTGCCAC
Found at i:34305 original size:140 final size:140
Alignment explanation
Indices: 34123--34402 Score: 506
Period size: 140 Copynumber: 2.0 Consensus size: 140
34113 CATCATCGAA
*
34123 AACCTTAGTGATAGAGAATTTAGAAATCTGACATTCTAAATCGCGGATAGGAAGGAAAGTGTCTA
1 AACCTTAGTGATAGAGAATTTAGAAATATGACATTCTAAATCGCGGATAGGAAGGAAAGTGTCTA
* * *
34188 TGGATTTCCACTTTTTGATTTTAAAAAAGTTGCCACAATATCTTTGGATGAAAGGTAAGAAATGA
66 AGGATTTCCACTTGTTGATTTTAAAAAAGTTGCCACAACATCTTTGGATGAAAGGTAAGAAATGA
34253 TGTGGAGAAG
131 TGTGGAGAAG
*
34263 AACCTTAGTGATAGAGAATTTAGAAATATGACATTCTAAATCGCGGATAGGAATGAAAGTGTCTA
1 AACCTTAGTGATAGAGAATTTAGAAATATGACATTCTAAATCGCGGATAGGAAGGAAAGTGTCTA
*
34328 AGGGTTTCCACTTGTTGATTTTAAAAAAGTTGCCACAACATCTTTGGATGAAAGGTAAGAAATGA
66 AGGATTTCCACTTGTTGATTTTAAAAAAGTTGCCACAACATCTTTGGATGAAAGGTAAGAAATGA
34393 TGTGGAGAAG
131 TGTGGAGAAG
34403 GTTTGCTAAT
Statistics
Matches: 134, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 134 1.00
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (140 bp):
AACCTTAGTGATAGAGAATTTAGAAATATGACATTCTAAATCGCGGATAGGAAGGAAAGTGTCTA
AGGATTTCCACTTGTTGATTTTAAAAAAGTTGCCACAACATCTTTGGATGAAAGGTAAGAAATGA
TGTGGAGAAG
Found at i:34777 original size:45 final size:46
Alignment explanation
Indices: 34691--34779 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 46
34681 GTTAGTATAT
34691 TAACACTCAAATTCAACAAAAAAAAACACTCTTGATTCTTGATTAC
1 TAACACTCAAATTCAACAAAAAAAAACACTCTTGATTCTTGATTAC
*
34737 TAACACTCAAATTCAAC-AAAGAAAACACTCTTGATTCTTGATT
1 TAACACTCAAATTCAACAAAAAAAAACACTCTTGATTCTTGATT
34780 TTAATTGCAG
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
45 25 0.60
46 17 0.40
ACGTcount: A:0.44, C:0.21, G:0.06, T:0.29
Consensus pattern (46 bp):
TAACACTCAAATTCAACAAAAAAAAACACTCTTGATTCTTGATTAC
Found at i:35575 original size:12 final size:12
Alignment explanation
Indices: 35558--35591 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
35548 ACCCCACATG
35558 TCAAGCAATAA-A
1 TCAAGCAA-AATA
35570 TCAAGCAAAATA
1 TCAAGCAAAATA
35582 TCAAGCAAAA
1 TCAAGCAAAA
35592 AGATCATCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 2 0.10
12 19 0.90
ACGTcount: A:0.59, C:0.18, G:0.09, T:0.15
Consensus pattern (12 bp):
TCAAGCAAAATA
Found at i:44221 original size:29 final size:29
Alignment explanation
Indices: 44187--44292 Score: 104
Period size: 30 Copynumber: 3.6 Consensus size: 29
44177 GACACGTGGT
44187 ACGTGGCATGCCACATGTCTTTTTTGTAC
1 ACGTGGCATGCCACATGTCTTTTTTGTAC
* *
44216 ACGTGGCGTGCCACATGTCCTTTTTTGTAT
1 ACGTGGCATGCCACATGT-CTTTTTTGTAC
* * * *
44246 ACGTGACGTGCCACGTGTCAATTTTTGGTAC
1 ACGTGGCATGCCACATGTC--TTTTTTGTAC
* * *
44277 ATGGGGCACGCCACAT
1 ACGTGGCATGCCACAT
44293 CGGACGCTGT
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
29 18 0.29
30 26 0.42
31 18 0.29
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.33
Consensus pattern (29 bp):
ACGTGGCATGCCACATGTCTTTTTTGTAC
Found at i:44241 original size:30 final size:30
Alignment explanation
Indices: 44187--44264 Score: 113
Period size: 30 Copynumber: 2.6 Consensus size: 30
44177 GACACGTGGT
*
44187 ACGTGGCATGCCACATGT-CTTTTTTGTAC
1 ACGTGGCGTGCCACATGTCCTTTTTTGTAC
*
44216 ACGTGGCGTGCCACATGTCCTTTTTTGTAT
1 ACGTGGCGTGCCACATGTCCTTTTTTGTAC
* *
44246 ACGTGACGTGCCACGTGTC
1 ACGTGGCGTGCCACATGTC
44265 AATTTTTGGT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 17 0.39
30 27 0.61
ACGTcount: A:0.15, C:0.26, G:0.24, T:0.35
Consensus pattern (30 bp):
ACGTGGCGTGCCACATGTCCTTTTTTGTAC
Found at i:48346 original size:21 final size:21
Alignment explanation
Indices: 48322--48363 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
48312 AATGAATAAA
* *
48322 GTCTCTTTGCCTCCTAAACTT
1 GTCTCTTTACCCCCTAAACTT
48343 GTCTCTTTACCCCCTAAACTT
1 GTCTCTTTACCCCCTAAACTT
48364 TAATTTGGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.36, G:0.07, T:0.40
Consensus pattern (21 bp):
GTCTCTTTACCCCCTAAACTT
Found at i:48511 original size:31 final size:32
Alignment explanation
Indices: 48435--48515 Score: 110
Period size: 32 Copynumber: 2.6 Consensus size: 32
48425 GGTATTGCTG
*
48435 ACGTGGCAATGCCACGCCGGACCAAATATGCA
1 ACGTGGCAATGCCACGTCGGACCAAATATGCA
* * *
48467 ATGTGGCAATGCCACGTTGGACCAAA-ATGCC
1 ACGTGGCAATGCCACGTCGGACCAAATATGCA
*
48498 ACGTGGCATTGCCACGTC
1 ACGTGGCAATGCCACGTC
48516 AGCAATATTG
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 19 0.45
32 23 0.55
ACGTcount: A:0.27, C:0.30, G:0.26, T:0.17
Consensus pattern (32 bp):
ACGTGGCAATGCCACGTCGGACCAAATATGCA
Found at i:59452 original size:30 final size:30
Alignment explanation
Indices: 59416--59558 Score: 153
Period size: 30 Copynumber: 4.7 Consensus size: 30
59406 CACGTGTACC
*
59416 GCCATGTGTACCAAAAATGACATGTGGCAT
1 GCCACGTGTACCAAAAATGACATGTGGCAT
* * *
59446 GCCATGTGTACAAAAAATGACATGTGGTAT
1 GCCACGTGTACCAAAAATGACATGTGGCAT
* **
59476 GCCACGTGTATCAAAAATGACACATGGCAT
1 GCCACGTGTACCAAAAATGACATGTGGCAT
* * * *
59506 GCCGCATGTACACAAGAATGACAAGTGGCAT
1 GCCACGTGTAC-CAAAAATGACATGTGGCAT
*
59537 GCCGCGTGTA-CACAAAATGACA
1 GCCACGTGTACCA-AAAATGACA
59559 CATAGCACGT
Statistics
Matches: 95, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
29 2 0.02
30 68 0.72
31 25 0.26
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (30 bp):
GCCACGTGTACCAAAAATGACATGTGGCAT
Found at i:59556 original size:61 final size:60
Alignment explanation
Indices: 59416--59561 Score: 161
Period size: 61 Copynumber: 2.4 Consensus size: 60
59406 CACGTGTACC
* ** ** * *
59416 GCCATGTGTAC-CAAAAATGACATGTGGCATGCCATGTGTACAAAAAATGACATGTGGTAT
1 GCCACGTGTACAC-AAAATGACACATGGCATGCCACATGTACAAAAAATGACAAGTGGCAT
* *
59476 GCCACGTGTATCA-AAAATGACACATGGCATGCCGCATGTACACAAGAATGACAAGTGGCAT
1 GCCACGTGTA-CACAAAATGACACATGGCATGCCACATGTACA-AAAAATGACAAGTGGCAT
*
59537 GCCGCGTGTACACAAAATGACACAT
1 GCCACGTGTACACAAAATGACACAT
59562 AGCACGTCAC
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
60 35 0.49
61 37 0.51
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.21
Consensus pattern (60 bp):
GCCACGTGTACACAAAATGACACATGGCATGCCACATGTACAAAAAATGACAAGTGGCAT
Found at i:59575 original size:30 final size:30
Alignment explanation
Indices: 59416--59575 Score: 137
Period size: 30 Copynumber: 5.3 Consensus size: 30
59406 CACGTGTACC
* **
59416 GCCATGTGTAC-CAAAAATGACATGTGGCAT
1 GCCACGTGTACAC-AAAATGACACATGGCAT
* * ** *
59446 GCCATGTGTACAAAAAATGACATGTGGTAT
1 GCCACGTGTACACAAAATGACACATGGCAT
59476 GCCACGTGTATCA-AAAATGACACATGGCAT
1 GCCACGTGTA-CACAAAATGACACATGGCAT
* *
59506 GCCGCATGTACACAAGAATGACA-AGTGGCAT
1 GCCACGTGTACACAA-AATGACACA-TGGCAT
* * *
59537 GCCGCGTGTACACAAAATGACACATAGCAC
1 GCCACGTGTACACAAAATGACACATGGCAT
*
59567 GTCACGTGT
1 GCCACGTGT
59576 TACAAATTGC
Statistics
Matches: 111, Mismatches: 13, Indels: 12
0.82 0.10 0.09
Matches are distributed among these distances:
29 2 0.02
30 79 0.71
31 30 0.27
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.21
Consensus pattern (30 bp):
GCCACGTGTACACAAAATGACACATGGCAT
Done.