Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005570.1 Corchorus capsularis cultivar CVL-1 contig05588, 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: 3187
ACGTcount: A:0.31, C:0.29, G:0.26, T:0.14
Found at i:67 original size:31 final size:31
Alignment explanation
Indices: 12--500 Score: 453
Period size: 31 Copynumber: 15.6 Consensus size: 31
2 CAAGGGCCAC
* *
12 CGGCAAATGACGACGCCAAAGCCATGGGCCAT
1 CGGCAAATGCCGACGCCAAGGCCATGGG-CAT
*
44 CGGCAAATGCCG-TGCCAAGGCCATGGGCAT
1 CGGCAAATGCCGACGCCAAGGCCATGGGCAT
* *
74 CGGTAAATGCCGACGCCAAGGCCAAGGGCAT
1 CGGCAAATGCCGACGCCAAGGCCATGGGCAT
* *
105 CGTCAAAAGCCGACGCCAAGGCCATGGGCAT
1 CGGCAAATGCCGACGCCAAGGCCATGGGCAT
* ** * * *
136 CGTCAAATGCCGATACCAAGGCAACGAGCCAT
1 CGGCAAATGCCGACGCCAAGGCCATG-GGCAT
* *
168 CGGCAAATGCCGATGCCAAGGCCAATGGCCAT
1 CGGCAAATGCCGACGCCAAGGCC-ATGGGCAT
* * * *
200 CGACAAATGCCAACGCCAAAGTCATGGGCCAT
1 CGGCAAATGCCGACGCCAAGGCCATGGG-CAT
*
232 CGGCAAATGCCG-TGCCAAGGCCATGGGCAT
1 CGGCAAATGCCGACGCCAAGGCCATGGGCAT
* * * * * *
262 CTGTAAATGCCGATGCAAAGGCTAAGGGCAT
1 CGGCAAATGCCGACGCCAAGGCCATGGGCAT
* *
293 CGGCAAAAGCCGACGCCAAGGCCAAGGGCCAT
1 CGGCAAATGCCGACGCCAAGGCCATGGG-CAT
* * *
325 TGGCAAATGCCCACACCAAGGCCATGGGCAT
1 CGGCAAATGCCGACGCCAAGGCCATGGGCAT
* * * * *
356 CGTCAAATGCCGACGGCAAGACCAAGGGCCAA
1 CGGCAAATGCCGACGCCAAGGCCATGGG-CAT
** * *
388 CATCAAAGGCCGACGTCAAGGCCATGGGCAT
1 CGGCAAATGCCGACGCCAAGGCCATGGGCAT
* * *
419 CGGCAACTACCGACGCCAAGGCCAAGGGCAT
1 CGGCAAATGCCGACGCCAAGGCCATGGGCAT
* * *
450 GGGCAAATGCCGACGACAAGGCC-TAGGACCAT
1 CGGCAAATGCCGACGCCAAGGCCAT-GG-GCAT
* *
482 CGACAAATGCCGATGCCAA
1 CGGCAAATGCCGACGCCAA
501 TGCAAAGGGG
Statistics
Matches: 370, Mismatches: 78, Indels: 18
0.79 0.17 0.04
Matches are distributed among these distances:
30 27 0.07
31 201 0.54
32 140 0.38
33 2 0.01
ACGTcount: A:0.30, C:0.30, G:0.28, T:0.11
Consensus pattern (31 bp):
CGGCAAATGCCGACGCCAAGGCCATGGGCAT
Found at i:305 original size:157 final size:155
Alignment explanation
Indices: 1--500 Score: 481
Period size: 157 Copynumber: 3.2 Consensus size: 155
* * * * * ** *
1 CCAAGGGCCACCGGCAAATGACGACGCCAAAGCCATGGGCCATCGGCAAATGCCGTGCCAAGGCC
1 CCAAGAGCCATCGGCAAATGCCGACGCCAAGGCCAT-GGCCATCGACAAATGCCACGCCAAAGCC
* * * *
66 ATGGG-CATCGGTAAATGCCGACGCCAAGGCCAAGGGCATCGTCAAAAGCCGACGCCAAGGCCAT
65 ATGGGCCATCGGCAAATGCCGACGCCAAGGCCATGGGCATCGT-AAATGCCGACGCCAAGGCCAA
* *
130 GGGCATCGTCAAATGCCGATACCAAGG
129 GGGCATCGGCAAATGCCGACACCAAGG
*
157 -CAACGAGCCATCGGCAAATGCCGATGCCAAGGCCAATGGCCATCGACAAATGCCAACGCCAAAG
1 CCAA-GAGCCATCGGCAAATGCCGACGCCAAGGCC-ATGGCCATCGACAAATGCC-ACGCCAAAG
* * * * *
221 TCATGGGCCATCGGCAAATGCCG-TGCCAAGGCCATGGGCATCTGTAAATGCCGATGCAAAGGCT
63 CCATGGGCCATCGGCAAATGCCGACGCCAAGGCCATGGGCATC-GTAAATGCCGACGCCAAGGCC
* *
285 AAGGGCATCGGCAAAAGCCGACGCCAAGG
127 AAGGGCATCGGCAAATGCCGACACCAAGG
* * * * * * *
314 CCAAGGGCCATTGGCAAATGCCCACACCAAGGCCATGGGCATCGTCAAATGCCGACGGC-AAGAC
1 CCAAGAGCCATCGGCAAATGCCGACGCCAAGGCCATGGCCATCGACAAATGCC-ACGCCAAAG-C
* * ** * * * * *
378 CAAGGGCCAACATCAAAGGCCGACGTCAAGGCCATGGGCATCGGCAACTACCGACGCCAAGGCCA
64 CATGGGCCATCGGCAAATGCCGACGCCAAGGCCATGGGCATC-GTAAATGCCGACGCCAAGGCCA
*
443 AGGGCATGGGCAAATGCCGACGA-CAAGG
128 AGGGCATCGGCAAATGCCGAC-ACCAAGG
* * *
471 CCTAG-GACCATCGACAAATGCCGATGCCAA
1 CCAAGAG-CCATCGGCAAATGCCGACGCCAA
501 TGCAAAGGGG
Statistics
Matches: 279, Mismatches: 55, Indels: 19
0.79 0.16 0.05
Matches are distributed among these distances:
155 6 0.02
156 80 0.29
157 174 0.62
158 19 0.07
ACGTcount: A:0.30, C:0.31, G:0.28, T:0.11
Consensus pattern (155 bp):
CCAAGAGCCATCGGCAAATGCCGACGCCAAGGCCATGGCCATCGACAAATGCCACGCCAAAGCCA
TGGGCCATCGGCAAATGCCGACGCCAAGGCCATGGGCATCGTAAATGCCGACGCCAAGGCCAAGG
GCATCGGCAAATGCCGACACCAAGG
Found at i:365 original size:188 final size:188
Alignment explanation
Indices: 1--509 Score: 585
Period size: 188 Copynumber: 2.7 Consensus size: 188
* * *
1 CCAAGGGCCACCGGCAAATGACGACGCCAAAGCCATGGGCCATCGGCAAATGCCGTGCCAAGGCC
1 CCAAGGGCCAACGACAAATGCCGACGCCAAAGCCATGGGCCATCGGCAAATGCCGTGCCAAGGCC
* * *
66 ATGGGCATCGGTAAATGCCGACGCCAAGGCCAAGGGCATCGTCAAAAGCCGACGCCAAGGCCATG
66 ATGGGCATCGGTAAATGCCGACGCAAAGGCCAAGGGCATCGGCAAAAGCCGACGCCAAGGCCAAG
* * * * *
131 GGCATCGTCAAATGCCGATACCAAGGCAACGAGCCATCGGCAAATGCCGATGCCAAGG
131 GGCATCGGCAAATGCCCACACCAAGGCAACGAGCCATCGGCAAATGCCGACGCCAAGA
* * * *
189 CCAATGGCCATCGACAAATGCCAACGCCAAAGTCATGGGCCATCGGCAAATGCCGTGCCAAGGCC
1 CCAAGGGCCAACGACAAATGCCGACGCCAAAGCCATGGGCCATCGGCAAATGCCGTGCCAAGGCC
* * *
254 ATGGGCATCTGTAAATGCCGATGCAAAGGCTAAGGGCATCGGCAAAAGCCGACGCCAAGGCCAAG
66 ATGGGCATCGGTAAATGCCGACGCAAAGGCCAAGGGCATCGGCAAAAGCCGACGCCAAGGCCAAG
* * * * * *
319 GGCCATTGGCAAATGCCCACACCAAGGCCATG-GGCATCGTCAAATGCCGACGGCAAGA
131 GG-CATCGGCAAATGCCCACACCAAGGCAACGAGCCATCGGCAAATGCCGACGCCAAGA
* * * * * *
377 CCAAGGGCCAAC-ATCAAAGGCCGACGTCAAGGCCATGGG-CATCGGCAACTACCGACGCCAAGG
1 CCAAGGGCCAACGA-CAAATGCCGACGCCAAAGCCATGGGCCATCGGCAAATGCCG-TGCCAAGG
* * * * * * * * *
440 CCAAGGGCATGGGCAAATGCCGACG-ACAAGGCCTAGGACCATCGACAAATGCCGATGCCAATGC
64 CCATGGGCATCGGTAAATGCCGACGCA-AAGGCCAAGG-GCATCGGCAAAAGCCGACGCCAAGGC
*
504 AAAGGG
127 CAAGGG
510 GACAAGGGAC
Statistics
Matches: 270, Mismatches: 46, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
187 15 0.06
188 206 0.76
189 49 0.18
ACGTcount: A:0.30, C:0.30, G:0.29, T:0.11
Consensus pattern (188 bp):
CCAAGGGCCAACGACAAATGCCGACGCCAAAGCCATGGGCCATCGGCAAATGCCGTGCCAAGGCC
ATGGGCATCGGTAAATGCCGACGCAAAGGCCAAGGGCATCGGCAAAAGCCGACGCCAAGGCCAAG
GGCATCGGCAAATGCCCACACCAAGGCAACGAGCCATCGGCAAATGCCGACGCCAAGA
Found at i:627 original size:32 final size:32
Alignment explanation
Indices: 539--648 Score: 141
Period size: 32 Copynumber: 3.5 Consensus size: 32
529 TTCCGACGCA
* * * *
539 ATCGGCAAATGTCGATGCCAAGGCAACGGACC
1 ATCGGCAAATGCCGACGCCAAGGCCATGGACC
* *
571 CTCAGCAAATGCCGACGCCAAGGCCATGGACC
1 ATCGGCAAATGCCGACGCCAAGGCCATGGACC
*
603 ATCGGCAAATGCCGACGCCAAGGCCATGG-GC
1 ATCGGCAAATGCCGACGCCAAGGCCATGGACC
*
634 ATTGGCAAATGCCGA
1 ATCGGCAAATGCCGA
649 TTCCAAGCTA
Statistics
Matches: 68, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
31 15 0.22
32 53 0.78
ACGTcount: A:0.29, C:0.31, G:0.28, T:0.12
Consensus pattern (32 bp):
ATCGGCAAATGCCGACGCCAAGGCCATGGACC
Found at i:701 original size:19 final size:19
Alignment explanation
Indices: 674--712 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
664 GCCAACATGA
*
674 CAAGGGACGTCATCAAATT
1 CAAGAGACGTCATCAAATT
693 CAAGAGACGTCATCAAATT
1 CAAGAGACGTCATCAAATT
712 C
1 C
713 CGACAAGGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (19 bp):
CAAGAGACGTCATCAAATT
Found at i:1067 original size:22 final size:22
Alignment explanation
Indices: 1036--1088 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
1026 CCCACGTTAG
* *
1036 GGCCCAAAGGTGCCCCCGAGGA
1 GGCCCCAAGGCGCCCCCGAGGA
*
1058 GGCCCCAAGGCGCCCCCGAGGT
1 GGCCCCAAGGCGCCCCCGAGGA
*
1080 TGCCCCAAG
1 GGCCCCAAG
1089 TGGCCACAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.19, C:0.42, G:0.34, T:0.06
Consensus pattern (22 bp):
GGCCCCAAGGCGCCCCCGAGGA
Found at i:1412 original size:63 final size:63
Alignment explanation
Indices: 1335--2104 Score: 303
Period size: 63 Copynumber: 12.3 Consensus size: 63
1325 TTCCAACGCA
* * ** * * * *
1335 ATCGGCAAATGCCGATAACAAGGAAACGGGCCAACGGCAAATGCCGACGCCTAGGCCATGGG-C
1 ATCGGCAAATGCCGACACCAAGGCCATGGG-CAACGACAAATGCCGACGCCAAGGCCAAGGGCC
* *
1398 ATCGGCAAATGCCGACGCCAAGGCCATGAG-AATCGACAAATGCCGACGCCAAGGCCAAGGGCC
1 ATCGGCAAATGCCGACACCAAGGCCATGGGCAA-CGACAAATGCCGACGCCAAGGCCAAGGGCC
* * * * *
1461 ATCGGCAAATTCCCACACCAAGGCCATGGGCATCGTCAAATGCCGACGCCAAGACCAAGGGCC
1 ATCGGCAAATGCCGACACCAAGGCCATGGGCAACGACAAATGCCGACGCCAAGGCCAAGGGCC
** * * *** * *
1524 ATCGGCAAATGCCGACGTCAAGGCCATGGGCATCGGCAACCACCGATGCCAAGTCCAAGGG-C
1 ATCGGCAAATGCCGACACCAAGGCCATGGGCAACGACAAATGCCGACGCCAAGGCCAAGGGCC
* * * *
1586 ATGGGCAAATGCCGA-AGCCAAGGCC-TAGGGCCATCGACAAATGCCGATGCCAATGCCAAGGGG
1 ATCGGCAAATGCCGACA-CCAAGGCCAT-GGG-CAACGACAAATGCCGACGCCAAGGCCAA-GGG
*
1649 AC
62 CC
* * * * * ** * ** * * * * * * *
1651 A-AGGGACAT--C-ATA-AAATTCCGA-CGCAATCGGCAAATGGCGATGCCAAGGCAACGGACC
1 ATCGGCAAATGCCGACACCAAGGCC-ATGGGCAACGACAAATGCCGACGCCAAGGCCAAGGGCC
* * * * * * * *
1709 ATCAGCAAATGACGACGCCAAGGCCATGGACCATCGGCAAATACCGACGCCAAGGCCATGGG-C
1 ATCGGCAAATGCCGACACCAAGGCCATGG-GCAACGACAAATGCCGACGCCAAGGCCAAGGGCC
* ** * * * * *
1772 ATTGGCAAATGCCGATTCCAAGGCCATGGGCCATCGGCAAATGCTGATGCC-AGTGCCAAGTGGA
1 ATCGGCAAATGCCGACACCAAGGCCATGGG-CAACGACAAATGCCGACGCCAAG-GCCAAG-GGC
1836 C
63 C
** * ** ** * * * * * * *
1837 AAGGGACATCAT-CAAATTCCGACGCAAT---C-A-G-CCAATGCCGACACCAAGGCCACGTGCC
1 ATCGG-CA-AATGCCGACACCAAGGCCATGGGCAACGACAAATGCCGACGCCAAGGCCAAGGGCC
* * ** * * * * * ** ** *
1895 ATCGTCAAATGTCGATGCCAATGCCAACGTGACAAGGGACATCAT-CAAATTCC---GACAA-GG
1 ATCGGCAAATGCCGACACCAAGGCC-ATG-GGCAA-CGACA-AATGCCGACGCCAAGGCCAAGGG
1955 CC
62 CC
* * * *
1957 ATCGGCAAATGCCGACGCCAAGGCCATGGGCCATCGGCAAATGCCGACGCCAAGGCCATGGGCC
1 ATCGGCAAATGCCGACACCAAGGCCATGGG-CAACGACAAATGCCGACGCCAAGGCCAAGGGCC
* * * * *
2021 ATCGGAAAATGCCGACGCCAAGGCCATGGGCCATCGGCAAATGCCGACGCCAAGGCCATGGGCC
1 ATCGGCAAATGCCGACACCAAGGCCATGGG-CAACGACAAATGCCGACGCCAAGGCCAAGGGCC
2085 ATCGGCAAATGCCGACACCA
1 ATCGGCAAATGCCGACACCA
2105 CATCGGAACT
Statistics
Matches: 530, Mismatches: 135, Indels: 83
0.71 0.18 0.11
Matches are distributed among these distances:
56 2 0.00
57 9 0.02
58 9 0.02
59 43 0.08
60 16 0.03
61 9 0.02
62 82 0.15
63 210 0.40
64 121 0.23
65 7 0.01
66 18 0.03
67 4 0.01
ACGTcount: A:0.30, C:0.31, G:0.27, T:0.12
Consensus pattern (63 bp):
ATCGGCAAATGCCGACACCAAGGCCATGGGCAACGACAAATGCCGACGCCAAGGCCAAGGGCC
Found at i:1460 original size:94 final size:95
Alignment explanation
Indices: 1362--2100 Score: 463
Period size: 94 Copynumber: 7.9 Consensus size: 95
1352 ACAAGGAAAC
* * * *
1362 GGGCCAACGGCAAATGCCGACGCCTAGGCCATGGGCATCGGCAAATGCCGACGCCAAGGCCATGA
1 GGGCCATCGGCAAATACCGACGCCAAGGCCATGGGCATCGGCAAATGCCGACGCCAAGGCCATGG
*
1427 G-AATCGACAAATGCCGACGCCAAGGCCAA
66 GCCATCGACAAATGCCGACGCCAAGGCCAA
* * * * * *
1456 GGGCCATCGGCAAATTCCCACACCAAGGCCATGGGCATCGTCAAATGCCGACGCCAAGACCAAGG
1 GGGCCATCGGCAAATACCGACGCCAAGGCCATGGGCATCGGCAAATGCCGACGCCAAGGCCATGG
* * *
1521 GCCATCGGCAAATGCCGACGTCAAGGCCAT
66 GCCATCGACAAATGCCGACGCCAAGGCCAA
** * * * * *
1551 GGG-CATCGGCAACCACCGATGCCAAGTCCAAGGGCATGGGCAAATGCCGAAGCCAAGGCC-TAG
1 GGGCCATCGGCAAATACCGACGCCAAGGCCATGGGCATCGGCAAATGCCGACGCCAAGGCCAT-G
* *
1614 GGCCATCGACAAATGCCGATGCCAATGCCAA
65 GGCCATCGACAAATGCCGACGCCAAGGCCAA
* * * * *** ** * * * *
1645 GGGGACA-AGGGACAT--C-A-TAAAATTCC--GACGCAATCGGCAAATGGCGATGCCAAGGCAA
1 -GGGCCATCGGCAAATACCGACGCCAAGGCCATG-GGC-ATCGGCAAATGCCGACGCCAAGGCCA
* * * *
1703 CGGACCATC-AGCAAATGACGACGCCAAGGCCAT
63 TGGGCCATCGA-CAAATGCCGACGCCAAGGCCAA
* * **
1736 GGACCATCGGCAAATACCGACGCCAAGGCCATGGGCATTGGCAAATGCCGATTCCAAGGCCATGG
1 GGGCCATCGGCAAATACCGACGCCAAGGCCATGGGCATCGGCAAATGCCGACGCCAAGGCCATGG
* * *
1801 GCCATCGGCAAATGCTGATGCC-AGTGCCAA
66 GCCATCGACAAATGCCGACGCCAAG-GCCAA
* * * * * * ** * * * *
1831 GTGGACA-AGGGACAT--C-A-TCAAATTCC--GACGCAATCAGCCAATGCCGACACCAAGGCCA
1 G-GGCCATCGGCAAATACCGACGCCAAGGCCATG-GGC-ATCGGCAAATGCCGACGCCAAGGCCA
* * * * *
1889 CGTGCCATCGTCAAATGTCGATGCCAATGCCAACGTGACAA
63 TGGGCCATCGACAAATGCCGA---C---GCCAA-G-GCCAA
* ** *
1930 GGGACATCATCAAATTCCGA---CAAGG-C-----CATCGGCAAATGCCGACGCCAAGGCCATGG
1 GGGCCATCGGCAAATACCGACGCCAAGGCCATGGGCATCGGCAAATGCCGACGCCAAGGCCATGG
* *
1986 GCCATCGGCAAATGCCGACGCCAAGGCCAT
66 GCCATCGACAAATGCCGACGCCAAGGCCAA
* *
2016 GGGCCATCGGAAAATGCCGACGCCAAGGCCATGGGCCATCGGCAAATGCCGACGCCAAGGCCATG
1 GGGCCATCGGCAAATACCGACGCCAAGGCCATGGG-CATCGGCAAATGCCGACGCCAAGGCCATG
*
2081 GGCCATCGGCAAATGCCGAC
65 GGCCATCGACAAATGCCGAC
2101 ACCACATCGG
Statistics
Matches: 486, Mismatches: 117, Indels: 82
0.71 0.17 0.12
Matches are distributed among these distances:
86 18 0.04
87 1 0.00
88 5 0.01
89 7 0.01
90 10 0.02
91 99 0.20
92 2 0.00
93 3 0.01
94 172 0.35
95 88 0.18
96 56 0.12
97 4 0.01
98 6 0.01
99 11 0.02
100 2 0.00
101 1 0.00
102 1 0.00
ACGTcount: A:0.30, C:0.31, G:0.28, T:0.12
Consensus pattern (95 bp):
GGGCCATCGGCAAATACCGACGCCAAGGCCATGGGCATCGGCAAATGCCGACGCCAAGGCCATGG
GCCATCGACAAATGCCGACGCCAAGGCCAA
Found at i:1711 original size:91 final size:91
Alignment explanation
Indices: 1589--2014 Score: 324
Period size: 91 Copynumber: 4.6 Consensus size: 91
1579 CAAGGGCATG
*
1589 GGCAAATGCCGAAGCCAAGGCCTA-GGGCCATCGACAAATGCCGATGCCAATGCCAAGGGGACAA
1 GGCAAATGCCGACGCCAAGGCC-ACGGGCCATCGACAAATGCCGATGCCAATGCCAAGGGGACAA
1653 GGGACATCATAAAATTCCGACGCAATC
65 GGGACATCATAAAATTCCGACGCAATC
* * * * * * * *
1680 GGCAAATGGCGATGCCAAGGCAACGGACCATC-AGCAAATGACGACGCCAAGGCC-A-TGGACCA
1 GGCAAATGCCGACGCCAAGGCCACGGGCCATCGA-CAAATGCCGATGCCAATGCCAAGGGGA-CA
** * ** ** * * *
1742 TCGG-CA-AATACCGACGCCAAGGCCATGGGCATT
64 AGGGACATCATA-AAATTCCGACG-CA-----ATC
** * * * * *
1775 GGCAAATGCCGATTCCAAGGCCATGGGCCATCGGCAAATGCTGATGCCAGTGCCAAGTGGACAAG
1 GGCAAATGCCGACGCCAAGGCCACGGGCCATCGACAAATGCCGATGCCAATGCCAAGGGGACAAG
*
1840 GGACATCATCAAATTCCGACGCAATC
66 GGACATCATAAAATTCCGACGCAATC
* * * * * * * *
1866 AGCCAATGCCGACACCAAGGCCACGTGCCATCGTCAAATGTCGATGCCAATGCCAACGTGACAAG
1 GGCAAATGCCGACGCCAAGGCCACGGGCCATCGACAAATGCCGATGCCAATGCCAAGGGGACAAG
* *
1931 GGACATCATCAAATTCCGACAAGGCCATC
66 GGACATCATAAAATTCCGAC---GCAATC
* * * *
1960 GGCAAATGCCGACGCCAAGGCCATGGGCCATCGGCAAATGCCGACGCCAAGGCCA
1 GGCAAATGCCGACGCCAAGGCCACGGGCCATCGACAAATGCCGATGCCAATGCCA
2015 TGGGCCATCG
Statistics
Matches: 254, Mismatches: 63, Indels: 33
0.73 0.18 0.09
Matches are distributed among these distances:
88 3 0.01
89 10 0.04
90 9 0.04
91 117 0.46
94 51 0.20
95 44 0.17
96 7 0.03
97 11 0.04
98 2 0.01
ACGTcount: A:0.31, C:0.30, G:0.26, T:0.13
Consensus pattern (91 bp):
GGCAAATGCCGACGCCAAGGCCACGGGCCATCGACAAATGCCGATGCCAATGCCAAGGGGACAAG
GGACATCATAAAATTCCGACGCAATC
Found at i:1765 original size:32 final size:32
Alignment explanation
Indices: 1677--1813 Score: 143
Period size: 32 Copynumber: 4.3 Consensus size: 32
1667 TTCCGACGCA
** * * *
1677 ATCGGCAAATGGCGATGCCAAGGCAACGGACC
1 ATCGGCAAATACCGACGCCAAGGCCATGGACC
*
1709 ATCAGCAAATGA-CGACGCCAAGGCCATGGACC
1 ATCGGCAAAT-ACCGACGCCAAGGCCATGGACC
*
1741 ATCGGCAAATACCGACGCCAAGGCCATGG-GC
1 ATCGGCAAATACCGACGCCAAGGCCATGGACC
* * ** *
1772 ATTGGCAAATGCCGATTCCAAGGCCATGGGCC
1 ATCGGCAAATACCGACGCCAAGGCCATGGACC
1804 ATCGGCAAAT
1 ATCGGCAAAT
1814 GCTGATGCCA
Statistics
Matches: 89, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
31 27 0.30
32 62 0.70
ACGTcount: A:0.31, C:0.29, G:0.28, T:0.12
Consensus pattern (32 bp):
ATCGGCAAATACCGACGCCAAGGCCATGGACC
Found at i:1783 original size:280 final size:278
Alignment explanation
Indices: 1398--2100 Score: 823
Period size: 280 Copynumber: 2.5 Consensus size: 278
1388 GGCCATGGGC
* * *
1398 ATCGGCAAATGCCGACGCCAAGGCCATGAGA--ATC-GACAAATGCCGACGCCAAGGCCAAGGGC
1 ATCGGCAAATGCCGACGCCAAGGCAACG-GACCATCAG-CAAATGCCGACGCCAAGGCCATGGGC
* * * * * *
1460 CATCGGCAAATTCCCACACCAAGGCCATGGGCATCGTCAAATGCCGACGCCAAGACCAAGGGCCA
64 CATCGGCAAATACCGACGCCAAGGCCATGGGCATCGGCAAATGCCGACGCCAAGGCCATGGGCCA
* * * *
1525 TCGGCAAATGCCGACGTCAAG-GCC-A-TGGGCATCGGCAACCACCGATGCCAAGTCCAAGGGC-
129 TCGGCAAATGCCGACG-CAAGTGCCAAGTGGACA-AGG-AA-CACC-AT-CAAAGTCCAA-CGCA
** *
1586 ATGGGCAAATGCCGA-AGCCAAGGCCTA-GGGCCATCGACAAATGCCGATGCCAATGCCAAGGGG
187 ATCAGCAAATGCCGACA-CCAAGGCC-ACGGGCCATCGACAAATGCCGATGCCAATGCCAACGGG
1649 ACAAGGGACATCATAAAATTCCGAC-GCA
250 ACAAGGGACATCATAAAATTCCGACAGCA
* * * *
1677 ATCGGCAAATGGCGATGCCAAGGCAACGGACCATCAGCAAATGACGACGCCAAGGCCATGGACCA
1 ATCGGCAAATGCCGACGCCAAGGCAACGGACCATCAGCAAATGCCGACGCCAAGGCCATGGGCCA
* **
1742 TCGGCAAATACCGACGCCAAGGCCATGGGCATTGGCAAATGCCGATTCCAAGGCCATGGGCCATC
66 TCGGCAAATACCGACGCCAAGGCCATGGGCATCGGCAAATGCCGACGCCAAGGCCATGGGCCATC
* * * * * * * *
1807 GGCAAATGCTGATGCCAGTGCCAAGTGGACAAGGGACATCATCAAATTCCGACGCAATCAGCCAA
131 GGCAAATGCCGACGCAAGTGCCAAGTGGACAAGGAACACCATCAAAGTCCAACGCAATCAGCAAA
* * * *
1872 TGCCGACACCAAGGCCACGTGCCATCGTCAAATGTCGATGCCAATGCCAACGTGACAAGGGACAT
196 TGCCGACACCAAGGCCACGGGCCATCGACAAATGCCGATGCCAATGCCAACGGGACAAGGGACAT
* *
1937 CATCAAATTCCGACAAGGCC
261 CATAAAATTCCGAC-A-GCA
* * * *
1957 ATCGGCAAATGCCGACGCCAAGGCCATGGGCCATCGGCAAATGCCGACGCCAAGGCCATGGGCCA
1 ATCGGCAAATGCCGACGCCAAGGCAACGGACCATCAGCAAATGCCGACGCCAAGGCCATGGGCCA
* *
2022 TCGGAAAATGCCGACGCCAAGGCCATGGGCCATCGGCAAATGCCGACGCCAAGGCCATGGGCCAT
66 TCGGCAAATACCGACGCCAAGGCCATGGG-CATCGGCAAATGCCGACGCCAAGGCCATGGGCCAT
2087 CGGCAAATGCCGAC
130 CGGCAAATGCCGAC
2101 ACCACATCGG
Statistics
Matches: 359, Mismatches: 52, Indels: 24
0.83 0.12 0.06
Matches are distributed among these distances:
276 3 0.01
277 82 0.23
278 5 0.01
279 30 0.08
280 186 0.52
281 48 0.13
282 5 0.01
ACGTcount: A:0.30, C:0.31, G:0.27, T:0.12
Consensus pattern (278 bp):
ATCGGCAAATGCCGACGCCAAGGCAACGGACCATCAGCAAATGCCGACGCCAAGGCCATGGGCCA
TCGGCAAATACCGACGCCAAGGCCATGGGCATCGGCAAATGCCGACGCCAAGGCCATGGGCCATC
GGCAAATGCCGACGCAAGTGCCAAGTGGACAAGGAACACCATCAAAGTCCAACGCAATCAGCAAA
TGCCGACACCAAGGCCACGGGCCATCGACAAATGCCGATGCCAATGCCAACGGGACAAGGGACAT
CATAAAATTCCGACAGCA
Found at i:1802 original size:31 final size:31
Alignment explanation
Indices: 1369--1643 Score: 300
Period size: 31 Copynumber: 8.8 Consensus size: 31
1359 AACGGGCCAA
*
1369 CGGCAAATGCCGACGCCTAGGCCATGGGCAT
1 CGGCAAATGCCGACGCCAAGGCCATGGGCAT
* *
1400 CGGCAAATGCCGACGCCAAGGCCATGAGAAT
1 CGGCAAATGCCGACGCCAAGGCCATGGGCAT
* *
1431 CGACAAATGCCGACGCCAAGGCCAAGGGCCAT
1 CGGCAAATGCCGACGCCAAGGCCATGGG-CAT
* * *
1463 CGGCAAATTCCCACACCAAGGCCATGGGCAT
1 CGGCAAATGCCGACGCCAAGGCCATGGGCAT
* * *
1494 CGTCAAATGCCGACGCCAAGACCAAGGGCCAT
1 CGGCAAATGCCGACGCCAAGGCCATGGG-CAT
*
1526 CGGCAAATGCCGACGTCAAGGCCATGGGCAT
1 CGGCAAATGCCGACGCCAAGGCCATGGGCAT
*** * * *
1557 CGGCAACCACCGATGCCAAGTCCAAGGGCAT
1 CGGCAAATGCCGACGCCAAGGCCATGGGCAT
* *
1588 GGGCAAATGCCGAAGCCAAGGCC-TAGGGCCAT
1 CGGCAAATGCCGACGCCAAGGCCAT-GGG-CAT
* * *
1620 CGACAAATGCCGATGCCAATGCCA
1 CGGCAAATGCCGACGCCAAGGCCA
1644 AGGGGACAAG
Statistics
Matches: 199, Mismatches: 40, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
31 125 0.63
32 74 0.37
ACGTcount: A:0.29, C:0.32, G:0.28, T:0.11
Consensus pattern (31 bp):
CGGCAAATGCCGACGCCAAGGCCATGGGCAT
Found at i:1886 original size:186 final size:183
Alignment explanation
Indices: 1497--1920 Score: 526
Period size: 186 Copynumber: 2.3 Consensus size: 183
1487 TGGGCATCGT
* * * * *
1497 CAAATGCCGACGCCAAGACCAAGGGCCATCGGCAAATGCCGACGTCAAGGCCATGGGCATCGGCA
1 CAAATGCCGACGCCAAG-GCAACGGCCATC-GCAAATGACGACGCCAAGGCCATGGCCATCGGCA
* * *
1562 ACCACCGATGCCAAGTCCAAGGGCATGGGCAAATGCCGAAGCCAAGGCCTAGGGCCATCGACAAA
64 AACACCGACGCCAAGGCCAAGGGCATGGGCAAATGCCGAAGCCAAGGCCTAGGGCCATCGACAAA
*
1627 TGCCGATGCCAATGCCAAGGGGACAAGGGACATCATAAAATTCCGACGCAATCGG
129 TGCCGATGCCAATGCCAAGGGGACAAGGGACATCATAAAATTCCGACGCAATCAG
* *
1682 CAAATGGCGATGCCAAGGCAACGGACCATCAGCAAATGACGACGCCAAGGCCATGGACCATCGGC
1 CAAATGCCGACGCCAAGGCAACGG-CCATC-GCAAATGACGACGCCAAGGCCATGG-CCATCGGC
* * * ** *
1747 AAATACCGACGCCAAGGCCATGGGCATTGGCAAATGCCGATTCCAAGGCC-ATGGGCCATCGGCA
63 AAACACCGACGCCAAGGCCAAGGGCATGGGCAAATGCCGAAGCCAAGGCCTA-GGGCCATCGACA
* * * *
1811 AATGCTGATGCCAGTGCCAAGTGGACAAGGGACATCATCAAATTCCGACGCAATCAG
127 AATGCCGATGCCAATGCCAAGGGGACAAGGGACATCATAAAATTCCGACGCAATCAG
* * * * * *
1868 CCAATGCCGACACCAAGGCCACGTGCCATCGTCAAATGTCGATGCCAATGCCA
1 CAAATGCCGACGCCAAGGCAACG-GCCATCG-CAAATGACGACGCCAAGGCCA
1921 ACGTGACAAG
Statistics
Matches: 204, Mismatches: 30, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
184 5 0.02
185 45 0.22
186 153 0.75
187 1 0.00
ACGTcount: A:0.31, C:0.30, G:0.27, T:0.12
Consensus pattern (183 bp):
CAAATGCCGACGCCAAGGCAACGGCCATCGCAAATGACGACGCCAAGGCCATGGCCATCGGCAAA
CACCGACGCCAAGGCCAAGGGCATGGGCAAATGCCGAAGCCAAGGCCTAGGGCCATCGACAAATG
CCGATGCCAATGCCAAGGGGACAAGGGACATCATAAAATTCCGACGCAATCAG
Found at i:1976 original size:19 final size:19
Alignment explanation
Indices: 1954--2008 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 19
1944 TTCCGACAAG
1954 GCCATCGGCAAATGCCGAC
1 GCCATCGGCAAATGCCGAC
* *
1973 GCCA-AGGC-CATG--G--
1 GCCATCGGCAAATGCCGAC
1986 GCCATCGGCAAATGCCGAC
1 GCCATCGGCAAATGCCGAC
2005 GCCA
1 GCCA
2009 AGGCCATGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 12
0.62 0.10 0.29
Matches are distributed among these distances:
13 4 0.15
14 3 0.12
15 4 0.15
17 4 0.15
18 3 0.12
19 8 0.31
ACGTcount: A:0.25, C:0.36, G:0.29, T:0.09
Consensus pattern (19 bp):
GCCATCGGCAAATGCCGAC
Found at i:1994 original size:32 final size:32
Alignment explanation
Indices: 1953--2100 Score: 287
Period size: 32 Copynumber: 4.6 Consensus size: 32
1943 ATTCCGACAA
1953 GGCCATCGGCAAATGCCGACGCCAAGGCCATG
1 GGCCATCGGCAAATGCCGACGCCAAGGCCATG
1985 GGCCATCGGCAAATGCCGACGCCAAGGCCATG
1 GGCCATCGGCAAATGCCGACGCCAAGGCCATG
*
2017 GGCCATCGGAAAATGCCGACGCCAAGGCCATG
1 GGCCATCGGCAAATGCCGACGCCAAGGCCATG
2049 GGCCATCGGCAAATGCCGACGCCAAGGCCATG
1 GGCCATCGGCAAATGCCGACGCCAAGGCCATG
2081 GGCCATCGGCAAATGCCGAC
1 GGCCATCGGCAAATGCCGAC
2101 ACCACATCGG
Statistics
Matches: 114, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 114 1.00
ACGTcount: A:0.26, C:0.34, G:0.31, T:0.09
Consensus pattern (32 bp):
GGCCATCGGCAAATGCCGACGCCAAGGCCATG
Found at i:2293 original size:22 final size:22
Alignment explanation
Indices: 2245--2286 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2235 GCCTAATGGT
*
2245 GCCCCCGAGGAGGCCCCAAGGC
1 GCCCCCGAGGAGGCCCAAAGGC
**
2267 GCCCCCGAGGTTGCCCAAAG
1 GCCCCCGAGGAGGCCCAAAG
2287 TGGCCCCAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.19, C:0.43, G:0.33, T:0.05
Consensus pattern (22 bp):
GCCCCCGAGGAGGCCCAAAGGC
Found at i:2862 original size:31 final size:32
Alignment explanation
Indices: 2715--2911 Score: 299
Period size: 32 Copynumber: 6.2 Consensus size: 32
2705 CACGTCATCA
* **
2715 CCAAGGGACATCGGCAAATGCCGACTACAAGG
1 CCAAGGGCCATCGGCAAATGCCGACGCCAAGG
2747 CCAAGGGCCATCGGCAAATGCCGACGCCAAGG
1 CCAAGGGCCATCGGCAAATGCCGACGCCAAGG
* *
2779 CCAAGGGTCATCGGCAAATGCCGACACCAAGG
1 CCAAGGGCCATCGGCAAATGCCGACGCCAAGG
*
2811 CCATGGGCCATCGGCAAATGCCGACGCCAAGG
1 CCAAGGGCCATCGGCAAATGCCGACGCCAAGG
* *
2843 CCATGGG-CATCCGCAAATGCCGACGCCAAGG
1 CCAAGGGCCATCGGCAAATGCCGACGCCAAGG
2874 CC-AGGGCCATCGGCAAATGCCGACGCCAAGG
1 CCAAGGGCCATCGGCAAATGCCGACGCCAAGG
*
2905 CCGAGGG
1 CCAAGGG
2912 GACAAGGGAC
Statistics
Matches: 152, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
30 3 0.02
31 50 0.33
32 99 0.65
ACGTcount: A:0.28, C:0.33, G:0.31, T:0.08
Consensus pattern (32 bp):
CCAAGGGCCATCGGCAAATGCCGACGCCAAGG
Found at i:2980 original size:32 final size:31
Alignment explanation
Indices: 2944--3185 Score: 220
Period size: 32 Copynumber: 7.7 Consensus size: 31
2934 CAACGCAATA
**
2944 GGCAAATGCCGATACCAAGGCAACGGGCCATC
1 GGCAAATGCCGACGCCAAGGCAA-GGGCCATC
*
2976 GGCAAATGCCAACGCCAAGGTCAAGGGCCATC
1 GGCAAATGCCGACGCCAAGG-CAAGGGCCATC
* * *
3008 GGCAAATGCCAACGCCAAAGCCATGGGCCATC
1 GGCAAATGCCGACGCC-AAGGCAAGGGCCATC
* * * *
3040 GGCAAATGCCG-TGCCATGGCCATGGG-CATT
1 GGCAAATGCCGACGCCAAGG-CAAGGGCCATC
* *
3070 GGTAAATGCCGACGCCAAGACCAAGGGCCATC
1 GGCAAATGCCGACGCCAAG-GCAAGGGCCATC
* * *
3102 GGCAAATGCCCACACCAAGGCCATGGG-CATC
1 GGCAAATGCCGACGCCAAGG-CAAGGGCCATC
* * *
3133 GTCAAATGCCGACGTCAAGACCAAGGGCCATC
1 GGCAAATGCCGACGCCAAG-GCAAGGGCCATC
* *
3165 GGCAGATGCCGACGTCAAGGC
1 GGCAAATGCCGACGCCAAGGC
3186 CA
Statistics
Matches: 171, Mismatches: 30, Indels: 19
0.78 0.14 0.09
Matches are distributed among these distances:
30 15 0.09
31 44 0.26
32 106 0.62
33 6 0.04
ACGTcount: A:0.29, C:0.31, G:0.29, T:0.11
Consensus pattern (31 bp):
GGCAAATGCCGACGCCAAGGCAAGGGCCATC
Found at i:3102 original size:217 final size:217
Alignment explanation
Indices: 2727--3123 Score: 620
Period size: 217 Copynumber: 1.8 Consensus size: 217
2717 AAGGGACATC
* *
2727 GGCAAATGCCGACTACAAGGCCAAGGGCCATCGGCAAATGCCGACGCCAAGGCCAAGGGTCATCG
1 GGCAAATGCCGACTACAAGGCCAAGGGCCATCGGCAAATGCCAACGCCAAGGCCAAGGGCCATCG
* *
2792 GCAAATGCCGACACCAAGGCCATGGGCCATCGGCAAATGCCGACGCCAAGGCCATGGGCATCCGC
66 GCAAATGCCAACACCAAAGCCATGGGCCATCGGCAAATGCCGACGCCAAGGCCATGGGCATCCGC
* * *
2857 AAATGCCGACGCCAAGGCCAGGGCCATCGGCAAATGCCGACGCCAAGGCCGAGGGGACAAGGGAC
131 AAATGCCGACGCCAAGACCAGGGCCATCGGCAAATGCCCACACCAAGGCCGAGGGGACAAGGGAC
2922 ATCATCAAATTCCAACGCAATA
196 ATCATCAAATTCCAACGCAATA
*
2944 GGCAAATGCCGA-TACCAAGG-CAACGGGCCATCGGCAAATGCCAACGCCAAGGTCAAGGGCCAT
1 GGCAAATGCCGACTA-CAAGGCCAA-GGGCCATCGGCAAATGCCAACGCCAAGGCCAAGGGCCAT
* * * **
3007 CGGCAAATGCCAACGCCAAAGCCATGGGCCATCGGCAAATGCCG-TGCCATGGCCATGGGCATTG
64 CGGCAAATGCCAACACCAAAGCCATGGGCCATCGGCAAATGCCGACGCCAAGGCCATGGGCATCC
*
3071 GTAAATGCCGACGCCAAGACCAAGGGCCATCGGCAAATGCCCACACCAAGGCC
129 GCAAATGCCGACGCCAAGACC-AGGGCCATCGGCAAATGCCCACACCAAGGCC
3124 ATGGGCATCG
Statistics
Matches: 163, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
216 40 0.25
217 123 0.75
ACGTcount: A:0.30, C:0.32, G:0.28, T:0.10
Consensus pattern (217 bp):
GGCAAATGCCGACTACAAGGCCAAGGGCCATCGGCAAATGCCAACGCCAAGGCCAAGGGCCATCG
GCAAATGCCAACACCAAAGCCATGGGCCATCGGCAAATGCCGACGCCAAGGCCATGGGCATCCGC
AAATGCCGACGCCAAGACCAGGGCCATCGGCAAATGCCCACACCAAGGCCGAGGGGACAAGGGAC
ATCATCAAATTCCAACGCAATA
Done.