Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017999.1 Corchorus olitorius cultivar O-4 contig18032, 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: 4293
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.30
Found at i:922 original size:30 final size:30
Alignment explanation
Indices: 895--1332 Score: 603
Period size: 30 Copynumber: 14.6 Consensus size: 30
885 GACCCTAAGC
*
895 CAGGATGAAAATAAAGCAATGATCCT-AAA
1 CAGGATTAAAATAAAGCAATGATCCTCAAA
* * * *
924 TCAGGATTAAAATGGAA-CACTCATCCTCAAC
1 -CAGGATTAAAAT-AAAGCAATGATCCTCAAA
*
955 CAGGATTAAAATAAAGCAATGATCCTCAAC
1 CAGGATTAAAATAAAGCAATGATCCTCAAA
* *
985 CAGGATTAAAATAAAGCAATGATCCTCGAC
1 CAGGATTAAAATAAAGCAATGATCCTCAAA
*
1015 CAGGATTAAAATAAAGCAATGATCCTCAAC
1 CAGGATTAAAATAAAGCAATGATCCTCAAA
1045 CAGGATTTAAAATAAAGCAATGATCCTCAAA
1 CAGGA-TTAAAATAAAGCAATGATCCTCAAA
* * *
1076 CAAGATTAAAATAAAGCAAGGATCATCAAA
1 CAGGATTAAAATAAAGCAATGATCCTCAAA
* *
1106 CAGGATTAAAATAAAGTAACGATCCTCAAA
1 CAGGATTAAAATAAAGCAATGATCCTCAAA
* *
1136 CATGATTAAAATAAAGCAAGGATCCTCAAA
1 CAGGATTAAAATAAAGCAATGATCCTCAAA
* * *
1166 CAAGATTAAAATAAAGTAACGATCCTCAAA
1 CAGGATTAAAATAAAGCAATGATCCTCAAA
* *
1196 CAGAATTAAAATAAAGCAACGATCCTC-AA
1 CAGGATTAAAATAAAGCAATGATCCTCAAA
1225 CTAGGATTAAAATAAAGCAATGATCCTCAAA
1 C-AGGATTAAAATAAAGCAATGATCCTCAAA
*
1256 CAGGATTAAAATAAAGCAACGATCCTCAAA
1 CAGGATTAAAATAAAGCAATGATCCTCAAA
* *
1286 CAGGATTAAAATAAAGCAACGATCCTCAAC
1 CAGGATTAAAATAAAGCAATGATCCTCAAA
1316 CAGGATTAAAATAAAGC
1 CAGGATTAAAATAAAGC
1333 TGATAAAGCA
Statistics
Matches: 371, Mismatches: 31, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
29 5 0.01
30 331 0.89
31 35 0.09
ACGTcount: A:0.49, C:0.18, G:0.13, T:0.19
Consensus pattern (30 bp):
CAGGATTAAAATAAAGCAATGATCCTCAAA
Found at i:1678 original size:71 final size:71
Alignment explanation
Indices: 1594--2077 Score: 535
Period size: 71 Copynumber: 6.8 Consensus size: 71
1584 CATTTTGCAG
* * * * * * * *
1594 TCAATTGAAATAAACT-ACAGAGAAGATCACCCTAGATCTACTGAAGTAAATTGAGGAAAGATCG
1 TCAATTGAAATAAACTGA-AGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCG
* *
1658 TCTTGGA
65 CCCTGGA
* * *
1665 TCACTTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAAGTGAAATAAACTGAAGAAAAGATCG
1 TCAATTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAG-AAAGACCG
1730 CCCTGGA
65 CCCTGGA
* *
1737 TCAATTGAAATAAATTGAAGAAAAGATTGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCGC
1 TCAATTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCGC
*
1802 CCTGAA
66 CCTGGA
*
1808 TCAATTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAATTGAAGAAAGACCGC
1 TCAATTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCGC
*
1873 CCTGGG
66 CCTGGA
* *
1879 TCAACTGAAATAAACTGAAGAAAAGGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAAACC
1 TCAATTGAAATAAACTGAAGAAAA-GATCGCCCTGGATCAACTGAAATAAACTGAAG-AAAGACC
*
1944 GCCCTGGG
64 GCCCTGGA
* * * * * * * * * *
1952 TCAACAT-AAATGAATTGAA-TAAGGATCGCCCTGGATCAACTGAAGTGAATTGAAGAAAGATCA
1 TCAA-TTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCG
2015 CCCTGGA
65 CCCTGGA
* * * * * * * *
2022 TCAAACTGAAATAAACTGAA-ATAGGACCACCCTGGGTCAACTGAAATGAATTGAAG
1 TC-AATTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAG
2078 CGTCTGAAAT
Statistics
Matches: 360, Mismatches: 46, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
70 14 0.04
71 218 0.61
72 99 0.28
73 28 0.08
74 1 0.00
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.19
Consensus pattern (71 bp):
TCAATTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCGC
CCTGGA
Found at i:1701 original size:36 final size:36
Alignment explanation
Indices: 1594--2077 Score: 518
Period size: 36 Copynumber: 13.6 Consensus size: 36
1584 CATTTTGCAG
* * * *
1594 TCAATTGAAATAAACT-ACAGAGAAGATCACCCTAGA
1 TCAACTGAAATAAACTGA-AGAAAAGATCGCCCTGGA
* * * * * *
1630 TCTACTGAAGTAAATTG-AGGAAAGATCGTCTTGGA
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
1665 TC-ACTTGAAATAAACTGAAGAAAAGATCGCCCTGGA
1 TCAAC-TGAAATAAACTGAAGAAAAGATCGCCCTGGA
*
1701 TCAAGTGAAATAAACTGAAGAAAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
* * *
1737 TCAATTGAAATAAATTGAAGAAAAGATTGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
* *
1773 TCAACTGAAATAAACTGAAG-AAAGACCGCCCTGAA
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
*
1808 TCAATTGAAATAAACTGAAGAAAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
* * *
1844 TCAACTGAAATAAATTGAAG-AAAGACCGCCCTGGG
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
1879 TCAACTGAAATAAACTGAAGAAAAGGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAAA-GATCGCCCTGGA
* * *
1916 TCAACTGAAATAAACTGAAGAAAAAACCGCCCTGGG
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
* * * *
1952 TCAACAT-AAATGAATTGAA-TAAGGATCGCCCTGGA
1 TCAAC-TGAAATAAACTGAAGAAAAGATCGCCCTGGA
* * * *
1987 TCAACTGAAGTGAATTGAAG-AAAGATCACCCTGGA
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
* * * * *
2022 TCAAACTGAAATAAACTGAA-ATAGGACCACCCTGGG
1 TC-AACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
* *
2058 TCAACTGAAATGAATTGAAG
1 TCAACTGAAATAAACTGAAG
2078 CGTCTGAAAT
Statistics
Matches: 379, Mismatches: 56, Indels: 26
0.82 0.12 0.06
Matches are distributed among these distances:
34 3 0.01
35 144 0.38
36 196 0.52
37 36 0.09
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.19
Consensus pattern (36 bp):
TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
Found at i:1853 original size:143 final size:142
Alignment explanation
Indices: 1594--2077 Score: 553
Period size: 143 Copynumber: 3.4 Consensus size: 142
1584 CATTTTGCAG
* * * * * * * * *
1594 TCAATTGAAATAAACT-ACAGAGAAGATCACCCTAGATCTACTGAAGTAAATTGAGGAAAGATCG
1 TCAACTGAAATAAACTGA-AGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCG
* * * * *
1658 TCTTGGATCACTTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAAGTGAAATAAACTGAAGAA
65 CCCTGGATCAATTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAATTGAAG-A
1723 AAGATCGCCCTGGA
129 AAGATCGCCCTGGA
* * *
1737 TCAATTGAAATAAATTGAAGAAAAGATTGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCGC
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCGC
*
1802 CCTGAATCAATTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAATTGAAGAAA
66 CCTGGATCAATTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAATTGAAGAAA
* *
1867 GACCGCCCTGGG
131 GATCGCCCTGGA
*
1879 TCAACTGAAATAAACTGAAGAAAAGGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAAACC
1 TCAACTGAAATAAACTGAAGAAAA-GATCGCCCTGGATCAACTGAAATAAACTGAAG-AAAGACC
* * * * * * * *
1944 GCCCTGGGTCAACAT-AAATGAATTGAA-TAAGGATCGCCCTGGATCAACTGAAGTGAATTGAAG
64 GCCCTGGATCAA-TTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAATTGAAG
*
2007 AAAGATCACCCTGGA
128 AAAGATCGCCCTGGA
* * * * * * *
2022 TCAAACTGAAATAAACTGAA-ATAGGACCACCCTGGGTCAACTGAAATGAATTGAAG
1 TC-AACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAG
2078 CGTCTGAAAT
Statistics
Matches: 295, Mismatches: 41, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
142 62 0.21
143 188 0.64
144 44 0.15
145 1 0.00
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.19
Consensus pattern (142 bp):
TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCGC
CCTGGATCAATTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAATTGAAGAAA
GATCGCCCTGGA
Found at i:1910 original size:179 final size:177
Alignment explanation
Indices: 1633--2077 Score: 536
Period size: 179 Copynumber: 2.5 Consensus size: 177
1623 CCCTAGATCT
* * * * * *
1633 ACTGAAGTAAATTGAGGAAAGATCGTCTTGGATC-ACTTGAAATAAACTGAAGAAAAGATCGCCC
1 ACTGAAATAAACTGAAGAAAGATCGCCCTGGATCAAC-TGAAATAAACTGAAG-AAAGACCGCCC
* * * * *
1697 TGGATCAAGTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAATTGAAATAAATTGAAGAAAAG
64 TGGGTCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAA
**
1762 ATTGCCCTGGATCAAC-TGAAATAAACTGAAGAAAGACCGCCCTGAATCA
129 ACCGCCCTGGATCAACAT-AAATAAACTGAAGAAAGACCGCCCTGAATCA
* *
1811 ATTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAATTGAAGAAAGACCGCCCT
1 ACTGAAATAAACTGAAG-AAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCGCCCT
1876 GGGTCAACTGAAATAAACTGAAGAAAAGGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAA
65 GGGTCAACTGAAATAAACTGAAGAAAA-GATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAA
* * * * * * *
1941 ACCGCCCTGGGTCAACATAAATGAATTGAATAAGGATCGCCCTGGATCA
129 ACCGCCCTGGATCAACATAAATAAACTGAAGAAAGACCGCCCTGAATCA
* * * * * *
1990 ACTGAAGTGAATTGAAGAAAGATCACCCTGGATCAAACTGAAATAAACTGAA-ATAGGACCACCC
1 ACTGAAATAAACTGAAGAAAGATCGCCCTGGATC-AACTGAAATAAACTGAAGA-AAGACCGCCC
* *
2054 TGGGTCAACTGAAATGAATTGAAG
64 TGGGTCAACTGAAATAAACTGAAG
2078 CGTCTGAAAT
Statistics
Matches: 229, Mismatches: 32, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
178 66 0.29
179 160 0.70
180 3 0.01
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.19
Consensus pattern (177 bp):
ACTGAAATAAACTGAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCGCCCTG
GGTCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAAAC
CGCCCTGGATCAACATAAATAAACTGAAGAAAGACCGCCCTGAATCA
Done.