Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010491.1 Corchorus olitorius cultivar O-4 contig10523, 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: 6476
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Found at i:676 original size:28 final size:27
Alignment explanation
Indices: 625--686 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 27
615 ACGTGAACTT
* *
625 AAAATGACCAAAATACCCCCGAATGTGC
1 AAAATGACCAAAATACCACCGAATGT-A
* *
653 AAAATGACCAAAATGCCACTGAATGTA
1 AAAATGACCAAAATACCACCGAATGTA
680 AAAATGA
1 AAAATGA
687 TTGAAAAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 7 0.23
28 23 0.77
ACGTcount: A:0.48, C:0.21, G:0.15, T:0.16
Consensus pattern (27 bp):
AAAATGACCAAAATACCACCGAATGTA
Found at i:1239 original size:30 final size:30
Alignment explanation
Indices: 1203--2016 Score: 1020
Period size: 30 Copynumber: 27.3 Consensus size: 30
1193 ACTGATGAAA
*
1203 CAATGATCCT-AAACCAAGATTAAAATAAAG
1 CAATGATCCTCAAA-CAGGATTAAAATAAAG
*
1233 CAATGATCCTCAACCAGGATTAAAATAAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
* *
1263 CAATGATCCTCGACCAGGATTAAAATAAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
* *
1293 CAATGATCCTCAACCAGGATTAAAAGAAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
* * *
1323 CGATGATCCTCAACCAGGATTAAAATAAAA
1 CAATGATCCTCAAACAGGATTAAAATAAAG
* * *
1353 TAACGATCCTCAAACAGGATTAAAATGAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
* * *
1383 CAACGATCCTCAAACAGGATTAAAATGAGG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
*
1413 CAAAT-ATCCTCAACCAGGATTAAAATAAAG
1 C-AATGATCCTCAAACAGGATTAAAATAAAG
1443 CAATGATCCTCAAACAGGATTAAAATGAAA-
1 CAATGATCCTCAAACAGGATTAAAAT-AAAG
1473 CAATGATCCTCAAACAGGATTAAAATAAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
* **
1503 CGATGATCCTCAAACAGGATTAAAACGAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
* * *
1533 CAATGATCATCAAACATGATCAAAATAAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
* *
1563 CGATGAGCCTCAAACAGGATTAAAATAAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
* *
1593 CAAAGATCCTCAAACAGGATAAAAATAAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
*
1623 CAATGATCCTCAAACAGGACTAAAATAAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
* *
1653 TAACGATCCTCAAACAGGATTAAAATAAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
* * * *
1683 CGACGATCCTCAAACAGGATTAAAATGAGG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
* * * *
1713 CAACGATCCTCAACCAGGATTAAAATGATG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
*
1743 CAAAT-ATCCTCAACCAGGATTAAAAT-AA-
1 C-AATGATCCTCAAACAGGATTAAAATAAAG
* *
1771 C---GATCTTCAACCAGGATTAAAATAAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
* * *
1798 TAACGATCCTCAACCAGGATTAAAATAAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
*
1828 CGAAT-ATCCTCAACCAGGATTAAAATAAAG
1 C-AATGATCCTCAAACAGGATTAAAATAAAG
* * *
1858 CGA-GAATCCTCAAACAGGATGAAAATGAAG
1 CAATG-ATCCTCAAACAGGATTAAAATAAAG
* *
1888 CAATGATCCTTAAACAGGATTAACATAAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
1918 CAATGATTCCTCAAACAGGATTAAAATAAAG
1 CAATGA-TCCTCAAACAGGATTAAAATAAAG
* *
1949 CAATGATCCTTAAACAGGATTAAAATGAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
*
1979 CAATGATCCTCAAACAGGATTAACATAAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAG
2009 CAATGATC
1 CAATGATC
2017 AAAATAAAGC
Statistics
Matches: 692, Mismatches: 75, Indels: 34
0.86 0.09 0.04
Matches are distributed among these distances:
25 20 0.03
26 2 0.00
28 1 0.00
29 8 0.01
30 621 0.90
31 40 0.06
ACGTcount: A:0.47, C:0.19, G:0.15, T:0.19
Consensus pattern (30 bp):
CAATGATCCTCAAACAGGATTAAAATAAAG
Found at i:2044 original size:47 final size:47
Alignment explanation
Indices: 1970--2063 Score: 143
Period size: 47 Copynumber: 2.0 Consensus size: 47
1960 AAACAGGATT
* *
1970 AAAATGAAGCAATGATCCTCAAACAGGATTAACATAAAGCAATGATC
1 AAAATAAAGCAATGATCCTCAAACAGGATTAAAATAAAGCAATGATC
* * *
2017 AAAATAAAGCAATGATCCTTAAGCAGGATTAAAATGAAGCAATGATC
1 AAAATAAAGCAATGATCCTCAAACAGGATTAAAATAAAGCAATGATC
2064 CTCAAACATG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.49, C:0.15, G:0.16, T:0.20
Consensus pattern (47 bp):
AAAATAAAGCAATGATCCTCAAACAGGATTAAAATAAAGCAATGATC
Found at i:2051 original size:30 final size:30
Alignment explanation
Indices: 2017--2263 Score: 253
Period size: 30 Copynumber: 8.5 Consensus size: 30
2007 AGCAATGATC
* *
2017 AAAATAAAGCAATGATCCTTAAGCAGGATT
1 AAAATAAAGCAATGATCCTCAAACAGGATT
* *
2047 AAAATGAAGCAATGATCCTCAAACATGATT
1 AAAATAAAGCAATGATCCTCAAACAGGATT
* *
2077 AACATGAAGCAATGATCCTCAAACAGGATT
1 AAAATAAAGCAATGATCCTCAAACAGGATT
*
2107 AACATAAAGCAATGATCCTTC-AACAGGATT
1 AAAATAAAGCAATGATCC-TCAAACAGGATT
*
2137 AAAATAAAGCAATGATCCT---------TA
1 AAAATAAAGCAATGATCCTCAAACAGGATT
* *
2158 AAAATGAAGCAATGATCCTTAAACAGGATT
1 AAAATAAAGCAATGATCCTCAAACAGGATT
* * *
2188 AACATAAAGCAATGATCCTCAACCAGGATC
1 AAAATAAAGCAATGATCCTCAAACAGGATT
** * * *
2218 AAAATAAAGTGACGATCCTCAACCAAGATT
1 AAAATAAAGCAATGATCCTCAAACAGGATT
2248 AAAATAAAGCAATGAT
1 AAAATAAAGCAATGAT
2264 GTAGAATAGT
Statistics
Matches: 182, Mismatches: 25, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
21 19 0.10
29 1 0.01
30 160 0.88
31 2 0.01
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.21
Consensus pattern (30 bp):
AAAATAAAGCAATGATCCTCAAACAGGATT
Found at i:2067 original size:77 final size:77
Alignment explanation
Indices: 1940--2093 Score: 281
Period size: 77 Copynumber: 2.0 Consensus size: 77
1930 AAACAGGATT
1940 AAAATAAAGCAATGATCCTTAAACAGGATTAAAATGAAGCAATGATCCTCAAACAGGATTAACAT
1 AAAATAAAGCAATGATCCTTAAACAGGATTAAAATGAAGCAATGATCCTCAAACAGGATTAACAT
2005 AAAGCAATGATC
66 AAAGCAATGATC
* *
2017 AAAATAAAGCAATGATCCTTAAGCAGGATTAAAATGAAGCAATGATCCTCAAACATGATTAACAT
1 AAAATAAAGCAATGATCCTTAAACAGGATTAAAATGAAGCAATGATCCTCAAACAGGATTAACAT
*
2082 GAAGCAATGATC
66 AAAGCAATGATC
2094 CTCAAACAGG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 74 1.00
ACGTcount: A:0.48, C:0.16, G:0.15, T:0.21
Consensus pattern (77 bp):
AAAATAAAGCAATGATCCTTAAACAGGATTAAAATGAAGCAATGATCCTCAAACAGGATTAACAT
AAAGCAATGATC
Found at i:2119 original size:107 final size:108
Alignment explanation
Indices: 1912--2123 Score: 363
Period size: 107 Copynumber: 2.0 Consensus size: 108
1902 CAGGATTAAC
*
1912 ATAAAGCAATGATTCCTCAAACAGGATTAAAATAAAGCAATGATCCTTAAACAGGATTAAAATGA
1 ATAAAGCAATGATTCCTCAAACAGGATTAAAATAAAGCAATGATCCTCAAACAGGATTAAAATGA
1977 AGCAATGATCCTCAAACAGGATTAACATAAAGCAATGATCAAA
66 AGCAATGATCCTCAAACAGGATTAACATAAAGCAATGATCAAA
* * * * *
2020 ATAAAGCAATGA-TCCTTAAGCAGGATTAAAATGAAGCAATGATCCTCAAACATGATTAACATGA
1 ATAAAGCAATGATTCCTCAAACAGGATTAAAATAAAGCAATGATCCTCAAACAGGATTAAAATGA
2084 AGCAATGATCCTCAAACAGGATTAACATAAAGCAATGATC
66 AGCAATGATCCTCAAACAGGATTAACATAAAGCAATGATC
2124 CTTCAACAGG
Statistics
Matches: 98, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
107 86 0.88
108 12 0.12
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.22
Consensus pattern (108 bp):
ATAAAGCAATGATTCCTCAAACAGGATTAAAATAAAGCAATGATCCTCAAACAGGATTAAAATGA
AGCAATGATCCTCAAACAGGATTAACATAAAGCAATGATCAAA
Found at i:2167 original size:21 final size:21
Alignment explanation
Indices: 2137--2180 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
2127 CAACAGGATT
2137 AAAATAAAGCAATGATCCTTA
1 AAAATAAAGCAATGATCCTTA
*
2158 AAAATGAAGCAATGATCCTTA
1 AAAATAAAGCAATGATCCTTA
2179 AA
1 AA
2181 CAGGATTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.52, C:0.14, G:0.11, T:0.23
Consensus pattern (21 bp):
AAAATAAAGCAATGATCCTTA
Found at i:2204 original size:111 final size:107
Alignment explanation
Indices: 1938--2263 Score: 368
Period size: 111 Copynumber: 3.0 Consensus size: 107
1928 TCAAACAGGA
* *
1938 TTAAAATAAAGCAATGATCCTTAAACAGGATTAAAATGAAGCAATGATCCTCAAACAGGATTAAC
1 TTAAAATGAAGCAATGATCCTTAAACAGGATTAACATGAAGCAATGATCCTCAAACAGGATTAAC
*** * * * *** * *
2003 ATAAAGCAATGATCAAAATAAAGCAATGATCCTTAAGC-AGGA-
66 ATAAAGCAATGATCCTCA-ACAG-GATTAAAATAAAGCAATGAT
* *
2045 TTAAAATGAAGCAATGATCCTCAAACATGATTAACATGAAGCAATGATCCTCAAACAGGATTAAC
1 TTAAAATGAAGCAATGATCCTTAAACAGGATTAACATGAAGCAATGATCCTCAAACAGGATTAAC
2110 ATAAAGCAATGATCCTTCAACAGGATTAAAATAAAGCAATGAT
66 ATAAAGCAATGATCC-TCAACAGGATTAAAATAAAGCAATGAT
* * *
2153 CCTTAAAAATGAAGCAATGATCCTTAAACAGGATTAACATAAAGCAATGATCCTCAACCAGGATC
1 --TT-AAAATGAAGCAATGATCCTTAAACAGGATTAACATGAAGCAATGATCCTCAAACAGGATT
* ** * *
2218 AAAATAAAGTGACGATCCTCAACCAAGATTAAAATAAAGCAATGAT
63 AACATAAAGCAATGATCCTCAA-CAGGATTAAAATAAAGCAATGAT
2264 GTAGAATAGT
Statistics
Matches: 187, Mismatches: 25, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
106 8 0.04
107 81 0.43
108 1 0.01
110 6 0.03
111 91 0.49
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (107 bp):
TTAAAATGAAGCAATGATCCTTAAACAGGATTAACATGAAGCAATGATCCTCAAACAGGATTAAC
ATAAAGCAATGATCCTCAACAGGATTAAAATAAAGCAATGAT
Found at i:2235 original size:81 final size:81
Alignment explanation
Indices: 2080--2236 Score: 253
Period size: 81 Copynumber: 1.9 Consensus size: 81
2070 CATGATTAAC
*
2080 ATGAAGCAATGATCCTCAAACAGGATTAACATAAAGCAATGATCCTTCAACAGGATTAAAATAAA
1 ATGAAGCAATGATCCTCAAACAGGATTAACATAAAGCAATGATCCTTCAACAGGATCAAAATAAA
*
2145 GCAATGATCCTTAAAA
66 GCAACGATCCTTAAAA
*
2161 ATGAAGCAATGATCCTTAAACAGGATTAACATAAAGCAATGATCC-TCAACCAGGATCAAAATAA
1 ATGAAGCAATGATCCTCAAACAGGATTAACATAAAGCAATGATCCTTCAA-CAGGATCAAAATAA
**
2225 AGTGACGATCCT
65 AGCAACGATCCT
2237 CAACCAAGAT
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
80 4 0.06
81 66 0.94
ACGTcount: A:0.45, C:0.18, G:0.15, T:0.22
Consensus pattern (81 bp):
ATGAAGCAATGATCCTCAAACAGGATTAACATAAAGCAATGATCCTTCAACAGGATCAAAATAAA
GCAACGATCCTTAAAA
Found at i:2515 original size:36 final size:36
Alignment explanation
Indices: 2470--2900 Score: 343
Period size: 36 Copynumber: 12.2 Consensus size: 36
2460 CAATTTGCGG
* *
2470 TCAACTGAAATAAACTGCAGAAAAGATCACCCTGGA
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
* **
2506 TCAATTGAAATAAACTGAAGAAAAGATTACCCTGGA
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
* * *
2542 TCCATTGAAATAAATTGAAGAAAAGATCGCCCTAGG-
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCT-GGA
2578 TCAA--G---TAAACTGAAGAAAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
* * * *
2609 TCAACTAAAAT-AACTTGAAG-TAAGATCGTCCTTGA
1 TCAACTGAAATAAAC-TGAAGAAAAGATCGCCCTGGA
* * * * *
2644 TCAATTGAAATGAATTGAAG-AAAGACCGCCCTGGG
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
* * * *
2679 TCAACTAAAAT-AACTTGAAG-AATGACCGCCCTGGG
1 TCAACTGAAATAAAC-TGAAGAAAAGATCGCCCTGGA
* * *
2714 TCAGCTAAAATAAATTGAACG-AAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAA-GAAAAGATCGCCCTGGA
** * * * *
2750 TTGACTGACATAAATTGAATAAAAGATCACCCTGGA
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
* * * * * *
2786 TCAACTGGAGTAAATTG-AGGAGAGATCACCCTGGA
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
* *
2821 TCAACTGACATAAACTGAATG--AAGATCACCCTGGA
1 TCAACTGAAATAAACTGAA-GAAAAGATCGCCCTGGA
* * *
2856 TCCATTGAAATAAACTGAAGAAAAGATCGCCCTGGG
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
2892 TCAACTGAA
1 TCAACTGAA
2901 GTGAACTAAA
Statistics
Matches: 321, Mismatches: 57, Indels: 34
0.78 0.14 0.08
Matches are distributed among these distances:
30 2 0.01
31 26 0.08
34 4 0.01
35 138 0.43
36 148 0.46
37 3 0.01
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.21
Consensus pattern (36 bp):
TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGA
Found at i:2883 original size:71 final size:70
Alignment explanation
Indices: 2470--2900 Score: 326
Period size: 70 Copynumber: 6.1 Consensus size: 70
2460 CAATTTGCGG
* **
2470 TCAACTGAAATAAACTGCAGAAAAGATCACCCTGGATCAATTGAAATAAACTGAAGAAAAGATTA
1 TCAACTGAAATAAACTG-A-AGAAGATCACCCTGGATCAATTGAAATAAACTGAAGAAAAGATCG
2535 CCCTGGA
64 CCCTGGA
* * * *
2542 TCCATTGAAATAAATTGAAGAAAAGATCGCCCTAGG-TCAA--G---TAAACTGAAGAAAAGATC
1 TCAACTGAAATAAACTGAAG--AAGATCACCCT-GGATCAATTGAAATAAACTGAAGAAAAGATC
2601 GCCCTGGA
63 GCCCTGGA
* ** * * * *
2609 TCAACTAAAAT-AACTTGAAGTAAGATCGTCCTTGATCAATTGAAATGAATTGAAG-AAAGACCG
1 TCAACTGAAATAAAC-TGAAG-AAGATCACCCTGGATCAATTGAAATAAACTGAAGAAAAGATCG
*
2672 CCCTGGG
64 CCCTGGA
* * * * ** * *
2679 TCAACTAAAAT-AACTTGAAGAATGACCGCCCTGGGTCAGCTAAAATAAATTGAACG-AAAGATC
1 TCAACTGAAATAAAC-TGAAGAA-GATCACCCTGGATCAATTGAAATAAACTGAA-GAAAAGATC
2742 GCCCTGGA
63 GCCCTGGA
** * * * * * * * * * *
2750 TTGACTGACATAAATTGAATAAAAGATCACCCTGGATCAACTGGAGTAAATTG-AGGAGAGATCA
1 TCAACTGAAATAAACTG-A-AGAAGATCACCCTGGATCAATTGAAATAAACTGAAGAAAAGATCG
2814 CCCTGGA
64 CCCTGGA
* *
2821 TCAACTGACATAAACTGAATGAAGATCACCCTGGATCCATTGAAATAAACTGAAGAAAAGATCGC
1 TCAACTGAAATAAACTGAA-GAAGATCACCCTGGATCAATTGAAATAAACTGAAGAAAAGATCGC
*
2886 CCTGGG
65 CCTGGA
2892 TCAACTGAA
1 TCAACTGAA
2901 GTGAACTAAA
Statistics
Matches: 284, Mismatches: 57, Indels: 37
0.75 0.15 0.10
Matches are distributed among these distances:
65 1 0.00
66 16 0.06
67 37 0.13
68 1 0.00
69 3 0.01
70 86 0.30
71 82 0.29
72 53 0.19
73 5 0.02
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.21
Consensus pattern (70 bp):
TCAACTGAAATAAACTGAAGAAGATCACCCTGGATCAATTGAAATAAACTGAAGAAAAGATCGCC
CTGGA
Found at i:4854 original size:2 final size:2
Alignment explanation
Indices: 4847--4877 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4837 GAACAATAGA
4847 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4878 CATAATGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.