Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023749.1 Corchorus olitorius cultivar O-4 contig23782, 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: 63999
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:6167 original size:69 final size:69
Alignment explanation
Indices: 6082--6219 Score: 249
Period size: 69 Copynumber: 2.0 Consensus size: 69
6072 GCCGGAAACC
* * *
6082 GTGCTTTCTAATGCGTTGGTAATGGTGTAGAAATGGTGGTTAATGGGAAATGGCTAGGATAGGGA
1 GTGCTTTCTAATGCGTTGGTAACGGTGTAGAAATGGTGGTGAATGGAAAATGGCTAGGATAGGGA
6147 AGAG
66 AGAG
6151 GTGCTTTCTAATGCGTTGGTAACGGTGTAGAAATGGTGGTGAATGGAAAATGGCTAGGATAGGGA
1 GTGCTTTCTAATGCGTTGGTAACGGTGTAGAAATGGTGGTGAATGGAAAATGGCTAGGATAGGGA
6216 AGAG
66 AGAG
6220 CACGAGAAAA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.28, C:0.07, G:0.38, T:0.28
Consensus pattern (69 bp):
GTGCTTTCTAATGCGTTGGTAACGGTGTAGAAATGGTGGTGAATGGAAAATGGCTAGGATAGGGA
AGAG
Found at i:12879 original size:27 final size:27
Alignment explanation
Indices: 12841--12897 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
12831 CCGGTCTGTT
12841 CTTGCTGCTATCTATATCAGATCCATA
1 CTTGCTGCTATCTATATCAGATCCATA
12868 CTTGCTGCTATCTATATCAGATCCATA
1 CTTGCTGCTATCTATATCAGATCCATA
12895 CTT
1 CTT
12898 CACTCTGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.25, C:0.26, G:0.11, T:0.39
Consensus pattern (27 bp):
CTTGCTGCTATCTATATCAGATCCATA
Found at i:13775 original size:19 final size:19
Alignment explanation
Indices: 13751--13787 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
13741 TTTGGTCCCA
*
13751 AAACGGTGGTGAAACGGTC
1 AAACGGTAGTGAAACGGTC
13770 AAACGGTAGTGAAACGGT
1 AAACGGTAGTGAAACGGT
13788 TACAGATAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.14, G:0.35, T:0.16
Consensus pattern (19 bp):
AAACGGTAGTGAAACGGTC
Found at i:16109 original size:24 final size:24
Alignment explanation
Indices: 16075--16124 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
16065 AGTGACCCAG
* **
16075 GGAAATTACTAGGGTCTTATGTGA
1 GGAAATCACTAGGGTCCCATGTGA
16099 GGAAATCACTAGGGTCCCATGTGA
1 GGAAATCACTAGGGTCCCATGTGA
16123 GG
1 GG
16125 CGAGGGGCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.28, C:0.14, G:0.32, T:0.26
Consensus pattern (24 bp):
GGAAATCACTAGGGTCCCATGTGA
Found at i:18959 original size:19 final size:19
Alignment explanation
Indices: 18935--18972 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
18925 TTTTTTTTTT
18935 GCCACGTGGATATTATTTG
1 GCCACGTGGATATTATTTG
*
18954 GCCACGTGGATTTTATTTG
1 GCCACGTGGATATTATTTG
18973 CTTTCATCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.18, C:0.16, G:0.26, T:0.39
Consensus pattern (19 bp):
GCCACGTGGATATTATTTG
Found at i:20983 original size:21 final size:20
Alignment explanation
Indices: 20949--21006 Score: 75
Period size: 19 Copynumber: 2.9 Consensus size: 20
20939 AAACTGATCG
20949 AATATTAATATATATAATTA
1 AATATTAATATATATAATTA
*
20969 AATATATATTATATATAA-T-
1 AATAT-TAATATATATAATTA
20988 AATATTAGATATATATAAT
1 AATATTA-ATATATATAAT
21007 ATTAGATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 2 0.06
19 14 0.42
20 6 0.18
21 11 0.33
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
AATATTAATATATATAATTA
Found at i:20988 original size:16 final size:16
Alignment explanation
Indices: 20950--21018 Score: 67
Period size: 14 Copynumber: 4.6 Consensus size: 16
20940 AACTGATCGA
*
20950 ATAT-TAATATATATA
1 ATATATAATATATATT
20965 AT-TA-AATATATATT
1 ATATATAATATATATT
20979 ATATATAATA-ATATT
1 ATATATAATATATATT
*
20994 AGATAT-ATATAATATT
1 ATATATAATAT-ATATT
*
21010 AGATATAAT
1 ATATATAAT
21019 TATTAAACGG
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
14 15 0.33
15 14 0.30
16 15 0.33
17 2 0.04
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
ATATATAATATATATT
Found at i:21001 original size:26 final size:25
Alignment explanation
Indices: 20950--21020 Score: 74
Period size: 26 Copynumber: 2.8 Consensus size: 25
20940 AACTGATCGA
20950 ATATTA-ATATATATAATTAAATAT
1 ATATTATATATATATAATTAAATAT
*
20974 ATATTATATATA-ATAATATTAGATAT
1 ATATTATATATATAT-A-ATTAAATAT
* *
21000 ATATAATATTAGATATAATTA
1 ATATTATA-TATATATAATTA
21021 TTAAACGGTC
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
24 8 0.21
25 6 0.15
26 19 0.49
27 4 0.10
28 2 0.05
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (25 bp):
ATATTATATATATATAATTAAATAT
Found at i:24074 original size:12 final size:12
Alignment explanation
Indices: 24057--24094 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
24047 TGAAAATGGT
24057 GAAGAAGAAAAA
1 GAAGAAGAAAAA
*
24069 GAAGAAGGAAAA
1 GAAGAAGAAAAA
24081 GAA-AAGAAAAA
1 GAAGAAGAAAAA
24092 GAA
1 GAA
24095 ATGGGAGAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:24405 original size:22 final size:21
Alignment explanation
Indices: 24378--24427 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
24368 AGTACCTGCC
24378 CTTAAACAGTCCGTAATACCCT
1 CTTAAACAGT-CGTAATACCCT
** * *
24400 CTTAAATTGTTGTAATTCCCT
1 CTTAAACAGTCGTAATACCCT
24421 CTTAAAC
1 CTTAAAC
24428 TTAACCCAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.30, C:0.26, G:0.08, T:0.36
Consensus pattern (21 bp):
CTTAAACAGTCGTAATACCCT
Found at i:25527 original size:10 final size:12
Alignment explanation
Indices: 25504--25535 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
25494 AACGAGGAAG
25504 AAGAAAAAGAGA
1 AAGAAAAAGAGA
25516 AA-AAAAAG-GA
1 AAGAAAAAGAGA
25526 AAGAAAAAGA
1 AAGAAAAAGA
25536 AAGGAAGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
10 4 0.22
11 12 0.67
12 2 0.11
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (12 bp):
AAGAAAAAGAGA
Found at i:25532 original size:14 final size:15
Alignment explanation
Indices: 25513--25541 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
25503 GAAGAAAAAG
25513 AGAAAAA-AAAGGAA
1 AGAAAAAGAAAGGAA
25527 AGAAAAAGAAAGGAA
1 AGAAAAAGAAAGGAA
25542 GAAGAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
AGAAAAAGAAAGGAA
Found at i:25535 original size:28 final size:26
Alignment explanation
Indices: 25479--25537 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
25469 TCCGGTTGCC
* *
25479 AGAAAAAAAAAAAAAAACGAGGAAGA
1 AGAAAAAAAAAAAAAAACGAAGAAAA
* *
25505 AGAAAAAGAGAAAAAAAAGGAAAGAAAA
1 AGAAAAA-AAAAAAAAAACG-AAGAAAA
25533 AGAAA
1 AGAAA
25538 GGAAGAAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 7 0.26
27 10 0.37
28 10 0.37
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (26 bp):
AGAAAAAAAAAAAAAAACGAAGAAAA
Found at i:25627 original size:18 final size:18
Alignment explanation
Indices: 25578--25627 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
25568 TTTGAAATTT
* *
25578 AAAAAATGGAAAAGGAAA
1 AAAAAAGGGAAAACGAAA
*
25596 AAAAATAGGAAAAACGAAA
1 AAAAA-AGGGAAAACGAAA
*
25615 AGAAAAGGGAAAA
1 AAAAAAGGGAAAA
25628 TAAGAAATGA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 12 0.46
19 14 0.54
ACGTcount: A:0.72, C:0.02, G:0.22, T:0.04
Consensus pattern (18 bp):
AAAAAAGGGAAAACGAAA
Found at i:28598 original size:158 final size:159
Alignment explanation
Indices: 28309--28626 Score: 530
Period size: 158 Copynumber: 2.0 Consensus size: 159
28299 TTTCTTTTTG
* * * * * *
28309 TTTAATATGTTGATCTAATGTGTACAATTAGATAATTAGAGTATGTTTGTGAAGATATAAGATCT
1 TTTAATATATTAATCTAATGTGTACAATTAGATAATTACAATATGTTTGTGAAGATATAAGAACC
** * *
28374 TTTTTTTCTTGATGCTGAAGAGTGAAAGTCAAAAAGATTTTTTTTCAACTCTAAATGATCAAAGT
66 TCATTATCTTGATGCTAAAGAGTGAAAGTCAAAAAGATTTTTTTTCAACTCTAAATGATCAAAGT
*
28439 TTTGGATTAGAAGAACCTTCTTATTAGTT
131 TTTGGATTAGAAGAACCTTCTCATTAGTT
28468 TTTAATATATTAATCTAATGTGTACAATTAGATAATTACAATATGTTTGTGAAGATATAA-AACC
1 TTTAATATATTAATCTAATGTGTACAATTAGATAATTACAATATGTTTGTGAAGATATAAGAACC
28532 TCATTATCTTGATGCTAAAGAGTGAAAGTCAAAAAGATTTTTTTTCAACTCTAAATGATCAAAGT
66 TCATTATCTTGATGCTAAAGAGTGAAAGTCAAAAAGATTTTTTTTCAACTCTAAATGATCAAAGT
28597 TTTGGATTAGAAGAACCTTCTCATTAGTT
131 TTTGGATTAGAAGAACCTTCTCATTAGTT
28626 T
1 T
28627 CATCAAAATT
Statistics
Matches: 148, Mismatches: 11, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
158 92 0.62
159 56 0.38
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (159 bp):
TTTAATATATTAATCTAATGTGTACAATTAGATAATTACAATATGTTTGTGAAGATATAAGAACC
TCATTATCTTGATGCTAAAGAGTGAAAGTCAAAAAGATTTTTTTTCAACTCTAAATGATCAAAGT
TTTGGATTAGAAGAACCTTCTCATTAGTT
Found at i:35399 original size:3 final size:3
Alignment explanation
Indices: 35391--35434 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
35381 GTTGTCAGGA
** *
35391 ATT ATT ATT ATT ATT ATT ATT ATT AAA AGTT ATT AAT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT A
35435 CGAGTAATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
3 33 0.97
4 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:44053 original size:13 final size:13
Alignment explanation
Indices: 44035--44059 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44025 TGCCGACCAA
44035 AATTGTTTTGGTC
1 AATTGTTTTGGTC
44048 AATTGTTTTGGT
1 AATTGTTTTGGT
44060 GGTTCCACAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.04, G:0.24, T:0.56
Consensus pattern (13 bp):
AATTGTTTTGGTC
Found at i:56242 original size:42 final size:42
Alignment explanation
Indices: 56183--56267 Score: 136
Period size: 42 Copynumber: 2.0 Consensus size: 42
56173 AAATGTTGAT
*
56183 ACATACCCCACTTGATAATTAAT-TATGTATTTAATATTCAAA
1 ACATACCCCACCTGATAATTAATAT-TGTATTTAATATTCAAA
*
56225 ACATACTCCACCTGATAATTAATATTGTATTTAATATTCAAA
1 ACATACCCCACCTGATAATTAATATTGTATTTAATATTCAAA
56267 A
1 A
56268 TTAATATCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
42 39 0.98
43 1 0.03
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (42 bp):
ACATACCCCACCTGATAATTAATATTGTATTTAATATTCAAA
Found at i:56518 original size:23 final size:23
Alignment explanation
Indices: 56492--56540 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
56482 AACCTGCCCA
* *
56492 ACCCGAGACTCGAATGACTCGAG
1 ACCCGAAACCCGAATGACTCGAG
*
56515 ACCCGAAACCCGCATGACTCGAG
1 ACCCGAAACCCGAATGACTCGAG
56538 ACC
1 ACC
56541 TGAATAACCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.31, C:0.37, G:0.22, T:0.10
Consensus pattern (23 bp):
ACCCGAAACCCGAATGACTCGAG
Found at i:58343 original size:17 final size:16
Alignment explanation
Indices: 58321--58375 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
58311 ATCACCCCCC
58321 AGATCACTAGTGATCTA
1 AGATCAC-AGTGATCTA
*
58338 AGATCAACAGTGATGTA
1 AGATC-ACAGTGATCTA
* *
58355 AGATCACCGGTGATCAA
1 AGATCA-CAGTGATCTA
58372 AGAT
1 AGAT
58376 TACATGGGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 1 0.03
17 29 0.91
18 2 0.06
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (16 bp):
AGATCACAGTGATCTA
Found at i:60572 original size:32 final size:32
Alignment explanation
Indices: 60536--60686 Score: 257
Period size: 32 Copynumber: 4.7 Consensus size: 32
60526 TTTTATAATG
* * * *
60536 TAGACGCTGCTAAATAAGGGTGTTTTTTTCTA
1 TAGACGCCGCTAAATAAGGGCGTGTTGTTCTA
60568 TAGACGCCGCTAAATAAGGGCGTGTTGTTCTA
1 TAGACGCCGCTAAATAAGGGCGTGTTGTTCTA
60600 TAGACGCCGCTAAATAAGGGCGTGTTGTTCTA
1 TAGACGCCGCTAAATAAGGGCGTGTTGTTCTA
60632 TAGACGCCGCTAAATAAGGGCGTGTTGTTCTA
1 TAGACGCCGCTAAATAAGGGCGTGTTGTTCTA
*
60664 TAGACACCGCTAAATAAGGGCGT
1 TAGACGCCGCTAAATAAGGGCGT
60687 TTTCTTTTCA
Statistics
Matches: 114, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 114 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (32 bp):
TAGACGCCGCTAAATAAGGGCGTGTTGTTCTA
Found at i:60590 original size:64 final size:64
Alignment explanation
Indices: 60512--60686 Score: 215
Period size: 64 Copynumber: 2.7 Consensus size: 64
60502 TAAAAGCAAT
* * * * * *
60512 TAAATATAGCGGCGTTTTATAATGTAGACGCTGCTAAATAAGGGTGTTTTTTTCTATAGACGCCG
1 TAAATA-AG-GGCGTGTTATAATATAGACGCCGCTAAATAAGGGCGTGTTGTTCTATAGACGCCG
60577 C
64 C
* **
60578 TAAATAAGGGCGTGTTGTTCTATAGACGCCGCTAAATAAGGGCGTGTTGTTCTATAGACGCCGC
1 TAAATAAGGGCGTGTTATAATATAGACGCCGCTAAATAAGGGCGTGTTGTTCTATAGACGCCGC
* ** *
60642 TAAATAAGGGCGTGTTGTTCTATAGACACCGCTAAATAAGGGCGT
1 TAAATAAGGGCGTGTTATAATATAGACGCCGCTAAATAAGGGCGT
60687 TTTCTTTTCA
Statistics
Matches: 99, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
64 91 0.92
65 2 0.02
66 6 0.06
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (64 bp):
TAAATAAGGGCGTGTTATAATATAGACGCCGCTAAATAAGGGCGTGTTGTTCTATAGACGCCGC
Found at i:62238 original size:17 final size:17
Alignment explanation
Indices: 62213--62247 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
62203 TGGATAATGT
62213 TAATATACCAACAAGAA
1 TAATATACCAACAAGAA
* *
62230 TAATGTACCCACAAGAA
1 TAATATACCAACAAGAA
62247 T
1 T
62248 GCACTTTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.20, G:0.09, T:0.20
Consensus pattern (17 bp):
TAATATACCAACAAGAA
Found at i:63100 original size:27 final size:27
Alignment explanation
Indices: 63061--63247 Score: 320
Period size: 27 Copynumber: 6.9 Consensus size: 27
63051 GAACCGACCC
63061 GGGTCGAAGTGGGAGGATCCACTGCTG
1 GGGTCGAAGTGGGAGGATCCACTGCTG
*
63088 GGGTCGAAATGGGAGGATCCACTGCTG
1 GGGTCGAAGTGGGAGGATCCACTGCTG
*
63115 GGGTCGAAGTGGGAGGATCCACTGTTG
1 GGGTCGAAGTGGGAGGATCCACTGCTG
* *
63142 GGGTCAAAGTGGGAGGATCCCCTGCTG
1 GGGTCGAAGTGGGAGGATCCACTGCTG
63169 GGGTCGAAGTGGGAGGATCCACTGCTG
1 GGGTCGAAGTGGGAGGATCCACTGCTG
* *
63196 GGGTCAAAGTGGGAGGATCCCCTGCTG
1 GGGTCGAAGTGGGAGGATCCACTGCTG
63223 GGGTCGAAGTGGGAGGATCCACTGC
1 GGGTCGAAGTGGGAGGATCCACTGC
63248 GGCAACAGTC
Statistics
Matches: 148, Mismatches: 12, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 148 1.00
ACGTcount: A:0.19, C:0.19, G:0.43, T:0.19
Consensus pattern (27 bp):
GGGTCGAAGTGGGAGGATCCACTGCTG
Done.