Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020896.1 Corchorus olitorius cultivar O-4 contig20929, 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: 25414
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:8270 original size:41 final size:41
Alignment explanation
Indices: 8225--8436 Score: 135
Period size: 41 Copynumber: 5.2 Consensus size: 41
8215 TTTCTAAAAC
*
8225 CAGGGACCAAATTGAATCAAATAGTAACTAAAATCCTAAAT
1 CAGGGACCAAATTGAATCAAATAGTAAATAAAATCCTAAAT
* * * *
8266 CAGGGGCTAAATTGCATCAAATAGTAAATAGAATCCTAAAT
1 CAGGGACCAAATTGAATCAAATAGTAAATAAAATCCTAAAT
* * * ** * ** * *
8307 TAAGGACTAAAACGTATCAAACGGTAAAT-TAATCTTAAAT
1 CAGGGACCAAATTGAATCAAATAGTAAATAAAATCCTAAAT
* * * * * *
8347 CAGGGACTAGATTGCATTAAATCAGGAAAT-AAATCTTAAAT
1 CAGGGACCAAATTGAATCAAAT-AGTAAATAAAATCCTAAAT
* * * * * *
8388 CAAGTACCAAATTGCATCAAACA--AAAGTAATATCTTAAAT
1 CAGGGACCAAATTGAATCAAATAGTAAA-TAAAATCCTAAAT
8428 CAGGGACCA
1 CAGGGACCA
8437 TGTTGAACAC
Statistics
Matches: 133, Mismatches: 35, Indels: 7
0.76 0.20 0.04
Matches are distributed among these distances:
38 3 0.02
39 1 0.01
40 41 0.31
41 88 0.66
ACGTcount: A:0.46, C:0.16, G:0.14, T:0.24
Consensus pattern (41 bp):
CAGGGACCAAATTGAATCAAATAGTAAATAAAATCCTAAAT
Found at i:8407 original size:81 final size:80
Alignment explanation
Indices: 8255--8434 Score: 184
Period size: 81 Copynumber: 2.2 Consensus size: 80
8245 ATAGTAACTA
* * * * *
8255 AAATCCTAAATCAGGGGCTAAATTGCATCAAATAGTAAATAGAATCCTAAATTAAGGACTAAAAC
1 AAATCTTAAATCAGGGACTAAATTGCATCAAATAGGAAATAGAATCCTAAATCAAGGACCAAAAC
* *
8320 GTATCAAACGGTAAA-T
66 GCATCAAAC--AAAAGT
* * * * * *
8336 TAATCTTAAATCAGGGACTAGATTGCATTAAATCAGGAAATA-AATCTTAAATCAAGTACCAAAT
1 AAATCTTAAATCAGGGACTAAATTGCATCAAAT-AGGAAATAGAATCCTAAATCAAGGACCAAAA
*
8400 TGCATCAAACAAAAGT
65 CGCATCAAACAAAAGT
8416 AATATCTTAAATCAGGGAC
1 AA-ATCTTAAATCAGGGAC
8435 CATGTTGAAC
Statistics
Matches: 81, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
79 3 0.04
80 2 0.02
81 69 0.85
82 7 0.09
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (80 bp):
AAATCTTAAATCAGGGACTAAATTGCATCAAATAGGAAATAGAATCCTAAATCAAGGACCAAAAC
GCATCAAACAAAAGT
Found at i:13783 original size:51 final size:51
Alignment explanation
Indices: 13711--13827 Score: 216
Period size: 51 Copynumber: 2.3 Consensus size: 51
13701 CAGCAATCAA
*
13711 AGTACTAGTGATTCCTCTTATTCCTAATCTATATAAATTATAAACTAAATC
1 AGTACTAGTTATTCCTCTTATTCCTAATCTATATAAATTATAAACTAAATC
*
13762 AGTACTAGTTATTCCTCTTATTCCTAATCTATATAAATTGTAAACTAAATC
1 AGTACTAGTTATTCCTCTTATTCCTAATCTATATAAATTATAAACTAAATC
13813 AGTACTAGTTATTCC
1 AGTACTAGTTATTCC
13828 CAAAGATAGC
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 64 1.00
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.40
Consensus pattern (51 bp):
AGTACTAGTTATTCCTCTTATTCCTAATCTATATAAATTATAAACTAAATC
Found at i:15037 original size:22 final size:22
Alignment explanation
Indices: 15012--15059 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
15002 TTCAGCAATG
*
15012 CTACATCAAGACTGCATTATTA
1 CTACATCAAGACTGCATCATTA
*
15034 CTACATCAAGGCTGCATCATTA
1 CTACATCAAGACTGCATCATTA
15056 CTAC
1 CTAC
15060 CTCATAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.33, C:0.27, G:0.10, T:0.29
Consensus pattern (22 bp):
CTACATCAAGACTGCATCATTA
Found at i:16182 original size:18 final size:18
Alignment explanation
Indices: 16161--16196 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
16151 CATCTTTTAA
*
16161 TTTTCTGATTTTTCCTTT
1 TTTTCTCATTTTTCCTTT
*
16179 TTTTTTCATTTTTCCTTT
1 TTTTCTCATTTTTCCTTT
16197 CTTCTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.06, C:0.17, G:0.03, T:0.75
Consensus pattern (18 bp):
TTTTCTCATTTTTCCTTT
Found at i:17031 original size:18 final size:18
Alignment explanation
Indices: 17004--17046 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
16994 CAAGTTAACT
17004 TTAATTTAAG-AAAAATC
1 TTAATTTAAGCAAAAATC
*
17021 TTAACTTTAAGCTAAAATC
1 TTAA-TTTAAGCAAAAATC
17040 TTAATTT
1 TTAATTT
17047 TCCAAATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 9 0.39
19 10 0.43
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (18 bp):
TTAATTTAAGCAAAAATC
Found at i:18357 original size:14 final size:14
Alignment explanation
Indices: 18338--18368 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
18328 CTTGCTGCTT
18338 CTGTTTAATCCTTA
1 CTGTTTAATCCTTA
18352 CTGTTTAATCCTTA
1 CTGTTTAATCCTTA
18366 CTG
1 CTG
18369 AATTAGGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.23, G:0.10, T:0.48
Consensus pattern (14 bp):
CTGTTTAATCCTTA
Found at i:20371 original size:158 final size:160
Alignment explanation
Indices: 20173--20658 Score: 548
Period size: 170 Copynumber: 2.9 Consensus size: 160
20163 TGACATGATA
* *
20173 CCCGGAGGACTTATCAGAATTAATATCCAGAGGTTTCTGAATTTGTGCCCGGAGGTCTTACCAAT
1 CCCGGAGGACTTATCAGAATTAATACCCAGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAAT
* * * * * *
20238 GTAAACTCTAAATAGAGACCTTGACCAAGGATTTTAAAC-T-T-TTTAATGAAAATCA-TGATGA
66 GCAAACTTTGAATTGAGACCTTGA-CAAGGATTTTAAACATATCTTTAATGAAAA-AATTAATGA
*
20299 AATGAAATGGTACCCGGAGGCTATACTAATTG
129 AATGAAATGGTACCCGGAGGCTATACCAATTG
* * *
20331 CCCGGAGGACTTGTCGGAATTAATACCCAGAGGTTTCTGAATTTATGCCCGGAGGACTTACCAAT
1 CCCGGAGGACTTATCAGAATTAATACCCAGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAAT
20396 GCAAACTTTGAATTGAGACCTTGGACAAGGATTTTAAATCTTAAACATGAATCTTTAATGAAAAA
66 GCAAACTTTGAATTGAGACCTT-GACAAGGA---T---T-TTAAACAT--ATCTTTAATGAAAAA
* * *
20461 ATTAATGAAATGAAATGGTATCCGGAGGCTTTACCGATTG
121 ATTAATGAAATGAAATGGTACCCGGAGGCTATACCAATTG
* ** *
20501 CCAGGAGGACTTATCAGAATTAATACCCAGAGGCATCTGAATTTGTGCCCGGGGGACTTACCAAT
1 CCCGGAGGACTTATCAGAATTAATACCCAGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAAT
* *
20566 GCAAATTTTGAATTGAGACCTTGAACAAGGATTTTAAATCTTAAACATGAATCTTTGATGAAAAA
66 GCAAACTTTGAATTGAGACCTTG-ACAAGGA---T---T-TTAAACAT--ATCTTTAATGAAAAA
*
20631 CTTAATGAAATGAAATGGTACCCGGAGG
121 ATTAATGAAATGAAATGGTACCCGGAGG
20659 TTTTAAAAAT
Statistics
Matches: 287, Mismatches: 26, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
158 84 0.29
159 2 0.01
161 1 0.00
164 1 0.00
165 6 0.02
166 1 0.00
169 3 0.01
170 189 0.66
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (160 bp):
CCCGGAGGACTTATCAGAATTAATACCCAGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAAT
GCAAACTTTGAATTGAGACCTTGACAAGGATTTTAAACATATCTTTAATGAAAAAATTAATGAAA
TGAAATGGTACCCGGAGGCTATACCAATTG
Found at i:20561 original size:170 final size:170
Alignment explanation
Indices: 20295--20663 Score: 594
Period size: 170 Copynumber: 2.2 Consensus size: 170
20285 GAAAATCATG
* * * * *
20295 ATGAAATGAAATGGTACCCGGAGGCTATACTAATTGCCCGGAGGACTTGTCGGAATTAATACCCA
1 ATGAAATGAAATGGTACCCGGAGGCTTTACCAATTGCCAGGAGGACTTATCAGAATTAATACCCA
** *
20360 GAGGTTTCTGAATTTATGCCCGGAGGACTTACCAATGCAAACTTTGAATTGAGACCTTGGACAAG
66 GAGGCATCTGAATTTATGCCCGGAGGACTTACCAATGCAAACTTTGAATTGAGACCTTGAACAAG
20425 GATTTTAAATCTTAAACATGAATCTTTAATGAAAAAATTA
131 GATTTTAAATCTTAAACATGAATCTTTAATGAAAAAATTA
* *
20465 ATGAAATGAAATGGTATCCGGAGGCTTTACCGATTGCCAGGAGGACTTATCAGAATTAATACCCA
1 ATGAAATGAAATGGTACCCGGAGGCTTTACCAATTGCCAGGAGGACTTATCAGAATTAATACCCA
* * *
20530 GAGGCATCTGAATTTGTGCCCGGGGGACTTACCAATGCAAATTTTGAATTGAGACCTTGAACAAG
66 GAGGCATCTGAATTTATGCCCGGAGGACTTACCAATGCAAACTTTGAATTGAGACCTTGAACAAG
* *
20595 GATTTTAAATCTTAAACATGAATCTTTGATGAAAAACTTA
131 GATTTTAAATCTTAAACATGAATCTTTAATGAAAAAATTA
*
20635 ATGAAATGAAATGGTACCCGGAGGTTTTA
1 ATGAAATGAAATGGTACCCGGAGGCTTTA
20664 AAAATGCAAA
Statistics
Matches: 182, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
170 182 1.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.28
Consensus pattern (170 bp):
ATGAAATGAAATGGTACCCGGAGGCTTTACCAATTGCCAGGAGGACTTATCAGAATTAATACCCA
GAGGCATCTGAATTTATGCCCGGAGGACTTACCAATGCAAACTTTGAATTGAGACCTTGAACAAG
GATTTTAAATCTTAAACATGAATCTTTAATGAAAAAATTA
Found at i:20897 original size:69 final size:69
Alignment explanation
Indices: 20797--21298 Score: 749
Period size: 69 Copynumber: 7.3 Consensus size: 69
20787 CTCATTAAAC
* * * * * * *
20797 TTGGCTTATGGAAAAGCCTCTGCT-G-TATGGATGGACCCAATGTTTAAACTAACTCGCATGGAA
1 TTGGCTTGTGGAAAAGCCTATG-TGGCT-TGGATGGAACCAAGGCTTAAACTGACTCGTATGGAA
*
20860 ATGAGT
64 ACGAGT
** * * * * *
20866 TTGATTTATGGAAAAGTCTATATGGCTTGGATGGAACCAAGGGTTGAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
20931 GAGT
66 GAGT
* *
20935 TTGGCTTGTGGAAAAGCCTATATGGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
21000 GAGT
66 GAGT
* *
21004 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAATGCTTAAACTCACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
21069 GAGT
66 GAGT
21073 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
21138 GAGT
66 GAGT
*
21142 TTGTCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGG-AAC
1 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
21206 GAGT
66 GAGT
* *
21210 TTGGCTTGTGAAAAATCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
21275 GAGT
66 GAGT
* *
21279 TTGACTTGTTGAAAAGCCTA
1 TTGGCTTGTGGAAAAGCCTA
21299 AGCATTCGGA
Statistics
Matches: 399, Mismatches: 31, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
68 66 0.17
69 332 0.83
70 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (69 bp):
TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
GAGT
Found at i:22306 original size:49 final size:50
Alignment explanation
Indices: 22128--22327 Score: 260
Period size: 50 Copynumber: 4.0 Consensus size: 50
22118 CCCTTCGAAC
* * * *
22128 AGCGAACTTTGGTCTTGGTCTCATAAATGGAATGCAATCTTAATT-TGAAA
1 AGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTT-ATTATGAAA
* *
22178 AGCGAACTTTGATCTTGGACTCACAAATGGAATGCAATCTTATTTTGAAA
1 AGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTATTATGAAA
* * *
22228 AGCGAATTTTGATCTTTGACACACGAATGGAATGCAATCTTATTAT-AAA
1 AGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTATTATGAAA
* * * *
22277 AGCGAATTTTGACCTCGGACTCACAAATGGGATGCAATCTTATTATAAAA
1 AGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTATTATGAAA
22327 A
1 A
22328 TTCTTGTTTT
Statistics
Matches: 134, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
49 46 0.34
50 88 0.66
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (50 bp):
AGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTATTATGAAA
Found at i:22921 original size:6 final size:6
Alignment explanation
Indices: 22910--22948 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
22900 ATCAATTCTC
22910 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA -TTTGA TTTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTT
22949 TTTTTATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.69
Consensus pattern (6 bp):
TTTTGA
Found at i:22961 original size:14 final size:15
Alignment explanation
Indices: 22916--22994 Score: 74
Period size: 14 Copynumber: 5.3 Consensus size: 15
22906 TCTCTTTTGA
22916 TTTTGATTTTGATTTT
1 TTTTGA-TTTGATTTT
22932 GATTTTGATTTGATTTT
1 --TTTTGATTTGATTTT
*
22949 TTTTTATTT-ATTTT
1 TTTTGATTTGATTTT
*
22963 TTTGGATTTGA-TTT
1 TTTTGATTTGATTTT
**
22977 GATTGA-TTGATTTT
1 TTTTGATTTGATTTT
22991 TTTT
1 TTTT
22995 TGTGATTTTC
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
13 4 0.08
14 23 0.45
15 9 0.18
17 9 0.18
18 6 0.12
ACGTcount: A:0.15, C:0.00, G:0.14, T:0.71
Consensus pattern (15 bp):
TTTTGATTTGATTTT
Found at i:23406 original size:16 final size:17
Alignment explanation
Indices: 23377--23414 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 17
23367 TTCATTTACC
23377 TTTTTTCATTTTTCATTT
1 TTTTTTCA-TTTTCATTT
23395 TTTTTTCA-TTTCATTT
1 TTTTTTCATTTTCATTT
23411 TTTT
1 TTTT
23415 GGATTATTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 12 0.60
18 8 0.40
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTTCATTTTCATTT
Done.