Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019237.1 Corchorus olitorius cultivar O-4 contig19270, 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: 11082
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:207 original size:2 final size:2
Alignment explanation
Indices: 200--245 Score: 83
Period size: 2 Copynumber: 22.5 Consensus size: 2
190 TCTTTACTAG
200 TA TA TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
243 TA T
1 TA T
246 TAGTCATAGG
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3684 original size:22 final size:22
Alignment explanation
Indices: 3642--3685 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3632 TATTCATATG
* *
3642 AAATTTTGATAATCTCCCTATT
1 AAATTATGATAATCTCACTATT
3664 AAATTATGATAAT-TACACTATT
1 AAATTATGATAATCT-CACTATT
3686 TTGGATAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.39, C:0.14, G:0.05, T:0.43
Consensus pattern (22 bp):
AAATTATGATAATCTCACTATT
Found at i:3716 original size:22 final size:22
Alignment explanation
Indices: 3683--3753 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
3673 TAATTACACT
3683 ATTTTGGATAACC-TCCTTATGAA
1 ATTTT-GATAACCTTCC-TATGAA
* *
3706 ATTTTTATAACCTTCCTATGCA
1 ATTTTGATAACCTTCCTATGAA
** *
3728 ATTTTGATAACGATACTATGAA
1 ATTTTGATAACCTTCCTATGAA
3750 ATTT
1 ATTT
3754 CAAGAACCTT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
22 32 0.80
23 8 0.20
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.42
Consensus pattern (22 bp):
ATTTTGATAACCTTCCTATGAA
Found at i:4044 original size:22 final size:22
Alignment explanation
Indices: 3945--4213 Score: 159
Period size: 22 Copynumber: 12.5 Consensus size: 22
3935 AATCAAACTC
* *
3945 TGAAATTTTGATAATC-ACACTA
1 TGAAATTTTGATAACCTTC-CTA
* *
3967 TGAAATTGTGACAACC-TCGCTA
1 TGAAATTTTGATAACCTTC-CTA
3989 TGAAATTTTGATAAACCTTCCTA
1 TGAAATTTTGAT-AACCTTCCTA
* *
4012 TAAAATTTTGATAA-TTTCCTTA
1 TGAAATTTTGATAACCTTCC-TA
*
4034 TGAAATCTTGATAA-----CTA
1 TGAAATTTTGATAACCTTCCTA
* **
4051 -CAAATTTTGATAACCACCCTA
1 TGAAATTTTGATAACCTTCCTA
** * *
4072 TGATTTTTTGAT-ACCCTCATTA
1 TGAAATTTTGATAACCTTC-CTA
* * *
4094 TGAAATTTTGTTAATCTCCCTA
1 TGAAATTTTGATAACCTTCCTA
* * *
4116 TGAAATTTTGACAACCCTCTTA
1 TGAAATTTTGATAACCTTCCTA
* **
4138 TGAAATTTTGA-AAACTAAACTA
1 TGAAATTTTGATAACCT-TCCTA
*
4160 TGAAATTTTGATAACCTTCATA
1 TGAAATTTTGATAACCTTCCTA
* *
4182 TGAAATTTTGATATCC-TCC-C
1 TGAAATTTTGATAACCTTCCTA
4202 TGAAATTTTGAT
1 TGAAATTTTGAT
4214 TACTCCATAA
Statistics
Matches: 190, Mismatches: 44, Indels: 28
0.73 0.17 0.11
Matches are distributed among these distances:
16 11 0.06
17 2 0.01
18 1 0.01
20 12 0.06
21 16 0.08
22 121 0.64
23 25 0.13
24 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.39
Consensus pattern (22 bp):
TGAAATTTTGATAACCTTCCTA
Found at i:4457 original size:88 final size:88
Alignment explanation
Indices: 4294--4460 Score: 228
Period size: 88 Copynumber: 1.9 Consensus size: 88
4284 AGAAATACTA
* * * **
4294 CTATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTC
1 CTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
**
4359 TTTATAAAATTTTGTTGACCCCT
66 ACTATAAAATTTTGTTGACCCCT
* *
4382 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAA
1 CTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTC-CTTATGAAATTTTGATAACAA
*
4446 CACTATGAAATTTTG
65 CACTATAAAATTTTG
4461 ATAATCTTCC
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
88 66 0.97
89 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.42
Consensus pattern (88 bp):
CTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
ACTATAAAATTTTGTTGACCCCT
Found at i:4640 original size:22 final size:22
Alignment explanation
Indices: 4293--4732 Score: 173
Period size: 22 Copynumber: 19.8 Consensus size: 22
4283 CAGAAATACT
* *
4293 ACTATGAAATTTTGGTAATCAC
1 ACTATGAAATTTTGATAACCAC
* * * *
4315 ATTTTGAAAATTTGATAACCTC
1 ACTATGAAATTTTGATAACCAC
** *
4337 TTTATGAAATTTTGATAACCTC
1 ACTATGAAATTTTGATAACCAC
** * * * *
4359 TTTATAAAATTTTGTTGACCCC
1 ACTATGAAATTTTGATAACCAC
* *
4381 TCTATGAAATTTTGATAATCAC
1 ACTATGAAATTTTGATAACCAC
* * *
4403 ATTATGTAATTTTGATAACCTC
1 ACTATGAAATTTTGATAACCAC
* * *
4425 GCTTTGAAATTTTGATAACAAC
1 ACTATGAAATTTTGATAACCAC
**
4447 ACTATGAAATTTTGATAATCTTC
1 ACTATGAAATTTTGATAA-CCAC
4470 -CTAT-AAATTTTGATAATCCGATC
1 ACTATGAAATTTTGATAA-CC-A-C
* * *
4493 TCTATGAAATTTCGATAATCAC
1 ACTATGAAATTTTGATAACCAC
** * * *
4515 TTTATGAGA-TTTGATAATC-T
1 ACTATGAAATTTTGATAACCAC
* * * * *
4535 TCTATCAAATTTTGGTACTCCTTATG
1 ACTATGAAATTTTGATA-ACC--A-C
* *
4561 A-AATTGAGAATTTT-ATAACCTTC
1 ACTA-TGA-AATTTTGATAACC-AC
*
4584 A-TATGAAATTTTCATAACCAC
1 ACTATGAAATTTTGATAACCAC
*
4605 ACTA-AAAATTTTTGATAACCAC
1 ACTATGAAA-TTTTGATAACCAC
*
4627 ACTATGAAATTTTGATAACCTC
1 ACTATGAAATTTTGATAACCAC
* * * * * *
4649 CCCATGATATATT-AGTAATCTC
1 ACTATGAAATTTTGA-TAACCAC
* *
4671 -CTTATGAAATTTTGTTAACCAT
1 AC-TATGAAATTTTGATAACCAC
**
4693 ACTATGAAATTCTT-ATAACTTC
1 ACTATGAAATT-TTGATAACCAC
* *
4715 CCTATGACATTTTGATAA
1 ACTATGAAATTTTGATAA
4733 TCTCTCTGAT
Statistics
Matches: 315, Mismatches: 80, Indels: 46
0.71 0.18 0.10
Matches are distributed among these distances:
20 6 0.02
21 44 0.14
22 223 0.71
23 12 0.04
24 6 0.02
25 14 0.04
26 4 0.01
27 6 0.02
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (22 bp):
ACTATGAAATTTTGATAACCAC
Found at i:4684 original size:66 final size:66
Alignment explanation
Indices: 4614--4971 Score: 224
Period size: 66 Copynumber: 5.2 Consensus size: 66
4604 CACTAAAAAT
* *
4614 TTTTGATAACCACACTATGAAATTTTGATAACCTCCCCATGATATATTAGTAATC-TCCTTATGA
1 TTTTGATAACCACACTATGAAATTTTGATAACCTCCCCATGAAAT-TTAGTAACCATCCTTATGA
4678 AA
65 AA
* * * * * *
4680 TTTTGTTAACCATACTATGAAATTCTT-ATAACTTCCCTATGACATTTTGATAATCTCTCTGATA
1 TTTTGATAACCACACTATGAAATT-TTGATAACCTCCCCATGAAATTTAG-TAA---C-C--AT-
*
4744 ACCTTTCTATAAAA
57 -CC--T-TATGAAA
* ** * * * * *
4758 TTGTGATAACCACACTATGAAATTTCAATAACATTCCTAAGAAATTTTAATAACCTGAT-CTTAT
1 TTTTGATAACCACACTATGAAATTTTGATAACCTCCCCATGAAA-TTTAGTAACC--ATCCTTAT
*
4822 TAAA
63 GAAA
* * * * * * *
4826 GTTTGGTAACCACACTATGAAATTTTGATAACTTTCCCATGAGATTTTGAG-AA-CTTCCATATG
1 TTTTGATAACCACACTATGAAATTTTGATAACCTCCCCATGA-AATTT-AGTAACCATCCTTATG
4889 AAA
64 AAA
* * * * *
4892 TTTTGGTAACCACACTATGAAATTTTTATAACCTACTCATGAAATTATAGTAACCAT-CTTACGA
1 TTTTGATAACCACACTATGAAATTTTGATAACCTCCCCATGAAATT-TAGTAACCATCCTTATGA
4956 AA
65 AA
4958 TTTTGATAACCACA
1 TTTTGATAACCACA
4972 TAGATACAAG
Statistics
Matches: 228, Mismatches: 42, Indels: 44
0.73 0.13 0.14
Matches are distributed among these distances:
65 9 0.04
66 107 0.47
67 5 0.02
68 45 0.20
69 3 0.01
70 1 0.00
71 1 0.00
73 1 0.00
74 5 0.02
75 3 0.01
77 2 0.01
78 43 0.19
79 3 0.01
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.37
Consensus pattern (66 bp):
TTTTGATAACCACACTATGAAATTTTGATAACCTCCCCATGAAATTTAGTAACCATCCTTATGAA
A
Found at i:4842 original size:68 final size:66
Alignment explanation
Indices: 4764--4916 Score: 173
Period size: 68 Copynumber: 2.3 Consensus size: 66
4754 AAAATTGTGA
* * * *
4764 TAACCACACTATGAAATTTCAATAACATTCCTAAGAAATTTTAATAACCTGAT-CTTATTAAAGT
1 TAACCACACTATGAAATTTCAATAACATTCCCAAGAAATTTTAAGAA-CT--TCCATATGAAAGT
4828 TTGG
63 TTGG
** * * * * *
4832 TAACCACACTATGAAATTTTGATAACTTTCCCATGAGATTTTGAGAACTTCCATATGAAATTTTG
1 TAACCACACTATGAAATTTCAATAACATTCCCAAGAAATTTTAAGAACTTCCATATGAAAGTTTG
4897 G
66 G
4898 TAACCACACTATGAAATTT
1 TAACCACACTATGAAATTT
4917 TTATAACCTA
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
65 1 0.01
66 31 0.42
67 2 0.03
68 39 0.53
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.35
Consensus pattern (66 bp):
TAACCACACTATGAAATTTCAATAACATTCCCAAGAAATTTTAAGAACTTCCATATGAAAGTTTG
G
Found at i:4857 original size:22 final size:22
Alignment explanation
Indices: 4750--4971 Score: 100
Period size: 22 Copynumber: 10.0 Consensus size: 22
4740 GATAACCTTT
* *
4750 CTATAAAATTGTGATAACCACA
1 CTATGAAATTTTGATAACCACA
**
4772 CTATGAAATTTCAATAA-CATTC-
1 CTATGAAATTTTGATAACCA--CA
* * **
4794 CTAAGAAATTTTAATAACCTGA
1 CTATGAAATTTTGATAACCACA
* * *
4816 TCTTATTAAAGTTTGGTAACCACA
1 -C-TATGAAATTTTGATAACCACA
**
4840 CTATGAAATTTTGATAACTTTC-
1 CTATGAAATTTTGATAAC-CACA
* * *
4862 CCATGAGATTTTGAGAACTTC-CA
1 CTATGAAATTTTGATAAC--CACA
*
4885 -TATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
* *
4906 CTATGAAATTTTTATAACC-TA
1 CTATGAAATTTTGATAACCACA
*
4927 CTCATGAAATTAT-AGTAACCATC-
1 CT-ATGAAATTTTGA-TAACCA-CA
* *
4950 TTACGAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCACA
4972 TAGATACAAG
Statistics
Matches: 147, Mismatches: 36, Indels: 34
0.68 0.17 0.16
Matches are distributed among these distances:
20 1 0.01
21 9 0.06
22 115 0.78
23 8 0.05
24 14 0.10
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:5406 original size:164 final size:166
Alignment explanation
Indices: 5186--5517 Score: 458
Period size: 165 Copynumber: 2.0 Consensus size: 166
5176 AATAGTAAAG
5186 GAAATTTGCATGTTCATCAACGAAAATAAATTTGACAAACTTATAATTCGGTCTAAATAGAAATT
1 GAAATTTGCATGTTCATCAACGAAAATAAATTTGACAAACTTATAATTCGGTCTAAATAGAAATT
* * *
5251 TT-TGAATAATA-AAATTATAC-TAAATTTTAATAATGGCAATTTAGAAATATATTTG-AAAAAA
66 TTAT-AAT--TAGAAATTAAACATAAATTTTAATAATGGAAATATAGAAATATATTTGAAAAAAA
* * *
5312 GGGTACAATCGGAAAACATAAAGTTTCCCATTATTCGTA
128 AGGTACAATCGAAAAACACAAAGTTTCCCATTATTCGTA
* * * *
5351 GAAATTTGCATGTTCATCAATGAAAATCAATTTTAC-AACTTATAATTCGGTCTAAATTGAAATT
1 GAAATTTGCATGTTCATCAACGAAAATAAATTTGACAAACTTATAATTCGGTCTAAATAGAAATT
*** *
5415 TTATAATTAGTTTTTAAACAATAAATTTTAATAATGGAAATATAGAAATATTTTTGAAAAAAAAA
66 TTATAATTAGAAATTAAAC-ATAAATTTTAATAATGGAAATATAGAAATATATTTG-AAAAAAAA
5480 GGTACAATCGAAAAACACAAAGTTTCCCATTATTCGTA
129 GGTACAATCGAAAAACACAAAGTTTCCCATTATTCGTA
5518 TTTTCATATA
Statistics
Matches: 147, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
162 2 0.01
163 5 0.03
164 32 0.22
165 66 0.45
167 42 0.29
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.34
Consensus pattern (166 bp):
GAAATTTGCATGTTCATCAACGAAAATAAATTTGACAAACTTATAATTCGGTCTAAATAGAAATT
TTATAATTAGAAATTAAACATAAATTTTAATAATGGAAATATAGAAATATATTTGAAAAAAAAGG
TACAATCGAAAAACACAAAGTTTCCCATTATTCGTA
Found at i:7384 original size:17 final size:17
Alignment explanation
Indices: 7362--7423 Score: 88
Period size: 17 Copynumber: 3.6 Consensus size: 17
7352 TTAGTCTAGT
7362 TCTTAGATTACTGGTGA
1 TCTTAGATTACTGGTGA
7379 TCTTAGATTACTGGTGA
1 TCTTAGATTACTGGTGA
* **
7396 TCTTAGATCACACGTGA
1 TCTTAGATTACTGGTGA
*
7413 TCTTTGATTAC
1 TCTTAGATTAC
7424 CTGGGTTTAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.40
Consensus pattern (17 bp):
TCTTAGATTACTGGTGA
Found at i:11035 original size:11 final size:11
Alignment explanation
Indices: 11011--11045 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
11001 TTGACAGCAC
11011 AACAAAAACAA
1 AACAAAAACAA
* *
11022 AACGAAAACGA
1 AACAAAAACAA
11033 AACAAAAACAA
1 AACAAAAACAA
11044 AA
1 AA
11046 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Done.