Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019858.1 Corchorus olitorius cultivar O-4 contig19891, 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: 37149
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:6110 original size:189 final size:189
Alignment explanation
Indices: 5790--6170 Score: 735
Period size: 189 Copynumber: 2.0 Consensus size: 189
5780 GCAAGAGTTC
5790 ATAGATGTAGAGTGAGGCAACGTCACAAACAAGTAAGGATTTGCAGGAGGTGGCAGGGAGGAAGA
1 ATAGATGTAGAGTGAGGCAACGTCACAAACAAGTAAGGATTTGCAGGAGGTGGCAGGGAGGAAGA
5855 CCGGAGCAGTTCCTTGAGGATGAGTGCACGGTGGCAGGCGTTGTAGATGGTGGTTGTTTGTGGTG
66 CCGGAGCAGTTCCTTGAGGATGAGTGCACGGTGGCAGGCGTTGTAGATGGTGGTTGTTTGTGGTG
5920 TTGGTAGTTTCTTTGAGTTAGAGAGATTTTTAGAGAGCAAAAGTCTTTGTATGCTGTGA
131 TTGGTAGTTTCTTTGAGTTAGAGAGATTTTTAGAGAGCAAAAGTCTTTGTATGCTGTGA
*
5979 ATAGATGTAGAGTGAGGCAACGTCACAAACAAGTAAGGATTTGCAGGAGGTGGCAGGGAGGAAGG
1 ATAGATGTAGAGTGAGGCAACGTCACAAACAAGTAAGGATTTGCAGGAGGTGGCAGGGAGGAAGA
*
6044 CCGGAGCAGTTCCTTGAGGATGAGTGCACGGTGGTAGGCGTTGTAGATGGTGGTTGTTTGTGGTG
66 CCGGAGCAGTTCCTTGAGGATGAGTGCACGGTGGCAGGCGTTGTAGATGGTGGTTGTTTGTGGTG
*
6109 TTGGTAGTTTCTTTGAGTTAGAGAGATTTTTAGAGAGCAAAAGTCTTTGTATGTTGTGA
131 TTGGTAGTTTCTTTGAGTTAGAGAGATTTTTAGAGAGCAAAAGTCTTTGTATGCTGTGA
6168 ATA
1 ATA
6171 ATGGAAGAAT
Statistics
Matches: 189, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
189 189 1.00
ACGTcount: A:0.25, C:0.10, G:0.36, T:0.29
Consensus pattern (189 bp):
ATAGATGTAGAGTGAGGCAACGTCACAAACAAGTAAGGATTTGCAGGAGGTGGCAGGGAGGAAGA
CCGGAGCAGTTCCTTGAGGATGAGTGCACGGTGGCAGGCGTTGTAGATGGTGGTTGTTTGTGGTG
TTGGTAGTTTCTTTGAGTTAGAGAGATTTTTAGAGAGCAAAAGTCTTTGTATGCTGTGA
Found at i:7200 original size:3 final size:3
Alignment explanation
Indices: 7192--7227 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
7182 TAAAAAATGT
7192 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
7228 TTTATTAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:16207 original size:40 final size:40
Alignment explanation
Indices: 16158--16603 Score: 278
Period size: 40 Copynumber: 10.4 Consensus size: 40
16148 TTTTCAGTTA
*
16158 GGAAA-GGCAAACTGGTAAAC-TAAACAACACCTTCCGGCG
1 GGAAAGGGCAAACTGG-AAACTTAAACAACACCTTCCGGTG
* * *
16197 GGAAAGGGCAAAATGGGAACTTAGACAACACCTTCCGGTG
1 GGAAAGGGCAAACTGGAAACTTAAACAACACCTTCCGGTG
* * * *
16237 GGGAAGGGCAAATTGGGTAAAGTAGATTTTAAACAACACCTTCCGAT-
1 GGAAAGGGCAAACT-GG---A--A-A-CTTAAACAACACCTTCCGGTG
*
16284 GGAGAAGGGCAAACTGGAAA-TTAGACAACACCTTCCGGTG
1 GGA-AAGGGCAAACTGGAAACTTAAACAACACCTTCCGGTG
* *
16324 GGGAAGGGCAAACTGGGAAAAGTGGACCTTAAACAACACCTTCCGATG
1 GGAAAGGGCAAACT-GG--AA----A-CTTAAACAACACCTTCCGGTG
*
16372 AGG-AAGGGCAAACTGGGAACTTAAACAACACCTTCCGGTG
1 -GGAAAGGGCAAACTGGAAACTTAAACAACACCTTCCGGTG
* ** *
16412 GGGAAGGGCAAACTGAGAAA-TTTTACAACAGCTTCCGGTG
1 GGAAAGGGCAAACTG-GAAACTTAAACAACACCTTCCGGTG
* * * *
16452 GGGAAGGGCGAATTGGGTAAAGTAGACTTTAAACAACACCTTCCGAT-
1 GGAAAGGGCAAACT-GG---A--A-AC-TTAAACAACACCTTCCGGTG
* *
16499 GGAGAAGGGCAAATTGGGAAAAATGGTCTTTAAACAACACCTTCCGATG
1 GGA-AAGGGCAAACT-GG--AAA----C-TTAAACAACACCTTCCGGTG
*
16548 AGGAAA-GGCAAACTGGGAACTTAAACAACACCTTCCGGTG
1 -GGAAAGGGCAAACTGGAAACTTAAACAACACCTTCCGGTG
*
16588 GGGAAGGGCAAACTGG
1 GGAAAGGGCAAACTGG
16604 GAAAAGTGGA
Statistics
Matches: 331, Mismatches: 35, Indels: 81
0.74 0.08 0.18
Matches are distributed among these distances:
39 42 0.13
40 133 0.40
41 9 0.03
42 3 0.01
43 1 0.00
44 2 0.01
45 5 0.02
46 3 0.01
47 14 0.04
48 112 0.34
49 4 0.01
50 3 0.01
ACGTcount: A:0.35, C:0.19, G:0.28, T:0.17
Consensus pattern (40 bp):
GGAAAGGGCAAACTGGAAACTTAAACAACACCTTCCGGTG
Found at i:16292 original size:48 final size:47
Alignment explanation
Indices: 16221--16607 Score: 253
Period size: 48 Copynumber: 8.8 Consensus size: 47
16211 GGGAACTTAG
* * *
16221 ACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTAAAGTAGATTTTAA
1 ACAACACCTTCCGATGGAGAAGGGCAAACTGGG-AAAGTAGATTTTAA
*
16269 ACAACACCTTCCGATGGAGAAGGGCAAACT-GG--A--A-A--TTAG
1 ACAACACCTTCCGATGGAGAAGGGCAAACTGGGAAAGTAGATTTTAA
* * * **
16308 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAAAGTGGACCTTAA
1 ACAACACCTTCCGATGGAGAAGGGCAAACTGGG-AAAGTAGATTTTAA
*
16356 ACAACACCTTCCGAT-GAGGAAGGGCAAACT-GG---G-A-A-CTTAA
1 ACAACACCTTCCGATGGA-GAAGGGCAAACTGGGAAAGTAGATTTTAA
* * *
16396 ACAACACCTTCCGGTGGGGAAGGGCAAACT--G--AG-AAATTTT--
1 ACAACACCTTCCGATGGAGAAGGGCAAACTGGGAAAGTAGATTTTAA
* * * * * *
16436 ACAACAGCTTCCGGTGGGGAAGGGCGAATTGGGTAAAGTAGACTTTAA
1 ACAACACCTTCCGATGGAGAAGGGCAAACTGGG-AAAGTAGATTTTAA
* * *
16484 ACAACACCTTCCGATGGAGAAGGGCAAATTGGGAAA-AATGGTCTTTAA
1 ACAACACCTTCCGATGGAGAAGGGCAAACTGGGAAAGTA-GAT-TTTAA
* *
16532 ACAACACCTTCCGAT-GAGGAAAGGCAAACT-GG---G-A-A-CTTAA
1 ACAACACCTTCCGATGGA-GAAGGGCAAACTGGGAAAGTAGATTTTAA
* *
16572 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAA
1 ACAACACCTTCCGATGGAGAAGGGCAAACTGGGAAA
16608 AGTGGACTAG
Statistics
Matches: 275, Mismatches: 33, Indels: 66
0.74 0.09 0.18
Matches are distributed among these distances:
39 32 0.12
40 91 0.33
41 7 0.03
42 4 0.01
43 2 0.01
44 2 0.01
45 2 0.01
46 7 0.03
47 13 0.05
48 115 0.42
ACGTcount: A:0.35, C:0.19, G:0.28, T:0.18
Consensus pattern (47 bp):
ACAACACCTTCCGATGGAGAAGGGCAAACTGGGAAAGTAGATTTTAA
Found at i:16573 original size:88 final size:86
Alignment explanation
Indices: 16178--16608 Score: 464
Period size: 88 Copynumber: 4.9 Consensus size: 86
16168 ACTGGTAAAC
** * *
16178 TAAACAACACCTTCCGGCGGGAAAGGGCAAAATGGGAACTTAGACAACACCTTCCGGTGGGGAAG
1 TAAACAACACCTTCCGATGGG-AAGGGCAAACTGGGAACTTAAACAACACCTTCCGGTGGGGAAG
* * * *
16243 GGCAAATTGGGTAAAGTAGATTT
65 GGCAAACTGGGAAAAAT-GGTTT
* *
16266 TAAACAACACCTTCCGATGGAGAAGGGCAAACT-GGAAATTAGACAACACCTTCCGGTGGGGAAG
1 TAAACAACACCTTCCGATGG-GAAGGGCAAACTGGGAACTTAAACAACACCTTCCGGTGGGGAAG
* **
16330 GGCAAACTGGGAAAAGTGGACCT
65 GGCAAACTGGGAAAAATGG-TTT
16353 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAACTTAAACAACACCTTCCGGTGGGGAAG
1 TAAACAACACCTTCCGATG-GGAAGGGCAAACTGGGAACTTAAACAACACCTTCCGGTGGGGAAG
*
16418 GGCAAACT--GAGAAA---TTT
65 GGCAAACTGGGAAAAATGGTTT
* * * * *
16435 T--ACAACAGCTTCCGGTGGGGAAGGGCGAATTGGGTAAAGTAGACTTTAAACAACACCTTCCGA
1 TAAACAACACCTTCCGAT-GGGAAGGGCAAACT-GG----G-A-AC-TTAAACAACACCTTCCGG
* *
16498 TGGAGAAGGGCAAATTGGGAAAAATGGTCTT
57 TGGGGAAGGGCAAACTGGGAAAAATGGT-TT
*
16529 TAAACAACACCTTCCGATGAGGAAAGGCAAACTGGGAACTTAAACAACACCTTCCGGTGGGGAAG
1 TAAACAACACCTTCCGATG-GGAAGGGCAAACTGGGAACTTAAACAACACCTTCCGGTGGGGAAG
16594 GGCAAACTGGGAAAA
65 GGCAAACTGGGAAAA
16609 GTGGACTAGG
Statistics
Matches: 290, Mismatches: 31, Indels: 44
0.79 0.08 0.12
Matches are distributed among these distances:
80 24 0.08
81 3 0.01
82 2 0.01
85 1 0.00
86 6 0.02
87 79 0.27
88 135 0.47
89 3 0.01
90 6 0.02
91 1 0.00
93 1 0.00
94 3 0.01
95 3 0.01
96 23 0.08
ACGTcount: A:0.35, C:0.19, G:0.28, T:0.17
Consensus pattern (86 bp):
TAAACAACACCTTCCGATGGGAAGGGCAAACTGGGAACTTAAACAACACCTTCCGGTGGGGAAGG
GCAAACTGGGAAAAATGGTTT
Found at i:32355 original size:4 final size:4
Alignment explanation
Indices: 32346--32500 Score: 83
Period size: 4 Copynumber: 39.5 Consensus size: 4
32336 CTATTTACCT
* * * *
32346 TTTA TTTA TTTA -CTA TTTA TATTT TTTA TTTA TTAATA TCTA TTTA TCTA
1 TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TT--TA TTTA TTTA TTTA
* ** *
32396 -TTA TTTA TTTA -TTA TTTA TCTT- TTTA TTTA TTAA TTTA ACTA -CTA
1 TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * **
32441 TCTA TTTA TTTA -CTA TTTA TCTT- TTTA TTTA TTAA TTTA GCTA -TTA
1 TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA
*
32487 TCTA TTTA TTTA TT
1 TTTA TTTA TTTA TT
32501 ATTATTTTTT
Statistics
Matches: 116, Mismatches: 22, Indels: 26
0.71 0.13 0.16
Matches are distributed among these distances:
3 18 0.16
4 88 0.76
5 7 0.06
6 3 0.03
ACGTcount: A:0.27, C:0.07, G:0.01, T:0.65
Consensus pattern (4 bp):
TTTA
Found at i:32362 original size:11 final size:11
Alignment explanation
Indices: 32347--32507 Score: 85
Period size: 11 Copynumber: 13.9 Consensus size: 11
32337 TATTTACCTT
32347 TTATTTATTTA
1 TTATTTATTTA
* *
32358 CTATTTATATTTT
1 TTA-TT-TATTTA
32371 TTATTTATTAATA
1 TTATTTATT--TA
*
32384 TCTATTTATCTA
1 T-TATTTATTTA
32396 TTATTTATTTA
1 TTATTTATTTA
*
32407 TTATTTATCTTT
1 TTATTTAT-TTA
*
32419 TTATTTATTAA
1 TTATTTATTTA
** *
32430 TTTAACTA-CTA
1 -TTATTTATTTA
32441 TCTATTTATTTA
1 T-TATTTATTTA
* *
32453 CTATTTATCTTT
1 TTATTTAT-TTA
*
32465 TTATTTATTAA
1 TTATTTATTTA
**
32476 TTTAGCTA-TTA
1 -TTATTTATTTA
32487 TCTATTTATTTA
1 T-TATTTATTTA
32499 TTA-TTATTT
1 TTATTTATTT
32508 TTTTCTTTTA
Statistics
Matches: 111, Mismatches: 26, Indels: 27
0.68 0.16 0.16
Matches are distributed among these distances:
10 8 0.07
11 45 0.41
12 42 0.38
13 9 0.08
14 7 0.06
ACGTcount: A:0.27, C:0.07, G:0.01, T:0.65
Consensus pattern (11 bp):
TTATTTATTTA
Found at i:32364 original size:15 final size:16
Alignment explanation
Indices: 32337--32500 Score: 101
Period size: 15 Copynumber: 10.2 Consensus size: 16
32327 TTTTGGTAGC
*
32337 TATTTACCT-TTTATT
1 TATTTATCTATTTATT
32352 TATTTA-CTATTTATAT
1 TATTTATCTATTTAT-T
* * *
32368 TTTTTATTTATTAATATC
1 TATTTATCTATT--TATT
32386 TATTTATCTA-TTATT
1 TATTTATCTATTTATT
32401 TATTTAT-TATTTATCT
1 TATTTATCTATTTAT-T
* *
32417 T-TTTATTTATTAATT
1 TATTTATCTATTTATT
** *
32432 TAACTA-CTATCTATT
1 TATTTATCTATTTATT
32447 TATTTA-CTATTTATCT
1 TATTTATCTATTTAT-T
* *
32463 T-TTTATTTATTAATT
1 TATTTATCTATTTATT
32478 TAGCTATTATCTATTTATT
1 TA--T-TTATCTATTTATT
32497 TATT
1 TATT
32501 ATTATTTTTT
Statistics
Matches: 115, Mismatches: 19, Indels: 29
0.71 0.12 0.18
Matches are distributed among these distances:
14 4 0.03
15 55 0.48
16 25 0.22
17 6 0.05
18 9 0.08
19 16 0.14
ACGTcount: A:0.27, C:0.08, G:0.01, T:0.65
Consensus pattern (16 bp):
TATTTATCTATTTATT
Found at i:32395 original size:8 final size:8
Alignment explanation
Indices: 32336--32599 Score: 77
Period size: 8 Copynumber: 34.8 Consensus size: 8
32326 TTTTTGGTAG
*
32336 CTATTTAC
1 CTATTTAT
32344 CT-TTTAT
1 CTATTTAT
*
32351 TTATTTA-
1 CTATTTAT
32358 CTATTTA-
1 CTATTTAT
32365 -TATTT-T
1 CTATTTAT
*
32371 TTATTTAT
1 CTATTTAT
*
32379 -TA-ATAT
1 CTATTTAT
32385 CTATTTAT
1 CTATTTAT
32393 CTA-TTAT
1 CTATTTAT
*
32400 TTATTTAT
1 CTATTTAT
32408 -TATTTAT
1 CTATTTAT
*
32415 CTTTTTAT
1 CTATTTAT
* *
32423 TTATTAAT
1 CTATTTAT
* **
32431 TTAACTA-
1 CTATTTAT
*
32438 CTATCTAT
1 CTATTTAT
*
32446 TTATTTA-
1 CTATTTAT
32453 CTATTTAT
1 CTATTTAT
32461 C--TTT-T
1 CTATTTAT
32466 -TATTTAT
1 CTATTTAT
*
32473 -TAATTTAG
1 CT-ATTTAT
32481 CTA-TTAT
1 CTATTTAT
32488 CTATTTAT
1 CTATTTAT
*
32496 TTA-TTAT
1 CTATTTAT
*
32503 -TATTTTTTT
1 CTA--TTTAT
32512 CT-TTTACCT
1 CTATTTA--T
32521 ACCTATTTAT
1 --CTATTTAT
32531 CTA-TTATT
1 CTATTTA-T
* *
32539 CTCTATAT
1 CTATTTAT
32547 CTATTTAT
1 CTATTTAT
32555 CTATTTAT
1 CTATTTAT
** * *
32563 CCCTATAC
1 CTATTTAT
32571 CTATTTAT
1 CTATTTAT
* *
32579 CTTTTTTT
1 CTATTTAT
*
32587 TTATTTAT
1 CTATTTAT
32595 -TATTT
1 CTATTT
32600 TTTAAACTTA
Statistics
Matches: 189, Mismatches: 40, Indels: 55
0.67 0.14 0.19
Matches are distributed among these distances:
5 1 0.01
6 16 0.08
7 67 0.35
8 90 0.48
9 7 0.04
10 2 0.01
11 2 0.01
12 4 0.02
ACGTcount: A:0.25, C:0.11, G:0.00, T:0.64
Consensus pattern (8 bp):
CTATTTAT
Found at i:32442 original size:27 final size:25
Alignment explanation
Indices: 32348--32501 Score: 86
Period size: 27 Copynumber: 6.5 Consensus size: 25
32338 ATTTACCTTT
*
32348 TATTTATTTACT-ATTTA-TAT-T-
1 TATTTATTTATTAATTTACTATATC
*
32369 T-TTTATTTATTAATATCTA-TTTATC
1 TATTTATTTATTAAT-T-TACTATATC
* *
32394 TA-TTATTTATTTA-TTA-TTTATC
1 TATTTATTTATTAATTTACTATATC
*
32416 TTTTTATTTATTAATTTAACTACTATC
1 TATTTATTTATTAATTT-ACTA-TATC
*
32443 TATTTATTTACT-A--T--T-TATC
1 TATTTATTTATTAATTTACTATATC
*
32462 TTTTTATTTATTAATTTAGCTATTATC
1 TATTTATTTATTAATTTA-CTA-TATC
32489 TATTTATTTATTA
1 TATTTATTTATTA
32502 TTATTTTTTT
Statistics
Matches: 103, Mismatches: 11, Indels: 32
0.71 0.08 0.22
Matches are distributed among these distances:
19 14 0.14
20 10 0.10
21 4 0.04
22 11 0.11
23 15 0.15
24 4 0.04
25 13 0.13
26 2 0.02
27 30 0.29
ACGTcount: A:0.28, C:0.07, G:0.01, T:0.64
Consensus pattern (25 bp):
TATTTATTTATTAATTTACTATATC
Found at i:32463 original size:46 final size:46
Alignment explanation
Indices: 32348--32511 Score: 206
Period size: 46 Copynumber: 3.5 Consensus size: 46
32338 ATTTACCTTT
* **
32348 TATTTATTTACTATTTATATTTTTTATTTATTAATATCTATTTATCTAT-
1 TATTTATTTACTATTTAT-CTTTTTATTTATTAAT-T-TAACTA-CTATC
*
32397 TATTTATTTATTATTTATCTTTTTATTTATTAATTTAACTACTATC
1 TATTTATTTACTATTTATCTTTTTATTTATTAATTTAACTACTATC
* *
32443 TATTTATTTACTATTTATCTTTTTATTTATTAATTTAGCTATTATC
1 TATTTATTTACTATTTATCTTTTTATTTATTAATTTAACTACTATC
* *
32489 TATTTATTTATTA-TTATTTTTTT
1 TATTTATTTACTATTTATCTTTTT
32512 CTTTTACCTA
Statistics
Matches: 105, Mismatches: 9, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
45 13 0.12
46 59 0.56
47 1 0.01
48 15 0.14
49 17 0.16
ACGTcount: A:0.27, C:0.07, G:0.01, T:0.66
Consensus pattern (46 bp):
TATTTATTTACTATTTATCTTTTTATTTATTAATTTAACTACTATC
Found at i:32550 original size:24 final size:24
Alignment explanation
Indices: 32520--32580 Score: 88
Period size: 24 Copynumber: 2.5 Consensus size: 24
32510 TTCTTTTACC
*
32520 TACCTATTTATCTA-TTATTCTCTA
1 TACCTATTTATCTATTTA-TCCCTA
*
32544 TATCTATTTATCTATTTATCCCTA
1 TACCTATTTATCTATTTATCCCTA
32568 TACCTATTTATCT
1 TACCTATTTATCT
32581 TTTTTTTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 30 0.91
25 3 0.09
ACGTcount: A:0.25, C:0.21, G:0.00, T:0.54
Consensus pattern (24 bp):
TACCTATTTATCTATTTATCCCTA
Found at i:36340 original size:29 final size:26
Alignment explanation
Indices: 36286--36349 Score: 83
Period size: 29 Copynumber: 2.3 Consensus size: 26
36276 CCAGGGGGGG
*
36286 TTTTGGTCATTTTCGCCTCAAGGGCA
1 TTTTGGTCATTTTCGCCCCAAGGGCA
*
36312 TTTTGGTCATTTTTCTCGCCCCAGGGGCA
1 TTTTGGTCA--TTT-TCGCCCCAAGGGCA
36341 TTTTGGTCA
1 TTTTGGTCA
36350 AAATTACTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 9 0.27
28 3 0.09
29 21 0.64
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.41
Consensus pattern (26 bp):
TTTTGGTCATTTTCGCCCCAAGGGCA
Done.