Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021535.1 Corchorus olitorius cultivar O-4 contig21568, 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: 31212
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1212 original size:25 final size:25
Alignment explanation
Indices: 1180--1365 Score: 250
Period size: 25 Copynumber: 7.5 Consensus size: 25
1170 CAAGCTCCTT
* *
1180 AAGAGGGACTACCACAAGCTCCCCA
1 AAGAGGGAATGCCACAAGCTCCCCA
*
1205 AAGAGGGAATGCCTCAAGCTCCCCA
1 AAGAGGGAATGCCACAAGCTCCCCA
* *
1230 AAAAGGGAATGCCTCAAGCTCCCCA
1 AAGAGGGAATGCCACAAGCTCCCCA
1255 AAGAGGGAATG-C-CAAGCTCCCCA
1 AAGAGGGAATGCCACAAGCTCCCCA
*
1278 AAGATGGAATGCCACAAGCTCCCCA
1 AAGAGGGAATGCCACAAGCTCCCCA
* * * *
1303 AAAACGGAATGCCTCAAGCTCCCTA
1 AAGAGGGAATGCCACAAGCTCCCCA
*
1328 AAGATGGAATGCCACAAGCTCCCCA
1 AAGAGGGAATGCCACAAGCTCCCCA
*
1353 AAGAGGGACTGCC
1 AAGAGGGAATGCC
1366 TATGCCCCCG
Statistics
Matches: 143, Mismatches: 16, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
23 21 0.15
24 2 0.01
25 120 0.84
ACGTcount: A:0.35, C:0.32, G:0.22, T:0.11
Consensus pattern (25 bp):
AAGAGGGAATGCCACAAGCTCCCCA
Found at i:1289 original size:73 final size:75
Alignment explanation
Indices: 1180--1366 Score: 288
Period size: 73 Copynumber: 2.5 Consensus size: 75
1170 CAAGCTCCTT
* * *
1180 AAGAGGGACTACCACAAGCTCCCCAAAGAGGGAATGCCTCAAGCTCCCCAAAAAGGGAATGCCTC
1 AAGAGGGAATGCCACAAGCTCCCCAAAGAGGGAATGCCTCAAGCTCCCCAAAAACGGAATGCCTC
1245 AAGCTCCCCA
66 AAGCTCCCCA
* *
1255 AAGAGGGAATG-C-CAAGCTCCCCAAAGATGGAATGCCACAAGCTCCCCAAAAACGGAATGCCTC
1 AAGAGGGAATGCCACAAGCTCCCCAAAGAGGGAATGCCTCAAGCTCCCCAAAAACGGAATGCCTC
*
1318 AAGCTCCCTA
66 AAGCTCCCCA
* *
1328 AAGATGGAATGCCACAAGCTCCCCAAAGAGGGACTGCCT
1 AAGAGGGAATGCCACAAGCTCCCCAAAGAGGGAATGCCT
1367 ATGCCCCCGT
Statistics
Matches: 100, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
73 67 0.67
74 2 0.02
75 31 0.31
ACGTcount: A:0.35, C:0.32, G:0.22, T:0.12
Consensus pattern (75 bp):
AAGAGGGAATGCCACAAGCTCCCCAAAGAGGGAATGCCTCAAGCTCCCCAAAAACGGAATGCCTC
AAGCTCCCCA
Found at i:1380 original size:23 final size:23
Alignment explanation
Indices: 1345--1397 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
1335 AATGCCACAA
**
1345 GCTCCCCAAAGAGGGACTGCCTAT
1 GCTCCCCGTAGAGGGACTGCCT-T
1369 GC-CCCCGTAGAGGGACTGCCTT
1 GCTCCCCGTAGAGGGACTGCCTT
1391 GCTCCCC
1 GCTCCCC
1398 AAGAGGAACG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 3 0.12
23 21 0.81
24 2 0.08
ACGTcount: A:0.17, C:0.40, G:0.26, T:0.17
Consensus pattern (23 bp):
GCTCCCCGTAGAGGGACTGCCTT
Found at i:1450 original size:34 final size:34
Alignment explanation
Indices: 1407--1477 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 34
1397 CAAGAGGAAC
1407 GTTAAATCAGGTCGTGCGCCGTAAGAA-CCCAATG
1 GTTAAATCAGGTCGTGCGCCGTAA-AACCCCAATG
* *
1441 GTTAAATCAGGTCGTGTGCTGTAAAACCCCAATG
1 GTTAAATCAGGTCGTGCGCCGTAAAACCCCAATG
1475 GTT
1 GTT
1478 GGCCCACTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 2 0.06
34 32 0.94
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.25
Consensus pattern (34 bp):
GTTAAATCAGGTCGTGCGCCGTAAAACCCCAATG
Found at i:5605 original size:45 final size:45
Alignment explanation
Indices: 5541--5634 Score: 170
Period size: 45 Copynumber: 2.1 Consensus size: 45
5531 GGTTAACACG
* *
5541 ATTAAAACACGTTTAACTATTTCTATTTATATGTCAACATGCTTA
1 ATTAAAACACCTTTAACTATTCCTATTTATATGTCAACATGCTTA
5586 ATTAAAACACCTTTAACTATTCCTATTTATATGTCAACATGCTTA
1 ATTAAAACACCTTTAACTATTCCTATTTATATGTCAACATGCTTA
5631 ATTA
1 ATTA
5635 CTATAATTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.41
Consensus pattern (45 bp):
ATTAAAACACCTTTAACTATTCCTATTTATATGTCAACATGCTTA
Found at i:6919 original size:23 final size:23
Alignment explanation
Indices: 6889--6934 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
6879 ATAAAAGGAT
6889 GGGATTATGGTAAAACTTGAGAC
1 GGGATTATGGTAAAACTTGAGAC
6912 GGGATTATGGTAAAACTTGAGAC
1 GGGATTATGGTAAAACTTGAGAC
6935 TTAATTTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.09, G:0.30, T:0.26
Consensus pattern (23 bp):
GGGATTATGGTAAAACTTGAGAC
Found at i:6957 original size:41 final size:43
Alignment explanation
Indices: 6912--7003 Score: 161
Period size: 41 Copynumber: 2.2 Consensus size: 43
6902 AACTTGAGAC
6912 GGGATTATGGTAAAACTTGAGACTTAAT-TT-GATAAAAGTAT
1 GGGATTATGGTAAAACTTGAGACTTAATATTCGATAAAAGTAT
6953 GGGATTATGGTAAAACTTGAGACTTAATAATTCGATAAAAGTAT
1 GGGATTATGGTAAAACTTGAGACTTAAT-ATTCGATAAAAGTAT
6997 GGGATTA
1 GGGATTA
7004 GTATTAGCAC
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
41 28 0.58
43 2 0.04
44 18 0.38
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.33
Consensus pattern (43 bp):
GGGATTATGGTAAAACTTGAGACTTAATATTCGATAAAAGTAT
Found at i:8612 original size:3 final size:3
Alignment explanation
Indices: 8604--8634 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
8594 TGACCATGGA
*
8604 TGT TGT TGT TGT TGT TGT TGT TGC TGT TGT T
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT T
8635 ATTCTCATGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.03, G:0.32, T:0.65
Consensus pattern (3 bp):
TGT
Found at i:13265 original size:33 final size:34
Alignment explanation
Indices: 13197--13267 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
13187 ATTGATAGAC
*
13197 AAAATAGCCCTTCAATTTTGAAAAAAAATAAAAT
1 AAAATAGCACTTCAATTTTGAAAAAAAATAAAAT
* ** *
13231 AAAATAGCACTTGAATTTTGGCAAAAAA-AGAAT
1 AAAATAGCACTTCAATTTTGAAAAAAAATAAAAT
13264 AAAA
1 AAAA
13268 ATTATAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 8 0.25
34 24 0.75
ACGTcount: A:0.56, C:0.10, G:0.10, T:0.24
Consensus pattern (34 bp):
AAAATAGCACTTCAATTTTGAAAAAAAATAAAAT
Found at i:16830 original size:54 final size:49
Alignment explanation
Indices: 16735--16837 Score: 143
Period size: 54 Copynumber: 2.0 Consensus size: 49
16725 GTTTCATTGG
* *
16735 ATCACAACTGTTTCTTGTTACATATATGTTGAATTTTAAAACTAATGTT
1 ATCACAACTGTTTCTGGTTACATATATGTTGAATTTCAAAACTAATGTT
16784 ATCACAACTGTTTCTGGTTTACAATATTGCATGTTGAATTTCAAAACTAATGTT
1 ATCACAACTGTTTCTGG-TTAC-ATA-T--ATGTTGAATTTCAAAACTAATGTT
16838 CCTGTTTATT
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
49 16 0.34
50 4 0.09
51 3 0.06
52 1 0.02
54 23 0.49
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.43
Consensus pattern (49 bp):
ATCACAACTGTTTCTGGTTACATATATGTTGAATTTCAAAACTAATGTT
Found at i:17102 original size:11 final size:11
Alignment explanation
Indices: 17086--17116 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
17076 AATTATATAT
17086 ATATATAAGTA
1 ATATATAAGTA
17097 ATATATAAGTA
1 ATATATAAGTA
17108 ATACTATAA
1 ATA-TATAA
17117 AATTATTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.74
12 5 0.26
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.35
Consensus pattern (11 bp):
ATATATAAGTA
Found at i:19656 original size:20 final size:22
Alignment explanation
Indices: 19620--19660 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
19610 CTACTCGGCC
19620 TCGACTCGAGAAAAATTCGAGT
1 TCGACTCGAGAAAAATTCGAGT
19642 TCGACTCG-G-AAAATTCGAG
1 TCGACTCGAGAAAAATTCGAG
19661 CCGAGCTCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
21 1 0.05
22 8 0.42
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (22 bp):
TCGACTCGAGAAAAATTCGAGT
Found at i:19669 original size:20 final size:20
Alignment explanation
Indices: 19621--19669 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
19611 TACTCGGCCT
*
19621 CGACTCGAGAAAAATTCGAGTT
1 CGACTCG-G-AAAATTCGAGTC
19643 CGACTCGGAAAATTCGAG-C
1 CGACTCGGAAAATTCGAGTC
19662 CGAGCTCG
1 CGA-CTCG
19670 AGCTCGAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 3 0.12
20 14 0.56
21 1 0.04
22 7 0.28
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.18
Consensus pattern (20 bp):
CGACTCGGAAAATTCGAGTC
Found at i:22579 original size:75 final size:73
Alignment explanation
Indices: 22437--22585 Score: 165
Period size: 75 Copynumber: 2.0 Consensus size: 73
22427 GTAATTAACT
* ** * *
22437 AAGCGAGAAAAGACGAAAAGGGGCGAAAAGGTTGTCCCTCATCGAAAGTTAAAAGGAGCTTTTAG
1 AAGCGAGAAAAGACGAAAAGGGGCGAAAAGGTTCTCCAACATCAAAAGTTAAAAGGAGCCTTTAG
22502 TAAATTCC
66 TAAATTCC
* * * * *
22510 AAGCGAGAAAAGACTAAAATGGGGCGAAAAGGGTTCTCCAACGTTAAAAGTT-GATGGAAGCCTT
1 AAGCGAGAAAAGACGAAAA-GGGGCGAAAA-GGTTCTCCAACATCAAAAGTTAAAAGG-AGCCTT
*
22574 TAGTAATTTCC
63 TAGTAAATTCC
22585 A
1 A
22586 GAGGGTATTC
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
73 18 0.29
74 13 0.21
75 31 0.50
ACGTcount: A:0.39, C:0.15, G:0.26, T:0.21
Consensus pattern (73 bp):
AAGCGAGAAAAGACGAAAAGGGGCGAAAAGGTTCTCCAACATCAAAAGTTAAAAGGAGCCTTTAG
TAAATTCC
Found at i:22859 original size:42 final size:43
Alignment explanation
Indices: 22807--22900 Score: 147
Period size: 45 Copynumber: 2.2 Consensus size: 43
22797 AGTGCATTAT
*
22807 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
22848 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
22893 CTAATATT
1 CTAATATT
22901 AATTGTTACT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
41 4 0.08
42 6 0.12
45 38 0.79
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:23759 original size:14 final size:14
Alignment explanation
Indices: 23715--23751 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
23705 GCCACTAAAA
23715 ATAA-TATATAGTAT
1 ATAATTATATA-TAT
23729 AT-ATTATATATAT
1 ATAATTATATATAT
23742 ATAATTATAT
1 ATAATTATAT
23752 TCATATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 6 0.29
14 15 0.71
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (14 bp):
ATAATTATATATAT
Found at i:27381 original size:12 final size:12
Alignment explanation
Indices: 27347--27381 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
27337 TATTTATATC
*
27347 TTTTTT-TTTTG
1 TTTTTTGTTTTT
27358 TTTTTTGTTTTT
1 TTTTTTGTTTTT
27370 TTTTTTGTTTTT
1 TTTTTTGTTTTT
27382 GTGCGTCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 6 0.27
12 16 0.73
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (12 bp):
TTTTTTGTTTTT
Found at i:31146 original size:36 final size:36
Alignment explanation
Indices: 31099--31168 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
31089 GAGATTTTGG
*
31099 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATTACAAAAAATGTAATA
31135 AGAAATATGATAACCAAAATTACAAAAAATGTAA
1 AGAAATATGATAACCAAAATTACAAAAAATGTAA
31169 GGTTATTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.61, C:0.07, G:0.09, T:0.23
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATTACAAAAAATGTAATA
Done.