Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018288.1 Corchorus olitorius cultivar O-4 contig18321, 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: 32893
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:5229 original size:179 final size:178
Alignment explanation
Indices: 4964--5294 Score: 497
Period size: 179 Copynumber: 1.9 Consensus size: 178
4954 CCAATTAAGG
* * * *
4964 TGATTTAAGTGTCTATTAAAAGATTGTTCCATGATTTACAACTTTCATGAAGTAGTCGAAAACTA
1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
* *
5029 AATTTAATGTTTCAAGTATAAAAAATGCTTCCGAAA-AATTTGTTGTTTCGCATAACAGGGAATA
66 AATTTAATGTTTCAAGTATAAAAAATGCTTCC-AAAGAATTAGTTGTTTCGCATAACA-GAAATA
*
5093 GACGGTAC-ACTTAATATTATATAACTTTTTCTCCATATGTCTGATTGAGA
129 GACGGT-CTACTTAATATTACATAACTTTTTCTCCATATGTCTGATTGAGA
* * *
5143 TGATTCAAGTGTCTCTTGAAAGGTTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
**
5208 AATTTAATG-TTCAAGGTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGGTTAACAGAAATAG
66 AATTTAATGTTTCAA-GTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGCATAACAGAAATAG
5272 ACGGTCTACTTAATATTACATAA
130 ACGGTCTACTTAATATTACATAA
5295 TTTGTGCTTA
Statistics
Matches: 137, Mismatches: 12, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
177 1 0.01
178 34 0.25
179 102 0.74
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.35
Consensus pattern (178 bp):
TGATTCAAGTGTCTATTAAAAGATTGTTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
AATTTAATGTTTCAAGTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGCATAACAGAAATAGA
CGGTCTACTTAATATTACATAACTTTTTCTCCATATGTCTGATTGAGA
Found at i:15405 original size:32 final size:32
Alignment explanation
Indices: 15356--15419 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
15346 GGGATACCGC
*
15356 CCCATGGGTGTGCCGTCC-CCTGAGGGCGGCAT
1 CCCATGGGTGTGCCGTCCTCAT-AGGGCGGCAT
* *
15388 CCCATGGTTGTGTCGTCCTCATAGGGCGGCAT
1 CCCATGGGTGTGCCGTCCTCATAGGGCGGCAT
15420 GCCGTCCATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 26 0.93
33 2 0.07
ACGTcount: A:0.11, C:0.31, G:0.34, T:0.23
Consensus pattern (32 bp):
CCCATGGGTGTGCCGTCCTCATAGGGCGGCAT
Found at i:15487 original size:14 final size:14
Alignment explanation
Indices: 15468--15509 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
15458 CGTCTAAATC
*
15468 AAAATTTTTTTAAA
1 AAAATTTATTTAAA
15482 AAAATTTATTTAAA
1 AAAATTTATTTAAA
* *
15496 ATAATTTAATTAAA
1 AAAATTTATTTAAA
15510 TCAATTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AAAATTTATTTAAA
Found at i:17556 original size:29 final size:29
Alignment explanation
Indices: 17517--17590 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
17507 CTTGTAGCGT
* *
17517 TTGGACGTTTTGCCCCCTAAACTTTAATC
1 TTGGACGTTTTGCCCCATAAACTTCAATC
* * * *
17546 TTGGACATTTTGGCCCATGAACTTCAATT
1 TTGGACGTTTTGCCCCATAAACTTCAATC
17575 TTGGGACGTTTTGCCC
1 TT-GGACGTTTTGCCC
17591 TCTCAACCTA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
29 25 0.69
30 11 0.31
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (29 bp):
TTGGACGTTTTGCCCCATAAACTTCAATC
Found at i:17770 original size:29 final size:29
Alignment explanation
Indices: 17724--17779 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
17714 CGTTAAGTTG
17724 AGGGGGAAAACGTCCCAAAATTGAAGTCC
1 AGGGGGAAAACGTCCCAAAATTGAAGTCC
* *
17753 AGGGGGTAAAATGT-CCAAGATTGAAGT
1 AGGGGG-AAAACGTCCCAAAATTGAAGT
17780 TCAATGGACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.38, C:0.14, G:0.30, T:0.18
Consensus pattern (29 bp):
AGGGGGAAAACGTCCCAAAATTGAAGTCC
Found at i:18516 original size:56 final size:56
Alignment explanation
Indices: 18426--18539 Score: 201
Period size: 56 Copynumber: 2.0 Consensus size: 56
18416 TATTCGTTTC
*
18426 CTTTCACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATATTATAATAAATCATATCCCCCTATCTCTACTTAATTATT
* *
18482 CTTTCACACAATATATATTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATATTATAATAAATCATATCCCCCTATCTCTACTTAATTATT
18538 CT
1 CT
18540 ACAAAATAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.34, C:0.25, G:0.01, T:0.40
Consensus pattern (56 bp):
CTTTCACACAATAAATATTATAATAAATCATATCCCCCTATCTCTACTTAATTATT
Found at i:18637 original size:21 final size:21
Alignment explanation
Indices: 18613--18679 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
18603 AGGATTTGAG
18613 ATTTGAGTTGAGTATTTCTTA
1 ATTTGAGTTGAGTATTTCTTA
*** * *
18634 ATTT-A-CAAAGAATTTTCTATG
1 ATTTGAGTTGAGTA-TTTCT-TA
18655 ATTTGAGTTGAGTATTTCTTA
1 ATTTGAGTTGAGTATTTCTTA
18676 ATTT
1 ATTT
18680 ACAGAGAATT
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
19 3 0.09
20 6 0.19
21 14 0.44
22 6 0.19
23 3 0.09
ACGTcount: A:0.28, C:0.06, G:0.15, T:0.51
Consensus pattern (21 bp):
ATTTGAGTTGAGTATTTCTTA
Found at i:18659 original size:42 final size:42
Alignment explanation
Indices: 18612--18692 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
18602 CAGGATTTGA
18612 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
*
18654 GATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
18693 AAGACTTAGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47
Consensus pattern (42 bp):
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Found at i:21306 original size:12 final size:11
Alignment explanation
Indices: 21280--21306 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
21270 GATCTTGGAG
21280 AAAAACTATTC
1 AAAAACTATTC
21291 AAAAACTATTC
1 AAAAACTATTC
21302 AAAAA
1 AAAAA
21307 TCGCAACTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.63, C:0.15, G:0.00, T:0.22
Consensus pattern (11 bp):
AAAAACTATTC
Found at i:22528 original size:30 final size:30
Alignment explanation
Indices: 22492--22567 Score: 125
Period size: 30 Copynumber: 2.5 Consensus size: 30
22482 CCTTAAGTCA
22492 TGCATATAATTTGTAATAACTCCATGACAT
1 TGCATATAATTTGTAATAACTCCATGACAT
** *
22522 TGCATATAATTTGTAATAGTTTCATGACAT
1 TGCATATAATTTGTAATAACTCCATGACAT
22552 TGCATATAATTTGTAA
1 TGCATATAATTTGTAA
22568 CAGGAAAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.41
Consensus pattern (30 bp):
TGCATATAATTTGTAATAACTCCATGACAT
Found at i:23633 original size:42 final size:43
Alignment explanation
Indices: 23558--23649 Score: 177
Period size: 42 Copynumber: 2.2 Consensus size: 43
23548 AGTAAGCTGG
23558 AGGGGGAAAAATGAATAAAATAAAAAAGAGGAGGAGGTTTCGA
1 AGGGGGAAAAATGAATAAAATAAAAAAGAGGAGGAGGTTTCGA
23601 AGGGGGAAAAATGAA-AAAATAAAAAAGAGGAGGAGGTTTCGA
1 AGGGGGAAAAATGAATAAAATAAAAAAGAGGAGGAGGTTTCGA
23643 AGGGGGA
1 AGGGGGA
23650 GGGAGAAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 34 0.69
43 15 0.31
ACGTcount: A:0.50, C:0.02, G:0.36, T:0.12
Consensus pattern (43 bp):
AGGGGGAAAAATGAATAAAATAAAAAAGAGGAGGAGGTTTCGA
Found at i:25126 original size:189 final size:189
Alignment explanation
Indices: 24806--25180 Score: 732
Period size: 189 Copynumber: 2.0 Consensus size: 189
24796 GACAGTGTTC
*
24806 CTCGTATAATTACTCAGTAAATTTGCATTGACCGGAATTCATGCATCACGTGCATTCATACATAT
1 CTCGTATAATTACTCAGTAAATTTGCATTAACCGGAATTCATGCATCACGTGCATTCATACATAT
24871 AAAAATTAGAATTAGTAATTACTATTAAATTCAAAAATTAAAATGAAATACTATGTTTTCCAAAA
66 AAAAATTAGAATTAGTAATTACTATTAAATTCAAAAATTAAAATGAAATACTATGTTTTCCAAAA
24936 ATTCCAAAAAAGATTTGTGTTTGTTATGGTTCTCTTCAAGTTTTTCTTAAATTAAAATA
131 ATTCCAAAAAAGATTTGTGTTTGTTATGGTTCTCTTCAAGTTTTTCTTAAATTAAAATA
*
24995 CTCGTATAATTACTCAGTAAATTTGCATTAATCGGAATTCATGCATCACGTGCATTCATACATAT
1 CTCGTATAATTACTCAGTAAATTTGCATTAACCGGAATTCATGCATCACGTGCATTCATACATAT
25060 AAAAATTAGAATTAGTAATTACTATTAAATTCAAAAATTAAAATGAAATACTATGTTTTCCAAAA
66 AAAAATTAGAATTAGTAATTACTATTAAATTCAAAAATTAAAATGAAATACTATGTTTTCCAAAA
25125 ATTCCAAAAAAGATTTGTGTTTGTTATGGTTCTCTTCAAGTTTTTCTTAAATTAAA
131 ATTCCAAAAAAGATTTGTGTTTGTTATGGTTCTCTTCAAGTTTTTCTTAAATTAAA
25181 GTTAAGAGTC
Statistics
Matches: 184, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
189 184 1.00
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (189 bp):
CTCGTATAATTACTCAGTAAATTTGCATTAACCGGAATTCATGCATCACGTGCATTCATACATAT
AAAAATTAGAATTAGTAATTACTATTAAATTCAAAAATTAAAATGAAATACTATGTTTTCCAAAA
ATTCCAAAAAAGATTTGTGTTTGTTATGGTTCTCTTCAAGTTTTTCTTAAATTAAAATA
Found at i:27977 original size:7 final size:7
Alignment explanation
Indices: 27962--27995 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
27952 TTCACACAAC
27962 AAAAA-A
1 AAAAACA
27968 AAAAACAA
1 AAAAAC-A
27976 AAAAACA
1 AAAAACA
27983 AAAAACA
1 AAAAACA
27990 AAAAAC
1 AAAAAC
27996 GAAGGCTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 5 0.19
7 14 0.54
8 7 0.27
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAACA
Found at i:27979 original size:8 final size:8
Alignment explanation
Indices: 27957--27994 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
27947 CATGTTTCAC
*
27957 ACAACAAA
1 ACAAAAAA
27965 A-AAAAAA
1 ACAAAAAA
27972 ACAAAAAA
1 ACAAAAAA
27980 AC-AAAAA
1 ACAAAAAA
27987 ACAAAAAA
1 ACAAAAAA
27995 CGAAGGCTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
7 13 0.48
8 14 0.52
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (8 bp):
ACAAAAAA
Found at i:27980 original size:15 final size:15
Alignment explanation
Indices: 27957--27994 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
27947 CATGTTTCAC
*
27957 ACAACAAAAAAAAAA
1 ACAAAAAAAAAAAAA
*
27972 ACAAAAAAACAAAAA
1 ACAAAAAAAAAAAAA
27987 ACAAAAAA
1 ACAAAAAA
27995 CGAAGGCTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (15 bp):
ACAAAAAAAAAAAAA
Found at i:29050 original size:5 final size:5
Alignment explanation
Indices: 29037--29088 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
29027 TTTCTCCAAT
*
29037 ATATT ATATC ATATC ATGTATC ATAT- ATATC ATATATC ATATC ATATC
1 ATATC ATATC ATATC A--TATC ATATC ATATC --ATATC ATATC ATATC
29085 ATAT
1 ATAT
29089 AATACAAGTG
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
4 4 0.10
5 27 0.66
7 10 0.24
ACGTcount: A:0.40, C:0.13, G:0.02, T:0.44
Consensus pattern (5 bp):
ATATC
Found at i:29067 original size:21 final size:21
Alignment explanation
Indices: 29041--29088 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
29031 TCCAATATAT
*
29041 TATATCATATCAT-GTATCATA
1 TATATCATAT-ATCATATCATA
29062 TATATCATATATCATATCATA
1 TATATCATATATCATATCATA
29083 TCATAT
1 T-ATAT
29089 AATACAAGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 2 0.08
21 18 0.75
22 4 0.17
ACGTcount: A:0.40, C:0.15, G:0.02, T:0.44
Consensus pattern (21 bp):
TATATCATATATCATATCATA
Found at i:29578 original size:11 final size:10
Alignment explanation
Indices: 29548--29572 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
29538 GGCAAGTGAG
29548 AAAAGACAAA
1 AAAAGACAAA
29558 AAAAGACAAA
1 AAAAGACAAA
29568 AAAAG
1 AAAAG
29573 TTCAAATAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.80, C:0.08, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAGACAAA
Found at i:29655 original size:2 final size:2
Alignment explanation
Indices: 29648--29687 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
29638 TACTATTTAG
29648 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29688 GCTAACAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29869 original size:21 final size:21
Alignment explanation
Indices: 29843--29886 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
29833 AAAAACTGAA
29843 TTGCTAAACACCGCCCCCTTT
1 TTGCTAAACACCGCCCCCTTT
***
29864 TTGCTACTTACCGCCCCCTTT
1 TTGCTAAACACCGCCCCCTTT
29885 TT
1 TT
29887 ACACTTTTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.41, G:0.09, T:0.36
Consensus pattern (21 bp):
TTGCTAAACACCGCCCCCTTT
Found at i:29892 original size:20 final size:21
Alignment explanation
Indices: 29852--29892 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
29842 ATTGCTAAAC
*
29852 ACCGCCCCCTTTTTGCTACTT
1 ACCGCCCCCTTTTTACTACTT
29873 ACCGCCCCCTTTTTAC-ACTT
1 ACCGCCCCCTTTTTACTACTT
29893 TTGCCCTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.12, C:0.44, G:0.07, T:0.37
Consensus pattern (21 bp):
ACCGCCCCCTTTTTACTACTT
Found at i:30351 original size:15 final size:15
Alignment explanation
Indices: 30333--30385 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
30323 TTAAAATTAA
*
30333 TTATTCTTAATTAGT
1 TTATTATTAATTAGT
*
30348 TTATTAGTTTGACTTAGT
1 TTATTA--TT-AATTAGT
*
30366 TTATAATTAATTAGT
1 TTATTATTAATTAGT
30381 TTATT
1 TTATT
30386 TACGATTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
15 15 0.50
16 2 0.07
17 2 0.07
18 11 0.37
ACGTcount: A:0.28, C:0.04, G:0.09, T:0.58
Consensus pattern (15 bp):
TTATTATTAATTAGT
Done.