Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013544.1 Corchorus olitorius cultivar O-4 contig13577, 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: 24090
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:381 original size:17 final size:16
Alignment explanation
Indices: 361--403 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
351 GGTTGCCGTC
361 GAAGAAGATGAGCCGAG
1 GAAGAAGATGAG-CGAG
* *
378 GAAGAGAGAAGTGCGAG
1 GAAGA-AGATGAGCGAG
395 GAAGAAGAT
1 GAAGAAGAT
404 ATGGCAGCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 3 0.14
17 14 0.64
18 5 0.23
ACGTcount: A:0.44, C:0.07, G:0.42, T:0.07
Consensus pattern (16 bp):
GAAGAAGATGAGCGAG
Found at i:5985 original size:16 final size:15
Alignment explanation
Indices: 5947--5988 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
5937 ACAGAGATTG
*
5947 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
5962 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
5977 ACTAGAAAACAA
1 AC-AGAAAACAA
5989 AGCAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:11520 original size:18 final size:19
Alignment explanation
Indices: 11497--11533 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
11487 CACCCTAGCC
11497 CTAAAACTAGAAGA-AAAA
1 CTAAAACTAGAAGAGAAAA
11515 CTAAAACTAGAAGAGAAAA
1 CTAAAACTAGAAGAGAAAA
11534 AGAAGAAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.65, C:0.11, G:0.14, T:0.11
Consensus pattern (19 bp):
CTAAAACTAGAAGAGAAAA
Found at i:17584 original size:15 final size:15
Alignment explanation
Indices: 17560--17635 Score: 80
Period size: 15 Copynumber: 4.9 Consensus size: 15
17550 CTCGGGCGGA
17560 TTCGGGTTCGGGTAC
1 TTCGGGTTCGGGTAC
* **
17575 TTCGGATTCGGGCTTT
1 TTCGGGTTCGGG-TAC
17591 TTCGGGTTCGGGTAC
1 TTCGGGTTCGGGTAC
* **
17606 TTTGGGTTCGGGCTTT
1 TTCGGGTTCGGG-TAC
17622 TTCGGGTTCGGGTA
1 TTCGGGTTCGGGTA
17636 TTTTTGGGCT
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
15 24 0.50
16 24 0.50
ACGTcount: A:0.05, C:0.17, G:0.38, T:0.39
Consensus pattern (15 bp):
TTCGGGTTCGGGTAC
Found at i:17595 original size:31 final size:31
Alignment explanation
Indices: 17560--17635 Score: 134
Period size: 31 Copynumber: 2.5 Consensus size: 31
17550 CTCGGGCGGA
17560 TTCGGGTTCGGGTACTTCGGATTCGGGCTTT
1 TTCGGGTTCGGGTACTTCGGATTCGGGCTTT
* *
17591 TTCGGGTTCGGGTACTTTGGGTTCGGGCTTT
1 TTCGGGTTCGGGTACTTCGGATTCGGGCTTT
17622 TTCGGGTTCGGGTA
1 TTCGGGTTCGGGTA
17636 TTTTTGGGCT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.05, C:0.17, G:0.38, T:0.39
Consensus pattern (31 bp):
TTCGGGTTCGGGTACTTCGGATTCGGGCTTT
Found at i:17600 original size:16 final size:15
Alignment explanation
Indices: 17560--17651 Score: 87
Period size: 16 Copynumber: 5.9 Consensus size: 15
17550 CTCGGGCGGA
**
17560 TTCGGGTTCGGGTAC
1 TTCGGGTTCGGGTTT
*
17575 TTCGGATTCGGGCTTT
1 TTCGGGTTCGGG-TTT
*
17591 TTCGGGTTCGGGTACT
1 TTCGGGTTCGGGT-TT
17607 TT-GGGTTCGGGCTTT
1 TTCGGGTTCGGG-TTT
17622 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGT-TT
* *
17638 TTTGGGCTCGGGTT
1 TTCGGGTTCGGGTT
17652 AAGTCAGGTT
Statistics
Matches: 64, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
15 26 0.41
16 38 0.59
ACGTcount: A:0.04, C:0.16, G:0.38, T:0.41
Consensus pattern (15 bp):
TTCGGGTTCGGGTTT
Found at i:17700 original size:32 final size:32
Alignment explanation
Indices: 17626--17707 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 32
17616 GGCTTTTTCG
* *
17626 GGTTCGGGTATTTTTGGGCTCGGGTTAAGTCA
1 GGTTCGGGTATTTTCGGGCTCAGGTTAAGTCA
* **
17658 GGTTCAGGTATTTTCGGGCTCAGGTTCTGTC-
1 GGTTCGGGTATTTTCGGGCTCAGGTTAAGTCA
*
17689 TGTCTCGGGTATTTTCGGG
1 GGT-TCGGGTATTTTCGGG
17708 TTCGGTCTCG
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 2 0.05
32 40 0.95
ACGTcount: A:0.10, C:0.16, G:0.35, T:0.39
Consensus pattern (32 bp):
GGTTCGGGTATTTTCGGGCTCAGGTTAAGTCA
Found at i:17731 original size:6 final size:6
Alignment explanation
Indices: 17702--17761 Score: 54
Period size: 6 Copynumber: 10.3 Consensus size: 6
17692 CTCGGGTATT
* * *
17702 TTCGGG TTC-GG TCTCGGG -TAGGG TTCGGG TTCGGC CTCGGG -TCGGG
1 TTCGGG TTCGGG T-TCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG
*
17748 TTCGGG CTCGGG TT
1 TTCGGG TTCGGG TT
17762 TGATTTCGAT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
5 12 0.28
6 29 0.67
7 2 0.05
ACGTcount: A:0.02, C:0.22, G:0.47, T:0.30
Consensus pattern (6 bp):
TTCGGG
Found at i:17732 original size:23 final size:23
Alignment explanation
Indices: 17702--17758 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
17692 CTCGGGTATT
*
17702 TTCGGGTTCGGTCTCGGGTAGGG
1 TTCGGGTTCGGCCTCGGGTAGGG
*
17725 TTCGGGTTCGGCCTCGGGTCGGG
1 TTCGGGTTCGGCCTCGGGTAGGG
*
17748 TTCGGGCTCGG
1 TTCGGGTTCGG
17759 GTTTGATTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.02, C:0.23, G:0.47, T:0.28
Consensus pattern (23 bp):
TTCGGGTTCGGCCTCGGGTAGGG
Found at i:17757 original size:17 final size:17
Alignment explanation
Indices: 17726--17760 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
17716 CGGGTAGGGT
17726 TCGGGTTCGGCCTCGGG
1 TCGGGTTCGGCCTCGGG
*
17743 TCGGGTTCGGGCTCGGG
1 TCGGGTTCGGCCTCGGG
17760 T
1 T
17761 TTGATTTCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.26, G:0.49, T:0.26
Consensus pattern (17 bp):
TCGGGTTCGGCCTCGGG
Found at i:18713 original size:21 final size:22
Alignment explanation
Indices: 18684--18724 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
18674 GAGAATTTTT
18684 TTATAAAATTTT-TTAACCTTC
1 TTATAAAATTTTGTTAACCTTC
*
18705 TTATGAAATTTTGTTAACCT
1 TTATAAAATTTTGTTAACCT
18725 CCCTAAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.32, C:0.12, G:0.05, T:0.51
Consensus pattern (22 bp):
TTATAAAATTTTGTTAACCTTC
Found at i:18758 original size:44 final size:45
Alignment explanation
Indices: 18706--18835 Score: 133
Period size: 45 Copynumber: 2.9 Consensus size: 45
18696 TTAACCTTCT
* * *
18706 TATGAAATTTTGTTAACCTCCCTAA-GGAATTTTGA-AGA-CATCAC
1 TATGAAATTTTGATAACCTCCC-AATGAAATTTTGATA-ACCAACAC
*
18750 TATGAAATTTTGATAACTTCCCAATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTCCCAATGAAATTTTGATAACCAACAC
* * * *
18795 TATGAGATGTTGATAACCT-CCATATGATATATTGATAACCA
1 TATGAAATTTTGATAACCTCCCA-ATGAAATTTTGATAACCA
18836 CCTTATGAAA
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
43 2 0.03
44 33 0.45
45 38 0.52
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (45 bp):
TATGAAATTTTGATAACCTCCCAATGAAATTTTGATAACCAACAC
Found at i:18834 original size:22 final size:22
Alignment explanation
Indices: 18706--19110 Score: 119
Period size: 22 Copynumber: 18.6 Consensus size: 22
18696 TTAACCTTCT
* * *
18706 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCACCA
* * *
18728 TAAGGAATTTTGA-AGA-CATCA
1 TATGAAATTTTGATA-ACCACCA
18749 CTATGAAATTTTGATAACTTC-CCA
1 -TATGAAATTTTGATAAC--CACCA
*
18773 -ATGAAATTTTGATAACCAACA
1 TATGAAATTTTGATAACCACCA
* * *
18794 CTATGAGATGTTGATAACCTCCA
1 -TATGAAATTTTGATAACCACCA
* * *
18817 TATGATATATTGATAACCACCT
1 TATGAAATTTTGATAACCACCA
* * * *
18839 TATGAAAATTT-AAAAACATTCA
1 TATGAAATTTTGATAACCA-CCA
* *
18861 TATG-AATTGTT-AGTAATCA-TA
1 TATGAAATT-TTGA-TAACCACCA
* *
18882 CTCTGAAATTTTGATAATCA-CA
1 -TATGAAATTTTGATAACCACCA
* * *
18904 CTATAAAATTGTGATAACCTCGC-
1 -TATGAAATTTTGATAACCAC-CA
*
18927 TATGAAATTTTGATAAACCTTCC-
1 TATGAAATTTTGAT-AACC-ACCA
* * * *
18950 TATAAAATTTTAATAACCTCCT
1 TATGAAATTTTGATAACCACCA
*
18972 TATGAAATCTTGAT-A--A-C-
1 TATGAAATTTTGATAACCACCA
* * *
18989 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCACCA
* ** *
19010 TATTATTTTTTGATAACC-TCA
1 TATGAAATTTTGATAACCACCA
** * * *
19031 TTATGAAATTTTTTTAATCTCCC
1 -TATGAAATTTTGATAACCACCA
* * *
19054 TATGAAATTTTGAAAACTA-AA
1 TATGAAATTTTGATAACCACCA
**
19075 CTATGAAATTTTGATAACCTTCA
1 -TATGAAATTTTGATAACCACCA
19098 TATGAAATTTTGA
1 TATGAAATTTTGA
19111 CATCCTGTCA
Statistics
Matches: 281, Mismatches: 72, Indels: 60
0.68 0.17 0.15
Matches are distributed among these distances:
16 9 0.03
17 3 0.01
18 1 0.00
20 2 0.01
21 21 0.07
22 193 0.69
23 46 0.16
24 5 0.02
25 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACCA
Found at i:19072 original size:82 final size:83
Alignment explanation
Indices: 18909--19072 Score: 188
Period size: 82 Copynumber: 2.0 Consensus size: 83
18899 TCACACTATA
* *
18909 AAATTGTGATAACCTCGCTATGAAATTTTGATAAACCTTCCTATAAAATTTTAATAACCTCCTTA
1 AAATTGTGATAACCTCCCTATGAAATTTTGATAAACCTTCCTATAAAATTTTAATAACCTCCCTA
*
18974 TGAAATCTTGATAACTAC
66 TGAAATCTTGAAAACTAC
* * ** * * ** *
18992 AAATTTTGATAACCTCCCTATTATTTTTTGAT-AACC-TCATTATGAAATTTTTTTAATCTCCCT
1 AAATTGTGATAACCTCCCTATGAAATTTTGATAAACCTTC-CTATAAAATTTTAATAACCTCCCT
*
19055 ATGAAATTTTGAAAACTA
65 ATGAAATCTTGAAAACTA
19073 AACTATGAAA
Statistics
Matches: 67, Mismatches: 13, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
81 2 0.03
82 38 0.57
83 27 0.40
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.40
Consensus pattern (83 bp):
AAATTGTGATAACCTCCCTATGAAATTTTGATAAACCTTCCTATAAAATTTTAATAACCTCCCTA
TGAAATCTTGAAAACTAC
Found at i:19261 original size:22 final size:22
Alignment explanation
Indices: 19236--19430 Score: 98
Period size: 22 Copynumber: 8.8 Consensus size: 22
19226 AATCACATTT
*
19236 TGAAAATTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTCTA
* *
19258 TGAAATTTTGATAACTTCTCTA
1 TGAAAATTTGATAACCTCTCTA
* * *
19280 T-AAAATTTTGTTGACCCCTCTA
1 TGAAAA-TTTGATAACCTCTCTA
* *
19302 TGAAATTTTGAT-A-CTCACATTA
1 TGAAAATTTGATAACCTCTC--TA
* * * *
19324 TGTAATTTTGATAACCTCGCTT
1 TGAAAATTTGATAACCTCTCTA
* *
19346 TAAAAATTTTGATAATCT-TCTTA
1 TGAAAA-TTTGATAACCTCTC-TA
* *
19369 T-AAATTTTGATAATCTGATCTCTA
1 TGAAAATTTGATAA-C--CTCTCTA
*
19393 TG-AAATTTCGATAACCACTCTA
1 TGAAAATTT-GATAACCTCTCTA
*
19415 TG-AGATTTGATAACCT
1 TGAAAATTTGATAACCT
19431 TCTCAAATCT
Statistics
Matches: 130, Mismatches: 29, Indels: 29
0.69 0.15 0.15
Matches are distributed among these distances:
20 3 0.02
21 19 0.15
22 71 0.55
23 16 0.12
24 14 0.11
25 7 0.05
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTCTA
Found at i:19357 original size:23 final size:21
Alignment explanation
Indices: 19327--19381 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
19317 CACATTATGT
19327 AATTTTGATAACCTCGCTTTAAA
1 AATTTTGATAACCT-GC-TTAAA
* * *
19350 AATTTTGATAATCTTCTTATA
1 AATTTTGATAACCTGCTTAAA
19371 AATTTTGATAA
1 AATTTTGATAA
19382 TCTGATCTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 15 0.52
22 1 0.03
23 13 0.45
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.45
Consensus pattern (21 bp):
AATTTTGATAACCTGCTTAAA
Found at i:19375 original size:44 final size:45
Alignment explanation
Indices: 19238--19381 Score: 140
Period size: 44 Copynumber: 3.3 Consensus size: 45
19228 TCACATTTTG
19238 AAAA-TTTGATAACCT-CTTTATGAAATTTTGATAA-CTTCTCTAT
1 AAAATTTTGATAACCTCCTTTATGAAATTTTGATAATCTTCT-TAT
* * * * *
19281 AAAATTTTGTTGACC-CCTCTATGAAATTTTGATACTC-ACATTAT
1 AAAATTTTGATAACCTCCTTTATGAAATTTTGATAATCTTC-TTAT
** *
19325 GTAATTTTGATAACCTCGCTTTA-AAAATTTTGATAATCTTCTTAT
1 AAAATTTTGATAACCTC-CTTTATGAAATTTTGATAATCTTCTTAT
19370 -AAATTTTGATAA
1 AAAATTTTGATAA
19382 TCTGATCTCT
Statistics
Matches: 80, Mismatches: 14, Indels: 13
0.75 0.13 0.12
Matches are distributed among these distances:
43 4 0.05
44 51 0.64
45 20 0.25
46 5 0.06
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.44
Consensus pattern (45 bp):
AAAATTTTGATAACCTCCTTTATGAAATTTTGATAATCTTCTTAT
Found at i:20624 original size:16 final size:16
Alignment explanation
Indices: 20583--20625 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
20573 TTGGACCGCC
* *
20583 TCGGGTTAGGGTATTT
1 TCGGGTTCGGGTAATT
* *
20599 TTGGGCTCGGGTAATT
1 TCGGGTTCGGGTAATT
20615 TCGGGTTCGGG
1 TCGGGTTCGGG
20626 ATGTTGACTT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.09, C:0.12, G:0.42, T:0.37
Consensus pattern (16 bp):
TCGGGTTCGGGTAATT
Found at i:21496 original size:20 final size:16
Alignment explanation
Indices: 21458--21490 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
21448 GCTCACTCAA
21458 TTCATGAGTGAGTAAT
1 TTCATGAGTGAGTAAT
21474 TTCATGAGTGAGTAAT
1 TTCATGAGTGAGTAAT
21490 T
1 T
21491 CTTTTCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.06, G:0.24, T:0.39
Consensus pattern (16 bp):
TTCATGAGTGAGTAAT
Done.