Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014418.1 Corchorus olitorius cultivar O-4 contig14451, 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: 34763
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:30 original size:18 final size:19
Alignment explanation
Indices: 1--37 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
1 ATTTAGCTATTATCTATTT
1 ATTTAGCTATTATCTATTT
20 ATTTA-CTATTATCTATTT
1 ATTTAGCTATTATCTATTT
38 TTTTTACCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.27, C:0.11, G:0.03, T:0.59
Consensus pattern (19 bp):
ATTTAGCTATTATCTATTT
Found at i:97 original size:8 final size:8
Alignment explanation
Indices: 49--139 Score: 53
Period size: 8 Copynumber: 11.6 Consensus size: 8
39 TTTTACCTAC
49 CTATTTAT
1 CTATTTAT
*
57 CTAATTAT
1 CTATTTAT
* *
65 CTATATAC
1 CTATTTAT
73 CTATTTAT
1 CTATTTAT
*
81 CTTTTTAT
1 CTATTTAT
* *
89 TTATCTAT
1 CTATTTAT
97 -TATTT-T
1 CTATTTAT
*
103 -TACTTAT
1 CTATTTAT
* *
110 TTTTTCTAT
1 CTATT-TAT
*
119 TTATTTAT
1 CTATTTAT
*
127 TTATTTAT
1 CTATTTAT
135 CTATT
1 CTATT
140 ACTTTTTTTA
Statistics
Matches: 64, Mismatches: 16, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
6 5 0.08
7 5 0.08
8 47 0.73
9 7 0.11
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.65
Consensus pattern (8 bp):
CTATTTAT
Found at i:125 original size:4 final size:4
Alignment explanation
Indices: 74--152 Score: 54
Period size: 4 Copynumber: 19.2 Consensus size: 4
64 TCTATATACC
* * * *
74 TATT TATCT T-TT TATT TATC TATT ATTTT TACT TATT TTTT CTATT TATT
1 TATT TAT-T TATT TATT TATT TATT -TATT TATT TATT TATT -TATT TATT
* *
124 TATT TATT TATC TA-T TACTT TTTT TATT T
1 TATT TATT TATT TATT TA-TT TATT TATT T
153 TAATATTTTT
Statistics
Matches: 57, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
3 4 0.07
4 43 0.75
5 10 0.18
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (4 bp):
TATT
Found at i:130 original size:42 final size:41
Alignment explanation
Indices: 73--153 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 41
63 ATCTATATAC
73 CTATTTATCTTTTTATTTATCTATTA-TTTTTACTTATTTTTT
1 CTATTTATCTTTTTATTTATCTATTACTTTTT--TTATTTTTT
115 CTATTTAT-TTATTTATTTATCTATTACTTTTTTTATTTT
1 CTATTTATCTT-TTTATTTATCTATTACTTTTTTTATTTT
154 AATATTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
41 9 0.24
42 23 0.62
43 5 0.14
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.72
Consensus pattern (41 bp):
CTATTTATCTTTTTATTTATCTATTACTTTTTTTATTTTTT
Found at i:1571 original size:19 final size:19
Alignment explanation
Indices: 1547--1590 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
1537 GAAATTCAAA
1547 ATGTATTTGAATTGGTCAG
1 ATGTATTTGAATTGGTCAG
1566 ATGTATTTGAATTGGTCAG
1 ATGTATTTGAATTGGTCAG
1585 AGTGTA
1 A-TGTA
1591 GGATAAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.27, C:0.05, G:0.27, T:0.41
Consensus pattern (19 bp):
ATGTATTTGAATTGGTCAG
Found at i:8422 original size:14 final size:13
Alignment explanation
Indices: 8403--8434 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
8393 AATTGAATGG
8403 AATTTTCAATTTTC
1 AATTTTCAA-TTTC
8417 AATTTTCAATTTC
1 AATTTTCAATTTC
8430 AATTT
1 AATTT
8435 CAAGGGTTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.31, C:0.12, G:0.00, T:0.56
Consensus pattern (13 bp):
AATTTTCAATTTC
Found at i:8437 original size:6 final size:7
Alignment explanation
Indices: 8403--8434 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
8393 AATTGAATGG
8403 AATTTTC
1 AATTTTC
8410 AATTTTC
1 AATTTTC
8417 AATTTTC
1 AATTTTC
8424 AA-TTTC
1 AATTTTC
8430 AATTT
1 AATTT
8435 CAAGGGTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.31, C:0.12, G:0.00, T:0.56
Consensus pattern (7 bp):
AATTTTC
Found at i:24440 original size:23 final size:23
Alignment explanation
Indices: 24410--24455 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
24400 GCCTGCCAAA
24410 ACCCTTCTTCAGAGTATCAGTAG
1 ACCCTTCTTCAGAGTATCAGTAG
24433 ACCCTTCTTCAGAGTATCAGTAG
1 ACCCTTCTTCAGAGTATCAGTAG
24456 CTTTTAAATA
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:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (23 bp):
ACCCTTCTTCAGAGTATCAGTAG
Found at i:30037 original size:22 final size:22
Alignment explanation
Indices: 30007--30212 Score: 160
Period size: 22 Copynumber: 9.6 Consensus size: 22
29997 TCCAAAGTAG
* *
30007 AAATATTGATAACCACACTGTGA
1 AAAT-TTGATAACCTCACTATGA
*
30030 AAATTTGATAACCTCATTAT-A
1 AAATTTGATAACCTCACTATGA
*
30051 AAATTCCGATAACCTCACTATGA
1 AAATT-TGATAACCTCACTATGA
*
30074 AAATTTGATAACCACACTATGA
1 AAATTTGATAACCTCACTATGA
* * *
30096 AATTTTGATAACCTCAATGTGA
1 AAATTTGATAACCTCACTATGA
*
30118 AATTTTGATAA--T--CTAT-A
1 AAATTTGATAACCTCACTATGA
* * *
30135 AAA-TTGGTAATCGCACTATGA
1 AAATTTGATAACCTCACTATGA
*
30156 AAATTTTGACAACCTCA-TCAT-A
1 AAA-TTTGATAACCTCACT-ATGA
* * *
30178 AATTTTGATAACCACACCATGA
1 AAATTTGATAACCTCACTATGA
*
30200 AATTTTGATAACC
1 AAATTTGATAACC
30213 CCCTAATTAT
Statistics
Matches: 147, Mismatches: 24, Indels: 25
0.75 0.12 0.13
Matches are distributed among these distances:
16 6 0.04
17 3 0.02
18 2 0.01
20 5 0.03
21 23 0.16
22 88 0.60
23 20 0.14
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (22 bp):
AAATTTGATAACCTCACTATGA
Found at i:30077 original size:44 final size:44
Alignment explanation
Indices: 30007--30212 Score: 183
Period size: 44 Copynumber: 4.8 Consensus size: 44
29997 TCCAAAGTAG
* *
30007 AAATATTGATAACCACACTGTGAAAATTTGATAACCTCATTATA
1 AAATTTTGATAACCACACTATGAAAATTTGATAACCTCATTATA
** * * * *
30051 AAATTCCGATAACCTCACTATGAAAATTTGATAACCACACTATG
1 AAATTTTGATAACCACACTATGAAAATTTGATAACCTCATTATA
* * * *
30095 AAATTTTGATAACCTCAATGTGAAATTTTGATAA--TC--TATA
1 AAATTTTGATAACCACACTATGAAAATTTGATAACCTCATTATA
* * * * *
30135 AAA--TTGGTAATCGCACTATGAAAATTTTGACAACCTCATCAT-
1 AAATTTTGATAACCACACTATGAAAA-TTTGATAACCTCATTATA
* *
30177 AAATTTTGATAACCACACCATGAAATTTTGATAACC
1 AAATTTTGATAACCACACTATGAAAATTTGATAACC
30213 CCCTAATTAT
Statistics
Matches: 126, Mismatches: 29, Indels: 15
0.74 0.17 0.09
Matches are distributed among these distances:
38 15 0.12
39 7 0.06
40 6 0.05
41 2 0.02
42 4 0.03
43 11 0.09
44 81 0.64
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (44 bp):
AAATTTTGATAACCACACTATGAAAATTTGATAACCTCATTATA
Found at i:30186 original size:82 final size:85
Alignment explanation
Indices: 30006--30211 Score: 233
Period size: 82 Copynumber: 2.4 Consensus size: 85
29996 CTCCAAAGTA
* * *
30006 GAAATATTGATAACCACACTGTGAAAATTTGATAACCTCATTATAAAATTCCGATAACCTCACTA
1 GAAATTTTGATAACCACACTGTGAAATTTTGATAA-CTCA-TATAAAATT-CGATAACCGCACTA
*
30071 TGAAAATTTGATAACCACACTAT
63 TGAAAATTTGACAACCACACTAT
* * * *
30094 GAAATTTTGATAACCTCAATGTGAAATTTTGATAA-TC-TATAAAATT-GGTAATCGCACTATGA
1 GAAATTTTGATAACCACACTGTGAAATTTTGATAACTCATATAAAATTCGATAACCGCACTATGA
*
30156 AAATTTTGACAACCTCA-TCAT
66 AAA-TTTGACAACCACACT-AT
**
30177 -AAATTTTGATAACCACACCATGAAATTTTGATAAC
1 GAAATTTTGATAACCACACTGTGAAATTTTGATAAC
30212 CCCCTAATTA
Statistics
Matches: 102, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
82 47 0.46
83 13 0.13
84 9 0.09
86 2 0.02
88 31 0.30
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (85 bp):
GAAATTTTGATAACCACACTGTGAAATTTTGATAACTCATATAAAATTCGATAACCGCACTATGA
AAATTTGACAACCACACTAT
Found at i:30286 original size:22 final size:22
Alignment explanation
Indices: 30261--30313 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
30251 TGTAATGTTG
30261 ATAACCTCTCC-ATAAAATTTTC
1 ATAACCTC-CCTATAAAATTTTC
* * *
30283 ATAATCTCCCTATGAAATTTTG
1 ATAACCTCCCTATAAAATTTTC
*
30305 TTAACCTCC
1 ATAACCTCC
30314 ATAGGAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 2 0.08
22 23 0.92
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.38
Consensus pattern (22 bp):
ATAACCTCCCTATAAAATTTTC
Found at i:30539 original size:44 final size:44
Alignment explanation
Indices: 30458--30563 Score: 106
Period size: 44 Copynumber: 2.4 Consensus size: 44
30448 TGCGGGCTCT
* * *
30458 TATGAAATTTTGATAACCACACTATAAAATTTCGATAAACTTGG
1 TATGAAATTTTGATAACTACACTAAAAAATTTCGATAAACTTGA
* * * * *
30502 TATGAAATTTTGTTAACTTCTCTAAAAAACTTT-GATAACCTTTA
1 TATGAAATTTTGATAACTACACTAAAAAA-TTTCGATAAACTTGA
* *
30546 TGTGAAATTTTGGTAACT
1 TATGAAATTTTGATAACT
30564 CTTGTATGAA
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
44 48 0.94
45 3 0.06
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (44 bp):
TATGAAATTTTGATAACTACACTAAAAAATTTCGATAAACTTGA
Found at i:30557 original size:22 final size:22
Alignment explanation
Indices: 30532--30585 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
30522 TCTAAAAAAC
30532 TTTGATAAC-CTT-TATGTGAAAT
1 TTTGATAACTCTTGTA--TGAAAT
*
30554 TTTGGTAACTCTTGTATGAAAT
1 TTTGATAACTCTTGTATGAAAT
*
30576 TCTGATAACT
1 TTTGATAACT
30586 ACACTATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 22 0.81
23 3 0.11
24 2 0.07
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (22 bp):
TTTGATAACTCTTGTATGAAAT
Found at i:31007 original size:2 final size:2
Alignment explanation
Indices: 31000--31025 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30990 GATAAATTAC
31000 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
31026 GTGTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32754 original size:12 final size:12
Alignment explanation
Indices: 32737--32779 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
32727 ATATAAGAAA
32737 AAAAAGAAAAGG
1 AAAAAGAAAAGG
32749 AAAAAGAAAA-G
1 AAAAAGAAAAGG
*
32760 AAAAA-AAAGGG
1 AAAAAGAAAAGG
*
32771 AAAAGGAAA
1 AAAAAGAAA
32780 TAAAACAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 3 0.11
11 11 0.41
12 13 0.48
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAGG
Found at i:32755 original size:21 final size:22
Alignment explanation
Indices: 32731--32790 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
32721 GGCCCAATAT
32731 AAGAAAAAAAAGAAAA-GGAAA
1 AAGAAAAAAAAGAAAAGGGAAA
32752 AAGAAAAGAAAA-AAAAGGGAAA
1 AAGAAAA-AAAAGAAAAGGGAAA
*
32774 AGGAAATAAAACAGAAA
1 AAGAAA-AAAA-AGAAA
32791 TTTTAGGATT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
21 11 0.33
22 17 0.52
23 2 0.06
24 3 0.09
ACGTcount: A:0.77, C:0.02, G:0.20, T:0.02
Consensus pattern (22 bp):
AAGAAAAAAAAGAAAAGGGAAA
Found at i:32784 original size:26 final size:25
Alignment explanation
Indices: 32726--32784 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
32716 GACTAGGCCC
*
32726 AATATAAGAAAAAAAAGAAAAGGAAA
1 AATAAAAGAAAAAAAAGAAAAGG-AA
*
32752 AAGAAAAGAAAAAAAAGGGAAAAGG-A
1 AATAAAAGAAAAAAAA--GAAAAGGAA
32778 AATAAAA
1 AATAAAA
32785 CAGAAATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
26 21 0.75
28 7 0.25
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (25 bp):
AATAAAAGAAAAAAAAGAAAAGGAA
Done.