Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023235.1 Corchorus olitorius cultivar O-4 contig23268, 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: 36170
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:8559 original size:63 final size:63
Alignment explanation
Indices: 8460--8586 Score: 191
Period size: 63 Copynumber: 2.0 Consensus size: 63
8450 ACAGAAACGT
* * * *
8460 GCGGATGAACAAAAGGAAGTGAAGATTGGTCATAGGAATAGGTAATGGGGACATCAAGCAAAC
1 GCGGATGAACAAAAGGAAGAGAAGATTCGTCATAGGAACAAGTAATGGGGACATCAAGCAAAC
* * *
8523 GCGGATGAATAGAAGGAAGAGAAGATTCGTCATAGGAACAAGTTATGGGGACATCAAGCAAAC
1 GCGGATGAACAAAAGGAAGAGAAGATTCGTCATAGGAACAAGTAATGGGGACATCAAGCAAAC
8586 G
1 G
8587 AACATCAGAA
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.41, C:0.12, G:0.31, T:0.16
Consensus pattern (63 bp):
GCGGATGAACAAAAGGAAGAGAAGATTCGTCATAGGAACAAGTAATGGGGACATCAAGCAAAC
Found at i:12734 original size:23 final size:23
Alignment explanation
Indices: 12704--12748 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
12694 TAGCTTCATT
12704 GTTCTAGTTTGAGCATACTTAGG
1 GTTCTAGTTTGAGCATACTTAGG
12727 GTTCTAGTTTGAGCATACTTAG
1 GTTCTAGTTTGAGCATACTTAG
12749 ACCTGCAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.13, G:0.24, T:0.40
Consensus pattern (23 bp):
GTTCTAGTTTGAGCATACTTAGG
Found at i:17531 original size:50 final size:50
Alignment explanation
Indices: 17469--17696 Score: 356
Period size: 50 Copynumber: 4.6 Consensus size: 50
17459 GATTCAACTT
* *
17469 CTTTGAATTGTCTTCCAA-TCTAATATTAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTACCAATTC-AATATTAAAAGGACCGTCTTCCGCTTATC
* *
17519 CTTTGAACTGTCTACCAATTCAATCTTGAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTACCAATTCAATATTAAAAGGACCGTCTTCCGCTTATC
*
17569 CTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTACCAATTCAATATTAAAAGGACCGTCTTCCGCTTATC
*
17619 CTTTGAACCGTCTACCAATTC-A-A-TAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTACCAATTCAATATTAAAAGGACCGTCTTCCGCTTATC
*
17666 CTTTGAACTGTCTACCAATTCAATCTTAAAA
1 CTTTGAACTGTCTACCAATTCAATATTAAAA
17697 AAAGGTAATG
Statistics
Matches: 165, Mismatches: 9, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
47 44 0.27
48 1 0.01
49 1 0.01
50 117 0.71
51 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.34
Consensus pattern (50 bp):
CTTTGAACTGTCTACCAATTCAATATTAAAAGGACCGTCTTCCGCTTATC
Found at i:17787 original size:50 final size:50
Alignment explanation
Indices: 17710--17942 Score: 351
Period size: 50 Copynumber: 4.7 Consensus size: 50
17700 GGTAATGCAC
* * *
17710 CGTATGGAAACG-GATGTGGCTTGTGGAAAAGCCTATGTTGATACTTGACT
1 CGTATGGAAACGAG-TTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACT
* *
17760 CATATGGAAACGAATTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACT
1 CGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACT
* * **
17810 CGTATGGGAACGAGTTCGGCTTGTGGAAAAGCCTGTGTTGATAATTGACT
1 CGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACT
*
17860 CGTATGGAAACGAGTTTGGCTTGTAGAAAAGCCCATGTTGATAATTGACT
1 CGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACT
*
17910 CGTATGGAAACGAGTTCGGCTTGTGGAAAAGCC
1 CGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
17943 AAAGCATTCG
Statistics
Matches: 164, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
50 164 1.00
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.29
Consensus pattern (50 bp):
CGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACT
Found at i:18168 original size:91 final size:92
Alignment explanation
Indices: 18027--18247 Score: 374
Period size: 91 Copynumber: 2.4 Consensus size: 92
18017 ATACCTTTGG
*
18027 AAAATAACTCTGAATCTGATGTTGTAACTGAAAACTTCTTGATTAATGATGAAAAAGGACCAATG
1 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTAATGATGAAAAAGGACCAATG
18092 TGCGGTCAAC-TTGAAAAACAACTTGA
66 TGCGGTCAACTTTGAAAAACAACTTGA
* *
18118 AAAATAACTCCGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAAGGACCAATG
1 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTAATGATGAAAAAGGACCAATG
*
18183 TGTGGTCAACTTTGAAAAACAACTTGA
66 TGCGGTCAACTTTGAAAAACAACTTGA
* *
18210 AAAATAACTCTGAGTCTGATGTTGTGATTG-AAACTTCT
1 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCT
18248 GGACTGTTGC
Statistics
Matches: 122, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
91 79 0.65
92 43 0.35
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (92 bp):
AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTAATGATGAAAAAGGACCAATG
TGCGGTCAACTTTGAAAAACAACTTGA
Found at i:18308 original size:25 final size:26
Alignment explanation
Indices: 18243--18308 Score: 73
Period size: 25 Copynumber: 2.5 Consensus size: 26
18233 GTGATTGAAA
18243 CTTCTGGACTGTTGCTTCGAATCTTTGCT
1 CTTCTGGA-T-TTGCTTC-AATCTTTGCT
*
18272 -TTCTTGGCTTTGCTTC-ATCTTTGCT
1 CTTC-TGGATTTGCTTCAATCTTTGCT
18297 CTTCTGGATTTG
1 CTTCTGGATTTG
18309 TCCTTGAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
25 16 0.48
26 3 0.09
27 7 0.21
28 4 0.12
29 3 0.09
ACGTcount: A:0.08, C:0.23, G:0.20, T:0.50
Consensus pattern (26 bp):
CTTCTGGATTTGCTTCAATCTTTGCT
Found at i:18750 original size:50 final size:50
Alignment explanation
Indices: 18649--18743 Score: 163
Period size: 50 Copynumber: 1.9 Consensus size: 50
18639 CTTAAATGCC
* * *
18649 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCAACCTTA
1 CTTTGAAAAGCAAATTTTGATCTTGAACTCACAAATGGAAAGCAACCTTA
18699 CTTTGAAAAGCAAATTTTGATCTTGAACTCACAAATGGAAAGCAA
1 CTTTGAAAAGCAAATTTTGATCTTGAACTCACAAATGGAAAGCAA
18744 TTTTACTGTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (50 bp):
CTTTGAAAAGCAAATTTTGATCTTGAACTCACAAATGGAAAGCAACCTTA
Found at i:19366 original size:23 final size:23
Alignment explanation
Indices: 19340--19461 Score: 137
Period size: 23 Copynumber: 5.2 Consensus size: 23
19330 ATCAATTCTC
19340 TTTTGATTTTGATTTGATTTGAT
1 TTTTGATTTTGATTTGATTTGAT
19363 TTTTGA---T--TTTGATTTGAT
1 TTTTGATTTTGATTTGATTTGAT
19381 TTTTGATTTTGATTTGATTTGAT
1 TTTTGATTTTGATTTGATTTGAT
19404 TTTTGATTTTGATTTGATTTTTGATTT
1 TTTTGATTTTGATTTGA--TTTGA--T
19431 TGATTTGATTTTTGATTTTGATTTGAT
1 T--TTTGA-TTTTGATT-TGATTTGAT
19458 TTTT
1 TTTT
19462 TGGATTTCTT
Statistics
Matches: 86, Mismatches: 0, Indels: 24
0.78 0.00 0.22
Matches are distributed among these distances:
18 17 0.20
20 1 0.01
21 1 0.01
23 34 0.40
25 8 0.09
27 4 0.05
29 10 0.12
30 8 0.09
31 3 0.03
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.67
Consensus pattern (23 bp):
TTTTGATTTTGATTTGATTTGAT
Found at i:19375 original size:18 final size:18
Alignment explanation
Indices: 19341--19461 Score: 183
Period size: 18 Copynumber: 6.6 Consensus size: 18
19331 TCAATTCTCT
19341 TTTGA-TTTTGA-TTTGA
1 TTTGATTTTTGATTTTGA
19357 TTTGATTTTTGATTTTGA
1 TTTGATTTTTGATTTTGA
19375 TTTGATTTTTGATTTTGATTTGA
1 TTTGATTTTTGA---T--TTTGA
19398 TTTGATTTTTGATTTTGA
1 TTTGATTTTTGATTTTGA
19416 TTTGATTTTTGATTTTGA
1 TTTGATTTTTGATTTTGA
19434 TTTGATTTTTGATTTTGA
1 TTTGATTTTTGATTTTGA
19452 TTTGATTTTT
1 TTTGATTTTT
19462 TGGATTTCTT
Statistics
Matches: 98, Mismatches: 0, Indels: 12
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.05
17 6 0.06
18 68 0.69
20 1 0.01
21 1 0.01
23 17 0.17
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.67
Consensus pattern (18 bp):
TTTGATTTTTGATTTTGA
Found at i:19397 original size:41 final size:41
Alignment explanation
Indices: 19340--19461 Score: 209
Period size: 41 Copynumber: 3.1 Consensus size: 41
19330 ATCAATTCTC
19340 TTTTGATTTTGATTTGATTTGATTTTTGATTTTGATTTGAT
1 TTTTGATTTTGATTTGATTTGATTTTTGATTTTGATTTGAT
19381 TTTTGATTTTGATTTGATTTGATTTTTGATTTTGATTTGAT
1 TTTTGATTTTGATTTGATTTGATTTTTGATTTTGATTTGAT
19422 TTTTGA---T--TTTGATTTGATTTTTGATTTTGATTTGAT
1 TTTTGATTTTGATTTGATTTGATTTTTGATTTTGATTTGAT
19458 TTTT
1 TTTT
19462 TGGATTTCTT
Statistics
Matches: 81, Mismatches: 0, Indels: 5
0.94 0.00 0.06
Matches are distributed among these distances:
36 33 0.41
38 1 0.01
41 47 0.58
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.67
Consensus pattern (41 bp):
TTTTGATTTTGATTTGATTTGATTTTTGATTTTGATTTGAT
Found at i:19771 original size:15 final size:13
Alignment explanation
Indices: 19734--19782 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
19724 AGAAAACAAG
19734 TTTCGAAATCATT
1 TTTCGAAATCATT
*
19747 TTTGGAAATCAATT
1 TTTCGAAATC-ATT
*
19761 TTATCGAAATCCTT
1 TT-TCGAAATCATT
*
19775 TTTTGAAA
1 TTTCGAAA
19783 ACAATGACTC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
13 14 0.47
14 9 0.30
15 7 0.23
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (13 bp):
TTTCGAAATCATT
Found at i:19876 original size:17 final size:17
Alignment explanation
Indices: 19837--19876 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
19827 TTCCAAGTGC
*
19837 TTTTATTTTCATTTCAT
1 TTTTTTTTTCATTTCAT
**
19854 CATTTTTTTCATTTCAT
1 TTTTTTTTTCATTTCAT
19871 TTTTTT
1 TTTTTT
19877 GATTATTGGG
Statistics
Matches: 18, Mismatches: 5, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTTTTTTCATTTCAT
Found at i:21380 original size:16 final size:15
Alignment explanation
Indices: 21342--21383 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
21332 ACAGAGGTTG
21342 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
21357 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
21372 ACTAGAAAACAA
1 AC-AGAAAACAA
21384 AACAAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:27236 original size:11 final size:10
Alignment explanation
Indices: 27199--27234 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
27189 GGTTTAATCG
**
27199 AAAAAATATC
1 AAAAAATAAA
27209 AAAAAATAAA
1 AAAAAATAAA
27219 AAAAAATAAA
1 AAAAAATAAA
27229 AAAAAA
1 AAAAAA
27235 ATTCGACCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.86, C:0.03, G:0.00, T:0.11
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:31790 original size:11 final size:10
Alignment explanation
Indices: 31774--31820 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
31764 ACGCTCGTGT
31774 TTGAAGACTCA
1 TTGAAGA-TCA
*
31785 TTGAAGATAA
1 TTGAAGATCA
31795 TTTGAAGAT--
1 -TTGAAGATCA
31804 TTGAAGATCA
1 TTGAAGATCA
31814 TTGAAGA
1 TTGAAGA
31821 ATTATTTCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 8 0.25
10 9 0.28
11 15 0.47
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.32
Consensus pattern (10 bp):
TTGAAGATCA
Found at i:31809 original size:19 final size:18
Alignment explanation
Indices: 31785--31820 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
31775 TGAAGACTCA
31785 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
31804 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
31821 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:35252 original size:21 final size:21
Alignment explanation
Indices: 35223--35272 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
35213 GGCCTGAGAG
*
35223 CCCAGGTCTTAAGCCTGATCA
1 CCCATGTCTTAAGCCTGATCA
*
35244 CTCATGTCTTAAGCCTGATCA
1 CCCATGTCTTAAGCCTGATCA
35265 CCCATGTC
1 CCCATGTC
35273 CTGTCCTCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.22, C:0.34, G:0.16, T:0.28
Consensus pattern (21 bp):
CCCATGTCTTAAGCCTGATCA
Done.