Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022166.1 Corchorus olitorius cultivar O-4 contig22199, 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: 8319
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.33
Found at i:185 original size:14 final size:16
Alignment explanation
Indices: 161--193 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
151 TTAGACCATA
161 AAAATGAAAATG-AAT
1 AAAATGAAAATGAAAT
176 AAAA-GAAAATGAAAT
1 AAAATGAAAATGAAAT
191 AAA
1 AAA
194 GGGAAGGTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.15
Consensus pattern (16 bp):
AAAATGAAAATGAAAT
Found at i:266 original size:11 final size:11
Alignment explanation
Indices: 250--289 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
240 ATGCAACATT
250 AAAATGAACTA
1 AAAATGAACTA
*
261 AAAATGCAACATT
1 AAAATG-AAC-TA
274 AAAATGAACTA
1 AAAATGAACTA
285 AAAAT
1 AAAAT
290 TTATGCAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 12 0.48
12 6 0.24
13 7 0.28
ACGTcount: A:0.62, C:0.10, G:0.07, T:0.20
Consensus pattern (11 bp):
AAAATGAACTA
Found at i:267 original size:24 final size:24
Alignment explanation
Indices: 238--289 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
228 ATGATATGCT
238 AAATGCAACATTAAAATGAACTAA
1 AAATGCAACATTAAAATGAACTAA
262 AAATGCAACATTAAAATGAACTAA
1 AAATGCAACATTAAAATGAACTAA
286 AAAT
1 AAAT
290 TTATGCAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.60, C:0.12, G:0.08, T:0.21
Consensus pattern (24 bp):
AAATGCAACATTAAAATGAACTAA
Found at i:279 original size:13 final size:13
Alignment explanation
Indices: 238--279 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
228 ATGATATGCT
238 AAATGCAACATTA
1 AAATGCAACATTA
*
251 AAATG-AAC-TAA
1 AAATGCAACATTA
262 AAATGCAACATTA
1 AAATGCAACATTA
275 AAATG
1 AAATG
280 AACTAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 7 0.28
12 6 0.24
13 12 0.48
ACGTcount: A:0.57, C:0.12, G:0.10, T:0.21
Consensus pattern (13 bp):
AAATGCAACATTA
Found at i:867 original size:51 final size:50
Alignment explanation
Indices: 629--1016 Score: 551
Period size: 50 Copynumber: 7.7 Consensus size: 50
619 CATTGAATTA
* *
629 TCTTCCAATCCAATATTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTG
1 TCTTCCAATTCAATTTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTG
*
679 TCTTCCAATTCTATTTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTG
1 TCTTCCAATTCAATTTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTG
* * ** * *
729 TCTTCCAATTCAATCTTAAAAAAAGGACCGCCTTTTGCTCATCCTCTGAACTG
1 TCTTCCAATTCAAT-TT--TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTG
* * * *
782 TCTTCCAATTCAATCTTAAAAAGACCGTCTTCCGCTCATCCTCTGAACTG
1 TCTTCCAATTCAATTTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTG
*
832 TCTTCCAATTCAATTTTGAAAAGGACCGTCTTCCGCTTATCCTTTTAACTG
1 TCTTCCAATTCAATTTT-AAAAGGACCGTCTTCCGCTTATCCTTTGAACTG
883 TCTTCCAATTCAATCTTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTG
1 TCTTCCAATTCAAT-TTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTG
* *
934 TCTACCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTG
1 TCTTCCAATTCAATTTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTG
* * **
984 TCTACCAATTCAATCTTAAAAGGATTGTCTTCC
1 TCTTCCAATTCAATTTTAAAAGGACCGTCTTCC
1017 AATCGTGTTT
Statistics
Matches: 307, Mismatches: 26, Indels: 10
0.90 0.08 0.03
Matches are distributed among these distances:
50 171 0.56
51 90 0.29
52 4 0.01
53 42 0.14
ACGTcount: A:0.26, C:0.28, G:0.11, T:0.36
Consensus pattern (50 bp):
TCTTCCAATTCAATTTTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTG
Found at i:1600 original size:124 final size:126
Alignment explanation
Indices: 1433--1777 Score: 412
Period size: 124 Copynumber: 2.7 Consensus size: 126
1423 CTTTTTAACA
* * * *
1433 AGATCGTCTTTCGATCAGCTTTTGAAGA-TTCTTGAGAAACCATCTTCTGGTGTACTTCTTGACA
1 AGATCGTCTTCCGATCATCTTCTGAAAACTT-TTGAGAAACCATCTTCTGGTGTACTTCTTGACA
*
1497 AGATCGTCTTCCGATCAACTTCTGAAAAACTTTTGAGAAG-C-T-TGACGTACTTCTTCGACT
65 AGATCGTCTTCCGATCATCTTCTG-AAAACTTTTGAGAAGCCTTCTGACGTACTTCTTCGACT
* * *
1557 AGATCGTCTTCCGATCATCTTCTGAAAACTTTTGAGAAGCCATCTTCTGGCGTACTTCTTCGACT
1 AGATCGTCTTCCGATCATCTTCTGAAAACTTTTGAGAAACCATCTTCTGGTGTACTTCTT-GACA
* *
1622 AGATCGTCTTCTGATCATCTTCTGAAAACTTTTGAGAAGCCATCTTCTGGCGTACTTCTTCGACT
65 AGATCGTCTTCCGATCATCTTCTGAAAACTTTTGAGAAG-C--CTTCTGACGTACTTCTTCGACT
* * *
1687 AGATCGTCTTCCGAACATCTTCTGAAAATTCTTTCT-AGCAAACCGTCTTCCGGTGTACTTCTTG
1 AGATCGTCTTCCGATCATCTTCTGAAAA--CTTT-TGAG-AAACCATCTTCTGGTGTACTTCTTG
** * *
1751 ATGAGATTGTCTTCCAATCATCTTCTG
62 ACAAGATCGTCTTCCGATCATCTTCTG
1778 CAAATTCTTT
Statistics
Matches: 189, Mismatches: 20, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
124 66 0.35
125 27 0.14
128 1 0.01
129 1 0.01
130 44 0.23
132 29 0.15
133 21 0.11
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (126 bp):
AGATCGTCTTCCGATCATCTTCTGAAAACTTTTGAGAAACCATCTTCTGGTGTACTTCTTGACAA
GATCGTCTTCCGATCATCTTCTGAAAACTTTTGAGAAGCCTTCTGACGTACTTCTTCGACT
Found at i:1615 original size:36 final size:36
Alignment explanation
Indices: 1575--1680 Score: 84
Period size: 36 Copynumber: 3.1 Consensus size: 36
1565 TTCCGATCAT
1575 CTTCTGAAAACTTTTGAGAAGCCATCTTCTGGCGTA
1 CTTCTGAAAACTTTTGAGAAGCCATCTTCTGGCGTA
*** * * * *
1611 CTTCT-TCGAC---T-AG-A-TCGTCTTCTGATCAT-
1 CTTCTGAAAACTTTTGAGAAGCCATCTTCTG-GCGTA
1640 CTTCTGAAAACTTTTGAGAAGCCATCTTCTGGCGTA
1 CTTCTGAAAACTTTTGAGAAGCCATCTTCTGGCGTA
1676 CTTCT
1 CTTCT
1681 TCGACTAGAT
Statistics
Matches: 47, Mismatches: 14, Indels: 18
0.59 0.18 0.23
Matches are distributed among these distances:
29 13 0.28
30 5 0.11
31 2 0.04
32 1 0.02
33 1 0.02
34 2 0.04
35 5 0.11
36 18 0.38
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.37
Consensus pattern (36 bp):
CTTCTGAAAACTTTTGAGAAGCCATCTTCTGGCGTA
Found at i:1638 original size:65 final size:65
Alignment explanation
Indices: 1362--1777 Score: 424
Period size: 65 Copynumber: 6.4 Consensus size: 65
1352 ATTTTTTTTA
* * * * *
1362 ACTAGACCGTCTTCCGATCAACTTCTTTGAAAACTGTTTGAGAAAACCATCTTCTGGTGTTCTT-
1 ACTAGATCGTCTTCCGATCATCTTC--TGAAAACT-TTTGAG-AAGCCATCTTCTGGCGTACTTC
**
1426 TTTA
62 TTCG
* * * * * * *
1430 ACAAGATCGTCTTTCGATCAGCTTTTGAAGA-TTCTTGAGAAACCATCTTCTGGTGTACTTCTT-
1 ACTAGATCGTCTTCCGATCATCTTCTGAAAACTT-TTGAGAAGCCATCTTCTGGCGTACTTCTTC
1493 G
65 G
* * *
1494 ACAAGATCGTCTTCCGATCAACTTCTGAAAAACTTTTGAGAAG----C-T-TGACGTACTTCTTC
1 ACTAGATCGTCTTCCGATCATCTTCTG-AAAACTTTTGAGAAGCCATCTTCTGGCGTACTTCTTC
1553 G
65 G
1554 ACTAGATCGTCTTCCGATCATCTTCTGAAAACTTTTGAGAAGCCATCTTCTGGCGTACTTCTTCG
1 ACTAGATCGTCTTCCGATCATCTTCTGAAAACTTTTGAGAAGCCATCTTCTGGCGTACTTCTTCG
*
1619 ACTAGATCGTCTTCTGATCATCTTCTGAAAACTTTTGAGAAGCCATCTTCTGGCGTACTTCTTCG
1 ACTAGATCGTCTTCCGATCATCTTCTGAAAACTTTTGAGAAGCCATCTTCTGGCGTACTTCTTCG
* * * * *
1684 ACTAGATCGTCTTCCGAACATCTTCTGAAAATTCTTTCT-AGCAAACCGTCTTCCGGTGTACTTC
1 ACTAGATCGTCTTCCGATCATCTTCTGAAAA--CTTT-TGAG-AAGCCATCTTCTGGCGTACTTC
1748 TT-G
62 TTCG
* *
1751 A-TGAGATTGTCTTCCAATCATCTTCTG
1 ACT-AGATCGTCTTCCGATCATCTTCTG
1778 CAAATTCTTT
Statistics
Matches: 304, Mismatches: 28, Indels: 33
0.83 0.08 0.09
Matches are distributed among these distances:
59 26 0.09
60 27 0.09
61 1 0.00
63 1 0.00
64 46 0.15
65 125 0.41
66 8 0.03
67 29 0.10
68 41 0.13
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (65 bp):
ACTAGATCGTCTTCCGATCATCTTCTGAAAACTTTTGAGAAGCCATCTTCTGGCGTACTTCTTCG
Found at i:1775 original size:67 final size:68
Alignment explanation
Indices: 1543--1875 Score: 345
Period size: 67 Copynumber: 5.0 Consensus size: 68
1533 GAAGCTTGAC
* * *
1543 GTACTTCTTCGACTAGATCGTCTTCCGATCATCTTCTGAAAA--CTTT-TGAG-AAGCCATCTTC
1 GTACTTCTTCGACTAGATCGTCTTCCAATCATCTTCTGAAAATTCTTTCT-AGCAAACCGTCTTC
*
1604 TGGC
65 TGGT
** * *
1608 GTACTTCTTCGACTAGATCGTCTTCTGATCATCTTCTGAAAA--CTTT-TGAG-AAGCCATCTTC
1 GTACTTCTTCGACTAGATCGTCTTCCAATCATCTTCTGAAAATTCTTTCT-AGCAAACCGTCTTC
*
1669 TGGC
65 TGGT
1673 GTACTTCTTCGACTAGATCGTCTTCCGAA-CATCTTCTGAAAATTCTTTCTAGCAAACCGTCTTC
1 GTACTTCTTCGACTAGATCGTCTTCC-AATCATCTTCTGAAAATTCTTTCTAGCAAACCGTCTTC
*
1737 CGGT
65 TGGT
* *
1741 GTACTTCTT-GA-TGAGATTGTCTTCCAATCATCTTCTGCAAATTCTTTCTAGCAAACCGTCTTC
1 GTACTTCTTCGACT-AGATCGTCTTCCAATCATCTTCTGAAAATTCTTTCTAGCAAACCGTCTTC
1804 TGGT
65 TGGT
* * * *
1808 GTA-TTCCTT--AATAAGATTGTCTTCCAATCAGCATT-TGAACATTCTTTCTAGCAAACCGTCT
1 GTACTT-CTTCGACT-AGATCGTCTTCCAATCATC-TTCTGAAAATTCTTTCTAGCAAACCGTCT
*
1869 TCCGGT
63 TCTGGT
1875 G
1 G
1876 CATTTTGATT
Statistics
Matches: 243, Mismatches: 15, Indels: 18
0.88 0.05 0.07
Matches are distributed among these distances:
65 102 0.42
66 7 0.03
67 111 0.46
68 23 0.09
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.37
Consensus pattern (68 bp):
GTACTTCTTCGACTAGATCGTCTTCCAATCATCTTCTGAAAATTCTTTCTAGCAAACCGTCTTCT
GGT
Found at i:3691 original size:12 final size:11
Alignment explanation
Indices: 3674--3721 Score: 78
Period size: 12 Copynumber: 4.2 Consensus size: 11
3664 TTAATTCGCT
3674 TTTGATTTGAA
1 TTTGATTTGAA
3685 CTTTGATTTGAA
1 -TTTGATTTGAA
3697 TTTCGATTTGAA
1 TTT-GATTTGAA
3709 TTTGATTTGAA
1 TTTGATTTGAA
3720 TT
1 TT
3722 ACTTAACGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
11 13 0.37
12 22 0.63
ACGTcount: A:0.25, C:0.04, G:0.17, T:0.54
Consensus pattern (11 bp):
TTTGATTTGAA
Found at i:3716 original size:23 final size:24
Alignment explanation
Indices: 3677--3721 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
3667 ATTCGCTTTT
3677 GATTTGAACTTTGATTTGAATTTC
1 GATTTGAACTTTGATTTGAATTTC
3701 GATTTGAA-TTTGATTTGAATT
1 GATTTGAACTTTGATTTGAATT
3722 ACTTAACGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.27, C:0.04, G:0.18, T:0.51
Consensus pattern (24 bp):
GATTTGAACTTTGATTTGAATTTC
Done.