Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018731.1 Corchorus olitorius cultivar O-4 contig18764, 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: 59023
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:686 original size:16 final size:16
Alignment explanation
Indices: 667--697 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
657 ATTATCCTTT
*
667 TTTATATTTATATATG
1 TTTATATATATATATG
683 TTTATATATATATAT
1 TTTATATATATATAT
698 ATACACCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
TTTATATATATATATG
Found at i:5448 original size:44 final size:44
Alignment explanation
Indices: 5388--5476 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 44
5378 TTGTGCAATT
* *
5388 TTATTATAAAATAAATGGCAAACTTCAACTACCAACTAGATCTA
1 TTATTAAAAAAAAAATGGCAAACTTCAACTACCAACTAGATCTA
*
5432 TTATTAAAAAAAAAATGGCAAACTTCAACTACCTACTAGATCTA
1 TTATTAAAAAAAAAATGGCAAACTTCAACTACCAACTAGATCTA
5476 T
1 T
5477 AATCGTGTGT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.46, C:0.18, G:0.07, T:0.29
Consensus pattern (44 bp):
TTATTAAAAAAAAAATGGCAAACTTCAACTACCAACTAGATCTA
Found at i:7437 original size:29 final size:31
Alignment explanation
Indices: 7405--7475 Score: 119
Period size: 32 Copynumber: 2.3 Consensus size: 31
7395 TGTCTGTGTG
7405 AGAAAAATAAGGTG-TTTTTTTGGC-CAAAA
1 AGAAAAATAAGGTGTTTTTTTTGGCACAAAA
7434 AGAAAAATAAGGTGTTTTTTTTTGGCACAAAA
1 AGAAAAATAAGGTG-TTTTTTTTGGCACAAAA
7466 AGAAAAATAA
1 AGAAAAATAA
7476 AGAAAAATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
29 14 0.36
31 10 0.26
32 15 0.38
ACGTcount: A:0.46, C:0.06, G:0.18, T:0.30
Consensus pattern (31 bp):
AGAAAAATAAGGTGTTTTTTTTGGCACAAAA
Found at i:11963 original size:80 final size:80
Alignment explanation
Indices: 11831--11983 Score: 236
Period size: 80 Copynumber: 1.9 Consensus size: 80
11821 CCAACACAGG
** *
11831 ACCTAGCACATTGAACAGGACAACTTACAAGCATCCAACAACAGAAACAAAAT-TGAGAACAGGA
1 ACCTAGCACATCAAACAGGAAAACTTACAAGCATCCAACAACAGAAACAAAATATGAGAACAGGA
11895 CAGAAACAGAGCCTA
66 CAGAAACAGAGCCTA
* * *
11910 ACCTAGCACATCAAACAGGAAAACTTTACAAGCATCCAACAACGGGAACAAAATATGTGAACAGG
1 ACCTAGCACATCAAACAGGAAAAC-TTACAAGCATCCAACAACAGAAACAAAATATGAGAACAGG
11975 ACAGAAACA
65 ACAGAAACA
11984 TAAACCAAGA
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
79 21 0.32
80 27 0.41
81 18 0.27
ACGTcount: A:0.48, C:0.24, G:0.16, T:0.12
Consensus pattern (80 bp):
ACCTAGCACATCAAACAGGAAAACTTACAAGCATCCAACAACAGAAACAAAATATGAGAACAGGA
CAGAAACAGAGCCTA
Found at i:12003 original size:80 final size:79
Alignment explanation
Indices: 11844--12012 Score: 200
Period size: 80 Copynumber: 2.1 Consensus size: 79
11834 TAGCACATTG
* * *
11844 AACAGGACAACTTACAAGCATCCAACAACAGAAACAAAATTGAGAACAGGACAGAAACAGAGCCT
1 AACAGGAAAACTTACAAGCATCCAACAACAGAAACAAAATTGAGAACAGGACAGAAACAAAACCT
* *
11909 AACCTAGCACATCA
66 AAACTAGCAAATCA
* * *
11923 AACAGGAAAACTTTACAAGCATCCAACAACGGGAACAAAATATGTGAACAGGACAGAAACATAAA
1 AACAGGAAAAC-TTACAAGCATCCAACAACAGAAACAAAAT-TGAGAACAGGACAGAAACA-AAA
11988 CC-AAGAC-AG-AAATCA
63 CCTAA-ACTAGCAAATCA
*
12003 AACAGCAAAA
1 AACAGGAAAA
12013 AGGCAAAATA
Statistics
Matches: 77, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
79 10 0.13
80 41 0.53
81 22 0.29
82 4 0.05
ACGTcount: A:0.52, C:0.22, G:0.15, T:0.10
Consensus pattern (79 bp):
AACAGGAAAACTTACAAGCATCCAACAACAGAAACAAAATTGAGAACAGGACAGAAACAAAACCT
AAACTAGCAAATCA
Found at i:15522 original size:18 final size:18
Alignment explanation
Indices: 15487--15528 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
15477 GCCGAGAAGG
*
15487 GAAGA-AGAAGAACTGAA
1 GAAGAGAGAAGAACGGAA
*
15504 GAAGAGAGAAGAAGGGAA
1 GAAGAGAGAAGAACGGAA
15522 G-AGAGAG
1 GAAGAGAG
15529 GTCGGGGTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.55, C:0.02, G:0.40, T:0.02
Consensus pattern (18 bp):
GAAGAGAGAAGAACGGAA
Found at i:17792 original size:28 final size:30
Alignment explanation
Indices: 17718--17792 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 30
17708 TTAATGCCCT
* *
17718 TTTTACCCCCTGAACTTCTATGATTTTGACG
1 TTTTGCCCCCTGAACTTCTA-GATTGTGACG
*
17749 TTTTGCCCCCTAAACTT-TA-ATTGTGAACG
1 TTTTGCCCCCTGAACTTCTAGATTGTG-ACG
17778 -TTTGCCCCCTGAACT
1 TTTTGCCCCCTGAACT
17793 CGCAATTTGG
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
28 19 0.49
29 3 0.08
30 2 0.05
31 15 0.38
ACGTcount: A:0.20, C:0.28, G:0.13, T:0.39
Consensus pattern (30 bp):
TTTTGCCCCCTGAACTTCTAGATTGTGACG
Found at i:21890 original size:8 final size:8
Alignment explanation
Indices: 21877--21907 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
21867 CCTAAGTAAA
21877 AAACAAAG
1 AAACAAAG
21885 AAACAAAG
1 AAACAAAG
21893 AAACAAAG
1 AAACAAAG
21901 AAACAAA
1 AAACAAA
21908 ACTGAAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.77, C:0.13, G:0.10, T:0.00
Consensus pattern (8 bp):
AAACAAAG
Found at i:23021 original size:16 final size:16
Alignment explanation
Indices: 23002--23045 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
22992 ACCCGTCCGA
*
23002 ACCCGAACCCGAAATT
1 ACCCGAACCCGAAAAT
*
23018 ACCCGAGCCCGAAAAT
1 ACCCGAACCCGAAAAT
23034 ACCCGAACCCGA
1 ACCCGAACCCGA
23046 GGCAGCCCGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.36, C:0.41, G:0.16, T:0.07
Consensus pattern (16 bp):
ACCCGAACCCGAAAAT
Found at i:23876 original size:13 final size:12
Alignment explanation
Indices: 23840--23886 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
23830 TCAATCTTTA
*
23840 TATATATTGATAA
1 TATATATT-ATAT
*
23853 TA-ATGTTATAT
1 TATATATTATAT
23864 TATATTATTATAT
1 TATA-TATTATAT
23877 TATATATTAT
1 TATATATTAT
23887 CAATAAACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:24082 original size:16 final size:15
Alignment explanation
Indices: 24061--24149 Score: 79
Period size: 16 Copynumber: 5.7 Consensus size: 15
24051 TACCCGAGAT
24061 CGAACCCGAAAATACC
1 CGAACCCG-AAATACC
*
24077 CGAACCCGACATAACC
1 CGAACCCGAAAT-ACC
* **
24093 CGAGCCCGACTTAACC
1 CGAACCCGAAAT-ACC
*
24109 CGAATCCGAAAATACC
1 CGAACCCG-AAATACC
*
24125 CGAACCCGAAGTACC
1 CGAACCCGAAATACC
*
24140 CGTACCCGAA
1 CGAACCCGAA
24150 CCCGCCCGAG
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
15 18 0.30
16 41 0.67
17 2 0.03
ACGTcount: A:0.36, C:0.39, G:0.16, T:0.09
Consensus pattern (15 bp):
CGAACCCGAAATACC
Found at i:28288 original size:17 final size:17
Alignment explanation
Indices: 28268--28310 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
28258 ACGTTCCACT
*
28268 TCTCTTCTTCATCCAAG
1 TCTCTTCTCCATCCAAG
28285 TCTCTTCTCCATCCAAG
1 TCTCTTCTCCATCCAAG
28302 TCTCTTCTC
1 TCTCTTCTC
28311 AATCTCTTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.14, C:0.40, G:0.05, T:0.42
Consensus pattern (17 bp):
TCTCTTCTCCATCCAAG
Found at i:29274 original size:18 final size:19
Alignment explanation
Indices: 29251--29286 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
29241 CTGATTTAGC
29251 ATTTATTCTT-ATATAATT
1 ATTTATTCTTCATATAATT
*
29269 ATTTATTGTTCATATAAT
1 ATTTATTCTTCATATAAT
29287 GAAATTTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (19 bp):
ATTTATTCTTCATATAATT
Found at i:29454 original size:35 final size:35
Alignment explanation
Indices: 29408--29478 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
29398 ATAAAACATA
29408 ATTTTATTTTATAATATTCTTGGGTCATTCAGGTT
1 ATTTTATTTTATAATATTCTTGGGTCATTCAGGTT
29443 ATTTTATTTTATAATATTCTTGGGTCATTCAGGTT
1 ATTTTATTTTATAATATTCTTGGGTCATTCAGGTT
29478 A
1 A
29479 ACTATTCGGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.24, C:0.08, G:0.14, T:0.54
Consensus pattern (35 bp):
ATTTTATTTTATAATATTCTTGGGTCATTCAGGTT
Found at i:29864 original size:23 final size:24
Alignment explanation
Indices: 29818--29869 Score: 70
Period size: 27 Copynumber: 2.1 Consensus size: 24
29808 GTCAATTAAT
29818 ATGTATATATTTTACTTAATTAAAAAA
1 ATGTATATATTTTAC---ATTAAAAAA
29845 ATGTATATATTTTAC-TTAAAAAA
1 ATGTATATATTTTACATTAAAAAA
29868 AT
1 AT
29870 CAATATGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 10 0.40
27 15 0.60
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (24 bp):
ATGTATATATTTTACATTAAAAAA
Found at i:29882 original size:23 final size:23
Alignment explanation
Indices: 29837--29882 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
29827 TTTTACTTAA
** *
29837 TTAAAAAAATGTATATATTTTAC
1 TTAAAAAAATCAATATATATTAC
*
29860 TTAAAAAAATCAATATGTATTAC
1 TTAAAAAAATCAATATATATTAC
29883 ATATAATAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (23 bp):
TTAAAAAAATCAATATATATTAC
Found at i:42567 original size:13 final size:13
Alignment explanation
Indices: 42549--42575 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42539 TGTTGTGGTC
42549 ACTCCTTATAATG
1 ACTCCTTATAATG
42562 ACTCCTTATAATG
1 ACTCCTTATAATG
42575 A
1 A
42576 TACAATGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.37
Consensus pattern (13 bp):
ACTCCTTATAATG
Found at i:47728 original size:30 final size:30
Alignment explanation
Indices: 47692--47761 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 30
47682 TAATGTTCAG
47692 CTTCAATCTTGATGTGTTCAAATAAGCCTA
1 CTTCAATCTTGATGTGTTCAAATAAGCCTA
* * *
47722 CTTCAATCTTGATGTGTTGAACTAAGGCTA
1 CTTCAATCTTGATGTGTTCAAATAAGCCTA
47752 CTTCAATCTT
1 CTTCAATCTT
47762 TCTTAACTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (30 bp):
CTTCAATCTTGATGTGTTCAAATAAGCCTA
Found at i:49402 original size:21 final size:21
Alignment explanation
Indices: 49364--49404 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
49354 GGCCCAAGTA
* *
49364 TGCAACCACCATTTGAGGAGG
1 TGCAACCACCAGTAGAGGAGG
*
49385 TGCAACCACCGGTAGAGGAG
1 TGCAACCACCAGTAGAGGAG
49405 AAAGTTCCTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.32, T:0.15
Consensus pattern (21 bp):
TGCAACCACCAGTAGAGGAGG
Found at i:54967 original size:35 final size:35
Alignment explanation
Indices: 54920--54990 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
54910 ATAAAACTTA
54920 AAGCATGCTGTGATATTTTTAATGTAAGTATTTTG
1 AAGCATGCTGTGATATTTTTAATGTAAGTATTTTG
* *
54955 AAGCATGTTGTGATATTTTTTATGTAAGTATTTTG
1 AAGCATGCTGTGATATTTTTAATGTAAGTATTTTG
54990 A
1 A
54991 TATATTTGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.28, C:0.04, G:0.20, T:0.48
Consensus pattern (35 bp):
AAGCATGCTGTGATATTTTTAATGTAAGTATTTTG
Found at i:59000 original size:13 final size:13
Alignment explanation
Indices: 58967--59019 Score: 60
Period size: 12 Copynumber: 4.4 Consensus size: 13
58957 GCACCCAAAA
*
58967 CATTTAT-TAAAA
1 CATTTATATAAAG
58979 CATTT-TATAAAG
1 CATTTATATAAAG
58991 CATTTATATAAAG
1 CATTTATATAAAG
*
59004 CAGTTATA-AAA-
1 CATTTATATAAAG
59015 CATTT
1 CATTT
59020 CCTC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
11 5 0.14
12 17 0.47
13 14 0.39
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40
Consensus pattern (13 bp):
CATTTATATAAAG
Done.