Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022620.1 Corchorus olitorius cultivar O-4 contig22653, 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: 27398
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:1901 original size:58 final size:58
Alignment explanation
Indices: 1810--2206 Score: 634
Period size: 58 Copynumber: 6.8 Consensus size: 58
1800 TCCTTTTGAC
* * *
1810 CTGTCTTCAGGTCTTAGTCTTAAAATCTTTTAGGAACTGTCTTCAGATCAATCTGTGAG
1 CTGTCTTCA-GCCTTAATCTTAAAATCTTTTAGGAACTGTCTTCAGATCCATCTGTGAG
*
1869 CTGTCTTCAGCCTTAATCTTAAAATCTTTTAGGAACTGTCTTCAGATCCGTCTGTGAG
1 CTGTCTTCAGCCTTAATCTTAAAATCTTTTAGGAACTGTCTTCAGATCCATCTGTGAG
* * * *
1927 CTGTCTTCAGTCTCAATCTTAAAATCTTTTAGGAACTGTCCTCAGATCCATCTGTAAG
1 CTGTCTTCAGCCTTAATCTTAAAATCTTTTAGGAACTGTCTTCAGATCCATCTGTGAG
* *
1985 CTGTCTTCAGCCTTAATCTCAAAATCTTTTAGGAACTGTCCTCAGATCCATCTGTGAG
1 CTGTCTTCAGCCTTAATCTTAAAATCTTTTAGGAACTGTCTTCAGATCCATCTGTGAG
* *
2043 CTGTCTTCAGCCTTAATCTTAAAATCTTTTAGGAACTATCCTCAGATCCATCTGTGAG
1 CTGTCTTCAGCCTTAATCTTAAAATCTTTTAGGAACTGTCTTCAGATCCATCTGTGAG
* *
2101 CTGTCTTCA-CTCTCAATCTTAAAATCTTCTAGGAACTGTCTTCAGATCCATCTGTGAG
1 CTGTCTTCAGC-CTTAATCTTAAAATCTTTTAGGAACTGTCTTCAGATCCATCTGTGAG
*
2159 CTGTCTTCAGCCTTAATCTTAAAATCTTCTAGGAACTGTCTTCAGATC
1 CTGTCTTCAGCCTTAATCTTAAAATCTTTTAGGAACTGTCTTCAGATC
2207 TATTTCTGAT
Statistics
Matches: 316, Mismatches: 20, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
57 1 0.00
58 305 0.97
59 10 0.03
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (58 bp):
CTGTCTTCAGCCTTAATCTTAAAATCTTTTAGGAACTGTCTTCAGATCCATCTGTGAG
Found at i:3708 original size:19 final size:19
Alignment explanation
Indices: 3684--3721 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3674 AGTGTAATCA
3684 TCGCCCTCTGGCATGTTGC
1 TCGCCCTCTGGCATGTTGC
3703 TCGCCCTCTGGCATGTTGC
1 TCGCCCTCTGGCATGTTGC
3722 CCCCAGTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.05, C:0.37, G:0.26, T:0.32
Consensus pattern (19 bp):
TCGCCCTCTGGCATGTTGC
Found at i:7079 original size:41 final size:41
Alignment explanation
Indices: 7018--7338 Score: 316
Period size: 42 Copynumber: 7.9 Consensus size: 41
7008 AAAATCTTTA
7018 ATGGGATCTTTCCCCT-AATTGAAAACTTTGAAAAAGACTAG
1 ATGGGATCTTT-CCCTAAATTGAAAACTTTGAAAAAGACTAG
*
7059 ATGGGATCTTTCCCTAAATTGAAAAC-TTG--AAA-ACTCG
1 ATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAAGACTAG
* * * * *
7096 ACGGGATCTTTCCATAAATTTAAAATTTTGAAGAAGACTAG
1 ATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAAGACTAG
*
7137 ATGGGATCTTTCCCTAAATT-AAAACTCTGAAAAAGAC-AGG
1 ATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAAGACTA-G
* ** *
7177 ATGGGATCTTTCCCTAAATT-AAAGGCTTTTGAAAACTACTTG
1 ATGGGATCTTTCCCTAAATTGAAA-AC-TTTGAAAAAGACTAG
** * *
7219 AAAGGATCTTTCCCTAAATTGAAAACTTTGAAAAATACTTTG
1 ATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAAGAC-TAG
* * * * * *
7261 GTGGGATCTTTCCCTAATTTGAAATCTTTAAAAAAATACTTTG
1 ATGGGATCTTTCCCTAAATTGAAAACTTT-GAAAAAGAC-TAG
* *
7304 GTGGGATCTTTCCCTAAATTGATAACTTTGAAAAA
1 ATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAA
7339 ACTTGATTTT
Statistics
Matches: 237, Mismatches: 31, Indels: 23
0.81 0.11 0.08
Matches are distributed among these distances:
37 26 0.11
38 6 0.03
39 1 0.00
40 47 0.20
41 55 0.23
42 61 0.26
43 41 0.17
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (41 bp):
ATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAAGACTAG
Found at i:7310 original size:43 final size:41
Alignment explanation
Indices: 7019--7339 Score: 189
Period size: 41 Copynumber: 7.8 Consensus size: 41
7009 AAATCTTTAA
* * * *
7019 TGGGATCTTTCCCCT-AATTGAAAACTTTGAAAAAGAC-TAGA
1 TGGGATCTTT-CCCTAAATTG-AAACTTTAAAAAATACTTTGG
* * *
7060 TGGGATCTTTCCCTAAATTGAAAAC-TT--GAAA-AC-TCGA
1 TGGGATCTTTCCCTAAATTG-AAACTTTAAAAAATACTTTGG
* * * * * * * * *
7097 CGGGATCTTTCCATAAATTTAAAATTTTGAAGAAGAC-TAGA
1 TGGGATCTTTCCCTAAA-TTGAAACTTTAAAAAATACTTTGG
* * * * *
7138 TGGGATCTTTCCCTAAATTAAAACTCTGAAAAAGAC--AGG
1 TGGGATCTTTCCCTAAATTGAAACTTTAAAAAATACTTTGG
* * *
7177 ATGGGATCTTTCCCTAAATT-AAAGGCTTTTGAAAACTAC-TTGA
1 -TGGGATCTTTCCCTAAATTGAAA--C-TTTAAAAAATACTTTGG
** *
7220 AAGGATCTTTCCCTAAATTGAAAACTTTGAAAAATACTTTGG
1 TGGGATCTTTCCCTAAATTG-AAACTTTAAAAAATACTTTGG
*
7262 TGGGATCTTTCCCTAATTTGAAATCTTTAAAAAAATACTTTGG
1 TGGGATCTTTCCCTAAATTGAAA-CTTT-AAAAAATACTTTGG
7305 TGGGATCTTTCCCTAAATTGATAACTTTGAAAAAA
1 TGGGATCTTTCCCTAAATTGA-AACTTT-AAAAAA
7340 CTTGATTTTT
Statistics
Matches: 233, Mismatches: 30, Indels: 32
0.79 0.10 0.11
Matches are distributed among these distances:
37 23 0.10
38 7 0.03
39 5 0.02
40 43 0.18
41 55 0.24
42 51 0.22
43 44 0.19
44 5 0.02
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (41 bp):
TGGGATCTTTCCCTAAATTGAAACTTTAAAAAATACTTTGG
Found at i:7331 original size:85 final size:84
Alignment explanation
Indices: 7018--7342 Score: 266
Period size: 78 Copynumber: 4.0 Consensus size: 84
7008 AAAATCTTTA
* * * *
7018 ATGGGATCTTTCCCCT-AATTGAAA-ACTTT-GAAAAAGACTAGATGGGATCTTTCCCTAAATTG
1 ATGGGATCTTT-CCCTAAATT-AAAGGCTTTAAAAAAATACTTGATGGGATCTTTCCCTAAATTG
*
7080 AAAAC-TTG--AAAAC-T-CG
64 AAAACTTTGAAAAAACTTAGG
* * * ** * * *
7096 ACGGGATCTTTCCATAAATTTAAA--ATTTTGAAGAAGACTAGATGGGATCTTTCCCTAAATT-A
1 ATGGGATCTTTCCCTAAA-TTAAAGGCTTTAAAAAAATACTTGATGGGATCTTTCCCTAAATTGA
*
7158 AAACTCTGAAAAAGAC--AGG
65 AAACTTTGAAAAA-ACTTAGG
** * **
7177 ATGGGATCTTTCCCTAAATTAAAGGCTTTTGAAAACTACTTGAAAGGATCTTTCCCTAAATTGAA
1 ATGGGATCTTTCCCTAAATTAAAGGCTTTAAAAAAATACTTGATGGGATCTTTCCCTAAATTGAA
*
7242 AACTTTGAAAAATACTTTGG
66 AACTTTGAAAAA-ACTTAGG
* * *
7262 -TGGGATCTTTCCCTAATTTGAAA-TCTTTAAAAAAATACTTTGGTGGGATCTTTCCCTAAATTG
1 ATGGGATCTTTCCCTAAATT-AAAGGCTTTAAAAAAATAC-TTGATGGGATCTTTCCCTAAATTG
*
7325 ATAACTTTGAAAAAACTT
64 AAAACTTTGAAAAAACTT
7343 GATTTTTGAT
Statistics
Matches: 205, Mismatches: 27, Indels: 24
0.80 0.11 0.09
Matches are distributed among these distances:
77 11 0.05
78 48 0.23
79 2 0.01
80 8 0.04
81 19 0.09
82 30 0.15
83 15 0.07
84 33 0.16
85 39 0.19
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (84 bp):
ATGGGATCTTTCCCTAAATTAAAGGCTTTAAAAAAATACTTGATGGGATCTTTCCCTAAATTGAA
AACTTTGAAAAAACTTAGG
Found at i:7434 original size:31 final size:30
Alignment explanation
Indices: 7396--7599 Score: 143
Period size: 31 Copynumber: 6.7 Consensus size: 30
7386 AAAGGCTAAT
7396 TGCTCAAATAAGGGCCTAACATTTGCCAAAA
1 TGCTCAAATAAGGGCCTAACATTTG-CAAAA
*
7427 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAACATTTG-CAAAA
* * * **
7458 TGCTCAAATAAGGGCCCGATC-TTT-TAATT
1 TGCTCAAATAAGGG-CCTAACATTTGCAAAA
*
7487 TGAC-CAAATAAGGGCCTAACGTTATTG-AAAA
1 TG-CTCAAATAAGGGCCTAAC-AT-TTGCAAAA
* * * * **
7518 TGCTCAAATAAGGACCCGATC-TTT-TAATT
1 TGCTCAAATAAGG-GCCTAACATTTGCAAAA
7547 TGGC-CAAATAAGGGCCTAACATTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACATTTG-CAAAA
* *
7578 TGTTCAAATAAGGGCCTGACAT
1 TGCTCAAATAAGGGCCTAACAT
7600 CAGTTTGGAT
Statistics
Matches: 136, Mismatches: 23, Indels: 28
0.73 0.12 0.15
Matches are distributed among these distances:
28 8 0.06
29 31 0.23
30 7 0.05
31 82 0.60
32 8 0.06
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAACATTTGCAAAA
Found at i:7506 original size:60 final size:60
Alignment explanation
Indices: 7431--7593 Score: 258
Period size: 60 Copynumber: 2.7 Consensus size: 60
7421 CCAAAATGCT
7431 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
* *
7491 CAAATAAGGGCCTAACGTTATTG--AAAATGCTCAAATAAGGACCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACG-T-TTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
* *
7551 CAAATAAGGGCCTAACATTTGCCAAAATGTTCAAATAAGGGCC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
7594 TGACATCAGT
Statistics
Matches: 94, Mismatches: 5, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
58 3 0.03
59 1 0.01
60 86 0.91
61 1 0.01
62 3 0.03
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
Found at i:7559 original size:29 final size:28
Alignment explanation
Indices: 7462--7559 Score: 81
Period size: 29 Copynumber: 3.3 Consensus size: 28
7452 CCAAAATGCT
*
7462 CAAATAAGGGCCCGATCTTTTAATTTGAC
1 CAAATAA-GGCCCGATCTTTTAATTTGGC
* * * **
7491 CAAATAAGGGCCTAACGTTATTGAAAAT-GC
1 CAAATAAGGCCCGATC-TT-TT-AATTTGGC
7521 TCAAATAAGGACCCGATCTTTTAATTTGGC
1 -CAAATAAGG-CCCGATCTTTTAATTTGGC
7551 CAAATAAGG
1 CAAATAAGG
7560 GCCTAACATT
Statistics
Matches: 52, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
28 6 0.12
29 21 0.40
30 7 0.13
31 14 0.27
32 4 0.08
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (28 bp):
CAAATAAGGCCCGATCTTTTAATTTGGC
Found at i:7671 original size:31 final size:31
Alignment explanation
Indices: 7632--7800 Score: 129
Period size: 31 Copynumber: 5.6 Consensus size: 31
7622 TTTTCGATAC
7632 CAGGCCCTTATTTGAGCATTTTGGCAAACGT
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGT
* ** * *
7663 CAGACCCTTATTTG-GCCAAATT---AAAAGAC
1 CAGGCCCTTATTTGAG-CATTTTGGCAAACG-T
*
7692 CGGGCCCTTATTTGAGCATTTTGGCAAACGT
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGT
* ** *
7723 TAGGCCCTTATTTG-GCCAAATT---AAAAGAT
1 CAGGCCCTTATTTGAG-CATTTTGGCAAACG-T
7752 CAGGCCCTTATTTGAGCATTTTGGCAAACGT
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGT
* * *
7783 TAGACCCTAATTTGAGCA
1 CAGGCCCTTATTTGAGCA
7801 ATTAGCCTTT
Statistics
Matches: 103, Mismatches: 23, Indels: 24
0.69 0.15 0.16
Matches are distributed among these distances:
28 8 0.08
29 34 0.33
30 4 0.04
31 49 0.48
32 8 0.08
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (31 bp):
CAGGCCCTTATTTGAGCATTTTGGCAAACGT
Found at i:7705 original size:29 final size:28
Alignment explanation
Indices: 7667--7765 Score: 76
Period size: 29 Copynumber: 3.4 Consensus size: 28
7657 AAACGTCAGA
7667 CCCTTATTTGGCCAAATTAAAAGACCGGG
1 CCCTTATTTGGCCAAATTAAAAGA-CGGG
** **
7696 CCCTTATTTGAG-CATTTTGGCAA-ACGTTAGG
1 CCCTTATTTG-GCCAAATT-AAAAGACG---GG
*
7727 CCCTTATTTGGCCAAATTAAAAGATCAGG
1 CCCTTATTTGGCCAAATTAAAAGA-CGGG
7756 CCCTTATTTG
1 CCCTTATTTG
7766 AGCATTTTGG
Statistics
Matches: 53, Mismatches: 9, Indels: 16
0.68 0.12 0.21
Matches are distributed among these distances:
28 2 0.04
29 27 0.51
30 6 0.11
31 17 0.32
32 1 0.02
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.31
Consensus pattern (28 bp):
CCCTTATTTGGCCAAATTAAAAGACGGG
Found at i:7731 original size:60 final size:60
Alignment explanation
Indices: 7630--7796 Score: 289
Period size: 60 Copynumber: 2.8 Consensus size: 60
7620 AATTTTCGAT
*
7630 ACCAGGCCCTTATTTGAGCATTTTGGCAAACGTCAGACCCTTATTTGGCCAAATTAAAAG
1 ACCAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGACCCTTATTTGGCCAAATTAAAAG
* *
7690 ACCGGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAG
1 ACCAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGACCCTTATTTGGCCAAATTAAAAG
* *
7750 ATCAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGACCCTAATTTG
1 ACCAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGACCCTTATTTG
7797 AGCAATTAGC
Statistics
Matches: 100, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 100 1.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.31
Consensus pattern (60 bp):
ACCAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGACCCTTATTTGGCCAAATTAAAAG
Found at i:8373 original size:22 final size:21
Alignment explanation
Indices: 8330--8373 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
8320 AAATAACTAA
*
8330 AACAAACAAAGCCCAAATTAT
1 AACAAACAAAGCCCAAAGTAT
* *
8351 AACAAAGCCAAGCCTAAAGTAT
1 AACAAA-CAAAGCCCAAAGTAT
8373 A
1 A
8374 TATGTTAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.55, C:0.23, G:0.09, T:0.14
Consensus pattern (21 bp):
AACAAACAAAGCCCAAAGTAT
Found at i:20077 original size:19 final size:19
Alignment explanation
Indices: 20053--20089 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
20043 CTAACTAATT
20053 GCCAAAAAGCCAAAAACTA
1 GCCAAAAAGCCAAAAACTA
*
20072 GCCAAAGAGCCAAAAACT
1 GCCAAAAAGCCAAAAACT
20090 TTTATCAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.27, G:0.14, T:0.05
Consensus pattern (19 bp):
GCCAAAAAGCCAAAAACTA
Done.