Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016300.1 Corchorus olitorius cultivar O-4 contig16333, 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: 26689
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.31
Found at i:1610 original size:33 final size:32
Alignment explanation
Indices: 1566--1663 Score: 124
Period size: 33 Copynumber: 3.0 Consensus size: 32
1556 ACTTTGTGGC
*
1566 GGTGCCTCCCCAACAGGGCGACGCCGCCATGGT
1 GGTGCC-CCCCAACAGGGCGACACCGCCATGGT
*
1599 GGTGCCACCCCAACAGGGCGACACCGCCAAGGT
1 GGTGCC-CCCCAACAGGGCGACACCGCCATGGT
* **
1632 GGTGCCGCCCAAGTTGGGCGACACCGCCATGG
1 GGTGCCCCCCAA-CAGGGCGACACCGCCATGG
1664 CGACGCCGCC
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
32 5 0.09
33 52 0.91
ACGTcount: A:0.18, C:0.38, G:0.34, T:0.10
Consensus pattern (32 bp):
GGTGCCCCCCAACAGGGCGACACCGCCATGGT
Found at i:1672 original size:33 final size:33
Alignment explanation
Indices: 1614--1695 Score: 103
Period size: 33 Copynumber: 2.5 Consensus size: 33
1604 CACCCCAACA
* **
1614 GGGCGACACCGCCAAGGTGGTGCCGCCCAAGTT
1 GGGCGACACCGCCAAGGCGACGCCGCCCAAGTT
*
1647 GGGCGACACCGCCATGGCGACGCCGCCCAAGTT
1 GGGCGACACCGCCAAGGCGACGCCGCCCAAGTT
*
1680 -GGCGACGCCGCTCAAG
1 GGGCGACACCGC-CAAG
1696 TTGGCGACAC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
32 10 0.24
33 32 0.76
ACGTcount: A:0.18, C:0.37, G:0.35, T:0.10
Consensus pattern (33 bp):
GGGCGACACCGCCAAGGCGACGCCGCCCAAGTT
Found at i:1684 original size:18 final size:18
Alignment explanation
Indices: 1635--1742 Score: 106
Period size: 18 Copynumber: 6.3 Consensus size: 18
1625 CCAAGGTGGT
1635 GCCGCCCAAGTTGGGCGAC
1 GCCGCCCAAGTT-GGCGAC
*
1654 ACCG-CC-A--TGGCGAC
1 GCCGCCCAAGTTGGCGAC
1668 GCCGCCCAAGTTGGCGAC
1 GCCGCCCAAGTTGGCGAC
*
1686 GCCGCTCAAGTTGGCGAC
1 GCCGCCCAAGTTGGCGAC
*
1704 ACCG-CC-A--TGGCGAC
1 GCCGCCCAAGTTGGCGAC
1718 GCCGCCCAAGTTGGGCGAC
1 GCCGCCCAAGTT-GGCGAC
*
1737 ACCGCC
1 GCCGCC
1743 ATGGCAGTGT
Statistics
Matches: 73, Mismatches: 7, Indels: 18
0.74 0.07 0.18
Matches are distributed among these distances:
14 19 0.26
15 5 0.07
16 3 0.04
17 2 0.03
18 30 0.41
19 14 0.19
ACGTcount: A:0.18, C:0.40, G:0.32, T:0.10
Consensus pattern (18 bp):
GCCGCCCAAGTTGGCGAC
Found at i:1710 original size:50 final size:52
Alignment explanation
Indices: 1635--1742 Score: 184
Period size: 50 Copynumber: 2.1 Consensus size: 52
1625 CCAAGGTGGT
1635 GCCGCCCAAGTTGGGCGACACCGCCATGGCGACGCCGCCCAAGTT-GGCGAC
1 GCCGCCCAAGTTGGGCGACACCGCCATGGCGACGCCGCCCAAGTTGGGCGAC
*
1686 GCCGCTCAAGTT-GGCGACACCGCCATGGCGACGCCGCCCAAGTTGGGCGAC
1 GCCGCCCAAGTTGGGCGACACCGCCATGGCGACGCCGCCCAAGTTGGGCGAC
*
1737 ACCGCC
1 GCCGCC
1743 ATGGCAGTGT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
50 32 0.60
51 21 0.40
ACGTcount: A:0.18, C:0.40, G:0.32, T:0.10
Consensus pattern (52 bp):
GCCGCCCAAGTTGGGCGACACCGCCATGGCGACGCCGCCCAAGTTGGGCGAC
Found at i:1740 original size:33 final size:33
Alignment explanation
Indices: 1679--1767 Score: 128
Period size: 33 Copynumber: 2.7 Consensus size: 33
1669 CCGCCCAAGT
*
1679 TGGCGACGCCGCTCAAGTT-GGCGACACCGCCA
1 TGGCGACGCCGCCCAAGTTGGGCGACACCGCCA
1711 TGGCGACGCCGCCCAAGTTGGGCGACACCGCCA
1 TGGCGACGCCGCCCAAGTTGGGCGACACCGCCA
* *
1744 TGGC-AGTGTCGCCCAAGTTGGGCG
1 TGGCGA-CGCCGCCCAAGTTGGGCG
1768 GCGTCACCAT
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 19 0.37
33 33 0.63
ACGTcount: A:0.17, C:0.35, G:0.35, T:0.13
Consensus pattern (33 bp):
TGGCGACGCCGCCCAAGTTGGGCGACACCGCCA
Found at i:1790 original size:33 final size:33
Alignment explanation
Indices: 1686--1790 Score: 88
Period size: 33 Copynumber: 3.2 Consensus size: 33
1676 AGTTGGCGAC
* * * *
1686 GCCGCTCAAGTT-GGCGACACCGCCATGGC-GAC
1 GCCGCCCAAGTTGGGCGACACCACCATAGCAG-T
* *
1718 GCCGCCCAAGTTGGGCGACACCGCCATGGCAGT
1 GCCGCCCAAGTTGGGCGACACCACCATAGCAGT
* * ** *
1751 GTCGCCCAAGTTGGGCGGCGTCACCATAGCGGT
1 GCCGCCCAAGTTGGGCGACACCACCATAGCAGT
1784 GCCGCCC
1 GCCGCCC
1791 CCCTGGGGCG
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
32 11 0.18
33 49 0.80
34 1 0.02
ACGTcount: A:0.16, C:0.37, G:0.33, T:0.13
Consensus pattern (33 bp):
GCCGCCCAAGTTGGGCGACACCACCATAGCAGT
Found at i:1940 original size:19 final size:19
Alignment explanation
Indices: 1916--1954 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1906 TATGATGTTC
1916 TTGAAGAAGTTTAGAGAGT
1 TTGAAGAAGTTTAGAGAGT
*
1935 TTGAAGAAGTTTTGAGAGT
1 TTGAAGAAGTTTAGAGAGT
1954 T
1 T
1955 AGAAAATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.31, T:0.36
Consensus pattern (19 bp):
TTGAAGAAGTTTAGAGAGT
Found at i:3837 original size:56 final size:57
Alignment explanation
Indices: 3751--3862 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 57
3741 CTGTTTCCTA
3751 TCACACAATAAATGTTATAATAAATCCTATC-CCCCTATCTCTACTTAATTATTCTT
1 TCACACAATAAATGTTATAATAAATCCTATCTCCCCTATCTCTACTTAATTATTCTT
3807 TCACACAATAAATGTTATAATAAATCCTATCTCCCCTATCTCTACTTAATTATTCT
1 TCACACAATAAATGTTATAATAAATCCTATCTCCCCTATCTCTACTTAATTATTCT
3863 ACAAAATAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
56 31 0.56
57 24 0.44
ACGTcount: A:0.34, C:0.25, G:0.02, T:0.39
Consensus pattern (57 bp):
TCACACAATAAATGTTATAATAAATCCTATCTCCCCTATCTCTACTTAATTATTCTT
Found at i:3980 original size:42 final size:42
Alignment explanation
Indices: 3933--4013 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
3923 ATCAGGATTG
3933 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
*
3975 GATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
4014 AAGACTTAGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47
Consensus pattern (42 bp):
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Found at i:7682 original size:16 final size:16
Alignment explanation
Indices: 7661--7746 Score: 88
Period size: 16 Copynumber: 5.4 Consensus size: 16
7651 CGAGACCTGA
*
7661 ATGACCAGAAACCCGT
1 ATGACCCGAAACCCGT
**
7677 ATGACCCGAGGCCCG-
1 ATGACCCGAAACCCGT
7692 ATTGACCCGAAACCCGT
1 A-TGACCCGAAACCCGT
*
7709 ATGACTCG-AACCCAG-
1 ATGACCCGAAACCC-GT
*
7724 ATGACCTGAAACCCGT
1 ATGACCCGAAACCCGT
7740 ATGACCC
1 ATGACCC
7747 AAAAAATTAC
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
15 13 0.23
16 42 0.75
17 1 0.02
ACGTcount: A:0.30, C:0.35, G:0.21, T:0.14
Consensus pattern (16 bp):
ATGACCCGAAACCCGT
Found at i:7735 original size:31 final size:31
Alignment explanation
Indices: 7648--7746 Score: 119
Period size: 32 Copynumber: 3.1 Consensus size: 31
7638 AACCCGCCCA
*
7648 ACCCGAGACCTGAATGACCAGAAACCCGTATG
1 ACCCGAGACCCG-ATGACCAGAAACCCGTATG
* *
7680 ACCCGAGGCCCGATTGACCCGAAACCCGTATG
1 ACCCGAGACCCGA-TGACCAGAAACCCGTATG
* *
7712 ACTCGA-ACCCAGATGACCTGAAACCCGTATG
1 ACCCGAGACCC-GATGACCAGAAACCCGTATG
7743 ACCC
1 ACCC
7747 AAAAAATTAC
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
31 24 0.41
32 34 0.59
ACGTcount: A:0.30, C:0.35, G:0.21, T:0.13
Consensus pattern (31 bp):
ACCCGAGACCCGATGACCAGAAACCCGTATG
Found at i:16898 original size:2 final size:2
Alignment explanation
Indices: 16893--16931 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
16883 TATGCGTGCA
16893 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
16932 CCATTTCTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:19139 original size:31 final size:29
Alignment explanation
Indices: 19077--19146 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 29
19067 CAGCAAATTA
19077 CAATTCAGGTTCTAACGTTAGTTCTTGTGT
1 CAATTCAGGTTCTAACGTTAG-TCTTGTGT
*
19107 CAATTCAGGTTCTAATGTTA-TCGGGTTGTGT
1 CAATTCAGGTTCTAACGTTAGTC---TTGTGT
19138 CAATTCAGG
1 CAATTCAGG
19147 ATAAAATCAG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
28 2 0.06
30 19 0.53
31 15 0.42
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.40
Consensus pattern (29 bp):
CAATTCAGGTTCTAACGTTAGTCTTGTGT
Found at i:19295 original size:13 final size:14
Alignment explanation
Indices: 19270--19309 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
19260 TTTTTATCAA
19270 TAAATAAAT-AAAT
1 TAAATAAATAAAAT
*
19283 TAAAT-GATAAAA-
1 TAAATAAATAAAAT
19295 TAAATAAATAAAAT
1 TAAATAAATAAAAT
19309 T
1 T
19310 TATTTGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
12 7 0.32
13 14 0.64
14 1 0.05
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (14 bp):
TAAATAAATAAAAT
Found at i:26174 original size:22 final size:22
Alignment explanation
Indices: 26163--26689 Score: 198
Period size: 22 Copynumber: 24.2 Consensus size: 22
26153 ATGATCTCCT
26163 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* ** *
26185 TATGAAATTTTAATAACGATAC
1 TATGAAATTTTGATAACCTTCC
* * * * **
26207 TATGGAATTTCGAGAATCTTTT
1 TATGAAATTTTGATAACCTTCC
* * *
26229 TATAAAATTTT-TTAACCTTCT
1 TATGAAATTTTGATAACCTTCC
*
26250 TATGAAATTTTGTTAACCTGT-C
1 TATGAAATTTTGATAACCT-TCC
* * * *
26272 TAAGGAATTTTGA-AGAGCTTAC
1 TATGAAATTTTGATA-ACCTTCC
26294 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* **
26316 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* *
26339 TATGAGATGTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * *
26360 ATATGATATATTGATAACC-ACGT
1 -TATGAAATTTTGATAACCTTC-C
* * * *
26383 TGTGAAAATTTAAAAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * *
26404 -ATAGGAATTGTT-AGTAATC-ACAC
1 TAT-GAAATT-TTGA-TAACCTTC-C
* *
26427 TCTGAAATTTTGATAATCACAT--
1 TATGAAATTTTGATAA-C-CTTCC
* *
26449 TATGAAATTGTGATAACCTTGC
1 TATGAAATTTTGATAACCTTCC
*
26471 TACGAAA-TTTGATAAACCTTCC
1 TATGAAATTTTGAT-AACCTTCC
* * *
26493 CATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTTCC
** *
26516 TAAAAAAATTTT-ATAACCTTCT
1 T-ATGAAATTTTGATAACCTTCC
*
26538 TATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTTCC
* *
26555 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
** *
26576 TATGATTTTTTGATAACC-TCAT
1 TATGAAATTTTGATAACCTTC-C
* * * *
26598 TCTGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
26620 TATGAAATTTTGATCTA-CATAC
1 TATGAAATTTTGAT-AACCTTCC
* *
26642 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
*
26664 TATGAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAACCTTCC
26686 TATG
1 TATG
Statistics
Matches: 368, Mismatches: 102, Indels: 70
0.68 0.19 0.13
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
20 3 0.01
21 45 0.12
22 252 0.68
23 44 0.12
24 11 0.03
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:26257 original size:21 final size:22
Alignment explanation
Indices: 26228--26268 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
26218 GAGAATCTTT
26228 TTATAAAATTTT-TTAACCTTC
1 TTATAAAATTTTGTTAACCTTC
*
26249 TTATGAAATTTTGTTAACCT
1 TTATAAAATTTTGTTAACCT
26269 GTCTAAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.32, C:0.12, G:0.05, T:0.51
Consensus pattern (22 bp):
TTATAAAATTTTGTTAACCTTC
Found at i:26352 original size:45 final size:45
Alignment explanation
Indices: 26292--26379 Score: 115
Period size: 45 Copynumber: 2.0 Consensus size: 45
26282 TGAAGAGCTT
* * *
26292 ACTATGAAATTTTGATAACTTCCCA-ATGAAATTTTGATAACCAAC
1 ACTATGAAATGTTGATAACCT-CCATATGAAATATTGATAACCAAC
* *
26337 ACTATGAGATGTTGATAACCTCCATATGATATATTGATAACCA
1 ACTATGAAATGTTGATAACCTCCATATGAAATATTGATAACCA
26380 CGTTGTGAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
44 3 0.08
45 34 0.92
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (45 bp):
ACTATGAAATGTTGATAACCTCCATATGAAATATTGATAACCAAC
Found at i:26522 original size:23 final size:24
Alignment explanation
Indices: 26478--26536 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 24
26468 TGCTACGAAA
*
26478 TTTGATAAACCTTCCC-ATAAAAT
1 TTTGATAAACCTTCCCAAAAAAAT
26501 TTTGATAAACC-TCCCTAAAAAAAT
1 TTTGATAAACCTTCCC-AAAAAAAT
26525 TTT-AT-AACCTTC
1 TTTGATAAACCTTC
26537 TTATGAAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 8 0.25
23 15 0.47
24 9 0.28
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.36
Consensus pattern (24 bp):
TTTGATAAACCTTCCCAAAAAAAT
Done.