Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024703.1 Corchorus olitorius cultivar O-4 contig24736, 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: 76981
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:5565 original size:42 final size:43
Alignment explanation
Indices: 5485--5581 Score: 144
Period size: 44 Copynumber: 2.3 Consensus size: 43
5475 ATAAAGCTTA
5485 ACCTATAAAAAGTGTATATATATATATATATAGTATAAATCTGT
1 ACCTATAAAAAGTGTATATATATATATATATAG-ATAAATCTGT
*
5529 ACCTATAAAAAGTGTATATATAT-TATAGTATA-ATAAATCTTT
1 ACCTATAAAAAGTGTATATATATATATA-TATAGATAAATCTGT
*
5571 ACCTATTAAAA
1 ACCTATAAAAA
5582 CTATATAAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
42 19 0.38
43 4 0.08
44 27 0.54
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.38
Consensus pattern (43 bp):
ACCTATAAAAAGTGTATATATATATATATATAGATAAATCTGT
Found at i:7739 original size:27 final size:26
Alignment explanation
Indices: 7667--7740 Score: 71
Period size: 27 Copynumber: 2.8 Consensus size: 26
7657 TGCCAAAATC
*
7667 GTGCC-AA-ATGTTGTGAACAAATAATT
1 GTGCCAAATATGTT-TGAA-AAATAACT
* *
7693 GTGCCAATTATCGTTAGAAAAATAACT
1 GTGCCAAATAT-GTTTGAAAAATAACT
7720 GTGCCAAATACTGTTTGAAAA
1 GTGCCAAATA-TGTTTGAAAA
7741 TCTCGTGCCA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
26 5 0.13
27 25 0.64
28 6 0.15
29 3 0.08
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.30
Consensus pattern (26 bp):
GTGCCAAATATGTTTGAAAAATAACT
Found at i:7836 original size:108 final size:109
Alignment explanation
Indices: 7718--7930 Score: 324
Period size: 108 Copynumber: 2.0 Consensus size: 109
7708 AGAAAAATAA
* ** * *
7718 CTGTGCCAAATACTGTTTGAAAATCTCGTGCCAAATAGCATGACAAATTTGAGAGCC-ATTCCAA
1 CTGTGCCAAATACAGTCAGAAAATCTCGTGCCAAACAGCATGAC-AATTTGAGAGCCGA-TCAAA
7782 ATTCCATGAGAAAA-ACAATGCCAAATACCGTGCC-AATTTGAGAG
64 ATTCCATGAGAAAAGACAATGCCAAATACCGTGCCAAATTTGAGAG
7826 CTGTGCCAAATACAGTCAGAAAATCTCGTGCCAAACAGCATGACAATTTGAGAGCCGATCAAAAT
1 CTGTGCCAAATACAGTCAGAAAATCTCGTGCCAAACAGCATGACAATTTGAGAGCCGATCAAAAT
* *
7891 TCCGTGAGAAAAGACAATGCCAAGTACCGTGCCAAATTTG
66 TCCATGAGAAAAGACAATGCCAAATACCGTGCCAAATTTG
7931 GCATAGACAC
Statistics
Matches: 95, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
107 29 0.31
108 60 0.63
109 6 0.06
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (109 bp):
CTGTGCCAAATACAGTCAGAAAATCTCGTGCCAAACAGCATGACAATTTGAGAGCCGATCAAAAT
TCCATGAGAAAAGACAATGCCAAATACCGTGCCAAATTTGAGAG
Found at i:7860 original size:54 final size:54
Alignment explanation
Indices: 7718--7880 Score: 150
Period size: 54 Copynumber: 3.0 Consensus size: 54
7708 AGAAAAATAA
* ** *
7718 CTGTGCCAAATACTGTTTGAAAATCTCGTGCCAAATAGCATGACAAATTTGAGAG
1 CTGTGCCAAATACAGTCAGAAAATCTCGTGCCAAATAGCATG-CCAATTTGAGAG
** * * * * ** * *
7773 CCATTCCAAATTCCA-TGAGAAAAAC-AATGCCAAATACCGTGCCAATTTGAGAG
1 CTGTGCCAAA-TACAGTCAGAAAATCTCGTGCCAAATAGCATGCCAATTTGAGAG
* *
7826 CTGTGCCAAATACAGTCAGAAAATCTCGTGCCAAACAGCATGACAATTTGAGAG
1 CTGTGCCAAATACAGTCAGAAAATCTCGTGCCAAATAGCATGCCAATTTGAGAG
7880 C
1 C
7881 CGATCAAAAT
Statistics
Matches: 80, Mismatches: 25, Indels: 7
0.71 0.22 0.06
Matches are distributed among these distances:
52 3 0.04
53 26 0.32
54 35 0.44
55 14 0.17
56 2 0.03
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (54 bp):
CTGTGCCAAATACAGTCAGAAAATCTCGTGCCAAATAGCATGCCAATTTGAGAG
Found at i:7901 original size:54 final size:54
Alignment explanation
Indices: 7736--7902 Score: 169
Period size: 54 Copynumber: 3.1 Consensus size: 54
7726 AATACTGTTT
*
7736 GAAAATCTCGTGCCAAATAGCATGACAAATTTGAGAGCC-ATTCCAAATTCCATGA
1 GAAAATCTCGTGCCAAATAGCATGAC-AATTTGAGAGCCGA-TCCAAATTCCGTGA
* ** * * * * * * *
7791 GAAAAAC-AATGCCAAATACCGTGCCAATTTGAGAGCTG-TGCCAAATACAGTCA
1 GAAAATCTCGTGCCAAATAGCATGACAATTTGAGAGCCGAT-CCAAATTCCGTGA
* *
7844 GAAAATCTCGTGCCAAACAGCATGACAATTTGAGAGCCGATCAAAATTCCGTGA
1 GAAAATCTCGTGCCAAATAGCATGACAATTTGAGAGCCGATCCAAATTCCGTGA
7898 GAAAA
1 GAAAA
7903 GACAATGCCA
Statistics
Matches: 85, Mismatches: 23, Indels: 9
0.73 0.20 0.08
Matches are distributed among these distances:
52 1 0.01
53 26 0.31
54 51 0.60
55 7 0.08
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.20
Consensus pattern (54 bp):
GAAAATCTCGTGCCAAATAGCATGACAATTTGAGAGCCGATCCAAATTCCGTGA
Found at i:9750 original size:18 final size:18
Alignment explanation
Indices: 9723--9757 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
9713 TTAGACTCAG
9723 CCTGAAGCTTCTCAAAAA
1 CCTGAAGCTTCTCAAAAA
*
9741 CCTGAGGCTTCTCAAAA
1 CCTGAAGCTTCTCAAAA
9758 GGTAAATGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.29, G:0.14, T:0.23
Consensus pattern (18 bp):
CCTGAAGCTTCTCAAAAA
Found at i:14076 original size:15 final size:15
Alignment explanation
Indices: 14066--14100 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
14056 GCCTCTTTTT
*
14066 CTTCTCTCTCTCTTC
1 CTTCCCTCTCTCTTC
14081 CTTCCCTCTCTCTTC
1 CTTCCCTCTCTCTTC
14096 CTTCC
1 CTTCC
14101 ACTCCGCACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (15 bp):
CTTCCCTCTCTCTTC
Found at i:17005 original size:82 final size:75
Alignment explanation
Indices: 16808--17041 Score: 369
Period size: 75 Copynumber: 3.0 Consensus size: 75
16798 TATCTTGTCA
*
16808 TTTCATTCAGATCAGAGTAGAAGTCATTATGAGATTTTGACAATCATCAATTTGGATTATATATG
1 TTTCATTCAGATCAGAGTAGAAGTCATTATGAGATTTTGACAATCATCAATCTGGATTATATATG
16873 TCTTACAACT
66 TCTTACAACT
* *
16883 TTTCATTCAGATCAGAGTAGAAGTCATTACGAGATATTGACAATCATCAATCTGGATTATATATG
1 TTTCATTCAGATCAGAGTAGAAGTCATTATGAGATTTTGACAATCATCAATCTGGATTATATATG
16948 TCTTACAACT
66 TCTTACAACT
16958 TTTCATTCAGATCAGAGTAGAAGTTATTACTCATTATGAGATTTTGACAATCATCAATCTGGATT
1 TTTCATTCAGATCAGAGTAGAAG-------TCATTATGAGATTTTGACAATCATCAATCTGGATT
*
17023 ATATATGTCTTATAACT
59 ATATATGTCTTACAACT
17040 TT
1 TT
17042 AAAGTGCTTC
Statistics
Matches: 146, Mismatches: 6, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
75 95 0.65
82 51 0.35
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.38
Consensus pattern (75 bp):
TTTCATTCAGATCAGAGTAGAAGTCATTATGAGATTTTGACAATCATCAATCTGGATTATATATG
TCTTACAACT
Found at i:20818 original size:66 final size:68
Alignment explanation
Indices: 20736--20868 Score: 191
Period size: 66 Copynumber: 2.0 Consensus size: 68
20726 TTATTATCAT
* * *
20736 AAATATGTTGTTTAGTCATTTCTCATTCGGATGTTCGAAAATAAAT-AAATTATCTTATG-ATTG
1 AAATATGTTGTTTAGTCAATTCTCATTCGAATATTCGAAAATAAATAAAATTATCTTA-GAATTG
20799 TAAC
65 TAAC
* *
20803 AAAT-TGTTGTTTAGTCAATTCTCATTCGAATATTTGAGAATAAATAAAATTATCTTAGAATTGT
1 AAATATGTTGTTTAGTCAATTCTCATTCGAATATTCGAAAATAAATAAAATTATCTTAGAATTGT
20867 AA
66 AA
20869 TGAAATTTGA
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
66 37 0.63
67 22 0.37
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (68 bp):
AAATATGTTGTTTAGTCAATTCTCATTCGAATATTCGAAAATAAATAAAATTATCTTAGAATTGT
AAC
Found at i:21208 original size:12 final size:13
Alignment explanation
Indices: 21182--21214 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
21172 TATTTTATAT
21182 TTTATATTATATTA
1 TTTAT-TTATATTA
21196 TTTATTTAT-TTA
1 TTTATTTATATTA
21208 TTTATTT
1 TTTATTT
21215 GTAGAGAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.53
13 4 0.21
14 5 0.26
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTATTTATATTA
Found at i:21475 original size:15 final size:15
Alignment explanation
Indices: 21455--21489 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
21445 GAGAAAAAGG
21455 GAAAAAGAAATAAAA
1 GAAAAAGAAATAAAA
21470 GAAAAAGAAATAAAA
1 GAAAAAGAAATAAAA
21485 GAAAA
1 GAAAA
21490 TTTGTTCAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (15 bp):
GAAAAAGAAATAAAA
Found at i:27057 original size:17 final size:17
Alignment explanation
Indices: 27035--27069 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
27025 CACTTCCCCA
27035 GTCCCACCATGTTAAAT
1 GTCCCACCATGTTAAAT
27052 GTCCCACCATGTTAAAT
1 GTCCCACCATGTTAAAT
27069 G
1 G
27070 AACACAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (17 bp):
GTCCCACCATGTTAAAT
Found at i:36377 original size:22 final size:22
Alignment explanation
Indices: 36335--36378 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
36325 TCTGTCTCCA
*
36335 TATATATACAGAGTAATATAAT
1 TATATATACAGAGTAAAATAAT
*
36357 TATATATAGAGAG-AGAAATAAT
1 TATATATACAGAGTA-AAATAAT
36379 AGTGGAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.52, C:0.02, G:0.14, T:0.32
Consensus pattern (22 bp):
TATATATACAGAGTAAAATAAT
Found at i:39100 original size:68 final size:68
Alignment explanation
Indices: 38991--39131 Score: 282
Period size: 68 Copynumber: 2.1 Consensus size: 68
38981 GATTCTTGTA
38991 GATTAATGCTAATGTAGTTCTTACTTAAAGATTGAATCAATGCTCCTCTTTGTGAATCATTGTAC
1 GATTAATGCTAATGTAGTTCTTACTTAAAGATTGAATCAATGCTCCTCTTTGTGAATCATTGTAC
39056 GGG
66 GGG
39059 GATTAATGCTAATGTAGTTCTTACTTAAAGATTGAATCAATGCTCCTCTTTGTGAATCATTGTAC
1 GATTAATGCTAATGTAGTTCTTACTTAAAGATTGAATCAATGCTCCTCTTTGTGAATCATTGTAC
39124 GGG
66 GGG
39127 GATTA
1 GATTA
39132 CCATGAAGCC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 73 1.00
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.38
Consensus pattern (68 bp):
GATTAATGCTAATGTAGTTCTTACTTAAAGATTGAATCAATGCTCCTCTTTGTGAATCATTGTAC
GGG
Found at i:49890 original size:20 final size:19
Alignment explanation
Indices: 49865--49905 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
49855 CGTTGTACAA
49865 TTATTTA-TTATTATTATTAT
1 TTATTTATTTA-TATTA-TAT
49885 TTATTTATTTATATTATAT
1 TTATTTATTTATATTATAT
49904 TT
1 TT
49906 CAGGTGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 12 0.60
21 3 0.15
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TTATTTATTTATATTATAT
Found at i:56067 original size:13 final size:13
Alignment explanation
Indices: 56049--56073 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56039 CCATTTGGTC
56049 AAAAAAAATAAAT
1 AAAAAAAATAAAT
56062 AAAAAAAATAAA
1 AAAAAAAATAAA
56074 AACACAGTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAAAATAAAT
Found at i:59853 original size:61 final size:61
Alignment explanation
Indices: 59775--59894 Score: 204
Period size: 61 Copynumber: 2.0 Consensus size: 61
59765 AACCCGATGT
* *
59775 AAATGCACAGGGATAATATCTAGTGCAAAATAAAATCAAGTAAATAAATTCCCCAACTAGC
1 AAATACACAGGGATAATATCTAGTGCAAAATAAAATCAAGTAAATAAATTCCCAAACTAGC
* *
59836 AAATACACGGGGATAATATCTAGTGCAAAATAAAATCAGGTAAATAAATTCCCAAACTA
1 AAATACACAGGGATAATATCTAGTGCAAAATAAAATCAAGTAAATAAATTCCCAAACTA
59895 AAAAGTGCTA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.22
Consensus pattern (61 bp):
AAATACACAGGGATAATATCTAGTGCAAAATAAAATCAAGTAAATAAATTCCCAAACTAGC
Found at i:60368 original size:29 final size:28
Alignment explanation
Indices: 60321--60380 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
60311 ATAATGTACC
60321 CAAAATAAAACATTTGGGTGCAATAAGAT
1 CAAAATAAAACATTTGGGTGCAATAAG-T
* *
60350 CAAAAT-AAACCTTTAGGGTGGAATAAGT
1 CAAAATAAAACATTT-GGGTGCAATAAGT
60378 CAA
1 CAA
60381 CCGTATAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 11 0.39
29 17 0.61
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.23
Consensus pattern (28 bp):
CAAAATAAAACATTTGGGTGCAATAAGT
Found at i:62058 original size:15 final size:15
Alignment explanation
Indices: 61993--62066 Score: 51
Period size: 15 Copynumber: 4.9 Consensus size: 15
61983 CATGGAAAGT
*
61993 ACTCTCCTGGGAATC
1 ACTCTCCTAGGAATC
* * * *
62008 ACACTTCTTGGAATG
1 ACTCTCCTAGGAATC
* *
62023 ATTCTCC-ATGGAGAGC
1 ACTCTCCTA-GGA-ATC
62039 ACTCTCCTAGGAATC
1 ACTCTCCTAGGAATC
*
62054 ACTCTCCTTGGAA
1 ACTCTCCTAGGAA
62067 AGCACTTCCC
Statistics
Matches: 43, Mismatches: 13, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
15 32 0.74
16 10 0.23
17 1 0.02
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.28
Consensus pattern (15 bp):
ACTCTCCTAGGAATC
Found at i:70910 original size:31 final size:30
Alignment explanation
Indices: 70842--70910 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
70832 AAAATGCAAT
* * *
70842 TCAGGATATACCGTTAGGACTTGTATCAAT
1 TCAGGATATAACGTTAGGACTTGGATCAAA
*
70872 TCAGGATATAACGTTATCGGA-TTGGGTCAAA
1 TCAGGATATAACGTTA--GGACTTGGATCAAA
70903 TCAGGATA
1 TCAGGATA
70911 AAATCAAACG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 15 0.45
31 15 0.45
32 3 0.09
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.30
Consensus pattern (30 bp):
TCAGGATATAACGTTAGGACTTGGATCAAA
Found at i:71887 original size:13 final size:13
Alignment explanation
Indices: 71871--71895 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
71861 TTTTTTTGGC
71871 TTTTTATTGATTA
1 TTTTTATTGATTA
71884 TTTTTATTGATT
1 TTTTTATTGATT
71896 TTGTTTCTGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (13 bp):
TTTTTATTGATTA
Done.