Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019948.1 Corchorus olitorius cultivar O-4 contig19981, 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: 111623
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:490 original size:11 final size:11
Alignment explanation
Indices: 464--505 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
454 ATTCTCTTAT
464 TTTCC-TTTTC
1 TTTCCTTTTTC
474 -TTCCTTTTTC
1 TTTCCTTTTTC
484 TTTCCTTTTTC
1 TTTCCTTTTTC
*
495 TTTTCTTTTTC
1 TTTCCTTTTTC
506 CTTCTTCCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 4 0.14
10 5 0.17
11 20 0.69
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTCCTTTTTC
Found at i:3838 original size:14 final size:15
Alignment explanation
Indices: 3799--3851 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 15
3789 AAAATATTAA
3799 ATAATTTTCAATACTTTT
1 ATAATTTT-AATA--TTT
3817 ATAATTTTAATATTT
1 ATAATTTTAATATTT
3832 A-AATTTTAATTATTAT
1 ATAATTTTAA-TATT-T
3848 ATAA
1 ATAA
3852 AATATGCATA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
14 8 0.25
15 8 0.25
16 2 0.06
17 6 0.19
18 8 0.25
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (15 bp):
ATAATTTTAATATTT
Found at i:6220 original size:19 final size:19
Alignment explanation
Indices: 6170--6220 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
6160 TGTGGGATTT
6170 TTAATAA-TAATTATTCAA
1 TTAATAATTAATTATTCAA
* *
6188 TAAAATAATT-ATTATTTAA
1 T-TAATAATTAATTATTCAA
6207 TTAATAATTAATTA
1 TTAATAATTAATTA
6221 ATTTCAGCCC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 8 0.30
19 18 0.67
20 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAATAATTAATTATTCAA
Found at i:9855 original size:23 final size:23
Alignment explanation
Indices: 9829--9873 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
9819 ATCTCACCTG
9829 TGAATCAAAATATACGTAGTACA
1 TGAATCAAAATATACGTAGTACA
9852 TGAATCAAAATATACGTAGTAC
1 TGAATCAAAATATACGTAGTAC
9874 GTATGTACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (23 bp):
TGAATCAAAATATACGTAGTACA
Found at i:9894 original size:4 final size:4
Alignment explanation
Indices: 9887--10013 Score: 254
Period size: 4 Copynumber: 31.8 Consensus size: 4
9877 TGTACGTACG
9887 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
9935 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
9983 TACA TACA TACA TACA TACA TACA TACA TAC
1 TACA TACA TACA TACA TACA TACA TACA TAC
10014 CCTAATATTG
Statistics
Matches: 123, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 123 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:17606 original size:126 final size:126
Alignment explanation
Indices: 17381--17638 Score: 516
Period size: 126 Copynumber: 2.0 Consensus size: 126
17371 TAAATTCAAG
17381 AAAAAGGAAGGAATGAAACTCTTGTCTGGCATATTCAGCACATCAGAATCAGATATGACTATACA
1 AAAAAGGAAGGAATGAAACTCTTGTCTGGCATATTCAGCACATCAGAATCAGATATGACTATACA
17446 ACCATAAAAATTAAGCCACCACAGGTTCCTTGACTTACGAGAGGATTGATAACCTTACACA
66 ACCATAAAAATTAAGCCACCACAGGTTCCTTGACTTACGAGAGGATTGATAACCTTACACA
17507 AAAAAGGAAGGAATGAAACTCTTGTCTGGCATATTCAGCACATCAGAATCAGATATGACTATACA
1 AAAAAGGAAGGAATGAAACTCTTGTCTGGCATATTCAGCACATCAGAATCAGATATGACTATACA
17572 ACCATAAAAATTAAGCCACCACAGGTTCCTTGACTTACGAGAGGATTGATAACCTTACACA
66 ACCATAAAAATTAAGCCACCACAGGTTCCTTGACTTACGAGAGGATTGATAACCTTACACA
17633 AAAAAG
1 AAAAAG
17639 TGGTCAACTC
Statistics
Matches: 132, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
126 132 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (126 bp):
AAAAAGGAAGGAATGAAACTCTTGTCTGGCATATTCAGCACATCAGAATCAGATATGACTATACA
ACCATAAAAATTAAGCCACCACAGGTTCCTTGACTTACGAGAGGATTGATAACCTTACACA
Found at i:27765 original size:12 final size:12
Alignment explanation
Indices: 27748--27789 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
27738 TCCTTCAAAG
*
27748 CATTTTTGTTGC
1 CATTTTTATTGC
* *
27760 CATTTTTCTTAC
1 CATTTTTATTGC
27772 C-TTTTTATTGC
1 CATTTTTATTGC
27783 CATTTTT
1 CATTTTT
27790 TTCCCTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.12, C:0.19, G:0.07, T:0.62
Consensus pattern (12 bp):
CATTTTTATTGC
Found at i:27782 original size:23 final size:22
Alignment explanation
Indices: 27750--27799 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 22
27740 CTTCAAAGCA
*
27750 TTTTTGTTGCCATTTTTCTTACC
1 TTTTTATTGCCATTTTT-TTACC
*
27773 TTTTTATTGCCATTTTTTTCCC
1 TTTTTATTGCCATTTTTTTACC
27795 TTTTT
1 TTTTT
27800 CTTGGCATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 9 0.36
23 16 0.64
ACGTcount: A:0.08, C:0.20, G:0.06, T:0.66
Consensus pattern (22 bp):
TTTTTATTGCCATTTTTTTACC
Found at i:33913 original size:15 final size:15
Alignment explanation
Indices: 33893--33924 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
33883 TGTTGTTGAT
33893 AAGAAGAATAAGAAG
1 AAGAAGAATAAGAAG
*
33908 AAGAAGAATAAGGAG
1 AAGAAGAATAAGAAG
33923 AA
1 AA
33925 TTTTTTGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.28, T:0.06
Consensus pattern (15 bp):
AAGAAGAATAAGAAG
Found at i:52761 original size:33 final size:33
Alignment explanation
Indices: 52710--52776 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
52700 TATGCACACC
* *
52710 AACAGTTTCTCGACCACTAACTTAAAAGGAAAA
1 AACAATTTATCGACCACTAACTTAAAAGGAAAA
52743 AACAATTTATCGACCACTAACTTAAAAGGAAAA
1 AACAATTTATCGACCACTAACTTAAAAGGAAAA
52776 A
1 A
52777 TCACAAGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.49, C:0.19, G:0.10, T:0.21
Consensus pattern (33 bp):
AACAATTTATCGACCACTAACTTAAAAGGAAAA
Found at i:56180 original size:76 final size:76
Alignment explanation
Indices: 56054--56207 Score: 308
Period size: 76 Copynumber: 2.0 Consensus size: 76
56044 ACAGGTTAAA
56054 GCAAGAGTGGTCCTGCCTCACAGATGAACCTACTTTAACTCTGTTTGTGCTCTCTTGTACCACCT
1 GCAAGAGTGGTCCTGCCTCACAGATGAACCTACTTTAACTCTGTTTGTGCTCTCTTGTACCACCT
56119 ATAGGCTTGTT
66 ATAGGCTTGTT
56130 GCAAGAGTGGTCCTGCCTCACAGATGAACCTACTTTAACTCTGTTTGTGCTCTCTTGTACCACCT
1 GCAAGAGTGGTCCTGCCTCACAGATGAACCTACTTTAACTCTGTTTGTGCTCTCTTGTACCACCT
56195 ATAGGCTTGTT
66 ATAGGCTTGTT
56206 GC
1 GC
56208 CCCAGCCTTC
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 78 1.00
ACGTcount: A:0.19, C:0.27, G:0.20, T:0.34
Consensus pattern (76 bp):
GCAAGAGTGGTCCTGCCTCACAGATGAACCTACTTTAACTCTGTTTGTGCTCTCTTGTACCACCT
ATAGGCTTGTT
Found at i:74922 original size:12 final size:12
Alignment explanation
Indices: 74902--74935 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
74892 TATCATATAT
*
74902 TATACTATAATA
1 TATAATATAATA
74914 TATAATATAATA
1 TATAATATAATA
74926 TATGAATATA
1 TAT-AATATA
74936 TAATACTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (12 bp):
TATAATATAATA
Found at i:78794 original size:21 final size:22
Alignment explanation
Indices: 78760--78800 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
78750 CTGCAAAGAA
78760 ATGAAGAATCCTTT-TTTTTGG
1 ATGAAGAATCCTTTCTTTTTGG
78781 ATGAAGAAAT-CTTTCTTTTT
1 ATGAAG-AATCCTTTCTTTTT
78801 TACATGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.27, C:0.10, G:0.15, T:0.49
Consensus pattern (22 bp):
ATGAAGAATCCTTTCTTTTTGG
Found at i:86341 original size:27 final size:29
Alignment explanation
Indices: 86279--86341 Score: 67
Period size: 31 Copynumber: 2.2 Consensus size: 29
86269 GCTTAATACC
86279 CAAATTAGCCCCTTAATTATCCATTTTGGGA
1 CAAATTAGCCCCTTAATTAT-C-TTTTGGGA
* * *
86310 TAAATTGGCCCCTTAATT-T-TTTTTGGA
1 CAAATTAGCCCCTTAATTATCTTTTGGGA
86337 CAAAT
1 CAAAT
86342 AAATCCCATA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
27 11 0.39
30 1 0.04
31 16 0.57
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.40
Consensus pattern (29 bp):
CAAATTAGCCCCTTAATTATCTTTTGGGA
Found at i:87036 original size:21 final size:21
Alignment explanation
Indices: 87011--87053 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
87001 ATGGAAAAGG
*
87011 CCAGACGGGAGAGAAAGAAAA
1 CCAGACAGGAGAGAAAGAAAA
*
87032 CCAGACAGGAGAGGAAGAAAA
1 CCAGACAGGAGAGAAAGAAAA
87053 C
1 C
87054 GAGGGGAGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.51, C:0.16, G:0.33, T:0.00
Consensus pattern (21 bp):
CCAGACAGGAGAGAAAGAAAA
Found at i:90074 original size:29 final size:30
Alignment explanation
Indices: 90042--90106 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 30
90032 TATGGGATTT
90042 ATTTGTCCCAAAA-AAAAGTTAAGGGGCCA
1 ATTTGTCCCAAAAGAAAAGTTAAGGGGCCA
* * *
90071 ATTTGTCCCAAAATGGATAGTTAAGGGGCTA
1 ATTTGTCCCAAAA-GAAAAGTTAAGGGGCCA
90102 ATTTG
1 ATTTG
90107 GGCATTAACC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 13 0.42
31 18 0.58
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (30 bp):
ATTTGTCCCAAAAGAAAAGTTAAGGGGCCA
Found at i:91943 original size:16 final size:16
Alignment explanation
Indices: 91922--91952 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
91912 GTGTGATCAA
91922 AGATGTTTCACAGCAG
1 AGATGTTTCACAGCAG
*
91938 AGATGTTTCAGAGCA
1 AGATGTTTCACAGCA
91953 CCCTTTCAAT
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:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (16 bp):
AGATGTTTCACAGCAG
Found at i:92414 original size:2 final size:2
Alignment explanation
Indices: 92409--92446 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
92399 ACACACACAC
92409 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
92447 GGAGGAGGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:92858 original size:22 final size:22
Alignment explanation
Indices: 92829--92877 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
92819 AGTAAGATGT
92829 AAAATTGAATTCCTTAGGAATG
1 AAAATTGAATTCCTTAGGAATG
* *
92851 GAAATTGAATTTCTTAGGAATG
1 AAAATTGAATTCCTTAGGAATG
92873 AAAAT
1 AAAAT
92878 GTTTAGATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.06, G:0.18, T:0.33
Consensus pattern (22 bp):
AAAATTGAATTCCTTAGGAATG
Found at i:95605 original size:37 final size:39
Alignment explanation
Indices: 95554--95726 Score: 166
Period size: 37 Copynumber: 4.7 Consensus size: 39
95544 CGTAATAACA
* * *
95554 CTCTTTGCCACAGAGCTCTC-CTTA-TAGCGGTAACACC
1 CTCTTTACCGCAGAGCTCTCTCTTACTAGCGGTAGCACC
* *
95591 CTCTTTACCGCAGAGCTC-CTCTTACTA-CGATAGCACA
1 CTCTTTACCGCAGAGCTCTCTCTTACTAGCGGTAGCACC
* *
95628 CTCTTTGCCGCAGAACT-TCTCTTAC-AGCGGTAGCACC
1 CTCTTTACCGCAGAGCTCTCTCTTACTAGCGGTAGCACC
* * * *
95665 CTCTTCACCGCAAAGCTTTC-CTTACT-GCGGTAGCATC
1 CTCTTTACCGCAGAGCTCTCTCTTACTAGCGGTAGCACC
* *
95702 CTCTTTACCGCAAAGCTTTCT-TTAC
1 CTCTTTACCGCAGAGCTCTCTCTTAC
95727 AAATCATTGT
Statistics
Matches: 114, Mismatches: 15, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
36 2 0.02
37 108 0.95
38 4 0.04
ACGTcount: A:0.21, C:0.35, G:0.15, T:0.29
Consensus pattern (39 bp):
CTCTTTACCGCAGAGCTCTCTCTTACTAGCGGTAGCACC
Found at i:96018 original size:6 final size:6
Alignment explanation
Indices: 96001--96038 Score: 67
Period size: 6 Copynumber: 6.2 Consensus size: 6
95991 ATATTTTCTC
96001 TCTTATT TCTTAT TCTTAT TCTTAT TCTTAT TCTTAT T
1 TCTTA-T TCTTAT TCTTAT TCTTAT TCTTAT TCTTAT T
96039 GTTCTTCAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (6 bp):
TCTTAT
Found at i:107768 original size:68 final size:68
Alignment explanation
Indices: 107689--107826 Score: 267
Period size: 68 Copynumber: 2.0 Consensus size: 68
107679 AAAAAATGAA
107689 TAAAAGAGGGTTTGGGTATAAAGTAAATACTTGGAGGCTTCCGCCTTGGTTTACTCTTGCAGTAA
1 TAAAAGAGGGTTTGGGTATAAAGTAAATACTTGGAGGCTTCCGCCTTGGTTTACTCTTGCAGTAA
107754 GCC
66 GCC
*
107757 TAAAAGAGGGTTTGGGTATAAAGTAAATACTTGGAGGCTTCCGCTTTGGTTTACTCTTGCAGTAA
1 TAAAAGAGGGTTTGGGTATAAAGTAAATACTTGGAGGCTTCCGCCTTGGTTTACTCTTGCAGTAA
107822 GCC
66 GCC
107825 TA
1 TA
107827 TTGTTTTGGG
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (68 bp):
TAAAAGAGGGTTTGGGTATAAAGTAAATACTTGGAGGCTTCCGCCTTGGTTTACTCTTGCAGTAA
GCC
Found at i:108682 original size:27 final size:29
Alignment explanation
Indices: 108624--108684 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
108614 AGTCCGTAGC
* **
108624 AATTTATATAATATTTATTCTTATTTGGT
1 AATTTATATAATATTTATTCATATTTAAT
108653 AATTTATATAATATTTA-T-ATATTTAAT
1 AATTTATATAATATTTATTCATATTTAAT
108680 AATTT
1 AATTT
108685 TGGCTTCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 11 0.38
28 1 0.03
29 17 0.59
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (29 bp):
AATTTATATAATATTTATTCATATTTAAT
Done.