Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017428.1 Corchorus olitorius cultivar O-4 contig17461, 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: 59456
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4338 original size:3 final size:3
Alignment explanation
Indices: 4330--4357 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
4320 AGGAAGAGGG
4330 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
4358 AAAGGGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:10819 original size:65 final size:66
Alignment explanation
Indices: 10715--10846 Score: 239
Period size: 65 Copynumber: 2.0 Consensus size: 66
10705 GACTGCATCA
*
10715 CTTGCCAATCCAGAAAGAGGATGTACTCTGAGAATTGGGTAACAAG-CCCATCCTCTCTAGTGTT
1 CTTGCCAATCCAGAAAGAGGATGTACCCTGAGAATTGGGTAACAAGCCCCATCCTCTCTAGTGTT
10779 C
66 C
10780 CTTGCCAATCCAGAAAGAGGATGTACCCTGAGAATTGGGTAACAAGCCCCCATCCTCTCTAGTGT
1 CTTGCCAATCCAGAAAGAGGATGTACCCTGAGAATTGGGTAACAAG-CCCCATCCTCTCTAGTGT
10845 TC
65 TC
10847 ATTTTAAGCA
Statistics
Matches: 64, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
65 45 0.70
67 19 0.30
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (66 bp):
CTTGCCAATCCAGAAAGAGGATGTACCCTGAGAATTGGGTAACAAGCCCCATCCTCTCTAGTGTT
C
Found at i:21248 original size:255 final size:252
Alignment explanation
Indices: 20763--21265 Score: 794
Period size: 255 Copynumber: 2.0 Consensus size: 252
20753 ATCTTTCGGT
* * * * *
20763 AAAAGTAGCCGGGAGGTCCCTGTATTATACGAAGTATTGATTTTGGTCCCTGTACTTTTTTTCTA
1 AAAAGTACCCGGGAGATCCCTGTACTATACAAAATATTGATTTTGGTCCCTGTACTTTTTTTCTA
* * *
20828 CAAATTCGTCTCTCTATTATCATAACCTATCACCCGAGGTCCCTCACGTTAGCATGCCGTGACAG
66 CAAATTCGTCCCTCTACTATCAGAACCTATCACCCGAGGTCCCTCACGTTAGCATGCCGTGACAG
* * *
20893 ACCCGTTAAATATGCTGATGTGGCACTAACACTGTCTTTTTTGCTGACGTGGCAGATGACACGTG
131 ACCCGTCAAATATGCTGACGTGGCACTAACACCGTCTTTTTTGCTGACGTGGCAGATGACACGTG
20958 GAATAAAAATTAAAATTTTTTTAATATATTTTTATTTTATTGAAATTTATTTTTGGTA
196 GAATAAAAATTAAAATTTTTTTAATATATTTTTATTTTATTG-AATTTATTTTTGGTA
*
21016 AAAAGTACCCGGGAGATCCCTGTACTATACAAAATGTTGATTTTGGTCCCTGTACTTTTTTTTTC
1 AAAAGTACCCGGGAGATCCCTGTACTATACAAAATATTGATTTTGGTCCCTGTAC--TTTTTTTC
* *
21081 TACAAATTCGTCCCTCTACTATTAGAACCTATCACCCGAGGTCCCTCACGTTAGCATGTCGTGAC
64 TACAAATTCGTCCCTCTACTATCAGAACCTATCACCCGAGGTCCCTCACGTTAGCATGCCGTGAC
*
21146 AGACCCGTCAAATATGCTGACGTGGCACTAACACCGTCTTTTTTTGCTGACGTGGCAGGTGACAC
129 AGACCCGTCAAATATGCTGACGTGGCACTAACACCGTC-TTTTTTGCTGACGTGGCAGATGACAC
* *
21211 GTGGAATAAAAATT-AAGTATTTTTTAATATA-TTTTATTTTATTGAATTTTTTTTT
193 GTGGAATAAAAATTAAAAT-TTTTTTAATATATTTTTATTTTATTGAATTTATTTTT
21266 AAAAAAAAGA
Statistics
Matches: 229, Mismatches: 17, Indels: 7
0.91 0.07 0.03
Matches are distributed among these distances:
253 49 0.21
254 10 0.04
255 119 0.52
256 51 0.22
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.37
Consensus pattern (252 bp):
AAAAGTACCCGGGAGATCCCTGTACTATACAAAATATTGATTTTGGTCCCTGTACTTTTTTTCTA
CAAATTCGTCCCTCTACTATCAGAACCTATCACCCGAGGTCCCTCACGTTAGCATGCCGTGACAG
ACCCGTCAAATATGCTGACGTGGCACTAACACCGTCTTTTTTGCTGACGTGGCAGATGACACGTG
GAATAAAAATTAAAATTTTTTTAATATATTTTTATTTTATTGAATTTATTTTTGGTA
Found at i:22943 original size:30 final size:31
Alignment explanation
Indices: 22907--22980 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 31
22897 GTCGCAATAT
22907 TCAATTCAGGATATAACGTTACCA-CTTGTG
1 TCAATTCAGGATATAACGTTACCATCTTGTG
* * *
22937 TCAATTCAGGATGTAACGTTATCATGTTGTG
1 TCAATTCAGGATATAACGTTACCATCTTGTG
* *
22968 CCAATTTAGGATA
1 TCAATTCAGGATA
22981 AAATCATATC
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 22 0.59
31 15 0.41
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (31 bp):
TCAATTCAGGATATAACGTTACCATCTTGTG
Found at i:23035 original size:157 final size:156
Alignment explanation
Indices: 22738--23049 Score: 423
Period size: 157 Copynumber: 2.0 Consensus size: 156
22728 GGACATAACA
*
22738 TTTGTGCAATATTCAATTCAGGATATAACATTATCACTTGTGTCAATTCAAGACATAACGTTATC
1 TTTGTGCAATATTCAATTCAGGATATAACATTACCACTTGTGTCAATTCAAGACATAACGTTATC
* * *
22803 GGGTTATGCCAATTCAGGATAAAATCAGACTGTTTGTTGTAAAAACACTCGTTCCTTTCATCGCC
66 AGGTTATGCCAATTCAGGATAAAATCAGACTGTCTGTTGTAAAAACACTCCTTCCTTTCATCGCC
*
22868 TGACCCAATCCACGTGGAATTTAATG
131 TGACCCAATCCACATGGAATTTAATG
* * **
22894 TTTGTCGCAATATTCAATTCAGGATATAACGTTACCACTTGTGTCAATTCAGGATGTAACGTTAT
1 TTTGT-GCAATATTCAATTCAGGATATAACATTACCACTTGTGTCAATTCAAGACATAACGTTAT
* * * *
22959 CATGTTGTGCCAATTTAGGATAAAATCATA-TCGTCTGTTGTAAAAACA-TGCACTT-CTTTCAT
65 CAGGTTATGCCAATTCAGGATAAAATCAGACT-GTCTGTTGTAAAAACACT-C-CTTCCTTTCAT
* * *
23021 CGCGTGGCCTAATCCACATGGAATTTAAT
127 CGCCTGACCCAATCCACATGGAATTTAAT
23050 AGCCAAGCCA
Statistics
Matches: 136, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
156 7 0.05
157 127 0.93
158 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.34
Consensus pattern (156 bp):
TTTGTGCAATATTCAATTCAGGATATAACATTACCACTTGTGTCAATTCAAGACATAACGTTATC
AGGTTATGCCAATTCAGGATAAAATCAGACTGTCTGTTGTAAAAACACTCCTTCCTTTCATCGCC
TGACCCAATCCACATGGAATTTAATG
Found at i:25375 original size:65 final size:65
Alignment explanation
Indices: 25265--25394 Score: 179
Period size: 65 Copynumber: 2.0 Consensus size: 65
25255 GGAAAAACTG
* * ** * *
25265 GTCCTACCCATGCATGGGGCACCCCTGGCCTATCCACGCTTGGGCTAGTGCAGAAAGTTTGAATC
1 GTCCAACCCATGCATGGGGCACCCCTGGCCTACCCACGCAAGGGCTAGTGCAGAAAATTGGAATC
* * *
25330 GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCATGCAAGGGCTAGTGCAGAAAATTGGAATC
1 GTCCAACCCATGCATGGGGCACCCCTGGCCTACCCACGCAAGGGCTAGTGCAGAAAATTGGAATC
25395 AATAGCAAGC
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
65 56 1.00
ACGTcount: A:0.23, C:0.29, G:0.26, T:0.22
Consensus pattern (65 bp):
GTCCAACCCATGCATGGGGCACCCCTGGCCTACCCACGCAAGGGCTAGTGCAGAAAATTGGAATC
Found at i:29585 original size:25 final size:24
Alignment explanation
Indices: 29557--29642 Score: 100
Period size: 25 Copynumber: 3.4 Consensus size: 24
29547 TGGACTGCTT
* *
29557 TTTTTTTTGTTAAATGGGTTGTTAC
1 TTTTTTTT-TTAAATGGGCTGCTAC
*
29582 TTTTTTTTTTCAAATGGCCTGCTAC
1 TTTTTTTTTT-AAATGGGCTGCTAC
*
29607 TTTTTTTTTTAAATGGGCTGATAATC
1 TTTTTTTTTTAAATGGGCTGCT-A-C
29633 TTTTTTTTTT
1 TTTTTTTTTT
29643 GTGTGTGTGA
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
24 12 0.23
25 30 0.57
26 11 0.21
ACGTcount: A:0.16, C:0.09, G:0.14, T:0.60
Consensus pattern (24 bp):
TTTTTTTTTTAAATGGGCTGCTAC
Found at i:29783 original size:25 final size:25
Alignment explanation
Indices: 29750--29801 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
29740 AATATACTGT
29750 ATAAATTATTTACATTTTCTTATTA
1 ATAAATTATTTACATTTTCTTATTA
*
29775 ATAATTTATTTACATTTTCTTATTA
1 ATAAATTATTTACATTTTCTTATTA
29800 AT
1 AT
29802 TTACTATAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.58
Consensus pattern (25 bp):
ATAAATTATTTACATTTTCTTATTA
Found at i:29909 original size:14 final size:14
Alignment explanation
Indices: 29876--29919 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
29866 TATTGAACTC
29876 TATAATGTTTTTTAT
1 TATAATGTTTTTT-T
*
29891 AATAATGTTTTTTT
1 TATAATGTTTTTTT
29905 TATAAT-TTTTATTT
1 TATAATGTTTT-TTT
29919 T
1 T
29920 GCATTTGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 4 0.15
14 10 0.38
15 12 0.46
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (14 bp):
TATAATGTTTTTTT
Found at i:30136 original size:16 final size:16
Alignment explanation
Indices: 30111--30174 Score: 58
Period size: 16 Copynumber: 4.0 Consensus size: 16
30101 TGTGACTTCC
* *
30111 TTTCCCTTCCTCCCAA
1 TTTCCTTTCCTCCCTA
**
30127 TTTCCTTTCCCTTGCTA
1 TTTCCTTT-CCTCCCTA
* *
30144 TTTCTTTTCCTTCCTA
1 TTTCCTTTCCTCCCTA
30160 TTT-CTTTCCTCCCTA
1 TTTCCTTTCCTCCCTA
30175 CCAAACAAAC
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
15 10 0.26
16 17 0.44
17 12 0.31
ACGTcount: A:0.08, C:0.39, G:0.02, T:0.52
Consensus pattern (16 bp):
TTTCCTTTCCTCCCTA
Found at i:42537 original size:20 final size:20
Alignment explanation
Indices: 42490--42537 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
42480 ACTGTTTTTG
*
42490 TTGTTTTATCTGTTAAATTA
1 TTGTTTTTTCTGTTAAATTA
* * *
42510 CTGTTTTTTTTGTTTAATTA
1 TTGTTTTTTCTGTTAAATTA
42530 TTGTTTTT
1 TTGTTTTT
42538 CATGCTTGTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.17, C:0.04, G:0.10, T:0.69
Consensus pattern (20 bp):
TTGTTTTTTCTGTTAAATTA
Found at i:43877 original size:47 final size:47
Alignment explanation
Indices: 43808--43898 Score: 155
Period size: 47 Copynumber: 1.9 Consensus size: 47
43798 GTGCTCAAGC
* *
43808 ATAACTTTGAAAATGATTGATGAAAATTTGGTTCTTGTCATAGAAAG
1 ATAACTTTAAAAATGATTGATGAAAATTTGGTTCATGTCATAGAAAG
*
43855 ATAACTTTAAAAATGATTGATGAAAATTTGGTTGATGTCATAGA
1 ATAACTTTAAAAATGATTGATGAAAATTTGGTTCATGTCATAGA
43899 TGAAAATCCA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (47 bp):
ATAACTTTAAAAATGATTGATGAAAATTTGGTTCATGTCATAGAAAG
Found at i:49096 original size:17 final size:16
Alignment explanation
Indices: 49056--49104 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
49046 CATGTAATCT
*
49056 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
49072 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
*
49089 TTAGATCACTAGTGAT
1 TT-GATCACTGGTGAT
49105 TTGGGGGTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 3 0.10
17 25 0.86
18 1 0.03
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:50523 original size:34 final size:31
Alignment explanation
Indices: 50426--50634 Score: 252
Period size: 34 Copynumber: 6.6 Consensus size: 31
50416 TTAAATTCAA
*
50426 TTGACACCAGAAGTTGTCATATTAAATTATC
1 TTGACACCAGAAGTTGTCATATCAAATTATC
*
50457 TTGACACCAGAAGTTGTCATA-GAAATTA--
1 TTGACACCAGAAGTTGTCATATCAAATTATC
*
50485 TTGACACCAGAAGTTGTCATATTATATTATTATC
1 TTGACACCAGAAGTTGTCATATCA-A--ATTATC
50519 TTGACACCAGAAGTTGTCATGA--AAATTA--
1 TTGACACCAGAAGTTGTCAT-ATCAAATTATC
50547 TTGACACCAGAAGTTGTCATATCAAATTATCATC
1 TTGACACCAGAAGTTGTCATATCAAA-T-T-ATC
50581 TTGACACCAGAAGTTGTCATATCAAATTATTATC
1 TTGACACCAGAAGTTGTCATATC-AA--ATTATC
50615 TTGACACCAGAAGTTGTCAT
1 TTGACACCAGAAGTTGTCAT
50635 GCTGAGGAAA
Statistics
Matches: 159, Mismatches: 2, Indels: 31
0.83 0.01 0.16
Matches are distributed among these distances:
27 1 0.01
28 41 0.26
29 4 0.03
30 12 0.08
31 22 0.14
32 6 0.04
33 1 0.01
34 66 0.42
35 4 0.03
36 1 0.01
37 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.33
Consensus pattern (31 bp):
TTGACACCAGAAGTTGTCATATCAAATTATC
Found at i:50545 original size:62 final size:60
Alignment explanation
Indices: 50425--50634 Score: 289
Period size: 62 Copynumber: 3.4 Consensus size: 60
50415 TTTAAATTCA
50425 ATTGACACCAGAAGTTGTCATATTAA--ATTATCTTGACACCAGAAGTTGTCATAGAAATT
1 ATTGACACCAGAAGTTGTCATATTAATTATTATCTTGACACCAGAAGTTGTCATA-AAATT
50484 ATTGACACCAGAAGTTGTCATATTATATTATTATCTTGACACCAGAAGTTGTCATGAAAATT
1 ATTGACACCAGAAGTTGTCATATTA-ATTATTATCTTGACACCAGAAGTTGTCAT-AAAATT
* *
50546 ATTGACACCAGAAGTTGTCATATCAAATTATCATCTTGACACCAGAAGTTGTCATATCAAATTAT
1 ATTGACACCAGAAGTTGTCATAT-TAATTATTATCTTGACACCAGAAGTTGTC--AT-AAA--AT
50611 T
60 T
50612 ATCTTGACACCAGAAGTTGTCAT
1 A--TTGACACCAGAAGTTGTCAT
50635 GCTGAGGAAA
Statistics
Matches: 137, Mismatches: 3, Indels: 13
0.90 0.02 0.08
Matches are distributed among these distances:
59 25 0.18
60 1 0.01
62 80 0.58
63 2 0.01
64 5 0.04
66 4 0.03
68 20 0.15
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (60 bp):
ATTGACACCAGAAGTTGTCATATTAATTATTATCTTGACACCAGAAGTTGTCATAAAATT
Found at i:50601 original size:96 final size:91
Alignment explanation
Indices: 50426--50667 Score: 317
Period size: 96 Copynumber: 2.5 Consensus size: 91
50416 TTAAATTCAA
* *
50426 TTGACACCAGAAGTTGTCAT-ATTAAATTATCTTGACACCAGAAGTTGTCATAGAAATTATTGAC
1 TTGACACCAGAAGTTGTCATGA-GAAATTA--TTGACACCAGAAGTTGTCATACAAATTATTGAC
* *
50490 ACCAGAAGTTGTCATATTATATTATTATC
63 ACCAGAAGTTGTCATATCAAATTATTATC
50519 TTGACACCAGAAGTTGTCATGA-AAATTATTGACACCAGAAGTTGTCATATCAAATTATCATCTT
1 TTGACACCAGAAGTTGTCATGAGAAATTATTGACACCAGAAGTTGTCATA-CAAA-T-T-A--TT
50583 GACACCAGAAGTTGTCATATCAAATTATTATC
60 GACACCAGAAGTTGTCATATCAAATTATTATC
50615 TTGACACCAGAAGTTGTCATGCTGAGGAAATTATTGACACCAGAAGTTGTCAT
1 TTGACACCAGAAGTTGTCA---TGA-GAAATTATTGACACCAGAAGTTGTCAT
50668 CCTAAGATTG
Statistics
Matches: 134, Mismatches: 3, Indels: 16
0.88 0.02 0.10
Matches are distributed among these distances:
90 21 0.16
91 3 0.02
92 7 0.05
93 21 0.16
94 2 0.01
96 51 0.38
99 3 0.02
101 26 0.19
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Consensus pattern (91 bp):
TTGACACCAGAAGTTGTCATGAGAAATTATTGACACCAGAAGTTGTCATACAAATTATTGACACC
AGAAGTTGTCATATCAAATTATTATC
Found at i:56079 original size:22 final size:23
Alignment explanation
Indices: 56030--56083 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
56020 CTGACTAGAT
* *
56030 ATTATCAAGTGATAAATGGAGAAA
1 ATTATC-AGAGATAAATAGAGAAA
*
56054 ATTATCAGAGATAAA-AGAGAAG
1 ATTATCAGAGATAAATAGAGAAA
56076 ATTATCAG
1 ATTATCAG
56084 CAACATTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 13 0.48
23 8 0.30
24 6 0.22
ACGTcount: A:0.50, C:0.06, G:0.20, T:0.24
Consensus pattern (23 bp):
ATTATCAGAGATAAATAGAGAAA
Found at i:57210 original size:30 final size:30
Alignment explanation
Indices: 57149--57225 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 30
57139 TGACACCAAA
57149 TTGTAAGTAGAGGGACCAAATTGACAATTT
1 TTGTAAGTAGAGGGACCAAATTGACAATTT
* * **
57179 TTGT-AGTAGGGGGACTAAATTGATCCCTTT
1 TTGTAAGTAGAGGGACCAAATTGA-CAATTT
* *
57209 TTATAAGTGGAGGGACC
1 TTGTAAGTAGAGGGACC
57226 TGTACTGTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
29 17 0.46
30 11 0.30
31 9 0.24
ACGTcount: A:0.30, C:0.12, G:0.27, T:0.31
Consensus pattern (30 bp):
TTGTAAGTAGAGGGACCAAATTGACAATTT
Found at i:59091 original size:12 final size:12
Alignment explanation
Indices: 59074--59100 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
59064 TGTTTTATGC
59074 AAAAAAAACAAA
1 AAAAAAAACAAA
59086 AAAAAAAACAAA
1 AAAAAAAACAAA
59098 AAA
1 AAA
59101 CATTATTGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAACAAA
Done.