Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016408.1 Corchorus olitorius cultivar O-4 contig16441, 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: 49962
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:4321 original size:35 final size:35
Alignment explanation
Indices: 4281--4355 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
4271 AGTTCGTTTA
*
4281 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
1 TGTTCACGAACAGACTCGTTTATTGTTAATTTAAG
4316 TGTTCACGAACAGACTCGTTTATTGTTAATTTAAG
1 TGTTCACGAACAGACTCGTTTATTGTTAATTTAAG
4351 TGTTC
1 TGTTC
4356 GTTTATATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.41
Consensus pattern (35 bp):
TGTTCACGAACAGACTCGTTTATTGTTAATTTAAG
Found at i:4587 original size:18 final size:18
Alignment explanation
Indices: 4560--4594 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4550 AATTATTACA
*
4560 TTGTTCATGAATAATTTT
1 TTGTTCATGAACAATTTT
*
4578 TTGTTTATGAACAATTT
1 TTGTTCATGAACAATTT
4595 CAGTTTTTGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.11, T:0.54
Consensus pattern (18 bp):
TTGTTCATGAACAATTTT
Found at i:7092 original size:40 final size:40
Alignment explanation
Indices: 7024--7101 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
7014 TTTCAATAGT
*
7024 TTTGCCTCAATTAATAAGTAAGCAATGCTGATTGCTATTG
1 TTTGCCTCAATTAATAAGTAAGCAATGCTGATGGCTATTG
* * * **
7064 TTTGCCTCATTTAATAGGTGAGTGATGCTGATGGCTAT
1 TTTGCCTCAATTAATAAGTAAGCAATGCTGATGGCTAT
7102 CTTGAGAGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (40 bp):
TTTGCCTCAATTAATAAGTAAGCAATGCTGATGGCTATTG
Found at i:15728 original size:328 final size:328
Alignment explanation
Indices: 14840--15900 Score: 1074
Period size: 328 Copynumber: 3.2 Consensus size: 328
14830 GGTTTCGATC
* * * * *
14840 AAAATTTTGTAAAAATAGAG-CGGAAATA-TATTTCCTCAATTTTTAGCCAAAATACTCAT-AAA
1 AAAATTTTGCAAAAAT-GAGCCCGAAATATTTTTTCCTCAATTTTTGGCCAAAATAATCATAAAA
* *** * * *
14902 AATATATAATTTAACTTAAAAAAGA-TCGGAGTGCTTTTCACCCTTCTAATATCGTATTCCCTAT
65 AATATATAATTAAACGCCAAAAAGATTGGGGGT-CTTTTCACACTTCTAATATCGTATTCCCTAT
*** * * *
14966 TTAAACTAAATTAATTTCCAATTAAATCGAAACCGATTTCAGAT-CTCGTAAAAACATATTCTAA
129 TTTTTCTAAATTAATTTCTAATTAAATCGAAACCGA-TTCAGATGCTCGTAAAAACATATCCTTA
* * *
15030 AATCCAACGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAA-TCTTTGCACCAAAA
193 AATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAA-GAAGTCTTGGCGCCAAAA
* * * *
15094 ATCATGTAAAACTGAGACTGAGCTGGGACCCAGAACGCGTTTCTAGCAAAAAAACCATGATGTTA
257 ATCATG--AAA---A-ACTGAGCCGGGACCCAGAACGCGTTTCTAGC--TAAAACCGTGAT-ATA
*
15159 GTACACAATTTCAGCT
313 GTACACGATTTCAGCT
* * * * * * * * *
15175 AAATTTTTGCAAAAATG-GACTCAAAATATTTTTTTCTTAATTTTCGACCAAAATACTCATAATA
1 AAAATTTTGCAAAAATGAG-CCCGAAATATTTTTTCCTCAATTTTTGGCCAAAATAATCATAAAA
* * * * *
15239 AATATATATTTAAACGCCAAAAAGATTAGAGGG-CTTTTCACATTTCTAATATTGTGTTCCCTA-
65 AATATATAATTAAACGCCAAAAAGATT-GGGGGTCTTTTCACACTTCTAATATCGTATTCCCTAT
* * * *
15302 ATTTTCTGAAA-TAATTTCTAATTAAATCGAAACTAGTTTCAGATGCTCATAAAAACATATCCTT
129 TTTTTCT-AAATTAATTTCTAATTAAATCGAAAC-CGATTCAGATGCTCGTAAAAACATATCCTT
* * * * * *
15366 AAATGCAATGAGACTGAGATTTGATTAGATGAATATAGATATTTCAAAAAGTCTCGGTGCCAAAA
192 AAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGAAGTCTTGGCGCCAAAA
* * * *
15431 ATCATGCAAAACTGAGCCGGGACCCCGGAACGCGTTTCTAGCTAAAACCGTGATATAGTTCATGA
257 ATCATGAAAAACTGAGCCGGGA-CCCAGAACGCGTTTCTAGCTAAAACCGTGATATAGTACACGA
*
15496 TTTCGGCT
321 TTTCAGCT
15504 AAAATTTTGCAAAAATGAGCCCGAAATA-TTTTTCCTCAATTTTTGGCCAAAATAATCCA-AAAA
1 AAAATTTTGCAAAAATGAGCCCGAAATATTTTTTCCTCAATTTTTGGCCAAAATAAT-CATAAAA
* * * * *
15567 AATATACAATTCAACGCCAAAAAGATTGGGGGTCTTTTCACACTTCTAATATCATTTTTCCTATT
65 AATATATAATTAAACGCCAAAAAGATTGGGGGTCTTTTCACACTTCTAATATCGTATTCCCTATT
15632 TTTTCTAAATTAATTTCTAATTAAATCGAAACCGGATTCAGATGCTCGT-AAAACATATCCTTAA
130 TTTTCTAAATTAATTTCTAATTAAATCGAAACC-GATTCAGATGCTCGTAAAAACATATCCTTAA
* * * * ** *
15696 ATCCAATGTGGCTGAAATTTTATTAAATGAATAAAGATATTTCAAGGTGTCTTTGGCGCAAAAAA
194 ATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGAAGTC-TTGGCGCCAAAAA
* * * * * * * * *
15761 TTATGAAAAACTAAACTGGGGCTCAGAACGCATTTCTAGTTAAAAACCGTGATA-ACATACACGA
258 TCATGAAAAACTGAGCCGGGACCCAGAACGCGTTTCTAGCT-AAAACCGTGATATA-GTACACGA
*
15825 -TTCTTGCT
321 TTTC-AGCT
* *
15833 AAAGTTTTGCAAAAATTGA-CCCGAAATATTTTTTTCTCAATTTTTGGCCAAAATAATCATAAAA
1 AAAATTTTGCAAAAA-TGAGCCCGAAATATTTTTTCCTCAATTTTTGGCCAAAATAATCATAAAA
15897 AATA
65 AATA
15901 ATTAGAGGGC
Statistics
Matches: 598, Mismatches: 104, Indels: 53
0.79 0.14 0.07
Matches are distributed among these distances:
327 4 0.01
328 154 0.26
329 150 0.25
330 49 0.08
331 11 0.02
332 19 0.03
333 1 0.00
334 1 0.00
335 21 0.04
336 58 0.10
337 127 0.21
338 1 0.00
339 2 0.00
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (328 bp):
AAAATTTTGCAAAAATGAGCCCGAAATATTTTTTCCTCAATTTTTGGCCAAAATAATCATAAAAA
ATATATAATTAAACGCCAAAAAGATTGGGGGTCTTTTCACACTTCTAATATCGTATTCCCTATTT
TTTCTAAATTAATTTCTAATTAAATCGAAACCGATTCAGATGCTCGTAAAAACATATCCTTAAAT
CCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGAAGTCTTGGCGCCAAAAATCA
TGAAAAACTGAGCCGGGACCCAGAACGCGTTTCTAGCTAAAACCGTGATATAGTACACGATTTCA
GCT
Found at i:16009 original size:21 final size:21
Alignment explanation
Indices: 15985--16025 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
15975 GATTTCTAAT
* *
15985 TCTGGTAACCTCCCTGTGAAC
1 TCTGATAACCTCCCTATGAAC
16006 TCTGATAACCTCCCTATGAA
1 TCTGATAACCTCCCTATGAA
16026 ATTATAATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.32, G:0.15, T:0.29
Consensus pattern (21 bp):
TCTGATAACCTCCCTATGAAC
Found at i:24786 original size:57 final size:57
Alignment explanation
Indices: 24691--24799 Score: 182
Period size: 57 Copynumber: 1.9 Consensus size: 57
24681 AGTGCGCAAC
* * * *
24691 ACGGGTCAGATCCGGATTAATCAGGGCAAAGCCTTGAATACCGGATGGGATACCTAA
1 ACGGGTCAGATCCGGATTAATCAAGGCAAAACCCTGAATACCGGATGAGATACCTAA
24748 ACGGGTCAGATCCGGATTAATCAAGGCAAAACCCTGAATACCGGATGAGATA
1 ACGGGTCAGATCCGGATTAATCAAGGCAAAACCCTGAATACCGGATGAGATA
24800 AAAAAAAAAC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.34, C:0.21, G:0.27, T:0.18
Consensus pattern (57 bp):
ACGGGTCAGATCCGGATTAATCAAGGCAAAACCCTGAATACCGGATGAGATACCTAA
Found at i:24875 original size:47 final size:48
Alignment explanation
Indices: 24785--24880 Score: 142
Period size: 47 Copynumber: 2.0 Consensus size: 48
24775 AAAACCCTGA
24785 ATACCGGATGAGATAAAAAAAAAACACCCGATGAATGAAAGTGTGAGAC
1 ATACCGGATGAGAT-AAAAAAAAACACCCGATGAATGAAAGTGTGAGAC
* *
24834 ATACCGGATGGGAT-AAAAAAAACACCCGATGAGT-AAGAGTGTGAGAC
1 ATACCGGATGAGATAAAAAAAAACACCCGATGAATGAA-AGTGTGAGAC
24881 GAGGAAAAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
46 2 0.05
47 29 0.66
49 13 0.30
ACGTcount: A:0.46, C:0.15, G:0.25, T:0.15
Consensus pattern (48 bp):
ATACCGGATGAGATAAAAAAAAACACCCGATGAATGAAAGTGTGAGAC
Found at i:25108 original size:3 final size:3
Alignment explanation
Indices: 25100--25129 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
25090 AATATTCCTG
25100 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
25130 ATATTGAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:28699 original size:52 final size:52
Alignment explanation
Indices: 28624--28729 Score: 167
Period size: 52 Copynumber: 2.0 Consensus size: 52
28614 TTTTTGGCCA
* * * *
28624 GGTTAGCATGCTAATTTTCATGGTAGGTTGATTACTTATCCTAATTGTATTT
1 GGTTAACATGCTAATTTTCATGGTAAGTTGATTACTCATCCTAACTGTATTT
*
28676 GGTTAACATGCTAATTTTCATGGTAAGTTGATTACTCATCCTAGCTGTATTT
1 GGTTAACATGCTAATTTTCATGGTAAGTTGATTACTCATCCTAACTGTATTT
28728 GG
1 GG
28730 CTTTCATGGT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (52 bp):
GGTTAACATGCTAATTTTCATGGTAAGTTGATTACTCATCCTAACTGTATTT
Found at i:29025 original size:2 final size:2
Alignment explanation
Indices: 29018--29047 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
29008 TCCGATCATC
29018 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
29048 TAATTAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49929 original size:2 final size:2
Alignment explanation
Indices: 49922--49949 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
49912 AGTGCTTTTA
49922 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
49950 TATTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.