Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013099.1 Corchorus olitorius cultivar O-4 contig13132, 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: 13423
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:126 original size:32 final size:32
Alignment explanation
Indices: 1--673 Score: 850
Period size: 32 Copynumber: 21.3 Consensus size: 32
**
1 AAGACCTGTCTGAGGTC-GAATTGAACTG-GTA
1 AAGACCTGTCTGAGGTCGGAATAAAACTGAG-A
* *
32 AAGACCTGTCTGAGGTCGAAATTAAAAGTTGAG-
1 AAGACCTGTCTGAGGTCGGAA-TAAAA-CTGAGA
*
65 AAGACCTGTCTGAGGTCGG-----AACTGTGA
1 AAGACCTGTCTGAGGTCGGAATAAAACTGAGA
92 AAGACCTGTCTGAGGTCGGAATAAAACTGAGA
1 AAGACCTGTCTGAGGTCGGAATAAAACTGAGA
* **
124 AAGACTTGTCTGAGGTCGGAATTGAACTG-GTA
1 AAGACCTGTCTGAGGTCGGAATAAAACTGAG-A
*
156 AAGACCTGTCTGAGGTCGAAATTAAAAGCTGAGA
1 AAGACCTGTCTGAGGTCGGAA-TAAAA-CTGAGA
190 AAGACCTGTCTGAGGTCGG-----AACTGAGA
1 AAGACCTGTCTGAGGTCGGAATAAAACTGAGA
*
217 AAGACCTGTCTGAGTTCGGAATAAAACTGAGA
1 AAGACCTGTCTGAGGTCGGAATAAAACTGAGA
249 AAGACCTGTCTGAGGTCGGAATAAAACTGAGA
1 AAGACCTGTCTGAGGTCGGAATAAAACTGAGA
* *
281 AAGACCTGTCTGAGGTCGGAATAAAAAT-ATA
1 AAGACCTGTCTGAGGTCGGAATAAAACTGAGA
312 AAGACCTGTCTGAGGTC-GAACTAAAACTGAGA
1 AAGACCTGTCTGAGGTCGGAA-TAAAACTGAGA
344 AAGACCTGTCTGAGGTCGGAATAAAAGCTGAGA
1 AAGACCTGTCTGAGGTCGGAATAAAA-CTGAGA
**
377 AAGACCTGTCTGAGGTCGGAATTGAACTG-GTA
1 AAGACCTGTCTGAGGTCGGAATAAAACTGAG-A
*
409 AAGACCTGTCTGAGGTCGAAATTAAAAGCTGAGA
1 AAGACCTGTCTGAGGTCGGAA-TAAAA-CTGAGA
443 AAGACCTGTCTGAGGTCGGAATAAAACTGAGA
1 AAGACCTGTCTGAGGTCGGAATAAAACTGAGA
*
475 AAGACCTGTCTGAGGTCGGAATAAAACTGAAA
1 AAGACCTGTCTGAGGTCGGAATAAAACTGAGA
* ** *
507 AAGACCTATCTGAGGTCGGAATTGAACTGATA
1 AAGACCTGTCTGAGGTCGGAATAAAACTGAGA
*
539 AAGACCTGTCTGAGGTCGAAATTAAAAGCTGAGA
1 AAGACCTGTCTGAGGTCGGAA-TAAAA-CTGAGA
* * *
573 AAGACCTGTCTGAGGTCGAAATAAAGCTGAAA
1 AAGACCTGTCTGAGGTCGGAATAAAACTGAGA
*
605 AAGACCCGTCTGAGGTC-G----AAACTGAGA
1 AAGACCTGTCTGAGGTCGGAATAAAACTGAGA
632 AAGACCTGTCTGAGGTCGGAATAAAACTGAGA
1 AAGACCTGTCTGAGGTCGGAATAAAACTGAGA
664 AAGACCTGTC
1 AAGACCTGTC
674 AGGTCCTTAA
Statistics
Matches: 563, Mismatches: 45, Indels: 67
0.83 0.07 0.10
Matches are distributed among these distances:
26 3 0.01
27 68 0.12
28 3 0.01
30 3 0.01
31 44 0.08
32 293 0.52
33 72 0.13
34 74 0.13
35 3 0.01
ACGTcount: A:0.36, C:0.16, G:0.28, T:0.21
Consensus pattern (32 bp):
AAGACCTGTCTGAGGTCGGAATAAAACTGAGA
Found at i:239 original size:125 final size:125
Alignment explanation
Indices: 1--673 Score: 938
Period size: 125 Copynumber: 5.3 Consensus size: 125
*
1 AAGACCTGTCTGAGGTC-GAATTGAACTGGTAAAGACCTGTCTGAGGTCGAAATTAAAAGTTGAG
1 AAGACCTGTCTGAGGTCGGAATTGAACTGGTAAAGACCTGTCTGAGGTCGAAATTAAAAGCTGAG
*
65 -AAGACCTGTCTGAGGTCGGAACTGTGAAAGACCTGTCTGAGGTCGGAATAAAACTGAGA
66 AAAGACCTGTCTGAGGTCGGAACTGAGAAAGACCTGTCTGAGGTCGGAATAAAACTGAGA
*
124 AAGACTTGTCTGAGGTCGGAATTGAACTGGTAAAGACCTGTCTGAGGTCGAAATTAAAAGCTGAG
1 AAGACCTGTCTGAGGTCGGAATTGAACTGGTAAAGACCTGTCTGAGGTCGAAATTAAAAGCTGAG
*
189 AAAGACCTGTCTGAGGTCGGAACTGAGAAAGACCTGTCTGAGTTCGGAATAAAACTGAGA
66 AAAGACCTGTCTGAGGTCGGAACTGAGAAAGACCTGTCTGAGGTCGGAATAAAACTGAGA
** * *
249 AAGACCTGTCTGAGGTCGGAATAAAACTGAG-AAAGACCTGTCTGAGGTCGGAA-TAAAA-AT-A
1 AAGACCTGTCTGAGGTCGGAATTGAACTG-GTAAAGACCTGTCTGAGGTCGAAATTAAAAGCTGA
* *
310 TAAAGACCTGTCTGAGGTCGAACTAAAACTGAGAAAGACCTGTCTGAGGTCGGAATAAAAGCTGA
65 GAAAGACCTGTCTGAGGTCG-----GAACTGAGAAAGACCTGTCTGAGGTCGGAATAAAA-CTGA
375 GA
124 GA
377 AAGACCTGTCTGAGGTCGGAATTGAACTGGTAAAGACCTGTCTGAGGTCGAAATTAAAAGCTGAG
1 AAGACCTGTCTGAGGTCGGAATTGAACTGGTAAAGACCTGTCTGAGGTCGAAATTAAAAGCTGAG
*
442 AAAGACCTGTCTGAGGTCGGAATAAAACTGAGAAAGACCTGTCTGAGGTCGGAATAAAACTGAAA
66 AAAGACCTGTCTGAGGTCGG-----AACTGAGAAAGACCTGTCTGAGGTCGGAATAAAACTGAGA
* *
507 AAGACCTATCTGAGGTCGGAATTGAACTGATAAAGACCTGTCTGAGGTCGAAATTAAAAGCTGAG
1 AAGACCTGTCTGAGGTCGGAATTGAACTGGTAAAGACCTGTCTGAGGTCGAAATTAAAAGCTGAG
* * *
572 AAAGACCTGTCTGAGGTCGAAATAAAGCTGAAAAAGACCCGTCTGAGGTC-G----AAACTGAGA
66 AAAGACCTGTCTGAGGTCG----GAA-CTGAGAAAGACCTGTCTGAGGTCGGAATAAAACTGAGA
**
632 AAGACCTGTCTGAGGTCGGAATAAAACTGAG-AAAGACCTGTC
1 AAGACCTGTCTGAGGTCGGAATTGAACTG-GTAAAGACCTGTC
674 AGGTCCTTAA
Statistics
Matches: 497, Mismatches: 29, Indels: 46
0.87 0.05 0.08
Matches are distributed among these distances:
122 20 0.04
123 17 0.03
124 51 0.10
125 149 0.30
126 1 0.00
127 34 0.07
128 54 0.11
129 8 0.02
130 109 0.22
131 54 0.11
ACGTcount: A:0.36, C:0.16, G:0.28, T:0.21
Consensus pattern (125 bp):
AAGACCTGTCTGAGGTCGGAATTGAACTGGTAAAGACCTGTCTGAGGTCGAAATTAAAAGCTGAG
AAAGACCTGTCTGAGGTCGGAACTGAGAAAGACCTGTCTGAGGTCGGAATAAAACTGAGA
Found at i:2176 original size:11 final size:11
Alignment explanation
Indices: 2160--2189 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
2150 TAATCGTGTT
2160 TCGTGTCATAA
1 TCGTGTCATAA
2171 TCGTGTCATAA
1 TCGTGTCATAA
2182 TCGTGTCA
1 TCGTGTCA
2190 AGACACGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (11 bp):
TCGTGTCATAA
Found at i:2607 original size:12 final size:12
Alignment explanation
Indices: 2590--2621 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
2580 TACCCTATGT
2590 AAACACGACACG
1 AAACACGACACG
2602 AAACACGACACG
1 AAACACGACACG
2614 AAACACGA
1 AAACACGA
2622 ATTGCCAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.53, C:0.31, G:0.16, T:0.00
Consensus pattern (12 bp):
AAACACGACACG
Found at i:2710 original size:35 final size:36
Alignment explanation
Indices: 2664--2736 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
2654 ACTTTCATAG
2664 GCTTTATTGTTGCTTTG-TTGATGGAGAAGAACTTT
1 GCTTTATTGTTGCTTTGCTTGATGGAGAAGAACTTT
*
2699 GCTTTGTTGTTGCTTTGCTTGATGGAGAAGAACTTT
1 GCTTTATTGTTGCTTTGCTTGATGGAGAAGAACTTT
2735 GC
1 GC
2737 CTTGCCTTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 16 0.44
36 20 0.56
ACGTcount: A:0.18, C:0.11, G:0.27, T:0.44
Consensus pattern (36 bp):
GCTTTATTGTTGCTTTGCTTGATGGAGAAGAACTTT
Found at i:7146 original size:31 final size:31
Alignment explanation
Indices: 7110--7257 Score: 206
Period size: 31 Copynumber: 4.8 Consensus size: 31
7100 GCATGCCATG
* * * *
7110 TGTACCAAAAAGCGACATGTGACACGCCACG
1 TGTACCAAAAAGTGACACGTGGCACGCCACA
*
7141 TGTACCAAAAAGCGACACGTGGCACGCCACA
1 TGTACCAAAAAGTGACACGTGGCACGCCACA
*
7172 TGTACCAAAAAGTGATACGTGGCACGCCACA
1 TGTACCAAAAAGTGACACGTGGCACGCCACA
* * **
7203 TGTACCAAAAAGTGACATGTGTCACGCCATT
1 TGTACCAAAAAGTGACACGTGGCACGCCACA
7234 TGTACCAAAAAGTGACACGTGGCA
1 TGTACCAAAAAGTGACACGTGGCA
7258 TGCCTTGTGC
Statistics
Matches: 105, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 105 1.00
ACGTcount: A:0.35, C:0.26, G:0.22, T:0.16
Consensus pattern (31 bp):
TGTACCAAAAAGTGACACGTGGCACGCCACA
Found at i:7275 original size:31 final size:31
Alignment explanation
Indices: 7147--7276 Score: 109
Period size: 31 Copynumber: 4.2 Consensus size: 31
7137 CACGTGTACC
* ** * *
7147 AAAAAGCGACACGTGGCACGCCACATGTACC
1 AAAAAGTGACACGTGGCACGCCATTTGCACA
* ** * *
7178 AAAAAGTGATACGTGGCACGCCACATGTACC
1 AAAAAGTGACACGTGGCACGCCATTTGCACA
* * * *
7209 AAAAAGTGACATGTGTCACGCCATTTGTACC
1 AAAAAGTGACACGTGGCACGCCATTTGCACA
*
7240 AAAAAGTGACACGTGGCATGCC-TTGTGCACA
1 AAAAAGTGACACGTGGCACGCCATT-TGCACA
7271 AAAAAG
1 AAAAAG
7277 GAAACGTATC
Statistics
Matches: 86, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
30 2 0.02
31 84 0.98
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.17
Consensus pattern (31 bp):
AAAAAGTGACACGTGGCACGCCATTTGCACA
Found at i:9817 original size:29 final size:28
Alignment explanation
Indices: 9761--9842 Score: 92
Period size: 29 Copynumber: 2.9 Consensus size: 28
9751 TGTTGGGAAC
* *
9761 AATTATTAGTGGTATTTCCGTCGCAAAA
1 AATTATTAGTGATATTTCCGTCACAAAA
* *
9789 AATTATTAGTAGATATTTCTGTCATAAAA
1 AATTATTAGT-GATATTTCCGTCACAAAA
* *
9818 AATTATTAATGGATATTTCCATCAC
1 AATTATTAGT-GATATTTCCGTCAC
9843 TAATTTTCCT
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
28 10 0.23
29 34 0.77
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (28 bp):
AATTATTAGTGATATTTCCGTCACAAAA
Found at i:10144 original size:4 final size:4
Alignment explanation
Indices: 10135--10170 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
10125 TCATTGCTAA
*
10135 ATTT ATTT ATTT ATTT ATTT ATTT A-TT ATTT TTTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT A
10171 AGTATGAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:13084 original size:8 final size:8
Alignment explanation
Indices: 13067--13096 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
13057 TCTCTGATGC
13067 AAAA-AAA
1 AAAAGAAA
13074 AAAAGAAA
1 AAAAGAAA
13082 AAAAGAAA
1 AAAAGAAA
13090 AAAAGAA
1 AAAAGAA
13097 TAAGATTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 4 0.18
8 18 0.82
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Done.