Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021804.1 Corchorus olitorius cultivar O-4 contig21837, 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: 23650
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.34
Found at i:3509 original size:68 final size:69
Alignment explanation
Indices: 3425--3566 Score: 268
Period size: 69 Copynumber: 2.1 Consensus size: 69
3415 TCAACATGCA
*
3425 AAATTTAATTACCAATTTTTAGG-GAAAAAAATAACCCTACCCAATAATGCTAATAATATTATGT
1 AAATTTAATTACCAATTTTTAGGAAAAAAAAATAACCCTACCCAATAATGCTAATAATATTATGT
3489 AATT
66 AATT
3493 AAATTTAATTACCAATTTTTAGGAAAAAAAAATAACCCTACCCAATAATGCTAATAATATTATGT
1 AAATTTAATTACCAATTTTTAGGAAAAAAAAATAACCCTACCCAATAATGCTAATAATATTATGT
3558 AATT
66 AATT
3562 AAATT
1 AAATT
3567 AAATATAAAT
Statistics
Matches: 72, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
68 23 0.32
69 49 0.68
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.34
Consensus pattern (69 bp):
AAATTTAATTACCAATTTTTAGGAAAAAAAAATAACCCTACCCAATAATGCTAATAATATTATGT
AATT
Found at i:8244 original size:29 final size:29
Alignment explanation
Indices: 8207--8265 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
8197 TTACTGTTAT
*
8207 TGTTGATAATATGAGATTATATAGTTTTA
1 TGTTAATAATATGAGATTATATAGTTTTA
8236 TGTTAATAATATGAGATTATATAGTTTTA
1 TGTTAATAATATGAGATTATATAGTTTTA
8265 T
1 T
8266 CTTATTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (29 bp):
TGTTAATAATATGAGATTATATAGTTTTA
Found at i:19572 original size:46 final size:46
Alignment explanation
Indices: 19519--19797 Score: 382
Period size: 46 Copynumber: 6.0 Consensus size: 46
19509 TAAATATTGC
*
19519 CCCAATTATTTTCCTTGTTTATTTTAAATTCTTTGTTGTATTCTTA
1 CCCAATTATTTTCCTTGTTTATTCTAAATTCTTTGTTGTATTCTTA
* * * * *
19565 CCCAATTATTTTCCTTGTTTATTCTAATTTCTGTGTT-TAAATATTGC
1 CCCAATTATTTTCCTTGTTTATTCTAAATTCTTTGTTGT-ATTCTT-A
*
19612 CCCAATTATTTTCCTTGTTTATTTTAAATTCTTTGTTGTATTCTTA
1 CCCAATTATTTTCCTTGTTTATTCTAAATTCTTTGTTGTATTCTTA
* * * * *
19658 CCCAATTATTTTCCTTGTTTATTCTAATTTCTGTGTT-TAAATATTGC
1 CCCAATTATTTTCCTTGTTTATTCTAAATTCTTTGTTGT-ATTCTT-A
*
19705 CCCAATTATTTTCCTTGTTTATTTTAAATTCTTTGTTGTATTCTTA
1 CCCAATTATTTTCCTTGTTTATTCTAAATTCTTTGTTGTATTCTTA
*
19751 CCCAATTATTTTCCTTGTTTATTCTAATTTCTTTGTTGTATTCTTA
1 CCCAATTATTTTCCTTGTTTATTCTAAATTCTTTGTTGTATTCTTA
19797 C
1 C
19798 TTCCTTGTTT
Statistics
Matches: 201, Mismatches: 26, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
45 2 0.01
46 121 0.60
47 76 0.38
48 2 0.01
ACGTcount: A:0.20, C:0.16, G:0.07, T:0.57
Consensus pattern (46 bp):
CCCAATTATTTTCCTTGTTTATTCTAAATTCTTTGTTGTATTCTTA
Found at i:19662 original size:93 final size:93
Alignment explanation
Indices: 19499--19787 Score: 562
Period size: 93 Copynumber: 3.1 Consensus size: 93
19489 TCTATCGCTG
19499 ATTT-TGTGTTTAAATATTGCCCCAATTATTTTCCTTGTTTATTTTAAATTCTTTGTTGTATTCT
1 ATTTCTGTGTTTAAATATTGCCCCAATTATTTTCCTTGTTTATTTTAAATTCTTTGTTGTATTCT
19563 TACCCAATTATTTTCCTTGTTTATTCTA
66 TACCCAATTATTTTCCTTGTTTATTCTA
19591 ATTTCTGTGTTTAAATATTGCCCCAATTATTTTCCTTGTTTATTTTAAATTCTTTGTTGTATTCT
1 ATTTCTGTGTTTAAATATTGCCCCAATTATTTTCCTTGTTTATTTTAAATTCTTTGTTGTATTCT
19656 TACCCAATTATTTTCCTTGTTTATTCTA
66 TACCCAATTATTTTCCTTGTTTATTCTA
19684 ATTTCTGTGTTTAAATATTGCCCCAATTATTTTCCTTGTTTATTTTAAATTCTTTGTTGTATTCT
1 ATTTCTGTGTTTAAATATTGCCCCAATTATTTTCCTTGTTTATTTTAAATTCTTTGTTGTATTCT
19749 TACCCAATTATTTTCCTTGTTTATTCTA
66 TACCCAATTATTTTCCTTGTTTATTCTA
*
19777 ATTTCTTTGTT
1 ATTTCTGTGTT
19788 GTATTCTTAC
Statistics
Matches: 195, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
92 4 0.02
93 191 0.98
ACGTcount: A:0.20, C:0.16, G:0.08, T:0.57
Consensus pattern (93 bp):
ATTTCTGTGTTTAAATATTGCCCCAATTATTTTCCTTGTTTATTTTAAATTCTTTGTTGTATTCT
TACCCAATTATTTTCCTTGTTTATTCTA
Found at i:19786 original size:18 final size:19
Alignment explanation
Indices: 19760--19831 Score: 85
Period size: 18 Copynumber: 3.9 Consensus size: 19
19750 ACCCAATTAT
19760 TTTCCTTGTT-TATTCTAA
1 TTTCCTTGTTGTATTCTAA
* *
19778 TTTCTTTGTTGTATTCTTA
1 TTTCCTTGTTGTATTCTAA
*
19797 CTTCCTTGTT-TATTCTAA
1 TTTCCTTGTTGTATTCTAA
**
19815 TTTTTTTGTTGTATTCT
1 TTTCCTTGTTGTATTCT
19832 TACATACCAA
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
18 23 0.52
19 21 0.48
ACGTcount: A:0.12, C:0.14, G:0.08, T:0.65
Consensus pattern (19 bp):
TTTCCTTGTTGTATTCTAA
Found at i:19802 original size:37 final size:37
Alignment explanation
Indices: 19761--19834 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
19751 CCCAATTATT
19761 TTCCTTGTTTATTCTAATTTCTTTGTTGTATTCTTAC
1 TTCCTTGTTTATTCTAATTTCTTTGTTGTATTCTTAC
*
19798 TTCCTTGTTTATTCTAATTTTTTTGTTGTATTCTTAC
1 TTCCTTGTTTATTCTAATTTCTTTGTTGTATTCTTAC
19835 ATACCAAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.14, C:0.15, G:0.08, T:0.64
Consensus pattern (37 bp):
TTCCTTGTTTATTCTAATTTCTTTGTTGTATTCTTAC
Found at i:19889 original size:18 final size:18
Alignment explanation
Indices: 19866--19902 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
19856 AAAACACCCC
19866 TCATCTCTAATTCTATTA
1 TCATCTCTAATTCTATTA
19884 TCATCTCTAATTCTATTA
1 TCATCTCTAATTCTATTA
19902 T
1 T
19903 TTTGTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.22, G:0.00, T:0.51
Consensus pattern (18 bp):
TCATCTCTAATTCTATTA
Found at i:20045 original size:49 final size:49
Alignment explanation
Indices: 19973--20100 Score: 256
Period size: 49 Copynumber: 2.6 Consensus size: 49
19963 AATCTACCAG
19973 ATCTACCAGCATTTGGATTAGGTCGACGAGGATAATACGCATTTGGATA
1 ATCTACCAGCATTTGGATTAGGTCGACGAGGATAATACGCATTTGGATA
20022 ATCTACCAGCATTTGGATTAGGTCGACGAGGATAATACGCATTTGGATA
1 ATCTACCAGCATTTGGATTAGGTCGACGAGGATAATACGCATTTGGATA
20071 ATCTACCAGCATTTGGATTAGGTCGACGAG
1 ATCTACCAGCATTTGGATTAGGTCGACGAG
20101 CGCCATGCTA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 79 1.00
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (49 bp):
ATCTACCAGCATTTGGATTAGGTCGACGAGGATAATACGCATTTGGATA
Found at i:20123 original size:25 final size:25
Alignment explanation
Indices: 20086--20134 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
20076 CCAGCATTTG
* *
20086 GATTAGGTCGACGAGCGCCATGCTA
1 GATTAGGTAGACGAGCACCATGCTA
20111 GATTAGGTAGACGAGCACCATGCT
1 GATTAGGTAGACGAGCACCATGCT
20135 GGAGAACTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.27, C:0.22, G:0.31, T:0.20
Consensus pattern (25 bp):
GATTAGGTAGACGAGCACCATGCTA
Found at i:20223 original size:20 final size:20
Alignment explanation
Indices: 20198--20238 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
20188 GAGAAATAGG
20198 TTGGATTAGGTCGATAATCA
1 TTGGATTAGGTCGATAATCA
20218 TTGGATTAGGTCGATAATCA
1 TTGGATTAGGTCGATAATCA
20238 T
1 T
20239 GACCAGCGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.37
Consensus pattern (20 bp):
TTGGATTAGGTCGATAATCA
Found at i:20455 original size:26 final size:27
Alignment explanation
Indices: 20426--20478 Score: 99
Period size: 26 Copynumber: 2.0 Consensus size: 27
20416 ACGCCTTAGG
20426 TGATCCAAAGCCTTCAAGTG-ATCCAA
1 TGATCCAAAGCCTTCAAGTGAATCCAA
20452 TGATCCAAAGCCTTCAAGTGAATCCAA
1 TGATCCAAAGCCTTCAAGTGAATCCAA
20479 ATGTATCAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 20 0.77
27 6 0.23
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (27 bp):
TGATCCAAAGCCTTCAAGTGAATCCAA
Found at i:20614 original size:90 final size:90
Alignment explanation
Indices: 20378--20622 Score: 436
Period size: 91 Copynumber: 2.7 Consensus size: 90
20368 AAGTGCCTTG
20378 AGTGATCCAAATGTATCAGCAAGTGAGGAGATTTCAGAACGCCTTAGGTGATCCAAAGCCTTCAA
1 AGTGATCCAAATGTATCAGCAAGTGAGGAGATTTCAGAACGCCTTAGGTGATCCAAAGCCTTCAA
20443 GTGATCCAATGATCCAAAGCCTTCA
66 GTGATCCAATGATCCAAAGCCTTCA
* *
20468 AGTGAATCCAAATGTATCAGCATGTGAGGAGATTTCAGAACGCCTTAGGTGGTCCAAAGCCTTCA
1 AGTG-ATCCAAATGTATCAGCAAGTGAGGAGATTTCAGAACGCCTTAGGTGATCCAAAGCCTTCA
*
20533 AGTGATTCAATGATCCAAAGCCTTCA
65 AGTGATCCAATGATCCAAAGCCTTCA
* *
20559 AGTGATCCAAACGTATCAGCAAGTGAGGAGATTTCAAAACGCCTTAGGTGATCCAAAGCCTTCA
1 AGTGATCCAAATGTATCAGCAAGTGAGGAGATTTCAGAACGCCTTAGGTGATCCAAAGCCTTCA
20623 GAACATATCA
Statistics
Matches: 147, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
90 60 0.41
91 87 0.59
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (90 bp):
AGTGATCCAAATGTATCAGCAAGTGAGGAGATTTCAGAACGCCTTAGGTGATCCAAAGCCTTCAA
GTGATCCAATGATCCAAAGCCTTCA
Found at i:20737 original size:16 final size:16
Alignment explanation
Indices: 20716--20748 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
20706 ATCACAATAT
*
20716 GATATAACAGGGTACA
1 GATATAAAAGGGTACA
20732 GATATAAAAGGGTACA
1 GATATAAAAGGGTACA
20748 G
1 G
20749 GGTGCTAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.09, G:0.27, T:0.18
Consensus pattern (16 bp):
GATATAAAAGGGTACA
Found at i:22890 original size:30 final size:30
Alignment explanation
Indices: 22854--22916 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
22844 TAATCTTTCA
* * *
22854 AAATTTTGTCATTGTACCTCTTAAATTTTT
1 AAATTTTATCATTGTACCGCTTAAACTTTT
*
22884 AAATTTTATCATTTTACCGCTTAAACTTTT
1 AAATTTTATCATTGTACCGCTTAAACTTTT
22914 AAA
1 AAA
22917 ATTGGTGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.49
Consensus pattern (30 bp):
AAATTTTATCATTGTACCGCTTAAACTTTT
Done.