Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021451.1 Corchorus olitorius cultivar O-4 contig21484, 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: 18363
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:761 original size:112 final size:112
Alignment explanation
Indices: 564--785 Score: 444
Period size: 112 Copynumber: 2.0 Consensus size: 112
554 TTTTGCTTTT
564 TCCACTTTTTTGTATTTTTTAATAACAATGCTATATTACAACTATTTAGTAGCAAATTGTAAATG
1 TCCACTTTTTTGTATTTTTTAATAACAATGCTATATTACAACTATTTAGTAGCAAATTGTAAATG
629 TAGATTCTACTTGTGCTATATTATGTGAAAATGCCTAATTAAATTTG
66 TAGATTCTACTTGTGCTATATTATGTGAAAATGCCTAATTAAATTTG
676 TCCACTTTTTTGTATTTTTTAATAACAATGCTATATTACAACTATTTAGTAGCAAATTGTAAATG
1 TCCACTTTTTTGTATTTTTTAATAACAATGCTATATTACAACTATTTAGTAGCAAATTGTAAATG
741 TAGATTCTACTTGTGCTATATTATGTGAAAATGCCTAATTAAATT
66 TAGATTCTACTTGTGCTATATTATGTGAAAATGCCTAATTAAATT
786 AGTTTTCCCA
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
112 110 1.00
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (112 bp):
TCCACTTTTTTGTATTTTTTAATAACAATGCTATATTACAACTATTTAGTAGCAAATTGTAAATG
TAGATTCTACTTGTGCTATATTATGTGAAAATGCCTAATTAAATTTG
Found at i:1878 original size:30 final size:30
Alignment explanation
Indices: 1842--2232 Score: 649
Period size: 30 Copynumber: 13.1 Consensus size: 30
1832 TTAACTGATG
*
1842 AAGCAATGATCCTAAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
1872 AAGCAATGATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
1902 AAGCAATGATCCTCAACCAGGATT-AAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
1931 AAGCAATGATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
1961 AAGCAATGATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
1991 AAGCAGTGATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* *
2021 AAGTAATGATCCTCAATCAGGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
2051 AAGCAATGATCCTCAACCAGGATTAAAATG
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
2081 AAGCAATGATCCTCAACCAGGATTAAAATG
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* * *
2111 AAGCAATGATCCTTAATCAAGATTAAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
2141 AAGCAATGATCCTCAACCAGGATTAAAACA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
* * *
2171 AAGGAAAGATCCTCAACCAGGATTAAAATG
1 AAGCAATGATCCTCAACCAGGATTAAAATA
*
2201 AAGCAATGATCCTCAACCAGGATTGAAATA
1 AAGCAATGATCCTCAACCAGGATTAAAATA
2231 AA
1 AA
2233 TTGATACAAC
Statistics
Matches: 336, Mismatches: 24, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
29 29 0.09
30 307 0.91
ACGTcount: A:0.46, C:0.19, G:0.15, T:0.20
Consensus pattern (30 bp):
AAGCAATGATCCTCAACCAGGATTAAAATA
Found at i:2481 original size:22 final size:22
Alignment explanation
Indices: 2456--2503 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
2446 TTAATACCCA
*
2456 GAGGTTTCTGAAATTGTGCCTG
1 GAGGTTTCTGAAATTGTGCCCG
*
2478 GAGGTTTCTGAATTTGTGCCCG
1 GAGGTTTCTGAAATTGTGCCCG
2500 GAGG
1 GAGG
2504 ACTTACAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.15, G:0.35, T:0.33
Consensus pattern (22 bp):
GAGGTTTCTGAAATTGTGCCCG
Found at i:2776 original size:25 final size:24
Alignment explanation
Indices: 2748--2806 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 24
2738 TTATCAATTG
2748 CCCGGAGGACTTGTCAGAATTAATA
1 CCCGGAGGACTT-TCAGAATTAATA
* * *
2773 CCCGGAGG--TTTCTGAATTAGTG
1 CCCGGAGGACTTTCAGAATTAATA
2795 CCCGGAGGACTT
1 CCCGGAGGACTT
2807 ACCAACGCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 17 0.59
23 2 0.07
24 2 0.07
25 8 0.28
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (24 bp):
CCCGGAGGACTTTCAGAATTAATA
Found at i:2821 original size:169 final size:168
Alignment explanation
Indices: 2533--2912 Score: 616
Period size: 169 Copynumber: 2.3 Consensus size: 168
2523 GAATTGAGAA
* * * *
2533 GAAAAACTTGATGAAATCAAATGGTACCCGGAGGTTTTACCAATTGTCCGGAGGACTTATCAGAA
1 GAAAAACTTGATGAAATGAAATGATACCCGGAGGTTTTATCAATTGCCCGGAGGACTTATCAGAA
* * * *
2598 TTAATATCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAATGTAAACTCTGAATAGAGAC
66 TTAATACCCGGAGGTTTCTGAATTAGTGCCCGGAGGACTTACCAACGCAAACTCTGAATAGAGAC
*
2663 CTTGACCAAGGATTTTAAACTTAAATATGAACTTTTAAT
131 CTTGACCAAGGATTTT-AACTTAAACATGAACTTTTAAT
* *
2702 GACAAACTTGATGAAATGAAATGATACCCGGAGGTTTTATCAATTGCCCGGAGGACTTGTCAGAA
1 GAAAAACTTGATGAAATGAAATGATACCCGGAGGTTTTATCAATTGCCCGGAGGACTTATCAGAA
2767 TTAATACCCGGAGGTTTCTGAATTAGTGCCCGGAGGACTTACCAACGCAAACTCTGAATAGAGAC
66 TTAATACCCGGAGGTTTCTGAATTAGTGCCCGGAGGACTTACCAACGCAAACTCTGAATAGAGAC
* **
2832 CTTGACCAAGGATTTTAACTTAAACATGAATTTTTGGT
131 CTTGACCAAGGATTTTAACTTAAACATGAACTTTTAAT
*
2870 GAAAAACTTGATAAAATGAAATGATACCCGGAGGTTTTATCAA
1 GAAAAACTTGATGAAATGAAATGATACCCGGAGGTTTTATCAA
2913 ATGGAAATAA
Statistics
Matches: 195, Mismatches: 16, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
168 59 0.30
169 136 0.70
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (168 bp):
GAAAAACTTGATGAAATGAAATGATACCCGGAGGTTTTATCAATTGCCCGGAGGACTTATCAGAA
TTAATACCCGGAGGTTTCTGAATTAGTGCCCGGAGGACTTACCAACGCAAACTCTGAATAGAGAC
CTTGACCAAGGATTTTAACTTAAACATGAACTTTTAAT
Found at i:3069 original size:69 final size:69
Alignment explanation
Indices: 2954--3409 Score: 804
Period size: 69 Copynumber: 6.6 Consensus size: 69
2944 AAGTAAGGCT
* * * * * *
2954 TGACTCATATGGAAACGAGCTTGGCTTGTAGAAAAACCTATATGGCTTGGATGAAACCAAGGCTT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTT
3019 AAAC
66 AAAC
*
3023 TGACTCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTT
3088 AAAC
66 AAAC
3092 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTT
3157 AAAC
66 AAAC
* *
3161 TGACTTGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGTCTTGGATGGAACCAAGGCTT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTT
3226 AAAC
66 AAAC
*
3230 TGACTCGTATGGAAACGAGTTTGGCTTGTGAAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTT
3295 AAAC
66 AAAC
* *
3299 TGACTCCTATGGAAACGAGTTTGGCTTGTAGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTT
3364 AAAC
66 AAAC
3368 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATG
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATG
3410 CATTCGGATG
Statistics
Matches: 371, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 371 1.00
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.27
Consensus pattern (69 bp):
TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTT
AAAC
Found at i:4596 original size:15 final size:15
Alignment explanation
Indices: 4558--4587 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4548 AGAGGTTGAA
*
4558 AGAAAGCAATTAAAC
1 AGAAAACAATTAAAC
4573 AGAAAACAATTAAAC
1 AGAAAACAATTAAAC
4588 TAGGAACAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.13, G:0.10, T:0.13
Consensus pattern (15 bp):
AGAAAACAATTAAAC
Found at i:11222 original size:22 final size:23
Alignment explanation
Indices: 11194--11238 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
11184 TTTTTTCAAA
11194 AAAAACGCA-AACACAA-AAAATT
1 AAAAACGCAGAA-ACAACAAAATT
11216 AAAAACGCAGAAACAACAAAATT
1 AAAAACGCAGAAACAACAAAATT
11239 TTTTAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.67, C:0.18, G:0.07, T:0.09
Consensus pattern (23 bp):
AAAAACGCAGAAACAACAAAATT
Found at i:11268 original size:26 final size:29
Alignment explanation
Indices: 11236--11311 Score: 113
Period size: 26 Copynumber: 2.7 Consensus size: 29
11226 AAACAACAAA
11236 ATTTTTTAGAAAAAACGCAGAAT-T-T-T
1 ATTTTTTAGAAAAAACGCAGAATATATAT
*
11262 TTTTTTTAGAAAAAACGCAGAATATATAT
1 ATTTTTTAGAAAAAACGCAGAATATATAT
*
11291 ATTTTTTAGAGAAAACGCAGA
1 ATTTTTTAGAAAAAACGCAGA
11312 CACAAAGAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
26 22 0.50
27 1 0.02
28 1 0.02
29 20 0.45
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.36
Consensus pattern (29 bp):
ATTTTTTAGAAAAAACGCAGAATATATAT
Found at i:11597 original size:15 final size:15
Alignment explanation
Indices: 11559--11588 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11549 AGAGGTTGAA
*
11559 AGAAATCAATTAAAC
1 AGAAAACAATTAAAC
11574 AGAAAACAATTAAAC
1 AGAAAACAATTAAAC
11589 TAGGAACAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.13, G:0.07, T:0.17
Consensus pattern (15 bp):
AGAAAACAATTAAAC
Found at i:12376 original size:14 final size:14
Alignment explanation
Indices: 12357--12387 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
12347 ACCCTTGCCT
12357 AAAAAACTAGAAGA
1 AAAAAACTAGAAGA
12371 AAAAAACTAGAAGA
1 AAAAAACTAGAAGA
12385 AAA
1 AAA
12388 GAAATTATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.74, C:0.06, G:0.13, T:0.06
Consensus pattern (14 bp):
AAAAAACTAGAAGA
Found at i:13915 original size:12 final size:12
Alignment explanation
Indices: 13887--14053 Score: 50
Period size: 14 Copynumber: 12.7 Consensus size: 12
13877 AATTCTCTTT
*
13887 TTATTTTGATT-
1 TTATTTTTATTA
* *
13898 TGATTTTTTTTA
1 TTATTTTTATTA
13910 TTATTTTTATTA
1 TTATTTTTATTA
* *
13922 TT-TTTTGATTT
1 TTATTTTTATTA
*
13933 TTGATTTTTGATTT
1 TT-ATTTTT-ATTA
*
13947 TTGATTTTTGATTT
1 TT-ATTTTT-ATTA
*
13961 TTGATTTTTGATTT
1 TT-ATTTTT-ATTA
*
13975 TTGATTTTTGATTT
1 TT-ATTTTT-ATTA
*
13989 TTGATTTTTGATTT
1 TT-ATTTTT-ATTA
*
14003 TTGATTTTTGATTT
1 TT-ATTTTT-ATTA
*
14017 TTGATTTTTGATTT
1 TT-ATTTTT-ATTA
*
14031 TTGATTTTTGATTT
1 TT-ATTTTT-ATTA
14045 TTGATTTTT
1 TT-ATTTTT
14054 GATTTTTTGA
Statistics
Matches: 144, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
11 17 0.12
12 12 0.08
13 4 0.03
14 111 0.77
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.73
Consensus pattern (12 bp):
TTATTTTTATTA
Found at i:14084 original size:7 final size:7
Alignment explanation
Indices: 13923--14076 Score: 290
Period size: 7 Copynumber: 21.7 Consensus size: 7
13913 TTTTTATTAT
13923 TTTTTGA
1 TTTTTGA
13930 TTTTTGA
1 TTTTTGA
13937 TTTTTGA
1 TTTTTGA
13944 TTTTTGA
1 TTTTTGA
13951 TTTTTGA
1 TTTTTGA
13958 TTTTTGA
1 TTTTTGA
13965 TTTTTGA
1 TTTTTGA
13972 TTTTTGA
1 TTTTTGA
13979 TTTTTGA
1 TTTTTGA
13986 TTTTTGA
1 TTTTTGA
13993 TTTTTGA
1 TTTTTGA
14000 TTTTTGA
1 TTTTTGA
14007 TTTTTGA
1 TTTTTGA
14014 TTTTTGA
1 TTTTTGA
14021 TTTTTGA
1 TTTTTGA
14028 TTTTTGA
1 TTTTTGA
14035 TTTTTGA
1 TTTTTGA
14042 TTTTTGA
1 TTTTTGA
14049 TTTTTGA
1 TTTTTGA
14056 TTTTTTGA
1 -TTTTTGA
14064 TTTTTTGA
1 -TTTTTGA
14072 TTTTT
1 TTTTT
14077 TTGATTTTGA
Statistics
Matches: 146, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
7 131 0.90
8 15 0.10
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.73
Consensus pattern (7 bp):
TTTTTGA
Done.