Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020465.1 Corchorus olitorius cultivar O-4 contig20498, 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: 11794
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Found at i:11 original size:1 final size:1
Alignment explanation
Indices: 6--31 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1 TTAGG
6 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
32 AAAGAAAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:137 original size:38 final size:38
Alignment explanation
Indices: 95--607 Score: 256
Period size: 38 Copynumber: 13.7 Consensus size: 38
85 TTTAAAGATG
* *
95 GACCTGAGCAGGTTTGATTAAACGAAACTCTAAGCGAA
1 GACCTAAGCAGGTTTAATTAAACGAAACTCTAAGCGAA
133 GACCTAAGCAGGTTTAATTAAACGAAACTCTAAGCGAA
1 GACCTAAGCAGGTTTAATTAAACGAAACTCTAAGCGAA
171 GACCTAAGCAGGTTTAATTAAACGAAACTCTAAGCAGAA
1 GACCTAAGCAGGTTTAATTAAACGAAACTCTAAGC-GAA
* * * *
210 GTCCTAAACAGGTTTACTTAAACGGAA--C---G-G-A
1 GACCTAAGCAGGTTTAATTAAACGAAACTCTAAGCGAA
* * * * *
241 GATCTAAGCAGGTTTACTTAAATGAAATTCTAAAC-ATA
1 GACCTAAGCAGGTTTAATTAAACGAAACTCTAAGCGA-A
* * * * *
279 GACCTAAGCAGGTTTACTTAAATG-AAGTTTTAGAC-ATA
1 GACCTAAGCAGGTTTAATTAAACGAAACTCTAAG-CGA-A
* * * * ** *
317 GACCTAAGCAGGTTTACTTAAAAGGGAATTCTAAATGAG
1 GACCTAAGCAGGTTTAATT-AAACGAAACTCTAAGCGAA
* * * *
356 GAGCTAAGCAGGTTTGATTAAACGACACTCTAAAC-AGA
1 GACCTAAGCAGGTTTAATTAAACGAAACTCTAAGCGA-A
* * * * * ** * **
394 GACATAAGTAGATTCACTTGAATGGAAGCTCTAA-ATAGA
1 GACCTAAGCAGGTTTAATT-AAACGAAACTCTAAGCGA-A
* * * * *
433 GACCTAAGCAGGTTTACTTAAATAGAGATTCTAAAC-ATA
1 GACCTAAGCAGGTTTAATTAAA-CGAAACTCTAAGCGA-A
* * *
472 GACCTAAGCAGGTTTGATTAAACGAAGCTCTAAGCTGAC
1 GACCTAAGCAGGTTTAATTAAACGAAACTCTAAGC-GAA
* * * * *
511 G-CCCATGCAGGTTT-A-T---GGAAATTCTACA-CGAG
1 GACCTAAGCAGGTTTAATTAAACGAAACTCTA-AGCGAA
* * **
543 GACCTAAGCAGGTTCGATTTAAACGAAACTTCTAAATGAA
1 GACCTAAGCAGGTT-TAATTAAACGAAAC-TCTAAGCGAA
* *
583 GACCTAAGCAGGTTTACTTGAACGA
1 GACCTAAGCAGGTTTAATTAAACGA
608 GAATTCTAGA
Statistics
Matches: 364, Mismatches: 81, Indels: 59
0.72 0.16 0.12
Matches are distributed among these distances:
31 23 0.06
32 4 0.01
33 19 0.05
34 2 0.01
36 2 0.01
37 8 0.02
38 162 0.45
39 117 0.32
40 27 0.07
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (38 bp):
GACCTAAGCAGGTTTAATTAAACGAAACTCTAAGCGAA
Found at i:368 original size:77 final size:76
Alignment explanation
Indices: 244--486 Score: 244
Period size: 77 Copynumber: 3.2 Consensus size: 76
234 GAACGGAGAT
*
244 CTAAGCAGGTTTACTTAAATGAAATTCTAAACATA-GACCTAAGCAGGTTTACTTAAATGA-AGT
1 CTAAGCAGGTTTACTTAAATGGAATTCT-AA-ATAGGACCTAAGCAGGTTTACTTAAATGACAGT
* *
307 TTTAGACATAGAC
64 TCTAAACATAGAC
* * *
320 CTAAGCAGGTTTACTTAAAAGGGAATTCTAAATGAGGAGCTAAGCAGGTTTGA-TTAAACGACA-
1 CTAAGCAGGTTTACTT-AAATGGAATTCTAAAT-AGGACCTAAGCAGGTTT-ACTTAAATGACAG
* *
383 CTCTAAACAGAGAC
63 TTCTAAACATAGAC
* * * * * * *
397 ATAAGTAGATTCACTTGAATGGAAGCTCTAAATAGAGACCTAAGCAGGTTTACTTAAAT-AGAGA
1 CTAAGCAGGTTTACTTAAATGGAA-TTCTAAATAG-GACCTAAGCAGGTTTACTTAAATGACAG-
461 TTCTAAACATAGAC
63 TTCTAAACATAGAC
475 CTAAGCAGGTTT
1 CTAAGCAGGTTT
487 GATTAAACGA
Statistics
Matches: 133, Mismatches: 24, Indels: 18
0.76 0.14 0.10
Matches are distributed among these distances:
75 2 0.02
76 30 0.23
77 79 0.59
78 22 0.17
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (76 bp):
CTAAGCAGGTTTACTTAAATGGAATTCTAAATAGGACCTAAGCAGGTTTACTTAAATGACAGTTC
TAAACATAGAC
Found at i:493 original size:39 final size:37
Alignment explanation
Indices: 244--486 Score: 222
Period size: 39 Copynumber: 6.3 Consensus size: 37
234 GAACGGAGAT
244 CTAAGCAGGTTTACTTAAATGAAATTCTAAACATAGAC
1 CTAAGCAGGTTTACTTAAATG-AATTCTAAACATAGAC
* *
282 CTAAGCAGGTTTACTTAAATGAAGTTTTAGACATAGAC
1 CTAAGCAGGTTTACTTAAATGAA-TTCTAAACATAGAC
* *
320 CTAAGCAGGTTTACTTAAAAGGGAATTCT-AA-ATGAGGAG
1 CTAAGCAGGTTTACTT-AAA-TGAATTCTAAACAT-A-GAC
* * *
359 CTAAGCAGGTTTGA-TTAAACGACACTCTAAACAGAGAC
1 CTAAGCAGGTTT-ACTTAAATGA-ATTCTAAACATAGAC
* * * * * * * *
397 ATAAGTAGATTCACTTGAATGGAAGCTCTAAATAGAGAC
1 CTAAGCAGGTTTACTTAAAT-GAA-TTCTAAACATAGAC
436 CTAAGCAGGTTTACTTAAATAGAGATTCTAAACATAGAC
1 CTAAGCAGGTTTACTTAAAT-GA-ATTCTAAACATAGAC
475 CTAAGCAGGTTT
1 CTAAGCAGGTTT
487 GATTAAACGA
Statistics
Matches: 166, Mismatches: 26, Indels: 25
0.76 0.12 0.12
Matches are distributed among these distances:
37 7 0.04
38 73 0.44
39 80 0.48
40 6 0.04
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (37 bp):
CTAAGCAGGTTTACTTAAATGAATTCTAAACATAGAC
Found at i:668 original size:71 final size:70
Alignment explanation
Indices: 582--717 Score: 186
Period size: 71 Copynumber: 1.9 Consensus size: 70
572 TTCTAAATGA
* *
582 AGACCTAAGCAGGTTTACTTGAAC-GAGAATTCTAGA-AAGGGACCTAAGCAGGTTTTACTTGAA
1 AGACCTAAGCAGGTTTACTTAAACGGA-AATTCTAGACAA-GGACCTAAGCAGG-TTTACTTAAA
645 TGGAACGG
63 TGGAACGG
* **
653 AGACCTAAGTAGGTTTGTTTAAACGGAAATTCTAGACAAGGACCTAAGCAGGTTTACTTAAATGG
1 AGACCTAAGCAGGTTTACTTAAACGGAAATTCTAGACAAGGACCTAAGCAGGTTTACTTAAATGG
718 CAACTTTAGA
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
70 12 0.21
71 42 0.72
72 4 0.07
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.26
Consensus pattern (70 bp):
AGACCTAAGCAGGTTTACTTAAACGGAAATTCTAGACAAGGACCTAAGCAGGTTTACTTAAATGG
AACGG
Found at i:714 original size:39 final size:38
Alignment explanation
Indices: 654--748 Score: 102
Period size: 39 Copynumber: 2.5 Consensus size: 38
644 ATGGAACGGA
**
654 GACCTAAGTAGGTTTGTTTAAACGG-AAATTCTAGACAAG
1 GACCTAAGTAGGTTTACTTAAACGGCAAATT-TAGA-AAG
* * * **
693 GACCTAAGCAGGTTTACTTAAATGGCAACTTTAGATGG
1 GACCTAAGTAGGTTTACTTAAACGGCAAATTTAGAAAG
731 GACCTAAGTAGGTTTACT
1 GACCTAAGTAGGTTTACT
749 AAGATAGAGA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
38 18 0.38
39 25 0.53
40 4 0.09
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (38 bp):
GACCTAAGTAGGTTTACTTAAACGGCAAATTTAGAAAG
Found at i:2080 original size:19 final size:18
Alignment explanation
Indices: 2056--2091 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2046 TGAAGACCAT
2056 TTGAAGATAATTTGAAGAC
1 TTGAAGAT-ATTTGAAGAC
*
2075 TTGAAGATTTTTGAAGA
1 TTGAAGATATTTGAAGA
2092 TCTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATATTTGAAGAC
Found at i:2696 original size:11 final size:11
Alignment explanation
Indices: 2680--2705 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2670 GAATAATTTC
2680 TTTTCTTCTAG
1 TTTTCTTCTAG
2691 TTTTCTTCTAG
1 TTTTCTTCTAG
2702 TTTT
1 TTTT
2706 TTAGGGCTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Done.