Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016948.1 Corchorus olitorius cultivar O-4 contig16981, 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: 17529
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:1295 original size:9 final size:9
Alignment explanation
Indices: 1281--1317 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
1271 TGGAGAAAAC
1281 AAAATGAAG
1 AAAATGAAG
*
1290 AAAATGAAC
1 AAAATGAAG
1299 ACAAATGAAG
1 A-AAATGAAG
1309 AAAATGAAG
1 AAAATGAAG
1318 TAACGGTGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.65, C:0.05, G:0.19, T:0.11
Consensus pattern (9 bp):
AAAATGAAG
Found at i:1306 original size:19 final size:18
Alignment explanation
Indices: 1278--1316 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 18
1268 CGGTGGAGAA
1278 AACAAAATGAAGAAAATG
1 AACAAAATGAAGAAAATG
1296 AACACAAATGAAGAAAATG
1 AACA-AAATGAAGAAAATG
1315 AA
1 AA
1317 GTAACGGTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.67, C:0.08, G:0.15, T:0.10
Consensus pattern (18 bp):
AACAAAATGAAGAAAATG
Found at i:1622 original size:17 final size:16
Alignment explanation
Indices: 1596--1629 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1586 ATTGATAATC
1596 TTATTCTTATTTTATTT
1 TTATTCTTATTTT-TTT
*
1613 TTATTTTTATTTTTTT
1 TTATTCTTATTTTTTT
1629 T
1 T
1630 GCATCAGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (16 bp):
TTATTCTTATTTTTTT
Found at i:2495 original size:25 final size:26
Alignment explanation
Indices: 2449--2498 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
2439 CATATTTATT
2449 TTTTTAAAATAAAACAATAATTTAAC
1 TTTTTAAAATAAAACAATAATTTAAC
*
2475 TTTTTAATAA-AAAATAA-AATTTAA
1 TTTTTAA-AATAAAACAATAATTTAA
2499 ACATTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 13 0.59
27 2 0.09
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (26 bp):
TTTTTAAAATAAAACAATAATTTAAC
Found at i:2651 original size:29 final size:30
Alignment explanation
Indices: 2593--2653 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
2583 GTTCTAATTA
* *
2593 ATGTATACATATAAATTATTCAATTTTATT
1 ATGTATAAATATAAATTATTCAATTATATT
*
2623 ATGTATAAATAT-AATTATTTAATTATATT
1 ATGTATAAATATAAATTATTCAATTATATT
2652 AT
1 AT
2654 ATAATTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (30 bp):
ATGTATAAATATAAATTATTCAATTATATT
Found at i:4810 original size:31 final size:30
Alignment explanation
Indices: 4718--4827 Score: 184
Period size: 30 Copynumber: 3.6 Consensus size: 30
4708 TCTCTCCAAA
4718 TGACACCAGAAGTTGTCATGATCTTACAAT
1 TGACACCAGAAGTTGTCATGATCTTACAAT
* *
4748 TGACACCAAAAGTTGTCATGATCTTATAAT
1 TGACACCAGAAGTTGTCATGATCTTACAAT
*
4778 TGACACCAGAAGTTGTCAATGTTCTTACAAT
1 TGACACCAGAAGTTGTC-ATGATCTTACAAT
4809 TGACACCAGAAGTTGTCAT
1 TGACACCAGAAGTTGTCAT
4828 AATAAATTTC
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
30 46 0.62
31 28 0.38
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (30 bp):
TGACACCAGAAGTTGTCATGATCTTACAAT
Found at i:4904 original size:39 final size:39
Alignment explanation
Indices: 4861--4960 Score: 182
Period size: 39 Copynumber: 2.6 Consensus size: 39
4851 AAGATATTCA
**
4861 ATTGACACAAGAAGTTGTCATATACACTATTAATTTGTT
1 ATTGACACCTGAAGTTGTCATATACACTATTAATTTGTT
4900 ATTGACACCTGAAGTTGTCATATACACTATTAATTTGTT
1 ATTGACACCTGAAGTTGTCATATACACTATTAATTTGTT
4939 ATTGACACCTGAAGTTGTCATA
1 ATTGACACCTGAAGTTGTCATA
4961 ACAATTTTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 59 1.00
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (39 bp):
ATTGACACCTGAAGTTGTCATATACACTATTAATTTGTT
Found at i:4907 original size:20 final size:20
Alignment explanation
Indices: 4884--4946 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
4874 GTTGTCATAT
4884 ACACTATTAATTTGTTATTG
1 ACACTATTAATTTGTTATTG
* * * *
4904 ACAC-CTGAAGTTGTCATAT-
1 ACACTATTAATTTGTTAT-TG
4923 ACACTATTAATTTGTTATTG
1 ACACTATTAATTTGTTATTG
4943 ACAC
1 ACAC
4947 CTGAAGTTGT
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
19 14 0.44
20 18 0.56
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (20 bp):
ACACTATTAATTTGTTATTG
Found at i:16125 original size:2 final size:2
Alignment explanation
Indices: 16118--16178 Score: 68
Period size: 2 Copynumber: 29.5 Consensus size: 2
16108 TAAGCAATAA
* * * *
16118 AT AT AT AT AT AT AT AT AT AT AT CT AT AT CT AT AT CT AT AT CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16160 AT AT ACT AT AT ACT AT AT A
1 AT AT A-T AT AT A-T AT AT A
16179 AGTCTAAATT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
2 45 0.92
3 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16485 original size:42 final size:40
Alignment explanation
Indices: 16426--16509 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 40
16416 TTTAATTCCT
16426 ATGTAATATATATAATAACTAAAATACTTATAACATTAATTAA
1 ATGTAATATATATAATAACTAAAATAC-T-T-ACATTAATTAA
* *
16469 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
16508 AT
1 AT
16510 TCTTAGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
39 13 0.33
40 1 0.03
41 1 0.03
42 16 0.41
43 8 0.21
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:16536 original size:25 final size:24
Alignment explanation
Indices: 16500--16546 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
16490 AATACTTACA
16500 TTAATTAAATTCTTAGGTATTTTT
1 TTAATTAAATTCTTAGGTATTTTT
16524 TTAATTCAAATTCTTAGGTATTT
1 TTAATT-AAATTCTTAGGTATTT
16547 GTGCAAACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (24 bp):
TTAATTAAATTCTTAGGTATTTTT
Done.