Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018241.1 Corchorus olitorius cultivar O-4 contig18274, 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: 36436
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:1367 original size:42 final size:42
Alignment explanation
Indices: 1308--1390 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
1298 GCTAAGGATC
* *
1308 ATGATTTGAGTTGAGTATTTCTTTATTTACAAAGAATTTTCT
1 ATGATTTGAGTTGAGTATTTCTTAATTTACAAAGAACTTTCT
*
1350 ATGATTTGAGTTGAGTATTTCTTAATTTACAGAGAACTTTC
1 ATGATTTGAGTTGAGTATTTCTTAATTTACAAAGAACTTTC
1391 AAGACTTAGC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.29, C:0.08, G:0.16, T:0.47
Consensus pattern (42 bp):
ATGATTTGAGTTGAGTATTTCTTAATTTACAAAGAACTTTCT
Found at i:8552 original size:16 final size:16
Alignment explanation
Indices: 8527--8557 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
8517 AAACGCTCAT
*
8527 CATTTTCTAACAACTC
1 CATTTCCTAACAACTC
8543 CATTTCCTAACAACT
1 CATTTCCTAACAACT
8558 TTATTCAAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (16 bp):
CATTTCCTAACAACTC
Found at i:11364 original size:6 final size:6
Alignment explanation
Indices: 11353--11380 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
11343 TATATTTCTT
11353 TTTTCA TTTTCA TTTTCA TTTTCA TTTT
1 TTTTCA TTTTCA TTTTCA TTTTCA TTTT
11381 GTCTGTTCCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTCA
Found at i:11952 original size:13 final size:13
Alignment explanation
Indices: 11917--11955 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
11907 GAGAATATTA
*
11917 TCAACAGAAGATG
1 TCAACAGAAGATT
*
11930 TCATCAGAAGATT
1 TCAACAGAAGATT
*
11943 TCAACTGAAGATT
1 TCAACAGAAGATT
11956 ATCTGGAGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (13 bp):
TCAACAGAAGATT
Found at i:11967 original size:11 final size:11
Alignment explanation
Indices: 11947--11977 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
11937 AAGATTTCAA
11947 CTGAAGATTAT
1 CTGAAGATTAT
*
11958 CTGGAGATTAT
1 CTGAAGATTAT
11969 CTGAAGATT
1 CTGAAGATT
11978 TAAGTAGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (11 bp):
CTGAAGATTAT
Found at i:15454 original size:32 final size:32
Alignment explanation
Indices: 15358--15438 Score: 153
Period size: 32 Copynumber: 2.5 Consensus size: 32
15348 AAGCATTATA
*
15358 TATACATGTAAATTTTACTAAATTGTCTTAAT
1 TATATATGTAAATTTTACTAAATTGTCTTAAT
15390 TATATATGTAAATTTTACTAAATTGTCTTAAT
1 TATATATGTAAATTTTACTAAATTGTCTTAAT
15422 TATATATGTAAATTTTA
1 TATATATGTAAATTTTA
15439 GAGAATTATA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.49
Consensus pattern (32 bp):
TATATATGTAAATTTTACTAAATTGTCTTAAT
Found at i:22892 original size:34 final size:29
Alignment explanation
Indices: 22816--22939 Score: 117
Period size: 33 Copynumber: 4.0 Consensus size: 29
22806 CAATCTTGGG
22816 ATGACAACTTCTGGTGTC-AATAATTTCCTCAGC
1 ATGACAACTTCTGGTGTCAAATAATTT--T---C
*
22849 ATGACAACTTCTGGTGTCAAGATAATAATTTGAT
1 ATGACAACTTCTGGTGTCAA-ATAAT--TTT--C
22883 ATGACAACTTCTGGTGTC-AATAATTTTC
1 ATGACAACTTCTGGTGTCAAATAATTTTC
*
22911 ATGACAACTTCTGGTGTCAATTAAATTTT
1 ATGACAACTTCTGGTGTCAAAT-AATTTT
22940 AAAAATAAAA
Statistics
Matches: 80, Mismatches: 5, Indels: 15
0.80 0.05 0.15
Matches are distributed among these distances:
28 18 0.22
29 2 0.03
30 9 0.11
32 5 0.06
33 19 0.24
34 19 0.24
35 6 0.08
37 2 0.03
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (29 bp):
ATGACAACTTCTGGTGTCAAATAATTTTC
Found at i:23767 original size:20 final size:19
Alignment explanation
Indices: 23722--23776 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 19
23712 AATGTCACCG
23722 GATATCCGTCGATATATCC
1 GATATCCGTCGATATATCC
*
23741 GTGTATCCGTCGATATTTAT-C
1 G-ATATCCGTCGATA--TATCC
23762 GATAT-C-TCGATATAT
1 GATATCCGTCGATATAT
23777 TCTCAATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
16 3 0.10
18 6 0.19
19 2 0.06
20 15 0.48
21 2 0.06
22 3 0.10
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.38
Consensus pattern (19 bp):
GATATCCGTCGATATATCC
Found at i:23799 original size:10 final size:10
Alignment explanation
Indices: 23784--23809 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
23774 TATTCTCAAT
23784 ATATCCGTAA
1 ATATCCGTAA
23794 ATATCCGTAA
1 ATATCCGTAA
23804 ATATCC
1 ATATCC
23810 ATATTAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (10 bp):
ATATCCGTAA
Found at i:24521 original size:39 final size:38
Alignment explanation
Indices: 24463--24537 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 38
24453 ATTTCTCATA
*
24463 TTTTTTTTTCTTTGATTTAAGATTTAACAAACTAATTT
1 TTTTTTTTTATTTGATTTAAGATTTAACAAACTAATTT
*
24501 TTTTCTTTTTATTTGTTTTAAGATTTAACAAACTAAT
1 TTTT-TTTTTATTTGATTTAAGATTTAACAAACTAAT
24538 ATCTTCCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 4 0.12
39 30 0.88
ACGTcount: A:0.29, C:0.08, G:0.05, T:0.57
Consensus pattern (38 bp):
TTTTTTTTTATTTGATTTAAGATTTAACAAACTAATTT
Found at i:28511 original size:17 final size:17
Alignment explanation
Indices: 28455--28521 Score: 63
Period size: 17 Copynumber: 4.2 Consensus size: 17
28445 TTTGTTTTTT
* *
28455 TTAATTATTAATTATAA
1 TTAATAATTAATAATAA
28472 TTAATAA-T-A-AA-AA
1 TTAATAATTAATAATAA
* *
28485 TTTA-AATTAATAATAC
1 TTAATAATTAATAATAA
28501 TTAATAATTAATAATAA
1 TTAATAATTAATAATAA
28518 TTAA
1 TTAA
28522 AAAAAATAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
12 2 0.05
13 6 0.15
14 2 0.05
15 3 0.08
16 5 0.13
17 21 0.54
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAATAATTAATAATAA
Found at i:30519 original size:16 final size:16
Alignment explanation
Indices: 30494--30527 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
30484 GAAAGCTGAC
*
30494 TAAGTGACATGATCAT
1 TAAGTAACATGATCAT
30510 TAAGTAACATGATCAT
1 TAAGTAACATGATCAT
30526 TA
1 TA
30528 GTACCTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (16 bp):
TAAGTAACATGATCAT
Found at i:35620 original size:2 final size:2
Alignment explanation
Indices: 35603--35646 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
35593 GTGTAATTGT
*
35603 TA TA TC TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35644 TA T
1 TA T
35647 CCTATTATGG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.