Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017036.1 Corchorus olitorius cultivar O-4 contig17069, 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: 30105
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Found at i:5966 original size:64 final size:64
Alignment explanation
Indices: 5865--5993 Score: 231
Period size: 64 Copynumber: 2.0 Consensus size: 64
5855 AGCGCCGAAG
* *
5865 AAGAATATAAACATTCAACTATAGTTTGTGTTTTAGAGTTGTCTTTGTACTCATCTGAACTTAC
1 AAGAATATAAACATTCAACTATAGTTTGTGTTTTAGAGTTGTCTGTGTACTCATCTAAACTTAC
*
5929 AAGAATATAAACATTCAACTATATTTTGTGTTTTAGAGTTGTCTGTGTACTCATCTAAACTTAC
1 AAGAATATAAACATTCAACTATAGTTTGTGTTTTAGAGTTGTCTGTGTACTCATCTAAACTTAC
5993 A
1 A
5994 GATTCTATTT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (64 bp):
AAGAATATAAACATTCAACTATAGTTTGTGTTTTAGAGTTGTCTGTGTACTCATCTAAACTTAC
Found at i:10816 original size:12 final size:12
Alignment explanation
Indices: 10799--10835 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
10789 CCCATATTAG
10799 ATATATATAATA
1 ATATATATAATA
10811 ATATATAT-AT-
1 ATATATATAATA
*
10821 ATATATATACTA
1 ATATATATAATA
10833 ATA
1 ATA
10836 CTAAATAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
10 8 0.36
11 3 0.14
12 11 0.50
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (12 bp):
ATATATATAATA
Found at i:16633 original size:2 final size:2
Alignment explanation
Indices: 16628--16662 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
16618 ATCCATTCTT
16628 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16663 TGGCTTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17242 original size:34 final size:35
Alignment explanation
Indices: 17163--17244 Score: 109
Period size: 34 Copynumber: 2.4 Consensus size: 35
17153 TTATGATATT
*
17163 TCAATAATTT-AATAGAGTTGTTGGCACAATTCTT
1 TCAATAATTTCAATAGAGTTGTTGGCACAATTCTA
17197 TCAATAA-TTCAATAGAGTTGTTGG-AC-ATATCTA
1 TCAATAATTTCAATAGAGTTGTTGGCACAAT-TCTA
*
17230 TCAAAAATTTCAATA
1 TCAATAATTTCAATA
17245 ATTTAATAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
32 2 0.05
33 13 0.30
34 28 0.65
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (35 bp):
TCAATAATTTCAATAGAGTTGTTGGCACAATTCTA
Found at i:17275 original size:34 final size:34
Alignment explanation
Indices: 17161--17275 Score: 81
Period size: 34 Copynumber: 3.1 Consensus size: 34
17151 AATTATGATA
*
17161 TTTCAATAATTTAATAGAGTTGTTG-GCA-CAATTC
1 TTTCAATAATTTAATAGAGTTG--GCACATCAATTC
* ***
17195 TTTCAATAATTCAATAGAGTTGTTGGACATATCTATCAAAAA
1 TTTCAATAATTTAATAGA---GTTGG-C--A-C-ATCAATTC
17237 TTTCAATAATTTAATAGAGTTGGCACATCAATTC
1 TTTCAATAATTTAATAGAGTTGGCACATCAATTC
17271 TTTCA
1 TTTCA
17276 CTCCTTGTAT
Statistics
Matches: 62, Mismatches: 9, Indels: 20
0.68 0.10 0.22
Matches are distributed among these distances:
34 27 0.44
35 2 0.03
36 1 0.02
37 4 0.06
38 1 0.02
39 5 0.08
40 1 0.02
41 1 0.02
42 20 0.32
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (34 bp):
TTTCAATAATTTAATAGAGTTGGCACATCAATTC
Found at i:17433 original size:15 final size:17
Alignment explanation
Indices: 17405--17453 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 17
17395 ATTTTAGTTT
17405 TTTTTTTAATTTTTAAG
1 TTTTTTTAATTTTTAAG
17422 TTTTTTT-A-TTTTAAG
1 TTTTTTTAATTTTTAAG
* *
17437 TTATCTTAATTTTTAAG
1 TTTTTTTAATTTTTAAG
17454 GTTTATTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 12 0.43
16 2 0.07
17 14 0.50
ACGTcount: A:0.24, C:0.02, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTTTTAATTTTTAAG
Found at i:18401 original size:21 final size:21
Alignment explanation
Indices: 18375--18415 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
18365 TATAATATAT
18375 TATATATTTAT-TAATTTAATG
1 TATATATTTATAT-ATTTAATG
18396 TATATATTTATATATTTAAT
1 TATATATTTATATATTTAAT
18416 AATGTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
TATATATTTATATATTTAATG
Found at i:18608 original size:2 final size:2
Alignment explanation
Indices: 18601--18634 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
18591 CATAATAATA
* *
18601 AT AT AT AT AG AT AT AT AG AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18635 TATCAACTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (2 bp):
AT
Found at i:18994 original size:42 final size:44
Alignment explanation
Indices: 18943--19036 Score: 131
Period size: 45 Copynumber: 2.2 Consensus size: 44
18933 AGTGCATTAC
* * *
18943 CTAA-ATTCTA-C-TCCATCTCTAGGTAATTCATCAAAATAATG
1 CTAATATTCTACCTTCCATCTATAGATAATTCATCAAAATAAAG
18984 CTAATATTCTACTCTTCCATCTATAGATAATTCATCAAAATAAAG
1 CTAATATTCTAC-CTTCCATCTATAGATAATTCATCAAAATAAAG
19029 CTAATATT
1 CTAATATT
19037 AATTGTTGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
44 1 0.02
45 35 0.76
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.36
Consensus pattern (44 bp):
CTAATATTCTACCTTCCATCTATAGATAATTCATCAAAATAAAG
Found at i:21801 original size:31 final size:28
Alignment explanation
Indices: 21732--21803 Score: 74
Period size: 31 Copynumber: 2.5 Consensus size: 28
21722 TTTGCCAGAT
* *
21732 TTAATAATA-GGTTTTTTTAGGACAAAA
1 TTAATAATATGCTTTTTTTAGGAAAAAA
* *
21759 TTAGTAGTATGCTTTTTTTATGGTAAAAAAA
1 TTAATAATATGCTTTTTTTA-GG--AAAAAA
21790 TTAATAATATGCTT
1 TTAATAATATGCTT
21804 AAAATTTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
27 7 0.20
28 9 0.26
29 2 0.06
31 17 0.49
ACGTcount: A:0.38, C:0.04, G:0.14, T:0.44
Consensus pattern (28 bp):
TTAATAATATGCTTTTTTTAGGAAAAAA
Done.