Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024510.1 Corchorus olitorius cultivar O-4 contig24543, 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: 37501
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:1233 original size:22 final size:22
Alignment explanation
Indices: 1208--1249 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1198 GACAAATCTG
* *
1208 TAACCTGAATGATCCGAGAAGT
1 TAACCCGAATGATCCAAGAAGT
*
1230 TAACCCGGATGATCCAAGAA
1 TAACCCGAATGATCCAAGAA
1250 TATCATAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (22 bp):
TAACCCGAATGATCCAAGAAGT
Found at i:2420 original size:23 final size:23
Alignment explanation
Indices: 2377--2420 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
2367 AAGTTTTTTT
*
2377 AATAAAATTAGTAAAATGATAAA
1 AATAAAATTAGTAAAAGGATAAA
*
2400 AATAAAA-TAGGTATAAGGATA
1 AATAAAATTA-GTAAAAGGATA
2421 TTAGATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 16 0.89
ACGTcount: A:0.61, C:0.00, G:0.14, T:0.25
Consensus pattern (23 bp):
AATAAAATTAGTAAAAGGATAAA
Found at i:2492 original size:100 final size:103
Alignment explanation
Indices: 2373--2572 Score: 300
Period size: 105 Copynumber: 2.0 Consensus size: 103
2363 ATATAAGTTT
* *
2373 TTTTAATAAAATTAGTAAAATGATAAAAATAAAAT-AGGTATAAGGATATTAGATTTAAT-TAA-
1 TTTTAATAAAATTAGTAAAATGATAAAAATAAAATAACGTATAAGGATATTAGATTTAATCAAAT
2435 AAAAATAGAGTTTTTAATTGAGTAAAACTATAAAAGTA
66 AAAAATAGAGTTTTTAATTGAGTAAAACTATAAAAGTA
* *
2473 TTTTAATTAAAA-TAGTAAAATGGTAAAAATAAAATAACACTTATAAGGATATTAGATTTAATCA
1 TTTTAA-TAAAATTAGTAAAATGATAAAAATAAAAT-A-ACGTATAAGGATATTAGATTTAATCA
*
2537 AATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAA
63 AATAAAAATAGAGTTTTTAATTGAGTAAAACTATAA
2573 TAAAAATTTA
Statistics
Matches: 89, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
100 28 0.31
101 5 0.06
103 22 0.25
104 2 0.02
105 32 0.36
ACGTcount: A:0.52, C:0.03, G:0.12, T:0.34
Consensus pattern (103 bp):
TTTTAATAAAATTAGTAAAATGATAAAAATAAAATAACGTATAAGGATATTAGATTTAATCAAAT
AAAAATAGAGTTTTTAATTGAGTAAAACTATAAAAGTA
Found at i:4804 original size:131 final size:132
Alignment explanation
Indices: 4647--4898 Score: 418
Period size: 131 Copynumber: 1.9 Consensus size: 132
4637 ATATTTTTTA
* * *
4647 AAATTCTAATATATCTAAGTTTTTTAATT-ATATCAGTAAAATGGTAAAAATAAAATAGGTATAA
1 AAATTCTAATATATATAAGTCTTTTAATTAAAAT-AGTAAAATGGTAAAAATAAAATAGGTATAA
*
4711 GGATATTAGATTTAATTAAATAAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATATTT
65 GGATATTACATTTAATTAAATAAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATATTT
4776 AAG
130 AAG
* *
4779 AAATTCTAATATATATAAG-CTTTTAATTAAAATAGTAAAATGGTAAAAATTAAATAGTTATAAG
1 AAATTCTAATATATATAAGTCTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAG
*
4843 GATATTACATTTAATTAAATAAAAAATAGAGTTTTTAGTTGAGTAAAATTATAAAA
66 GATATTACATTTAATTAAATAAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
4899 AGTTTATACA
Statistics
Matches: 112, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
131 91 0.81
132 21 0.19
ACGTcount: A:0.49, C:0.03, G:0.11, T:0.37
Consensus pattern (132 bp):
AAATTCTAATATATATAAGTCTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAG
GATATTACATTTAATTAAATAAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATATTTA
AG
Found at i:7882 original size:16 final size:16
Alignment explanation
Indices: 7861--7892 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
7851 TATAATTATT
7861 TATATATTAATAATAA
1 TATATATTAATAATAA
*
7877 TATATATTATTAATAA
1 TATATATTAATAATAA
7893 ATTCTATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATATATTAATAATAA
Found at i:7887 original size:19 final size:19
Alignment explanation
Indices: 7845--7892 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
7835 GAACGTTCGT
* *
7845 TTATTATATAATTATTTATA
1 TTATTA-ATAATAATATATA
7865 -TATTAATAATAATATATA
1 TTATTAATAATAATATATA
7883 TTATTAATAA
1 TTATTAATAA
7893 ATTCTATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTATTAATAATAATATATA
Found at i:8045 original size:18 final size:18
Alignment explanation
Indices: 8018--8052 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
8008 AATTATTACA
8018 TTGTTCATGAACAATTTT
1 TTGTTCATGAACAATTTT
*
8036 TTGTTTATGAACAATTT
1 TTGTTCATGAACAATTT
8053 AAGTTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (18 bp):
TTGTTCATGAACAATTTT
Found at i:8376 original size:2 final size:2
Alignment explanation
Indices: 8371--8399 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
8361 TCTTGGCCCA
8371 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
8400 AATGTTGGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:13107 original size:15 final size:15
Alignment explanation
Indices: 13079--13121 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
13069 TTTAATTGTT
13079 ACTCTTCCTA-GAATC
1 ACTC-TCCTAGGAATC
*
13094 ACTCTCCTTGGAATC
1 ACTCTCCTAGGAATC
*
13109 GCTCTCCTAGGAA
1 ACTCTCCTAGGAA
13122 AAGTGTTTCC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 4 0.17
15 20 0.83
ACGTcount: A:0.23, C:0.33, G:0.14, T:0.30
Consensus pattern (15 bp):
ACTCTCCTAGGAATC
Found at i:15753 original size:40 final size:40
Alignment explanation
Indices: 15698--15778 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
15688 ACCACAGAAA
*
15698 ATTCAAGTTTGTATTTCTAGGATGTAGTAAGGAAAGTAAC
1 ATTCAAGTTTGTATTTCTAGGATGCAGTAAGGAAAGTAAC
*
15738 ATTCAAGTTTGTATTTCTATGATGCAGTAAGGAAAGTAAC
1 ATTCAAGTTTGTATTTCTAGGATGCAGTAAGGAAAGTAAC
15778 A
1 A
15779 GAGGAGTGGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.35
Consensus pattern (40 bp):
ATTCAAGTTTGTATTTCTAGGATGCAGTAAGGAAAGTAAC
Found at i:17108 original size:18 final size:18
Alignment explanation
Indices: 17075--17109 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17065 TGAAGCTCGT
**
17075 GAAGAAGAAGGCGTGAAG
1 GAAGAAGAAGAAGTGAAG
17093 GAAGAAGAAGAAGTGAA
1 GAAGAAGAAGAAGTGAA
17110 AAAAAGAAGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.03, G:0.40, T:0.06
Consensus pattern (18 bp):
GAAGAAGAAGAAGTGAAG
Found at i:24752 original size:38 final size:38
Alignment explanation
Indices: 24701--24778 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
24691 ATCACAATTT
24701 AGAATTTTGTGGGGTCCATCAAGGAGCCCACACTCATA
1 AGAATTTTGTGGGGTCCATCAAGGAGCCCACACTCATA
24739 AGAATTTTGTGGGGTCCATCAAGGAGCCCACACTCATA
1 AGAATTTTGTGGGGTCCATCAAGGAGCCCACACTCATA
24777 AG
1 AG
24779 TGGTGGACCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.23
Consensus pattern (38 bp):
AGAATTTTGTGGGGTCCATCAAGGAGCCCACACTCATA
Found at i:30009 original size:2 final size:2
Alignment explanation
Indices: 30004--30035 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
29994 AAATGAAAAA
30004 AT AT AT AT AT AT AT AT 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
30036 GCAAAGAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37087 original size:14 final size:14
Alignment explanation
Indices: 37068--37096 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
37058 AAGAGTCTAG
37068 CACTTGATGGTTGA
1 CACTTGATGGTTGA
37082 CACTTGATGGTTGA
1 CACTTGATGGTTGA
37096 C
1 C
37097 GGCAACAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.17, G:0.28, T:0.34
Consensus pattern (14 bp):
CACTTGATGGTTGA
Done.