Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020446.1 Corchorus olitorius cultivar O-4 contig20479, 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: 28132
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:6148 original size:3 final size:3
Alignment explanation
Indices: 6140--6167 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
6130 AATTTTCATT
6140 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
6168 TTGATTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:6945 original size:14 final size:14
Alignment explanation
Indices: 6926--6977 Score: 59
Period size: 14 Copynumber: 3.4 Consensus size: 14
6916 ATATAAGAAC
6926 ATATATTATTCTAT
1 ATATATTATTCTAT
*
6940 ATATATAATCGTACTAGT
1 ATATATTAT--T-CTA-T
6958 ATATATTATTCTAT
1 ATATATTATTCTAT
6972 ATATAT
1 ATATAT
6978 AATTGTACTA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
14 15 0.47
15 3 0.09
16 2 0.06
17 3 0.09
18 9 0.28
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (14 bp):
ATATATTATTCTAT
Found at i:6967 original size:32 final size:32
Alignment explanation
Indices: 6926--6989 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
6916 ATATAAGAAC
6926 ATATATTATTCTATATATATAATCGTACTAGT
1 ATATATTATTCTATATATATAATCGTACTAGT
*
6958 ATATATTATTCTATATATATAATTGTACTAGT
1 ATATATTATTCTATATATATAATCGTACTAGT
6990 CTTAGCTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.48
Consensus pattern (32 bp):
ATATATTATTCTATATATATAATCGTACTAGT
Found at i:7194 original size:17 final size:18
Alignment explanation
Indices: 7158--7194 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
7148 CTTTTCTATG
*
7158 AAAATGAGTATACATTTT
1 AAAATGAGTAAACATTTT
7176 AAAATGAGTAAAC-TTTT
1 AAAATGAGTAAACATTTT
7193 AA
1 AA
7195 GATTTCCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.49, C:0.05, G:0.11, T:0.35
Consensus pattern (18 bp):
AAAATGAGTAAACATTTT
Found at i:7410 original size:22 final size:22
Alignment explanation
Indices: 7385--7465 Score: 96
Period size: 22 Copynumber: 3.7 Consensus size: 22
7375 AACCTCCCCG
7385 TGAAACTTTGATAACCACACTA
1 TGAAACTTTGATAACCACACTA
*
7407 TGAAATTTTGAT-ACCATC-CTA
1 TGAAACTTTGATAACCA-CACTA
*
7428 TGAAATTTTGATAACCACACTA
1 TGAAACTTTGATAACCACACTA
*
7450 T-AATACTGTGATAACC
1 TGAA-ACTTTGATAACC
7466 TCTATATGAA
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
21 22 0.42
22 30 0.58
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (22 bp):
TGAAACTTTGATAACCACACTA
Found at i:7428 original size:21 final size:21
Alignment explanation
Indices: 7385--7450 Score: 89
Period size: 21 Copynumber: 3.0 Consensus size: 21
7375 AACCTCCCCG
*
7385 TGAAACTTTGATAACCACACTA
1 TGAAATTTTGAT-ACCACACTA
7407 TGAAATTTTGATACCATC-CTA
1 TGAAATTTTGATACCA-CACTA
7428 TGAAATTTTGATAACCACACTA
1 TGAAATTTTGAT-ACCACACTA
7450 T
1 T
7451 AATACTGTGA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
21 20 0.50
22 20 0.50
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (21 bp):
TGAAATTTTGATACCACACTA
Found at i:7591 original size:22 final size:22
Alignment explanation
Indices: 7542--7754 Score: 120
Period size: 22 Copynumber: 9.9 Consensus size: 22
7532 TGATTTGGTA
*
7542 CACTATGAAATTTGGATAACCAT
1 CACTATGAAATTTTGATAACC-T
7565 -ACTATGAAATTTTGATAACCT
1 CACTATGAAATTTTGATAACCT
* * *
7586 CCCTAT-AGAATGTTGATAACTT
1 CACTATGA-AATTTTGATAACCT
* * * *
7608 CCCTAT-AGAATTTCGTTAAGCT
1 CACTATGA-AATTTTGATAACCT
* * * * *
7630 AACAATAAAATTTTGATAAGCA
1 CACTATGAAATTTTGATAACCT
* *
7652 CAATATGAAATTTTGATTACCT
1 CACTATGAAATTTTGATAACCT
*
7674 ---T-TGAAATTTTTG-TAACCA
1 CACTATGAAA-TTTTGATAACCT
* * *
7692 CATTATGAAATTTTGACAACCA
1 CACTATGAAATTTTGATAACCT
* *
7714 CATTATGAAATTTTGAT-AGCT
1 CACTATGAAATTTTGATAACCT
*
7735 ACACTATGAAATTTCGATAA
1 -CACTATGAAATTTTGATAA
7755 TCTGCAAAGT
Statistics
Matches: 149, Mismatches: 30, Indels: 22
0.74 0.15 0.11
Matches are distributed among these distances:
18 9 0.06
19 6 0.04
21 10 0.07
22 122 0.82
23 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (22 bp):
CACTATGAAATTTTGATAACCT
Found at i:10182 original size:6 final size:7
Alignment explanation
Indices: 10167--10191 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
10157 GATAGAACCC
10167 TTTTCTT
1 TTTTCTT
10174 TTTTCTT
1 TTTTCTT
10181 TTTTCTT
1 TTTTCTT
10188 TTTT
1 TTTT
10192 ATATATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTCTT
Found at i:14143 original size:22 final size:22
Alignment explanation
Indices: 14116--14161 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
14106 ATTAGATATG
*
14116 AAAAAAGTGTTTTCT-TTTCAAA
1 AAAAAAGTGGTTTCTATTT-AAA
14138 AAAAAAGTGGTTTCTATTTAAA
1 AAAAAAGTGGTTTCTATTTAAA
14160 AA
1 AA
14162 TGTTAGTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.37
Consensus pattern (22 bp):
AAAAAAGTGGTTTCTATTTAAA
Found at i:23278 original size:26 final size:27
Alignment explanation
Indices: 23249--23302 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
23239 AATGTATAGC
23249 AAAGTAG-AAAGAATAGATCAAAAACA
1 AAAGTAGAAAAGAATAGATCAAAAACA
*
23275 AAAGTAGAAAAGAATATATCAAAAACA
1 AAAGTAGAAAAGAATAGATCAAAAACA
23302 A
1 A
23303 GAGAAGAGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.67, C:0.07, G:0.13, T:0.13
Consensus pattern (27 bp):
AAAGTAGAAAAGAATAGATCAAAAACA
Done.