Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017026.1 Corchorus olitorius cultivar O-4 contig17059, 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: 30545
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:1028 original size:2 final size:2
Alignment explanation
Indices: 1021--1057 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
1011 AAACTACTAA
*
1021 AT AT AT AT AT AT AT AT AT AT GT AT AT A- AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1058 ACTTAAAGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1345 original size:22 final size:23
Alignment explanation
Indices: 1285--1346 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 23
1275 TCTATCAGCT
1285 TTTAATTTG-TTTAATTTAAGAC
1 TTTAATTTGATTTAATTTAAGAC
* * * *
1307 TTTCATTTTAATCAATTTAATG-C
1 TTTAATTTGATTTAATTTAA-GAC
1330 -TTAATTTGATTTAATTT
1 TTTAATTTGATTTAATTT
1347 GCAATAATTT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
22 20 0.67
23 9 0.30
24 1 0.03
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.56
Consensus pattern (23 bp):
TTTAATTTGATTTAATTTAAGAC
Found at i:1637 original size:13 final size:12
Alignment explanation
Indices: 1601--1647 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
1591 TCAATCTTTA
*
1601 TATATATTGATAA
1 TATATATT-ATAT
*
1614 TA-ATGTTATAT
1 TATATATTATAT
1625 TATATTATTATAT
1 TATA-TATTATAT
1638 TATATATTAT
1 TATATATTAT
1648 CAATAAACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:1783 original size:6 final size:6
Alignment explanation
Indices: 1772--1849 Score: 65
Period size: 6 Copynumber: 13.3 Consensus size: 6
1762 ATCGAAATCA
* * *
1772 AACCCG AGCCCG AGCCCG AACCCG AACCCG AACCC- TACCCG AGA-CCG
1 AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG A-ACCCG
* *
1819 AACCCG AATCC- TACCCG AGA-CCG AACCCG AA
1 AACCCG AACCCG AACCCG A-ACCCG AACCCG AA
1850 AATACCCAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
5 9 0.16
6 47 0.81
7 2 0.03
ACGTcount: A:0.31, C:0.46, G:0.19, T:0.04
Consensus pattern (6 bp):
AACCCG
Found at i:1819 original size:23 final size:23
Alignment explanation
Indices: 1793--1849 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
1783 GAGCCCGAAC
1793 CCGAACCCGAACCCTACCCGAGA
1 CCGAACCCGAACCCTACCCGAGA
*
1816 CCGAACCCGAATCCTACCCGAGA
1 CCGAACCCGAACCCTACCCGAGA
1839 CCGAACCCGAA
1 CCGAACCCGAA
1850 AATACCCAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.32, C:0.46, G:0.18, T:0.05
Consensus pattern (23 bp):
CCGAACCCGAACCCTACCCGAGA
Found at i:1881 original size:32 final size:32
Alignment explanation
Indices: 1839--1926 Score: 122
Period size: 32 Copynumber: 2.8 Consensus size: 32
1829 CTACCCGAGA
* * *
1839 CCGAACCCGAAAATACCCAAACCCGACAAAAT
1 CCGAGCCCGAAAATACCCGAACCCGACAAAAC
* **
1871 CCGAGCCCGAAAATACCGGAACCCGACTTAAC
1 CCGAGCCCGAAAATACCCGAACCCGACAAAAC
1903 CCGAGCCCGAAAATACCCGAACCC
1 CCGAGCCCGAAAATACCCGAACCC
1927 AAACCCGCCC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.39, C:0.40, G:0.15, T:0.07
Consensus pattern (32 bp):
CCGAGCCCGAAAATACCCGAACCCGACAAAAC
Found at i:1920 original size:16 final size:16
Alignment explanation
Indices: 1839--1926 Score: 81
Period size: 16 Copynumber: 5.5 Consensus size: 16
1829 CTACCCGAGA
1839 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
* *
1855 CCAAACCCGACAAA-AT
1 CCGAACCCGA-AAATAC
*
1871 CCGAGCCCGAAAATAC
1 CCGAACCCGAAAATAC
* **
1887 CGGAACCCG-ACTTAAC
1 CCGAACCCGAAAAT-AC
*
1903 CCGAGCCCGAAAATAC
1 CCGAACCCGAAAATAC
1919 CCGAACCC
1 CCGAACCC
1927 AAACCCGCCC
Statistics
Matches: 54, Mismatches: 14, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
15 5 0.09
16 44 0.81
17 5 0.09
ACGTcount: A:0.39, C:0.40, G:0.15, T:0.07
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:2981 original size:29 final size:29
Alignment explanation
Indices: 2924--2981 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
2914 AAATAATTAT
** *
2924 AAAGATATTAGATTTATTTCACTATAAAA
1 AAAGATATTAGATTTAAATCAATATAAAA
2953 AAAGATATTAGATTTAAATCAA-ATAAAA
1 AAAGATATTAGATTTAAATCAATATAAAA
2981 A
1 A
2982 TATGTTGTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 7 0.27
29 19 0.73
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (29 bp):
AAAGATATTAGATTTAAATCAATATAAAA
Found at i:5645 original size:26 final size:26
Alignment explanation
Indices: 5609--5669 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
5599 GCCCACTGAC
*
5609 TTGGACTTTTAATTTCTCTTATGCAT
1 TTGGGCTTTTAATTTCTCTTATGCAT
* *
5635 TTGGGCTTTTAATTTCTTTTATGCTT
1 TTGGGCTTTTAATTTCTCTTATGCAT
5661 TTGGG-TTTT
1 TTGGGCTTTT
5670 GTTTGGGCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
25 4 0.12
26 28 0.88
ACGTcount: A:0.13, C:0.11, G:0.16, T:0.59
Consensus pattern (26 bp):
TTGGGCTTTTAATTTCTCTTATGCAT
Found at i:8267 original size:13 final size:13
Alignment explanation
Indices: 8225--8271 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
8215 TCATGCACCC
*
8225 AAAACAATTTATTT
1 AAAACAATTTA-AT
8239 AAAA-ACATTT-AT
1 AAAACA-ATTTAAT
8251 AAAACAATTTAAT
1 AAAACAATTTAAT
8264 AAAACAAT
1 AAAACAAT
8272 AATAAAATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
12 9 0.31
13 12 0.41
14 8 0.28
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAACAATTTAAT
Found at i:10187 original size:9 final size:9
Alignment explanation
Indices: 10173--10209 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
10163 GGAGAAAACA
10173 AAAATGAAG
1 AAAATGAAG
*
10182 AAAATGAAC
1 AAAATGAAG
10191 ACAAATGAAG
1 A-AAATGAAG
10201 AAAATGAAG
1 AAAATGAAG
10210 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:10196 original size:19 final size:19
Alignment explanation
Indices: 10169--10208 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
10159 CGGTGGAGAA
10169 AACAAAAATGAAGAAAATG
1 AACAAAAATGAAGAAAATG
*
10188 AACACAAATGAAGAAAATG
1 AACAAAAATGAAGAAAATG
10207 AA
1 AA
10209 GTAACGGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.68, C:0.07, G:0.15, T:0.10
Consensus pattern (19 bp):
AACAAAAATGAAGAAAATG
Found at i:27945 original size:23 final size:22
Alignment explanation
Indices: 27914--27958 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
27904 TAGATCTAGA
* *
27914 TTTAATTTACTCTGCTTTGTTTT
1 TTTAATTTAAT-TGCTTTCTTTT
*
27937 TTTAGTTTAATTGCTTTCTTTT
1 TTTAATTTAATTGCTTTCTTTT
27959 CAATTGTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.13, C:0.11, G:0.09, T:0.67
Consensus pattern (22 bp):
TTTAATTTAATTGCTTTCTTTT
Found at i:28237 original size:31 final size:31
Alignment explanation
Indices: 28175--28244 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
28165 CTCTATAATT
*
28175 CGCCACTATTTAGCGGCGTTTATATAGGAAA
1 CGCCACTATTTAGCGGCGTTTATACAGGAAA
*
28206 CGCCACTATTTAGCGGCGTTTATGCCA-GAAA
1 CGCCACTATTTAGCGGCGTTTAT-ACAGGAAA
28237 CGCCACTA
1 CGCCACTA
28245 AATAGCAGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 35 0.97
32 1 0.03
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (31 bp):
CGCCACTATTTAGCGGCGTTTATACAGGAAA
Done.