Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021840.1 Corchorus olitorius cultivar O-4 contig21873, 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: 35476
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:1243 original size:2 final size:2
Alignment explanation
Indices: 1236--1269 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1226 AAAGATGACT
* *
1236 TA TA TA TA TA TA TA TA TA TA TA TG TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1270 GTGTCGGCAT
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:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1944 original size:36 final size:37
Alignment explanation
Indices: 1904--1974 Score: 101
Period size: 36 Copynumber: 1.9 Consensus size: 37
1894 AAGAAGTTAC
*
1904 TTTTCAGC-TCAAATGCAATAT-TAAATAAGTTTTATT
1 TTTTCA-CTTCAAATACAATATATAAATAAGTTTTATT
1940 TTTTCACTTCAAATACAATATAATAAATAAGTTTT
1 TTTTCACTTCAAATACAATAT-ATAAATAAGTTTT
1975 GGTTTGTCTC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 1 0.03
36 18 0.58
38 12 0.39
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (37 bp):
TTTTCACTTCAAATACAATATATAAATAAGTTTTATT
Found at i:4072 original size:18 final size:18
Alignment explanation
Indices: 4049--4089 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
4039 GTAAATGATT
4049 AAGTAGTATAAAGTAGAA
1 AAGTAGTATAAAGTAGAA
*
4067 AAGTAGTATAAAGTATAA
1 AAGTAGTATAAAGTAGAA
4085 AAGTA
1 AAGTA
4090 TGAGGGTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.20, T:0.24
Consensus pattern (18 bp):
AAGTAGTATAAAGTAGAA
Found at i:6280 original size:16 final size:16
Alignment explanation
Indices: 6259--6297 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
6249 CCCGAAATCT
**
6259 AAATGACTTGTGACCA
1 AAATGACTCATGACCA
6275 AAATGACTCATGACCA
1 AAATGACTCATGACCA
*
6291 ATATGAC
1 AAATGAC
6298 CACAAACCCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.23
Consensus pattern (16 bp):
AAATGACTCATGACCA
Found at i:7237 original size:16 final size:17
Alignment explanation
Indices: 7192--7247 Score: 57
Period size: 16 Copynumber: 3.4 Consensus size: 17
7182 TCAAGGGTCG
7192 TTTGTTATCGTTTTCGTT
1 TTTGTT-TCGTTTTCGTT
*
7210 TTTCTGTT--TTTT-GTT
1 TTTGT-TTCGTTTTCGTT
7225 TTTGTTTCGTTTTCG-T
1 TTTGTTTCGTTTTCGTT
7241 TTTGTTT
1 TTTGTTT
7248 TTGTTGTGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
14 2 0.06
15 7 0.22
16 16 0.50
17 1 0.03
18 5 0.16
19 1 0.03
ACGTcount: A:0.02, C:0.09, G:0.16, T:0.73
Consensus pattern (17 bp):
TTTGTTTCGTTTTCGTT
Found at i:10244 original size:10 final size:10
Alignment explanation
Indices: 10218--10260 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
10208 GTAAGACCGC
10218 CTTTCTCT-T
1 CTTTCTCTCT
10227 CTTCTCTCTCT
1 CTT-TCTCTCT
10238 CTTTCTCTCT
1 CTTTCTCTCT
*
10248 CTTTTTCTC-
1 CTTTCTCTCT
10257 CTTT
1 CTTT
10261 TTTTTCCCTG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 7 0.23
10 20 0.65
11 4 0.13
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (10 bp):
CTTTCTCTCT
Found at i:10263 original size:10 final size:12
Alignment explanation
Indices: 10221--10256 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
10211 AGACCGCCTT
*
10221 TCTCTTCTTCTC
1 TCTCTTTTTCTC
*
10233 TCTCTCTTTCTC
1 TCTCTTTTTCTC
10245 TCTCTTTTTCTC
1 TCTCTTTTTCTC
10257 CTTTTTTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (12 bp):
TCTCTTTTTCTC
Found at i:12920 original size:16 final size:16
Alignment explanation
Indices: 12899--12931 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
12889 CTCTCTCTAG
12899 TTATGAACAAAATTCA
1 TTATGAACAAAATTCA
*
12915 TTATGACCAAAATTCA
1 TTATGAACAAAATTCA
12931 T
1 T
12932 CATTGGCTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.33
Consensus pattern (16 bp):
TTATGAACAAAATTCA
Found at i:15002 original size:19 final size:21
Alignment explanation
Indices: 14956--15014 Score: 95
Period size: 19 Copynumber: 2.9 Consensus size: 21
14946 ATTTGATTTT
14956 TCATTACACCAAATAATGATA
1 TCATTACACCAAATAATGATA
*
14977 CCATTACACCAAATAA-GA-A
1 TCATTACACCAAATAATGATA
14996 TCATTACACCAAATAATGA
1 TCATTACACCAAATAATGA
15015 CAGATTTCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
19 16 0.46
20 4 0.11
21 15 0.43
ACGTcount: A:0.49, C:0.22, G:0.05, T:0.24
Consensus pattern (21 bp):
TCATTACACCAAATAATGATA
Found at i:15665 original size:29 final size:23
Alignment explanation
Indices: 15610--15658 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
15600 TGTATCAATT
15610 TGAATTACCTGCCACATATCAAA
1 TGAATTACCTGCCACATATCAAA
15633 TGAATTACCTGCCACATATCAAA
1 TGAATTACCTGCCACATATCAAA
15656 TGA
1 TGA
15659 GAATGAAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (23 bp):
TGAATTACCTGCCACATATCAAA
Found at i:18088 original size:21 final size:21
Alignment explanation
Indices: 18063--18145 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 21
18053 TATCTTAGAT
18063 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
18084 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
* **
18105 ATAAATAATGA-GTTCAAAATAA
1 AT-AATAAT-ATATTTTAAATAA
18127 ATAAATAATATATATTTAA
1 AT-AATAATATAT-TTTAA
18146 TTACTAAACG
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
21 18 0.37
22 21 0.43
23 10 0.20
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:18096 original size:25 final size:25
Alignment explanation
Indices: 18065--18113 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
18055 TCTTAGATAT
*
18065 AATATATATT-ATTAAATAAATAATA
1 AATATATATTAAAT-AATAAATAATA
*
18090 AATATATTTTAAATAATAAATAAT
1 AATATATATTAAATAATAAATAAT
18114 GAGTTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATATATATTAAATAATAAATAATA
Found at i:18477 original size:75 final size:75
Alignment explanation
Indices: 18373--18514 Score: 239
Period size: 75 Copynumber: 1.9 Consensus size: 75
18363 AAGCTCAATG
* * * *
18373 TTTCCTACACAAGCTATTGGGTTCGAGTCTTGTTTTTTGCTACTCATTAATATGATATTGAAATG
1 TTTCCTACACAAGCTATTGGATTCGAGTCTTGTTTTTTGCTACTCATGAACAGGATATTGAAATG
18438 GATTACCTCC
66 GATTACCTCC
*
18448 TTTCCTAGACAAGCTATTGGATTCGAGTCTTGTTTTTTGCTACTCATGAACAGGATATTGAAATG
1 TTTCCTACACAAGCTATTGGATTCGAGTCTTGTTTTTTGCTACTCATGAACAGGATATTGAAATG
18513 GA
66 GA
18515 CTACACAATA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 62 1.00
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.39
Consensus pattern (75 bp):
TTTCCTACACAAGCTATTGGATTCGAGTCTTGTTTTTTGCTACTCATGAACAGGATATTGAAATG
GATTACCTCC
Found at i:19191 original size:29 final size:29
Alignment explanation
Indices: 19158--19217 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
19148 AAAAGTCAAG
19158 TGTTTAACAATTGAAAAGGCATATATAAA
1 TGTTTAACAATTGAAAAGGCATATATAAA
19187 TGTTTAACAATTGAAAAGGCATATATAAA
1 TGTTTAACAATTGAAAAGGCATATATAAA
19216 TG
1 TG
19218 AACTTCAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.32
Consensus pattern (29 bp):
TGTTTAACAATTGAAAAGGCATATATAAA
Found at i:27773 original size:24 final size:25
Alignment explanation
Indices: 27744--27794 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
27734 TTATGTGAAC
*
27744 AATAAAATAAATAAACAAGA-AAAT
1 AATAAAATAAAGAAACAAGATAAAT
* *
27768 AATAAAATTAAGCAACAAGATAAAT
1 AATAAAATAAAGAAACAAGATAAAT
27793 AA
1 AA
27795 ATACTCCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.18
Consensus pattern (25 bp):
AATAAAATAAAGAAACAAGATAAAT
Found at i:30700 original size:21 final size:21
Alignment explanation
Indices: 30640--30704 Score: 76
Period size: 26 Copynumber: 2.9 Consensus size: 21
30630 TGAGATGATA
30640 TAATATTTCATCAAACAATTG
1 TAATATTTCATCAAACAATTG
30661 TAATACACAATTTCATCAAACAATTG
1 TAAT-----ATTTCATCAAACAATTG
*
30687 TAATATTCCATCAAACAA
1 TAATATTTCATCAAACAA
30705 GTGAAACCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
21 17 0.45
26 21 0.55
ACGTcount: A:0.46, C:0.18, G:0.03, T:0.32
Consensus pattern (21 bp):
TAATATTTCATCAAACAATTG
Found at i:32133 original size:41 final size:41
Alignment explanation
Indices: 32069--32192 Score: 153
Period size: 41 Copynumber: 3.0 Consensus size: 41
32059 ACTGCGGGAG
*
32069 CTTCAGCATGAG-TCCTAATTGCGGGAGCTTTGGCATGAGTC
1 CTTCAGCATGAGTTCC-AACTGCGGGAGCTTTGGCATGAGTC
* * *
32110 CTTTAGCATGAGTTCCAACTGCGGGAACTTCGGCATGAGTC
1 CTTCAGCATGAGTTCCAACTGCGGGAGCTTTGGCATGAGTC
* * *
32151 CTTCAGCACGAGTCCCAACTG-TGGAGGCTTTGGCATGAGTC
1 CTTCAGCATGAGTTCCAACTGCGGGA-GCTTTGGCATGAGTC
32192 C
1 C
32193 CAACTGCGGG
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
40 3 0.04
41 65 0.92
42 3 0.04
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.27
Consensus pattern (41 bp):
CTTCAGCATGAGTTCCAACTGCGGGAGCTTTGGCATGAGTC
Found at i:32198 original size:27 final size:27
Alignment explanation
Indices: 32160--32234 Score: 114
Period size: 27 Copynumber: 2.8 Consensus size: 27
32150 CCTTCAGCAC
*
32160 GAGTCCCAACTGTGGAGGCTTTGGCAT
1 GAGTCCCAACTGTGGAGGCTTTGCCAT
* *
32187 GAGTCCCAACTGCGGGGGCTTTGCCAT
1 GAGTCCCAACTGTGGAGGCTTTGCCAT
*
32214 GAGTCCCAACTGTGGAAGCTT
1 GAGTCCCAACTGTGGAGGCTT
32235 GATCGGTCGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.19, C:0.25, G:0.32, T:0.24
Consensus pattern (27 bp):
GAGTCCCAACTGTGGAGGCTTTGCCAT
Done.