Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016721.1 Corchorus olitorius cultivar O-4 contig16754, 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: 33250
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:94 original size:33 final size:33
Alignment explanation
Indices: 4--109 Score: 124
Period size: 33 Copynumber: 3.2 Consensus size: 33
1 AGA
* * **
4 GGGCGGCCTAACCATGGTTATGCCGCCCTCGGT
1 GGGCGGCATAGCCATGGTTATGCCGCCCTCCTT
* **
37 GGGCGGTAT-GCCATGGGCATGCCGCCCTCCTT
1 GGGCGGCATAGCCATGGTTATGCCGCCCTCCTT
* *
69 AGGCGGCATAGCCATGGTTACGCCGCCCTCCTT
1 GGGCGGCATAGCCATGGTTATGCCGCCCTCCTT
102 GGGCGGCA
1 GGGCGGCA
110 CCAATAAATA
Statistics
Matches: 59, Mismatches: 13, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
32 25 0.42
33 34 0.58
ACGTcount: A:0.12, C:0.34, G:0.34, T:0.20
Consensus pattern (33 bp):
GGGCGGCATAGCCATGGTTATGCCGCCCTCCTT
Found at i:3379 original size:39 final size:39
Alignment explanation
Indices: 3334--3417 Score: 150
Period size: 39 Copynumber: 2.2 Consensus size: 39
3324 CAGCAGCAGC
*
3334 CTCCCTCTCCCTATACATCCGAGCAGCCTCAGCCTCCCT
1 CTCCCTCTCCCGATACATCCGAGCAGCCTCAGCCTCCCT
*
3373 CTCCCTCTCCCGATACATCCGAGCAGCCTCAGCCTCTCT
1 CTCCCTCTCCCGATACATCCGAGCAGCCTCAGCCTCCCT
3412 CTCCCT
1 CTCCCT
3418 TTGCAACTGC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.14, C:0.51, G:0.11, T:0.24
Consensus pattern (39 bp):
CTCCCTCTCCCGATACATCCGAGCAGCCTCAGCCTCCCT
Found at i:3900 original size:33 final size:33
Alignment explanation
Indices: 3815--3891 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 33
3805 ACTTTCCGGC
* * * *
3815 GGTGCCGCACCAACACGGTGACGCCGCCATGGT
1 GGTGCCGCCCCAACAGGGCGACACCGCCATGGT
*
3848 GGTGCCGCCCCAACAGGGCGACACCGCTATGGT
1 GGTGCCGCCCCAACAGGGCGACACCGCCATGGT
3881 GGTGCCGCCCC
1 GGTGCCGCCCC
3892 CCGGGGGCGG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.16, C:0.39, G:0.34, T:0.12
Consensus pattern (33 bp):
GGTGCCGCCCCAACAGGGCGACACCGCCATGGT
Found at i:4073 original size:19 final size:19
Alignment explanation
Indices: 4049--4087 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
4039 CATGATGTTC
4049 TTGAAGAAGTTTAGAGAGT
1 TTGAAGAAGTTTAGAGAGT
*
4068 TTGAAGAAGTTTTGAGAGT
1 TTGAAGAAGTTTAGAGAGT
4087 T
1 T
4088 AGAAAATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.31, T:0.36
Consensus pattern (19 bp):
TTGAAGAAGTTTAGAGAGT
Found at i:4598 original size:21 final size:21
Alignment explanation
Indices: 4560--4607 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
4550 TCAATGCTTT
* ** *
4560 AGGATGCAAGAGGGATTTCGA
1 AGGAAGCAAGAGCCATTTCCA
4581 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCCA
4602 A-GAAGC
1 AGGAAGC
4608 TACAATTCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.38, C:0.17, G:0.31, T:0.15
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCCA
Found at i:10548 original size:21 final size:21
Alignment explanation
Indices: 10524--10568 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
10514 ATGACATTGC
* *
10524 CCACCTAGGTGATCAGACAAA
1 CCACATAGGTCATCAGACAAA
* *
10545 CCACATGGGTCTTCAGACAAA
1 CCACATAGGTCATCAGACAAA
10566 CCA
1 CCA
10569 TGTGGACGCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.31, G:0.18, T:0.16
Consensus pattern (21 bp):
CCACATAGGTCATCAGACAAA
Found at i:15952 original size:32 final size:32
Alignment explanation
Indices: 15911--15975 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
15901 TACGATGTGG
15911 TCATTTTTTAATCTTGATTGCAATTATTAAAT
1 TCATTTTTTAATCTTGATTGCAATTATTAAAT
* * *
15943 TCATTTTTTAATCTTGGTTGTAATTGTTAAAT
1 TCATTTTTTAATCTTGATTGCAATTATTAAAT
15975 T
1 T
15976 AATAGAATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.28, C:0.08, G:0.09, T:0.55
Consensus pattern (32 bp):
TCATTTTTTAATCTTGATTGCAATTATTAAAT
Found at i:17510 original size:11 final size:11
Alignment explanation
Indices: 17496--17533 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
17486 ATTCATAACA
17496 AATTTATAATT
1 AATTTATAATT
17507 AATTTATAATT
1 AATTTATAATT
17518 -ATTTGATAATT
1 AATTT-ATAATT
*
17529 TATTT
1 AATTT
17534 TATATAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:24826 original size:12 final size:12
Alignment explanation
Indices: 24811--24835 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24801 CAATCTTGAA
24811 GAAAATCATGTC
1 GAAAATCATGTC
24823 GAAAATCATGTC
1 GAAAATCATGTC
24835 G
1 G
24836 GATTTTGTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (12 bp):
GAAAATCATGTC
Found at i:24952 original size:10 final size:10
Alignment explanation
Indices: 24939--25019 Score: 59
Period size: 10 Copynumber: 8.7 Consensus size: 10
24929 TTTTTATTTT
24939 TTAATTATTA
1 TTAATTATTA
24949 TTAATTA-T-
1 TTAATTATTA
24957 TT-A--ATTA
1 TTAATTATTA
24964 TTAATTATTA
1 TTAATTATTA
*
24974 TTAATT-TAAA
1 TTAATTAT-TA
*
24984 TT-GTTATTA
1 TTAATTATTA
*
24993 TTAATTATAA
1 TTAATTATTA
*
25003 TTAATAATTA
1 TTAATTATTA
*
25013 ATAATTA
1 TTAATTA
25020 AAAAACAAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 16
0.68 0.11 0.20
Matches are distributed among these distances:
5 1 0.02
6 1 0.02
7 3 0.06
8 3 0.06
9 7 0.13
10 39 0.72
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (10 bp):
TTAATTATTA
Found at i:24955 original size:7 final size:7
Alignment explanation
Indices: 24945--25019 Score: 66
Period size: 7 Copynumber: 10.6 Consensus size: 7
24935 TTTTTTAATT
24945 ATTATTA
1 ATTATTA
24952 ATTATTTA
1 ATTA-TTA
24960 ATTATTA
1 ATTATTA
24967 ATTATT-
1 ATTATTA
24973 ATTAATTTAA
1 ATT-A-TT-A
*
24983 ATTGTT-
1 ATTATTA
24989 ATTATTA
1 ATTATTA
24996 ATTA-TA
1 ATTATTA
*
25002 ATTAATA
1 ATTATTA
*
25009 ATTAATA
1 ATTATTA
25016 ATTA
1 ATTA
25020 AAAAACAAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
6 14 0.24
7 31 0.53
8 11 0.19
10 3 0.05
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (7 bp):
ATTATTA
Found at i:24992 original size:29 final size:26
Alignment explanation
Indices: 24939--25007 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 26
24929 TTTTTATTTT
24939 TTAATTATTATTAA-TTATTTAATTA
1 TTAATTATTATTAATTTATTTAATTA
*
24964 TTAATTATTATTAATTTAAATTGTTATTA
1 TTAATTATTATTAATTT--ATT-TAATTA
*
24993 TTAATTATAATTAAT
1 TTAATTATTATTAAT
25008 AATTAATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 14 0.37
26 2 0.05
28 3 0.08
29 19 0.50
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (26 bp):
TTAATTATTATTAATTTATTTAATTA
Found at i:28162 original size:33 final size:34
Alignment explanation
Indices: 28125--28198 Score: 82
Period size: 33 Copynumber: 2.2 Consensus size: 34
28115 GCGCCCTGCC
*
28125 GGGGCGGCGTCACCAT-ATCGGTGGCG-CCCCCTG
1 GGGGCGCCGTCACCATGAT-GGTGGCGCCCCCCTG
** *
28158 GGGGCGCCGTCGGCATGGTGGTGGCGCCCCCCT-
1 GGGGCGCCGTCACCATGATGGTGGCGCCCCCCTG
28191 GGGGCGCC
1 GGGGCGCC
28199 ACAGCCGGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
33 28 0.80
34 7 0.20
ACGTcount: A:0.05, C:0.36, G:0.45, T:0.14
Consensus pattern (34 bp):
GGGGCGCCGTCACCATGATGGTGGCGCCCCCCTG
Found at i:28676 original size:27 final size:27
Alignment explanation
Indices: 28613--28680 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
28603 AAGGGAGAAA
*
28613 GAGGCTGAGGCTGCTCGGATGTATAGG
1 GAGGCGGAGGCTGCTCGGATGTATAGG
* *
28640 GAGGCTGAGGCTGCTCGGAT-TATCCGG
1 GAGGCGGAGGCTGCTCGGATGTAT-AGG
28667 GAGAG-GGAGGCTGC
1 GAG-GCGGAGGCTGC
28681 CGCTGGTGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
26 3 0.08
27 33 0.89
28 1 0.03
ACGTcount: A:0.18, C:0.18, G:0.46, T:0.19
Consensus pattern (27 bp):
GAGGCGGAGGCTGCTCGGATGTATAGG
Found at i:28977 original size:20 final size:20
Alignment explanation
Indices: 28952--28993 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
28942 TATTATGTGA
*
28952 TATTATAAATTGAAATTAAT
1 TATTATAAATTGAAATAAAT
28972 TATTATAAATTGAAATAAAT
1 TATTATAAATTGAAATAAAT
28992 TA
1 TA
28994 AATAAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (20 bp):
TATTATAAATTGAAATAAAT
Found at i:30500 original size:21 final size:21
Alignment explanation
Indices: 30474--30514 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
30464 ATATTTTGGG
30474 ATTTTTATGGATGTTTATGTC
1 ATTTTTATGGATGTTTATGTC
* *
30495 ATTTTTTTGGATTTTTATGT
1 ATTTTTATGGATGTTTATGT
30515 ATATTGGGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.02, G:0.17, T:0.63
Consensus pattern (21 bp):
ATTTTTATGGATGTTTATGTC
Found at i:32733 original size:12 final size:12
Alignment explanation
Indices: 32718--32742 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32708 ATACATTAAT
32718 AAATAATAATAA
1 AAATAATAATAA
32730 AAATAATAATAA
1 AAATAATAATAA
32742 A
1 A
32743 TATTACAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATAATAATAA
Found at i:32736 original size:19 final size:19
Alignment explanation
Indices: 32714--32766 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
32704 ATGAATACAT
32714 TAATAAATAATAATAAAAA
1 TAATAAATAATAATAAAAA
* * *
32733 TAAT-AATAAATATTACAAC
1 TAATAAAT-AATAATAAAAA
*
32752 TATTAAATAATAATA
1 TAATAAATAATAATA
32767 CCACCTGATG
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
18 3 0.11
19 21 0.78
20 3 0.11
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (19 bp):
TAATAAATAATAATAAAAA
Done.