Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017019.1 Corchorus olitorius cultivar O-4 contig17052, 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: 20144
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Found at i:2782 original size:18 final size:18
Alignment explanation
Indices: 2739--2794 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 18
2729 GATAATGATG
2739 TGAAAATTTGATAACATCATTA
1 TGAAAATTTGATAAC--C--TA
2761 TG-AAATTTCGATAACCTA
1 TGAAAATTT-GATAACCTA
2779 TGAAAATTTGATAACC
1 TGAAAATTTGATAACC
2795 ACACTGTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 11 0.34
19 6 0.19
20 1 0.03
21 6 0.19
22 8 0.25
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.34
Consensus pattern (18 bp):
TGAAAATTTGATAACCTA
Found at i:2810 original size:22 final size:22
Alignment explanation
Indices: 2739--2956 Score: 155
Period size: 22 Copynumber: 10.1 Consensus size: 22
2729 GATAATGATG
* *
2739 TGAAAATTTGATAA-CATCATTA
1 TGAAATTTTGATAACCA-CACTA
*
2761 TGAAATTTCGAT-A--AC-CTA
1 TGAAATTTTGATAACCACACTA
* *
2779 TGAAAATTTGATAACCACACTG
1 TGAAATTTTGATAACCACACTA
* * *
2801 TGAAATTTTGATAATCTCCCTA
1 TGAAATTTTGATAACCACACTA
* * *
2823 TGAAATTTTGATAATCTCCCTA
1 TGAAATTTTGATAACCACACTA
*
2845 TGAAATTTTGATAATCACACTA
1 TGAAATTTTGATAACCACACTA
*
2867 T-AAA-ATTGATAACCACACTA
1 TGAAATTTTGATAACCACACTA
* *
2887 TGAAAATTTTGATAACCTC-TTCA
1 TG-AAATTTTGATAACCACACT-A
* *
2910 TTAAATTTTGATAACCACACCA
1 TGAAATTTTGATAACCACACTA
* * * * *
2932 TTAAGTTTCGATAACCTCCCTA
1 TGAAATTTTGATAACCACACTA
2954 TGA
1 TGA
2957 GAATGAAACA
Statistics
Matches: 159, Mismatches: 28, Indels: 18
0.78 0.14 0.09
Matches are distributed among these distances:
18 12 0.08
19 2 0.01
20 16 0.10
21 6 0.04
22 111 0.70
23 12 0.08
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (22 bp):
TGAAATTTTGATAACCACACTA
Found at i:2833 original size:44 final size:44
Alignment explanation
Indices: 2739--2956 Score: 182
Period size: 44 Copynumber: 5.1 Consensus size: 44
2729 GATAATGATG
* * *
2739 TGAAAATTTGATAA-CATCATTATGAAATTTCGATAA----CCTA
1 TGAAATTTTGATAACCA-CACTATGAAATTTTGATAACCTCCCTA
* * *
2779 TGAAAATTTGATAACCACACTGTGAAATTTTGATAATCTCCCTA
1 TGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCTA
* * * * * *
2823 TGAAATTTTGATAATCTCCCTATGAAATTTTGATAATCACACTA
1 TGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCTA
* *
2867 T-AAA-ATTGATAACCACACTATGAAAATTTTGATAACCT-CTTCA
1 TGAAATTTTGATAACCACACTATG-AAATTTTGATAACCTCCCT-A
* * * * *
2910 TTAAATTTTGATAACCACACCATTAAGTTTCGATAACCTCCCTA
1 TGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCTA
2954 TGA
1 TGA
2957 GAATGAAACA
Statistics
Matches: 143, Mismatches: 25, Indels: 16
0.78 0.14 0.09
Matches are distributed among these distances:
40 30 0.21
41 2 0.01
42 15 0.10
43 18 0.13
44 61 0.43
45 17 0.12
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (44 bp):
TGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCTA
Found at i:2945 original size:87 final size:88
Alignment explanation
Indices: 2759--2945 Score: 210
Period size: 87 Copynumber: 2.2 Consensus size: 88
2749 ATAACATCAT
* *
2759 TATGAAATTTCGAT-A--AC-CTATGAAAATTTGATAACCACACTGTGAAATTTTGATAATCTCC
1 TATGAAATTTCGATAATCACACTATGAAAATTTGATAACCACACTATGAAATTTTGATAACCTCC
* *
2820 CTATGAAATTTTGATAATCTCCC
66 CTATGAAATTTTGATAACCACCC
*
2843 TATGAAATTTTGATAATCACACTAT-AAAA-TTGATAACCACACTATGAAAATTTTGATAACCT-
1 TATGAAATTTCGATAATCACACTATGAAAATTTGATAACCACACTATG-AAATTTTGATAACCTC
* *
2905 CTTCATTAAATTTTGATAACCACACC
65 CCT-ATGAAATTTTGATAACCAC-CC
* *
2931 -ATTAAGTTTCGATAA
1 TATGAAATTTCGATAA
2946 CCTCCCTATG
Statistics
Matches: 86, Mismatches: 10, Indels: 11
0.80 0.09 0.10
Matches are distributed among these distances:
84 13 0.15
85 1 0.01
86 18 0.21
87 48 0.56
88 6 0.07
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (88 bp):
TATGAAATTTCGATAATCACACTATGAAAATTTGATAACCACACTATGAAATTTTGATAACCTCC
CTATGAAATTTTGATAACCACCC
Found at i:3052 original size:22 final size:22
Alignment explanation
Indices: 2985--3090 Score: 65
Period size: 22 Copynumber: 4.6 Consensus size: 22
2975 CTCTTTATTT
* *
2985 AATTTTGATAACATCTCCATA-A
1 AATTTTGATAACCTC-CCTTAGA
* *
3007 AATTTTTG-TAACCTTCC-AATGA
1 AA-TTTTGATAACCTCCCTTA-GA
*
3029 AATTTTGTTAACCTCCCTTAGA
1 AATTTTGATAACCTCCCTTAGA
* *
3051 AACTTTGATAACCTGCCTCCCTATGA
1 AATTTTGATAACCT--C-CCTTA-GA
3077 AATTTTGATAACCT
1 AATTTTGATAACCT
3091 TCATATAAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
20 1 0.02
21 7 0.11
22 32 0.48
23 6 0.09
24 1 0.02
25 4 0.06
26 15 0.23
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (22 bp):
AATTTTGATAACCTCCCTTAGA
Found at i:3069 original size:26 final size:26
Alignment explanation
Indices: 3040--3090 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
3030 ATTTTGTTAA
3040 CCTCCCT-TAGAAACTTTGATAACCTG
1 CCTCCCTAT-GAAACTTTGATAACCTG
*
3066 CCTCCCTATGAAATTTTGATAACCT
1 CCTCCCTATGAAACTTTGATAACCT
3091 TCATATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 22 0.96
27 1 0.04
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.33
Consensus pattern (26 bp):
CCTCCCTATGAAACTTTGATAACCTG
Found at i:3104 original size:22 final size:22
Alignment explanation
Indices: 2985--3105 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
2975 CTCTTTATTT
*
2985 AATTTTGATAACATCTCCATA-AA
1 AATTTTGATAAC--CTTCATATAA
* *
3008 ATTTTTG-TAACCTTCCA-ATGA
1 AATTTTGATAACCTT-CATATAA
* * *
3029 AATTTTGTTAACCTCCCT-TAGA
1 AATTTTGATAACCTTCATATA-A
* * *
3051 AACTTTGATAACCTGCCTCCCTATGA
1 AATTTTGATAACCT---T-CATATAA
3077 AATTTTGATAACCTTCATATAA
1 AATTTTGATAACCTTCATATAA
3099 AATTTTG
1 AATTTTG
3106 TTAATGACAC
Statistics
Matches: 74, Mismatches: 14, Indels: 21
0.68 0.13 0.19
Matches are distributed among these distances:
20 3 0.04
21 11 0.15
22 35 0.47
23 7 0.09
26 17 0.23
27 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (22 bp):
AATTTTGATAACCTTCATATAA
Found at i:3187 original size:22 final size:22
Alignment explanation
Indices: 3162--3231 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
3152 GTAATGTCTG
3162 TATGGAATTTTGATAACTACAC
1 TATGGAATTTTGATAACTACAC
* *
3184 TAT-GACGTTTTGATAACCTCCA-
1 TATGGA-ATTTTGATAA-CTACAC
* *
3206 TATGAAATTTT-AGTAACCACAC
1 TATGGAATTTTGA-TAACTACAC
3228 TATG
1 TATG
3232 AAAATTTCAT
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
21 6 0.16
22 26 0.70
23 5 0.14
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (22 bp):
TATGGAATTTTGATAACTACAC
Found at i:4729 original size:120 final size:118
Alignment explanation
Indices: 4461--4814 Score: 552
Period size: 118 Copynumber: 3.0 Consensus size: 118
4451 TTATTAACGA
*
4461 GTTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGG
1 GTTTGGGATCTAAGAATTAAGGAGTAATTTATATTATTTTTATTGGAAGAGTTGGTTTGAAGTGG
*
4526 AAAAGTTAAGGACTTGAAATTCCTCAAAAGAATATTCATGGTTGTGGTGGAAC
66 AAAATTTAAGGACTTGAAATTCCTCAAAAGAATATTCATGGTTGTGGTGGAAC
* *
4579 GTTTGGGATCTAAGAATTAAGGAGTAATTTATATTATTTTCAATGGAAGAGTTGGTTTGAAGTGG
1 GTTTGGGATCTAAGAATTAAGGAGTAATTTATATTATTTTTATTGGAAGAGTTGGTTTGAAGTGG
* *
4644 AAAATTTAAGGACTTGAGAAATTCCTCAAACA-AATATTAATGGTTGTGGTGGAGC
66 AAAATTTAAGGACTT--GAAATTCCTCAAA-AGAATATTCATGGTTGTGGTGGAAC
* *
4699 GTTTGGGATCTAAGAAATAAGGAGTAATTTAT-TCTATTTTTATTGGAAGAGTTGGTTTGAAATG
1 GTTTGGGATCTAAGAATTAAGGAGTAATTTATAT-TATTTTTATTGGAAGAGTTGGTTTGAAGTG
* *
4763 G-AAATTTGAAGGACTTGAAATTCCTCAAAATAATATTCATGGTTTTGGTGGA
65 GAAAATTT-AAGGACTTGAAATTCCTCAAAAGAATATTCATGGTTGTGGTGGA
4815 TGTTCTTCCA
Statistics
Matches: 218, Mismatches: 12, Indels: 12
0.90 0.05 0.05
Matches are distributed among these distances:
117 1 0.00
118 108 0.50
119 7 0.03
120 101 0.46
121 1 0.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (118 bp):
GTTTGGGATCTAAGAATTAAGGAGTAATTTATATTATTTTTATTGGAAGAGTTGGTTTGAAGTGG
AAAATTTAAGGACTTGAAATTCCTCAAAAGAATATTCATGGTTGTGGTGGAAC
Found at i:5361 original size:34 final size:32
Alignment explanation
Indices: 5311--5400 Score: 121
Period size: 34 Copynumber: 2.8 Consensus size: 32
5301 TCGGCCCTGT
*
5311 CCAGTGGCTT-ATAATAACTGGAAGACCCAGC
1 CCAGTGGGTTGATAATAACTGGAAGACCCAGC
* *
5342 CCAGTGGGTTATGATAATAACTGGAAGATCCTGC
1 CCAGTGGG-T-TGATAATAACTGGAAGACCCAGC
5376 CCAGTGGGTTG-TAATAACTGGAAGA
1 CCAGTGGGTTGATAATAACTGGAAGA
5401 TGGCCCTGCT
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
31 21 0.40
32 3 0.06
33 2 0.04
34 27 0.51
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (32 bp):
CCAGTGGGTTGATAATAACTGGAAGACCCAGC
Found at i:5409 original size:34 final size:32
Alignment explanation
Indices: 5305--5401 Score: 117
Period size: 31 Copynumber: 3.0 Consensus size: 32
5295 GTTTTCTCGG
* * *
5305 CCCTGTCCAGTGGCTTATAATAACTGGAAGA-
1 CCCTGCCCAGTGGGTTGTAATAACTGGAAGAT
*
5336 CCCAGCCCAGTGGGTTATGATAATAACTGGAAGAT
1 CCCTGCCCAGTGGG-T-TG-TAATAACTGGAAGAT
5371 -CCTGCCCAGTGGGTTGTAATAACTGGAAGAT
1 CCCTGCCCAGTGGGTTGTAATAACTGGAAGAT
5402 GGCCCTGCTA
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
31 26 0.46
32 3 0.05
33 2 0.04
34 26 0.46
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.25
Consensus pattern (32 bp):
CCCTGCCCAGTGGGTTGTAATAACTGGAAGAT
Found at i:5564 original size:26 final size:26
Alignment explanation
Indices: 5516--5566 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
5506 ATAGAGGTGT
*
5516 ATATCATTTGATGATTTTATGGTTTG
1 ATATCATTTGATGATTGTATGGTTTG
5542 ATATCATTTGATGATTAGT-TGGTTT
1 ATATCATTTGATGATT-GTATGGTTT
5567 TCAACTTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 22 0.96
27 1 0.04
ACGTcount: A:0.24, C:0.04, G:0.20, T:0.53
Consensus pattern (26 bp):
ATATCATTTGATGATTGTATGGTTTG
Found at i:5816 original size:28 final size:28
Alignment explanation
Indices: 5785--5849 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
5775 GTGTGTGGGG
*
5785 AGACTTACTGAGCATGTGTTGCTCACGC
1 AGACTTACTGAGCATGTGTTGCTCACCC
5813 AGACTTACTGAGCATGTGTTGCTCACCC
1 AGACTTACTGAGCATGTGTTGCTCACCC
5841 AGACTTACT
1 AGACTTACT
5850 TTGATTTGTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (28 bp):
AGACTTACTGAGCATGTGTTGCTCACCC
Found at i:18228 original size:16 final size:15
Alignment explanation
Indices: 18190--18231 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
18180 ACAGAGATTG
*
18190 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
18205 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
18220 ACTAGAAAACAA
1 AC-AGAAAACAA
18232 AGCAGAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.