Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018947.1 Corchorus olitorius cultivar O-4 contig18980, 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: 33681
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:433 original size:27 final size:27
Alignment explanation
Indices: 409--462 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
399 ATTTATGAGT
409 AAAAATCAAGAATAAGTAATAATGAAA
1 AAAAATCAAGAATAAGTAATAATGAAA
436 AAAAATCAAGAATAAGTAATAATGAAA
1 AAAAATCAAGAATAAGTAATAATGAAA
463 TATAATTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.67, C:0.04, G:0.11, T:0.19
Consensus pattern (27 bp):
AAAAATCAAGAATAAGTAATAATGAAA
Found at i:1125 original size:21 final size:21
Alignment explanation
Indices: 1101--1141 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1091 CCTTTTGTCT
1101 TTTTATTTCTTTAAATAATAA
1 TTTTATTTCTTTAAATAATAA
1122 TTTTATTTCTTTAAATAATA
1 TTTTATTTCTTTAAATAATA
1142 GCTGATGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTTATTTCTTTAAATAATAA
Found at i:5523 original size:122 final size:124
Alignment explanation
Indices: 5340--5669 Score: 490
Period size: 122 Copynumber: 2.7 Consensus size: 124
5330 AATAACCTTT
* * *
5340 TAAATTAAAATAGTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAGAAT
1 TAAA-TAAAATGGTAAAAATAAAATAATTAT-AAAATATTGAATTTAATTAAAAGAAAATAGAGT
5405 TTTTAGTAGAATAAAACTGTATATT-AAAATTTTTTAATATATCCAAGTTTTTAATG-AAAA
64 TTTTAGTAGAATAAAACTGTATATTGAAAA-TTTTTAATATATCCAAGTTTTTAATGAAAAA
* *
5465 T-AGTAAAATGGTAAAAATAAAATAATCATAAAATATTGAATTTAATTAAAAGAAAATAGAGTTT
1 TAAATAAAATGGTAAAAATAAAATAATTATAAAATATTGAATTTAATTAAAAGAAAATAGAGTTT
*
5529 TTAGTAGAATAAAACTGTATTTTGAAAATTTTTAATATATCCAAGTTTTTAATGAAAAA
66 TTAGTAGAATAAAACTGTATATTGAAAATTTTTAATATATCCAAGTTTTTAATGAAAAA
* * *
5588 TAAAAAAAATGGTAAAAATAAAGTAATTATAAAGATGTT-AGATTTAATTAAATA-AAAATAGAG
1 TAAATAAAATGGTAAAAATAAAATAATTATAAA-ATATTGA-ATTTAATTAAA-AGAAAATAGAG
5651 TTTTTAGTAGAATAAAACT
63 TTTTTAGTAGAATAAAACT
5670 ATAATAGTTT
Statistics
Matches: 188, Mismatches: 11, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
122 81 0.43
123 33 0.18
124 29 0.15
125 44 0.23
126 1 0.01
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.35
Consensus pattern (124 bp):
TAAATAAAATGGTAAAAATAAAATAATTATAAAATATTGAATTTAATTAAAAGAAAATAGAGTTT
TTAGTAGAATAAAACTGTATATTGAAAATTTTTAATATATCCAAGTTTTTAATGAAAAA
Found at i:8488 original size:16 final size:16
Alignment explanation
Indices: 8447--8491 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
8437 AATTTTGGGT
8447 ACCCGAACCCGAAAATG
1 ACCCGAACCC-AAAATG
*
8464 ACCCAAACCCAAAATG
1 ACCCGAACCCAAAATG
*
8480 ACCTGAACCCAA
1 ACCCGAACCCAA
8492 TCAACCCGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 16 0.64
17 9 0.36
ACGTcount: A:0.44, C:0.38, G:0.11, T:0.07
Consensus pattern (16 bp):
ACCCGAACCCAAAATG
Found at i:10069 original size:16 final size:16
Alignment explanation
Indices: 10023--10076 Score: 58
Period size: 15 Copynumber: 3.4 Consensus size: 16
10013 GAACCGTATA
* *
10023 ACCCGAAACCGAAAACG
1 ACCCG-AACCCAAAATG
10040 ACCC-AACCCAAAATTG
1 ACCCGAACCCAAAA-TG
10056 ACCCGAACCC-AAATG
1 ACCCGAACCCAAAATG
10071 ACCCGA
1 ACCCGA
10077 CATTTGAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 16 0.48
16 8 0.24
17 9 0.27
ACGTcount: A:0.43, C:0.39, G:0.13, T:0.06
Consensus pattern (16 bp):
ACCCGAACCCAAAATG
Found at i:18768 original size:33 final size:30
Alignment explanation
Indices: 18698--18773 Score: 89
Period size: 33 Copynumber: 2.4 Consensus size: 30
18688 TCAGGAAATT
** *
18698 AAAGAAGAAGAAGAAATTGTAGGATTTCTC
1 AAAGAAGAAGAAGAAATTGTAGGAGCTCAC
*
18728 AAGGAAGAAGAAGAAAATTGTAGGGCAGCTCAC
1 AAAGAAGAAGAAG-AAATTGTA-GG-AGCTCAC
18761 AAAGAAGAAGAAG
1 AAAGAAGAAGAAG
18774 TCTAAACGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
30 12 0.32
31 8 0.21
32 2 0.05
33 16 0.42
ACGTcount: A:0.50, C:0.08, G:0.28, T:0.14
Consensus pattern (30 bp):
AAAGAAGAAGAAGAAATTGTAGGAGCTCAC
Found at i:19459 original size:68 final size:68
Alignment explanation
Indices: 19378--19560 Score: 267
Period size: 77 Copynumber: 2.6 Consensus size: 68
19368 AATGAAACAC
* *
19378 CATAATGATCTCATAATAATATACACATGTTATCATATCATACATCTATAAATCTATAATGTAGC
1 CATAATAATCTCATAATAATATATACATGTTATCATATCATACATCTATAAATCTATAATGTAGC
19443 TTA
66 TTA
19446 CATAATAATCTCATAATAATATATACATGTTATCATATTATATATATCATACATCTATAAATCTA
1 CATAATAATCTCATAATAATATATACATGTTATC---------ATATCATACATCTATAAATCTA
19511 TAATGTAGCTTA
57 TAATGTAGCTTA
19523 CATAATAATCTCATAATAATATATACATGTTATCATAT
1 CATAATAATCTCATAATAATATATACATGTTATCATAT
19561 TATATATACA
Statistics
Matches: 104, Mismatches: 2, Indels: 18
0.84 0.02 0.15
Matches are distributed among these distances:
68 36 0.35
77 68 0.65
ACGTcount: A:0.43, C:0.14, G:0.04, T:0.39
Consensus pattern (68 bp):
CATAATAATCTCATAATAATATATACATGTTATCATATCATACATCTATAAATCTATAATGTAGC
TTA
Found at i:19504 original size:77 final size:77
Alignment explanation
Indices: 19412--19568 Score: 314
Period size: 77 Copynumber: 2.0 Consensus size: 77
19402 ACATGTTATC
19412 ATATCATACATCTATAAATCTATAATGTAGCTTACATAATAATCTCATAATAATATATACATGTT
1 ATATCATACATCTATAAATCTATAATGTAGCTTACATAATAATCTCATAATAATATATACATGTT
19477 ATCATATTATAT
66 ATCATATTATAT
19489 ATATCATACATCTATAAATCTATAATGTAGCTTACATAATAATCTCATAATAATATATACATGTT
1 ATATCATACATCTATAAATCTATAATGTAGCTTACATAATAATCTCATAATAATATATACATGTT
19554 ATCATATTATAT
66 ATCATATTATAT
19566 ATA
1 ATA
19569 CATCTATAAT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 80 1.00
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.40
Consensus pattern (77 bp):
ATATCATACATCTATAAATCTATAATGTAGCTTACATAATAATCTCATAATAATATATACATGTT
ATCATATTATAT
Found at i:19849 original size:20 final size:21
Alignment explanation
Indices: 19824--19863 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
19814 AATGACATGA
*
19824 CATGAAA-GGCAAACCCTAAC
1 CATGAAATGACAAACCCTAAC
19844 CATGAAATGACAAACCCTAA
1 CATGAAATGACAAACCCTAA
19864 GTGAGATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.47, C:0.28, G:0.12, T:0.12
Consensus pattern (21 bp):
CATGAAATGACAAACCCTAAC
Found at i:19925 original size:25 final size:25
Alignment explanation
Indices: 19819--19912 Score: 85
Period size: 25 Copynumber: 4.0 Consensus size: 25
19809 AAAAAAATGA
*
19819 CATGACATGAAAGGCAAACCCTAAC
1 CATGACATGAAAGCCAAACCCTAAC
*
19844 CATGAAATG--A--CAAACCCTAA-
1 CATGACATGAAAGCCAAACCCTAAC
* * *
19864 -GTGAGATG-AAGACTAAACCCTAAC
1 CATGACATGAAAG-CCAAACCCTAAC
19888 CATGACATGAAAGCCAAACCCTAAC
1 CATGACATGAAAGCCAAACCCTAAC
19913 ATGTCATCTA
Statistics
Matches: 55, Mismatches: 7, Indels: 14
0.72 0.09 0.18
Matches are distributed among these distances:
19 6 0.11
20 1 0.02
21 10 0.18
23 10 0.18
25 25 0.45
26 3 0.05
ACGTcount: A:0.45, C:0.27, G:0.15, T:0.14
Consensus pattern (25 bp):
CATGACATGAAAGCCAAACCCTAAC
Found at i:20000 original size:31 final size:32
Alignment explanation
Indices: 19955--20018 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
19945 GTAGAAAAAA
*
19955 ATTGGAATACCCAAATTATCCTAAAGGCTTAT
1 ATTGGAATACCCAAATTACCCTAAAGGCTTAT
* **
19987 ATTGG-ATGCCCAAATTACCCTCGAGGCTTAT
1 ATTGGAATACCCAAATTACCCTAAAGGCTTAT
20018 A
1 A
20019 CGAAATAACA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 23 0.82
32 5 0.18
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.30
Consensus pattern (32 bp):
ATTGGAATACCCAAATTACCCTAAAGGCTTAT
Found at i:20709 original size:48 final size:48
Alignment explanation
Indices: 20654--21118 Score: 720
Period size: 48 Copynumber: 9.7 Consensus size: 48
20644 GGGAATTTAA
* *** * *
20654 ACAACACCTTCCGATGGGGAAGGGCAAAACAGGG-AAAAGCAAACTTAG
1 ACAACACCTTCCGATGAGGAAGGGC-AATTTGGGAAAAAGTAGACTTAG
*
20702 ACAACACCTTCCGATGAGGAAGGGCAATTTGGGAAAAAGTAGACTTAA
1 ACAACACCTTCCGATGAGGAAGGGCAATTTGGGAAAAAGTAGACTTAG
* * *
20750 ACAACACCTTCCGATGAGGAAGGGAAATTTGGGAAAAAGCAAACTTAG
1 ACAACACCTTCCGATGAGGAAGGGCAATTTGGGAAAAAGTAGACTTAG
*
20798 ACAATACCTTCCGATGAGGAAGGGCAATTTGGGAAAAAGTAGACTTAG
1 ACAACACCTTCCGATGAGGAAGGGCAATTTGGGAAAAAGTAGACTTAG
****
20846 ACAACACCTTCCGATGAGGAAGGGCAAAACAGGAAAAAGTAGACTTAG
1 ACAACACCTTCCGATGAGGAAGGGCAATTTGGGAAAAAGTAGACTTAG
*
20894 ACAACACCTTCCGATGAGGAAGGGCAATTTGGG-AAAAGCAGACTTAG
1 ACAACACCTTCCGATGAGGAAGGGCAATTTGGGAAAAAGTAGACTTAG
20941 ACAACACCTTCCGATGAGGAAGGGCAATTTGGGAAAAAGTAGACTTAG
1 ACAACACCTTCCGATGAGGAAGGGCAATTTGGGAAAAAGTAGACTTAG
* *
20989 ACAACACCTTCCGATGAGGAAGGGCAGTTTGGG-AAAAGCAGACTTAG
1 ACAACACCTTCCGATGAGGAAGGGCAATTTGGGAAAAAGTAGACTTAG
* *
21036 ACAACACCTTCCGATAAGGAAGGACAATTTGGGAAAAAGTAGACTTAG
1 ACAACACCTTCCGATGAGGAAGGGCAATTTGGGAAAAAGTAGACTTAG
21084 ACAACACCTTCCGATGAGGAAGGGCAATTTGGGAA
1 ACAACACCTTCCGATGAGGAAGGGCAATTTGGGAA
21119 TGTTGAAGGA
Statistics
Matches: 380, Mismatches: 34, Indels: 6
0.90 0.08 0.01
Matches are distributed among these distances:
47 94 0.25
48 286 0.75
ACGTcount: A:0.39, C:0.18, G:0.26, T:0.17
Consensus pattern (48 bp):
ACAACACCTTCCGATGAGGAAGGGCAATTTGGGAAAAAGTAGACTTAG
Found at i:20980 original size:95 final size:95
Alignment explanation
Indices: 20654--21118 Score: 716
Period size: 95 Copynumber: 4.9 Consensus size: 95
20644 GGGAATTTAA
* *** * *
20654 ACAACACCTTCCGATGGGGAAGGGCAAAACAGGG-AAAAGCAAACTTAGACAACACCTTCCGATG
1 ACAACACCTTCCGATGAGGAAGGGC-AATTTGGGAAAAAGTAGACTTAGACAACACCTTCCGATG
* *
20718 AGGAAGGGCAATTTGGGAAAAAGTAGACTTAA
65 AGGAAGGGCAATTTGGG-AAAAGCAGACTTAG
* * * *
20750 ACAACACCTTCCGATGAGGAAGGGAAATTTGGGAAAAAGCAAACTTAGACAATACCTTCCGATGA
1 ACAACACCTTCCGATGAGGAAGGGCAATTTGGGAAAAAGTAGACTTAGACAACACCTTCCGATGA
*
20815 GGAAGGGCAATTTGGGAAAAAGTAGACTTAG
66 GGAAGGGCAATTTGGG-AAAAGCAGACTTAG
****
20846 ACAACACCTTCCGATGAGGAAGGGCAAAACAGGAAAAAGTAGACTTAGACAACACCTTCCGATGA
1 ACAACACCTTCCGATGAGGAAGGGCAATTTGGGAAAAAGTAGACTTAGACAACACCTTCCGATGA
20911 GGAAGGGCAATTTGGGAAAAGCAGACTTAG
66 GGAAGGGCAATTTGGGAAAAGCAGACTTAG
20941 ACAACACCTTCCGATGAGGAAGGGCAATTTGGGAAAAAGTAGACTTAGACAACACCTTCCGATGA
1 ACAACACCTTCCGATGAGGAAGGGCAATTTGGGAAAAAGTAGACTTAGACAACACCTTCCGATGA
*
21006 GGAAGGGCAGTTTGGGAAAAGCAGACTTAG
66 GGAAGGGCAATTTGGGAAAAGCAGACTTAG
* *
21036 ACAACACCTTCCGATAAGGAAGGACAATTTGGGAAAAAGTAGACTTAGACAACACCTTCCGATGA
1 ACAACACCTTCCGATGAGGAAGGGCAATTTGGGAAAAAGTAGACTTAGACAACACCTTCCGATGA
21101 GGAAGGGCAATTTGGGAA
66 GGAAGGGCAATTTGGGAA
21119 TGTTGAAGGA
Statistics
Matches: 344, Mismatches: 24, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
95 188 0.55
96 156 0.45
ACGTcount: A:0.39, C:0.18, G:0.26, T:0.17
Consensus pattern (95 bp):
ACAACACCTTCCGATGAGGAAGGGCAATTTGGGAAAAAGTAGACTTAGACAACACCTTCCGATGA
GGAAGGGCAATTTGGGAAAAGCAGACTTAG
Found at i:21864 original size:45 final size:45
Alignment explanation
Indices: 21807--21892 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
21797 TCTTTGTAAT
* * * *
21807 CAACTCATCAAAATCT-AAACTGTTTGAGTCTAAATATTGTATTAC
1 CAACTCACCAAAAT-TGAAACTGTTTAAGACTAAAGATTGTATTAC
*
21852 CAACTCACCAAAATTGAAACTTTTTAAGACTAAAGATTGTA
1 CAACTCACCAAAATTGAAACTGTTTAAGACTAAAGATTGTA
21893 ATTTTATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 1 0.03
45 34 0.97
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (45 bp):
CAACTCACCAAAATTGAAACTGTTTAAGACTAAAGATTGTATTAC
Found at i:22259 original size:52 final size:53
Alignment explanation
Indices: 22129--22260 Score: 144
Period size: 52 Copynumber: 2.5 Consensus size: 53
22119 AGCATGAACC
* * *
22129 CAAAA-ATCTAATCTTTAAGCT-AAAAGCTTTTACTCTTTACACATTATAAGAA
1 CAAAAGATCTAATCTTTAAACTAAAAAGATTATACTCTTTACACATTAT-AGAA
* * * **
22181 CAAAAGATTTGATCTTTAAATTAAAAAGATTATACTCTTTACATGTTAT-GAA
1 CAAAAGATCTAATCTTTAAACTAAAAAGATTATACTCTTTACACATTATAGAA
* *
22233 CAAAAGATCCAATCTCTAAACTAAAAAG
1 CAAAAGATCTAATCTTTAAACTAAAAAG
22261 TTTTTATATA
Statistics
Matches: 65, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
52 31 0.48
53 12 0.18
54 22 0.34
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.33
Consensus pattern (53 bp):
CAAAAGATCTAATCTTTAAACTAAAAAGATTATACTCTTTACACATTATAGAA
Found at i:25173 original size:17 final size:17
Alignment explanation
Indices: 25151--25191 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
25141 CATAGAAGGG
25151 GAGAGACAGACGAAATT
1 GAGAGACAGACGAAATT
25168 GAGAGACAGACGAAATT
1 GAGAGACAGACGAAATT
25185 GAGAGAC
1 GAGAGAC
25192 TCCTTCTACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.46, C:0.12, G:0.32, T:0.10
Consensus pattern (17 bp):
GAGAGACAGACGAAATT
Found at i:29068 original size:21 final size:21
Alignment explanation
Indices: 29029--29077 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
29019 TCAATGCTTT
**
29029 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
29051 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
29072 A-GAAGC
1 AGGAAGC
29078 TACAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Done.