Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013942.1 Corchorus olitorius cultivar O-4 contig13975, 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: 77423
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1656 original size:93 final size:93
Alignment explanation
Indices: 1541--1717 Score: 291
Period size: 93 Copynumber: 1.9 Consensus size: 93
1531 ATTTTTTAAT
* * * *
1541 TAAATTAGTAATATCGTTAAAATAAAATAGATATAAGGATATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATCGTAAAAATAAAAAAGATATAAGGATATTAGATTTAATTAAATAAAAATAG
1606 AGTTTTTAGTTGAGTAAAACTATAAAAG
66 AGTTTTTAGTTGAGTAAAACTATAAAAG
* *
1634 TAAAATAGTAAAATGGTAAAAATAAAAAAGTTATAAGGATATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATCGTAAAAATAAAAAAGATATAAGGATATTAGATTTAATTAAATAAAAATAG
*
1699 AGTTTTTAGTTGATTAAAA
66 AGTTTTTAGTTGAGTAAAA
1718 TAAGGATATG
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 77 1.00
ACGTcount: A:0.52, C:0.01, G:0.13, T:0.34
Consensus pattern (93 bp):
TAAAATAGTAAAATCGTAAAAATAAAAAAGATATAAGGATATTAGATTTAATTAAATAAAAATAG
AGTTTTTAGTTGAGTAAAACTATAAAAG
Found at i:1763 original size:31 final size:31
Alignment explanation
Indices: 1716--1777 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
1706 AGTTGATTAA
* *
1716 AATAAGGATATGATAGGCGATTCAAAAGTTT
1 AATAAGGATATAATAGGCAATTCAAAAGTTT
*
1747 AATAAGGGTATAATAGGCAATTCAAAAGTTT
1 AATAAGGATATAATAGGCAATTCAAAAGTTT
1778 TACAAAACTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29
Consensus pattern (31 bp):
AATAAGGATATAATAGGCAATTCAAAAGTTT
Found at i:1863 original size:24 final size:24
Alignment explanation
Indices: 1836--1883 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
1826 GAACCGGTTC
*
1836 CTAAATAGGCTAGATTTAAGCCGA
1 CTAAATAGACTAGATTTAAGCCGA
1860 CTAAATAGACTAGATTTAAGCCGA
1 CTAAATAGACTAGATTTAAGCCGA
1884 AACCGTTTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.25
Consensus pattern (24 bp):
CTAAATAGACTAGATTTAAGCCGA
Found at i:1944 original size:26 final size:28
Alignment explanation
Indices: 1888--1946 Score: 86
Period size: 30 Copynumber: 2.1 Consensus size: 28
1878 AGCCGAAACC
1888 GTTTCCTAGTTGGACATGATATATAAGGTT
1 GTTTCCTAGTTGGACA--ATATATAAGGTT
1918 GTTTCCTAGTTGGAC-A-ATATAAGGTT
1 GTTTCCTAGTTGGACAATATATAAGGTT
1944 GTT
1 GTT
1947 GTCTTCTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 13 0.45
27 1 0.03
30 15 0.52
ACGTcount: A:0.25, C:0.10, G:0.24, T:0.41
Consensus pattern (28 bp):
GTTTCCTAGTTGGACAATATATAAGGTT
Found at i:8413 original size:19 final size:19
Alignment explanation
Indices: 8371--8414 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
8361 AGTATTAGTT
*
8371 AAGAGAGTGAGTATGAAGA
1 AAGAGAGTGAGTAGGAAGA
* * *
8390 TAGAGAGTGAGTGGGGAGA
1 AAGAGAGTGAGTAGGAAGA
8409 AAGAGA
1 AAGAGA
8415 ATAGGGTAAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.43, T:0.14
Consensus pattern (19 bp):
AAGAGAGTGAGTAGGAAGA
Found at i:10063 original size:16 final size:16
Alignment explanation
Indices: 10039--10069 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
10029 AGTAGATGTG
10039 TTTGCTTTAGACTTTC
1 TTTGCTTTAGACTTTC
*
10055 TTTGTTTTAGACTTT
1 TTTGCTTTAGACTTT
10070 GCATGTTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.61
Consensus pattern (16 bp):
TTTGCTTTAGACTTTC
Found at i:14340 original size:16 final size:16
Alignment explanation
Indices: 14316--14346 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
14306 ATTAGATGTG
14316 TTTGCTTTAGACTTTT
1 TTTGCTTTAGACTTTT
*
14332 TTTGTTTTAGACTTT
1 TTTGCTTTAGACTTT
14347 GCATGTTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.10, G:0.13, T:0.65
Consensus pattern (16 bp):
TTTGCTTTAGACTTTT
Found at i:21354 original size:17 final size:17
Alignment explanation
Indices: 21332--21366 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
21322 TGAAAATTAA
21332 TGCTATGAAAAAGACAT
1 TGCTATGAAAAAGACAT
*
21349 TGCTATGAAAAGGACAT
1 TGCTATGAAAAAGACAT
21366 T
1 T
21367 AGGGACAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.43, C:0.11, G:0.20, T:0.26
Consensus pattern (17 bp):
TGCTATGAAAAAGACAT
Found at i:38787 original size:33 final size:33
Alignment explanation
Indices: 38748--38815 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
38738 TTAAATGTTC
38748 AATTATGTATTAATTTGGTTAATTTCCTAGACA
1 AATTATGTATTAATTTGGTTAATTTCCTAGACA
38781 AATTATGTATTAATTTGGTTAATTTCCTAGACA
1 AATTATGTATTAATTTGGTTAATTTCCTAGACA
38814 AA
1 AA
38816 AAACAGCTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (33 bp):
AATTATGTATTAATTTGGTTAATTTCCTAGACA
Found at i:39578 original size:24 final size:24
Alignment explanation
Indices: 39546--39591 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
39536 AACATCAAGA
39546 TTTATCTTCTCCCTCTTCTCTTTT
1 TTTATCTTCTCCCTCTTCTCTTTT
*
39570 TTTATCTTCTCCCTCTTTTCTT
1 TTTATCTTCTCCCTCTTCTCTT
39592 GTTACTGCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.04, C:0.33, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTATCTTCTCCCTCTTCTCTTTT
Found at i:53818 original size:2 final size:2
Alignment explanation
Indices: 53811--53841 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
53801 TTGATTACTC
53811 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
53842 TTCTTATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54350 original size:31 final size:31
Alignment explanation
Indices: 54312--54413 Score: 132
Period size: 31 Copynumber: 3.3 Consensus size: 31
54302 TGATTAATTA
*
54312 AGTCCCTAACATTACAAAATCGGCTAAAATC
1 AGTCCCTAACATTACAAAATCGGCTCAAATC
* * *
54343 AGTCCCTAACGTTGCAAAATCGACTCAAATC
1 AGTCCCTAACATTACAAAATCGGCTCAAATC
* * * *
54374 AGTCCCTAATATTTCAAAATCAGCTCAAATT
1 AGTCCCTAACATTACAAAATCGGCTCAAATC
54405 AGTCCCTAA
1 AGTCCCTAA
54414 TGTCAATTTA
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 61 1.00
ACGTcount: A:0.38, C:0.26, G:0.10, T:0.25
Consensus pattern (31 bp):
AGTCCCTAACATTACAAAATCGGCTCAAATC
Found at i:55338 original size:2 final size:2
Alignment explanation
Indices: 55331--55369 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
55321 GCTAAACTAT
55331 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
55370 GAAAGCATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:56322 original size:19 final size:19
Alignment explanation
Indices: 56302--56338 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
56292 AATTAATTAT
56302 TTTA-ATATTAAATTTTTA
1 TTTATATATTAAATTTTTA
*
56320 TTTATATATTATATTTTTA
1 TTTATATATTAAATTTTTA
56339 CTTAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATATATTAAATTTTTA
Found at i:56794 original size:29 final size:29
Alignment explanation
Indices: 56761--56818 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
56751 AATGAGCCTG
56761 CGTAAATATCTAAATCATGACTATAACTA
1 CGTAAATATCTAAATCATGACTATAACTA
56790 CGTAAATATCTAAATCATGACTATAACTA
1 CGTAAATATCTAAATCATGACTATAACTA
56819 TAAGTTTGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.31
Consensus pattern (29 bp):
CGTAAATATCTAAATCATGACTATAACTA
Found at i:68999 original size:145 final size:145
Alignment explanation
Indices: 68708--69135 Score: 689
Period size: 145 Copynumber: 3.0 Consensus size: 145
68698 AAATCGTTCG
* * *
68708 ATGCCCCTTAAACAAGATCTTTGATTATTTGATTTAAGTCCTGCAAATGAAGAATATAGACACGG
1 ATGCCCCTTAAACAAGATCTTTGATTCTTTGATCTAAGTCTTGCAAATGAAGAATATAGACACGG
* *
68773 AGAAAAGCTTCCCTATATT-TGATGGAATTCGGATTCGGATTACTCGGTGCTCAATGTAGCTACC
66 AGAAAA-CTTCCCTAT-TTCTGACGGAATTCGGATTCGGATTACTCGGGGCTCAATGTAGCTACC
*
68837 AAATATAGGGTCGTTCA
129 AAATATAGGGTCATTCA
* * *
68854 ATGCCCCTTAAACAAGATCTTTGATTCTTTGGTCCAAGTCTTGCAAATGAAGAATATAGGCACGG
1 ATGCCCCTTAAACAAGATCTTTGATTCTTTGATCTAAGTCTTGCAAATGAAGAATATAGACACGG
* * *
68919 AGAAAACTTCCCTATTTCTGACGAAATTCGGATTCGGATTACTCGGGGTTAAATGTAGCTACCAA
66 AGAAAACTTCCCTATTTCTGACGGAATTCGGATTCGGATTACTCGGGGCTCAATGTAGCTACCAA
68984 ATATAGGGTCATTCA
131 ATATAGGGTCATTCA
68999 ATGCCCCTTAAACAAGATCTTTGATTCTTTGATCTAAGTCTTGCAAATGAAGAATATAGACAC-G
1 ATGCCCCTTAAACAAGATCTTTGATTCTTTGATCTAAGTCTTGCAAATGAAGAATATAGACACGG
* * *
69063 AGAAAGCTTCCCTATTTCTGGCGGAATTCGGATTCGGATGACTCGGGGCTCAATGTAGCTACCAA
66 AGAAAACTTCCCTATTTCTGACGGAATTCGGATTCGGATTACTCGGGGCTCAATGTAGCTACCAA
69128 ATATAGGG
131 ATATAGGG
69136 ATTGGGGAAT
Statistics
Matches: 260, Mismatches: 21, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
144 70 0.27
145 125 0.48
146 65 0.25
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.30
Consensus pattern (145 bp):
ATGCCCCTTAAACAAGATCTTTGATTCTTTGATCTAAGTCTTGCAAATGAAGAATATAGACACGG
AGAAAACTTCCCTATTTCTGACGGAATTCGGATTCGGATTACTCGGGGCTCAATGTAGCTACCAA
ATATAGGGTCATTCA
Found at i:73262 original size:17 final size:17
Alignment explanation
Indices: 73231--73276 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
73221 TTATTTACTG
* *
73231 AAATAATGATAATTATA
1 AAATAATTATTATTATA
*
73248 AAATAATTATTATTATC
1 AAATAATTATTATTATA
*
73265 CAATAATTATTA
1 AAATAATTATTA
73277 CTAATTTCGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.41
Consensus pattern (17 bp):
AAATAATTATTATTATA
Found at i:74207 original size:211 final size:214
Alignment explanation
Indices: 73823--74250 Score: 610
Period size: 211 Copynumber: 2.0 Consensus size: 214
73813 GCGCAAAATT
* * * * *
73823 CAGTATCCCCAAAGTGATATACTCTATATCGAAATCATTTCTTATCATCCCCAAATAATCATAAG
1 CAGTATCCCCAAACTGATATACTCTATACCCAAATCATTTCTCATCATCCCAAAATAATCATAAG
* * *
73888 CACCATCCCCAAATTCATTAGAAATTGACATTTTTTTATATACCTAAAATTGGCTTTAAAACGTG
66 ---C-TCCCCAAACTCATTAGAAATTGACATTTTTTCATATACCCAAAATTGGCTTTAAAACGTG
* * * *
73953 TTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCTGTCTATATGAATTTAGTGTCATCT
127 CTTTAATCCATATTTTCATCCTAACTAATTGAATAAACCCTGTCTACATGAATTTAGTATCATCT
74018 AATAATTAAACAAAATGCAAAAC
192 AATAATTAAACAAAATGCAAAAC
* * * *
74041 CAGTATCCCCAAACTGATATACTTTATACCCAACTCATTTGTCATCATCCCAAAATAATCATATG
1 CAGTATCCCCAAACTGATATACTCTATACCCAAATCATTTCTCATCATCCCAAAATAATCATAAG
* * *
74106 -TCCCCAAACTCTTTTGAGATTGACA-TTTTTCATATACCCAAAATTGGCTTT-AAACGTGCTTT
66 CTCCCCAAACTCATTAGAAATTGACATTTTTTCATATACCCAAAATTGGCTTTAAAACGTGCTTT
* *
74168 AATTCATATTTTTATCCTAACTAATTGAATAAACCCTGTCTACATGAATTTAGTATCATCTAATA
131 AATCCATATTTTCATCCTAACTAATTGAATAAACCCTGTCTACATGAATTTAGTATCATCTAATA
74233 ATTAAACAAAATGCAAAA
196 ATTAAACAAAATGCAAAA
74251 TTAAGCATCC
Statistics
Matches: 189, Mismatches: 21, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
211 88 0.47
212 24 0.13
213 21 0.11
218 56 0.30
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.35
Consensus pattern (214 bp):
CAGTATCCCCAAACTGATATACTCTATACCCAAATCATTTCTCATCATCCCAAAATAATCATAAG
CTCCCCAAACTCATTAGAAATTGACATTTTTTCATATACCCAAAATTGGCTTTAAAACGTGCTTT
AATCCATATTTTCATCCTAACTAATTGAATAAACCCTGTCTACATGAATTTAGTATCATCTAATA
ATTAAACAAAATGCAAAAC
Found at i:75067 original size:41 final size:41
Alignment explanation
Indices: 75010--75096 Score: 124
Period size: 41 Copynumber: 2.1 Consensus size: 41
75000 ATTAGCCATA
*
75010 GTATCAGCGGGAATTAGAACAAGCATTC-GTTTCTCATCATT
1 GTATCAGCGGGAATTAGAACAAGCA-TCGGCTTCTCATCATT
* *
75051 GTATCAGCGGGGATTAGAGCAAGCATCGGCTTCTCATCATT
1 GTATCAGCGGGAATTAGAACAAGCATCGGCTTCTCATCATT
75092 G-ATCA
1 GTATCA
75097 AAAAATCTAC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
40 6 0.14
41 36 0.86
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.29
Consensus pattern (41 bp):
GTATCAGCGGGAATTAGAACAAGCATCGGCTTCTCATCATT
Found at i:75502 original size:25 final size:25
Alignment explanation
Indices: 75468--75519 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
75458 ATTGTTTATT
75468 AATAACAATGTCTTTACAAATTGCA
1 AATAACAATGTCTTTACAAATTGCA
75493 AATAACAATGTCTTTACAAATTGCA
1 AATAACAATGTCTTTACAAATTGCA
75518 AA
1 AA
75520 GAGGGGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (25 bp):
AATAACAATGTCTTTACAAATTGCA
Found at i:77391 original size:2 final size:2
Alignment explanation
Indices: 77384--77423 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
77374 CACGTGTAGT
77384 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.