Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023415.1 Corchorus olitorius cultivar O-4 contig23448, 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: 70882
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Found at i:5282 original size:27 final size:27
Alignment explanation
Indices: 5240--5301 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
5230 ACTGTACTTG
*
5240 AAATGACCAAAATGCCCTTGGACATGC
1 AAATGACCAAAATGCCCCTGGACATGC
* *
5267 AAATGACCAAATTGCCCCTGGACGTGC
1 AAATGACCAAAATGCCCCTGGACATGC
5294 AAATGACC
1 AAATGACC
5302 CCAATGCTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.18
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGGACATGC
Found at i:12131 original size:36 final size:36
Alignment explanation
Indices: 12088--12159 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
12078 GGTGGTGGTA
12088 ATTGAGCTTGATCAGCCCTTGGTTGATTTTGAGCTT
1 ATTGAGCTTGATCAGCCCTTGGTTGATTTTGAGCTT
12124 ATTGAGCTTGATCAGCCCTTGGTTGATTTTGAGCTT
1 ATTGAGCTTGATCAGCCCTTGGTTGATTTTGAGCTT
12160 GCCTTACTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.17, C:0.17, G:0.25, T:0.42
Consensus pattern (36 bp):
ATTGAGCTTGATCAGCCCTTGGTTGATTTTGAGCTT
Found at i:12155 original size:21 final size:21
Alignment explanation
Indices: 12095--12155 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
12085 GTAATTGAGC
12095 TTGATCAGCCCTTGGTTGATT
1 TTGATCAGCCCTTGGTTGATT
* **
12116 TTG---AG--CTT-ATTGAGC
1 TTGATCAGCCCTTGGTTGATT
12131 TTGATCAGCCCTTGGTTGATT
1 TTGATCAGCCCTTGGTTGATT
12152 TTGA
1 TTGA
12156 GCTTGCCTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 12
0.61 0.13 0.26
Matches are distributed among these distances:
15 7 0.25
16 3 0.11
18 4 0.14
20 3 0.11
21 11 0.39
ACGTcount: A:0.16, C:0.16, G:0.25, T:0.43
Consensus pattern (21 bp):
TTGATCAGCCCTTGGTTGATT
Found at i:15802 original size:21 final size:21
Alignment explanation
Indices: 15778--15817 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
15768 CTCTTGTCAT
*
15778 TGGATCTAATGGCATCTTTAA
1 TGGATCAAATGGCATCTTTAA
15799 TGGATCAAATGGCATCTTT
1 TGGATCAAATGGCATCTTT
15818 GGCATCTCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.38
Consensus pattern (21 bp):
TGGATCAAATGGCATCTTTAA
Found at i:20421 original size:83 final size:84
Alignment explanation
Indices: 20248--20441 Score: 311
Period size: 83 Copynumber: 2.3 Consensus size: 84
20238 GACATTAGGC
20248 GGACTTTAGGCTTAGCAATTGATAGTTTAACAATTAATTTAAATTGCCTTTTGGTTTTTTGGAAA
1 GGACTTTAGGCTTAGCAATTGATAG--TAACAATTAATTTAAATTGCCTTTTGGTTTTTTGGAAA
20313 CAATTTAGGAATCCGAAAGTT
64 CAATTTAGGAATCCGAAAGTT
*
20334 -GACTTTAGGCTTAGCAATTGATAGTAACAATTAATTTAATTTGCCTTTTGG-TTTTTGGAAACA
1 GGACTTTAGGCTTAGCAATTGATAGTAACAATTAATTTAAATTGCCTTTTGGTTTTTTGGAAACA
*
20397 ATTTAGGAATCTGAAAGTT
66 ATTTAGGAATCCGAAAGTT
* * *
20416 GGACTTTAGGTTTAGGAATTGGTAGT
1 GGACTTTAGGCTTAGCAATTGATAGT
20442 TAAATATTTT
Statistics
Matches: 102, Mismatches: 5, Indels: 5
0.91 0.04 0.04
Matches are distributed among these distances:
82 30 0.29
83 48 0.47
85 24 0.24
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (84 bp):
GGACTTTAGGCTTAGCAATTGATAGTAACAATTAATTTAAATTGCCTTTTGGTTTTTTGGAAACA
ATTTAGGAATCCGAAAGTT
Found at i:21628 original size:62 final size:61
Alignment explanation
Indices: 21513--21656 Score: 202
Period size: 62 Copynumber: 2.3 Consensus size: 61
21503 ATTTCATTCA
* *
21513 AAAGTTTCAAAGTATTAAATCCAAGTTTTTCAAAGTTTTCAATTTAGGGAAAGTTCCTATC
1 AAAGTTTCAAAGTATTCAATCCAAGTTTTTCAAAGTTTTCAATTTAGGGAAAGTTCCCATC
*
21574 -AAGTTGTC-AAGTATTCAATCCAAGTTTTTTTAAAGGTTTTCAATTTAGGGAAAGTTCCCATC
1 AAAGTT-TCAAAGTATTCAATCCAAG-TTTTTCAAA-GTTTTCAATTTAGGGAAAGTTCCCATC
*
21636 AAAATTTTCAAAGTATTCAAT
1 -AAAGTTTCAAAGTATTCAAT
21657 TTAGCTCTTT
Statistics
Matches: 73, Mismatches: 4, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
60 20 0.27
61 10 0.14
62 26 0.36
63 2 0.03
64 15 0.21
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.38
Consensus pattern (61 bp):
AAAGTTTCAAAGTATTCAATCCAAGTTTTTCAAAGTTTTCAATTTAGGGAAAGTTCCCATC
Found at i:21721 original size:52 final size:52
Alignment explanation
Indices: 21622--21748 Score: 139
Period size: 52 Copynumber: 2.4 Consensus size: 52
21612 TTCAATTTAG
* * * **
21622 GGAAAGTTCCCATCAAAATTTTCAAAGTATTCAATTTAGCTCTTTTTCAGGTTC
1 GGAAAGTTCCCATC--AGTTTTCAAAGTATTCAATTAAGCTCGTTTTCAAATTC
** *
21676 GGAAAGTTCCCATCAGTTTTCAAAGTATTTGATTAAGC-CGGTTTTCAAATTG
1 GGAAAGTTCCCATCAGTTTTCAAAGTATTCAATTAAGCTC-GTTTTCAAATTC
21728 GGAAAGTTCCCATCAGGTTTT
1 GGAAAGTTCCCATCA-GTTTT
21749 AGTTTTTTAA
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
51 1 0.02
52 43 0.68
53 5 0.08
54 14 0.22
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.37
Consensus pattern (52 bp):
GGAAAGTTCCCATCAGTTTTCAAAGTATTCAATTAAGCTCGTTTTCAAATTC
Found at i:28494 original size:33 final size:32
Alignment explanation
Indices: 28434--28495 Score: 79
Period size: 33 Copynumber: 1.9 Consensus size: 32
28424 CCATCCGAGG
*
28434 CTCATGCCCGGCACCACCTGCCCCAGCCGCGC
1 CTCATGCCCGGCACCACCTGCCACAGCCGCGC
** *
28466 CTCATGCCCGGCTAGGACCTGTCACAGCCG
1 CTCATGCCCGGC-ACCACCTGCCACAGCCG
28496 AGCCATTCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 12 0.48
33 13 0.52
ACGTcount: A:0.15, C:0.48, G:0.24, T:0.13
Consensus pattern (32 bp):
CTCATGCCCGGCACCACCTGCCACAGCCGCGC
Found at i:38242 original size:17 final size:17
Alignment explanation
Indices: 38220--38257 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
38210 TTCACTTGGC
*
38220 TTGCCTTGACTCTGTGT
1 TTGCCTTGACTCTGTAT
38237 TTGCCTTGACTCTGTAT
1 TTGCCTTGACTCTGTAT
38254 TTGC
1 TTGC
38258 TGCTGATAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.08, C:0.24, G:0.21, T:0.47
Consensus pattern (17 bp):
TTGCCTTGACTCTGTAT
Found at i:39350 original size:28 final size:28
Alignment explanation
Indices: 39308--39371 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 28
39298 GTACTTGAAG
39308 TGACCAAAATACCCCTGGACATACAAAA
1 TGACCAAAATACCCCTGGACATACAAAA
* **
39336 TGACCAAAATGCCCCTGGACATGTAAAA
1 TGACCAAAATACCCCTGGACATACAAAA
*
39364 TGATCAAA
1 TGACCAAA
39372 GAAGAAGTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.44, C:0.25, G:0.14, T:0.17
Consensus pattern (28 bp):
TGACCAAAATACCCCTGGACATACAAAA
Found at i:39830 original size:36 final size:35
Alignment explanation
Indices: 39789--40031 Score: 310
Period size: 36 Copynumber: 6.8 Consensus size: 35
39779 TCAACTTTTA
*
39789 AAGATGCTACACCGAGTCATCTGAATTCATCCATT-G
1 AAGATGCTACACCGAGTCATCTGAATTCA--CTTTGG
* * * **
39825 AAGATGCTACACCGAGCCATCTAAATTCAATTTTAA
1 AAGATGCTACACCGAGTCATCTGAATTC-ACTTTGG
* * *
39861 AAAATGCTACACCGAGTCATCTAAATTCAAATTTGG
1 AAGATGCTACACCGAGTCATCTGAATTC-ACTTTGG
* *
39897 GAGATGCTACACCGAGTCATCTAAATTCAACTTTGG
1 AAGATGCTACACCGAGTCATCTGAATTC-ACTTTGG
39933 AAGATGCTACACCGAGTCATCTGAATTCAACTTTGG
1 AAGATGCTACACCGAGTCATCTGAATTC-ACTTTGG
39969 AAGATGCTACACCGAGTCATCTGAATTCATCTTT-G
1 AAGATGCTACACCGAGTCATCTGAATTCA-CTTTGG
40004 AAGATGCTACACCGAGTCATCTGAATTC
1 AAGATGCTACACCGAGTCATCTGAATTC
40032 CTGAAAATTT
Statistics
Matches: 189, Mismatches: 15, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
35 32 0.17
36 156 0.83
37 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (35 bp):
AAGATGCTACACCGAGTCATCTGAATTCACTTTGG
Found at i:39917 original size:108 final size:107
Alignment explanation
Indices: 39789--40031 Score: 344
Period size: 108 Copynumber: 2.3 Consensus size: 107
39779 TCAACTTTTA
*
39789 AAGATGCTACACCGAGTCATCTGAATTCATCCATT-GAAGATGCTACACCGAGCCATCTAAATTC
1 AAGATGCTACACCGAGTCATCTGAATTCA-ACATTGGAAGATGCTACACCGAGCCATCTAAATTC
*
39853 AATTTTAAAAAATGCTACACCGAGTCATCTAAATTCAAATTTGG
65 AACTTTAAAAAATGCTACACCGAGTCATCTAAATTCAAATTT-G
* * * * *
39897 GAGATGCTACACCGAGTCATCTAAATTCAACTTTGGAAGATGCTACACCGAGTCATCTGAATTCA
1 AAGATGCTACACCGAGTCATCTGAATTCAACATTGGAAGATGCTACACCGAGCCATCTAAATTCA
** * * **
39962 ACTTTGGAAGATGCTACACCGAGTCATCTGAATTCATCTTTG
66 ACTTTAAAAAATGCTACACCGAGTCATCTAAATTCAAATTTG
40004 AAGATGCTACACCGAGTCATCTGAATTC
1 AAGATGCTACACCGAGTCATCTGAATTC
40032 CTGAAAATTT
Statistics
Matches: 119, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
107 30 0.25
108 89 0.75
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (107 bp):
AAGATGCTACACCGAGTCATCTGAATTCAACATTGGAAGATGCTACACCGAGCCATCTAAATTCA
ACTTTAAAAAATGCTACACCGAGTCATCTAAATTCAAATTTG
Found at i:51384 original size:12 final size:12
Alignment explanation
Indices: 51362--51393 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
51352 ATCTAGTGTG
51362 TGAGA-GGAAGA
1 TGAGAGGGAAGA
51373 TGAGAGGGAAGA
1 TGAGAGGGAAGA
51385 TGAGAGGGA
1 TGAGAGGGA
51394 GAGAATTCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.41, C:0.00, G:0.50, T:0.09
Consensus pattern (12 bp):
TGAGAGGGAAGA
Found at i:52404 original size:17 final size:17
Alignment explanation
Indices: 52382--52415 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
52372 ACTGGCTTGG
*
52382 CTTGACTCTGTGTTTGC
1 CTTGACTCTGTATTTGC
52399 CTTGACTCTGTATTTGC
1 CTTGACTCTGTATTTGC
52416 TGCTGATAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (17 bp):
CTTGACTCTGTATTTGC
Found at i:53503 original size:28 final size:28
Alignment explanation
Indices: 53461--53527 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
53451 GTACTTGAAG
*
53461 TGACGAAAATACCCCTGGACATGCAAAA
1 TGACCAAAATACCCCTGGACATGCAAAA
* *
53489 TGACCAAAATGCCCCTGGACATGTAAAA
1 TGACCAAAATACCCCTGGACATGCAAAA
*
53517 TGATCAAAATA
1 TGACCAAAATA
53528 AGAAGTAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.18
Consensus pattern (28 bp):
TGACCAAAATACCCCTGGACATGCAAAA
Found at i:54041 original size:29 final size:29
Alignment explanation
Indices: 53990--54057 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
53980 TGTCTCTTAA
*
53990 ATTGGTCA--TTTGCACGTTCAGGGGCAT
1 ATTGGTCATTTTTGCACATTCAGGGGCAT
* * *
54017 TTTGGTCATTTTTGCACATTTAGGGGCCT
1 ATTGGTCATTTTTGCACATTCAGGGGCAT
54046 ATTGGTCATTTT
1 ATTGGTCATTTT
54058 GCATCCTCGG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 7 0.21
29 27 0.79
ACGTcount: A:0.16, C:0.16, G:0.25, T:0.43
Consensus pattern (29 bp):
ATTGGTCATTTTTGCACATTCAGGGGCAT
Found at i:59622 original size:104 final size:105
Alignment explanation
Indices: 59434--59631 Score: 346
Period size: 104 Copynumber: 1.9 Consensus size: 105
59424 TTGTGCGAAA
59434 AACCTCCACCCAACGAGACCTTGCCAGGTCGAAATTGAGAACCTACTAAGTACGTGTGGACTAAC
1 AACCTCCACCCAACGAGACCTTGCCAGGTCGAAATTGAGAACCTACTAAGTACGTGTGGACTAAC
59499 CCAGCATATAAGTATGT-ACATAAGGAATTGGGACTTGGG
66 CCAGCATATAAGTATGTAACATAAGGAATTGGGACTTGGG
* *
59538 AACCTCCACCCAACGAGACCTTGCCGGGTCGAAATTGGGAACCTACTAAGTACGTGTGGACTAAC
1 AACCTCCACCCAACGAGACCTTGCCAGGTCGAAATTGAGAACCTACTAAGTACGTGTGGACTAAC
59603 CCAGCATATAAGT-TGGTACACATAAGGAA
66 CCAGCATATAAGTAT-GTA-ACATAAGGAA
59632 CATTCCGAAC
Statistics
Matches: 89, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
103 1 0.01
104 78 0.88
106 10 0.11
ACGTcount: A:0.33, C:0.24, G:0.23, T:0.20
Consensus pattern (105 bp):
AACCTCCACCCAACGAGACCTTGCCAGGTCGAAATTGAGAACCTACTAAGTACGTGTGGACTAAC
CCAGCATATAAGTATGTAACATAAGGAATTGGGACTTGGG
Found at i:68971 original size:38 final size:40
Alignment explanation
Indices: 68929--69014 Score: 113
Period size: 38 Copynumber: 2.2 Consensus size: 40
68919 AGGAGCTAAA
* * *
68929 AAAAAAACTTGACTTAAAATAGAAAGAGGTC-GAAAA-AG
1 AAAAAAACTGGACCTAAAACAGAAAGAGGTCAGAAAATAG
*
68967 AAAAAAACTGGGCCTAAAACAGAAAGAGGTCAGAAAATAG
1 AAAAAAACTGGACCTAAAACAGAAAGAGGTCAGAAAATAG
69007 AAATAAAA
1 AAA-AAAA
69015 AGGAGGGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
38 27 0.66
39 5 0.12
40 5 0.12
41 4 0.10
ACGTcount: A:0.59, C:0.09, G:0.19, T:0.13
Consensus pattern (40 bp):
AAAAAAACTGGACCTAAAACAGAAAGAGGTCAGAAAATAG
Done.