Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023590.1 Corchorus olitorius cultivar O-4 contig23623, 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: 5919
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Found at i:4428 original size:162 final size:159
Alignment explanation
Indices: 4005--4439 Score: 477
Period size: 162 Copynumber: 2.7 Consensus size: 159
3995 CAAAGGCAAG
* **
4005 TAAACAACCCCTTCCGGTGGGGGAAGG-ACAAACTAGGAAAGTAAACAACACCTTCCGGTGGGGA
1 TAAACAACACCTTCCGGT-GGGGAAGGCA-AAAC-AGGAATTTAAACAACACCTTCCGGTGGGGA
* * * * * *
4069 AGGGCAAAACGGGAATTTAAACCACACCTTCCGCT-GGGAAAGGGAAAAACAAGAAAGTAAACAA
63 AGGGC-AAACAGGAATTTAAACAACAACTCCCGGTGGGGAAA-GGCAAAACAAGAAAGTAAACAA
*
4133 CACATACCCGTAGGAGAAGGGCAAAACATGAATT
126 CACATACCCGTAGGAGAAGGGCAAAACAGGAATT
* *
4167 TAAACAA-AGCCTTCCAGTGGGGAAGGACAAAACAGGAATTTAAACAACACCTTTCGGTGGGGAA
1 TAAACAACA-CCTTCCGGTGGGGAAGG-CAAAACAGGAATTTAAACAACACCTTCCGGTGGGGAA
* * * * **
4231 -GGCTATACTGTGAATTTAAACAAC-ACCCTCCGGTGGGGAAAGGCAAAACAGGAATTTAATCAC
64 GGGC-AAACAG-GAATTTAAACAACAACTC-CCGGTGGGGAAAGGCAAAACAAGAAAGTAA--AC
* * * *
4294 AACACCTTCCGGT-GGGGAAGGGCAAAACAGGAATT
124 AACACATACCCGTAGGAGAAGGGCAAAACAGGAATT
*
4329 TAAACAACACCTTCCGGTGGGGAAGAGCAAAACAAGAATTTAAACAACACCTTCCGGTGGGGAAG
1 TAAACAACACCTTCCGGTGGGGAAG-GCAAAACAGGAATTTAAACAACACCTTCCGGTGGGGAAG
* *
4394 GGCAAACCAGGACTTTAAACAACAACTCCCGGTGGGGAAGGGCAAA
65 GGCAAA-CAGGAATTTAAACAACAACTCCCGGTGGGGAAAGGCAAA
4440 CTGGGAAAAA
Statistics
Matches: 230, Mismatches: 30, Indels: 26
0.80 0.10 0.09
Matches are distributed among these distances:
160 8 0.03
161 66 0.29
162 133 0.58
163 23 0.10
ACGTcount: A:0.39, C:0.21, G:0.26, T:0.15
Consensus pattern (159 bp):
TAAACAACACCTTCCGGTGGGGAAGGCAAAACAGGAATTTAAACAACACCTTCCGGTGGGGAAGG
GCAAACAGGAATTTAAACAACAACTCCCGGTGGGGAAAGGCAAAACAAGAAAGTAAACAACACAT
ACCCGTAGGAGAAGGGCAAAACAGGAATT
Found at i:4440 original size:40 final size:40
Alignment explanation
Indices: 4005--4439 Score: 507
Period size: 40 Copynumber: 10.8 Consensus size: 40
3995 CAAAGGCAAG
* * **
4005 TAAACAACCCCTTCCGGTGGGGGAAGGAC-AAACTAGGAAAG
1 TAAACAACACCTTCCGGT-GGGGAAGGGCAAAAC-AGGAATT
*
4046 TAAACAACACCTTCCGGTGGGGAAGGGCAAAACGGGAATT
1 TAAACAACACCTTCCGGTGGGGAAGGGCAAAACAGGAATT
* * * * * **
4086 TAAACCACACCTTCCGCTGGGAAAGGGAAAAACAAGAAAG
1 TAAACAACACCTTCCGGTGGGGAAGGGCAAAACAGGAATT
* * * * *
4126 TAAACAACACATACCCGTAGGAGAAGGGCAAAACATGAATT
1 TAAACAACACCTTCCGGT-GGGGAAGGGCAAAACAGGAATT
* *
4167 TAAACAA-AGCCTTCCAGTGGGGAAGGACAAAACAGGAATT
1 TAAACAACA-CCTTCCGGTGGGGAAGGGCAAAACAGGAATT
* * * *
4207 TAAACAACACCTTTCGGTGGGGAA-GGCTATACTGTGAATT
1 TAAACAACACCTTCCGGTGGGGAAGGGCAAAACAG-GAATT
* *
4247 TAAACAACACCCTCCGGTGGGGAAAGGCAAAACAGGAATT
1 TAAACAACACCTTCCGGTGGGGAAGGGCAAAACAGGAATT
4287 TAATCACAACACCTTCCGGTGGGGAAGGGCAAAACAGGAATT
1 TAA--ACAACACCTTCCGGTGGGGAAGGGCAAAACAGGAATT
* *
4329 TAAACAACACCTTCCGGTGGGGAAGAGCAAAACAAGAATT
1 TAAACAACACCTTCCGGTGGGGAAGGGCAAAACAGGAATT
* *
4369 TAAACAACACCTTCCGGTGGGGAAGGGCAAACCAGGACTT
1 TAAACAACACCTTCCGGTGGGGAAGGGCAAAACAGGAATT
* *
4409 TAAACAACAACTCCCGGTGGGGAAGGGCAAA
1 TAAACAACACCTTCCGGTGGGGAAGGGCAAA
4440 CTGGGAAAAA
Statistics
Matches: 335, Mismatches: 51, Indels: 17
0.83 0.13 0.04
Matches are distributed among these distances:
39 6 0.02
40 233 0.70
41 58 0.17
42 38 0.11
ACGTcount: A:0.39, C:0.21, G:0.26, T:0.15
Consensus pattern (40 bp):
TAAACAACACCTTCCGGTGGGGAAGGGCAAAACAGGAATT
Found at i:4511 original size:47 final size:47
Alignment explanation
Indices: 4408--5693 Score: 1510
Period size: 47 Copynumber: 27.7 Consensus size: 47
4398 AACCAGGACT
* * * *
4408 TTAAACAACAACTCCCGGTGGGGAAGGGCAAACTGGGAAAAAGCAGAC
1 TTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGG-AAAAGCAGAC
* * * * *
4456 TTACACAACACCTTCCAATGAGGAAGAGCAATCTAGGAAAAGCAGAC
1 TTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAAGCAGAC
* **
4503 TTAAACAACACCTTCTGATGAGGAAGGGCAATTTGGGAAAAGCAGAC
1 TTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAAGCAGAC
*
4550 TTAAACAACACCTTCCGATGAGGAAGGGCAATCTGGGAAAAGCAGAC
1 TTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAAGCAGAC
4597 TTAAACAACACCTTCCGATGAGGAAGGG-AAACCTGGGAAAAGCAGAC
1 TTAAACAACACCTTCCGATGAGGAAGGGCAAA-CTGGGAAAAGCAGAC
* * * * *
4644 TTAAACAACACCTTCCAATGAGGAAGGGCAACCTAGGAAAAGTAGAT
1 TTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAAGCAGAC
* *
4691 TTAAACAACACCTTCCGATGGGGAAGGACAAACTGGGAAAAGCAGAC
1 TTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAAGCAGAC
* *
4738 TTAAACAACACCTTCCGATGAGGAAGTGCAAACTGGGAAAAGTAGAC
1 TTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAAGCAGAC
** **
4785 TTAAACAACACCTTCCGATGAGGAAGTACAAACTCAGAAAAGCAGAC
1 TTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAAGCAGAC
* * * *
4832 TTAAAAAAAACCTTCTGATGAGGACGGGCAAACTGGGAAAAGCAGAC
1 TTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAAGCAGAC
* * *
4879 TTTAAA-AACACCTTCCGATGAGGAAGTGCGAACTGGGAAAAACAGAC
1 -TTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAAGCAGAC
* *
4926 TTAAACAACACCTTCCGATGAGGAAGGGCAAATTGGGAAAAACAGAC
1 TTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAAGCAGAC
* * * * * ***
4973 TTAAACAACACCTTCCGGTGGGGAAGGGTAAAATAGG-AATTTA-A-
1 TTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAAGCAGAC
* * * * * *
5017 --ACACAACACGTTCC-AGTGGGGAAGGGCAAA----G--CAGGA-AT
1 TTAAACAACACCTTCCGA-TGAGGAAGGGCAAACTGGGAAAAGCAGAC
* * *
5055 TTAAACAACACCTTCCGATGGGGAAGGGCAAAC-----CAAG-A-AT
1 TTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAAGCAGAC
* *
5095 TTAAACAACACCTTCTCGTTG-GGAAGGGCAAACTGGGGAAAAACAAGAC
1 TTAAACAACACCTTC-CGATGAGGAAGGGCAAACT-GGGAAAAGC-AGAC
* * *
5144 TTAAACAACACTTTCCGATGAGGAAGGGCAATCTAGGAAAAGCAGAC
1 TTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAAGCAGAC
*
5191 TTAAACAACACCTTCCGATGAGGAAGGGC-AATTAGGGTAAAA-CAGAC
1 TTAAACAACACCTTCCGATGAGGAAGGGCAAACT-GGG-AAAAGCAGAC
* * * * *
5238 TTAAACAACACCTACCGATGAGGAACGACAATCTGGGAAAAACAGAC
1 TTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAAGCAGAC
* * *
5285 TTAAACAACCCCTTCTGATGAGGAAGGGAAAACTGGG-AAAGCAGAC
1 TTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAAGCAGAC
* * * *
5331 CTAAACAACACCTTTCGATGAGGAAGGGTAACCTGGGAAAAGCAGAC
1 TTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAAGCAGAC
* * *
5378 GTAAACAACACCTTCCGATGAGGAAGGGCAAATTGGGAAAAGTAGAC
1 TTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAAGCAGAC
* * * *
5425 CTAAACAACACCTTCCTATGACGAAGGGC-AACTAGGGAAAAGTAGAC
1 TTAAACAACACCTTCCGATGAGGAAGGGCAAACT-GGGAAAAGCAGAC
* *
5472 TTAAACAACACCTTCCGATGAGGAAGGGCAAATTGGGAAAATCAGAC
1 TTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAAGCAGAC
* *
5519 TTAAACAACACCTTCCGATGAGGAAGTGCAAACTGGGAAAAGTAGAC
1 TTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAAGCAGAC
* * * *
5566 TTAAACAACACCTTCGGATGAGGTAGGGCAAACTAGGAAAAACAGAC
1 TTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAAGCAGAC
*
5613 TTAAACAACACCTTCCGATGAGGAAGGGAAAACTGGGAAAAGCAGAC
1 TTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAAGCAGAC
*
5660 TTAAACAACACCTTCCGATGAGAAAGGGCAAACT
1 TTAAACAACACCTTCCGATGAGGAAGGGCAAACT
5694 AGGATAGGAC
Statistics
Matches: 1070, Mismatches: 139, Indels: 59
0.84 0.11 0.05
Matches are distributed among these distances:
37 2 0.00
38 1 0.00
40 56 0.05
41 7 0.01
42 25 0.02
45 1 0.00
46 60 0.06
47 835 0.78
48 56 0.05
49 27 0.03
ACGTcount: A:0.41, C:0.20, G:0.24, T:0.15
Consensus pattern (47 bp):
TTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAAGCAGAC
Found at i:5077 original size:82 final size:80
Alignment explanation
Indices: 4973--5126 Score: 211
Period size: 82 Copynumber: 1.9 Consensus size: 80
4963 AAAAACAGAC
* * * * *
4973 TTAAACAACACCTTCCGGTGGGGAAGGGTAAAATAGGAATTTAAACACAACACGTTC-CAGTGGG
1 TTAAACAACACCTTCCGATGGGGAAGGGCAAAACAAGAATTT-AA-ACAACACCTTCTC-GTGGG
5037 GAAGGGCAAAGCAGGAAT
63 GAAGGGCAAAGCAGGAAT
* *
5055 TTAAACAACACCTTCCGATGGGGAAGGGCAAACCAAGAATTTAAACAACACCTTCTCGTTGGGAA
1 TTAAACAACACCTTCCGATGGGGAAGGGCAAAACAAGAATTTAAACAACACCTTCTCGTGGGGAA
5120 GGGCAAA
66 GGGCAAA
5127 CTGGGGAAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
80 24 0.38
81 3 0.05
82 37 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.18
Consensus pattern (80 bp):
TTAAACAACACCTTCCGATGGGGAAGGGCAAAACAAGAATTTAAACAACACCTTCTCGTGGGGAA
GGGCAAAGCAGGAAT
Found at i:5127 original size:40 final size:40
Alignment explanation
Indices: 4973--5127 Score: 188
Period size: 40 Copynumber: 3.8 Consensus size: 40
4963 AAAAACAGAC
* * **
4973 TTAAACAACACCTTCCGGTGGGGAAGGGTAAAATAGGAAT
1 TTAAACAACACCTTCCAGTGGGGAAGGGCAAACCAGGAAT
* *
5013 TTAAACACAACACGTTCCAGTGGGGAAGGGCAAAGCAGGAAT
1 TT-AA-ACAACACCTTCCAGTGGGGAAGGGCAAACCAGGAAT
*
5055 TTAAACAACACCTTCC-GATGGGGAAGGGCAAACCAAGAAT
1 TTAAACAACACCTTCCAG-TGGGGAAGGGCAAACCAGGAAT
*
5095 TTAAACAACACCTTCTC-GTTGGGAAGGGCAAAC
1 TTAAACAACACCTTC-CAGTGGGGAAGGGCAAAC
5128 TGGGGAAAAA
Statistics
Matches: 102, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
39 1 0.01
40 62 0.61
41 6 0.06
42 33 0.32
ACGTcount: A:0.37, C:0.20, G:0.25, T:0.17
Consensus pattern (40 bp):
TTAAACAACACCTTCCAGTGGGGAAGGGCAAACCAGGAAT
Found at i:5810 original size:40 final size:41
Alignment explanation
Indices: 5722--5919 Score: 233
Period size: 41 Copynumber: 4.9 Consensus size: 41
5712 CGACAAAGGG
* *
5722 AAGTAAATAACACCTTCCTGTGGGGGAAGAGC-AAACTAGGA
1 AAGTAAATAACACCTTCCGGTGGGGGAAGGGCAAAAC-AGGA
*
5763 AAGTAAACAACACCTTCCGGT-GGGGAAGGGCAAAAC-GAGA
1 AAGTAAATAACACCTTCCGGTGGGGGAAGGGCAAAACAG-GA
** ** * * *
5803 ATTTAAACCACACGTTCTGGT-GGGGAAGGGCAAAACAAGA
1 AAGTAAATAACACCTTCCGGTGGGGGAAGGGCAAAACAGGA
* *
5843 AAGTAAATAACACCTTCCGTTGGGGGAAGTGCAAAACAGGA
1 AAGTAAATAACACCTTCCGGTGGGGGAAGGGCAAAACAGGA
*
5884 AAGTAAATAACACCTTCCGTTGGGGGAAGGGCAAAA
1 AAGTAAATAACACCTTCCGGTGGGGGAAGGGCAAAA
Statistics
Matches: 134, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
39 1 0.01
40 58 0.43
41 75 0.56
ACGTcount: A:0.39, C:0.18, G:0.28, T:0.16
Consensus pattern (41 bp):
AAGTAAATAACACCTTCCGGTGGGGGAAGGGCAAAACAGGA
Done.