Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013947.1 Corchorus olitorius cultivar O-4 contig13980, 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: 23938
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Found at i:484 original size:2 final size:2
Alignment explanation
Indices: 477--508 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
467 TAAGGTTCAA
477 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
509 GAGATTAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:798 original size:36 final size:36
Alignment explanation
Indices: 751--820 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
741 ACAAAACAAA
*
751 ACTTGTCACCAAGTCCAAGAGAGTAGCCTTTCTCCC
1 ACTTGTCACCAAGTCCAAGAGAGTAGCATTTCTCCC
787 ACTTGTCACCAAGTCCAAGAGAGTAGCATTTCTC
1 ACTTGTCACCAAGTCCAAGAGAGTAGCATTTCTC
821 GGGAGACAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (36 bp):
ACTTGTCACCAAGTCCAAGAGAGTAGCATTTCTCCC
Found at i:884 original size:22 final size:22
Alignment explanation
Indices: 856--903 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
846 AAGCCAGTAA
856 AAGACCAGGAACTTTCAAAGTG
1 AAGACCAGGAACTTTCAAAGTG
878 AAGACCAGGAACTTTCAAAGTG
1 AAGACCAGGAACTTTCAAAGTG
900 AAGA
1 AAGA
904 AAATATTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.17
Consensus pattern (22 bp):
AAGACCAGGAACTTTCAAAGTG
Found at i:11485 original size:23 final size:21
Alignment explanation
Indices: 11434--11530 Score: 90
Period size: 23 Copynumber: 4.4 Consensus size: 21
11424 TTGTGGTCAC
11434 AAGTGGTCGAGCGCCGCGTTATGG
1 AAGTGGTC-AGCGCCG-GTT-TGG
11458 AAGTGGTCAGTCGCCAGGTTTGG
1 AAGTGGTCAG-CGCC-GGTTTGG
* * *
11481 AAGTGGTC-G-GGCGCTATGG
1 AAGTGGTCAGCGCCGGTTTGG
11500 AAGTGGTCAGTCGCCAGGTTTGG
1 AAGTGGTCAG-CGCC-GGTTTGG
11523 AAGTGGTC
1 AAGTGGTC
11531 GGGCGTCAAG
Statistics
Matches: 61, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
19 13 0.21
20 3 0.05
22 3 0.05
23 26 0.43
24 15 0.25
25 1 0.02
ACGTcount: A:0.18, C:0.18, G:0.41, T:0.24
Consensus pattern (21 bp):
AAGTGGTCAGCGCCGGTTTGG
Found at i:11512 original size:42 final size:42
Alignment explanation
Indices: 11453--11535 Score: 166
Period size: 42 Copynumber: 2.0 Consensus size: 42
11443 AGCGCCGCGT
11453 TATGGAAGTGGTCAGTCGCCAGGTTTGGAAGTGGTCGGGCGC
1 TATGGAAGTGGTCAGTCGCCAGGTTTGGAAGTGGTCGGGCGC
11495 TATGGAAGTGGTCAGTCGCCAGGTTTGGAAGTGGTCGGGCG
1 TATGGAAGTGGTCAGTCGCCAGGTTTGGAAGTGGTCGGGCG
11536 TCAAGCAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.17, C:0.16, G:0.43, T:0.24
Consensus pattern (42 bp):
TATGGAAGTGGTCAGTCGCCAGGTTTGGAAGTGGTCGGGCGC
Found at i:12000 original size:60 final size:60
Alignment explanation
Indices: 11914--12101 Score: 209
Period size: 60 Copynumber: 3.0 Consensus size: 60
11904 GATGGCCAGA
* * *
11914 TTTTTTTTTTGTGGTTGACCGTCTAGATCCATTTGTGCGCTCGACCACATGTGTGTGTTG
1 TTTTTTTTTGGTGGTCGACCGCCTAGATCCATTTGTGCGCTCGACCACATGTGTGTGTTG
*
11974 TTTTTTTTTGGTGGTCGATCGCCTAGATCCATTT-TGGCGCTCGACCACGTGTGTGTATGTGTGT
1 TTTTTTTTTGGTGGTCGACCGCCTAGATCCATTTGT-GCGCTCGACCAC--------ATGTGTGT
*
12038 GTTT
57 GTTG
12042 TTCTTTTTTTGGGTGGTCGACCGCCTAGATCCATTTG-GACGCTCGACCACATGTGTGTGT
1 TT-TTTTTTT-GGTGGTCGACCGCCTAGATCCATTTGTG-CGCTCGACCACATGTGTGTGT
12102 GTGTGTGTGT
Statistics
Matches: 109, Mismatches: 6, Indels: 24
0.78 0.04 0.17
Matches are distributed among these distances:
59 1 0.01
60 42 0.39
62 10 0.09
68 13 0.12
69 8 0.07
70 35 0.32
ACGTcount: A:0.12, C:0.20, G:0.27, T:0.42
Consensus pattern (60 bp):
TTTTTTTTTGGTGGTCGACCGCCTAGATCCATTTGTGCGCTCGACCACATGTGTGTGTTG
Found at i:12073 original size:70 final size:70
Alignment explanation
Indices: 11962--12170 Score: 237
Period size: 70 Copynumber: 2.9 Consensus size: 70
11952 GCTCGACCAC
* *
11962 ATGTGTGTGTTGTTTTTTTTT-GGTGGTCGATCGCCTAGATCCATTTTGGCGCTCGACCAC-GTG
1 ATGTGTGTGTTTTTTTTTTTTGGGTGGTCGACCGCCTAGATCCATTTTGGCGCTCGACCACAGTG
12025 TGTGT
66 TGTGT
12030 ATGTGTGTGTTTTTCTTTTTTTGGGTGGTCGACCGCCTAGATCCA-TTTGGACGCTCGACCACAT
1 ATGTGTGTGTTTTT-TTTTTTTGGGTGGTCGACCGCCTAGATCCATTTTGG-CGCTCGACCACA-
12094 GTGTGTGTGT
63 --GTGTGTGT
* * * *
12104 GTGTGTGTGTGCTTTTTTTTTTTGGTGTATGGTCGAGCGCCTAGATCTATTTGGGCG-TCCGACC
1 ATGTGTGTGT--TTTTTTTTTTTGG-G--TGGTCGACCGCCTAGATCCATTTTGGCGCT-CGACC
12168 ACA
60 ACA
12171 TGGTATTATA
Statistics
Matches: 121, Mismatches: 6, Indels: 18
0.83 0.04 0.12
Matches are distributed among these distances:
68 13 0.11
69 12 0.10
70 32 0.26
74 17 0.14
75 9 0.07
76 5 0.04
77 1 0.01
78 28 0.23
79 4 0.03
ACGTcount: A:0.11, C:0.18, G:0.29, T:0.41
Consensus pattern (70 bp):
ATGTGTGTGTTTTTTTTTTTTGGGTGGTCGACCGCCTAGATCCATTTTGGCGCTCGACCACAGTG
TGTGT
Found at i:12279 original size:78 final size:79
Alignment explanation
Indices: 12118--12281 Score: 217
Period size: 78 Copynumber: 2.1 Consensus size: 79
12108 GTGTGTGCTT
*
12118 TTTTTTTTTGGTGTATGGTCGAGCGCCTAGATCTATTTGGGCGTCCGACCACATGGTATTATAAT
1 TTTTTTTTTGGTGTATGGTCGAGCGCCTAGACCTATTTGGGCGTCCGACCACATGGTATTATAAT
* *
12183 TCATTTTCTCTCT-
66 TCATTTGCTATCTA
* * **
12196 TTTTTTTTTTGTGTGTGGTCGAGCGCCTAGACCTATTTGGGCGTCCGACCACATGG-ATGTATGC
1 TTTTTTTTTGGTGTATGGTCGAGCGCCTAGACCTATTTGGGCGTCCGACCACATGGTAT-TATAA
*
12260 TTC-TTTGCTAATGTA
65 TTCATTTGCT-ATCTA
12275 TTTTTTT
1 TTTTTTT
12282 AACTTTGTTG
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
77 7 0.09
78 61 0.81
79 7 0.09
ACGTcount: A:0.15, C:0.18, G:0.22, T:0.45
Consensus pattern (79 bp):
TTTTTTTTTGGTGTATGGTCGAGCGCCTAGACCTATTTGGGCGTCCGACCACATGGTATTATAAT
TCATTTGCTATCTA
Found at i:13926 original size:127 final size:127
Alignment explanation
Indices: 13686--14087 Score: 603
Period size: 127 Copynumber: 3.2 Consensus size: 127
13676 GGGAATTCGT
* * * *
13686 CGTTGA-CCCCTTGGGGGCGTTCATTACTTTTCGTACTTGTGCAAGGATCGCTTCTTGGCGACCA
1 CGTTGAGCCCTTTGCGGGCGTTCATTACTTTCCGTACTTGTGCAAGGATCGCTTCTTGGCGACCG
* * *
13750 CCCACAAGTCGGGGGCCATGCTAAGTC-GAGTTCTGATCCTTC-CCGATCGCCCCGCCTGCTGG
66 CCCACAAGTCGGGGGCCATGCTAAGTCGGGGTT-GGAT-CTTCGTCGATCGCCCCGCCTGCTGG
* * *
13812 CGTTGAGCCCTTCGCGGGCGTTCATTACTTTCCGTACTTGTGTAGGGATCGCTTCTTGGCGACCG
1 CGTTGAGCCCTTTGCGGGCGTTCATTACTTTCCGTACTTGTGCAAGGATCGCTTCTTGGCGACCG
*
13877 CCCACAAGTCGGGGGCCATGCTAAGTCGGGGTTGGATCTTCGTCGATCGCCCCGCTTGCTGG
66 CCCACAAGTCGGGGGCCATGCTAAGTCGGGGTTGGATCTTCGTCGATCGCCCCGCCTGCTGG
* * *
13939 CGTTGAGCCCTTTGCGGGCATTTATTACTTTCCGTACTTGTGCATGGATCGCTTCTTGGCGACCG
1 CGTTGAGCCCTTTGCGGGCGTTCATTACTTTCCGTACTTGTGCAAGGATCGCTTCTTGGCGACCG
* * * *
14004 CCCTCAAGTCGGGGGCCATGCTAAGTTGGGGTTGGATCTTCGTCGATCGCCCCGTCTACTGG
66 CCCACAAGTCGGGGGCCATGCTAAGTCGGGGTTGGATCTTCGTCGATCGCCCCGCCTGCTGG
14066 CGTTGAGCCCTTTGCGGGCGTT
1 CGTTGAGCCCTTTGCGGGCGTT
14088 GTTGGGCGTA
Statistics
Matches: 251, Mismatches: 22, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
126 10 0.04
127 237 0.94
128 4 0.02
ACGTcount: A:0.12, C:0.29, G:0.30, T:0.29
Consensus pattern (127 bp):
CGTTGAGCCCTTTGCGGGCGTTCATTACTTTCCGTACTTGTGCAAGGATCGCTTCTTGGCGACCG
CCCACAAGTCGGGGGCCATGCTAAGTCGGGGTTGGATCTTCGTCGATCGCCCCGCCTGCTGG
Done.