Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022738.1 Corchorus olitorius cultivar O-4 contig22771, 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: 14868
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4623 original size:113 final size:112
Alignment explanation
Indices: 4478--4972 Score: 568
Period size: 113 Copynumber: 4.5 Consensus size: 112
4468 AATATAAACA
*
4478 GCGTTTCTGG-GCAAGACGCCGCTAAATGGGGGCGTTTGAGGTTTAAAACGCCGCCATATTTAAA
1 GCGTTTCTGGCCCAA-ACGCCGCTAAATGGGGGCGTTTGAGGTTTAAAACGCCGCCATATTTAAA
* * *
4542 TCTTTCTGGGAAATAGAAATTGGGGAAAAATTAATACTAAAATATAGCG
65 TTTTTCTGGGAAATACAAATTGGGGAAAAA-TAAGACTAAAATATAGCG
* * *
4591 GCGTTT-TGGCCTCAAACGCCGCTAAATTGGGGCGTTTGAGGTTAAAAACGCCGTCATATTTAAT
1 GCGTTTCTGGCC-CAAACGCCGCTAAATGGGGGCGTTTGAGGTTTAAAACGCCGCCATATTTAA-
* * * * ** *
4655 TTTTTTCCGGGAAATGCCAATTGGATAAAAATGAGACTAAAATATAGCG
64 ATTTTTCTGGGAAATACAAATTGGGGAAAAATAAGACTAAAATATAGCG
* ** * * * **
4704 GGGTTT-TTACCCAAAACGCCGCTAAATGGGGGCGGTTGAGATTTACAACGCCGTTATATTTAAA
1 GCGTTTCTGGCCC-AAACGCCGCTAAATGGGGGCGTTTGAGGTTTAAAACGCCGCCATATTTAAA
*
4768 TTTTTCTGGGAAATACAAATTGGGTAAAAATGAAGACTAAAATATAGCG
65 TTTTTCTGGGAAATACAAATTGGGGAAAAAT-AAGACTAAAATATAGCG
* *
4817 GCGTTTCAGG-GCAAGACGCCGCTAAATGGGGGCGTTTGAGGTTTAAAACGCCGCCATATTTAAA
1 GCGTTTCTGGCCCAA-ACGCCGCTAAATGGGGGCGTTTGAGGTTTAAAACGCCGCCATATTTAAA
4881 TTTTTCTGGGAAATACAAA-T---G------AAGACTAAAATATAGCG
65 TTTTTCTGGGAAATACAAATTGGGGAAAAATAAGACTAAAATATAGCG
* * * *
4919 GCGTTTCGGGCCAAAACGCCGCTAAATTGGGGCGTTTGAGGTTAAAAACGCCGC
1 GCGTTTCTGGCCCAAACGCCGCTAAATGGGGGCGTTTGAGGTTTAAAACGCCGC
4973 TATGTTATTA
Statistics
Matches: 329, Mismatches: 45, Indels: 27
0.82 0.11 0.07
Matches are distributed among these distances:
102 63 0.19
103 2 0.01
112 34 0.10
113 204 0.62
114 26 0.08
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.27
Consensus pattern (112 bp):
GCGTTTCTGGCCCAAACGCCGCTAAATGGGGGCGTTTGAGGTTTAAAACGCCGCCATATTTAAAT
TTTTCTGGGAAATACAAATTGGGGAAAAATAAGACTAAAATATAGCG
Found at i:8541 original size:33 final size:33
Alignment explanation
Indices: 8498--8587 Score: 137
Period size: 33 Copynumber: 2.7 Consensus size: 33
8488 GTTTTGACGG
*
8498 AAACGCCACTAAATAGCGGCGTTTCCGTAC-AA
1 AAACGCCACTAAATAGTGGCGTTTCCGTACGAA
*
8530 CAAACGTCACTAAATAGTGGCGTTTCCGTACGAA
1 -AAACGCCACTAAATAGTGGCGTTTCCGTACGAA
*
8564 AAACGCCGCTAAATAGTGGCGTTT
1 AAACGCCACTAAATAGTGGCGTTT
8588 TTTGTACGGA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 50 0.96
34 2 0.04
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.22
Consensus pattern (33 bp):
AAACGCCACTAAATAGTGGCGTTTCCGTACGAA
Found at i:8607 original size:33 final size:32
Alignment explanation
Indices: 8478--8603 Score: 121
Period size: 33 Copynumber: 3.9 Consensus size: 32
8468 AAAAAAGCCA
* *
8478 AAATAGCGGCGTTT-TG-ACGGAAACGCCACT
1 AAATAGTGGCGTTTCCGTACGGAAACGCCACT
* ** *
8508 AAATAGCGGCGTTTCCGTACAACAAACGTCACT
1 AAATAGTGGCGTTTCCGTAC-GGAAACGCCACT
* *
8541 AAATAGTGGCGTTTCCGTACGAAAAACGCCGCT
1 AAATAGTGGCGTTTCCGTACG-GAAACGCCACT
**
8574 AAATAGTGGCGTTTTTTGTACGGAAACGCC
1 AAATAGTGGCG-TTTCCGTACGGAAACGCC
8604 GCTATTCCAA
Statistics
Matches: 79, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
30 14 0.18
31 1 0.01
32 2 0.03
33 54 0.68
34 8 0.10
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.23
Consensus pattern (32 bp):
AAATAGTGGCGTTTCCGTACGGAAACGCCACT
Found at i:11656 original size:21 final size:21
Alignment explanation
Indices: 11621--11662 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
11611 TGTGTGTGTG
*
11621 TGTGATTGTTTGGTTTGGTAGA
1 TGTGATTGATTGGTTT-GTAGA
11643 TGTGA-TGATTGGTTTGTAGA
1 TGTGATTGATTGGTTTGTAGA
11663 GACCGAGCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.17, C:0.00, G:0.36, T:0.48
Consensus pattern (21 bp):
TGTGATTGATTGGTTTGTAGA
Found at i:12899 original size:131 final size:130
Alignment explanation
Indices: 12665--12927 Score: 463
Period size: 131 Copynumber: 2.0 Consensus size: 130
12655 CAATACATTC
*
12665 ATGACAAGAACAAATAAATATGGTGAAATAGGATCACCTTGCTTAACCCCTTTCTCACAAAAAAA
1 ATGACAAGAACAAATAAATATGGTGAAATAGGATCACCTTGCTTAACCCCTTTCCCACAAAAAAA
**
12730 GTAGCCTACTAAACCACCATTGAGCCTTAATGAAAACTTAGGAGTAGTTAAACAAATATGAATCC
66 GTAGCCTACTAAACCACCATTGAGCCCCAATGAAAACTTAGGAGTAGTTAAACAAATATG-ATCC
12795 A
130 A
* * *
12796 ATGACAAGAACAAATAAGTATGGTGAAATAGGATCACCTTGCTTAACCCCTTTCCCACCAGAAAA
1 ATGACAAGAACAAATAAATATGGTGAAATAGGATCACCTTGCTTAACCCCTTTCCCACAAAAAAA
12861 GTAGCCTACTAAACCACCATTGAGCCCCAATGAAAACTTAGGAGTAGTTAAACAAATATGATCCA
66 GTAGCCTACTAAACCACCATTGAGCCCCAATGAAAACTTAGGAGTAGTTAAACAAATATGATCCA
12926 AT
1 AT
12928 TTCAGAATTC
Statistics
Matches: 126, Mismatches: 6, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
130 7 0.06
131 119 0.94
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.23
Consensus pattern (130 bp):
ATGACAAGAACAAATAAATATGGTGAAATAGGATCACCTTGCTTAACCCCTTTCCCACAAAAAAA
GTAGCCTACTAAACCACCATTGAGCCCCAATGAAAACTTAGGAGTAGTTAAACAAATATGATCCA
Done.