Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016671.1 Corchorus olitorius cultivar O-4 contig16704, 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: 5600
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Found at i:4569 original size:39 final size:38
Alignment explanation
Indices: 4479--4998 Score: 217
Period size: 39 Copynumber: 13.4 Consensus size: 38
4469 TTTTTATCTT
** *
4479 AGCAAACCTGCTTAGG-TCTATATTTAGAATTTCATTTA
1 AGCAAACCTGCTTAGGTTCT-TGCTTAGAATTTCGTTTA
* *
4517 AGTAAACCTGCTTAGGTTCTTGCTTAAAATTTCCGTTTA
1 AGCAAACCTGCTTAGGTTCTTGCTTAGAATTT-CGTTTA
* * * * **
4556 AGCAAACCCGCTTAAGTCCTTGTTTAGAACTCCCG-TTA
1 AGCAAACCTGCTTAGGTTCTTGCTTAGAA-TTTCGTTTA
* * * *
4594 AGTAAACCTGCTT-GGGTCTTCGTTTGGAAGTTTCGTTTA
1 AGCAAACCTGCTTAGGTTCTT-GCTTAGAA-TTTCGTTTA
* * *
4633 ATCAAACTTGCTTAGGTTCTTG-TGTAGAATTCCCGTTTGA
1 AGCAAACCTGCTTAGGTTCTTGCT-TAGAATT-TCGTTT-A
*
4673 ATG--AACCTGCTTAGG-TCTATGCTTAGAATTTCGCTTA
1 A-GCAAACCTGCTTAGGTTCT-TGCTTAGAATTTCGTTTA
* * *
4710 ATCAAACCTGCTTAGG-TCTACGCTTAGAGTTTTCGTTTA
1 AGCAAACCTGCTTAGGTTCT-TGCTTAGA-ATTTCGTTTA
* * * * *
4749 ATCAAACCTGCTTAGGTCCCT-CTTTGTAATCTT-GCCTT-
1 AGCAAACCTGCTTAGGTTCTTGCTTAG-AAT-TTCG-TTTA
* * * * * *
4787 AGAAAAATCTGATCACG-TCTCTGCTTAGAAATTTCATTTA
1 AG-CAAACCTGCTTAGGTTCT-TGCTTAG-AATTTCGTTTA
* * * * * * *
4827 AGAAAACATGTTTAGGATCTCTGCTTAGAGCTTT-GATCA
1 AGCAAACCTGCTTAGGTTCT-TGCTTAGA-ATTTCGTTTA
* * * * * * * * *
4866 AGTAAGCCTGTTTAGGTCCCT-ATATAGAGTTGCCATTTA
1 AGCAAACCTGCTTAGGTTCTTGCT-TAGAATT-TCGTTTA
*
4905 AGTAAACCTGCTTAGG-TCTATG-TTCAGAATTTCGTTTA
1 AGCAAACCTGCTTAGGTTCT-TGCTT-AGAATTTCGTTTA
* * *
4943 AGAAAACCTGCTTAGGTTCTTGTTTAGAATTCTTGTTTA
1 AGCAAACCTGCTTAGGTTCTTGCTTAGAATT-TCGTTTA
*
4982 ATCAAACCTGCTTAGGT
1 AGCAAACCTGCTTAGGT
4999 CCCCCCTCTA
Statistics
Matches: 361, Mismatches: 86, Indels: 69
0.70 0.17 0.13
Matches are distributed among these distances:
37 9 0.02
38 124 0.34
39 194 0.54
40 34 0.09
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.38
Consensus pattern (38 bp):
AGCAAACCTGCTTAGGTTCTTGCTTAGAATTTCGTTTA
Found at i:4569 original size:77 final size:74
Alignment explanation
Indices: 4479--4765 Score: 229
Period size: 77 Copynumber: 3.7 Consensus size: 74
4469 TTTTTATCTT
* * *
4479 AGCAAACCTGCTTAGGTCTATATTTAGAATTTCATTTAAGTAAACCTGCTTAGGTTCTTGCTTAA
1 AGCAAACCTGCTTAGGTCT-TGTTTAGAATTCCGTTTAA-TAAACCTGCTTAGGTTCTTGCTTAA
4544 AATTTCCGTTTA
64 AATTT-CGTTTA
* * * * *
4556 AGCAAACCCGCTTAAGTCCTTGTTTAGAACTCCCG-TTAAGTAAACCTGCTT-GGGTCTTCGTTT
1 AGCAAACCTGCTTAGGT-CTTGTTTAGAA-TTCCGTTTAA-TAAACCTGCTTAGGTTCTT-GCTT
* *
4619 GGAAGTTTCGTTTA
62 -AAAATTTCGTTTA
* * * *
4633 ATCAAACTTGCTTAGGTTCTTGTGTAGAATTCCCGTTTGAATGAACCTGCTTAGG-TCTATGCTT
1 AGCAAACCTGCTTAGG-TCTTGTTTAGAATT-CCGTTT-AATAAACCTGCTTAGGTTCT-TGCTT
* *
4697 AGAATTTCGCTTA
62 AAAATTTCGTTTA
* * * * *
4710 ATCAAACCTGCTTAGGTCTACGCTTAGAGTTTTCGTTTAATCAAACCTGCTTAGGT
1 AGCAAACCTGCTTAGGTCT-TGTTTAGA-ATTCCGTTTAAT-AAACCTGCTTAGGT
4766 CCCTCTTTGT
Statistics
Matches: 167, Mismatches: 29, Indels: 27
0.75 0.13 0.12
Matches are distributed among these distances:
76 13 0.08
77 119 0.71
78 30 0.18
79 5 0.03
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.38
Consensus pattern (74 bp):
AGCAAACCTGCTTAGGTCTTGTTTAGAATTCCGTTTAATAAACCTGCTTAGGTTCTTGCTTAAAA
TTTCGTTTA
Found at i:4997 original size:116 final size:113
Alignment explanation
Indices: 4482--5001 Score: 304
Period size: 116 Copynumber: 4.5 Consensus size: 113
4472 TTATCTTAGC
** ** * * * *
4482 AAACCTGCTTAGGTCTATATTTAGAATTTCATTTAAGT-AAACCTGCTTAGGTTCTTGCTTAAAA
1 AAACCTGCTTAGGTCTATGCTTAGAATTTTGTTTAA-TCAAACCTGCTTAGGTCCCT-ATTAGAA
* * * * * ** *
4546 TTTCCGTTTAAGCAAACCCGCTTAAGTCCT-TGTTTAGAACTCCCG-TTAAGT
64 TTGCC-TTTAAGTAAACCTGCTTAGGT-CTATGCTTAGAA-TTTCGTTTAAGA
* * * * * * * *
4597 AAACCTGCTTGGGTCT-TCGTTTGGAAGTTTCGTTTAATCAAACTTGCTTAGGTTCTTGTGTAGA
1 AAACCTGCTTAGGTCTAT-GCTTAGAA-TTTTGTTTAATCAAACCTGCTTAGGTCCCTAT-TAGA
* * * **
4661 ATTCCCGTTTGAA-TGAACCTGCTTAGGTCTATGCTTAGAATTTCGCTTAATC
63 ATTGCC-TTT-AAGTAAACCTGCTTAGGTCTATGCTTAGAATTTCGTTTAAGA
* * * *
4713 AAACCTGCTTAGGTCTACGCTTAGAGTTTTCGTTTAATCAAACCTGCTTAGGTCCCTCTTTGTAA
1 AAACCTGCTTAGGTCTATGCTTAGAATTTT-GTTTAATCAAACCTGCTTAGGTCCCTATTAG-AA
* * * * * * *
4778 TCTTGCC-TT-AGAAAAATCTGATCACGTCTCTGCTTAGAAATTTCATTTAAGA
64 --TTGCCTTTAAG-TAAACCTGCTTAGGTCTATGCTTAG-AATTTCGTTTAAGA
* * * ** * * * *
4830 AAACATGTTTAGGATCTCTGCTTAGAGCTTTGATCAAGT-AAGCCTGTTTAGGTCCCTATATAGA
1 AAACCTGCTTAGG-TCTATGCTTAGAATTTTGTTTAA-TCAAACCTGCTTAGGTCCCTAT-TAGA
*
4894 GTTGCCATTTAAGTAAACCTGCTTAGGTCTATG-TTCAGAATTTCGTTTAAGA
63 ATTGCC-TTTAAGTAAACCTGCTTAGGTCTATGCTT-AGAATTTCGTTTAAGA
*
4946 AAACCTGCTTAGGTTCT-TGTTTAGAATTCTTGTTTAATCAAACCTGCTTAGGTCCC
1 AAACCTGCTTAGG-TCTATGCTTAGAATT-TTGTTTAATCAAACCTGCTTAGGTCCC
5002 CCCTCTACAA
Statistics
Matches: 312, Mismatches: 69, Indels: 47
0.73 0.16 0.11
Matches are distributed among these distances:
114 2 0.01
115 47 0.15
116 177 0.57
117 63 0.20
118 23 0.07
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (113 bp):
AAACCTGCTTAGGTCTATGCTTAGAATTTTGTTTAATCAAACCTGCTTAGGTCCCTATTAGAATT
GCCTTTAAGTAAACCTGCTTAGGTCTATGCTTAGAATTTCGTTTAAGA
Done.