Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018828.1 Corchorus olitorius cultivar O-4 contig18861, 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: 10930
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35


Found at i:3178 original size:31 final size:31

Alignment explanation


    Indices: 3140--3200  Score: 122
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       3130 GCCAGCGAGA

                                           
       3140 ACGCAACCTTGGTGCTTGTTTCCACTGTTCC
          1 ACGCAACCTTGGTGCTTGTTTCCACTGTTCC

                                          
       3171 ACGCAACCTTGGTGCTTGTTTCCACTGTTC
          1 ACGCAACCTTGGTGCTTGTTTCCACTGTTC

       3201 TCACTGGACC


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  31   30  1.00

ACGTcount: A:0.13, C:0.31, G:0.20, T:0.36


Consensus pattern (31 bp):   
ACGCAACCTTGGTGCTTGTTTCCACTGTTCC

Found at i:4564 original size:39 final size:39

Alignment explanation


    Indices: 4521--4596  Score: 116
    Period size: 39  Copynumber: 1.9  Consensus size: 39

       4511 GTATTTCTGA

                          *           *            
       4521 TTCTGATGAACATTTCAATTCTGTTTTTCCTTGTAATTG
          1 TTCTGATGAACATTACAATTCTGTTTCTCCTTGTAATTG

                    *                    *       
       4560 TTCTGATGCACATTACAATTCTGTTTCTCTTTGTAAT
          1 TTCTGATGAACATTACAATTCTGTTTCTCCTTGTAAT

       4597 CATGTTAATG


Statistics
Matches: 33,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  39   33  1.00

ACGTcount: A:0.21, C:0.17, G:0.12, T:0.50


Consensus pattern (39 bp):   
TTCTGATGAACATTACAATTCTGTTTCTCCTTGTAATTG

Found at i:5726 original size:24 final size:24

Alignment explanation


    Indices: 5699--5747  Score: 89
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       5689 CCAGAATCCT

                         *          
       5699 CCTGTAGTACAAATTTCTCTTCAA
          1 CCTGTAGTACAAACTTCTCTTCAA

                                    
       5723 CCTGTAGTACAAACTTCTCTTCAA
          1 CCTGTAGTACAAACTTCTCTTCAA

             
       5747 C
          1 C

       5748 ACACTTCAGA


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.29, C:0.29, G:0.08, T:0.35


Consensus pattern (24 bp):   
CCTGTAGTACAAACTTCTCTTCAA

Found at i:9389 original size:23 final size:24

Alignment explanation


    Indices: 9363--9408  Score: 67
    Period size: 25  Copynumber: 1.9  Consensus size: 24

       9353 TCTAAAAAAA

                          *         
       9363 AATAATA-TTCTACTTTTATTGAT
          1 AATAATATTTCTACATTTATTGAT

                                   
       9386 AATAATATTTTCTACATTTATTG
          1 AATAATA-TTTCTACATTTATTG

       9409 CTCATTTTAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  23    7  0.35
  25   13  0.65

ACGTcount: A:0.35, C:0.09, G:0.04, T:0.52


Consensus pattern (24 bp):   
AATAATATTTCTACATTTATTGAT

Found at i:9484 original size:13 final size:13

Alignment explanation


    Indices: 9466--9493  Score: 56
    Period size: 13  Copynumber: 2.2  Consensus size: 13

       9456 ATATATCAAC

                         
       9466 AAATAAAAATAAA
          1 AAATAAAAATAAA

                         
       9479 AAATAAAAATAAA
          1 AAATAAAAATAAA

              
       9492 AA
          1 AA

       9494 GAAGCATATT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   15  1.00

ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14


Consensus pattern (13 bp):   
AAATAAAAATAAA
Done.