Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017886.1 Corchorus olitorius cultivar O-4 contig17919, 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: 31274
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:1117 original size:13 final size:13

Alignment explanation


    Indices: 1099--1139  Score: 55
    Period size: 13  Copynumber: 3.2  Consensus size: 13

       1089 TCTTTCTCCC

                    *    
       1099 TTTTTTTTGTTTT
          1 TTTTTTTTATTTT

                     *   
       1112 TTTTTTTTAATTT
          1 TTTTTTTTATTTT

             *           
       1125 TCTTTTTTATTTT
          1 TTTTTTTTATTTT

              
       1138 TT
          1 TT

       1140 AATGCAACCC


Statistics
Matches: 23,  Mismatches: 5, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  13   23  1.00

ACGTcount: A:0.07, C:0.02, G:0.02, T:0.88


Consensus pattern (13 bp):   
TTTTTTTTATTTT

Found at i:22887 original size:33 final size:33

Alignment explanation


    Indices: 22848--22915  Score: 118
    Period size: 33  Copynumber: 2.1  Consensus size: 33

      22838 CAGCCAATAG

                                        *    
      22848 ATATCGCGCGTTTGGAGTAGTCTACTTATCGAT
          1 ATATCGCGCGTTTGGAGTAGTCTACTTACCGAT

                                   *         
      22881 ATATCGCGCGTTTGGAGTAGTCTGCTTACCGAT
          1 ATATCGCGCGTTTGGAGTAGTCTACTTACCGAT

              
      22914 AT
          1 AT

      22916 CGCGCGATCG


Statistics
Matches: 33,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  33   33  1.00

ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35


Consensus pattern (33 bp):   
ATATCGCGCGTTTGGAGTAGTCTACTTACCGAT

Found at i:23499 original size:1 final size:1

Alignment explanation


    Indices: 23495--23528  Score: 68
    Period size: 1  Copynumber: 34.0  Consensus size: 1

      23485 TACAAACTAC

                                              
      23495 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

      23529 CAGATGGTGC


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   33  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:27342 original size:73 final size:72

Alignment explanation


    Indices: 27250--27389  Score: 226
    Period size: 73  Copynumber: 1.9  Consensus size: 72

      27240 AGATATTATA

                        *         *                     **                   
      27250 GAAGTAACAGAAGAAGTGGCTTGTCATTAGATATTTGGTCTATTGGTAAAGTGTTTAGACTTTTA
          1 GAAGTAACAGAAAAAGTGGCTTATCATTAGATATTTGGTCTATTAATAAAGTG-TTAGACTTTTA

                    
      27315 ATTTTAAT
         65 ATTTTAAT

                                                                      *      
      27323 GAAGTAACAGAAAAAGTGGCTTATCATTAGATATTTGGTCTATTAATAAAGTGTTAGATTTTTAA
          1 GAAGTAACAGAAAAAGTGGCTTATCATTAGATATTTGGTCTATTAATAAAGTGTTAGACTTTTAA

              
      27388 TT
         66 TT

      27390 CTAGTGATTA


Statistics
Matches: 62,  Mismatches: 5, Indels: 1
        0.91            0.07        0.01

Matches are distributed among these distances:
  72   13  0.21
  73   49  0.79

ACGTcount: A:0.34, C:0.06, G:0.20, T:0.39


Consensus pattern (72 bp):   
GAAGTAACAGAAAAAGTGGCTTATCATTAGATATTTGGTCTATTAATAAAGTGTTAGACTTTTAA
TTTTAAT

Found at i:27752 original size:11 final size:12

Alignment explanation


    Indices: 27729--27764  Score: 56
    Period size: 11  Copynumber: 3.0  Consensus size: 12

      27719 GAGATGATCT

                         
      27729 TTTATACTATTTA
          1 TTTATA-TATTTA

                        
      27742 TTTAT-TATTTA
          1 TTTATATATTTA

                        
      27753 TTTATATATTTA
          1 TTTATATATTTA

      27765 AATCTTGAAT


Statistics
Matches: 22,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  11   11  0.50
  12    6  0.27
  13    5  0.23

ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67


Consensus pattern (12 bp):   
TTTATATATTTA
Done.