Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019942.1 Corchorus olitorius cultivar O-4 contig19975, 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: 18117
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:1522 original size:33 final size:32

Alignment explanation


    Indices: 1485--1553  Score: 84
    Period size: 33  Copynumber: 2.1  Consensus size: 32

       1475 AAATTTATAG

                      ** *       *           
       1485 ACAAAATAGCCCTTGAACTTTGACAAAAAAAGT
          1 ACAAAATAGCAATCGAACTTTAAC-AAAAAAGT

                                        *   
       1518 ACAAAATAGCAATCGAACTTTAACAAAATAGT
          1 ACAAAATAGCAATCGAACTTTAACAAAAAAGT

                
       1550 ACAA
          1 ACAA

       1554 CCCCTGAATG


Statistics
Matches: 31,  Mismatches: 5, Indels: 1
        0.84            0.14        0.03

Matches are distributed among these distances:
  32   11  0.35
  33   20  0.65

ACGTcount: A:0.52, C:0.17, G:0.10, T:0.20


Consensus pattern (32 bp):   
ACAAAATAGCAATCGAACTTTAACAAAAAAGT

Found at i:11810 original size:21 final size:21

Alignment explanation


    Indices: 11781--11821  Score: 55
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      11771 TATGTTTTCA

                         *       
      11781 CTTTGTTTTATTTCCTTTATG
          1 CTTTGTTTTATTTACTTTATG

                *    *          
      11802 CTTTTTTTTTTTTACTTTAT
          1 CTTTGTTTTATTTACTTTAT

      11822 ATTGTAGTAT


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.10, C:0.12, G:0.05, T:0.73


Consensus pattern (21 bp):   
CTTTGTTTTATTTACTTTATG

Found at i:14537 original size:25 final size:28

Alignment explanation


    Indices: 14498--14558  Score: 74
    Period size: 27  Copynumber: 2.2  Consensus size: 28

      14488 CCTTTTTTTC

                                         
      14498 AAATATATATCTAAA-T-TGCCATTATT-
          1 AAATA-ATATCTAAATTATGCCATTATTA

                     *        *         
      14524 AAATAATATTTAAATTATTCCATTATTA
          1 AAATAATATCTAAATTATGCCATTATTA

                   
      14552 AAATAAT
          1 AAATAAT

      14559 GGAAATTTAG


Statistics
Matches: 30,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  25    8  0.27
  26    6  0.20
  27    9  0.30
  28    7  0.23

ACGTcount: A:0.48, C:0.08, G:0.02, T:0.43


Consensus pattern (28 bp):   
AAATAATATCTAAATTATGCCATTATTA

Found at i:15252 original size:37 final size:37

Alignment explanation


    Indices: 15206--15287  Score: 96
    Period size: 37  Copynumber: 2.2  Consensus size: 37

      15196 ATATTACTTT

                                          *        
      15206 ATAATAAATAATATAAT-ATATATAATTTAGATAAAAAA
          1 ATAA-AAATAAT-TAATAATATATAATTTAAATAAAAAA

                     *  *                       *
      15244 ATAAAAATACTTTATAATATATAATTTAAATAAAAAT
          1 ATAAAAATAATTAATAATATATAATTTAAATAAAAAA

                    
      15281 A-AAAAAT
          1 ATAAAAAT

      15288 CAAAATGACG


Statistics
Matches: 39,  Mismatches: 4, Indels: 4
        0.83            0.09        0.09

Matches are distributed among these distances:
  36    9  0.23
  37   26  0.67
  38    4  0.10

ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34


Consensus pattern (37 bp):   
ATAAAAATAATTAATAATATATAATTTAAATAAAAAA
Done.