Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023044.1 Corchorus olitorius cultivar O-4 contig23077, 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: 32998
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:1983 original size:26 final size:27

Alignment explanation


    Indices: 1954--2010  Score: 89
    Period size: 27  Copynumber: 2.1  Consensus size: 27

       1944 AAATTAAAAG

                             *         
       1954 TGAACCTA-AAATGACCTAAATGCCCC
          1 TGAACCTACAAATGACCAAAATGCCCC

                 *                     
       1980 TGAACGTACAAATGACCAAAATGCCCC
          1 TGAACCTACAAATGACCAAAATGCCCC

                
       2007 TGAA
          1 TGAA

       2011 TTTTTGGAAA


Statistics
Matches: 28,  Mismatches: 2, Indels: 1
        0.90            0.06        0.03

Matches are distributed among these distances:
  26    7  0.25
  27   21  0.75

ACGTcount: A:0.40, C:0.28, G:0.14, T:0.18


Consensus pattern (27 bp):   
TGAACCTACAAATGACCAAAATGCCCC

Found at i:11693 original size:22 final size:22

Alignment explanation


    Indices: 11668--11710  Score: 68
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      11658 AAATACCATT

                                  
      11668 CGAATTAGGGTTTTAGGAATTC
          1 CGAATTAGGGTTTTAGGAATTC

                  *       *      
      11690 CGAATTGGGGTTTTTGGAATT
          1 CGAATTAGGGTTTTAGGAATT

      11711 AATGAATCAA


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.23, C:0.07, G:0.30, T:0.40


Consensus pattern (22 bp):   
CGAATTAGGGTTTTAGGAATTC

Found at i:12123 original size:29 final size:29

Alignment explanation


    Indices: 12080--12160  Score: 112
    Period size: 29  Copynumber: 2.8  Consensus size: 29

      12070 GTTTCAGAAA

                      *                  
      12080 ATATTAATATGTATAA-ATAATAAAAATC
          1 ATATTAATATATATAATATAATAAAAATC

                                           
      12108 ATATGTAATATATATATATATAATAAAAATC
          1 ATAT-TAATATATATA-ATATAATAAAAATC

                  *                
      12139 ATA-TATTATATATAATATAATA
          1 ATATTAATATATATAATATAATA

      12161 TTAAATTATA


Statistics
Matches: 48,  Mismatches: 2, Indels: 6
        0.86            0.04        0.11

Matches are distributed among these distances:
  28   12  0.25
  29   20  0.42
  30    1  0.02
  31   15  0.31

ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40


Consensus pattern (29 bp):   
ATATTAATATATATAATATAATAAAAATC

Found at i:12134 original size:31 final size:29

Alignment explanation


    Indices: 12086--12160  Score: 98
    Period size: 31  Copynumber: 2.6  Consensus size: 29

      12076 GAAAATATTA

                *    *                     
      12086 ATATGTATAAATAATAAAAATCATATGTAAT
          1 ATATATATATATAATAAAAATCATA--TAAT

                                       * 
      12117 ATATATATATATAATAAAAATCATATATT
          1 ATATATATATATAATAAAAATCATATAAT

                            
      12146 ATATATA-ATATAATA
          1 ATATATATATATAATA

      12161 TTAAATTATA


Statistics
Matches: 41,  Mismatches: 3, Indels: 3
        0.87            0.06        0.06

Matches are distributed among these distances:
  28    8  0.20
  29   10  0.24
  31   23  0.56

ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39


Consensus pattern (29 bp):   
ATATATATATATAATAAAAATCATATAAT

Found at i:20823 original size:31 final size:32

Alignment explanation


    Indices: 20766--20828  Score: 94
    Period size: 31  Copynumber: 2.0  Consensus size: 32

      20756 CAAGATTGAA

                                            
      20766 GTATGAAAAATGACAAGAACAAGTAAGAACTT
          1 GTATGAAAAATGACAAGAACAAGTAAGAACTT

                            *                
      20798 GTATG-AAAATGA-AATAACAATGTAAGAACTT
          1 GTATGAAAAATGACAAGAACAA-GTAAGAACTT

      20829 TCAGAGAAAA


Statistics
Matches: 29,  Mismatches: 1, Indels: 3
        0.88            0.03        0.09

Matches are distributed among these distances:
  30    7  0.24
  31   17  0.59
  32    5  0.17

ACGTcount: A:0.52, C:0.08, G:0.17, T:0.22


Consensus pattern (32 bp):   
GTATGAAAAATGACAAGAACAAGTAAGAACTT

Found at i:23005 original size:31 final size:30

Alignment explanation


    Indices: 22942--23004  Score: 81
    Period size: 30  Copynumber: 2.1  Consensus size: 30

      22932 TTATTCTGAC

                  *           **  *   *   
      22942 AAAGAATTTTGCTTATGATCCTCTTTGAAA
          1 AAAGAAATTTGCTTATGAAACTATTTAAAA

                                          
      22972 AAAGAAATTTGCTTATGAAACTATTTAAAA
          1 AAAGAAATTTGCTTATGAAACTATTTAAAA

               
      23002 AAA
          1 AAA

      23005 ATTGATACCA


Statistics
Matches: 28,  Mismatches: 5, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  30   28  1.00

ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35


Consensus pattern (30 bp):   
AAAGAAATTTGCTTATGAAACTATTTAAAA

Found at i:25773 original size:19 final size:19

Alignment explanation


    Indices: 25749--25786  Score: 76
    Period size: 19  Copynumber: 2.0  Consensus size: 19

      25739 TATTTCACAT

                               
      25749 TTTTTTATTAGGAAATTAG
          1 TTTTTTATTAGGAAATTAG

                               
      25768 TTTTTTATTAGGAAATTAG
          1 TTTTTTATTAGGAAATTAG

      25787 GAATTCTAGT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   19  1.00

ACGTcount: A:0.32, C:0.00, G:0.16, T:0.53


Consensus pattern (19 bp):   
TTTTTTATTAGGAAATTAG
Done.