Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021737.1 Corchorus olitorius cultivar O-4 contig21770, 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: 15785
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:1027 original size:25 final size:26

Alignment explanation


    Indices: 974--1034  Score: 72
    Period size: 26  Copynumber: 2.4  Consensus size: 26

        964 TTTTCTAAAA

                                    * 
        974 ACGCAGAACAAAAATTTTTTTTTATG
          1 ACGCAGAACAAAAATTTTTTTTTACG

                          *            
       1000 ACGCAGAA-AAACACTTTTTTTTT-CG
          1 ACGCAGAACAAA-AATTTTTTTTTACG

                 *    
       1025 ACGCAAAACA
          1 ACGCAGAACA

       1035 CAAACAGATT


Statistics
Matches: 30,  Mismatches: 3, Indels: 4
        0.81            0.08        0.11

Matches are distributed among these distances:
  25   11  0.37
  26   19  0.63

ACGTcount: A:0.39, C:0.18, G:0.11, T:0.31


Consensus pattern (26 bp):   
ACGCAGAACAAAAATTTTTTTTTACG

Found at i:1464 original size:16 final size:15

Alignment explanation


    Indices: 1426--1467  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       1416 ACAGAGATTG

                   *       
       1426 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
       1441 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       1456 ACTAGAAAACAA
          1 AC-AGAAAACAA

       1468 AGCAAAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:11057 original size:15 final size:15

Alignment explanation


    Indices: 11039--11070  Score: 55
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      11029 AAGTTGTTTC

                       *   
      11039 CTTTAATATTGTTGT
          1 CTTTAATATTGCTGT

                           
      11054 CTTTAATATTGCTGT
          1 CTTTAATATTGCTGT

              
      11069 CT
          1 CT

      11071 ACTAGGGAGG


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.19, C:0.12, G:0.12, T:0.56


Consensus pattern (15 bp):   
CTTTAATATTGCTGT

Found at i:12652 original size:67 final size:65

Alignment explanation


    Indices: 12339--12777  Score: 385
    Period size: 67  Copynumber: 6.6  Consensus size: 65

      12329 ACAAAGCTTG

                 *           *            * *                      *         
      12339 CCCTTTGACCGAAAGGGCATTTTTGGAAAGTAGAA-TAAAC-TGAAGTGCGAAAATGATGAAACT
          1 CCCTTCGACCGAAAGGGTATTTTTGGAAAGAAAAACTAAACTTGAA-TGC-AAAAAGATGAAACT

              
      12402 GA
         64 GA

               *                          **    *       *            *   *   
      12404 CCTTTTC-ACCGAAAGGGTATTTTTGGAAATCAAAAGTAAAC-TCAA-GCTCAAGAATGA-CAGA
          1 CC-CTTCGACCGAAAGGGTATTTTTGGAAAGAAAAACTAAACTTGAATG--CAA-AAAGATGA-A

             *   
      12465 ATTGA
         61 ACTGA

                                            * *    *                 **      
      12470 CCCTTCGACCGAAAGGGTATTCTTTGGAAAGAGAGACTAGACTT-AGATGCAATATCCTGATGAA
          1 CCCTTCGACCGAAAGGGTATT-TTTGGAAAGAAAAACTAAACTTGA-ATGCAA-A--AAGATGAA

                 
      12534 ACTGA
         61 ACTGA

                       *                   *         *                       
      12539 CCCTTCGACCGGAAGGGTATTTTTGGAAAGAGAAACTAAACCTGAATGCAAAAAGATGAAACTGA
          1 CCCTTCGACCGAAAGGGTATTTTTGGAAAGAAAAACTAAACTTGAATGCAAAAAGATGAAACTGA

                                                                      *      
      12604 CCCTTCGACCGAAAGGGTATTTTTGGAAATGAAAATACTAAACTTGAATGCAAAAAGACGAAA-T
          1 CCCTTCGACCGAAAGGGTATTTTTGGAAA-GAAAA-ACTAAACTTGAATGCAAAAAGATGAAACT

               
      12668 CGA
         64 -GA

                 *                                  *    *                   
      12671 CCCTTTGACCGAAAGGGTATTTTTGGAAAAGAAAATACTACACTTAAATGCAAAAAGATGAAACT
          1 CCCTTCGACCGAAAGGGTATTTTTGG-AAAGAAAA-ACTAAACTTGAATGCAAAAAGATGAAACT

              
      12736 GA
         64 GA

                            **         *              
      12738 CCC-TCTGACCGAAAGATTATTTTTGGGAAGAGAAAA-TAAA
          1 CCCTTC-GACCGAAAGGGTATTTTTGGAAAGA-AAAACTAAA

      12778 ACATTACTTT


Statistics
Matches: 313,  Mismatches: 39, Indels: 44
        0.79            0.10        0.11

Matches are distributed among these distances:
  64    1  0.00
  65   74  0.24
  66   48  0.15
  67  128  0.41
  68   31  0.10
  69   30  0.10
  70    1  0.00

ACGTcount: A:0.39, C:0.16, G:0.21, T:0.23


Consensus pattern (65 bp):   
CCCTTCGACCGAAAGGGTATTTTTGGAAAGAAAAACTAAACTTGAATGCAAAAAGATGAAACTGA

Done.