Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013993.1 Corchorus capsularis cultivar CVL-1 contig14014, 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: 26811
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32


Found at i:8959 original size:17 final size:16

Alignment explanation


    Indices: 8919--8960  Score: 66
    Period size: 16  Copynumber: 2.6  Consensus size: 16

       8909 CAGAAATCGG

                            
       8919 AAAGAAAGAATAACAC
          1 AAAGAAAGAATAACAC

               *             
       8935 AAAAAAAGAATAACAGC
          1 AAAGAAAGAATAACA-C

                     
       8952 AAAGAAAGA
          1 AAAGAAAGA

       8961 GTAAGTTGGA


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  16   14  0.61
  17    9  0.39

ACGTcount: A:0.71, C:0.10, G:0.14, T:0.05


Consensus pattern (16 bp):   
AAAGAAAGAATAACAC

Found at i:25758 original size:94 final size:94

Alignment explanation


    Indices: 25577--25816  Score: 390
    Period size: 94  Copynumber: 2.5  Consensus size: 94

      25567 TACTTTGTAC

                      *                  *                                   
      25577 TATTGACATAATTGGAGACAATTTTTGCATAGATTCCTTCATAATTCGGATAACTTTGCAGACCA
          1 TATTGACATAGTTGGAGACAATTTTTGCAGAGATT-CTTC---A-T--GATAACTTTGCAGACCA

                            *                   
      25642 TTTGCTTTATCTTCATTCAATGAGTCAGCCTTGCAT
         59 TTTGCTTTATCTTCATCCAATGAGTCAGCCTTGCAT

                                                                             
      25678 TATTGACATAGTTGGAGACAATTTTTGCAGAGATTCTTCATGATAACTTTGCAGACCATTTGCTT
          1 TATTGACATAGTTGGAGACAATTTTTGCAGAGATTCTTCATGATAACTTTGCAGACCATTTGCTT

                                         
      25743 TATCTTCATCCAATGAGTCAGCCTTGCAT
         66 TATCTTCATCCAATGAGTCAGCCTTGCAT

                                                         
      25772 TATTGACATAGTTGGAGACAATTTTTGCAGAGATTCTTCATGATA
          1 TATTGACATAGTTGGAGACAATTTTTGCAGAGATTCTTCATGATA

      25817 GGGTTAACTT


Statistics
Matches: 136,  Mismatches: 3, Indels: 7
        0.93            0.02        0.05

Matches are distributed among these distances:
  94   97  0.71
  96    1  0.01
  97    1  0.01
 100    4  0.03
 101   33  0.24

ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38


Consensus pattern (94 bp):   
TATTGACATAGTTGGAGACAATTTTTGCAGAGATTCTTCATGATAACTTTGCAGACCATTTGCTT
TATCTTCATCCAATGAGTCAGCCTTGCAT

Found at i:25845 original size:94 final size:93

Alignment explanation


    Indices: 25577--25849  Score: 315
    Period size: 94  Copynumber: 2.8  Consensus size: 93

      25567 TACTTTGTAC

                      *                  *            *   *                  
      25577 TATTGACATAATTGGAGACAATTTTTGCATAGATTCCTTCATAATTCGGATAACTTTGCAGACCA
          1 TATTGACATAGTTGGAGACAATTTTTGCAGAGATT-CTTCATGA-TAGG-TAACTTTGCAGACCA

                            *                   
      25642 TTTGCTTTATCTTCATTCAATGAGTCAGCCTTGCAT
         63 -----TTTATCTTCATCCAATGAGTCAGCCTTGCAT

                                                                             
      25678 TATTGACATAGTTGGAGACAATTTTTGCAGAGATTCTTCATG--A--TAACTTTGCAGACCATTT
          1 TATTGACATAGTTGGAGACAATTTTTGCAGAGATTCTTCATGATAGGTAACTTTGCAGACCA---

                                             
      25739 GCTTTATCTTCATCCAATGAGTCAGCCTTGCAT
         63 --TTTATCTTCATCCAATGAGTCAGCCTTGCAT

                                                                             
      25772 TATTGACATAGTTGGAGACAATTTTTGCAGAGATTCTTCATGATAGGGTTAACTTTTGCAGACCA
          1 TATTGACATAGTTGGAGACAATTTTTGCAGAGATTCTTCATGATA-GG-TAAC-TTTGCAGACCA

                           
      25837 -TTAT-TTCATCCAA
         63 TTTATCTTCATCCAA

      25850 CTTTTTCCCT


Statistics
Matches: 160,  Mismatches: 5, Indels: 21
        0.86            0.03        0.11

Matches are distributed among these distances:
  94  101  0.63
  95    4  0.03
  96    1  0.01
 100   10  0.06
 101   44  0.28

ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38


Consensus pattern (93 bp):   
TATTGACATAGTTGGAGACAATTTTTGCAGAGATTCTTCATGATAGGTAACTTTGCAGACCATTT
ATCTTCATCCAATGAGTCAGCCTTGCAT
Done.