Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020374.1 Corchorus olitorius cultivar O-4 contig20407, 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: 23458
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:4956 original size:38 final size:38

Alignment explanation


    Indices: 4886--4960  Score: 116
    Period size: 38  Copynumber: 2.0  Consensus size: 38

       4876 GATCTAAATT

                                     * *          
       4886 CTATTAGCATCATCCTAAAAATGGGTGTTTTTAGGATA
          1 CTATTAGCATCATCCTAAAAATGGGCGATTTTAGGATA

                                                  
       4924 CTATTAGCATCATCCTAAAAA-GGGACGATTTTAGGAT
          1 CTATTAGCATCATCCTAAAAATGGG-CGATTTTAGGAT

       4961 TCCTGGTGCC


Statistics
Matches: 34,  Mismatches: 2, Indels: 2
        0.89            0.05        0.05

Matches are distributed among these distances:
  37    3  0.09
  38   31  0.91

ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33


Consensus pattern (38 bp):   
CTATTAGCATCATCCTAAAAATGGGCGATTTTAGGATA

Found at i:13841 original size:17 final size:17

Alignment explanation


    Indices: 13819--13860  Score: 84
    Period size: 17  Copynumber: 2.5  Consensus size: 17

      13809 ACTTTACCTT

                             
      13819 CTTATTCTAATTTTACC
          1 CTTATTCTAATTTTACC

                             
      13836 CTTATTCTAATTTTACC
          1 CTTATTCTAATTTTACC

                    
      13853 CTTATTCT
          1 CTTATTCT

      13861 CTTTCTCCCA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   25  1.00

ACGTcount: A:0.21, C:0.24, G:0.00, T:0.55


Consensus pattern (17 bp):   
CTTATTCTAATTTTACC

Found at i:20243 original size:35 final size:35

Alignment explanation


    Indices: 20197--20267  Score: 99
    Period size: 35  Copynumber: 2.0  Consensus size: 35

      20187 TTATTGTAAT

                                                
      20197 AAAATTATAATAAAATTCACTTATAGC-AGTAAAAA
          1 AAAATTATAATAAAATTCACTTATA-CAAGTAAAAA

                  *      *        *            
      20232 AAAATTGTAATAAGATTCACTTGTACAAGTAAAAA
          1 AAAATTATAATAAAATTCACTTATACAAGTAAAAA

             
      20267 A
          1 A

      20268 TGAAAGAAAG


Statistics
Matches: 32,  Mismatches: 3, Indels: 2
        0.86            0.08        0.05

Matches are distributed among these distances:
  34    1  0.03
  35   31  0.97

ACGTcount: A:0.55, C:0.08, G:0.08, T:0.28


Consensus pattern (35 bp):   
AAAATTATAATAAAATTCACTTATACAAGTAAAAA

Found at i:21481 original size:21 final size:19

Alignment explanation


    Indices: 21424--21481  Score: 62
    Period size: 21  Copynumber: 2.9  Consensus size: 19

      21414 CTGTTTAGCA

                    *          
      21424 ACTGTACAAATGAGATTAC
          1 ACTGTACAGATGAGATTAC

               *       * *       
      21443 ACTATACAGATTAAATTAGGC
          1 ACTGTACAGATGAGATTA--C

                              
      21464 ACTGTACAGATGAGATTA
          1 ACTGTACAGATGAGATTA

      21482 TTAGAGCAGC


Statistics
Matches: 30,  Mismatches: 7, Indels: 2
        0.77            0.18        0.05

Matches are distributed among these distances:
  19   14  0.47
  21   16  0.53

ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28


Consensus pattern (19 bp):   
ACTGTACAGATGAGATTAC

Found at i:23063 original size:31 final size:32

Alignment explanation


    Indices: 23022--23084  Score: 101
    Period size: 31  Copynumber: 2.0  Consensus size: 32

      23012 GCTCCCTTTT

                           *                
      23022 CCTTTATGCAAGTAGGTTGGCACAAAAGTTTC
          1 CCTTTATGCAAGTAGATTGGCACAAAAGTTTC

                                  *         
      23054 CCTTT-TGCAAGTAGATTGGCATAAAAGTTTC
          1 CCTTTATGCAAGTAGATTGGCACAAAAGTTTC

      23085 ATTTTGACAT


Statistics
Matches: 29,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  31   24  0.83
  32    5  0.17

ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33


Consensus pattern (32 bp):   
CCTTTATGCAAGTAGATTGGCACAAAAGTTTC
Done.