Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010156.1 Corchorus capsularis cultivar CVL-1 contig10177, 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: 29856
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33


Found at i:176 original size:27 final size:24

Alignment explanation


    Indices: 145--205  Score: 68
    Period size: 25  Copynumber: 2.4  Consensus size: 24

        135 CGTAGCAAGG

                                       
        145 GAGTCTCCCATAGCGCGCGCAACACGT
          1 GAGTCTCCC-TA--GCGCGCAACACGT

            *                     *  
        172 TAGTCTCTCCTAGCGCGCAACAGGT
          1 GAGTCTC-CCTAGCGCGCAACACGT

                     
        197 GAGTCTCCC
          1 GAGTCTCCC

        206 CTGAGACGCA


Statistics
Matches: 30,  Mismatches: 3, Indels: 5
        0.79            0.08        0.13

Matches are distributed among these distances:
  24    2  0.07
  25   18  0.60
  27    8  0.27
  28    2  0.07

ACGTcount: A:0.20, C:0.36, G:0.25, T:0.20


Consensus pattern (24 bp):   
GAGTCTCCCTAGCGCGCAACACGT

Found at i:3234 original size:16 final size:16

Alignment explanation


    Indices: 3212--3304  Score: 89
    Period size: 16  Copynumber: 5.7  Consensus size: 16

       3202 TGACCTCACT

                           *
       3212 AGGTGAGTATTGTACT
          1 AGGTGAGTATTGTACC

            *            *   
       3228 GGGTGAGTATCT-CACC
          1 AGGTGAGTAT-TGTACC

                        *   
       3244 AGGTGAGTATTGCACC
          1 AGGTGAGTATTGTACC

                     *      *
       3260 AGGTGAGTGTTTGTACG
          1 AGGTGAGT-ATTGTACC

                     *       
       3277 AGGTGAGTGTTTGTACC
          1 AGGTGAGT-ATTGTACC

                       
       3294 AGGTGAGTATT
          1 AGGTGAGTATT

       3305 TGTATTGGGT


Statistics
Matches: 65,  Mismatches: 9, Indels: 6
        0.81            0.11        0.08

Matches are distributed among these distances:
  15    1  0.02
  16   34  0.52
  17   30  0.46

ACGTcount: A:0.22, C:0.12, G:0.34, T:0.32


Consensus pattern (16 bp):   
AGGTGAGTATTGTACC

Found at i:3282 original size:17 final size:17

Alignment explanation


    Indices: 3241--3308  Score: 93
    Period size: 17  Copynumber: 4.1  Consensus size: 17

       3231 TGAGTATCTC

                        *   *
       3241 ACCAGGTGAGT-ATTGC
          1 ACCAGGTGAGTGTTTGT

                             
       3257 ACCAGGTGAGTGTTTGT
          1 ACCAGGTGAGTGTTTGT

              *              
       3274 ACGAGGTGAGTGTTTGT
          1 ACCAGGTGAGTGTTTGT

                       *     
       3291 ACCAGGTGAGTATTTGT
          1 ACCAGGTGAGTGTTTGT

             
       3308 A
          1 A

       3309 TTGGGTGAGT


Statistics
Matches: 46,  Mismatches: 5, Indels: 1
        0.88            0.10        0.02

Matches are distributed among these distances:
  16   11  0.24
  17   35  0.76

ACGTcount: A:0.22, C:0.12, G:0.34, T:0.32


Consensus pattern (17 bp):   
ACCAGGTGAGTGTTTGT

Done.