Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008843.1 Corchorus capsularis cultivar CVL-1 contig08864, 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: 22388
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:1286 original size:2 final size:2

Alignment explanation


    Indices: 1279--1317  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

       1269 TAGGACCTGC

                                                                      
       1279 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       1318 CTTCAACATG


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:4793 original size:3 final size:3

Alignment explanation


    Indices: 4785--4826  Score: 84
    Period size: 3  Copynumber: 14.0  Consensus size: 3

       4775 ATTGCATGAC

                                                                   
       4785 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT

       4827 TACAAGTTAA


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   39  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
ATT

Found at i:21394 original size:33 final size:33

Alignment explanation


    Indices: 21357--21459  Score: 115
    Period size: 33  Copynumber: 3.1  Consensus size: 33

      21347 ACCTCCAGTG

                                             
      21357 AAAATAAGCTACTTTTAGCTTGTCACGTAGGAC
          1 AAAATAAGCTACTTTTAGCTTGTCACGTAGGAC

                                       *         
      21390 AAAATAAGCTACTTTTAGC-T-TCAACCTCCAGTG--
          1 AAAATAAGCTACTTTTAGCTTGTC-ACGT--AG-GAC

                                   *          
      21423 AAAATAAGCTACTTTTAGCTTTGCCACGTAGGAC
          1 AAAATAAGCTACTTTTAGC-TTGTCACGTAGGAC

               
      21457 AAA
          1 AAA

      21460 TGGCACCTCA


Statistics
Matches: 58,  Mismatches: 3, Indels: 17
        0.74            0.04        0.22

Matches are distributed among these distances:
  31    2  0.03
  32    5  0.09
  33   40  0.69
  34    5  0.09
  35    5  0.09
  36    1  0.02

ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29


Consensus pattern (33 bp):   
AAAATAAGCTACTTTTAGCTTGTCACGTAGGAC

Found at i:21544 original size:13 final size:13

Alignment explanation


    Indices: 21526--21552  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

      21516 GCACTAAAAA

                         
      21526 GGTGCTTTTCATT
          1 GGTGCTTTTCATT

                         
      21539 GGTGCTTTTCATT
          1 GGTGCTTTTCATT

             
      21552 G
          1 G

      21553 CACCGCTATA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.07, C:0.15, G:0.26, T:0.52


Consensus pattern (13 bp):   
GGTGCTTTTCATT
Done.