Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006924.1 Corchorus capsularis cultivar CVL-1 contig06945, 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: 24701
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32


Found at i:21 original size:11 final size:11

Alignment explanation


    Indices: 4--33  Score: 51
    Period size: 11  Copynumber: 2.7  Consensus size: 11

          1 AAA

                       
          4 ATATATATTAT
          1 ATATATATTAT

            *          
         15 GTATATATTAT
          1 ATATATATTAT

                    
         26 ATATATAT
          1 ATATATAT

         34 ATTAATATAT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  11   17  1.00

ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53


Consensus pattern (11 bp):   
ATATATATTAT

Found at i:6053 original size:7 final size:7

Alignment explanation


    Indices: 6037--6070  Score: 54
    Period size: 7  Copynumber: 5.1  Consensus size: 7

       6027 GTTGACATAC

                   
       6037 TTTC-TT
          1 TTTCTTT

                   
       6043 TTTCTTT
          1 TTTCTTT

                   
       6050 TTTCTTT
          1 TTTCTTT

                   
       6057 TTTCTTT
          1 TTTCTTT

                   
       6064 TTT-TTT
          1 TTTCTTT

             
       6070 T
          1 T

       6071 ACCTTCAAAA


Statistics
Matches: 27,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   6    8  0.30
   7   19  0.70

ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88


Consensus pattern (7 bp):   
TTTCTTT

Found at i:8184 original size:31 final size:31

Alignment explanation


    Indices: 8137--8216  Score: 117
    Period size: 31  Copynumber: 2.6  Consensus size: 31

       8127 ATTTTTAGCC

                 *                         
       8137 ACCAAATTGAGTCTAAAACTTTCAAAAGTTG
          1 ACCAATTTGAGTCTAAAACTTTCAAAAGTTG

                        *     *             
       8168 -CTCAATTTGAGGCTAAATCTTTCAAAAGTTG
          1 AC-CAATTTGAGTCTAAAACTTTCAAAAGTTG

                              
       8199 ACCAATTTGAGTCTAAAA
          1 ACCAATTTGAGTCTAAAA

       8217 ACAGAAACGA


Statistics
Matches: 42,  Mismatches: 5, Indels: 4
        0.82            0.10        0.08

Matches are distributed among these distances:
  30    1  0.02
  31   40  0.95
  32    1  0.02

ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31


Consensus pattern (31 bp):   
ACCAATTTGAGTCTAAAACTTTCAAAAGTTG

Found at i:12831 original size:27 final size:28

Alignment explanation


    Indices: 12796--12863  Score: 88
    Period size: 27  Copynumber: 2.5  Consensus size: 28

      12786 ATCCTAGGGA

                                         
      12796 ACTAACTTTGAATGGGA-AACTGT-TGTG
          1 ACTAACTTTGAATGGGAGAACTGTGT-TG

                *                       
      12823 ACTAGCTTTGAAT-GGAGAACTGTGTTG
          1 ACTAACTTTGAATGGGAGAACTGTGTTG

                    *     
      12850 ACTAACTTGGAATG
          1 ACTAACTTTGAATG

      12864 AGAGTCTGAC


Statistics
Matches: 35,  Mismatches: 3, Indels: 5
        0.81            0.07        0.12

Matches are distributed among these distances:
  26    3  0.09
  27   31  0.89
  28    1  0.03

ACGTcount: A:0.29, C:0.12, G:0.26, T:0.32


Consensus pattern (28 bp):   
ACTAACTTTGAATGGGAGAACTGTGTTG
Done.