Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012816.1 Corchorus capsularis cultivar CVL-1 contig12837, 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: 34561
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33


Found at i:23137 original size:3 final size:3

Alignment explanation


    Indices: 23129--23175  Score: 94
    Period size: 3  Copynumber: 15.7  Consensus size: 3

      23119 CTCATTAGCA

                                                                          
      23129 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
          1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC

      23176 ACTCATCTTA


Statistics
Matches: 44,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   44  1.00

ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66


Consensus pattern (3 bp):   
TCT

Found at i:31613 original size:9 final size:9

Alignment explanation


    Indices: 31591--31619  Score: 51
    Period size: 9  Copynumber: 3.3  Consensus size: 9

      31581 CACCCAAAAC

                     
      31591 AAAAGAAA-
          1 AAAAGAAAG

                     
      31599 AAAAGAAAG
          1 AAAAGAAAG

                     
      31608 AAAAGAAAG
          1 AAAAGAAAG

               
      31617 AAA
          1 AAA

      31620 CAACTTGAAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
   8    8  0.40
   9   12  0.60

ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00


Consensus pattern (9 bp):   
AAAAGAAAG

Found at i:33857 original size:12 final size:12

Alignment explanation


    Indices: 33840--33864  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

      33830 ACTAGTCATC

                        
      33840 CATAGGATGATA
          1 CATAGGATGATA

                        
      33852 CATAGGATGATA
          1 CATAGGATGATA

             
      33864 C
          1 C

      33865 TTAGTTGGAA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24


Consensus pattern (12 bp):   
CATAGGATGATA

Found at i:34117 original size:32 final size:33

Alignment explanation


    Indices: 34076--34150  Score: 98
    Period size: 32  Copynumber: 2.3  Consensus size: 33

      34066 AAATTGGTCT

                                      *      
      34076 AGCCGCCCCACCGGGGCGCCCTG-CCGTGGCGA
          1 AGCCGCCCCACCGGGGCGCCCTGCCCATGGCGA

                      **      *           *  
      34108 AGCCGCCCCAGTGGGGCGGCCTGCCCATGGTGA
          1 AGCCGCCCCACCGGGGCGCCCTGCCCATGGCGA

                      
      34141 AGCCGCCCCA
          1 AGCCGCCCCA

      34151 TTGGGGAGGC


Statistics
Matches: 37,  Mismatches: 5, Indels: 1
        0.86            0.12        0.02

Matches are distributed among these distances:
  32   20  0.54
  33   17  0.46

ACGTcount: A:0.12, C:0.44, G:0.36, T:0.08


Consensus pattern (33 bp):   
AGCCGCCCCACCGGGGCGCCCTGCCCATGGCGA

Found at i:34148 original size:33 final size:32

Alignment explanation


    Indices: 34076--34156  Score: 99
    Period size: 33  Copynumber: 2.5  Consensus size: 32

      34066 AAATTGGTCT

                       *             *      
      34076 AGCCGCCCCACCGGGGCGCCCTGCCGTGGCGA
          1 AGCCGCCCCACTGGGGCGCCCTGCCATGGCGA

                      *       *           *  
      34108 AGCCGCCCCAGTGGGGCGGCCTGCCCATGGTGA
          1 AGCCGCCCCACTGGGGCGCCCTG-CCATGGCGA

                      *     
      34141 AGCCGCCCCATTGGGG
          1 AGCCGCCCCACTGGGG

      34157 AGGCTCCGCC


Statistics
Matches: 42,  Mismatches: 6, Indels: 1
        0.86            0.12        0.02

Matches are distributed among these distances:
  32   20  0.48
  33   22  0.52

ACGTcount: A:0.11, C:0.41, G:0.38, T:0.10


Consensus pattern (32 bp):   
AGCCGCCCCACTGGGGCGCCCTGCCATGGCGA

Found at i:34178 original size:33 final size:33

Alignment explanation


    Indices: 34076--34178  Score: 88
    Period size: 33  Copynumber: 3.2  Consensus size: 33

      34066 AAATTGGTCT

                      **     *                
      34076 AGCCGCCCCACCGGGG-CGCCCTGCCGTGGC-GA
          1 AGCCGCCCCAGTGGGGAGGCCC-GCCGTGGCTGA

                            *    *    *       
      34108 AGCCGCCCCAGTGGGGCGGCCTGCCCATGG-TGA
          1 AGCCGCCCCAGTGGGGAGGCCCG-CCGTGGCTGA

                      *                       
      34141 AGCCGCCCCATTGGGGAGGCTCCGCCGTGGCTG-
          1 AGCCGCCCCAGTGGGGAGGC-CCGCCGTGGCTGA

                 
      34174 AGCCG
          1 AGCCG

      34179 TCATAGTGGG


Statistics
Matches: 57,  Mismatches: 9, Indels: 9
        0.76            0.12        0.12

Matches are distributed among these distances:
  32   15  0.26
  33   38  0.67
  34    4  0.07

ACGTcount: A:0.11, C:0.40, G:0.39, T:0.11


Consensus pattern (33 bp):   
AGCCGCCCCAGTGGGGAGGCCCGCCGTGGCTGA

Found at i:34415 original size:18 final size:19

Alignment explanation


    Indices: 34392--34433  Score: 59
    Period size: 18  Copynumber: 2.3  Consensus size: 19

      34382 GTCTTTATTA

                               
      34392 TTTTTTATTTTTAC-TTTC
          1 TTTTTTATTTTTACTTTTC

                  *     *      
      34410 TTTTTTCTTTTTTCTTTTC
          1 TTTTTTATTTTTACTTTTC

                 
      34429 TTTTT
          1 TTTTT

      34434 CTTCTCTCTC


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  18   12  0.57
  19    9  0.43

ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83


Consensus pattern (19 bp):   
TTTTTTATTTTTACTTTTC

Done.