Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018669.1 Corchorus olitorius cultivar O-4 contig18702, 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: 38419
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:16912 original size:17 final size:17

Alignment explanation


    Indices: 16892--16942  Score: 52
    Period size: 17  Copynumber: 3.1  Consensus size: 17

      16882 CTGCCTATTA

                             
      16892 ATTGCTTCTTCAATCTG
          1 ATTGCTTCTTCAATCTG

                *    *    * *
      16909 ATTGATTCTGC--TTTA
          1 ATTGCTTCTTCAATCTG

                             
      16924 ATTGCTTCTTCAATCTG
          1 ATTGCTTCTTCAATCTG

              
      16941 AT
          1 AT

      16943 CTCTCTGAAA


Statistics
Matches: 24,  Mismatches: 8, Indels: 4
        0.67            0.22        0.11

Matches are distributed among these distances:
  15   11  0.46
  17   13  0.54

ACGTcount: A:0.20, C:0.20, G:0.12, T:0.49


Consensus pattern (17 bp):   
ATTGCTTCTTCAATCTG

Found at i:23456 original size:21 final size:22

Alignment explanation


    Indices: 23431--23472  Score: 68
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      23421 GAGTATTAAG

                     *            
      23431 TTTTTG-ATTAGTTTTTGTTTT
          1 TTTTTGCATCAGTTTTTGTTTT

                                 
      23452 TTTTTGCATCAGTTTTTGTTT
          1 TTTTTGCATCAGTTTTTGTTT

      23473 GTTTAGAAAG


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  21    6  0.32
  22   13  0.68

ACGTcount: A:0.10, C:0.05, G:0.14, T:0.71


Consensus pattern (22 bp):   
TTTTTGCATCAGTTTTTGTTTT

Found at i:27716 original size:17 final size:17

Alignment explanation


    Indices: 27694--27730  Score: 74
    Period size: 17  Copynumber: 2.2  Consensus size: 17

      27684 TCCCTCTCTC

                             
      27694 TCCATAATCTCTTCCCA
          1 TCCATAATCTCTTCCCA

                             
      27711 TCCATAATCTCTTCCCA
          1 TCCATAATCTCTTCCCA

               
      27728 TCC
          1 TCC

      27731 CCTCTCTTTT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   20  1.00

ACGTcount: A:0.22, C:0.43, G:0.00, T:0.35


Consensus pattern (17 bp):   
TCCATAATCTCTTCCCA

Found at i:28629 original size:41 final size:41

Alignment explanation


    Indices: 28580--28685  Score: 142
    Period size: 41  Copynumber: 2.6  Consensus size: 41

      28570 TCCCTTATTA

                         *          *   *           * 
      28580 ATTCAATTTTGTCACTGATTTAGGTTAATATTTATTAAT-TG
          1 ATTCAATTTTGTCCCTGATTTAGGGTAACATTTATT-ATCAG

                                                     
      28621 ATTCAATTTTGTCCCTGATTTAGGGTAACATTTATTATCAG
          1 ATTCAATTTTGTCCCTGATTTAGGGTAACATTTATTATCAG

              *       *             
      28662 ATGCAATTTTATCCCTGATTTAGG
          1 ATTCAATTTTGTCCCTGATTTAGG

      28686 ATTTTACTTG


Statistics
Matches: 58,  Mismatches: 6, Indels: 2
        0.88            0.09        0.03

Matches are distributed among these distances:
  40    2  0.03
  41   56  0.97

ACGTcount: A:0.27, C:0.12, G:0.14, T:0.46


Consensus pattern (41 bp):   
ATTCAATTTTGTCCCTGATTTAGGGTAACATTTATTATCAG

Found at i:38020 original size:18 final size:18

Alignment explanation


    Indices: 37997--38042  Score: 56
    Period size: 18  Copynumber: 2.6  Consensus size: 18

      37987 TGAAATTAAT

                              
      37997 TAATTATTAATTAAATAA
          1 TAATTATTAATTAAATAA

                    **  *     
      38015 TAATTATTTTTTGAATAA
          1 TAATTATTAATTAAATAA

             *        
      38033 TTATTATTAA
          1 TAATTATTAA

      38043 ATTTCTAGTG


Statistics
Matches: 22,  Mismatches: 6, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  18   22  1.00

ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52


Consensus pattern (18 bp):   
TAATTATTAATTAAATAA
Done.