Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019947.1 Corchorus olitorius cultivar O-4 contig19980, 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: 24044
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30


Found at i:604 original size:3 final size:3

Alignment explanation


    Indices: 589--665  Score: 57
    Period size: 3  Copynumber: 25.7  Consensus size: 3

        579 CTCCTCATGG

                    *                 *   *      **            *        
        589 TCA TCA CCA TCA TCA TCA TCG TCC TCA TTG TCA TC- TCCG TCA TCA
          1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T-CA TCA TCA

                          *   *           *           
        634 TCA TCA TCA TCC TCG TCA TCA TCC TCA TCA TC
          1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC

        666 GCCATCAACT


Statistics
Matches: 57,  Mismatches: 15, Indels: 4
        0.75            0.20        0.05

Matches are distributed among these distances:
   2    1  0.02
   3   55  0.96
   4    1  0.02

ACGTcount: A:0.22, C:0.39, G:0.05, T:0.34


Consensus pattern (3 bp):   
TCA

Found at i:616 original size:30 final size:29

Alignment explanation


    Indices: 580--665  Score: 91
    Period size: 30  Copynumber: 2.9  Consensus size: 29

        570 GAGCTAAATC

                   *                     *
        580 TCCTCATGGTCATCACCATCATCATCATCG
          1 TCCTCATCGTCATCACC-TCATCATCATCA

                   *      *               
        610 TCCTCATTGTCATCTCCGTCATCATCATCA
          1 TCCTCATCGTCATCACC-TCATCATCATCA

              *  *                    
        640 TCATCCTCGTCATCATCCTCATCATC
          1 TCCTCATCGTCATCA-CCTCATCATC

        666 GCCATCAACT


Statistics
Matches: 47,  Mismatches: 8, Indels: 2
        0.82            0.14        0.04

Matches are distributed among these distances:
  30   45  0.96
  31    2  0.04

ACGTcount: A:0.21, C:0.38, G:0.07, T:0.34


Consensus pattern (29 bp):   
TCCTCATCGTCATCACCTCATCATCATCA

Found at i:622 original size:21 final size:20

Alignment explanation


    Indices: 588--665  Score: 79
    Period size: 21  Copynumber: 3.9  Consensus size: 20

        578 TCTCCTCATG

                   *             
        588 GTCATCACCATCATCATCATC
          1 GTCATCATCATCATCATC-TC

               *    **          
        609 GTCCTCATTGTCATC-TC-C
          1 GTCATCATCATCATCATCTC

                                 
        627 GTCATCATCATCATCATCCTC
          1 GTCATCATCATCATCAT-CTC

                     *        
        648 GTCATCATCCTCATCATC
          1 GTCATCATCATCATCATC

        666 GCCATCAACT


Statistics
Matches: 46,  Mismatches: 8, Indels: 7
        0.75            0.13        0.11

Matches are distributed among these distances:
  18   13  0.28
  19    1  0.02
  20    4  0.09
  21   28  0.61

ACGTcount: A:0.22, C:0.38, G:0.06, T:0.33


Consensus pattern (20 bp):   
GTCATCATCATCATCATCTC

Found at i:8818 original size:11 final size:11

Alignment explanation


    Indices: 8802--8826  Score: 50
    Period size: 11  Copynumber: 2.3  Consensus size: 11

       8792 ACCATCCCAC

                       
       8802 AGAGGCTGTTT
          1 AGAGGCTGTTT

                       
       8813 AGAGGCTGTTT
          1 AGAGGCTGTTT

               
       8824 AGA
          1 AGA

       8827 AGCTTGAACC


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

Matches are distributed among these distances:
  11   14  1.00

ACGTcount: A:0.24, C:0.08, G:0.36, T:0.32


Consensus pattern (11 bp):   
AGAGGCTGTTT

Found at i:10033 original size:12 final size:12

Alignment explanation


    Indices: 10012--10068  Score: 69
    Period size: 12  Copynumber: 4.5  Consensus size: 12

      10002 AAAATGGGAG

                        
      10012 TTTAAAACGGAA
          1 TTTAAAACGGAA

               *         
      10024 TTTCAAACGGAAA
          1 TTTAAAACGG-AA

                          
      10037 GTTTAAAAACGGAA
          1 -TTT-AAAACGGAA

                        
      10051 TTTAAAACGGAA
          1 TTTAAAACGGAA

             *    
      10063 TATAAA
          1 TTTAAA

      10069 TATCCATCTC


Statistics
Matches: 39,  Mismatches: 3, Indels: 6
        0.81            0.06        0.12

Matches are distributed among these distances:
  12   23  0.59
  13    5  0.13
  14    5  0.13
  15    6  0.15

ACGTcount: A:0.51, C:0.09, G:0.16, T:0.25


Consensus pattern (12 bp):   
TTTAAAACGGAA

Found at i:10050 original size:27 final size:26

Alignment explanation


    Indices: 10010--10062  Score: 88
    Period size: 27  Copynumber: 2.0  Consensus size: 26

      10000 GGAAAATGGG

                             *        
      10010 AGTTTAAAACGGAATTTCAAACGGAA
          1 AGTTTAAAACGGAATTTAAAACGGAA

                                       
      10036 AGTTTAAAAACGGAATTTAAAACGGAA
          1 AGTTT-AAAACGGAATTTAAAACGGAA

      10063 TATAAATATC


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  26    5  0.20
  27   20  0.80

ACGTcount: A:0.49, C:0.09, G:0.19, T:0.23


Consensus pattern (26 bp):   
AGTTTAAAACGGAATTTAAAACGGAA

Found at i:19615 original size:6 final size:6

Alignment explanation


    Indices: 19604--19635  Score: 64
    Period size: 6  Copynumber: 5.3  Consensus size: 6

      19594 GTTACGTGCT

                                                 
      19604 GAAAGA GAAAGA GAAAGA GAAAGA GAAAGA GA
          1 GAAAGA GAAAGA GAAAGA GAAAGA GAAAGA GA

      19636 TGATTTTTTT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   26  1.00

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


Consensus pattern (6 bp):   
GAAAGA

Done.