Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017288.1 Corchorus olitorius cultivar O-4 contig17321, 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: 11256
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32


Found at i:440 original size:19 final size:18

Alignment explanation


    Indices: 416--451  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

        406 TGAAGACTTA

                               
        416 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
        435 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

        452 ATTATTTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAT

Found at i:3698 original size:21 final size:21

Alignment explanation


    Indices: 3672--3712  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       3662 TTTAAACCCT

                                  
       3672 ATTGGAGAC-AAGTGGTACTAA
          1 ATTGGA-ACTAAGTGGTACTAA

                  *             
       3693 ATTGGATCTAAGTGGTACTA
          1 ATTGGAACTAAGTGGTACTA

       3713 GGGTTTATAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  20    1  0.06
  21   17  0.94

ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29


Consensus pattern (21 bp):   
ATTGGAACTAAGTGGTACTAA

Found at i:5724 original size:26 final size:23

Alignment explanation


    Indices: 5675--5724  Score: 73
    Period size: 26  Copynumber: 2.0  Consensus size: 23

       5665 CTATCCTTCT

                                   
       5675 ATTCATCTATCATCAAGTTTTTC
          1 ATTCATCTATCATCAAGTTTTTC

                                      
       5698 ATTCATCTCATCCATCAAAGTTTTTC
          1 ATTCATCT-AT-CATC-AAGTTTTTC

             
       5724 A
          1 A

       5725 AATTTTCTAG


Statistics
Matches: 24,  Mismatches: 0, Indels: 3
        0.89            0.00        0.11

Matches are distributed among these distances:
  23    8  0.33
  24    2  0.08
  25    4  0.17
  26   10  0.42

ACGTcount: A:0.28, C:0.24, G:0.04, T:0.44


Consensus pattern (23 bp):   
ATTCATCTATCATCAAGTTTTTC
Done.