Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009863.1 Corchorus olitorius cultivar O-4 contig09895, 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: 2357
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


Found at i:135 original size:20 final size:21

Alignment explanation


    Indices: 110--155  Score: 67
    Period size: 21  Copynumber: 2.2  Consensus size: 21

        100 GTGATAGTTA

                     *          *
        110 TTTCTAT-TTAAAATATGAAG
          1 TTTCTATGTAAAAATATGAAC

                                 
        130 TTTCTATGTAAAAATATGAAC
          1 TTTCTATGTAAAAATATGAAC

                 
        151 TTTCT
          1 TTTCT

        156 CATAACTAAC


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  20    7  0.30
  21   16  0.70

ACGTcount: A:0.37, C:0.09, G:0.09, T:0.46


Consensus pattern (21 bp):   
TTTCTATGTAAAAATATGAAC

Found at i:743 original size:13 final size:13

Alignment explanation


    Indices: 727--751  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

        717 AAAAATTTTA

                         
        727 AAAAAAAAAAGAT
          1 AAAAAAAAAAGAT

                        
        740 AAAAAAAAAAGA
          1 AAAAAAAAAAGA

        752 CGAAGGAAGA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.88, C:0.00, G:0.08, T:0.04


Consensus pattern (13 bp):   
AAAAAAAAAAGAT

Found at i:910 original size:16 final size:16

Alignment explanation


    Indices: 891--922  Score: 55
    Period size: 16  Copynumber: 2.0  Consensus size: 16

        881 TATGACAGGT

                            
        891 TCCGTTTACTTCGTGG
          1 TCCGTTTACTTCGTGG

                    *       
        907 TCCGTTTATTTCGTGG
          1 TCCGTTTACTTCGTGG

        923 AAAATAGTGG


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.06, C:0.22, G:0.25, T:0.47


Consensus pattern (16 bp):   
TCCGTTTACTTCGTGG

Found at i:1076 original size:27 final size:30

Alignment explanation


    Indices: 1038--1092  Score: 89
    Period size: 27  Copynumber: 1.9  Consensus size: 30

       1028 CTCAAGTGCG

                                          
       1038 AAAATGGTGGG-AA-TG-ACATTCCCATCT
          1 AAAATGGTGGGAAAGTGAACATTCCCATCT

                                        
       1065 AAAATGGTGGGAAAGTGAACATTCCCAT
          1 AAAATGGTGGGAAAGTGAACATTCCCAT

       1093 GAAAGTGTTG


Statistics
Matches: 25,  Mismatches: 0, Indels: 3
        0.89            0.00        0.11

Matches are distributed among these distances:
  27   11  0.44
  28    2  0.08
  29    2  0.08
  30   10  0.40

ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24


Consensus pattern (30 bp):   
AAAATGGTGGGAAAGTGAACATTCCCATCT

Found at i:1802 original size:23 final size:23

Alignment explanation


    Indices: 1766--1816  Score: 72
    Period size: 23  Copynumber: 2.3  Consensus size: 23

       1756 TTTACTATCT

                                    
       1766 TAGAT-ATAACATATATTATTAAA
          1 TAGATAATAACATATATT-TTAAA

                                   
       1789 TAGATAATAA-ATATATTTTAAA
          1 TAGATAATAACATATATTTTAAA

                   
       1811 TA-ATAA
          1 TAGATAA

       1817 ATAATGAGTT


Statistics
Matches: 27,  Mismatches: 0, Indels: 4
        0.87            0.00        0.13

Matches are distributed among these distances:
  21    4  0.15
  22    7  0.26
  23   12  0.44
  24    4  0.15

ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39


Consensus pattern (23 bp):   
TAGATAATAACATATATTTTAAA
Done.