Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016837.1 Corchorus olitorius cultivar O-4 contig16870, 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: 12595
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32


Found at i:2087 original size:14 final size:15

Alignment explanation


    Indices: 2068--2097  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       2058 CAATTAAAGC

                           
       2068 AATAAT-CAAGGAAA
          1 AATAATGCAAGGAAA

                           
       2082 AATAATGCAAGGAAA
          1 AATAATGCAAGGAAA

             
       2097 A
          1 A

       2098 TTAAAGAGAT


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

Matches are distributed among these distances:
  14    6  0.40
  15    9  0.60

ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13


Consensus pattern (15 bp):   
AATAATGCAAGGAAA

Found at i:2506 original size:21 final size:21

Alignment explanation


    Indices: 2452--2506  Score: 74
    Period size: 21  Copynumber: 2.6  Consensus size: 21

       2442 GGCAGTGAAT

                *       *     *  
       2452 GGTGATGGCACGAGCATAGCC
          1 GGTGGTGGCACGGGCATAACC

                           *     
       2473 GGTGGTGGCACGGGCTTAACC
          1 GGTGGTGGCACGGGCATAACC

                         
       2494 GGTGGTGGCACGG
          1 GGTGGTGGCACGG

       2507 TGAATGGGCG


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   30  1.00

ACGTcount: A:0.16, C:0.22, G:0.45, T:0.16


Consensus pattern (21 bp):   
GGTGGTGGCACGGGCATAACC

Found at i:6853 original size:13 final size:13

Alignment explanation


    Indices: 6835--6860  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       6825 TGAATTTAGC

                         
       6835 TACCCATGGATTT
          1 TACCCATGGATTT

                         
       6848 TACCCATGGATTT
          1 TACCCATGGATTT

       6861 GGGAAAATCC


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

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38


Consensus pattern (13 bp):   
TACCCATGGATTT

Found at i:9470 original size:21 final size:21

Alignment explanation


    Indices: 9454--9500  Score: 76
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       9444 ATGGTGATGT

                      *          
       9454 CACGGGCATAGCCGGTGGTGG
          1 CACGGGCATAACCGGTGGTGG

                   *             
       9475 CACGGGCTTAACCGGTGGTGG
          1 CACGGGCATAACCGGTGGTGG

                 
       9496 CACGG
          1 CACGG

       9501 TGAATGGGCG


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  21   24  1.00

ACGTcount: A:0.15, C:0.26, G:0.45, T:0.15


Consensus pattern (21 bp):   
CACGGGCATAACCGGTGGTGG
Done.