Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013517.1 Corchorus capsularis cultivar CVL-1 contig13538, 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: 23855
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31


Found at i:4969 original size:15 final size:16

Alignment explanation


    Indices: 4943--4973  Score: 55
    Period size: 15  Copynumber: 2.0  Consensus size: 16

       4933 TAAAAATTAG

                            
       4943 ATATATTTTTATTTTA
          1 ATATATTTTTATTTTA

                            
       4959 ATATA-TTTTATTTTA
          1 ATATATTTTTATTTTA

       4974 TTGAAATATA


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

Matches are distributed among these distances:
  15   10  0.67
  16    5  0.33

ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68


Consensus pattern (16 bp):   
ATATATTTTTATTTTA

Found at i:5958 original size:15 final size:15

Alignment explanation


    Indices: 5926--5955  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       5916 TAAATTGCAA

                           
       5926 TAAAATAAAATATAT
          1 TAAAATAAAATATAT

                           
       5941 TAAAATAAAA-ATAT
          1 TAAAATAAAATATAT

             
       5955 T
          1 T

       5956 TAATTTTCAT


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

Matches are distributed among these distances:
  14    5  0.33
  15   10  0.67

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (15 bp):   
TAAAATAAAATATAT

Found at i:6617 original size:16 final size:17

Alignment explanation


    Indices: 6580--6618  Score: 55
    Period size: 17  Copynumber: 2.4  Consensus size: 17

       6570 TAATCCCAAA

                             
       6580 TTAAAAGAAAGTTTTAT
          1 TTAAAAGAAAGTTTTAT

                              
       6597 TTAAAA-AATAGTTTT-T
          1 TTAAAAGAA-AGTTTTAT

                  
       6613 TTAAAA
          1 TTAAAA

       6619 TTCTCCTAAC


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  16    9  0.43
  17   12  0.57

ACGTcount: A:0.49, C:0.00, G:0.08, T:0.44


Consensus pattern (17 bp):   
TTAAAAGAAAGTTTTAT

Found at i:6765 original size:14 final size:15

Alignment explanation


    Indices: 6738--6767  Score: 53
    Period size: 14  Copynumber: 2.1  Consensus size: 15

       6728 GACTGGTTAT

                           
       6738 TTTTATTGTTTTTAA
          1 TTTTATTGTTTTTAA

                           
       6753 TTTTATT-TTTTTAA
          1 TTTTATTGTTTTTAA

             
       6767 T
          1 T

       6768 AAAAAATCAA


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

Matches are distributed among these distances:
  14    8  0.53
  15    7  0.47

ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77


Consensus pattern (15 bp):   
TTTTATTGTTTTTAA

Found at i:20243 original size:15 final size:15

Alignment explanation


    Indices: 20223--20253  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      20213 ATTCATAATG

                      *    
      20223 TCAATATGCCTTGAA
          1 TCAATATGCCCTGAA

                           
      20238 TCAATATGCCCTGAA
          1 TCAATATGCCCTGAA

             
      20253 T
          1 T

      20254 TATAGCTTTG


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

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32


Consensus pattern (15 bp):   
TCAATATGCCCTGAA
Done.