Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011768.1 Corchorus capsularis cultivar CVL-1 contig11789, 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: 26741
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35


Found at i:10357 original size:2 final size:2

Alignment explanation


    Indices: 10350--10375  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

      10340 TTAATTCTTG

                                                  
      10350 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

      10376 TAGAAAAATT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:17743 original size:15 final size:17

Alignment explanation


    Indices: 17723--17755  Score: 52
    Period size: 15  Copynumber: 2.1  Consensus size: 17

      17713 TTCGTCTGCG

                             
      17723 AGCAATTC-TTTT-ATT
          1 AGCAATTCATTTTCATT

                             
      17738 AGCAATTCATTTTCATT
          1 AGCAATTCATTTTCATT

             
      17755 A
          1 A

      17756 CAGGTGACTT


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  15    8  0.50
  16    4  0.25
  17    4  0.25

ACGTcount: A:0.30, C:0.15, G:0.06, T:0.48


Consensus pattern (17 bp):   
AGCAATTCATTTTCATT

Found at i:19686 original size:13 final size:12

Alignment explanation


    Indices: 19663--19695  Score: 50
    Period size: 11  Copynumber: 2.8  Consensus size: 12

      19653 CGGCTCTTAA

                        
      19663 TTTTTTCTTTCT
          1 TTTTTTCTTTCT

                        
      19675 TTTTTTCTTT-T
          1 TTTTTTCTTTCT

            *         
      19686 CTTTTTCTTT
          1 TTTTTTCTTT

      19696 TGTTTGGTGA


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  11   10  0.50
  12   10  0.50

ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85


Consensus pattern (12 bp):   
TTTTTTCTTTCT

Found at i:26269 original size:21 final size:22

Alignment explanation


    Indices: 26245--26287  Score: 61
    Period size: 21  Copynumber: 2.0  Consensus size: 22

      26235 ATATCGTGAA

                                  
      26245 TTACTAAATACCGCCC-CCTTT
          1 TTACTAAATACCGCCCTCCTTT

                  **              
      26266 TTACTAGGTACCGCCCTCCTTT
          1 TTACTAAATACCGCCCTCCTTT

      26288 GGACAATTTT


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  21   14  0.74
  22    5  0.26

ACGTcount: A:0.19, C:0.37, G:0.09, T:0.35


Consensus pattern (22 bp):   
TTACTAAATACCGCCCTCCTTT
Done.