Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007738.1 Corchorus capsularis cultivar CVL-1 contig07759, 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: 28572
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:11902 original size:22 final size:22

Alignment explanation


    Indices: 11874--11941  Score: 77
    Period size: 22  Copynumber: 3.2  Consensus size: 22

      11864 CTAAGAAGTT

                                  
      11874 TGATAACCATACTATGAAATTC
          1 TGATAACCATACTATGAAATTC

                    *             
      11896 TGATAACCCT--TATGAAATTC
          1 TGATAACCATACTATGAAATTC

            *    *  *            *
      11916 GGATAGCCTTACTATGAAATTT
          1 TGATAACCATACTATGAAATTC

                
      11938 TGAT
          1 TGAT

      11942 GATTTCCCAA


Statistics
Matches: 38,  Mismatches: 6, Indels: 4
        0.79            0.12        0.08

Matches are distributed among these distances:
  20   17  0.45
  22   21  0.55

ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35


Consensus pattern (22 bp):   
TGATAACCATACTATGAAATTC

Found at i:22291 original size:15 final size:15

Alignment explanation


    Indices: 22271--22302  Score: 55
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      22261 ACTTGTTTTA

                           
      22271 TTTGAGGATAAACAT
          1 TTTGAGGATAAACAT

                       *   
      22286 TTTGAGGATAACCAT
          1 TTTGAGGATAAACAT

              
      22301 TT
          1 TT

      22303 CTCCTGTGTT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38


Consensus pattern (15 bp):   
TTTGAGGATAAACAT

Found at i:22408 original size:10 final size:11

Alignment explanation


    Indices: 22388--22412  Score: 50
    Period size: 11  Copynumber: 2.3  Consensus size: 11

      22378 ATTAGTTAGG

                       
      22388 AAAAAGAAAAA
          1 AAAAAGAAAAA

                       
      22399 AAAAAGAAAAA
          1 AAAAAGAAAAA

               
      22410 AAA
          1 AAA

      22413 CTAAAGAGCA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   14  1.00

ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00


Consensus pattern (11 bp):   
AAAAAGAAAAA
Done.