Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009129.1 Corchorus capsularis cultivar CVL-1 contig09150, 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: 66300
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:29957 original size:19 final size:18

Alignment explanation


    Indices: 29933--29968  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      29923 TGAAGATTTC

                               
      29933 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
      29952 TTGAAGATCATTGAAGA
          1 TTGAAGATAATTGAAGA

      29969 ATTATTTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33


Consensus pattern (18 bp):   
TTGAAGATAATTGAAGAT

Found at i:41821 original size:15 final size:16

Alignment explanation


    Indices: 41801--41834  Score: 52
    Period size: 16  Copynumber: 2.2  Consensus size: 16

      41791 GATTGCTCTC

                         *  
      41801 TTAGTTA-ATTTACTT
          1 TTAGTTAGATTTAATT

                            
      41816 TTAGTTAGATTTAATT
          1 TTAGTTAGATTTAATT

               
      41832 TTA
          1 TTA

      41835 ATTCTTCTTT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  15    7  0.41
  16   10  0.59

ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59


Consensus pattern (16 bp):   
TTAGTTAGATTTAATT

Found at i:45355 original size:43 final size:43

Alignment explanation


    Indices: 45307--45399  Score: 168
    Period size: 43  Copynumber: 2.2  Consensus size: 43

      45297 TAAAAATCTA

                  *                                    
      45307 GCCAACTATGATGATAATTTGACTTCTTGTCATTGATGAATAT
          1 GCCAACCATGATGATAATTTGACTTCTTGTCATTGATGAATAT

                                                     * 
      45350 GCCAACCATGATGATAATTTGACTTCTTGTCATTGATGAATTT
          1 GCCAACCATGATGATAATTTGACTTCTTGTCATTGATGAATAT

                   
      45393 GCCAACC
          1 GCCAACC

      45400 CCATCTTCAT


Statistics
Matches: 48,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  43   48  1.00

ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37


Consensus pattern (43 bp):   
GCCAACCATGATGATAATTTGACTTCTTGTCATTGATGAATAT

Found at i:54487 original size:30 final size:31

Alignment explanation


    Indices: 54428--54495  Score: 120
    Period size: 31  Copynumber: 2.2  Consensus size: 31

      54418 AGACAATCCT

                                           
      54428 CCCAAGTTCTTAAGTTCTTCTTAATTAATGC
          1 CCCAAGTTCTTAAGTTCTTCTTAATTAATGC

                                           
      54459 CCCAAGTTCTTAAGTTCTTCTT-ATTAATGC
          1 CCCAAGTTCTTAAGTTCTTCTTAATTAATGC

              *    
      54489 CCTAAGT
          1 CCCAAGT

      54496 AGTAGAAAAT


Statistics
Matches: 36,  Mismatches: 1, Indels: 1
        0.95            0.03        0.03

Matches are distributed among these distances:
  30   14  0.39
  31   22  0.61

ACGTcount: A:0.25, C:0.24, G:0.10, T:0.41


Consensus pattern (31 bp):   
CCCAAGTTCTTAAGTTCTTCTTAATTAATGC
Done.