Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015909.1 Corchorus olitorius cultivar O-4 contig15942, 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: 22549
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35


Found at i:635 original size:31 final size:30

Alignment explanation


    Indices: 592--673  Score: 89
    Period size: 28  Copynumber: 2.8  Consensus size: 30

        582 CTAATCAAAT

                   *                *       
        592 AATAATACACCAATAATTAATTATTACTAATG
          1 AATAATAAACCAATAATTAATTATCA-T-ATG

                               *       *  
        624 -ATAATAAACCAATAATT-CTT-TCATGTG
          1 AATAATAAACCAATAATTAATTATCATATG

                                   
        651 AATAATAAACCAATAATTAATTA
          1 AATAATAAACCAATAATTAATTA

        674 CTAAGGCCCA


Statistics
Matches: 42,  Mismatches: 5, Indels: 8
        0.76            0.09        0.15

Matches are distributed among these distances:
  27    2  0.05
  28   18  0.43
  29    4  0.10
  30    2  0.05
  31   16  0.38

ACGTcount: A:0.50, C:0.12, G:0.04, T:0.34


Consensus pattern (30 bp):   
AATAATAAACCAATAATTAATTATCATATG

Found at i:10943 original size:27 final size:28

Alignment explanation


    Indices: 10913--10965  Score: 74
    Period size: 28  Copynumber: 1.9  Consensus size: 28

      10903 TAATCTGATT

                                         
      10913 ATTTAT-TTT-GGTATTTTATGATTTCAG
          1 ATTTATCTTTAGGT-TTTTATGATTTCAG

                       *              
      10940 ATTTATCTTTATGTTTTTATGATTTC
          1 ATTTATCTTTAGGTTTTTATGATTTC

      10966 TAATTGATTT


Statistics
Matches: 23,  Mismatches: 1, Indels: 3
        0.85            0.04        0.11

Matches are distributed among these distances:
  27    6  0.26
  28   15  0.65
  29    2  0.09

ACGTcount: A:0.21, C:0.06, G:0.11, T:0.62


Consensus pattern (28 bp):   
ATTTATCTTTAGGTTTTTATGATTTCAG

Found at i:17223 original size:21 final size:21

Alignment explanation


    Indices: 17197--17236  Score: 64
    Period size: 21  Copynumber: 1.9  Consensus size: 21

      17187 TGGAGTTGTG

                                  
      17197 AGATTA-AACACTGTACATATC
          1 AGATTAGAA-ACTGTACATATC

                               
      17218 AGATTAGAAACTGTACATA
          1 AGATTAGAAACTGTACATA

      17237 ACAGCGATAG


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  21   16  0.89
  22    2  0.11

ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28


Consensus pattern (21 bp):   
AGATTAGAAACTGTACATATC

Found at i:17396 original size:14 final size:14

Alignment explanation


    Indices: 17377--17407  Score: 62
    Period size: 14  Copynumber: 2.2  Consensus size: 14

      17367 TAAATTAGTG

                          
      17377 TATGAGTATATAAT
          1 TATGAGTATATAAT

                          
      17391 TATGAGTATATAAT
          1 TATGAGTATATAAT

               
      17405 TAT
          1 TAT

      17408 TATTAATAAA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   17  1.00

ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45


Consensus pattern (14 bp):   
TATGAGTATATAAT
Done.