Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007949.1 Corchorus capsularis cultivar CVL-1 contig07970, 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: 22282
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


Found at i:446 original size:16 final size:15

Alignment explanation


    Indices: 427--500  Score: 96
    Period size: 16  Copynumber: 4.7  Consensus size: 15

        417 CAAACCCGAT

                           
        427 CCGAACCCGAAAATA
          1 CCGAACCCGAAAATA

                            
        442 TCCGAACCCG-AAATA
          1 -CCGAACCCGAAAATA

                         *   
        457 CCCGAACCCGACAGATA
          1 -CCGAACCCGA-AAATA

                           
        474 CCGAACCCGAAAATA
          1 CCGAACCCGAAAATA

                        
        489 CTCGAACCCGAA
          1 C-CGAACCCGAA

        501 CCCACCCAAT


Statistics
Matches: 52,  Mismatches: 3, Indels: 6
        0.85            0.05        0.10

Matches are distributed among these distances:
  15   19  0.37
  16   29  0.56
  17    4  0.08

ACGTcount: A:0.41, C:0.36, G:0.15, T:0.08


Consensus pattern (15 bp):   
CCGAACCCGAAAATA

Found at i:465 original size:31 final size:31

Alignment explanation


    Indices: 427--500  Score: 105
    Period size: 31  Copynumber: 2.4  Consensus size: 31

        417 CAAACCCGAT

                                            
        427 CCGAACCCGAAAATATCCGAACCCG-AAATAC
          1 CCGAACCCGAAAATA-CCGAACCCGAAAATAC

                        *                   
        458 CCGAACCCGACAGATACCGAACCCGAAAATAC
          1 CCGAACCCGA-AAATACCGAACCCGAAAATAC

            *          
        490 TCGAACCCGAA
          1 CCGAACCCGAA

        501 CCCACCCAAT


Statistics
Matches: 39,  Mismatches: 2, Indels: 4
        0.87            0.04        0.09

Matches are distributed among these distances:
  31   20  0.51
  32   19  0.49

ACGTcount: A:0.41, C:0.36, G:0.15, T:0.08


Consensus pattern (31 bp):   
CCGAACCCGAAAATACCGAACCCGAAAATAC

Found at i:2836 original size:2 final size:2

Alignment explanation


    Indices: 2829--2853  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       2819 GGATGAATCC

                                                 
       2829 AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT A

       2854 AATCATGGAT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:12932 original size:23 final size:23

Alignment explanation


    Indices: 12902--12947  Score: 74
    Period size: 23  Copynumber: 2.0  Consensus size: 23

      12892 AAATAGGGTG

                        *          
      12902 TTGCTAAACACCGCCCCATTTTT
          1 TTGCTAAACACCACCCCATTTTT

                            *      
      12925 TTGCTAAACACCACCCTATTTTT
          1 TTGCTAAACACCACCCCATTTTT

      12948 GACACTTTTG


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  23   21  1.00

ACGTcount: A:0.24, C:0.33, G:0.07, T:0.37


Consensus pattern (23 bp):   
TTGCTAAACACCACCCCATTTTT

Found at i:15410 original size:3 final size:3

Alignment explanation


    Indices: 15402--15437  Score: 72
    Period size: 3  Copynumber: 12.0  Consensus size: 3

      15392 TAATTAAGAA

                                                           
      15402 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT

      15438 AGTAATTAAG


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   33  1.00

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


Consensus pattern (3 bp):   
TAT

Found at i:21787 original size:2 final size:2

Alignment explanation


    Indices: 21739--21770  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

      21729 GTGATGATTA

                                                           
      21739 AT AT AT 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 AT AT AT

      21771 GCATTCAGCA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

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


Consensus pattern (2 bp):   
AT
Done.