Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001218.1 Corchorus capsularis cultivar CVL-1 contig01218, 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: 10879
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35


Found at i:142 original size:2 final size:2

Alignment explanation


    Indices: 130--166  Score: 51
    Period size: 2  Copynumber: 19.5  Consensus size: 2

        120 TTATTTTCAT

                                                          *           
        130 TA TA T- TA TA TA TA -A TA TA TA TA TA TA TA TG TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

        167 TGGACACGAA


Statistics
Matches: 31,  Mismatches: 2, Indels: 4
        0.84            0.05        0.11

Matches are distributed among these distances:
   1    2  0.06
   2   29  0.94

ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:3445 original size:31 final size:30

Alignment explanation


    Indices: 3410--3496  Score: 120
    Period size: 31  Copynumber: 2.8  Consensus size: 30

       3400 ATGTTTTCTG

                                           
       3410 ATTGTACCCTTGTTTTTAAAACATATTTCCA
          1 ATTGTACCCTT-TTTTTAAAACATATTTCCA

                  *                        
       3441 ATTGTATCCTTATTTTTAAAACATATTTCCA
          1 ATTGTACCCTT-TTTTTAAAACATATTTCCA

            *              *    *    
       3472 TTTGTACCCTTTTTTAAAAAAATAT
          1 ATTGTACCCTTTTTTTAAAACATAT

       3497 ATTTCTAAAT


Statistics
Matches: 50,  Mismatches: 6, Indels: 1
        0.88            0.11        0.02

Matches are distributed among these distances:
  30   12  0.24
  31   38  0.76

ACGTcount: A:0.32, C:0.16, G:0.05, T:0.47


Consensus pattern (30 bp):   
ATTGTACCCTTTTTTTAAAACATATTTCCA

Found at i:5612 original size:2 final size:2

Alignment explanation


    Indices: 5607--5631  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       5597 ACATATATTC

                                                 
       5607 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

       5632 ATGTTAAGGT


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:7125 original size:2 final size:2

Alignment explanation


    Indices: 7118--7143  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       7108 GTGGTATCAC

                                                  
       7118 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

       7144 GTGTGTGTGT


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:8131 original size:39 final size:38

Alignment explanation


    Indices: 8041--8131  Score: 91
    Period size: 39  Copynumber: 2.4  Consensus size: 38

       8031 GAATTAAAGC

                                                    
       8041 TATAATATTTA-TTTGGCCAAAAAAAGGCTATAATATATA
          1 TATAATATTTATTTTGGCC--AAAAAGGCTATAATATATA

                    *            *                 
       8080 TAT-ATATATATTTTGGCC-ACAA-GCTATAATATATTA
          1 TATAATATTTATTTTGGCCAAAAAGGCTATAATATA-TA

                            
       8116 TTTATAATATTTATTT
          1 --TATAATATTTATTT

       8132 ACAAGTACAA


Statistics
Matches: 44,  Mismatches: 3, Indels: 10
        0.77            0.05        0.18

Matches are distributed among these distances:
  35   11  0.25
  36    5  0.11
  38    9  0.20
  39   19  0.43

ACGTcount: A:0.41, C:0.08, G:0.08, T:0.44


Consensus pattern (38 bp):   
TATAATATTTATTTTGGCCAAAAAGGCTATAATATATA
Done.