Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009173.1 Corchorus capsularis cultivar CVL-1 contig09194, 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: 17139
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31


Found at i:984 original size:2 final size:2

Alignment explanation


    Indices: 977--1006  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

        967 CCAATACCTA

                                                        
        977 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

       1007 GAGGGAGAGA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:13384 original size:2 final size:2

Alignment explanation


    Indices: 13377--13408  Score: 55
    Period size: 2  Copynumber: 16.0  Consensus size: 2

      13367 AAGGTTAACG

                                       *                   
      13377 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      13409 TTAAAATGAA


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:16961 original size:2 final size:2

Alignment explanation


    Indices: 16954--17023  Score: 64
    Period size: 2  Copynumber: 37.0  Consensus size: 2

      16944 CTCCCTGAGG

                                                                            
      16954 TA TA TA TA TA TA TA TA TA -A T- TCA TA TA TA TA -A T- TA TA TGA
          1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA T-A

                                                            
      16994 -A TCA -A TA -A TA TA TA TA TA TA TA TA TA TA TA
          1 TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      17024 GAATAAAAGA


Statistics
Matches: 58,  Mismatches: 0, Indels: 20
        0.74            0.00        0.26

Matches are distributed among these distances:
   1    7  0.12
   2   48  0.83
   3    3  0.05

ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46


Consensus pattern (2 bp):   
TA

Found at i:16981 original size:13 final size:12

Alignment explanation


    Indices: 16954--17023  Score: 65
    Period size: 13  Copynumber: 5.7  Consensus size: 12

      16944 CTCCCTGAGG

                        
      16954 TATATAT-A-TA
          1 TATATATAATTA

                         
      16964 TATATATAATTCA
          1 TATATATAATT-A

                        
      16977 TATATATAATTA
          1 TATATATAATTA

                        * 
      16989 TATGA-ATCAATAA
          1 TAT-ATAT-AATTA

                          
      17002 TATATATATATATA
          1 TATATATA-AT-TA

                    
      17016 TATATATA
          1 TATATATA

      17024 GAATAAAAGA


Statistics
Matches: 50,  Mismatches: 2, Indels: 12
        0.78            0.03        0.19

Matches are distributed among these distances:
  10    7  0.14
  11    1  0.02
  12    9  0.18
  13   24  0.48
  14    9  0.18

ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46


Consensus pattern (12 bp):   
TATATATAATTA

Found at i:16981 original size:21 final size:21

Alignment explanation


    Indices: 16955--17015  Score: 72
    Period size: 21  Copynumber: 2.8  Consensus size: 21

      16945 TCCCTGAGGT

                                  
      16955 ATATATATATATATATAATTC-
          1 ATATATATATATATATAA-TCA

                                   
      16976 ATATATATA-ATTATATGAATCA
          1 ATATATATATA-TATAT-AATCA

                              
      16998 ATAATATATATATATATA
          1 AT-ATATATATATATATA

      17016 TATATATAGA


Statistics
Matches: 35,  Mismatches: 0, Indels: 9
        0.80            0.00        0.20

Matches are distributed among these distances:
  20    1  0.03
  21   16  0.46
  22    5  0.14
  23   12  0.34
  24    1  0.03

ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44


Consensus pattern (21 bp):   
ATATATATATATATATAATCA
Done.