Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013650.1 Corchorus capsularis cultivar CVL-1 contig13671, 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: 10816
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35


Found at i:1231 original size:2 final size:2

Alignment explanation


    Indices: 1224--1259  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

       1214 AATCAAGACT

                                                                 
       1224 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       1260 CTATCATCCT


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   34  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:7435 original size:2 final size:2

Alignment explanation


    Indices: 7428--7481  Score: 72
    Period size: 2  Copynumber: 27.0  Consensus size: 2

       7418 TGCATGTTGC

                                  *                       *  *  *         
       7428 AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AC AC AC AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                             
       7470 AT AT AT AT AT AT
          1 AT AT AT AT AT AT

       7482 GGCTATGAAT


Statistics
Matches: 48,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   2   48  1.00

ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43


Consensus pattern (2 bp):   
AT

Found at i:7448 original size:16 final size:16

Alignment explanation


    Indices: 7427--7481  Score: 83
    Period size: 16  Copynumber: 3.4  Consensus size: 16

       7417 TTGCATGTTG

                            
       7427 CATATATATATATATA
          1 CATATATATATATATA

                            
       7443 CATATATATATATATA
          1 CATATATATATATATA

              * *           
       7459 CACACATATATATATA
          1 CATATATATATATATA

            *      
       7475 TATATAT
          1 CATATAT

       7482 GGCTATGAAT


Statistics
Matches: 34,  Mismatches: 5, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  16   34  1.00

ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42


Consensus pattern (16 bp):   
CATATATATATATATA

Found at i:9794 original size:2 final size:2

Alignment explanation


    Indices: 9787--9821  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       9777 TAGAAGATAC

                                                                
       9787 AT AT AT AT AT 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 AT AT AT AT AT A

       9822 ATAATGATCA


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

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:10442 original size:27 final size:27

Alignment explanation


    Indices: 10405--10476  Score: 135
    Period size: 27  Copynumber: 2.6  Consensus size: 27

      10395 TTATGAGAAT

                                        
      10405 ACCATTTATTAGGGATTTTTTTAGGTAA
          1 ACCA-TTATTAGGGATTTTTTTAGGTAA

                                       
      10433 ACCATTATTAGGGATTTTTTTAGGTAA
          1 ACCATTATTAGGGATTTTTTTAGGTAA

                             
      10460 ACCATTATTAGGGATTT
          1 ACCATTATTAGGGATTT

      10477 AAAGTACTGT


Statistics
Matches: 44,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  27   40  0.91
  28    4  0.09

ACGTcount: A:0.29, C:0.08, G:0.18, T:0.44


Consensus pattern (27 bp):   
ACCATTATTAGGGATTTTTTTAGGTAA
Done.