Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006662.1 Corchorus capsularis cultivar CVL-1 contig06683, 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: 9620
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32


Found at i:6349 original size:2 final size:2

Alignment explanation


    Indices: 6342--6374  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

       6332 TCAGTTGCAT

                                                             
       6342 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       6375 TAAAATCGCA


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:7720 original size:17 final size:17

Alignment explanation


    Indices: 7672--7721  Score: 54
    Period size: 15  Copynumber: 3.2  Consensus size: 17

       7662 GTAATATAAA

                             
       7672 CATGGAGAAAAAACCA-
          1 CATGGAGAAAAAACCAT

                *         *  
       7688 -ATGCA-AAAAAA-AAT
          1 CATGGAGAAAAAACCAT

                             
       7702 CATGGAGAAAAAACCAT
          1 CATGGAGAAAAAACCAT

               
       7719 CAT
          1 CAT

       7722 TTCATGAATT


Statistics
Matches: 26,  Mismatches: 4, Indels: 7
        0.70            0.11        0.19

Matches are distributed among these distances:
  13    1  0.04
  14    6  0.23
  15    8  0.31
  16    6  0.23
  17    5  0.19

ACGTcount: A:0.58, C:0.16, G:0.14, T:0.12


Consensus pattern (17 bp):   
CATGGAGAAAAAACCAT

Found at i:7763 original size:27 final size:27

Alignment explanation


    Indices: 7733--7803  Score: 79
    Period size: 27  Copynumber: 2.6  Consensus size: 27

       7723 TCATGAATTT

                             * *       
       7733 ATAAGATTATAATAATTTTTTTTGAAA
          1 ATAAGATTATAATAATTCTATTTGAAA

                  *      *            *
       7760 ATAAGACTATAATCATTCTATTTGAAC
          1 ATAAGATTATAATAATTCTATTTGAAA

                *            
       7787 ATAAAATGTATAATAAT
          1 ATAAGAT-TATAATAAT

       7804 GCATTATCTA


Statistics
Matches: 35,  Mismatches: 8, Indels: 1
        0.80            0.18        0.02

Matches are distributed among these distances:
  27   27  0.77
  28    8  0.23

ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41


Consensus pattern (27 bp):   
ATAAGATTATAATAATTCTATTTGAAA

Found at i:8566 original size:2 final size:2

Alignment explanation


    Indices: 8559--8608  Score: 75
    Period size: 2  Copynumber: 24.5  Consensus size: 2

       8549 CATGGGGATA

                                                                           
       8559 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT -T
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT

                       
       8601 ACT AT AT A
          1 A-T AT AT A

       8609 GCTAGCAGGT


Statistics
Matches: 45,  Mismatches: 0, Indels: 6
        0.88            0.00        0.12

Matches are distributed among these distances:
   1    1  0.02
   2   40  0.89
   3    4  0.09

ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.