Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009962.1 Corchorus capsularis cultivar CVL-1 contig09983, 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: 20080
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31


Found at i:1639 original size:15 final size:15

Alignment explanation


    Indices: 1619--1650  Score: 64
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       1609 TATTAGTCGA

                           
       1619 CTGTGAATACCTCTC
          1 CTGTGAATACCTCTC

                           
       1634 CTGTGAATACCTCTC
          1 CTGTGAATACCTCTC

              
       1649 CT
          1 CT

       1651 AGGATTAAGA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.19, C:0.34, G:0.12, T:0.34


Consensus pattern (15 bp):   
CTGTGAATACCTCTC

Found at i:4557 original size:22 final size:22

Alignment explanation


    Indices: 4511--4557  Score: 58
    Period size: 22  Copynumber: 2.1  Consensus size: 22

       4501 ATGACCTCTT

                       *      * * 
       4511 TATGAAATTTTGATAACCTTCC
          1 TATGAAATTTTAATAACCATAC

                             *    
       4533 TATGAAATTTTAATAACGATAC
          1 TATGAAATTTTAATAACCATAC

               
       4555 TAT
          1 TAT

       4558 AGAATTTCGA


Statistics
Matches: 21,  Mismatches: 4, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  22   21  1.00

ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40


Consensus pattern (22 bp):   
TATGAAATTTTAATAACCATAC

Found at i:15498 original size:3 final size:3

Alignment explanation


    Indices: 15492--15516  Score: 50
    Period size: 3  Copynumber: 8.3  Consensus size: 3

      15482 GTAGGAGGAG

                                             
      15492 GAA GAA GAA GAA GAA GAA GAA GAA G
          1 GAA GAA GAA GAA GAA GAA GAA GAA G

      15517 GAAAGAGGGA


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   22  1.00

ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00


Consensus pattern (3 bp):   
GAA

Found at i:18874 original size:21 final size:21

Alignment explanation


    Indices: 18848--18892  Score: 56
    Period size: 21  Copynumber: 2.1  Consensus size: 21

      18838 CTGACATTTC

                     *            
      18848 ACATTAGTTCACA-AAGAAAAT
          1 ACATTA-TTAACACAAGAAAAT

                             *   
      18869 ACATTATTAACACAAGATAAT
          1 ACATTATTAACACAAGAAAAT

               
      18890 ACA
          1 ACA

      18893 CCCTAAACAG


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  20    5  0.24
  21   16  0.76

ACGTcount: A:0.53, C:0.16, G:0.07, T:0.24


Consensus pattern (21 bp):   
ACATTATTAACACAAGAAAAT

Found at i:19876 original size:21 final size:21

Alignment explanation


    Indices: 19850--19894  Score: 65
    Period size: 21  Copynumber: 2.1  Consensus size: 21

      19840 ATAAACTAGA

                                  
      19850 TTGCTAAAT-ACCGCCCCATTT
          1 TTGCT-AATCACCGCCCCATTT

                  *              
      19871 TTGCTATTCACCGCCCCATTT
          1 TTGCTAATCACCGCCCCATTT

               
      19892 TTG
          1 TTG

      19895 ACATTTTTTT


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  20    2  0.09
  21   20  0.91

ACGTcount: A:0.18, C:0.33, G:0.11, T:0.38


Consensus pattern (21 bp):   
TTGCTAATCACCGCCCCATTT
Done.