Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012711.1 Corchorus capsularis cultivar CVL-1 contig12732, 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: 7774
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32


Found at i:2649 original size:11 final size:11

Alignment explanation


    Indices: 2633--2664  Score: 55
    Period size: 11  Copynumber: 2.9  Consensus size: 11

       2623 GAAGTTCGTG

                       
       2633 TTTGAAGATTA
          1 TTTGAAGATTA

                     * 
       2644 TTTGAAGATAA
          1 TTTGAAGATTA

                      
       2655 TTTGAAGATT
          1 TTTGAAGATT

       2665 TGAAGACAAT


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  11   19  1.00

ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44


Consensus pattern (11 bp):   
TTTGAAGATTA

Found at i:2661 original size:22 final size:22

Alignment explanation


    Indices: 2633--2692  Score: 65
    Period size: 22  Copynumber: 2.9  Consensus size: 22

       2623 GAAGTTCGTG

                               *  
       2633 TTTGAAGATTATTTGAAGATAA
          1 TTTGAAGATTATTTGAAGACAA

                                  
       2655 TTTGAAG---ATTTGAAGACAA
          1 TTTGAAGATTATTTGAAGACAA

                           *    
       2674 -TTGAAGAATTATTTCAAGA
          1 TTTGAAG-ATTATTTGAAGA

       2693 AGCAAGAATT


Statistics
Matches: 32,  Mismatches: 2, Indels: 8
        0.76            0.05        0.19

Matches are distributed among these distances:
  18    6  0.19
  19   11  0.34
  22   15  0.47

ACGTcount: A:0.42, C:0.03, G:0.18, T:0.37


Consensus pattern (22 bp):   
TTTGAAGATTATTTGAAGACAA

Found at i:2667 original size:19 final size:18

Alignment explanation


    Indices: 2643--2680  Score: 58
    Period size: 19  Copynumber: 2.1  Consensus size: 18

       2633 TTTGAAGATT

                     *         
       2643 ATTTGAAGATAATTTGAAG
          1 ATTTGAAGACAA-TTGAAG

                              
       2662 ATTTGAAGACAATTGAAG
          1 ATTTGAAGACAATTGAAG

             
       2680 A
          1 A

       2681 ATTATTTCAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  18    7  0.39
  19   11  0.61

ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32


Consensus pattern (18 bp):   
ATTTGAAGACAATTGAAG

Found at i:4025 original size:6 final size:6

Alignment explanation


    Indices: 4014--4044  Score: 55
    Period size: 6  Copynumber: 5.3  Consensus size: 6

       4004 ATAATTGCCA

                                                 
       4014 TAGATT TAGATT TAGATT TAGATT TA-ATT TA
          1 TAGATT TAGATT TAGATT TAGATT TAGATT TA

       4045 TTCTGCTTTG


Statistics
Matches: 25,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   5    5  0.20
   6   20  0.80

ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52


Consensus pattern (6 bp):   
TAGATT

Found at i:5507 original size:15 final size:15

Alignment explanation


    Indices: 5487--5527  Score: 73
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       5477 TCTTGCTAAG

                           
       5487 CCAGAAGATGAGCCA
          1 CCAGAAGATGAGCCA

                           
       5502 CCAGAAGATGAGCCA
          1 CCAGAAGATGAGCCA

             *         
       5517 CAAGAAGATGA
          1 CCAGAAGATGA

       5528 ACAACTTGGA


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  15   25  1.00

ACGTcount: A:0.44, C:0.22, G:0.27, T:0.07


Consensus pattern (15 bp):   
CCAGAAGATGAGCCA

Found at i:7122 original size:9 final size:9

Alignment explanation


    Indices: 7104--7137  Score: 59
    Period size: 9  Copynumber: 3.8  Consensus size: 9

       7094 TGATTGATGC

                 *   
       7104 CTTGAATTG
          1 CTTGATTTG

                     
       7113 CTTGATTTG
          1 CTTGATTTG

                     
       7122 CTTGATTTG
          1 CTTGATTTG

                   
       7131 CTTGATT
          1 CTTGATT

       7138 GGGTCGACAC


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   9   24  1.00

ACGTcount: A:0.15, C:0.12, G:0.21, T:0.53


Consensus pattern (9 bp):   
CTTGATTTG
Done.