Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013988.1 Corchorus capsularis cultivar CVL-1 contig14009, 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: 16578
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:46 original size:2 final size:2

Alignment explanation


    Indices: 39--82  Score: 74
    Period size: 2  Copynumber: 23.0  Consensus size: 2

         29 AAAAATTCCA

                                                                          
         39 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT A- AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                 
         79 AT AT
          1 AT AT

         83 GAAAAGCTTC


Statistics
Matches: 40,  Mismatches: 0, Indels: 4
        0.91            0.00        0.09

Matches are distributed among these distances:
   1    2  0.05
   2   38  0.95

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


Consensus pattern (2 bp):   
AT

Found at i:1167 original size:109 final size:109

Alignment explanation


    Indices: 1035--1309  Score: 446
    Period size: 109  Copynumber: 2.5  Consensus size: 109

       1025 AAAAAAATTA

                                           *                                 
       1035 TATAAA-ATATT-GAATTTAATTAAATGAAATTAGAGTTTTTAGTAGAATAAAATTGTATATTAG
          1 TATAAAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG

                                                         
       1098 AAAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
         65 AAAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT

                                                                             
       1143 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
          1 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA

                      *                                 
       1208 AAAAATTTTAGTATATCCAAATTTTTTGGTAAAAATAAAGTAAT
         66 AAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT

                                           *            *             
       1252 TATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTAGTAGAATAAAA
          1 TATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTAGTAGAATAAAA

       1310 CTATAATAGT


Statistics
Matches: 156,  Mismatches: 4, Indels: 8
        0.93            0.02        0.05

Matches are distributed among these distances:
 108    6  0.04
 109  118  0.76
 110    3  0.02
 111    1  0.01
 114   28  0.18

ACGTcount: A:0.48, C:0.02, G:0.11, T:0.39


Consensus pattern (109 bp):   
TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
AAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT

Found at i:1565 original size:13 final size:13

Alignment explanation


    Indices: 1544--1580  Score: 56
    Period size: 13  Copynumber: 2.8  Consensus size: 13

       1534 GATAATTCTT

                         
       1544 TTTGACCCTCCAA
          1 TTTGACCCTCCAA

                *        
       1557 TTTGTCCCTCCAA
          1 TTTGACCCTCCAA

            *          
       1570 CTTGACCCTCC
          1 TTTGACCCTCC

       1581 TTACTAGTTA


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  13   21  1.00

ACGTcount: A:0.16, C:0.43, G:0.08, T:0.32


Consensus pattern (13 bp):   
TTTGACCCTCCAA

Found at i:10983 original size:3 final size:3

Alignment explanation


    Indices: 10975--11001  Score: 54
    Period size: 3  Copynumber: 9.0  Consensus size: 3

      10965 GACATCAACC

                                               
      10975 TCA TCA TCA TCA TCA TCA TCA TCA TCA
          1 TCA TCA TCA TCA TCA TCA TCA TCA TCA

      11002 AAATCTGGCT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   24  1.00

ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33


Consensus pattern (3 bp):   
TCA

Found at i:13521 original size:2 final size:2

Alignment explanation


    Indices: 13514--13547  Score: 54
    Period size: 2  Copynumber: 18.0  Consensus size: 2

      13504 TTAACTAAAC

                                                                 
      13514 TA TA TA TA TA -A T- 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

      13548 ATTAAAGATC


Statistics
Matches: 30,  Mismatches: 0, Indels: 4
        0.88            0.00        0.12

Matches are distributed among these distances:
   1    2  0.07
   2   28  0.93

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


Consensus pattern (2 bp):   
TA

Found at i:13803 original size:42 final size:43

Alignment explanation


    Indices: 13721--13803  Score: 107
    Period size: 42  Copynumber: 2.0  Consensus size: 43

      13711 CTTAAATGTG

                        *             *        *       
      13721 TTAATCGTGTCTTGACACGATTACGATACGAAACATGATAATC
          1 TTAATCGTGTCTCGACACGATTACGACACGAAACACGATAATC

                                            *         
      13764 TTAATCGTGTC-CGACACGATT-CAGACACGAGACACGATAA
          1 TTAATCGTGTCTCGACACGATTAC-GACACGAAACACGATAA

      13804 ACCAAACATG


Statistics
Matches: 35,  Mismatches: 4, Indels: 3
        0.83            0.10        0.07

Matches are distributed among these distances:
  41    1  0.03
  42   23  0.66
  43   11  0.31

ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25


Consensus pattern (43 bp):   
TTAATCGTGTCTCGACACGATTACGACACGAAACACGATAATC
Done.