Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005473.1 Corchorus capsularis cultivar CVL-1 contig05491, 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: 35366
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30


Found at i:904 original size:3 final size:3

Alignment explanation


    Indices: 896--929  Score: 68
    Period size: 3  Copynumber: 11.3  Consensus size: 3

        886 AACGCACGAC

                                                         
        896 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
          1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A

        930 TGATGAATCC


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

Matches are distributed among these distances:
   3   31  1.00

ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00


Consensus pattern (3 bp):   
AAG

Found at i:4049 original size:45 final size:45

Alignment explanation


    Indices: 3985--4075  Score: 164
    Period size: 45  Copynumber: 2.0  Consensus size: 45

       3975 ACTGAAAGTG

                                *                 *      
       3985 CTGTTGATCCTTTATAAAAATAGTAAAAACAATCTACATGCTGAC
          1 CTGTTGATCCTTTATAAAAACAGTAAAAACAATCTACAAGCTGAC

                                                         
       4030 CTGTTGATCCTTTATAAAAACAGTAAAAACAATCTACAAGCTGAC
          1 CTGTTGATCCTTTATAAAAACAGTAAAAACAATCTACAAGCTGAC

             
       4075 C
          1 C

       4076 GTAACAAAGA


Statistics
Matches: 44,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  45   44  1.00

ACGTcount: A:0.41, C:0.20, G:0.11, T:0.29


Consensus pattern (45 bp):   
CTGTTGATCCTTTATAAAAACAGTAAAAACAATCTACAAGCTGAC

Found at i:5882 original size:4 final size:4

Alignment explanation


    Indices: 5873--5899  Score: 54
    Period size: 4  Copynumber: 6.8  Consensus size: 4

       5863 TTTCTATACA

                                             
       5873 AAAT AAAT AAAT AAAT AAAT AAAT AAA
          1 AAAT AAAT AAAT AAAT AAAT AAAT AAA

       5900 ACACAATTTG


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   23  1.00

ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22


Consensus pattern (4 bp):   
AAAT

Found at i:13977 original size:7 final size:7

Alignment explanation


    Indices: 13967--13994  Score: 56
    Period size: 7  Copynumber: 4.0  Consensus size: 7

      13957 TTGGCTTGGG

                   
      13967 ACCCAAA
          1 ACCCAAA

                   
      13974 ACCCAAA
          1 ACCCAAA

                   
      13981 ACCCAAA
          1 ACCCAAA

                   
      13988 ACCCAAA
          1 ACCCAAA

      13995 GGCTTTGCAG


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   21  1.00

ACGTcount: A:0.57, C:0.43, G:0.00, T:0.00


Consensus pattern (7 bp):   
ACCCAAA

Found at i:14754 original size:13 final size:13

Alignment explanation


    Indices: 14736--14766  Score: 62
    Period size: 13  Copynumber: 2.4  Consensus size: 13

      14726 TAAATAAACC

                         
      14736 CCCTAGTACCCTA
          1 CCCTAGTACCCTA

                         
      14749 CCCTAGTACCCTA
          1 CCCTAGTACCCTA

                 
      14762 CCCTA
          1 CCCTA

      14767 CCTGTTGCAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   18  1.00

ACGTcount: A:0.23, C:0.48, G:0.06, T:0.23


Consensus pattern (13 bp):   
CCCTAGTACCCTA

Found at i:23214 original size:1 final size:1

Alignment explanation


    Indices: 23208--23242  Score: 70
    Period size: 1  Copynumber: 35.0  Consensus size: 1

      23198 CTTCCCCAAG

                                               
      23208 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

      23243 CAAGTCCATT


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

Matches are distributed among these distances:
   1   34  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:24743 original size:2 final size:2

Alignment explanation


    Indices: 24736--24772  Score: 74
    Period size: 2  Copynumber: 18.5  Consensus size: 2

      24726 TGATCTGATA

                                                                   
      24736 AT 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 AT A

      24773 ACATAACACA


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   35  1.00

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


Consensus pattern (2 bp):   
AT

Done.