Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013203.1 Corchorus capsularis cultivar CVL-1 contig13224, 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: 28596
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34


Found at i:11211 original size:13 final size:14

Alignment explanation


    Indices: 11193--11221  Score: 51
    Period size: 13  Copynumber: 2.1  Consensus size: 14

      11183 ATAACCGGAC

                          
      11193 TTTGCATTCAT-CA
          1 TTTGCATTCATGCA

                          
      11206 TTTGCATTCATGCA
          1 TTTGCATTCATGCA

              
      11220 TT
          1 TT

      11222 GAGTACAAGT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13   11  0.73
  14    4  0.27

ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48


Consensus pattern (14 bp):   
TTTGCATTCATGCA

Found at i:11309 original size:13 final size:12

Alignment explanation


    Indices: 11293--11322  Score: 51
    Period size: 12  Copynumber: 2.4  Consensus size: 12

      11283 AGATGCAATA

                         
      11293 AAAAATGTTTTTC
          1 AAAAATG-TTTTC

                        
      11306 AAAAATGTTTTC
          1 AAAAATGTTTTC

                 
      11318 AAAAA
          1 AAAAA

      11323 ATCATGTTTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  12   10  0.59
  13    7  0.41

ACGTcount: A:0.50, C:0.07, G:0.07, T:0.37


Consensus pattern (12 bp):   
AAAAATGTTTTC

Found at i:11323 original size:13 final size:14

Alignment explanation


    Indices: 11292--11324  Score: 52
    Period size: 13  Copynumber: 2.5  Consensus size: 14

      11282 AAGATGCAAT

                          
      11292 AAAAAATGTTTTTC
          1 AAAAAATGTTTTTC

                          
      11306 -AAAAATG-TTTTC
          1 AAAAAATGTTTTTC

                   
      11318 AAAAAAT
          1 AAAAAAT

      11325 CATGTTTTCT


Statistics
Matches: 18,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  12    5  0.28
  13   13  0.72

ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36


Consensus pattern (14 bp):   
AAAAAATGTTTTTC

Found at i:19330 original size:2 final size:2

Alignment explanation


    Indices: 19323--19350  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

      19313 CTATTACATC

                                                     
      19323 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      19351 TGATAGATGG


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:20715 original size:2 final size:2

Alignment explanation


    Indices: 20708--20733  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

      20698 ATTCAAAGGA

                                                  
      20708 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

      20734 TTATGTACAG


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

Matches are distributed among these distances:
   2   24  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:23974 original size:17 final size:18

Alignment explanation


    Indices: 23954--23996  Score: 54
    Period size: 16  Copynumber: 2.4  Consensus size: 18

      23944 AATCCCACCC

                     *        
      23954 AAAAAAAAGGAAA-AAAT
          1 AAAAAAAAGAAAATAAAT

                              
      23971 -AAAAAAAGAAAATAAAT
          1 AAAAAAAAGAAAATAAAT

                     
      23988 AATAAAAAA
          1 AA-AAAAAA

      23997 ACCCTAATCG


Statistics
Matches: 22,  Mismatches: 1, Indels: 4
        0.81            0.04        0.15

Matches are distributed among these distances:
  16   11  0.50
  17    4  0.18
  18    1  0.05
  19    6  0.27

ACGTcount: A:0.84, C:0.00, G:0.07, T:0.09


Consensus pattern (18 bp):   
AAAAAAAAGAAAATAAAT
Done.