Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013845.1 Corchorus olitorius cultivar O-4 contig13878, 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: 11327
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35


Found at i:1052 original size:21 final size:21

Alignment explanation


    Indices: 1026--1067  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       1016 AAAATCAGAA

                  *  *     *     
       1026 CAAGTCTTGTCCAGATCTTGG
          1 CAAGTCCTGCCCAGAACTTGG

                                 
       1047 CAAGTCCTGCCCAGAACTTGG
          1 CAAGTCCTGCCCAGAACTTGG

       1068 GCTGTTGAGG


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

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26


Consensus pattern (21 bp):   
CAAGTCCTGCCCAGAACTTGG

Found at i:2106 original size:15 final size:16

Alignment explanation


    Indices: 2071--2112  Score: 59
    Period size: 15  Copynumber: 2.7  Consensus size: 16

       2061 CACCGACTTA

                  *         
       2071 ACCCGAGCCCGAAAAT
          1 ACCCGAACCCGAAAAT

                          * 
       2087 ACCCGAACCCG-AAGT
          1 ACCCGAACCCGAAAAT

                       
       2102 ACCCGAACCCG
          1 ACCCGAACCCG

       2113 CCTAATTGCC


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  15   14  0.58
  16   10  0.42

ACGTcount: A:0.33, C:0.43, G:0.19, T:0.05


Consensus pattern (16 bp):   
ACCCGAACCCGAAAAT

Found at i:6444 original size:2 final size:2

Alignment explanation


    Indices: 6437--6465  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       6427 CTGCACTTAA

                                                       
       6437 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T

       6466 ATAATTTCTT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52


Consensus pattern (2 bp):   
TC

Found at i:11247 original size:2 final size:2

Alignment explanation


    Indices: 11242--11285  Score: 56
    Period size: 2  Copynumber: 22.5  Consensus size: 2

      11232 TTATTTGATG

                                                *                          
      11242 AT AT AT AT AT AT AT AT AT AT AT AT TT CAT AT AT AT A- 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

                
      11283 AT A
          1 AT A

      11286 AAATACTTAA


Statistics
Matches: 37,  Mismatches: 2, Indels: 6
        0.82            0.04        0.13

Matches are distributed among these distances:
   1    2  0.05
   2   34  0.92
   3    1  0.03

ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.