Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010764.1 Corchorus capsularis cultivar CVL-1 contig10785, 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: 26120
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:6464 original size:2 final size:2

Alignment explanation


    Indices: 6457--6482  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       6447 TAGTTGATGC

                                                  
       6457 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

       6483 TTGTTAAAAA


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:8200 original size:20 final size:21

Alignment explanation


    Indices: 8167--8205  Score: 62
    Period size: 20  Copynumber: 1.9  Consensus size: 21

       8157 TGTTTTTTCT

                                 
       8167 TATATAAATATTTTATTATAA
          1 TATATAAATATTTTATTATAA

                     *         
       8188 TATA-AAATTTTTTATTAT
          1 TATATAAATATTTTATTAT

       8206 TGTATTTTTT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  20   13  0.76
  21    4  0.24

ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56


Consensus pattern (21 bp):   
TATATAAATATTTTATTATAA

Found at i:13723 original size:2 final size:2

Alignment explanation


    Indices: 13716--13753  Score: 67
    Period size: 2  Copynumber: 19.0  Consensus size: 2

      13706 GAGGGTCATG

                                                            *       
      13716 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      13754 GTACTAGTAT


Statistics
Matches: 34,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   34  1.00

ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:22145 original size:57 final size:57

Alignment explanation


    Indices: 22055--22167  Score: 172
    Period size: 57  Copynumber: 2.0  Consensus size: 57

      22045 GCAGTCGGTC

                                        *         **                 
      22055 GGGTTAGTCGATTTTGAGACTAACAATTCATTTTCTTTTTCCTGTTAAATTTTCTAT
          1 GGGTTAGTCGATTTTGAGACTAACAATTAATTTTCTTTCCCCTGTTAAATTTTCTAT

                      *     *        *                              
      22112 GGGTTAGTCGGTTTTGGGACTAACATTTAATTTTCTTTCCCCTGTTAAATTTTCTA
          1 GGGTTAGTCGATTTTGAGACTAACAATTAATTTTCTTTCCCCTGTTAAATTTTCTA

      22168 CATACAATGG


Statistics
Matches: 50,  Mismatches: 6, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  57   50  1.00

ACGTcount: A:0.21, C:0.15, G:0.16, T:0.48


Consensus pattern (57 bp):   
GGGTTAGTCGATTTTGAGACTAACAATTAATTTTCTTTCCCCTGTTAAATTTTCTAT

Found at i:24765 original size:2 final size:2

Alignment explanation


    Indices: 24758--24784  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

      24748 AATTCATAAT

                                                    
      24758 TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA T

      24785 TTGGATCAAT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

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


Consensus pattern (2 bp):   
TA

Done.