Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007037.1 Corchorus capsularis cultivar CVL-1 contig07058, 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: 21210
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35


Found at i:10023 original size:24 final size:24

Alignment explanation


    Indices: 9991--10050  Score: 93
    Period size: 24  Copynumber: 2.5  Consensus size: 24

       9981 AAATAATTTT

                *        *          
       9991 AGATTAATATAAGTAAGCTATATA
          1 AGATGAATATAAGAAAGCTATATA

                            *       
      10015 AGATGAATATAAGAAATCTATATA
          1 AGATGAATATAAGAAAGCTATATA

                        
      10039 AGATGAATATAA
          1 AGATGAATATAA

      10051 TAGTATCCAT


Statistics
Matches: 33,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  24   33  1.00

ACGTcount: A:0.53, C:0.03, G:0.13, T:0.30


Consensus pattern (24 bp):   
AGATGAATATAAGAAAGCTATATA

Found at i:11389 original size:27 final size:27

Alignment explanation


    Indices: 11338--11389  Score: 68
    Period size: 27  Copynumber: 1.9  Consensus size: 27

      11328 TACTCAACTT

                        *   **         
      11338 TTCCTACTCCTTTACATTACCAAACGA
          1 TTCCTACTCCTTAACAACACCAAACGA

                                *    
      11365 TTCCTACTCCTTAACAACACTAAAC
          1 TTCCTACTCCTTAACAACACCAAAC

      11390 TACACCAAAA


Statistics
Matches: 21,  Mismatches: 4, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  27   21  1.00

ACGTcount: A:0.33, C:0.35, G:0.02, T:0.31


Consensus pattern (27 bp):   
TTCCTACTCCTTAACAACACCAAACGA

Found at i:12896 original size:33 final size:33

Alignment explanation


    Indices: 12859--12926  Score: 127
    Period size: 33  Copynumber: 2.1  Consensus size: 33

      12849 ATCCTCATAC

                                             
      12859 TTTTTATGCTTTATGCTATTTAATCCTTTACAA
          1 TTTTTATGCTTTATGCTATTTAATCCTTTACAA

                                 *           
      12892 TTTTTATGCTTTATGCTATTTGATCCTTTACAA
          1 TTTTTATGCTTTATGCTATTTAATCCTTTACAA

              
      12925 TT
          1 TT

      12927 ATGGATTGGA


Statistics
Matches: 34,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  33   34  1.00

ACGTcount: A:0.22, C:0.15, G:0.07, T:0.56


Consensus pattern (33 bp):   
TTTTTATGCTTTATGCTATTTAATCCTTTACAA

Found at i:13898 original size:30 final size:30

Alignment explanation


    Indices: 13857--13913  Score: 89
    Period size: 30  Copynumber: 1.9  Consensus size: 30

      13847 TGTCTTCAAG

                  *                        
      13857 TCCATAGTAAGTCCTT-GGCGCATCATTCCT
          1 TCCATAATAAGT-CTTGGGCGCATCATTCCT

                                       
      13887 TCCATAATAAGTCTTGGGCGCATCATT
          1 TCCATAATAAGTCTTGGGCGCATCATT

      13914 ATTGATACGA


Statistics
Matches: 25,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  29    3  0.12
  30   22  0.88

ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33


Consensus pattern (30 bp):   
TCCATAATAAGTCTTGGGCGCATCATTCCT

Found at i:19496 original size:34 final size:34

Alignment explanation


    Indices: 19455--19524  Score: 122
    Period size: 34  Copynumber: 2.1  Consensus size: 34

      19445 ACATTATTAA

                                              
      19455 TAAATTCAGTAATATCTTACATTCTTATTAATTT
          1 TAAATTCAGTAATATCTTACATTCTTATTAATTT

                      **                      
      19489 TAAATTCAGTGTTATCTTACATTCTTATTAATTT
          1 TAAATTCAGTAATATCTTACATTCTTATTAATTT

              
      19523 TA
          1 TA

      19525 GTGGCTTTTC


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

Matches are distributed among these distances:
  34   34  1.00

ACGTcount: A:0.33, C:0.11, G:0.04, T:0.51


Consensus pattern (34 bp):   
TAAATTCAGTAATATCTTACATTCTTATTAATTT

Found at i:19800 original size:33 final size:33

Alignment explanation


    Indices: 19763--19828  Score: 123
    Period size: 33  Copynumber: 2.0  Consensus size: 33

      19753 ATTTAATAAA

                                        *    
      19763 CATAAGTGACTAATACGTTACTTTTTATTTAGT
          1 CATAAGTGACTAATACGTTACTTTTTATATAGT

                                             
      19796 CATAAGTGACTAATACGTTACTTTTTATATAGT
          1 CATAAGTGACTAATACGTTACTTTTTATATAGT

      19829 TTGATGACTA


Statistics
Matches: 32,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  33   32  1.00

ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44


Consensus pattern (33 bp):   
CATAAGTGACTAATACGTTACTTTTTATATAGT

Found at i:21142 original size:2 final size:2

Alignment explanation


    Indices: 21137--21210  Score: 148
    Period size: 2  Copynumber: 37.0  Consensus size: 2

      21127 ATATATATAT

                                                                          
      21137 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

                                                           
      21179 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG


Statistics
Matches: 72,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   72  1.00

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


Consensus pattern (2 bp):   
AG

Done.