Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005012.1 Corchorus capsularis cultivar CVL-1 contig05030, 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: 15812
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.33


Found at i:3108 original size:29 final size:29

Alignment explanation


    Indices: 3075--3134  Score: 120
    Period size: 29  Copynumber: 2.1  Consensus size: 29

       3065 TCTTGGGTTC

                                         
       3075 AAGTCTCACGGAATGTGAGTTTAGTGTGT
          1 AAGTCTCACGGAATGTGAGTTTAGTGTGT

                                         
       3104 AAGTCTCACGGAATGTGAGTTTAGTGTGT
          1 AAGTCTCACGGAATGTGAGTTTAGTGTGT

              
       3133 AA
          1 AA

       3135 TTTATTTGTT


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

Matches are distributed among these distances:
  29   31  1.00

ACGTcount: A:0.27, C:0.10, G:0.30, T:0.33


Consensus pattern (29 bp):   
AAGTCTCACGGAATGTGAGTTTAGTGTGT

Found at i:3195 original size:18 final size:18

Alignment explanation


    Indices: 3172--3209  Score: 76
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       3162 TGTACAGTAG

                              
       3172 TTTCTAGTTTGGTTGAAT
          1 TTTCTAGTTTGGTTGAAT

                              
       3190 TTTCTAGTTTGGTTGAAT
          1 TTTCTAGTTTGGTTGAAT

              
       3208 TT
          1 TT

       3210 GTTGGCTCAT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   20  1.00

ACGTcount: A:0.16, C:0.05, G:0.21, T:0.58


Consensus pattern (18 bp):   
TTTCTAGTTTGGTTGAAT

Found at i:4351 original size:2 final size:2

Alignment explanation


    Indices: 4346--4373  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       4336 TTTATGCAAC

                                                     
       4346 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

       4374 GATAATTGCA


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:11156 original size:26 final size:26

Alignment explanation


    Indices: 11119--11171  Score: 97
    Period size: 26  Copynumber: 2.0  Consensus size: 26

      11109 TTAAATTCCA

                   *                  
      11119 ACTATTATAGAGCTTTTCGTTTACAT
          1 ACTATTACAGAGCTTTTCGTTTACAT

                                      
      11145 ACTATTACAGAGCTTTTCGTTTACAT
          1 ACTATTACAGAGCTTTTCGTTTACAT

             
      11171 A
          1 A

      11172 GTCACGAGTA


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  26   26  1.00

ACGTcount: A:0.28, C:0.17, G:0.11, T:0.43


Consensus pattern (26 bp):   
ACTATTACAGAGCTTTTCGTTTACAT

Found at i:11256 original size:51 final size:51

Alignment explanation


    Indices: 11180--11283  Score: 199
    Period size: 51  Copynumber: 2.0  Consensus size: 51

      11170 TAGTCACGAG

                                                               
      11180 TAACTCCACCCAAACCTTGCAACTTCAATCTAATGAAATTACCAATCAATC
          1 TAACTCCACCCAAACCTTGCAACTTCAATCTAATGAAATTACCAATCAATC

                         *                                     
      11231 TAACTCCACCCAAGCCTTGCAACTTCAATCTAATGAAATTACCAATCAATC
          1 TAACTCCACCCAAACCTTGCAACTTCAATCTAATGAAATTACCAATCAATC

              
      11282 TA
          1 TA

      11284 TCTAATCTAT


Statistics
Matches: 52,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  51   52  1.00

ACGTcount: A:0.38, C:0.31, G:0.05, T:0.26


Consensus pattern (51 bp):   
TAACTCCACCCAAACCTTGCAACTTCAATCTAATGAAATTACCAATCAATC

Found at i:13629 original size:2 final size:2

Alignment explanation


    Indices: 13622--13652  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

      13612 TGAGAAAGAA

                                                          
      13622 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 A

      13653 GAAAATTCGT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:14084 original size:7 final size:7

Alignment explanation


    Indices: 14072--14098  Score: 54
    Period size: 7  Copynumber: 3.9  Consensus size: 7

      14062 CTTAATTATA

                   
      14072 CTTGAGC
          1 CTTGAGC

                   
      14079 CTTGAGC
          1 CTTGAGC

                   
      14086 CTTGAGC
          1 CTTGAGC

                  
      14093 CTTGAG
          1 CTTGAG

      14099 GTGGTGTGTA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   20  1.00

ACGTcount: A:0.15, C:0.26, G:0.30, T:0.30


Consensus pattern (7 bp):   
CTTGAGC

Done.