Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011988.1 Corchorus capsularis cultivar CVL-1 contig12009, 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: 60315
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:12 original size:2 final size:2

Alignment explanation


    Indices: 6--56  Score: 102
    Period size: 2  Copynumber: 25.5  Consensus size: 2

          1 TTCCT

                                                                          
          6 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

                         
         48 TC TC TC TC T
          1 TC TC TC TC T

         57 TTCTTTTCTT


Statistics
Matches: 49,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   49  1.00

ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51


Consensus pattern (2 bp):   
TC

Found at i:17507 original size:36 final size:36

Alignment explanation


    Indices: 17455--17527  Score: 137
    Period size: 36  Copynumber: 2.0  Consensus size: 36

      17445 GTTGGCTAAC

                                                
      17455 AATGCTAATACCAATGAAACTACAGAGCAACCGCAA
          1 AATGCTAATACCAATGAAACTACAGAGCAACCGCAA

                *                               
      17491 AATGGTAATACCAATGAAACTACAGAGCAACCGCAA
          1 AATGCTAATACCAATGAAACTACAGAGCAACCGCAA

             
      17527 A
          1 A

      17528 GTGATCGAGG


Statistics
Matches: 36,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  36   36  1.00

ACGTcount: A:0.48, C:0.23, G:0.15, T:0.14


Consensus pattern (36 bp):   
AATGCTAATACCAATGAAACTACAGAGCAACCGCAA

Found at i:25971 original size:2 final size:2

Alignment explanation


    Indices: 25964--25989  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

      25954 CTTCACCTAA

                                                  
      25964 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

      25990 TACGATTTCT


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:27524 original size:21 final size:21

Alignment explanation


    Indices: 27478--27536  Score: 66
    Period size: 21  Copynumber: 2.8  Consensus size: 21

      27468 ATATTCTCAT

                             *  *
      27478 CTGTACAGTAACAAATTTTAT
          1 CTGTACAGTAACAAATTCTAA

                                 
      27499 CTGTACAGTAACAAA-TCTAA
          1 CTGTACAGTAACAAATTCTAA

                    *    *    
      27519 CATGTACAATAACCAATT
          1 C-TGTACAGTAACAAATT

      27537 TTACTATCAC


Statistics
Matches: 32,  Mismatches: 4, Indels: 3
        0.82            0.10        0.08

Matches are distributed among these distances:
  20    4  0.12
  21   27  0.84
  22    1  0.03

ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31


Consensus pattern (21 bp):   
CTGTACAGTAACAAATTCTAA

Found at i:31759 original size:2 final size:2

Alignment explanation


    Indices: 31752--31781  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

      31742 GTTAGTATCA

                                                        
      31752 AT 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 AT

      31782 TGTTAAAGAA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:40848 original size:2 final size:2

Alignment explanation


    Indices: 40841--40874  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

      40831 AATTCGGCGC

                                                              
      40841 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      40875 GATACAATCA


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:58756 original size:3 final size:3

Alignment explanation


    Indices: 58725--58782  Score: 71
    Period size: 3  Copynumber: 18.0  Consensus size: 3

      58715 AGGGGACAAA

                          *                                                
      58725 AAT AAT ATAT AGT ATAT ATAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT
          1 AAT AAT A-AT AAT A-AT A-AT A-AT AAT AAT AAT AAT AAT AAT AAT AAT

                       
      58774 AAT AAT AAT
          1 AAT AAT AAT

      58783 GAAGGAAAGA


Statistics
Matches: 51,  Mismatches: 2, Indels: 4
        0.89            0.04        0.07

Matches are distributed among these distances:
   3   38  0.75
   4   13  0.25

ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38


Consensus pattern (3 bp):   
AAT

Found at i:59253 original size:18 final size:18

Alignment explanation


    Indices: 59210--59244  Score: 61
    Period size: 18  Copynumber: 1.9  Consensus size: 18

      59200 TATCGCCGGC

                              
      59210 CCGGATCCACTACTGTCA
          1 CCGGATCCACTACTGTCA

                     *       
      59228 CCGGATCCATTACTGTC
          1 CCGGATCCACTACTGTC

      59245 GCTGGATCCG


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.20, C:0.37, G:0.17, T:0.26


Consensus pattern (18 bp):   
CCGGATCCACTACTGTCA
Done.