Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012740.1 Corchorus olitorius cultivar O-4 contig12773, 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: 6134
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:15 original size:2 final size:2

Alignment explanation


    Indices: 9--40  Score: 55
    Period size: 2  Copynumber: 16.0  Consensus size: 2

          1 TTCTTGAA

                               *                           
          9 AT AT AT AT AT AT AC 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 AT

         41 TCATCTAACC


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   2   28  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:2524 original size:22 final size:22

Alignment explanation


    Indices: 2499--2573  Score: 71
    Period size: 22  Copynumber: 3.2  Consensus size: 22

       2489 TGTTTGATCA

                                  
       2499 ACCCTATCTTTTACTTTTCATC
          1 ACCCTATCTTTTACTTTTCATC

                    *           * *   
       2521 ACCCT-TGTTTTTACAAGTTGTGATC
          1 ACCCTAT-CTTTTAC---TTTTCATC

                                   
       2546 AACCCTATCTTTTACTTTTCATC
          1 -ACCCTATCTTTTACTTTTCATC

                 
       2569 ACCCT
          1 ACCCT

       2574 TGTTGTTACA


Statistics
Matches: 41,  Mismatches: 6, Indels: 12
        0.69            0.10        0.20

Matches are distributed among these distances:
  21    1  0.02
  22   16  0.39
  23    6  0.15
  25    6  0.15
  26   11  0.27
  27    1  0.02

ACGTcount: A:0.20, C:0.29, G:0.05, T:0.45


Consensus pattern (22 bp):   
ACCCTATCTTTTACTTTTCATC

Found at i:2548 original size:48 final size:48

Alignment explanation


    Indices: 2493--2585  Score: 177
    Period size: 48  Copynumber: 1.9  Consensus size: 48

       2483 AACTCTTGTT

                                                 *          
       2493 TGATCAACCCTATCTTTTACTTTTCATCACCCTTGTTTTTACAAGTTG
          1 TGATCAACCCTATCTTTTACTTTTCATCACCCTTGTTGTTACAAGTTG

                                                         
       2541 TGATCAACCCTATCTTTTACTTTTCATCACCCTTGTTGTTACAAG
          1 TGATCAACCCTATCTTTTACTTTTCATCACCCTTGTTGTTACAAG

       2586 GTGTAATCTT


Statistics
Matches: 44,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  48   44  1.00

ACGTcount: A:0.22, C:0.26, G:0.09, T:0.44


Consensus pattern (48 bp):   
TGATCAACCCTATCTTTTACTTTTCATCACCCTTGTTGTTACAAGTTG

Found at i:2582 original size:22 final size:21

Alignment explanation


    Indices: 2507--2582  Score: 62
    Period size: 22  Copynumber: 3.3  Consensus size: 21

       2497 CAACCCTATC

                                 
       2507 TTTTACTTTTCATCACCCTTG
          1 TTTTACTTTTCATCACCCTTG

                        * *           *
       2528 TTTTTACAAGTTGTGATCAACCCTATC
          1 -TTTTAC---TTTTCATC-ACCCT-TG

                                 
       2555 TTTTACTTTTCATCACCCTTG
          1 TTTTACTTTTCATCACCCTTG

                   
       2576 TTGTTAC
          1 TT-TTAC

       2583 AAGGTGTAAT


Statistics
Matches: 42,  Mismatches: 6, Indels: 12
        0.70            0.10        0.20

Matches are distributed among these distances:
  21    3  0.07
  22   15  0.36
  23    6  0.14
  25    6  0.14
  26   11  0.26
  27    1  0.02

ACGTcount: A:0.18, C:0.25, G:0.08, T:0.49


Consensus pattern (21 bp):   
TTTTACTTTTCATCACCCTTG

Found at i:6113 original size:2 final size:2

Alignment explanation


    Indices: 6106--6134  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       6096 GTATAAACGG

                                                       
       6106 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 A


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


Consensus pattern (2 bp):   
AT

Done.