Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012848.1 Corchorus capsularis cultivar CVL-1 contig12869, 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: 53735
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30


Found at i:244 original size:3 final size:3

Alignment explanation


    Indices: 231--263  Score: 59
    Period size: 3  Copynumber: 11.3  Consensus size: 3

        221 ATATATATAT

                                                         
        231 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA T
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T

        264 ATATACATAT


Statistics
Matches: 29,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   2    2  0.07
   3   27  0.93

ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70


Consensus pattern (3 bp):   
TTA

Found at i:5811 original size:1 final size:1

Alignment explanation


    Indices: 5805--5832  Score: 56
    Period size: 1  Copynumber: 28.0  Consensus size: 1

       5795 AACGGGCCGG

                                        
       5805 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT

       5833 CTGTTTCCTG


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   27  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:15812 original size:26 final size:26

Alignment explanation


    Indices: 15783--15869  Score: 156
    Period size: 26  Copynumber: 3.3  Consensus size: 26

      15773 TATATGGTTG

                *   *                 
      15783 TCATCCGTGCTCATTTCCTGCCATGT
          1 TCATTCGTACTCATTTCCTGCCATGT

                                      
      15809 TCATTCGTACTCATTTCCTGCCATGT
          1 TCATTCGTACTCATTTCCTGCCATGT

                                      
      15835 TCATTCGTACTCATTTCCTGCCATGT
          1 TCATTCGTACTCATTTCCTGCCATGT

                     
      15861 TCATTCGTA
          1 TCATTCGTA

      15870 AATGTTATCC


Statistics
Matches: 59,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  26   59  1.00

ACGTcount: A:0.15, C:0.31, G:0.13, T:0.41


Consensus pattern (26 bp):   
TCATTCGTACTCATTTCCTGCCATGT

Found at i:27919 original size:5 final size:5

Alignment explanation


    Indices: 27909--27936  Score: 56
    Period size: 5  Copynumber: 5.6  Consensus size: 5

      27899 TGCTCCCCCA

                                             
      27909 TTTCT TTTCT TTTCT TTTCT TTTCT TTT
          1 TTTCT TTTCT TTTCT TTTCT TTTCT TTT

      27937 TAATTTCTAC


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   23  1.00

ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82


Consensus pattern (5 bp):   
TTTCT

Found at i:33418 original size:16 final size:16

Alignment explanation


    Indices: 33397--33429  Score: 66
    Period size: 16  Copynumber: 2.1  Consensus size: 16

      33387 TAGTAAGATA

                            
      33397 TAATTTTGATTATTAT
          1 TAATTTTGATTATTAT

                            
      33413 TAATTTTGATTATTAT
          1 TAATTTTGATTATTAT

             
      33429 T
          1 T

      33430 GTTAGATATA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64


Consensus pattern (16 bp):   
TAATTTTGATTATTAT

Found at i:46191 original size:75 final size:75

Alignment explanation


    Indices: 45998--46197  Score: 323
    Period size: 75  Copynumber: 2.7  Consensus size: 75

      45988 TATGCATCGC

                                                                             
      45998 AACTCAACGGACGAACGTCCCGAATGGGACTTATCCGCAAAAAAACAAACGAGAGCCGAAACAGG
          1 AACTCAACGGACGAACGTCCCGAATGGGAC-TATCCGCAAAAAAACAAACGAGAGCCGAAACAGG

                   *   
      46063 TTCCCTCGTAA
         65 TTCCCTCATAA

                       *                                          *          
      46074 AACTCAACGGATGAACGTCCCGAATGGGACTAATCCGC-AAAAAACAAACGAGATCCGAAACAGG
          1 AACTCAACGGACGAACGTCCCGAATGGGACT-ATCCGCAAAAAAACAAACGAGAGCCGAAACAGG

                *      
      46138 TTCCTTCATAA
         65 TTCCCTCATAA

                                                              
      46149 AACTCAACGGACGAACGTCCCGAATGGGAC-ATCCGCAAAAAAAACAAAC
          1 AACTCAACGGACGAACGTCCCGAATGGGACTATCCGC-AAAAAAACAAAC

      46198 AAGAACCAAA


Statistics
Matches: 116,  Mismatches: 5, Indels: 7
        0.91            0.04        0.05

Matches are distributed among these distances:
  73    6  0.05
  75   75  0.65
  76   35  0.30

ACGTcount: A:0.41, C:0.27, G:0.20, T:0.13


Consensus pattern (75 bp):   
AACTCAACGGACGAACGTCCCGAATGGGACTATCCGCAAAAAAACAAACGAGAGCCGAAACAGGT
TCCCTCATAA

Found at i:46259 original size:10 final size:10

Alignment explanation


    Indices: 46244--46282  Score: 50
    Period size: 8  Copynumber: 4.3  Consensus size: 10

      46234 GTACGTATAA

                      
      46244 ATAATAATAT
          1 ATAATAATAT

                      
      46254 ATAATAATA-
          1 ATAATAATAT

                      
      46263 ATAA-AATAT
          1 ATAATAATAT

                      
      46272 AT-AT-ATAT
          1 ATAATAATAT

               
      46280 ATA
          1 ATA

      46283 CTGAAAAGGT


Statistics
Matches: 26,  Mismatches: 0, Indels: 7
        0.79            0.00        0.21

Matches are distributed among these distances:
   8   11  0.42
   9    6  0.23
  10    9  0.35

ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38


Consensus pattern (10 bp):   
ATAATAATAT
Done.