Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022079.1 Corchorus olitorius cultivar O-4 contig22112, 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: 6826
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31


Found at i:466 original size:32 final size:32

Alignment explanation


    Indices: 370--528  Score: 221
    Period size: 32  Copynumber: 5.0  Consensus size: 32

        360 TAAGAATAGC

                          * * *   *         
        370 GGCGTTTCCGTA-AAAAATGCCACTATTTAGT
          1 GGCGTTTCCGTACAGAGACGCCGCTATTTAGT

                           * * *   *         
        401 GGCGTTTCCGTACAAAAAATGCCACTATTTAGT
          1 GGCGTTTCCGTAC-AGAGACGCCGCTATTTAGT

                                            
        434 GGCGTTTCCGTACAGAGACGCCGCTATTTAGT
          1 GGCGTTTCCGTACAGAGACGCCGCTATTTAGT

                     *                      
        466 GGCGTTTCCATACAGAGACGCCGCTATTTAGT
          1 GGCGTTTCCGTACAGAGACGCCGCTATTTAGT

                                           
        498 GGCGTTTCCGTACAGAGACGCCGCTATTTAG
          1 GGCGTTTCCGTACAGAGACGCCGCTATTTAG

        529 GCTTTTTTCA


Statistics
Matches: 120,  Mismatches: 6, Indels: 3
        0.93            0.05        0.02

Matches are distributed among these distances:
  31   12  0.10
  32   76  0.63
  33   32  0.27

ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29


Consensus pattern (32 bp):   
GGCGTTTCCGTACAGAGACGCCGCTATTTAGT

Found at i:4581 original size:16 final size:16

Alignment explanation


    Indices: 4557--4590  Score: 50
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       4547 TTAATTTTAT

                            
       4557 TTCAGGTCATTTCGGG
          1 TTCAGGTCATTTCGGG

                *       *   
       4573 TTCATGTCATTTTGGG
          1 TTCAGGTCATTTCGGG

              
       4589 TT
          1 TT

       4591 TGGGTCGTTT


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.12, C:0.15, G:0.26, T:0.47


Consensus pattern (16 bp):   
TTCAGGTCATTTCGGG

Found at i:5885 original size:14 final size:15

Alignment explanation


    Indices: 5861--5891  Score: 55
    Period size: 14  Copynumber: 2.1  Consensus size: 15

       5851 GTGAGGCTTA

                           
       5861 AAAATCATTAAGAAC
          1 AAAATCATTAAGAAC

                           
       5876 AAAA-CATTAAGAAC
          1 AAAATCATTAAGAAC

              
       5890 AA
          1 AA

       5892 TTATTCACAC


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

Matches are distributed among these distances:
  14   12  0.75
  15    4  0.25

ACGTcount: A:0.65, C:0.13, G:0.06, T:0.16


Consensus pattern (15 bp):   
AAAATCATTAAGAAC

Found at i:6382 original size:12 final size:12

Alignment explanation


    Indices: 6365--6397  Score: 57
    Period size: 12  Copynumber: 2.8  Consensus size: 12

       6355 ACCCTCTTCT

                        
       6365 AAAACTAGAGAG
          1 AAAACTAGAGAG

                   *    
       6377 AAAACTAAAGAG
          1 AAAACTAGAGAG

                     
       6389 AAAACTAGA
          1 AAAACTAGA

       6398 TGAAGAGAAA


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  12   19  1.00

ACGTcount: A:0.64, C:0.09, G:0.18, T:0.09


Consensus pattern (12 bp):   
AAAACTAGAGAG
Done.