Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020788.1 Corchorus olitorius cultivar O-4 contig20821, 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: 12115
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35


Found at i:10936 original size:56 final size:56

Alignment explanation


    Indices: 10847--10958  Score: 206
    Period size: 56  Copynumber: 2.0  Consensus size: 56

      10837 GTACGTGATA

                                  *     *                           
      10847 TGGGTCGGATCCATCTCACCCATCATAATCAGGTGCACGACGCGGGTCGGATCCGG
          1 TGGGTCGGATCCATCTCACCCACCATAACCAGGTGCACGACGCGGGTCGGATCCGG

                                                                    
      10903 TGGGTCGGATCCATCTCACCCACCATAACCAGGTGCACGACGCGGGTCGGATCCGG
          1 TGGGTCGGATCCATCTCACCCACCATAACCAGGTGCACGACGCGGGTCGGATCCGG

      10959 ATTAGTCAGG


Statistics
Matches: 54,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  56   54  1.00

ACGTcount: A:0.20, C:0.32, G:0.30, T:0.18


Consensus pattern (56 bp):   
TGGGTCGGATCCATCTCACCCACCATAACCAGGTGCACGACGCGGGTCGGATCCGG

Found at i:11260 original size:19 final size:20

Alignment explanation


    Indices: 11233--11284  Score: 70
    Period size: 19  Copynumber: 2.6  Consensus size: 20

      11223 ACTACAGATA

                                
      11233 ATCAAAAATCACCACAGGTG
          1 ATCAAAAATCACCACAGGTG

                     * *        
      11253 AT-AAAAATTATCACAGGTG
          1 ATCAAAAATCACCACAGGTG

                  *      
      11272 ATCAAAGATCACC
          1 ATCAAAAATCACC

      11285 CCCAACTAAA


Statistics
Matches: 26,  Mismatches: 5, Indels: 2
        0.79            0.15        0.06

Matches are distributed among these distances:
  19   17  0.65
  20    9  0.35

ACGTcount: A:0.46, C:0.21, G:0.13, T:0.19


Consensus pattern (20 bp):   
ATCAAAAATCACCACAGGTG

Found at i:11817 original size:28 final size:29

Alignment explanation


    Indices: 11785--11842  Score: 91
    Period size: 29  Copynumber: 2.0  Consensus size: 29

      11775 TTCTTCAAAC

                                 *       
      11785 TTTCTAAT-TTCAAAAACGCTCAAGAACA
          1 TTTCTAATCTTCAAAAACGCTAAAGAACA

                          *              
      11813 TTTCTAATCTTCAAGAACGCTAAAGAACA
          1 TTTCTAATCTTCAAAAACGCTAAAGAACA

             
      11842 T
          1 T

      11843 GGAATAACCA


Statistics
Matches: 27,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
  28    8  0.30
  29   19  0.70

ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29


Consensus pattern (29 bp):   
TTTCTAATCTTCAAAAACGCTAAAGAACA

Found at i:12025 original size:22 final size:21

Alignment explanation


    Indices: 11992--12049  Score: 73
    Period size: 22  Copynumber: 2.7  Consensus size: 21

      11982 ATTATTAATT

                                  
      11992 ATAATTAATAATAACAATTTAA
          1 ATAATTAATAATAACAA-TTAA

                            *      
      12014 ATTAA-TAATAATTAATAATTAA
          1 A-TAATTAATAA-TAACAATTAA

                          
      12036 ATAATTAATAATAA
          1 ATAATTAATAATAA

      12050 TTAAAAAAAA


Statistics
Matches: 32,  Mismatches: 1, Indels: 7
        0.80            0.03        0.17

Matches are distributed among these distances:
  21    6  0.19
  22   18  0.56
  23    8  0.25

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


Consensus pattern (21 bp):   
ATAATTAATAATAACAATTAA

Found at i:12031 original size:7 final size:7

Alignment explanation


    Indices: 11973--12047  Score: 66
    Period size: 7  Copynumber: 10.6  Consensus size: 7

      11963 TTTTGTTTTT

                  *
      11973 TAATTAT
          1 TAATTAA

                  *
      11980 TAATTAT
          1 TAATTAA

                   
      11987 TAATT-A
          1 TAATTAA

                   
      11993 TAATTAA
          1 TAATTAA

                   
      12000 TAA-TAA
          1 TAATTAA

            *        
      12006 CAATTTAAA
          1 TAA-TT-AA

                    
      12015 TTAA-TAA
          1 -TAATTAA

                   
      12022 TAATTAA
          1 TAATTAA

                    
      12029 TAATTAAA
          1 TAATT-AA

                   
      12037 TAATTAA
          1 TAATTAA

                
      12044 TAAT
          1 TAAT

      12048 AATTAAAAAA


Statistics
Matches: 58,  Mismatches: 3, Indels: 14
        0.77            0.04        0.19

Matches are distributed among these distances:
   6   13  0.22
   7   32  0.55
   8    9  0.16
   9    2  0.03
  10    2  0.03

ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44


Consensus pattern (7 bp):   
TAATTAA
Done.