Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013848.1 Corchorus olitorius cultivar O-4 contig13881, 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: 12713
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30


Found at i:5751 original size:75 final size:74

Alignment explanation


    Indices: 5608--5760  Score: 184
    Period size: 75  Copynumber: 2.0  Consensus size: 74

       5598 TTTATTGCGT

                  *               *    *                           *         
       5608 AATATTGAGTTGTTGCGTAAAATACAATTCTTTTAACAACAATAAAATGACGCTCTGAAAATATT
          1 AATATTCAGTTGTTGCGTAAAACACAACTCTTTTAACAACAATAAAATGA-GCTCAGAAAATATT

                *     
       5673 TTTTCGCAAC
         65 TTTTAGCAAC

                                    *          *                             
       5683 AATATTCAGTTGTTGCGTAAAACATAACTCTTTTAGCAACAATAAAATG-GCATAACAGAAAGA-
          1 AATATTCAGTTGTTGCGTAAAACACAACTCTTTTAACAACAATAAAATGAGC-T--CAGAAA-AT

                         
       5746 ATTTTTTAGCAAC
         62 ATTTTTTAGCAAC

              
       5759 AA
          1 AA

       5761 CCACCTTAAA


Statistics
Matches: 67,  Mismatches: 7, Indels: 7
        0.83            0.09        0.09

Matches are distributed among these distances:
  73    2  0.03
  74    1  0.01
  75   44  0.66
  76   19  0.28
  77    1  0.01

ACGTcount: A:0.41, C:0.14, G:0.12, T:0.32


Consensus pattern (74 bp):   
AATATTCAGTTGTTGCGTAAAACACAACTCTTTTAACAACAATAAAATGAGCTCAGAAAATATTT
TTTAGCAAC

Found at i:7092 original size:136 final size:136

Alignment explanation


    Indices: 6930--7200  Score: 490
    Period size: 136  Copynumber: 2.0  Consensus size: 136

       6920 AATTTGAAAA

                                                                             
       6930 GAAAAAAAAACATGCAAAAAGGAAGTAATCTTTTATTTTATTTTAGAAAATTTTGTGGACTTTCA
          1 GAAAAAAAAACATGCAAAAAGGAAGTAATCTTTTATTTTATTTTAGAAAATTTTGTGGACTTTCA

                *                                 *                          
       6995 CAGGTGCCGGAAATTGGAGAAAGATGTAGATTGTCGAGGAACAGGATATTTATAGAAGAATTATG
         66 CAGGGGCCGGAAATTGGAGAAAGATGTAGATTGTCGAGAAACAGGATATTTATAGAAGAATTATG

                  
       7060 GGATTT
        131 GGATTT

                                                                             
       7066 GAAAAGAAAAA-ATGCAAAAAGGAAGTAATCTTTTATTTTATTTTAGAAAATTTTGTGGACTTTC
          1 GAAAA-AAAAACATGCAAAAAGGAAGTAATCTTTTATTTTATTTTAGAAAATTTTGTGGACTTTC

                    *                                     *                  
       7130 ACAGGGGCGGGAAATTGGAGAAAGATGTAGATTGTCGAGAAACAGGGTATTTATAGAAGAATTAT
         65 ACAGGGGCCGGAAATTGGAGAAAGATGTAGATTGTCGAGAAACAGGATATTTATAGAAGAATTAT

                  
       7195 GGGATT
        130 GGGATT

       7201 CAATTCTTTA


Statistics
Matches: 130,  Mismatches: 4, Indels: 2
        0.96            0.03        0.01

Matches are distributed among these distances:
 136  125  0.96
 137    5  0.04

ACGTcount: A:0.39, C:0.07, G:0.24, T:0.30


Consensus pattern (136 bp):   
GAAAAAAAAACATGCAAAAAGGAAGTAATCTTTTATTTTATTTTAGAAAATTTTGTGGACTTTCA
CAGGGGCCGGAAATTGGAGAAAGATGTAGATTGTCGAGAAACAGGATATTTATAGAAGAATTATG
GGATTT

Found at i:7452 original size:2 final size:2

Alignment explanation


    Indices: 7445--7473  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       7435 TAACATTTAG

                                                       
       7445 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       7474 TAGACAATTA


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


Consensus pattern (2 bp):   
TA

Found at i:11208 original size:19 final size:19

Alignment explanation


    Indices: 11171--11209  Score: 53
    Period size: 19  Copynumber: 2.1  Consensus size: 19

      11161 GCTAATCCTT

                          *    
      11171 AAGTGTTTTTGCGTTTTAA
          1 AAGTGTTTTTGCGTATTAA

                                
      11190 AAGTGTTTTTG-GATATTAA
          1 AAGTGTTTTTGCG-TATTAA

             
      11209 A
          1 A

      11210 TGACTAAAAT


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  18    1  0.06
  19   17  0.94

ACGTcount: A:0.28, C:0.03, G:0.21, T:0.49


Consensus pattern (19 bp):   
AAGTGTTTTTGCGTATTAA
Done.