Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019325.1 Corchorus olitorius cultivar O-4 contig19358, 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: 16276
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33


Found at i:1655 original size:15 final size:15

Alignment explanation


    Indices: 1635--1664  Score: 60
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       1625 ACTTATAATA

                           
       1635 TATATTATATAATGT
          1 TATATTATATAATGT

                           
       1650 TATATTATATAATGT
          1 TATATTATATAATGT

       1665 CATAAAATAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53


Consensus pattern (15 bp):   
TATATTATATAATGT

Found at i:1675 original size:22 final size:22

Alignment explanation


    Indices: 1650--1693  Score: 79
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       1640 TATATAATGT

                *                 
       1650 TATATTATATAATGTCATAAAA
          1 TATAATATATAATGTCATAAAA

                                  
       1672 TATAATATATAATGTCATAAAA
          1 TATAATATATAATGTCATAAAA

       1694 ATTCTACATC


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  22   21  1.00

ACGTcount: A:0.52, C:0.05, G:0.05, T:0.39


Consensus pattern (22 bp):   
TATAATATATAATGTCATAAAA

Found at i:2771 original size:19 final size:19

Alignment explanation


    Indices: 2739--2785  Score: 58
    Period size: 19  Copynumber: 2.4  Consensus size: 19

       2729 CTAATTTTTG

                  *           *  
       2739 TTTTTTGAATAAAAAAATTCA
          1 TTTTTTTAA-AAAAAAA-CCA

                               
       2760 TTTTTTTAAAAAAAAACCA
          1 TTTTTTTAAAAAAAAACCA

                   
       2779 TTTTTTT
          1 TTTTTTT

       2786 CTTTCTTTTT


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  19    9  0.38
  20    7  0.29
  21    8  0.33

ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49


Consensus pattern (19 bp):   
TTTTTTTAAAAAAAAACCA

Found at i:12838 original size:16 final size:16

Alignment explanation


    Indices: 12817--12848  Score: 64
    Period size: 16  Copynumber: 2.0  Consensus size: 16

      12807 AGGACTAGGC

                            
      12817 AATCAATCAAAGCAAT
          1 AATCAATCAAAGCAAT

                            
      12833 AATCAATCAAAGCAAT
          1 AATCAATCAAAGCAAT

      12849 GCAAAGAAAA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.56, C:0.19, G:0.06, T:0.19


Consensus pattern (16 bp):   
AATCAATCAAAGCAAT

Found at i:13251 original size:21 final size:21

Alignment explanation


    Indices: 13225--13271  Score: 67
    Period size: 21  Copynumber: 2.2  Consensus size: 21

      13215 TTGGGGCGTG

                      **         
      13225 GATGGCCGGTGGTGGCACGGT
          1 GATGGCCGGTCCTGGCACGGT

                           *     
      13246 GATGGCCGGTCCTGGTACGGT
          1 GATGGCCGGTCCTGGCACGGT

                 
      13267 GATGG
          1 GATGG

      13272 GTGCATGGGT


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   23  1.00

ACGTcount: A:0.11, C:0.19, G:0.49, T:0.21


Consensus pattern (21 bp):   
GATGGCCGGTCCTGGCACGGT
Done.