Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024528.1 Corchorus olitorius cultivar O-4 contig24561, 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: 9864
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31


Found at i:1048 original size:16 final size:15

Alignment explanation


    Indices: 1010--1051  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       1000 ACAAAGATTG

                   *       
       1010 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
       1025 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       1040 ACTAGAAAACAA
          1 AC-AGAAAACAA

       1052 AGCAGAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:7949 original size:16 final size:15

Alignment explanation


    Indices: 7909--7950  Score: 57
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       7899 ACAGAGATTG

                   *       
       7909 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

               *           
       7924 ACAAAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       7939 ACTAGAAAACAA
          1 AC-AGAAAACAA

       7951 AGCAGAGTAA


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  15   15  0.65
  16    8  0.35

ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:9348 original size:29 final size:29

Alignment explanation


    Indices: 9314--9390  Score: 145
    Period size: 29  Copynumber: 2.6  Consensus size: 29

       9304 CTTGAAATAA

                                         
       9314 ATCTTCAATGGTCTTCAAGTCTCCAATTT
          1 ATCTTCAATGGTCTTCAAGTCTCCAATTT

                                         
       9343 ATCTTCAATGGTCTTCAAGTCTCCAATTT
          1 ATCTTCAATGGTCTTCAAGTCTCCAATTT

                               
       9372 ATCTTCAAATGGTCTTCAA
          1 ATCTTC-AATGGTCTTCAA

       9391 ACACGAAAAA


Statistics
Matches: 47,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  29   35  0.74
  30   12  0.26

ACGTcount: A:0.26, C:0.23, G:0.10, T:0.40


Consensus pattern (29 bp):   
ATCTTCAATGGTCTTCAAGTCTCCAATTT

Found at i:9424 original size:12 final size:12

Alignment explanation


    Indices: 9407--9437  Score: 62
    Period size: 12  Copynumber: 2.6  Consensus size: 12

       9397 AAAAGTCATT

                        
       9407 AAAATAGCTACA
          1 AAAATAGCTACA

                        
       9419 AAAATAGCTACA
          1 AAAATAGCTACA

                   
       9431 AAAATAG
          1 AAAATAG

       9438 TGAAAAACAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   19  1.00

ACGTcount: A:0.61, C:0.13, G:0.10, T:0.16


Consensus pattern (12 bp):   
AAAATAGCTACA

Found at i:9609 original size:27 final size:26

Alignment explanation


    Indices: 9578--9663  Score: 91
    Period size: 27  Copynumber: 3.2  Consensus size: 26

       9568 AGCTCAATCA

                                   *   
       9578 GTGGTCCAAGTGGGGCTGAAAATCTTG
          1 GTGGTCCAAG-GGGGCTGAAAATGTTG

                          *    *       
       9605 GTGGTCCAAGGGTGTCTGACAATGTTG
          1 GTGGTCCAAGGG-GGCTGAAAATGTTG

                *       *  *           
       9632 GTGGGCCAAGAGTGGTTGAAAATGTTG
          1 GTGGTCCAAG-GGGGCTGAAAATGTTG

                 
       9659 GTGGT
          1 GTGGT

       9664 GGGGCAAGTG


Statistics
Matches: 48,  Mismatches: 9, Indels: 4
        0.79            0.15        0.07

Matches are distributed among these distances:
  26    2  0.04
  27   45  0.94
  28    1  0.02

ACGTcount: A:0.21, C:0.12, G:0.40, T:0.28


Consensus pattern (26 bp):   
GTGGTCCAAGGGGGCTGAAAATGTTG
Done.