Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010073.1 Corchorus olitorius cultivar O-4 contig10105, 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: 2344
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33


Found at i:1551 original size:26 final size:26

Alignment explanation


    Indices: 1504--1571  Score: 84
    Period size: 27  Copynumber: 2.6  Consensus size: 26

       1494 CACGCACGAT

                 *           *         
       1504 GTCACATGTGGAGGTGTCCG-TTGGAG
          1 GTCACGTGT-GAGGTGTACGTTTGGAG

                                       
       1530 GTCACGTGTGAGGTCGTACGTTTGGAG
          1 GTCACGTGTGAGGT-GTACGTTTGGAG

                      *    
       1557 GTCACGTGTGGGGTG
          1 GTCACGTGTGAGGTG

       1572 CCAGCTGGTT


Statistics
Matches: 37,  Mismatches: 3, Indels: 4
        0.84            0.07        0.09

Matches are distributed among these distances:
  25    5  0.14
  26   13  0.35
  27   19  0.51

ACGTcount: A:0.13, C:0.15, G:0.44, T:0.28


Consensus pattern (26 bp):   
GTCACGTGTGAGGTGTACGTTTGGAG

Found at i:1731 original size:42 final size:42

Alignment explanation


    Indices: 1672--1755  Score: 159
    Period size: 42  Copynumber: 2.0  Consensus size: 42

       1662 AGCGCCGCGA

                              *                       
       1672 TATGGAAGTGGTCGGTCGTCAGGTTTGGAAGTGGTCGGGCGC
          1 TATGGAAGTGGTCGGTCGCCAGGTTTGGAAGTGGTCGGGCGC

                                                      
       1714 TATGGAAGTGGTCGGTCGCCAGGTTTGGAAGTGGTCGGGCGC
          1 TATGGAAGTGGTCGGTCGCCAGGTTTGGAAGTGGTCGGGCGC

       1756 CAAGCAATTG


Statistics
Matches: 41,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  42   41  1.00

ACGTcount: A:0.14, C:0.15, G:0.45, T:0.25


Consensus pattern (42 bp):   
TATGGAAGTGGTCGGTCGCCAGGTTTGGAAGTGGTCGGGCGC

Found at i:1756 original size:23 final size:23

Alignment explanation


    Indices: 1674--1757  Score: 104
    Period size: 23  Copynumber: 3.8  Consensus size: 23

       1664 CGCCGCGATA

                         *  *      
       1674 TGGAAGTGGTCGGTCGTCAGGTT
          1 TGGAAGTGGTCGGGCGCCAGGTT

                                  *
       1697 TGGAAGTGGTCGGGCG-C---TA
          1 TGGAAGTGGTCGGGCGCCAGGTT

                         *         
       1716 TGGAAGTGGTCGGTCGCCAGGTT
          1 TGGAAGTGGTCGGGCGCCAGGTT

                               
       1739 TGGAAGTGGTCGGGCGCCA
          1 TGGAAGTGGTCGGGCGCCA

       1758 AGCAATTGTG


Statistics
Matches: 52,  Mismatches: 5, Indels: 8
        0.80            0.08        0.12

Matches are distributed among these distances:
  19   16  0.31
  20    1  0.02
  22    1  0.02
  23   34  0.65

ACGTcount: A:0.14, C:0.17, G:0.45, T:0.24


Consensus pattern (23 bp):   
TGGAAGTGGTCGGGCGCCAGGTT
Done.