Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011237.1 Corchorus olitorius cultivar O-4 contig11270, 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: 6508
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30


Found at i:199 original size:2 final size:2

Alignment explanation


    Indices: 188--222  Score: 63
    Period size: 2  Copynumber: 18.0  Consensus size: 2

        178 TTGAGCTAGC

                                                                 
        188 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

        223 GCAATTAAGA


Statistics
Matches: 32,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   31  0.97

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:1395 original size:15 final size:16

Alignment explanation


    Indices: 1365--1398  Score: 52
    Period size: 15  Copynumber: 2.2  Consensus size: 16

       1355 ACTTCACCTG

                            
       1365 AAATCTACATATCTTC
          1 AAATCTACATATCTTC

                  *         
       1381 AAATCTTCA-ATCTTC
          1 AAATCTACATATCTTC

               
       1396 AAA
          1 AAA

       1399 CTCTGACCTG


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  15    9  0.53
  16    8  0.47

ACGTcount: A:0.41, C:0.24, G:0.00, T:0.35


Consensus pattern (16 bp):   
AAATCTACATATCTTC

Found at i:3478 original size:76 final size:76

Alignment explanation


    Indices: 3341--3493  Score: 175
    Period size: 76  Copynumber: 2.0  Consensus size: 76

       3331 ACAAGGACCC

                    *         *            **                  *           * 
       3341 TGACTCCATCTGGGCGCCTACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
          1 TGACTCCAGCTGGGCGCCCACATGGTTGCCTAAAGCACCCATGTGGTTTGCCTGAGAACCCAGAT

                       
       3406 GGGCAGTGTCA
         66 GGGCAGTGTCA

                          *              *                           **      
       3417 TGACTCCAGCTGGGTGCCCACATGGTTTGTCTAAAG-ACCCATGT-GTTTCGCCTGATCACCCAG
          1 TGACTCCAGCTGGGCGCCCACATGG-TTGCCTAAAGCACCCATGTGGTTT-GCCTGAGAACCCAG

                  *      
       3480 ATGGGCTGTGTCA
         64 ATGGGCAGTGTCA

             
       3493 T
          1 T

       3494 AGCTCATCAC


Statistics
Matches: 64,  Mismatches: 11, Indels: 4
        0.81            0.14        0.05

Matches are distributed among these distances:
  75    4  0.06
  76   53  0.83
  77    7  0.11

ACGTcount: A:0.18, C:0.27, G:0.28, T:0.27


Consensus pattern (76 bp):   
TGACTCCAGCTGGGCGCCCACATGGTTGCCTAAAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Done.