Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024883.1 Corchorus olitorius cultivar O-4 contig24916, 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: 1865
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31


Found at i:1027 original size:48 final size:49

Alignment explanation


    Indices: 964--1057  Score: 133
    Period size: 48  Copynumber: 1.9  Consensus size: 49

        954 TTTTAGAAAA

                                                               
        964 ACGCAAAAACTTTTTTTTTAT-GACGCAGAAACA-AAAA-AAATTTTTATG
          1 ACGCAAAAACTTTTTTTTT-TCGACGCA-AAACACAAAACAAATTTTTATG

                                                           
       1012 ACGCAAAAA-TATTTTTTTTTCGACGCAAAACACAAAACAAATTTTT
          1 ACGCAAAAACT-TTTTTTTTTCGACGCAAAACACAAAACAAATTTTT

       1058 TTTTTCAAAA


Statistics
Matches: 42,  Mismatches: 0, Indels: 7
        0.86            0.00        0.14

Matches are distributed among these distances:
  47    7  0.17
  48   27  0.64
  49    8  0.19

ACGTcount: A:0.44, C:0.15, G:0.09, T:0.33


Consensus pattern (49 bp):   
ACGCAAAAACTTTTTTTTTTCGACGCAAAACACAAAACAAATTTTTATG

Found at i:1205 original size:29 final size:30

Alignment explanation


    Indices: 1164--1236  Score: 112
    Period size: 29  Copynumber: 2.4  Consensus size: 30

       1154 AGTCTATTTT

                                           
       1164 CCTTCCCCTGGCAAAAACCAGAAAAAGTT-C
          1 CCTTCCCC-GGCAAAAACCAGAAAAAGTTAC

                  *                       
       1194 CCTTCCTCGGCAAAAACCAGAAAAAGTTAC
          1 CCTTCCCCGGCAAAAACCAGAAAAAGTTAC

            *            
       1224 TCTTCCCCGGCAA
          1 CCTTCCCCGGCAA

       1237 CGGCGCCAAA


Statistics
Matches: 39,  Mismatches: 3, Indels: 2
        0.89            0.07        0.05

Matches are distributed among these distances:
  29   20  0.51
  30   19  0.49

ACGTcount: A:0.34, C:0.34, G:0.14, T:0.18


Consensus pattern (30 bp):   
CCTTCCCCGGCAAAAACCAGAAAAAGTTAC

Found at i:1327 original size:16 final size:15

Alignment explanation


    Indices: 1287--1328  Score: 57
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       1277 ACAGAGATTG

                   *       
       1287 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

               *           
       1302 ACAAAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       1317 ACTAGAAAACAA
          1 AC-AGAAAACAA

       1329 AGCAAAGTAA


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
Done.