Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018812.1 Corchorus olitorius cultivar O-4 contig18845, 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: 20365
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:10028 original size:41 final size:42

Alignment explanation


    Indices: 9971--10060  Score: 137
    Period size: 42  Copynumber: 2.2  Consensus size: 42

       9961 GCGACAACTA

                                        *             
       9971 GTGTCAAAGATAATTTTAA-TTTACCAAGGTAACAACTTCTG
          1 GTGTCAAAGATAATTTTAATTTTACCAAAGTAACAACTTCTG

                     *                     *         *
      10012 GTGTCAAAGGTAATTTTAATTTTACCAAAGTGACAACTTCTT
          1 GTGTCAAAGATAATTTTAATTTTACCAAAGTAACAACTTCTG

                   
      10054 GTGTCAA
          1 GTGTCAA

      10061 TTATATTCAC


Statistics
Matches: 44,  Mismatches: 4, Indels: 1
        0.90            0.08        0.02

Matches are distributed among these distances:
  41   18  0.41
  42   26  0.59

ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36


Consensus pattern (42 bp):   
GTGTCAAAGATAATTTTAATTTTACCAAAGTAACAACTTCTG

Found at i:10150 original size:47 final size:47

Alignment explanation


    Indices: 10042--10260  Score: 332
    Period size: 47  Copynumber: 4.7  Consensus size: 47

      10032 TTTACCAAAG

                       *          *   *          *         
      10042 TGACAACTTCTTGTGTCAATTATATTCACTAAAGTAAGA-TTTAATT
          1 TGACAACTTCTGGTGTCAATTAAATTTACTAAAGTAAAATTTTAATT

                                                 *         
      10088 TGACAACTTCTGGTGTCAATTAAATTTACTAAAGTAAGATTTTAATT
          1 TGACAACTTCTGGTGTCAATTAAATTTACTAAAGTAAAATTTTAATT

                                   **        *             
      10135 TGACAACTTCTGGTGTCAATTAAGGTTACTAAAATAAAATTTTAATT
          1 TGACAACTTCTGGTGTCAATTAAATTTACTAAAGTAAAATTTTAATT

                      **                                   
      10182 TGACAACTTCAAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATT
          1 TGACAACTTCTGGTGTCAATTAAATTTACTAAAGTAAAATTTTAATT

                                            
      10229 TGACAACTTCTGGTGTCAATTAAAATTTACTA
          1 TGACAACTTCTGGTGTCAATT-AAATTTACTA

      10261 GAGCTCTCGT


Statistics
Matches: 157,  Mismatches: 14, Indels: 2
        0.91            0.08        0.01

Matches are distributed among these distances:
  46   36  0.23
  47  111  0.71
  48   10  0.06

ACGTcount: A:0.37, C:0.12, G:0.11, T:0.39


Consensus pattern (47 bp):   
TGACAACTTCTGGTGTCAATTAAATTTACTAAAGTAAAATTTTAATT

Found at i:17733 original size:32 final size:33

Alignment explanation


    Indices: 17688--17764  Score: 120
    Period size: 33  Copynumber: 2.4  Consensus size: 33

      17678 TTTTACAAAA

                    *               *        
      17688 TTTCTTTAACATGCATAATC-CCTTCTTCTACC
          1 TTTCTTTATCATGCATAATCTCCTCCTTCTACC

               *                             
      17720 TTTTTTTATCATGCATAATCTCCTCCTTCTACC
          1 TTTCTTTATCATGCATAATCTCCTCCTTCTACC

                        
      17753 TTTCTTTATCAT
          1 TTTCTTTATCAT

      17765 TAAAAAAAAA


Statistics
Matches: 40,  Mismatches: 4, Indels: 1
        0.89            0.09        0.02

Matches are distributed among these distances:
  32   18  0.45
  33   22  0.55

ACGTcount: A:0.19, C:0.29, G:0.03, T:0.49


Consensus pattern (33 bp):   
TTTCTTTATCATGCATAATCTCCTCCTTCTACC

Found at i:19283 original size:38 final size:38

Alignment explanation


    Indices: 19235--19351  Score: 209
    Period size: 38  Copynumber: 3.1  Consensus size: 38

      19225 CTATATTGGG

                *                                 
      19235 TGTGAAAATTTGATTGATGGCTCCGGAAGAGCTAGTAT
          1 TGTGCAAATTTGATTGATGGCTCCGGAAGAGCTAGTAT

                                                  
      19273 TGTGCAAATTTGATTGATGGCTCCGGAAGAGCTAGTAT
          1 TGTGCAAATTTGATTGATGGCTCCGGAAGAGCTAGTAT

                                                   
      19311 TGTGCAAATTTGATTGAAT-GCTCCGGAAGAGCTAGTAT
          1 TGTGCAAATTTGATTG-ATGGCTCCGGAAGAGCTAGTAT

               
      19349 TGT
          1 TGT

      19352 TTTATTTGGA


Statistics
Matches: 77,  Mismatches: 1, Indels: 2
        0.96            0.01        0.03

Matches are distributed among these distances:
  38   75  0.97
  39    2  0.03

ACGTcount: A:0.27, C:0.12, G:0.28, T:0.32


Consensus pattern (38 bp):   
TGTGCAAATTTGATTGATGGCTCCGGAAGAGCTAGTAT

Found at i:20200 original size:82 final size:82

Alignment explanation


    Indices: 20063--20226  Score: 328
    Period size: 82  Copynumber: 2.0  Consensus size: 82

      20053 GTCTATTGGC

                                                                             
      20063 ATTGATGTTGGACATCCTGTAACACATGTTCATACACACAATGGTCTGGCAGAATCATTTCTCAA
          1 ATTGATGTTGGACATCCTGTAACACATGTTCATACACACAATGGTCTGGCAGAATCATTTCTCAA

                             
      20128 ACATCTGCAATTAATTG
         66 ACATCTGCAATTAATTG

                                                                             
      20145 ATTGATGTTGGACATCCTGTAACACATGTTCATACACACAATGGTCTGGCAGAATCATTTCTCAA
          1 ATTGATGTTGGACATCCTGTAACACATGTTCATACACACAATGGTCTGGCAGAATCATTTCTCAA

                             
      20210 ACATCTGCAATTAATTG
         66 ACATCTGCAATTAATTG

      20227 CTAGACTAAT


Statistics
Matches: 82,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  82   82  1.00

ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32


Consensus pattern (82 bp):   
ATTGATGTTGGACATCCTGTAACACATGTTCATACACACAATGGTCTGGCAGAATCATTTCTCAA
ACATCTGCAATTAATTG
Done.