Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014472.1 Corchorus olitorius cultivar O-4 contig14505, 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: 16524
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34


Found at i:1454 original size:13 final size:13

Alignment explanation


    Indices: 1436--1461  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       1426 CTTGGCATGA

                         
       1436 GTGATGATTTTTG
          1 GTGATGATTTTTG

                         
       1449 GTGATGATTTTTG
          1 GTGATGATTTTTG

       1462 TTGTTACCTT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54


Consensus pattern (13 bp):   
GTGATGATTTTTG

Found at i:1838 original size:19 final size:19

Alignment explanation


    Indices: 1816--1866  Score: 61
    Period size: 19  Copynumber: 2.7  Consensus size: 19

       1806 GGTCTGAAAT

                               
       1816 TAATTAATTATTAATTAAA
          1 TAATTAATTATTAATTAAA

                         *   *  
       1835 TAA-TAATTATTTTATTGAA
          1 TAATTAATTA-TTAATTAAA

                          
       1854 TAATT-ATTATTAA
          1 TAATTAATTATTAA

       1867 AAATCTTATG


Statistics
Matches: 27,  Mismatches: 3, Indels: 5
        0.77            0.09        0.14

Matches are distributed among these distances:
  18    9  0.33
  19   17  0.63
  20    1  0.04

ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51


Consensus pattern (19 bp):   
TAATTAATTATTAATTAAA

Found at i:14369 original size:39 final size:40

Alignment explanation


    Indices: 14313--14393  Score: 137
    Period size: 39  Copynumber: 2.0  Consensus size: 40

      14303 TTTAATTCCT

                                                    
      14313 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

                     *          *                   
      14353 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

              
      14392 AT
          1 AT

      14394 TCTTAGGTAT


Statistics
Matches: 39,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  39   31  0.79
  40    8  0.21

ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37


Consensus pattern (40 bp):   
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

Found at i:15473 original size:29 final size:29

Alignment explanation


    Indices: 15430--15489  Score: 75
    Period size: 29  Copynumber: 2.1  Consensus size: 29

      15420 ATTTTGGAGA

                *     *      *           
      15430 AATATGATAATCAAAATTACAAAAAATGT
          1 AATAAGATAACCAAAATCACAAAAAATGT

                               *    *    
      15459 AATAAGATAACCAAAATCATAAAAGATGT
          1 AATAAGATAACCAAAATCACAAAAAATGT

              
      15488 AA
          1 AA

      15490 GGTTATTGAA


Statistics
Matches: 26,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  29   26  1.00

ACGTcount: A:0.60, C:0.08, G:0.08, T:0.23


Consensus pattern (29 bp):   
AATAAGATAACCAAAATCACAAAAAATGT
Done.