Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000809.1 Corchorus capsularis cultivar CVL-1 contig00809, 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: 7870
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33


Found at i:4186 original size:22 final size:21

Alignment explanation


    Indices: 4151--4195  Score: 56
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       4141 AATGTCTCCA

                                  
       4151 TTTTTTTACTTTTTCTTT-TGT
          1 TTTTTTTACTTTTT-TTTATGT

                   *              
       4172 TTTTTTTCCTATTTTTTTATGT
          1 TTTTTTTACT-TTTTTTTATGT

              
       4194 TT
          1 TT

       4196 ATATTTATAT


Statistics
Matches: 21,  Mismatches: 1, Indels: 3
        0.84            0.04        0.12

Matches are distributed among these distances:
  21   12  0.57
  22    9  0.43

ACGTcount: A:0.07, C:0.09, G:0.04, T:0.80


Consensus pattern (21 bp):   
TTTTTTTACTTTTTTTTATGT

Found at i:7352 original size:41 final size:41

Alignment explanation


    Indices: 7305--7403  Score: 126
    Period size: 41  Copynumber: 2.4  Consensus size: 41

       7295 CTTGTGTTAC

                   **             *    **            
       7305 ATGTGCTCAAGGACTTTGATATGGATGTTTCTGTGTTATAA
          1 ATGTGCTTGAGGACTTTGATATAGATGCCTCTGTGTTATAA

                       *        *  *                 
       7346 ATGTGCTTGAGAACTTTGATGTATATGCCTCTGTGTTATAA
          1 ATGTGCTTGAGGACTTTGATATAGATGCCTCTGTGTTATAA

                             
       7387 ATGTGCTTGAGGACTTT
          1 ATGTGCTTGAGGACTTT

       7404 TAGGGAGAGT


Statistics
Matches: 49,  Mismatches: 9, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  41   49  1.00

ACGTcount: A:0.23, C:0.11, G:0.24, T:0.41


Consensus pattern (41 bp):   
ATGTGCTTGAGGACTTTGATATAGATGCCTCTGTGTTATAA

Found at i:7803 original size:2 final size:2

Alignment explanation


    Indices: 7798--7831  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       7788 TTTTTTCCTT

                                                              
       7798 TA TA 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

       7832 GAGTTTTAGA


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Done.