Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012354.1 Corchorus capsularis cultivar CVL-1 contig12375, 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: 15180
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32


Found at i:7 original size:1 final size:1

Alignment explanation


    Indices: 2--32  Score: 62
    Period size: 1  Copynumber: 31.0  Consensus size: 1

          1 T

                                           
          2 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

         33 CTCACTACAG


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   30  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:2816 original size:21 final size:21

Alignment explanation


    Indices: 2767--2816  Score: 57
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       2757 CATTTGATCA

                         *        
       2767 ACTTGTTCCTTTCTTTGTCTTT
          1 ACTT-TTCCTTTCCTTGTCTTT

               *                  
       2789 -CAATTTCCTTTCCTTGTCTTT
          1 AC-TTTTCCTTTCCTTGTCTTT

                   
       2810 ACTTTTC
          1 ACTTTTC

       2817 GATCACCCTT


Statistics
Matches: 23,  Mismatches: 3, Indels: 5
        0.74            0.10        0.16

Matches are distributed among these distances:
  21   21  0.91
  22    2  0.09

ACGTcount: A:0.08, C:0.26, G:0.06, T:0.60


Consensus pattern (21 bp):   
ACTTTTCCTTTCCTTGTCTTT

Found at i:14522 original size:2 final size:2

Alignment explanation


    Indices: 14515--14544  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

      14505 CAATATGCAA

                                                        
      14515 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      14545 TTCTTGTTAC


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:15135 original size:17 final size:17

Alignment explanation


    Indices: 15101--15156  Score: 53
    Period size: 17  Copynumber: 3.3  Consensus size: 17

      15091 TAATTCTATT

                              
      15101 TATTATA-TAATATATAA
          1 TATTATATTAATAT-TAA

                      *      
      15118 TATTATATTACTATTAA
          1 TATTATATTAATATTAA

                       *     *
      15135 TA-TATTATTATTATTAC
          1 TATTA-TATTAATATTAA

                 
      15152 TATTA
          1 TATTA

      15157 AATAATTAAC


Statistics
Matches: 33,  Mismatches: 3, Indels: 5
        0.80            0.07        0.12

Matches are distributed among these distances:
  16    2  0.06
  17   24  0.73
  18    7  0.21

ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54


Consensus pattern (17 bp):   
TATTATATTAATATTAA
Done.