Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003240.1 Corchorus capsularis cultivar CVL-1 contig03248, 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: 2035
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33


Found at i:275 original size:15 final size:15

Alignment explanation


    Indices: 255--291  Score: 58
    Period size: 15  Copynumber: 2.5  Consensus size: 15

        245 AAAAGGAAAG

                           
        255 AGAAAGAAGGAAAAC
          1 AGAAAGAAGGAAAAC

                  *        
        270 AGAAAGGAGGAAAAC
          1 AGAAAGAAGGAAAAC

                    
        285 A-AAAGAA
          1 AGAAAGAA

        292 ATAGTTAGAT


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  14    5  0.25
  15   15  0.75

ACGTcount: A:0.68, C:0.05, G:0.27, T:0.00


Consensus pattern (15 bp):   
AGAAAGAAGGAAAAC

Found at i:1584 original size:26 final size:25

Alignment explanation


    Indices: 1555--1604  Score: 82
    Period size: 26  Copynumber: 2.0  Consensus size: 25

       1545 TTGATTGCCA

                    *                 
       1555 ATTACCATTTTTTACTCTTTGTACTG
          1 ATTACCATATTTTACTCTTT-TACTG

                                    
       1581 ATTACCATATTTTACTCTTTTACT
          1 ATTACCATATTTTACTCTTTTACT

       1605 TTAATTACCC


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  25    4  0.17
  26   19  0.83

ACGTcount: A:0.22, C:0.20, G:0.04, T:0.54


Consensus pattern (25 bp):   
ATTACCATATTTTACTCTTTTACTG

Found at i:1619 original size:26 final size:25

Alignment explanation


    Indices: 1554--1624  Score: 81
    Period size: 26  Copynumber: 2.7  Consensus size: 25

       1544 TTTGATTGCC

                                      
       1554 AATTACCATTTTTTACTCTTTGTACT
          1 AATTACCA-TTTTTACTCTTTGTACT

            *                           
       1580 GATTACCATATTTTACTCTTT-TACTTT
          1 AATTACCAT-TTTTACTCTTTGTAC--T

                   *          
       1607 AATTACCCTTTTTACTCT
          1 AATTACCATTTTTACTCT

       1625 CTCTTTCTTA


Statistics
Matches: 39,  Mismatches: 3, Indels: 6
        0.81            0.06        0.12

Matches are distributed among these distances:
  25    4  0.10
  26   27  0.69
  27    8  0.21

ACGTcount: A:0.23, C:0.21, G:0.03, T:0.54


Consensus pattern (25 bp):   
AATTACCATTTTTACTCTTTGTACT

Found at i:1662 original size:30 final size:32

Alignment explanation


    Indices: 1600--1662  Score: 85
    Period size: 30  Copynumber: 2.0  Consensus size: 32

       1590 TTTTACTCTT

                          *    *            
       1600 TTACTTTAATTACCCTTTTTACTCTCTCTTTC
          1 TTACTTTAATTACCATTTTCACTCTCTCTTTC

                                       *    
       1632 TTAC-TTAA-TACCATTTTCACTCTCTTTTTC
          1 TTACTTTAATTACCATTTTCACTCTCTCTTTC

             
       1662 T
          1 T

       1663 ATTGATCACC


Statistics
Matches: 28,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  30   20  0.71
  31    4  0.14
  32    4  0.14

ACGTcount: A:0.17, C:0.27, G:0.00, T:0.56


Consensus pattern (32 bp):   
TTACTTTAATTACCATTTTCACTCTCTCTTTC

Found at i:1684 original size:30 final size:30

Alignment explanation


    Indices: 1600--1684  Score: 84
    Period size: 30  Copynumber: 2.8  Consensus size: 30

       1590 TTTTACTCTT

                          *                 
       1600 TTACTTTAATTACCCTTTTTACTCTCTCTTTC
          1 TTAC-TTAA-TACCATTTTTACTCTCTCTTTC

                             *       *    
       1632 TTACTTAATACCATTTTCACTCTCTTTTTC
          1 TTACTTAATACCATTTTTACTCTCTCTTTC

                  *                  
       1662 -TA-TTGATCACCATTTCTTACTCT
          1 TTACTTAAT-ACCATTT-TTACTCT

       1685 TTACTACTAA


Statistics
Matches: 46,  Mismatches: 5, Indels: 6
        0.81            0.09        0.11

Matches are distributed among these distances:
  28    4  0.09
  29    9  0.20
  30   25  0.54
  31    4  0.09
  32    4  0.09

ACGTcount: A:0.19, C:0.27, G:0.01, T:0.53


Consensus pattern (30 bp):   
TTACTTAATACCATTTTTACTCTCTCTTTC
Done.