Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010927.1 Corchorus capsularis cultivar CVL-1 contig10948, 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: 8313
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:5118 original size:37 final size:37

Alignment explanation


    Indices: 5074--5144  Score: 115
    Period size: 37  Copynumber: 1.9  Consensus size: 37

       5064 CTTGATCAAC

                        ** *                     
       5074 ATACATGTCTTTTTATATAGACATAACTTTATGATCA
          1 ATACATGTCTTTCCAAATAGACATAACTTTATGATCA

                                              
       5111 ATACATGTCTTTCCAAATAGACATAACTTTATGA
          1 ATACATGTCTTTCCAAATAGACATAACTTTATGA

       5145 ATAATTATAT


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  37   31  1.00

ACGTcount: A:0.37, C:0.15, G:0.08, T:0.39


Consensus pattern (37 bp):   
ATACATGTCTTTCCAAATAGACATAACTTTATGATCA

Found at i:5210 original size:31 final size:31

Alignment explanation


    Indices: 5173--5232  Score: 102
    Period size: 31  Copynumber: 1.9  Consensus size: 31

       5163 TACCTTTTAT

                      *    *               
       5173 AGACAAATAATTCTCTTCATAATTGTTCATA
          1 AGACAAATAAGTCTCGTCATAATTGTTCATA

                                         
       5204 AGACAAATAAGTCTCGTCATAATTGTTCA
          1 AGACAAATAAGTCTCGTCATAATTGTTCA

       5233 CTTATGAACA


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  31   27  1.00

ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35


Consensus pattern (31 bp):   
AGACAAATAAGTCTCGTCATAATTGTTCATA

Found at i:6403 original size:31 final size:32

Alignment explanation


    Indices: 6355--6418  Score: 94
    Period size: 31  Copynumber: 2.0  Consensus size: 32

       6345 CATCATAGTG

                                        *   
       6355 ATATAACTCTTTTGTTTCTCTAAGAAACTAAC
          1 ATATAACTCTTTTGTTTCTCTAAGAAACCAAC

                 *             *            
       6387 ATATATCTC-TTTGTTTCTTTAAGAAACCAAC
          1 ATATAACTCTTTTGTTTCTCTAAGAAACCAAC

             
       6418 A
          1 A

       6419 CGCCCCCACT


Statistics
Matches: 29,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  31   21  0.72
  32    8  0.28

ACGTcount: A:0.34, C:0.19, G:0.06, T:0.41


Consensus pattern (32 bp):   
ATATAACTCTTTTGTTTCTCTAAGAAACCAAC

Found at i:7610 original size:37 final size:38

Alignment explanation


    Indices: 7555--7633  Score: 115
    Period size: 37  Copynumber: 2.1  Consensus size: 38

       7545 CTTATATACT

                                *  *               
       7555 TGATCAACATACATGTCTTTTCATATAAACATAACTTTA
          1 TGATCAACA-ACATGTCTTTCCAAATAAACATAACTTTA

                                      *           
       7594 TGATCAAC-ACATGTCTTTCCAAATAGACATAACTTTA
          1 TGATCAACAACATGTCTTTCCAAATAAACATAACTTTA

               
       7631 TGA
          1 TGA

       7634 ATAATTATAT


Statistics
Matches: 37,  Mismatches: 3, Indels: 2
        0.88            0.07        0.05

Matches are distributed among these distances:
  37   29  0.78
  39    8  0.22

ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35


Consensus pattern (38 bp):   
TGATCAACAACATGTCTTTCCAAATAAACATAACTTTA

Found at i:7699 original size:31 final size:31

Alignment explanation


    Indices: 7662--7721  Score: 102
    Period size: 31  Copynumber: 1.9  Consensus size: 31

       7652 TACCTTTTAT

                      *    *               
       7662 AGACAAATAATTCTCTTCATAATTGTTCATA
          1 AGACAAATAAGTCTCGTCATAATTGTTCATA

                                         
       7693 AGACAAATAAGTCTCGTCATAATTGTTCA
          1 AGACAAATAAGTCTCGTCATAATTGTTCA

       7722 CTTATGAACA


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  31   27  1.00

ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35


Consensus pattern (31 bp):   
AGACAAATAAGTCTCGTCATAATTGTTCATA

Found at i:8282 original size:1 final size:1

Alignment explanation


    Indices: 8276--8308  Score: 57
    Period size: 1  Copynumber: 33.0  Consensus size: 1

       8266 GCTTACTCTC

                                   *         
       8276 TTTTTTTTTTTTTTTTTTTTTTTNTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

       8309 ACATA


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   1   30  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:0.97


Consensus pattern (1 bp):   
T

Done.