Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011444.1 Corchorus olitorius cultivar O-4 contig11477, 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: 15828
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.31


Found at i:6548 original size:39 final size:37

Alignment explanation


    Indices: 6504--6584  Score: 99
    Period size: 37  Copynumber: 2.1  Consensus size: 37

       6494 TTAAAATCTT

                                              **   
       6504 TTTGAAAAAAACATTTTTTCTCGTTTCAAAAGATTGCAC
          1 TTTGAAAAAAAC-TTTTTTC-CGTTTCAAAAGATCACAC

                  *             *   *            
       6543 TTTGAATAAAACTTTTTTCCTTTTGAAAAGATCACAC
          1 TTTGAAAAAAACTTTTTTCCGTTTCAAAAGATCACAC

                 
       6580 TTTGA
          1 TTTGA

       6585 GGAAGGTTTC


Statistics
Matches: 37,  Mismatches: 5, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
  37   19  0.51
  38    7  0.19
  39   11  0.30

ACGTcount: A:0.35, C:0.15, G:0.10, T:0.41


Consensus pattern (37 bp):   
TTTGAAAAAAACTTTTTTCCGTTTCAAAAGATCACAC

Found at i:7202 original size:14 final size:13

Alignment explanation


    Indices: 7167--7214  Score: 53
    Period size: 14  Copynumber: 3.5  Consensus size: 13

       7157 GAAAACCGAT

                       * 
       7167 TTTTTGAAAACCC
          1 TTTTTGAAAACAC

                          
       7180 TTTTCTGAAAACAC
          1 TTTT-TGAAAACAC

                           
       7194 TTTCTTGAAAAGCA-
          1 TTT-TTGAAAA-CAC

                   
       7208 TTTTTGA
          1 TTTTTGA

       7215 CATTTGAAAA


Statistics
Matches: 31,  Mismatches: 1, Indels: 6
        0.82            0.03        0.16

Matches are distributed among these distances:
  13    8  0.26
  14   20  0.65
  15    3  0.10

ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42


Consensus pattern (13 bp):   
TTTTTGAAAACAC

Found at i:13980 original size:5 final size:5

Alignment explanation


    Indices: 13952--13993  Score: 50
    Period size: 5  Copynumber: 8.4  Consensus size: 5

      13942 TCATTTCTTA

                                **                             
      13952 TTATT ATTATT TT-TT TCCTT TTATT TTATT TTATT TTATT TT
          1 TTATT -TTATT TTATT TTATT TTATT TTATT TTATT TTATT TT

      13994 CCTTTTCTTT


Statistics
Matches: 32,  Mismatches: 3, Indels: 3
        0.84            0.08        0.08

Matches are distributed among these distances:
   4    3  0.09
   5   24  0.75
   6    5  0.16

ACGTcount: A:0.17, C:0.05, G:0.00, T:0.79


Consensus pattern (5 bp):   
TTATT

Found at i:15790 original size:21 final size:22

Alignment explanation


    Indices: 15742--15809  Score: 77
    Period size: 21  Copynumber: 3.0  Consensus size: 22

      15732 CGTTTCATAA

                         *         
      15742 TTATATATAT-TATTATATATGT
          1 TTATATATATATAATATATAT-T

                        *           
      15764 AATTATATATATCTAATAT-TATT
          1 --TTATATATATATAATATATATT

                                  
      15787 TTATATATATATAATATATATT
          1 TTATATATATATAATATATATT

             
      15809 T
          1 T

      15810 AATTATAAAT


Statistics
Matches: 40,  Mismatches: 2, Indels: 6
        0.83            0.04        0.12

Matches are distributed among these distances:
  21   16  0.40
  22    5  0.12
  23    1  0.03
  24   13  0.32
  25    5  0.12

ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56


Consensus pattern (22 bp):   
TTATATATATATAATATATATT

Found at i:15810 original size:21 final size:20

Alignment explanation


    Indices: 15742--15823  Score: 71
    Period size: 21  Copynumber: 4.0  Consensus size: 20

      15732 CGTTTCATAA

                                   *
      15742 TTATATATATTATTATATATGTAA
          1 TTATATATA-TA-TA-ATAT-TAT

                      *          
      15766 TTATATATATCTAATATTATT
          1 TTATATATATATAATATTA-T

                                 
      15787 TTATATATATATAATATATAT
          1 TTATATATATATAATAT-TAT

                               
      15808 TTA-AT-TATA-AATATTA
          1 TTATATATATATAATATTA

      15824 CTAAA


Statistics
Matches: 53,  Mismatches: 3, Indels: 11
        0.79            0.04        0.16

Matches are distributed among these distances:
  17    2  0.04
  18    5  0.09
  19    4  0.08
  20    4  0.08
  21   24  0.45
  22    4  0.08
  23    1  0.02
  24    9  0.17

ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54


Consensus pattern (20 bp):   
TTATATATATATAATATTAT
Done.