Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011891.1 Corchorus olitorius cultivar O-4 contig11924, 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: 11632
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32


Found at i:2828 original size:21 final size:22

Alignment explanation


    Indices: 2799--2842  Score: 54
    Period size: 21  Copynumber: 2.0  Consensus size: 22

       2789 GATTGGAGTA

                        *         
       2799 TTTATTTATCTTGTTGCTTAAT
          1 TTTATTTATCTTCTTGCTTAAT

                     *      *     
       2821 TTTA-TTATTTTCTTGTTTAAT
          1 TTTATTTATCTTCTTGCTTAAT

             
       2842 T
          1 T

       2843 ATTTTATTGT


Statistics
Matches: 19,  Mismatches: 3, Indels: 1
        0.83            0.13        0.04

Matches are distributed among these distances:
  21   15  0.79
  22    4  0.21

ACGTcount: A:0.18, C:0.07, G:0.07, T:0.68


Consensus pattern (22 bp):   
TTTATTTATCTTCTTGCTTAAT

Found at i:6933 original size:23 final size:23

Alignment explanation


    Indices: 6907--6952  Score: 56
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       6897 TTACAATTAT

                       *           
       6907 GAAAATTATGAGAATTATCATGA
          1 GAAAATTATGAAAATTATCATGA

                *  *          *    
       6930 GAAAGTTGTGAAAATTATGATGA
          1 GAAAATTATGAAAATTATCATGA

       6953 TGAATTTCTA


Statistics
Matches: 19,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  23   19  1.00

ACGTcount: A:0.46, C:0.02, G:0.22, T:0.30


Consensus pattern (23 bp):   
GAAAATTATGAAAATTATCATGA

Found at i:8657 original size:16 final size:15

Alignment explanation


    Indices: 8619--8660  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       8609 ACAGAGATTG

                   *       
       8619 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
       8634 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       8649 ACTAGAAAACAA
          1 AC-AGAAAACAA

       8661 AGCAAAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:11492 original size:16 final size:16

Alignment explanation


    Indices: 11449--11496  Score: 55
    Period size: 16  Copynumber: 3.1  Consensus size: 16

      11439 TCGTTTGGCA

                           *
      11449 TCGTTTTCGTTTT-TC
          1 TCGTTTTCGTTTTGTT

                   *         
      11464 T-GTTTTTGTTTTTGTT
          1 TCGTTTTCG-TTTTGTT

                            
      11480 TCGTTTTCGTTTTGTT
          1 TCGTTTTCGTTTTGTT

             
      11496 T
          1 T

      11497 TTGTTGCGCT


Statistics
Matches: 27,  Mismatches: 3, Indels: 5
        0.77            0.09        0.14

Matches are distributed among these distances:
  14    6  0.22
  15    5  0.19
  16   10  0.37
  17    6  0.22

ACGTcount: A:0.00, C:0.10, G:0.17, T:0.73


Consensus pattern (16 bp):   
TCGTTTTCGTTTTGTT

Found at i:11495 original size:22 final size:25

Alignment explanation


    Indices: 11453--11501  Score: 77
    Period size: 22  Copynumber: 2.1  Consensus size: 25

      11443 TTGGCATCGT

                                     
      11453 TTTCGTTTTTCTGTTTTTGTTTTTG
          1 TTTCGTTTTTCTGTTTTTGTTTTTG

                                     
      11478 TTTCG-TTTTC-G-TTTTGTTTTTG
          1 TTTCGTTTTTCTGTTTTTGTTTTTG

              
      11500 TT
          1 TT

      11502 GCGCTGTCAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 3
        0.89            0.00        0.11

Matches are distributed among these distances:
  22   13  0.54
  23    1  0.04
  24    5  0.21
  25    5  0.21

ACGTcount: A:0.00, C:0.08, G:0.16, T:0.76


Consensus pattern (25 bp):   
TTTCGTTTTTCTGTTTTTGTTTTTG
Done.