Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006976.1 Corchorus capsularis cultivar CVL-1 contig06997, 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: 6737
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:2600 original size:12 final size:13

Alignment explanation


    Indices: 2559--2603  Score: 74
    Period size: 13  Copynumber: 3.5  Consensus size: 13

       2549 AATTATTGTT

                         
       2559 TGCTTTATTAATC
          1 TGCTTTATTAATC

                        *
       2572 TGCTTTATTAATT
          1 TGCTTTATTAATC

                         
       2585 TGCTTTA-TAATC
          1 TGCTTTATTAATC

                   
       2597 TGCTTTA
          1 TGCTTTA

       2604 GATTTAGATT


Statistics
Matches: 30,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  12   11  0.37
  13   19  0.63

ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56


Consensus pattern (13 bp):   
TGCTTTATTAATC

Found at i:2611 original size:6 final size:6

Alignment explanation


    Indices: 2600--2633  Score: 59
    Period size: 6  Copynumber: 5.5  Consensus size: 6

       2590 TATAATCTGC

                                                   
       2600 TTTAGA TTTAGA TTTAAGA TTTAGA TTTAGA TTT
          1 TTTAGA TTTAGA TTT-AGA TTTAGA TTTAGA TTT

       2634 GCTTTGCTTT


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

Matches are distributed among these distances:
   6   21  0.78
   7    6  0.22

ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53


Consensus pattern (6 bp):   
TTTAGA

Found at i:2621 original size:13 final size:12

Alignment explanation


    Indices: 2600--2633  Score: 59
    Period size: 13  Copynumber: 2.8  Consensus size: 12

       2590 TATAATCTGC

                        
       2600 TTTAGATTTAGA
          1 TTTAGATTTAGA

                         
       2612 TTTAAGATTTAGA
          1 TTT-AGATTTAGA

                     
       2625 TTTAGATTT
          1 TTTAGATTT

       2634 GCTTTGCTTT


Statistics
Matches: 21,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  12    9  0.43
  13   12  0.57

ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53


Consensus pattern (12 bp):   
TTTAGATTTAGA

Found at i:3152 original size:3 final size:3

Alignment explanation


    Indices: 3144--3175  Score: 55
    Period size: 3  Copynumber: 10.7  Consensus size: 3

       3134 AATTTAATTA

                                              *       
       3144 ATT ATT ATT ATT ATT ATT ATT ATT ATA ATT AT
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT

       3176 CAAGTTAGTA


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

Matches are distributed among these distances:
   3   27  1.00

ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62


Consensus pattern (3 bp):   
ATT

Done.