Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006725.1 Corchorus capsularis cultivar CVL-1 contig06746, 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: 8023
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29


Found at i:5385 original size:21 final size:21

Alignment explanation


    Indices: 5356--5398  Score: 77
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       5346 ATAGAGGTGG

                                 
       5356 CAAACGATTAAGTCTAGCAAT
          1 CAAACGATTAAGTCTAGCAAT

                *                
       5377 CAAATGATTAAGTCTAGCAAT
          1 CAAACGATTAAGTCTAGCAAT

             
       5398 C
          1 C

       5399 TCTACAGTCA


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.42, C:0.19, G:0.14, T:0.26


Consensus pattern (21 bp):   
CAAACGATTAAGTCTAGCAAT

Found at i:5758 original size:13 final size:13

Alignment explanation


    Indices: 5742--5766  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       5732 TGAAAAATAG

                         
       5742 GGAAAAAAAAACT
          1 GGAAAAAAAAACT

                        
       5755 GGAAAAAAAAAC
          1 GGAAAAAAAAAC

       5767 AACAGAACAT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.72, C:0.08, G:0.16, T:0.04


Consensus pattern (13 bp):   
GGAAAAAAAAACT

Found at i:7366 original size:17 final size:16

Alignment explanation


    Indices: 7312--7367  Score: 78
    Period size: 16  Copynumber: 3.5  Consensus size: 16

       7302 TTGGGTTCGG

                             
       7312 GTTTTTTCGGATTCTGA
          1 GTTTTTTCGGATT-TGA

                            
       7329 -TTTTTTCGGATTTGA
          1 GTTTTTTCGGATTTGA

             *             *
       7344 GCTTTTTCGGATTTGG
          1 GTTTTTTCGGATTTGA

                    
       7360 GTTTTTTC
          1 GTTTTTTC

       7368 AGGTTCGGAT


Statistics
Matches: 35,  Mismatches: 3, Indels: 3
        0.85            0.07        0.07

Matches are distributed among these distances:
  15    3  0.09
  16   32  0.91

ACGTcount: A:0.09, C:0.11, G:0.23, T:0.57


Consensus pattern (16 bp):   
GTTTTTTCGGATTTGA

Found at i:7869 original size:3 final size:3

Alignment explanation


    Indices: 7861--7909  Score: 82
    Period size: 3  Copynumber: 16.3  Consensus size: 3

       7851 CTACTCATCG

                                                                        
       7861 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TC GTTC
          1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC

                 
       7906 TTC T
          1 TTC T

       7910 CCTTGGCTTA


Statistics
Matches: 44,  Mismatches: 0, Indels: 4
        0.92            0.00        0.08

Matches are distributed among these distances:
   2    2  0.05
   3   40  0.91
   4    2  0.05

ACGTcount: A:0.00, C:0.33, G:0.02, T:0.65


Consensus pattern (3 bp):   
TTC

Done.