Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001328.1 Corchorus capsularis cultivar CVL-1 contig01328, 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: 1759
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30


Found at i:275 original size:8 final size:8

Alignment explanation


    Indices: 262--295  Score: 50
    Period size: 8  Copynumber: 4.1  Consensus size: 8

        252 TTCTTGAAAA

                    
        262 AAAAATTC
          1 AAAAATTC

                    
        270 AAAAATTC
          1 AAAAATTC

                 *   
        278 AGAAACTTC
          1 A-AAAATTC

                    
        287 AAAAATTC
          1 AAAAATTC

             
        295 A
          1 A

        296 TACCCGATTC


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
   8   16  0.70
   9    7  0.30

ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24


Consensus pattern (8 bp):   
AAAAATTC

Found at i:393 original size:16 final size:17

Alignment explanation


    Indices: 368--399  Score: 57
    Period size: 16  Copynumber: 1.9  Consensus size: 17

        358 AGTTATATCG

                             
        368 AAAAATATAAAAAAAAT
          1 AAAAATATAAAAAAAAT

                            
        385 AAAAA-ATAAAAAAAA
          1 AAAAATATAAAAAAAA

        400 ATTCGACCAG


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16   10  0.67
  17    5  0.33

ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12


Consensus pattern (17 bp):   
AAAAATATAAAAAAAAT

Found at i:396 original size:17 final size:18

Alignment explanation


    Indices: 368--401  Score: 61
    Period size: 17  Copynumber: 1.9  Consensus size: 18

        358 AGTTATATCG

                              
        368 AAAAATATAAAAAAAATA
          1 AAAAATATAAAAAAAATA

                             
        386 AAAAATA-AAAAAAAAT
          1 AAAAATATAAAAAAAAT

        402 TCGACCAGAA


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  17    9  0.56
  18    7  0.44

ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15


Consensus pattern (18 bp):   
AAAAATATAAAAAAAATA
Done.