Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015266.1 Corchorus olitorius cultivar O-4 contig15299, 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: 16113
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:388 original size:14 final size:14

Alignment explanation


    Indices: 369--405  Score: 74
    Period size: 14  Copynumber: 2.6  Consensus size: 14

        359 ATTGTTTCCG

                          
        369 TTTTCTGTTGCCAA
          1 TTTTCTGTTGCCAA

                          
        383 TTTTCTGTTGCCAA
          1 TTTTCTGTTGCCAA

                     
        397 TTTTCTGTT
          1 TTTTCTGTT

        406 TTTGGAAACA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   23  1.00

ACGTcount: A:0.11, C:0.19, G:0.14, T:0.57


Consensus pattern (14 bp):   
TTTTCTGTTGCCAA

Found at i:687 original size:11 final size:11

Alignment explanation


    Indices: 671--702  Score: 55
    Period size: 11  Copynumber: 2.9  Consensus size: 11

        661 ACAGCGCAAT

                       
        671 AAAAACAAAAC
          1 AAAAACAAAAC

                  *    
        682 AAAAACGAAAC
          1 AAAAACAAAAC

                      
        693 AAAAACAAAA
          1 AAAAACAAAA

        703 AACAGAAAAA


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  11   19  1.00

ACGTcount: A:0.81, C:0.16, G:0.03, T:0.00


Consensus pattern (11 bp):   
AAAAACAAAAC

Found at i:4298 original size:21 final size:21

Alignment explanation


    Indices: 4274--4316  Score: 86
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       4264 CTCAAATTGG

                                 
       4274 ATTCACGTTATCTCGGTTTGA
          1 ATTCACGTTATCTCGGTTTGA

                                 
       4295 ATTCACGTTATCTCGGTTTGA
          1 ATTCACGTTATCTCGGTTTGA

             
       4316 A
          1 A

       4317 ATGTTTTAGT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   22  1.00

ACGTcount: A:0.21, C:0.19, G:0.19, T:0.42


Consensus pattern (21 bp):   
ATTCACGTTATCTCGGTTTGA

Found at i:15675 original size:18 final size:18

Alignment explanation


    Indices: 15647--15681  Score: 54
    Period size: 17  Copynumber: 1.9  Consensus size: 18

      15637 TGTTTAAATA

                               
      15647 AATTGAAAATTAAATTAAT
          1 AATTGAAAATT-AATTAAT

                             
      15666 AATT-AAAATTAATTAA
          1 AATTGAAAATTAATTAA

      15682 CACCGTATAT


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  17    6  0.38
  18    6  0.38
  19    4  0.25

ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37


Consensus pattern (18 bp):   
AATTGAAAATTAATTAAT
Done.