Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018775.1 Corchorus olitorius cultivar O-4 contig18808, 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: 7152
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:509 original size:21 final size:20

Alignment explanation


    Indices: 470--509  Score: 53
    Period size: 21  Copynumber: 1.9  Consensus size: 20

        460 ATTTGATGGG

                         **     
        470 GAAAATCCAAGCTTGATGAA
          1 GAAAATCCAAGCTCCATGAA

                                
        490 GAAAATCCCAAGCTCCATGA
          1 GAAAAT-CCAAGCTCCATGA

        510 GAGGTCTCCA


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  20    6  0.35
  21   11  0.65

ACGTcount: A:0.42, C:0.23, G:0.17, T:0.17


Consensus pattern (20 bp):   
GAAAATCCAAGCTCCATGAA

Found at i:1321 original size:18 final size:18

Alignment explanation


    Indices: 1298--1334  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       1288 CTCCTCTTGC

                     *        
       1298 ATGAAAACACTTCTTTTT
          1 ATGAAAACAATTCTTTTT

                        *     
       1316 ATGAAAACAATTTTTTTT
          1 ATGAAAACAATTCTTTTT

             
       1334 A
          1 A

       1335 ACTACCCTTT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46


Consensus pattern (18 bp):   
ATGAAAACAATTCTTTTT

Found at i:6403 original size:19 final size:18

Alignment explanation


    Indices: 6370--6405  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       6360 TTGAGATAAT

                              
       6370 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
       6388 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

       6406 TAAGTCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:7067 original size:19 final size:18

Alignment explanation


    Indices: 7047--7094  Score: 60
    Period size: 19  Copynumber: 2.6  Consensus size: 18

       7037 AATTAATTAT

                              
       7047 TTTAATATTAAATTTTTA
          1 TTTAATATTAAATTTTTA

                       *       
       7065 TTTATATATTATATTTTTA
          1 TTTA-ATATTAAATTTTTA

                  *    
       7084 CTTTAAAATTA
          1 -TTTAATATTA

       7095 CTCCTAATTA


Statistics
Matches: 26,  Mismatches: 2, Indels: 3
        0.84            0.06        0.10

Matches are distributed among these distances:
  18    4  0.15
  19   18  0.69
  20    4  0.15

ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60


Consensus pattern (18 bp):   
TTTAATATTAAATTTTTA
Done.