Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017935.1 Corchorus olitorius cultivar O-4 contig17968, 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: 5804
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33


Found at i:3272 original size:21 final size:21

Alignment explanation


    Indices: 3255--3294  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       3245 TTCTCATTAT

                                 
       3255 CATCAGCTTCATCTTCATCTA
          1 CATCAGCTTCATCTTCATCTA

                **             
       3276 CATCTTCTTCATCTTCATC
          1 CATCAGCTTCATCTTCATC

       3295 ATCTGGATCT


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

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.20, C:0.35, G:0.03, T:0.42


Consensus pattern (21 bp):   
CATCAGCTTCATCTTCATCTA

Found at i:5033 original size:14 final size:15

Alignment explanation


    Indices: 5005--5035  Score: 55
    Period size: 14  Copynumber: 2.1  Consensus size: 15

       4995 ACTTTTTAGA

                           
       5005 TTTATTTTATTTATT
          1 TTTATTTTATTTATT

                           
       5020 TTTATTTT-TTTATT
          1 TTTATTTTATTTATT

              
       5034 TT
          1 TT

       5036 CTGAATTTTT


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

Matches are distributed among these distances:
  14    8  0.50
  15    8  0.50

ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84


Consensus pattern (15 bp):   
TTTATTTTATTTATT

Found at i:5033 original size:23 final size:23

Alignment explanation


    Indices: 5005--5053  Score: 62
    Period size: 23  Copynumber: 2.1  Consensus size: 23

       4995 ACTTTTTAGA

                      **       *   
       5005 TTTATTTTATTTATTTTTATTTT
          1 TTTATTTTATGAATTTTTAATTT

                    *              
       5028 TTTATTTTCTGAATTTTTAATTT
          1 TTTATTTTATGAATTTTTAATTT

               
       5051 TTT
          1 TTT

       5054 CCAAAATTAT


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  23   22  1.00

ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78


Consensus pattern (23 bp):   
TTTATTTTATGAATTTTTAATTT

Found at i:5287 original size:29 final size:27

Alignment explanation


    Indices: 5209--5287  Score: 68
    Period size: 29  Copynumber: 2.7  Consensus size: 27

       5199 GGCTCACTTT

                  *                      
       5209 TGAAACGTAAGGGATTAATTTGTCCCAAA
          1 TGAAACATAAGGGATT--TTTGTCCCAAA

            **        *                   
       5238 AAAAACATAAAGGATTATTTTGTCCCGAAA
          1 TGAAACATAAGGGA-T-TTTTGTCCC-AAA

                                
       5268 GTGAAACATAAGGGATTTTT
          1 -TGAAACATAAGGGATTTTT

       5288 TTGGGTATTT


Statistics
Matches: 39,  Mismatches: 7, Indels: 8
        0.72            0.13        0.15

Matches are distributed among these distances:
  29   22  0.56
  30    5  0.13
  31   12  0.31

ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29


Consensus pattern (27 bp):   
TGAAACATAAGGGATTTTTGTCCCAAA
Done.