Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015561.1 Corchorus capsularis cultivar CVL-1 contig15582, 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: 8938
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32


Found at i:1309 original size:14 final size:14

Alignment explanation


    Indices: 1290--1317  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

       1280 GGCCGATTAG

                          
       1290 AGGAGAAGTCGACT
          1 AGGAGAAGTCGACT

                          
       1304 AGGAGAAGTCGACT
          1 AGGAGAAGTCGACT

       1318 TTACAAAGAG


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.36, C:0.14, G:0.36, T:0.14


Consensus pattern (14 bp):   
AGGAGAAGTCGACT

Found at i:3955 original size:19 final size:18

Alignment explanation


    Indices: 3931--3966  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       3921 TGAAGATTTC

                               
       3931 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
       3950 TTGAAGATCATTGAAGA
          1 TTGAAGATAATTGAAGA

       3967 ATTATTTCAA


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

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

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


Consensus pattern (18 bp):   
TTGAAGATAATTGAAGAT

Found at i:5269 original size:15 final size:16

Alignment explanation


    Indices: 5249--5282  Score: 52
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       5239 GATTGCTTTC

                         *  
       5249 TTAGTTA-ATTTACTT
          1 TTAGTTAGATTTAATT

                            
       5264 TTAGTTAGATTTAATT
          1 TTAGTTAGATTTAATT

               
       5280 TTA
          1 TTA

       5283 ATTCTTCTCT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  15    7  0.41
  16   10  0.59

ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59


Consensus pattern (16 bp):   
TTAGTTAGATTTAATT

Done.