Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012389.1 Corchorus capsularis cultivar CVL-1 contig12410, 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: 27123
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:6006 original size:4 final size:4

Alignment explanation


    Indices: 5997--6023  Score: 54
    Period size: 4  Copynumber: 6.8  Consensus size: 4

       5987 TCCCTCTTCT

                                             
       5997 TTTC TTTC TTTC TTTC TTTC TTTC TTT
          1 TTTC TTTC TTTC TTTC TTTC TTTC TTT

       6024 TTCTCAGGAA


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

Matches are distributed among these distances:
   4   23  1.00

ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78


Consensus pattern (4 bp):   
TTTC

Found at i:20215 original size:17 final size:17

Alignment explanation


    Indices: 20187--20239  Score: 88
    Period size: 17  Copynumber: 3.1  Consensus size: 17

      20177 GCCTTGCACG

                             
      20187 TGGCACGTGACCTAATA
          1 TGGCACGTGACCTAATA

               * *           
      20204 TGGTATGTGACCTAATA
          1 TGGCACGTGACCTAATA

                             
      20221 TGGCACGTGACCTAATA
          1 TGGCACGTGACCTAATA

              
      20238 TG
          1 TG

      20240 TTTTAATTAA


Statistics
Matches: 32,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  17   32  1.00

ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28


Consensus pattern (17 bp):   
TGGCACGTGACCTAATA

Found at i:25625 original size:30 final size:30

Alignment explanation


    Indices: 25589--25648  Score: 93
    Period size: 30  Copynumber: 2.0  Consensus size: 30

      25579 CGGTAGGAAC

                                 *        
      25589 ATGCATTAATCACATTGAAGCTAACTTGAG
          1 ATGCATTAATCACATTGAAGCCAACTTGAG

                         *    *           
      25619 ATGCATTAATCACGTTGAGGCCAACTTGAG
          1 ATGCATTAATCACATTGAAGCCAACTTGAG

      25649 GGTTTAATTC


Statistics
Matches: 27,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  30   27  1.00

ACGTcount: A:0.33, C:0.18, G:0.20, T:0.28


Consensus pattern (30 bp):   
ATGCATTAATCACATTGAAGCCAACTTGAG
Done.