Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022995.1 Corchorus olitorius cultivar O-4 contig23028, 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: 29157
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:3689 original size:2 final size:2

Alignment explanation


    Indices: 3682--3706  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       3672 TATTTACTAG

                                                 
       3682 TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T

       3707 TATCCCATAA


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

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:8168 original size:2 final size:2

Alignment explanation


    Indices: 8161--8194  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       8151 TTTACTAGTG

                                                              
       8161 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       8195 AGGATTGCTT


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:10104 original size:13 final size:13

Alignment explanation


    Indices: 10075--10103  Score: 51
    Period size: 13  Copynumber: 2.3  Consensus size: 13

      10065 TAATGCACCC

                         
      10075 AAAATCATTTAAT
          1 AAAATCATTTAAT

                         
      10088 AAAATCATTT-AT
          1 AAAATCATTTAAT

                
      10100 AAAA
          1 AAAA

      10104 AAAAATTAAT


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

Matches are distributed among these distances:
  12    6  0.38
  13   10  0.62

ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34


Consensus pattern (13 bp):   
AAAATCATTTAAT

Found at i:11677 original size:2 final size:2

Alignment explanation


    Indices: 11670--11702  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

      11660 TGTCTCAATA

                                                             
      11670 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
          1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A

      11703 TATATATATA


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00


Consensus pattern (2 bp):   
AC

Found at i:14439 original size:15 final size:15

Alignment explanation


    Indices: 14419--14451  Score: 66
    Period size: 15  Copynumber: 2.2  Consensus size: 15

      14409 TTATATATCC

                           
      14419 ATCACATTTCCTTAA
          1 ATCACATTTCCTTAA

                           
      14434 ATCACATTTCCTTAA
          1 ATCACATTTCCTTAA

               
      14449 ATC
          1 ATC

      14452 GAAATTATTT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   18  1.00

ACGTcount: A:0.33, C:0.27, G:0.00, T:0.39


Consensus pattern (15 bp):   
ATCACATTTCCTTAA

Found at i:25861 original size:11 final size:11

Alignment explanation


    Indices: 25845--25869  Score: 50
    Period size: 11  Copynumber: 2.3  Consensus size: 11

      25835 TTTTGGCAAG

                       
      25845 ATAATTTCCAA
          1 ATAATTTCCAA

                       
      25856 ATAATTTCCAA
          1 ATAATTTCCAA

               
      25867 ATA
          1 ATA

      25870 TTTGATTTTT


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

Matches are distributed among these distances:
  11   14  1.00

ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36


Consensus pattern (11 bp):   
ATAATTTCCAA
Done.