Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014534.1 Corchorus olitorius cultivar O-4 contig14567, 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: 22881
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:4511 original size:14 final size:14

Alignment explanation


    Indices: 4492--4536  Score: 81
    Period size: 14  Copynumber: 3.2  Consensus size: 14

       4482 ATATCCAAAA

                          
       4492 TTTTTAAGGCCCAC
          1 TTTTTAAGGCCCAC

                         *
       4506 TTTTTAAGGCCCAA
          1 TTTTTAAGGCCCAC

                          
       4520 TTTTTAAGGCCCAC
          1 TTTTTAAGGCCCAC

               
       4534 TTT
          1 TTT

       4537 ATTCCTATAA


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  14   29  1.00

ACGTcount: A:0.22, C:0.24, G:0.13, T:0.40


Consensus pattern (14 bp):   
TTTTTAAGGCCCAC

Found at i:14128 original size:6 final size:6

Alignment explanation


    Indices: 14117--14143  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

      14107 AACCCATAAT

                                           
      14117 ATAAAG ATAAAG ATAAAG ATAAAG ATA
          1 ATAAAG ATAAAG ATAAAG ATAAAG ATA

      14144 TATCTTCTCC


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.67, C:0.00, G:0.15, T:0.19


Consensus pattern (6 bp):   
ATAAAG

Found at i:21368 original size:12 final size:12

Alignment explanation


    Indices: 21337--21374  Score: 51
    Period size: 12  Copynumber: 3.1  Consensus size: 12

      21327 TATATTAGGC

                         
      21337 TAATAAAAAAAGA
          1 TAATAAAAAAA-A

                         
      21350 -AAGTAAAAAAAA
          1 TAA-TAAAAAAAA

                        
      21362 TAATAAAAAAAA
          1 TAATAAAAAAAA

             
      21374 T
          1 T

      21375 CAAAATCAAG


Statistics
Matches: 23,  Mismatches: 0, Indels: 5
        0.82            0.00        0.18

Matches are distributed among these distances:
  12   13  0.57
  13   10  0.43

ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16


Consensus pattern (12 bp):   
TAATAAAAAAAA

Found at i:21379 original size:22 final size:23

Alignment explanation


    Indices: 21338--21421  Score: 70
    Period size: 22  Copynumber: 3.7  Consensus size: 23

      21328 ATATTAGGCT

                                     
      21338 AATAA-AAAAAGAAAGT-AAAAAA-
          1 AATAATAAAAA-AAA-TCAAAAAAG

                                     
      21360 AATAATAAAAAAAATCAAAATCAAG
          1 AATAATAAAAAAAATCAAAA--AAG

              *  *                 
      21385 AAAAAGAAAAAAAA-CAAAAAAG
          1 AATAATAAAAAAAATCAAAAAAG

                            
      21407 ACA-AATAAAAAAAAT
          1 A-ATAATAAAAAAAAT

      21422 TGATTAAAAA


Statistics
Matches: 52,  Mismatches: 3, Indels: 13
        0.76            0.04        0.19

Matches are distributed among these distances:
  21    1  0.02
  22   26  0.50
  23    6  0.12
  24    7  0.13
  25   12  0.23

ACGTcount: A:0.80, C:0.05, G:0.06, T:0.10


Consensus pattern (23 bp):   
AATAATAAAAAAAATCAAAAAAG
Done.