Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008787.1 Corchorus olitorius cultivar O-4 contig08814, 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, 603

Length: 1005
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33


Found at i:424 original size:13 final size:14

Alignment explanation


    Indices: 405--452  Score: 57
    Period size: 12  Copynumber: 3.6  Consensus size: 14

        395 AGATAGATCT

                          
        405 TTTCATAAACAGAA
          1 TTTCATAAACAGAA

                       *  
        419 -TTCATAAACATAA
          1 TTTCATAAACAGAA

                       *  
        432 TTTCAT--ACATAA
          1 TTTCATAAACAGAA

                     
        444 TTTCATAAA
          1 TTTCATAAA

        453 TTTTCTATCT


Statistics
Matches: 30,  Mismatches: 1, Indels: 6
        0.81            0.03        0.16

Matches are distributed among these distances:
  12   12  0.40
  13   12  0.40
  14    6  0.20

ACGTcount: A:0.48, C:0.15, G:0.02, T:0.35


Consensus pattern (14 bp):   
TTTCATAAACAGAA

Found at i:507 original size:14 final size:14

Alignment explanation


    Indices: 488--516  Score: 58
    Period size: 14  Copynumber: 2.1  Consensus size: 14

        478 AGATAGAAAA

                          
        488 TCAAAAATATATTC
          1 TCAAAAATATATTC

                          
        502 TCAAAAATATATTC
          1 TCAAAAATATATTC

             
        516 T
          1 T

        517 ATATATAATA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38


Consensus pattern (14 bp):   
TCAAAAATATATTC

Found at i:548 original size:22 final size:23

Alignment explanation


    Indices: 516--575  Score: 63
    Period size: 22  Copynumber: 2.7  Consensus size: 23

        506 AAATATATTC

                                    
        516 TATATATAATAGAATAA-ATAGAA
          1 TATATA-AATAGAATAATATAGAA

                          *         
        539 T-TATAGAATA-AAGAATATAGAA
          1 TATATA-AATAGAATAATATAGAA

              *            
        561 TAAATAAATAGAATA
          1 TATATAAATAGAATA

        576 TAGAAAATAG


Statistics
Matches: 30,  Mismatches: 4, Indels: 6
        0.75            0.10        0.15

Matches are distributed among these distances:
  21    4  0.13
  22   19  0.63
  23    7  0.23

ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28


Consensus pattern (23 bp):   
TATATAAATAGAATAATATAGAA

Found at i:559 original size:14 final size:14

Alignment explanation


    Indices: 524--595  Score: 76
    Period size: 14  Copynumber: 5.1  Consensus size: 14

        514 TCTATATATA

                             
        524 ATAGAATAAATAGAATT
          1 ATAGAAT-AA-AGAA-T

                          
        541 ATAGAATAAAGAAT
          1 ATAGAATAAAGAAT

                      *   
        555 ATAGAATAAATAA-
          1 ATAGAATAAAGAAT

                    *    *
        568 ATAGAATATAGAAA
          1 ATAGAATAAAGAAT

                          
        582 ATAGAATAAA-AAT
          1 ATAGAATAAAGAAT

             
        595 A
          1 A

        596 AATTTCGAAT


Statistics
Matches: 49,  Mismatches: 5, Indels: 6
        0.82            0.08        0.10

Matches are distributed among these distances:
  13   14  0.29
  14   22  0.45
  15    4  0.08
  16    2  0.04
  17    7  0.14

ACGTcount: A:0.65, C:0.00, G:0.11, T:0.24


Consensus pattern (14 bp):   
ATAGAATAAAGAAT

Found at i:740 original size:15 final size:15

Alignment explanation


    Indices: 720--748  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

        710 GTTTTGCAGT

                           
        720 TATATAGTACTATAC
          1 TATATAGTACTATAC

                          
        735 TATATAGTACTATA
          1 TATATAGTACTATA

        749 ATCGAAATTA


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

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41


Consensus pattern (15 bp):   
TATATAGTACTATAC
Done.