Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012291.1 Corchorus olitorius cultivar O-4 contig12324, 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: 14779
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31


Found at i:883 original size:24 final size:24

Alignment explanation


    Indices: 851--953  Score: 101
    Period size: 24  Copynumber: 4.3  Consensus size: 24

        841 AAAAATTTTC

                                    
        851 TTTTTTTTTATGACGCAAAAACTA
          1 TTTTTTTTTATGACGCAAAAACTA

                                         
        875 TTTTTTTTT-TAGAAAAACGCAAAAAC--
          1 TTTTTTTTTAT-G----ACGCAAAAACTA

                             *    * 
        901 --TTTTTTTATGACGCAGAAACAA
          1 TTTTTTTTTATGACGCAAAAACTA

                                    
        923 TTTTTTTTTATGACGCAAAAA-TA
          1 TTTTTTTTTATGACGCAAAAACTA

                    
        946 TTTTTTTT
          1 TTTTTTTT

        954 CCGACGCAAA


Statistics
Matches: 66,  Mismatches: 3, Indels: 21
        0.73            0.03        0.23

Matches are distributed among these distances:
  20    9  0.14
  23   10  0.15
  24   36  0.55
  25    1  0.02
  28   10  0.15

ACGTcount: A:0.34, C:0.11, G:0.09, T:0.47


Consensus pattern (24 bp):   
TTTTTTTTTATGACGCAAAAACTA

Found at i:953 original size:22 final size:21

Alignment explanation


    Indices: 852--964  Score: 84
    Period size: 22  Copynumber: 4.9  Consensus size: 21

        842 AAAATTTTCT

                                   
        852 TTTTTTTTATGACGCAAAAACTA
          1 TTTTTTTTATGACGCAAAAA--A

                    *                 
        875 TTTTTTTTTTAGAAAAACGC-AAAAA
          1 TTTTTTTTAT-G----ACGCAAAAAA

            *                      
        900 CTTTTTTTATGACGCAGAAACAA
          1 TTTTTTTTATGACGCA-AAA-AA

                                   
        923 TTTTTTTTTATGACGCAAAAATA
          1 -TTTTTTTTATGACGCAAAAA-A

                    **         
        946 TTTTTTTTCCGACGCAAAA
          1 TTTTTTTTATGACGCAAAA

        965 CACAACACAA


Statistics
Matches: 74,  Mismatches: 6, Indels: 21
        0.73            0.06        0.21

Matches are distributed among these distances:
  20    4  0.05
  22   21  0.28
  23   15  0.20
  24   17  0.23
  25    9  0.12
  27    4  0.05
  28    4  0.05

ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42


Consensus pattern (21 bp):   
TTTTTTTTATGACGCAAAAAA

Found at i:1414 original size:16 final size:15

Alignment explanation


    Indices: 1376--1417  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       1366 ACAGAGATTG

                   *       
       1376 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
       1391 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       1406 ACTAGAAAACAA
          1 AC-AGAAAACAA

       1418 AGCAAAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:11046 original size:19 final size:18

Alignment explanation


    Indices: 11013--11048  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      11003 TTGAGATAAT

                              
      11013 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
      11031 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

      11049 TAAGTCTTCA


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

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

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


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:11921 original size:18 final size:18

Alignment explanation


    Indices: 11898--11934  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

      11888 CTCCTCTATC

                     *        
      11898 ATGAAAACACTTCTTTTT
          1 ATGAAAACAATTCTTTTT

                        *     
      11916 ATGAAAACAATTTTTTTT
          1 ATGAAAACAATTCTTTTT

             
      11934 A
          1 A

      11935 ATTACCCTTT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46


Consensus pattern (18 bp):   
ATGAAAACAATTCTTTTT
Done.