Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010720.1 Corchorus olitorius cultivar O-4 contig10752, 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: 3855
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:1027 original size:13 final size:14

Alignment explanation


    Indices: 1009--1039  Score: 55
    Period size: 13  Copynumber: 2.3  Consensus size: 14

        999 AGCTTCCTAG

                          
       1009 AAAAACTCAAAA-A
          1 AAAAACTCAAAAGA

                          
       1022 AAAAACTCAAAAGA
          1 AAAAACTCAAAAGA

                
       1036 AAAA
          1 AAAA

       1040 TTGTTAGTAG


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13   12  0.71
  14    5  0.29

ACGTcount: A:0.77, C:0.13, G:0.03, T:0.06


Consensus pattern (14 bp):   
AAAAACTCAAAAGA

Found at i:1228 original size:21 final size:21

Alignment explanation


    Indices: 1198--1244  Score: 60
    Period size: 20  Copynumber: 2.2  Consensus size: 21

       1188 TTTTTTTTTC

                           *      
       1198 AAAAAGACGCAAACACAAAAAT
          1 AAAAAGACGCAAA-AAAAAAAT

                                 
       1220 AAAAA-ACGCAAAAAAAAAAT
          1 AAAAAGACGCAAAAAAAAAAT

            *    
       1240 CAAAA
          1 AAAAA

       1245 TTTTTTTATA


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  20   11  0.48
  21    7  0.30
  22    5  0.22

ACGTcount: A:0.74, C:0.15, G:0.06, T:0.04


Consensus pattern (21 bp):   
AAAAAGACGCAAAAAAAAAAT

Found at i:1629 original size:16 final size:15

Alignment explanation


    Indices: 1588--1629  Score: 57
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       1578 ACAGAGATTG

                   *       
       1588 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                *          
       1603 ACAGTAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       1618 ACTAGAAAACAA
          1 AC-AGAAAACAA

       1630 AGCAGAGTAA


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  15   15  0.65
  16    8  0.35

ACGTcount: A:0.62, C:0.14, G:0.10, T:0.14


Consensus pattern (15 bp):   
ACAGAAAACAATTAA
Done.