Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018778.1 Corchorus olitorius cultivar O-4 contig18811, 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: 2254
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30


Found at i:1049 original size:26 final size:27

Alignment explanation


    Indices: 1020--1080  Score: 81
    Period size: 26  Copynumber: 2.3  Consensus size: 27

       1010 CACGCAGACA

                                        
       1020 AAAAATTTTTTT-AGAAAACGCAAAAC-
          1 AAAAATTTTTTTCA-AAAACGCAAAACT

                *                      
       1046 AAAATTTTTTTTCAAAAACGCAAAACT
          1 AAAAATTTTTTTCAAAAACGCAAAACT

                    
       1073 AATAAATT
          1 AA-AAATT

       1081 AAAAACGTAA


Statistics
Matches: 30,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  26   23  0.77
  27    3  0.10
  28    4  0.13

ACGTcount: A:0.52, C:0.11, G:0.05, T:0.31


Consensus pattern (27 bp):   
AAAAATTTTTTTCAAAAACGCAAAACT

Found at i:1131 original size:25 final size:25

Alignment explanation


    Indices: 1092--1141  Score: 84
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       1082 AAAACGTAAG

                                      
       1092 AAAACTTTTTTTTATGACGCAGAAAT
          1 AAAACTTTTTTTTATGACGCA-AAAT

                                     
       1118 AAAA-TTTTTTTTATGACGCAAAAT
          1 AAAACTTTTTTTTATGACGCAAAAT

       1142 TTTTTTTTTT


Statistics
Matches: 24,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  24    4  0.17
  25   16  0.67
  26    4  0.17

ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40


Consensus pattern (25 bp):   
AAAACTTTTTTTTATGACGCAAAAT

Found at i:1147 original size:22 final size:23

Alignment explanation


    Indices: 1097--1162  Score: 73
    Period size: 25  Copynumber: 2.8  Consensus size: 23

       1087 GTAAGAAAAC

                                     
       1097 TTTTTTTTATGACGCAGAAATAAAA
          1 TTTTTTTTATGACGCA-AAAT-AAA

                                  *
       1122 TTTTTTTTATGACGCAAAAT--T
          1 TTTTTTTTATGACGCAAAATAAA

                    *           
       1143 TTTTTTTTTTCGACGCAAAA
          1 TTTTTTTTAT-GACGCAAAA

       1163 CACAAAATTT


Statistics
Matches: 38,  Mismatches: 2, Indels: 5
        0.84            0.04        0.11

Matches are distributed among these distances:
  21    9  0.24
  22    9  0.24
  24    4  0.11
  25   16  0.42

ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47


Consensus pattern (23 bp):   
TTTTTTTTATGACGCAAAATAAA

Found at i:1534 original size:16 final size:15

Alignment explanation


    Indices: 1495--1536  Score: 57
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       1485 CTCAAAAATG

                   *       
       1495 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
       1510 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

               *        
       1525 ACTGGAAAACAA
          1 AC-AGAAAACAA

       1537 AGCAGAGTAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  15   16  0.67
  16    8  0.33

ACGTcount: A:0.62, C:0.14, G:0.12, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA
Done.