Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009442.1 Corchorus capsularis cultivar CVL-1 contig09463, 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: 3481
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31


Found at i:770 original size:35 final size:35

Alignment explanation


    Indices: 730--812  Score: 139
    Period size: 35  Copynumber: 2.4  Consensus size: 35

        720 TTTAGTTTCA

                                               
        730 GAACAATGGTTTGTAATCCTTAATTCCTAGTATCG
          1 GAACAATGGTTTGTAATCCTTAATTCCTAGTATCG

                                 *   *     *   
        765 GAACAATGGTTTGTAATCCTTGATTTCTAGTCTCG
          1 GAACAATGGTTTGTAATCCTTAATTCCTAGTATCG

                         
        800 GAACAATGGTTTG
          1 GAACAATGGTTTG

        813 ATGTTAGCAG


Statistics
Matches: 45,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  35   45  1.00

ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37


Consensus pattern (35 bp):   
GAACAATGGTTTGTAATCCTTAATTCCTAGTATCG

Found at i:1350 original size:6 final size:6

Alignment explanation


    Indices: 1341--1379  Score: 78
    Period size: 6  Copynumber: 6.5  Consensus size: 6

       1331 AAAGCAAAGC

                                                         
       1341 AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAA
          1 AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAA

       1380 GCAGATTATA


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   33  1.00

ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31


Consensus pattern (6 bp):   
AAATCT

Found at i:1391 original size:12 final size:13

Alignment explanation


    Indices: 1376--1420  Score: 74
    Period size: 13  Copynumber: 3.5  Consensus size: 13

       1366 AATCTAAATC

                         
       1376 TAAAGCAGATT-A
          1 TAAAGCAGATTAA

                   *     
       1388 TAAAGCAAATTAA
          1 TAAAGCAGATTAA

                         
       1401 TAAAGCAGATTAA
          1 TAAAGCAGATTAA

                   
       1414 TAAAGCA
          1 TAAAGCA

       1421 AACAATAATT


Statistics
Matches: 30,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  12   10  0.33
  13   20  0.67

ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22


Consensus pattern (13 bp):   
TAAAGCAGATTAA

Found at i:1427 original size:25 final size:25

Alignment explanation


    Indices: 1376--1428  Score: 81
    Period size: 25  Copynumber: 2.1  Consensus size: 25

       1366 AATCTAAATC

                                  *  
       1376 TAAAGCAGATTATAAAGCAAATTAA
          1 TAAAGCAGATTATAAAGCAAATCAA

                                      
       1401 TAAAGCAGATTAATAAAGCAAA-CAA
          1 TAAAGCAGATT-ATAAAGCAAATCAA

               
       1426 TAA
          1 TAA

       1429 TTAAAAAGCA


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  25   16  0.62
  26   10  0.38

ACGTcount: A:0.58, C:0.09, G:0.11, T:0.21


Consensus pattern (25 bp):   
TAAAGCAGATTATAAAGCAAATCAA
Done.