Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019285.1 Corchorus olitorius cultivar O-4 contig19318, 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: 9836
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.34


Found at i:2609 original size:35 final size:35

Alignment explanation


    Indices: 2569--2700  Score: 151
    Period size: 35  Copynumber: 3.7  Consensus size: 35

       2559 CACCAGGTCA

                   *                           
       2569 AAGTTTTTAAATTGGGAAAGTTCCCACCAGTTTTT
          1 AAGTTTTCAAATTGGGAAAGTTCCCACCAGTTTTT

                                       * *     **
       2604 AAGTTTTCAAATTGGGAAAGTTCCCATTCGGTTTCCA
          1 AAGTTTTCAAATTGGGAAAGTTCCCA-CCAGTTT-TT

                   *                            
       2641 AAGTTTTTAAATTGGGAAAGTTCCCACCAAG-TTTT
          1 AAGTTTTCAAATTGGGAAAGTTCCCACC-AGTTTTT

                      *               
       2676 -AGTTTTCAATTTAGGGAAAGTTCCC
          1 AAGTTTTCAAATT-GGGAAAGTTCCC

       2701 GTCATTTTCG


Statistics
Matches: 81,  Mismatches: 12, Indels: 8
        0.80            0.12        0.08

Matches are distributed among these distances:
  34   10  0.12
  35   37  0.46
  36    8  0.10
  37   26  0.32

ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37


Consensus pattern (35 bp):   
AAGTTTTCAAATTGGGAAAGTTCCCACCAGTTTTT

Found at i:2693 original size:72 final size:72

Alignment explanation


    Indices: 2567--2700  Score: 227
    Period size: 72  Copynumber: 1.9  Consensus size: 72

       2557 TTCACCAGGT

                                                                             
       2567 CAAAGTTTTTAAATTGGGAAAGTTCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGTTCCCATT
          1 CAAAGTTTTTAAATTGGGAAAGTTCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGTTCCCATT

                   
       2632 CGGTTTC
         66 CGGTTTC

                                                            *               
       2639 CAAAGTTTTTAAATTGGGAAAGTTCCCACCAAG-TTTT-AGTTTTCAATTTAGGGAAAGTTCCC
          1 CAAAGTTTTTAAATTGGGAAAGTTCCCACC-AGTTTTTAAGTTTTCAAATT-GGGAAAGTTCCC

       2701 GTCATTTTCG


Statistics
Matches: 59,  Mismatches: 1, Indels: 4
        0.92            0.02        0.06

Matches are distributed among these distances:
  71   11  0.19
  72   46  0.78
  73    2  0.03

ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37


Consensus pattern (72 bp):   
CAAAGTTTTTAAATTGGGAAAGTTCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGTTCCCATT
CGGTTTC

Found at i:3721 original size:21 final size:21

Alignment explanation


    Indices: 3691--3730  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       3681 TGAAATCGAT

                 *       *       
       3691 TTGCTTAAGTCGATTTCTCCC
          1 TTGCTCAAGTCGACTTCTCCC

                               
       3712 TTGCTCAAGTCGACTTCTC
          1 TTGCTCAAGTCGACTTCTC

       3731 TCTTAAACAA


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

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.15, C:0.30, G:0.15, T:0.40


Consensus pattern (21 bp):   
TTGCTCAAGTCGACTTCTCCC
Done.