Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023969.1 Corchorus olitorius cultivar O-4 contig24002, 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: 11352
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.29


Found at i:2671 original size:22 final size:21

Alignment explanation


    Indices: 2619--2672  Score: 60
    Period size: 19  Copynumber: 2.6  Consensus size: 21

       2609 TGCTTCTTGA

                                  
       2619 AATAATTCTTC-AATGATCTTC
          1 AATAA-TCTTCAAATGATCTTC

                          *      
       2640 -A-AATCTTCAAATTATCTTC
          1 AATAATCTTCAAATGATCTTC

                          
       2659 AATAAGTCTTCAAA
          1 AATAA-TCTTCAAA

       2673 CACGAACTTC


Statistics
Matches: 28,  Mismatches: 1, Indels: 7
        0.78            0.03        0.19

Matches are distributed among these distances:
  18    5  0.18
  19   11  0.39
  20    2  0.07
  21    2  0.07
  22    8  0.29

ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39


Consensus pattern (21 bp):   
AATAATCTTCAAATGATCTTC

Found at i:4435 original size:17 final size:18

Alignment explanation


    Indices: 4403--4437  Score: 54
    Period size: 17  Copynumber: 1.9  Consensus size: 18

       4393 TGAAGACCAT

                               
       4403 TTGAAGATAATTTGAAGAC
          1 TTGAAGAT-ATTTGAAGAC

                             
       4422 TTGAAGAT-TTTGAAGA
          1 TTGAAGATATTTGAAGA

       4438 TTTATTTCAA


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  17    8  0.50
  19    8  0.50

ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34


Consensus pattern (18 bp):   
TTGAAGATATTTGAAGAC

Found at i:5842 original size:15 final size:16

Alignment explanation


    Indices: 5815--5853  Score: 55
    Period size: 15  Copynumber: 2.5  Consensus size: 16

       5805 CTTTGCTTTG

                             
       5815 TTTTCTAGTTTAATT-C
          1 TTTTCT-GTTTAATTGC

                            
       5831 TTTTCTGTTTAATTGC
          1 TTTTCTGTTTAATTGC

                    
       5847 -TTTCTGT
          1 TTTTCTGT

       5854 CAACCTCTGT


Statistics
Matches: 22,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  15   15  0.68
  16    7  0.32

ACGTcount: A:0.13, C:0.13, G:0.10, T:0.64


Consensus pattern (16 bp):   
TTTTCTGTTTAATTGC

Found at i:7623 original size:24 final size:24

Alignment explanation


    Indices: 7591--7637  Score: 85
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       7581 CCAGATGGGA

                          *         
       7591 ACCCATGGTATCATTATATTTTGT
          1 ACCCATGGTATCATGATATTTTGT

                                   
       7615 ACCCATGGTATCATGATATTTTG
          1 ACCCATGGTATCATGATATTTTG

       7638 AAGTATATCA


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   22  1.00

ACGTcount: A:0.26, C:0.17, G:0.15, T:0.43


Consensus pattern (24 bp):   
ACCCATGGTATCATGATATTTTGT
Done.