Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012021.1 Corchorus olitorius cultivar O-4 contig12054, 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: 23306
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34


Found at i:6538 original size:33 final size:33

Alignment explanation


    Indices: 6487--6550  Score: 110
    Period size: 33  Copynumber: 1.9  Consensus size: 33

       6477 CTTCAGCTCG

                    *    *                   
       6487 CTTGGATTGATCATCTCACTGACCTTTTGCTGA
          1 CTTGGATTAATCAGCTCACTGACCTTTTGCTGA

                                           
       6520 CTTGGATTAATCAGCTCACTGACCTTTTGCT
          1 CTTGGATTAATCAGCTCACTGACCTTTTGCT

       6551 AATCAGATGC


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  33   29  1.00

ACGTcount: A:0.19, C:0.25, G:0.17, T:0.39


Consensus pattern (33 bp):   
CTTGGATTAATCAGCTCACTGACCTTTTGCTGA

Found at i:9832 original size:80 final size:80

Alignment explanation


    Indices: 9705--9867  Score: 326
    Period size: 80  Copynumber: 2.0  Consensus size: 80

       9695 TTCTTTTCTC

                                                                             
       9705 TCTTTCTTTCTTCTTTTTATTTTTCTCCTTACAGTTTCTCACTCCATTTCCTCCCACCTTAACAA
          1 TCTTTCTTTCTTCTTTTTATTTTTCTCCTTACAGTTTCTCACTCCATTTCCTCCCACCTTAACAA

                           
       9770 TCTATCATCCCTTCA
         66 TCTATCATCCCTTCA

                                                                             
       9785 TCTTTCTTTCTTCTTTTTATTTTTCTCCTTACAGTTTCTCACTCCATTTCCTCCCACCTTAACAA
          1 TCTTTCTTTCTTCTTTTTATTTTTCTCCTTACAGTTTCTCACTCCATTTCCTCCCACCTTAACAA

                           
       9850 TCTATCATCCCTTCA
         66 TCTATCATCCCTTCA

               
       9865 TCT
          1 TCT

       9868 AATCCTTTGC


Statistics
Matches: 83,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  80   83  1.00

ACGTcount: A:0.16, C:0.34, G:0.01, T:0.49


Consensus pattern (80 bp):   
TCTTTCTTTCTTCTTTTTATTTTTCTCCTTACAGTTTCTCACTCCATTTCCTCCCACCTTAACAA
TCTATCATCCCTTCA

Found at i:11176 original size:18 final size:20

Alignment explanation


    Indices: 11153--11194  Score: 70
    Period size: 18  Copynumber: 2.2  Consensus size: 20

      11143 AATTAATTGA

                                
      11153 TTTTTTATTTTTT-AA-CTT
          1 TTTTTTATTTTTTCAACCTT

                                
      11171 TTTTTTATTTTTTCAACCTT
          1 TTTTTTATTTTTTCAACCTT

                
      11191 TTTT
          1 TTTT

      11195 CTTTCACATA


Statistics
Matches: 22,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  18   13  0.59
  19    2  0.09
  20    7  0.32

ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76


Consensus pattern (20 bp):   
TTTTTTATTTTTTCAACCTT

Found at i:11894 original size:19 final size:18

Alignment explanation


    Indices: 11859--11893  Score: 54
    Period size: 18  Copynumber: 1.9  Consensus size: 18

      11849 TGGACTCCTA

                              
      11859 TTTTCTTTGGGCCTTTTC
          1 TTTTCTTTGGGCCTTTTC

                              
      11877 TTTTCTTTTGGG-CTTTT
          1 TTTTC-TTTGGGCCTTTT

      11894 TTTATGTATC


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

Matches are distributed among these distances:
  18   10  0.62
  19    6  0.38

ACGTcount: A:0.00, C:0.17, G:0.17, T:0.66


Consensus pattern (18 bp):   
TTTTCTTTGGGCCTTTTC

Found at i:12732 original size:17 final size:17

Alignment explanation


    Indices: 12712--12746  Score: 70
    Period size: 17  Copynumber: 2.1  Consensus size: 17

      12702 CGCAATGCCC

                             
      12712 TTCAATCTTCAATCGGA
          1 TTCAATCTTCAATCGGA

                             
      12729 TTCAATCTTCAATCGGA
          1 TTCAATCTTCAATCGGA

             
      12746 T
          1 T

      12747 CTTTGATTGT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   18  1.00

ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37


Consensus pattern (17 bp):   
TTCAATCTTCAATCGGA

Found at i:16171 original size:16 final size:15

Alignment explanation


    Indices: 16131--16172  Score: 75
    Period size: 15  Copynumber: 2.7  Consensus size: 15

      16121 ACTACACACT

                           
      16131 CATGGTTGAAACAAC
          1 CATGGTTGAAACAAC

                           
      16146 CATGGTTGAAACAAC
          1 CATGGTTGAAACAAC

                        
      16161 CATGAGTTGAAA
          1 CATG-GTTGAAA

      16173 ACTTACAAAG


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   19  0.73
  16    7  0.27

ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21


Consensus pattern (15 bp):   
CATGGTTGAAACAAC
Done.