Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021079.1 Corchorus olitorius cultivar O-4 contig21112, 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: 33101
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33


Found at i:1247 original size:12 final size:12

Alignment explanation


    Indices: 1232--1264  Score: 57
    Period size: 12  Copynumber: 2.8  Consensus size: 12

       1222 TAAGAATTAT

                *       
       1232 GAAAAGAACAAG
          1 GAAAGGAACAAG

                        
       1244 GAAAGGAACAAG
          1 GAAAGGAACAAG

                     
       1256 GAAAGGAAC
          1 GAAAGGAAC

       1265 TATATTCAAT


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  12   20  1.00

ACGTcount: A:0.61, C:0.09, G:0.30, T:0.00


Consensus pattern (12 bp):   
GAAAGGAACAAG

Found at i:3245 original size:52 final size:52

Alignment explanation


    Indices: 3183--3330  Score: 240
    Period size: 44  Copynumber: 3.0  Consensus size: 52

       3173 AGCAGCGATC

                                                                
       3183 ACCAAAGCATCAACCTCACAAATCACATTTCTATATCCCTCATCCCAAGCCA
          1 ACCAAAGCATCAACCTCACAAATCACATTTCTATATCCCTCATCCCAAGCCA

                                                                
       3235 ACCAAAGCATCAACCTCACAAATCACA----T-T-T--CTCATCCCAAGCCA
          1 ACCAAAGCATCAACCTCACAAATCACATTTCTATATCCCTCATCCCAAGCCA

                                                                
       3279 ACCAAAGCATCAACCTCACAAATCACATTTCTATATCCCTCATCCCAAGCCA
          1 ACCAAAGCATCAACCTCACAAATCACATTTCTATATCCCTCATCCCAAGCCA

       3331 GCAAAAGGCC


Statistics
Matches: 88,  Mismatches: 0, Indels: 16
        0.85            0.00        0.15

Matches are distributed among these distances:
  44   41  0.47
  46    1  0.01
  47    1  0.01
  48    2  0.02
  49    1  0.01
  50    1  0.01
  52   41  0.47

ACGTcount: A:0.37, C:0.39, G:0.04, T:0.20


Consensus pattern (52 bp):   
ACCAAAGCATCAACCTCACAAATCACATTTCTATATCCCTCATCCCAAGCCA

Found at i:25727 original size:13 final size:13

Alignment explanation


    Indices: 25709--25751  Score: 54
    Period size: 13  Copynumber: 3.5  Consensus size: 13

      25699 ATATATATAC

                         
      25709 CAATTGCAAATAG
          1 CAATTGCAAATAG

                     *  *
      25722 CAATTG--ACTAC
          1 CAATTGCAAATAG

                         
      25733 CAATTGCAAATAG
          1 CAATTGCAAATAG

                  
      25746 CAATTG
          1 CAATTG

      25752 ACATGACTAG


Statistics
Matches: 24,  Mismatches: 4, Indels: 4
        0.75            0.12        0.12

Matches are distributed among these distances:
  11    9  0.38
  13   15  0.62

ACGTcount: A:0.42, C:0.19, G:0.14, T:0.26


Consensus pattern (13 bp):   
CAATTGCAAATAG

Found at i:25733 original size:24 final size:24

Alignment explanation


    Indices: 25706--25753  Score: 96
    Period size: 24  Copynumber: 2.0  Consensus size: 24

      25696 TATATATATA

                                    
      25706 TACCAATTGCAAATAGCAATTGAC
          1 TACCAATTGCAAATAGCAATTGAC

                                    
      25730 TACCAATTGCAAATAGCAATTGAC
          1 TACCAATTGCAAATAGCAATTGAC

      25754 ATGACTAGCT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.42, C:0.21, G:0.12, T:0.25


Consensus pattern (24 bp):   
TACCAATTGCAAATAGCAATTGAC

Found at i:28440 original size:42 final size:42

Alignment explanation


    Indices: 28389--28479  Score: 148
    Period size: 42  Copynumber: 2.2  Consensus size: 42

      28379 AGTGCGTTAC

                                   *                 *
      28389 CTAA-ATTCTACTCCATCTCTAGGTAATTCATCAAAATAAAG
          1 CTAATATTCTACTCCATCTCTAGATAATTCATCAAAATAAAA

                             *                        
      28430 CTAATATTCTACTCCATTTCTAGATAATTCATCAAAATAAAA
          1 CTAATATTCTACTCCATCTCTAGATAATTCATCAAAATAAAA

                    
      28472 CTAATATT
          1 CTAATATT

      28480 AATTGTTGTT


Statistics
Matches: 46,  Mismatches: 3, Indels: 1
        0.92            0.06        0.02

Matches are distributed among these distances:
  41    4  0.09
  42   42  0.91

ACGTcount: A:0.41, C:0.20, G:0.04, T:0.35


Consensus pattern (42 bp):   
CTAATATTCTACTCCATCTCTAGATAATTCATCAAAATAAAA
Done.