Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017606.1 Corchorus olitorius cultivar O-4 contig17639, 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: 15560
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:5039 original size:43 final size:43

Alignment explanation


    Indices: 4978--5063  Score: 172
    Period size: 43  Copynumber: 2.0  Consensus size: 43

       4968 AAACAGAGTT

                                                       
       4978 GGTAGGCATGGAATGGCAACCGAAACGTGGGATTTGAGATTTA
          1 GGTAGGCATGGAATGGCAACCGAAACGTGGGATTTGAGATTTA

                                                       
       5021 GGTAGGCATGGAATGGCAACCGAAACGTGGGATTTGAGATTTA
          1 GGTAGGCATGGAATGGCAACCGAAACGTGGGATTTGAGATTTA

       5064 AGGAGCGACC


Statistics
Matches: 43,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  43   43  1.00

ACGTcount: A:0.30, C:0.12, G:0.35, T:0.23


Consensus pattern (43 bp):   
GGTAGGCATGGAATGGCAACCGAAACGTGGGATTTGAGATTTA

Found at i:5460 original size:21 final size:21

Alignment explanation


    Indices: 5434--5476  Score: 86
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       5424 TGCATATTAG

                                 
       5434 ATTACCTATGAGAGTAAGTGA
          1 ATTACCTATGAGAGTAAGTGA

                                 
       5455 ATTACCTATGAGAGTAAGTGA
          1 ATTACCTATGAGAGTAAGTGA

             
       5476 A
          1 A

       5477 ATGTAAGGAT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   22  1.00

ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28


Consensus pattern (21 bp):   
ATTACCTATGAGAGTAAGTGA

Found at i:10439 original size:89 final size:89

Alignment explanation


    Indices: 10335--10498  Score: 256
    Period size: 89  Copynumber: 1.8  Consensus size: 89

      10325 AAATTCATCT

                                                   *            *            
      10335 ATAATTAAAGTGACTACTAAATTCCCAACTTAGTTCCCATCTTAAAATCCTATGACTAAAAATAT
          1 ATAATTAAAGTGACTACTAAATTCCCAACTTAGTTCCCAACTTAAAATCCTAGGACTAAAAATAT

                                    
      10400 ATCACCTGCAAATTCTTATTTATA
         66 ATCACCTGCAAATTCTTATTTATA

                            *      *    *  *              *  *               
      10424 ATAATTAAAGTGACTATTAAATTTCCAATTTGGTTCCCAACTTAAATTCTTAGGACTAAAAATAT
          1 ATAATTAAAGTGACTACTAAATTCCCAACTTAGTTCCCAACTTAAAATCCTAGGACTAAAAATAT

                      
      10489 ATCACCTGCA
         66 ATCACCTGCA

      10499 GCGAAACGCA


Statistics
Matches: 67,  Mismatches: 8, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  89   67  1.00

ACGTcount: A:0.39, C:0.19, G:0.07, T:0.35


Consensus pattern (89 bp):   
ATAATTAAAGTGACTACTAAATTCCCAACTTAGTTCCCAACTTAAAATCCTAGGACTAAAAATAT
ATCACCTGCAAATTCTTATTTATA

Found at i:10870 original size:25 final size:25

Alignment explanation


    Indices: 10814--10870  Score: 62
    Period size: 27  Copynumber: 2.2  Consensus size: 25

      10804 AACAAATGCA

                                * *  
      10814 CAAACTGGTATATATGAATTTTTTG
          1 CAAACTGGTATATATGAATTATGTG

                                        
      10839 CATAAACTGGTATATATGAATTGATGT-
          1 C--AAACTGGTATATATGAATT-ATGTG

                 
      10866 CAAAC
          1 CAAAC

      10871 AATAAAAATA


Statistics
Matches: 27,  Mismatches: 2, Indels: 6
        0.77            0.06        0.17

Matches are distributed among these distances:
  25    5  0.19
  27   20  0.74
  28    2  0.07

ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37


Consensus pattern (25 bp):   
CAAACTGGTATATATGAATTATGTG

Found at i:10894 original size:13 final size:13

Alignment explanation


    Indices: 10876--10902  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

      10866 CAAACAATAA

                         
      10876 AAATAACTGGTAT
          1 AAATAACTGGTAT

                         
      10889 AAATAACTGGTAT
          1 AAATAACTGGTAT

             
      10902 A
          1 A

      10903 TATGAATATG


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.48, C:0.07, G:0.15, T:0.30


Consensus pattern (13 bp):   
AAATAACTGGTAT

Found at i:11624 original size:49 final size:47

Alignment explanation


    Indices: 11523--11664  Score: 171
    Period size: 49  Copynumber: 3.0  Consensus size: 47

      11513 GAGCGTGCCA

                        *         *                  *      
      11523 ATCAATTTTGTCCAAAAATTGATAAAAAGTGCAA-TGAAAATTAAAAG
          1 ATCAATTTTGTCTAAAAATTGACAAAAAGTGCAAGT-AAAAATAAAAG

                                   *                         
      11570 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGTAAAAATAAAAG
          1 ATCAATTTTGTC-TAAAAATTGACAAAAAG-TGCAAGTAAAAATAAAAG

            *           *                                  
      11619 TTCAATTTTGTAGTAAAAATTGACAAAAAGTGC-AGTAAAAAGTAAA
          1 ATCAATTTTGT-CTAAAAATTGACAAAAAGTGCAAGTAAAAA-TAAA

      11665 GGATTGCTTG


Statistics
Matches: 84,  Mismatches: 6, Indels: 9
        0.85            0.06        0.09

Matches are distributed among these distances:
  47   20  0.24
  48   22  0.26
  49   41  0.49
  50    1  0.01

ACGTcount: A:0.51, C:0.07, G:0.14, T:0.27


Consensus pattern (47 bp):   
ATCAATTTTGTCTAAAAATTGACAAAAAGTGCAAGTAAAAATAAAAG
Done.