Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018544.1 Corchorus olitorius cultivar O-4 contig18577, 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: 24221
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31


Found at i:8143 original size:26 final size:23

Alignment explanation


    Indices: 8113--8159  Score: 67
    Period size: 26  Copynumber: 1.9  Consensus size: 23

       8103 CTTGAAAATT

                                      
       8113 TGAAAAACTTTGATGGATGAGATGTA
          1 TGAAAAAC-TTGAT-GAT-AGATGTA

                                 
       8139 TGAAAAACTTGATGATAGATG
          1 TGAAAAACTTGATGATAGATG

       8160 AATAGAAGGA


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    5  0.24
  24    3  0.14
  25    5  0.24
  26    8  0.38

ACGTcount: A:0.40, C:0.04, G:0.26, T:0.30


Consensus pattern (23 bp):   
TGAAAAACTTGATGATAGATGTA

Found at i:10753 original size:21 final size:22

Alignment explanation


    Indices: 10729--10769  Score: 57
    Period size: 21  Copynumber: 1.9  Consensus size: 22

      10719 TGCCTCATGC

                                  
      10729 ATTCATTCAT-CATACCATGGA
          1 ATTCATTCATGCATACCATGGA

                *         *     
      10750 ATTCGTTCATGCATTCCATG
          1 ATTCATTCATGCATACCATG

      10770 AAGCTTTAGC


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  21    9  0.53
  22    8  0.47

ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37


Consensus pattern (22 bp):   
ATTCATTCATGCATACCATGGA

Found at i:12426 original size:76 final size:74

Alignment explanation


    Indices: 12286--12427  Score: 162
    Period size: 76  Copynumber: 1.9  Consensus size: 74

      12276 TCTGGACTGT

                       **                                            * *     
      12286 GAGCAAAGGAATGACGAGTTTCAATCAAAAAGTTTTCAAAATCAGTTTTAATCAAAGCTTTGATT
          1 GAGCAAAGGAACAACGAGTTTCAATCAAAAAGTTTTCAAAATCAGTTTTAATCAAAGATATGATT

                     
      12351 TTGAGTTGC
         66 TTGAGTTGC

                                  *                 *           **           
      12360 GAGCAAAGGAACAACGATGTTTTAATC-AAAAGATGTTTCTAAATCAGTTTTGGTCAAA-ATAAT
          1 GAGCAAAGGAACAACGA-GTTTCAATCAAAAAG-T-TTTCAAAATCAGTTTTAATCAAAGAT-AT

                 
      12423 GATTT
         62 GATTT

      12428 CGAGGTGACT


Statistics
Matches: 56,  Mismatches: 8, Indels: 6
        0.80            0.11        0.09

Matches are distributed among these distances:
  74   20  0.36
  75   10  0.18
  76   26  0.46

ACGTcount: A:0.38, C:0.11, G:0.18, T:0.32


Consensus pattern (74 bp):   
GAGCAAAGGAACAACGAGTTTCAATCAAAAAGTTTTCAAAATCAGTTTTAATCAAAGATATGATT
TTGAGTTGC

Found at i:19220 original size:27 final size:26

Alignment explanation


    Indices: 19189--19285  Score: 108
    Period size: 27  Copynumber: 3.7  Consensus size: 26

      19179 GGTCACATAT

                                     * 
      19189 GGGCATTTTGGTCATTTGCACATTCGA
          1 GGGCATTTTGGTCATTTGC-CATTCAA

                                       *
      19216 GGGCATTTTGGTCATTTG-CATGTCCAG
          1 GGGCATTTTGGTCATTTGCCAT-T-CAA

                              *   *    
      19243 GGGCATTTTGGTCATTTTTCCACT-AA
          1 GGGCATTTTGGTCA-TTTGCCATTCAA

                             
      19269 GGGCATTTTGGTCATTT
          1 GGGCATTTTGGTCATTT

      19286 TAGGTTCACT


Statistics
Matches: 61,  Mismatches: 5, Indels: 10
        0.80            0.07        0.13

Matches are distributed among these distances:
  25    6  0.10
  26   16  0.26
  27   33  0.54
  28    4  0.07
  29    2  0.03

ACGTcount: A:0.16, C:0.18, G:0.26, T:0.40


Consensus pattern (26 bp):   
GGGCATTTTGGTCATTTGCCATTCAA

Found at i:23805 original size:16 final size:16

Alignment explanation


    Indices: 23787--23846  Score: 75
    Period size: 16  Copynumber: 3.7  Consensus size: 16

      23777 AATTTTAGGT

                           *
      23787 ACCCGAACCCGAAATT
          1 ACCCGAACCCGAAATG

                             
      23803 ACCCGAACCCGAAAATG
          1 ACCCGAACCCG-AAATG

             *  *     *     
      23820 ATCCAAACCCAAAATG
          1 ACCCGAACCCGAAATG

                       
      23836 ACCCGAACCCG
          1 ACCCGAACCCG

      23847 TTCAACCCGA


Statistics
Matches: 36,  Mismatches: 7, Indels: 2
        0.80            0.16        0.04

Matches are distributed among these distances:
  16   24  0.67
  17   12  0.33

ACGTcount: A:0.40, C:0.38, G:0.13, T:0.08


Consensus pattern (16 bp):   
ACCCGAACCCGAAATG

Done.