Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013471.1 Corchorus olitorius cultivar O-4 contig13504, 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: 23014
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31


Found at i:1454 original size:52 final size:51

Alignment explanation


    Indices: 1353--1454  Score: 125
    Period size: 52  Copynumber: 2.0  Consensus size: 51

       1343 GTTCTTCATA

                       **                           * **       
       1353 TTTCCTTGTTTGGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGTTT
          1 TTTCCTTGTTTCAATCTTGTCTCCGGACAAACAAACACTCGTACAGTGTTT

                                          *                     
       1404 TTTCTCTTGTTTCAATCTTGTCTCCGGACATACAAACACT-GTACACGTGTT
          1 TTTC-CTTGTTTCAATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGTT

       1455 CTTCATTCAG


Statistics
Matches: 43,  Mismatches: 6, Indels: 3
        0.83            0.12        0.06

Matches are distributed among these distances:
  51    6  0.14
  52   37  0.86

ACGTcount: A:0.21, C:0.24, G:0.15, T:0.41


Consensus pattern (51 bp):   
TTTCCTTGTTTCAATCTTGTCTCCGGACAAACAAACACTCGTACAGTGTTT

Found at i:4892 original size:106 final size:102

Alignment explanation


    Indices: 4700--4892  Score: 287
    Period size: 106  Copynumber: 1.9  Consensus size: 102

       4690 TTAATAAAAT

                                     *     **              *                 
       4700 TAGTAAAATGATAAAAATAAAATAGGCATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTT
          1 TAGTAAAATGATAAAAATAAAATAGCCATAAAAATATTAGATTTAATCAAATAAAAATAGAGTTT

                    *       *                    
       4765 TTAGTTGAGTAAAACTGTAAAAGTATTTTAATTTAAA
         66 TTAGTTGAATAAAACTATAAAAGTATTTTAATTTAAA

                      *                                                      
       4802 TAGTAAAATGGTAAAAATAAAATAGTCCTTATAAAAATATTAGATTTAATCAAATAAAAAATAGA
          1 TAGTAAAATGATAAAAATAAAATAG-CC--ATAAAAATATTAGATTTAATCAAAT-AAAAATAGA

                                      
       4867 GTTTTTAGTTGAATAAAACTATAAAA
         62 GTTTTTAGTTGAATAAAACTATAAAA

       4893 ATTTAAGCAA


Statistics
Matches: 80,  Mismatches: 7, Indels: 4
        0.88            0.08        0.04

Matches are distributed among these distances:
 102   24  0.30
 103    1  0.01
 105   22  0.28
 106   33  0.41

ACGTcount: A:0.52, C:0.03, G:0.12, T:0.33


Consensus pattern (102 bp):   
TAGTAAAATGATAAAAATAAAATAGCCATAAAAATATTAGATTTAATCAAATAAAAATAGAGTTT
TTAGTTGAATAAAACTATAAAAGTATTTTAATTTAAA

Found at i:5496 original size:51 final size:51

Alignment explanation


    Indices: 5436--5543  Score: 207
    Period size: 51  Copynumber: 2.1  Consensus size: 51

       5426 TTTAAGAAAT

                                                               
       5436 ATATTTGAAAAAGAAGGGTATAATGGACAATTCAAAATTTTACAAACAAAC
          1 ATATTTGAAAAAGAAGGGTATAATGGACAATTCAAAATTTTACAAACAAAC

                                                               
       5487 ATATTTGAAAAAGAAGGGTATAATGGACAATTCAAAATTTTACAAACAAAC
          1 ATATTTGAAAAAGAAGGGTATAATGGACAATTCAAAATTTTACAAACAAAC

            *     
       5538 GTATTT
          1 ATATTT

       5544 TTTAATATAT


Statistics
Matches: 56,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  51   56  1.00

ACGTcount: A:0.49, C:0.09, G:0.14, T:0.28


Consensus pattern (51 bp):   
ATATTTGAAAAAGAAGGGTATAATGGACAATTCAAAATTTTACAAACAAAC

Found at i:19837 original size:20 final size:20

Alignment explanation


    Indices: 19812--19851  Score: 80
    Period size: 20  Copynumber: 2.0  Consensus size: 20

      19802 TTAGGTTCAA

                                
      19812 CTCTCACGGAATGTGAGTTT
          1 CTCTCACGGAATGTGAGTTT

                                
      19832 CTCTCACGGAATGTGAGTTT
          1 CTCTCACGGAATGTGAGTTT

      19852 GTTTGTAATT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35


Consensus pattern (20 bp):   
CTCTCACGGAATGTGAGTTT

Found at i:22484 original size:101 final size:101

Alignment explanation


    Indices: 22335--22571  Score: 288
    Period size: 101  Copynumber: 2.3  Consensus size: 101

      22325 GGTATTTTGG

                 *                                *    *                     
      22335 CTCTGTTTTTTGTTCACTTATTGAAGGCCACCAGCATCTATATGGAGTTGA-AGACCATT-TGGA
          1 CTCTGATTTTTGTTCACTTATTGAAGGCCACCAGCATCCATATAGAGTTGACA-A-C-TTCTGGA

                                                     
      22398 ATGATGAATGAAGATTTTGGAAGCTACAC-G-AATTTTTTA
         63 ATGATGAATGAAGATTTTGGAAGCT-C-CTGAAATTTTTTA

                            *                                                
      22437 CTCT-ATTTTTGTTCATTTATTGAAGGCCACCAGCATCCATATAGAGTTGACAACTTGCTGGAAT
          1 CTCTGATTTTTGTTCACTTATTGAAGGCCACCAGCATCCATATAGAGTTGACAACTT-CTGGAAT

                     * *      *                 *
      22501 GATGAATGACGGTTTTGGGAGCTCCTGAAATTTTTTG
         65 GATGAATGAAGATTTTGGAAGCTCCTGAAATTTTTTA

                 *                             
      22538 CTCTGTTTTTTGTTC-CTTATGTGAAGGCCACCAG
          1 CTCTGATTTTTGTTCACTTAT-TGAAGGCCACCAG

      22572 AATTTATAGC


Statistics
Matches: 118,  Mismatches: 10, Indels: 14
        0.83            0.07        0.10

Matches are distributed among these distances:
  99    3  0.03
 100    3  0.03
 101   85  0.72
 102   27  0.23

ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37


Consensus pattern (101 bp):   
CTCTGATTTTTGTTCACTTATTGAAGGCCACCAGCATCCATATAGAGTTGACAACTTCTGGAATG
ATGAATGAAGATTTTGGAAGCTCCTGAAATTTTTTA
Done.