Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024058.1 Corchorus olitorius cultivar O-4 contig24091, 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: 4576
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31


Found at i:1126 original size:31 final size:30

Alignment explanation


    Indices: 1083--1151  Score: 93
    Period size: 31  Copynumber: 2.2  Consensus size: 30

       1073 CAAGAAAATG

                *                          
       1083 AAATTTTTTTTTTTTAAAATAAAAACGCAAA
          1 AAATCTTTTTTTTTTAAAA-AAAAACGCAAA

                            * *            
       1114 AAATCTTTTTTTTTTTCAGAAAAAACGCAAA
          1 AAATC-TTTTTTTTTTAAAAAAAAACGCAAA

                   
       1145 AAATCTT
          1 AAATCTT

       1152 AAAAACAATT


Statistics
Matches: 34,  Mismatches: 3, Indels: 3
        0.85            0.08        0.08

Matches are distributed among these distances:
  30    2  0.06
  31   20  0.59
  32   12  0.35

ACGTcount: A:0.45, C:0.10, G:0.04, T:0.41


Consensus pattern (30 bp):   
AAATCTTTTTTTTTTAAAAAAAAACGCAAA

Found at i:1295 original size:33 final size:33

Alignment explanation


    Indices: 1258--1321  Score: 85
    Period size: 33  Copynumber: 1.9  Consensus size: 33

       1248 ACAACACAAG

                     *   *                    
       1258 TTTTTTTTTTA-ATTAAAGACACAAAGAAAAATA
          1 TTTTTTTTTCAGAATAAA-ACACAAAGAAAAATA

                                   *       
       1291 TTTTTTTTTCAGAATAAAACACAGAGAAAAA
          1 TTTTTTTTTCAGAATAAAACACAAAGAAAAA

       1322 GAAAAACGCA


Statistics
Matches: 27,  Mismatches: 3, Indels: 2
        0.84            0.09        0.06

Matches are distributed among these distances:
  33   22  0.81
  34    5  0.19

ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36


Consensus pattern (33 bp):   
TTTTTTTTTCAGAATAAAACACAAAGAAAAATA

Found at i:1579 original size:27 final size:28

Alignment explanation


    Indices: 1506--1585  Score: 101
    Period size: 29  Copynumber: 2.9  Consensus size: 28

       1496 TTAGGATTAC

                                         
       1506 CTAGGGGCATTTTGGTCATTTTCAAAAAT
          1 CTAGGGGCATTTTGGTCATTTT-AAAAAT

                         *           * * 
       1535 CTAGGGGCATTTTAGTCATTTGT-ATATT
          1 CTAGGGGCATTTTGGTCATTT-TAAAAAT

                                    
       1563 C-AGGGGCATTTTGGTCATTTTAA
          1 CTAGGGGCATTTTGGTCATTTTAA

       1586 GTCCATGCTT


Statistics
Matches: 45,  Mismatches: 4, Indels: 6
        0.82            0.07        0.11

Matches are distributed among these distances:
  26    1  0.02
  27   19  0.42
  28    4  0.09
  29   20  0.44
  30    1  0.02

ACGTcount: A:0.24, C:0.12, G:0.23, T:0.41


Consensus pattern (28 bp):   
CTAGGGGCATTTTGGTCATTTTAAAAAT

Found at i:1852 original size:17 final size:17

Alignment explanation


    Indices: 1830--1864  Score: 70
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       1820 ATATGCATGC

                             
       1830 TTTCACATTAGTTTAAT
          1 TTTCACATTAGTTTAAT

                             
       1847 TTTCACATTAGTTTAAT
          1 TTTCACATTAGTTTAAT

             
       1864 T
          1 T

       1865 AATTATAGGC


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:0.11, G:0.06, T:0.54


Consensus pattern (17 bp):   
TTTCACATTAGTTTAAT
Done.