Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013463.1 Corchorus olitorius cultivar O-4 contig13496, 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: 4873
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.34


Found at i:1314 original size:29 final size:29

Alignment explanation


    Indices: 1247--1352  Score: 112
    Period size: 29  Copynumber: 3.7  Consensus size: 29

       1237 AGGATCACCT

                                      *    
       1247 AGGGGCATTTTGGTCATTT-T-CAAAAATCC
          1 AGGGGCATTTTGGTCATTTCTGC--ACATCC

              **                       * 
       1276 AGAAGCATTTTGGTCATTTCTGCACATTC
          1 AGGGGCATTTTGGTCATTTCTGCACATCC

                 *     *                 
       1305 AGGGGTATTTTAGTCA-TT-TGCACATCC
          1 AGGGGCATTTTGGTCATTTCTGCACATCC

                                 
       1332 AGGGGCATTTTGGTCATTTCT
          1 AGGGGCATTTTGGTCATTTCT

       1353 ACTCCATTGC


Statistics
Matches: 62,  Mismatches: 11, Indels: 8
        0.77            0.14        0.10

Matches are distributed among these distances:
  27   22  0.35
  28    4  0.06
  29   34  0.55
  30    1  0.02
  31    1  0.02

ACGTcount: A:0.23, C:0.18, G:0.22, T:0.38


Consensus pattern (29 bp):   
AGGGGCATTTTGGTCATTTCTGCACATCC

Found at i:1588 original size:55 final size:55

Alignment explanation


    Indices: 1504--1614  Score: 222
    Period size: 55  Copynumber: 2.0  Consensus size: 55

       1494 CATTTACATG

                                                                   
       1504 ATCCCAATTAGTAATTGAGCCTTGATACTTTGGTCACTTGGCTTAGTGCAGAATC
          1 ATCCCAATTAGTAATTGAGCCTTGATACTTTGGTCACTTGGCTTAGTGCAGAATC

                                                                   
       1559 ATCCCAATTAGTAATTGAGCCTTGATACTTTGGTCACTTGGCTTAGTGCAGAATC
          1 ATCCCAATTAGTAATTGAGCCTTGATACTTTGGTCACTTGGCTTAGTGCAGAATC

             
       1614 A
          1 A

       1615 ATTGGTAAAC


Statistics
Matches: 56,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  55   56  1.00

ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34


Consensus pattern (55 bp):   
ATCCCAATTAGTAATTGAGCCTTGATACTTTGGTCACTTGGCTTAGTGCAGAATC

Found at i:1897 original size:14 final size:14

Alignment explanation


    Indices: 1878--1907  Score: 60
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       1868 CCCAATGATC

                          
       1878 AAATGACTTGCCTT
          1 AAATGACTTGCCTT

                          
       1892 AAATGACTTGCCTT
          1 AAATGACTTGCCTT

              
       1906 AA
          1 AA

       1908 GTGCTCTTGA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   16  1.00

ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33


Consensus pattern (14 bp):   
AAATGACTTGCCTT
Done.