Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016947.1 Corchorus olitorius cultivar O-4 contig16980, 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: 3708
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.36


Found at i:392 original size:41 final size:41

Alignment explanation


    Indices: 335--419  Score: 161
    Period size: 41  Copynumber: 2.1  Consensus size: 41

        325 CAAAATTGCC

                                                   * 
        335 AAATGGTCCCCTTGCCTTTATGCCATTTTCAATCAAGCATA
          1 AAATGGTCCCCTTGCCTTTATGCCATTTTCAATCAAGCACA

                                                     
        376 AAATGGTCCCCTTGCCTTTATGCCATTTTCAATCAAGCACA
          1 AAATGGTCCCCTTGCCTTTATGCCATTTTCAATCAAGCACA

               
        417 AAA
          1 AAA

        420 CTCTTCTTTG


Statistics
Matches: 43,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  41   43  1.00

ACGTcount: A:0.29, C:0.27, G:0.12, T:0.32


Consensus pattern (41 bp):   
AAATGGTCCCCTTGCCTTTATGCCATTTTCAATCAAGCACA

Found at i:1528 original size:61 final size:61

Alignment explanation


    Indices: 1453--1575  Score: 246
    Period size: 61  Copynumber: 2.0  Consensus size: 61

       1443 TTTATATACT

                                                                         
       1453 ATATAAGTCTAAACTTCAAAACCATTGACCTGAAATTTCTAAAATAACCTTTTTAATTTTA
          1 ATATAAGTCTAAACTTCAAAACCATTGACCTGAAATTTCTAAAATAACCTTTTTAATTTTA

                                                                         
       1514 ATATAAGTCTAAACTTCAAAACCATTGACCTGAAATTTCTAAAATAACCTTTTTAATTTTA
          1 ATATAAGTCTAAACTTCAAAACCATTGACCTGAAATTTCTAAAATAACCTTTTTAATTTTA

             
       1575 A
          1 A

       1576 AAGTTTAGTA


Statistics
Matches: 62,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  61   62  1.00

ACGTcount: A:0.41, C:0.16, G:0.05, T:0.37


Consensus pattern (61 bp):   
ATATAAGTCTAAACTTCAAAACCATTGACCTGAAATTTCTAAAATAACCTTTTTAATTTTA

Found at i:1790 original size:39 final size:40

Alignment explanation


    Indices: 1734--1814  Score: 119
    Period size: 39  Copynumber: 2.0  Consensus size: 40

       1724 TTTAATTCCT

                                      *             
       1734 ATGTAATATATATAATAACTAAAATAGTTAAATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTAAATTAATTAA

                     *          *         *         
       1774 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTAAATTAATTAA

              
       1813 AT
          1 AT

       1815 TCTTAGGTAT


Statistics
Matches: 37,  Mismatches: 4, Indels: 1
        0.88            0.10        0.02

Matches are distributed among these distances:
  39   29  0.78
  40    8  0.22

ACGTcount: A:0.52, C:0.06, G:0.05, T:0.37


Consensus pattern (40 bp):   
ATGTAATATATATAATAACTAAAATACTTAAATTAATTAA

Found at i:1841 original size:25 final size:24

Alignment explanation


    Indices: 1805--1851  Score: 85
    Period size: 25  Copynumber: 1.9  Consensus size: 24

       1795 AATACTTACA

                                    
       1805 TTAATTAAATTCTTAGGTATTTTT
          1 TTAATTAAATTCTTAGGTATTTTT

                                   
       1829 TTAATTCAAATTCTTAGGTATTT
          1 TTAATT-AAATTCTTAGGTATTT

       1852 GTGCAAACGT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  24    6  0.27
  25   16  0.73

ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55


Consensus pattern (24 bp):   
TTAATTAAATTCTTAGGTATTTTT

Found at i:2162 original size:198 final size:194

Alignment explanation


    Indices: 1926--2324  Score: 604
    Period size: 198  Copynumber: 2.0  Consensus size: 194

       1916 TTAATAATAA

                                                                             
       1926 ATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATT
          1 ATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATT

             *                              *                               *
       1991 TGATAAATCAACCACTAATGTTCAACTAATTTTTTTTTTTTGGTATAGTTCTATATATATAATAG
         66 TAATAAATCAACCACTAATGTTCAACT-A---CTTTTTTTTGGTATAGTT-T-TATATATAATAA

                                                                            *
       2056 TAATGTGTTG-T-CTACAACTTTGTTAGTAATCTTAGAATTAAAAAATTAATAACATTCACCATT
        125 TAATGTGTTGTTACTACAACTTTGTTAGTAATCTTAGAATTAAAAAATTAATAACATTCACCATC

                 
       2119 GATAT
        190 GATAT

                                                                             
       2124 ATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATT
          1 ATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATT

                                                                             
       2189 TAATAAATCAACCACTAATGTTCAACTACTTTTTTTTGGTATAGTTTTATATATAATAATAATGT
         66 TAATAAATCAACCACTAATGTTCAACTACTTTTTTTTGGTATAGTTTTATATATAATAATAATGT

                                                    *                     *  
       2254 GTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCATCA
        131 GTTG-------TT-ACTACAACTTTGTTAGTAATCTTAGAATTAAAAAATTAATAACATTCACCA

                  
       2319 TCGATA
        188 TCGATA

       2325 AAATTATTAA


Statistics
Matches: 185,  Mismatches: 6, Indels: 16
        0.89            0.03        0.08

Matches are distributed among these distances:
 192   21  0.11
 193    1  0.01
 194   17  0.09
 197    1  0.01
 198   91  0.49
 200    1  0.01
 202   53  0.29

ACGTcount: A:0.35, C:0.11, G:0.09, T:0.45


Consensus pattern (194 bp):   
ATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAATT
TAATAAATCAACCACTAATGTTCAACTACTTTTTTTTGGTATAGTTTTATATATAATAATAATGT
GTTGTTACTACAACTTTGTTAGTAATCTTAGAATTAAAAAATTAATAACATTCACCATCGATAT
Done.