Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007608.1 Corchorus olitorius cultivar O-4 contig07634, 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: 2831
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.27


Found at i:1056 original size:22 final size:22

Alignment explanation


    Indices: 1028--1071  Score: 88
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       1018 CATGTCTCGT

                                  
       1028 CAAAATGCAGATAGTTTCTGGC
          1 CAAAATGCAGATAGTTTCTGGC

                                  
       1050 CAAAATGCAGATAGTTTCTGGC
          1 CAAAATGCAGATAGTTTCTGGC

       1072 TTTGGAATCA


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   22  1.00

ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27


Consensus pattern (22 bp):   
CAAAATGCAGATAGTTTCTGGC

Found at i:1334 original size:13 final size:13

Alignment explanation


    Indices: 1316--1346  Score: 55
    Period size: 13  Copynumber: 2.5  Consensus size: 13

       1306 CTATTGATGC

                         
       1316 GTTGAAGTCCTCT
          1 GTTGAAGTCCTCT

                         
       1329 GTTGAAGTCCTCT
          1 GTTGAAGTCCTCT

                  
       1342 -TTGAA
          1 GTTGAA

       1347 TAAAAGCTCT


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  12    5  0.28
  13   13  0.72

ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39


Consensus pattern (13 bp):   
GTTGAAGTCCTCT

Found at i:1837 original size:18 final size:19

Alignment explanation


    Indices: 1799--1844  Score: 58
    Period size: 18  Copynumber: 2.4  Consensus size: 19

       1789 AAAAAGAAAG

                                
       1799 ATAAAAAGATGAAAGAAAAA
          1 ATAAAAA-ATGAAAGAAAAA

                           *   
       1819 ATAAAAAAT-AAAGATAAA
          1 ATAAAAAATGAAAGAAAAA

             *      
       1837 AGAAAAAA
          1 ATAAAAAA

       1845 AGGAAAACAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  18   15  0.62
  19    2  0.08
  20    7  0.29

ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11


Consensus pattern (19 bp):   
ATAAAAAATGAAAGAAAAA

Found at i:1859 original size:24 final size:25

Alignment explanation


    Indices: 1803--1866  Score: 69
    Period size: 25  Copynumber: 2.6  Consensus size: 25

       1793 AGAAAGATAA

                  *                 *
       1803 AAAGATGAAAGAAAAAATAAAAAAT
          1 AAAGATAAAAGAAAAAATAAAAAAC

                                *     
       1828 AAAGATAAAAGAAAAAA-AGGAAAAC
          1 AAAGATAAAAGAAAAAATA-AAAAAC

                     *     
       1853 AAA-ATAAAGGAAAA
          1 AAAGATAAAAGAAAA

       1867 GACACGTCAA


Statistics
Matches: 34,  Mismatches: 4, Indels: 3
        0.83            0.10        0.07

Matches are distributed among these distances:
  24   11  0.32
  25   23  0.68

ACGTcount: A:0.77, C:0.02, G:0.14, T:0.08


Consensus pattern (25 bp):   
AAAGATAAAAGAAAAAATAAAAAAC

Found at i:1861 original size:15 final size:15

Alignment explanation


    Indices: 1823--1866  Score: 54
    Period size: 15  Copynumber: 2.9  Consensus size: 15

       1813 GAAAAAATAA

                      *    *
       1823 AAAATAAAGATAAAAG
          1 AAAATAAAG-GAAAAC

                           
       1839 AAAA-AAAGGAAAAC
          1 AAAATAAAGGAAAAC

                          
       1853 AAAATAAAGGAAAA
          1 AAAATAAAGGAAAA

       1867 GACACGTCAA


Statistics
Matches: 25,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  14    8  0.32
  15   13  0.52
  16    4  0.16

ACGTcount: A:0.77, C:0.02, G:0.14, T:0.07


Consensus pattern (15 bp):   
AAAATAAAGGAAAAC

Found at i:2692 original size:31 final size:30

Alignment explanation


    Indices: 2673--2733  Score: 79
    Period size: 31  Copynumber: 2.0  Consensus size: 30

       2663 AAAACAGATT

                                            
       2673 AAGCATTAAATTAAACAAA-TAATTAAAATGA
          1 AAGCATTAAATTAAACAAATTAA--AAAATGA

                *                    *    
       2704 AAGCCTTAAATTAAACAAATTAAAAGATGA
          1 AAGCATTAAATTAAACAAATTAAAAAATGA

       2734 TAGACCCTTA


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

Matches are distributed among these distances:
  30    6  0.22
  31   18  0.67
  32    3  0.11

ACGTcount: A:0.59, C:0.08, G:0.08, T:0.25


Consensus pattern (30 bp):   
AAGCATTAAATTAAACAAATTAAAAAATGA
Done.