Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022927.1 Corchorus olitorius cultivar O-4 contig22960, 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: 17733
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35


Found at i:823 original size:6 final size:6

Alignment explanation


    Indices: 805--845  Score: 64
    Period size: 6  Copynumber: 6.7  Consensus size: 6

        795 GTTTAGACTT

                                                     *     
        805 ATATAG TATATAG ATATAG ATATAG ATATAG ATATAT ATAT
          1 ATATAG -ATATAG ATATAG ATATAG ATATAG ATATAG ATAT

        846 CTTTATTTTT


Statistics
Matches: 33,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
   6   27  0.82
   7    6  0.18

ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39


Consensus pattern (6 bp):   
ATATAG

Found at i:5200 original size:5 final size:5

Alignment explanation


    Indices: 5178--5221  Score: 72
    Period size: 5  Copynumber: 8.8  Consensus size: 5

       5168 TGATTAGACG

                                                                 
       5178 TAATA T-ATA TATATA TAATA TAATA TAATA TAATA TAATA TAAT
          1 TAATA TAATA TA-ATA TAATA TAATA TAATA TAATA TAATA TAAT

       5222 TTAGATCAAC


Statistics
Matches: 37,  Mismatches: 0, Indels: 4
        0.90            0.00        0.10

Matches are distributed among these distances:
   4    4  0.11
   5   28  0.76
   6    5  0.14

ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43


Consensus pattern (5 bp):   
TAATA

Found at i:6821 original size:44 final size:44

Alignment explanation


    Indices: 6773--6887  Score: 230
    Period size: 44  Copynumber: 2.6  Consensus size: 44

       6763 CTTGCAGCCC

                                                        
       6773 TTGCATATCCTTTCCATGCTCTCCATGTTCTCCACTGTCATCCT
          1 TTGCATATCCTTTCCATGCTCTCCATGTTCTCCACTGTCATCCT

                                                        
       6817 TTGCATATCCTTTCCATGCTCTCCATGTTCTCCACTGTCATCCT
          1 TTGCATATCCTTTCCATGCTCTCCATGTTCTCCACTGTCATCCT

                                       
       6861 TTGCATATCCTTTCCATGCTCTCCATG
          1 TTGCATATCCTTTCCATGCTCTCCATG

       6888 ATAAGCCCTT


Statistics
Matches: 71,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  44   71  1.00

ACGTcount: A:0.14, C:0.36, G:0.10, T:0.41


Consensus pattern (44 bp):   
TTGCATATCCTTTCCATGCTCTCCATGTTCTCCACTGTCATCCT

Found at i:9742 original size:7 final size:7

Alignment explanation


    Indices: 9722--9751  Score: 51
    Period size: 7  Copynumber: 4.1  Consensus size: 7

       9712 TTTATAATGA

                   
       9722 GGTTTAG
          1 GGTTTAG

                    
       9729 GGTTTTAG
          1 GG-TTTAG

                   
       9737 GGTTTAG
          1 GGTTTAG

                   
       9744 GGTTTAG
          1 GGTTTAG

             
       9751 G
          1 G

       9752 TTTGGCCCTA


Statistics
Matches: 22,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
   7   15  0.68
   8    7  0.32

ACGTcount: A:0.13, C:0.00, G:0.43, T:0.43


Consensus pattern (7 bp):   
GGTTTAG

Found at i:14154 original size:21 final size:23

Alignment explanation


    Indices: 14094--14154  Score: 72
    Period size: 23  Copynumber: 2.7  Consensus size: 23

      14084 AACAAATTTA

                *                 * 
      14094 TGTGAATTTTTAATGTTGATTGTT
          1 TGTGGATTTTT-ATGTTGATTGCT

                                   
      14118 TGTGGATTTTTATGTTGATTGCT
          1 TGTGGATTTTTATGTTGATTGCT

                       *    
      14141 TG-GG-TTTTTCTGTT
          1 TGTGGATTTTTATGTT

      14155 TTATGTTGAT


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

Matches are distributed among these distances:
  21    9  0.26
  22    2  0.06
  23   13  0.38
  24   10  0.29

ACGTcount: A:0.13, C:0.03, G:0.25, T:0.59


Consensus pattern (23 bp):   
TGTGGATTTTTATGTTGATTGCT

Found at i:15659 original size:19 final size:19

Alignment explanation


    Indices: 15635--15676  Score: 59
    Period size: 19  Copynumber: 2.2  Consensus size: 19

      15625 CCATGTGGCC

                           *    
      15635 AAAATTAT-TTTTCCCGAAA
          1 AAAATTATATTTT-CAGAAA

                               
      15654 AAAATTATATTTTCAGAAA
          1 AAAATTATATTTTCAGAAA

                
      15673 AAAA
          1 AAAA

      15677 AAATTAAAGT


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  19   17  0.81
  20    4  0.19

ACGTcount: A:0.52, C:0.10, G:0.05, T:0.33


Consensus pattern (19 bp):   
AAAATTATATTTTCAGAAA

Found at i:15867 original size:30 final size:29

Alignment explanation


    Indices: 15833--15902  Score: 86
    Period size: 30  Copynumber: 2.4  Consensus size: 29

      15823 TTAAAAAAAA

                          ***             
      15833 GGGTTTATTTGGCCTTTTTAAAGAGTTCAG
          1 GGGTTTATTTGGCCAAATTAAA-AGTTCAG

                        *                
      15863 GGGTTTATTTGGTCAAATTAAAAGTTCAG
          1 GGGTTTATTTGGCCAAATTAAAAGTTCAG

               *       
      15892 GGGCTTATTTG
          1 GGGTTTATTTG

      15903 ATCATTTTAT


Statistics
Matches: 35,  Mismatches: 5, Indels: 1
        0.85            0.12        0.02

Matches are distributed among these distances:
  29   17  0.49
  30   18  0.51

ACGTcount: A:0.23, C:0.09, G:0.27, T:0.41


Consensus pattern (29 bp):   
GGGTTTATTTGGCCAAATTAAAAGTTCAG
Done.