Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023811.1 Corchorus olitorius cultivar O-4 contig23844, 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: 23401
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29


Found at i:13670 original size:16 final size:15

Alignment explanation


    Indices: 13632--13673  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

      13622 ACAAAGATTG

                   *       
      13632 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
      13647 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
      13662 ACTAGAAAACAA
          1 AC-AGAAAACAA

      13674 AGCAAAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:13929 original size:47 final size:47

Alignment explanation


    Indices: 13860--13954  Score: 172
    Period size: 47  Copynumber: 2.0  Consensus size: 47

      13850 TTTAGATAAG

                  *                                        
      13860 ATTAGCTGTCAAGCCTTAAATTACCCATTTTTCCTCCTAACTAATCA
          1 ATTAGCCGTCAAGCCTTAAATTACCCATTTTTCCTCCTAACTAATCA

                                      *                    
      13907 ATTAGCCGTCAAGCCTTAAATTACCCCTTTTTCCTCCTAACTAATCA
          1 ATTAGCCGTCAAGCCTTAAATTACCCATTTTTCCTCCTAACTAATCA

             
      13954 A
          1 A

      13955 AGCATTAAGA


Statistics
Matches: 46,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  47   46  1.00

ACGTcount: A:0.29, C:0.29, G:0.06, T:0.35


Consensus pattern (47 bp):   
ATTAGCCGTCAAGCCTTAAATTACCCATTTTTCCTCCTAACTAATCA

Found at i:16589 original size:14 final size:15

Alignment explanation


    Indices: 16570--16599  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      16560 CAATCAAAGC

                           
      16570 AATAAT-CAAGGAAA
          1 AATAATGCAAGGAAA

                           
      16584 AATAATGCAAGGAAA
          1 AATAATGCAAGGAAA

             
      16599 A
          1 A

      16600 TTAAAGAGAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    6  0.40
  15    9  0.60

ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13


Consensus pattern (15 bp):   
AATAATGCAAGGAAA

Found at i:16982 original size:21 final size:21

Alignment explanation


    Indices: 16956--17023  Score: 64
    Period size: 21  Copynumber: 3.2  Consensus size: 21

      16946 CGAATGGTGA

                                 
      16956 TGGCACGGGCATGGCCGGTAG
          1 TGGCACGGGCATGGCCGGTAG

                      * **     * 
      16977 TGGCACGGGCTTAACCGGTGG
          1 TGGCACGGGCATGGCCGGTAG

              *       *          *
      16998 TGACACGGTGAATGGCCGGTAA
          1 TGGCACGG-GCATGGCCGGTAG

                
      17020 TGGC
          1 TGGC

      17024 TTGGTAGTGG


Statistics
Matches: 34,  Mismatches: 12, Indels: 1
        0.72            0.26        0.02

Matches are distributed among these distances:
  21   24  0.71
  22   10  0.29

ACGTcount: A:0.18, C:0.22, G:0.43, T:0.18


Consensus pattern (21 bp):   
TGGCACGGGCATGGCCGGTAG

Found at i:19776 original size:87 final size:81

Alignment explanation


    Indices: 19587--19777  Score: 233
    Period size: 87  Copynumber: 2.2  Consensus size: 81

      19577 TTTTTTTATG

                                                                             
      19587 ACGC-AAAATTTTTTTTTTTTTCGACGCAAAACACAAAACAAATTTTTTTTTTTCAAAAACGCAA
          1 ACGCAAAAATTTTTTTTTTTTTCGACGCAAAACACAAAACAAATTTTTTTTTTTCAAAAACGCAA

                  *         
      19651 AACTAATAAAATAAAA
         66 AACTAAAAAAATAAAA

                                                                             
      19667 ACGCAAGAAAACTTTTTCTTTTTTTTTCCGACGCAAAACACAAAACAAAATTTTTTTTTTTCTCA
          1 ACGC-A-AAAA--TTTT-TTTTTTTTT-CGACGCAAAACACAAAAC-AAA-TTTTTTTTTT-TCA

            *   *                       
      19732 TAAAGGCACAAAC-ACAAAAAATAAAAA
         57 AAAACGCA-AAACTA-AAAAAAT-AAAA

                               
      19759 ACGCAAAAATTTTTTTTTT
          1 ACGCAAAAATTTTTTTTTT

      19778 AGATTAAAAA


Statistics
Matches: 95,  Mismatches: 3, Indels: 19
        0.81            0.03        0.16

Matches are distributed among these distances:
  80    4  0.04
  83    4  0.04
  85    4  0.04
  86    9  0.09
  87   24  0.25
  88    7  0.07
  89   10  0.11
  90   14  0.15
  91   11  0.12
  92    8  0.08

ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34


Consensus pattern (81 bp):   
ACGCAAAAATTTTTTTTTTTTTCGACGCAAAACACAAAACAAATTTTTTTTTTTCAAAAACGCAA
AACTAAAAAAATAAAA

Found at i:22774 original size:21 final size:21

Alignment explanation


    Indices: 22726--22775  Score: 57
    Period size: 21  Copynumber: 2.4  Consensus size: 21

      22716 CTGCCGCTGG

                                *
      22726 GCGCCCAGGCGAAATGCCTCG
          1 GCGCCCAGGCGAAATGCCTCA

              *              *    
      22747 GCACCCAGGCGACAA-GGCTCA
          1 GCGCCCAGGCGA-AATGCCTCA

                    
      22768 GCGCCCAG
          1 GCGCCCAG

      22776 CTCGATCCCT


Statistics
Matches: 24,  Mismatches: 4, Indels: 2
        0.80            0.13        0.07

Matches are distributed among these distances:
  21   22  0.92
  22    2  0.08

ACGTcount: A:0.22, C:0.40, G:0.32, T:0.06


Consensus pattern (21 bp):   
GCGCCCAGGCGAAATGCCTCA
Done.