Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016797.1 Corchorus olitorius cultivar O-4 contig16830, 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: 22135
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32


Found at i:2726 original size:15 final size:15

Alignment explanation


    Indices: 2706--2749  Score: 70
    Period size: 15  Copynumber: 2.9  Consensus size: 15

       2696 GTTTCCGTTA

                           
       2706 TTATTTACACCATTG
          1 TTATTTACACCATTG

                  *        
       2721 TTATTTGCACCATTG
          1 TTATTTACACCATTG

              *           
       2736 TTGTTTACACCATT
          1 TTATTTACACCATT

       2750 CACCCTAGCA


Statistics
Matches: 26,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  15   26  1.00

ACGTcount: A:0.23, C:0.20, G:0.09, T:0.48


Consensus pattern (15 bp):   
TTATTTACACCATTG

Found at i:3668 original size:49 final size:47

Alignment explanation


    Indices: 3567--3712  Score: 161
    Period size: 49  Copynumber: 3.0  Consensus size: 47

       3557 GAGCGTGCCA

                        *         *                  *      
       3567 ATCAATTTTGTCAAAAAATTGATAAAAAGTGCAA-TGAAAATTAAAAG
          1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGT-AAAAATAAAAG

                              *                              
       3614 ATCAATTTTGTCTTAAAATTTGAGAAAAAGATGCAAGTAAAAATAAAAG
          1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGCAAGTAAAAATAAAAG

            *        *  *               *                    
       3663 TTCAATTTTATAGTAAAAATTGAGAAAAGGTGC-AGTAAAAAGTAAAAG
          1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAAGTAAAAA-TAAAAG

              
       3711 AT
          1 AT

       3713 TGCTTGGAGT


Statistics
Matches: 84,  Mismatches: 10, Indels: 9
        0.82            0.10        0.09

Matches are distributed among these distances:
  47   20  0.24
  48   24  0.29
  49   39  0.46
  50    1  0.01

ACGTcount: A:0.51, C:0.05, G:0.15, T:0.28


Consensus pattern (47 bp):   
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGTAAAAATAAAAG

Found at i:14813 original size:20 final size:20

Alignment explanation


    Indices: 14776--14813  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      14766 TCCAACGGCT

                         *      
      14776 AGTAGTTTTGACCGTTGAGA
          1 AGTAGTTTTGACCATTGAGA

                       *      
      14796 AGTAGTTTTGAGCATTGA
          1 AGTAGTTTTGACCATTGA

      14814 AGAACTCCTT


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   16  1.00

ACGTcount: A:0.26, C:0.08, G:0.29, T:0.37


Consensus pattern (20 bp):   
AGTAGTTTTGACCATTGAGA

Found at i:20080 original size:42 final size:41

Alignment explanation


    Indices: 20032--20176  Score: 125
    Period size: 41  Copynumber: 3.5  Consensus size: 41

      20022 CGTCAAAAAT

                           *       *          *      *
      20032 AAATAAAATCCTAAAGCAGGGACGAAATTGCATTTAATCAGG
          1 AAATAAAATCCTAAATCAGGGACAAAATTGCATTAAATCA-A

                                    * ****            
      20074 AAATAAAA-CCTTAAATCAGGGACTAGGCAGCA-TAAATCAA
          1 AAATAAAATCC-TAAATCAGGGACAAAATTGCATTAAATCAA

                                             *       
      20114 AAATAAAATCCTAAATCAGGGACAAAATTGCATCAAA-CAA
          1 AAATAAAATCCTAAATCAGGGACAAAATTGCATTAAATCAA

                  **  *            
      20154 AAGATAGTATTCTAAATCAGGGA
          1 AA-ATAAAATCCTAAATCAGGGA

      20177 AACGCTTAAA


Statistics
Matches: 82,  Mismatches: 17, Indels: 9
        0.76            0.16        0.08

Matches are distributed among these distances:
  40   29  0.35
  41   30  0.37
  42   23  0.28

ACGTcount: A:0.49, C:0.15, G:0.16, T:0.20


Consensus pattern (41 bp):   
AAATAAAATCCTAAATCAGGGACAAAATTGCATTAAATCAA

Found at i:20155 original size:40 final size:40

Alignment explanation


    Indices: 20016--20176  Score: 121
    Period size: 40  Copynumber: 4.0  Consensus size: 40

      20006 ATCAGAGATT

                   *                        *       *
      20016 AAATTGCGTCAAA-AATAAATAAAATCCTAAAGCAGGGACG
          1 AAATTGCATCAAACAA-AAATAAAATCCTAAATCAGGGACA

                      *  *   *                        *
      20056 AAATTGCATTTAATCAGGAAATAAAA-CCTTAAATCAGGGACT
          1 AAATTGCA-TCAAACA-AAAATAAAATCC-TAAATCAGGGACA

             ****                                    
      20098 AGGCAGCAT-AAATCAAAAATAAAATCCTAAATCAGGGACA
          1 AAATTGCATCAAA-CAAAAATAAAATCCTAAATCAGGGACA

                                  **  *            
      20138 AAATTGCATCAAACAAAAGATAGTATTCTAAATCAGGGA
          1 AAATTGCATCAAACAAAA-ATAAAATCCTAAATCAGGGA

      20177 AACGCTTAAA


Statistics
Matches: 93,  Mismatches: 20, Indels: 15
        0.73            0.16        0.12

Matches are distributed among these distances:
  40   39  0.42
  41   30  0.32
  42   24  0.26

ACGTcount: A:0.49, C:0.15, G:0.16, T:0.20


Consensus pattern (40 bp):   
AAATTGCATCAAACAAAAATAAAATCCTAAATCAGGGACA
Done.