Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_319 ID=scaffold_319-JGI_221_v2.0

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: 8247
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31


Found at i:567 original size:48 final size:48

Alignment explanation


    Indices: 515--745  Score: 291
    Period size: 48  Copynumber: 4.7  Consensus size: 48

        505 CACAAATATT

                  *        *                       *  *     
        515 TGGACAACATTTAAGTACCAATTTGGACAGCATTAATATACTCAAAAA
          1 TGGACAGCATTTAAGCACCAATTTGGACAGCATTAATATGCTAAAAAA

                     *       *         *                          
        563 TGGACAGCAATTAAGCATCAATTTGGATAGCATTAATATGCTCAAAAAAAAAAA
          1 TGGACAGCATTTAAGCACCAATTTGGACAGCATTAATATGCT------AAAAAA

                   *          *             *               
        617 TGGACAGTATTTAAGCACTAATTTGGACAGCACTAATATGCTAAAAAA
          1 TGGACAGCATTTAAGCACCAATTTGGACAGCATTAATATGCTAAAAAA

                *             *                             
        665 TGGAAAGCATTTAAGCACTAATTTGGACAGCATTAATATGCTAAAAAA
          1 TGGACAGCATTTAAGCACCAATTTGGACAGCATTAATATGCTAAAAAA

                     *                       
        713 TGGACAGCAATTAAGCACCAATTTGGACAGCAT
          1 TGGACAGCATTTAAGCACCAATTTGGACAGCAT

        746 CTTATCATCA


Statistics
Matches: 158,  Mismatches: 19, Indels: 12
        0.84            0.10        0.06

Matches are distributed among these distances:
  48  117  0.74
  54   41  0.26

ACGTcount: A:0.43, C:0.15, G:0.16, T:0.26


Consensus pattern (48 bp):   
TGGACAGCATTTAAGCACCAATTTGGACAGCATTAATATGCTAAAAAA

Found at i:691 original size:102 final size:96

Alignment explanation


    Indices: 515--744  Score: 291
    Period size: 102  Copynumber: 2.3  Consensus size: 96

        505 CACAAATATT

                  *        *                *         *         *            
        515 TGGACAACATTTAAGTACCAATTTGGACAGCATTAATATACTCAAAAATGGACAGCAATTAAGCA
          1 TGGACAGCATTTAAGCACCAATTTGGACAGCACTAATATACTAAAAAATGGAAAGCAATTAAGCA

                      *                          
        580 TCAATTTGGATAGCATTAATATGCTCAAAAAAAAAAA
         66 TCAATTTGGACAGCATTAATATGCT------AAAAAA

                   *          *                    *                 *       
        617 TGGACAGTATTTAAGCACTAATTTGGACAGCACTAATATGCTAAAAAATGGAAAGCATTTAAGCA
          1 TGGACAGCATTTAAGCACCAATTTGGACAGCACTAATATACTAAAAAATGGAAAGCAATTAAGCA

                                            
        682 -CTAATTTGGACAGCATTAATATGCTAAAAAA
         66 TC-AATTTGGACAGCATTAATATGCTAAAAAA

                     *                      
        713 TGGACAGCAATTAAGCACCAATTTGGACAGCA
          1 TGGACAGCATTTAAGCACCAATTTGGACAGCA

        745 TCTTATCATC


Statistics
Matches: 114,  Mismatches: 13, Indels: 8
        0.84            0.10        0.06

Matches are distributed among these distances:
  96   35  0.31
 101    1  0.01
 102   78  0.68

ACGTcount: A:0.43, C:0.15, G:0.16, T:0.25


Consensus pattern (96 bp):   
TGGACAGCATTTAAGCACCAATTTGGACAGCACTAATATACTAAAAAATGGAAAGCAATTAAGCA
TCAATTTGGACAGCATTAATATGCTAAAAAA

Found at i:696 original size:23 final size:23

Alignment explanation


    Indices: 617--745  Score: 73
    Period size: 23  Copynumber: 5.4  Consensus size: 23

        607 AAAAAAAAAA

                   *          *    
        617 TGGACAGTATTTAAGCACTAATT
          1 TGGACAGCATTTAAGCACAAATT

                        *  *        **
        640 TGGACAGCACTAATATGCTA-AAAAA
          1 TGGACAGCA-T-TTAAGC-ACAAATT

                *             *    
        665 TGGAAAGCATTTAAGCACTAATT
          1 TGGACAGCATTTAAGCACAAATT

                           *        **
        688 TGGACAGCATTAATATGCTA-AAAAA
          1 TGGACAGCATT--TAAGC-ACAAATT

                     *        *    
        713 TGGACAGCAATTAAGCACCAATT
          1 TGGACAGCATTTAAGCACAAATT

                      
        736 TGGACAGCAT
          1 TGGACAGCAT

        746 CTTATCATCA


Statistics
Matches: 75,  Mismatches: 23, Indels: 16
        0.66            0.20        0.14

Matches are distributed among these distances:
  22    2  0.03
  23   39  0.52
  24    2  0.03
  25   30  0.40
  26    2  0.03

ACGTcount: A:0.41, C:0.16, G:0.18, T:0.26


Consensus pattern (23 bp):   
TGGACAGCATTTAAGCACAAATT

Found at i:721 original size:25 final size:25

Alignment explanation


    Indices: 640--726  Score: 81
    Period size: 25  Copynumber: 3.5  Consensus size: 25

        630 AGCACTAATT

                     *               
        640 TGGACAGCACTAATATGCTAAAAAA
          1 TGGACAGCATTAATATGCTAAAAAA

                *          *     *  **
        665 TGGAAAGCATT--TAAGC-ACTAATT
          1 TGGACAGCATTAATATGCTA-AAAAA

                                     
        688 TGGACAGCATTAATATGCTAAAAAA
          1 TGGACAGCATTAATATGCTAAAAAA

                          
        713 TGGACAGCAATTAA
          1 TGGACAGC-ATTAA

        727 GCACCAATTT


Statistics
Matches: 46,  Mismatches: 11, Indels: 9
        0.70            0.17        0.14

Matches are distributed among these distances:
  22    1  0.02
  23   16  0.35
  25   23  0.50
  26    6  0.13

ACGTcount: A:0.45, C:0.14, G:0.17, T:0.24


Consensus pattern (25 bp):   
TGGACAGCATTAATATGCTAAAAAA

Found at i:1385 original size:42 final size:41

Alignment explanation


    Indices: 1321--1404  Score: 114
    Period size: 42  Copynumber: 2.0  Consensus size: 41

       1311 ATGTTATAAG

                     *  *    *                       
       1321 ATATCGATGTCACTGTCTCAGACAGGGTCTTACACGAAATC
          1 ATATCGATGCCAATGTCCCAGACAGGGTCTTACACGAAATC

                                     *          *     
       1362 ATATACGATGCCAATGTCCCAGACATGGTCTTACACTAAATC
          1 ATAT-CGATGCCAATGTCCCAGACAGGGTCTTACACGAAATC

             
       1404 A
          1 A

       1405 CACCTCGGAA


Statistics
Matches: 37,  Mismatches: 5, Indels: 1
        0.86            0.12        0.02

Matches are distributed among these distances:
  41    4  0.11
  42   33  0.89

ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26


Consensus pattern (41 bp):   
ATATCGATGCCAATGTCCCAGACAGGGTCTTACACGAAATC
Done.