Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_351 ID=scaffold_351-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: 7985
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32


Found at i:430 original size:33 final size:33

Alignment explanation


    Indices: 388--453  Score: 132
    Period size: 33  Copynumber: 2.0  Consensus size: 33

        378 ACTCGGAATG

                                             
        388 TTATCCGTTATCGGTGGATTCAGCACTTAGCAA
          1 TTATCCGTTATCGGTGGATTCAGCACTTAGCAA

                                             
        421 TTATCCGTTATCGGTGGATTCAGCACTTAGCAA
          1 TTATCCGTTATCGGTGGATTCAGCACTTAGCAA

        454 CCACCAGTGA


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  33   33  1.00

ACGTcount: A:0.24, C:0.21, G:0.21, T:0.33


Consensus pattern (33 bp):   
TTATCCGTTATCGGTGGATTCAGCACTTAGCAA

Found at i:548 original size:42 final size:43

Alignment explanation


    Indices: 469--573  Score: 158
    Period size: 43  Copynumber: 2.5  Consensus size: 43

        459 AGTGATTCGG

                                                   *   
        469 GGAATCAGCACTTAGCAACCCCTTTCACATTCAAAAATACGGT
          1 GGAATCAGCACTTAGCAACCCCTTTCACATTCAAAAATAAGGT

                                 *          *       *  
        512 GGAATCAGCACTTAGCAACCCTTTTCACATT-TAAAATAATGT
          1 GGAATCAGCACTTAGCAACCCCTTTCACATTCAAAAATAAGGT

              *                 
        554 GGGATCAGCACTTAGCAACC
          1 GGAATCAGCACTTAGCAACC

        574 ACCAATAATT


Statistics
Matches: 57,  Mismatches: 5, Indels: 1
        0.90            0.08        0.02

Matches are distributed among these distances:
  42   27  0.47
  43   30  0.53

ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25


Consensus pattern (43 bp):   
GGAATCAGCACTTAGCAACCCCTTTCACATTCAAAAATAAGGT

Found at i:595 original size:33 final size:34

Alignment explanation


    Indices: 557--706  Score: 111
    Period size: 33  Copynumber: 4.4  Consensus size: 34

        547 ATAATGTGGG

                                              
        557 ATCAGCACTTAGCAACCACCAAT-AATTCGGGGA
          1 ATCAGCACTTAGCAACCACCAATAAATTCGGGGA

                       *                *     
        590 ATCAGCACTTAACAACC-CC------TTGGGGGA
          1 ATCAGCACTTAGCAACCACCAATAAATTCGGGGA

                              *               *       
        617 ATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGA
          1 ATCAGCACTTAGCAA-CCAC--CA-A--T-AAATTCGG-GGA

                                   *         *
        659 ATCAGCACTTAGCAACCACCAATGAA-TCGGGGC
          1 ATCAGCACTTAGCAACCACCAATAAATTCGGGGA

                           
        692 ATCAGCACTTAGCAA
          1 ATCAGCACTTAGCAA

        707 TGCATTGGGG


Statistics
Matches: 93,  Mismatches: 9, Indels: 30
        0.70            0.07        0.23

Matches are distributed among these distances:
  27   21  0.23
  28    2  0.02
  29    1  0.01
  31    1  0.01
  32    2  0.02
  33   33  0.35
  34    3  0.03
  35    2  0.02
  36    1  0.01
  38    1  0.01
  39    2  0.02
  41    6  0.06
  42   18  0.19

ACGTcount: A:0.34, C:0.29, G:0.18, T:0.19


Consensus pattern (34 bp):   
ATCAGCACTTAGCAACCACCAATAAATTCGGGGA

Found at i:689 original size:102 final size:102

Alignment explanation


    Indices: 512--740  Score: 343
    Period size: 102  Copynumber: 2.2  Consensus size: 102

        502 AAAATACGGT

                                 **                *    *                    
        512 GGAATCAGCACTTAGCAACCCTTTTCACATTTAAAATAATGTGGGATCAGCACTTAGCAACCACC
          1 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATAAGGTGGAATCAGCACTTAGCAACCACC

                                           *     
        577 AATAATTCGGGGAATCAGCACTTAACAACCCCTTGGG
         66 AATAATTCGGGGAATCAGCACTTAACAACCCATTGGG

                                                  *                          
        614 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCACC
          1 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATAAGGTGGAATCAGCACTTAGCAACCACC

                         *           *   **       
        679 AATGAA-TCGGGGCATCAGCACTTAGCAATGCATTGGG
         66 AAT-AATTCGGGGAATCAGCACTTAACAACCCATTGGG

                 *                   
        716 GGAATTAGCACTTAGCAACCCCCTT
          1 GGAATCAGCACTTAGCAACCCCCTT

        741 TATATTCAAT


Statistics
Matches: 115,  Mismatches: 11, Indels: 2
        0.90            0.09        0.02

Matches are distributed among these distances:
 102  113  0.98
 103    2  0.02

ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22


Consensus pattern (102 bp):   
GGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATAAGGTGGAATCAGCACTTAGCAACCACC
AATAATTCGGGGAATCAGCACTTAACAACCCATTGGG

Found at i:707 original size:26 final size:27

Alignment explanation


    Indices: 678--733  Score: 69
    Period size: 27  Copynumber: 2.1  Consensus size: 27

        668 TAGCAACCAC

                          *            
        678 CAATG-AATCGGGGCATCAGCACTTAG
          1 CAATGCAATCGGGGAATCAGCACTTAG

                   * *       *         
        704 CAATGCATTGGGGGAATTAGCACTTAG
          1 CAATGCAATCGGGGAATCAGCACTTAG

               
        731 CAA
          1 CAA

        734 CCCCCTTTAT


Statistics
Matches: 25,  Mismatches: 4, Indels: 1
        0.83            0.13        0.03

Matches are distributed among these distances:
  26    5  0.20
  27   20  0.80

ACGTcount: A:0.32, C:0.20, G:0.27, T:0.21


Consensus pattern (27 bp):   
CAATGCAATCGGGGAATCAGCACTTAG
Done.