Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_842 ID=scaffold_842-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: 3220
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.34


Found at i:177 original size:39 final size:43

Alignment explanation


    Indices: 123--232  Score: 138
    Period size: 45  Copynumber: 2.6  Consensus size: 43

        113 TTTTCCATTA

                              *              *         
        123 TGCTATTACACCTCTATTACATT-CAATCAA-ACACAG-GA-T
          1 TGCTATTACACCTCTATTCCATTACAATCAACAAACAGTGATT

                     *                *                  
        162 TGCTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
          1 TGCTATTACACCTCTATTCCATTACAATCAA-CAAACAG-TGATT

                                      
        207 TGCTATTACACCTCTATTCCATTACA
          1 TGCTATTACACCTCTATTCCATTACA

        233 CCTCTATTCC


Statistics
Matches: 60,  Mismatches: 5, Indels: 6
        0.85            0.07        0.08

Matches are distributed among these distances:
  39   21  0.35
  40    6  0.10
  42    5  0.08
  44    2  0.03
  45   26  0.43

ACGTcount: A:0.31, C:0.27, G:0.07, T:0.35


Consensus pattern (43 bp):   
TGCTATTACACCTCTATTCCATTACAATCAACAAACAGTGATT

Found at i:232 original size:16 final size:16

Alignment explanation


    Indices: 211--264  Score: 90
    Period size: 16  Copynumber: 3.4  Consensus size: 16

        201 TTGATTTGCT

                            
        211 ATTACACCTCTATTCC
          1 ATTACACCTCTATTCC

                            
        227 ATTACACCTCTATTCC
          1 ATTACACCTCTATTCC

                        *   
        243 ATTACACCTCTAATCC
          1 ATTACACCTCTATTCC

             *    
        259 AATACA
          1 ATTACA

        265 GCGAACCAAA


Statistics
Matches: 36,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  16   36  1.00

ACGTcount: A:0.31, C:0.35, G:0.00, T:0.33


Consensus pattern (16 bp):   
ATTACACCTCTATTCC

Found at i:1460 original size:50 final size:53

Alignment explanation


    Indices: 1354--1538  Score: 168
    Period size: 50  Copynumber: 3.5  Consensus size: 53

       1344 TCTATACTGT

                     *       *        *         *         *       
       1354 CAATGCCATATCCCAGATATGGTCTTCCATG-GGA-GT-TC-TCATATCGATGC
          1 CAATGCCATGTCCCAGACATGGTCTTACA-GAGGACCTCTCATCATCTCGATGC

             *               *          *                    *   
       1404 CCATGCCATGTCCCAGAAATGGTCTTACGGAGGA-C-CT-ATCATCTCGGTGC
          1 CAATGCCATGTCCCAGACATGGTCTTACAGAGGACCTCTCATCATCTCGATGC

                                    *    *            *           * 
       1454 CAATGCCATGTCCCAGACATGGTCGTACATAGGACCTCTCATAATCTCAATGATTC
          1 CAATGCCATGTCCCAGACATGGTCTTACAGAGGACCTCTCATCATCTC---GATGC

                                         
       1510 CAATGCCATGTCCCAGACATGGTCTTACA
          1 CAATGCCATGTCCCAGACATGGTCTTACA

       1539 TGGGATCTCA


Statistics
Matches: 109,  Mismatches: 17, Indels: 12
        0.79            0.12        0.09

Matches are distributed among these distances:
  49    1  0.01
  50   67  0.61
  51    1  0.01
  52    2  0.02
  53    7  0.06
  56   31  0.28

ACGTcount: A:0.25, C:0.29, G:0.19, T:0.26


Consensus pattern (53 bp):   
CAATGCCATGTCCCAGACATGGTCTTACAGAGGACCTCTCATCATCTCGATGC
Done.