Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold9756.1

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: 4244
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.29


Found at i:1246 original size:59 final size:59

Alignment explanation


    Indices: 1152--1269  Score: 200
    Period size: 59  Copynumber: 2.0  Consensus size: 59

       1142 GAACTCACAC

                                                       *               
       1152 TTACTGAACTTAGCATATAACTGCTTATCCCGCAAAATTTACAGCACTAGCCTCAGATG
          1 TTACTGAACTTAGCATATAACTGCTTATCCCGCAAAATTTACAACACTAGCCTCAGATG

                                          *         *       *          
       1211 TTACTGAACTTAGCATATAACTGCTTATCCTGCAAAATTTGCAACACTTGCCTCAGATG
          1 TTACTGAACTTAGCATATAACTGCTTATCCCGCAAAATTTACAACACTAGCCTCAGATG

       1270 CTCAGCATGT


Statistics
Matches: 55,  Mismatches: 4, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  59   55  1.00

ACGTcount: A:0.31, C:0.25, G:0.14, T:0.31


Consensus pattern (59 bp):   
TTACTGAACTTAGCATATAACTGCTTATCCCGCAAAATTTACAACACTAGCCTCAGATG

Found at i:1319 original size:11 final size:11

Alignment explanation


    Indices: 1303--1327  Score: 50
    Period size: 11  Copynumber: 2.3  Consensus size: 11

       1293 TTGAATAGAC

                       
       1303 CAAGATGTCAT
          1 CAAGATGTCAT

                       
       1314 CAAGATGTCAT
          1 CAAGATGTCAT

               
       1325 CAA
          1 CAA

       1328 TAAATACAAC


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   14  1.00

ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24


Consensus pattern (11 bp):   
CAAGATGTCAT

Found at i:3804 original size:38 final size:37

Alignment explanation


    Indices: 3694--3825  Score: 178
    Period size: 37  Copynumber: 3.6  Consensus size: 37

       3684 GATCTATCTT

                       * *                       
       3694 AACCTTTTTAAAGATTGCCTTAGACAAGGTCTATCCC
          1 AACCTTTTTAAGGGTTGCCTTAGACAAGGTCTATCCC

                       *      *      **          
       3731 AACCTTTTT-ACGGTTGCTTTAGA-TGGGTCTATCCC
          1 AACCTTTTTAAGGGTTGCCTTAGACAAGGTCTATCCC

                *                                 
       3766 AATCTTTTTTAAGGGTTGCCTTAGACAAGGTCTATCCC
          1 AA-CCTTTTTAAGGGTTGCCTTAGACAAGGTCTATCCC

                                  
       3804 AACCTTTTTAAGGGTTGCCTTA
          1 AACCTTTTTAAGGGTTGCCTTA

       3826 AACGAGTCAA


Statistics
Matches: 81,  Mismatches: 11, Indels: 6
        0.83            0.11        0.06

Matches are distributed among these distances:
  35   12  0.15
  36   17  0.21
  37   40  0.49
  38   12  0.15

ACGTcount: A:0.23, C:0.22, G:0.17, T:0.37


Consensus pattern (37 bp):   
AACCTTTTTAAGGGTTGCCTTAGACAAGGTCTATCCC
Done.