Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold10571.1

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: 3472
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.37


Found at i:736 original size:16 final size:16

Alignment explanation


    Indices: 717--747  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

        707 CTTCTTCACT

                            
        717 TACTCACTTACTTAAA
          1 TACTCACTTACTTAAA

                *          
        733 TACTTACTTACTTAA
          1 TACTCACTTACTTAA

        748 TCAAATTTAT


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42


Consensus pattern (16 bp):   
TACTCACTTACTTAAA

Found at i:753 original size:20 final size:20

Alignment explanation


    Indices: 714--753  Score: 53
    Period size: 20  Copynumber: 2.0  Consensus size: 20

        704 AAACTTCTTC

                         * *    
        714 ACTTACTCACTTACTTAAAT
          1 ACTTACTCACTTAATCAAAT

                   *            
        734 ACTTACTTACTTAATCAAAT
          1 ACTTACTCACTTAATCAAAT

        754 TTATTAATAC


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  20   17  1.00

ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40


Consensus pattern (20 bp):   
ACTTACTCACTTAATCAAAT

Found at i:1129 original size:55 final size:53

Alignment explanation


    Indices: 939--1193  Score: 229
    Period size: 55  Copynumber: 4.8  Consensus size: 53

        929 ACGCGGGTAC

                   *       *    *           *   *                 
        939 CTTACCATTGCCATGACTTGTCATGGTCTTACGTGGTATCC-T---TT-TGAAA
          1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG-AA

                   *                            *                
        988 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAA
          1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAA

              *            *    *                                   
       1041 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAA
          1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCC-TTGCCTTAT-G-AA

                *                              ***                
       1096 CTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTA-GAAA
          1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG-AA

                       *     *                     *      
       1149 CCTTACCAATTCCCATGCCTT-AGCATGGTCTTACATGGTATCCTT
          1 -CTTACCAA-TGCCATGTCTTGA-CATGGTCTTACATGGGATCCTT

       1194 AAACCCTAAT


Statistics
Matches: 173,  Mismatches: 21, Indels: 18
        0.82            0.10        0.08

Matches are distributed among these distances:
  49   38  0.22
  50    1  0.01
  52    2  0.01
  53   49  0.28
  54   11  0.06
  55   70  0.40
  56    2  0.01

ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36


Consensus pattern (53 bp):   
CTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAA

Found at i:1130 original size:108 final size:110

Alignment explanation


    Indices: 986--1186  Score: 309
    Period size: 108  Copynumber: 1.8  Consensus size: 110

        976 ATCCTTTTGA

                     *                           *                           
        986 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACCAA
          1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTA-GAAACCTCACCAA

              *         *                                 
       1049 -TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
         65 TTCCCATGCCTTAGCATGGTCTTACATGGGACCTTTGCCTTATAGT

                  *                                *                  *      
       1094 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGAAACCTTACCAAT
          1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT

                                        
       1159 TCCCATGCCTTAGCATGGTCTTACATGG
         66 TCCCATGCCTTAGCATGGTCTTACATGG

       1187 TATCCTTAAA


Statistics
Matches: 83,  Mismatches: 7, Indels: 4
        0.88            0.07        0.04

Matches are distributed among these distances:
 107    1  0.01
 108   49  0.59
 109    7  0.08
 110   26  0.31

ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34


Consensus pattern (110 bp):   
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
TCCCATGCCTTAGCATGGTCTTACATGGGACCTTTGCCTTATAGT
Done.