Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_3499

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: 18380
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33


Found at i:11094 original size:30 final size:30

Alignment explanation


    Indices: 11022--11243  Score: 236
    Period size: 30  Copynumber: 7.5  Consensus size: 30

      11012 TCGGCTATCG

                          *     *         
      11022 ATTATGAAAAGGGAAGGTGATGACCATC-A
          1 ATTATGAAAAGGGATGGTGACGACCATCAA

                  *                     * 
      11051 ATTATGGAAAGGGATGGTGACGACCATCGA
          1 ATTATGAAAAGGGATGGTGACGACCATCAA

             *              *  *  * *     
      11081 ACTATGAAAAGGGATGCT-TCGGCTATCAA
          1 ATTATGAAAAGGGATGGTGACGACCATCAA

                                        * 
      11110 ATTATGAAAAGGGATGGTGACGACCATCGA
          1 ATTATGAAAAGGGATGGTGACGACCATCAA

             *              *  *  * *     
      11140 ACTATGAAAAGGGATGCT-TCGGCTATCAA
          1 ATTATGAAAAGGGATGGTGACGACCATCAA

                                        * 
      11169 ATTATGAAAAGGGATGGTGACGACCATCGA
          1 ATTATGAAAAGGGATGGTGACGACCATCAA

             **            *               
      11199 ACAATGAAAAGGGATAGTGAAC-ACCATCAA
          1 ATTATGAAAAGGGATGGTG-ACGACCATCAA

                           
      11229 ATTATGAAAAGGGAT
          1 ATTATGAAAAGGGAT

      11244 AGTTTCAGGT


Statistics
Matches: 155,  Mismatches: 34, Indels: 7
        0.79            0.17        0.04

Matches are distributed among these distances:
  29   71  0.46
  30   82  0.53
  31    2  0.01

ACGTcount: A:0.39, C:0.14, G:0.27, T:0.21


Consensus pattern (30 bp):   
ATTATGAAAAGGGATGGTGACGACCATCAA

Found at i:11094 original size:59 final size:59

Alignment explanation


    Indices: 11024--11243  Score: 277
    Period size: 59  Copynumber: 3.7  Consensus size: 59

      11014 GGCTATCGAT

                          *                    *                         
      11024 TATGAAAAGGGAAGGTGAT-GACCATC-AATTATGGAAAGGGATGGTGACGACCATCGAAC
          1 TATGAAAAGGGAAGCT--TCGACCATCAAATTATGAAAAGGGATGGTGACGACCATCGAAC

                        *      * *                                     
      11083 TATGAAAAGGGATGCTTCGGCTATCAAATTATGAAAAGGGATGGTGACGACCATCGAAC
          1 TATGAAAAGGGAAGCTTCGACCATCAAATTATGAAAAGGGATGGTGACGACCATCGAAC

                        *      * *                                     
      11142 TATGAAAAGGGATGCTTCGGCTATCAAATTATGAAAAGGGATGGTGACGACCATCGAAC
          1 TATGAAAAGGGAAGCTTCGACCATCAAATTATGAAAAGGGATGGTGACGACCATCGAAC

            *                  *                         
      11201 AATGAAAAGGGATAG-TGAAC-ACCATCAAATTATGAAAAGGGAT
          1 TATGAAAAGGGA-AGCT--TCGACCATCAAATTATGAAAAGGGAT

      11244 AGTTTCAGGT


Statistics
Matches: 146,  Mismatches: 10, Indels: 9
        0.88            0.06        0.05

Matches are distributed among these distances:
  57    1  0.01
  58    5  0.03
  59  117  0.80
  60   22  0.15
  61    1  0.01

ACGTcount: A:0.39, C:0.14, G:0.27, T:0.20


Consensus pattern (59 bp):   
TATGAAAAGGGAAGCTTCGACCATCAAATTATGAAAAGGGATGGTGACGACCATCGAAC

Found at i:11287 original size:30 final size:30

Alignment explanation


    Indices: 11224--11303  Score: 90
    Period size: 30  Copynumber: 2.7  Consensus size: 30

      11214 AGTGAACACC

                                  **      
      11224 ATCAAATTATGAAAAGGGATAGTTTCAGGT
          1 ATCAAATTATGAAAAGGGATAGCCTCAGGT

                           *               
      11254 ATCAAATTATGAAAATGGATAGCCTC-GGCT
          1 ATCAAATTATGAAAAGGGATAGCCTCAGG-T

                *  * *          
      11284 ATCAGATAAAGAAAAGGGAT
          1 ATCAAATTATGAAAAGGGAT

      11304 GTGTCAACCA


Statistics
Matches: 42,  Mismatches: 7, Indels: 2
        0.82            0.14        0.04

Matches are distributed among these distances:
  29    2  0.05
  30   40  0.95

ACGTcount: A:0.42, C:0.10, G:0.23, T:0.25


Consensus pattern (30 bp):   
ATCAAATTATGAAAAGGGATAGCCTCAGGT
Done.