Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold8015.1

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: 5703
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.32


Found at i:240 original size:59 final size:59

Alignment explanation


    Indices: 143--262  Score: 170
    Period size: 59  Copynumber: 2.0  Consensus size: 59

        133 GAGAACCTAA

                             *                                          
        143 ATATCTCTTAACATACTGTCCATATGATCATTTCGTTAC-TTCTATATGAAAATAGACTC
          1 ATATCTCTTAACATACTATCCATATGATCATTTCGTTACTTTC-ATATGAAAATAGACTC

                                *        *   *         *            *  
        202 ATATCTCTTAACATACTATCTATATGATCGTTTTGTTACTTTCCTATGAAAATAGATTC
          1 ATATCTCTTAACATACTATCCATATGATCATTTCGTTACTTTCATATGAAAATAGACTC

              
        261 AT
          1 AT

        263 CAAGGTTCGT


Statistics
Matches: 54,  Mismatches: 6, Indels: 2
        0.87            0.10        0.03

Matches are distributed among these distances:
  59   51  0.94
  60    3  0.06

ACGTcount: A:0.32, C:0.18, G:0.08, T:0.42


Consensus pattern (59 bp):   
ATATCTCTTAACATACTATCCATATGATCATTTCGTTACTTTCATATGAAAATAGACTC

Found at i:1120 original size:37 final size:37

Alignment explanation


    Indices: 1070--1148  Score: 113
    Period size: 37  Copynumber: 2.1  Consensus size: 37

       1060 TTATTACGAA

                          *    *           *   * 
       1070 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
          1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCAG

                                       *         
       1107 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCAG
          1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCAG

                 
       1144 GTCTT
          1 GTCTT

       1149 TAGAGCTCGG


Statistics
Matches: 37,  Mismatches: 5, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  37   37  1.00

ACGTcount: A:0.27, C:0.32, G:0.18, T:0.24


Consensus pattern (37 bp):   
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCAG

Found at i:4716 original size:40 final size:40

Alignment explanation


    Indices: 4671--4945  Score: 197
    Period size: 40  Copynumber: 6.9  Consensus size: 40

       4661 CGAATACACG

                     *  *          *  *             
       4671 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATA
          1 TCACCAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA

            *                      ***     *        
       4711 ACACCAGCACGAATGCTCTTCGGGGTTTAGCACGGATATA
          1 TCACCAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA

                *                                 * 
       4751 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
          1 TCACCAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA

                *    *                           *  
       4791 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATTTA
          1 TCACCAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA

              *  *      *             *                  
       4831 GTAATTC-GCACCAATGC-CTTCGG-GCTTAGCCCGGAATTAGTA
          1 -TCA-CCAGCACGAATGCTCTTCGGAACTTAGCCCGG-A-TA-TA

               *      *             *     *         *
       4873 TC-TC-GCACAAATGC-CTTCGGATCTTAGTCCGGATATGG
          1 TCACCAGCACGAATGCTCTTCGGAACTTAGCCCGGATAT-A

                 *        *         *            
       4911 TCACTTAGCAC-AAAGC-CTTCGGGACTTAGCCCGGA
          1 TCAC-CAGCACGAATGCTCTTCGGAACTTAGCCCGGA

       4946 CATCATTCGA


Statistics
Matches: 190,  Mismatches: 35, Indels: 20
        0.78            0.14        0.08

Matches are distributed among these distances:
  37    1  0.01
  38    4  0.02
  39   28  0.15
  40  139  0.73
  41   16  0.08
  42    2  0.01

ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25


Consensus pattern (40 bp):   
TCACCAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA

Found at i:4871 original size:39 final size:40

Alignment explanation


    Indices: 4802--4905  Score: 131
    Period size: 39  Copynumber: 2.6  Consensus size: 40

       4792 CACTAGCATG

                         *           *               
       4802 AATGCTCTTCGGAACTTAGCCCGGATTTAGTAATTCGCACC
          1 AATGC-CTTCGGAGCTTAGCCCGGAATTAGTAATTCGCACC

                                                    *
       4843 AATGCCTTCGG-GCTTAGCCCGGAATTAGT-ATCTCGCACA
          1 AATGCCTTCGGAGCTTAGCCCGGAATTAGTAAT-TCGCACC

                        *     *     
       4882 AATGCCTTCGGATCTTAGTCCGGA
          1 AATGCCTTCGGAGCTTAGCCCGGA

       4906 TATGGTCACT


Statistics
Matches: 56,  Mismatches: 5, Indels: 5
        0.85            0.08        0.08

Matches are distributed among these distances:
  38    2  0.04
  39   33  0.59
  40   16  0.29
  41    5  0.09

ACGTcount: A:0.23, C:0.27, G:0.22, T:0.28


Consensus pattern (40 bp):   
AATGCCTTCGGAGCTTAGCCCGGAATTAGTAATTCGCACC

Found at i:5290 original size:29 final size:29

Alignment explanation


    Indices: 5251--5329  Score: 97
    Period size: 29  Copynumber: 2.7  Consensus size: 29

       5241 CTTAATAATC

                                   *       
       5251 AACCACGCACACTTAGTGCCATGTACTTT-A
          1 AACC-CGCACACTTAGTGCCATGCA-TTTCA

               *              *          
       5281 AACTCGCACACTTAGTGCTATGCATTTCA
          1 AACCCGCACACTTAGTGCCATGCATTTCA

             *                  
       5310 AGCCCGCACACTTAGTGCCA
          1 AACCCGCACACTTAGTGCCA

       5330 ATCTCACAAC


Statistics
Matches: 42,  Mismatches: 6, Indels: 3
        0.82            0.12        0.06

Matches are distributed among these distances:
  28    3  0.07
  29   36  0.86
  30    3  0.07

ACGTcount: A:0.28, C:0.32, G:0.15, T:0.25


Consensus pattern (29 bp):   
AACCCGCACACTTAGTGCCATGCATTTCA
Done.