Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold840

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: 10008
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30


Found at i:1179 original size:45 final size:47

Alignment explanation


    Indices: 1128--1241  Score: 124
    Period size: 56  Copynumber: 2.3  Consensus size: 47

       1118 TATTCTTATT

                                                           
       1128 CAACATGTTTCATTTGCCCAT-TTCTTATTTT-TTCTTCCATTAACA
          1 CAACATGTTTCATTTGCCCATCTTCTTATTTTATTCTTCCATTAACA

                                                        *           
       1173 CAACATGTTTCATGACATGTTTTGCCCATGCTTCTTATTTTATTTTTCCATTAACA
          1 CAACATG-TT--T--CA---TTTGCCCAT-CTTCTTATTTTATTCTTCCATTAACA

                         
       1229 CAACATGTTTCAT
          1 CAACATGTTTCAT

       1242 GACATGTTTT


Statistics
Matches: 57,  Mismatches: 1, Indels: 19
        0.74            0.01        0.25

Matches are distributed among these distances:
  45    7  0.12
  46    2  0.04
  48    2  0.04
  50    2  0.04
  51    2  0.04
  53   10  0.18
  55   12  0.21
  56   20  0.35

ACGTcount: A:0.24, C:0.23, G:0.07, T:0.46


Consensus pattern (47 bp):   
CAACATGTTTCATTTGCCCATCTTCTTATTTTATTCTTCCATTAACA

Found at i:1227 original size:56 final size:53

Alignment explanation


    Indices: 1140--1257  Score: 200
    Period size: 56  Copynumber: 2.2  Consensus size: 53

       1130 ACATGTTTCA

                                                                 
       1140 TTTGCCCATTTCTTATTTTTTCTTCCATTAACACAACATGTTTCATGACATGT
          1 TTTGCCCATTTCTTATTTTTTCTTCCATTAACACAACATGTTTCATGACATGT

                                    *                               
       1193 TTTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGT
          1 TTTGCCCAT--TTCTTATTTT-TTCTTCCATTAACACAACATGTTTCATGACATGT

                     
       1249 TTTGCCCAT
          1 TTTGCCCAT

       1258 CATCCCTTGT


Statistics
Matches: 61,  Mismatches: 1, Indels: 3
        0.94            0.02        0.05

Matches are distributed among these distances:
  53    9  0.15
  55   10  0.16
  56   42  0.69

ACGTcount: A:0.22, C:0.23, G:0.08, T:0.47


Consensus pattern (53 bp):   
TTTGCCCATTTCTTATTTTTTCTTCCATTAACACAACATGTTTCATGACATGT

Found at i:7750 original size:40 final size:40

Alignment explanation


    Indices: 7713--7937  Score: 278
    Period size: 40  Copynumber: 5.7  Consensus size: 40

       7703 GCTACTCGTT

                            *  *                     
       7713 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA

                                                    
       7753 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

                                                    
       7793 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

             *                 *      *      *      
       7833 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
          1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

                                **      * *  *    *   
       7872 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
          1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA

                               *      
       7913 CAAA-GCCTTCGGGACTTAGCCCGGA
          1 CAAATGCCTTCGGGACTTAACCCGGA

       7938 CATCATTCGA


Statistics
Matches: 165,  Mismatches: 15, Indels: 10
        0.87            0.08        0.05

Matches are distributed among these distances:
  38    2  0.01
  39   32  0.19
  40  118  0.72
  41   13  0.08

ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24


Consensus pattern (40 bp):   
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

Found at i:7897 original size:119 final size:120

Alignment explanation


    Indices: 7715--7937  Score: 301
    Period size: 119  Copynumber: 1.9  Consensus size: 120

       7705 TACTCGTTCA

                                   *                                         
       7715 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
          1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT

            *         *                                             
       7780 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
         66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC

                          *                 *                          **    
       7835 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
          1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG

                *  *                          *      
       7897 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
         64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA

       7938 CATCATTCGA


Statistics
Matches: 90,  Mismatches: 10, Indels: 7
        0.84            0.09        0.07

Matches are distributed among these distances:
 118    4  0.04
 119   66  0.73
 120   20  0.22

ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25


Consensus pattern (120 bp):   
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC

Found at i:9164 original size:55 final size:56

Alignment explanation


    Indices: 9063--9181  Score: 231
    Period size: 55  Copynumber: 2.1  Consensus size: 56

       9053 TATTAGTTTA

                                                                    
       9063 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
          1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT

                                                                    
       9119 TTGCCCATGCTTCTTATTTTATT-TTCCATTAACACAACATGTTTCATGACATGTT
          1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT

                    
       9174 TTGCCCAT
          1 TTGCCCAT

       9182 CATCCCTTGT


Statistics
Matches: 63,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  55   40  0.63
  56   23  0.37

ACGTcount: A:0.23, C:0.24, G:0.09, T:0.45


Consensus pattern (56 bp):   
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Done.