Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1751

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: 17895
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30


Found at i:1386 original size:47 final size:46

Alignment explanation


    Indices: 1269--1441  Score: 187
    Period size: 45  Copynumber: 3.8  Consensus size: 46

       1259 GGATGGTTGA

                                               *           
       1269 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAT
          1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCAAT

                                             *        *    
       1316 G--TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GATGTAACT
          1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCAA-T

                                               * *           *
       1359 AGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAAC
          1 --GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGC-AAT

                    *                          
       1409 GC--CCGAGCTCGTTGAGTTGAGTCCGAGTTCACT
          1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACT

       1442 TAGGGGCGGG


Statistics
Matches: 108,  Mismatches: 9, Indels: 19
        0.79            0.07        0.14

Matches are distributed among these distances:
  42    6  0.06
  43    1  0.01
  44    2  0.02
  45   30  0.28
  46   29  0.27
  47   30  0.28
  48    4  0.04
  50    4  0.04
  51    2  0.02

ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29


Consensus pattern (46 bp):   
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCAAT

Found at i:1437 original size:46 final size:45

Alignment explanation


    Indices: 1273--1443  Score: 204
    Period size: 46  Copynumber: 3.7  Consensus size: 45

       1263 GGTTGAGCAT

                                                      * *
       1273 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAATGT
          1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACGC

                                         * *       *        
       1318 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGC
          1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAC---GC

                                           *                
       1363 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGC
          1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC-AACGC

                *                            
       1411 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
          1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA

       1444 GGGGCGGGTT


Statistics
Matches: 107,  Mismatches: 10, Indels: 17
        0.80            0.07        0.13

Matches are distributed among these distances:
  42    6  0.06
  44    2  0.02
  45   29  0.27
  46   31  0.29
  47   28  0.26
  48    4  0.04
  50    4  0.04
  51    3  0.03

ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29


Consensus pattern (45 bp):   
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACGC

Found at i:1705 original size:19 final size:20

Alignment explanation


    Indices: 1668--1705  Score: 53
    Period size: 19  Copynumber: 1.9  Consensus size: 20

       1658 ATAAGGTGGT

                                
       1668 AAGATGATGAATGATGTTTA
          1 AAGATGATGAATGATGTTTA

                                
       1688 AAGATG-TGATAT-ATGTTT
          1 AAGATGATGA-ATGATGTTT

       1706 TGGTGGTACC


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

Matches are distributed among these distances:
  19    9  0.53
  20    8  0.47

ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39


Consensus pattern (20 bp):   
AAGATGATGAATGATGTTTA

Found at i:7648 original size:19 final size:20

Alignment explanation


    Indices: 7611--7648  Score: 53
    Period size: 19  Copynumber: 1.9  Consensus size: 20

       7601 ATAAGGTGGT

                                
       7611 AAGATGATGAATGATGTTTA
          1 AAGATGATGAATGATGTTTA

                                
       7631 AAGATG-TGATAT-ATGTTT
          1 AAGATGATGA-ATGATGTTT

       7649 TGGTGGTACC


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

Matches are distributed among these distances:
  19    9  0.53
  20    8  0.47

ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39


Consensus pattern (20 bp):   
AAGATGATGAATGATGTTTA

Found at i:11574 original size:24 final size:24

Alignment explanation


    Indices: 11542--11588  Score: 76
    Period size: 24  Copynumber: 2.0  Consensus size: 24

      11532 CTGTCAGGAG

                        **          
      11542 AGGATTTAGGAGTTGATAAGGGAT
          1 AGGATTTAGGAGCAGATAAGGGAT

                                   
      11566 AGGATTTAGGAGCAGATAAGGGA
          1 AGGATTTAGGAGCAGATAAGGGA

      11589 GGAAATCTAG


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  24   21  1.00

ACGTcount: A:0.36, C:0.02, G:0.38, T:0.23


Consensus pattern (24 bp):   
AGGATTTAGGAGCAGATAAGGGAT

Found at i:13060 original size:27 final size:26

Alignment explanation


    Indices: 13000--13110  Score: 134
    Period size: 27  Copynumber: 4.2  Consensus size: 26

      12990 AGGAAGCGTC

                     *               * 
      13000 CTGGTGGCTATGCCACAATTAT-TGAT
          1 CTGGTGGCTCTGCCAC-ATTATCTGTT

                                *      
      13026 CTGGTGGCTCTGCCACATATTTCTGTT
          1 CTGGTGGCTCTGCCACAT-TATCTGTT

                                        
      13053 CTGGTGGCTCTGCCACGATTATCTGTAT
          1 CTGGTGGCTCTGCCAC-ATTATCTGT-T

                  *     *             
      13081 CTGGTGACTCTGTCACATTATCTGTT
          1 CTGGTGGCTCTGCCACATTATCTGTT

                
      13107 CTGG
          1 CTGG

      13111 CAGCCATGCT


Statistics
Matches: 75,  Mismatches: 6, Indels: 8
        0.84            0.07        0.09

Matches are distributed among these distances:
  25    2  0.03
  26   22  0.29
  27   34  0.45
  28   17  0.23

ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38


Consensus pattern (26 bp):   
CTGGTGGCTCTGCCACATTATCTGTT
Done.