Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1735

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: 4907
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29


Found at i:388 original size:81 final size:82

Alignment explanation


    Indices: 253--415  Score: 247
    Period size: 81  Copynumber: 2.0  Consensus size: 82

        243 GTGTTGATGC

                                              *           *                 *
        253 ATCACCAAGCCTAATTTCCTTGAGGCAAGGTGCAGCCCACACATTCTCAATCATATCCCCTTCAT
          1 ATCACCAAGCCTAATTTCCTTGAGGCAAGGTGCAACCCACACATTCCCAATCATATCCCCTTCAC

                     *       
        318 CCAACCA-TTGATGGTA
         66 CCAACCACTAGATGGTA

                 *                       *      *                   *        
        334 ATCACTAAGCCTAATTTCCTTGAGGCAAGTTGCAACTCACACATTCCCAATCATATTCCCTTCAC
          1 ATCACCAAGCCTAATTTCCTTGAGGCAAGGTGCAACCCACACATTCCCAATCATATCCCCTTCAC

                             
        399 CCAACCACTAGATGGTA
         66 CCAACCACTAGATGGTA

        416 CTGATACATC


Statistics
Matches: 73,  Mismatches: 8, Indels: 1
        0.89            0.10        0.01

Matches are distributed among these distances:
  81   65  0.89
  82    8  0.11

ACGTcount: A:0.29, C:0.32, G:0.12, T:0.26


Consensus pattern (82 bp):   
ATCACCAAGCCTAATTTCCTTGAGGCAAGGTGCAACCCACACATTCCCAATCATATCCCCTTCAC
CCAACCACTAGATGGTA

Found at i:1190 original size:20 final size:20

Alignment explanation


    Indices: 1167--1239  Score: 101
    Period size: 20  Copynumber: 3.6  Consensus size: 20

       1157 ACAATTCAAA

                                
       1167 GTATCGATACATGTTGCAAT
          1 GTATCGATACATGTTGCAAT

                         ****    
       1187 GTATCGATACATGAAAAAGAT
          1 GTATCGATACATGTTGCA-AT

                                
       1208 GTATCGATACATGTTGCAAT
          1 GTATCGATACATGTTGCAAT

                        
       1228 GTATCGATACAT
          1 GTATCGATACAT

       1240 AAAAAAGATG


Statistics
Matches: 44,  Mismatches: 8, Indels: 2
        0.81            0.15        0.04

Matches are distributed among these distances:
  20   28  0.64
  21   16  0.36

ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32


Consensus pattern (20 bp):   
GTATCGATACATGTTGCAAT

Found at i:1211 original size:21 final size:21

Alignment explanation


    Indices: 1185--1260  Score: 100
    Period size: 21  Copynumber: 3.7  Consensus size: 21

       1175 ACATGTTGCA

                                 
       1185 ATGTATCGATACATGAAAAAG
          1 ATGTATCGATACATGAAAAAG

                           ****  
       1206 ATGTATCGATACATGTTGCA-
          1 ATGTATCGATACATGAAAAAG

                          *      
       1226 ATGTATCGATACATAAAAAAG
          1 ATGTATCGATACATGAAAAAG

                          
       1247 ATGTATCGATACAT
          1 ATGTATCGATACAT

       1261 TTCTTGGCAG


Statistics
Matches: 45,  Mismatches: 9, Indels: 2
        0.80            0.16        0.04

Matches are distributed among these distances:
  20   15  0.33
  21   30  0.67

ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29


Consensus pattern (21 bp):   
ATGTATCGATACATGAAAAAG

Found at i:1218 original size:41 final size:41

Alignment explanation


    Indices: 1167--1260  Score: 179
    Period size: 41  Copynumber: 2.3  Consensus size: 41

       1157 ACAATTCAAA

                                            *        
       1167 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
          1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT

                                                     
       1208 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
          1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT

                        
       1249 GTATCGATACAT
          1 GTATCGATACAT

       1261 TTCTTGGCAG


Statistics
Matches: 52,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  41   52  1.00

ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30


Consensus pattern (41 bp):   
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT

Found at i:1317 original size:13 final size:13

Alignment explanation


    Indices: 1299--1324  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       1289 TACAGCAAGT

                         
       1299 ATGTATCGATACA
          1 ATGTATCGATACA

                         
       1312 ATGTATCGATACA
          1 ATGTATCGATACA

       1325 CAAAAAATTG


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31


Consensus pattern (13 bp):   
ATGTATCGATACA
Done.