Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold805

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: 8491
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30


Found at i:1233 original size:54 final size:54

Alignment explanation


    Indices: 1144--1251  Score: 162
    Period size: 54  Copynumber: 2.0  Consensus size: 54

       1134 TTTTTCCAAC

                                       *  *                       
       1144 AACTTTATATTGATACATAAAGCAAAGTATTGATACATTACTTAAAAAACTAAT
          1 AACTTTATATTGATACATAAAGCAAAGCATCGATACATTACTTAAAAAACTAAT

                  *                * *             *              
       1198 AACTTTGTATTGATACATAAAGCCAGGCATCGATACATTTCTTAAAAAACTAAT
          1 AACTTTATATTGATACATAAAGCAAAGCATCGATACATTACTTAAAAAACTAAT

       1252 TATTGTGACT


Statistics
Matches: 48,  Mismatches: 6, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  54   48  1.00

ACGTcount: A:0.44, C:0.14, G:0.09, T:0.32


Consensus pattern (54 bp):   
AACTTTATATTGATACATAAAGCAAAGCATCGATACATTACTTAAAAAACTAAT

Found at i:1429 original size:20 final size:20

Alignment explanation


    Indices: 1400--1449  Score: 57
    Period size: 20  Copynumber: 2.5  Consensus size: 20

       1390 TCACTTAATG

                 *               
       1400 TATCGTTACATTGT-ACATTA
          1 TATCGATACATTGTGAC-TTA

                        *      *
       1420 TATCGATACATTTTGACTTG
          1 TATCGATACATTGTGACTTA

                      
       1440 TATCGATACA
          1 TATCGATACA

       1450 AATGAGGGTT


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  20   24  0.92
  21    2  0.08

ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42


Consensus pattern (20 bp):   
TATCGATACATTGTGACTTA

Found at i:1523 original size:112 final size:113

Alignment explanation


    Indices: 1284--1499  Score: 267
    Period size: 113  Copynumber: 1.9  Consensus size: 113

       1274 ACATTTAGGG

                       **    **   *                                          
       1284 ATGTATCGATATGTTGTGTATTGTATCGATACATTTTCATGTGTATCGATACAAATGAGAGTTTC
          1 ATGTATCGATACATTGTACATTATATCGATACATTTTCATGTGTATCGATACAAATGAGAGTTTC

                *           * *                   *         
       1349 AAGATTTCTTTAGCTATTGCCAACCAGATGTATCGATACTTTCACTTA
         66 AAGACTTCTTTAGCTACTACCAACCAGATGTATCGATAATTTCACTTA

                    *                            *                      *    
       1397 ATGTATCGTTACATTGTACATTATATCGATACATTTTGACT-TGTATCGATACAAATGAGGGTTT
          1 ATGTATCGATACATTGTACATTATATCGATACATTTTCA-TGTGTATCGATACAAATGAGAGTTT

             *                          *            
       1461 -TAGCACTT-TTTAGCTACTACCAACCATATGTATCGATAA
         65 CAAG-ACTTCTTTAGCTACTACCAACCAGATGTATCGATAA

       1500 ATTTATATGA


Statistics
Matches: 87,  Mismatches: 14, Indels: 5
        0.82            0.13        0.05

Matches are distributed among these distances:
 112   29  0.33
 113   57  0.66
 114    1  0.01

ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39


Consensus pattern (113 bp):   
ATGTATCGATACATTGTACATTATATCGATACATTTTCATGTGTATCGATACAAATGAGAGTTTC
AAGACTTCTTTAGCTACTACCAACCAGATGTATCGATAATTTCACTTA

Found at i:4155 original size:20 final size:20

Alignment explanation


    Indices: 4130--4186  Score: 80
    Period size: 20  Copynumber: 2.9  Consensus size: 20

       4120 GAAACCCAAA

                                 
       4130 TGTATCAATACATTATT-CAT
          1 TGTATCAATACATT-TTGCAT

                                
       4150 TGTATCAATACATTTTGCAT
          1 TGTATCAATACATTTTGCAT

             *        *      
       4170 TATATCAATATATTTTG
          1 TGTATCAATACATTTTG

       4187 GAAAAACCTA


Statistics
Matches: 34,  Mismatches: 2, Indels: 2
        0.89            0.05        0.05

Matches are distributed among these distances:
  19    2  0.06
  20   32  0.94

ACGTcount: A:0.33, C:0.12, G:0.07, T:0.47


Consensus pattern (20 bp):   
TGTATCAATACATTTTGCAT
Done.