Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1950

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, 715

Length: 1192
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25


Found at i:170 original size:24 final size:24

Alignment explanation


    Indices: 143--202  Score: 68
    Period size: 24  Copynumber: 2.5  Consensus size: 24

        133 ATGATGACAT

                                *   
        143 TAATAATAATAATAATACTATTAA
          1 TAATAATAATAATAATACTACTAA

                           * *       
        167 TAAT-ATAAATAATATTGCTACTAA
          1 TAATAAT-AATAATAATACTACTAA

                  *     
        191 TAATAAAAATAA
          1 TAATAATAATAA

        203 CGATAAAATA


Statistics
Matches: 30,  Mismatches: 4, Indels: 4
        0.79            0.11        0.11

Matches are distributed among these distances:
  23    2  0.07
  24   27  0.90
  25    1  0.03

ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35


Consensus pattern (24 bp):   
TAATAATAATAATAATACTACTAA

Found at i:196 original size:3 final size:3

Alignment explanation


    Indices: 75--180  Score: 69
    Period size: 3  Copynumber: 35.7  Consensus size: 3

         65 GTAGTAGTAG

                                                                          
         75 TAA TAA TAA TAA TAA TAA TAA -AA GTAA TAA -AA GTAA TAA -AA GTAA
          1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA -TAA TAA TAA -TAA

                  *       *      *   *  * *                       *   *    
        120 TAA TAC T-A TAG TAA TGA TGA CAT TAA TAA TAA TAA TAA TAC TAT TAA
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA

                               
        167 TAA T-A TAAA TAA TA
          1 TAA TAA T-AA TAA TA

        181 TTGCTACTAA


Statistics
Matches: 81,  Mismatches: 13, Indels: 18
        0.72            0.12        0.16

Matches are distributed among these distances:
   2    9  0.11
   3   64  0.79
   4    8  0.10

ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32


Consensus pattern (3 bp):   
TAA

Found at i:441 original size:100 final size:98

Alignment explanation


    Indices: 251--445  Score: 327
    Period size: 100  Copynumber: 2.0  Consensus size: 98

        241 AGCTAAAAAC

                               *                                    *        
        251 AAAATTTCGGGGAAAATTCGAAATAAATAAAAAAGAAAAAGACCAAAATAAACGCGCAAAAAACT
          1 AAAATTTCGGGGAAAATTCAAAATAAATAAAAAAGAAAAAGACCAAAATAAACGCGAAAAAAACT

                                             
        316 AGGAGGGGGCAAATGGGAAATAATCCCATTCTT
         66 AGGAGGGGGCAAATGGGAAATAATCCCATTCTT

                   *    *                                     *              
        349 AAAATTTTGGGGCAAATTCAAAATAAATAAAAAAGGAAAAAGACCAAAATGAACGCGAAAAAAAA
          1 AAAATTTCGGGGAAAATTCAAAATAAATAAAAAA-GAAAAAGACCAAAATAAACGCG-AAAAAAA

                                            
        414 CTAGGAGGGGGCAAATGGGAAATAATCCCATT
         64 CTAGGAGGGGGCAAATGGGAAATAATCCCATT

        446 ATGCAAAACG


Statistics
Matches: 90,  Mismatches: 5, Indels: 2
        0.93            0.05        0.02

Matches are distributed among these distances:
  98   31  0.34
  99   21  0.23
 100   38  0.42

ACGTcount: A:0.52, C:0.12, G:0.20, T:0.16


Consensus pattern (98 bp):   
AAAATTTCGGGGAAAATTCAAAATAAATAAAAAAGAAAAAGACCAAAATAAACGCGAAAAAAACT
AGGAGGGGGCAAATGGGAAATAATCCCATTCTT

Found at i:947 original size:122 final size:122

Alignment explanation


    Indices: 730--955  Score: 407
    Period size: 122  Copynumber: 1.9  Consensus size: 122

        720 CAAAAAAAAT

                   *                                       *                 
        730 ATCATTCCTTCCTTTTCACACCAAAAAAAACTGATATGCTCTCCCTCTCTTCTTCTCCGTTCAGA
          1 ATCATTCATTCCTTTTCACACCAAAAAAAACTGATATGCTCTCCCTCCCTTCTTCTCCGTTCAGA

                                *                                    
        795 ATTCGGACAGAGGACGGGCCGACCACCGCCGTGCCGGCCGCCGGTCACCGACGACGA
         66 ATTCGGACAGAGGACGGGCCAACCACCGCCGTGCCGGCCGCCGGTCACCGACGACGA

                                                                             
        852 ATCATTCATTCCTTTTCACACCAAAAAAAACTGATATGCTCTCCCTCCCTTCTTCTCCGTTCAGA
          1 ATCATTCATTCCTTTTCACACCAAAAAAAACTGATATGCTCTCCCTCCCTTCTTCTCCGTTCAGA

                  *                *               
        917 ATTCGGCCAGAGGACGGGCCAACGACCGCCGTGCCGGCC
         66 ATTCGGACAGAGGACGGGCCAACCACCGCCGTGCCGGCC

        956 ACTGGTCATC


Statistics
Matches: 99,  Mismatches: 5, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
 122   99  1.00

ACGTcount: A:0.23, C:0.36, G:0.19, T:0.23


Consensus pattern (122 bp):   
ATCATTCATTCCTTTTCACACCAAAAAAAACTGATATGCTCTCCCTCCCTTCTTCTCCGTTCAGA
ATTCGGACAGAGGACGGGCCAACCACCGCCGTGCCGGCCGCCGGTCACCGACGACGA

Done.