Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_515 ID=scaffold_515-JGI_221_v2.0

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: 7107
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.27

Warning! 871 characters in sequence are not A, C, G, or T


Found at i:1053 original size:16 final size:16

Alignment explanation


    Indices: 1032--1083  Score: 77
    Period size: 16  Copynumber: 3.2  Consensus size: 16

       1022 TTTGGTTCGC

                           *
       1032 TGTATTGGATTAGAGA
          1 TGTATTGGATTAGAGG

                            
       1048 TGTATTGGATTAGAGG
          1 TGTATTGGATTAGAGG

                *    *      
       1064 TGTAATGGAATAGAGG
          1 TGTATTGGATTAGAGG

                
       1080 TGTA
          1 TGTA

       1084 ATAGCAAATC


Statistics
Matches: 33,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  16   33  1.00

ACGTcount: A:0.31, C:0.00, G:0.35, T:0.35


Consensus pattern (16 bp):   
TGTATTGGATTAGAGG

Found at i:1169 original size:39 final size:43

Alignment explanation


    Indices: 1064--1173  Score: 129
    Period size: 45  Copynumber: 2.6  Consensus size: 43

       1054 GGATTAGAGG

                                                         
       1064 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
          1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A

                            *        *    ***          
       1109 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
          1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA

                                      
       1149 TG-AATGGAATAGAGGTGTAATAGCA
          1 TGTAATGGAATAGAGGTGTAATAGCA

       1174 TAATGGAAAA


Statistics
Matches: 57,  Mismatches: 7, Indels: 7
        0.80            0.10        0.10

Matches are distributed among these distances:
  39   20  0.35
  40    2  0.04
  43    1  0.02
  44   11  0.19
  45   23  0.40

ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32


Consensus pattern (43 bp):   
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA

Found at i:1340 original size:18 final size:17

Alignment explanation


    Indices: 1319--1353  Score: 52
    Period size: 18  Copynumber: 2.0  Consensus size: 17

       1309 TTATTATTAA

                 *            
       1319 ATATATTTTAATTAAAAT
          1 ATATAATTTAA-TAAAAT

                             
       1337 ATATAATTTAATAAAAT
          1 ATATAATTTAATAAAAT

       1354 TCTTAATAAT


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  17    6  0.38
  18   10  0.62

ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46


Consensus pattern (17 bp):   
ATATAATTTAATAAAAT

Found at i:1799 original size:40 final size:41

Alignment explanation


    Indices: 1753--1839  Score: 158
    Period size: 40  Copynumber: 2.1  Consensus size: 41

       1743 TAAGTGAGTA

                                                     
       1753 AGAATTGAACTCTAAAAATAAAA-AAAAAACATAACCATAT
          1 AGAATTGAACTCTAAAAATAAAATAAAAAACATAACCATAT

                                                     
       1793 AGAATTGAACTCTAAAAATAAAATAAAAAACATAACCATAT
          1 AGAATTGAACTCTAAAAATAAAATAAAAAACATAACCATAT

            *     
       1834 CGAATT
          1 AGAATT

       1840 ATCATCAACA


Statistics
Matches: 45,  Mismatches: 1, Indels: 1
        0.96            0.02        0.02

Matches are distributed among these distances:
  40   23  0.51
  41   22  0.49

ACGTcount: A:0.60, C:0.13, G:0.06, T:0.22


Consensus pattern (41 bp):   
AGAATTGAACTCTAAAAATAAAATAAAAAACATAACCATAT

Done.