Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_322 ID=scaffold_322-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: 8221
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32


Found at i:1295 original size:40 final size:40

Alignment explanation


    Indices: 1137--1313  Score: 133
    Period size: 40  Copynumber: 4.2  Consensus size: 40

       1127 ACAACGTCAA

                             *                      
       1137 GGAGATAAGACTTGATGTGATCTGCTCCACTACTGCTTAG
          1 GGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAG

                             * ***  *            *  *   *
       1177 GGAGATAAGATCTGTGGTTTTAATTTGCTCCACTGCAAT-TTTAA
          1 GGAGATAAGA-CT-T-GATGCGATCTGCTCCACT--ACTGCTTAG

                       *     ** *       *               
       1221 GGAGATATGATTACTTTCTTCCG-TCTGTTCCACTACTGCTTAG
          1 GGAGATA--A-GAC-TTGATGCGATCTGCTCCACTACTGCTTAG

                                                    
       1264 GGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAG
          1 GGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAG

                      
       1304 GGAGATAAGA
          1 GGAGATAAGA

       1314 TCTGTGGTCT


Statistics
Matches: 104,  Mismatches: 22, Indels: 22
        0.70            0.15        0.15

Matches are distributed among these distances:
  39    5  0.05
  40   41  0.39
  41    3  0.03
  42    3  0.03
  43   24  0.23
  44   19  0.18
  45    4  0.04
  46    3  0.03
  47    2  0.02

ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33


Consensus pattern (40 bp):   
GGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAG

Found at i:1440 original size:86 final size:86

Alignment explanation


    Indices: 1335--1844  Score: 835
    Period size: 86  Copynumber: 6.0  Consensus size: 86

       1325 CAGTCTGCTC

                         *           *  *                        *           
       1335 CGCTGTTAACGCAAGAAGGCAAGATTTGTTTCTTTAACCAGCTCCACTGCAACTGATGGAGGCAA
          1 CGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAA

                              *  
       1400 GGCTTTGTTTTTGATCTATTT
         66 GGCTTTGTTTTTGATCTACTT

                                                                             
       1421 CGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAA
          1 CGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAA

             *         *         
       1486 GACTTTGTTTTCGATCTACTT
         66 GGCTTTGTTTTTGATCTACTT

                                                                             
       1507 CGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAA
          1 CGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAA

             *         *     *   
       1572 GACTTTGTTTTCGATCTGCTT
         66 GGCTTTGTTTTTGATCTACTT

                                     *                                       
       1593 CGCTGTTAACGCAGGAAGGCAAGATTTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAA
          1 CGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAA

                             *   
       1658 GGCTTTGTTTTTGATCTGCTT
         66 GGCTTTGTTTTTGATCTACTT

            *          *                                                     
       1679 TGCTGTTAACGTAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAA
          1 CGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAA

                  *          *   
       1744 GGC-TTATTTTT-ATCTGCTT
         66 GGCTTTGTTTTTGATCTACTT

                             *    *                             *            
       1763 CGCTGTTAACGCAGGAATGCAATATCTGCTTCTTTAACCAGCTCCACTGCAATCGATGGAGGCAA
          1 CGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAA

                             
       1828 GGCTTTGTTTTTGATCT
         66 GGCTTTGTTTTTGATCT

       1845 TCACTGATCT


Statistics
Matches: 401,  Mismatches: 21, Indels: 4
        0.94            0.05        0.01

Matches are distributed among these distances:
  84   71  0.18
  85   14  0.03
  86  316  0.79

ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30


Consensus pattern (86 bp):   
CGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAA
GGCTTTGTTTTTGATCTACTT

Found at i:3095 original size:7 final size:7

Alignment explanation


    Indices: 3085--3118  Score: 54
    Period size: 7  Copynumber: 5.1  Consensus size: 7

       3075 TCCATTTTAC

                   
       3085 TTTTT-A
          1 TTTTTCA

                   
       3091 TTTTTCA
          1 TTTTTCA

                   
       3098 TTTTTCA
          1 TTTTTCA

                   
       3105 -TTTTCA
          1 TTTTTCA

                   
       3111 TTTTTCA
          1 TTTTTCA

             
       3118 T
          1 T

       3119 CTCTCTTTTT


Statistics
Matches: 26,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
   6   11  0.42
   7   15  0.58

ACGTcount: A:0.15, C:0.12, G:0.00, T:0.74


Consensus pattern (7 bp):   
TTTTTCA

Found at i:3101 original size:13 final size:13

Alignment explanation


    Indices: 3092--3118  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

       3082 TACTTTTTAT

                         
       3092 TTTTCATTTTTCA
          1 TTTTCATTTTTCA

                         
       3105 TTTTCATTTTTCA
          1 TTTTCATTTTTCA

             
       3118 T
          1 T

       3119 CTCTCTTTTT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70


Consensus pattern (13 bp):   
TTTTCATTTTTCA

Found at i:3128 original size:20 final size:19

Alignment explanation


    Indices: 3084--3128  Score: 54
    Period size: 20  Copynumber: 2.3  Consensus size: 19

       3074 CTCCATTTTA

                           * * 
       3084 CTTTTTATTTTTCATTTTT
          1 CTTTTTATTTTTCATCTCT

                  *             
       3103 CATTTTCATTTTTCATCTCT
          1 C-TTTTTATTTTTCATCTCT

                  
       3123 CTTTTT
          1 CTTTTT

       3129 TTTGAACTTC


Statistics
Matches: 21,  Mismatches: 4, Indels: 2
        0.78            0.15        0.07

Matches are distributed among these distances:
  19    5  0.24
  20   16  0.76

ACGTcount: A:0.11, C:0.18, G:0.00, T:0.71


Consensus pattern (19 bp):   
CTTTTTATTTTTCATCTCT
Done.