Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_274 ID=scaffold_274-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: 8758
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35


Found at i:1337 original size:40 final size:40

Alignment explanation


    Indices: 1288--1533  Score: 314
    Period size: 40  Copynumber: 6.1  Consensus size: 40

       1278 TAATTAATGT

                         *                  *       
       1288 CTGAATGCACATATGTGCCCCTGTTTGTACTTTGGTACCC
          1 CTGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCC

                *               *             *     
       1328 CTGAGTGCACATACGTGCCCTTGTTTGTACTTCGATACCC
          1 CTGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCC

            *         *  *      *                   
       1368 TTGAATGCACTTATGTGCCCTTGTTTGTACTTCGGTACCC
          1 CTGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCC

              *           *    *                    
       1408 CTAAATGCACATACATGCCTCTGTTTGTACTTCGGTACCC
          1 CTGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCC

                         *        *                  
       1448 CTGAATGCACATATGTGCCCCTATTTGTACTTCGGTACCCC
          1 CTGAATGCACATACGTGCCCCTGTTTGTACTTCGGTA-CCC

                        *            *             * 
       1489 CTGAATGCACATGCGTGCCCCTGTTAGTACCTTC-GTACTC
          1 CTGAATGCACATACGTGCCCCTGTTTGTA-CTTCGGTACCC

                 
       1529 CTGAA
          1 CTGAA

       1534 GGCATATTCA


Statistics
Matches: 177,  Mismatches: 27, Indels: 4
        0.85            0.13        0.02

Matches are distributed among these distances:
  40  142  0.80
  41   31  0.18
  42    4  0.02

ACGTcount: A:0.19, C:0.29, G:0.19, T:0.33


Consensus pattern (40 bp):   
CTGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCC

Found at i:1370 original size:20 final size:19

Alignment explanation


    Indices: 1345--1407  Score: 54
    Period size: 20  Copynumber: 3.2  Consensus size: 19

       1335 CACATACGTG

                                
       1345 CCCTTGTTTGTACTTCGATA
          1 CCCTTGTTTGTACTTCG-TA

                  **  *     *  *
       1365 CCCTTGAATGCACTTATGTG
          1 CCCTTGTTTGTACTT-CGTA

                                
       1385 CCCTTGTTTGTACTTCGGTA
          1 CCCTTGTTTGTACTTC-GTA

               
       1405 CCC
          1 CCC

       1408 CTAAATGCAC


Statistics
Matches: 31,  Mismatches: 10, Indels: 4
        0.69            0.22        0.09

Matches are distributed among these distances:
  20   30  0.97
  21    1  0.03

ACGTcount: A:0.14, C:0.29, G:0.17, T:0.40


Consensus pattern (19 bp):   
CCCTTGTTTGTACTTCGTA

Found at i:3614 original size:20 final size:20

Alignment explanation


    Indices: 3588--3691  Score: 86
    Period size: 20  Copynumber: 5.2  Consensus size: 20

       3578 TTGTATGAGA

                     *           
       3588 TTTGCACTTTGATGCCCCTAG
          1 TTTGCACTTCGATGCCCCT-G

                          *     
       3609 -TTGCACTTCGATGTCCCTG
          1 TTTGCACTTCGATGCCCCTG

                       *        
       3628 TTTGCACTTCGGTGCCCCTG
          1 TTTGCACTTCGATGCCCCTG

             * *       *  **   *
       3648 TATACACTTCGGTGTTCCTA
          1 TTTGCACTTCGATGCCCCTG

              *                  
       3668 TTCGCACTAT-GATGCCCCTG
          1 TTTGCACT-TCGATGCCCCTG

                
       3688 TTTG
          1 TTTG

       3692 GACATTTGTG


Statistics
Matches: 64,  Mismatches: 17, Indels: 5
        0.74            0.20        0.06

Matches are distributed among these distances:
  19    1  0.02
  20   62  0.97
  21    1  0.02

ACGTcount: A:0.12, C:0.30, G:0.20, T:0.38


Consensus pattern (20 bp):   
TTTGCACTTCGATGCCCCTG

Found at i:3675 original size:40 final size:40

Alignment explanation


    Indices: 3591--3688  Score: 101
    Period size: 40  Copynumber: 2.5  Consensus size: 40

       3581 TATGAGATTT

                 *               *               *  *
       3591 GCACTTTGATGCCCCTAGT-TGCACTTCGATGTCCCTGTTT
          1 GCACTATGATGCCCCT-GTATACACTTCGATGTCCCTATTC

                     *                   *   *       
       3631 GCACT-TCGGTGCCCCTGTATACACTTCGGTGTTCCTATTC
          1 GCACTAT-GATGCCCCTGTATACACTTCGATGTCCCTATTC

                              
       3671 GCACTATGATGCCCCTGT
          1 GCACTATGATGCCCCTGT

       3689 TTGGACATTT


Statistics
Matches: 48,  Mismatches: 7, Indels: 6
        0.79            0.11        0.10

Matches are distributed among these distances:
  39    3  0.06
  40   44  0.92
  41    1  0.02

ACGTcount: A:0.13, C:0.32, G:0.20, T:0.35


Consensus pattern (40 bp):   
GCACTATGATGCCCCTGTATACACTTCGATGTCCCTATTC
Done.