Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_53 ID=scaffold_53-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: 22536
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.35

Warning! 675 characters in sequence are not A, C, G, or T


Found at i:1352 original size:25 final size:27

Alignment explanation


    Indices: 1314--1365  Score: 74
    Period size: 25  Copynumber: 2.0  Consensus size: 27

       1304 AATGTATGTA

                                       
       1314 TTTTTGAAATATTAA-TGT-TATATTT
          1 TTTTTGAAATATTAATTGTATATATTT

                                        
       1339 TTTTGTGAAA-ATTAATTGTATATATTT
          1 TTTT-TGAAATATTAATTGTATATATTT

       1366 AATGTACTAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 4
        0.86            0.00        0.14

Matches are distributed among these distances:
  25    9  0.38
  26    8  0.33
  27    7  0.29

ACGTcount: A:0.33, C:0.00, G:0.10, T:0.58


Consensus pattern (27 bp):   
TTTTTGAAATATTAATTGTATATATTT

Found at i:5586 original size:2 final size:2

Alignment explanation


    Indices: 5575--5611  Score: 58
    Period size: 2  Copynumber: 18.5  Consensus size: 2

       5565 GAATTTAAGT

                                                                    
       5575 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TGA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA T

       5612 TACTTAAAAT


Statistics
Matches: 33,  Mismatches: 0, Indels: 4
        0.89            0.00        0.11

Matches are distributed among these distances:
   1    1  0.03
   2   30  0.91
   3    2  0.06

ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:10286 original size:23 final size:23

Alignment explanation


    Indices: 10260--10303  Score: 72
    Period size: 23  Copynumber: 1.9  Consensus size: 23

      10250 AATGTATGTA

                                    
      10260 TTTT-TGAAATATTAATGGTATTT
          1 TTTTGTGAAA-ATTAATGGTATTT

                                 
      10283 TTTTGTGAAAATTAATGGTAT
          1 TTTTGTGAAAATTAATGGTAT

      10304 ATATTTAATG


Statistics
Matches: 20,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  23   15  0.75
  24    5  0.25

ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52


Consensus pattern (23 bp):   
TTTTGTGAAAATTAATGGTATTT

Found at i:12883 original size:2 final size:2

Alignment explanation


    Indices: 12878--12902  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

      12868 TAGAATATTC

                                                 
      12878 TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T

      12903 NNNNNNNNNN


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:16642 original size:153 final size:153

Alignment explanation


    Indices: 16257--16625  Score: 584
    Period size: 153  Copynumber: 2.4  Consensus size: 153

      16247 ATATTCCACC

                                *      **      *                    *        
      16257 TGATATTTCTGGTCTATCCTGTTTG-GAAATACTTGATCTTAGTGGTAACAATTTCGTCAGCATA
          1 TGATATTTCTGGTCTATCCTCTTTGAGTTAT-CTTAATCTTAGTGGTAACAATTTCATCAGCATA

                                   *       *                         *       
      16321 CCTGCATCTCTTACTCGACTCTCGAAGCTTGCATATCTTATATTGTCAAATTGCAACTTGTGCAC
         65 CCTGCATCTCTTACTCGACTCTCAAAGCTTGAATATCTTATATTGTCAAATTGCAACATGTGCAC

                                    
      16386 TTTTGGTGAAGCAGATACTCATAG
        130 TTTTGGTGAAGCAGATACTCATAG

                                                                             
      16410 TGATATTTCTGGTCTATCCTCTTTGAGTTATCTTAATCTTAGTGGTAACAATTTCATCAGCATAC
          1 TGATATTTCTGGTCTATCCTCTTTGAGTTATCTTAATCTTAGTGGTAACAATTTCATCAGCATAC

                                              *                              
      16475 CTGCATCTCTTACTCGACTCTCAAAGCTT-AAGTCTCTTGA-ATTGTCAAATTGCAACATGTGCA
         66 CTGCATCTCTTACTCGACTCTCAAAGCTTGAA-TATCTT-ATATTGTCAAATTGCAACATGTGCA

                                      
      16538 -TTCTTGGTGAAGCAGATACTCATAG
        129 CTT-TTGGTGAAGCAGATACTCATAG

                                              *                            
      16563 TGATATTTCTGGTCTATCCTCTTTGAGTTATCTTTATCTTAGTGGTAACAATTTCATCAGCAT
          1 TGATATTTCTGGTCTATCCTCTTTGAGTTATCTTAATCTTAGTGGTAACAATTTCATCAGCAT

      16626 TCCTTTGGCT


Statistics
Matches: 202,  Mismatches: 10, Indels: 8
        0.92            0.05        0.04

Matches are distributed among these distances:
 152    3  0.01
 153  195  0.97
 154    4  0.02

ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39


Consensus pattern (153 bp):   
TGATATTTCTGGTCTATCCTCTTTGAGTTATCTTAATCTTAGTGGTAACAATTTCATCAGCATAC
CTGCATCTCTTACTCGACTCTCAAAGCTTGAATATCTTATATTGTCAAATTGCAACATGTGCACT
TTTGGTGAAGCAGATACTCATAG

Found at i:17987 original size:2 final size:2

Alignment explanation


    Indices: 17980--18008  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

      17970 ATTTCCACAT

                                                       
      17980 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      18009 TCACTTACAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Done.