Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold7706.1

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: 6292
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29


Found at i:403 original size:40 final size:40

Alignment explanation


    Indices: 348--426  Score: 149
    Period size: 40  Copynumber: 2.0  Consensus size: 40

        338 ATTAAAGTCA

                                 *                  
        348 CATATATATATGGAAATCATGCATCAAACTCAACATTTTC
          1 CATATATATATGGAAATCATGAATCAAACTCAACATTTTC

                                                   
        388 CATATATATATGGAAATCATGAATCAAACTCAACATTTT
          1 CATATATATATGGAAATCATGAATCAAACTCAACATTTT

        427 AGCCCCCACT


Statistics
Matches: 38,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  40   38  1.00

ACGTcount: A:0.42, C:0.18, G:0.08, T:0.33


Consensus pattern (40 bp):   
CATATATATATGGAAATCATGAATCAAACTCAACATTTTC

Found at i:6023 original size:20 final size:21

Alignment explanation


    Indices: 5985--6023  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       5975 TTTGGTCAGT

                          *      
       5985 TACTTTTTCTGTTATCACCGG
          1 TACTTTTTCTGTTAACACCGG

                               
       6006 TACTTTTTCTG-TAACACC
          1 TACTTTTTCTGTTAACACC

       6024 CCGTACCCGA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  20    6  0.35
  21   11  0.65

ACGTcount: A:0.18, C:0.26, G:0.10, T:0.46


Consensus pattern (21 bp):   
TACTTTTTCTGTTAACACCGG

Found at i:6029 original size:21 final size:21

Alignment explanation


    Indices: 5985--6029  Score: 56
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       5975 TTTGGTCAGT

                          *    * 
       5985 TACTTTTTCTGTTATCACCGG
          1 TACTTTTTCTGTTAACACCCG

                                  
       6006 TACTTTTTCTG-TAACACCCCG
          1 TACTTTTTCTGTTAACA-CCCG

               
       6027 TAC
          1 TAC

       6030 CCGAGACCGT


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  20    4  0.19
  21   17  0.81

ACGTcount: A:0.18, C:0.29, G:0.11, T:0.42


Consensus pattern (21 bp):   
TACTTTTTCTGTTAACACCCG
Done.