Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold691

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: 9857
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.32


Found at i:6036 original size:22 final size:22

Alignment explanation


    Indices: 6006--6067  Score: 74
    Period size: 22  Copynumber: 2.8  Consensus size: 22

       5996 CATATAACCT

                                   
       6006 CATTTCAATC-ATAA-TTTCTCA
          1 CATTTCAATCAATAATTTTC-CA

                           *        
       6027 CATTTTCAATTCAATCATTTTCCA
          1 CA-TTTCAA-TCAATAATTTTCCA

                             
       6051 CATTTCAATCAATAATT
          1 CATTTCAATCAATAATT

       6068 AATCCACAAT


Statistics
Matches: 35,  Mismatches: 2, Indels: 7
        0.80            0.05        0.16

Matches are distributed among these distances:
  21    2  0.06
  22   14  0.40
  23    8  0.23
  24    7  0.20
  25    4  0.11

ACGTcount: A:0.34, C:0.23, G:0.00, T:0.44


Consensus pattern (22 bp):   
CATTTCAATCAATAATTTTCCA

Found at i:6052 original size:24 final size:25

Alignment explanation


    Indices: 6009--6063  Score: 71
    Period size: 27  Copynumber: 2.2  Consensus size: 25

       5999 ATAACCTCAT

                                       
       6009 TTCAATCATAATTTCTCACATTTTCAA
          1 TTCAATCAT-ATTTCTCACA-TTTCAA

                                     
       6036 TTCAATCAT-TTTC-CACATTTCAA
          1 TTCAATCATATTTCTCACATTTCAA

                  
       6059 -TCAAT
          1 TTCAAT

       6064 AATTAATCCA


Statistics
Matches: 28,  Mismatches: 0, Indels: 5
        0.85            0.00        0.15

Matches are distributed among these distances:
  22    5  0.18
  23    6  0.21
  24    4  0.14
  25    4  0.14
  27    9  0.32

ACGTcount: A:0.33, C:0.24, G:0.00, T:0.44


Consensus pattern (25 bp):   
TTCAATCATATTTCTCACATTTCAA

Found at i:6227 original size:3 final size:3

Alignment explanation


    Indices: 6219--6369  Score: 302
    Period size: 3  Copynumber: 50.3  Consensus size: 3

       6209 CCACTCATTT

                                                                           
       6219 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA

                                                                           
       6267 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA

                                                                           
       6315 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA

                     
       6363 TAA TAA T
          1 TAA TAA T

       6370 GTATTTTACA


Statistics
Matches: 148,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3  148  1.00

ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34


Consensus pattern (3 bp):   
TAA

Found at i:7255 original size:30 final size:31

Alignment explanation


    Indices: 7221--7284  Score: 76
    Period size: 30  Copynumber: 2.1  Consensus size: 31

       7211 TACATTTGTC

                 *    *    *               
       7221 TTAATCTAATTACTTCATTAA-AAAAATCTT
          1 TTAATATAATAACTTAATTAATAAAAATCTT

                        *            *     
       7251 TTAATATAATAATTTAATTAATAAATATCTT
          1 TTAATATAATAACTTAATTAATAAAAATCTT

               
       7282 TTA
          1 TTA

       7285 CTTCAATTAT


Statistics
Matches: 28,  Mismatches: 5, Indels: 1
        0.82            0.15        0.03

Matches are distributed among these distances:
  30   17  0.61
  31   11  0.39

ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47


Consensus pattern (31 bp):   
TTAATATAATAACTTAATTAATAAAAATCTT

Found at i:7439 original size:3 final size:3

Alignment explanation


    Indices: 7387--7424  Score: 67
    Period size: 3  Copynumber: 12.7  Consensus size: 3

       7377 TTGGTTTATT

                                              *               
       7387 TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TA
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA

       7425 TAAAACCATA


Statistics
Matches: 33,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   3   33  1.00

ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34


Consensus pattern (3 bp):   
TAA
Done.