Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold808

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: 37435
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:13024 original size:16 final size:17

Alignment explanation


    Indices: 13005--13037  Score: 50
    Period size: 17  Copynumber: 2.0  Consensus size: 17

      12995 ATAAAAATAA

                             
      13005 ACTTT-ACAACTTGGCC
          1 ACTTTGACAACTTGGCC

                      *      
      13021 ACTTTGACAATTTGGCC
          1 ACTTTGACAACTTGGCC

      13038 TGATTTCAAC


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  16    5  0.33
  17   10  0.67

ACGTcount: A:0.24, C:0.27, G:0.15, T:0.33


Consensus pattern (17 bp):   
ACTTTGACAACTTGGCC

Found at i:16455 original size:4 final size:4

Alignment explanation


    Indices: 16439--16468  Score: 53
    Period size: 4  Copynumber: 7.8  Consensus size: 4

      16429 GTTGTAAAGT

                                                  
      16439 TTTA TTT- TTTA TTTA TTTA TTTA TTTA TTT
          1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT

      16469 TACTTAGTTT


Statistics
Matches: 25,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   3    3  0.12
   4   22  0.88

ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80


Consensus pattern (4 bp):   
TTTA

Found at i:29205 original size:12 final size:11

Alignment explanation


    Indices: 29170--29202  Score: 66
    Period size: 11  Copynumber: 3.0  Consensus size: 11

      29160 TAGTAGTTTC

                       
      29170 TTCAAAAAAAA
          1 TTCAAAAAAAA

                       
      29181 TTCAAAAAAAA
          1 TTCAAAAAAAA

                       
      29192 TTCAAAAAAAA
          1 TTCAAAAAAAA

      29203 ATTGGTTTCC


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   22  1.00

ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18


Consensus pattern (11 bp):   
TTCAAAAAAAA

Found at i:33966 original size:4 final size:4

Alignment explanation


    Indices: 33957--33984  Score: 56
    Period size: 4  Copynumber: 7.0  Consensus size: 4

      33947 TTAAACTAAG

                                              
      33957 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
          1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA

      33985 AATAAAACTT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   24  1.00

ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25


Consensus pattern (4 bp):   
TAAA

Found at i:35374 original size:23 final size:22

Alignment explanation


    Indices: 35322--35374  Score: 56
    Period size: 23  Copynumber: 2.4  Consensus size: 22

      35312 TCCACGTCTT

                    *             
      35322 TTTCTTTTGTTTCTTTTTCTAA
          1 TTTCTTTTCTTTCTTTTTCTAA

                                     
      35344 -TTCATTTTCTCTTCTTTCTTC-AA
          1 TTTC-TTTTCT-TTCTTT-TTCTAA

                    
      35367 TTTCTTTT
          1 TTTCTTTT

      35375 TCACTCTCAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 7
        0.76            0.03        0.21

Matches are distributed among these distances:
  21    3  0.12
  22    5  0.19
  23   12  0.46
  24    6  0.23

ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70


Consensus pattern (22 bp):   
TTTCTTTTCTTTCTTTTTCTAA
Done.