Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold973

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: 20947
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.31


Found at i:5207 original size:38 final size:40

Alignment explanation


    Indices: 5106--5268  Score: 176
    Period size: 40  Copynumber: 4.1  Consensus size: 40

       5096 TTGAATGATG

                                         *        *   
       5106 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATA
          1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTATA

                 *                                   
       5146 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-A
          1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTATA

                                            *       
       5185 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATA
          1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATA

            *        *                **             
       5224 ACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
          1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATA-CTATA

                 
       5264 TCCGG
          1 TCCGG

       5269 TTAAATTCCG


Statistics
Matches: 106,  Mismatches: 10, Indels: 14
        0.82            0.08        0.11

Matches are distributed among these distances:
  38   24  0.23
  39   23  0.22
  40   48  0.45
  41   10  0.09
  42    1  0.01

ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24


Consensus pattern (40 bp):   
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATA

Found at i:9573 original size:53 final size:53

Alignment explanation


    Indices: 9496--9702  Score: 201
    Period size: 53  Copynumber: 3.9  Consensus size: 53

       9486 CCATGGCAAC

                          *                 *                    
       9496 AAGTGATAAGTGATATCCGTATAAGA-CATAGTTGGGCTATGGCATCGGAAAA
          1 AAGTGATAAGTGATTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGAAAA

                             *                * *        *     ** 
       9548 CAAGTGATAAGTGATTTTCGTATAAGACCATAGCCGAGCTATGGCTTCGGATTA
          1 -AAGTGATAAGTGATTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGAAAA

                               *                                    
       9602 AAGTGATACAAGTGA--TCTGTATAAGACCATAGCTGGGCTATGGCATC--AAAGA
          1 AAGTGAT--AAGTGATTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGAAA-A

                                 *          *   ***           
       9654 AATGTGATAAGTG-TTTCCGTGTAAGACCATATCTGAAATATGGCATCGG
          1 AA-GTGATAAGTGATTTCCGTATAAGACCATAGCTGGGCTATGGCATCGG

       9703 TATGATATAT


Statistics
Matches: 124,  Mismatches: 21, Indels: 17
        0.77            0.13        0.10

Matches are distributed among these distances:
  51    6  0.05
  52   29  0.23
  53   63  0.51
  54   20  0.16
  55    6  0.05

ACGTcount: A:0.33, C:0.14, G:0.25, T:0.27


Consensus pattern (53 bp):   
AAGTGATAAGTGATTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGAAAA

Found at i:15867 original size:55 final size:53

Alignment explanation


    Indices: 15791--15996  Score: 224
    Period size: 55  Copynumber: 3.8  Consensus size: 53

      15781 ATTAGGGTTT

                *                      *                           
      15791 AAGGTTACCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTTTAAGGC
          1 AAGGATACCATGTAAGACCATGCCAAGTCATGGCAA-TGGTAAGGTTTTTAA-GC

                 * *                                          *     
      15846 AAGGAAATCATGTAAGACCATGCCAAGTCATGGCAATTGGTAAGGTTACTATAAGC
          1 AAGGATACCATGTAAGACCATGCCAAGTCATGGCAA-TGGTAAGGTT--TTTAAGC

                    *                    *                         
      15902 TAAAGG-TCCCATGTAAGACCATGCCAAGACATGGCAATGGTAA-G-TTTTAA--
          1 --AAGGATACCATGTAAGACCATGCCAAGTCATGGCAATGGTAAGGTTTTTAAGC

                      **          *                      
      15952 AAGGATACCACATAAGACCATGACAAGTCATGGCAATGGTAAGGT
          1 AAGGATACCATGTAAGACCATGCCAAGTCATGGCAATGGTAAGGT

      15997 ACTTGCGTAT


Statistics
Matches: 129,  Mismatches: 15, Indels: 18
        0.80            0.09        0.11

Matches are distributed among these distances:
  48    4  0.03
  49   32  0.25
  50    1  0.01
  52    4  0.03
  54    1  0.01
  55   44  0.34
  56    8  0.06
  57   31  0.24
  58    4  0.03

ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23


Consensus pattern (53 bp):   
AAGGATACCATGTAAGACCATGCCAAGTCATGGCAATGGTAAGGTTTTTAAGC

Found at i:16207 original size:16 final size:16

Alignment explanation


    Indices: 16186--16216  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

      16176 ATAAATTTGA

                            
      16186 TTAAGTAAGTAAGTAT
          1 TTAAGTAAGTAAGTAT

                      *    
      16202 TTAAGTAAGTGAGTA
          1 TTAAGTAAGTAAGTA

      16217 ACTGAAGAAG


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35


Consensus pattern (16 bp):   
TTAAGTAAGTAAGTAT

Found at i:19813 original size:15 final size:15

Alignment explanation


    Indices: 19793--19825  Score: 66
    Period size: 15  Copynumber: 2.2  Consensus size: 15

      19783 AGTTGTGTTC

                           
      19793 ATTGATGATATCTTG
          1 ATTGATGATATCTTG

                           
      19808 ATTGATGATATCTTG
          1 ATTGATGATATCTTG

               
      19823 ATT
          1 ATT

      19826 TATTCTCATG


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   18  1.00

ACGTcount: A:0.27, C:0.06, G:0.18, T:0.48


Consensus pattern (15 bp):   
ATTGATGATATCTTG
Done.