Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: CotAD_25772

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: 7136
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:2425 original size:43 final size:46

Alignment explanation


    Indices: 2377--2465  Score: 148
    Period size: 45  Copynumber: 2.0  Consensus size: 46

       2367 TACGTATGAT

                                                          
       2377 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
          1 CACTTATCACTTTGTCACCTGATCAGATAAGTGTAGCTAAGGCTAC

                              *                           
       2420 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
          1 CACTTATCACTTTGTCACCTGATCAGATAAGTGTAGCTAAGGCTAC

       2466 TTTTTCACTT


Statistics
Matches: 42,  Mismatches: 1, Indels: 3
        0.91            0.02        0.07

Matches are distributed among these distances:
  43   10  0.24
  44    5  0.12
  45   20  0.48
  46    7  0.17

ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31


Consensus pattern (46 bp):   
CACTTATCACTTTGTCACCTGATCAGATAAGTGTAGCTAAGGCTAC

Found at i:2636 original size:36 final size:36

Alignment explanation


    Indices: 2420--2636  Score: 357
    Period size: 36  Copynumber: 6.0  Consensus size: 36

       2410 GCTAGGCTAC

                         *                      
       2420 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
          1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG

                *  *                          *   
       2456 --CTAAGGCTACTTTTTCACTTGATCAGATAAGTATAG
          1 CACTTA-TC-ACTTTTTCACTTGATCAGATAAGTGTAG

                                            *   
       2492 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
          1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG

                                                
       2528 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
          1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG

                                                
       2564 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
          1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG

                                                
       2600 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
          1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG

             
       2636 C
          1 C

       2637 TAAAGCTACC


Statistics
Matches: 170,  Mismatches: 7, Indels: 8
        0.92            0.04        0.04

Matches are distributed among these distances:
  34    3  0.02
  35    1  0.01
  36  162  0.95
  37    1  0.01
  38    3  0.02

ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38


Consensus pattern (36 bp):   
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG

Found at i:5338 original size:20 final size:21

Alignment explanation


    Indices: 5310--5360  Score: 61
    Period size: 20  Copynumber: 2.4  Consensus size: 21

       5300 ATAAAATTTA

                                   
       5310 ATTAGAATATATAAACTAT-ATT
          1 ATTA-AATATATAAA-TATAATT

                     *           
       5332 -TTAAATATTTAAATATAATT
          1 ATTAAATATATAAATATAATT

                     
       5352 ATTAAATAT
          1 ATTAAATAT

       5361 TTGTAATTAG


Statistics
Matches: 26,  Mismatches: 1, Indels: 5
        0.81            0.03        0.16

Matches are distributed among these distances:
  19    3  0.12
  20   12  0.46
  21   11  0.42

ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45


Consensus pattern (21 bp):   
ATTAAATATATAAATATAATT

Found at i:5358 original size:21 final size:21

Alignment explanation


    Indices: 5310--5362  Score: 65
    Period size: 21  Copynumber: 2.5  Consensus size: 21

       5300 ATAAAATTTA

                      *           
       5310 ATTAGAATATATAAACTATATT
          1 ATTA-AATATTTAAACTATATT

                                  
       5332 -TTAAATATTTAAA-TATAATT
          1 ATTAAATATTTAAACTAT-ATT

                       
       5352 ATTAAATATTT
          1 ATTAAATATTT

       5363 GTAATTAGAT


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

Matches are distributed among these distances:
  19    3  0.11
  20   12  0.43
  21   13  0.46

ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47


Consensus pattern (21 bp):   
ATTAAATATTTAAACTATATT
Done.