Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold854

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: 21728
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31


Found at i:1371 original size:45 final size:46

Alignment explanation


    Indices: 1307--1481  Score: 216
    Period size: 45  Copynumber: 3.8  Consensus size: 46

       1297 TGTAACCCGC

                                           *              
       1307 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG-CGTTCGCAT
          1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT

                   *                                       *   
       1352 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
          1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C--GTTCGCAT

                *                                 *       
       1402 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
          1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT

                   *                             
       1445 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
          1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA

       1482 TGCTCAACCA


Statistics
Matches: 111,  Mismatches: 9, Indels: 19
        0.80            0.06        0.14

Matches are distributed among these distances:
  42    2  0.02
  43    3  0.03
  44    2  0.02
  45   36  0.32
  46   29  0.26
  47   29  0.26
  48    2  0.02
  49    2  0.02
  50    3  0.03
  51    3  0.03

ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21


Consensus pattern (46 bp):   
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT

Found at i:1472 original size:93 final size:92

Alignment explanation


    Indices: 1314--1484  Score: 315
    Period size: 93  Copynumber: 1.8  Consensus size: 92

       1304 CGCCCATAAG

                                          *                                  
       1314 CGAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
          1 CGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA

                                       
       1379 CGAGTTCGGATGCCTAGTTACATCTCA
         66 CGAGTTCGGATGCCTAGTTACATCTCA

                                    *                                        
       1406 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
          1 CGAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCATCCATAAGTGAACTCGGACTCAACTCA

                          
       1471 ACGAGTTCGGATGC
         65 ACGAGTTCGGATGC

       1485 TCAACCATCC


Statistics
Matches: 76,  Mismatches: 2, Indels: 1
        0.96            0.03        0.01

Matches are distributed among these distances:
  92   28  0.37
  93   48  0.63

ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21


Consensus pattern (92 bp):   
CGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCA

Found at i:8946 original size:47 final size:49

Alignment explanation


    Indices: 8870--9002  Score: 172
    Period size: 47  Copynumber: 2.8  Consensus size: 49

       8860 TGTAACCCGC

                                                               
       8870 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
          1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A-TTCACAT

                *                                        *   
       8920 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTCGCAT
          1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT

                   *                                
       8963 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
          1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGC

       9003 TCAACATCCT


Statistics
Matches: 72,  Mismatches: 4, Indels: 15
        0.79            0.04        0.16

Matches are distributed among these distances:
  42    2  0.03
  43    4  0.06
  44    2  0.03
  45    2  0.03
  46   29  0.40
  47   30  0.42
  48    2  0.03
  49    1  0.01

ACGTcount: A:0.29, C:0.29, G:0.20, T:0.21


Consensus pattern (49 bp):   
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT

Found at i:17388 original size:40 final size:40

Alignment explanation


    Indices: 17344--17490  Score: 237
    Period size: 40  Copynumber: 3.7  Consensus size: 40

      17334 GCTACTTGCT

                                                    
      17344 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA

                                                    
      17384 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA

                                      *      *   *   
      17424 CAAATGCCTTCGGG--TTAGCCCGG-AATTAGTCACTAGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA

                                         
      17462 CAAATGCCTTCGGGACTTAGCCCGGTTAT
          1 CAAATGCCTTCGGGACTTAGCCCGGTTAT

      17491 CATCCGAATA


Statistics
Matches: 99,  Mismatches: 4, Indels: 8
        0.89            0.04        0.07

Matches are distributed among these distances:
  37    1  0.01
  38   33  0.33
  40   64  0.65
  41    1  0.01

ACGTcount: A:0.24, C:0.27, G:0.23, T:0.25


Consensus pattern (40 bp):   
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA

Found at i:17468 original size:78 final size:79

Alignment explanation


    Indices: 17344--17490  Score: 235
    Period size: 78  Copynumber: 1.9  Consensus size: 79

      17334 GCTACTTGCT

                                     *          *                            
      17344 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
          1 CAAATGCCTTCGGGA-TTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGG

                           
      17409 TTATAGTAACTCGCA
         65 TTATAGTAACTCGCA

                                            *                                
      17424 CAAATGCCTTCGGG-TTAGCCCGGA-ATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGG
          1 CAAATGCCTTCGGGATTAGCCCGGATA-TAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGG

                
      17487 TTAT
         65 TTAT

      17491 CATCCGAATA


Statistics
Matches: 63,  Mismatches: 3, Indels: 4
        0.90            0.04        0.06

Matches are distributed among these distances:
  77    1  0.02
  78   48  0.76
  80   14  0.22

ACGTcount: A:0.24, C:0.27, G:0.23, T:0.25


Consensus pattern (79 bp):   
CAAATGCCTTCGGGATTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGT
TATAGTAACTCGCA
Done.