Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1259

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: 31600
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32


Found at i:2425 original size:28 final size:28

Alignment explanation


    Indices: 2354--2427  Score: 114
    Period size: 28  Copynumber: 2.6  Consensus size: 28

       2344 TTGTTAAGCC

                                 *  *    
       2354 CGCACACTTAGTGCT-TAATAGTCGAACT
          1 CGCACACTTAGTGCTAT-ATAATCAAACT

                                        
       2382 CGCACACTTAGTGCTATATAATCAAACT
          1 CGCACACTTAGTGCTATATAATCAAACT

                              
       2410 CGCACACTTAGTGCTATA
          1 CGCACACTTAGTGCTATA

       2428 CAATTTGAAC


Statistics
Matches: 43,  Mismatches: 2, Indels: 2
        0.91            0.04        0.04

Matches are distributed among these distances:
  28   42  0.98
  29    1  0.02

ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28


Consensus pattern (28 bp):   
CGCACACTTAGTGCTATATAATCAAACT

Found at i:8260 original size:40 final size:40

Alignment explanation


    Indices: 8076--8247  Score: 267
    Period size: 40  Copynumber: 4.3  Consensus size: 40

       8066 AATATGGTCG

                                                     
       8076 CTAGCACAAATGCCTTCGGGACTTAGCCCGG-ATATAGTAA
          1 CTAGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAA

                               *                     
       8116 CTCA-CACAAATGCCTTCGAGACTTAGCCCGGAATTAGTAA
          1 CT-AGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAA

              *                                     
       8156 CTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAA
          1 CTAGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAA

              *                                 * * 
       8196 CTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAATCA
          1 CTAGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAA

                        
       8236 CTAGCACAAATG
          1 CTAGCACAAATG

       8248 TCTTTGAGAC


Statistics
Matches: 123,  Mismatches: 6, Indels: 6
        0.91            0.04        0.04

Matches are distributed among these distances:
  40  120  0.98
  41    3  0.02

ACGTcount: A:0.30, C:0.27, G:0.20, T:0.22


Consensus pattern (40 bp):   
CTAGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAA

Found at i:11031 original size:17 final size:17

Alignment explanation


    Indices: 11009--11065  Score: 66
    Period size: 17  Copynumber: 3.4  Consensus size: 17

      10999 AATAGCAGAG

                             
      11009 ATAAAATTAGATGATGA
          1 ATAAAATTAGATGATGA

                         *     
      11026 ATAAAA-TATGA-AATTG-
          1 ATAAAATTA-GATGA-TGA

                             
      11042 ATAAAATTAGATGATGA
          1 ATAAAATTAGATGATGA

                   
      11059 ATAAAAT
          1 ATAAAAT

      11066 ATGAAATTGA


Statistics
Matches: 33,  Mismatches: 2, Indels: 10
        0.73            0.04        0.22

Matches are distributed among these distances:
  16   13  0.39
  17   20  0.61

ACGTcount: A:0.56, C:0.00, G:0.14, T:0.30


Consensus pattern (17 bp):   
ATAAAATTAGATGATGA

Found at i:11046 original size:33 final size:33

Alignment explanation


    Indices: 11008--11075  Score: 136
    Period size: 33  Copynumber: 2.1  Consensus size: 33

      10998 AAATAGCAGA

                                             
      11008 GATAAAATTAGATGATGAATAAAATATGAAATT
          1 GATAAAATTAGATGATGAATAAAATATGAAATT

                                             
      11041 GATAAAATTAGATGATGAATAAAATATGAAATT
          1 GATAAAATTAGATGATGAATAAAATATGAAATT

              
      11074 GA
          1 GA

      11076 AGCTTATTGA


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  33   35  1.00

ACGTcount: A:0.54, C:0.00, G:0.16, T:0.29


Consensus pattern (33 bp):   
GATAAAATTAGATGATGAATAAAATATGAAATT

Found at i:11047 original size:16 final size:16

Alignment explanation


    Indices: 11026--11075  Score: 50
    Period size: 16  Copynumber: 3.1  Consensus size: 16

      11016 TAGATGATGA

                            
      11026 ATAAAATATGAAATTG
          1 ATAAAATATGAAATTG

                       *      
      11042 ATAAAAT-T-AGATGATG
          1 ATAAAATATGAAAT--TG

                             
      11058 AATAAAATATGAAATTG
          1 -ATAAAATATGAAATTG

             
      11075 A
          1 A

      11076 AGCTTATTGA


Statistics
Matches: 27,  Mismatches: 2, Indels: 10
        0.69            0.05        0.26

Matches are distributed among these distances:
  14    3  0.11
  15    1  0.04
  16   10  0.37
  17    9  0.33
  18    1  0.04
  19    3  0.11

ACGTcount: A:0.56, C:0.00, G:0.14, T:0.30


Consensus pattern (16 bp):   
ATAAAATATGAAATTG

Found at i:11076 original size:17 final size:17

Alignment explanation


    Indices: 11023--11076  Score: 60
    Period size: 17  Copynumber: 3.2  Consensus size: 17

      11013 AATTAGATGA

                             
      11023 TGAATAAAATATGAAAT
          1 TGAATAAAATATGAAAT

                          *  
      11040 TG-ATAAAAT-T-AGAT
          1 TGAATAAAATATGAAAT

                               
      11054 GATGAATAAAATATGAAAT
          1 --TGAATAAAATATGAAAT

                
      11073 TGAA
          1 TGAA

      11077 GCTTATTGAG


Statistics
Matches: 30,  Mismatches: 2, Indels: 10
        0.71            0.05        0.24

Matches are distributed among these distances:
  14    3  0.10
  15    1  0.03
  16    9  0.30
  17   13  0.43
  18    1  0.03
  19    3  0.10

ACGTcount: A:0.56, C:0.00, G:0.15, T:0.30


Consensus pattern (17 bp):   
TGAATAAAATATGAAAT
Done.