Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold2980

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, 489

Length: 816
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30


Found at i:194 original size:33 final size:32

Alignment explanation


    Indices: 125--378  Score: 125
    Period size: 33  Copynumber: 7.5  Consensus size: 32

        115 TGTGAAAGGG

                                             
        125 GGTTGCTAAGTGCTGATTCCCC---CGA--GG-
          1 GGTTGCTAAGTGCTGATTCCCCATTC-ATTGGT

                                             
        152 GGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
          1 GGTTGCTAAGTGCTGATTCCCC-ATTCATTGGT

                                           *        *
        185 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGG
          1 GGTTGCTAAGTGCTGATTCC-CC--A--TT-CAT-TG--GT

                                         *   
        226 GGATTGCTAAGTGCTGATTCCCC---CA-AGG-
          1 GG-TTGCTAAGTGCTGATTCCCCATTCATTGGT

                                    * *      
        254 GGTTGCTAAGTGCTGATTCCCCGAATGATTGGT
          1 GGTTGCTAAGTGCTGATTCCCC-ATTCATTGGT

                        *               *        
        287 GGTTGCTAAGTGTTGATTCCACCATATCTTTGAATGT
          1 GGTTGCTAAGTGCTGATTCC-CCAT-TCATTG---GT

                                          *   *    
        324 GAAAGGGATTGCTAAGTGCTGATTCCCCGAATCACTGGT
          1 -----GG-TTGCTAAGTGCTGATTCCCC-ATTCATTGGT

                            
        363 GGTTGCTAAGTGCTGA
          1 GGTTGCTAAGTGCTGA

        379 ATCCACCGAT


Statistics
Matches: 179,  Mismatches: 14, Indels: 62
        0.70            0.05        0.24

Matches are distributed among these distances:
  27   42  0.23
  28    2  0.01
  29    1  0.01
  30    1  0.01
  31    3  0.02
  32    4  0.02
  33   55  0.31
  34   10  0.06
  35    2  0.01
  37    4  0.02
  38    2  0.01
  39    4  0.02
  41    5  0.03
  42   26  0.15
  43   18  0.10

ACGTcount: A:0.20, C:0.20, G:0.28, T:0.32


Consensus pattern (32 bp):   
GGTTGCTAAGTGCTGATTCCCCATTCATTGGT

Found at i:258 original size:102 final size:102

Alignment explanation


    Indices: 45--351  Score: 472
    Period size: 103  Copynumber: 3.0  Consensus size: 102

         35 ATTGCATGTA

                       **         *                                         *
         45 AAGGGGTTGCTGTGTGCTGATTTCCCAATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
          1 AAGGGGTTGCTAAGTGCTGATTCCCCAATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC

                            *                     
        110 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
         66 TTAAATGTG-AAGGGGATTGCTAAGTGCTGATTCCCCC

            *                         *                                      
        148 GAGGGGTTGCTAAGTGCTGATTCCCCTATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
          1 AAGGGGTTGCTAAGTGCTGATTCCCCAATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC

                                                 
        213 TTAAATGTGAAGGGGATTGCTAAGTGCTGATTCCCCC
         66 TTAAATGTGAAGGGGATTGCTAAGTGCTGATTCCCCC

                                           *                  *          *   
        250 AAGGGGTTGCTAAGTGCTGATTCCCCGAA-TGATTGGTGGTTGCTAAGTGTTGATTCCACCATAT
          1 AAGGGGTTGCTAAGTGCTGATTCCCC-AATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTAT

                *        *                        
        314 CTTTGAATGTGAAAGGGATTGCTAAGTGCTGATTCCCC
         65 C-TTAAATGTGAAGGGGATTGCTAAGTGCTGATTCCCC

        352 GAATCACTGG


Statistics
Matches: 188,  Mismatches: 14, Indels: 4
        0.91            0.07        0.02

Matches are distributed among these distances:
 102   85  0.45
 103  103  0.55

ACGTcount: A:0.21, C:0.19, G:0.28, T:0.33


Consensus pattern (102 bp):   
AAGGGGTTGCTAAGTGCTGATTCCCCAATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTAAATGTGAAGGGGATTGCTAAGTGCTGATTCCCCC

Found at i:261 original size:27 final size:28

Alignment explanation


    Indices: 222--275  Score: 101
    Period size: 27  Copynumber: 2.0  Consensus size: 28

        212 CTTAAATGTG

                                        
        222 AAGGGGATTGCTAAGTGCTGATTCCCCC
          1 AAGGGGATTGCTAAGTGCTGATTCCCCC

                                       
        250 AAGGGG-TTGCTAAGTGCTGATTCCCC
          1 AAGGGGATTGCTAAGTGCTGATTCCCC

        276 GAATGATTGG


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  27   20  0.77
  28    6  0.23

ACGTcount: A:0.20, C:0.24, G:0.30, T:0.26


Consensus pattern (28 bp):   
AAGGGGATTGCTAAGTGCTGATTCCCCC

Found at i:550 original size:24 final size:24

Alignment explanation


    Indices: 523--571  Score: 98
    Period size: 24  Copynumber: 2.0  Consensus size: 24

        513 AGTATCAAAA

                                    
        523 ACTACAAAAGAGCAAATTAAATAT
          1 ACTACAAAAGAGCAAATTAAATAT

                                    
        547 ACTACAAAAGAGCAAATTAAATAT
          1 ACTACAAAAGAGCAAATTAAATAT

             
        571 A
          1 A

        572 AAACTGTTTT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   25  1.00

ACGTcount: A:0.59, C:0.12, G:0.08, T:0.20


Consensus pattern (24 bp):   
ACTACAAAAGAGCAAATTAAATAT
Done.