Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga05g03293.N4

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: 2627
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34


Found at i:99 original size:42 final size:40

Alignment explanation


    Indices: 39--205  Score: 129
    Period size: 40  Copynumber: 4.1  Consensus size: 40

         29 ATGCTGCAAT

                      *  *        *                    
         39 AGGTAAAGCAGTACCGGTGTTTTTGATAAAAAAACGCAACAAA
          1 AGGT-AAGCAATAGCGGTGTTTGTGAT--AAAAACGCAACAAA

                                              **    
         82 AGGTAAGCAATAGCGGTGTTTGTGATAAAAACGCCGCAAA
          1 AGGTAAGCAATAGCGGTGTTTGTGATAAAAACGCAACAAA

              *           ****   *             **    
        122 AGATAAGCAATAGCTACATTTAT-AGTAAAAACGCTGCAAA
          1 AGGTAAGCAATAGCGGTGTTTGTGA-TAAAAACGCAACAAA

                           ***      *         *     
        162 AGGTAAGCAATAGCGACATTTGTGTTAAAAACGCTACAAA
          1 AGGTAAGCAATAGCGGTGTTTGTGATAAAAACGCAACAAA

                
        202 AGGT
          1 AGGT

        206 TTTTTACTTT


Statistics
Matches: 105,  Mismatches: 17, Indels: 7
        0.81            0.13        0.05

Matches are distributed among these distances:
  39    1  0.01
  40   81  0.77
  42   19  0.18
  43    4  0.04

ACGTcount: A:0.43, C:0.14, G:0.22, T:0.22


Consensus pattern (40 bp):   
AGGTAAGCAATAGCGGTGTTTGTGATAAAAACGCAACAAA

Found at i:120 original size:43 final size:39

Alignment explanation


    Indices: 34--135  Score: 96
    Period size: 42  Copynumber: 2.5  Consensus size: 39

         24 GGAAAATGCT

                *          *  *        *            
         34 GCAATAGGTAAAGCAGTACCGGTGTTTTTGATAAAAAAAC
          1 GCAAAAGGT-AAGCAATAGCGGTGTTTGTGATAAAAAAAC

                                                    ** 
         74 GCAACAAAAGGTAAGCAATAGCGGTGTTTGTGATAAAAACGCC
          1 G---CAAAAGGTAAGCAATAGCGGTGTTTGTGATAAAAA-AAC

                   *           
        117 GCAAAAGATAAGCAATAGC
          1 GCAAAAGGTAAGCAATAGC

        136 TACATTTATA


Statistics
Matches: 51,  Mismatches: 7, Indels: 8
        0.77            0.11        0.12

Matches are distributed among these distances:
  40   18  0.35
  42   24  0.47
  43    9  0.18

ACGTcount: A:0.42, C:0.15, G:0.24, T:0.20


Consensus pattern (39 bp):   
GCAAAAGGTAAGCAATAGCGGTGTTTGTGATAAAAAAAC

Found at i:123 original size:40 final size:40

Alignment explanation


    Indices: 68--205  Score: 161
    Period size: 40  Copynumber: 3.5  Consensus size: 40

         58 TTTTTGATAA

                    **                   ***        
         68 AAAAACGCAACAAAAGGTAAGCAATAGCGGTGTTTGTGAT
          1 AAAAACGCTGCAAAAGGTAAGCAATAGCGACATTTGTGAT

                    *       *           *      *     
        108 AAAAACGCCGCAAAAGATAAGCAATAGCTACATTTAT-AGT
          1 AAAAACGCTGCAAAAGGTAAGCAATAGCGACATTTGTGA-T

                                                  * 
        148 AAAAACGCTGCAAAAGGTAAGCAATAGCGACATTTGTGTT
          1 AAAAACGCTGCAAAAGGTAAGCAATAGCGACATTTGTGAT

                     *        
        188 AAAAACGCTACAAAAGGT
          1 AAAAACGCTGCAAAAGGT

        206 TTTTTACTTT


Statistics
Matches: 82,  Mismatches: 14, Indels: 4
        0.82            0.14        0.04

Matches are distributed among these distances:
  39    1  0.01
  40   81  0.99

ACGTcount: A:0.45, C:0.15, G:0.20, T:0.20


Consensus pattern (40 bp):   
AAAAACGCTGCAAAAGGTAAGCAATAGCGACATTTGTGAT

Found at i:371 original size:46 final size:46

Alignment explanation


    Indices: 274--425  Score: 144
    Period size: 46  Copynumber: 3.2  Consensus size: 46

        264 ATACGAATTA

                          *                  *       ***    
        274 TTTTCTTTCTCGATATTTTCTTTGCTTGAAACCTCAAAATCATTTCCC
          1 TTTTCTTTCTCGA-CTTTT-TTTGCTTGAAACCACAAAATCCCATCCC

                                                           
        322 TTTTCTTTCTCGGACTTTTTTTGCTTGAAACCAC-AAATCCCATCCC
          1 TTTTCTTTCTC-GACTTTTTTTGCTTGAAACCACAAAATCCCATCCC

                         *            *       *         *   *
        368 TTTTCTTTCTCAGTCTTTTTGTTGCTCGAAAACCCCAAAATCCCGTCCT
          1 TTTTCTTTCTC-GACTTTTT-TTGCTTG-AAACCACAAAATCCCATCCC

                     
        417 TTATTCTTT
          1 TT-TTCTTT

        426 TATTTTAGCT


Statistics
Matches: 88,  Mismatches: 11, Indels: 8
        0.82            0.10        0.07

Matches are distributed among these distances:
  46   27  0.31
  47   20  0.23
  48   21  0.24
  49   14  0.16
  50    6  0.07

ACGTcount: A:0.19, C:0.28, G:0.08, T:0.45


Consensus pattern (46 bp):   
TTTTCTTTCTCGACTTTTTTTGCTTGAAACCACAAAATCCCATCCC
Done.