Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga03g00383.F3

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: 3789
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34


Found at i:689 original size:143 final size:143

Alignment explanation


    Indices: 449--744  Score: 407
    Period size: 143  Copynumber: 2.1  Consensus size: 143

        439 CGACTATCGT

                            *                                                
        449 TGGGCGCAAAATCGTTGGTTTATCCAACTAGAGCTGGGCTCACTAAATTATTTGTCAGTTTATCC
          1 TGGGCGCAAAATCGTTAGTTTATCCAACTAGAGCTGGGCTCACTAAATTATTTGTCAGTTTATCC

               * *             * *                     *                     
        514 GACTAGCGCTAGGCGCAACTTTCGTCAATTTATCTAACTAGTGGTAGACACACATTCGTCT-GTT
         66 GACCAACGCTAGGCGCAACCTCCGTCAATTTATCTAACTAGTGCTAGACACACATTCGT-TGGTT

                          
        578 TATCCGACTAGTAC
        130 TATCCGACTAGTAC

                *        *                                                   
        592 TGGGTGCAAATATTGTTAGTTTATCCAACTAGAGCTGGGCTCACT-AATTATTTGTCAGTTTATC
          1 TGGGCGCAAA-ATCGTTAGTTTATCCAACTAGAGCTGGGCTCACTAAATTATTTGTCAGTTTATC

            *          *                *       *         * *        *       
        656 TGACCAACGCTGGGCGCAACCTCCGTCAGTTTATCTGACTAGTGCTGGGCACACATTTGTTGGTT
         65 CGACCAACGCTAGGCGCAACCTCCGTCAATTTATCTAACTAGTGCTAGACACACATTCGTTGGTT

                       ** 
        721 TATCCGACTAGCGC
        130 TATCCGACTAGTAC

                      
        735 TGGGCGCAAA
          1 TGGGCGCAAA

        745 CTCTTTCGCG


Statistics
Matches: 133,  Mismatches: 18, Indels: 4
        0.86            0.12        0.03

Matches are distributed among these distances:
 142    1  0.01
 143  100  0.75
 144   32  0.24

ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32


Consensus pattern (143 bp):   
TGGGCGCAAAATCGTTAGTTTATCCAACTAGAGCTGGGCTCACTAAATTATTTGTCAGTTTATCC
GACCAACGCTAGGCGCAACCTCCGTCAATTTATCTAACTAGTGCTAGACACACATTCGTTGGTTT
ATCCGACTAGTAC

Found at i:743 original size:69 final size:69

Alignment explanation


    Indices: 506--743  Score: 194
    Period size: 69  Copynumber: 3.4  Consensus size: 69

        496 TTATTTGTCA

                              *        *       *               * * *        *
        506 GTTTATCCGACTAGCGCTAGGCGCAACTTTCGTCAATTTATCTAACTAGTGGTAGACACACATTC
          1 GTTTATCCGACTAGCGCTGGGCGCAACATTCGTCAGTTTATCTAACTAGTGCTGGGCACACATTT

                 
        571 GTCT-
         66 GT-TG

                          **     *         *  *        *      *       *      
        575 GTTTATCCGACTAGTACTGGGTGCAA-ATATTGTTAGTTTATCCAACTAGAGCTGGGCTCACTAA
          1 GTTTATCCGACTAGCGCTGGGCGCAACAT-TCGTCAGTTTATCTAACTAGTGCTGGGCACAC--A

                    
        639 TTAT-TTG
         63 TT-TGTTG

                      *   * *             * *             *                  
        646 TCAGTTTATCTGACCAACGCTGGGCGCAACCTCCGTCAGTTTATCTGACTAGTGCTGGGCACACA
          1 ---GTTTATCCGACTAGCGCTGGGCGCAACATTCGTCAGTTTATCTAACTAGTGCTGGGCACACA

                   
        711 TTTGTTG
         63 TTTGTTG

                                      
        718 GTTTATCCGACTAGCGCTGGGCGCAA
          1 GTTTATCCGACTAGCGCTGGGCGCAA

        744 ACTCTTTCGC


Statistics
Matches: 127,  Mismatches: 32, Indels: 20
        0.71            0.18        0.11

Matches are distributed among these distances:
  68    1  0.01
  69   68  0.54
  70    1  0.01
  71    5  0.04
  72    6  0.05
  74   45  0.35
  75    1  0.01

ACGTcount: A:0.23, C:0.23, G:0.22, T:0.32


Consensus pattern (69 bp):   
GTTTATCCGACTAGCGCTGGGCGCAACATTCGTCAGTTTATCTAACTAGTGCTGGGCACACATTT
GTTG
Done.