Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g00589.F1

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: 2781
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.35


Found at i:795 original size:159 final size:159

Alignment explanation


    Indices: 425--1085  Score: 1079
    Period size: 159  Copynumber: 4.2  Consensus size: 159

        415 AGTATCCGTG

                                            *                *       *       
        425 ATTCAATTGAGGTTGGCTTGTTGGTTGAGGATACACCAAGCTGTCACTCTGCACTGAGTTCGTTA
          1 ATTCAATTGAGGTTGGCTTGTTGGTTGAGGATGCACCAAGCTGTCACTCGGCACTGAATTCGTTA

                  *              *                                           
        490 GATCTGCTTGACTCTGACCTGGTACATTCG-ATCGAAATTGCCCAGTATGCTGAGAGTTCGAGTG
         66 GATCTGTTTGACTCTGACCTGCTACATTCGAAT-GAAATTGCCCAGTATGCTGAGAGTTCGAGTG

                                          
        554 ATGAATC--AGTCTGGTTCTGACGTGTTTC
        130 ATGAATCAGAGTCTGGTTCTGACGTGTTTC

                           *                                                 
        582 ATTCAATTGAGGTTGACTTGTTGGTTGAGGATGCACCAAGCTGTCACTCGGCACTGAATTCGTTA
          1 ATTCAATTGAGGTTGGCTTGTTGGTTGAGGATGCACCAAGCTGTCACTCGGCACTGAATTCGTTA

                              *                              *               
        647 GATCTGTTTGACTCTGACGTGCTACATTCGAATGAAATTGCCCAGTATGGTGAGAGTTCGAGTGA
         66 GATCTGTTTGACTCTGACCTGCTACATTCGAATGAAATTGCCCAGTATGCTGAGAGTTCGAGTGA

                                         
        712 TGAATCAGAGTCTGGTTCTGACGTGTTTC
        131 TGAATCAGAGTCTGGTTCTGACGTGTTTC

                                                                     *       
        741 ATTCAATTGAGGTTGGCTTGTTGGTTGAGGATGCACCAAGCTGTCACTCGGCACTGAGTTCGTTA
          1 ATTCAATTGAGGTTGGCTTGTTGGTTGAGGATGCACCAAGCTGTCACTCGGCACTGAATTCGTTA

                                           *       *         *        *      
        806 GATCTG--T---T-TGACCTGCTACATTCGATTGAAATTTCCCAGTATGGTGAGAGTTTGAGTGA
         66 GATCTGTTTGACTCTGACCTGCTACATTCGAATGAAATTGCCCAGTATGCTGAGAGTTCGAGTGA

                                         
        865 TGAATCAGAGTCTGGTTCTGACGTGTTTC
        131 TGAATCAGAGTCTGGTTCTGACGTGTTTC

                                                                  *     *    
        894 ATTCAATTGAGGTTGGCTTGTTGGTTGAGGATGCACCAAGCTGTCACTCGGCACAGAATTTGTTA
          1 ATTCAATTGAGGTTGGCTTGTTGGTTGAGGATGCACCAAGCTGTCACTCGGCACTGAATTCGTTA

                                           *                          ** *   
        959 GATCTGTTTGACTCTGACCTGCTACATTCGATTGAAATTGCCCAGTATGCTGAGAGTTTAACTGA
         66 GATCTGTTTGACTCTGACCTGCTACATTCGAATGAAATTGCCCAGTATGCTGAGAGTTCGAGTGA

                                         
       1024 TGAATCAGAGTCTGGTTCTGACGTGTTTC
        131 TGAATCAGAGTCTGGTTCTGACGTGTTTC

                                             
       1053 ATTCAATTGAGGTTGGCTTGTTGGTTGAGGATG
          1 ATTCAATTGAGGTTGGCTTGTTGGTTGAGGATG

       1086 TTCCCAAAAG


Statistics
Matches: 474,  Mismatches: 21, Indels: 16
        0.93            0.04        0.03

Matches are distributed among these distances:
 153  144  0.30
 154    1  0.00
 155    1  0.00
 157  126  0.27
 158    3  0.01
 159  199  0.42

ACGTcount: A:0.22, C:0.18, G:0.27, T:0.34


Consensus pattern (159 bp):   
ATTCAATTGAGGTTGGCTTGTTGGTTGAGGATGCACCAAGCTGTCACTCGGCACTGAATTCGTTA
GATCTGTTTGACTCTGACCTGCTACATTCGAATGAAATTGCCCAGTATGCTGAGAGTTCGAGTGA
TGAATCAGAGTCTGGTTCTGACGTGTTTC

Found at i:997 original size:312 final size:313

Alignment explanation


    Indices: 425--1085  Score: 1112
    Period size: 312  Copynumber: 2.1  Consensus size: 313

        415 AGTATCCGTG

                                            *                *               
        425 ATTCAATTGAGGTTGGCTTGTTGGTTGAGGATACACCAAGCTGTCACTCTGCACTGAGTTCGTTA
          1 ATTCAATTGAGGTTGGCTTGTTGGTTGAGGATGCACCAAGCTGTCACTCGGCACTGAGTTCGTTA

                                 *                                           
        490 GATCTGCTTGACTCTGACCTGGTACATTCGATCGAAATTGCCCAGTATGCTGAGAGTTCGAGTGA
         66 GATCTGC-T-A-TCTGACCTGCTACATTCGATCGAAATTGCCCAGTATGCTGAGAGTTCGAGTGA

                                                                             
        555 TGAATCAGTCTGGTTCTGACGTGTTTCATTCAATTGAGGTTGACTTGTTGGTTGAGGATGCACCA
        128 TGAATCAGTCTGGTTCTGACGTGTTTCATTCAATTGAGGTTGACTTGTTGGTTGAGGATGCACCA

                            *                            *                   
        620 AGCTGTCACTCGGCACTGAATTCGTTAGATCTGTTTGACTCTGACGTGCTACATTCGAATGAAAT
        193 AGCTGTCACTCGGCACAGAATTCGTTAGATCTGTTTGACTCTGACCTGCTACATTCGAATGAAAT

                       *         * *                                
        685 TGCCCAGTATGGTGAGAGTTCGAGTGATGAATCAGAGTCTGGTTCTGACGTGTTTC
        258 TGCCCAGTATGCTGAGAGTTCAACTGATGAATCAGAGTCTGGTTCTGACGTGTTTC

                                                                             
        741 ATTCAATTGAGGTTGGCTTGTTGGTTGAGGATGCACCAAGCTGTCACTCGGCACTGAGTTCGTTA
          1 ATTCAATTGAGGTTGGCTTGTTGGTTGAGGATGCACCAAGCTGTCACTCGGCACTGAGTTCGTTA

                                         *      *         *        *         
        806 GATCTG-T-T-TGACCTGCTACATTCGATTGAAATTTCCCAGTATGGTGAGAGTTTGAGTGATGA
         66 GATCTGCTATCTGACCTGCTACATTCGATCGAAATTGCCCAGTATGCTGAGAGTTCGAGTGATGA

                                                     *                       
        868 ATCAGAGTCTGGTTCTGACGTGTTTCATTCAATTGAGGTTGGCTTGTTGGTTGAGGATGCACCAA
        131 ATC--AGTCTGGTTCTGACGTGTTTCATTCAATTGAGGTTGACTTGTTGGTTGAGGATGCACCAA

                                 *                                   *       
        933 GCTGTCACTCGGCACAGAATTTGTTAGATCTGTTTGACTCTGACCTGCTACATTCGATTGAAATT
        194 GCTGTCACTCGGCACAGAATTCGTTAGATCTGTTTGACTCTGACCTGCTACATTCGAATGAAATT

                               *                                   
        998 GCCCAGTATGCTGAGAGTTTAACTGATGAATCAGAGTCTGGTTCTGACGTGTTTC
        259 GCCCAGTATGCTGAGAGTTCAACTGATGAATCAGAGTCTGGTTCTGACGTGTTTC

                                             
       1053 ATTCAATTGAGGTTGGCTTGTTGGTTGAGGATG
          1 ATTCAATTGAGGTTGGCTTGTTGGTTGAGGATG

       1086 TTCCCAAAAG


Statistics
Matches: 327,  Mismatches: 16, Indels: 8
        0.93            0.05        0.02

Matches are distributed among these distances:
 310   52  0.16
 311    1  0.00
 312  204  0.62
 314    1  0.00
 316   69  0.21

ACGTcount: A:0.22, C:0.18, G:0.27, T:0.34


Consensus pattern (313 bp):   
ATTCAATTGAGGTTGGCTTGTTGGTTGAGGATGCACCAAGCTGTCACTCGGCACTGAGTTCGTTA
GATCTGCTATCTGACCTGCTACATTCGATCGAAATTGCCCAGTATGCTGAGAGTTCGAGTGATGA
ATCAGTCTGGTTCTGACGTGTTTCATTCAATTGAGGTTGACTTGTTGGTTGAGGATGCACCAAGC
TGTCACTCGGCACAGAATTCGTTAGATCTGTTTGACTCTGACCTGCTACATTCGAATGAAATTGC
CCAGTATGCTGAGAGTTCAACTGATGAATCAGAGTCTGGTTCTGACGTGTTTC

Found at i:1202 original size:159 final size:158

Alignment explanation


    Indices: 425--1232  Score: 656
    Period size: 159  Copynumber: 5.1  Consensus size: 158

        415 AGTATCCGTG

                                            *         *           *  * * *** 
        425 ATTCAATTGAGGTTGGCTTGTTGGTTGAGGATACACCAAGCTGTCACTCTGCACTGAGTTCGTTA
          1 ATTCAATTGAGGTTGGCTTGTTGGTTGAGGATGCACCAAGCTATCACTC-GCACAGAATGCAACA

                *        *        *  *    *  *     *     *     *             
        490 GATCTGCTT-GACTCTGACCTGGTACATTCGATCGAAATTGCCCAGTATGCTGAGAGT-TCGAGT
         65 GATCAG-TTAGACGCTGACCTGCTAAATTCAATTGAAATGGCCCACTATGCAGAGAGTCT-GAGT

                                           
        553 GATGAATC--AGTCTGGTTCTGACGTGTTTC
        128 GATGAATCAGAGTCTGGTTCTGACGTGTTTC

                           *                          *           *    * *** 
        582 ATTCAATTGAGGTTGACTTGTTGGTTGAGGATGCACCAAGCTGTCACTCGGCACTGAATTCGTTA
          1 ATTCAATTGAGGTTGGCTTGTTGGTTGAGGATGCACCAAGCTATCACTC-GCACAGAATGCAACA

                *   *   *     *     *              *     *    **             
        647 GATCTGTTTGACTCTGACGTGCTACATTCGAA-TGAAATTGCCCAGTATGGTGAGAGT-TCGAGT
         65 GATCAGTTAGACGCTGACCTGCTAAATTC-AATTGAAATGGCCCACTATGCAGAGAGTCT-GAGT

                                           
        710 GATGAATCAGAGTCTGGTTCTGACGTGTTTC
        128 GATGAATCAGAGTCTGGTTCTGACGTGTTTC

                                                      *           *  * * *** 
        741 ATTCAATTGAGGTTGGCTTGTTGGTTGAGGATGCACCAAGCTGTCACTCGGCACTGAGTTCGTTA
          1 ATTCAATTGAGGTTGGCTTGTTGGTTGAGGATGCACCAAGCTATCACTC-GCACAGAATGCAACA

                *                   *    *        **    *    **      *       
        806 GATCTGTT------TGACCTGCTACATTCGATTGAAATTTCCCAGTATGGTGAGAGTTTGAGTGA
         65 GATCAGTTAGACGCTGACCTGCTAAATTCAATTGAAATGGCCCACTATGCAGAGAGTCTGAGTGA

                                         
        865 TGAATCAGAGTCTGGTTCTGACGTGTTTC
        130 TGAATCAGAGTCTGGTTCTGACGTGTTTC

                                                      *                ***** 
        894 ATTCAATTGAGGTTGGCTTGTTGGTTGAGGATGCACCAAGCTGTCACTCGGCACAGAATTTGTTA
          1 ATTCAATTGAGGTTGGCTTGTTGGTTGAGGATGCACCAAGCTATCACTC-GCACAGAATGCAACA

                *   *   *           *    *        *     *     *      * * *   
        959 GATCTGTTTGACTCTGACCTGCTACATTCGATTGAAATTGCCCAGTATGCTGAGAGTTTAACTGA
         65 GATCAGTTAGACGCTGACCTGCTAAATTCAATTGAAATGGCCCACTATGCAGAGAGTCTGAGTGA

                                         
       1024 TGAATCAGAGTCTGGTTCTGACGTGTTTC
        130 TGAATCAGAGTCTGGTTCTGACGTGTTTC

                                                        *   *        *  *    
       1053 ATTCAATTGAGGTTGGCTTGTTGGTTGAGGATGTTC-CCAAAAGGTATTA-TC-CACTGAGTGCA
          1 ATTCAATTGAGGTTGGCTTGTTGGTTGAGGATG--CACC--AAGCTATCACTCGCACAGAATGCA

                                                  *     **           *       
       1115 ACAGATCAGTTAGACGCTGACCTGCTAAATTCAATTGACATGGCTGACTATGCAGAGGGTCTGAG
         62 ACAGATCAGTTAGACGCTGACCTGCTAAATTCAATTGAAATGGCCCACTATGCAGAGAGTCTGAG

                        *  ***      **      
       1180 TGATGAATCAGACTCCAATTCTGATATGTTTC
        127 TGATGAATCAGAGTCTGGTTCTGACGTGTTTC

            *   *    *           
       1212 CTTCGATTGGGGTTGGCTTGT
          1 ATTCAATTGAGGTTGGCTTGT

       1233 GTGATTAAAG


Statistics
Matches: 580,  Mismatches: 55, Indels: 30
        0.87            0.08        0.05

Matches are distributed among these distances:
 152    1  0.00
 153  143  0.25
 154    1  0.00
 156    2  0.00
 157  122  0.21
 158    1  0.00
 159  299  0.52
 160    2  0.00
 161    3  0.01
 162    6  0.01

ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33


Consensus pattern (158 bp):   
ATTCAATTGAGGTTGGCTTGTTGGTTGAGGATGCACCAAGCTATCACTCGCACAGAATGCAACAG
ATCAGTTAGACGCTGACCTGCTAAATTCAATTGAAATGGCCCACTATGCAGAGAGTCTGAGTGAT
GAATCAGAGTCTGGTTCTGACGTGTTTC
Done.