Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g01435.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: 4431
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.33


Found at i:176 original size:50 final size:50

Alignment explanation


    Indices: 1--231  Score: 203
    Period size: 52  Copynumber: 4.5  Consensus size: 50

                     *                        *     *  *      
          1 TAGCCTACAGTTAGTACTACACATGTGACCTAACCATCTGATAGACGTAG
          1 TAGCCTACACTTAGTACTACACATGTGACCTAACTATCTGGTACACGTAG

                                   *     *   **  *  *     * *   
         51 TAGCCTACACTTAGTACTACACACGTGA-TTGAGGTCGTCGGGTACGCATAG
          1 TAGCCTACACTTAGTACTACACATGTGACCT-AACT-ATCTGGTACACGTAG

                   *         *                                 
        102 TAGCCATGCACTTAGTATTACACATGTGACCTAACTATCTGGTACACGTAG
          1 TAGCC-TACACTTAGTACTACACATGTGACCTAACTATCTGGTACACGTAG

                         *                      *    ***    *   
        153 TAGCCTACACTTAATACTACACATGTGACCTAAAACCATCTTAAACACATAG
          1 TAGCCTACACTTAGTACTACACATGTGACCT--AACTATCTGGTACACGTAG

                * *   *                
        205 TAGCTTGCACATAGTACTACACATGTG
          1 TAGCCTACACTTAGTACTACACATGTG

        232 TTCTCACAAT


Statistics
Matches: 141,  Mismatches: 34, Indels: 10
        0.76            0.18        0.05

Matches are distributed among these distances:
  49    1  0.01
  50   50  0.35
  51   30  0.21
  52   59  0.42
  53    1  0.01

ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27


Consensus pattern (50 bp):   
TAGCCTACACTTAGTACTACACATGTGACCTAACTATCTGGTACACGTAG

Found at i:214 original size:102 final size:102

Alignment explanation


    Indices: 11--231  Score: 255
    Period size: 102  Copynumber: 2.2  Consensus size: 102

          1 TAGCCTACAG

                                             *                   *           
         11 TTAGTACTACACATGTGACCTAACCATCTGATAGACGTAGTAGCCTACACTTAGTACTACACACG
          1 TTAGTACTACACATGTGACCTAACCATCTGATACACGTAGTAGCCTACACTTAATACTACACACG

               * * *** *    **  *                
         76 TGATTGAGGTCGTCGGGTACGCATAGTAGCCATGCAC
         66 TGACTAAAACCATCGGAAACACATAGTAGCCATGCAC

                  *                 *     *                                * 
        113 TTAGTATTACACATGTGACCTAACTATCTGGTACACGTAGTAGCCTACACTTAATACTACACATG
          1 TTAGTACTACACATGTGACCTAACCATCTGATACACGTAGTAGCCTACACTTAATACTACACACG

                           **               *     
        178 TGACCTAAAACCATCTTAAACACATAGTAG-CTTGCAC
         66 TGA-CTAAAACCATCGGAAACACATAGTAGCCATGCAC

            *                
        215 ATAGTACTACACATGTG
          1 TTAGTACTACACATGTG

        232 TTCTCACAAT


Statistics
Matches: 98,  Mismatches: 20, Indels: 2
        0.82            0.17        0.02

Matches are distributed among these distances:
 102   83  0.85
 103   15  0.15

ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27


Consensus pattern (102 bp):   
TTAGTACTACACATGTGACCTAACCATCTGATACACGTAGTAGCCTACACTTAATACTACACACG
TGACTAAAACCATCGGAAACACATAGTAGCCATGCAC

Found at i:3901 original size:28 final size:28

Alignment explanation


    Indices: 3855--3915  Score: 70
    Period size: 28  Copynumber: 2.2  Consensus size: 28

       3845 GGCATTATCG

                               *        
       3855 TAAATATGGAAGTCCATCAGGACGATCA
          1 TAAATATGGAAGTCCATCAAGACGATCA

                 *                 *    *
       3883 TAAATCTGGAAG-CCTATCAAGATGATCT
          1 TAAATATGGAAGTCC-ATCAAGACGATCA

                 
       3911 TAAAT
          1 TAAAT

       3916 GTGAAAATAC


Statistics
Matches: 28,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  27    2  0.07
  28   26  0.93

ACGTcount: A:0.39, C:0.16, G:0.18, T:0.26


Consensus pattern (28 bp):   
TAAATATGGAAGTCCATCAAGACGATCA

Found at i:3979 original size:28 final size:28

Alignment explanation


    Indices: 3899--4022  Score: 99
    Period size: 28  Copynumber: 4.4  Consensus size: 28

       3889 TGGAAGCCTA

                  *                 * *  
       3899 TCAAGATGATCTTAAATGT-GAAAATACG
          1 TCAAGACGATCTT-AATGTGGAAAGTTCG

             * *         *               
       3927 TTAGGACGATCTGAAATGTGG-AAGTTCG
          1 TCAAGACGATCT-TAATGTGGAAAGTTCG

                                      * 
       3955 TCAAGACGATCTTAATGTGGAAAGTTTG
          1 TCAAGACGATCTTAATGTGGAAAGTTCG

            *  * * *                   *
       3983 CCAGGGCTATCTTAATGTGGAAAGTTCA
          1 TCAAGACGATCTTAATGTGGAAAGTTCG

                   *    
       4011 TCAAGACTATCT
          1 TCAAGACGATCT

       4023 CTTGTGGAAG


Statistics
Matches: 74,  Mismatches: 19, Indels: 6
        0.75            0.19        0.06

Matches are distributed among these distances:
  27    7  0.09
  28   66  0.89
  29    1  0.01

ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30


Consensus pattern (28 bp):   
TCAAGACGATCTTAATGTGGAAAGTTCG
Done.