Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga08g02417.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: 3160
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26


Found at i:1265 original size:66 final size:66

Alignment explanation


    Indices: 1149--1277  Score: 213
    Period size: 66  Copynumber: 2.0  Consensus size: 66

       1139 ATTCATATAT

                                                    *    *           *       
       1149 CATTCATAACACATCTAATTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGAC
          1 CATTCATAACACATCTAATTAGGAGCATTTGATTCATTTCAATCAGAGCATCCTAATCATTTGAC

             
       1214 A
         66 A

                             *                         *                   
       1215 CATTCATAACACATCTAGTTAGGAGCATTTGATTCATTTCAATTAGAGCATCCTAATCATTTG
          1 CATTCATAACACATCTAATTAGGAGCATTTGATTCATTTCAATCAGAGCATCCTAATCATTTG

       1278 GCATAAGTAC


Statistics
Matches: 58,  Mismatches: 5, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  66   58  1.00

ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36


Consensus pattern (66 bp):   
CATTCATAACACATCTAATTAGGAGCATTTGATTCATTTCAATCAGAGCATCCTAATCATTTGAC
A

Found at i:1416 original size:45 final size:44

Alignment explanation


    Indices: 1302--1515  Score: 168
    Period size: 44  Copynumber: 4.8  Consensus size: 44

       1292 AACTGATTTT

                           *                         *  
       1302 ACAGATCTTATCCCCCTAAGCAGTAGGGAAACAGATCGAAGGTG
          1 ACAGATCTTATCCCCTTAAGCAGTAGGGAAACAGATCGAAGTTG

                  *    *         *       *      *         *
       1346 ACA-AGCCTTAACCCCTTAAGTAGTAGGGTAACAG-GCTGAAGATTT
          1 ACAGA-TCTTATCCCCTTAAGCAGTAGGGAAACAGATC-GAAG-TTG

                                                     ** 
       1391 ACAGATCTTATCCCCTTAAGCAGTAGGGAAACAGATCGAAGGCG
          1 ACAGATCTTATCCCCTTAAGCAGTAGGGAAACAGATCGAAGTTG

                   *   *   *             *      *  *     *
       1435 AC-GAGTTTTAACCCGTTAAGCAGTAGGGTAACA-AGCTAAAGTTC
          1 ACAGA-TCTTATCCCCTTAAGCAGTAGGGAAACAGATC-GAAGTTG

             *                             *      
       1479 ATAGATCTTATCACCC-TAAGCAGTAGGGAAGCAGATC
          1 ACAGATCTTATC-CCCTTAAGCAGTAGGGAAACAGATC

       1516 AAAAGACGGC


Statistics
Matches: 128,  Mismatches: 32, Indels: 19
        0.72            0.18        0.11

Matches are distributed among these distances:
  43    6  0.05
  44   81  0.63
  45   39  0.30
  46    2  0.02

ACGTcount: A:0.34, C:0.21, G:0.23, T:0.21


Consensus pattern (44 bp):   
ACAGATCTTATCCCCTTAAGCAGTAGGGAAACAGATCGAAGTTG

Found at i:1454 original size:89 final size:87

Alignment explanation


    Indices: 1299--1515  Score: 299
    Period size: 89  Copynumber: 2.4  Consensus size: 87

       1289 TGAAACTGAT

                                                         *                   
       1299 TTTACAGATCTTATCCCCCTAAGCAGTAGGGAAACAGATCGAAGGTGACAAGCCTTAACCCCTTA
          1 TTTACAGATCTTAT-CCCCTAAGCAGTAGGGAAACAGATCGAAGGCGACAAGCCTTAACCCCTTA

              *            *   *   
       1364 AGTAGTAGGGTAACAGGCTGAAG
         65 AGCAGTAGGGTAACAAGCTAAAG

                                                              *  **       *  
       1387 ATTTACAGATCTTATCCCCTTAAGCAGTAGGGAAACAGATCGAAGGCGACGAGTTTTAACCCGTT
          1 -TTTACAGATCTTATCCCC-TAAGCAGTAGGGAAACAGATCGAAGGCGACAAGCCTTAACCCCTT

                                    
       1452 AAGCAGTAGGGTAACAAGCTAAAG
         64 AAGCAGTAGGGTAACAAGCTAAAG

              * *                            *      
       1476 TTCATAGATCTTATCACCCTAAGCAGTAGGGAAGCAGATC
          1 TTTACAGATCTTATC-CCCTAAGCAGTAGGGAAACAGATC

       1516 AAAAGACGGC


Statistics
Matches: 115,  Mismatches: 11, Indels: 5
        0.88            0.08        0.04

Matches are distributed among these distances:
  88   37  0.32
  89   78  0.68

ACGTcount: A:0.34, C:0.21, G:0.23, T:0.23


Consensus pattern (87 bp):   
TTTACAGATCTTATCCCCTAAGCAGTAGGGAAACAGATCGAAGGCGACAAGCCTTAACCCCTTAA
GCAGTAGGGTAACAAGCTAAAG

Found at i:1639 original size:45 final size:43

Alignment explanation


    Indices: 1575--1728  Score: 148
    Period size: 43  Copynumber: 3.5  Consensus size: 43

       1565 ACCACTAAGC

                          *       *  *  * *       *      
       1575 CTTAATCCCCTAAGTAGTAGGGTAATAGGTTGAAGATCTACAGAT
          1 CTTAATCCCCTAAGCAGTAGGGAAACAGATCGAAGAT-GA-AGAT

                                                   *   
       1620 CTTAATCCCCTAAGCAGTAGGGAAACAGATCGAAGATGATGAT
          1 CTTAATCCCCTAAGCAGTAGGGAAACAGATCGAAGATGAAGAT

                                            *    *   * **
       1663 CTT-ATCACCCTAAGCAGTAGGGAAACAGATCAAAGAAGATGGGC
          1 CTTAATC-CCCTAAGCAGTAGGGAAACAGATCGAAGATGA-AGAT

                 *                
       1707 CTTAACCCCCTAAGCAGTAGGG
          1 CTTAATCCCCTAAGCAGTAGGG

       1729 TAATAGGCTG


Statistics
Matches: 93,  Mismatches: 13, Indels: 7
        0.82            0.12        0.06

Matches are distributed among these distances:
  42    3  0.03
  43   36  0.39
  44   20  0.22
  45   34  0.37

ACGTcount: A:0.35, C:0.20, G:0.23, T:0.21


Consensus pattern (43 bp):   
CTTAATCCCCTAAGCAGTAGGGAAACAGATCGAAGATGAAGAT

Found at i:2024 original size:87 final size:88

Alignment explanation


    Indices: 1836--2043  Score: 251
    Period size: 87  Copynumber: 2.4  Consensus size: 88

       1826 CAAACCACCA

                                              *  *    *   *    *             
       1836 AGCTTTAACCCCCTAAGCAGTAGGGTAACAAGCTGAAGTTTATAGATATTATTGCCCTAAGAAGT
          1 AGCTTTAACCCCCTAAGCAGTAGGGTAACAAGCTCAAATTTACAGACATTAATGCCCTAAGAAGT

                            * *  * 
       1901 AGGGAAACAGATCGAATATGATG
         66 AGGGAAACAGATCGAAGACGACG

            *    *            *                            *              *  
       1924 GGC-TAAACCCCCTAAGCGGTAGGGTAACAAGC-CAAATTTACAGACCTTGAAT-CCCTAAGCAG
          1 AGCTTTAACCCCCTAAGCAGTAGGGTAACAAGCTCAAATTTACAGACATT-AATGCCCTAAGAAG

                              *     
       1986 TAGGGAAACAGATCGAAGGCGACG
         65 TAGGGAAACAGATCGAAGACGACG

                     *                        
       2010 AGCTTTAACTCCCTAAGCAGTAGGGTAACAAGCT
          1 AGCTTTAACCCCCTAAGCAGTAGGGTAACAAGCT

       2044 GACGTTCATA


Statistics
Matches: 99,  Mismatches: 18, Indels: 6
        0.80            0.15        0.05

Matches are distributed among these distances:
  86   42  0.42
  87   55  0.56
  88    2  0.02

ACGTcount: A:0.35, C:0.21, G:0.24, T:0.21


Consensus pattern (88 bp):   
AGCTTTAACCCCCTAAGCAGTAGGGTAACAAGCTCAAATTTACAGACATTAATGCCCTAAGAAGT
AGGGAAACAGATCGAAGACGACG
Done.