Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold65

Parameters: 2 7 7 80 10 50 500

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500

Length: 67362
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.26


Found at i:10386 original size:16 final size:17

Alignment explanation


    Indices: 10360--10391  Score: 57
    Period size: 16  Copynumber: 1.9  Consensus size: 17

      10350 AGCTGCGGTT

                             
      10360 GGCCGCGGCACGGTGGA
          1 GGCCGCGGCACGGTGGA

                            
      10377 GGCC-CGGCACGGTGG
          1 GGCCGCGGCACGGTGG

      10392 CGTGCGGGCC


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16   11  0.73
  17    4  0.27

ACGTcount: A:0.09, C:0.31, G:0.53, T:0.06


Consensus pattern (17 bp):   
GGCCGCGGCACGGTGGA

Left flanking sequence: Indices 9860 -- 10359
GTGGCCAAACTTCGAGTTGTTGGGGTGCAAGTCGCTGATCACGCTCGGGGGCACCGAGTCGGCAA
TCAGGGCTTGCTCGTGCACCGGCTGGAACCCGTGGCCCAGCAGCCGGCCATTGGTCTTGTAGGCA
AAGTCGTCGGTCATCACCAGCGGCATGGTGTTGTTGGAGGTGATGCTGGCGTCGTCTCGTTTATT
CTTCTTGCCCAACTTGAATCTCGCCATGTTGTTGGAACGAAAAAATTCCCAAAACGGTTAAGGGA
GTGGAGAAATTCCTAAGTCGCGTTGAAGAATAGTCCGGTGTGCATATGGCCGCGGTCAGGGCTAA
AACCAGCCGTGCCAGCCCCCCTGGGCCATAACAACGCTAATTGTTGCCGACGACGTCATGTGGCA
ATACGTGTTGGGGCTAGCGATTTTCTTTGTCGAAGTGGCGGTGGTGCTCATGCTGCAGCTCCTCG
ACACCCTTGCCTACCACCCGTTCTGAGTGTGGGGTAGCTGCGGTT


Right flanking sequence: Indices 10392 -- 10891
CGTGCGGGCCGACCACGGCACGAGGGAGACTCCCCGGGCCATAGCGGCCCACGATTACCCGGGCA
TTTGTTTACTTCCACGGTGGGCGCCGGCGTTCACGTATATTCACTTAGTACACCTAATACCATGT
TTAATTTCCATGTGCCCTCGTGGCCGATGTAGGACACTGGTGCCGATTCGGCAGGCGAAGCGCAG
ACTCACGTCTGATGCCAGGCTCCACCTTGCTACCGTGCGTGCTTCATATGCCGAGGCATTGTAAG
CGAGCGGTTGTGAGACCGGAGATATACAATAGGCGGGGATGGTGTTACGCAGACGCCTTGGGCGG
AGGGCGCCCACTTGTCAGTTGGCGAACTGGCCCAGCCTTTCTGTCTGGATATCGCCAATATCTTG
GGTAATCTCCGTCCGACATTTGCTCAAAACTTGTCCAGTTCCCAACCCGCATACTCACGCTACGT
CTCTTGTCCATGCCTACCAGTCCCGCGAACTCACTAATCCAATAA



Found at i:20491 original size:181 final size:181

Alignment explanation


    Indices: 20187--20527  Score: 592
    Period size: 181  Copynumber: 1.9  Consensus size: 181

      20177 CATGTGGGAG

                    *                *                                       
      20187 AGCATCACTGGTAGTTGGAGCACGGGCAAAACCATGCTTGCGAGCTGCTCTATGTAGGATTCCTC
          1 AGCATCACCGGTAGTTGGAGCACGGACAAAACCATGCTTGCGAGCTGCTCTATGTAGGATTCCTC

                                            *   *                       * *  
      20252 TCGACCTCCCGAGCACAACGTGGGCGACAAGCGGCCTCAAAAAAAAATGAAATTTACGGGGTTAG
         66 TCGACCTCCCGAGCACAACGTGGGCGACAAGCAGCCCCAAAAAAAAATGAAATTTACGGGATCAG

                    *                                          
      20317 TGGTGATTCCTAAACTTCGACCGTGACCCACTCCGAATTAGGAAAACTCAA
        131 TGGTGATTACTAAACTTCGACCGTGACCCACTCCGAATTAGGAAAACTCAA

                                        *                                    
      20368 AGCATCACCGGTAGTTGGAGCACGGACACAACCATGCTTGCGAGCTGCTCTATGTAGGATTCCTC
          1 AGCATCACCGGTAGTTGGAGCACGGACAAAACCATGCTTGCGAGCTGCTCTATGTAGGATTCCTC

                                                     *                       
      20433 TCGACCTCCCGAGCACAACGTGGGCGACAAGCAGCCCCAAATAAAAATGAAATTTACGGGATCAG
         66 TCGACCTCCCGAGCACAACGTGGGCGACAAGCAGCCCCAAAAAAAAATGAAATTTACGGGATCAG

                                *         
      20498 TGGTGATTACTAAACTTCGATCGTGACCCA
        131 TGGTGATTACTAAACTTCGACCGTGACCCA

      20528 ACGTCGTCGT


Statistics
Matches: 150,  Mismatches: 10, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
 181  150  1.00

ACGTcount: A:0.29, C:0.26, G:0.24, T:0.21


Consensus pattern (181 bp):   
AGCATCACCGGTAGTTGGAGCACGGACAAAACCATGCTTGCGAGCTGCTCTATGTAGGATTCCTC
TCGACCTCCCGAGCACAACGTGGGCGACAAGCAGCCCCAAAAAAAAATGAAATTTACGGGATCAG
TGGTGATTACTAAACTTCGACCGTGACCCACTCCGAATTAGGAAAACTCAA

Left flanking sequence: Indices 19687 -- 20186
AGCTTCGAAGATCCAGCGGGGTCCGCAGCGAAAACAGGGAATTGCGAGCCGAATAAACGGAATCG
TATTCACCATAGCGCAGCAGCTGTCCGATGGGGCTACTACGCACAGCCTCTCTGATTGAATGGTG
TATTTCACACTGGGCAGGCGTTCCACAACACAACTTTCTGGTAGGGTGCCAAAATGGTGCCACCG
TAGCACTAGGCGAGGTCGGAGTCGGTAGTTTCTCTGGCAGGGTCGCCTTGACCTTCATTGCTGGC
TGCAACGTTCCATTGGGGTACATTACAAATAGGTTCCCCAAATTGTCGCGAATTAGCGAGTATCC
GAGATCAAAAGAGACAGTTGATTTTGGAGATTGGGACAATCCCCCCAGATTACCATCGGCCATGA
CAAAAACTGGTGTTTTTAGACACCACGACTTATAGAAATCACTACAAGCGGCTTAATGCATCTTA
GGGGGGCATGGTGGGAACTCCGAATTAGGGGAATTCATGTGGGAG


Right flanking sequence: Indices 20528 -- 21027
ACGTCGTCGTTTTTGGCCAGCGAGGATCGGTGCCGTTAGAGCAATTGTGCACAAAACAAAGTTTG
ACCATCTCTTTGTCCTGGGCTGAAAAATTAAGGAGTCATGCACTTCACTGGAACTGAATGAATTC
GAACAATCAACTGAGTCAATTGATCGAGTAGAAAACGTCCCCCCCTGACACTTTCGGCGTACGTT
TGCTGGAGGGGCGCTCCGAAGCGGCGCTACCTTCGATAACCGCCTTCCCCCCACCGCTTTTCCCC
GGTCCTGCATACCACACAGAGGCAGGCGCGGATATCTCCGCAAGTTATCCAGTATAAAATGTCGA
ACAAATCTGTCCCCCATTGGTTGATGCAAAGAAGCTTGTTCTCAAGATTAACCAGAATTAGATTC
CGTCCGTATACCACAATGTCTGCCTGCCCTTACAAACAGCCCGAGCACAAGTTGACCATGATCCC
TGGTCCTATTGAGTTCTCCAACGAGGTGCTCTACGCCATGTCCAC


Done.