Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NC_063515

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: 456448
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28

Warning! 36 characters in sequence are not A, C, G, or T


Found at i:178655 original size:23 final size:23

Alignment explanation


    Indices: 178625--178674  Score: 84
    Period size: 23  Copynumber: 2.2  Consensus size: 23

     178615 TTAGCAAGGG

                                    
     178625 ATTCGTTGAAC-ATAGTTCAACTC
          1 ATTCGTTGAACTAT-GTTCAACTC

                                   
     178648 ATTCGTTGAACTATGTTCAACTC
          1 ATTCGTTGAACTATGTTCAACTC

                
     178671 ATTC
          1 ATTC

     178675 AGTCAAAATA


Statistics
Matches: 26,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  23   24  0.92
  24    2  0.08

ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38


Consensus pattern (23 bp):   
ATTCGTTGAACTATGTTCAACTC

Left flanking sequence: Indices 178125 -- 178624
GAACAACTCATTCAGCCAGAAGCCTTGGTGTGCTAACCAGTTTCCAAAAGATTGAGTGGTCTGCG
CATAACACCTCCTGACGGGGCATCTCCTCCATCCCCGTTGGTCCTTCCAAAACCTACTTCTCTTT
TATTTTCTTCTTTTTCACTCTGGCGCAGCATTGTCCACTGGGGATTAGTAACAAAATAAAGTAAC
TGGCTGATGGGAGACCTGTTCCACGTCTTAGCTTCGACCTCCCAGTCACAGCACAGACATGCCTG
ACTGACAGCCTTGTTCCGAGAGTATAAAGAACCCAAAACAAGGATGACTTTGGTCCTTATACCGA
AACAAGGTCCCAGATCAATTTGCTGAAGCCTCCTTGACTTTGCTTGAAGCGGGAAAGAAAGTATA
CTATGAATAATAGCTCTTCCTAACAAATGGAATCGAAAGCTAGAGCTATTAGTCTACAATAGGGC
TTTCTATCAATCAATAGTGATATCTCACTTCGATATTAGCAAGGG


Right flanking sequence: Indices 178675 -- 179174
AGTCAAAATAACGCCAAGGACGGTGGGTGTAGCGGATTTTATCCTCCCCCTGCTGAAGATCAGAC
AATATGCTATGTCACGAAGACCATAAGAGGAGCACTTTGGTTGAGGTAGTATATCATTTGGATCA
AAGACTTTATAAAAGAGACCTTGCCTTCGCCTGAACCGGAAGCACACGAAAGAGGTACGAAGTTG
CTCGAAAGAGGGGAGGCCGGGAACGTAGCCTCTTCAGAATCGTAGTTCCTAGGCGCATTCATTTC
GGGCTCCGTCTCAAAGCCCTTTTGCCAGCTTAGCGCCTTGATGTTCTGTTCAATCAGTTGATTAT
GTCAATATGTCAAAACAGGGAAAAGAAGACCTGCTTTTGTTCCAGTTTCTGATTCAAGAATGTTC
CTATCATTTCTGAACGTTTAGGTGAGCCAATTTGCAGAGTTCTCCGCATGCATTCGCTTCTGCCA
ACAAAAATAATTTGAATCATTTCATATGGACGAACAGTCTAAGTA



Found at i:182232 original size:20 final size:20

Alignment explanation


    Indices: 182203--182241  Score: 53
    Period size: 20  Copynumber: 1.9  Consensus size: 20

     182193 TAATAACCAA

                                 
     182203 AGCTACCGTGGCT-ACTATGG
          1 AGCTACCGT-GCTGACTATGG

                 *             
     182223 AGCTATCGTGCTGACTATG
          1 AGCTACCGTGCTGACTATG

     182242 ATGCTCTGTG


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  19    3  0.18
  20   14  0.82

ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28


Consensus pattern (20 bp):   
AGCTACCGTGCTGACTATGG

Left flanking sequence: Indices 181703 -- 182202
TACTCGGTAAACCAAGCCGAAACCTCTGATCTACTGTCAGCCATTTCATTAGGACAGCACTTGAT
TAGTCTTTTTCTAGCTTGATTTCGAAGCGGAAAGCTGAAACGGTATATCTTAAAAAGCCTATTCC
TTTGTGACTGGCCCCAGTGCTTAACGTCAGGTTGCCTCCACATATGAAAAGTAAGCCAGCCGTAT
TAGCTCATAAACTCGCCTTAAGGCACCGTGTTGAGTAGGGAATTGAATAGAAAATTTTGTGTCCC
GCTCCGCTCTATACCCAAAGCTTCAACTCAATCACTTGTACAGAGGCCTACCAACAGCGGGCTCC
GGTGGGGGAACTGTATCCATTTCCTGCTGCCCCATCCCAATAATACGTGTTTATCAACCACCCCT
GTCAACTTCGCACAAGCCAACACTGGCTCCTGCCCTATACATACATTAGGGGAGTCGATAATCCC
GGTAGATCCTCTGCATGAATGGGCGCGTTCTCCTGTAATAACCAA


Right flanking sequence: Indices 182242 -- 182741
ATGCTCTGTGAGGCCAGTTCCCTGCGGTGAAGTTTCTTCCTTCCCATAAGGGAAAGCTAGTCTTC
TTATTAGGTGAGTTTTGACTATTTGGATTGGGGAAATGGAGCACTTCTCGCATTTAAGGTGCCGG
AGCGTCCCAAACAGTTGTAGTTGACCTCTAACTATCACTTCAAGCCGTCAGTCTTAACTGTCCAA
TAGGCGGAAAGATATGAAACTTCAACAGACTCCTCACTGCAACCTTATCCTCAGTTTGACTTACG
GTTAAAAGATTGAATTCATTGAAAGTTGACCCCTAAGCAGTCCCAGAAGTCTCAGTCTAAGTACT
TCTTACCAATCCGGGCAGAAAGTGGGAGCCCGAGTTCACTATTTAGATTGAGGCCATACTCGGAT
AGAGAAGCCAGTGATTAAGTTACTGACTTTCCTGACCAGAGAAAGAAGTAAGCAGAAAGCTCATC
TTCTTTTCTTGGTCTTGCTATTGACTTAGACCTCGGTACAGAGAG


Done.