Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NC_026540

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: 106727
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30


Found at i:1008 original size:2 final size:2

Alignment explanation


    Indices: 1001--1031  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

        991 TAGTATAGAC

                                                          
       1001 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       1032 TGGCTAATAA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Left flanking sequence: Indices 501 -- 1000
GGTGTATAGCTTAATTGGTAGAGCATTAGGCTTTTAACTTAATGGTCGCAGGTTCAAGTCCTGCT
ATACCCAAATGTTTTTATAGAAGTTCTCCAGGCAGTTCATATGCACATCAAAATATACATTGTAC
GTTGACTCGTCTAGTACGATTAATTACGTTAAACTAAAATATATATATATTTTTAATGTCTTTAT
GGCCGCTCACGCCCTTTTTTTTTCTTTGCGAAAAAAGGCCGCGGGCCTCTAATCTAAGCTTAGAG
TGGGTGAATAGAACGTCGCAGCGTTTGATGCGGCTCTGAAAAGATAGAAGTTAAGTAGGTGTTAC
CAACTACTTAACTATTTAACTTATCTATATTATACAATCTGCAGCAATCCTGCATTCTGCAATTA
AGGAGTTGTTTGATAGCAACTGTGAATAACAGTATAAATATAGATATTTTCATAAAATAAATAAA
TAGCTTATTTATTATTGGCCAAATACATAATATTTTAGTATAGAC


Right flanking sequence: Indices 1032 -- 1531
TGGCTAATAATGCCGTATTGATTGTTGTTTCATTAAAGCTAATTGCTGTTGGAATAAAAGCTCTA
GTAAACTAGAAGTCTCGATTACATGTGCCGCGTTTTGCGCTTTTCGGACAGCATTGCTGGAGCTG
GCAACATGAAGAGCGGATTCCCGTTATTTTCAAATTCCTAAGTAATCTACGTCACCGTCAACCTT
AATTCATGAGATATGCGTCTCTTTCATTAATTATCTAAATTATGCCAACCTATCTTATGAAAGCC
AGCCCGGCAGTATAATATAATAAATACTGGCTCGCTCGCGTATATTCCCACATTCATTCGTCAAA
TCAGGCAATCTCTATTGAATAAAAGAGAAGATATGATAATAAATTGAATAAGAAGCTTCCGAGTA
CGCAAATGGTAGGAATACACCAGAAGTATTGGCAACCTAGAAATAGGCCGGCAAAAGGTACAAGA
ATAGCATGTCGCCACTAGCTGTGTTATGGCATTGGCCGCCTCCAA



Found at i:19051 original size:19 final size:20

Alignment explanation


    Indices: 19009--19051  Score: 52
    Period size: 19  Copynumber: 2.2  Consensus size: 20

      18999 GGATGTTGGT

                   *           *
      19009 CATGACTTTCGAAAAGTTCC
          1 CATGACTATCGAAAAGTTCA

                           *    
      19029 CATGACTAT-GAAAATTTCA
          1 CATGACTATCGAAAAGTTCA

                
      19048 CATG
          1 CATG

      19052 GAGGAGTTTG


Statistics
Matches: 20,  Mismatches: 3, Indels: 1
        0.83            0.12        0.04

Matches are distributed among these distances:
  19   12  0.60
  20    8  0.40

ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30


Consensus pattern (20 bp):   
CATGACTATCGAAAAGTTCA

Left flanking sequence: Indices 18509 -- 19008
GAGCTAAAAATGCATTTTTTTTCTTTTTTATTTTCATTTTCAATTTTTTTATTTTCAAATTTATG
GGAGACTTGTCATATTTAGAATCTTTCTGTGGTGTGCTTTGTTTTTTATTATTTTGTACTTTTTT
TTTATCATCTAAATATAGGCGCGATACGTGGGCAAACAAGGAGCGTAGGCTTGAAATAAAAAAAA
AAATAAAACCGCGTAAGCGGGCACAGAGAACAAAGCGCCAAGCGCTTTGTTGGCCTAACGAAAAA
AAGAAACAAAGAAATAAAAATAAAGAAAATTTTTCCTTTTTATTTCTTTCAAATAAATCAAAAAT
ATTTTTGATTTATTTGCTACAATTTTTAAAAACCTTCGGCTTCAACGAAAAAGCAAAAATTTTGA
CTTTTTCTTCTCTGCTTGCTTTTTCGCAAGCTTATTCTTCCGTCCCTGAAAATATTTGGAATAGA
TTTTTTATTGTTCGCGCCTTACCAAAAAGACTGATGGATGTTGGT


Right flanking sequence: Indices 19052 -- 19551
GAGGAGTTTGCATCTTTATTATGGGTGTTATTTTGTCGTGCGACCCTGCAGCTTATGCGCGACTA
TCTCGTGTTTAAGCTCACGCCATGTAGGCGTGAACTCTGGTTGAATTCGGGTTCTCAATCCCGCC
GCTGAAATGCTCAGTCGACTCTTGAACCTTGATAGGAAGACGGCTTCTTCCTAAATTAGTGCAAA
AGGTTCAAGGACTTAGGATGAACTTAATGTGAATGGGTATAAGCTTCGCTGCTCAAAAACACCCA
GTATTGACCACACTGAGAGACTTGCCAATGGCAAGAAAGGCCGCGGGTAACGCTAGTTGGCGAAA
TGGCGTTAAGCATTCCTAGCGATACGGAAAGAGAGGTCGTGATGATATCATCTACGTTCGTACTG
TTCTTCGTGGAGTAAATCTCACATCCAAAAATCTAACCAGGGAACGGGATAATTCCCATTAAGTT
CCAGTAAAACTGGCAGGCCAGCCGGGCCGTAAGCTAGTGGGAACA



Found at i:37881 original size:24 final size:24

Alignment explanation


    Indices: 37854--37899  Score: 58
    Period size: 23  Copynumber: 2.0  Consensus size: 24

      37844 TGCTAATACG

                 *                  
      37854 AAAAATAAAAAGA-AGACTAAAGA
          1 AAAAAAAAAAAGAGAGACTAAAGA

                     *     *       
      37877 AAAAAAAAATAGAGATACTAAAG
          1 AAAAAAAAAAAGAGAGACTAAAG

      37900 TGAGCACTTC


Statistics
Matches: 19,  Mismatches: 3, Indels: 1
        0.83            0.13        0.04

Matches are distributed among these distances:
  23   11  0.58
  24    8  0.42

ACGTcount: A:0.72, C:0.04, G:0.13, T:0.11


Consensus pattern (24 bp):   
AAAAAAAAAAAGAGAGACTAAAGA

Left flanking sequence: Indices 37354 -- 37853
CTCAGTGAAATTGAACTCTCCGTGAAGATGCGGAGTACCAACGGCTAGACGGTAAGACCCCGTGC
ACCTTTACTATAGCTTTGCAGTGACAACCTTGATTGAATGTGTAGGATAGGTGGGAGGTGGTGAC
GTTGCACGTCACCACCAATCTTGAAATACCACTCTTTCGTCTAAGGATGTCTAACTGCCGAAACA
GAGGCGGGACACTGCATGGTGGTTAGTTTATCTGGGGCGGATGCCTTTAAGTAAGGGGCGCTTGG
ATGGTAACATCCCAGGCCAATCTGGCTATATGCTGAAATCTCCATTTCTTGGACAATCAGCAGGG
AAGGCTGAAAAAAGCCACTGCGAAAAATTTATTTGGCTCCCTCAACGACTGCATGCCAGGTATCC
AACAATGCAATAATGATTGGATAATGATACAGTCTGAACTTCCAGTAAACTGGAAGCCTAAAGTA
CTGTTCACTACGAAACAGTGATAGGACATTCAAACTGCTAATACG


Right flanking sequence: Indices 37900 -- 38399
TGAGCACTTCAATTGAATCAAATACAACGACAAGTATGTTGCAGAGTGAATGAACATAATTGCCC
AAAGAGTAACGGAGGTGTGCGAAGGTAGGCTCGAGCTAATATTATGACAGCTTTAGAGCGTAATG
GTAGAAGCCTGCCTGACTGTGAGACTTACCAGTCGAACAGAGACGAAAGTCGGCCATAGTGATCC
GGGAGTCCCGTGTGGAAGGGCTCTCGCTCAACGGATCAAAGGTACGCCGGGGATAACAGGCTGAT
GACTCCCAAGAGCTCTTATCGACGGAGTCGTTTGGCACCTCGATGTCGACTCATCACATCCTGGG
GTTGAAGAAGGTCCCAAGGGTTCGGTTGTTCGCCGATGAAAGTGGTACGTGAGTTGGGTTTAGAA
CGTCGTGAGACAGTTCGGTTCCTATCTACCGTTGGTGTTTAAGAGAGAACTGCGAGAAGCCAACC
CTAGTACGAGAGGACTGGGTTGGGTCAACCTATGGTGTACCGGTT



Found at i:41587 original size:81 final size:81

Alignment explanation


    Indices: 41452--41600  Score: 255
    Period size: 81  Copynumber: 1.8  Consensus size: 81

      41442 TAAATACTCG

                                                   *                         
      41452 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTGAGACTGCCGTGTTTACCATTTTCAC
          1 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC

                            
      41517 CAAGCGAGTATGCTCA
         66 CAAGCGAGTATGCTCA

                                                       *   *                 
      41533 CTATCGGACTT-GAACCGATAACCCATAGGAACAGATTTTAAGTCTGTCGTGTTTACCATTTTCA
          1 CTATCGGA-TTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCA

                
      41597 CCAA
         65 CCAA

      41601 ATGAGCTTAG


Statistics
Matches: 64,  Mismatches: 3, Indels: 2
        0.93            0.04        0.03

Matches are distributed among these distances:
  81   62  0.97
  82    2  0.03

ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29


Consensus pattern (81 bp):   
CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
CAAGCGAGTATGCTCA

Left flanking sequence: Indices 40952 -- 41451
AACTTCAATCTACTTTAGTCAATCATATGGATATAAAAAAAGCGGCTAATTTAGAAATAACATCA
GTATTTCAACAACTTTTTGAGCTCATTTTTTACCCATATAATTCTTTATGCTCTTGTTTGAACAA
GCCAATTTGTGCTTCATCCACTATACAAGAAAAGACGCAAGGAGGGTTACTTAGTCACCAGAGGA
TAACCACTTAGTAACTTGGGTCCCCACTTTGCCAATTAAAGCCTGCGGCTTTATTGACAGAACTG
GGGACCCAAGTTTGTAGCGAACCTTTTTTTTTAATATTTCGGGAACCCCCCAAAAATATTAAAAA
TATTTTTTGCTGCGAAAAACAGCGTCCTCAAAAATTATAAAGATTTAAACTAATGGATGATTTGT
TTTTTTGGCGAATAACGGGATTCGAACCCGTGTTTTCAAATTCACAATCTGACACTTTCACCTAT
TAAGTTATACTCGCCCTTTTTCCAATTTAGACATTTAAATACTCG


Right flanking sequence: Indices 41601 -- 42100
ATGAGCTTAGGGAAGCGAAGCGCAGAGTGGAAACACAATCTTTTTGTTTCGTTTTATTTTCGCCA
TTTTATTTTATAGACATCCCCGGCTTATTCCGGCTCGGCTGGACCTGCGGCATTTTTTCAAATAT
TTGAAAAATCTATAGTCCCTTGTCTTAAGGCGTGTAGAGACTCCTTTTTTATTGATTTATACTAA
TCTATCTTAGATCCGAGATAGTGCCGAAAAAATGATTCAATTTCATCTAACCACGGTTGCCTTGG
CAATGGCAATTACTCTTATACGATATGCAGAATACTCCAAAACCTCTATTTATTCTATTTAGAAC
TAAAAGAAGATAATGCTTTTTTATAAAAAAATCATAAAGTGCAAAGATTCAAATTTTGAGCTTTG
TTTTACGTAGTTTTGCCATCTATATAATATAATATAGTAAGAAATAATAAGTTGGCGAGGAATTA
AAAAAAAATATATATATATATATTTTTTTTTTATTCTGTGGTCCT


Done.