Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015836.1 Corchorus capsularis cultivar CVL-1 contig15857, whole genome shotgun sequence

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: 15190
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35


Found at i:1311 original size:15 final size:15

Alignment explanation


    Indices: 1288--1317  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       1278 ATATTCTTAT

                *          
       1288 ATAATTATATATATA
          1 ATAAATATATATATA

                           
       1303 ATAAATATATATATA
          1 ATAAATATATATATA

       1318 TATATTCGTT


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43


Consensus pattern (15 bp):   
ATAAATATATATATA

Found at i:13974 original size:2 final size:2

Alignment explanation


    Indices: 13967--13994  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

      13957 GTCAGTCCAA

                                                     
      13967 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      13995 TTTATGAATC


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:14200 original size:22 final size:22

Alignment explanation


    Indices: 14163--14224  Score: 63
    Period size: 22  Copynumber: 2.8  Consensus size: 22

      14153 ATAATTTACC

                     * *       ** 
      14163 TATGAAATTGTGATAAACTCCA
          1 TATGAAATTTTAATAAACTAAA

                             *     
      14185 TATGAAACTTTT-ATAACCTAAA
          1 TATGAAA-TTTTAATAAACTAAA

                              
      14207 TATGAAATTTTAATAAAC
          1 TATGAAATTTTAATAAAC

      14225 CTTTCTTTTT


Statistics
Matches: 33,  Mismatches: 5, Indels: 4
        0.79            0.12        0.10

Matches are distributed among these distances:
  21    4  0.12
  22   26  0.79
  23    3  0.09

ACGTcount: A:0.45, C:0.11, G:0.08, T:0.35


Consensus pattern (22 bp):   
TATGAAATTTTAATAAACTAAA

Found at i:14214 original size:66 final size:66

Alignment explanation


    Indices: 14097--14222  Score: 152
    Period size: 66  Copynumber: 1.9  Consensus size: 66

      14087 TGAATATTTT

                                 *   *                             *         
      14097 TATGAAATTTCGATAACTACCCTATTAAATTTTGATAACCACAATAAGAAATTTTGATAATTTAC
          1 TATGAAATTTCGATAACTACCATATGAAATTTTGATAACCACAATAAGAAATTTTAATAATTTAC

             
      14162 C
         66 C

                                                              *             
      14163 TATGAAATTGT-GATAAACT-CCATATGAAACTTTT-ATAACCTA-AATATGAAATTTTAATAA
          1 TATGAAATT-TCGAT-AACTACCATATGAAA-TTTTGATAACC-ACAATAAGAAATTTTAATAA

      14223 ACCTTTCTTT


Statistics
Matches: 52,  Mismatches: 4, Indels: 8
        0.81            0.06        0.12

Matches are distributed among these distances:
  66   42  0.81
  67   10  0.19

ACGTcount: A:0.43, C:0.13, G:0.08, T:0.37


Consensus pattern (66 bp):   
TATGAAATTTCGATAACTACCATATGAAATTTTGATAACCACAATAAGAAATTTTAATAATTTAC
C

Found at i:15118 original size:2 final size:2

Alignment explanation


    Indices: 15111--15150  Score: 80
    Period size: 2  Copynumber: 20.0  Consensus size: 2

      15101 AAAGCCACAC

                                                                       
      15111 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      15151 GAGAGAGAGA


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   38  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:15155 original size:2 final size:2

Alignment explanation


    Indices: 15150--15190  Score: 82
    Period size: 2  Copynumber: 20.5  Consensus size: 2

      15140 ATATATATAT

                                                                         
      15150 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   39  1.00

ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00


Consensus pattern (2 bp):   
AG

Done.