Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013531.1 Corchorus olitorius cultivar O-4 contig13564, 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: 13559
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29


Found at i:1352 original size:20 final size:20

Alignment explanation


    Indices: 1327--1365  Score: 78
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       1317 TCTCAACAAA

                                
       1327 AATTTGATGGGTTTAGAAAC
          1 AATTTGATGGGTTTAGAAAC

                               
       1347 AATTTGATGGGTTTAGAAA
          1 AATTTGATGGGTTTAGAAA

       1366 AGGGAAAGAC


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.36, C:0.03, G:0.26, T:0.36


Consensus pattern (20 bp):   
AATTTGATGGGTTTAGAAAC

Found at i:1744 original size:23 final size:25

Alignment explanation


    Indices: 1718--1764  Score: 62
    Period size: 23  Copynumber: 2.0  Consensus size: 25

       1708 AATGCATTAG

                           *         
       1718 ACAAGAATAA-AAT-TAATAAAAAC
          1 ACAAGAATAATAATAAAATAAAAAC

                  *                 
       1741 ACAAGATTAATAATAAAATAAAAA
          1 ACAAGAATAATAATAAAATAAAAA

       1765 GTTTGAAAAG


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  23    9  0.45
  24    3  0.15
  25    8  0.40

ACGTcount: A:0.70, C:0.06, G:0.04, T:0.19


Consensus pattern (25 bp):   
ACAAGAATAATAATAAAATAAAAAC

Found at i:7332 original size:24 final size:24

Alignment explanation


    Indices: 7300--7357  Score: 80
    Period size: 24  Copynumber: 2.4  Consensus size: 24

       7290 AATGGGAATT

                      *             
       7300 GGTGGAGGAATATTCCGATCCTGA
          1 GGTGGAGGAACATTCCGATCCTGA

                     * *       *    
       7324 GGTGGAGGAGCGTTCCGATTCTGA
          1 GGTGGAGGAACATTCCGATCCTGA

                      
       7348 GGTGGAGGAA
          1 GGTGGAGGAA

       7358 GTGCAGGTGG


Statistics
Matches: 29,  Mismatches: 5, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  24   29  1.00

ACGTcount: A:0.22, C:0.14, G:0.41, T:0.22


Consensus pattern (24 bp):   
GGTGGAGGAACATTCCGATCCTGA

Found at i:12075 original size:66 final size:66

Alignment explanation


    Indices: 11976--12239  Score: 332
    Period size: 66  Copynumber: 3.9  Consensus size: 66

      11966 CCGATTGTTT

                         *                                   *   *          *
      11976 GTTCCGCT-GGGAAACTGCAGGGGGGCCAACCACTGGGGGTCTTACGGCACACGACCTGATTTAG
          1 GTTCCGCTGGGGAGACTGCAGGGGGGCCAACCACTGGGGGTCTTACGGCGCACCACCTGATTTAA

             
      12040 C
         66 C

                                                 *                           
      12041 GTTCCGCTGGGGAGACTGCAGGGGGGCCAACCACTGGAGGTCTTACGGCGCACCACCTGATTTAA
          1 GTTCCGCTGGGGAGACTGCAGGGGGGCCAACCACTGGGGGTCTTACGGCGCACCACCTGATTTAA

             
      12106 C
         66 C

                *          *           *       *           *                 
      12107 GTTCTGCTGGGGAGATTGCAGGGGGGCTAACCACTAGGGGTCTTACGACGCACCACCTGATTTAA
          1 GTTCCGCTGGGGAGACTGCAGGGGGGCCAACCACTGGGGGTCTTACGGCGCACCACCTGATTTAA

             
      12172 C
         66 C

                                    *                                    *   
      12173 GTGTCGCTGGGGAGACTGGGGAGATTGCAGGGGGGCCAACCACTGGGGGTCTTACGGCGCATCAC
          1 GT-TC-C------G-CTGGGGAGACTGCAGGGGGGCCAACCACTGGGGGTCTTACGGCGCACCAC

              
      12238 CT
         57 CT

      12240 AATTCCACCG


Statistics
Matches: 173,  Mismatches: 16, Indels: 10
        0.87            0.08        0.05

Matches are distributed among these distances:
  65    8  0.05
  66  114  0.66
  67    2  0.01
  74    1  0.01
  75   48  0.28

ACGTcount: A:0.19, C:0.26, G:0.35, T:0.19


Consensus pattern (66 bp):   
GTTCCGCTGGGGAGACTGCAGGGGGGCCAACCACTGGGGGTCTTACGGCGCACCACCTGATTTAA
C

Found at i:13506 original size:37 final size:37

Alignment explanation


    Indices: 13456--13555  Score: 155
    Period size: 37  Copynumber: 2.7  Consensus size: 37

      13446 TGCAGTGTAG

                                                 
      13456 CCGAGGATGCCTCTGGGGGACTTACAGCGCTCGGTGA
          1 CCGAGGATGCCTCTGGGGGACTTACAGCGCTCGGTGA

                          *      *              *
      13493 CCGAGGATGCCTCTAGGGGACATACAGCGCTCGGTGG
          1 CCGAGGATGCCTCTGGGGGACTTACAGCGCTCGGTGA

               *  *                   
      13530 CCGTGGCTGCCTCTGGGGGACTTACA
          1 CCGAGGATGCCTCTGGGGGACTTACA

      13556 ACGC


Statistics
Matches: 56,  Mismatches: 7, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  37   56  1.00

ACGTcount: A:0.16, C:0.28, G:0.37, T:0.19


Consensus pattern (37 bp):   
CCGAGGATGCCTCTGGGGGACTTACAGCGCTCGGTGA
Done.