Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015619.1 Corchorus olitorius cultivar O-4 contig15652, 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: 15969
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35


Found at i:4955 original size:22 final size:22

Alignment explanation


    Indices: 4902--4955  Score: 56
    Period size: 23  Copynumber: 2.5  Consensus size: 22

       4892 TATTTAGTGG

                      *           
       4902 GGTT-TTGTTTTTGCAATTTTA
          1 GGTTATTGTTCTTGCAATTTTA

                  *          *    *
       4923 GGTATACTGTTCTTGCATTTTTT
          1 GGT-TATTGTTCTTGCAATTTTA

                      
       4946 GGTTATTGTT
          1 GGTTATTGTT

       4956 TTAATAATAC


Statistics
Matches: 26,  Mismatches: 5, Indels: 3
        0.76            0.15        0.09

Matches are distributed among these distances:
  21    3  0.12
  22    7  0.27
  23   16  0.62

ACGTcount: A:0.13, C:0.07, G:0.20, T:0.59


Consensus pattern (22 bp):   
GGTTATTGTTCTTGCAATTTTA

Found at i:5451 original size:55 final size:56

Alignment explanation


    Indices: 5372--5482  Score: 172
    Period size: 55  Copynumber: 2.0  Consensus size: 56

       5362 AAAGGTTGGG

                    *                                                
       5372 CCTAGATTTTTTGTTTCCCATTTTTTCTATATAAATCAAAC-AGAACAAAAGGAATT
          1 CCTAGATTCTTTGTTTCCCATTTTTTCTATATAAATCAAACTAG-ACAAAAGGAATT

                               *                      *             
       5428 CCTAGATTCTTT-TTTCCCCTTTTTTCTATATAAATCAAACTTGACAAAAGGAATT
          1 CCTAGATTCTTTGTTTCCCATTTTTTCTATATAAATCAAACTAGACAAAAGGAATT

       5483 TGCTGACTAT


Statistics
Matches: 51,  Mismatches: 3, Indels: 3
        0.89            0.05        0.05

Matches are distributed among these distances:
  55   39  0.76
  56   12  0.24

ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41


Consensus pattern (56 bp):   
CCTAGATTCTTTGTTTCCCATTTTTTCTATATAAATCAAACTAGACAAAAGGAATT

Found at i:9178 original size:39 final size:40

Alignment explanation


    Indices: 9122--9202  Score: 137
    Period size: 39  Copynumber: 2.0  Consensus size: 40

       9112 TTTAATTCCT

                                                    
       9122 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

                     *          *                   
       9162 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

              
       9201 AT
          1 AT

       9203 TCTTAGGTAT


Statistics
Matches: 39,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  39   31  0.79
  40    8  0.21

ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37


Consensus pattern (40 bp):   
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

Found at i:9229 original size:25 final size:24

Alignment explanation


    Indices: 9193--9239  Score: 85
    Period size: 25  Copynumber: 1.9  Consensus size: 24

       9183 AATACTTACA

                                    
       9193 TTAATTAAATTCTTAGGTATTTTT
          1 TTAATTAAATTCTTAGGTATTTTT

                                   
       9217 TTAATTCAAATTCTTAGGTATTT
          1 TTAATT-AAATTCTTAGGTATTT

       9240 GTGCAAACGT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  24    6  0.27
  25   16  0.73

ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55


Consensus pattern (24 bp):   
TTAATTAAATTCTTAGGTATTTTT

Found at i:11636 original size:58 final size:58

Alignment explanation


    Indices: 11535--11647  Score: 167
    Period size: 58  Copynumber: 1.9  Consensus size: 58

      11525 AGCATCATGC

                                                                      
      11535 CTCGGTCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAAGT
          1 CTCGGTCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAAGT

                                      *             *           *    
      11593 CTCGGT-CTGAAAACGTCTTTTTTTATGCATCTAAT-AAAGAACATGTCACTTGATA
          1 CTCGGTCCT-AAAACGTC-TTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATA

      11648 TTTGATTAAT


Statistics
Matches: 50,  Mismatches: 3, Indels: 4
        0.88            0.05        0.07

Matches are distributed among these distances:
  57    2  0.04
  58   32  0.64
  59   16  0.32

ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34


Consensus pattern (58 bp):   
CTCGGTCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAAGT

Found at i:15242 original size:24 final size:24

Alignment explanation


    Indices: 15210--15257  Score: 87
    Period size: 24  Copynumber: 2.0  Consensus size: 24

      15200 ATGGAATTAG

                               *    
      15210 GAGGGTGTTTAGTGAAGGTGGTGC
          1 GAGGGTGTTTAGTGAAGGTAGTGC

                                    
      15234 GAGGGTGTTTAGTGAAGGTAGTGC
          1 GAGGGTGTTTAGTGAAGGTAGTGC

      15258 AATGGATATG


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   23  1.00

ACGTcount: A:0.19, C:0.04, G:0.48, T:0.29


Consensus pattern (24 bp):   
GAGGGTGTTTAGTGAAGGTAGTGC
Done.