Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009830.1 Corchorus capsularis cultivar CVL-1 contig09851, 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: 41717
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:7849 original size:54 final size:54

Alignment explanation


    Indices: 7780--7888  Score: 218
    Period size: 54  Copynumber: 2.0  Consensus size: 54

       7770 TTTGAGGTTC

                                                                  
       7780 TCAATTTGAGAATATATTATCCTATATATATAAGTCATGAATGAGGAGGTTAGG
          1 TCAATTTGAGAATATATTATCCTATATATATAAGTCATGAATGAGGAGGTTAGG

                                                                  
       7834 TCAATTTGAGAATATATTATCCTATATATATAAGTCATGAATGAGGAGGTTAGG
          1 TCAATTTGAGAATATATTATCCTATATATATAAGTCATGAATGAGGAGGTTAGG

             
       7888 T
          1 T

       7889 AAGAATTGAT


Statistics
Matches: 55,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  54   55  1.00

ACGTcount: A:0.37, C:0.07, G:0.20, T:0.36


Consensus pattern (54 bp):   
TCAATTTGAGAATATATTATCCTATATATATAAGTCATGAATGAGGAGGTTAGG

Found at i:17056 original size:29 final size:29

Alignment explanation


    Indices: 16999--17067  Score: 95
    Period size: 29  Copynumber: 2.3  Consensus size: 29

      16989 GAGTTTTTTA

                                          
      16999 CCAAATTATAACAGTTTAAAAACTTATTTC
          1 CCAAATTATAACAGTTT-AAAACTTATTTC

            *          *                  
      17029 TCAAATTATAATAGATTT-AAACTTATTTC
          1 CCAAATTATAACAG-TTTAAAACTTATTTC

                      
      17058 CCAAATTATA
          1 CCAAATTATA

      17068 CCAATTCTTG


Statistics
Matches: 35,  Mismatches: 3, Indels: 3
        0.85            0.07        0.07

Matches are distributed among these distances:
  29   20  0.57
  30   12  0.34
  31    3  0.09

ACGTcount: A:0.43, C:0.14, G:0.03, T:0.39


Consensus pattern (29 bp):   
CCAAATTATAACAGTTTAAAACTTATTTC

Found at i:23728 original size:6 final size:6

Alignment explanation


    Indices: 23717--23743  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

      23707 CCTCAAGGTA

                                           
      23717 GTGTAG GTGTAG GTGTAG GTGTAG GTG
          1 GTGTAG GTGTAG GTGTAG GTGTAG GTG

      23744 AAGGGCGAAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.15, C:0.00, G:0.52, T:0.33


Consensus pattern (6 bp):   
GTGTAG

Found at i:32262 original size:25 final size:28

Alignment explanation


    Indices: 32218--32270  Score: 85
    Period size: 25  Copynumber: 2.0  Consensus size: 28

      32208 GCATTGAAAT

                                        
      32218 TAATTGCATAATAAGACCATCAGCTGAA
          1 TAATTGCATAATAAGACCATCAGCTGAA

                                        
      32246 TAATTGCAT-A-AA-ACCATCAGCTGAA
          1 TAATTGCATAATAAGACCATCAGCTGAA

      32271 AAGAAGCATC


Statistics
Matches: 25,  Mismatches: 0, Indels: 3
        0.89            0.00        0.11

Matches are distributed among these distances:
  25   13  0.52
  26    2  0.08
  27    1  0.04
  28    9  0.36

ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25


Consensus pattern (28 bp):   
TAATTGCATAATAAGACCATCAGCTGAA

Found at i:32279 original size:25 final size:25

Alignment explanation


    Indices: 32228--32279  Score: 61
    Period size: 25  Copynumber: 2.1  Consensus size: 25

      32218 TAATTGCATA

                *                **  
      32228 ATAAGACCATCAGCTGAATAATTGC
          1 ATAAAACCATCAGCTGAATAAAAGC

                                      
      32253 ATAAAACCATCAGCTGAA-AAGAAGC
          1 ATAAAACCATCAGCTGAATAA-AAGC

              
      32278 AT
          1 AT

      32280 CTCCAACAGA


Statistics
Matches: 23,  Mismatches: 3, Indels: 2
        0.82            0.11        0.07

Matches are distributed among these distances:
  24    2  0.09
  25   21  0.91

ACGTcount: A:0.46, C:0.19, G:0.15, T:0.19


Consensus pattern (25 bp):   
ATAAAACCATCAGCTGAATAAAAGC

Found at i:36715 original size:6 final size:6

Alignment explanation


    Indices: 36706--36730  Score: 50
    Period size: 6  Copynumber: 4.2  Consensus size: 6

      36696 AGAAGTGGTT

                                         
      36706 GTTGCA GTTGCA GTTGCA GTTGCA G
          1 GTTGCA GTTGCA GTTGCA GTTGCA G

      36731 AGAGTGAAAG


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

Matches are distributed among these distances:
   6   19  1.00

ACGTcount: A:0.16, C:0.16, G:0.36, T:0.32


Consensus pattern (6 bp):   
GTTGCA

Found at i:36797 original size:7 final size:7

Alignment explanation


    Indices: 36785--36811  Score: 54
    Period size: 7  Copynumber: 3.9  Consensus size: 7

      36775 GATAGATAGT

                   
      36785 TTAGGAC
          1 TTAGGAC

                   
      36792 TTAGGAC
          1 TTAGGAC

                   
      36799 TTAGGAC
          1 TTAGGAC

                  
      36806 TTAGGA
          1 TTAGGA

      36812 GTAGTTCTTT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   20  1.00

ACGTcount: A:0.30, C:0.11, G:0.30, T:0.30


Consensus pattern (7 bp):   
TTAGGAC

Done.