Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009015.1 Corchorus capsularis cultivar CVL-1 contig09036, 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: 14616
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33


Found at i:346 original size:144 final size:144

Alignment explanation


    Indices: 86--348  Score: 510
    Period size: 144  Copynumber: 1.8  Consensus size: 144

         76 TTTTTCTTTT

                                                                             
         86 AAAAAAAATACTTTCAATCCGAAAATTCCTTTACCCATCCTGGATGTCGCTACTCCATGAATTTT
          1 AAAAAAAATACTTTCAATCCGAAAATTCCTTTACCCATCCTGGATGTCGCTACTCCATGAATTTT

                                                                             
        151 GATGTTGTTTTGTTTGAATGATTGAAATTTGAAAGTTTGAAGGTTGAGAGAATTGAAAATTTTGA
         66 GATGTTGTTTTGTTTGAATGATTGAAATTTGAAAGTTTGAAGGTTGAGAGAATTGAAAATTTTGA

                          
        216 AGTTTGAAGGAATA
        131 AGTTTGAAGGAATA

                                                                             
        230 AAAAAAAATACTTTCAATCCGAAAATTCCTTTACCCATCCCT-GATGTCGCTACTCCATGAATTT
          1 AAAAAAAATACTTTCAATCCGAAAATTCCTTTACCCAT-CCTGGATGTCGCTACTCCATGAATTT

                                                                   
        294 TGATGTTGTTTTGTTTGAATGATTGAAATTTGAAAGTTTGAAGGTTGAGAGAATT
         65 TGATGTTGTTTTGTTTGAATGATTGAAATTTGAAAGTTTGAAGGTTGAGAGAATT

        349 TGAGAGAATT


Statistics
Matches: 118,  Mismatches: 0, Indels: 2
        0.98            0.00        0.02

Matches are distributed among these distances:
 144  115  0.97
 145    3  0.03

ACGTcount: A:0.33, C:0.13, G:0.18, T:0.37


Consensus pattern (144 bp):   
AAAAAAAATACTTTCAATCCGAAAATTCCTTTACCCATCCTGGATGTCGCTACTCCATGAATTTT
GATGTTGTTTTGTTTGAATGATTGAAATTTGAAAGTTTGAAGGTTGAGAGAATTGAAAATTTTGA
AGTTTGAAGGAATA

Found at i:7197 original size:45 final size:45

Alignment explanation


    Indices: 7133--7222  Score: 171
    Period size: 45  Copynumber: 2.0  Consensus size: 45

       7123 AAAAGTTTGC

                                                         
       7133 AGCTTGGATGTGCTACACCTTATCATAATTGAAATCTCTTTAATT
          1 AGCTTGGATGTGCTACACCTTATCATAATTGAAATCTCTTTAATT

                 *                                       
       7178 AGCTTTGATGTGCTACACCTTATCATAATTGAAATCTCTTTAATT
          1 AGCTTGGATGTGCTACACCTTATCATAATTGAAATCTCTTTAATT

       7223 TTGGTTGAAA


Statistics
Matches: 44,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  45   44  1.00

ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41


Consensus pattern (45 bp):   
AGCTTGGATGTGCTACACCTTATCATAATTGAAATCTCTTTAATT

Found at i:7752 original size:28 final size:28

Alignment explanation


    Indices: 7720--7777  Score: 116
    Period size: 28  Copynumber: 2.1  Consensus size: 28

       7710 AAAAATTCAA

                                        
       7720 TTAAATAACAAGAACCAACTCATTTTTG
          1 TTAAATAACAAGAACCAACTCATTTTTG

                                        
       7748 TTAAATAACAAGAACCAACTCATTTTTG
          1 TTAAATAACAAGAACCAACTCATTTTTG

              
       7776 TT
          1 TT

       7778 CAATGGAGTT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  28   30  1.00

ACGTcount: A:0.41, C:0.17, G:0.07, T:0.34


Consensus pattern (28 bp):   
TTAAATAACAAGAACCAACTCATTTTTG

Found at i:10066 original size:18 final size:19

Alignment explanation


    Indices: 10032--10069  Score: 69
    Period size: 19  Copynumber: 2.1  Consensus size: 19

      10022 CTTATTTCCT

                               
      10032 AATAATGTAATAAATGCAA
          1 AATAATGTAATAAATGCAA

                               
      10051 AATAATGTAA-AAATGCAA
          1 AATAATGTAATAAATGCAA

             
      10069 A
          1 A

      10070 GAAAAACTAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  18    9  0.47
  19   10  0.53

ACGTcount: A:0.61, C:0.05, G:0.11, T:0.24


Consensus pattern (19 bp):   
AATAATGTAATAAATGCAA
Done.