Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001028.1 Corchorus capsularis cultivar CVL-1 contig01028, 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: 17626
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:2851 original size:6 final size:6

Alignment explanation


    Indices: 2842--2871  Score: 60
    Period size: 6  Copynumber: 5.0  Consensus size: 6

       2832 TTTTTTATTC

                                              
       2842 TTCTAG TTCTAG TTCTAG TTCTAG TTCTAG
          1 TTCTAG TTCTAG TTCTAG TTCTAG TTCTAG

       2872 ATGCACAAAT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   24  1.00

ACGTcount: A:0.17, C:0.17, G:0.17, T:0.50


Consensus pattern (6 bp):   
TTCTAG

Found at i:4995 original size:15 final size:15

Alignment explanation


    Indices: 4955--4995  Score: 50
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       4945 AAAATTAGGG

                            
       4955 TATTATATAGT-ATAT
          1 TATTATATA-TAATAT

                            
       4970 TATTA-ACTATAATAT
          1 TATTATA-TATAATAT

                       
       4985 TATTATATATA
          1 TATTATATATA

       4996 TGTAGCGGTA


Statistics
Matches: 23,  Mismatches: 0, Indels: 6
        0.79            0.00        0.21

Matches are distributed among these distances:
  14    2  0.09
  15   20  0.87
  16    1  0.04

ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51


Consensus pattern (15 bp):   
TATTATATATAATAT

Found at i:5196 original size:6 final size:6

Alignment explanation


    Indices: 5187--5214  Score: 56
    Period size: 6  Copynumber: 4.7  Consensus size: 6

       5177 TTGATCTTTT

                                            
       5187 CCCTGA CCCTGA CCCTGA CCCTGA CCCT
          1 CCCTGA CCCTGA CCCTGA CCCTGA CCCT

       5215 CATGATGATG


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   22  1.00

ACGTcount: A:0.14, C:0.54, G:0.14, T:0.18


Consensus pattern (6 bp):   
CCCTGA

Found at i:6467 original size:2 final size:2

Alignment explanation


    Indices: 6456--6490  Score: 56
    Period size: 2  Copynumber: 18.5  Consensus size: 2

       6446 ACCGCCTCCC

                                                                   
       6456 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       6491 AAATTAAAAT


Statistics
Matches: 31,  Mismatches: 0, Indels: 4
        0.89            0.00        0.11

Matches are distributed among these distances:
   1    2  0.06
   2   29  0.94

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


Consensus pattern (2 bp):   
AT

Found at i:7630 original size:2 final size:2

Alignment explanation


    Indices: 7623--7651  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       7613 CTATTAAGGA

                                                       
       7623 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       7652 GTCAAGACCA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:10762 original size:92 final size:92

Alignment explanation


    Indices: 10632--10815  Score: 368
    Period size: 92  Copynumber: 2.0  Consensus size: 92

      10622 AATTTTGGAC

                                                                             
      10632 TCCACAAGCGAGTTGTGGAGTTGACACATGTCCATTTTTTGAATTATTTAAGTTTTAAATATTTC
          1 TCCACAAGCGAGTTGTGGAGTTGACACATGTCCATTTTTTGAATTATTTAAGTTTTAAATATTTC

                                       
      10697 AATCTAGTCCCTAAGGGACACATGTCA
         66 AATCTAGTCCCTAAGGGACACATGTCA

                                                                             
      10724 TCCACAAGCGAGTTGTGGAGTTGACACATGTCCATTTTTTGAATTATTTAAGTTTTAAATATTTC
          1 TCCACAAGCGAGTTGTGGAGTTGACACATGTCCATTTTTTGAATTATTTAAGTTTTAAATATTTC

                                       
      10789 AATCTAGTCCCTAAGGGACACATGTCA
         66 AATCTAGTCCCTAAGGGACACATGTCA

      10816 CCCTTCAAGA


Statistics
Matches: 92,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  92   92  1.00

ACGTcount: A:0.29, C:0.17, G:0.17, T:0.36


Consensus pattern (92 bp):   
TCCACAAGCGAGTTGTGGAGTTGACACATGTCCATTTTTTGAATTATTTAAGTTTTAAATATTTC
AATCTAGTCCCTAAGGGACACATGTCA
Done.