Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012935.1 Corchorus olitorius cultivar O-4 contig12968, 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: 9199
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31


Found at i:5311 original size:11 final size:11

Alignment explanation


    Indices: 5291--5325  Score: 61
    Period size: 11  Copynumber: 3.2  Consensus size: 11

       5281 TTGACAGCGC

                       
       5291 AACAAAAACAA
          1 AACAAAAACAA

               *       
       5302 AACGAAAACAA
          1 AACAAAAACAA

                       
       5313 AACAAAAACAA
          1 AACAAAAACAA

              
       5324 AA
          1 AA

       5326 AAATAGAAAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  11   22  1.00

ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00


Consensus pattern (11 bp):   
AACAAAAACAA

Found at i:5325 original size:16 final size:17

Alignment explanation


    Indices: 5295--5343  Score: 59
    Period size: 16  Copynumber: 3.0  Consensus size: 17

       5285 CAGCGCAACA

                             
       5295 AAAAC-AAAACGAAAAC
          1 AAAACAAAAACGAAAAC

                             
       5311 AAAACAAAAAC-AAAA-
          1 AAAACAAAAACGAAAAC

                 *            
       5326 AAATAGAAAAACGAAAAC
          1 AAA-ACAAAAACGAAAAC

       5344 GATACCAAAC


Statistics
Matches: 28,  Mismatches: 1, Indels: 6
        0.80            0.03        0.17

Matches are distributed among these distances:
  15    3  0.11
  16   16  0.57
  17    9  0.32

ACGTcount: A:0.78, C:0.14, G:0.06, T:0.02


Consensus pattern (17 bp):   
AAAACAAAAACGAAAAC

Found at i:6083 original size:7 final size:7

Alignment explanation


    Indices: 6073--6117  Score: 90
    Period size: 7  Copynumber: 6.4  Consensus size: 7

       6063 AGTTTTTTTA

                   
       6073 AATCTTG
          1 AATCTTG

                   
       6080 AATCTTG
          1 AATCTTG

                   
       6087 AATCTTG
          1 AATCTTG

                   
       6094 AATCTTG
          1 AATCTTG

                   
       6101 AATCTTG
          1 AATCTTG

                   
       6108 AATCTTG
          1 AATCTTG

               
       6115 AAT
          1 AAT

       6118 GCCAATGACA


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   38  1.00

ACGTcount: A:0.31, C:0.13, G:0.13, T:0.42


Consensus pattern (7 bp):   
AATCTTG

Found at i:7041 original size:2 final size:2

Alignment explanation


    Indices: 7034--7074  Score: 73
    Period size: 2  Copynumber: 20.0  Consensus size: 2

       7024 TAATACATAG

                                                                        
       7034 TA TA TA TA TA TA TA TA TA CTA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA

       7075 CAAGACACAT


Statistics
Matches: 38,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   2   36  0.95
   3    2  0.05

ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:7060 original size:23 final size:23

Alignment explanation


    Indices: 7026--7076  Score: 86
    Period size: 23  Copynumber: 2.2  Consensus size: 23

       7016 ACTAAAAATA

                                   
       7026 ATACATAGTATATATATATATAT
          1 ATACATAGTATATATATATATAT

                                    
       7049 ATACTATA-TATATATATATATAT
          1 ATAC-ATAGTATATATATATATAT

                 
       7072 ATACA
          1 ATACA

       7077 AGACACATGG


Statistics
Matches: 27,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  22    1  0.04
  23   23  0.85
  24    3  0.11

ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43


Consensus pattern (23 bp):   
ATACATAGTATATATATATATAT
Done.