Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009541.1 Corchorus olitorius cultivar O-4 contig09573, 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: 9330
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33


Found at i:4531 original size:39 final size:39

Alignment explanation


    Indices: 4487--4564  Score: 147
    Period size: 39  Copynumber: 2.0  Consensus size: 39

       4477 ATGAGGCTGA

                                    *              
       4487 AATACTTGCAATCAAGGAAGCTGTTGTCATTTTTGGAGC
          1 AATACTTGCAATCAAGGAAGCTGTAGTCATTTTTGGAGC

                                                   
       4526 AATACTTGCAATCAAGGAAGCTGTAGTCATTTTTGGAGC
          1 AATACTTGCAATCAAGGAAGCTGTAGTCATTTTTGGAGC

       4565 CTCAAGGTGG


Statistics
Matches: 38,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  39   38  1.00

ACGTcount: A:0.29, C:0.15, G:0.23, T:0.32


Consensus pattern (39 bp):   
AATACTTGCAATCAAGGAAGCTGTAGTCATTTTTGGAGC

Found at i:4654 original size:15 final size:15

Alignment explanation


    Indices: 4634--4662  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

       4624 GGGTATCTAA

                           
       4634 ACCGATAAATTCCCC
          1 ACCGATAAATTCCCC

                          
       4649 ACCGATAAATTCCC
          1 ACCGATAAATTCCC

       4663 TTGGAGATTA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.34, C:0.38, G:0.07, T:0.21


Consensus pattern (15 bp):   
ACCGATAAATTCCCC

Found at i:5082 original size:11 final size:11

Alignment explanation


    Indices: 5062--5096  Score: 61
    Period size: 11  Copynumber: 3.2  Consensus size: 11

       5052 TTGACAGCGC

                       
       5062 AACAAAAACAA
          1 AACAAAAACAA

               *       
       5073 AACGAAAACAA
          1 AACAAAAACAA

                       
       5084 AACAAAAACAA
          1 AACAAAAACAA

              
       5095 AA
          1 AA

       5097 AACAGAAAAA


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:7448 original size:27 final size:27

Alignment explanation


    Indices: 7410--7464  Score: 85
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       7400 AACTAATCTA

                                       
       7410 AATCCGATCCGCATCGCACACCTAGTT
          1 AATCCGATCCGCATCGCACACCTAGTT

                               *        
       7437 AATCC-ATCCCGCATCGCATACCTAGTT
          1 AATCCGAT-CCGCATCGCACACCTAGTT

             
       7464 A
          1 A

       7465 TGGTGGGTGA


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  26    2  0.08
  27   24  0.92

ACGTcount: A:0.27, C:0.36, G:0.13, T:0.24


Consensus pattern (27 bp):   
AATCCGATCCGCATCGCACACCTAGTT

Found at i:7810 original size:21 final size:21

Alignment explanation


    Indices: 7784--7826  Score: 68
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       7774 ACACTCCATC

                    *  *         
       7784 ATCTAACCGTATATCAATTAA
          1 ATCTAACCATACATCAATTAA

                                 
       7805 ATCTAACCATACATCAATTAA
          1 ATCTAACCATACATCAATTAA

             
       7826 A
          1 A

       7827 AGGTTTATTA


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.47, C:0.21, G:0.02, T:0.30


Consensus pattern (21 bp):   
ATCTAACCATACATCAATTAA

Found at i:8976 original size:2 final size:2

Alignment explanation


    Indices: 8969--9011  Score: 86
    Period size: 2  Copynumber: 21.5  Consensus size: 2

       8959 TCCTAGATAC

                                                                          
       8969 TA TA TA TA TA TA TA TA TA TA TA 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 TA

             
       9011 T
          1 T

       9012 TAGTAAAGAC


Statistics
Matches: 41,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   41  1.00

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


Consensus pattern (2 bp):   
TA

Done.