Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007558.1 Corchorus capsularis cultivar CVL-1 contig07579, 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: 11874
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:2510 original size:2 final size:2

Alignment explanation


    Indices: 2503--2531  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       2493 CTCATTATCA

                                                       
       2503 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

       2532 GAGAGAGAGA


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:2536 original size:2 final size:2

Alignment explanation


    Indices: 2531--2562  Score: 55
    Period size: 2  Copynumber: 16.0  Consensus size: 2

       2521 ATATATATAT

                                           *               
       2531 AG AG AG AG AG AG AG AG AG AG AC AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

       2563 TATAATTCAC


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00


Consensus pattern (2 bp):   
AG

Found at i:5043 original size:24 final size:24

Alignment explanation


    Indices: 4998--5043  Score: 58
    Period size: 24  Copynumber: 1.9  Consensus size: 24

       4988 GGAGACCCAG

                       *     *      
       4998 AATGCAAATCAGCAAATGCGCTAA
          1 AATGCAAATCAACAAATACGCTAA

                                   
       5022 AATGCAAATCAACGAAA-ACGCT
          1 AATGCAAATCAAC-AAATACGCT

       5044 CTTTTTTTAG


Statistics
Matches: 19,  Mismatches: 2, Indels: 2
        0.83            0.09        0.09

Matches are distributed among these distances:
  24   16  0.84
  25    3  0.16

ACGTcount: A:0.48, C:0.22, G:0.15, T:0.15


Consensus pattern (24 bp):   
AATGCAAATCAACAAATACGCTAA

Found at i:6129 original size:22 final size:22

Alignment explanation


    Indices: 6083--6130  Score: 55
    Period size: 22  Copynumber: 2.2  Consensus size: 22

       6073 TCTCATCTAA

                                * 
       6083 TTCTGCTCTATTTCTCACCTTT
          1 TTCTGCTCTATTTCTCACCTCT

                                    
       6105 TTCT-CTCTATATTCTCATCC-CT
          1 TTCTGCTCTAT-TTCTCA-CCTCT

                
       6127 TTCT
          1 TTCT

       6131 TCTTCTCAAA


Statistics
Matches: 23,  Mismatches: 1, Indels: 4
        0.82            0.04        0.14

Matches are distributed among these distances:
  21    6  0.26
  22   15  0.65
  23    2  0.09

ACGTcount: A:0.10, C:0.33, G:0.02, T:0.54


Consensus pattern (22 bp):   
TTCTGCTCTATTTCTCACCTCT

Found at i:6615 original size:14 final size:14

Alignment explanation


    Indices: 6596--6623  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

       6586 AATGTTTCAC

                          
       6596 CTATCAAAGATCAA
          1 CTATCAAAGATCAA

                          
       6610 CTATCAAAGATCAA
          1 CTATCAAAGATCAA

       6624 AGAATATAAT


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

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.50, C:0.21, G:0.07, T:0.21


Consensus pattern (14 bp):   
CTATCAAAGATCAA

Found at i:9116 original size:10 final size:10

Alignment explanation


    Indices: 9101--9125  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

       9091 ATTGTAGGTG

                      
       9101 AACAAATTGA
          1 AACAAATTGA

                      
       9111 AACAAATTGA
          1 AACAAATTGA

                 
       9121 AACAA
          1 AACAA

       9126 GGAAACGTGG


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   15  1.00

ACGTcount: A:0.64, C:0.12, G:0.08, T:0.16


Consensus pattern (10 bp):   
AACAAATTGA
Done.