Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023863.1 Corchorus olitorius cultivar O-4 contig23896, 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: 19302
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33


Found at i:3414 original size:6 final size:6

Alignment explanation


    Indices: 3403--3428  Score: 52
    Period size: 6  Copynumber: 4.3  Consensus size: 6

       3393 AATTGGCCAC

                                          
       3403 TTCTTG TTCTTG TTCTTG TTCTTG TT
          1 TTCTTG TTCTTG TTCTTG TTCTTG TT

       3429 TCTGAACCAC


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   20  1.00

ACGTcount: A:0.00, C:0.15, G:0.15, T:0.69


Consensus pattern (6 bp):   
TTCTTG

Found at i:5413 original size:3 final size:3

Alignment explanation


    Indices: 5405--5434  Score: 60
    Period size: 3  Copynumber: 10.0  Consensus size: 3

       5395 CTCTTAGTAT

                                                   
       5405 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
          1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC

       5435 GAAAGCTACA


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

Matches are distributed among these distances:
   3   27  1.00

ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67


Consensus pattern (3 bp):   
TTC

Found at i:7333 original size:165 final size:167

Alignment explanation


    Indices: 7055--7406  Score: 591
    Period size: 165  Copynumber: 2.1  Consensus size: 167

       7045 GACAGAACCC

                 *           *  *                                            
       7055 AGACTTGGTTCTGTTTCGCTCTCAACAAATGTTCGAGGAATTAGGGTTTCGACTCTGCCACAACC
          1 AGACTGGGTTCTGTTTCACTATCAACAAATGTTCGAGGAATTAGGGTTTCGACTCTGCCACAACC

                                                *                            
       7120 CTCAGGGAAATCACGAATCGCAAATACCCTCGGCTTGTTGTGCCGAAA-T-TCAACCAAATCGTT
         66 CTCAGGGAAATCACGAATCGCAAATACCCTCGGCTTCTTGTGCCGAAATTATCAACCAAATCGTT

                *   * *                        * 
       7183 AGAATCTATCGAATCATCAGAATTCGAATGAGAATTA
        131 AGAAGCTAACAAATCATCAGAATTCGAATGAGAATAA

                                      *                                      
       7220 AGACTGGGTTCTGTTTCACTATCAACGAATGTTCGAGGAATTAGGGTTTCGACTCTGCCACAACC
          1 AGACTGGGTTCTGTTTCACTATCAACAAATGTTCGAGGAATTAGGGTTTCGACTCTGCCACAACC

                                                                             
       7285 CTCAGGGAAATCACGAATCGCAAATACCCTCGGCTTCTTGTGCCGAAATTCATCAACCAAATCGT
         66 CTCAGGGAAATCACGAATCGCAAATACCCTCGGCTTCTTGTGCCGAAATT-ATCAACCAAATCGT

                                                  
       7350 TAGAAGCTAACAAATCATCAGAATTCGAATGAGAATAA
        130 TAGAAGCTAACAAATCATCAGAATTCGAATGAGAATAA

             *                 
       7388 AAACTGGGTTCTGTTTCAC
          1 AGACTGGGTTCTGTTTCAC

       7407 AATCGGCGAA


Statistics
Matches: 174,  Mismatches: 10, Indels: 3
        0.93            0.05        0.02

Matches are distributed among these distances:
 165  108  0.62
 166    1  0.01
 168   65  0.37

ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27


Consensus pattern (167 bp):   
AGACTGGGTTCTGTTTCACTATCAACAAATGTTCGAGGAATTAGGGTTTCGACTCTGCCACAACC
CTCAGGGAAATCACGAATCGCAAATACCCTCGGCTTCTTGTGCCGAAATTATCAACCAAATCGTT
AGAAGCTAACAAATCATCAGAATTCGAATGAGAATAA

Found at i:18447 original size:30 final size:29

Alignment explanation


    Indices: 18413--18488  Score: 134
    Period size: 30  Copynumber: 2.6  Consensus size: 29

      18403 TGTTAGCATT

                                          
      18413 AAATGTATAGGAAATTTTCTTTTTGATGTA
          1 AAATGTATAGGAAATTTT-TTTTTGATGTA

                                          
      18443 AAATGTATAGGAAAATTTTTTTTTGATGTA
          1 AAATGTATAGG-AAATTTTTTTTTGATGTA

                            
      18473 AAATGTATAGGAAATT
          1 AAATGTATAGGAAATT

      18489 ATCTCTACTA


Statistics
Matches: 45,  Mismatches: 0, Indels: 3
        0.94            0.00        0.06

Matches are distributed among these distances:
  29    5  0.11
  30   33  0.73
  31    7  0.16

ACGTcount: A:0.38, C:0.01, G:0.17, T:0.43


Consensus pattern (29 bp):   
AAATGTATAGGAAATTTTTTTTTGATGTA

Found at i:18726 original size:24 final size:26

Alignment explanation


    Indices: 18676--18728  Score: 74
    Period size: 27  Copynumber: 2.1  Consensus size: 26

      18666 GTATATTAGT

                                       
      18676 AATATTGTAATTAAATTGTAACCAAAA
          1 AATATTGTAATT-AATTGTAACCAAAA

                         *            
      18703 AATATTGTAATT-CTT-TAACCAAAA
          1 AATATTGTAATTAATTGTAACCAAAA

              
      18727 AA
          1 AA

      18729 AAATTATTAT


Statistics
Matches: 25,  Mismatches: 1, Indels: 3
        0.86            0.03        0.10

Matches are distributed among these distances:
  24   11  0.44
  25    2  0.08
  27   12  0.48

ACGTcount: A:0.51, C:0.09, G:0.06, T:0.34


Consensus pattern (26 bp):   
AATATTGTAATTAATTGTAACCAAAA

Found at i:18740 original size:25 final size:24

Alignment explanation


    Indices: 18694--18740  Score: 58
    Period size: 25  Copynumber: 1.9  Consensus size: 24

      18684 AATTAAATTG

                       *   *        
      18694 TAACCAAAAAATATTGTAATTCTT
          1 TAACCAAAAAAAATTATAATTCTT

                              *    
      18718 TAACCAAAAAAAAATTATTATTC
          1 TAACC-AAAAAAAATTATAATTC

      18741 GATAGTCAAA


Statistics
Matches: 19,  Mismatches: 3, Indels: 1
        0.83            0.13        0.04

Matches are distributed among these distances:
  24    5  0.26
  25   14  0.74

ACGTcount: A:0.51, C:0.13, G:0.02, T:0.34


Consensus pattern (24 bp):   
TAACCAAAAAAAATTATAATTCTT
Done.