Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014193.1 Corchorus olitorius cultivar O-4 contig14226, 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: 44652
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:5595 original size:54 final size:55

Alignment explanation


    Indices: 5467--5602  Score: 150
    Period size: 54  Copynumber: 2.5  Consensus size: 55

       5457 CAATGTTGGC

                              *                        *             
       5467 GTTTCTGTCCTGACAGCACTATCATATTTGTTTTGGTTTTCCATGGGCTCGTAAGTA
          1 GTTTCTGTCCTGACAGCAGTATCATA--TGTTTTGGTTTTCCAAGGGCTCGTAAGTA

             *          *                          **   *   *    *  
       5524 GCTTCTGTCCTGCCAGCAGTATCATA-GTATTT-GTTTTGTAAGTGCTTGTAATTA
          1 GTTTCTGTCCTGACAGCAGTATCATATGT-TTTGGTTTTCCAAGGGCTCGTAAGTA

                                     
       5578 GTTTCTGTCCTGACAGCAGTATCAT
          1 GTTTCTGTCCTGACAGCAGTATCAT

       5603 CCCTGTTTTC


Statistics
Matches: 67,  Mismatches: 11, Indels: 5
        0.81            0.13        0.06

Matches are distributed among these distances:
  54   41  0.61
  55    3  0.04
  57   23  0.34

ACGTcount: A:0.19, C:0.19, G:0.21, T:0.41


Consensus pattern (55 bp):   
GTTTCTGTCCTGACAGCAGTATCATATGTTTTGGTTTTCCAAGGGCTCGTAAGTA

Found at i:9346 original size:21 final size:21

Alignment explanation


    Indices: 9302--9364  Score: 56
    Period size: 21  Copynumber: 3.0  Consensus size: 21

       9292 ATTCAACTTC

                  * *     *    * 
       9302 AAAAAAACATATAAAATTACT
          1 AAAAAATCGTATAAGATTATT

                            *     
       9323 AAAAAATC-TATTAAGCTTATT
          1 AAAAAATCGTA-TAAGATTATT

                *                
       9344 AAAAGATCGTATAAGATTATT
          1 AAAAAATCGTATAAGATTATT

       9365 TTTAAAACGA


Statistics
Matches: 34,  Mismatches: 6, Indels: 4
        0.77            0.14        0.09

Matches are distributed among these distances:
  20    2  0.06
  21   30  0.88
  22    2  0.06

ACGTcount: A:0.54, C:0.08, G:0.06, T:0.32


Consensus pattern (21 bp):   
AAAAAATCGTATAAGATTATT

Found at i:16243 original size:22 final size:23

Alignment explanation


    Indices: 16199--16245  Score: 85
    Period size: 23  Copynumber: 2.0  Consensus size: 23

      16189 ACTTGGTGTC

                                   
      16199 AACTGTCATGAAACCAAAAAAAA
          1 AACTGTCATGAAACCAAAAAAAA

                          *        
      16222 AACTGTCATGAAACGAAAAAAAA
          1 AACTGTCATGAAACCAAAAAAAA

             
      16245 A
          1 A

      16246 TGTGGTTTTT


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  23   23  1.00

ACGTcount: A:0.62, C:0.15, G:0.11, T:0.13


Consensus pattern (23 bp):   
AACTGTCATGAAACCAAAAAAAA

Found at i:28044 original size:15 final size:15

Alignment explanation


    Indices: 28024--28055  Score: 55
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      28014 CAGATCGAAA

                  *        
      28024 CAGATCTGAAAATGG
          1 CAGATCCGAAAATGG

                           
      28039 CAGATCCGAAAATGG
          1 CAGATCCGAAAATGG

              
      28054 CA
          1 CA

      28056 AAAAAGACCC


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.41, C:0.19, G:0.25, T:0.16


Consensus pattern (15 bp):   
CAGATCCGAAAATGG

Found at i:31113 original size:58 final size:58

Alignment explanation


    Indices: 31023--31139  Score: 225
    Period size: 58  Copynumber: 2.0  Consensus size: 58

      31013 CTCTCATACA

                          *                                           
      31023 CCCACTTGGAAATGTCAGTTTCAAGCTCTTCTTCTGCACTACCAAGTACCAACCTCCC
          1 CCCACTTGGAAATGCCAGTTTCAAGCTCTTCTTCTGCACTACCAAGTACCAACCTCCC

                                                                      
      31081 CCCACTTGGAAATGCCAGTTTCAAGCTCTTCTTCTGCACTACCAAGTACCAACCTCCC
          1 CCCACTTGGAAATGCCAGTTTCAAGCTCTTCTTCTGCACTACCAAGTACCAACCTCCC

             
      31139 C
          1 C

      31140 AAGCAATTCC


Statistics
Matches: 58,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  58   58  1.00

ACGTcount: A:0.24, C:0.38, G:0.12, T:0.26


Consensus pattern (58 bp):   
CCCACTTGGAAATGCCAGTTTCAAGCTCTTCTTCTGCACTACCAAGTACCAACCTCCC

Found at i:37130 original size:19 final size:19

Alignment explanation


    Indices: 37108--37158  Score: 61
    Period size: 19  Copynumber: 2.7  Consensus size: 19

      37098 GGGCTGAAAT

                               
      37108 TAATTAATTATTAATTAAA
          1 TAATTAATTATTAATTAAA

                         *   *  
      37127 TAA-TAATTATTTTATTGAA
          1 TAATTAATTA-TTAATTAAA

                          
      37146 TAATT-ATTATTAA
          1 TAATTAATTATTAA

      37159 AAATCCCATG


Statistics
Matches: 27,  Mismatches: 3, Indels: 5
        0.77            0.09        0.14

Matches are distributed among these distances:
  18    9  0.33
  19   17  0.63
  20    1  0.04

ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51


Consensus pattern (19 bp):   
TAATTAATTATTAATTAAA
Done.