Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013458.1 Corchorus olitorius cultivar O-4 contig13491, 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: 31109
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32


Found at i:7039 original size:17 final size:17

Alignment explanation


    Indices: 7010--7044  Score: 54
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       7000 CAACCATGAG

                             
       7010 AAATATAATAATAATAT
          1 AAATATAATAATAATAT

                              
       7027 AAATA-AATAAATAATAT
          1 AAATATAAT-AATAATAT

             
       7044 A
          1 A

       7045 TACTTCAATA


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  16    3  0.18
  17   14  0.82

ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31


Consensus pattern (17 bp):   
AAATATAATAATAATAT

Found at i:8428 original size:54 final size:56

Alignment explanation


    Indices: 8342--8456  Score: 207
    Period size: 54  Copynumber: 2.1  Consensus size: 56

       8332 AGGACAAAAG

                                                                  * 
       8342 GATGACTCATGGGTGTGTGTATAATTGTTTGGTTTGGTGTTGGTTTTGGTTGATGT
          1 GATGACTCATGGGTGTGTGTATAATTGTTTGGTTTGGTGTTGGTTTTGGTTGATAT

                                                                    
       8398 GATGACTCATGGGTGTGT-T-TAATTGTTTGGTTTGGTGTTGGTTTTGGTTGATAT
          1 GATGACTCATGGGTGTGTGTATAATTGTTTGGTTTGGTGTTGGTTTTGGTTGATAT

                 
       8452 GATGA
          1 GATGA

       8457 TTGTTTTGTA


Statistics
Matches: 58,  Mismatches: 1, Indels: 2
        0.95            0.02        0.03

Matches are distributed among these distances:
  54   39  0.67
  55    1  0.02
  56   18  0.31

ACGTcount: A:0.14, C:0.03, G:0.35, T:0.48


Consensus pattern (56 bp):   
GATGACTCATGGGTGTGTGTATAATTGTTTGGTTTGGTGTTGGTTTTGGTTGATAT

Found at i:10182 original size:60 final size:60

Alignment explanation


    Indices: 10099--10227  Score: 188
    Period size: 60  Copynumber: 2.1  Consensus size: 60

      10089 GTTAAAAAAA

                     *    *   *           *           *                  
      10099 CTCAAATAAGAATCTGATTTTTTAATTTGGTCAAATAAGAG-TCTAACGTTATCGAAAATG
          1 CTCAAATAAAAATCCGATCTTTTAATTTGGCCAAATAAG-GCCCTAACGTTATCGAAAATG

              *                                                         
      10159 CTTAAATAAAAATCCGATCTTTTAATTTGGCCAAATAAGGCCCTAACGTTATCGAAAATG
          1 CTCAAATAAAAATCCGATCTTTTAATTTGGCCAAATAAGGCCCTAACGTTATCGAAAATG

                     
      10219 CTCAAATAA
          1 CTCAAATAA

      10228 GGGTTTGTCG


Statistics
Matches: 61,  Mismatches: 7, Indels: 2
        0.87            0.10        0.03

Matches are distributed among these distances:
  59    1  0.02
  60   60  0.98

ACGTcount: A:0.40, C:0.16, G:0.13, T:0.32


Consensus pattern (60 bp):   
CTCAAATAAAAATCCGATCTTTTAATTTGGCCAAATAAGGCCCTAACGTTATCGAAAATG

Found at i:10312 original size:31 final size:31

Alignment explanation


    Indices: 10274--10375  Score: 88
    Period size: 31  Copynumber: 3.4  Consensus size: 31

      10264 TTGACACCAA

                                           
      10274 GCCCTTATTTGAGCATTTTAGCAAACATTAG
          1 GCCCTTATTTGAGCATTTTAGCAAACATTAG

                            **           ** 
      10305 GCCCTTATTTG-GCCAAATTA--AAA-A-CCG
          1 GCCCTTATTTGAG-CATTTTAGCAAACATTAG

                                *      *    
      10332 GCCCCTTATTTGAGCATTTTGGCAAACGTTAG
          1 G-CCCTTATTTGAGCATTTTAGCAAACATTAG

            *           
      10364 ACCCTTATTTGA
          1 GCCCTTATTTGA

      10376 CAAAAAAAAG


Statistics
Matches: 53,  Mismatches: 11, Indels: 14
        0.68            0.14        0.18

Matches are distributed among these distances:
  27    2  0.04
  28   15  0.28
  29    4  0.08
  30    4  0.08
  31   27  0.51
  32    1  0.02

ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33


Consensus pattern (31 bp):   
GCCCTTATTTGAGCATTTTAGCAAACATTAG

Found at i:11976 original size:52 final size:49

Alignment explanation


    Indices: 11893--11995  Score: 170
    Period size: 52  Copynumber: 2.0  Consensus size: 49

      11883 AATAAATAGC

                                      *                      
      11893 AGTAATAAATATACTTATATAGATACTAATAAATAATAAACTAGTTAGT
          1 AGTAATAAATATACTTATATAGATACCAATAAATAATAAACTAGTTAGT

                                                                
      11942 AGTAATATAATATACTTATATATAGATACCAATAAATAATAAACTAGTTAGT
          1 AGTAATA-AATATAC-T-TATATAGATACCAATAAATAATAAACTAGTTAGT

              
      11994 AG
          1 AG

      11996 CAAAAAGAAC


Statistics
Matches: 50,  Mismatches: 1, Indels: 3
        0.93            0.02        0.06

Matches are distributed among these distances:
  49    7  0.14
  50    7  0.14
  51    1  0.02
  52   35  0.70

ACGTcount: A:0.50, C:0.07, G:0.09, T:0.34


Consensus pattern (49 bp):   
AGTAATAAATATACTTATATAGATACCAATAAATAATAAACTAGTTAGT

Found at i:30687 original size:2 final size:2

Alignment explanation


    Indices: 30680--30709  Score: 51
    Period size: 2  Copynumber: 15.0  Consensus size: 2

      30670 CGGAGAATAA

                                                *       
      30680 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      30710 TACATATACA


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
AT

Done.