Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021622.1 Corchorus olitorius cultivar O-4 contig21655, 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: 35929
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:577 original size:18 final size:18

Alignment explanation


    Indices: 554--601  Score: 54
    Period size: 14  Copynumber: 3.0  Consensus size: 18

        544 ACCTAAAAAA

                              
        554 AAAAAGTAGATATTCAAG
          1 AAAAAGTAGATATTCAAG

                              
        572 AAAAAGT--A-ATT-AAG
          1 AAAAAGTAGATATTCAAG

                              
        586 AAAAA-TAGATA-TCAAG
          1 AAAAAGTAGATATTCAAG

        602 TGATGGAAAT


Statistics
Matches: 26,  Mismatches: 0, Indels: 10
        0.72            0.00        0.28

Matches are distributed among these distances:
  13    1  0.04
  14    8  0.31
  15    5  0.19
  16    5  0.19
  18    7  0.27

ACGTcount: A:0.60, C:0.04, G:0.15, T:0.21


Consensus pattern (18 bp):   
AAAAAGTAGATATTCAAG

Found at i:5209 original size:19 final size:18

Alignment explanation


    Indices: 5185--5220  Score: 54
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       5175 TGAAGACCAT

                               
       5185 TTGAAGATAATTTGAAGAC
          1 TTGAAGAT-ATTTGAAGAC

                    *        
       5204 TTGAAGATTTTTGAAGA
          1 TTGAAGATATTTGAAGA

       5221 ATTATTTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    8  0.50
  19    8  0.50

ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36


Consensus pattern (18 bp):   
TTGAAGATATTTGAAGAC

Found at i:10967 original size:13 final size:13

Alignment explanation


    Indices: 10949--10973  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

      10939 GAAATTACAA

                         
      10949 TTATGAAAGTATC
          1 TTATGAAAGTATC

                        
      10962 TTATGAAAGTAT
          1 TTATGAAAGTAT

      10974 TTCTGCATAC


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.40, C:0.04, G:0.16, T:0.40


Consensus pattern (13 bp):   
TTATGAAAGTATC

Found at i:11893 original size:19 final size:18

Alignment explanation


    Indices: 11869--11904  Score: 54
    Period size: 18  Copynumber: 1.9  Consensus size: 18

      11859 TGAAGACCAT

                               
      11869 TTGAAGATAATTTGAAGAC
          1 TTGAAGAT-ATTTGAAGAC

                    *        
      11888 TTGAAGATTTTTGAAGA
          1 TTGAAGATATTTGAAGA

      11905 ATTATTTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    8  0.50
  19    8  0.50

ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36


Consensus pattern (18 bp):   
TTGAAGATATTTGAAGAC

Found at i:14469 original size:22 final size:23

Alignment explanation


    Indices: 14408--14470  Score: 69
    Period size: 22  Copynumber: 2.9  Consensus size: 23

      14398 AGAAGGTTTC

                    *            * 
      14408 GGGGAAGAGAAAG-AA-AAAATT
          1 GGGGAAGAAAAAGAAAGAAAACT

                                   
      14429 GGGGAAGAAAAAGAAAGAAAACT
          1 GGGGAAGAAAAAGAAAGAAAACT

                *      *        
      14452 GGGGTAG-AAACGAAAGAAA
          1 GGGGAAGAAAAAGAAAGAAA

      14471 GAACGTGGGA


Statistics
Matches: 36,  Mismatches: 4, Indels: 3
        0.84            0.09        0.07

Matches are distributed among these distances:
  21   12  0.33
  22   13  0.36
  23   11  0.31

ACGTcount: A:0.57, C:0.03, G:0.33, T:0.06


Consensus pattern (23 bp):   
GGGGAAGAAAAAGAAAGAAAACT

Found at i:25224 original size:21 final size:21

Alignment explanation


    Indices: 25198--25245  Score: 69
    Period size: 21  Copynumber: 2.3  Consensus size: 21

      25188 GCAAGCTTGA

                                 
      25198 CCGGGCAGGTGGCACGGATGG
          1 CCGGGCAGGTGGCACGGATGG

                         **  *   
      25219 CCGGGCAGGTGGCTTGGGTGG
          1 CCGGGCAGGTGGCACGGATGG

                  
      25240 CCGGGC
          1 CCGGGC

      25246 CATGGCCGGG


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   24  1.00

ACGTcount: A:0.08, C:0.25, G:0.54, T:0.12


Consensus pattern (21 bp):   
CCGGGCAGGTGGCACGGATGG

Found at i:34038 original size:27 final size:26

Alignment explanation


    Indices: 33977--34051  Score: 87
    Period size: 27  Copynumber: 2.8  Consensus size: 26

      33967 TTAGGGTCAC

                                  *    
      33977 CTAGGGGCATTTTGGTCATTTTTAAAA
          1 CTAGGGGCATTTTGGTCA-TTTGAAAA

               *                  * * 
      34004 CTAAGGGCATTTTGGTCATTTGCATA
          1 CTAGGGGCATTTTGGTCATTTGAAAA

                     *            
      34030 CTTAGGGGCGTTTTGGTCATTT
          1 C-TAGGGGCATTTTGGTCATTT

      34052 TGGGCATTTT


Statistics
Matches: 41,  Mismatches: 6, Indels: 2
        0.84            0.12        0.04

Matches are distributed among these distances:
  26    6  0.15
  27   35  0.85

ACGTcount: A:0.20, C:0.13, G:0.25, T:0.41


Consensus pattern (26 bp):   
CTAGGGGCATTTTGGTCATTTGAAAA
Done.