Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008141.1 Corchorus capsularis cultivar CVL-1 contig08162, 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: 17436
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31


Found at i:1749 original size:13 final size:13

Alignment explanation


    Indices: 1714--1754  Score: 55
    Period size: 13  Copynumber: 3.2  Consensus size: 13

       1704 TGCGCGGACA

                     *  *
       1714 GCACCCATGACAA
          1 GCACCCATGCCAT

                         
       1727 GCACCCATGCCAT
          1 GCACCCATGCCAT

                      *  
       1740 GCACCCATGCTAT
          1 GCACCCATGCCAT

              
       1753 GC
          1 GC

       1755 CGATGTCACC


Statistics
Matches: 25,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  13   25  1.00

ACGTcount: A:0.27, C:0.41, G:0.17, T:0.15


Consensus pattern (13 bp):   
GCACCCATGCCAT

Found at i:1832 original size:54 final size:54

Alignment explanation


    Indices: 1750--1859  Score: 211
    Period size: 54  Copynumber: 2.0  Consensus size: 54

       1740 GCACCCATGC

                                                                  
       1750 TATGCCGATGTCACCCAACTCACTACACCCATCACTCATCTCAAACACTATAAA
          1 TATGCCGATGTCACCCAACTCACTACACCCATCACTCATCTCAAACACTATAAA

                                                          *       
       1804 TATGCCGATGTCACCCAACTCACTACACCCATCACTCATCTCAAACGCTATAAA
          1 TATGCCGATGTCACCCAACTCACTACACCCATCACTCATCTCAAACACTATAAA

              
       1858 TA
          1 TA

       1860 CCGCCCAACA


Statistics
Matches: 55,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  54   55  1.00

ACGTcount: A:0.35, C:0.36, G:0.06, T:0.23


Consensus pattern (54 bp):   
TATGCCGATGTCACCCAACTCACTACACCCATCACTCATCTCAAACACTATAAA

Found at i:13177 original size:41 final size:39

Alignment explanation


    Indices: 13132--13213  Score: 101
    Period size: 41  Copynumber: 2.1  Consensus size: 39

      13122 AAATAAAATA

                   *          *            *         
      13132 AAAAGCAGAAACAGAAAATAAAAATATATTTTTTTTTATTT
          1 AAAAGCAAAAACAGAAAAGAAAAAT-TATTTATTTTT-TTT

                 *      *                          
      13173 AAAAGGAAAAACGGAAAAGAAAAATTATTTATTTTTTTT
          1 AAAAGCAAAAACAGAAAAGAAAAATTATTTATTTTTTTT

              
      13212 AA
          1 AA

      13214 TCGACGCAAA


Statistics
Matches: 36,  Mismatches: 5, Indels: 2
        0.84            0.12        0.05

Matches are distributed among these distances:
  39    5  0.14
  40   10  0.28
  41   21  0.58

ACGTcount: A:0.52, C:0.04, G:0.10, T:0.34


Consensus pattern (39 bp):   
AAAAGCAAAAACAGAAAAGAAAAATTATTTATTTTTTTT

Found at i:14683 original size:115 final size:115

Alignment explanation


    Indices: 14480--14692  Score: 302
    Period size: 115  Copynumber: 1.9  Consensus size: 115

      14470 AGAGGAATAG

                               **     *                                 **   
      14480 GGTAGGACGGTTTAGCCTTTTCTAGGTCTCCAAGTTGGATTACGTGTCATCCTAGAGTAGGCTCC
          1 GGTAGGACGGTTTAGCCTTAACTAGGACTCCAAGTTGGATTACGTGTCATCCTAGAGTAGAATCC

                * * *                                         
      14545 AAGTTAGATGAGGACTCTAGAATTTTCTGGAATTTTCTAACTTGGAGTGA
         66 AAGTCAAAAGAGGACTCTAGAATTTTCTGGAATTTTCTAACTTGGAGTGA

                                    *                  *                     
      14595 GGTAGGACGGTTTAG-CTCTAACTTGGACTCCAAGTTGGATTAGGTGTCATCCTAGAGTAGAATC
          1 GGTAGGACGGTTTAGCCT-TAACTAGGACTCCAAGTTGGATTACGTGTCATCCTAGAGTAGAATC

                           *   *              
      14659 CAAGTCAAAAGAGGATTCTGGAATTTTCTGGAAT
         65 CAAGTCAAAAGAGGACTCTAGAATTTTCTGGAAT

      14693 CTAGCAGGAA


Statistics
Matches: 85,  Mismatches: 12, Indels: 2
        0.86            0.12        0.02

Matches are distributed among these distances:
 114    2  0.02
 115   83  0.98

ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32


Consensus pattern (115 bp):   
GGTAGGACGGTTTAGCCTTAACTAGGACTCCAAGTTGGATTACGTGTCATCCTAGAGTAGAATCC
AAGTCAAAAGAGGACTCTAGAATTTTCTGGAATTTTCTAACTTGGAGTGA

Found at i:15119 original size:11 final size:10

Alignment explanation


    Indices: 15101--15134  Score: 50
    Period size: 11  Copynumber: 3.2  Consensus size: 10

      15091 AATGGTCTTC

                      
      15101 AAATCTTCAA
          1 AAATCTTCAA

                       
      15111 AATATCTTCAA
          1 AA-ATCTTCAA

                       
      15122 GAAATCTTCAA
          1 -AAATCTTCAA

              
      15133 AA
          1 AA

      15135 CACGAACTTC


Statistics
Matches: 22,  Mismatches: 0, Indels: 4
        0.85            0.00        0.15

Matches are distributed among these distances:
  10    4  0.18
  11   16  0.73
  12    2  0.09

ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29


Consensus pattern (10 bp):   
AAATCTTCAA

Found at i:15319 original size:20 final size:21

Alignment explanation


    Indices: 15286--15324  Score: 53
    Period size: 20  Copynumber: 1.9  Consensus size: 21

      15276 AGCAAAATAG

                          *      
      15286 GGTAAAAACACATATAAAAGT
          1 GGTAAAAACACATAGAAAAGT

                     *         
      15307 GGTAAAAA-GCATAGAAAA
          1 GGTAAAAACACATAGAAAA

      15325 ATAGCTATAA


Statistics
Matches: 16,  Mismatches: 2, Indels: 1
        0.84            0.11        0.05

Matches are distributed among these distances:
  20    8  0.50
  21    8  0.50

ACGTcount: A:0.59, C:0.08, G:0.18, T:0.15


Consensus pattern (21 bp):   
GGTAAAAACACATAGAAAAGT
Done.