Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008400.1 Corchorus capsularis cultivar CVL-1 contig08421, 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: 20196
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32


Found at i:2780 original size:18 final size:18

Alignment explanation


    Indices: 2757--2794  Score: 76
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       2747 TTAACGATGA

                              
       2757 ACTAAACCGGATTAAACT
          1 ACTAAACCGGATTAAACT

                              
       2775 ACTAAACCGGATTAAACT
          1 ACTAAACCGGATTAAACT

              
       2793 AC
          1 AC

       2795 CACAAAGCTA


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

Matches are distributed among these distances:
  18   20  1.00

ACGTcount: A:0.45, C:0.24, G:0.11, T:0.21


Consensus pattern (18 bp):   
ACTAAACCGGATTAAACT

Found at i:4386 original size:18 final size:18

Alignment explanation


    Indices: 4363--4400  Score: 58
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       4353 TCTCCTTTAA

                           *  
       4363 GCTTGTCCAAGCTTCGTT
          1 GCTTGTCCAAGCTTCCTT

                     *        
       4381 GCTTGTCCATGCTTCCTT
          1 GCTTGTCCAAGCTTCCTT

              
       4399 GC
          1 GC

       4401 AATCCTTGAT


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.08, C:0.32, G:0.21, T:0.39


Consensus pattern (18 bp):   
GCTTGTCCAAGCTTCCTT

Found at i:4535 original size:32 final size:32

Alignment explanation


    Indices: 4473--4537  Score: 94
    Period size: 32  Copynumber: 2.0  Consensus size: 32

       4463 CGCATCACTC

                                 * *        
       4473 CTAAATTATGCACGTTTATACGATACGATACA
          1 CTAAATTATGCACGTTTATACAACACGATACA

                        *            *      
       4505 CTAAATTATGCATGTTTATACAACATGATACA
          1 CTAAATTATGCACGTTTATACAACACGATACA

             
       4537 C
          1 C

       4538 GACATGAAAC


Statistics
Matches: 29,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  32   29  1.00

ACGTcount: A:0.38, C:0.18, G:0.11, T:0.32


Consensus pattern (32 bp):   
CTAAATTATGCACGTTTATACAACACGATACA

Found at i:16669 original size:33 final size:33

Alignment explanation


    Indices: 16591--16695  Score: 88
    Period size: 33  Copynumber: 3.2  Consensus size: 33

      16581 TTGCAAAGAG

                    *         **    *      * 
      16591 TGTTTTAGATGTTGTTTGCGATGATACTAAACC
          1 TGTTTTAGGTGTTGTTTGTAATGAAACTAAATC

             **                       *     *  
      16624 TAATTT-GAGTGTTGTTT-TCAATGACACTAATTC
          1 TGTTTTAG-GTGTTGTTTGT-AATGAAACTAAATC

                               *             
      16657 TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC
          1 TGTTTTAGGTGTTGTTTGTAATGAAACTAAATC

                  
      16690 TGTTTT
          1 TGTTTT

      16696 GAATGCTAAT


Statistics
Matches: 55,  Mismatches: 13, Indels: 8
        0.72            0.17        0.11

Matches are distributed among these distances:
  32    1  0.02
  33   52  0.95
  34    2  0.04

ACGTcount: A:0.24, C:0.10, G:0.20, T:0.47


Consensus pattern (33 bp):   
TGTTTTAGGTGTTGTTTGTAATGAAACTAAATC

Found at i:16751 original size:33 final size:34

Alignment explanation


    Indices: 16711--16784  Score: 116
    Period size: 33  Copynumber: 2.2  Consensus size: 34

      16701 CTAATTATGA

                                           *  
      16711 TGAAAATAAATT-TGTTTTGGTTGATCATAGCAT
          1 TGAAAATAAATTCTGTTTTGGTTGATCATAGAAT

              *                               
      16744 TGCAAAT-AATTCTGTTTTGGTTGATCATAGAAT
          1 TGAAAATAAATTCTGTTTTGGTTGATCATAGAAT

                    
      16777 TGAAAATA
          1 TGAAAATA

      16785 GGACTATTTT


Statistics
Matches: 36,  Mismatches: 3, Indels: 3
        0.86            0.07        0.07

Matches are distributed among these distances:
  32    4  0.11
  33   32  0.89

ACGTcount: A:0.35, C:0.07, G:0.18, T:0.41


Consensus pattern (34 bp):   
TGAAAATAAATTCTGTTTTGGTTGATCATAGAAT

Found at i:16795 original size:33 final size:33

Alignment explanation


    Indices: 16725--16796  Score: 90
    Period size: 33  Copynumber: 2.2  Consensus size: 33

      16715 AATAAATTTG

                            *    *      **  *
      16725 TTTTGGTTGATCATAGCATTGCAAATAATTCTG
          1 TTTTGGTTGATCATAGAATTGAAAATAAGACTA

                                       *     
      16758 TTTTGGTTGATCATAGAATTGAAAATAGGACTA
          1 TTTTGGTTGATCATAGAATTGAAAATAAGACTA

                  
      16791 TTTTGG
          1 TTTTGG

      16797 GTGAAAAGAA


Statistics
Matches: 33,  Mismatches: 6, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  33   33  1.00

ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42


Consensus pattern (33 bp):   
TTTTGGTTGATCATAGAATTGAAAATAAGACTA

Found at i:17282 original size:9 final size:9

Alignment explanation


    Indices: 17268--17292  Score: 50
    Period size: 9  Copynumber: 2.8  Consensus size: 9

      17258 GGAAAGGATG

                     
      17268 TGCAAGGGC
          1 TGCAAGGGC

                     
      17277 TGCAAGGGC
          1 TGCAAGGGC

                   
      17286 TGCAAGG
          1 TGCAAGG

      17293 AAGCATGAAG


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   16  1.00

ACGTcount: A:0.24, C:0.20, G:0.44, T:0.12


Consensus pattern (9 bp):   
TGCAAGGGC
Done.