Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006993.1 Corchorus capsularis cultivar CVL-1 contig07014, 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: 43222
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:4539 original size:29 final size:30

Alignment explanation


    Indices: 4506--4571  Score: 98
    Period size: 29  Copynumber: 2.2  Consensus size: 30

       4496 ACTTGTACGG

                        *      *          
       4506 TTTGGACACTTTGCCCCTTTAACT-TCAAT
          1 TTTGGACACTTTACCCCTTAAACTCTCAAT

                    *                     
       4535 TTTGGACATTTTACCCCTTAAACTCTCAAT
          1 TTTGGACACTTTACCCCTTAAACTCTCAAT

                   
       4565 TTTGGAC
          1 TTTGGAC

       4572 GTTTCAGACC


Statistics
Matches: 33,  Mismatches: 3, Indels: 1
        0.89            0.08        0.03

Matches are distributed among these distances:
  29   21  0.64
  30   12  0.36

ACGTcount: A:0.23, C:0.26, G:0.11, T:0.41


Consensus pattern (30 bp):   
TTTGGACACTTTACCCCTTAAACTCTCAAT

Found at i:25098 original size:2 final size:2

Alignment explanation


    Indices: 25091--25190  Score: 56
    Period size: 2  Copynumber: 54.0  Consensus size: 2

      25081 AATAACTTAT

                                           *              *    *          
      25091 TA TA TA TA TA TA -A TA TA -A TT TA TA TA T- TT TA CA TA TA T-
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

             *                      *            *                    *    
      25129 TT TA TA TA TA TA -A TA AA TA TA T- TT TA TA TA TA TCA TA AA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA

                   *                           
      25170 TA T- TT TA TA TA TA -A TA -A TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA

      25191 ATCAGTCGGT


Statistics
Matches: 76,  Mismatches: 12, Indels: 20
        0.70            0.11        0.19

Matches are distributed among these distances:
   1    9  0.12
   2   65  0.86
   3    2  0.03

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


Consensus pattern (2 bp):   
TA

Found at i:25138 original size:22 final size:22

Alignment explanation


    Indices: 25090--25188  Score: 125
    Period size: 22  Copynumber: 4.6  Consensus size: 22

      25080 AAATAACTTA

                                * 
      25090 TTATATATAT-AT-AATATAAT
          1 TTATATATATAATAAATATATT

                       *  *       
      25110 TTATATAT-T-TTACATATATT
          1 TTATATATATAATAAATATATT

                                  
      25130 TTATATATATAATAAATATATT
          1 TTATATATATAATAAATATATT

                      *           
      25152 TTATATATATCATAAATATATT
          1 TTATATATATAATAAATATATT

                           
      25174 TTATATATAATAATA
          1 TTATATAT-ATAATA

      25189 TAATCAGTCG


Statistics
Matches: 68,  Mismatches: 7, Indels: 5
        0.85            0.09        0.06

Matches are distributed among these distances:
  19    2  0.03
  20   22  0.32
  21    1  0.01
  22   38  0.56
  23    5  0.07

ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52


Consensus pattern (22 bp):   
TTATATATATAATAAATATATT

Found at i:35488 original size:42 final size:42

Alignment explanation


    Indices: 35408--35491  Score: 114
    Period size: 42  Copynumber: 2.0  Consensus size: 42

      35398 AATGGATCGA

                                          *           
      35408 ATGGCCAGTTGTGGCCGGATGGCGCATGCGTTGGCCCGTGCG
          1 ATGGCCAGTTGTGGCCGGATGGCGCATGCGATGGCCCGTGCG

                  *                ***       *        
      35450 ATGGCCGGTTGTGGCCGGATGGCTTGTGCGATGTCCCGTGCG
          1 ATGGCCAGTTGTGGCCGGATGGCGCATGCGATGGCCCGTGCG

      35492 GTGTCCCATG


Statistics
Matches: 36,  Mismatches: 6, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  42   36  1.00

ACGTcount: A:0.08, C:0.25, G:0.43, T:0.24


Consensus pattern (42 bp):   
ATGGCCAGTTGTGGCCGGATGGCGCATGCGATGGCCCGTGCG
Done.