Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000222.1 Corchorus capsularis cultivar CVL-1 contig00222, 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: 5444
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.31


Found at i:428 original size:20 final size:20

Alignment explanation


    Indices: 392--429  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 20

        382 TTTAGAAGCA

                       **       
        392 ATTAATTAAAAGCATTAAAC
          1 ATTAATTAAAAAAATTAAAC

                              
        412 ATTAATTAAAAAAATTAA
          1 ATTAATTAAAAAAATTAA

        430 GGAATGTGTA


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   16  1.00

ACGTcount: A:0.61, C:0.05, G:0.03, T:0.32


Consensus pattern (20 bp):   
ATTAATTAAAAAAATTAAAC

Found at i:524 original size:74 final size:74

Alignment explanation


    Indices: 435--586  Score: 252
    Period size: 74  Copynumber: 2.1  Consensus size: 74

        425 ATTAAGGAAT

                      *                *       *                             
        435 GTGTAATTACGAAAAAGGGTAGAAGGATAAGGAATGGGGGAAACTCATAGAGGGGCTTTTTAGTC
          1 GTGTAATTACAAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTTTAGTC

                      
        500 ATCC-GAAAA
         66 A-CCTGAAAA

                                          *                                  
        509 GTGTAATTACAAAAAAGGGTAGAAGGAAAATGAATAGGGGAAACTCATAGAGGGGCTTTTTAGTC
          1 GTGTAATTACAAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTTTAGTC

                     
        574 ACCTGAAAA
         66 ACCTGAAAA

                
        583 GTGT
          1 GTGT

        587 GAAAAGACCA


Statistics
Matches: 73,  Mismatches: 4, Indels: 2
        0.92            0.05        0.03

Matches are distributed among these distances:
  73    2  0.03
  74   71  0.97

ACGTcount: A:0.39, C:0.09, G:0.30, T:0.22


Consensus pattern (74 bp):   
GTGTAATTACAAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTTTAGTC
ACCTGAAAA

Found at i:712 original size:51 final size:51

Alignment explanation


    Indices: 639--735  Score: 151
    Period size: 51  Copynumber: 1.9  Consensus size: 51

        629 TCAATTTGGT

                  *      *                        *            
        639 CTTTTAGTAATTTCCTATGTAGTTAAAAATAATATATAGTATATATTTGCC
          1 CTTTTAATAATTTACTATGTAGTTAAAAATAATATATAATATATATTTGCC

                                                           
        690 CTTTTAATAATTTAC-ATGGTAGTTAAAAATAATATATAATATATAT
          1 CTTTTAATAATTTACTAT-GTAGTTAAAAATAATATATAATATATAT

        736 ATATTATCAA


Statistics
Matches: 42,  Mismatches: 3, Indels: 2
        0.89            0.06        0.04

Matches are distributed among these distances:
  50    2  0.05
  51   40  0.95

ACGTcount: A:0.40, C:0.07, G:0.08, T:0.44


Consensus pattern (51 bp):   
CTTTTAATAATTTACTATGTAGTTAAAAATAATATATAATATATATTTGCC

Found at i:937 original size:31 final size:32

Alignment explanation


    Indices: 893--955  Score: 85
    Period size: 32  Copynumber: 2.0  Consensus size: 32

        883 ATTTTGTAAG

                                             
        893 CGGACCTTAAAA-TTTTGTCCAAACCCATCCAA
          1 CGGACCTTAAAATTTTTGTCCAAACCC-TCCAA

                    *           *           
        925 CGGA-CTTCAAATTTTTGTCTAAACCCTCCAA
          1 CGGACCTTAAAATTTTTGTCCAAACCCTCCAA

        956 ATATCGGGTG


Statistics
Matches: 28,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  31   11  0.39
  32   17  0.61

ACGTcount: A:0.32, C:0.30, G:0.10, T:0.29


Consensus pattern (32 bp):   
CGGACCTTAAAATTTTTGTCCAAACCCTCCAA

Found at i:1351 original size:5 final size:5

Alignment explanation


    Indices: 1314--1350  Score: 65
    Period size: 5  Copynumber: 7.4  Consensus size: 5

       1304 GTGTACACGG

                                                  *     
       1314 GACAC GACAC GACAC GACAC GACAC GACAC GATAC GA
          1 GACAC GACAC GACAC GACAC GACAC GACAC GACAC GA

       1351 TTAAACCGTG


Statistics
Matches: 31,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
   5   31  1.00

ACGTcount: A:0.41, C:0.35, G:0.22, T:0.03


Consensus pattern (5 bp):   
GACAC

Found at i:1450 original size:12 final size:12

Alignment explanation


    Indices: 1435--1460  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       1425 AAACTATATA

                        
       1435 TATATATATAAT
          1 TATATATATAAT

                        
       1447 TATATATATAAT
          1 TATATATATAAT

              
       1459 TA
          1 TA

       1461 AAGATAATTG


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (12 bp):   
TATATATATAAT

Found at i:1636 original size:20 final size:21

Alignment explanation


    Indices: 1599--1641  Score: 61
    Period size: 20  Copynumber: 2.1  Consensus size: 21

       1589 TAACCGTTAA

                         *       
       1599 TTAAAGCGTGTCACTCGTGTC
          1 TTAAAGCGTGTCAATCGTGTC

                       *         
       1620 TTAAA-CGTGTTAATCGTGTC
          1 TTAAAGCGTGTCAATCGTGTC

              
       1640 TT
          1 TT

       1642 GACACGATTA


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  20   15  0.75
  21    5  0.25

ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40


Consensus pattern (21 bp):   
TTAAAGCGTGTCAATCGTGTC
Done.