Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012522.1 Corchorus capsularis cultivar CVL-1 contig12543, 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: 35230
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30


Found at i:4767 original size:65 final size:65

Alignment explanation


    Indices: 4691--4814  Score: 185
    Period size: 65  Copynumber: 1.9  Consensus size: 65

       4681 CACAAGATAA

                  *      *                                    *              
       4691 TTGGAATTTGAGATCTTGTTTAAGGAGTATTGAATTCATTATACTCAACCCAACAAACAAGACTT
          1 TTGGAAGTTGAGACCTTGTTTAAGGAGTATTGAATTCATTATACTCAACCAAACAAACAAGACTT

                                      * *        *  *                  
       4756 TTGGAAGTTGAGACCTTGTTTAAGGATTGTTGAATTCGTTCTACTCAACCAAACAAACA
          1 TTGGAAGTTGAGACCTTGTTTAAGGAGTATTGAATTCATTATACTCAACCAAACAAACA

       4815 TATTGGTCTT


Statistics
Matches: 52,  Mismatches: 7, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  65   52  1.00

ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33


Consensus pattern (65 bp):   
TTGGAAGTTGAGACCTTGTTTAAGGAGTATTGAATTCATTATACTCAACCAAACAAACAAGACTT

Found at i:6464 original size:2 final size:2

Alignment explanation


    Indices: 6451--6493  Score: 77
    Period size: 2  Copynumber: 21.0  Consensus size: 2

       6441 GTTTATACTT

                                                                           
       6451 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       6494 AAGGCTAGCC


Statistics
Matches: 40,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   2   38  0.95
   3    2  0.05

ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:12836 original size:21 final size:21

Alignment explanation


    Indices: 12807--12848  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      12797 AATAATTACT

                            *    
      12807 TAAAAAAATGAAAAATTAAAA
          1 TAAAAAAATGAAAAATGAAAA

                *    *           
      12828 TAAAGAAATTAAAAATGAAAA
          1 TAAAAAAATGAAAAATGAAAA

      12849 GAAATTATTA


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19


Consensus pattern (21 bp):   
TAAAAAAATGAAAAATGAAAA

Found at i:14291 original size:71 final size:71

Alignment explanation


    Indices: 14175--14319  Score: 281
    Period size: 71  Copynumber: 2.0  Consensus size: 71

      14165 ATCTCACATG

                                                                             
      14175 AAAGTAAGGTTTAAAAGTTTGTTTAATTATCAAATAGAAATGCATCAAACCAACGTAAATCAAAA
          1 AAAGTAAGGTTTAAAAGTTTGTTTAATTATCAAATAGAAATGCATCAAACCAACGTAAATCAAAA

                  
      14240 CAATGT
         66 CAATGT

                                                                            *
      14246 AAAGTAAGGTTTAAAAGTTTGTTTAATTATCAAATAGAAATGCATCAAACCAACGTAAATCAAAC
          1 AAAGTAAGGTTTAAAAGTTTGTTTAATTATCAAATAGAAATGCATCAAACCAACGTAAATCAAAA

                  
      14311 CAATGT
         66 CAATGT

               
      14317 AAA
          1 AAA

      14320 CTCTCAAGAT


Statistics
Matches: 73,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  71   73  1.00

ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28


Consensus pattern (71 bp):   
AAAGTAAGGTTTAAAAGTTTGTTTAATTATCAAATAGAAATGCATCAAACCAACGTAAATCAAAA
CAATGT

Found at i:14307 original size:15 final size:15

Alignment explanation


    Indices: 14289--14319  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      14279 ATAGAAATGC

                           
      14289 ATCAAACCAACGTAA
          1 ATCAAACCAACGTAA

                      *    
      14304 ATCAAACCAATGTAA
          1 ATCAAACCAACGTAA

             
      14319 A
          1 A

      14320 CTCTCAAGAT


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.55, C:0.23, G:0.06, T:0.16


Consensus pattern (15 bp):   
ATCAAACCAACGTAA

Found at i:26380 original size:3 final size:3

Alignment explanation


    Indices: 26374--26402  Score: 58
    Period size: 3  Copynumber: 9.7  Consensus size: 3

      26364 TCATCATCAT

                                                  
      26374 CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
          1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CA

      26403 TCATCATCAT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   26  1.00

ACGTcount: A:0.34, C:0.66, G:0.00, T:0.00


Consensus pattern (3 bp):   
CAC

Found at i:26407 original size:3 final size:3

Alignment explanation


    Indices: 26401--26435  Score: 70
    Period size: 3  Copynumber: 11.7  Consensus size: 3

      26391 CCACCACCAC

                                                          
      26401 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
          1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA

      26436 AGGCTAGATT


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   32  1.00

ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31


Consensus pattern (3 bp):   
CAT

Done.