Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007842.1 Corchorus capsularis cultivar CVL-1 contig07863, 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: 50073
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33


Found at i:1302 original size:29 final size:28

Alignment explanation


    Indices: 1259--1316  Score: 89
    Period size: 29  Copynumber: 2.0  Consensus size: 28

       1249 GTTACCAACC

                               *         
       1259 ATTAGTATAGCACCTAATATTGAATTTTG
          1 ATTAGTATAGCACCT-ATAATGAATTTTG

                      *                 
       1288 ATTAGTATAGTACCTATAATGAATTTTG
          1 ATTAGTATAGCACCTATAATGAATTTTG

             
       1316 A
          1 A

       1317 GGTTTCATAT


Statistics
Matches: 27,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
  28   13  0.48
  29   14  0.52

ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41


Consensus pattern (28 bp):   
ATTAGTATAGCACCTATAATGAATTTTG

Found at i:3947 original size:20 final size:20

Alignment explanation


    Indices: 3924--3961  Score: 76
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       3914 CTTAACTCAA

                                
       3924 AAAAAAAAAACTAAAAACTT
          1 AAAAAAAAAACTAAAAACTT

                              
       3944 AAAAAAAAAACTAAAAAC
          1 AAAAAAAAAACTAAAAAC

       3962 AATGAACCTT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.79, C:0.11, G:0.00, T:0.11


Consensus pattern (20 bp):   
AAAAAAAAAACTAAAAACTT

Found at i:5372 original size:21 final size:21

Alignment explanation


    Indices: 5343--5391  Score: 89
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       5333 TTACCCAATT

                *                
       5343 AACTTAACATTTATGTAACAA
          1 AACTAAACATTTATGTAACAA

                                 
       5364 AACTAAACATTTATGTAACAA
          1 AACTAAACATTTATGTAACAA

                   
       5385 AACTAAA
          1 AACTAAA

       5392 GAAGAGAAAT


Statistics
Matches: 27,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  21   27  1.00

ACGTcount: A:0.53, C:0.14, G:0.04, T:0.29


Consensus pattern (21 bp):   
AACTAAACATTTATGTAACAA

Found at i:14416 original size:2 final size:2

Alignment explanation


    Indices: 14409--14447  Score: 62
    Period size: 2  Copynumber: 19.5  Consensus size: 2

      14399 TCTTATGATC

                                                                       
      14409 TA TA TA TA TA TA TA TA GTA TA -A TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA T

      14448 TCTTACCTAA


Statistics
Matches: 35,  Mismatches: 0, Indels: 4
        0.90            0.00        0.10

Matches are distributed among these distances:
   1    1  0.03
   2   32  0.91
   3    2  0.06

ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:14923 original size:73 final size:74

Alignment explanation


    Indices: 14818--14965  Score: 253
    Period size: 74  Copynumber: 2.0  Consensus size: 74

      14808 TCTGAACGAA

                    *                  *                   *                 
      14818 TTAAGGCATTTTGTATTTTTGTAGGTAGAATAAAAT-AAAAAGAATTTGTATTTTTAGTAGTACT
          1 TTAAGGCAATTTGTATTTTTGTAGGTAAAATAAAATAAAAAAGAATTAGTATTTTTAGTAGTACT

                     
      14882 ACTATCATT
         66 ACTATCATT

                                                      *                      
      14891 TTAAGGCAATTTGTATTTTTGTAGGTAAAATAAAATAAAAAATAATTAGTATTTTTAGTAGTACT
          1 TTAAGGCAATTTGTATTTTTGTAGGTAAAATAAAATAAAAAAGAATTAGTATTTTTAGTAGTACT

                     
      14956 ACTATCATT
         66 ACTATCATT

             
      14965 T
          1 T

      14966 ATTCATTATA


Statistics
Matches: 70,  Mismatches: 4, Indels: 1
        0.93            0.05        0.01

Matches are distributed among these distances:
  73   34  0.49
  74   36  0.51

ACGTcount: A:0.38, C:0.05, G:0.14, T:0.43


Consensus pattern (74 bp):   
TTAAGGCAATTTGTATTTTTGTAGGTAAAATAAAATAAAAAAGAATTAGTATTTTTAGTAGTACT
ACTATCATT

Found at i:41001 original size:1 final size:1

Alignment explanation


    Indices: 40995--41020  Score: 52
    Period size: 1  Copynumber: 26.0  Consensus size: 1

      40985 GTGTTCGCAT

                                      
      40995 AAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAA

      41021 GAAGAAGTAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   25  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Done.