Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010925.1 Corchorus capsularis cultivar CVL-1 contig10946, 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: 9014
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35


Found at i:832 original size:35 final size:36

Alignment explanation


    Indices: 786--855  Score: 124
    Period size: 35  Copynumber: 2.0  Consensus size: 36

        776 GATAAGTGGA

                                                
        786 CAATAAATTGGGTTTCCTTCGGA-TGATTTCTTGGG
          1 CAATAAATTGGGTTTCCTTCGGATTGATTTCTTGGG

                               *               
        821 CAATAAATTGGGTTTCCTTGGGATTGATTTCTTGG
          1 CAATAAATTGGGTTTCCTTCGGATTGATTTCTTGG

        856 TGATCCAAAG


Statistics
Matches: 33,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  35   22  0.67
  36   11  0.33

ACGTcount: A:0.20, C:0.13, G:0.26, T:0.41


Consensus pattern (36 bp):   
CAATAAATTGGGTTTCCTTCGGATTGATTTCTTGGG

Found at i:2843 original size:2 final size:2

Alignment explanation


    Indices: 2831--2861  Score: 53
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       2821 TACAAATAAG

                  *                                       
       2831 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       2862 AAGAAGTTAA


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:3754 original size:198 final size:195

Alignment explanation


    Indices: 3344--3751  Score: 581
    Period size: 198  Copynumber: 2.1  Consensus size: 195

       3334 AATTGAGCTT

                                                               *             
       3344 TTTCATAATTAATTAAATATTTAATATTAACACATATTCCCTAAGCCGACATATGTCAACCCTTA
          1 TTTCATAATTAATTAAATATTTAATATTAACACATATTCCCTAAGCCGACACATGTCAACCCTTA

              * *     *        *     *   ** *                                
       3409 AATCTCACACGTGCAGTCTTCTAAATTCCGTTGATGGTGTATTGTATAATTTTTCTTATATGATT
         66 AACCCCACACATGCAGTCTGCTAAACTCCACTAATGGTGTATTGTATAATTTTTCTTATATGATT

                                                       *        *            
       3474 ATTATACAATACACTGTAAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAGGTTGACACATAC
        131 ATTATACAATACACTGTAAGTGTAAATTTT-G--TCCATAAGCAGGTTAAGAAGTTGACACATAC

               
       3539 CCA
        193 CCA

                                          *              **  *               
       3542 TTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGATACATGTCAACCCTTA
          1 TTTCATAATTAATTAAATATTTAATATTAACACATATTCCCTAAGCCGACACATGTCAACCCTTA

                  *                                                          
       3607 AACCCCGCACATGCAGTCTGCTAAACTCCACTAACT-GTGTATTGTATAATTTTTCTTAT-TGTA
         66 AACCCCACACATGCAGTCTGCTAAACTCCACTAA-TGGTGTATTGTATAATTTTTCTTATATG-A

                               *                                             
       3670 TTATTATACAATACACTGTCAGTGTAAA-TTT-TCCATAAGCAGGTTAAGAAGTTGACACATACC
        129 TTATTATACAATACACTGTAAGTGTAAATTTTGTCCATAAGCAGGTTAAGAAGTTGACACATACC

               
       3733 TCA
        194 -CA

                            
       3736 TTTCATAATTAATTAA
          1 TTTCATAATTAATTAA

       3752 TTATATATAT


Statistics
Matches: 190,  Mismatches: 17, Indels: 10
        0.88            0.08        0.05

Matches are distributed among these distances:
 193   30  0.16
 194   18  0.09
 197    5  0.03
 198  136  0.72
 199    1  0.01

ACGTcount: A:0.34, C:0.18, G:0.12, T:0.37


Consensus pattern (195 bp):   
TTTCATAATTAATTAAATATTTAATATTAACACATATTCCCTAAGCCGACACATGTCAACCCTTA
AACCCCACACATGCAGTCTGCTAAACTCCACTAATGGTGTATTGTATAATTTTTCTTATATGATT
ATTATACAATACACTGTAAGTGTAAATTTTGTCCATAAGCAGGTTAAGAAGTTGACACATACCCA

Found at i:4637 original size:28 final size:28

Alignment explanation


    Indices: 4583--4637  Score: 76
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       4573 AGTAAGTATA

                                 **     
       4583 AAAATTAAGGATATTAATTGTGGTAATT
          1 AAAATTAAGGATATTAATTGTACTAATT

                                        
       4611 AAAATTAAGGATACTTAA-TGTACTAAT
          1 AAAATTAAGGATA-TTAATTGTACTAAT

       4638 ACATGTATTA


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  28   20  0.83
  29    4  0.17

ACGTcount: A:0.45, C:0.04, G:0.15, T:0.36


Consensus pattern (28 bp):   
AAAATTAAGGATATTAATTGTACTAATT

Found at i:5389 original size:22 final size:21

Alignment explanation


    Indices: 5341--5384  Score: 61
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       5331 TATAAAGCTT

                             *   
       5341 TATTTTAGTAATTGTATTAAG
          1 TATTTTAGTAATTGTATCAAG

                                   
       5362 TATTTTAGTAATTTGTTATCAAG
          1 TATTTTAGTAA-TTG-TATCAAG

       5385 CTTTTCACCA


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

Matches are distributed among these distances:
  21   11  0.55
  22    3  0.15
  23    6  0.30

ACGTcount: A:0.32, C:0.02, G:0.14, T:0.52


Consensus pattern (21 bp):   
TATTTTAGTAATTGTATCAAG
Done.