Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001513.1 Corchorus capsularis cultivar CVL-1 contig01513, 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: 5933
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34


Found at i:2300 original size:2 final size:2

Alignment explanation


    Indices: 2295--2323  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       2285 CTATTACAAC

                                                       
       2295 AT AT 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 A

       2324 ACACAACATT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:3629 original size:2 final size:2

Alignment explanation


    Indices: 3622--3649  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       3612 TAACTTGTAA

                                                     
       3622 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       3650 CTTTATCTTT


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

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:3656 original size:6 final size:6

Alignment explanation


    Indices: 3647--3676  Score: 51
    Period size: 6  Copynumber: 5.0  Consensus size: 6

       3637 TATATATATA

                                         *    
       3647 TATCTT TATCTT TATCTT TATCTT TTTCTT
          1 TATCTT TATCTT TATCTT TATCTT TATCTT

       3677 CATATTATAT


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   6   23  1.00

ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70


Consensus pattern (6 bp):   
TATCTT

Found at i:5029 original size:42 final size:43

Alignment explanation


    Indices: 4981--5062  Score: 114
    Period size: 42  Copynumber: 1.9  Consensus size: 43

       4971 CACGACACGA

                            *            *              
       4981 TATCGTGTCTCGTGT-TTGAATCGTGTC-GGACACGATTAAGAT
          1 TATCGTGTCTCGTGTCGT-AATCGTGTCAAGACACGATTAAGAT

                    *                               
       5023 TATCGTGTTTCGTGTCGTAATCGTGTCAAGACACGATTAA
          1 TATCGTGTCTCGTGTCGTAATCGTGTCAAGACACGATTAA

       5063 CACGTTTAAG


Statistics
Matches: 35,  Mismatches: 3, Indels: 3
        0.85            0.07        0.07

Matches are distributed among these distances:
  42   23  0.66
  43   12  0.34

ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35


Consensus pattern (43 bp):   
TATCGTGTCTCGTGTCGTAATCGTGTCAAGACACGATTAAGAT

Found at i:5075 original size:20 final size:21

Alignment explanation


    Indices: 5050--5092  Score: 61
    Period size: 20  Copynumber: 2.1  Consensus size: 21

       5040 TAATCGTGTC

                     *           
       5050 AAGACACGATTAACACG-TTT
          1 AAGACACGAGTAACACGCTTT

                       *         
       5070 AAGACACGAGTGACACGCTTT
          1 AAGACACGAGTAACACGCTTT

              
       5091 AA
          1 AA

       5093 TTAACGGGTT


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


Consensus pattern (21 bp):   
AAGACACGAGTAACACGCTTT

Found at i:5913 original size:2 final size:2

Alignment explanation


    Indices: 5906--5933  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       5896 AAAGATAACT

                                                     
       5906 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA


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

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
TA

Done.