Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008694.1 Corchorus capsularis cultivar CVL-1 contig08715, 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: 6016
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30


Found at i:3765 original size:19 final size:20

Alignment explanation


    Indices: 3739--3787  Score: 75
    Period size: 18  Copynumber: 2.5  Consensus size: 20

       3729 CGCAAACCCT

                                
       3739 AATTTTTTTTT-TCGACAC-
          1 AATTTTTTTTTCTCGACACA

                             *  
       3757 AATTTTTTTTTCTCGACGCA
          1 AATTTTTTTTTCTCGACACA

                       
       3777 AATTTTTTTTT
          1 AATTTTTTTTT

       3788 ATAGAAAAGA


Statistics
Matches: 28,  Mismatches: 1, Indels: 2
        0.90            0.03        0.06

Matches are distributed among these distances:
  18   11  0.39
  19    6  0.21
  20   11  0.39

ACGTcount: A:0.20, C:0.14, G:0.06, T:0.59


Consensus pattern (20 bp):   
AATTTTTTTTTCTCGACACA

Found at i:4117 original size:6 final size:6

Alignment explanation


    Indices: 4101--4155  Score: 103
    Period size: 6  Copynumber: 9.3  Consensus size: 6

       4091 CAAAGCAAAA

                                                                   
       4101 TAAAT- TAAATC TAAATC TAAATC TAAATC TAAATC TAAATC TAAATC
          1 TAAATC TAAATC TAAATC TAAATC TAAATC TAAATC TAAATC TAAATC

                     
       4148 TAAATC TA
          1 TAAATC TA

       4156 TGGCAATTAT


Statistics
Matches: 49,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
   5    5  0.10
   6   44  0.90

ACGTcount: A:0.51, C:0.15, G:0.00, T:0.35


Consensus pattern (6 bp):   
TAAATC

Found at i:5520 original size:22 final size:21

Alignment explanation


    Indices: 5490--5548  Score: 61
    Period size: 19  Copynumber: 2.9  Consensus size: 21

       5480 AATTCTTGCT

                *                *
       5490 TCTTGAAATAATTCTTCAATTG
          1 TCTTCAAATAA-TCTTCAATTA

                                  
       5512 TCTTC--A-AATCTTCAAATTA
          1 TCTTCAAATAATCTTC-AATTA

                              
       5531 TCTTCAAATAATCTTCAA
          1 TCTTCAAATAATCTTCAA

       5549 ACACGAACTT


Statistics
Matches: 31,  Mismatches: 2, Indels: 9
        0.74            0.05        0.21

Matches are distributed among these distances:
  18    5  0.16
  19   11  0.35
  20    1  0.03
  21    3  0.10
  22   11  0.35

ACGTcount: A:0.36, C:0.19, G:0.03, T:0.42


Consensus pattern (21 bp):   
TCTTCAAATAATCTTCAATTA

Found at i:5535 original size:11 final size:11

Alignment explanation


    Indices: 5518--5549  Score: 55
    Period size: 11  Copynumber: 2.9  Consensus size: 11

       5508 ATTGTCTTCA

                       
       5518 AATCTTCAAAT
          1 AATCTTCAAAT

            *          
       5529 TATCTTCAAAT
          1 AATCTTCAAAT

                      
       5540 AATCTTCAAA
          1 AATCTTCAAA

       5550 CACGAACTTC


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  11   19  1.00

ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38


Consensus pattern (11 bp):   
AATCTTCAAAT

Found at i:5549 original size:22 final size:22

Alignment explanation


    Indices: 5490--5549  Score: 65
    Period size: 22  Copynumber: 2.9  Consensus size: 22

       5480 AATTCTTGCT

                *                 *
       5490 TCTTGAAATAATTCTTC-AATTG
          1 TCTTCAAATAA-TCTTCAAATTA

                                  
       5512 TCTTC--A-AATCTTCAAATTA
          1 TCTTCAAATAATCTTCAAATTA

                               
       5531 TCTTCAAATAATCTTCAAA
          1 TCTTCAAATAATCTTCAAA

       5550 CACGAACTTC


Statistics
Matches: 32,  Mismatches: 2, Indels: 8
        0.76            0.05        0.19

Matches are distributed among these distances:
  18    5  0.16
  19   11  0.34
  20    1  0.03
  21    1  0.03
  22   14  0.44

ACGTcount: A:0.37, C:0.18, G:0.03, T:0.42


Consensus pattern (22 bp):   
TCTTCAAATAATCTTCAAATTA
Done.