Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020934.1 Corchorus olitorius cultivar O-4 contig20967, 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: 12536
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34


Found at i:4701 original size:21 final size:21

Alignment explanation


    Indices: 4672--4718  Score: 85
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       4662 GTTGTGTGCT

                *                
       4672 TCTCAATTAGCACTTCAACAA
          1 TCTCTATTAGCACTTCAACAA

                                 
       4693 TCTCTATTAGCACTTCAACAA
          1 TCTCTATTAGCACTTCAACAA

                 
       4714 TCTCT
          1 TCTCT

       4719 GGAAACCAAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  21   25  1.00

ACGTcount: A:0.32, C:0.30, G:0.04, T:0.34


Consensus pattern (21 bp):   
TCTCTATTAGCACTTCAACAA

Found at i:6538 original size:2 final size:2

Alignment explanation


    Indices: 6531--6559  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       6521 CCCACAAAAC

                                                       
       6531 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

       6560 GGTTTAATTA


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:7666 original size:31 final size:31

Alignment explanation


    Indices: 7630--7707  Score: 77
    Period size: 31  Copynumber: 2.5  Consensus size: 31

       7620 GCGGACCGGC

                            *               
       7630 TTTTTTATAGTTGTCCCG-CACTTGAAGAGTT
          1 TTTTTTATAGTTGT-CAGACACTTGAAGAGTT

                  * **                     
       7661 TTTTTTTTTTTTGTCAGACACTTGAAGAGTT
          1 TTTTTTATAGTTGTCAGACACTTGAAGAGTT

            *               
       7692 GTTTTTAGTATGTTGT
          1 TTTTTTA-TA-GTTGT

       7708 ACTTGGAATT


Statistics
Matches: 36,  Mismatches: 8, Indels: 4
        0.75            0.17        0.08

Matches are distributed among these distances:
  30    2  0.06
  31   29  0.81
  32    1  0.03
  33    4  0.11

ACGTcount: A:0.18, C:0.10, G:0.19, T:0.53


Consensus pattern (31 bp):   
TTTTTTATAGTTGTCAGACACTTGAAGAGTT

Found at i:9434 original size:127 final size:127

Alignment explanation


    Indices: 9208--9511  Score: 581
    Period size: 127  Copynumber: 2.4  Consensus size: 127

       9198 ACTTGGTTAA

                       *                         *                           
       9208 TTACTAAGAAGGCCCTCAATTAGTTTCTCACCATTCCCTTTTCCTCCAACCCTTTTTCGTAATTG
          1 TTACTAAGAAGTCCCTCAATTAGTTTCTCACCATTCCTTTTTCCTCCAACCCTTTTTCGTAATTG

                                                                          
       9273 CAAAGGTTTCAACCAGTTGAATGTGAAAGCATTTATTAACCATAAAATCATGTATTATTTAT
         66 CAAAGGTTTCAACCAGTTGAATGTGAAAGCATTTATTAACCATAAAATCATGTATTATTTAT

                                                                             
       9335 TTACTAAGAAGTCCCTCAATTAGTTTCTCACCATTCCTTTTTCCTCCAACCCTTTTTCGTAATTG
          1 TTACTAAGAAGTCCCTCAATTAGTTTCTCACCATTCCTTTTTCCTCCAACCCTTTTTCGTAATTG

                                                                          
       9400 CAAAGGTTTCAACCAGTTGAATGTGAAAGCATTTATTAACCATAAAATCATGTATTATTTAT
         66 CAAAGGTTTCAACCAGTTGAATGTGAAAGCATTTATTAACCATAAAATCATGTATTATTTAT

                                      *                       
       9462 TTACTAAGAAGTCCCTCAATTAGTTTTTCACCATTCCTTTTTCCTCCAAC
          1 TTACTAAGAAGTCCCTCAATTAGTTTCTCACCATTCCTTTTTCCTCCAAC

       9512 TTTATGAATT


Statistics
Matches: 174,  Mismatches: 3, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 127  174  1.00

ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38


Consensus pattern (127 bp):   
TTACTAAGAAGTCCCTCAATTAGTTTCTCACCATTCCTTTTTCCTCCAACCCTTTTTCGTAATTG
CAAAGGTTTCAACCAGTTGAATGTGAAAGCATTTATTAACCATAAAATCATGTATTATTTAT
Done.