Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015919.1 Corchorus olitorius cultivar O-4 contig15952, 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: 16003
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34


Found at i:663 original size:15 final size:14

Alignment explanation


    Indices: 640--669  Score: 51
    Period size: 15  Copynumber: 2.1  Consensus size: 14

        630 ATAAAAATTA

                          
        640 AATATTTTTATTTT
          1 AATATTTTTATTTT

                           
        654 AATATATTTTATTTT
          1 AATAT-TTTTATTTT

             
        669 A
          1 A

        670 TTGAAATTTA


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    5  0.33
  15   10  0.67

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (14 bp):   
AATATTTTTATTTT

Found at i:1499 original size:15 final size:15

Alignment explanation


    Indices: 1467--1496  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       1457 TAAATTTCAA

                           
       1467 TAAAATAAAATATAT
          1 TAAAATAAAATATAT

                           
       1482 TAAAATAAAA-ATAT
          1 TAAAATAAAATATAT

             
       1496 T
          1 T

       1497 TAATTTTTAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    5  0.33
  15   10  0.67

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (15 bp):   
TAAAATAAAATATAT

Found at i:3167 original size:22 final size:22

Alignment explanation


    Indices: 3128--3170  Score: 61
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       3118 TTAAATAACC

                                  
       3128 AAAATCGAAAATGAAATTAAAA
          1 AAAATCGAAAATGAAATTAAAA

                          *       
       3150 AAAATTCGAAAAT-TAATTAAA
          1 AAAA-TCGAAAATGAAATTAAA

       3171 CAGAAGCCAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  22   11  0.58
  23    8  0.42

ACGTcount: A:0.65, C:0.05, G:0.07, T:0.23


Consensus pattern (22 bp):   
AAAATCGAAAATGAAATTAAAA

Found at i:9012 original size:2 final size:2

Alignment explanation


    Indices: 9007--9049  Score: 86
    Period size: 2  Copynumber: 21.5  Consensus size: 2

       8997 AAAAACCAAG

                                                                          
       9007 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA

             
       9049 T
          1 T

       9050 TGATTGTAGC


Statistics
Matches: 41,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   41  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:12625 original size:1 final size:1

Alignment explanation


    Indices: 12619--12659  Score: 82
    Period size: 1  Copynumber: 41.0  Consensus size: 1

      12609 GACTTGTGTT

                                                     
      12619 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

      12660 CAACAACAAC


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   40  1.00

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


Consensus pattern (1 bp):   
A

Done.