Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011871.1 Corchorus capsularis cultivar CVL-1 contig11892, 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: 11685
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33


Found at i:263 original size:22 final size:23

Alignment explanation


    Indices: 238--281  Score: 72
    Period size: 23  Copynumber: 2.0  Consensus size: 23

        228 TTTTCACTTA

                                   
        238 ATTACTA-TTACTTTGACTCTTG
          1 ATTACTATTTACTTTGACTCTTG

                       *          
        260 ATTACTATTTATTTTGACTCTT
          1 ATTACTATTTACTTTGACTCTT

        282 AATTTTTATT


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  22    7  0.35
  23   13  0.65

ACGTcount: A:0.23, C:0.16, G:0.07, T:0.55


Consensus pattern (23 bp):   
ATTACTATTTACTTTGACTCTTG

Found at i:1253 original size:16 final size:16

Alignment explanation


    Indices: 1232--1262  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       1222 CTAATTAACA

                            
       1232 ATATATAAAAAAATAT
          1 ATATATAAAAAAATAT

                   *       
       1248 ATATATATAAAAATA
          1 ATATATAAAAAAATA

       1263 AACAAGGCCG


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32


Consensus pattern (16 bp):   
ATATATAAAAAAATAT

Found at i:3758 original size:2 final size:2

Alignment explanation


    Indices: 3751--3822  Score: 64
    Period size: 2  Copynumber: 37.5  Consensus size: 2

       3741 TTTTAATTGA

                         *                                *                
       3751 AT AT AT AT AA AT AT AT AT AT AT AT A- AT AT AA AT GA- AT A- AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT

                   *                                          
       3791 -T AGT TT AT AT AT AT AT AT AT AT AT -T AT AT AT A
          1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       3823 CTACATATTA


Statistics
Matches: 57,  Mismatches: 6, Indels: 14
        0.74            0.08        0.18

Matches are distributed among these distances:
   1    5  0.09
   2   50  0.88
   3    2  0.04

ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46


Consensus pattern (2 bp):   
AT

Found at i:3834 original size:19 final size:19

Alignment explanation


    Indices: 3795--3834  Score: 55
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       3785 AATAATTAGT

                       *       
       3795 TTATATATATATATATATA
          1 TTATATATATACATATATA

                                
       3814 TTATATATACTACATAT-TA
          1 TTATATATA-TACATATATA

              
       3833 TT
          1 TT

       3835 TGAATAGAGT


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

Matches are distributed among these distances:
  19   13  0.68
  20    6  0.32

ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53


Consensus pattern (19 bp):   
TTATATATATACATATATA

Found at i:5148 original size:22 final size:22

Alignment explanation


    Indices: 5102--5146  Score: 74
    Period size: 21  Copynumber: 2.1  Consensus size: 22

       5092 ATAAAAATTC

                                  
       5102 TTCTTCTTCTTTTTTCCTTTTT
          1 TTCTTCTTCTTTTTTCCTTTTT

                            *     
       5124 TTCTT-TTCTTTTTTCTTTTTT
          1 TTCTTCTTCTTTTTTCCTTTTT

              
       5145 TT
          1 TT

       5147 TCAATTTTTA


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  21   17  0.77
  22    5  0.23

ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82


Consensus pattern (22 bp):   
TTCTTCTTCTTTTTTCCTTTTT

Found at i:5566 original size:43 final size:43

Alignment explanation


    Indices: 5503--5608  Score: 140
    Period size: 43  Copynumber: 2.5  Consensus size: 43

       5493 GATCTACATA

                           *        *      *  *        
       5503 TCTGACACTTCTGCCGATCTTCGATGTTTCTGTTTTCCTATAC
          1 TCTGACACTTCTGCCAATCTTCGAGGTTTCTATTCTCCTATAC

                                                     **
       5546 TCTGACACTTCTGCCAATCTTCGAGGTTTCTATTCTCCTATGT
          1 TCTGACACTTCTGCCAATCTTCGAGGTTTCTATTCTCCTATAC

                      *  *      
       5589 TCTGACACTTTTGGCAATCT
          1 TCTGACACTTCTGCCAATCT

       5609 ACAATGTTGT


Statistics
Matches: 55,  Mismatches: 8, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  43   55  1.00

ACGTcount: A:0.16, C:0.27, G:0.14, T:0.42


Consensus pattern (43 bp):   
TCTGACACTTCTGCCAATCTTCGAGGTTTCTATTCTCCTATAC

Found at i:7396 original size:36 final size:36

Alignment explanation


    Indices: 7356--7425  Score: 131
    Period size: 36  Copynumber: 1.9  Consensus size: 36

       7346 ATAAAAAACT

                                                
       7356 CTGACGGAAATGTTGTCAACCATGAATCTGAAAAAA
          1 CTGACGGAAATGTTGTCAACCATGAATCTGAAAAAA

                   *                          
       7392 CTGACGGGAATGTTGTCAACCATGAATCTGAAAA
          1 CTGACGGAAATGTTGTCAACCATGAATCTGAAAA

       7426 GGCAAAATTG


Statistics
Matches: 33,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  36   33  1.00

ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23


Consensus pattern (36 bp):   
CTGACGGAAATGTTGTCAACCATGAATCTGAAAAAA
Done.