Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007824.1 Corchorus capsularis cultivar CVL-1 contig07845, 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: 27278
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33


Found at i:1376 original size:12 final size:12

Alignment explanation


    Indices: 1342--1384  Score: 61
    Period size: 12  Copynumber: 3.5  Consensus size: 12

       1332 AGGAGACAAA

                         
       1342 AATAATATATAGT
          1 AATAATATATA-T

                         
       1355 -ATATATATATAT
          1 AATA-ATATATAT

                        
       1367 AATAATATATAT
          1 AATAATATATAT

                  
       1379 AATAAT
          1 AATAAT

       1385 GAAAATAAAA


Statistics
Matches: 28,  Mismatches: 0, Indels: 5
        0.85            0.00        0.15

Matches are distributed among these distances:
  12   18  0.64
  13   10  0.36

ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42


Consensus pattern (12 bp):   
AATAATATATAT

Found at i:8110 original size:1 final size:1

Alignment explanation


    Indices: 8104--8132  Score: 58
    Period size: 1  Copynumber: 29.0  Consensus size: 1

       8094 TTTGTTCTCC

                                         
       8104 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT

       8133 GTGCAGATAC


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   28  1.00

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


Consensus pattern (1 bp):   
T

Found at i:11681 original size:58 final size:61

Alignment explanation


    Indices: 11578--11815  Score: 221
    Period size: 67  Copynumber: 3.7  Consensus size: 61

      11568 CACCTTCGAG

                           ***         **                                 
      11578 TACGATTCAAGGATCACACAATTTTTGGCAAAACGGTCTCGAGGGAGACGTTCG-T-C-TTT
          1 TACGATTCAAGGATCGTTCAA-TTTTGATAAAACGGTCTCGAGGGAGACGTTCGTTACTTTT

                                                                             
      11637 TACGATTCAAGGATCGTTCAATTTTGATAAAACGGTCTCGAGGGAGACGTTCGTCTTACTTAAAT
          1 TACGATTCAAGGATCGTTCAATTTTGATAAAACGGTCTCGAGGGAGACGTTCG--TTACTT---T

             
      11702 T
         61 T

              *             *  *       * *                                   
      11703 TATGATTCAAGGATCATTTTAATTTTGGTTAAACGGTCTCGAGGGAGACGTTCGTCTTACTTAAT
          1 TACGATTCAAGGATC-GTTCAATTTTGATAAAACGGTCTCGAGGGAGACGTTCG--TTAC-T--T

              
      11768 TT
         60 TT

                      *        *            *             
      11770 TACGATTCAAAGATCGTTTTAATTTTGATAAAGCGGTCTCGAGGGA
          1 TACGATTCAAGGATCG-TTCAATTTTGATAAAACGGTCTCGAGGGA

      11816 ACGAACGCAC


Statistics
Matches: 150,  Mismatches: 16, Indels: 18
        0.82            0.09        0.10

Matches are distributed among these distances:
  58   30  0.20
  59   18  0.12
  61    1  0.01
  62    1  0.01
  63    1  0.01
  66   16  0.11
  67   81  0.54
  68    1  0.01
  70    1  0.01

ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34


Consensus pattern (61 bp):   
TACGATTCAAGGATCGTTCAATTTTGATAAAACGGTCTCGAGGGAGACGTTCGTTACTTTT

Found at i:11747 original size:67 final size:66

Alignment explanation


    Indices: 11635--11815  Score: 256
    Period size: 67  Copynumber: 2.7  Consensus size: 66

      11625 ACGTTCGTCT

                             *  *       * *                                  
      11635 TTTACGATTCAAGGATCGTTCAATTTTGATAAAACGGTCTCGAGGGAGACGTTCGTCTTACTTAA
          1 TTTACGATTCAAGGATCTTTTAATTTTGGTTAAACGGTCTCGAGGGAGACGTTCGTCTTACTTAA

             
      11700 A
         66 A

                *                                                            
      11701 TTTATGATTCAAGGATCATTTTAATTTTGGTTAAACGGTCTCGAGGGAGACGTTCGTCTTACTTA
          1 TTTACGATTCAAGGATC-TTTTAATTTTGGTTAAACGGTCTCGAGGGAGACGTTCGTCTTACTTA

             *
      11766 AT
         65 AA

                        *                 *                  
      11768 TTTACGATTCAAAGATCGTTTTAATTTT-GATAAAGCGGTCTCGAGGGA
          1 TTTACGATTCAAGGATC-TTTTAATTTTGGTTAAA-CGGTCTCGAGGGA

      11816 ACGAACGCAC


Statistics
Matches: 103,  Mismatches: 10, Indels: 3
        0.89            0.09        0.03

Matches are distributed among these distances:
  66   21  0.20
  67   82  0.80

ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36


Consensus pattern (66 bp):   
TTTACGATTCAAGGATCTTTTAATTTTGGTTAAACGGTCTCGAGGGAGACGTTCGTCTTACTTAA
A

Found at i:21378 original size:29 final size:29

Alignment explanation


    Indices: 21318--21388  Score: 88
    Period size: 29  Copynumber: 2.4  Consensus size: 29

      21308 ACACCGAACC

                            *   *   **** 
      21318 GTCAAATAAGCCCCTGTACTTTTATTTCA
          1 GTCAAATAAGCCCCTGAACTCTTAAAAAA

                                         
      21347 GTCAAATAAGCCCCTGAACTCTTAAAAAA
          1 GTCAAATAAGCCCCTGAACTCTTAAAAAA

                         
      21376 GTCAAATAAGCCC
          1 GTCAAATAAGCCC

      21389 TGTTTCCAAG


Statistics
Matches: 36,  Mismatches: 6, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  29   36  1.00

ACGTcount: A:0.37, C:0.25, G:0.11, T:0.27


Consensus pattern (29 bp):   
GTCAAATAAGCCCCTGAACTCTTAAAAAA
Done.