Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008862.1 Corchorus capsularis cultivar CVL-1 contig08883, 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: 32955
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32


Found at i:90 original size:19 final size:19

Alignment explanation


    Indices: 50--90  Score: 57
    Period size: 19  Copynumber: 2.2  Consensus size: 19

         40 GACCCTCTCC

                     *         
         50 TTTCATTTTTCCTCTTTTT
          1 TTTCATTTTCCCTCTTTTT

                                
         69 TTTCTATTTTCCCT-TTTTT
          1 TTTC-ATTTTCCCTCTTTTT

               
         88 TTT
          1 TTT

         91 GCTAAGAACG


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  19   12  0.60
  20    8  0.40

ACGTcount: A:0.05, C:0.20, G:0.00, T:0.76


Consensus pattern (19 bp):   
TTTCATTTTCCCTCTTTTT

Found at i:8976 original size:32 final size:32

Alignment explanation


    Indices: 8935--8998  Score: 128
    Period size: 32  Copynumber: 2.0  Consensus size: 32

       8925 CCCTCCCCTT

                                            
       8935 TCCTTTCTTTTCCTTCAAAAACTTGAATCCAA
          1 TCCTTTCTTTTCCTTCAAAAACTTGAATCCAA

                                            
       8967 TCCTTTCTTTTCCTTCAAAAACTTGAATCCAA
          1 TCCTTTCTTTTCCTTCAAAAACTTGAATCCAA

       8999 GGCGATAATA


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  32   32  1.00

ACGTcount: A:0.28, C:0.28, G:0.03, T:0.41


Consensus pattern (32 bp):   
TCCTTTCTTTTCCTTCAAAAACTTGAATCCAA

Found at i:23243 original size:2 final size:2

Alignment explanation


    Indices: 23236--23264  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

      23226 GAAAATATTT

                                                       
      23236 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      23265 CTGCATAGAA


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:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:26707 original size:36 final size:36

Alignment explanation


    Indices: 26667--26738  Score: 108
    Period size: 36  Copynumber: 2.0  Consensus size: 36

      26657 CTAAACAACC

                          *                     
      26667 GAAACCATAACAATGAACACACATAAATTTAACACA
          1 GAAACCATAACAATCAACACACATAAATTTAACACA

                    **          *               
      26703 GAAACCATCGCAATCAACACCCATAAATTTAACACA
          1 GAAACCATAACAATCAACACACATAAATTTAACACA

      26739 TTCATCGAGA


Statistics
Matches: 32,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  36   32  1.00

ACGTcount: A:0.51, C:0.26, G:0.06, T:0.17


Consensus pattern (36 bp):   
GAAACCATAACAATCAACACACATAAATTTAACACA

Found at i:31446 original size:21 final size:20

Alignment explanation


    Indices: 31409--31447  Score: 60
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      31399 TTTAGAAGCA

                       *        
      31409 ATTAATTAAAAGCATTAAAC
          1 ATTAATTAAAAACATTAAAC

                               
      31429 ATTAATTAAAAACAATTAA
          1 ATTAATTAAAAAC-ATTAA

      31448 GGAAGGGAGA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  20   12  0.71
  21    5  0.29

ACGTcount: A:0.59, C:0.08, G:0.03, T:0.31


Consensus pattern (20 bp):   
ATTAATTAAAAACATTAAAC

Found at i:31531 original size:95 final size:95

Alignment explanation


    Indices: 31368--31562  Score: 383
    Period size: 95  Copynumber: 2.1  Consensus size: 95

      31358 AGCGAGAGAA

                                                                             
      31368 ACATTAATTAAAAGTAATTAAGGGTTTAGAGTTTAGAAGCAATTAATTAAAAGCATTAAACATTA
          1 ACATTAATTAAAAGTAATTAAGGGTTTAGAGTTTAGAAGCAATTAATTAAAAGCATTAAACATTA

                                          
      31433 ATTAAAAACAATTAAGGAAGGGAGATGTGT
         66 ATTAAAAACAATTAAGGAAGGGAGATGTGT

                                                                             
      31463 ACATTAATTAAAAGTAATTAAGGGTTTAGAGTTTAGAAGCAATTAATTAAAAGCATTAAACATTA
          1 ACATTAATTAAAAGTAATTAAGGGTTTAGAGTTTAGAAGCAATTAATTAAAAGCATTAAACATTA

                                          
      31528 ATTAAAAACAATTAAGGAAGGGAGATGTGT
         66 ATTAAAAACAATTAAGGAAGGGAGATGTGT

                  
      31558 A-ATTA
          1 ACATTA

      31563 CGAAAAATGG


Statistics
Matches: 100,  Mismatches: 0, Indels: 1
        0.99            0.00        0.01

Matches are distributed among these distances:
  94    4  0.04
  95   96  0.96

ACGTcount: A:0.48, C:0.05, G:0.17, T:0.30


Consensus pattern (95 bp):   
ACATTAATTAAAAGTAATTAAGGGTTTAGAGTTTAGAAGCAATTAATTAAAAGCATTAAACATTA
ATTAAAAACAATTAAGGAAGGGAGATGTGT

Found at i:31541 original size:21 final size:20

Alignment explanation


    Indices: 31504--31542  Score: 60
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      31494 TTTAGAAGCA

                       *        
      31504 ATTAATTAAAAGCATTAAAC
          1 ATTAATTAAAAACATTAAAC

                               
      31524 ATTAATTAAAAACAATTAA
          1 ATTAATTAAAAAC-ATTAA

      31543 GGAAGGGAGA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  20   12  0.71
  21    5  0.29

ACGTcount: A:0.59, C:0.08, G:0.03, T:0.31


Consensus pattern (20 bp):   
ATTAATTAAAAACATTAAAC
Done.