Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005849.1 Corchorus capsularis cultivar CVL-1 contig05867, 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: 9657
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30


Found at i:5394 original size:21 final size:21

Alignment explanation


    Indices: 5364--5403  Score: 71
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       5354 GGCATTGGTG

                                 
       5364 TTGAGACAAACTATAGCTCAC
          1 TTGAGACAAACTATAGCTCAC

                 *             
       5385 TTGAGGCAAACTATAGCTC
          1 TTGAGACAAACTATAGCTC

       5404 TCACCTTGTC


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25


Consensus pattern (21 bp):   
TTGAGACAAACTATAGCTCAC

Found at i:5502 original size:64 final size:65

Alignment explanation


    Indices: 5385--5536  Score: 225
    Period size: 64  Copynumber: 2.3  Consensus size: 65

       5375 TATAGCTCAC

                 *                                       *  *                
       5385 TTGAGGCAAACTATAGCTCTCACCTTGTCTTTATTTACAAAAGGTTCAGTTTGTGGCAAGGCATT
          1 TTGAGACAAACTATAGCTCTCA-C---TCTTTATTTACAAAAGGTCCACTTTGTGGCAAGGCATT

                
       5450 GGTG
         62 GGTG

                                                                *            
       5454 TTGAGACAAACTATAGCTCTCA-TCTTTATTTACAAAAGGTCCACTTTGTGGTAAGGCATTGGTG
          1 TTGAGACAAACTATAGCTCTCACTCTTTATTTACAAAAGGTCCACTTTGTGGCAAGGCATTGGTG

                               
       5518 TTGAGACAAACTATAGCTC
          1 TTGAGACAAACTATAGCTC

       5537 ACTTGAGGCA


Statistics
Matches: 79,  Mismatches: 4, Indels: 5
        0.90            0.05        0.06

Matches are distributed among these distances:
  64   58  0.73
  69   21  0.27

ACGTcount: A:0.28, C:0.18, G:0.21, T:0.34


Consensus pattern (65 bp):   
TTGAGACAAACTATAGCTCTCACTCTTTATTTACAAAAGGTCCACTTTGTGGCAAGGCATTGGTG

Found at i:5548 original size:21 final size:21

Alignment explanation


    Indices: 5518--5557  Score: 71
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       5508 GGCATTGGTG

                                 
       5518 TTGAGACAAACTATAGCTCAC
          1 TTGAGACAAACTATAGCTCAC

                 *             
       5539 TTGAGGCAAACTATAGCTC
          1 TTGAGACAAACTATAGCTC

       5558 TCACCTTATC


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25


Consensus pattern (21 bp):   
TTGAGACAAACTATAGCTCAC

Found at i:5604 original size:90 final size:91

Alignment explanation


    Indices: 5475--5717  Score: 398
    Period size: 91  Copynumber: 2.7  Consensus size: 91

       5465 TATAGCTCTC

                                          *                 *                
       5475 ATCTTTATTTACAAAAGGTCCACTTTGTGGTAAGGCATTGGTGTTGAGACAAACTATAGCTCACT
          1 ATCTTTATTTACAAAAGGTCCACTTTGTGGCAAGGCATTGGTGTTGAGGCAAACTATAGCTCACT

                *                     
       5540 TGAGGC-AAACTATAGCTCTCACCTT
         66 TGAGCCAAAACTATAGCTCTCACCTT

                            *                 *                              
       5565 ATCTTTATTTACAAAAAGTCCACTTTGTGGCAAGACATTGGTGTTGAGGCAAACTATAGCTCACT
          1 ATCTTTATTTACAAAAGGTCCACTTTGTGGCAAGGCATTGGTGTTGAGGCAAACTATAGCTCACT

                      *         *     
       5630 TGAGCCAAAAGTATAGCTCTTACCTT
         66 TGAGCCAAAACTATAGCTCTCACCTT

            **                                                            
       5656 GCCTTTATTTACAAAAGGTCCACTTTGTGGCAAGGCATTGGTGTTGAGGCAAACTATAGCTC
          1 ATCTTTATTTACAAAAGGTCCACTTTGTGGCAAGGCATTGGTGTTGAGGCAAACTATAGCTC

       5718 TCACCTTGTC


Statistics
Matches: 141,  Mismatches: 11, Indels: 1
        0.92            0.07        0.01

Matches are distributed among these distances:
  90   66  0.47
  91   75  0.53

ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32


Consensus pattern (91 bp):   
ATCTTTATTTACAAAAGGTCCACTTTGTGGCAAGGCATTGGTGTTGAGGCAAACTATAGCTCACT
TGAGCCAAAACTATAGCTCTCACCTT

Found at i:5618 original size:154 final size:154

Alignment explanation


    Indices: 5333--5626  Score: 525
    Period size: 154  Copynumber: 1.9  Consensus size: 154

       5323 TTACTATTAT

                                                                             
       5333 AAAAGGTCCACTTTGTGGCAAGGCATTGGTGTTGAGACAAACTATAGCTCACTTGAGGCAAACTA
          1 AAAAGGTCCACTTTGTGGCAAGGCATTGGTGTTGAGACAAACTATAGCTCACTTGAGGCAAACTA

                         *               *  *  *           *                 
       5398 TAGCTCTCACCTTGTCTTTATTTACAAAAGGTTCAGTTTGTGGCAAGGCATTGGTGTTGAGACAA
         66 TAGCTCTCACCTTATCTTTATTTACAAAAAGTCCACTTTGTGGCAAGACATTGGTGTTGAGACAA

                                    
       5463 ACTATAGCTCTCATCTTTATTTAC
        131 ACTATAGCTCTCATCTTTATTTAC

                              *                                              
       5487 AAAAGGTCCACTTTGTGGTAAGGCATTGGTGTTGAGACAAACTATAGCTCACTTGAGGCAAACTA
          1 AAAAGGTCCACTTTGTGGCAAGGCATTGGTGTTGAGACAAACTATAGCTCACTTGAGGCAAACTA

                                                                         *   
       5552 TAGCTCTCACCTTATCTTTATTTACAAAAAGTCCACTTTGTGGCAAGACATTGGTGTTGAGGCAA
         66 TAGCTCTCACCTTATCTTTATTTACAAAAAGTCCACTTTGTGGCAAGACATTGGTGTTGAGACAA

                      
       5617 ACTATAGCTC
        131 ACTATAGCTC

       5627 ACTTGAGCCA


Statistics
Matches: 133,  Mismatches: 7, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
 154  133  1.00

ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31


Consensus pattern (154 bp):   
AAAAGGTCCACTTTGTGGCAAGGCATTGGTGTTGAGACAAACTATAGCTCACTTGAGGCAAACTA
TAGCTCTCACCTTATCTTTATTTACAAAAAGTCCACTTTGTGGCAAGACATTGGTGTTGAGACAA
ACTATAGCTCTCATCTTTATTTAC

Done.