Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015581.1 Corchorus capsularis cultivar CVL-1 contig15602, 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: 15211
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29


Found at i:1799 original size:21 final size:21

Alignment explanation


    Indices: 1775--1823  Score: 64
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       1765 CAGCTGGGGG

                                 *
       1775 CCCATGTGGTATG-CTTGGCGC
          1 CCCATGTGGTATGCCTT-GCGA

                      *          
       1796 CCCATGTGGTTTGCCTTGCGA
          1 CCCATGTGGTATGCCTTGCGA

                   
       1817 CCCATGT
          1 CCCATGT

       1824 CCTCCAATGC


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  21   22  0.88
  22    3  0.12

ACGTcount: A:0.10, C:0.31, G:0.29, T:0.31


Consensus pattern (21 bp):   
CCCATGTGGTATGCCTTGCGA

Found at i:5003 original size:27 final size:27

Alignment explanation


    Indices: 4973--5044  Score: 108
    Period size: 27  Copynumber: 2.7  Consensus size: 27

       4963 AGGGTCATCT

                                       
       4973 AGGGGCATTTTGGTCATTTTCACATTC
          1 AGGGGCATTTTGGTCATTTTCACATTC

                                **    *
       5000 AGGGGCATTTTGGTCATTTTTGCATTT
          1 AGGGGCATTTTGGTCATTTTCACATTC

                 *            
       5027 AGGGGTATTTTGGTCATT
          1 AGGGGCATTTTGGTCATT

       5045 CTTAATCTAC


Statistics
Matches: 41,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  27   41  1.00

ACGTcount: A:0.17, C:0.12, G:0.26, T:0.44


Consensus pattern (27 bp):   
AGGGGCATTTTGGTCATTTTCACATTC

Found at i:5578 original size:20 final size:20

Alignment explanation


    Indices: 5539--5579  Score: 55
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       5529 ATGAATACAA

                          **    
       5539 GGCATTTGATTTACGGATTG
          1 GGCATTTGATTTACAAATTG

                        *       
       5559 GGCATTTGATTTGCAAATTG
          1 GGCATTTGATTTACAAATTG

             
       5579 G
          1 G

       5580 TGCTTTTTTT


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.22, C:0.10, G:0.29, T:0.39


Consensus pattern (20 bp):   
GGCATTTGATTTACAAATTG

Found at i:6374 original size:10 final size:11

Alignment explanation


    Indices: 6341--6381  Score: 57
    Period size: 11  Copynumber: 3.7  Consensus size: 11

       6331 AACACCAAAA

                        
       6341 ACAGAGACAATT
          1 ACAGAG-CAATT

                 *     
       6353 ACAGATCAATT
          1 ACAGAGCAATT

                       
       6364 ACAG-GCAATT
          1 ACAGAGCAATT

                    
       6374 ACAGAGCA
          1 ACAGAGCA

       6382 TCAATACAGC


Statistics
Matches: 26,  Mismatches: 2, Indels: 3
        0.84            0.06        0.10

Matches are distributed among these distances:
  10    9  0.35
  11   12  0.46
  12    5  0.19

ACGTcount: A:0.46, C:0.20, G:0.17, T:0.17


Consensus pattern (11 bp):   
ACAGAGCAATT

Found at i:9545 original size:21 final size:21

Alignment explanation


    Indices: 9519--9571  Score: 54
    Period size: 21  Copynumber: 2.5  Consensus size: 21

       9509 CCCTTCTTGA

                                  
       9519 TCAAATCATCATCAA-AGCTCT
          1 TCAAATCATCATCAATAG-TCT

                  * * *          
       9540 TCAAATGAACCTCAATAGTCT
          1 TCAAATCATCATCAATAGTCT

               *       
       9561 TCATATCATCA
          1 TCAAATCATCA

       9572 AGATGAGTTC


Statistics
Matches: 24,  Mismatches: 7, Indels: 2
        0.73            0.21        0.06

Matches are distributed among these distances:
  21   22  0.92
  22    2  0.08

ACGTcount: A:0.38, C:0.26, G:0.06, T:0.30


Consensus pattern (21 bp):   
TCAAATCATCATCAATAGTCT

Found at i:13678 original size:24 final size:24

Alignment explanation


    Indices: 13665--13716  Score: 86
    Period size: 24  Copynumber: 2.2  Consensus size: 24

      13655 AGTGGGGATG

                                    
      13665 AAGTCAGTGAAGAGAGAAGGAATC
          1 AAGTCAGTGAAGAGAGAAGGAATC

                 *                 *
      13689 AAGTCCGTGAAGAGAGAAGGAATG
          1 AAGTCAGTGAAGAGAGAAGGAATC

                
      13713 AAGT
          1 AAGT

      13717 GAGGAAAAAA


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  24   26  1.00

ACGTcount: A:0.44, C:0.08, G:0.35, T:0.13


Consensus pattern (24 bp):   
AAGTCAGTGAAGAGAGAAGGAATC

Found at i:14992 original size:30 final size:31

Alignment explanation


    Indices: 14918--15010  Score: 118
    Period size: 33  Copynumber: 2.9  Consensus size: 31

      14908 TCCGGAAGGC

                                             
      14918 CCAATCGATGGCCGGTTGTGGCCGGTTGGTGCA
          1 CCAATCGATGGCCGGTTGTGGCCGG-T-GTGCA

                                          *
      14951 CCAATCGATGGCCGGTTGTGGCCGGT-TGCT
          1 CCAATCGATGGCCGGTTGTGGCCGGTGTGCA

                                           
      14981 CC-ATGCGATGGCCGGTCATGTGGCCGGTGT
          1 CCAAT-CGATGGCCGGT--TGTGGCCGGTGT

      15011 TGCGCGGCTT


Statistics
Matches: 55,  Mismatches: 1, Indels: 8
        0.86            0.02        0.12

Matches are distributed among these distances:
  29    2  0.04
  30   16  0.29
  32   11  0.20
  33   26  0.47

ACGTcount: A:0.11, C:0.26, G:0.39, T:0.25


Consensus pattern (31 bp):   
CCAATCGATGGCCGGTTGTGGCCGGTGTGCA
Done.