Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014785.1 Corchorus capsularis cultivar CVL-1 contig14806, 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: 18677
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.30


Found at i:39 original size:2 final size:2

Alignment explanation


    Indices: 32--65  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

         22 ATAGAAACTA

                                                              
         32 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

         66 GCCAATGAAT


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

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:369 original size:106 final size:109

Alignment explanation


    Indices: 243--529  Score: 338
    Period size: 106  Copynumber: 2.7  Consensus size: 109

        233 AGAAAATCGC

                 *      *                 *       *       *    *         *   
        243 AATTAATTGATAGATAATTTATAAGAAAAACCAAAAT-CGA-AAA-AAAAAACATTTAATTGGAA
          1 AATTAGTTGATAAATAATTTATAAGAAAAAACAAAATGGGATAAAGGAAAAGCATTTAATTTGAA

                                               **   **  
        305 GATTCATAATTTACCCA-TACAAGTAATTAGAAAATTAAATTGA
         66 GATTCATAATTTACCCATTACAAGTAATTAGAAAAAAAAAAAGA

                            *                 *                              
        348 AATTAGTTGATAAAATTATTTATGTAAGAAAAAATAAAATGGGGATAAAGGAAAAGCATTTAATT
          1 AATTAGTTGAT-AAATAATTTA--TAAGAAAAAACAAAAT-GGGATAAAGGAAAAGCATTTAATT

                        *                    *              
        413 TGAA-A---ATATTTTACCCATTACAAGTAATTTGAAAAAAAAAAAGA
         62 TGAAGATTCATAATTTACCCATTACAAGTAATTAGAAAAAAAAAAAGA

                                                                             
        457 AATTAGTTGATAAATAATTTATAAGAAAAAACAAAATGGGGATAAAGGAAAAGCATTTAATTTGA
          1 AATTAGTTGATAAATAATTTATAAGAAAAAACAAAAT-GGGATAAAGGAAAAGCATTTAATTTGA

                    
        522 AGATTCAT
         65 AGATTCAT

        530 GTTTTTTTTG


Statistics
Matches: 153,  Mismatches: 17, Indels: 19
        0.81            0.09        0.10

Matches are distributed among these distances:
 105   10  0.07
 106   52  0.34
 107    1  0.01
 108   34  0.22
 109   32  0.21
 110    4  0.03
 111    4  0.03
 112   16  0.10

ACGTcount: A:0.52, C:0.06, G:0.13, T:0.29


Consensus pattern (109 bp):   
AATTAGTTGATAAATAATTTATAAGAAAAAACAAAATGGGATAAAGGAAAAGCATTTAATTTGAA
GATTCATAATTTACCCATTACAAGTAATTAGAAAAAAAAAAAGA

Found at i:1495 original size:25 final size:24

Alignment explanation


    Indices: 1460--1518  Score: 75
    Period size: 25  Copynumber: 2.5  Consensus size: 24

       1450 TTCAAACCCT

                  *            *     
       1460 AAACTTAATTTCTAACAACTTCTTC
          1 AAACTTCATTTCTAACAA-ATCTTC

                       *            
       1485 AAACTTCATTTTTAACAAATCTTC
          1 AAACTTCATTTCTAACAAATCTTC

                       
       1509 AAA-TTCATTT
          1 AAACTTCATTT

       1519 TCCTTCATTT


Statistics
Matches: 31,  Mismatches: 3, Indels: 2
        0.86            0.08        0.06

Matches are distributed among these distances:
  23    7  0.23
  24    8  0.26
  25   16  0.52

ACGTcount: A:0.37, C:0.20, G:0.00, T:0.42


Consensus pattern (24 bp):   
AAACTTCATTTCTAACAAATCTTC

Found at i:1557 original size:26 final size:26

Alignment explanation


    Indices: 1528--1595  Score: 100
    Period size: 26  Copynumber: 2.6  Consensus size: 26

       1518 TTCCTTCATT

                                      
       1528 TTAATCATAAACTAATTAAATACTAA
          1 TTAATCATAAACTAATTAAATACTAA

                 *     *      *       
       1554 TTAATAATAAAATAATTAGATACTAA
          1 TTAATCATAAACTAATTAAATACTAA

                *           
       1580 TTAAACATAAACTAAT
          1 TTAATCATAAACTAAT

       1596 AAACTAAGTA


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

Matches are distributed among these distances:
  26   36  1.00

ACGTcount: A:0.56, C:0.09, G:0.01, T:0.34


Consensus pattern (26 bp):   
TTAATCATAAACTAATTAAATACTAA

Found at i:3330 original size:17 final size:18

Alignment explanation


    Indices: 3283--3333  Score: 61
    Period size: 17  Copynumber: 2.9  Consensus size: 18

       3273 AAAAATAAGT

                  *           
       3283 TTTTTTCATAAAAAATCA
          1 TTTTTTAATAAAAAATCA

                   * *        
       3301 -TTTTTAGTGAAAAAT-A
          1 TTTTTTAATAAAAAATCA

                             
       3317 TTTTTTAATAAAAAATC
          1 TTTTTTAATAAAAAATC

       3334 TGATGTGGAC


Statistics
Matches: 26,  Mismatches: 5, Indels: 4
        0.74            0.14        0.11

Matches are distributed among these distances:
  16    1  0.04
  17   25  0.96

ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45


Consensus pattern (18 bp):   
TTTTTTAATAAAAAATCA

Found at i:5838 original size:27 final size:27

Alignment explanation


    Indices: 5808--5861  Score: 90
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       5798 AATTCTTTTA

                           *           
       5808 AGAAAATTGAGTTAAGAAATGAAATTT
          1 AGAAAATTGAGTTAACAAATGAAATTT

                    *                  
       5835 AGAAAATTTAGTTAACAAATGAAATTT
          1 AGAAAATTGAGTTAACAAATGAAATTT

       5862 TGTTGTGAAA


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  27   25  1.00

ACGTcount: A:0.52, C:0.02, G:0.15, T:0.31


Consensus pattern (27 bp):   
AGAAAATTGAGTTAACAAATGAAATTT
Done.