Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015128.1 Corchorus capsularis cultivar CVL-1 contig15149, 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: 23734
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33


Found at i:5729 original size:219 final size:219

Alignment explanation


    Indices: 5199--5789  Score: 731
    Period size: 219  Copynumber: 2.7  Consensus size: 219

       5189 AGAGAGAGAG

                       *    *       *        * **                   * *      
       5199 AGACTGACTGATTGATAGGTGAACAATTTAGGCCTATAGAATTTGACATGAGAGATCTATTTCTT
          1 AGACTGACTGACTGATGGGTG-ACGATTTAGGCATGCAGAATTTGACATGAGAGATATGTTTCTT

                                         *                      *            
       5264 AGAAGTTCTTTATATGTAGTTTCACGATATATTTTTTGCAGTATCTCACATTGAATGCAATAAGT
         65 AGAAGTTCTTTATATGTAGTTTCACGATACATTTTTTGCAGTATCTCACATTAAATGCAATAAGT

                                               *        *      *             
       5329 TAATTGCATTTTTCCTTTATAGACAGTTGTAATTACACGAGTTGGTAAAAGGTGAACACCTCAAA
        130 TAATTGCA-TTTTCCTTTATAGACAGTTGTAATTAAACGAGTTGATAAAAGATGAACACCTCAAA

                         *       **   *
       5394 ATAAGAGAAAGAGTGAGAGTGTGAGAG
        194 AT-AGAGAAAGAGAGAGAGTGACAGAC

                               *   *  * *      *      *                      
       5421 AGACTGACTGACTGACTGGCTGATGAATGAGCGACTTGCAGAGTTTGACATGAGAGATATGTTTC
          1 AGACTGACTGACTGA-TGGGTGACGATTTAG-G-CATGCAGAATTTGACATGAGAGATATGTTTC

                             *                    *      *  *                
       5486 TTAGAAGTTCTTTATATATAGTTTCACGATACA-TTTTCGACAGTGTCCCACATTAAATGCAATA
         63 TTAGAAGTTCTTTATATGTAGTTTCACGATACATTTTTTG-CAGTATCTCACATTAAATGCAATA

            **    *               *    *                     *               
       5550 CTTTAACTGCATTTTCCTTTATGGACATTTGTAATTAAACGAGTTGATACAAGATGAACACCTCA
        127 AGTTAATTGCATTTTCCTTTATAGACAGTTGTAATTAAACGAGTTGATAAAAGATGAACACCTCA

                     *                   
       5615 AAAT-GAGATAGAGAGAG-GCTGACAGAC
        192 AAATAGAGAAAGAGAGAGAG-TGACAGAC

                      *                                                      
       5642 AGACTGACTGGCTGATGGGTGAGCGATTTAGGCATGCAGAATTTGACATGAGAGATATGTTTCTT
          1 AGACTGACTGACTGATGGGTGA-CGATTTAGGCATGCAGAATTTGACATGAGAGATATGTTTCTT

                  *                 *                                        
       5707 AGAAGTCCTTTATATGTAGTTTCATGATACATTTTTTGC-GATATCTCACATTAAATGCAATAAG
         65 AGAAGTTCTTTATATGTAGTTTCACGATACATTTTTTGCAG-TATCTCACATTAAATGCAATAAG

                               
       5771 TTAATTGCATTTTCCTTTA
        129 TTAATTGCATTTTCCTTTA

       5790 CACGAGTTGG


Statistics
Matches: 312,  Mismatches: 49, Indels: 19
        0.82            0.13        0.05

Matches are distributed among these distances:
 218    1  0.00
 219   97  0.31
 220   13  0.04
 221   35  0.11
 222   19  0.06
 223   62  0.20
 224   85  0.27

ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34


Consensus pattern (219 bp):   
AGACTGACTGACTGATGGGTGACGATTTAGGCATGCAGAATTTGACATGAGAGATATGTTTCTTA
GAAGTTCTTTATATGTAGTTTCACGATACATTTTTTGCAGTATCTCACATTAAATGCAATAAGTT
AATTGCATTTTCCTTTATAGACAGTTGTAATTAAACGAGTTGATAAAAGATGAACACCTCAAAAT
AGAGAAAGAGAGAGAGTGACAGAC

Found at i:12134 original size:17 final size:17

Alignment explanation


    Indices: 12107--12140  Score: 52
    Period size: 17  Copynumber: 2.0  Consensus size: 17

      12097 CTTGATCCTG

                             
      12107 ACTATTGTCCT-CCAGA
          1 ACTATTGTCCTACCAGA

                              
      12123 ACTATATGTCCTACCAGA
          1 ACTAT-TGTCCTACCAGA

      12141 GGAAACACCG


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  16    5  0.31
  17    6  0.38
  18    5  0.31

ACGTcount: A:0.29, C:0.29, G:0.12, T:0.29


Consensus pattern (17 bp):   
ACTATTGTCCTACCAGA

Found at i:23323 original size:30 final size:30

Alignment explanation


    Indices: 23280--23363  Score: 125
    Period size: 30  Copynumber: 2.8  Consensus size: 30

      23270 ATTGTATATT

                               *       *  
      23280 ATAGA-TTTAACATTATTTGTGAGGACGCA
          1 ATAGATTTTAACATTATTTTTGAGGACCCA

              *      *                    
      23309 ATGGATTTTCACATTATTTTTGAGGACCCA
          1 ATAGATTTTAACATTATTTTTGAGGACCCA

                                     
      23339 ATAGATTTTAACATTATTTTTGAGG
          1 ATAGATTTTAACATTATTTTTGAGG

      23364 GTAAACCTTA


Statistics
Matches: 48,  Mismatches: 6, Indels: 1
        0.87            0.11        0.02

Matches are distributed among these distances:
  29    4  0.08
  30   44  0.92

ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40


Consensus pattern (30 bp):   
ATAGATTTTAACATTATTTTTGAGGACCCA

Found at i:23379 original size:2 final size:2

Alignment explanation


    Indices: 23372--23399  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

      23362 GGGTAAACCT

                                                     
      23372 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      23400 CTAGTAATGA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:23498 original size:27 final size:28

Alignment explanation


    Indices: 23438--23500  Score: 83
    Period size: 27  Copynumber: 2.2  Consensus size: 28

      23428 TAATATATTA

                            *  *         
      23438 TAATTTGTAATATATATAAGATGAATAAT
          1 TAATTT-TAATATATAAAAAATGAATAAT

                   *                    
      23467 TAATTTTCATATATAAAAAAT-AATAAT
          1 TAATTTTAATATATAAAAAATGAATAAT

                   
      23494 TAATTTT
          1 TAATTTT

      23501 TATAAATTAT


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

Matches are distributed among these distances:
  27   13  0.42
  28   12  0.39
  29    6  0.19

ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44


Consensus pattern (28 bp):   
TAATTTTAATATATAAAAAATGAATAAT
Done.