Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010407.1 Corchorus capsularis cultivar CVL-1 contig10428, 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: 19227
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:6163 original size:6 final size:6

Alignment explanation


    Indices: 6115--6159  Score: 63
    Period size: 6  Copynumber: 7.5  Consensus size: 6

       6105 AGCAAGATGG

                 *    *                                  *      
       6115 GATTGG GATCGA GATTGA GATTGA GATTGA GATTGA GATAGA GAT
          1 GATTGA GATTGA GATTGA GATTGA GATTGA GATTGA GATTGA GAT

       6160 AGAGCCTTGA


Statistics
Matches: 35,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
   6   35  1.00

ACGTcount: A:0.33, C:0.02, G:0.36, T:0.29


Consensus pattern (6 bp):   
GATTGA

Found at i:6369 original size:24 final size:24

Alignment explanation


    Indices: 6342--6387  Score: 74
    Period size: 24  Copynumber: 1.9  Consensus size: 24

       6332 ATCATGAGGT

                                    
       6342 GAAGGTCGAAGAAAAAGAAAACCG
          1 GAAGGTCGAAGAAAAAGAAAACCG

                  *       *       
       6366 GAAGGTTGAAGAAAGAGAAAAC
          1 GAAGGTCGAAGAAAAAGAAAAC

       6388 GGTGTAAGAG


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  24   20  1.00

ACGTcount: A:0.54, C:0.09, G:0.30, T:0.07


Consensus pattern (24 bp):   
GAAGGTCGAAGAAAAAGAAAACCG

Found at i:8280 original size:32 final size:31

Alignment explanation


    Indices: 8180--8447  Score: 156
    Period size: 32  Copynumber: 8.6  Consensus size: 31

       8170 TCCAATGATA

                              *          * *   
       8180 TGTGCATCTCCCGCACATTATCAATTTAAAACTCG
          1 TGTGCATCTCCCGCACA-CAT--A-TTAATATTCG

                               *  **         
       8215 TGTGCATCTCCCGCACACTTTAACAATAATT-G
          1 TGTGCATCTCCCGCACAC-ATATTAAT-ATTCG

                 *                        * 
       8247 TGTGCTTCTCCCGCACATCATATTAATATTTG
          1 TGTGCATCTCCCGCACA-CATATTAATATTCG

                * *                    *    
       8279 TGTGAACCTCCCGCACACTATATTAATGTTCG
          1 TGTGCATCTCCCGCACAC-ATATTAATATTCG

               * *       *                *
       8311 TGTACTTCTCCCGTACAC-TA-TAATATTCA
          1 TGTGCATCTCCCGCACACATATTAATATTCG

                                  *       *
       8340 TGTGCATCTCCCGCACAC-T-TGAATATTCA
          1 TGTGCATCTCCCGCACACATATTAATATTCG

                 *     *   *      * *        
       8369 TGTGCGTCTCCTGCATACTATACTGATACTT-G
          1 TGTGCATCTCCCGCACAC-ATATTAATA-TTCG

                      *  *         *      *
       8401 TGTGCATCTCTCGTACAC-TA-TCATATTCA
          1 TGTGCATCTCCCGCACACATATTAATATTCG

                              
       8430 TGTGCATCTCCCGCACAC
          1 TGTGCATCTCCCGCACAC

       8448 TTTTTCTATC


Statistics
Matches: 180,  Mismatches: 42, Indels: 28
        0.72            0.17        0.11

Matches are distributed among these distances:
  28    2  0.01
  29   66  0.37
  30    4  0.02
  31    5  0.03
  32   79  0.44
  33    6  0.03
  35   18  0.10

ACGTcount: A:0.24, C:0.29, G:0.13, T:0.34


Consensus pattern (31 bp):   
TGTGCATCTCCCGCACACATATTAATATTCG

Found at i:9960 original size:11 final size:11

Alignment explanation


    Indices: 9946--9983  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

       9936 ATTCATAACA

                       
       9946 AATTTATAATT
          1 AATTTATAATT

                       
       9957 AATTTATAATT
          1 AATTTATAATT

                        
       9968 -ATTTGATAATT
          1 AATTT-ATAATT

            *    
       9979 TATTT
          1 AATTT

       9984 TATATAGGAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 3
        0.89            0.00        0.11

Matches are distributed among these distances:
  10    4  0.16
  11   17  0.68
  12    4  0.16

ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58


Consensus pattern (11 bp):   
AATTTATAATT

Found at i:14305 original size:20 final size:19

Alignment explanation


    Indices: 14276--14318  Score: 50
    Period size: 20  Copynumber: 2.2  Consensus size: 19

      14266 CATGCCTTGC

                       *        
      14276 TTTCACTCCTCTATACCATA
          1 TTTCACTCCTCAAT-CCATA

                 *    *        
      14296 TTTCAGTCCTGAATCCATA
          1 TTTCACTCCTCAATCCATA

                
      14315 TTTC
          1 TTTC

      14319 GTCTAGCAGA


Statistics
Matches: 20,  Mismatches: 3, Indels: 1
        0.83            0.12        0.04

Matches are distributed among these distances:
  19    9  0.45
  20   11  0.55

ACGTcount: A:0.23, C:0.30, G:0.05, T:0.42


Consensus pattern (19 bp):   
TTTCACTCCTCAATCCATA
Done.