Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016114.1 Corchorus capsularis cultivar CVL-1 contig16135, 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: 13034
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31


Found at i:925 original size:36 final size:36

Alignment explanation


    Indices: 873--1044  Score: 136
    Period size: 36  Copynumber: 4.8  Consensus size: 36

        863 TAAAATAAAT

                 *     *                       *
        873 AACTGGAGAAAAACCACCCTGGATCATTCCGAACTG
          1 AACTGAAGAAAGACCACCCTGGATCATTCCGAACTA

                                 *              * 
        909 AACTGAA-AAATGACCACCCTCGATCATTCCG-ACGCA
          1 AACTGAAGAAA-GACCACCCTGGATCATTCCGAAC-TA

               *            *          * *   *  
        945 AACCGAAGAAAGACCAACCTGGATCA-ACTGAAATA
          1 AACTGAAGAAAGACCACCCTGGATCATTCCGAACTA

              *                  *       *  *    
        980 AATTGAA-AAACGACCACCCTCGATCATTTCGGACTA
          1 AACTGAAGAAA-GACCACCCTGGATCATTCCGAACTA

                *                  *     
       1016 AACTAAAGAAAAGACCACCCTGGGTCATT
          1 AACTGAAG-AAAGACCACCCTGGATCATT

       1045 GAAGCAATGA


Statistics
Matches: 103,  Mismatches: 25, Indels: 15
        0.72            0.17        0.10

Matches are distributed among these distances:
  34    3  0.03
  35   26  0.25
  36   53  0.51
  37   18  0.17
  38    3  0.03

ACGTcount: A:0.40, C:0.27, G:0.16, T:0.17


Consensus pattern (36 bp):   
AACTGAAGAAAGACCACCCTGGATCATTCCGAACTA

Found at i:1162 original size:35 final size:34

Alignment explanation


    Indices: 1068--1162  Score: 93
    Period size: 35  Copynumber: 2.8  Consensus size: 34

       1058 ATTGGAGAAT

                      *    *                  
       1068 TGAAGAAAGACCACCATGGATC-ATTGAAGTAAA
          1 TGAAGAAAGATCACCCTGGATCAATTGAAGTAAA

                    *    *      **         *   *
       1101 TGGAAGAATGATCGCCCTGGGCCAATTGAAATTAAC
          1 T-GAAGAAAGATCACCCTGGATCAATTG-AAGTAAA

                                      
       1137 TGAAGAAAGATCACCCTGGATCAATT
          1 TGAAGAAAGATCACCCTGGATCAATT

       1163 AATTGAGGGC


Statistics
Matches: 47,  Mismatches: 12, Indels: 4
        0.75            0.19        0.06

Matches are distributed among these distances:
  33    1  0.02
  34   15  0.32
  35   25  0.53
  36    6  0.13

ACGTcount: A:0.39, C:0.18, G:0.22, T:0.21


Consensus pattern (34 bp):   
TGAAGAAAGATCACCCTGGATCAATTGAAGTAAA

Found at i:1279 original size:34 final size:34

Alignment explanation


    Indices: 1234--1299  Score: 105
    Period size: 34  Copynumber: 1.9  Consensus size: 34

       1224 GATAAATAAC

                               *              
       1234 TGAAGAAAGACCACCTTGGGTCAATTGAAATTAT
          1 TGAAGAAAGACCACCTTGGATCAATTGAAATTAT

                  *     *                   
       1268 TGAAGAGAGACCGCCTTGGATCAATTGAAATT
          1 TGAAGAAAGACCACCTTGGATCAATTGAAATT

       1300 TACTGAATGG


Statistics
Matches: 29,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  34   29  1.00

ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26


Consensus pattern (34 bp):   
TGAAGAAAGACCACCTTGGATCAATTGAAATTAT

Found at i:7235 original size:15 final size:16

Alignment explanation


    Indices: 7203--7236  Score: 52
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       7193 AAAGAAGAAT

                 *          
       7203 TAAAATTAAATCTAAC
          1 TAAAAGTAAATCTAAC

                            
       7219 TAAAAGTAAAT-TAAC
          1 TAAAAGTAAATCTAAC

               
       7234 TAA
          1 TAA

       7237 GAAATCAATC


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  15    7  0.41
  16   10  0.59

ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29


Consensus pattern (16 bp):   
TAAAAGTAAATCTAAC

Found at i:8553 original size:19 final size:18

Alignment explanation


    Indices: 8520--8555  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       8510 TTGAAATAAT

                              
       8520 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
       8538 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

       8556 GAAATCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:10164 original size:34 final size:32

Alignment explanation


    Indices: 10126--10193  Score: 82
    Period size: 34  Copynumber: 2.1  Consensus size: 32

      10116 CCTACGATGC

                                              
      10126 TTAAAAATAAAATCCTAAATCTAGAAAACATAAA
          1 TTAAAAATAAAATCCT-AAT-TAGAAAACATAAA

                 **             *      *    
      10160 TTAAACTTAAAATCCTAATTTGAAAACCTAAA
          1 TTAAAAATAAAATCCTAATTAGAAAACATAAA

              
      10192 TT
          1 TT

      10194 GGTTTAGGAA


Statistics
Matches: 30,  Mismatches: 4, Indels: 2
        0.83            0.11        0.06

Matches are distributed among these distances:
  32   13  0.43
  33    3  0.10
  34   14  0.47

ACGTcount: A:0.54, C:0.13, G:0.03, T:0.29


Consensus pattern (32 bp):   
TTAAAAATAAAATCCTAATTAGAAAACATAAA
Done.