Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018250.1 Corchorus olitorius cultivar O-4 contig18283, 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: 23961
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32


Found at i:627 original size:29 final size:29

Alignment explanation


    Indices: 595--653  Score: 100
    Period size: 29  Copynumber: 2.0  Consensus size: 29

        585 CTATCTTAAA

                         *               
        595 TGTGGACATTATTGTGCCACTTCAAATAT
          1 TGTGGACATTATTATGCCACTTCAAATAT

                            *            
        624 TGTGGACATTATTATGTCACTTCAAATAT
          1 TGTGGACATTATTATGCCACTTCAAATAT

             
        653 T
          1 T

        654 TTGAAAACTA


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  29   28  1.00

ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41


Consensus pattern (29 bp):   
TGTGGACATTATTATGCCACTTCAAATAT

Found at i:1180 original size:23 final size:23

Alignment explanation


    Indices: 1153--1208  Score: 112
    Period size: 23  Copynumber: 2.4  Consensus size: 23

       1143 AAAAAAACTA

                                   
       1153 AACACAAACTGTTTATTTATACT
          1 AACACAAACTGTTTATTTATACT

                                   
       1176 AACACAAACTGTTTATTTATACT
          1 AACACAAACTGTTTATTTATACT

                      
       1199 AACACAAACT
          1 AACACAAACT

       1209 TGGACTCCAA


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   33  1.00

ACGTcount: A:0.43, C:0.20, G:0.04, T:0.34


Consensus pattern (23 bp):   
AACACAAACTGTTTATTTATACT

Found at i:5556 original size:36 final size:34

Alignment explanation


    Indices: 5496--5566  Score: 88
    Period size: 36  Copynumber: 2.0  Consensus size: 34

       5486 TGTTTTTTTA

                            *  *                
       5496 GATGGGTTTAGTATATGGGTCGGGTGGGGTATATTT
          1 GATGGGTTTAGTATATAGGCCGGGT-GGG-ATATTT

                        * *                   
       5532 GATGGGTTTAGTGTTTAGGCCGGGTGGGATATTT
          1 GATGGGTTTAGTATATAGGCCGGGTGGGATATTT

             
       5566 G
          1 G

       5567 TTGTCTTGGT


Statistics
Matches: 31,  Mismatches: 4, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
  34    7  0.23
  35    3  0.10
  36   21  0.68

ACGTcount: A:0.15, C:0.04, G:0.42, T:0.38


Consensus pattern (34 bp):   
GATGGGTTTAGTATATAGGCCGGGTGGGATATTT

Found at i:6284 original size:75 final size:75

Alignment explanation


    Indices: 6154--6297  Score: 252
    Period size: 75  Copynumber: 1.9  Consensus size: 75

       6144 CACTCTTCGC

                *                                                            
       6154 TACTGTTCTTTTCTGCAGCTGAGGACTCCTCTTTACTTTCTTCTTCACCACCGTCCTTCTTCTCT
          1 TACTCTTCTTTTCTGCAGCTGAGGACTCCTCTTTACTTTCTTCTTCACCACCGTCCTTCTTCTCT

                      
       6219 TCCTCATCTA
         66 TCCTCATCTA

                                              *            *  *              
       6229 TACTCTTCTTTTCTGCAGCTGAGGACTCCTCTTTGCTTTCTTCTTCAGCAGCGTCCTTCTTCTCT
          1 TACTCTTCTTTTCTGCAGCTGAGGACTCCTCTTTACTTTCTTCTTCACCACCGTCCTTCTTCTCT

                
       6294 TCCT
         66 TCCT

       6298 TTTCTTCCTC


Statistics
Matches: 65,  Mismatches: 4, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  75   65  1.00

ACGTcount: A:0.10, C:0.34, G:0.11, T:0.44


Consensus pattern (75 bp):   
TACTCTTCTTTTCTGCAGCTGAGGACTCCTCTTTACTTTCTTCTTCACCACCGTCCTTCTTCTCT
TCCTCATCTA

Found at i:7580 original size:27 final size:27

Alignment explanation


    Indices: 7538--7589  Score: 77
    Period size: 27  Copynumber: 1.9  Consensus size: 27

       7528 GTATTCGAGC

                      *         *      
       7538 TACTTATCTTGCAAGTTACTTTAAGAT
          1 TACTTATCTTACAAGTTACTCTAAGAT

                       *             
       7565 TACTTATCTTATAAGTTACTCTAAG
          1 TACTTATCTTACAAGTTACTCTAAG

       7590 CCGAAATCCA


Statistics
Matches: 22,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  27   22  1.00

ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44


Consensus pattern (27 bp):   
TACTTATCTTACAAGTTACTCTAAGAT

Found at i:16771 original size:7 final size:7

Alignment explanation


    Indices: 16759--16785  Score: 54
    Period size: 7  Copynumber: 3.9  Consensus size: 7

      16749 ATATACAATG

                   
      16759 TCAAGAC
          1 TCAAGAC

                   
      16766 TCAAGAC
          1 TCAAGAC

                   
      16773 TCAAGAC
          1 TCAAGAC

                  
      16780 TCAAGA
          1 TCAAGA

      16786 GTAAGCAAAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   20  1.00

ACGTcount: A:0.44, C:0.26, G:0.15, T:0.15


Consensus pattern (7 bp):   
TCAAGAC

Found at i:18759 original size:22 final size:21

Alignment explanation


    Indices: 18725--18765  Score: 55
    Period size: 22  Copynumber: 1.9  Consensus size: 21

      18715 TAGGAAGGAG

                    *            
      18725 AAGGAAAATGAATAAAAGAAA
          1 AAGGAAAAAGAATAAAAGAAA

                          *     
      18746 AAGGAAAAAAGAATTAAAGA
          1 AAGG-AAAAAGAATAAAAGA

      18766 GCTAATTAAG


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  21    4  0.24
  22   13  0.76

ACGTcount: A:0.71, C:0.00, G:0.20, T:0.10


Consensus pattern (21 bp):   
AAGGAAAAAGAATAAAAGAAA
Done.