Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017938.1 Corchorus olitorius cultivar O-4 contig17971, 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: 21306
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:12578 original size:32 final size:32

Alignment explanation


    Indices: 12542--12607  Score: 114
    Period size: 32  Copynumber: 2.1  Consensus size: 32

      12532 AAATATTTTA

                                 *          
      12542 TTTTTACCATTTTACTATTTTGATTAAAAAAC
          1 TTTTTACCATTTTACTATTTTAATTAAAAAAC

                  *                         
      12574 TTTTTATCATTTTACTATTTTAATTAAAAAAC
          1 TTTTTACCATTTTACTATTTTAATTAAAAAAC

              
      12606 TT
          1 TT

      12608 AGATATATTA


Statistics
Matches: 32,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  32   32  1.00

ACGTcount: A:0.35, C:0.11, G:0.02, T:0.53


Consensus pattern (32 bp):   
TTTTTACCATTTTACTATTTTAATTAAAAAAC

Found at i:13990 original size:33 final size:34

Alignment explanation


    Indices: 13939--14002  Score: 112
    Period size: 33  Copynumber: 1.9  Consensus size: 34

      13929 ACGAAACTCA

                         *                    
      13939 AAAATCTTAATTAGTCAATTACTAAAATACCTTT
          1 AAAATCTTAATTAATCAATTACTAAAATACCTTT

                                           
      13973 AAAA-CTTAATTAATCAATTACTAAAATACC
          1 AAAATCTTAATTAATCAATTACTAAAATACC

      14003 CTTGATATTA


Statistics
Matches: 29,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  33   25  0.86
  34    4  0.14

ACGTcount: A:0.48, C:0.16, G:0.02, T:0.34


Consensus pattern (34 bp):   
AAAATCTTAATTAATCAATTACTAAAATACCTTT

Found at i:14189 original size:30 final size:30

Alignment explanation


    Indices: 14154--14215  Score: 115
    Period size: 30  Copynumber: 2.1  Consensus size: 30

      14144 TATAATTTTT

                             *            
      14154 AATCATTAAACTTTTATTTATTAATTATAA
          1 AATCATTAAACTTTTATCTATTAATTATAA

                                          
      14184 AATCATTAAACTTTTATCTATTAATTATAA
          1 AATCATTAAACTTTTATCTATTAATTATAA

              
      14214 AA
          1 AA

      14216 AGATATTGAA


Statistics
Matches: 31,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  30   31  1.00

ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47


Consensus pattern (30 bp):   
AATCATTAAACTTTTATCTATTAATTATAA

Found at i:16557 original size:18 final size:19

Alignment explanation


    Indices: 16522--16561  Score: 64
    Period size: 18  Copynumber: 2.2  Consensus size: 19

      16512 TTGAAGATTT

                               
      16522 ATTGAAGATAATTTGAAGA
          1 ATTGAAGATAATTTGAAGA

                     *         
      16541 ATTGAAGATCA-TTGAAGA
          1 ATTGAAGATAATTTGAAGA

               
      16559 ATT
          1 ATT

      16562 ATCTCAATAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  18   10  0.50
  19   10  0.50

ACGTcount: A:0.45, C:0.03, G:0.20, T:0.33


Consensus pattern (19 bp):   
ATTGAAGATAATTTGAAGA

Found at i:17871 original size:21 final size:21

Alignment explanation


    Indices: 17841--17895  Score: 58
    Period size: 21  Copynumber: 2.6  Consensus size: 21

      17831 ATTGTCATAG

                *           *     
      17841 TTTAGATTTAATTTACTTTGC-
          1 TTTATATTTAATTTA-ATTGCT

                 *    *          
      17862 TTTATTTTTAGTTTAATTGCT
          1 TTTATATTTAATTTAATTGCT

                         
      17883 TTTATATTTAATT
          1 TTTATATTTAATT

      17896 GTTTTAATCC


Statistics
Matches: 27,  Mismatches: 6, Indels: 2
        0.77            0.17        0.06

Matches are distributed among these distances:
  20    4  0.15
  21   23  0.85

ACGTcount: A:0.24, C:0.05, G:0.07, T:0.64


Consensus pattern (21 bp):   
TTTATATTTAATTTAATTGCT

Found at i:19805 original size:19 final size:18

Alignment explanation


    Indices: 19781--19816  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      19771 TGAAGACTTA

                               
      19781 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
      19800 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

      19817 ATAATTTCAA


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

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAT

Found at i:19823 original size:30 final size:30

Alignment explanation


    Indices: 19769--19828  Score: 77
    Period size: 30  Copynumber: 2.0  Consensus size: 30

      19759 GAAGTTCGTG

                      *              *    
      19769 TTTGAAGACTTATTGAAGACAATTTGAAGA
          1 TTTGAAGACTCATTGAAGACAATTTCAAGA

                                *          
      19799 TTTGAAGAC-CATTGAAGAATAATTTCAAGA
          1 TTTGAAGACTCATTGAAG-ACAATTTCAAGA

      19829 ACAAGAATTG


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  29    7  0.27
  30   19  0.73

ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32


Consensus pattern (30 bp):   
TTTGAAGACTCATTGAAGACAATTTCAAGA
Done.