Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019177.1 Corchorus olitorius cultivar O-4 contig19210, 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: 8903
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34


Found at i:3157 original size:39 final size:39

Alignment explanation


    Indices: 3104--3244  Score: 173
    Period size: 39  Copynumber: 3.6  Consensus size: 39

       3094 GCGGAACAGA

                            *                       
       3104 GACCTAAGCAGGTTTGCTTAAACGAAAATTCTAAACATA-
          1 GACCTAAGCAGGTTTGATTAAACGAAAATTCTAAACA-AG

                                     ** *     *     
       3143 GACCTAAGCAGGTTT-ACTT-AACGGGAGTTCTAGACAAG
          1 GACCTAAGCAGGTTTGA-TTAAACGAAAATTCTAAACAAG

                   *                                
       3181 GACCTAAACAGGTTTGATTAAAC-AAAAGTTCTAAACAAG
          1 GACCTAAGCAGGTTTGATTAAACGAAAA-TTCTAAACAAG

                                     
       3220 GACCTAAGCAGGTTTGATTAAACGA
          1 GACCTAAGCAGGTTTGATTAAACGA

       3245 GTCTCTAAGC


Statistics
Matches: 85,  Mismatches: 11, Indels: 11
        0.79            0.10        0.10

Matches are distributed among these distances:
  37    1  0.01
  38   30  0.35
  39   53  0.62
  40    1  0.01

ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24


Consensus pattern (39 bp):   
GACCTAAGCAGGTTTGATTAAACGAAAATTCTAAACAAG

Found at i:5539 original size:26 final size:23

Alignment explanation


    Indices: 5485--5539  Score: 74
    Period size: 26  Copynumber: 2.2  Consensus size: 23

       5475 TAAATCTATC

                                    
       5485 TTTCTATTCATCTATCATCAAGTT
          1 TTTC-ATTCATCTATCATCAAGTT

                                      
       5509 TTTCATTCATCTCATCCATCAAAGTT
          1 TTTCATTCATCT-AT-CATC-AAGTT

                 
       5535 TTTCA
          1 TTTCA

       5540 AATTTTCTAG


Statistics
Matches: 28,  Mismatches: 0, Indels: 4
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    8  0.29
  24    6  0.21
  25    4  0.14
  26   10  0.36

ACGTcount: A:0.25, C:0.24, G:0.04, T:0.47


Consensus pattern (23 bp):   
TTTCATTCATCTATCATCAAGTT

Found at i:7134 original size:33 final size:33

Alignment explanation


    Indices: 7089--7169  Score: 101
    Period size: 33  Copynumber: 2.5  Consensus size: 33

       7079 GTGTTTTAGA

                   *       *                  
       7089 TGTTGTTAGTGATGATACTAAACCTAATTTGA-G
          1 TGTTGTTTGTGATGACACTAAACCT-ATTTGAGG

                                  *  *   *   
       7122 TGTTGTTTGTGATGACACTAAATCTGTTTTAGG
          1 TGTTGTTTGTGATGACACTAAACCTATTTGAGG

                           
       7155 TGTTGTTTGTGATGA
          1 TGTTGTTTGTGATGA

       7170 AACAAATTCT


Statistics
Matches: 42,  Mismatches: 5, Indels: 2
        0.86            0.10        0.04

Matches are distributed among these distances:
  32    4  0.10
  33   38  0.90

ACGTcount: A:0.23, C:0.07, G:0.25, T:0.44


Consensus pattern (33 bp):   
TGTTGTTTGTGATGACACTAAACCTATTTGAGG

Found at i:7181 original size:33 final size:32

Alignment explanation


    Indices: 7116--7220  Score: 106
    Period size: 33  Copynumber: 3.2  Consensus size: 32

       7106 CTAAACCTAA

                                 *            
       7116 TTTGAGTGTTGTTTGTGATGACACTAAA-TCTGT
          1 TTTG-GTGTTGTTTGTGATGAAAC-AAATTCTGT

                                             
       7149 TTTAGGTGTTGTTTGTGATGAAACAAATTCTGT
          1 TTT-GGTGTTGTTTGTGATGAAACAAATTCTGT

                    * **                    * 
       7182 TTTGGATGCTAATTGTGATGAAAACAAA-TCTAT
          1 TTTGG-TGTTGTTTGTGATG-AAACAAATTCTGT

                  
       7215 TTTGGT
          1 TTTGGT

       7221 TGATCATAGC


Statistics
Matches: 63,  Mismatches: 5, Indels: 9
        0.82            0.06        0.12

Matches are distributed among these distances:
  32    6  0.10
  33   49  0.78
  34    8  0.13

ACGTcount: A:0.26, C:0.08, G:0.23, T:0.44


Consensus pattern (32 bp):   
TTTGGTGTTGTTTGTGATGAAACAAATTCTGT

Found at i:7814 original size:19 final size:18

Alignment explanation


    Indices: 7790--7825  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       7780 TGAAGACTTA

                               
       7790 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
       7809 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

       7826 ATTATTTTCA


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
Done.