Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009731.1 Corchorus olitorius cultivar O-4 contig09763, 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: 9380
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34


Found at i:623 original size:13 final size:13

Alignment explanation


    Indices: 599--631  Score: 57
    Period size: 13  Copynumber: 2.5  Consensus size: 13

        589 AAGGAAGATT

                          
        599 ATATATTTTATTTA
          1 ATATA-TTTATTTA

                         
        613 ATATATTTATTTA
          1 ATATATTTATTTA

                  
        626 ATATAT
          1 ATATAT

        632 GATATATAAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  13   14  0.74
  14    5  0.26

ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61


Consensus pattern (13 bp):   
ATATATTTATTTA

Found at i:733 original size:21 final size:22

Alignment explanation


    Indices: 688--733  Score: 53
    Period size: 21  Copynumber: 2.2  Consensus size: 22

        678 TTATTTCATA

                                  
        688 AATA-CATTTATATATGATATC
          1 AATATCATTTATATATGATATC

                      *        *  
        709 -ATATCATTTTTATAT-ATTTC
          1 AATATCATTTATATATGATATC

                 
        729 AATAT
          1 AATAT

        734 AAACAACGAC


Statistics
Matches: 21,  Mismatches: 2, Indels: 4
        0.78            0.07        0.15

Matches are distributed among these distances:
  20    7  0.33
  21   14  0.67

ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50


Consensus pattern (22 bp):   
AATATCATTTATATATGATATC

Found at i:1222 original size:15 final size:15

Alignment explanation


    Indices: 1204--1239  Score: 63
    Period size: 15  Copynumber: 2.4  Consensus size: 15

       1194 CGCGTCATAC

                     *     
       1204 TAATTTCTGTCAGAA
          1 TAATTTCTGGCAGAA

                           
       1219 TAATTTCTGGCAGAA
          1 TAATTTCTGGCAGAA

                  
       1234 TAATTT
          1 TAATTT

       1240 ACATTCAATT


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  15   20  1.00

ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42


Consensus pattern (15 bp):   
TAATTTCTGGCAGAA

Found at i:3744 original size:3 final size:3

Alignment explanation


    Indices: 3738--3762  Score: 50
    Period size: 3  Copynumber: 8.3  Consensus size: 3

       3728 TGTTGCACAT

                                             
       3738 AAC AAC AAC AAC AAC AAC AAC AAC A
          1 AAC AAC AAC AAC AAC AAC AAC AAC A

       3763 GGATATTATA


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   22  1.00

ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00


Consensus pattern (3 bp):   
AAC

Found at i:5578 original size:105 final size:105

Alignment explanation


    Indices: 5391--5593  Score: 343
    Period size: 105  Copynumber: 1.9  Consensus size: 105

       5381 ATGTCACTAA

                        *                                  *                 
       5391 ACATAGACATGGGTTATCCAAATCCCAAGATACTTCTTCCCATTTTAGTAATTCTGTCACTAAAC
          1 ACATAGACATGGATTATCCAAATCCCAAGATACTTCTTCCCATTTTAATAATTCTGTCACTAAAC

                                        *           
       5456 GTAGACATGAGTAATCCAAGATACCCCTGGAAGCCCGGCT
         66 GTAGACATGAGTAATCCAAGATACCCCTAGAAGCCCGGCT

                *                                   *            *           
       5496 ACATCGACATGGATTATCCAAATCCCAAGATACTTCTTCCTATTTTAATAATTTTGTCACTAAAC
          1 ACATAGACATGGATTATCCAAATCCCAAGATACTTCTTCCCATTTTAATAATTCTGTCACTAAAC

                                    *        
       5561 GTAGACATGAGTAATCCAAGATACTCCTAGAAG
         66 GTAGACATGAGTAATCCAAGATACCCCTAGAAG

       5594 GGTGCGGCTC


Statistics
Matches: 91,  Mismatches: 7, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
 105   91  1.00

ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29


Consensus pattern (105 bp):   
ACATAGACATGGATTATCCAAATCCCAAGATACTTCTTCCCATTTTAATAATTCTGTCACTAAAC
GTAGACATGAGTAATCCAAGATACCCCTAGAAGCCCGGCT

Found at i:7435 original size:27 final size:26

Alignment explanation


    Indices: 7411--7461  Score: 66
    Period size: 27  Copynumber: 1.9  Consensus size: 26

       7401 TATCATATTG

                        *              
       7411 TTTCATAAATATTTATATATGATATCA
          1 TTTCATAAATATATATATAT-ATATCA

               *   *                
       7438 TTTTATATATATATATATATATAT
          1 TTTCATAAATATATATATATATAT

       7462 ATATATTTCA


Statistics
Matches: 21,  Mismatches: 3, Indels: 1
        0.84            0.12        0.04

Matches are distributed among these distances:
  26    4  0.19
  27   17  0.81

ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53


Consensus pattern (26 bp):   
TTTCATAAATATATATATATATATCA

Found at i:7446 original size:2 final size:2

Alignment explanation


    Indices: 7419--7467  Score: 55
    Period size: 2  Copynumber: 24.0  Consensus size: 2

       7409 TGTTTCATAA

                  *                         *                               
       7419 AT AT TT AT AT AT GAT AT CAT -T TT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT -AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT

                    
       7462 AT AT AT
          1 AT AT AT

       7468 TTCATTATAA


Statistics
Matches: 41,  Mismatches: 3, Indels: 6
        0.82            0.06        0.12

Matches are distributed among these distances:
   1    1  0.02
   2   36  0.88
   3    4  0.10

ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53


Consensus pattern (2 bp):   
AT

Done.