Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022131.1 Corchorus olitorius cultivar O-4 contig22164, 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: 10173
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33


Found at i:545 original size:10 final size:11

Alignment explanation


    Indices: 528--556  Score: 51
    Period size: 10  Copynumber: 2.7  Consensus size: 11

        518 TGTATAAGTT

                       
        528 TAATAATATAA
          1 TAATAATATAA

                       
        539 T-ATAATATAA
          1 TAATAATATAA

                    
        549 TAATAATA
          1 TAATAATA

        557 GTGTAGATGT


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  10   10  0.59
  11    7  0.41

ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38


Consensus pattern (11 bp):   
TAATAATATAA

Found at i:1369 original size:20 final size:21

Alignment explanation


    Indices: 1346--1389  Score: 63
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       1336 TGAAAACCAT

                                 
       1346 AAATATGAA-AGTCAAACCCC
          1 AAATATGAATAGTCAAACCCC

                  *   *          
       1366 AAATATTAATGGTCAAACCCC
          1 AAATATGAATAGTCAAACCCC

               
       1387 AAA
          1 AAA

       1390 GCATCCATTG


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  20    8  0.38
  21   13  0.62

ACGTcount: A:0.50, C:0.23, G:0.09, T:0.18


Consensus pattern (21 bp):   
AAATATGAATAGTCAAACCCC

Found at i:1382 original size:21 final size:21

Alignment explanation


    Indices: 1356--1426  Score: 79
    Period size: 21  Copynumber: 3.3  Consensus size: 21

       1346 AAATATGAAA

                                 
       1356 GTCAAACCCCAAATATTAATG
          1 GTCAAACCCCAAATATTAATG

                          *  **  *
       1377 GTCAAACCCCAAAGCATCCATT
          1 GTCAAACCCCAAA-TATTAATG

              *           *      
       1399 GTAAAACCCCAAATGTTAATG
          1 GTCAAACCCCAAATATTAATG

                   
       1420 GTCAAAC
          1 GTCAAAC

       1427 TACAAATCAT


Statistics
Matches: 38,  Mismatches: 11, Indels: 2
        0.75            0.22        0.04

Matches are distributed among these distances:
  21   22  0.58
  22   16  0.42

ACGTcount: A:0.41, C:0.27, G:0.11, T:0.21


Consensus pattern (21 bp):   
GTCAAACCCCAAATATTAATG

Found at i:1580 original size:87 final size:88

Alignment explanation


    Indices: 1402--1592  Score: 296
    Period size: 87  Copynumber: 2.2  Consensus size: 88

       1392 ATCCATTGTA

                         *            *                                      
       1402 AAACCCCAAATG-TTAATGGTCAAACTACAAATCATGTATGGTCAAATTGTAAAGCATGATTAGG
          1 AAACCCCAAA-GCATAATGGTCAAACCACAAATCATGTATGGTCAAATTGTAAAGCATGATTAGG

                                    
       1466 CAAACCCCTACTAGTAATGGGATC
         65 CAAACCCCTACTAGTAATGGGATC

                 *    *               *               *                      
       1490 AAACCTCAAATCATAATGGTCAAACCCCAAATCATGTATGGTGAAATT-TAAAGCATGATTAGGC
          1 AAACCCCAAAGCATAATGGTCAAACCACAAATCATGTATGGTCAAATTGTAAAGCATGATTAGGC

                  *                
       1554 AAACCCTTACTAGTAATGGGATC
         66 AAACCCCTACTAGTAATGGGATC

                            
       1577 AAACCCCAAAGCATAA
          1 AAACCCCAAAGCATAA

       1593 CTAAATAATT


Statistics
Matches: 93,  Mismatches: 9, Indels: 3
        0.89            0.09        0.03

Matches are distributed among these distances:
  87   52  0.56
  88   41  0.44

ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24


Consensus pattern (88 bp):   
AAACCCCAAAGCATAATGGTCAAACCACAAATCATGTATGGTCAAATTGTAAAGCATGATTAGGC
AAACCCCTACTAGTAATGGGATC

Found at i:8730 original size:32 final size:32

Alignment explanation


    Indices: 8694--8754  Score: 122
    Period size: 32  Copynumber: 1.9  Consensus size: 32

       8684 TTAAAATAAA

                                            
       8694 GAATATAATTTCAATAAAAAGGGAAAAATGAG
          1 GAATATAATTTCAATAAAAAGGGAAAAATGAG

                                         
       8726 GAATATAATTTCAATAAAAAGGGAAAAAT
          1 GAATATAATTTCAATAAAAAGGGAAAAAT

       8755 TAATTTTGTC


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  32   29  1.00

ACGTcount: A:0.57, C:0.03, G:0.16, T:0.23


Consensus pattern (32 bp):   
GAATATAATTTCAATAAAAAGGGAAAAATGAG
Done.