Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010174.1 Corchorus capsularis cultivar CVL-1 contig10195, 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: 2636
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.31


Found at i:491 original size:18 final size:19

Alignment explanation


    Indices: 468--511  Score: 81
    Period size: 18  Copynumber: 2.4  Consensus size: 19

        458 GTAGGTAAAA

                               
        468 AAATAAATAGATAATAG-T
          1 AAATAAATAGATAATAGCT

                               
        486 AAATAAATAGATAATAGCT
          1 AAATAAATAGATAATAGCT

                   
        505 AAATAAA
          1 AAATAAA

        512 AGGAAAAATT


Statistics
Matches: 25,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  18   17  0.68
  19    8  0.32

ACGTcount: A:0.64, C:0.02, G:0.09, T:0.25


Consensus pattern (19 bp):   
AAATAAATAGATAATAGCT

Found at i:900 original size:16 final size:16

Alignment explanation


    Indices: 874--916  Score: 59
    Period size: 16  Copynumber: 2.6  Consensus size: 16

        864 AAGCTATTAA

                             
        874 AAATAAAATTAAATCCT
          1 AAAT-AAATTAAATCCT

                       *    
        891 AAATAAATTAATTCCT
          1 AAATAAATTAAATCCT

              *       
        907 AATTAAATTA
          1 AAATAAATTA

        917 TGAAATTAAG


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  16   20  0.83
  17    4  0.17

ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35


Consensus pattern (16 bp):   
AAATAAATTAAATCCT

Found at i:1512 original size:16 final size:16

Alignment explanation


    Indices: 1491--1529  Score: 53
    Period size: 15  Copynumber: 2.5  Consensus size: 16

       1481 TGTGTAAGTG

                            
       1491 ACCCGAACCTGAATTA
          1 ACCCGAACCTGAATTA

                    *       
       1507 ACCCGAA-TTGAATTA
          1 ACCCGAACCTGAATTA

             *      
       1522 AACCGAAC
          1 ACCCGAAC

       1530 TCAATTTATG


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  15   13  0.65
  16    7  0.35

ACGTcount: A:0.41, C:0.28, G:0.13, T:0.18


Consensus pattern (16 bp):   
ACCCGAACCTGAATTA

Found at i:2453 original size:25 final size:24

Alignment explanation


    Indices: 2419--2477  Score: 75
    Period size: 25  Copynumber: 2.5  Consensus size: 24

       2409 TTCAAACCCT

                               * *   
       2419 AAACTTCATTTCTAACAACTTTTTC
          1 AAACTTCATTTCTAACAA-ATCTTC

                       *            
       2444 AAACTTCATTTTTAACAAATCTTC
          1 AAACTTCATTTCTAACAAATCTTC

                       
       2468 AAA-TTCATTT
          1 AAACTTCATTT

       2478 TCCTTCATTT


Statistics
Matches: 31,  Mismatches: 3, Indels: 2
        0.86            0.08        0.06

Matches are distributed among these distances:
  23    7  0.23
  24    7  0.23
  25   17  0.55

ACGTcount: A:0.36, C:0.20, G:0.00, T:0.44


Consensus pattern (24 bp):   
AAACTTCATTTCTAACAAATCTTC

Found at i:2516 original size:26 final size:26

Alignment explanation


    Indices: 2487--2550  Score: 92
    Period size: 26  Copynumber: 2.5  Consensus size: 26

       2477 TTCCTTCATT

                                      
       2487 TTAATCATAAACTAATTAAATACTAA
          1 TTAATCATAAACTAATTAAATACTAA

                 *            *   *   
       2513 TTAATAATAAACTAATTAGATATTAA
          1 TTAATCATAAACTAATTAAATACTAA

                *       
       2539 TTAAACATAAAC
          1 TTAATCATAAAC

       2551 GAATAAACTA


Statistics
Matches: 33,  Mismatches: 5, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  26   33  1.00

ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34


Consensus pattern (26 bp):   
TTAATCATAAACTAATTAAATACTAA

Found at i:2517 original size:15 final size:15

Alignment explanation


    Indices: 2487--2530  Score: 51
    Period size: 15  Copynumber: 3.2  Consensus size: 15

       2477 TTCCTTCATT

                 *         
       2487 TTAATCATAAACTAA
          1 TTAATAATAAACTAA

                           
       2502 TT-A-AAT--ACTAA
          1 TTAATAATAAACTAA

                           
       2513 TTAATAATAAACTAA
          1 TTAATAATAAACTAA

               
       2528 TTA
          1 TTA

       2531 GATATTAATT


Statistics
Matches: 24,  Mismatches: 1, Indels: 8
        0.73            0.03        0.24

Matches are distributed among these distances:
  11    7  0.29
  12    1  0.04
  13    5  0.21
  14    1  0.04
  15   10  0.42

ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36


Consensus pattern (15 bp):   
TTAATAATAAACTAA
Done.