Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010760.1 Corchorus olitorius cultivar O-4 contig10792, 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: 4367
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30


Found at i:631 original size:21 final size:22

Alignment explanation


    Indices: 579--632  Score: 60
    Period size: 21  Copynumber: 2.6  Consensus size: 22

        569 GGGATTGGAG

                           *      
        579 TATTTA-TTTATTTTGTTGCTT
          1 TATTTATTTTATTTTCTTGCTT

            *      *              
        600 AATTT-TATTATTTTCTTG-TT
          1 TATTTATTTTATTTTCTTGCTT

                         
        620 TATTTATTTTATT
          1 TATTTATTTTATT

        633 GTTCACATAA


Statistics
Matches: 26,  Mismatches: 5, Indels: 4
        0.74            0.14        0.11

Matches are distributed among these distances:
  20    6  0.23
  21   20  0.77

ACGTcount: A:0.19, C:0.04, G:0.06, T:0.72


Consensus pattern (22 bp):   
TATTTATTTTATTTTCTTGCTT

Found at i:1478 original size:22 final size:22

Alignment explanation


    Indices: 1451--1508  Score: 82
    Period size: 21  Copynumber: 2.7  Consensus size: 22

       1441 AGTTTAGTTT

                 *                
       1451 TCAAATTTTCATAGGGGGT-AA
          1 TCAAAATTTCATAGGGGGTAAA

                          * *     
       1472 TCAAAATTTCATAGTGTGTAAA
          1 TCAAAATTTCATAGGGGGTAAA

                           
       1494 TCAAAATTTCATAGG
          1 TCAAAATTTCATAGG

       1509 TAGGCTAATA


Statistics
Matches: 32,  Mismatches: 4, Indels: 1
        0.86            0.11        0.03

Matches are distributed among these distances:
  21   16  0.50
  22   16  0.50

ACGTcount: A:0.38, C:0.10, G:0.17, T:0.34


Consensus pattern (22 bp):   
TCAAAATTTCATAGGGGGTAAA

Found at i:1498 original size:43 final size:43

Alignment explanation


    Indices: 1409--1528  Score: 118
    Period size: 43  Copynumber: 2.7  Consensus size: 43

       1399 AACATTATCA

                          *  *          *      *    **  
       1409 AAATTTTCATGAGGAGGAAATCAAAATTCCATAGTTTAGTTTTC
          1 AAATTTTCAT-AGGGGGTAATCAAAATTTCATAGTGTAGTAATC

                                                        
       1453 AAATTTTCATAGGGGGTAATCAAAATTTCATAGTGT-GTAAATC
          1 AAATTTTCATAGGGGGTAATCAAAATTTCATAGTGTAGT-AATC

               *             *                
       1496 AAAATTTCATAGGTAGGCTAAT-AAAATTTCATA
          1 AAATTTTCATAGG--GGGTAATCAAAATTTCATA

       1529 ACTATCAAAA


Statistics
Matches: 65,  Mismatches: 8, Indels: 6
        0.82            0.10        0.08

Matches are distributed among these distances:
  42    2  0.03
  43   36  0.55
  44   21  0.32
  45    6  0.09

ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35


Consensus pattern (43 bp):   
AAATTTTCATAGGGGGTAATCAAAATTTCATAGTGTAGTAATC

Found at i:3558 original size:19 final size:18

Alignment explanation


    Indices: 3534--3569  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       3524 TGAAGATTTA

                               
       3534 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
       3553 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

       3570 AATATTTCCA


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.