Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014651.1 Corchorus olitorius cultivar O-4 contig14684, 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: 24105
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:1288 original size:15 final size:15

Alignment explanation


    Indices: 1268--1297  Score: 60
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       1258 AATATTCAAA

                           
       1268 ATCAAAATCAAAATG
          1 ATCAAAATCAAAATG

                           
       1283 ATCAAAATCAAAATG
          1 ATCAAAATCAAAATG

       1298 CTAAAGTCAG


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.60, C:0.13, G:0.07, T:0.20


Consensus pattern (15 bp):   
ATCAAAATCAAAATG

Found at i:1577 original size:14 final size:14

Alignment explanation


    Indices: 1534--1584  Score: 59
    Period size: 14  Copynumber: 3.6  Consensus size: 14

       1524 ATATATTAGT

                          
       1534 ATTATTATTATGAG
          1 ATTATTATTATGAG

                  *  *  *  
       1548 ATT-TTTTTTTAAAG
          1 ATTATTATTAT-GAG

                          
       1562 ATTATTATTATGAG
          1 ATTATTATTATGAG

                     
       1576 ATTATTATT
          1 ATTATTATT

       1585 TCTTAATCTT


Statistics
Matches: 29,  Mismatches: 6, Indels: 4
        0.74            0.15        0.10

Matches are distributed among these distances:
  13    5  0.17
  14   19  0.66
  15    5  0.17

ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57


Consensus pattern (14 bp):   
ATTATTATTATGAG

Found at i:1897 original size:5 final size:5

Alignment explanation


    Indices: 1887--1917  Score: 62
    Period size: 5  Copynumber: 6.2  Consensus size: 5

       1877 TGTCACTGAC

                                                 
       1887 ACACA ACACA ACACA ACACA ACACA ACACA A
          1 ACACA ACACA ACACA ACACA ACACA ACACA A

       1918 AGAGAAAGAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   26  1.00

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


Consensus pattern (5 bp):   
ACACA

Found at i:12126 original size:5 final size:5

Alignment explanation


    Indices: 12116--12146  Score: 62
    Period size: 5  Copynumber: 6.2  Consensus size: 5

      12106 CTTCTTCCAC

                                                 
      12116 TCTGT TCTGT TCTGT TCTGT TCTGT TCTGT T
          1 TCTGT TCTGT TCTGT TCTGT TCTGT TCTGT T

      12147 ATAATAACAG


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   26  1.00

ACGTcount: A:0.00, C:0.19, G:0.19, T:0.61


Consensus pattern (5 bp):   
TCTGT

Found at i:15199 original size:29 final size:29

Alignment explanation


    Indices: 15165--15239  Score: 96
    Period size: 29  Copynumber: 2.6  Consensus size: 29

      15155 ACTTGTAGCG

                  *          *       *   
      15165 TTTGGATGTTTTGCCCCCTAAACTTTAAT
          1 TTTGGACGTTTTGCCCCATAAACTTCAAT

                   *     *               
      15194 TTTGGACATTTTGTCCCATAAACTTCAAT
          1 TTTGGACGTTTTGCCCCATAAACTTCAAT

                             
      15223 TTTGGGACGTTTTGCCC
          1 TTT-GGACGTTTTGCCC

      15240 TCTCATGCTA


Statistics
Matches: 38,  Mismatches: 7, Indels: 1
        0.83            0.15        0.02

Matches are distributed among these distances:
  29   27  0.71
  30   11  0.29

ACGTcount: A:0.20, C:0.21, G:0.16, T:0.43


Consensus pattern (29 bp):   
TTTGGACGTTTTGCCCCATAAACTTCAAT

Found at i:15458 original size:29 final size:29

Alignment explanation


    Indices: 15407--15485  Score: 115
    Period size: 29  Copynumber: 2.7  Consensus size: 29

      15397 CGTTAGGCTG

                  *                   *   
      15407 AGGGGGTAAAACGTCCCAAAATTGAAGTTC
          1 AGGGGGCAAAACGTCCC-AAATTGAAATTC

                       *                 
      15437 AGGGGGCAAAATGTCCCAAATTGAAATTC
          1 AGGGGGCAAAACGTCCCAAATTGAAATTC

                                 
      15466 AGGGGGCAAAACGT-CCAAAT
          1 AGGGGGCAAAACGTCCCAAAT

      15486 GCTACAAATT


Statistics
Matches: 45,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
  28    6  0.13
  29   24  0.53
  30   15  0.33

ACGTcount: A:0.38, C:0.18, G:0.27, T:0.18


Consensus pattern (29 bp):   
AGGGGGCAAAACGTCCCAAATTGAAATTC
Done.