Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016746.1 Corchorus olitorius cultivar O-4 contig16779, 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: 9232
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35


Found at i:1203 original size:17 final size:17

Alignment explanation


    Indices: 1181--1214  Score: 50
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       1171 CTAACACTAG

                             
       1181 GGAAAATACTAGGGAAA
          1 GGAAAATACTAGGGAAA

                   **        
       1198 GGAAAATTTTAGGGAAA
          1 GGAAAATACTAGGGAAA

       1215 ATTGAAATCA


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.50, C:0.03, G:0.29, T:0.18


Consensus pattern (17 bp):   
GGAAAATACTAGGGAAA

Found at i:1293 original size:12 final size:12

Alignment explanation


    Indices: 1273--1307  Score: 52
    Period size: 12  Copynumber: 2.9  Consensus size: 12

       1263 TATTTGTTGT

                        
       1273 CAAGGAAAATAC
          1 CAAGGAAAATAC

            * *         
       1285 TATGGAAAATAC
          1 CAAGGAAAATAC

                       
       1297 CAAGGAAAATA
          1 CAAGGAAAATA

       1308 TTTTCTCAAG


Statistics
Matches: 19,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  12   19  1.00

ACGTcount: A:0.57, C:0.11, G:0.17, T:0.14


Consensus pattern (12 bp):   
CAAGGAAAATAC

Found at i:2072 original size:2 final size:2

Alignment explanation


    Indices: 2059--2095  Score: 65
    Period size: 2  Copynumber: 18.5  Consensus size: 2

       2049 AAAGCTATTG

                   *                                               
       2059 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       2096 ACAACTATTG


Statistics
Matches: 33,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46


Consensus pattern (2 bp):   
AT

Found at i:7785 original size:18 final size:18

Alignment explanation


    Indices: 7762--7798  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       7752 CGGTTATTTG

                        *     
       7762 TTTGGTTTCTTTTCTTAT
          1 TTTGGTTTCTTTGCTTAT

                    *         
       7780 TTTGGTTTGTTTGCTTAT
          1 TTTGGTTTCTTTGCTTAT

             
       7798 T
          1 T

       7799 GGGCTATTGT


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

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.05, C:0.08, G:0.16, T:0.70


Consensus pattern (18 bp):   
TTTGGTTTCTTTGCTTAT

Found at i:7864 original size:2 final size:2

Alignment explanation


    Indices: 7857--7894  Score: 76
    Period size: 2  Copynumber: 19.0  Consensus size: 2

       7847 TTTTATTTGT

                                                                    
       7857 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       7895 CTAAGGACCC


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   36  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:8434 original size:25 final size:25

Alignment explanation


    Indices: 8391--8441  Score: 61
    Period size: 23  Copynumber: 2.0  Consensus size: 25

       8381 TGATAAATTT

                                       
       8391 TTATATATAGTTATGATTTCTTAAAAA
          1 TTATATATAGTTATGA-TT-TTAAAAA

                  *                  
       8418 TTATATGTA-TTAT-ATTTTAAAAA
          1 TTATATATAGTTATGATTTTAAAAA

             
       8441 T
          1 T

       8442 AATGTGGAGA


Statistics
Matches: 23,  Mismatches: 1, Indels: 4
        0.82            0.04        0.14

Matches are distributed among these distances:
  23    8  0.35
  24    2  0.09
  25    1  0.04
  26    4  0.17
  27    8  0.35

ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51


Consensus pattern (25 bp):   
TTATATATAGTTATGATTTTAAAAA
Done.