Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011672.1 Corchorus capsularis cultivar CVL-1 contig11693, 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: 11654
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.31


Found at i:4080 original size:17 final size:17

Alignment explanation


    Indices: 4054--4120  Score: 116
    Period size: 17  Copynumber: 3.9  Consensus size: 17

       4044 CCACCCTCAT

                             
       4054 GGTACCAGGTAGCATGA
          1 GGTACCAGGTAGCATGA

                 *           
       4071 GGTACTAGGTAGCATGA
          1 GGTACCAGGTAGCATGA

             *               
       4088 GATACCAGGTAGCATGA
          1 GGTACCAGGTAGCATGA

                            
       4105 GGTACCAGGTAGCATG
          1 GGTACCAGGTAGCATG

       4121 TGTGACAACT


Statistics
Matches: 46,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  17   46  1.00

ACGTcount: A:0.30, C:0.16, G:0.34, T:0.19


Consensus pattern (17 bp):   
GGTACCAGGTAGCATGA

Found at i:6688 original size:14 final size:14

Alignment explanation


    Indices: 6661--6698  Score: 58
    Period size: 14  Copynumber: 2.6  Consensus size: 14

       6651 GGATTAGCCG

                     *     
       6661 CTCCTCTCTTCCCTT
          1 CTCC-CTCTCCCCTT

                          
       6676 CTCCCTCTCCCCTT
          1 CTCCCTCTCCCCTT

                     
       6690 CTCCCTCTC
          1 CTCCCTCTC

       6699 TAGTTCTCGT


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  14   18  0.82
  15    4  0.18

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


Consensus pattern (14 bp):   
CTCCCTCTCCCCTT

Found at i:6859 original size:26 final size:26

Alignment explanation


    Indices: 6824--6875  Score: 70
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       6814 GTTTTATTTG

                           *          
       6824 AGTTTGTTTTGAGTCGGTTT-GAGTC
          1 AGTTTGTTTTGAGTCAGTTTCGAGTC

                       *               
       6849 AGTTTGTTTTTTAGTCAGTTTCGAGTC
          1 AGTTTG-TTTTGAGTCAGTTTCGAGTC

       6876 TAGTGATCGA


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  25    6  0.26
  26   12  0.52
  27    5  0.22

ACGTcount: A:0.13, C:0.10, G:0.27, T:0.50


Consensus pattern (26 bp):   
AGTTTGTTTTGAGTCAGTTTCGAGTC

Found at i:7141 original size:19 final size:18

Alignment explanation


    Indices: 7117--7152  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       7107 TGAAGATTTC

                               
       7117 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
       7136 TTGAAGATCATTGAAGA
          1 TTGAAGATAATTGAAGA

       7153 ATTATTTCAA


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:0.03, G:0.22, T:0.33


Consensus pattern (18 bp):   
TTGAAGATAATTGAAGAT
Done.