Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019246.1 Corchorus olitorius cultivar O-4 contig19279, 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: 5520
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--32  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

                                                           
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

         33 TAGAAAACCC


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:296 original size:2 final size:2

Alignment explanation


    Indices: 271--328  Score: 72
    Period size: 2  Copynumber: 31.0  Consensus size: 2

        261 TTAAAACTAC

                                                                           
        271 TA TA TA T- TA T- TA TA T- TA TA T- TA TA TA TA GTA -A TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA

                                         
        309 TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA

        329 CATGGTAAAA


Statistics
Matches: 50,  Mismatches: 0, Indels: 12
        0.81            0.00        0.19

Matches are distributed among these distances:
   1    5  0.10
   2   43  0.86
   3    2  0.04

ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:1173 original size:21 final size:22

Alignment explanation


    Indices: 1147--1205  Score: 72
    Period size: 21  Copynumber: 2.9  Consensus size: 22

       1137 GTAGTCGAAA

                                  
       1147 ATATTATTATTATAT-TATACT
          1 ATATTATTATTATATATATACT

                       *        * 
       1168 ATATTATTATTGT-TATATATT
          1 ATATTATTATTATATATATACT

                               
       1189 ATA-TATTA-TATATATAT
          1 ATATTATTATTATATATAT

       1206 TAGAACCAAC


Statistics
Matches: 33,  Mismatches: 3, Indels: 5
        0.80            0.07        0.12

Matches are distributed among these distances:
  19    2  0.06
  20   11  0.33
  21   20  0.61

ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58


Consensus pattern (22 bp):   
ATATTATTATTATATATATACT

Found at i:1174 original size:18 final size:17

Alignment explanation


    Indices: 1147--1207  Score: 69
    Period size: 16  Copynumber: 3.8  Consensus size: 17

       1137 GTAGTCGAAA

                             
       1147 ATAT-TATTATTATATT
          1 ATATATATTATTATATT

                               
       1163 ATACTATATTATTAT-TGT
          1 ATA-TATATTATTATAT-T

                             
       1181 -TATATATTA-TATATT
          1 ATATATATTATTATATT

                         
       1196 ATATATA-TATTA
          1 ATATATATTATTA

       1208 GAACCAACCC


Statistics
Matches: 39,  Mismatches: 0, Indels: 12
        0.76            0.00        0.24

Matches are distributed among these distances:
  15    6  0.15
  16   19  0.49
  17    4  0.10
  18   10  0.26

ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57


Consensus pattern (17 bp):   
ATATATATTATTATATT

Found at i:1186 original size:16 final size:18

Alignment explanation


    Indices: 1147--1207  Score: 67
    Period size: 18  Copynumber: 3.6  Consensus size: 18

       1137 GTAGTCGAAA

                               
       1147 ATAT-TATTATTATATTAT
          1 ATATATATTA-TATATTAT

              *             * 
       1165 A-CTATATTAT-TATTGT
          1 ATATATATTATATATTAT

                              
       1181 -TATATATTATATATTAT
          1 ATATATATTATATATTAT

                      
       1198 ATATATATTA
          1 ATATATATTA

       1208 GAACCAACCC


Statistics
Matches: 35,  Mismatches: 4, Indels: 8
        0.74            0.09        0.17

Matches are distributed among these distances:
  16   13  0.37
  17    7  0.20
  18   15  0.43

ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57


Consensus pattern (18 bp):   
ATATATATTATATATTAT

Found at i:3212 original size:31 final size:31

Alignment explanation


    Indices: 3174--3235  Score: 115
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       3164 GAGTTTTGTA

                               *           
       3174 AAACTTTTGAATCGCCTATTATACCCTTATT
          1 AAACTTTTGAATCGCCTATCATACCCTTATT

                                           
       3205 AAACTTTTGAATCGCCTATCATACCCTTATT
          1 AAACTTTTGAATCGCCTATCATACCCTTATT

       3236 TTTAGAATAT


Statistics
Matches: 30,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  31   30  1.00

ACGTcount: A:0.29, C:0.24, G:0.06, T:0.40


Consensus pattern (31 bp):   
AAACTTTTGAATCGCCTATCATACCCTTATT
Done.