Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014876.1 Corchorus olitorius cultivar O-4 contig14909, 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: 13337
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34


Found at i:1425 original size:21 final size:21

Alignment explanation


    Indices: 1374--1437  Score: 78
    Period size: 21  Copynumber: 3.1  Consensus size: 21

       1364 TTGACACTGT

                          *      
       1374 TTAGGAACTGTACATATGAGA
          1 TTAGGAACTGTACAGATGAGA

                 *           *   
       1395 TTA--CACTGTACAGATTAGA
          1 TTAGGAACTGTACAGATGAGA

                 *               
       1414 TTAGGTACTGTACAGATGAGA
          1 TTAGGAACTGTACAGATGAGA

               
       1435 TTA
          1 TTA

       1438 TTAGAACAGC


Statistics
Matches: 36,  Mismatches: 5, Indels: 4
        0.80            0.11        0.09

Matches are distributed among these distances:
  19   16  0.44
  21   20  0.56

ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31


Consensus pattern (21 bp):   
TTAGGAACTGTACAGATGAGA

Found at i:2743 original size:12 final size:12

Alignment explanation


    Indices: 2726--2750  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

       2716 ACAAAAGTTG

                        
       2726 CTAAATTAATAA
          1 CTAAATTAATAA

                        
       2738 CTAAATTAATAA
          1 CTAAATTAATAA

             
       2750 C
          1 C

       2751 AACCACATAA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32


Consensus pattern (12 bp):   
CTAAATTAATAA

Found at i:3153 original size:42 final size:43

Alignment explanation


    Indices: 3106--3188  Score: 125
    Period size: 42  Copynumber: 2.0  Consensus size: 43

       3096 CGTGTTTGGC

                                          *             
       3106 TTATCGTGTCTCGTGT-CTGAATCGTGTC-GGACACGATTAAGA
          1 TTATCGTGTCTCGTGTCCT-AATCGTGTCAAGACACGATTAAGA

                     *                               
       3148 TTATCGTGTTTCGTGTCCTAATCGTGTCAAGACACGATTAA
          1 TTATCGTGTCTCGTGTCCTAATCGTGTCAAGACACGATTAA

       3189 CACGTTTAAG


Statistics
Matches: 37,  Mismatches: 2, Indels: 3
        0.88            0.05        0.07

Matches are distributed among these distances:
  42   24  0.65
  43   13  0.35

ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35


Consensus pattern (43 bp):   
TTATCGTGTCTCGTGTCCTAATCGTGTCAAGACACGATTAAGA

Found at i:12922 original size:2 final size:2

Alignment explanation


    Indices: 12915--12980  Score: 66
    Period size: 2  Copynumber: 32.5  Consensus size: 2

      12905 AATAATAATC

                                                                          * 
      12915 AT AT AT AT CAT AT A- AT AT CAT AT A- AT AT AT AT AT AT AT AT GT
          1 AT AT AT AT -AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT

                                                
      12957 AT CAT AT AT AT CAT AT AT -T AT AT A
          1 AT -AT AT AT AT -AT AT AT AT AT AT A

      12981 ATGATAACAA


Statistics
Matches: 55,  Mismatches: 2, Indels: 14
        0.77            0.03        0.20

Matches are distributed among these distances:
   1    3  0.05
   2   44  0.80
   3    8  0.15

ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45


Consensus pattern (2 bp):   
AT

Found at i:12940 original size:30 final size:28

Alignment explanation


    Indices: 12906--12982  Score: 99
    Period size: 26  Copynumber: 2.8  Consensus size: 28

      12896 ATTTGTAAAA

                                          
      12906 ATAATAATCATATATATCATATAATATCAT
          1 ATAAT-ATCATATATAT-ATATAATATCAT

                                 *      
      12936 ATAATAT-ATATATATATAT-GTATCAT
          1 ATAATATCATATATATATATAATATCAT

                                   
      12962 AT-ATATCATATAT-TATATAAT
          1 ATAATATCATATATATATATAAT

      12983 GATAACAATG


Statistics
Matches: 43,  Mismatches: 2, Indels: 8
        0.81            0.04        0.15

Matches are distributed among these distances:
  25    9  0.21
  26   15  0.35
  27    4  0.09
  28    8  0.19
  29    2  0.05
  30    5  0.12

ACGTcount: A:0.48, C:0.06, G:0.01, T:0.44


Consensus pattern (28 bp):   
ATAATATCATATATATATATAATATCAT
Done.