Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001399.1 Corchorus capsularis cultivar CVL-1 contig01399, 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: 2666
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33


Found at i:1853 original size:127 final size:127

Alignment explanation


    Indices: 1702--1944  Score: 357
    Period size: 127  Copynumber: 1.9  Consensus size: 127

       1692 TGATGAAGTG

                                                   *     *  *                
       1702 AATAAATAATACATAATTTTATGGTCAAT-AAGTGCTTTTACATTGAATTGGTTAAAAACTCTTG
          1 AATAAATAATACATAATTTTATGGTCAATGAA-TGCTTTCACATTCAACTGGTTAAAAAC-CTTG

            *             *   **                                             
       1766 TAATTACAAAAAAATG-CTGGAGGAATAA-GGAATGGTGAGAAACTAATTGAGGACTTCTTTGTA
         64 CAATTACAAAAAAAGGACCAGAGGAA-AACGGAATGGTGAGAAACTAATTGAGGACTTCTTTGTA

                          *                                      *           
       1829 AATAAATAATACATGATTTTATGGTCAATGAATGCTTTCACATTCAACTGGTTGAAAACCTTGCA
          1 AATAAATAATACATAATTTTATGGTCAATGAATGCTTTCACATTCAACTGGTTAAAAACCTTGCA

                                                               
       1894 ATTACAAAAAAAGGACCAGAGGAAAACGGAATGGTGAGAAACTAATTGAGG
         66 ATTACAAAAAAAGGACCAGAGGAAAACGGAATGGTGAGAAACTAATTGAGG

       1945 GTCTTTTTAG


Statistics
Matches: 104,  Mismatches: 9, Indels: 6
        0.87            0.08        0.05

Matches are distributed among these distances:
 126   20  0.19
 127   82  0.79
 128    2  0.02

ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29


Consensus pattern (127 bp):   
AATAAATAATACATAATTTTATGGTCAATGAATGCTTTCACATTCAACTGGTTAAAAACCTTGCA
ATTACAAAAAAAGGACCAGAGGAAAACGGAATGGTGAGAAACTAATTGAGGACTTCTTTGTA

Found at i:2100 original size:21 final size:19

Alignment explanation


    Indices: 2064--2142  Score: 90
    Period size: 19  Copynumber: 4.2  Consensus size: 19

       2054 ATTGAAAATA

                                
       2064 ATATATA-ATATAGTATAGT
          1 ATATATATATATAGTATA-T

                 *       *      
       2083 ATATGGTATATATGGTATAT
          1 ATAT-ATATATATAGTATAT

                               
       2103 ATATATATATATA-TATAT
          1 ATATATATATATAGTATAT

                     *   *     
       2121 ATATATATACATACTATAT
          1 ATATATATATATAGTATAT

               
       2140 ATA
          1 ATA

       2143 ATTTTTATCC


Statistics
Matches: 52,  Mismatches: 5, Indels: 6
        0.83            0.08        0.10

Matches are distributed among these distances:
  18   17  0.33
  19   19  0.37
  20    7  0.13
  21    9  0.17

ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44


Consensus pattern (19 bp):   
ATATATATATATAGTATAT

Found at i:2103 original size:2 final size:2

Alignment explanation


    Indices: 2064--2142  Score: 79
    Period size: 2  Copynumber: 37.5  Consensus size: 2

       2054 ATTGAAAATA

                                                *            *             
       2064 AT AT AT A- AT AT AGT AT AGT AT AT GGT AT AT AT GGT AT AT AT AT
          1 AT AT AT AT AT AT A-T AT A-T AT AT -AT AT AT AT -AT AT AT AT AT

                                              *                  
       2107 AT AT AT AT AT AT AT AT AT AT AT AC AT ACT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A

       2143 ATTTTTATCC


Statistics
Matches: 65,  Mismatches: 6, Indels: 12
        0.78            0.07        0.14

Matches are distributed among these distances:
   1    1  0.02
   2   56  0.86
   3    8  0.12

ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44


Consensus pattern (2 bp):   
AT

Done.