Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022283.1 Corchorus olitorius cultivar O-4 contig22316, 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: 12000
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31


Found at i:1171 original size:15 final size:16

Alignment explanation


    Indices: 1142--1172  Score: 55
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       1132 CTTGCCATCG

                            
       1142 CTTCATCTCTCTTACT
          1 CTTCATCTCTCTTACT

                            
       1158 CTTCATCT-TCTTACT
          1 CTTCATCTCTCTTACT

       1173 GATTGAAAGC


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  15    7  0.47
  16    8  0.53

ACGTcount: A:0.13, C:0.35, G:0.00, T:0.52


Consensus pattern (16 bp):   
CTTCATCTCTCTTACT

Found at i:2995 original size:40 final size:40

Alignment explanation


    Indices: 2929--3309  Score: 559
    Period size: 40  Copynumber: 9.6  Consensus size: 40

       2919 TTGTCTAGTC

                      *                *            
       2929 TAAATACCCAATTTGCCCTTCCCCACCAGAAGGTGTTGTT
          1 TAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTT

               * *                                  
       2969 TAATTTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTT
          1 TAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTT

                      *   *                         
       3009 TAAATACCCATTTTACCCTTCCCCACCGGAAGGTGTTGTT
          1 TAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTT

                                                     
       3049 TAAATTACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTT
          1 TAAA-TACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTT

                        *       *                   
       3090 TAAATACCCAGTCTGCCCTTTCCCACCGGAAGGTGTTGTT
          1 TAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTT

                                                   *
       3130 TAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTC
          1 TAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTT

                                      *             
       3170 TAAATACCCAGTTTGCCCTTCCCCACTGGAAGGTGTTGTT
          1 TAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTT

                                       *            
       3210 TAAATA-CCAGTTTGCCCTTCCCCACCTGAAGGTGTTGTT
          1 TAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTT

                          ** *     *       *       *
       3249 TAAATA-CCAGTTTATCTTTCCCTACCGGAAAGTGTTGTC
          1 TAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTT

                 * **             
       3288 TAAATTCTTAGTTTGCCCTTCC
          1 TAAATACCCAGTTTGCCCTTCC

       3310 TCATCGGGAG


Statistics
Matches: 307,  Mismatches: 32, Indels: 4
        0.90            0.09        0.01

Matches are distributed among these distances:
  39   68  0.22
  40  201  0.65
  41   38  0.12

ACGTcount: A:0.21, C:0.29, G:0.18, T:0.33


Consensus pattern (40 bp):   
TAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTT

Found at i:3149 original size:121 final size:120

Alignment explanation


    Indices: 2926--3309  Score: 583
    Period size: 121  Copynumber: 3.2  Consensus size: 120

       2916 GTCTTGTCTA

                         *                *               * *                
       2926 GTCTAAATACCCAATTTGCCCTTCCCCACCAGAAGGTGTTGTTTAATTTCCCAGTTTGCCCTTCC
          1 GTCTAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACCCAGTTTGCCCTTCC

                                        *                          
       2991 CCACCGGAAGGTGTTGTTTAAATACCCATTTTACCCTTCCCCACCGGAAGGTGTT
         66 CCACCGGAAGGTGTTGTTTAAATACCCAGTTTACCCTTCCCCACCGGAAGGTGTT

              *                                                     *       *
       3046 GTTTAAATTACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACCCAGTCTGCCCTTT
          1 GTCTAAA-TACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACCCAGTTTGCCCTTC

                                             *                      
       3111 CCCACCGGAAGGTGTTGTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTT
         65 CCCACCGGAAGGTGTTGTTTAAATACCCAGTTTACCCTTCCCCACCGGAAGGTGTT

                                         *                                   
       3167 GTCTAAATACCCAGTTTGCCCTTCCCCACTGGAAGGTGTTGTTTAAATA-CCAGTTTGCCCTTCC
          1 GTCTAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACCCAGTTTGCCCTTCC

                 *                           * *     *       *     
       3231 CCACCTGAAGGTGTTGTTTAAATA-CCAGTTTATCTTTCCCTACCGGAAAGTGTT
         66 CCACCGGAAGGTGTTGTTTAAATACCCAGTTTACCCTTCCCCACCGGAAGGTGTT

                    * **             
       3285 GTCTAAATTCTTAGTTTGCCCTTCC
          1 GTCTAAATACCCAGTTTGCCCTTCC

       3310 TCATCGGGAG


Statistics
Matches: 241,  Mismatches: 22, Indels: 4
        0.90            0.08        0.01

Matches are distributed among these distances:
 118   47  0.20
 119   36  0.15
 120   47  0.20
 121  111  0.46

ACGTcount: A:0.21, C:0.29, G:0.18, T:0.33


Consensus pattern (120 bp):   
GTCTAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACCCAGTTTGCCCTTCC
CCACCGGAAGGTGTTGTTTAAATACCCAGTTTACCCTTCCCCACCGGAAGGTGTT

Found at i:4171 original size:22 final size:21

Alignment explanation


    Indices: 4149--4190  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       4139 CCCACATGGT

                     *     *     
       4149 TTCCTTGAGCACCCATGTGGG
          1 TTCCTTGAGAACCCAGGTGGG

              *                  
       4170 TTGCTTGAGAACCCAGGTGGG
          1 TTCCTTGAGAACCCAGGTGGG

       4191 CAGTGTCACG


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.17, C:0.24, G:0.33, T:0.26


Consensus pattern (21 bp):   
TTCCTTGAGAACCCAGGTGGG

Found at i:11818 original size:26 final size:23

Alignment explanation


    Indices: 11763--11826  Score: 65
    Period size: 24  Copynumber: 2.6  Consensus size: 23

      11753 AAAGTTCAAA

                            *       
      11763 TCAAAAAGAAGAAAAAGGAAAAAT
          1 TCAAAAAGAA-AAAAAAGAAAAAT

                                      
      11787 TCAAAAAGAAAAGAAAAGAAAGAAGT
          1 TCAAAAAGAAAA-AAAAGAAA-AA-T

             *      *     
      11813 TGAAAAAGTAAAAA
          1 TCAAAAAGAAAAAA

      11827 TGGACGAAAG


Statistics
Matches: 34,  Mismatches: 3, Indels: 5
        0.81            0.07        0.12

Matches are distributed among these distances:
  23    2  0.06
  24   17  0.50
  25    4  0.12
  26   11  0.32

ACGTcount: A:0.70, C:0.03, G:0.17, T:0.09


Consensus pattern (23 bp):   
TCAAAAAGAAAAAAAAGAAAAAT
Done.