Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010149.1 Corchorus capsularis cultivar CVL-1 contig10170, 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: 7772
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:1924 original size:17 final size:16

Alignment explanation


    Indices: 1900--1949  Score: 55
    Period size: 17  Copynumber: 3.0  Consensus size: 16

       1890 GTAGGTAGGT

                            
       1900 AAGAAATAGGAAGGAA
          1 AAGAAATAGGAAGGAA

                      *       
       1916 AAGGAAATAGCAAGGGAA
          1 AA-GAAATAGGAA-GGAA

                 *    *     
       1934 AAGAATTAGGGAGGAA
          1 AAGAAATAGGAAGGAA

       1950 GGGAAAGCAA


Statistics
Matches: 28,  Mismatches: 4, Indels: 4
        0.78            0.11        0.11

Matches are distributed among these distances:
  16    6  0.21
  17   16  0.57
  18    6  0.21

ACGTcount: A:0.56, C:0.02, G:0.34, T:0.08


Consensus pattern (16 bp):   
AAGAAATAGGAAGGAA

Found at i:3215 original size:108 final size:108

Alignment explanation


    Indices: 3055--3312  Score: 396
    Period size: 108  Copynumber: 2.4  Consensus size: 108

       3045 TGGAATTAAA

                                              *                              
       3055 TATCCGTCGATATCTTGAT--ATATCCGTCGATATAT-TCGATATCTGTACCCCTCGATATAAAT
          1 TATCCGTCGATAT-TT-ATCGATAT-C-TCGATAAATCTCGATATCTGTACCCCTCGATATAAAT

                                                  *  *    *
       3117 ATCCATAAAAATTTCAATGTCACGAAATATCCGTCGATGTATCCGTT
         62 ATCCATAAAAATTTCAATGTCACGAAATATCCGTCGATATAGCCGTG

                 *                                     *                     
       3164 TATCCTTCGATATTTATCGATATCTCGATAAATCTCGATATCTTTACCCCTCGATATAAATATCC
          1 TATCCGTCGATATTTATCGATATCTCGATAAATCTCGATATCTGTACCCCTCGATATAAATATCC

                                          *            
       3229 ATAAAAATTTCAATGTCACGAAATATCCGTTGATATAGCCGTG
         66 ATAAAAATTTCAATGTCACGAAATATCCGTCGATATAGCCGTG

                                                     
       3272 TATCCGTCGATATTTATCGATATCTCGATAAATCTCGATAT
          1 TATCCGTCGATATTTATCGATATCTCGATAAATCTCGATAT

       3313 ATCCGTAAAT


Statistics
Matches: 138,  Mismatches: 8, Indels: 7
        0.90            0.05        0.05

Matches are distributed among these distances:
 107   10  0.07
 108  112  0.81
 109   16  0.12

ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36


Consensus pattern (108 bp):   
TATCCGTCGATATTTATCGATATCTCGATAAATCTCGATATCTGTACCCCTCGATATAAATATCC
ATAAAAATTTCAATGTCACGAAATATCCGTCGATATAGCCGTG

Found at i:4691 original size:13 final size:13

Alignment explanation


    Indices: 4673--4697  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       4663 TCATCGATAC

                         
       4673 TTCGATATATCCG
          1 TTCGATATATCCG

                        
       4686 TTCGATATATCC
          1 TTCGATATATCC

       4698 ATCGATACCT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.24, C:0.24, G:0.12, T:0.40


Consensus pattern (13 bp):   
TTCGATATATCCG

Found at i:6379 original size:55 final size:55

Alignment explanation


    Indices: 6320--6425  Score: 194
    Period size: 55  Copynumber: 1.9  Consensus size: 55

       6310 AATAGCTTGA

                                                                   
       6320 TCCTGATGGTGTTGCCTTCAACTTATCATTCAGATCATCTGGACCAAAAAATTGG
          1 TCCTGATGGTGTTGCCTTCAACTTATCATTCAGATCATCTGGACCAAAAAATTGG

                          *      *                             
       6375 TCCTGATGGTGTTGTCTTCAATTTATCATTCAGATCATCTGGACCAAAAAA
          1 TCCTGATGGTGTTGCCTTCAACTTATCATTCAGATCATCTGGACCAAAAAA

       6426 AAAAAAATGG


Statistics
Matches: 49,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  55   49  1.00

ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34


Consensus pattern (55 bp):   
TCCTGATGGTGTTGCCTTCAACTTATCATTCAGATCATCTGGACCAAAAAATTGG

Found at i:7409 original size:2 final size:2

Alignment explanation


    Indices: 7402--7434  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

       7392 CAATCAATCA

                                                             
       7402 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       7435 ATCAAGTTGT


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.