Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009762.1 Corchorus capsularis cultivar CVL-1 contig09783, 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: 8269
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40


Found at i:1188 original size:110 final size:109

Alignment explanation


    Indices: 1054--1258  Score: 234
    Period size: 108  Copynumber: 1.9  Consensus size: 109

       1044 ATCATTAAGA

                              *                 *                *    *  *   
       1054 ATGATAAGAACCGAGTGAAAAAAAAAACTCTATAA-TTAAAATGATTTGCTAGCCACACATTAAG
          1 ATGATAAGAACCGA--GAGAAAAAAAACTCTA-AAGCTAAAATGATTTGCTAGACACAAATCAAG

                    *                                      
       1118 AATGCTCGTCGCGCCAGCGCGAGCCGAT-AACTACCTATTCACATAT
         63 AATGCTCGACGCGCCAGCGCGAGCCGATCAACTACCTATTCACATAT

                      *      **      * *                  *                  
       1164 ATGATAAGAATCGAGAGGGAAAAAATTTTAAAGCTAAAATGATTTGTTAGACACAAATCAAGAAT
          1 ATGATAAGAACCGAGAGAAAAAAAACTCTAAAGCTAAAATGATTTGCTAGACACAAATCAAGAAT

                      *    **             
       1229 GCTCGACGCGTCAGCTTGAGCCGATCAACT
         66 GCTCGACGCGCCAGCGCGAGCCGATCAACT

       1259 TGTAATAGAT


Statistics
Matches: 78,  Mismatches: 15, Indels: 5
        0.80            0.15        0.05

Matches are distributed among these distances:
 107    2  0.03
 108   59  0.76
 109    4  0.05
 110   13  0.17

ACGTcount: A:0.40, C:0.19, G:0.19, T:0.23


Consensus pattern (109 bp):   
ATGATAAGAACCGAGAGAAAAAAAACTCTAAAGCTAAAATGATTTGCTAGACACAAATCAAGAAT
GCTCGACGCGCCAGCGCGAGCCGATCAACTACCTATTCACATAT

Found at i:3070 original size:3 final size:3

Alignment explanation


    Indices: 3062--3103  Score: 84
    Period size: 3  Copynumber: 14.0  Consensus size: 3

       3052 ATTACTAACT

                                                                   
       3062 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA

       3104 AAAAATTATT


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   39  1.00

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (3 bp):   
TAA

Found at i:3701 original size:21 final size:21

Alignment explanation


    Indices: 3675--3720  Score: 83
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       3665 ATTCGGATAA

                   *             
       3675 CTTTGCATACCATTATTTTTC
          1 CTTTGCAGACCATTATTTTTC

                                 
       3696 CTTTGCAGACCATTATTTTTC
          1 CTTTGCAGACCATTATTTTTC

                
       3717 CTTT
          1 CTTT

       3721 TTTTTTTGAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  21   24  1.00

ACGTcount: A:0.17, C:0.24, G:0.07, T:0.52


Consensus pattern (21 bp):   
CTTTGCAGACCATTATTTTTC
Done.