Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006658.1 Corchorus capsularis cultivar CVL-1 contig06679, 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: 16279
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.28


Found at i:1232 original size:30 final size:30

Alignment explanation


    Indices: 1170--1232  Score: 90
    Period size: 30  Copynumber: 2.1  Consensus size: 30

       1160 CCCTGCCCCG

                            *     *    *  
       1170 AAAGCGAACATATGCTTTTTCTTCATTTTC
          1 AAAGCGAACATATGCTATTTCTGCATTCTC

                                   *      
       1200 AAAGCGAACATATGCTATTTCTGGATTCTC
          1 AAAGCGAACATATGCTATTTCTGCATTCTC

               
       1230 AAA
          1 AAA

       1233 TAGATTGGAT


Statistics
Matches: 29,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  30   29  1.00

ACGTcount: A:0.32, C:0.19, G:0.13, T:0.37


Consensus pattern (30 bp):   
AAAGCGAACATATGCTATTTCTGCATTCTC

Found at i:2568 original size:19 final size:19

Alignment explanation


    Indices: 2544--2581  Score: 76
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       2534 GCAAGAAAAG

                               
       2544 CCCTAACTATTCTATTAGT
          1 CCCTAACTATTCTATTAGT

                               
       2563 CCCTAACTATTCTATTAGT
          1 CCCTAACTATTCTATTAGT

       2582 AAAGCCTAAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   19  1.00

ACGTcount: A:0.26, C:0.26, G:0.05, T:0.42


Consensus pattern (19 bp):   
CCCTAACTATTCTATTAGT

Found at i:5471 original size:33 final size:33

Alignment explanation


    Indices: 5434--5502  Score: 138
    Period size: 33  Copynumber: 2.1  Consensus size: 33

       5424 TCGAACCCAC

                                             
       5434 ATTTTGAAAGGTTCTGTTAGGTTCTTAGTAGCA
          1 ATTTTGAAAGGTTCTGTTAGGTTCTTAGTAGCA

                                             
       5467 ATTTTGAAAGGTTCTGTTAGGTTCTTAGTAGCA
          1 ATTTTGAAAGGTTCTGTTAGGTTCTTAGTAGCA

               
       5500 ATT
          1 ATT

       5503 AGCGGCCTTT


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  33   36  1.00

ACGTcount: A:0.25, C:0.09, G:0.23, T:0.43


Consensus pattern (33 bp):   
ATTTTGAAAGGTTCTGTTAGGTTCTTAGTAGCA

Found at i:12246 original size:11 final size:11

Alignment explanation


    Indices: 12230--12256  Score: 54
    Period size: 11  Copynumber: 2.5  Consensus size: 11

      12220 GTATATCCTG

                       
      12230 TGAATCAGTTA
          1 TGAATCAGTTA

                       
      12241 TGAATCAGTTA
          1 TGAATCAGTTA

                 
      12252 TGAAT
          1 TGAAT

      12257 ATGATTCATT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   16  1.00

ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37


Consensus pattern (11 bp):   
TGAATCAGTTA
Done.