Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006685.1 Corchorus capsularis cultivar CVL-1 contig06706, 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: 29460
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33


Found at i:9193 original size:108 final size:108

Alignment explanation


    Indices: 9004--9223  Score: 440
    Period size: 108  Copynumber: 2.0  Consensus size: 108

       8994 GAATCAATAG

                                                                             
       9004 CAAGCAAAGTGATGAACTTGTAATTGATTGGTGTTTTCTTGCTCAAATCATCATCAAAGCTCTTC
          1 CAAGCAAAGTGATGAACTTGTAATTGATTGGTGTTTTCTTGCTCAAATCATCATCAAAGCTCTTC

                                                       
       9069 AATTGAACTTGAATGGTCTTCATATCATCAAGATGAGTTCGAA
         66 AATTGAACTTGAATGGTCTTCATATCATCAAGATGAGTTCGAA

                                                                             
       9112 CAAGCAAAGTGATGAACTTGTAATTGATTGGTGTTTTCTTGCTCAAATCATCATCAAAGCTCTTC
          1 CAAGCAAAGTGATGAACTTGTAATTGATTGGTGTTTTCTTGCTCAAATCATCATCAAAGCTCTTC

                                                       
       9177 AATTGAACTTGAATGGTCTTCATATCATCAAGATGAGTTCGAA
         66 AATTGAACTTGAATGGTCTTCATATCATCAAGATGAGTTCGAA

                
       9220 CAAG
          1 CAAG

       9224 GCCCATGAGT


Statistics
Matches: 112,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
 108  112  1.00

ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34


Consensus pattern (108 bp):   
CAAGCAAAGTGATGAACTTGTAATTGATTGGTGTTTTCTTGCTCAAATCATCATCAAAGCTCTTC
AATTGAACTTGAATGGTCTTCATATCATCAAGATGAGTTCGAA

Found at i:9452 original size:30 final size:30

Alignment explanation


    Indices: 9416--9478  Score: 101
    Period size: 30  Copynumber: 2.1  Consensus size: 30

       9406 TGTCTTCAAG

                                *          
       9416 TCCATGATAAGTCCTT-GGCGCATCATTCCC
          1 TCCATGATAAG-CCTTGGGCACATCATTCCC

                                          
       9446 TCCATGATAAGCCTTGGGCACATCATTCCC
          1 TCCATGATAAGCCTTGGGCACATCATTCCC

               
       9476 TCC
          1 TCC

       9479 CCTTTGAAGA


Statistics
Matches: 31,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  29    4  0.13
  30   27  0.87

ACGTcount: A:0.21, C:0.35, G:0.16, T:0.29


Consensus pattern (30 bp):   
TCCATGATAAGCCTTGGGCACATCATTCCC

Found at i:11271 original size:59 final size:59

Alignment explanation


    Indices: 11170--11297  Score: 213
    Period size: 59  Copynumber: 2.2  Consensus size: 59

      11160 GCAATAGAGT

                            *                   * *                   *
      11170 AAAAT-TGAAGTATGTTAAAGACAAGAGAATAGAGATATAATAGAATATGGAGAAGAAG
          1 AAAATATGAAGTATGTAAAAGACAAGAGAATAGAGAGACAATAGAATATGGAGAAGAAA

                                                                       
      11228 AAAATATGAAGTATGTAAAAGACAAGAGAATAGAGAGACAATAGAATATGGAGAAGAAA
          1 AAAATATGAAGTATGTAAAAGACAAGAGAATAGAGAGACAATAGAATATGGAGAAGAAA

                       
      11287 AAAATATGAAG
          1 AAAATATGAAG

      11298 AATGGGAGAA


Statistics
Matches: 65,  Mismatches: 4, Indels: 1
        0.93            0.06        0.01

Matches are distributed among these distances:
  58    5  0.08
  59   60  0.92

ACGTcount: A:0.56, C:0.02, G:0.23, T:0.18


Consensus pattern (59 bp):   
AAAATATGAAGTATGTAAAAGACAAGAGAATAGAGAGACAATAGAATATGGAGAAGAAA

Found at i:12648 original size:19 final size:19

Alignment explanation


    Indices: 12621--12657  Score: 56
    Period size: 19  Copynumber: 1.9  Consensus size: 19

      12611 ACCATTTATA

                *              
      12621 ACCGTTTCACCATCGTTTG
          1 ACCGGTTCACCATCGTTTG

                         *    
      12640 ACCGGTTCACCATTGTTT
          1 ACCGGTTCACCATCGTTT

      12658 TGGACCCAAT


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  19   16  1.00

ACGTcount: A:0.16, C:0.30, G:0.16, T:0.38


Consensus pattern (19 bp):   
ACCGGTTCACCATCGTTTG

Found at i:21730 original size:2 final size:2

Alignment explanation


    Indices: 21723--21749  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

      21713 AGGTTTTGCT

                                                    
      21723 TC TC TC TC TC TC TC TC TC TC TC TC TC T
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC T

      21750 GTGGCTTTAT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

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


Consensus pattern (2 bp):   
TC

Done.