Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004754.1 Corchorus capsularis cultivar CVL-1 contig04772, 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: 14426
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32


Found at i:4522 original size:91 final size:92

Alignment explanation


    Indices: 4363--4604  Score: 377
    Period size: 91  Copynumber: 2.7  Consensus size: 92

       4353 AAGATCCAAG

                                                                             
       4363 GAGG-ATTATTGAAAGAAGATCCACGTATGTGGAGTATTCTTCTTTCAAA-AAAACTCCAATTAT
          1 GAGGAATTATTGAAAGAAGATCCACGTATGTGGAGTATTCTTCTTTCAAAGAAAACTCCAATTAT

                              *        
       4426 TGGAGAATTACTGAAGACTCAGTTATT
         66 TGGAGAATTACTGAAGACCCAGTTATT

                                               *   *            **    *      
       4453 GAGGAATTATTGAAAGAAGATCCACGTATGTGGAGGATTTTTCTTTCAAAGACGA-TCTAATTAT
          1 GAGGAATTATTGAAAGAAGATCCACGTATGTGGAGTATTCTTCTTTCAAAGAAAACTCCAATTAT

                                       
       4517 TGGAGAATTACTGAAGACCCAGTTATT
         66 TGGAGAATTACTGAAGACCCAGTTATT

                                                                  *        
       4544 G-GGAAATTATTGAAAGAAGATCCACGTATGTGGAGTATTCTTCTTTCAAAGAATA-TCCAAT
          1 GAGG-AATTATTGAAAGAAGATCCACGTATGTGGAGTATTCTTCTTTCAAAGAAAACTCCAAT

       4605 GAGGATTATC


Statistics
Matches: 138,  Mismatches: 11, Indels: 5
        0.90            0.07        0.03

Matches are distributed among these distances:
  90    6  0.04
  91  130  0.94
  92    2  0.01

ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32


Consensus pattern (92 bp):   
GAGGAATTATTGAAAGAAGATCCACGTATGTGGAGTATTCTTCTTTCAAAGAAAACTCCAATTAT
TGGAGAATTACTGAAGACCCAGTTATT

Found at i:4865 original size:59 final size:59

Alignment explanation


    Indices: 4767--4896  Score: 190
    Period size: 59  Copynumber: 2.2  Consensus size: 59

       4757 AAGACCCTCG

                                           *             *       *      
       4767 AATCAAATCAAACTCCCTCATCAATTCAAGATCAAGTCATACGACTCTTGAATGAAATCA
          1 AATCAAATCAAACT-CCTCATCAATTCAAGACCAAGTCATACGACCCTTGAATCAAATCA

                             *                      *                   
       4827 AATCAAATCAAACT-CTTATCAAGTTCAAGACCAAGTCATTCGACCCTTGAATCAAATCA
          1 AATCAAATCAAACTCCTCATCAA-TTCAAGACCAAGTCATACGACCCTTGAATCAAATCA

                       
       4886 AATCAAATCAA
          1 AATCAAATCAA

       4897 GTTCTCAGAT


Statistics
Matches: 64,  Mismatches: 5, Indels: 3
        0.89            0.07        0.04

Matches are distributed among these distances:
  58    7  0.11
  59   43  0.67
  60   14  0.22

ACGTcount: A:0.43, C:0.25, G:0.08, T:0.25


Consensus pattern (59 bp):   
AATCAAATCAAACTCCTCATCAATTCAAGACCAAGTCATACGACCCTTGAATCAAATCA

Found at i:10608 original size:13 final size:15

Alignment explanation


    Indices: 10592--10623  Score: 50
    Period size: 15  Copynumber: 2.3  Consensus size: 15

      10582 ATTTTGAAAG

                           
      10592 GAGGA-GGTT-GAGA
          1 GAGGAGGGTTGGAGA

                           
      10605 GAGGAGGGTTGGAGA
          1 GAGGAGGGTTGGAGA

                
      10620 GAGG
          1 GAGG

      10624 CTAGGGTTTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  13    5  0.29
  14    4  0.24
  15    8  0.47

ACGTcount: A:0.28, C:0.00, G:0.59, T:0.12


Consensus pattern (15 bp):   
GAGGAGGGTTGGAGA

Found at i:13355 original size:1 final size:1

Alignment explanation


    Indices: 13349--13385  Score: 74
    Period size: 1  Copynumber: 37.0  Consensus size: 1

      13339 CAATTTACAC

                                                 
      13349 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

      13386 CTGCTAGATC


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

Matches are distributed among these distances:
   1   36  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Done.