Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009297.1 Corchorus capsularis cultivar CVL-1 contig09318, 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: 11838
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:5919 original size:26 final size:26

Alignment explanation


    Indices: 5883--5936  Score: 108
    Period size: 26  Copynumber: 2.1  Consensus size: 26

       5873 TATAATATTT

                                      
       5883 ATAATTTAGATTTAAAGTTTTCTACC
          1 ATAATTTAGATTTAAAGTTTTCTACC

                                      
       5909 ATAATTTAGATTTAAAGTTTTCTACC
          1 ATAATTTAGATTTAAAGTTTTCTACC

              
       5935 AT
          1 AT

       5937 CGAAATAAAT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   28  1.00

ACGTcount: A:0.35, C:0.11, G:0.07, T:0.46


Consensus pattern (26 bp):   
ATAATTTAGATTTAAAGTTTTCTACC

Found at i:6126 original size:22 final size:22

Alignment explanation


    Indices: 6093--6142  Score: 91
    Period size: 22  Copynumber: 2.2  Consensus size: 22

       6083 TGAAACAAAT

                                   
       6093 AATTATTTTATTATTATAAATTA
          1 AATT-TTTTATTATTATAAATTA

                                  
       6116 AATTTTTTATTATTATAAATTA
          1 AATTTTTTATTATTATAAATTA

                 
       6138 AATTT
          1 AATTT

       6143 AATATATTCT


Statistics
Matches: 27,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  22   23  0.85
  23    4  0.15

ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58


Consensus pattern (22 bp):   
AATTTTTTATTATTATAAATTA

Found at i:6278 original size:2 final size:2

Alignment explanation


    Indices: 6273--6302  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       6263 CGTGTGTGTC

                                                        
       6273 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       6303 CACGTGAATT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:8363 original size:52 final size:53

Alignment explanation


    Indices: 8285--8391  Score: 198
    Period size: 52  Copynumber: 2.0  Consensus size: 53

       8275 TCTTAGGATA

                                                                 
       8285 TAATCATTTTGATATACTTGCTGATAG-TTTTTTCCCTTGCAATAAATAGAAT
          1 TAATCATTTTGATATACTTGCTGATAGTTTTTTTCCCTTGCAATAAATAGAAT

                                                *                
       8337 TAATCATTTTGATATACTTGCTGATAGTTTTTTTCCTTTGCAATAAATAGAAT
          1 TAATCATTTTGATATACTTGCTGATAGTTTTTTTCCCTTGCAATAAATAGAAT

              
       8390 TA
          1 TA

       8392 GTTGGAAAGT


Statistics
Matches: 53,  Mismatches: 1, Indels: 1
        0.96            0.02        0.02

Matches are distributed among these distances:
  52   27  0.51
  53   26  0.49

ACGTcount: A:0.31, C:0.12, G:0.11, T:0.46


Consensus pattern (53 bp):   
TAATCATTTTGATATACTTGCTGATAGTTTTTTTCCCTTGCAATAAATAGAAT

Found at i:8881 original size:2 final size:2

Alignment explanation


    Indices: 8874--8908  Score: 54
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       8864 TAACTTGTAA

                                                                 
       8874 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AGT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A

       8909 AAGTATGCTT


Statistics
Matches: 31,  Mismatches: 0, Indels: 4
        0.89            0.00        0.11

Matches are distributed among these distances:
   1    1  0.03
   2   28  0.90
   3    2  0.06

ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:11352 original size:3 final size:3

Alignment explanation


    Indices: 11344--11383  Score: 64
    Period size: 3  Copynumber: 13.7  Consensus size: 3

      11334 GTGTATATAT

                                    *                             
      11344 ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA ATA A-A ATA AT
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT

      11384 TATTTATTCC


Statistics
Matches: 34,  Mismatches: 2, Indels: 2
        0.89            0.05        0.05

Matches are distributed among these distances:
   2    2  0.06
   3   32  0.94

ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33


Consensus pattern (3 bp):   
ATA

Done.