Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019764.1 Corchorus olitorius cultivar O-4 contig19797, 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: 42939
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32

Warning! 2 characters in sequence are not A, C, G, or T


Found at i:545 original size:3 final size:3

Alignment explanation


    Indices: 537--564  Score: 56
    Period size: 3  Copynumber: 9.3  Consensus size: 3

        527 ATAGTATTAT

                                                 
        537 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A

        565 AGTTAACATT


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

Matches are distributed among these distances:
   3   25  1.00

ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32


Consensus pattern (3 bp):   
ATA

Found at i:28169 original size:42 final size:44

Alignment explanation


    Indices: 28118--28211  Score: 140
    Period size: 45  Copynumber: 2.2  Consensus size: 44

      28108 AGTGCATTAT

                                     *                  
      28118 CTAA-ATTCTACT-CT-ATCTCTAGGTAATTCATCAAAATAAAG
          1 CTAATATTCTACTCCTCATCTCTAGATAATTCATCAAAATAAAG

              *                                          
      28159 CTGATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
          1 CTAATATTCTACTCCT-CATCTCTAGATAATTCATCAAAATAAAG

                    
      28204 CTAATATT
          1 CTAATATT

      28212 AATTTTTGCT


Statistics
Matches: 46,  Mismatches: 3, Indels: 4
        0.87            0.06        0.08

Matches are distributed among these distances:
  41    3  0.07
  42    8  0.17
  43    2  0.04
  45   33  0.72

ACGTcount: A:0.37, C:0.21, G:0.06, T:0.35


Consensus pattern (44 bp):   
CTAATATTCTACTCCTCATCTCTAGATAATTCATCAAAATAAAG

Found at i:30566 original size:45 final size:44

Alignment explanation


    Indices: 30482--30577  Score: 149
    Period size: 45  Copynumber: 2.2  Consensus size: 44

      30472 AGTGCATTAC

                                *    *                  
      30482 CTAA-ATTCTACTCCTCCATTTCTGGTAATTCATCAAAATAAAG
          1 CTAATATTCTACTCCTCCATCTCTGATAATTCATCAAAATAAAG

                                     *                   
      30525 CTAATATTCTACTCCTCCATCTCTATATAATTCATCAAAATAAAG
          1 CTAATATTCTACTCCTCCATCTCT-GATAATTCATCAAAATAAAG

                    
      30570 CTAATATT
          1 CTAATATT

      30578 AATTGTGGTT


Statistics
Matches: 48,  Mismatches: 3, Indels: 2
        0.91            0.06        0.04

Matches are distributed among these distances:
  43    4  0.08
  44   18  0.38
  45   26  0.54

ACGTcount: A:0.36, C:0.23, G:0.04, T:0.36


Consensus pattern (44 bp):   
CTAATATTCTACTCCTCCATCTCTGATAATTCATCAAAATAAAG

Found at i:33933 original size:2 final size:2

Alignment explanation


    Indices: 33926--33976  Score: 58
    Period size: 2  Copynumber: 27.5  Consensus size: 2

      33916 GGTTTAATTA

                                                                           
      33926 AT AT AT AT AT AT AT AT AT AT -T AGT AT AT AT -T AT -T AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT

                               
      33966 -T AT AT AT -T AT A
          1 AT AT AT AT AT AT A

      33977 AGCATAAAAA


Statistics
Matches: 43,  Mismatches: 0, Indels: 12
        0.78            0.00        0.22

Matches are distributed among these distances:
   1    5  0.12
   2   36  0.84
   3    2  0.05

ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53


Consensus pattern (2 bp):   
AT

Found at i:33941 original size:10 final size:9

Alignment explanation


    Indices: 33927--33972  Score: 65
    Period size: 10  Copynumber: 4.8  Consensus size: 9

      33917 GTTTAATTAA

                     
      33927 TATATATAT
          1 TATATATAT

                      
      33936 ATATATATAT
          1 -TATATATAT

                      
      33946 TAGTATATAT
          1 TA-TATATAT

                      
      33956 TATTATATAT
          1 TA-TATATAT

                   
      33966 TATATAT
          1 TATATAT

      33973 TATAAGCATA


Statistics
Matches: 34,  Mismatches: 1, Indels: 3
        0.89            0.03        0.08

Matches are distributed among these distances:
   9    7  0.21
  10   27  0.79

ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54


Consensus pattern (9 bp):   
TATATATAT

Done.