Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015693.1 Corchorus olitorius cultivar O-4 contig15726, 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: 16152
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34


Found at i:1870 original size:15 final size:14

Alignment explanation


    Indices: 1836--1877  Score: 50
    Period size: 15  Copynumber: 3.0  Consensus size: 14

       1826 CAACAGGGGC

                 *        
       1836 TAAGGGAAAC-AAT
          1 TAAGGAAAACTAAT

                          
       1849 TAAGGAAAACTAAT
          1 TAAGGAAAACTAAT

                      *    
       1863 TGAAGGAAAAATAAT
          1 T-AAGGAAAACTAAT

       1878 GGTCACTTGG


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  13    9  0.36
  14    4  0.16
  15   12  0.48

ACGTcount: A:0.57, C:0.05, G:0.19, T:0.19


Consensus pattern (14 bp):   
TAAGGAAAACTAAT

Found at i:2894 original size:125 final size:124

Alignment explanation


    Indices: 2571--2908  Score: 478
    Period size: 124  Copynumber: 2.7  Consensus size: 124

       2561 AAATGTCACG

                                               **                      *     
       2571 AATATCTATACCAACGCTTAAAAATGTCGGAATACAACGAAATCAAATGATGTGAAGAAATTGTT
          1 AATATCTATACCAACGC-TAAAAATGTCGGAATACGTCGAAATCAAATGATGTGAAGAACTTGTT

            **                      *              *                    
       2636 ATGACATTTGCAAACGTCGGTATATTATTTTTTAGCGACGTTTAATAAATGTCACAATAT
         65 CCGACATTTGCAAACGTCGGTATAGTATTTTTTAGCGACATTTAATAAATGTCACAATAT

                              * *   *                              *     *   
       2696 AATATCTATACCAACGCTTATAATATCGGAATACGTCGAAATCAAATGATGTGAAAAACTTATTC
          1 AATATCTATACCAACGCTAAAAATGTCGGAATACGTCGAAATCAAATGATGTGAAGAACTTGTTC

                                              *  *     *       *  *    
       2761 CGACATTTGCAAACGTCGGTATAGTATTTTTTAGTGATATTTAGTAAATGTTACGATAT
         66 CGACATTTGCAAACGTCGGTATAGTATTTTTTAGCGACATTTAATAAATGTCACAATAT

                        *  *                      *                          
       2820 AATATCTATACCGACACTAACAAATGTCGGAATACGTCAAAATCAAATGATGTGAAGAACTTGTT
          1 AATATCTATACCAACGCTAA-AAATGTCGGAATACGTCGAAATCAAATGATGTGAAGAACTTGTT

                                    
       2885 CCGACATTTGCAAACGTCGGTATA
         65 CCGACATTTGCAAACGTCGGTATA

       2909 ATATATATAT


Statistics
Matches: 187,  Mismatches: 25, Indels: 2
        0.87            0.12        0.01

Matches are distributed among these distances:
 124  107  0.57
 125   80  0.43

ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31


Consensus pattern (124 bp):   
AATATCTATACCAACGCTAAAAATGTCGGAATACGTCGAAATCAAATGATGTGAAGAACTTGTTC
CGACATTTGCAAACGTCGGTATAGTATTTTTTAGCGACATTTAATAAATGTCACAATAT

Found at i:4350 original size:22 final size:21

Alignment explanation


    Indices: 4308--4350  Score: 52
    Period size: 22  Copynumber: 2.0  Consensus size: 21

       4298 CTTGTACACT

                            *    
       4308 ACAATTTTCGCCACAATGACA
          1 ACAATTTTCGCCACAAAGACA

                                   
       4329 ACAATGTTTC-CCAGCAAAGACA
          1 ACAAT-TTTCGCCA-CAAAGACA

       4351 TCAACGATGT


Statistics
Matches: 19,  Mismatches: 1, Indels: 3
        0.83            0.04        0.13

Matches are distributed among these distances:
  21    8  0.42
  22   11  0.58

ACGTcount: A:0.40, C:0.28, G:0.12, T:0.21


Consensus pattern (21 bp):   
ACAATTTTCGCCACAAAGACA

Found at i:9153 original size:10 final size:10

Alignment explanation


    Indices: 9138--9162  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

       9128 ATATTGATCA

                      
       9138 AATTAAAATC
          1 AATTAAAATC

                      
       9148 AATTAAAATC
          1 AATTAAAATC

                 
       9158 AATTA
          1 AATTA

       9163 GTATTAATGT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   15  1.00

ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32


Consensus pattern (10 bp):   
AATTAAAATC

Found at i:10188 original size:21 final size:21

Alignment explanation


    Indices: 10159--10212  Score: 99
    Period size: 21  Copynumber: 2.6  Consensus size: 21

      10149 AATACTATTT

                *                
      10159 AATCTATTGATAGAGATTATA
          1 AATCAATTGATAGAGATTATA

                                 
      10180 AATCAATTGATAGAGATTATA
          1 AATCAATTGATAGAGATTATA

                        
      10201 AATCAATTGATA
          1 AATCAATTGATA

      10213 TAATTAGTAG


Statistics
Matches: 32,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  21   32  1.00

ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35


Consensus pattern (21 bp):   
AATCAATTGATAGAGATTATA

Found at i:14596 original size:30 final size:31

Alignment explanation


    Indices: 14533--14605  Score: 91
    Period size: 31  Copynumber: 2.4  Consensus size: 31

      14523 GAAGTAGTTG

                                *          
      14533 ATAAAAAATAAAATAAAAAGCTAGAAAACGA
          1 ATAAAAAATAAAATAAAAAGATAGAAAACGA

                                             
      14564 ATAAAAAA-AAGAATAAGAAAGAT-GAAAA-GA
          1 ATAAAAAATAA-AATAA-AAAGATAGAAAACGA

                         
      14594 AT-AAAAATAAAA
          1 ATAAAAAATAAAA

      14606 AGTTAGAGAA


Statistics
Matches: 38,  Mismatches: 1, Indels: 8
        0.81            0.02        0.17

Matches are distributed among these distances:
  29    7  0.18
  30    8  0.21
  31   18  0.47
  32    5  0.13

ACGTcount: A:0.74, C:0.03, G:0.11, T:0.12


Consensus pattern (31 bp):   
ATAAAAAATAAAATAAAAAGATAGAAAACGA

Done.