Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022549.1 Corchorus olitorius cultivar O-4 contig22582, 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: 4386
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32


Found at i:573 original size:85 final size:86

Alignment explanation


    Indices: 429--603  Score: 343
    Period size: 85  Copynumber: 2.0  Consensus size: 86

        419 TAAATTTAAA

                                                                             
        429 TATTAAATAATATAATCAACGAATAAATCCAGATTTATCTCAAAATGTTGCGGTGAGAAGTGAAA
          1 TATTAAATAATATAATCAACGAATAAATCCAGATTTATCTCAAAATGTTGCGGTGAGAAGTGAAA

                                 
        494 GCTCCCCACTTTAGTTTGTCC
         66 GCTCCCCACTTTAGTTTGTCC

                                                                             
        515 TATTAAATAATATAA-CAACGAATAAATCCAGATTTATCTCAAAATGTTGCGGTGAGAAGTGAAA
          1 TATTAAATAATATAATCAACGAATAAATCCAGATTTATCTCAAAATGTTGCGGTGAGAAGTGAAA

                                 
        579 GCTCCCCACTTTAGTTTGTCC
         66 GCTCCCCACTTTAGTTTGTCC

                
        600 TATT
          1 TATT

        604 CTAAGGCACC


Statistics
Matches: 89,  Mismatches: 0, Indels: 1
        0.99            0.00        0.01

Matches are distributed among these distances:
  85   74  0.83
  86   15  0.17

ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32


Consensus pattern (86 bp):   
TATTAAATAATATAATCAACGAATAAATCCAGATTTATCTCAAAATGTTGCGGTGAGAAGTGAAA
GCTCCCCACTTTAGTTTGTCC

Found at i:1752 original size:139 final size:141

Alignment explanation


    Indices: 1601--1863  Score: 349
    Period size: 139  Copynumber: 1.9  Consensus size: 141

       1591 TTTTTTACTT

                                                      *                      
       1601 TTAACAATAATTTAAAATTTGTTAAAATAAAGGAGGAGTAATTTGCAACTATTTC-AT-TTA-AC
          1 TTAACAATAATTTAAAATTTGTTAAAATAAAGGAGGAGTAATGTGCAAC--TTTCAATATTATA-

             *              *                                                
       1663 TTA-TAATCCTCTAGGGACAAAATTAA-A-AGTTTAAGATTTTAATTTTCAATTAATTTAAACAT
         63 TAATTAA-CCTCTAGGCACAAAATTAATATAGTTTAAGATTTTAATTTTCAATTAATTTAAACAT

                           
       1725 GTTGGGTCACGTGTG
        127 GTTGGGTCACGTGTG

                            *      *            *                            
       1740 TTAACAATAATTTAAATTTTGTTTAAATAAAGGAGGGGTAATGTGCAACTTTCAATATTATATAA
          1 TTAACAATAATTTAAAATTTGTTAAAATAAAGGAGGAGTAATGTGCAACTTTCAATATTATATAA

                   *                    *                    *         
       1805 TTAACCTTTAGGCACAAAATTAATAGTTTGTTTAAGATTTTAATTTTCATTTAATTTAA
         66 TTAACCTCTAGGCACAAAATTAATA--TAGTTTAAGATTTTAATTTTCAATTAATTTAA

       1864 GCACGTTAAG


Statistics
Matches: 107,  Mismatches: 9, Indels: 12
        0.84            0.07        0.09

Matches are distributed among these distances:
 137    4  0.04
 138    2  0.02
 139   67  0.63
 140    5  0.05
 143   29  0.27

ACGTcount: A:0.39, C:0.08, G:0.13, T:0.40


Consensus pattern (141 bp):   
TTAACAATAATTTAAAATTTGTTAAAATAAAGGAGGAGTAATGTGCAACTTTCAATATTATATAA
TTAACCTCTAGGCACAAAATTAATATAGTTTAAGATTTTAATTTTCAATTAATTTAAACATGTTG
GGTCACGTGTG

Found at i:4290 original size:45 final size:45

Alignment explanation


    Indices: 4222--4316  Score: 129
    Period size: 45  Copynumber: 2.1  Consensus size: 45

       4212 AGTGCATTAC

                       *     *        *        *         
       4222 CTAA-ATTCTAGTACTCTATCTCTAGGTAATTCATTAAAATAAAA
          1 CTAATATTCTACTACTCCATCTCTAGATAATTCATCAAAATAAAA

                         *                              *
       4266 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
          1 CTAATATTCTACTACTCCATCTCTAGATAATTCATCAAAATAAAA

                  
       4311 CTAATA
          1 CTAATA

       4317 ATAATTGTTA


Statistics
Matches: 44,  Mismatches: 6, Indels: 1
        0.86            0.12        0.02

Matches are distributed among these distances:
  44    4  0.09
  45   40  0.91

ACGTcount: A:0.40, C:0.20, G:0.05, T:0.35


Consensus pattern (45 bp):   
CTAATATTCTACTACTCCATCTCTAGATAATTCATCAAAATAAAA
Done.