Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014636.1 Corchorus capsularis cultivar CVL-1 contig14657, 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: 6598
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34


Found at i:577 original size:132 final size:130

Alignment explanation


    Indices: 233--556  Score: 427
    Period size: 131  Copynumber: 2.5  Consensus size: 130

        223 AAAAAAACTC

                    *      *         *                                       
        233 TTTT-TAGCGACTTTCAAGGTCGCTACGAAAATCAATTTGTAAAATATATTAAACAACGACTAAC
          1 TTTTGTAGAGACTTTTAAGGTCGCTGCGAAAATCAATTTGTAAAATATATTAAACAACGACTAAC

                                                      * * *             *    
        297 AATAGTCGTTGCGAAAAGAGTAAGATTTCACAGCGACTTAATTTGTGGCTTCAAAAGTAATTGTG
         66 AA-AGTCGTTGCGAAAAGAGTAAGATTTCACAGCGACTTAATCTATCGCTTCAAAAGTAAATGTG

             
        362 T
        130 T

                     *        **             *                   *   *       
        363 TTTTGTAGAAACTTTTAAAATCGCTGCGAAAATTAATTTGTAAAATATATTAAGCAATGACTAAC
          1 TTTTGTAGAGACTTTTAAGGTCGCTGCGAAAATCAATTTGTAAAATATATTAAACAACGACTAAC

                  *           **                            *                
        428 AAAAGTTGTTGCGAAAAGTTTAAGATTTCACAGCGACTTAATCTATCGTTTCAAAAGTAACCATG
         66 -AAAGTCGTTGCGAAAAGAGTAAGATTTCACAGCGACTTAATCTATCGCTTCAAAAGTAA--ATG

               
        493 T-T
        128 TGT

                    *                       *                             
        495 TTTTGTAGTGACTTTTAAGGTCGCTGCGAAAACCAATTTGTAAAATATATTAAACAACGACT
          1 TTTTGTAGAGACTTTTAAGGTCGCTGCGAAAATCAATTTGTAAAATATATTAAACAACGACT

        557 TGCAGAAGTC


Statistics
Matches: 165,  Mismatches: 25, Indels: 6
        0.84            0.13        0.03

Matches are distributed among these distances:
 130    4  0.02
 131  101  0.61
 132   57  0.35
 133    3  0.02

ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33


Consensus pattern (130 bp):   
TTTTGTAGAGACTTTTAAGGTCGCTGCGAAAATCAATTTGTAAAATATATTAAACAACGACTAAC
AAAGTCGTTGCGAAAAGAGTAAGATTTCACAGCGACTTAATCTATCGCTTCAAAAGTAAATGTGT

Found at i:698 original size:61 final size:61

Alignment explanation


    Indices: 603--722  Score: 240
    Period size: 61  Copynumber: 2.0  Consensus size: 61

        593 CGACTAATAG

                                                                         
        603 AAGTCGTTGTAAAAAGGGTAGGATTTTTAGCAGCGACTTTGTTTTTGTCATTGCGAATGCT
          1 AAGTCGTTGTAAAAAGGGTAGGATTTTTAGCAGCGACTTTGTTTTTGTCATTGCGAATGCT

                                                                       
        664 AAGTCGTTGTAAAAAGGGTAGGATTTTTAGCAGCGACTTTGTTTTTGTCATTGCGAATG
          1 AAGTCGTTGTAAAAAGGGTAGGATTTTTAGCAGCGACTTTGTTTTTGTCATTGCGAATG

        723 ATGTTAGCAT


Statistics
Matches: 59,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  61   59  1.00

ACGTcount: A:0.25, C:0.11, G:0.27, T:0.38


Consensus pattern (61 bp):   
AAGTCGTTGTAAAAAGGGTAGGATTTTTAGCAGCGACTTTGTTTTTGTCATTGCGAATGCT

Found at i:2121 original size:15 final size:15

Alignment explanation


    Indices: 2101--2169  Score: 58
    Period size: 15  Copynumber: 4.8  Consensus size: 15

       2091 TTTGAGAATA

                           
       2101 TATTTTTAAAGGATT
          1 TATTTTTAAAGGATT

                   *       
       2116 TATTTTTGAAGGA--
          1 TATTTTTAAAGGATT

                       *  *
       2129 TA--TTT-AAGAATG
          1 TATTTTTAAAGGATT

                            
       2141 TATTTTTTAAAGGATT
          1 TA-TTTTTAAAGGATT

                         
       2157 TATTTTTGAAAGG
          1 TATTTTT-AAAGG

       2170 TATATTATGA


Statistics
Matches: 43,  Mismatches: 4, Indels: 13
        0.72            0.07        0.22

Matches are distributed among these distances:
  10    4  0.09
  11    3  0.07
  12    2  0.05
  13    2  0.05
  15   20  0.47
  16   12  0.28

ACGTcount: A:0.33, C:0.00, G:0.17, T:0.49


Consensus pattern (15 bp):   
TATTTTTAAAGGATT

Found at i:2126 original size:40 final size:40

Alignment explanation


    Indices: 2081--2190  Score: 148
    Period size: 41  Copynumber: 2.6  Consensus size: 40

       2071 TCCTCGACTG

                                                    
       2081 TTGAAGGATATTTGAGAATATATTTTTAAAGGATTTATTT
          1 TTGAAGGATATTTGAGAATATATTTTTAAAGGATTTATTT

                         *     *                     
       2121 TTGAAGGATATTTAAGAATGTATTTTTTAAAGGATTTATTT
          1 TTGAAGGATATTTGAGAATATA-TTTTTAAAGGATTTATTT

                                         
       2162 TTGAAAGGTATATTATGATGATATATATT
          1 TTG-AAGG-ATATT-TGA-GA-ATATATT

       2191 ACATTACTAG


Statistics
Matches: 60,  Mismatches: 4, Indels: 7
        0.85            0.06        0.10

Matches are distributed among these distances:
  40   20  0.33
  41   21  0.35
  42    4  0.07
  43    5  0.08
  44    2  0.03
  45    4  0.07
  46    4  0.07

ACGTcount: A:0.35, C:0.00, G:0.17, T:0.47


Consensus pattern (40 bp):   
TTGAAGGATATTTGAGAATATATTTTTAAAGGATTTATTT

Done.