Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012755.1 Corchorus capsularis cultivar CVL-1 contig12776, 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: 11028
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30


Found at i:3096 original size:18 final size:20

Alignment explanation


    Indices: 3056--3105  Score: 61
    Period size: 18  Copynumber: 2.6  Consensus size: 20

       3046 TTTTGTTTGC

                                
       3056 ATACATTTATATATTTACTT
          1 ATACATTTATATATTTACTT

                                 
       3076 ATAC-TTTAT-TATTT-CTCT
          1 ATACATTTATATATTTACT-T

                  *     
       3094 ATACATATATAT
          1 ATACATTTATAT

       3106 TCTCTTCATT


Statistics
Matches: 26,  Mismatches: 1, Indels: 6
        0.79            0.03        0.18

Matches are distributed among these distances:
  17    2  0.08
  18   10  0.38
  19    9  0.35
  20    5  0.19

ACGTcount: A:0.34, C:0.12, G:0.00, T:0.54


Consensus pattern (20 bp):   
ATACATTTATATATTTACTT

Found at i:6094 original size:6 final size:6

Alignment explanation


    Indices: 6083--6108  Score: 52
    Period size: 6  Copynumber: 4.3  Consensus size: 6

       6073 ATAATTGCCA

                                          
       6083 TAGATT TAGATT TAGATT TAGATT TA
          1 TAGATT TAGATT TAGATT TAGATT TA

       6109 TTTTGCTTTG


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   20  1.00

ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50


Consensus pattern (6 bp):   
TAGATT

Found at i:9482 original size:63 final size:62

Alignment explanation


    Indices: 9409--9784  Score: 425
    Period size: 63  Copynumber: 6.0  Consensus size: 62

       9399 TTTATTCAAC

                        *            *                     *              
       9409 TCAAATCCTAGTTGAGGTCTCTAGTTGAGAGTTTCTTGTTTCAATTCGAAATCTTGTTTCTT
          1 TCAAATCCTAGTCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCTAAATCTTGTTTCTT

                               *                *      *                   * 
       9471 GTCAAATCCTAGTCGAGGTTTCTAGTCGAGAGTTTCATGTTTCGATT-TAAAGTCTTGTTTCGCT
          1 -TCAAATCCTAGTCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCTAAA-TCTTGTTTC-TT

                        *                                  *              
       9535 TCAAATCCTAGTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCAAAATCTTGTTTCTT
          1 TCAAATCCTAGTCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCTAAATCTTGTTTCTT

                               *                *                          * 
       9597 GTCAAATCCTAGTCGAGGTTTCTAGTCGAGAGTTTCATGTTTCAATT-TAAAGTCTTGTTTCGCT
          1 -TCAAATCCTAGTCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCTAAA-TCTTGTTTC-TT

                        *              *                      **    *   *    
       9661 TCAAATCCTAGTTGAGGTCTCTATGTCAAGAGTTTTCTTGTTTCAATTCCGGAATCATG-CTCTT
          1 TCAAATCCTAGTCGAGGTCTCTA-GTCGAGAG-TTTCTTGTTTCAATT-CTAAATCTTGTTTC-T

             
       9725 T
         62 T

             *        *                  *        * *           *      
       9726 TAAAATCCTAATCGAGGTCTCTAGTCGAGGGTTTCTTGCTCCAATTCTAAATTTTGTTT
          1 TCAAATCCTAGTCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCTAAATCTTGTTT

       9785 TATTTCGAGT


Statistics
Matches: 262,  Mismatches: 40, Indels: 22
        0.81            0.12        0.07

Matches are distributed among these distances:
  62   13  0.05
  63  188  0.72
  64   18  0.07
  65   37  0.14
  66    4  0.02
  67    2  0.01

ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42


Consensus pattern (62 bp):   
TCAAATCCTAGTCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCTAAATCTTGTTTCTT

Found at i:9634 original size:126 final size:126

Alignment explanation


    Indices: 9409--9760  Score: 562
    Period size: 126  Copynumber: 2.8  Consensus size: 126

       9399 TTTATTCAAC

                                     *                                       
       9409 TCAAATCCTAGTTGAGGTCTCTAGTTGAGAGTTTCTTGTTTCAATTCGAAATCTTGTTTCTTGTC
          1 TCAAATCCTAGTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCGAAATCTTGTTTCTTGTC

                                                    *                    
       9474 AAATCCTAGTCGAGGTTTCTAGTCGAGAGTTTCATGTTTCGATTTAAAGTCTTGTTTCGCT
         66 AAATCCTAGTCGAGGTTTCTAGTCGAGAGTTTCATGTTTCAATTTAAAGTCTTGTTTCGCT

                                                           *                 
       9535 TCAAATCCTAGTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCAAAATCTTGTTTCTTGTC
          1 TCAAATCCTAGTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCGAAATCTTGTTTCTTGTC

                                                                         
       9600 AAATCCTAGTCGAGGTTTCTAGTCGAGAGTTTCATGTTTCAATTTAAAGTCTTGTTTCGCT
         66 AAATCCTAGTCGAGGTTTCTAGTCGAGAGTTTCATGTTTCAATTTAAAGTCTTGTTTCGCT

                                       *                       *    *   *    
       9661 TCAAATCCTAGTTGAGGTCTCTATGTCAAGAGTTTTCTTGTTTCAATTCCGGAATCATG-CTCTT
          1 TCAAATCCTAGTTGAGGTCTCTA-GTCGAGAG-TTTCTTGTTTCAATT-CGAAATCTTGTTTCTT

            * *        *       *          *     
       9725 TTAAAATCCTAATCGAGGTCTCTAGTCGAGGGTTTC
         63 GTCAAATCCTAGTCGAGGTTTCTAGTCGAGAGTTTC

       9761 TTGCTCCAAT


Statistics
Matches: 210,  Mismatches: 13, Indels: 4
        0.93            0.06        0.02

Matches are distributed among these distances:
 126  146  0.70
 127    7  0.03
 128   50  0.24
 129    7  0.03

ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41


Consensus pattern (126 bp):   
TCAAATCCTAGTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCGAAATCTTGTTTCTTGTC
AAATCCTAGTCGAGGTTTCTAGTCGAGAGTTTCATGTTTCAATTTAAAGTCTTGTTTCGCT
Done.