Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001183.1 Corchorus capsularis cultivar CVL-1 contig01183, 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: 8217
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33


Found at i:1644 original size:21 final size:22

Alignment explanation


    Indices: 1620--1661  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 22

       1610 TGCATCACTT

                                  
       1620 TCCCAATTCCCCTC-TTTCCTC
          1 TCCCAATTCCCCTCGTTTCCTC

                **               
       1641 TCCCCCTTCCCCTCGTTTCCT
          1 TCCCAATTCCCCTCGTTTCCT

       1662 TCTCAACCCT


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  21   12  0.67
  22    6  0.33

ACGTcount: A:0.05, C:0.55, G:0.02, T:0.38


Consensus pattern (22 bp):   
TCCCAATTCCCCTCGTTTCCTC

Found at i:1662 original size:68 final size:70

Alignment explanation


    Indices: 1526--1664  Score: 174
    Period size: 71  Copynumber: 2.0  Consensus size: 70

       1516 AGATTACATA

                            *  *     * *                                 *   
       1526 AAAAAAAAAATCATACTTCTCTTTCTCGATTCCCCTCTTTCCATTCTCTCCCCTTCCCATATTTT
          1 AAAAAAAAAATCATACATCACTTTCCCAATTCCCCTCTTTCCA-TCTCTCCCCTTCCCATAGTTT

                  
       1591 CCTTCT
         65 CCTTCT

                       *  *                                          * *     
       1597 AAAAAAAAAATTATGCATCACTTTCCCAATTCCCCTCTTTCC-TCTC-CCCCTTCCCCTCGTTTC
          1 AAAAAAAAAATCATACATCACTTTCCCAATTCCCCTCTTTCCATCTCTCCCCTTCCCATAGTTTC

                 
       1660 CTTCT
         66 CTTCT

       1665 CAACCCTACC


Statistics
Matches: 59,  Mismatches: 9, Indels: 3
        0.83            0.13        0.04

Matches are distributed among these distances:
  68   19  0.32
  69    4  0.07
  71   36  0.61

ACGTcount: A:0.22, C:0.37, G:0.02, T:0.38


Consensus pattern (70 bp):   
AAAAAAAAAATCATACATCACTTTCCCAATTCCCCTCTTTCCATCTCTCCCCTTCCCATAGTTTC
CTTCT

Found at i:7356 original size:18 final size:18

Alignment explanation


    Indices: 7333--7369  Score: 74
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       7323 ACGTGTCATT

                              
       7333 ATTTGGTGGTTGGGGCAC
          1 ATTTGGTGGTTGGGGCAC

                              
       7351 ATTTGGTGGTTGGGGCAC
          1 ATTTGGTGGTTGGGGCAC

             
       7369 A
          1 A

       7370 ATGGGGCACA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   19  1.00

ACGTcount: A:0.14, C:0.11, G:0.43, T:0.32


Consensus pattern (18 bp):   
ATTTGGTGGTTGGGGCAC
Done.