Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012407.1 Corchorus capsularis cultivar CVL-1 contig12428, 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: 20664
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34


Found at i:1141 original size:5 final size:6

Alignment explanation


    Indices: 1124--1148  Score: 50
    Period size: 6  Copynumber: 4.2  Consensus size: 6

       1114 AGCATACATA

                                         
       1124 TCTTTT TCTTTT TCTTTT TCTTTT T
          1 TCTTTT TCTTTT TCTTTT TCTTTT T

       1149 TGGTTTCTTG


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

Matches are distributed among these distances:
   6   19  1.00

ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84


Consensus pattern (6 bp):   
TCTTTT

Found at i:2611 original size:21 final size:21

Alignment explanation


    Indices: 2587--2627  Score: 64
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       2577 AAAAATGCCA

                      *   *      
       2587 AAAGGGGGCGGTAAGTAGCAC
          1 AAAGGGGGCGATAAATAGCAC

                                
       2608 AAAGGGGGCGATAAATAGCA
          1 AAAGGGGGCGATAAATAGCA

       2628 ACTCTCAATA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.39, C:0.12, G:0.39, T:0.10


Consensus pattern (21 bp):   
AAAGGGGGCGATAAATAGCAC

Found at i:2677 original size:2 final size:2

Alignment explanation


    Indices: 2670--2697  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       2660 CTCTTAATAC

                                                     
       2670 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       2698 ATTCTAAACT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:11646 original size:11 final size:11

Alignment explanation


    Indices: 11622--11656  Score: 52
    Period size: 11  Copynumber: 3.2  Consensus size: 11

      11612 TTGACAATAC

                       
      11622 AACAAAAACAA
          1 AACAAAAACAA

               *     * 
      11633 AACGAAAACGA
          1 AACAAAAACAA

                       
      11644 AACAAAAACAA
          1 AACAAAAACAA

              
      11655 AA
          1 AA

      11657 AACAGAAAAA


Statistics
Matches: 20,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  11   20  1.00

ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00


Consensus pattern (11 bp):   
AACAAAAACAA

Found at i:17978 original size:11 final size:11

Alignment explanation


    Indices: 17957--17995  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

      17947 CCATCTTATC

                        
      17957 TTCTCTTTTTTT
          1 TTCT-TTTTTTT

                       
      17969 TTCTTTTTTTT
          1 TTCTTTTTTTT

               *   *   
      17980 TTCCTTTCTTT
          1 TTCTTTTTTTT

                 
      17991 TTCTT
          1 TTCTT

      17996 GTTTCTTAGA


Statistics
Matches: 24,  Mismatches: 3, Indels: 1
        0.86            0.11        0.04

Matches are distributed among these distances:
  11   20  0.83
  12    4  0.17

ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82


Consensus pattern (11 bp):   
TTCTTTTTTTT
Done.