Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013295.1 Corchorus capsularis cultivar CVL-1 contig13316, 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: 2957
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30


Found at i:1275 original size:13 final size:14

Alignment explanation


    Indices: 1257--1310  Score: 67
    Period size: 13  Copynumber: 3.9  Consensus size: 14

       1247 TTTTTTTTTT

                          
       1257 AAAATA-ATAAAAA
          1 AAAATATATAAAAA

                            
       1270 AAAATAAATATAAAAA
          1 AAAAT--ATATAAAAA

                      *   
       1286 AAAATATA-ATAAA
          1 AAAATATATAAAAA

                        
       1299 AAAATATATAAA
          1 AAAATATATAAA

       1311 TTGCTGAAAA


Statistics
Matches: 35,  Mismatches: 2, Indels: 7
        0.80            0.05        0.16

Matches are distributed among these distances:
  13   17  0.49
  14    5  0.14
  15    1  0.03
  16   12  0.34

ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20


Consensus pattern (14 bp):   
AAAATATATAAAAA

Found at i:1278 original size:17 final size:17

Alignment explanation


    Indices: 1258--1302  Score: 69
    Period size: 16  Copynumber: 2.8  Consensus size: 17

       1248 TTTTTTTTTA

                             
       1258 AAATAATAAAAAAAAAT
          1 AAATAATAAAAAAAAAT

                             
       1275 AAAT-ATAAAAAAAAAT
          1 AAATAATAAAAAAAAAT

                          
       1291 --ATAATAAAAAAA
          1 AAATAATAAAAAAA

       1303 TATATAAATT


Statistics
Matches: 27,  Mismatches: 0, Indels: 4
        0.87            0.00        0.13

Matches are distributed among these distances:
  14    2  0.07
  15    9  0.33
  16   12  0.44
  17    4  0.15

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


Consensus pattern (17 bp):   
AAATAATAAAAAAAAAT

Found at i:1307 original size:15 final size:15

Alignment explanation


    Indices: 1257--1309  Score: 67
    Period size: 15  Copynumber: 3.7  Consensus size: 15

       1247 TTTTTTTTTT

                           
       1257 AAAATA-ATAA-AAA
          1 AAAATATATAATAAA

                  *        
       1270 AAAATAAAT-ATAAA
          1 AAAATATATAATAAA

                *          
       1284 AAAAAATATAATAAA
          1 AAAATATATAATAAA

                       
       1299 AAAATATATAA
          1 AAAATATATAA

       1310 ATTGCTGAAA


Statistics
Matches: 34,  Mismatches: 3, Indels: 4
        0.83            0.07        0.10

Matches are distributed among these distances:
  13    7  0.21
  14   12  0.35
  15   15  0.44

ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21


Consensus pattern (15 bp):   
AAAATATATAATAAA

Found at i:1999 original size:27 final size:27

Alignment explanation


    Indices: 1969--2020  Score: 86
    Period size: 27  Copynumber: 1.9  Consensus size: 27

       1959 GCATTGGGGT

                      *                
       1969 CGCCCAAGGGTATTTTGGTCATTTTCG
          1 CGCCCAAGGGCATTTTGGTCATTTTCG

                  *                  
       1996 CGCCCAGGGGCATTTTGGTCATTTT
          1 CGCCCAAGGGCATTTTGGTCATTTT

       2021 TACACTCGGG


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  27   23  1.00

ACGTcount: A:0.13, C:0.23, G:0.27, T:0.37


Consensus pattern (27 bp):   
CGCCCAAGGGCATTTTGGTCATTTTCG

Found at i:2697 original size:21 final size:21

Alignment explanation


    Indices: 2673--2716  Score: 54
    Period size: 22  Copynumber: 2.0  Consensus size: 21

       2663 GGCTTTTATT

                                  
       2673 TACAAA-ACAGTACCAAATAAA
          1 TACAAATACA-TACCAAATAAA

                        *         
       2694 TACAAATTACATGCCAAATAAA
          1 TACAAA-TACATACCAAATAAA

             
       2716 T
          1 T

       2717 GTAAAGTAGA


Statistics
Matches: 20,  Mismatches: 1, Indels: 3
        0.83            0.04        0.12

Matches are distributed among these distances:
  21    6  0.30
  22   11  0.55
  23    3  0.15

ACGTcount: A:0.57, C:0.18, G:0.05, T:0.20


Consensus pattern (21 bp):   
TACAAATACATACCAAATAAA
Done.