Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014489.1 Corchorus capsularis cultivar CVL-1 contig14510, 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: 25041
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Found at i:1298 original size:6 final size:6

Alignment explanation


    Indices: 1289--1321  Score: 66
    Period size: 6  Copynumber: 5.5  Consensus size: 6

       1279 TGCATGCCCA

                                                  
       1289 TGTTTC TGTTTC TGTTTC TGTTTC TGTTTC TGT
          1 TGTTTC TGTTTC TGTTTC TGTTTC TGTTTC TGT

       1322 CCGTGCATGT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   27  1.00

ACGTcount: A:0.00, C:0.15, G:0.18, T:0.67


Consensus pattern (6 bp):   
TGTTTC

Found at i:2458 original size:24 final size:24

Alignment explanation


    Indices: 2412--2457  Score: 78
    Period size: 22  Copynumber: 2.0  Consensus size: 24

       2402 ACAATGTCAT

                                    
       2412 GATCCTTTCTTTGGGTTTAAAAAA
          1 GATCCTTTCTTTGGGTTTAAAAAA

                                    
       2436 GATCCTTT-TTT-GGTTTAAAAAA
          1 GATCCTTTCTTTGGGTTTAAAAAA

       2458 ATAAAGTGTG


Statistics
Matches: 22,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  22   11  0.50
  23    3  0.14
  24    8  0.36

ACGTcount: A:0.30, C:0.11, G:0.15, T:0.43


Consensus pattern (24 bp):   
GATCCTTTCTTTGGGTTTAAAAAA

Found at i:7043 original size:2 final size:2

Alignment explanation


    Indices: 7036--7064  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       7026 AGTTGTTTTA

                                                       
       7036 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       7065 ATTATATTTT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:7103 original size:23 final size:23

Alignment explanation


    Indices: 7077--7139  Score: 126
    Period size: 23  Copynumber: 2.7  Consensus size: 23

       7067 TATATTTTTG

                                   
       7077 TTACAAATCATGCATGTTTATTA
          1 TTACAAATCATGCATGTTTATTA

                                   
       7100 TTACAAATCATGCATGTTTATTA
          1 TTACAAATCATGCATGTTTATTA

                             
       7123 TTACAAATCATGCATGT
          1 TTACAAATCATGCATGT

       7140 GAATTGTGAT


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   40  1.00

ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41


Consensus pattern (23 bp):   
TTACAAATCATGCATGTTTATTA

Found at i:7574 original size:2 final size:2

Alignment explanation


    Indices: 7567--7599  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

       7557 ACAATAGCAA

                                                             
       7567 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       7600 CACACACACA


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:24732 original size:14 final size:14

Alignment explanation


    Indices: 24690--24734  Score: 51
    Period size: 14  Copynumber: 3.4  Consensus size: 14

      24680 TGAAGAAGAG

                  *       
      24690 TATAAGAAGAATC-
          1 TATAAGGAGAATCA

                       *  
      24703 TA-AAGGA-AAGCA
          1 TATAAGGAGAATCA

                          
      24715 TATAAGGAGAATCA
          1 TATAAGGAGAATCA

                  
      24729 TATAAG
          1 TATAAG

      24735 TCAAGGAAGT


Statistics
Matches: 26,  Mismatches: 3, Indels: 5
        0.76            0.09        0.15

Matches are distributed among these distances:
  11    3  0.12
  12    6  0.23
  13    7  0.27
  14   10  0.38

ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20


Consensus pattern (14 bp):   
TATAAGGAGAATCA
Done.