Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012757.1 Corchorus capsularis cultivar CVL-1 contig12778, 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: 15538
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32


Found at i:3446 original size:15 final size:16

Alignment explanation


    Indices: 3428--3466  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

       3418 AAACTCATTT

                            
       3428 TTGAAAAACC-TTTTC
          1 TTGAAAAACCATTTTC

                  *         
       3443 TTG-AAGACCATTTTC
          1 TTGAAAAACCATTTTC

                     
       3458 TTGAAAAAC
          1 TTGAAAAAC

       3467 GTCTCTTGTT


Statistics
Matches: 20,  Mismatches: 2, Indels: 3
        0.80            0.08        0.12

Matches are distributed among these distances:
  14    5  0.25
  15   11  0.55
  16    4  0.20

ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36


Consensus pattern (16 bp):   
TTGAAAAACCATTTTC

Found at i:3581 original size:41 final size:42

Alignment explanation


    Indices: 3523--3620  Score: 171
    Period size: 41  Copynumber: 2.3  Consensus size: 42

       3513 GTTGCAATTC

                                                    * 
       3523 TTTTTCTTTTCTTTTTGCGACCTCTTTCTTTTTTAGGCCCGG
          1 TTTTTCTTTTCTTTTTGCGACCTCTTTCTTTTTTAGGCCCAG

                                                      
       3565 TTTTT-TTTTCTTTTTGCGACCTCTTTCTTTTTTAGGCCCAG
          1 TTTTTCTTTTCTTTTTGCGACCTCTTTCTTTTTTAGGCCCAG

                           
       3606 TTTTTCTTCTTCTTT
          1 TTTTTCTT-TTCTTT

       3621 GATGGGAATT


Statistics
Matches: 53,  Mismatches: 1, Indels: 3
        0.93            0.02        0.05

Matches are distributed among these distances:
  41   40  0.75
  42    7  0.13
  43    6  0.11

ACGTcount: A:0.05, C:0.22, G:0.11, T:0.61


Consensus pattern (42 bp):   
TTTTTCTTTTCTTTTTGCGACCTCTTTCTTTTTTAGGCCCAG

Found at i:6305 original size:17 final size:17

Alignment explanation


    Indices: 6283--6322  Score: 62
    Period size: 17  Copynumber: 2.4  Consensus size: 17

       6273 ATGAAATTCT

                   *         
       6283 TTTTTGATTTTTTTGAA
          1 TTTTTGACTTTTTTGAA

                           * 
       6300 TTTTTGACTTTTTTGGA
          1 TTTTTGACTTTTTTGAA

                  
       6317 TTTTTG
          1 TTTTTG

       6323 GAAAACTTTT


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  17   21  1.00

ACGTcount: A:0.12, C:0.03, G:0.15, T:0.70


Consensus pattern (17 bp):   
TTTTTGACTTTTTTGAA

Found at i:9760 original size:25 final size:25

Alignment explanation


    Indices: 9728--9779  Score: 95
    Period size: 25  Copynumber: 2.1  Consensus size: 25

       9718 AAATGTGTTT

                                     
       9728 AACCCAAAATTGAAACAAAATTTAG
          1 AACCCAAAATTGAAACAAAATTTAG

                          *          
       9753 AACCCAAAATTGAAGCAAAATTTAG
          1 AACCCAAAATTGAAACAAAATTTAG

              
       9778 AA
          1 AA

       9780 TGAATCAAAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  25   26  1.00

ACGTcount: A:0.56, C:0.15, G:0.10, T:0.19


Consensus pattern (25 bp):   
AACCCAAAATTGAAACAAAATTTAG

Found at i:12050 original size:21 final size:21

Alignment explanation


    Indices: 12024--12075  Score: 59
    Period size: 21  Copynumber: 2.5  Consensus size: 21

      12014 CCAGGGCACA

                         *    *  
      12024 TGGGTGCCCAAGCCAACCGGC
          1 TGGGTGCCCAAGCAAACCAGC

                   *        *    
      12045 TGGGTGCTCAAGCAAAGCAGC
          1 TGGGTGCCCAAGCAAACCAGC

                *     
      12066 TGGGGGCCCA
          1 TGGGTGCCCA

      12076 CCGTGAGTCG


Statistics
Matches: 25,  Mismatches: 6, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  21   25  1.00

ACGTcount: A:0.21, C:0.31, G:0.37, T:0.12


Consensus pattern (21 bp):   
TGGGTGCCCAAGCAAACCAGC
Done.