Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009553.1 Corchorus capsularis cultivar CVL-1 contig09574, 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: 15240
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35


Found at i:1450 original size:26 final size:26

Alignment explanation


    Indices: 1416--1470  Score: 65
    Period size: 26  Copynumber: 2.1  Consensus size: 26

       1406 TGGATCTTCT

                      *            *  
       1416 TTCAATAATTTTCCAATAACTGGGTC
          1 TTCAATAATTCTCCAATAACTGGATC

                *       *      *      
       1442 TTCAGTAATTCTGCAATAATTGGATC
          1 TTCAATAATTCTCCAATAACTGGATC

               
       1468 TTC
          1 TTC

       1471 TTTGAAAGAA


Statistics
Matches: 24,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  26   24  1.00

ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40


Consensus pattern (26 bp):   
TTCAATAATTCTCCAATAACTGGATC

Found at i:1509 original size:90 final size:91

Alignment explanation


    Indices: 1380--1602  Score: 340
    Period size: 90  Copynumber: 2.5  Consensus size: 91

       1370 TTCTTGATAA

                          *     *    *                  * **         *       
       1380 TTTGAAAGAAGAATCCTCCATATACGTGGATCTTCTTTCAATAATTTTCCAATAACTGGGTCTTC
          1 TTTGAAAGAAGAATACTCCACATACATGGATCTTCTTTCAATAACTCCCCAATAACTAGGTCTTC

                     *         *      
       1445 AGTAATTCTGCAATAATTGGATCTTC
         66 AGTAATTCTCCAATAATTGAATCTTC

                                                                             
       1471 TTTGAAAGAAGAATACT-CACATACATGGATCTTCTTTCAATAACTCCCCAATAACTAGGTCTTC
          1 TTTGAAAGAAGAATACTCCACATACATGGATCTTCTTTCAATAACTCCCCAATAACTAGGTCTTC

                                      
       1535 AGTAATTCTCCAATAATTGAATCTTC
         66 AGTAATTCTCCAATAATTGAATCTTC

                          **                          
       1561 TTTGAAAGAAGAATTTTCCACATACATGGATCTTCTTTCAAT
          1 TTTGAAAGAAGAATACTCCACATACATGGATCTTCTTTCAAT

       1603 CTTCTTAAGC


Statistics
Matches: 120,  Mismatches: 11, Indels: 2
        0.90            0.08        0.02

Matches are distributed among these distances:
  90   80  0.67
  91   40  0.33

ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36


Consensus pattern (91 bp):   
TTTGAAAGAAGAATACTCCACATACATGGATCTTCTTTCAATAACTCCCCAATAACTAGGTCTTC
AGTAATTCTCCAATAATTGAATCTTC

Found at i:5823 original size:38 final size:38

Alignment explanation


    Indices: 5769--5842  Score: 130
    Period size: 38  Copynumber: 1.9  Consensus size: 38

       5759 AGCAACAATT

                                      *           
       5769 AATATTAGCTTAATTTTGATGAATTATCTAGAGATGAG
          1 AATATTAGCTTAATTTTGATGAATTACCTAGAGATGAG

                       *                        
       5807 AATATTAGCTTTATTTTGATGAATTACCTAGAGATG
          1 AATATTAGCTTAATTTTGATGAATTACCTAGAGATG

       5843 GAGTAGAATT


Statistics
Matches: 34,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  38   34  1.00

ACGTcount: A:0.35, C:0.07, G:0.18, T:0.41


Consensus pattern (38 bp):   
AATATTAGCTTAATTTTGATGAATTACCTAGAGATGAG

Found at i:12465 original size:2 final size:2

Alignment explanation


    Indices: 12460--12486  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

      12450 TGTGTGAATA

                                                    
      12460 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 A

      12487 GGTGTGGAGG


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:14489 original size:29 final size:31

Alignment explanation


    Indices: 14457--14523  Score: 93
    Period size: 31  Copynumber: 2.2  Consensus size: 31

      14447 ATGCAATTTG

                                       *   
      14457 GGATATAACGTTAC-AAAA-CAAACAATTAA
          1 GGATATAACGTTACGAAAATCAAACAAATAA

                                 * *       
      14486 GGATATAACGTTACGAAAATCGAGCAAATAA
          1 GGATATAACGTTACGAAAATCAAACAAATAA

                   
      14517 GGATATA
          1 GGATATA

      14524 GTCCGTTAGA


Statistics
Matches: 33,  Mismatches: 3, Indels: 2
        0.87            0.08        0.05

Matches are distributed among these distances:
  29   14  0.42
  30    4  0.12
  31   15  0.45

ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21


Consensus pattern (31 bp):   
GGATATAACGTTACGAAAATCAAACAAATAA

Found at i:14740 original size:31 final size:31

Alignment explanation


    Indices: 14641--14752  Score: 93
    Period size: 31  Copynumber: 3.7  Consensus size: 31

      14631 GCCCTAACTG

                              * *   *      
      14641 ATTATATCCTTAATTGCTCGAAATCGAAAAC
          1 ATTATATCCTTAATTGCTTGCAATAGAAAAC

            *              *     ** *  *   
      14672 GTTATATCCTTAATTACTTG-TTTTG-TAAC
          1 ATTATATCCTTAATTGCTTGCAATAGAAAAC

            *                    **        
      14701 GTTATATCCTTAATTGCTTGCGGTAGAAAAC
          1 ATTATATCCTTAATTGCTTGCAATAGAAAAC

                      *          
      14732 ATTATATCCTAAATTGCTTGC
          1 ATTATATCCTTAATTGCTTGC

      14753 TTATCATCTA


Statistics
Matches: 65,  Mismatches: 14, Indels: 4
        0.78            0.17        0.05

Matches are distributed among these distances:
  29   22  0.34
  30    4  0.06
  31   39  0.60

ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40


Consensus pattern (31 bp):   
ATTATATCCTTAATTGCTTGCAATAGAAAAC
Done.