Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005101.1 Corchorus capsularis cultivar CVL-1 contig05119, 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: 13643
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34


Found at i:3193 original size:27 final size:28

Alignment explanation


    Indices: 3162--3228  Score: 109
    Period size: 29  Copynumber: 2.4  Consensus size: 28

       3152 AGTAGGGGAT

                                        
       3162 CAAAATGCCCCTGAATGC-AAAAATGAC
          1 CAAAATGCCCCTGAATGCAAAAAATGAC

            *                            
       3189 TAAAATGCCCCTGAATGCAAAAAAATGAC
          1 CAAAATGCCCCTGAATGC-AAAAAATGAC

                       
       3218 CAAAATGCCCC
          1 CAAAATGCCCC

       3229 CTAGATGACC


Statistics
Matches: 36,  Mismatches: 2, Indels: 2
        0.90            0.05        0.05

Matches are distributed among these distances:
  27   17  0.47
  29   19  0.53

ACGTcount: A:0.45, C:0.27, G:0.13, T:0.15


Consensus pattern (28 bp):   
CAAAATGCCCCTGAATGCAAAAAATGAC

Found at i:4366 original size:42 final size:43

Alignment explanation


    Indices: 4319--4401  Score: 125
    Period size: 42  Copynumber: 2.0  Consensus size: 43

       4309 CGTGTTTGGC

                                          *             
       4319 TTATCGTGTCTCGTGTC-TGAATCGTGTC-GGACACGATTAAGA
          1 TTATCGTGTCTCGTGTCGT-AATCGTGTCAAGACACGATTAAGA

                     *                               
       4361 TTATCGTGTTTCGTGTCGTAATCGTGTCAAGACACGATTAA
          1 TTATCGTGTCTCGTGTCGTAATCGTGTCAAGACACGATTAA

       4402 CACGTTTAAG


Statistics
Matches: 37,  Mismatches: 2, Indels: 3
        0.88            0.05        0.07

Matches are distributed among these distances:
  42   25  0.68
  43   12  0.32

ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35


Consensus pattern (43 bp):   
TTATCGTGTCTCGTGTCGTAATCGTGTCAAGACACGATTAAGA

Found at i:4414 original size:20 final size:21

Alignment explanation


    Indices: 4389--4431  Score: 61
    Period size: 20  Copynumber: 2.1  Consensus size: 21

       4379 TAATCGTGTC

                     *           
       4389 AAGACACGATTAACACG-TTT
          1 AAGACACGAGTAACACGCTTT

                       *         
       4409 AAGACACGAGTGACACGCTTT
          1 AAGACACGAGTAACACGCTTT

              
       4430 AA
          1 AA

       4432 TTAACGGGTT


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  20   15  0.75
  21    5  0.25

ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21


Consensus pattern (21 bp):   
AAGACACGAGTAACACGCTTT

Found at i:4590 original size:14 final size:14

Alignment explanation


    Indices: 4571--4597  Score: 54
    Period size: 14  Copynumber: 1.9  Consensus size: 14

       4561 CAATTATCTT

                          
       4571 TAATTATATATATG
          1 TAATTATATATATG

                         
       4585 TAATTATATATAT
          1 TAATTATATATAT

       4598 ATTTTAGTTA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   13  1.00

ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52


Consensus pattern (14 bp):   
TAATTATATATATG

Found at i:8525 original size:26 final size:26

Alignment explanation


    Indices: 8473--8521  Score: 75
    Period size: 26  Copynumber: 1.9  Consensus size: 26

       8463 GTCAATATTT

                                      
       8473 ATTTTTTAAAATAAAATAATAATTAA
          1 ATTTTTTAAAATAAAATAATAATTAA

                                     
       8499 ATTTTTTAATAA-AAAATAA-AATT
          1 ATTTTTTAA-AATAAAATAATAATT

       8522 TAAACATTAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  25    4  0.18
  26   16  0.73
  27    2  0.09

ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43


Consensus pattern (26 bp):   
ATTTTTTAAAATAAAATAATAATTAA
Done.