Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001454.1 Corchorus capsularis cultivar CVL-1 contig01454, 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: 6708
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35


Found at i:1567 original size:15 final size:15

Alignment explanation


    Indices: 1547--1576  Score: 60
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       1537 ATTCATTGAA

                           
       1547 AATGTAAGAACAGAT
          1 AATGTAAGAACAGAT

                           
       1562 AATGTAAGAACAGAT
          1 AATGTAAGAACAGAT

       1577 GGGAAACTTA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   15  1.00

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


Consensus pattern (15 bp):   
AATGTAAGAACAGAT

Found at i:2663 original size:51 final size:50

Alignment explanation


    Indices: 2566--2674  Score: 166
    Period size: 51  Copynumber: 2.2  Consensus size: 50

       2556 AAATTTTTCC

                *                                    *        
       2566 ATTTCTTTAACACTTTCTATTCAATTCTTTAAACTAATTTTGGCTAGTTG
          1 ATTTTTTTAACACTTTCTATTCAATTCTTTAAACTAATTTTAGCTAGTTG

                                       *                        
       2616 ATTTTTTTAACACTTTCTA-TCAATTATTTGTAAACTAATTTTAGCTAGTTG
          1 ATTTTTTTAACACTTTCTATTCAATT-CTT-TAAACTAATTTTAGCTAGTTG

                    
       2667 ATTTTTTT
          1 ATTTTTTT

       2675 TTCTAACACC


Statistics
Matches: 54,  Mismatches: 3, Indels: 3
        0.90            0.05        0.05

Matches are distributed among these distances:
  49    6  0.11
  50   20  0.37
  51   28  0.52

ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53


Consensus pattern (50 bp):   
ATTTTTTTAACACTTTCTATTCAATTCTTTAAACTAATTTTAGCTAGTTG

Found at i:2817 original size:2 final size:2

Alignment explanation


    Indices: 2775--2799  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       2765 ATGTTGTTAT

                                                 
       2775 TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T

       2800 TAAAATTATT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:3545 original size:33 final size:35

Alignment explanation


    Indices: 3503--3575  Score: 105
    Period size: 37  Copynumber: 2.1  Consensus size: 35

       3493 TAATTACCCC

                                               
       3503 TATTTCAATTTGGGG-A-GAAATCATTATTATATA
          1 TATTTCAATTTGGGGAATGAAATCATTATTATATA

                                  *              
       3536 TATTTCAATTTGGGGAAAATGATATCATTATTATATA
          1 TATTTCAATTTGGGG--AATGAAATCATTATTATATA

               
       3573 TAT
          1 TAT

       3576 ATATATATAT


Statistics
Matches: 35,  Mismatches: 1, Indels: 4
        0.88            0.03        0.10

Matches are distributed among these distances:
  33   15  0.43
  36    1  0.03
  37   19  0.54

ACGTcount: A:0.37, C:0.05, G:0.14, T:0.44


Consensus pattern (35 bp):   
TATTTCAATTTGGGGAATGAAATCATTATTATATA

Done.