Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016413.1 Corchorus capsularis cultivar CVL-1 contig16434, 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: 7032
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33


Found at i:407 original size:22 final size:22

Alignment explanation


    Indices: 298--574  Score: 139
    Period size: 22  Copynumber: 12.5  Consensus size: 22

        288 AATAACATGC

                                  
        298 AATCAGTAAAAAGTAAAAAGGT
          1 AATCAGTAAAAAGTAAAAAGGT

             *  *      *      *   
        320 -GTCTG-AAAAGGTAAAATGGT
          1 AATCAGTAAAAAGTAAAAAGGT

                       *  *         
        340 AATCA--ACAAGAGCAAAATA-GT
          1 AATCAGTA-AAAAGTAAAA-AGGT

             *   *         *  *    
        361 AGTCAATAAAAAGT-GAATGGTT
          1 AATCAGTAAAAAGTAAAAAGG-T

                     *            
        383 AATCAGTAAGAAGTAAAAAGGT
          1 AATCAGTAAAAAGTAAAAAGGT

                           *      *
        405 AATCAGTAAAAAAG-CAAAAGGC
          1 AATCAGT-AAAAAGTAAAAAGGT

                                   
        427 AATCAGTAAAAAGT-AAAAGAGT
          1 AATCAGTAAAAAGTAAAAAG-GT

                 *           *       *  
        449 AATCATTAAAAAAGGAGCAGAAAATAGT
          1 AATCAGT--AAAA--AGTA-AAAA-GGT

                               *   
        477 AATCAGTAAAAGAGTAAAATGGT
          1 AATCAGTAAAA-AGTAAAAAGGT

                            *     
        500 AATCAGTAAAAAGTAAGAAGGT
          1 AATCAGTAAAAAGTAAAAAGGT

                       *            
        522 AATCA--ACAAGAGTAAAATA-GT
          1 AATCAGTA-AAAAGTAAAA-AGGT

                    **             
        543 AATCAGTACGAAGTAAAGAA--T
          1 AATCAGTAAAAAGTAAA-AAGGT

                       
        564 AATCAGTAAAA
          1 AATCAGTAAAA

        575 TAGTGATGGT


Statistics
Matches: 192,  Mismatches: 40, Indels: 47
        0.69            0.14        0.17

Matches are distributed among these distances:
  20   15  0.08
  21   57  0.30
  22   66  0.34
  23   25  0.13
  24    7  0.04
  25    4  0.02
  26    6  0.03
  28   12  0.06

ACGTcount: A:0.55, C:0.07, G:0.19, T:0.19


Consensus pattern (22 bp):   
AATCAGTAAAAAGTAAAAAGGT

Found at i:492 original size:15 final size:15

Alignment explanation


    Indices: 438--493  Score: 53
    Period size: 15  Copynumber: 3.9  Consensus size: 15

        428 ATCAGTAAAA

                           
        438 AGTAAAAGAGTAATC
          1 AGTAAAAGAGTAATC

             *     *   * * 
        453 ATTAAAAAAG-GAGC
          1 AGTAAAAGAGTAATC

                   *       
        467 AG-AAAATAGTAATC
          1 AGTAAAAGAGTAATC

                         
        481 AGTAAAAGAGTAA
          1 AGTAAAAGAGTAA

        494 AATGGTAATC


Statistics
Matches: 30,  Mismatches: 9, Indels: 4
        0.70            0.21        0.09

Matches are distributed among these distances:
  13    6  0.20
  14    7  0.23
  15   17  0.57

ACGTcount: A:0.57, C:0.05, G:0.20, T:0.18


Consensus pattern (15 bp):   
AGTAAAAGAGTAATC

Found at i:6551 original size:26 final size:27

Alignment explanation


    Indices: 6503--6553  Score: 68
    Period size: 27  Copynumber: 1.9  Consensus size: 27

       6493 GTGTTCATGA

                *           *          
       6503 TTTGGGGTTACTAACTCCCTTTTTTAT
          1 TTTGAGGTTACTAACTACCTTTTTTAT

                              *      
       6530 TTTGAGGTTACTAAC-ACTTTTTTT
          1 TTTGAGGTTACTAACTACCTTTTTT

       6554 TCAGAGAGAC


Statistics
Matches: 21,  Mismatches: 3, Indels: 1
        0.84            0.12        0.04

Matches are distributed among these distances:
  26    7  0.33
  27   14  0.67

ACGTcount: A:0.18, C:0.16, G:0.14, T:0.53


Consensus pattern (27 bp):   
TTTGAGGTTACTAACTACCTTTTTTAT

Found at i:6975 original size:2 final size:2

Alignment explanation


    Indices: 6968--6994  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       6958 TAATCACTTA

                                                    
       6968 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

       6995 ATTCAAAATA


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

Done.