Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015479.1 Corchorus capsularis cultivar CVL-1 contig15500, 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: 11263
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33


Found at i:637 original size:2 final size:2

Alignment explanation


    Indices: 630--654  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

        620 ACAGTTTTTA

                                                 
        630 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 A

        655 ATTTAGTACT


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


Consensus pattern (2 bp):   
AT

Found at i:1535 original size:20 final size:21

Alignment explanation


    Indices: 1510--1555  Score: 67
    Period size: 20  Copynumber: 2.2  Consensus size: 21

       1500 AATTAAAGTT

                   *  *          
       1510 TCAACCATCTTAATTAA-CAC
          1 TCAACCACCTAAATTAATCAC

                                 
       1530 TCAACCACCTAAATTAATCAC
          1 TCAACCACCTAAATTAATCAC

                 
       1551 TCAAC
          1 TCAAC

       1556 TATATATGGA


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  20   15  0.65
  21    8  0.35

ACGTcount: A:0.41, C:0.33, G:0.00, T:0.26


Consensus pattern (21 bp):   
TCAACCACCTAAATTAATCAC

Found at i:2163 original size:2 final size:2

Alignment explanation


    Indices: 2156--2180  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       2146 CCATCTTCTA

                                                 
       2156 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 A

       2181 AACCAAAATA


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


Consensus pattern (2 bp):   
AT

Found at i:2407 original size:3 final size:3

Alignment explanation


    Indices: 2399--2436  Score: 76
    Period size: 3  Copynumber: 12.7  Consensus size: 3

       2389 ATGTTCATTC

                                                              
       2399 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT

       2437 GTTTGCAGCT


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   35  1.00

ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66


Consensus pattern (3 bp):   
ATT

Found at i:3961 original size:132 final size:130

Alignment explanation


    Indices: 3569--4023  Score: 497
    Period size: 132  Copynumber: 3.5  Consensus size: 130

       3559 AGTGGATGCC

                            *                                                
       3569 AAAGTTTGGTTGAACTTCCTTGCATGAGGCATTTGATATCTCTTAAGAAGCTAGATCTTTCATAT
          1 AAAGTTTGGTTGAACTCCCTTGCATGAGGCATTTGATATCTCTTAAGAAGCTAGATCTTTCATAT

                                     **                         *       * *  
       3634 TGCTCAAATCTTACTAAATTTTCAGCGCTTCCAACAAACTTAGAAGAATTACATTTATCTAGCTG
         66 TGCTCAAAT-TTACTAAATTTTCAGAACTTCCAACAAACTTAGAAGAATTA-TTTTATCTGGGTG

              
       3699 CG
        129 CG

                            *              *    *          **                
       3701 AAAGTTTGGTTGAACTTCCTTGCATGAGGCAATTGACATCTCTTAAGGTGCTAGATCTTTCATCA
          1 AAAGTTTGGTTGAACTCCCTTGCATGAGGCATTTGATATCTCTTAAGAAGCTAGATCTTTCAT-A

                                                          *           *      
       3766 -TGCTCAAAATTTACTAAATTTTCAGAACTTCCAACAAACTTAGAAAAATTATGTTT-GCGTGGG
         65 TTGCTC-AAATTTACTAAATTTTCAGAACTTCCAACAAACTTAGAAGAATTAT-TTTATC-TGGG

              * 
       3829 TGTG
        127 TGCG

                                        *        *  *                   **  *
       3833 AAAGTTTGGTTGAACTCCCTTGCATGAGCCATTTGATGTCACTTGAA-AAGCTAGATCTTAGATT
          1 AAAGTTTGGTTGAACTCCCTTGCATGAGGCATTTGATATCTCTT-AAGAAGCTAGATCTTTCATA

                    *                   *     *    *        *                
       3897 TTGCTCAAGTTTCACTAAATTTTCAGAATTTCCACCAAATTTAGAAGAGTTATTCTTATCTGGGT
         65 TTGCTCAAATTT-ACTAAATTTTCAGAACTTCCAACAAACTTAGAAGAATTATT-TTATCTGGGT

              *
       3962 GCA
        128 GCG

               * *                   * *    *                            
       3965 AAAATCTGGTTGAACTCCCTTGCATAATGCATCTGATATCTC-TAA-AAGTCCTAGATCTT
          1 AAAGTTTGGTTGAACTCCCTTGCATGAGGCATTTGATATCTCTTAAGAAG--CTAGATCTT

       4024 AGTGATTGCC


Statistics
Matches: 272,  Mismatches: 40, Indels: 22
        0.81            0.12        0.07

Matches are distributed among these distances:
 130    5  0.02
 131    8  0.03
 132  251  0.92
 133    8  0.03

ACGTcount: A:0.30, C:0.18, G:0.16, T:0.35


Consensus pattern (130 bp):   
AAAGTTTGGTTGAACTCCCTTGCATGAGGCATTTGATATCTCTTAAGAAGCTAGATCTTTCATAT
TGCTCAAATTTACTAAATTTTCAGAACTTCCAACAAACTTAGAAGAATTATTTTATCTGGGTGCG

Found at i:8553 original size:1 final size:1

Alignment explanation


    Indices: 8515--8540  Score: 52
    Period size: 1  Copynumber: 26.0  Consensus size: 1

       8505 GTAAATAAAT

                                      
       8515 AAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAA

       8541 GGGAAAAAAA


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

Matches are distributed among these distances:
   1   25  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Done.