Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016486.1 Corchorus capsularis cultivar CVL-1 contig16507, 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: 15915
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35


Found at i:490 original size:26 final size:26

Alignment explanation


    Indices: 461--512  Score: 77
    Period size: 26  Copynumber: 2.0  Consensus size: 26

        451 ATAGAATTAG

                *                     
        461 TTGATACGATCCCAATCTAAAATGAC
          1 TTGACACGATCCCAATCTAAAATGAC

                 *            *       
        487 TTGACCCGATCCCAATCTGAAATGAC
          1 TTGACACGATCCCAATCTAAAATGAC

        513 ATGTTCCGAG


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  26   23  1.00

ACGTcount: A:0.35, C:0.27, G:0.13, T:0.25


Consensus pattern (26 bp):   
TTGACACGATCCCAATCTAAAATGAC

Found at i:1182 original size:28 final size:28

Alignment explanation


    Indices: 1151--1209  Score: 84
    Period size: 27  Copynumber: 2.1  Consensus size: 28

       1141 TGGAAAATAA

                                         
       1151 GGAAAAAGGACAATTAAAAAGGAACA-AG
          1 GGAAAAA-GACAATTAAAAAGGAACAGAG

                **                      
       1179 GGAATGAGACAATTAAAAAGGAACAGAG
          1 GGAAAAAGACAATTAAAAAGGAACAGAG

               
       1207 GGA
          1 GGA

       1210 GTAATTATTA


Statistics
Matches: 28,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  27   18  0.64
  28   10  0.36

ACGTcount: A:0.56, C:0.07, G:0.29, T:0.08


Consensus pattern (28 bp):   
GGAAAAAGACAATTAAAAAGGAACAGAG

Found at i:2263 original size:2 final size:2

Alignment explanation


    Indices: 2258--2283  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       2248 ATATATATAG

                                                  
       2258 AC AC AC AC AC AC AC AC AC AC AC AC AC
          1 AC AC AC AC AC AC AC AC AC AC AC AC AC

       2284 TCGAAGTCGA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00


Consensus pattern (2 bp):   
AC

Found at i:4646 original size:1 final size:1

Alignment explanation


    Indices: 4640--4664  Score: 50
    Period size: 1  Copynumber: 25.0  Consensus size: 1

       4630 TGATCTAGGG

                                     
       4640 TTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTT

       4665 CATCTTTATT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   24  1.00

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


Consensus pattern (1 bp):   
T

Found at i:11286 original size:25 final size:25

Alignment explanation


    Indices: 11252--11302  Score: 102
    Period size: 25  Copynumber: 2.0  Consensus size: 25

      11242 TCAATGATTC

                                     
      11252 AATTTAGCAAGAAACACTCTATCTG
          1 AATTTAGCAAGAAACACTCTATCTG

                                     
      11277 AATTTAGCAAGAAACACTCTATCTG
          1 AATTTAGCAAGAAACACTCTATCTG

             
      11302 A
          1 A

      11303 TTAGAACTCA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  25   26  1.00

ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27


Consensus pattern (25 bp):   
AATTTAGCAAGAAACACTCTATCTG

Found at i:12726 original size:24 final size:22

Alignment explanation


    Indices: 12669--12715  Score: 76
    Period size: 22  Copynumber: 2.1  Consensus size: 22

      12659 GTACTACATT

                   *              
      12669 AATTAACCATATTCCATGAAAA
          1 AATTAACAATATTCCATGAAAA

                         *        
      12691 AATTAACAATATTTCATGAAAA
          1 AATTAACAATATTCCATGAAAA

               
      12713 AAT
          1 AAT

      12716 ATTAACTATA


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  22   23  1.00

ACGTcount: A:0.53, C:0.13, G:0.04, T:0.30


Consensus pattern (22 bp):   
AATTAACAATATTCCATGAAAA

Found at i:14309 original size:17 final size:17

Alignment explanation


    Indices: 14254--14310  Score: 50
    Period size: 15  Copynumber: 3.6  Consensus size: 17

      14244 TTCGTGTTGT

                *            
      14254 TAATTTTAATTTTTAAC
          1 TAATGTTAATTTTTAAC

                          * *
      14271 TAATGTT--TTTTTGAG
          1 TAATGTTAATTTTTAAC

            *                
      14286 GAA--TTAATTTTTAAC
          1 TAATGTTAATTTTTAAC

                      
      14301 TAATGTTAAT
          1 TAATGTTAAT

      14311 AGTAGCTTAA


Statistics
Matches: 29,  Mismatches: 7, Indels: 8
        0.66            0.16        0.18

Matches are distributed among these distances:
  13    2  0.07
  15   16  0.55
  17   11  0.38

ACGTcount: A:0.33, C:0.04, G:0.09, T:0.54


Consensus pattern (17 bp):   
TAATGTTAATTTTTAAC

Found at i:15517 original size:2 final size:2

Alignment explanation


    Indices: 15510--15535  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

      15500 CTTTTATGTT

                                                  
      15510 TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA

      15536 ATTTATAAAT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Done.