Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016270.1 Corchorus olitorius cultivar O-4 contig16303, 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: 44179
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:1331 original size:2 final size:2

Alignment explanation


    Indices: 1324--1351  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       1314 AACTTACAGA

                                                     
       1324 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       1352 TCAATTATTC


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

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:1398 original size:19 final size:19

Alignment explanation


    Indices: 1376--1417  Score: 50
    Period size: 19  Copynumber: 2.2  Consensus size: 19

       1366 TATTTCATTC

                 *              
       1376 ATCAATATCAGAT-TCATCA
          1 ATCAACATCA-ATATCATCA

                *              
       1395 ATCACCATCAATATCATCA
          1 ATCAACATCAATATCATCA

                
       1414 ATCA
          1 ATCA

       1418 TTTACTTAGC


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  18    2  0.10
  19   18  0.90

ACGTcount: A:0.43, C:0.26, G:0.02, T:0.29


Consensus pattern (19 bp):   
ATCAACATCAATATCATCA

Found at i:1446 original size:20 final size:20

Alignment explanation


    Indices: 1410--1450  Score: 57
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       1400 CATCAATATC

                     *          
       1410 ATCAATCATTTACTTAGCAA
          1 ATCAATCATATACTTAGCAA

                                 
       1430 ATCAATCATCATA-TTAGCAA
          1 ATCAATCAT-ATACTTAGCAA

             
       1450 A
          1 A

       1451 AAATGAAAAT


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  20   17  0.89
  21    2  0.11

ACGTcount: A:0.44, C:0.20, G:0.05, T:0.32


Consensus pattern (20 bp):   
ATCAATCATATACTTAGCAA

Found at i:20685 original size:22 final size:22

Alignment explanation


    Indices: 20659--20700  Score: 57
    Period size: 22  Copynumber: 1.9  Consensus size: 22

      20649 TGTCCACCCA

                   *  *           
      20659 TTAGGACCCTTCACGCGCCATT
          1 TTAGGACACTCCACGCGCCATT

                 *              
      20681 TTAGGTCACTCCACGCGCCA
          1 TTAGGACACTCCACGCGCCA

      20701 CCTAGGGGGT


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  22   17  1.00

ACGTcount: A:0.19, C:0.38, G:0.19, T:0.24


Consensus pattern (22 bp):   
TTAGGACACTCCACGCGCCATT

Found at i:21574 original size:13 final size:13

Alignment explanation


    Indices: 21556--21591  Score: 54
    Period size: 13  Copynumber: 2.7  Consensus size: 13

      21546 AAGCAATTAA

                         
      21556 TAATTAATTAATT
          1 TAATTAATTAATT

                      *  
      21569 TAATTAATTACTT
          1 TAATTAATTAATT

                      
      21582 TAATTCAATT
          1 TAATT-AATT

      21592 TGTTAATCTG


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  13   17  0.81
  14    4  0.19

ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53


Consensus pattern (13 bp):   
TAATTAATTAATT

Found at i:30308 original size:19 final size:19

Alignment explanation


    Indices: 30276--30313  Score: 51
    Period size: 19  Copynumber: 2.0  Consensus size: 19

      30266 TTTCTTTGGG

                                
      30276 CTTTGCTTTATTTCTTCTTT
          1 CTTTGCTTTATTTC-TCTTT

                     *         
      30296 CTTT-CTTTCTTTCTCTTT
          1 CTTTGCTTTATTTCTCTTT

      30314 TTCCTCTCTT


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  18    5  0.29
  19    8  0.47
  20    4  0.24

ACGTcount: A:0.03, C:0.24, G:0.03, T:0.71


Consensus pattern (19 bp):   
CTTTGCTTTATTTCTCTTT

Found at i:32136 original size:11 final size:11

Alignment explanation


    Indices: 32112--32146  Score: 52
    Period size: 11  Copynumber: 3.2  Consensus size: 11

      32102 TTGACAGCGC

                       
      32112 AACAAAAACAA
          1 AACAAAAACAA

               *     * 
      32123 AACGAAAACGA
          1 AACAAAAACAA

                       
      32134 AACAAAAACAA
          1 AACAAAAACAA

              
      32145 AA
          1 AA

      32147 AACAGAAAAA


Statistics
Matches: 20,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  11   20  1.00

ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00


Consensus pattern (11 bp):   
AACAAAAACAA

Found at i:39080 original size:22 final size:22

Alignment explanation


    Indices: 39052--39105  Score: 90
    Period size: 22  Copynumber: 2.5  Consensus size: 22

      39042 CGAAAATATA

                     *            
      39052 GCCACCGACTGACGGGGGAGCT
          1 GCCACCGACCGACGGGGGAGCT

                        *         
      39074 GCCACCGACCGATGGGGGAGCT
          1 GCCACCGACCGACGGGGGAGCT

                      
      39096 GCCACCGACC
          1 GCCACCGACC

      39106 ACCGACTATA


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  22   30  1.00

ACGTcount: A:0.19, C:0.37, G:0.37, T:0.07


Consensus pattern (22 bp):   
GCCACCGACCGACGGGGGAGCT
Done.