Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018608.1 Corchorus olitorius cultivar O-4 contig18641, 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: 18024
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34


Found at i:1342 original size:22 final size:20

Alignment explanation


    Indices: 1317--1363  Score: 67
    Period size: 20  Copynumber: 2.2  Consensus size: 20

       1307 CTGTTTTGTG

                                  
       1317 TTTTGCATCAAAGAAAAAAAAA
          1 TTTTGCATC--AGAAAAAAAAA

                      *         
       1339 TTTTGCATCATAAAAAAAAA
          1 TTTTGCATCAGAAAAAAAAA

                 
       1359 TTTTG
          1 TTTTG

       1364 TTCCTGCGTC


Statistics
Matches: 24,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  20   15  0.62
  22    9  0.38

ACGTcount: A:0.51, C:0.09, G:0.09, T:0.32


Consensus pattern (20 bp):   
TTTTGCATCAGAAAAAAAAA

Found at i:9424 original size:19 final size:19

Alignment explanation


    Indices: 9400--9436  Score: 65
    Period size: 19  Copynumber: 1.9  Consensus size: 19

       9390 TGCAAGTTTG

                               
       9400 AATGTTCTTAGTGATCATA
          1 AATGTTCTTAGTGATCATA

                         *    
       9419 AATGTTCTTAGTGTTCAT
          1 AATGTTCTTAGTGATCAT

       9437 GAGAAAAAAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  19   17  1.00

ACGTcount: A:0.27, C:0.11, G:0.16, T:0.46


Consensus pattern (19 bp):   
AATGTTCTTAGTGATCATA

Found at i:11121 original size:29 final size:29

Alignment explanation


    Indices: 11062--11121  Score: 68
    Period size: 29  Copynumber: 2.1  Consensus size: 29

      11052 CATGATGTAG

                      *             ***  
      11062 GGTTACTAACCCTTTTATTTTTATTTTGA
          1 GGTTACTAACACTTTTATTTTTATCAAGA

                                          
      11091 GGTTACTAACACTCTTTATTTTT-TCAAGA
          1 GGTTACTAACACT-TTTATTTTTATCAAGA

              
      11120 GG
          1 GG

      11122 GACAACACTT


Statistics
Matches: 26,  Mismatches: 4, Indels: 2
        0.81            0.12        0.06

Matches are distributed among these distances:
  29   17  0.65
  30    9  0.35

ACGTcount: A:0.23, C:0.15, G:0.13, T:0.48


Consensus pattern (29 bp):   
GGTTACTAACACTTTTATTTTTATCAAGA

Found at i:12876 original size:17 final size:17

Alignment explanation


    Indices: 12832--12878  Score: 76
    Period size: 17  Copynumber: 2.8  Consensus size: 17

      12822 TCCCTTCATA

                 *    *      
      12832 CATGGTATTGCCTATCT
          1 CATGGAATTGTCTATCT

                             
      12849 CATGGAATTGTCTATCT
          1 CATGGAATTGTCTATCT

                         
      12866 CATGGAATTGTCT
          1 CATGGAATTGTCT

      12879 CTTAAAGTTC


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  17   28  1.00

ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40


Consensus pattern (17 bp):   
CATGGAATTGTCTATCT

Found at i:13235 original size:30 final size:30

Alignment explanation


    Indices: 13183--13242  Score: 77
    Period size: 30  Copynumber: 2.0  Consensus size: 30

      13173 GAAGTTCGTG

                      *              *    
      13183 TTTGAAGACTTATTAAAGATAATTTGAAGA
          1 TTTGAAGACTCATTAAAGATAATTTCAAGA

                          *                
      13213 TTTGAAGAC-CATTGAAGAATAATTTCAAGA
          1 TTTGAAGACTCATTAAAG-ATAATTTCAAGA

      13243 GCAAGAATTA


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  29    6  0.23
  30   20  0.77

ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33


Consensus pattern (30 bp):   
TTTGAAGACTCATTAAAGATAATTTCAAGA

Found at i:17712 original size:2 final size:2

Alignment explanation


    Indices: 17705--17729  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

      17695 TTATTATCTT

                                                 
      17705 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

      17730 TAGATTTGCA


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

Done.