Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001225.1 Corchorus capsularis cultivar CVL-1 contig01225, 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: 2204
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.41


Found at i:1273 original size:25 final size:25

Alignment explanation


    Indices: 1245--1296  Score: 95
    Period size: 25  Copynumber: 2.1  Consensus size: 25

       1235 TATTTGTACT

                                     
       1245 TAACTATATTATCCTTAAATGTAAA
          1 TAACTATATTATCCTTAAATGTAAA

                            *        
       1270 TAACTATATTATCCTTGAATGTAAA
          1 TAACTATATTATCCTTAAATGTAAA

              
       1295 TA
          1 TA

       1297 TCATCTTTAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  25   26  1.00

ACGTcount: A:0.42, C:0.12, G:0.06, T:0.40


Consensus pattern (25 bp):   
TAACTATATTATCCTTAAATGTAAA

Found at i:1391 original size:48 final size:48

Alignment explanation


    Indices: 1335--1431  Score: 185
    Period size: 48  Copynumber: 2.0  Consensus size: 48

       1325 TATTCTGAGA

                                  *                         
       1335 AACATTATATTGTAAATAACCTTTACAGTTCTTCTACCGAACCAAGCT
          1 AACATTATATTGTAAATAACCTCTACAGTTCTTCTACCGAACCAAGCT

                                                            
       1383 AACATTATATTGTAAATAACCTCTACAGTTCTTCTACCGAACCAAGCT
          1 AACATTATATTGTAAATAACCTCTACAGTTCTTCTACCGAACCAAGCT

             
       1431 A
          1 A

       1432 TACTTCTACC


Statistics
Matches: 48,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  48   48  1.00

ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32


Consensus pattern (48 bp):   
AACATTATATTGTAAATAACCTCTACAGTTCTTCTACCGAACCAAGCT

Found at i:1483 original size:19 final size:20

Alignment explanation


    Indices: 1445--1485  Score: 66
    Period size: 19  Copynumber: 2.1  Consensus size: 20

       1435 TTCTACCCGC

                         *      
       1445 ATATTTATTATTATTTAAAT
          1 ATATTTATTATTAATTAAAT

                                
       1465 ATATTTATT-TTAATTAAAT
          1 ATATTTATTATTAATTAAAT

              
       1484 AT
          1 AT

       1486 TTGTGATTTC


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  19   11  0.55
  20    9  0.45

ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59


Consensus pattern (20 bp):   
ATATTTATTATTAATTAAAT

Found at i:1603 original size:145 final size:146

Alignment explanation


    Indices: 1432--1724  Score: 552
    Period size: 145  Copynumber: 2.0  Consensus size: 146

       1422 AACCAAGCTA

                                                                         *   
       1432 TACTTCTACCCGCATATTTATTATTATTTAAATATATTTATTTTAATTAAATATTTGTGATTTCT
          1 TACTTCTACCCGCATATTTATTATTATTTAAATATATTTATTTTAATTAAATATTTGTGATGTCT

                                                                             
       1497 TATTATTTTTAAGTATTT-AAAAATTATATTTTGTTCACACGCGTTGTACCATGTGCAACGCACG
         66 TATTATTTTTAAGTATTTAAAAAATTATATTTTGTTCACACGCGTTGTACCATGTGCAACGCACG

                            
       1561 TGAAGGTGAAAACTAG
        131 TGAAGGTGAAAACTAG

                     *                                      *                
       1577 TACTTCTACTCGCATATTTATTATTATTTAAATATATTTATTTTAATTGAATATTTGTGATGTCT
          1 TACTTCTACCCGCATATTTATTATTATTTAAATATATTTATTTTAATTAAATATTTGTGATGTCT

                                                                             
       1642 TATTATTTTTAAGTATTTAAAAAATTATATTTTGTTCACACGCGTTGTACCATGTGCAACGCACG
         66 TATTATTTTTAAGTATTTAAAAAATTATATTTTGTTCACACGCGTTGTACCATGTGCAACGCACG

                            
       1707 TGAAGGTGAAAACTAG
        131 TGAAGGTGAAAACTAG

              
       1723 TA
          1 TA

       1725 TATTAAAAAG


Statistics
Matches: 144,  Mismatches: 3, Indels: 1
        0.97            0.02        0.01

Matches are distributed among these distances:
 145   80  0.56
 146   64  0.44

ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44


Consensus pattern (146 bp):   
TACTTCTACCCGCATATTTATTATTATTTAAATATATTTATTTTAATTAAATATTTGTGATGTCT
TATTATTTTTAAGTATTTAAAAAATTATATTTTGTTCACACGCGTTGTACCATGTGCAACGCACG
TGAAGGTGAAAACTAG

Found at i:2006 original size:79 final size:78

Alignment explanation


    Indices: 1814--2061  Score: 390
    Period size: 78  Copynumber: 3.2  Consensus size: 78

       1804 ATTGTTTAGG

                          *                       *         *       *        
       1814 TTTTA-TAGTTTTAGTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAACT
          1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACT

               *          
       1878 ATTTTATTTTACCA
         65 ATTATATTTTACCA

                                                          *                  
       1892 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAAGCTAATATCCTTATAACTA
          1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA

            **            
       1957 AAATATTTTAACCA
         66 TTATATTTT-ACCA

                                    *                                        
       1971 TTTTACTATTTTACTCAACTAAAATCTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
          1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA

                         
       2036 TTATATTTTACCA
         66 TTATATTTTACCA

                         
       2049 TTTTACTATTTTA
          1 TTTTACTATTTTA

       2062 ATTAAAAACT


Statistics
Matches: 156,  Mismatches: 12, Indels: 4
        0.91            0.07        0.02

Matches are distributed among these distances:
  78   80  0.51
  79   76  0.49

ACGTcount: A:0.37, C:0.13, G:0.01, T:0.49


Consensus pattern (78 bp):   
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
TTATATTTTACCA
Done.