Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008784.1 Corchorus capsularis cultivar CVL-1 contig08805, 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: 2305
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37


Found at i:1454 original size:11 final size:11

Alignment explanation


    Indices: 1438--1472  Score: 52
    Period size: 11  Copynumber: 3.1  Consensus size: 11

       1428 TTTCTCTATC

                       
       1438 ACAAAAAAAAA
          1 ACAAAAAAAAA

                  *    
       1449 ACAAAACAAAA
          1 ACAAAAAAAAA

                        
       1460 ACAAAACAAAAA
          1 ACAAAA-AAAAA

             
       1472 A
          1 A

       1473 GAGGAAGGAT


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  11   16  0.76
  12    5  0.24

ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00


Consensus pattern (11 bp):   
ACAAAAAAAAA

Found at i:1459 original size:16 final size:16

Alignment explanation


    Indices: 1438--1470  Score: 57
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       1428 TTTCTCTATC

                            
       1438 ACAAAAAAAAAACAAA
          1 ACAAAAAAAAAACAAA

                   *        
       1454 ACAAAAACAAAACAAA
          1 ACAAAAAAAAAACAAA

             
       1470 A
          1 A

       1471 AAGAGGAAGG


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00


Consensus pattern (16 bp):   
ACAAAAAAAAAACAAA

Found at i:1796 original size:166 final size:166

Alignment explanation


    Indices: 1521--1856  Score: 450
    Period size: 166  Copynumber: 2.0  Consensus size: 166

       1511 TGTACATCTA

                         *      *           *                                
       1521 ATTTTATACTTCCTCATGTTGCATTAAGTTTATTTATAACCTTATACAAATTTGACTTACAGGTC
          1 ATTTTATACTTCCGCATGTTACATTAAGTTTAGTTATAACCTTATACAAATTTGACTTACAGGTC

                                  *                            * *           
       1586 TAGGTGTGTTTGGTTGAATTGTGAGATTTGTTTTGAAGAGATTGAAA-AATTAGA-A-ATTACAG
         66 TAGGTGTGTTTGGTTGAATTGTAAGATTTGTTTTGAAGAGATTGAAATAATGAAATAGATTACAG

             *                                   
       1648 TGTGATAT-TAGAATAACAATAATAAAAATAAAATTT
        131 TCTGATATCT-GAATAACAATAATAAAAATAAAATTT

                                       *                                    *
       1684 ATTTTATACTTCCGCATGTTACATTAATTTTAGTTATAACCTTATACAAATTATTTGACTTACAT
          1 ATTTTATACTTCCGCATGTTACATTAAGTTTAGTTATAACCTTATAC-AA--ATTTGACTTACAG

                                                                  *          
       1749 GT-TCAGGTGTGTTTGGTTGAATTGTAAGATTTGTTTTGGAA-AGATTGAAATAGTGAAATTAGA
         63 GTCT-AGGTGTGTTTGGTTGAATTGTAAGATTTGTTTT-GAAGAGATTGAAATAATGAAA-TAGA

                *     *                    *          
       1812 TTACGGTCTGGTATCTGAATAACAATAATAAGAATAAAATTT
        125 TTACAGTCTGATATCTGAATAACAATAATAAAAATAAAATTT

               
       1854 ATT
          1 ATT

       1857 GAAAATTTTC


Statistics
Matches: 150,  Mismatches: 13, Indels: 13
        0.85            0.07        0.07

Matches are distributed among these distances:
 163   43  0.29
 164    2  0.01
 165    1  0.01
 166   55  0.37
 167    7  0.05
 169    1  0.01
 170   40  0.27
 171    1  0.01

ACGTcount: A:0.35, C:0.08, G:0.16, T:0.40


Consensus pattern (166 bp):   
ATTTTATACTTCCGCATGTTACATTAAGTTTAGTTATAACCTTATACAAATTTGACTTACAGGTC
TAGGTGTGTTTGGTTGAATTGTAAGATTTGTTTTGAAGAGATTGAAATAATGAAATAGATTACAG
TCTGATATCTGAATAACAATAATAAAAATAAAATTT
Done.