Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011097.1 Corchorus capsularis cultivar CVL-1 contig11118, 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: 3554
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32


Found at i:649 original size:323 final size:321

Alignment explanation


    Indices: 112--758  Score: 987
    Period size: 323  Copynumber: 2.0  Consensus size: 321

        102 AATATGAAAA

                                                 *    **                     
        112 AAACGATATGAAAAAGCGTGAAAAAGTCCTCCAACCATTTTGTTGTTAAATTATATATATATTTC
          1 AAACGATATGAAAAAGCGTGAAAAAGTCCTCCAACCACTTTGGCGTTAAATTATATATATATTTC

            *                      *                                         
        177 TTGAGTATTTTAGCCAAAATGGAGGAAAAAAATTTGGTCATTTTTTGCAAAATTTTAGCCGAAAT
         66 ATGAGTATTTTAGCCAAAATGGAAGAAAAAAATTTGGTCATTTTTTGCAAAATTTTAGCCGAAAT

                   *                                *    *                   
        242 CGTGTACTAACCATCACGGTTTTTGGCTAAAAACGTGTTTTGGGGCCTCGGCTCAGTTTTGCATG
        131 CGTGTACAAACCATCACGGTTTTTGGCTAAAAACGTGTTTCGGGGACTCGGCTCAGTTTTGCATG

                                            *                                
        307 ATTTTTGGTGCCCAGACTCCTTGAAATATCTATATTCATCTAATGAAATCTTAGCC-ACATTGCA
        196 ATTTTTGGTGCCCAGACTCCTTGAAATATCTACATTCATCTAATGAAATCTTAGCCGA-ATTGCA

               **                  *  *             * *             *      
        371 TTTCTGGATTTGTCTT-AACGAGTATTTAAATCTTGTTTCGATTTAATTAGAAATTTATTCAG
        260 TTTAAGGATTTGT-TTCAACGAGCATCTAAATCTTGTTTCAAATTAATTAGAAATTAATTCAG

                                                *                            
        433 AAACGATATG-AAAAGCGTG-AAAAGTCCTCCAACCCCTTTGGCGTTAAATTATATATATATTTC
          1 AAACGATATGAAAAAGCGTGAAAAAGTCCTCCAACCACTTTGGCGTTAAATTATATATATATTTC

                                             **                              
        496 ATGAGTATTTTAGCCAAAAATGGAAGAAAAATTTTTTTGGTCATTTTTTGCAAAATTTTAGCCGA
         66 ATGAGTATTTTAGCC-AAAATGGAAGAAAAA--AATTTGGTCATTTTTTGCAAAATTTTAGCCGA

                                                                             
        561 AATCGTGTACAAACCATCACGGTTTTTTGGCTAAAAACGTGTTTCGGGGACTCGGCTCAGTTTTG
        128 AATCGTGTACAAACCATCACGG-TTTTTGGCTAAAAACGTGTTTCGGGGACTCGGCTCAGTTTTG

               *            *                                *               
        626 CATTATTTTTGGTGCCGAGACTCCTTGAAATATCTACATTCATCTAATGGAATCTTAGCCGAATT
        192 CATGATTTTTGGTGCCCAGACTCCTTGAAATATCTACATTCATCTAATGAAATCTTAGCCGAATT

                               **         *                                  
        691 GCATTTAAGGATTTGTTTCTGCGAGCATCTGAATCTTGTTTCAAATTAATTAGAAATTAATTCAG
        257 GCATTTAAGGATTTGTTTCAACGAGCATCTAAATCTTGTTTCAAATTAATTAGAAATTAATTCAG

               
        756 AAA
          1 AAA

        759 AAATATATAA


Statistics
Matches: 295,  Mismatches: 25, Indels: 10
        0.89            0.08        0.03

Matches are distributed among these distances:
 319   54  0.18
 320   23  0.08
 321   10  0.03
 322   53  0.18
 323  154  0.52
 324    1  0.00

ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36


Consensus pattern (321 bp):   
AAACGATATGAAAAAGCGTGAAAAAGTCCTCCAACCACTTTGGCGTTAAATTATATATATATTTC
ATGAGTATTTTAGCCAAAATGGAAGAAAAAAATTTGGTCATTTTTTGCAAAATTTTAGCCGAAAT
CGTGTACAAACCATCACGGTTTTTGGCTAAAAACGTGTTTCGGGGACTCGGCTCAGTTTTGCATG
ATTTTTGGTGCCCAGACTCCTTGAAATATCTACATTCATCTAATGAAATCTTAGCCGAATTGCAT
TTAAGGATTTGTTTCAACGAGCATCTAAATCTTGTTTCAAATTAATTAGAAATTAATTCAG

Found at i:1249 original size:13 final size:13

Alignment explanation


    Indices: 1231--1265  Score: 61
    Period size: 13  Copynumber: 2.7  Consensus size: 13

       1221 GATCTAAATC

                   *     
       1231 TAAAGCAGATTAA
          1 TAAAGCAAATTAA

                         
       1244 TAAAGCAAATTAA
          1 TAAAGCAAATTAA

                     
       1257 TAAAGCAAA
          1 TAAAGCAAA

       1266 CAATAATTAA


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  13   21  1.00

ACGTcount: A:0.60, C:0.09, G:0.11, T:0.20


Consensus pattern (13 bp):   
TAAAGCAAATTAA
Done.