Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024885.1 Corchorus olitorius cultivar O-4 contig24918, 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: 12619
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34


Found at i:4720 original size:34 final size:34

Alignment explanation


    Indices: 4609--4763  Score: 224
    Period size: 34  Copynumber: 4.6  Consensus size: 34

       4599 AAATATTATG

                                               
       4609 TGACAACTTCTGGTGTCAACGATAATAATTTAATA
          1 TGACAACTTCTGGTGTCAA-GATAATAATTTAATA

                       *                * *  * 
       4644 TGACAACTTCTAGTGTC-A-ATAATATACTCAACA
          1 TGACAACTTCTGGTGTCAAGATAATA-ATTTAATA

             *                                
       4677 TTACAACTTCTGGTGTCAAGATAATAATTTAATA
          1 TGACAACTTCTGGTGTCAAGATAATAATTTAATA

                                             *
       4711 TGACAACTTCTGGTGTCAAGATAATAATTTAATG
          1 TGACAACTTCTGGTGTCAAGATAATAATTTAATA

                               
       4745 TGACAACTTCTGGTGTCAA
          1 TGACAACTTCTGGTGTCAA

       4764 TTAAATTCTA


Statistics
Matches: 106,  Mismatches: 11, Indels: 7
        0.85            0.09        0.06

Matches are distributed among these distances:
  32    6  0.06
  33   20  0.19
  34   58  0.55
  35   22  0.21

ACGTcount: A:0.36, C:0.15, G:0.14, T:0.34


Consensus pattern (34 bp):   
TGACAACTTCTGGTGTCAAGATAATAATTTAATA

Found at i:11692 original size:178 final size:178

Alignment explanation


    Indices: 11379--11717  Score: 479
    Period size: 178  Copynumber: 1.9  Consensus size: 178

      11369 TTTCCACCAT

                         *                       *             *      *      
      11379 AAGCACAAATTATGTAATATTAAGTAGACTGTCTATTTCCGTTAACCGAAAGAACTAATTCTTTG
          1 AAGCACAAATTATATAATATTAAGTAGACTGTCTATTCCCGTTAACCGAAACAACTAAATCTTTG

               *       *                               *                   * 
      11444 GAATCATTTTTTATACCTTGAACATTAAATTTAGTTTTCGAGTTCTTCATAAAAGTTGTAGATCA
         66 GAAGCATTTTTGATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATAAAAGTTGTAGATAA

                                     *                      
      11509 TGGAACAACCTTTGAAAAGACACTTGAATCATCTCAATCAAACATCTG
        131 TGGAACAACCTTTGAAAAGACACTTAAATCATCTCAATCAAACATCTG

                                      *                                      
      11557 AAGCA-AAAGTTATATAATATTAAGTGGA-TCGTCTATTCCCGTTAACCGAAACAAC-AAATCTT
          1 AAGCACAAA-TTATATAATATTAAGTAGACT-GTCTATTCCCGTTAACCGAAACAACTAAATCTT

                                                                  *          
      11619 TCGGAAGCATTTTTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAG
         64 T-GGAAGCATTTTTGATACCTTG-AACATTAAATTTAGTTTTCGAGTCCTTCATAAAAGTTGTAG

                        *    *  **             
      11683 ATAATGGAACAATCTTTTAATGGACACTTAAATCA
        127 ATAATGGAACAACCTTTGAAAAGACACTTAAATCA

      11718 CCCTAATCGG


Statistics
Matches: 142,  Mismatches: 15, Indels: 8
        0.86            0.09        0.05

Matches are distributed among these distances:
 177   15  0.11
 178  127  0.89

ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34


Consensus pattern (178 bp):   
AAGCACAAATTATATAATATTAAGTAGACTGTCTATTCCCGTTAACCGAAACAACTAAATCTTTG
GAAGCATTTTTGATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATAAAAGTTGTAGATAA
TGGAACAACCTTTGAAAAGACACTTAAATCATCTCAATCAAACATCTG

Found at i:11750 original size:178 final size:178

Alignment explanation


    Indices: 11379--11763  Score: 465
    Period size: 178  Copynumber: 2.2  Consensus size: 178

      11369 TTTCCACCAT

                 *       *                       *             *      *      
      11379 AAGCACAAATTATGTAATATTAAGTAGACTGTCTATTTCCGTTAACCGAAAGAACTAATTCTTTG
          1 AAGCAAAAATTATATAATATTAAGTAGACTGTCTATTCCCGTTAACCGAAACAACTAAATCTTTG

               *       *                               *                   * 
      11444 GAATCATTTTTTATACCTTGAACATTAAATTTAGTTTTCGAGTTCTTCATAAAAGTTGTAGATCA
         66 GAAGCATTTTTGATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATAAAAGTTGTAGATAA

                                     *     *            * * 
      11509 TGGAACAACCTTTGAAAAGACACTTGAATCATCTCAATCAAACATCTG
        131 TGGAACAACCTTTGAAAAGACACTTAAATCACCTCAATCAAACAACCG

                    *                *                                       
      11557 AAGCAAAAGTTATATAATATTAAGTGGA-TCGTCTATTCCCGTTAACCGAAACAAC-AAATCTTT
          1 AAGCAAAAATTATATAATATTAAGTAGACT-GTCTATTCCCGTTAACCGAAACAACTAAATCTTT

                                                                 *           
      11620 CGGAAGCATTTTTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGA
         65 -GGAAGCATTTTTGATACCTTG-AACATTAAATTTAGTTTTCGAGTCCTTCATAAAAGTTGTAGA

                       *    *  **                      ** *     
      11684 TAATGGAACAATCTTTTAATGGACACTTAAATCACC-CTAATCGGATAACCG
        128 TAATGGAACAACCTTTGAAAAGACACTTAAATCACCTC-AATCAAACAACCG

                               *    *     
      11735 AAG-ATAAAATTATATAATGTTAAATAGAC
          1 AAGCA-AAAATTATATAATATTAAGTAGAC

      11764 CGTTTAGGCA


Statistics
Matches: 174,  Mismatches: 27, Indels: 11
        0.82            0.13        0.05

Matches are distributed among these distances:
 177   14  0.08
 178  160  0.92

ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33


Consensus pattern (178 bp):   
AAGCAAAAATTATATAATATTAAGTAGACTGTCTATTCCCGTTAACCGAAACAACTAAATCTTTG
GAAGCATTTTTGATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATAAAAGTTGTAGATAA
TGGAACAACCTTTGAAAAGACACTTAAATCACCTCAATCAAACAACCG
Done.