Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015318.1 Corchorus capsularis cultivar CVL-1 contig15339, 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: 17568
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36


Found at i:1035 original size:5 final size:5

Alignment explanation


    Indices: 1025--1062  Score: 58
    Period size: 5  Copynumber: 7.6  Consensus size: 5

       1015 AACTTCTTAG

                                            *     *      
       1025 TTGTT TTGTT TTGTT TTGTT TTGTT TTTTT TTTTT TTG
          1 TTGTT TTGTT TTGTT TTGTT TTGTT TTGTT TTGTT TTG

       1063 ACAGAAAGGT


Statistics
Matches: 31,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   5   31  1.00

ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84


Consensus pattern (5 bp):   
TTGTT

Found at i:11583 original size:23 final size:23

Alignment explanation


    Indices: 11540--11583  Score: 54
    Period size: 23  Copynumber: 1.9  Consensus size: 23

      11530 CTGCTGAGGC

                         *         
      11540 TACTGCAGCCTCCTTTGTTGGGT
          1 TACTGCAGCCTCCCTTGTTGGGT

                    *             
      11563 TACTGCAATCCTCCCTT-TTGG
          1 TACTGC-AGCCTCCCTTGTTGG

      11584 TGTTCTCAGC


Statistics
Matches: 18,  Mismatches: 2, Indels: 2
        0.82            0.09        0.09

Matches are distributed among these distances:
  23   10  0.56
  24    8  0.44

ACGTcount: A:0.11, C:0.30, G:0.20, T:0.39


Consensus pattern (23 bp):   
TACTGCAGCCTCCCTTGTTGGGT

Found at i:13191 original size:40 final size:39

Alignment explanation


    Indices: 13131--13217  Score: 102
    Period size: 40  Copynumber: 2.2  Consensus size: 39

      13121 TCCTAGGGCC

                    *               *           *  
      13131 AACATTGAGAAAAGGAAGTAGACATGAATCATTGAAGTT
          1 AACATTGAAAAAAGGAAGTAGACAAGAATCATTGAACTT

                            *          *  *         
      13170 AACATTGATAAAAAGGGAGTAGACAAGTATGATTGAACTT
          1 AACATTGA-AAAAAGGAAGTAGACAAGAATCATTGAACTT

                    
      13210 AAGCATTG
          1 AA-CATTG

      13218 CTTTGATTAT


Statistics
Matches: 40,  Mismatches: 6, Indels: 2
        0.83            0.12        0.04

Matches are distributed among these distances:
  39    8  0.20
  40   27  0.68
  41    5  0.12

ACGTcount: A:0.45, C:0.08, G:0.23, T:0.24


Consensus pattern (39 bp):   
AACATTGAAAAAAGGAAGTAGACAAGAATCATTGAACTT

Found at i:14927 original size:18 final size:17

Alignment explanation


    Indices: 14891--14924  Score: 59
    Period size: 17  Copynumber: 2.0  Consensus size: 17

      14881 AAAAAGGTTT

                        *    
      14891 TTTTTTTTTTTTTTGAA
          1 TTTTTTTTTTTTGTGAA

                             
      14908 TTTTTTTTTTTTGTGAA
          1 TTTTTTTTTTTTGTGAA

      14925 ATTCATATTC


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

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.12, C:0.00, G:0.09, T:0.79


Consensus pattern (17 bp):   
TTTTTTTTTTTTGTGAA

Found at i:16083 original size:21 final size:21

Alignment explanation


    Indices: 16057--16102  Score: 83
    Period size: 21  Copynumber: 2.2  Consensus size: 21

      16047 CTATGTTATT

                       *         
      16057 TTAGATCACATTGATCATTCA
          1 TTAGATCACATAGATCATTCA

                                 
      16078 TTAGATCACATAGATCATTCA
          1 TTAGATCACATAGATCATTCA

                
      16099 TTAG
          1 TTAG

      16103 TTTGGTAGAG


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  21   24  1.00

ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37


Consensus pattern (21 bp):   
TTAGATCACATAGATCATTCA

Found at i:16388 original size:3 final size:3

Alignment explanation


    Indices: 16380--16431  Score: 95
    Period size: 3  Copynumber: 17.3  Consensus size: 3

      16370 ATATCAAAAT

                                                                         * 
      16380 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AGA
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA

                 
      16428 ATA A
          1 ATA A

      16432 AATTTGTTGA


Statistics
Matches: 47,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   3   47  1.00

ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31


Consensus pattern (3 bp):   
ATA

Done.