Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021782.1 Corchorus olitorius cultivar O-4 contig21815, 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: 17241
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32


Found at i:6631 original size:65 final size:65

Alignment explanation


    Indices: 6550--6680  Score: 244
    Period size: 65  Copynumber: 2.0  Consensus size: 65

       6540 TCGGCCATTC

                                                                             
       6550 AGCAATCTACTTCTTTGAACAATTTTCAATTCGAATTAAATTGTTTGATACATAGGAAATTTCGA
          1 AGCAATCTACTTCTTTGAACAATTTTCAATTCGAATTAAATTGTTTGATACATAGGAAATTTCGA

                                       *                       *             
       6615 AGCAATCTACTTCTTTGAACAATTTTCTATTCGAATTAAATTGTTTGATACGTAGGAAATTTCGA
          1 AGCAATCTACTTCTTTGAACAATTTTCAATTCGAATTAAATTGTTTGATACATAGGAAATTTCGA

             
       6680 A
          1 A

       6681 AGTACTATGA


Statistics
Matches: 64,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  65   64  1.00

ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39


Consensus pattern (65 bp):   
AGCAATCTACTTCTTTGAACAATTTTCAATTCGAATTAAATTGTTTGATACATAGGAAATTTCGA

Found at i:7709 original size:8 final size:8

Alignment explanation


    Indices: 7696--7736  Score: 55
    Period size: 8  Copynumber: 4.9  Consensus size: 8

       7686 GATTATAATT

                    
       7696 TATCTTAC
          1 TATCTTAC

                   *
       7704 TATCTTAT
          1 TATCTTAC

                     
       7712 TATCTTATC
          1 TATCTTA-C

                     
       7721 TTATCTTAC
          1 -TATCTTAC

                   
       7730 TATCTTA
          1 TATCTTA

       7737 TATTATATAA


Statistics
Matches: 29,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
   8   21  0.72
   9    1  0.03
  10    7  0.24

ACGTcount: A:0.24, C:0.20, G:0.00, T:0.56


Consensus pattern (8 bp):   
TATCTTAC

Found at i:7720 original size:13 final size:13

Alignment explanation


    Indices: 7695--7737  Score: 54
    Period size: 13  Copynumber: 3.3  Consensus size: 13

       7685 AGATTATAAT

                         
       7695 TTATCTTACTATC
          1 TTATCTTACTATC

                           
       7708 TTA--TTATCTTATC
          1 TTATCTTA-C-TATC

                         
       7721 TTATCTTACTATC
          1 TTATCTTACTATC

                
       7734 TTAT
          1 TTAT

       7738 ATTATATAAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 8
        0.76            0.00        0.24

Matches are distributed among these distances:
  11    3  0.12
  12    1  0.04
  13   18  0.69
  14    1  0.04
  15    3  0.12

ACGTcount: A:0.23, C:0.19, G:0.00, T:0.58


Consensus pattern (13 bp):   
TTATCTTACTATC

Found at i:16180 original size:29 final size:30

Alignment explanation


    Indices: 16125--16187  Score: 74
    Period size: 29  Copynumber: 2.1  Consensus size: 30

      16115 AGATTTTAAT

                            *** *         
      16125 AAAACTTTGATTCTCTTTGTGGCAAAAAA-
          1 AAAACTTTGATTCTCTACATAGCAAAAAAG

                                  *       
      16154 AAAACTTTGATTCTCTACATAGTAAAAAAG
          1 AAAACTTTGATTCTCTACATAGCAAAAAAG

                
      16184 AAAA
          1 AAAA

      16188 GTAAAGTTCT


Statistics
Matches: 28,  Mismatches: 5, Indels: 1
        0.82            0.15        0.03

Matches are distributed among these distances:
  29   24  0.86
  30    4  0.14

ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30


Consensus pattern (30 bp):   
AAAACTTTGATTCTCTACATAGCAAAAAAG

Found at i:16881 original size:31 final size:28

Alignment explanation


    Indices: 16811--16884  Score: 78
    Period size: 31  Copynumber: 2.6  Consensus size: 28

      16801 CCAAATTGCG

                                *       
      16811 AGTTCAGGGGGC-AAACATCCAAATTAA
          1 AGTTCAGGGGGCAAAACATCAAAATTAA

                *  *         *             
      16838 AGTTTAGAGGGCAAAACGTCAAAATCGTAAA
          1 AGTTCAGGGGGCAAAACATCAAAAT--T-AA

                            
      16869 AGTTCAGGGGGCAAAA
          1 AGTTCAGGGGGCAAAA

      16885 AGGGCATTAA


Statistics
Matches: 37,  Mismatches: 6, Indels: 4
        0.79            0.13        0.09

Matches are distributed among these distances:
  27   10  0.27
  28   10  0.27
  30    1  0.03
  31   16  0.43

ACGTcount: A:0.42, C:0.15, G:0.26, T:0.18


Consensus pattern (28 bp):   
AGTTCAGGGGGCAAAACATCAAAATTAA
Done.