Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022136.1 Corchorus olitorius cultivar O-4 contig22169, 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: 9863
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:1593 original size:18 final size:19

Alignment explanation


    Indices: 1570--1606  Score: 67
    Period size: 18  Copynumber: 2.0  Consensus size: 19

       1560 CACCCTAGCC

                               
       1570 CTAAAACTAGAAGA-AAAA
          1 CTAAAACTAGAAGAGAAAA

                               
       1588 CTAAAACTAGAAGAGAAAA
          1 CTAAAACTAGAAGAGAAAA

       1607 AGAAGAAGAG


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  18   14  0.78
  19    4  0.22

ACGTcount: A:0.65, C:0.11, G:0.14, T:0.11


Consensus pattern (19 bp):   
CTAAAACTAGAAGAGAAAA

Found at i:2240 original size:18 final size:19

Alignment explanation


    Indices: 2217--2252  Score: 56
    Period size: 19  Copynumber: 1.9  Consensus size: 19

       2207 TGGAAATAAT

                               
       2217 TCTTCAA-TGGTCTTCAAA
          1 TCTTCAATTGGTCTTCAAA

                     *        
       2235 TCTTCAATTTGTCTTCAA
          1 TCTTCAATTGGTCTTCAA

       2253 TAAATCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.25, C:0.22, G:0.08, T:0.44


Consensus pattern (19 bp):   
TCTTCAATTGGTCTTCAAA

Found at i:3125 original size:20 final size:19

Alignment explanation


    Indices: 3100--3137  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 19

       3090 CTCCTCTATC

                     *          
       3100 ATGAAAACACTTTTCTTTTT
          1 ATGAAAACAATTTT-TTTTT

                              
       3120 ATGAAAACAATTTTTTTT
          1 ATGAAAACAATTTTTTTT

       3138 AATTACCCTT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  19    4  0.24
  20   13  0.76

ACGTcount: A:0.34, C:0.11, G:0.05, T:0.50


Consensus pattern (19 bp):   
ATGAAAACAATTTTTTTTT

Found at i:4426 original size:28 final size:27

Alignment explanation


    Indices: 4390--4463  Score: 85
    Period size: 27  Copynumber: 2.7  Consensus size: 27

       4380 GATCAACTAG

                        *               
       4390 GGGGCATTTTGGCCATTTTCAAAATCCA
          1 GGGGCATTTTGGTCATTTTC-AAATCCA

                      *       *  *   * 
       4418 GGGGCATTTTAGTCATTTGCACATCTA
          1 GGGGCATTTTGGTCATTTTCAAATCCA

            *                  
       4445 AGGGCATTTTGGTCATTTT
          1 GGGGCATTTTGGTCATTTT

       4464 AGGTTCACTT


Statistics
Matches: 38,  Mismatches: 8, Indels: 1
        0.81            0.17        0.02

Matches are distributed among these distances:
  27   21  0.55
  28   17  0.45

ACGTcount: A:0.22, C:0.18, G:0.23, T:0.38


Consensus pattern (27 bp):   
GGGGCATTTTGGTCATTTTCAAATCCA

Found at i:8776 original size:18 final size:19

Alignment explanation


    Indices: 8749--8793  Score: 51
    Period size: 18  Copynumber: 2.5  Consensus size: 19

       8739 AAATTCAAAG

                       *        
       8749 AAAAATTAAT-GTAAAAATT
          1 AAAAATTAATAAT-AAAATT

                               
       8768 AAAAA-TAATAATAAAATT
          1 AAAAATTAATAATAAAATT

                     
       8786 -AAAATTAA
          1 AAAAATTAA

       8794 AATTAAACAT


Statistics
Matches: 23,  Mismatches: 1, Indels: 5
        0.79            0.03        0.17

Matches are distributed among these distances:
  17    4  0.17
  18   13  0.57
  19    6  0.26

ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29


Consensus pattern (19 bp):   
AAAAATTAATAATAAAATT

Found at i:8788 original size:6 final size:6

Alignment explanation


    Indices: 8762--8800  Score: 53
    Period size: 6  Copynumber: 6.5  Consensus size: 6

       8752 AATTAATGTA

                       *                                  
       8762 AAAATT AAAAAT AATAA-T AAAATT AAAATT AAAATT AAA
          1 AAAATT AAAATT AA-AATT AAAATT AAAATT AAAATT AAA

       8801 CATGCAAAGA


Statistics
Matches: 30,  Mismatches: 1, Indels: 4
        0.86            0.03        0.11

Matches are distributed among these distances:
   5    2  0.07
   6   26  0.87
   7    2  0.07

ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28


Consensus pattern (6 bp):   
AAAATT

Done.