Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017077.1 Corchorus olitorius cultivar O-4 contig17110, 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: 12557
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31


Found at i:1187 original size:21 final size:22

Alignment explanation


    Indices: 1161--1205  Score: 65
    Period size: 23  Copynumber: 2.0  Consensus size: 22

       1151 CCTTTCTTAG

                                  
       1161 CTACTT-GTCGACAATTTGCTT
          1 CTACTTAGTCGACAATTTGCTT

                         *         
       1182 CTACTTGAGTCGATAATTTGCTT
          1 CTACTT-AGTCGACAATTTGCTT

             
       1205 C
          1 C

       1206 CTTTGGTCGA


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  21    6  0.29
  23   15  0.71

ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42


Consensus pattern (22 bp):   
CTACTTAGTCGACAATTTGCTT

Found at i:1220 original size:21 final size:22

Alignment explanation


    Indices: 1167--1220  Score: 67
    Period size: 23  Copynumber: 2.5  Consensus size: 22

       1157 TTAGCTACTT

                                   
       1167 GTCGACAATTTGCTTCTACTTGA
          1 GTCGACAATTTGCTTCTA-TTGA

                 *                 
       1190 GTCGATAATTTGCTTCCT-TTG-
          1 GTCGACAATTTGCTT-CTATTGA

                      
       1211 GTCGACAATT
          1 GTCGACAATT

       1221 CCCTAGTCGA


Statistics
Matches: 28,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  21    9  0.32
  22    3  0.11
  23   14  0.50
  24    2  0.07

ACGTcount: A:0.20, C:0.20, G:0.19, T:0.41


Consensus pattern (22 bp):   
GTCGACAATTTGCTTCTATTGA

Found at i:1250 original size:15 final size:15

Alignment explanation


    Indices: 1232--1273  Score: 57
    Period size: 16  Copynumber: 2.7  Consensus size: 15

       1222 CCTAGTCGAC

                 *         
       1232 ACTTGCTCCTTATCG
          1 ACTTGATCCTTATCG

                            
       1247 ACTTTGATCCTTATCG
          1 AC-TTGATCCTTATCG

                 *     
       1263 ACTTGGTCCTT
          1 ACTTGATCCTT

       1274 TAAGTCGACA


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  15   10  0.42
  16   14  0.58

ACGTcount: A:0.14, C:0.29, G:0.14, T:0.43


Consensus pattern (15 bp):   
ACTTGATCCTTATCG

Found at i:2091 original size:6 final size:6

Alignment explanation


    Indices: 2080--2122  Score: 86
    Period size: 6  Copynumber: 7.2  Consensus size: 6

       2070 TTAGTGTAAG

                                                              
       2080 AATTAA AATTAA AATTAA AATTAA AATTAA AATTAA AATTAA A
          1 AATTAA AATTAA AATTAA AATTAA AATTAA AATTAA AATTAA A

       2123 TATGCAAAGA


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   37  1.00

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (6 bp):   
AATTAA

Found at i:8437 original size:22 final size:23

Alignment explanation


    Indices: 8388--8442  Score: 69
    Period size: 23  Copynumber: 2.5  Consensus size: 23

       8378 ATGGTCGATG

                                 * 
       8388 GTTTTGCTTCCTTAAATCGACTA
          1 GTTTTGCTTCCTTAAATCGACAA

                           *       
       8411 GTTTTGCTTCCTT-AGTCGACAA
          1 GTTTTGCTTCCTTAAATCGACAA

                 *     
       8433 -TTTTTCTTCC
          1 GTTTTGCTTCC

       8443 ACTTGTCGAC


Statistics
Matches: 29,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  21    9  0.31
  22    7  0.24
  23   13  0.45

ACGTcount: A:0.16, C:0.24, G:0.13, T:0.47


Consensus pattern (23 bp):   
GTTTTGCTTCCTTAAATCGACAA
Done.