Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001204.1 Corchorus olitorius cultivar O-4 contig01204, 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, 963

Length: 1605
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32


Found at i:740 original size:2 final size:2

Alignment explanation


    Indices: 733--771  Score: 53
    Period size: 2  Copynumber: 19.0  Consensus size: 2

        723 ATTAGGAAGA

                                                                      
        733 AT AT AT AT AT AT AT AT AT AT ACT -T AT AT ACT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT

        772 TTTCAGTGAC


Statistics
Matches: 34,  Mismatches: 0, Indels: 6
        0.85            0.00        0.15

Matches are distributed among these distances:
   1    1  0.03
   2   30  0.88
   3    3  0.09

ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:1030 original size:31 final size:30

Alignment explanation


    Indices: 995--1163  Score: 159
    Period size: 31  Copynumber: 5.6  Consensus size: 30

        985 ATTGGCTAAT

                                           
        995 TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
          1 TGCTCAAATAAGGGCCTAAC-TTTGTCAAAA

                            *            **
       1026 TGCTCAAATAAGGGCCCAATCTTT-T-AATT
          1 TGCTCAAATAAGGGCCTAA-CTTTGTCAAAA

                                      *     
       1055 TGGC-CAAATAAGGGCCTAACTTTTGCCAAAA
          1 T-GCTCAAATAAGGGCCTAAC-TTTGTCAAAA

                             * *         **
       1086 TGCTCAAATAAGGGCCCGATCTTT-T-AATT
          1 TGCTCAAATAAGGG-CCTAACTTTGTCAAAA

              *                      *     
       1115 TGGTCAAATAAGGGCCTAACGTTTGCCAAAA
          1 TGCTCAAATAAGGGCCTAAC-TTTGTCAAAA

                              
       1146 TGCTCAAATAAGGGCCTA
          1 TGCTCAAATAAGGGCCTA

       1164 GCATCAAAAA


Statistics
Matches: 109,  Mismatches: 19, Indels: 20
        0.74            0.13        0.14

Matches are distributed among these distances:
  28    5  0.05
  29   38  0.35
  30    5  0.05
  31   56  0.51
  32    5  0.05

ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27


Consensus pattern (30 bp):   
TGCTCAAATAAGGGCCTAACTTTGTCAAAA

Found at i:1092 original size:60 final size:60

Alignment explanation


    Indices: 999--1161  Score: 290
    Period size: 60  Copynumber: 2.7  Consensus size: 60

        989 GCTAATTGCT

                                 *                                      
        999 CAAATAAGGGCCTAACGTTTGTCAAAATGCTCAAATAAGGGCCCAATCTTTTAATTTGGC
          1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCAATCTTTTAATTTGGC

                            *                           *              *
       1059 CAAATAAGGGCCTAACTTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGT
          1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCAATCTTTTAATTTGGC

                                                       
       1119 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
          1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC

       1162 TAGCATCAAA


Statistics
Matches: 98,  Mismatches: 5, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  60   98  1.00

ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26


Consensus pattern (60 bp):   
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCAATCTTTTAATTTGGC

Found at i:1129 original size:29 final size:29

Alignment explanation


    Indices: 1029--1130  Score: 116
    Period size: 29  Copynumber: 3.4  Consensus size: 29

       1019 GTCAAAATGC

                                         
       1029 TCAAATAAGGGCCCAATCTTTTAATTTGG
          1 TCAAATAAGGGCCCAATCTTTTAATTTGG

            *            *             **  *
       1058 CCAAATAAGGGCCTAA-CTTTTGCCAAAATGC
          1 TCAAATAAGGGCCCAATCTTTT---AATTTGG

                          *              
       1089 TCAAATAAGGGCCCGATCTTTTAATTTGG
          1 TCAAATAAGGGCCCAATCTTTTAATTTGG

                         
       1118 TCAAATAAGGGCC
          1 TCAAATAAGGGCC

       1131 TAACGTTTGC


Statistics
Matches: 58,  Mismatches: 11, Indels: 8
        0.75            0.14        0.10

Matches are distributed among these distances:
  28    5  0.09
  29   31  0.53
  31   17  0.29
  32    5  0.09

ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28


Consensus pattern (29 bp):   
TCAAATAAGGGCCCAATCTTTTAATTTGG

Found at i:1241 original size:31 final size:30

Alignment explanation


    Indices: 1201--1309  Score: 114
    Period size: 31  Copynumber: 3.6  Consensus size: 30

       1191 AAACTGACGC

                                           
       1201 TAGGCCCTTATTTGAGCATTTTGGCAAACAT
          1 TAGGCCCTTATTTGAGCATTTT-GCAAACAT

                *              **   *   *  
       1232 TAGGTCCTTATTTG-GCCAAATT-AAAAGAT
          1 TAGGCCCTTATTTGAG-CATTTTGCAAACAT

            *                           *  
       1261 CAGGCCCTTATTTGAGCATTTTGACAAATAT
          1 TAGGCCCTTATTTGAGCATTTTG-CAAACAT

                              
       1292 TAGGCCCTTATTTGAGCA
          1 TAGGCCCTTATTTGAGCA

       1310 ATTAGCCATT


Statistics
Matches: 62,  Mismatches: 12, Indels: 8
        0.76            0.15        0.10

Matches are distributed among these distances:
  29   21  0.34
  30    2  0.03
  31   39  0.63

ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35


Consensus pattern (30 bp):   
TAGGCCCTTATTTGAGCATTTTGCAAACAT
Done.