Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006480.1 Hibiscus syriacus cultivar Beakdansim tig00015714_pilon, 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: 52235
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:6261 original size:15 final size:13
Alignment explanation
Indices: 6233--6258 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6223 AAAGTTTGAT
6233 TGATTTTTTTAAA
1 TGATTTTTTTAAA
6246 TGATTTTTTTAAA
1 TGATTTTTTTAAA
6259 AATAAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
TGATTTTTTTAAA
Found at i:8724 original size:45 final size:46
Alignment explanation
Indices: 8636--8726 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 46
8626 TTGAAAAAGC
* *
8636 CTGAGTGCATCGATGCATAGTCTTATGCATCGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATAGTCATATGCATCGATGCATAAAATGCA
* *
8682 CTGAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 CTGAGTGCATCGATGCATAGTCATATGCATCGATGCATAAAATGCA
8727 TTCGATGTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 21 0.51
46 20 0.49
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (46 bp):
CTGAGTGCATCGATGCATAGTCATATGCATCGATGCATAAAATGCA
Found at i:11526 original size:44 final size:44
Alignment explanation
Indices: 11437--11533 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 44
11427 GCTCTTGTGC
* *
11437 ATCGATGCACATTCAAGGGCGTGCATCAGTGCATCAGCTGATGT
1 ATCGATGCACATTCAAGGGCATGCATCAGTGCATCAGCTAATGT
* * *
11481 ATCGATGCACATTCAAAGGG-ATGCATCGGTGCA-CTGTTAAGTGT
1 ATCGATGCACATTC-AAGGGCATGCATCAGTGCATCAGCTAA-TGT
11525 ATCGATGCA
1 ATCGATGCA
11534 TTAAGCACAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
43 4 0.09
44 37 0.80
45 5 0.11
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGGCATGCATCAGTGCATCAGCTAATGT
Found at i:14948 original size:17 final size:17
Alignment explanation
Indices: 14926--14982 Score: 96
Period size: 17 Copynumber: 3.4 Consensus size: 17
14916 AATTTCTAAT
14926 TTTTGGTACCCAAATCC
1 TTTTGGTACCCAAATCC
*
14943 TTTTGGTACCCAGATCC
1 TTTTGGTACCCAAATCC
*
14960 TTTTGGTACCCAAACCC
1 TTTTGGTACCCAAATCC
14977 TTTTGG
1 TTTTGG
14983 GTCCATATTC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.19, C:0.28, G:0.16, T:0.37
Consensus pattern (17 bp):
TTTTGGTACCCAAATCC
Found at i:16139 original size:592 final size:592
Alignment explanation
Indices: 15008--16198 Score: 2190
Period size: 592 Copynumber: 2.0 Consensus size: 592
14998 TTTCTAAAAT
15008 CCTTGT-C-CCCTTTGGTATCCATTTATGAAGGACATCCTTATCTTTAGTAGTAATGAATTCTTT
1 CCTTGTGCTCCCTTTGGTATCCATTTATGAAGGACATCCTTATCTTTAGTAGTAATGAATTCTTT
*
15071 AGGAACCCATATACTCCTAACAATTTTACCATTCAAGGTTCGTTGAGGACTTCTATGATTATAGC
66 AGGAACCCATATACTCCTAACAATTTTACCATTCAAGGTTCGTTGAGGACTTCTATGATTATAAC
*
15136 TTCTAAAACTTTTCTTAATAAAGTTGGATTTTGAATTCTCACCTTTTTCAAAACTTTTTGTTCCA
131 TTCTAAAACTTTTCTTAACAAAGTTGGATTTTGAATTCTCACCTTTTTCAAAACTTTTTGTTCCA
15201 ACCTTATTAAAAGAAGTTTTAAGATCATCAATCTTCTTTTGATGATCATCATGAACTTTTGAAAG
196 ACCTTATTAAAAGAAGTTTTAAGATCATCAATCTTCTTTTGATGATCATCATGAACTTTTGAAAG
15266 TAAGTTATGCAAATCAGTAGTTTTCTTTTCAAAATCATTAATTTTGATTTGCAATTATTTGATCT
261 TAAGTTATGCAAATCAGTAGTTTTCTTTTCAAAATCATTAATTTTGATTTGCAATTATTTGATCT
*
15331 TACTTTCAAGCTCACTGTTGGTCATGGATATAAGACTATTTTTGTTTTTCAATTTTAAAATATCA
326 TACTTTCAAGCTCACTGTTGGTCATGGATATAAGACTATTTTCGTTTTTCAATTTTAAAATATCA
*
15396 TTTTTGTATTTTGAAAATAGAGTCTTATAATCTGAAGCCAACCCATTATAATCCTCTAATAACTC
391 TTTTTGTATTTTAAAAATAGAGTCTTATAATCTGAAGCCAACCCATTATAATCCTCTAATAACTC
*
15461 ATCATAAGATAATTCATCCAAATCGAATGAGTTGGAGGTTACCTTAGAATCTTCCCCGATAGCCA
456 ATCATAAGATAATTCATCCAAATCGAATGAGTTAGAGGTTACCTTAGAATCTTCCCCGATAGCCA
15526 TCAAGCACAAGTTCGCAACTTCTTGTTCCTCTTCATCGGAACCTTCTTCATCGCTCCATGTAGCT
521 TCAAGCACAAGTTCGCAACTTCTTGTTCCTCTTCATCGGAACCTTCTTCATCGCTCCATGTAGCT
15591 ACATGAG
586 ACATGAG
*
15598 CCTTGTGCTCCCTTTGGTATCCATTTATGAAGGACATCTTTATCTTTAGTAGTAATGAATTCTTT
1 CCTTGTGCTCCCTTTGGTATCCATTTATGAAGGACATCCTTATCTTTAGTAGTAATGAATTCTTT
* *
15663 AGGAACCCATATACTCTTAATAATTTTACCATTCAAGGTTCGTTGAGGACTTCTATGATTATAAC
66 AGGAACCCATATACTCCTAACAATTTTACCATTCAAGGTTCGTTGAGGACTTCTATGATTATAAC
15728 TTCTAAAACTTTTCTTAACAAAGTTGGATTTTGAATTCTCACCTTTTTCAAAACTTTTTGTTCCA
131 TTCTAAAACTTTTCTTAACAAAGTTGGATTTTGAATTCTCACCTTTTTCAAAACTTTTTGTTCCA
15793 ACCTTATTAAAAGAAGTTTTAAGATCATCAATCTTCTTTTGATGATCATCATGAACTTTTGAAAG
196 ACCTTATTAAAAGAAGTTTTAAGATCATCAATCTTCTTTTGATGATCATCATGAACTTTTGAAAG
* *
15858 TAAGTTATGCAAATCAGTATTTTTCTTTTCAAAATCATTAATTTTGATTTGCAATTCTTTGATCT
261 TAAGTTATGCAAATCAGTAGTTTTCTTTTCAAAATCATTAATTTTGATTTGCAATTATTTGATCT
* * *
15923 TACTTTCAAGCTCATTGTTGGTCTTGGATATAAGACTATTTTCGTTTTTCAATTTTGAAATATCA
326 TACTTTCAAGCTCACTGTTGGTCATGGATATAAGACTATTTTCGTTTTTCAATTTTAAAATATCA
15988 TTTTTGTATTTTAAAAATAGAGTCTTATAAT-TCGAAGCCAACCCATTATAATCCTCTAATAACT
391 TTTTTGTATTTTAAAAATAGAGTCTTATAATCT-GAAGCCAACCCATTATAATCCTCTAATAACT
*
16052 CATCATAAGATAATTCATCCAAATCGAATGAGTTAGAGGTTACCTTAGAATCTTCTCCGATAGCC
455 CATCATAAGATAATTCATCCAAATCGAATGAGTTAGAGGTTACCTTAGAATCTTCCCCGATAGCC
* * *
16117 ATCAAGCACAAGTTTGCAACTTCTTGTTTCTCTTCATCGGAACCTTCTTCATCGTTCCATGTAGC
520 ATCAAGCACAAGTTCGCAACTTCTTGTTCCTCTTCATCGGAACCTTCTTCATCGCTCCATGTAGC
*
16182 TATATGAG
585 TACATGAG
16190 CCTTGTGCT
1 CCTTGTGCT
16199 TCTTTTTGGA
Statistics
Matches: 580, Mismatches: 18, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
590 6 0.01
591 2 0.00
592 572 0.99
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (592 bp):
CCTTGTGCTCCCTTTGGTATCCATTTATGAAGGACATCCTTATCTTTAGTAGTAATGAATTCTTT
AGGAACCCATATACTCCTAACAATTTTACCATTCAAGGTTCGTTGAGGACTTCTATGATTATAAC
TTCTAAAACTTTTCTTAACAAAGTTGGATTTTGAATTCTCACCTTTTTCAAAACTTTTTGTTCCA
ACCTTATTAAAAGAAGTTTTAAGATCATCAATCTTCTTTTGATGATCATCATGAACTTTTGAAAG
TAAGTTATGCAAATCAGTAGTTTTCTTTTCAAAATCATTAATTTTGATTTGCAATTATTTGATCT
TACTTTCAAGCTCACTGTTGGTCATGGATATAAGACTATTTTCGTTTTTCAATTTTAAAATATCA
TTTTTGTATTTTAAAAATAGAGTCTTATAATCTGAAGCCAACCCATTATAATCCTCTAATAACTC
ATCATAAGATAATTCATCCAAATCGAATGAGTTAGAGGTTACCTTAGAATCTTCCCCGATAGCCA
TCAAGCACAAGTTCGCAACTTCTTGTTCCTCTTCATCGGAACCTTCTTCATCGCTCCATGTAGCT
ACATGAG
Found at i:18073 original size:45 final size:46
Alignment explanation
Indices: 17985--18073 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 46
17975 TTGAAAAAGC
* * *
17985 CTGAGTGCATCGATGCATAGTCTTGTGCATCGATGAATCAAATGAA
1 CTGAGTGAATCGATGCATAGTCATGTGCATCGATGAATAAAATGAA
* *
18031 CTGAGTGAATCGATGCATGGT-ATGTGCATCGATGCATAAAATG
1 CTGAGTGAATCGATGCATAGTCATGTGCATCGATGAATAAAATG
18074 CATTCGATGT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
45 19 0.50
46 19 0.50
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (46 bp):
CTGAGTGAATCGATGCATAGTCATGTGCATCGATGAATAAAATGAA
Found at i:27072 original size:11 final size:11
Alignment explanation
Indices: 27049--27091 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
27039 TTAATTTAAG
27049 TAAATATATTTT
1 TAAATA-ATTTT
27061 TAAATAATTTT
1 TAAATAATTTT
* *
27072 TTAATTATTTT
1 TAAATAATTTT
27083 T-AATAATTT
1 TAAATAATTT
27092 AACATAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 7 0.25
11 15 0.54
12 6 0.21
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TAAATAATTTT
Found at i:27709 original size:2 final size:2
Alignment explanation
Indices: 27702--27755 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
27692 AGAAATCAAC
27702 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27744 AT AT AT AT AT AT
1 AT AT AT AT AT AT
27756 CAAGATACTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29049 original size:167 final size:168
Alignment explanation
Indices: 28773--29111 Score: 662
Period size: 167 Copynumber: 2.0 Consensus size: 168
28763 ATTCCAAACC
28773 CATATGATATGAACCACTCAAATGCTGTCACACCACACGACTGCCATGAGTGTCAACTTGCTTTG
1 CATATGATATGAACCACTCAAATGCTGTCACACCACACGACTGCCATGAGTGTCAACTTGCTTTG
28838 ATTTGTTCCTACACCATTAAAAAGAATTAATTATCAATGGCATTTATGTAATTAAGCTGTATATA
66 ATTTGTTCCTACACCATTAAAAAGAATTAATTATCAATGGCATTTATGTAATTAAGCTGTATATA
28903 TCTGTCTTGATTCACAAC-TTTTTTTTTTTTTAGTTTG
131 TCTGTCTTGATTCACAACTTTTTTTTTTTTTTAGTTTG
28940 CATATGATATGAACCACTCAAATGCTGTCACACCACACGACTGCCATGAGTGTCAACTTGCTTTG
1 CATATGATATGAACCACTCAAATGCTGTCACACCACACGACTGCCATGAGTGTCAACTTGCTTTG
29005 ATTTGTTCCTACACCATTAAAAAGAATTAATTATCAATGGCATTTATGTAATTAAGCTGTATATA
66 ATTTGTTCCTACACCATTAAAAAGAATTAATTATCAATGGCATTTATGTAATTAAGCTGTATATA
29070 TCTGTCTTGATTCACAACTTTTTTTTTTTTTTTAGTTTG
131 TCTGTCTTGATTCACAAC-TTTTTTTTTTTTTTAGTTTG
29109 CAT
1 CAT
29112 GAAAGTGACT
Statistics
Matches: 170, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
167 148 0.87
169 22 0.13
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (168 bp):
CATATGATATGAACCACTCAAATGCTGTCACACCACACGACTGCCATGAGTGTCAACTTGCTTTG
ATTTGTTCCTACACCATTAAAAAGAATTAATTATCAATGGCATTTATGTAATTAAGCTGTATATA
TCTGTCTTGATTCACAACTTTTTTTTTTTTTTAGTTTG
Found at i:32634 original size:6 final size:6
Alignment explanation
Indices: 32623--32707 Score: 152
Period size: 6 Copynumber: 14.2 Consensus size: 6
32613 GACACGTATT
*
32623 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCTCG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
*
32671 ACCTCG ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
32708 GCCGAGCCGA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 77 1.00
ACGTcount: A:0.32, C:0.49, G:0.16, T:0.02
Consensus pattern (6 bp):
ACCACG
Found at i:32715 original size:5 final size:5
Alignment explanation
Indices: 32705--32743 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
32695 ACCACGACCA
* * *
32705 CGAGC CGAGC CGAGC CGTGC CGAGC CGAGA CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
32744 ACGGACGGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.23, C:0.33, G:0.41, T:0.03
Consensus pattern (5 bp):
CGAGC
Found at i:36717 original size:6 final size:6
Alignment explanation
Indices: 36706--36802 Score: 176
Period size: 6 Copynumber: 16.2 Consensus size: 6
36696 GACACGTATT
36706 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
* *
36754 ACCACG ACCTCG ACCTCG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
36802 A
1 A
36803 GCCGAGCCGA
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 89 1.00
ACGTcount: A:0.32, C:0.49, G:0.16, T:0.02
Consensus pattern (6 bp):
ACCACG
Found at i:36810 original size:5 final size:5
Alignment explanation
Indices: 36800--36838 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
36790 ACCACGACCA
* * *
36800 CGAGC CGAGC CGAGC CGTGC CGAGC CGAGA CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
36839 ACGGACGGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.23, C:0.33, G:0.41, T:0.03
Consensus pattern (5 bp):
CGAGC
Found at i:37105 original size:24 final size:24
Alignment explanation
Indices: 37073--37121 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
37063 CCCACTCATG
37073 CATGAATGATAGATCTTAACCCTA
1 CATGAATGATAGATCTTAACCCTA
*
37097 CATGAATGATAGATCTTAAGCCTA
1 CATGAATGATAGATCTTAACCCTA
37121 C
1 C
37122 GATTAGGGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (24 bp):
CATGAATGATAGATCTTAACCCTA
Found at i:39813 original size:24 final size:24
Alignment explanation
Indices: 39781--39828 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
39771 GAATTCGATG
*
39781 CCCCTTAGCCCCTCTTTTTGACTT
1 CCCCTTAGCCCCCCTTTTTGACTT
39805 CCCCTTAGCCCCCCTTTTTGACTT
1 CCCCTTAGCCCCCCTTTTTGACTT
39829 TTCTAACAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.08, C:0.44, G:0.08, T:0.40
Consensus pattern (24 bp):
CCCCTTAGCCCCCCTTTTTGACTT
Found at i:43981 original size:20 final size:21
Alignment explanation
Indices: 43950--43989 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
43940 ATGCATGTGG
43950 ATTTGATGTATGAAATGATAT
1 ATTTGATGTATGAAATGATAT
*
43971 ATTTG-TGTATGATATGATA
1 ATTTGATGTATGAAATGATA
43990 GTAGTAATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.45
Consensus pattern (21 bp):
ATTTGATGTATGAAATGATAT
Done.