Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004537.1 Hibiscus syriacus cultivar Beakdansim tig00010019_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: 48168
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Found at i:2549 original size:21 final size:21
Alignment explanation
Indices: 2519--2567 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
2509 GAGAAGAAGA
*
2519 AATGAGAGAGAAAAAGTTAA-
1 AATGAAAGAGAAAAAGTTAAT
2539 AGATGAAAGAGAAAAAGTTAAT
1 A-ATGAAAGAGAAAAAGTTAAT
2561 AATGAAA
1 AATGAAA
2568 TATAAAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.16
Consensus pattern (21 bp):
AATGAAAGAGAAAAAGTTAAT
Found at i:2637 original size:22 final size:22
Alignment explanation
Indices: 2597--2639 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2587 AATGAGAGGG
*
2597 AAATGAGTGATGGATGGTTAAA
1 AAATGAGTGATGGAGGGTTAAA
2619 AAATGAGTGGAT-GAGGGTTAA
1 AAATGAGT-GATGGAGGGTTAA
2640 TGTGTATGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.40, C:0.00, G:0.35, T:0.26
Consensus pattern (22 bp):
AAATGAGTGATGGAGGGTTAAA
Found at i:11266 original size:36 final size:36
Alignment explanation
Indices: 11226--11358 Score: 230
Period size: 36 Copynumber: 3.7 Consensus size: 36
11216 ACGGTGCTAG
* *
11226 ACATTGATACACGAATGTACCAAAGGTGATATGATA
1 ACATTGATACACGAATGTATCAAAGATGATATGATA
*
11262 ACATTGATACACGAATGTATCAAAGCTGATATGATA
1 ACATTGATACACGAATGTATCAAAGATGATATGATA
*
11298 ACATTGATACACGAATATATCAAAGATGATATGATA
1 ACATTGATACACGAATGTATCAAAGATGATATGATA
11334 ACATTGATACACGAATGTATCAAAG
1 ACATTGATACACGAATGTATCAAAG
11359 CTGACAATGG
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 92 1.00
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.26
Consensus pattern (36 bp):
ACATTGATACACGAATGTATCAAAGATGATATGATA
Found at i:16013 original size:23 final size:23
Alignment explanation
Indices: 15987--16039 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
15977 CACCACAGCT
*
15987 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
16010 CGTAGAATTGCACCGAAGTTCCA
1 CGTAGAAATGCACCGAAGTGCCA
16033 CGTAGAA
1 CGTAGAA
16040 TTGTACCATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:16040 original size:23 final size:23
Alignment explanation
Indices: 15995--16055 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
15985 CTCGTATAAA
15995 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
16018 TGCACCGAAGTTCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
16041 TGTACC-ATAGTGCCA
1 TGCACCGA-AGTGCCA
16056 TATAAGATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 1 0.03
23 33 0.97
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:16321 original size:31 final size:30
Alignment explanation
Indices: 16277--16336 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
16267 TATTGTATAG
16277 ACATATAATTTCCAT-ACCTTCATCACATAA
1 ACATATAATTTCCATCA-CTTCATCACATAA
* *
16307 ACATATCATGTTCCATCACTTTATCACATA
1 ACATATAAT-TTCCATCACTTCATCACATA
16337 GCTTATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 8 0.31
31 17 0.65
32 1 0.04
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.35
Consensus pattern (30 bp):
ACATATAATTTCCATCACTTCATCACATAA
Found at i:21343 original size:23 final size:23
Alignment explanation
Indices: 21313--21382 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
21303 CTGGTATAAA
21313 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGAAGTGCCACATAGAAT
* * * *
21336 TGCACCGATGTGCCGCGTAAAAT
1 TGCACCGAAGTGCCACATAGAAT
* *
21359 TGCACCGTAGTGCCATATAAGAAT
1 TGCACCGAAGTGCCACAT-AGAAT
21383 GTCCCTAAGG
Statistics
Matches: 36, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
23 32 0.89
24 4 0.11
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCCACATAGAAT
Found at i:21641 original size:31 final size:30
Alignment explanation
Indices: 21596--21655 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
21586 TATTGTATAG
21596 ACATATAATTTCCAT-ACCTTCATCACATAA
1 ACATATAATTTCCATCA-CTTCATCACATAA
* *
21626 ACATATCATGTTCCATCACTTTATCACATA
1 ACATATAAT-TTCCATCACTTCATCACATA
21656 GCTTATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 8 0.31
31 17 0.65
32 1 0.04
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.35
Consensus pattern (30 bp):
ACATATAATTTCCATCACTTCATCACATAA
Found at i:26784 original size:12 final size:12
Alignment explanation
Indices: 26767--26805 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
26757 ATTGGATTCG
26767 TCTGAACTTGAT
1 TCTGAACTTGAT
* *
26779 TCTGAATTTGGT
1 TCTGAACTTGAT
*
26791 TATGAACTTGAT
1 TCTGAACTTGAT
26803 TCT
1 TCT
26806 AGATCTAATT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (12 bp):
TCTGAACTTGAT
Found at i:28742 original size:28 final size:28
Alignment explanation
Indices: 28699--28783 Score: 134
Period size: 28 Copynumber: 3.0 Consensus size: 28
28689 TCAACCAGAA
* * *
28699 CTGAGTCAACTAATCCAAGTTAACTCGT
1 CTGATTCAACTCATCCGAGTTAACTCGT
28727 CTGATTCAACTCATCCGAGTTAACTCGT
1 CTGATTCAACTCATCCGAGTTAACTCGT
*
28755 CTGATTCAACTCATCCGAGTCAACTCGT
1 CTGATTCAACTCATCCGAGTTAACTCGT
28783 C
1 C
28784 CGAGTTAACC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.27, C:0.29, G:0.14, T:0.29
Consensus pattern (28 bp):
CTGATTCAACTCATCCGAGTTAACTCGT
Found at i:28787 original size:14 final size:14
Alignment explanation
Indices: 28701--28788 Score: 77
Period size: 14 Copynumber: 6.3 Consensus size: 14
28691 AACCAGAACT
*
28701 GAGTCAACTAATCC
1 GAGTCAACTCATCC
* * * *
28715 AAGTTAACTCGTCT
1 GAGTCAACTCATCC
*
28729 GATTCAACTCATCC
1 GAGTCAACTCATCC
* * *
28743 GAGTTAACTCGTCT
1 GAGTCAACTCATCC
*
28757 GATTCAACTCATCC
1 GAGTCAACTCATCC
*
28771 GAGTCAACTCGTCC
1 GAGTCAACTCATCC
28785 GAGT
1 GAGT
28789 TAACCCGTTG
Statistics
Matches: 54, Mismatches: 20, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
14 54 1.00
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.28
Consensus pattern (14 bp):
GAGTCAACTCATCC
Found at i:31892 original size:26 final size:26
Alignment explanation
Indices: 31853--31902 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
31843 CCAGAAGGCA
*
31853 CTGACTAGATCTTCTAGAAACTGTTG
1 CTGACTAGACCTTCTAGAAACTGTTG
*
31879 CTGACTGGACCTTCTAGAAACTGT
1 CTGACTAGACCTTCTAGAAACTGT
31903 CACATCAGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (26 bp):
CTGACTAGACCTTCTAGAAACTGTTG
Found at i:40177 original size:26 final size:27
Alignment explanation
Indices: 40141--40194 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
40131 AATTGACCGT
40141 TATAATTGATGATACTAA-AAAACAAA
1 TATAATTGATGATACTAATAAAACAAA
* *
40167 TATAATTGATGATATTAATTAAACAAA
1 TATAATTGATGATACTAATAAAACAAA
40194 T
1 T
40195 GGTATCAGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 17 0.68
27 8 0.32
ACGTcount: A:0.54, C:0.06, G:0.07, T:0.33
Consensus pattern (27 bp):
TATAATTGATGATACTAATAAAACAAA
Done.