Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008317.1 Hibiscus syriacus cultivar Beakdansim tig00111014_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: 312147
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:286110 original size:19 final size:18
Alignment explanation
Indices: 286084--286189 Score: 103
Period size: 19 Copynumber: 5.9 Consensus size: 18
286074 ACGAAACTTA
286084 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
*
286102 ACTATCGCAACGCGGAAATGG
1 A-AATCGCAACGC-GAAAT-G
** *
286123 CTATCGCAATGCGAAATG
1 AAATCGCAACGCGAAATG
*
286141 AAAATCGCAA--CGACA--
1 -AAATCGCAACGCGAAATG
286156 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
286174 AAATCGCAACGCGAAA
1 AAATCGCAACGCGAAA
286190 CACAAATCGC
Statistics
Matches: 73, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 4 0.05
18 18 0.25
19 22 0.30
20 15 0.21
21 1 0.01
ACGTcount: A:0.42, C:0.24, G:0.22, T:0.12
Consensus pattern (18 bp):
AAATCGCAACGCGAAATG
Found at i:286110 original size:39 final size:37
Alignment explanation
Indices: 286067--286200 Score: 102
Period size: 39 Copynumber: 3.6 Consensus size: 37
286057 TAGTTTACTT
*
286067 TCGCAACACGAAACTTAAAATCGCAACGCGAAATGACTA
1 TCGCAACACGAAAC-TAAAATCGCAACGCGAAATGA-AA
* *** *
286106 TCGCAACGCGGAAA-TGGCTATCGCAATGCGAAATGAAAA
1 TCGCAACAC-GAAACT-AAAATCGCAACGCGAAATG-AAA
286145 TCGC-A-ACG--AC-AAAATCGCAACGCGAAATGAAA
1 TCGCAACACGAAACTAAAATCGCAACGCGAAATGAAA
*
286177 TCGCAACGCGAAAC-ACAAATCGCA
1 TCGCAACACGAAACTA-AAATCGCA
286201 TTGCGATTTC
Statistics
Matches: 74, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
32 7 0.09
33 16 0.22
34 3 0.04
36 4 0.05
37 9 0.12
38 2 0.03
39 28 0.38
40 5 0.07
ACGTcount: A:0.43, C:0.25, G:0.19, T:0.13
Consensus pattern (37 bp):
TCGCAACACGAAACTAAAATCGCAACGCGAAATGAAA
Found at i:286198 original size:19 final size:18
Alignment explanation
Indices: 286156--286200 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
286146 CGCAACGACA
**
286156 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAAAC
286174 AAATCGCAACGCGAAACAC
1 AAATCGCAACGCGAAA-AC
286193 AAATCGCA
1 AAATCGCA
286201 TTGCGATTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.09
Consensus pattern (18 bp):
AAATCGCAACGCGAAAAC
Found at i:286236 original size:14 final size:14
Alignment explanation
Indices: 286217--286274 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
286207 TTTCATTTCG
286217 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
286231 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
286247 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
286263 CGTTGCGATTTT
1 CGTTGCGATTTT
286275 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:286242 original size:32 final size:32
Alignment explanation
Indices: 286201--286290 Score: 162
Period size: 32 Copynumber: 2.8 Consensus size: 32
286191 ACAAATCGCA
286201 TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
286233 TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
*
286265 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGA-TTTCATTTCGCGTTGCGAT
286291 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 38 0.68
33 18 0.32
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (32 bp):
TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
Found at i:286309 original size:20 final size:19
Alignment explanation
Indices: 286275--286329 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
286265 TTGCGATTTT
*
286275 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
286294 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
286314 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
286330 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:286828 original size:18 final size:18
Alignment explanation
Indices: 286802--286846 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
286792 GTCGATCAGA
*
286802 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
286820 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
286838 TGATGGCTC
1 TGATGGCTC
286847 CCGAAGTGGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:288181 original size:20 final size:20
Alignment explanation
Indices: 288156--288193 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
288146 AATAGTTTCT
288156 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
288176 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
288194 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:288482 original size:22 final size:22
Alignment explanation
Indices: 288457--288500 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
288447 GATTTAGATA
288457 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
288479 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
288501 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:288713 original size:20 final size:20
Alignment explanation
Indices: 288688--288780 Score: 87
Period size: 20 Copynumber: 4.7 Consensus size: 20
288678 GATTATGTAT
288688 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
288708 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* * *** * *
288728 TATCTCGTTGTGATTTTTAT
1 TATCGCGTTGCGAAAGTCAG
* *
288748 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
288768 TATCGCATTGCGA
1 TATCGCGTTGCGA
288781 TTTTCCCAAT
Statistics
Matches: 58, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:288781 original size:20 final size:20
Alignment explanation
Indices: 288668--288781 Score: 86
Period size: 20 Copynumber: 5.7 Consensus size: 20
288658 CGCTTTGAAA
*
288668 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
288689 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
288709 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * * ** * *
288729 ATCTCGTTGTGATTTTTATT
1 ATCGCATTGCGATAGTCAGT
288749 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
288769 ATCGCATTGCGAT
1 ATCGCATTGCGAT
288782 TTTCCCAATT
Statistics
Matches: 74, Mismatches: 18, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
19 2 0.03
20 61 0.82
21 11 0.15
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:288783 original size:40 final size:40
Alignment explanation
Indices: 288708--288784 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
288698 CGAAAGTCAG
* * * *
288708 TATCGCGTTGCGAAAGTAAGTATCTCGTTGTGATTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTAT
* *
288748 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
288785 CCCAATTCGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (40 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTAT
Found at i:288814 original size:40 final size:41
Alignment explanation
Indices: 288770--288864 Score: 174
Period size: 40 Copynumber: 2.3 Consensus size: 41
288760 ATAGTCAGTA
*
288770 TCGCATTGCGATTTTCCCAATTCGCGTTGCGA-TTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
288810 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
288851 TCGCATTGCGAATT
1 TCGCATTGCGAATT
288865 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 31 0.58
41 22 0.42
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.39
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:288852 original size:20 final size:20
Alignment explanation
Indices: 288770--288861 Score: 87
Period size: 21 Copynumber: 4.5 Consensus size: 20
288760 ATAGTCAGTA
* **
288770 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
288791 TCGCGTTGCGA-TTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
288810 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
288831 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
288851 TCGCATTGCGA
1 TCGCATTGCGA
288862 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 13, Indels: 5
0.76 0.18 0.07
Matches are distributed among these distances:
19 14 0.25
20 18 0.32
21 24 0.43
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:290736 original size:35 final size:35
Alignment explanation
Indices: 290692--290761 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
290682 TGGTATTGAG
* *
290692 TCTCTGTAGGTTCAACTCCGATCAAGCTGGTAATT
1 TCTCAGTAGGTTCAACACCGATCAAGCTGGTAATT
290727 TCTCAGTAGGTTCAACACCGATCAAGCTGGTAATT
1 TCTCAGTAGGTTCAACACCGATCAAGCTGGTAATT
290762 CATTATGGAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (35 bp):
TCTCAGTAGGTTCAACACCGATCAAGCTGGTAATT
Found at i:295793 original size:5 final size:5
Alignment explanation
Indices: 295742--295775 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
295732 GTAATCTAAT
* *
295742 AAATA AAATA AAATA AAATA AAATG AAATG AAAT
1 AAATA AAATA AAATA AAATA AAATA AAATA AAAT
295776 GGTGATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:307244 original size:21 final size:20
Alignment explanation
Indices: 307211--307259 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
307201 GAATAATAAT
* *
307211 AAAAATATTATTTTATTCAA
1 AAAAATATGATTTAATTCAA
* *
307231 TAAAATAGTGATTTAATTGAA
1 AAAAATA-TGATTTAATTCAA
307252 AAAAATAT
1 AAAAATAT
307260 ATATAGAGGG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (20 bp):
AAAAATATGATTTAATTCAA
Found at i:307892 original size:12 final size:13
Alignment explanation
Indices: 307872--307903 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
307862 ATCTTCAATT
307872 TTTTA-AAATA-A
1 TTTTATAAATATA
307883 TTTTATAAATATA
1 TTTTATAAATATA
307896 TTTTATAA
1 TTTTATAA
307904 TTTTAGATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 5 0.26
12 5 0.26
13 9 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTTTATAAATATA
Found at i:309426 original size:51 final size:52
Alignment explanation
Indices: 309371--309485 Score: 133
Period size: 52 Copynumber: 2.2 Consensus size: 52
309361 AACATCGTTA
* * * *
309371 TATTTTTAAATTATTATT-TCATTTTTAATTAATCCTTAAATCTTTAAATTT
1 TATTTTTAAATTATAATTCTCATTTTAAATTAATACTTAAATATTTAAATTT
* * * *
309422 TATTTTCAAATTATAATTCTTATTTTAAATTGATATTTAAATATTTAAATTT
1 TATTTTTAAATTATAATTCTCATTTTAAATTAATACTTAAATATTTAAATTT
* *
309474 CATTCTTAAATT
1 TATTTTTAAATT
309486 TGGTCTTCAT
Statistics
Matches: 52, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
51 16 0.31
52 36 0.69
ACGTcount: A:0.36, C:0.07, G:0.01, T:0.57
Consensus pattern (52 bp):
TATTTTTAAATTATAATTCTCATTTTAAATTAATACTTAAATATTTAAATTT
Done.