Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000187.1 Hibiscus syriacus cultivar Beakdansim tig00000336_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: 209407
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:176948 original size:14 final size:14
Alignment explanation
Indices: 176929--176965 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
176919 CATCAATTAA
176929 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
176943 ACAAATCACCTTTT
1 ACAAATCAACTTTT
176957 ACAAATCAA
1 ACAAATCAA
176966 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:178389 original size:21 final size:21
Alignment explanation
Indices: 178323--178389 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
178313 GTGAATCGGG
*
178323 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
178343 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
178365 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
178386 CTCT
1 CTCT
178390 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:178408 original size:42 final size:41
Alignment explanation
Indices: 178323--178445 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
178313 GTGAATCGGG
* * * *
178323 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
178365 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
178407 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
178446 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:180478 original size:20 final size:19
Alignment explanation
Indices: 180433--180592 Score: 79
Period size: 19 Copynumber: 8.8 Consensus size: 19
180423 TCTTTTGGTT
180433 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
180452 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
180473 GAAATGACTATCGCAAC--
1 GAAATGAAAATCGCAACGA
* *
180490 --AA-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGA
** * *
180506 GAAATGACTATTGCGACGA
1 GAAATGAAAATCGCAACGA
*
180525 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
* * *
180539 GAAATAAAAATCACAACGC
1 GAAATGAAAATCGCAACGA
* * *
180558 GAAATGAAAATTGCAAAGC
1 GAAATGAAAATCGCAACGA
180577 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
180593 TGCGATTTTT
Statistics
Matches: 107, Mismatches: 22, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
14 18 0.17
15 2 0.02
16 2 0.02
17 1 0.01
18 2 0.02
19 52 0.49
20 28 0.26
21 2 0.02
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:180488 original size:40 final size:37
Alignment explanation
Indices: 180433--180543 Score: 103
Period size: 33 Copynumber: 3.1 Consensus size: 37
180423 TCTTTTGGTT
**
180433 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGACTATCGCAACGAGA-AA-GAGAATCGCAACGC
180472 GGAAATGACTATCGCAAC----AAGAGAATCGCAACGC
1 -GAAATGACTATCGCAACGAGAAAGAGAATCGCAACGC
* *
180506 GAAATGACTATTGCGAC--G--AGAGAATCGCAACGC
1 GAAATGACTATCGCAACGAGAAAGAGAATCGCAACGC
180539 GAAAT
1 GAAAT
180544 AAAAATCACA
Statistics
Matches: 66, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
33 35 0.53
34 14 0.21
35 2 0.03
40 15 0.23
ACGTcount: A:0.42, C:0.20, G:0.24, T:0.14
Consensus pattern (37 bp):
GAAATGACTATCGCAACGAGAAAGAGAATCGCAACGC
Found at i:180515 original size:33 final size:33
Alignment explanation
Indices: 180458--180543 Score: 136
Period size: 33 Copynumber: 2.6 Consensus size: 33
180448 ACGAGATAAT
180458 GAGAATCGCAACGCGGAAATGACTATCGCAACAA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACAA
* * *
180492 GAGAATCGCAACGCGAAATGACTATTGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACAA
180525 GAGAATCGCAACGCGAAAT
1 GAGAATCGCAACGCGAAAT
180544 AAAAATCACA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 35 0.71
34 14 0.29
ACGTcount: A:0.40, C:0.22, G:0.26, T:0.13
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACAA
Found at i:180550 original size:19 final size:19
Alignment explanation
Indices: 180528--180597 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
180518 GCGACGAGAG
*
180528 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATGAA
*
180547 AATCACAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
* *
180566 AATTGCAAAGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
180585 AATCGCAATGCGA
1 AATCGCAACGCGA
180598 TTTTTGTTTC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.50, C:0.19, G:0.19, T:0.13
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:181220 original size:20 final size:20
Alignment explanation
Indices: 181197--181241 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
181187 TGTAAATCGT
181197 GTTGCGAAAGTCAGAATCAC
1 GTTGCGAAAGTCAGAATCAC
* *
181217 GTTGCGAAAGTCAGTATCTC
1 GTTGCGAAAGTCAGAATCAC
181237 GTTGC
1 GTTGC
181242 CATTTTGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (20 bp):
GTTGCGAAAGTCAGAATCAC
Found at i:181277 original size:20 final size:20
Alignment explanation
Indices: 181252--181305 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
181242 CATTTTGTAT
181252 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
181272 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
181292 TATCGCATTGCGAT
1 TATCGCATTGCGAT
181306 TTTTCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:184093 original size:12 final size:12
Alignment explanation
Indices: 184076--184100 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
184066 AAGAGTTGAT
184076 AAGTTGAATTTG
1 AAGTTGAATTTG
184088 AAGTTGAATTTG
1 AAGTTGAATTTG
184100 A
1 A
184101 CTTGTCATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (12 bp):
AAGTTGAATTTG
Found at i:190359 original size:24 final size:24
Alignment explanation
Indices: 190332--190407 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
190322 TATATCAAAA
190332 ATCAAAACATAAAT-CAGGTCAAGT
1 ATCAAAACA-AAATCCAGGTCAAGT
* * *
190356 ATCATATCAAACTCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
190380 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
190404 ATCA
1 ATCA
190408 GATCAGAATC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 3 0.07
24 41 0.93
ACGTcount: A:0.43, C:0.21, G:0.13, T:0.22
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:190408 original size:24 final size:24
Alignment explanation
Indices: 190349--190464 Score: 155
Period size: 24 Copynumber: 4.8 Consensus size: 24
190339 CATAAATCAG
* *
190349 GTCAAGTATCATATCA-AACTCCAG
1 GTCAAGTATCAGATCAGAA-TCCAT
*
190373 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
*
190397 GTCAAGTATCAGATCAGAATCTAT
1 GTCAAGTATCAGATCAGAATCCAT
190421 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
*
190445 GTCAAGTATCATATCAGAAT
1 GTCAAGTATCAGATCAGAAT
190465 TCAAATCGAA
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
23 2 0.02
24 77 0.93
25 4 0.05
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:191467 original size:26 final size:26
Alignment explanation
Indices: 191438--191490 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
191428 TCAGTTTTAT
*
191438 TCCATTCATTTCAGAGCTCGAGGATA
1 TCCAATCATTTCAGAGCTCGAGGATA
* * *
191464 TCCAATCATTTCTGAGCTTGATGATA
1 TCCAATCATTTCAGAGCTCGAGGATA
191490 T
1 T
191491 TCTTGGGTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (26 bp):
TCCAATCATTTCAGAGCTCGAGGATA
Found at i:192920 original size:8 final size:8
Alignment explanation
Indices: 192890--192938 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 8
192880 AGTCAACAGT
192890 GGTCAACG
1 GGTCAACG
192898 CCGGTCAAC-
1 --GGTCAACG
192907 GGTCAACG
1 GGTCAACG
192915 GGTCAACG
1 GGTCAACG
192923 GGT---CG
1 GGTCAACG
192928 GGTCAACG
1 GGTCAACG
192936 GGT
1 GGT
192939 TGGTCAACAG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
5 5 0.14
7 7 0.20
8 16 0.46
10 7 0.20
ACGTcount: A:0.20, C:0.27, G:0.39, T:0.14
Consensus pattern (8 bp):
GGTCAACG
Found at i:192920 original size:15 final size:16
Alignment explanation
Indices: 192890--192923 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
192880 AGTCAACAGT
192890 GGTCAACGCCGGTCAAC
1 GGTCAACG-CGGTCAAC
192907 GGTCAACG-GGTCAAC
1 GGTCAACGCGGTCAAC
192922 GG
1 GG
192924 GTCGGGTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.24, C:0.29, G:0.35, T:0.12
Consensus pattern (16 bp):
GGTCAACGCGGTCAAC
Found at i:192931 original size:13 final size:13
Alignment explanation
Indices: 192913--192956 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
192903 CAACGGTCAA
192913 CGGGTCAACGGGT
1 CGGGTCAACGGGT
192926 CGGGTCAACGGGT
1 CGGGTCAACGGGT
* *
192939 -TGGTCAACAGGT
1 CGGGTCAACGGGT
*
192951 TGGGTC
1 CGGGTC
192957 GGGTAAACGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 10 0.37
13 17 0.63
ACGTcount: A:0.16, C:0.20, G:0.43, T:0.20
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:192945 original size:12 final size:12
Alignment explanation
Indices: 192915--192953 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
192905 ACGGTCAACG
*
192915 GGTCAACGGGTCG
1 GGTCAACGGGT-T
192928 GGTCAACGGGTT
1 GGTCAACGGGTT
*
192940 GGTCAACAGGTT
1 GGTCAACGGGTT
192952 GG
1 GG
192954 GTCGGGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.18, C:0.18, G:0.44, T:0.21
Consensus pattern (12 bp):
GGTCAACGGGTT
Found at i:201766 original size:27 final size:30
Alignment explanation
Indices: 201732--201793 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
201722 AATAATTTAA
*
201732 TAATTTT-AA-GCATAAATTAAAATAATAG
1 TAATTTTAAAGGCAAAAATTAAAATAATAG
*
201760 -AATTTTAAAGGGAAAAATTAAAATAATAG
1 TAATTTTAAAGGCAAAAATTAAAATAATAG
201789 TAATT
1 TAATT
201794 AAACAATCGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 6 0.21
28 2 0.07
29 17 0.59
30 4 0.14
ACGTcount: A:0.55, C:0.02, G:0.10, T:0.34
Consensus pattern (30 bp):
TAATTTTAAAGGCAAAAATTAAAATAATAG
Found at i:202455 original size:22 final size:22
Alignment explanation
Indices: 202430--202478 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
202420 TAAAAAAATC
202430 TTTTTTTC-CTTTTCCTTCTCAT
1 TTTTTTTCACTTTTCCTT-TCAT
* *
202452 TTTTCTTCATTTTTCCTTTCAT
1 TTTTTTTCACTTTTCCTTTCAT
202474 TTTTT
1 TTTTT
202479 AGAGAGATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTTTTCACTTTTCCTTTCAT
Found at i:202463 original size:10 final size:12
Alignment explanation
Indices: 202439--202477 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
202429 CTTTTTTTCC
202439 TTTTCCTTCTCAT
1 TTTTCCTT-TCAT
202452 TTTT-C-TTCAT
1 TTTTCCTTTCAT
202462 TTTTCCTTTCAT
1 TTTTCCTTTCAT
202474 TTTT
1 TTTT
202478 TAGAGAGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 8 0.33
11 2 0.08
12 10 0.42
13 4 0.17
ACGTcount: A:0.08, C:0.23, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTCCTTTCAT
Found at i:204828 original size:26 final size:26
Alignment explanation
Indices: 204792--204846 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
204782 TTATATATGC
204792 TACGAAGGGAGTCAGCCCAGCACACA
1 TACGAAGGGAGTCAGCCCAGCACACA
*
204818 TACGAAGGGAGTCAGCCCAGTACACA
1 TACGAAGGGAGTCAGCCCAGCACACA
204844 TAC
1 TAC
204847 TCTTCAAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.35, C:0.29, G:0.25, T:0.11
Consensus pattern (26 bp):
TACGAAGGGAGTCAGCCCAGCACACA
Found at i:206976 original size:19 final size:20
Alignment explanation
Indices: 206954--206995 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
206944 AGAAAAAAAT
*
206954 AAAGTTAA-AATGAAATAGA
1 AAAGTTAAGAATGAAAGAGA
*
206973 AAAGTTAAGGATGAAAGAGA
1 AAAGTTAAGAATGAAAGAGA
206993 AAA
1 AAA
206996 TAAAAGTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.17
Consensus pattern (20 bp):
AAAGTTAAGAATGAAAGAGA
Done.