Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001890.1 Hibiscus syriacus cultivar Beakdansim tig00003835_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: 56880
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:5507 original size:31 final size:31
Alignment explanation
Indices: 5472--5535 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
5462 CATATTGTTT
5472 AGCTCAACTTGACTCGAAAAGTTTAAAATTG
1 AGCTCAACTTGACTCGAAAAGTTTAAAATTG
*
5503 AGCTCGACTTGACTCGAAAAGTTTAAAATTG
1 AGCTCAACTTGACTCGAAAAGTTTAAAATTG
5534 AG
1 AG
5536 TTTGACTCGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.28
Consensus pattern (31 bp):
AGCTCAACTTGACTCGAAAAGTTTAAAATTG
Found at i:5540 original size:26 final size:28
Alignment explanation
Indices: 5479--5545 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 28
5469 TTTAGCTCAA
5479 CTTGACTCGAAAAGTTTAAAATTGAGCT
1 CTTGACTCGAAAAGTTTAAAATTGAGCT
5507 CGACTTGACTCGAAAAGTTTAAAATTGAG-T
1 ---CTTGACTCGAAAAGTTTAAAATTGAGCT
5537 -TTGACTCGA
1 CTTGACTCGA
5546 CTTTAAAACT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
26 9 0.25
30 1 0.03
31 26 0.72
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.31
Consensus pattern (28 bp):
CTTGACTCGAAAAGTTTAAAATTGAGCT
Found at i:6644 original size:26 final size:27
Alignment explanation
Indices: 6599--6660 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
6589 ATTTTATGTT
* *
6599 AATAGTAAATTTTTATAATTTT-GAAAC
1 AATA-TAAATTTATAAAATTTTAGAAAC
*
6626 AATATAAATTTATAAAATTTTAGAAAG
1 AATATAAATTTATAAAATTTTAGAAAC
6653 AATA-AAAT
1 AATATAAAT
6661 AAATTAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 19 0.61
27 12 0.39
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (27 bp):
AATATAAATTTATAAAATTTTAGAAAC
Found at i:15814 original size:22 final size:22
Alignment explanation
Indices: 15774--15815 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
15764 TCTATTTTCA
**
15774 TCTCCCAAAATTTTTAAGTTCG
1 TCTCCCAAAATTTAGAAGTTCG
*
15796 TCTCCTAAAATTTAGAAGTT
1 TCTCCCAAAATTTAGAAGTT
15816 TGCCCTCTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (22 bp):
TCTCCCAAAATTTAGAAGTTCG
Found at i:18175 original size:18 final size:20
Alignment explanation
Indices: 18130--18175 Score: 51
Period size: 23 Copynumber: 2.2 Consensus size: 20
18120 TTTTTCAATT
18130 TTATAATAAAATATCTAACTA
1 TTATAATAAAATA-CTAACTA
18151 TAGTATAATAAAATA-TAA-TA
1 T--TATAATAAAATACTAACTA
18171 TTATA
1 TTATA
18176 TTCTTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
18 4 0.17
20 3 0.13
21 4 0.17
23 12 0.52
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (20 bp):
TTATAATAAAATACTAACTA
Found at i:21453 original size:20 final size:20
Alignment explanation
Indices: 21416--21454 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
21406 GATTCGAATG
* *
21416 TTTAATAATTAAATTAAAAT
1 TTTAATAATGAAAATAAAAT
*
21436 TTTAATGATGAAAATAAAA
1 TTTAATAATGAAAATAAAA
21455 GTGAGAATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (20 bp):
TTTAATAATGAAAATAAAAT
Found at i:22848 original size:29 final size:30
Alignment explanation
Indices: 22815--22989 Score: 120
Period size: 29 Copynumber: 5.9 Consensus size: 30
22805 TAAATTCATA
22815 ATATTTTA-TATATCTTAACTTTTAAAAAT
1 ATATTTTATTATATCTTAACTTTTAAAAAT
* *
22844 ATATTTTATTTTTATTTTAACTTATT--AAAT
1 ATATTTTA-TTATATCTTAACTT-TTAAAAAT
* * *
22874 ATATTTTATTCTTATTTTAA-TTTAAAAAAT
1 ATATTTTATT-ATATCTTAACTTTTAAAAAT
*
22904 AT-TTTTATTCTTATCTTCAA---TTAAAAAT
1 ATATTTTATT-ATATCTT-AACTTTTAAAAAT
* *
22932 ATATTTTATTTTTATTTTAAC--TTAAAAAT
1 ATATTTTA-TTATATCTTAACTTTTAAAAAT
22961 ATAATTTT-TTATTATCTTTAACTTTTAAA
1 AT-ATTTTATTA-TATC-TTAACTTTTAAA
22990 TTTTAAAAAT
Statistics
Matches: 123, Mismatches: 8, Indels: 27
0.78 0.05 0.17
Matches are distributed among these distances:
28 14 0.11
29 50 0.41
30 41 0.33
31 11 0.09
32 7 0.06
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (30 bp):
ATATTTTATTATATCTTAACTTTTAAAAAT
Found at i:22876 original size:30 final size:29
Alignment explanation
Indices: 22836--22984 Score: 178
Period size: 29 Copynumber: 5.1 Consensus size: 29
22826 ATCTTAACTT
*
22836 TTAAAAATATATTTTATTTTTATTTTAAC
1 TTAAAAATATATTTTATTCTTATTTTAAC
* *
22865 TTATTAAATATATTTTATTCTTATTTTAAT
1 TTA-AAAATATATTTTATTCTTATTTTAAC
*
22895 TTAAAAA-ATATTTTTATTCTTATCTTCAA-
1 TTAAAAATATA-TTTTATTCTTAT-TTTAAC
*
22924 TTAAAAATATATTTTATTTTTATTTTAAC
1 TTAAAAATATATTTTATTCTTATTTTAAC
*
22953 TTAAAAATATAATTTT-TTATTATCTTTAAC
1 TTAAAAATAT-ATTTTATTCTTAT-TTTAAC
22983 TT
1 TT
22985 TTAAATTTTA
Statistics
Matches: 105, Mismatches: 8, Indels: 13
0.83 0.06 0.10
Matches are distributed among these distances:
28 7 0.07
29 52 0.50
30 46 0.44
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (29 bp):
TTAAAAATATATTTTATTCTTATTTTAAC
Found at i:23198 original size:28 final size:28
Alignment explanation
Indices: 23122--23211 Score: 82
Period size: 28 Copynumber: 3.3 Consensus size: 28
23112 TTTTATTTAT
*
23122 TTTTAAGTTAAT-ATAAGAATAATATATA
1 TTTTAA-TTAATAATAAGAATAAAATATA
* *
23150 -TAT-A-TATATATATAA-ATTAAAATATA
1 TTTTAATTA-ATA-ATAAGAATAAAATATA
*
23176 TTTTAATTAATAATAAGAATAAATTATA
1 TTTTAATTAATAATAAGAATAAAATATA
23204 TTTTAATT
1 TTTTAATT
23212 GAAGATAACA
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
24 2 0.04
25 2 0.04
26 10 0.20
27 12 0.24
28 21 0.43
29 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (28 bp):
TTTTAATTAATAATAAGAATAAAATATA
Found at i:32947 original size:25 final size:26
Alignment explanation
Indices: 32898--32949 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
32888 AATTATATTT
* **
32898 TAAAAAAACCTAAAATATTTTAAATC
1 TAAAAAAACCTAAAACATTAAAAATC
32924 TAAAAAAACC-AAAACATTAAAAATC
1 TAAAAAAACCTAAAACATTAAAAATC
32949 T
1 T
32950 TAATTCCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.25
Consensus pattern (26 bp):
TAAAAAAACCTAAAACATTAAAAATC
Found at i:33110 original size:12 final size:12
Alignment explanation
Indices: 33093--33117 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33083 AATCACAAAT
33093 ATTCACATCTTA
1 ATTCACATCTTA
33105 ATTCACATCTTA
1 ATTCACATCTTA
33117 A
1 A
33118 AAAATCTCTT
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:0.24, G:0.00, T:0.40
Consensus pattern (12 bp):
ATTCACATCTTA
Found at i:34137 original size:51 final size:52
Alignment explanation
Indices: 34072--34171 Score: 123
Period size: 51 Copynumber: 1.9 Consensus size: 52
34062 TACATTTCAA
* * * *
34072 TAGTTTAGATGAAAATGTCTTA-TTTATGCGATTAATTTATTGTTATTTTAAT
1 TAGTTTAGAGGAAAATGT-TTAGCTTATACGATTAATTTATTATTATTTTAAT
* *
34124 TAGTTTA-AGGAAAATGTTTAGCTTATATGATTAGTTTATTATTATTTT
1 TAGTTTAGAGGAAAATGTTTAGCTTATACGATTAATTTATTATTATTTT
34172 TGTGAATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
50 3 0.07
51 31 0.76
52 7 0.17
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.52
Consensus pattern (52 bp):
TAGTTTAGAGGAAAATGTTTAGCTTATACGATTAATTTATTATTATTTTAAT
Found at i:39253 original size:41 final size:41
Alignment explanation
Indices: 39208--39362 Score: 186
Period size: 41 Copynumber: 3.8 Consensus size: 41
39198 TAAGAGATTC
* *
39208 ATACAAACGTCGCTAAAGACTCATACTTTAGTGGCGTTTTT
1 ATACAAACGTCGCTATAGACTCGTACTTTAGTGGCGTTTTT
* * * * *
39249 ATACAAATGTTGTTATAGACTCTTAC-TTAGTGGCGTTTCT
1 ATACAAACGTCGCTATAGACTCGTACTTTAGTGGCGTTTTT
* * * *
39289 ATACAAATGTCTCTATAGACTCGTATTTTAGTGACGTTTTT
1 ATACAAACGTCGCTATAGACTCGTACTTTAGTGGCGTTTTT
* *
39330 ATACAAACGTTGCTATAGACTTGTACTTTAGTG
1 ATACAAACGTCGCTATAGACTCGTACTTTAGTG
39363 TTTACAATTT
Statistics
Matches: 95, Mismatches: 18, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
40 34 0.36
41 61 0.64
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (41 bp):
ATACAAACGTCGCTATAGACTCGTACTTTAGTGGCGTTTTT
Found at i:39357 original size:81 final size:82
Alignment explanation
Indices: 39208--39362 Score: 215
Period size: 81 Copynumber: 1.9 Consensus size: 82
39198 TAAGAGATTC
* * *
39208 ATACAAACGTCGCTAAAGACTCATACTTTAGTGGCGTTTTTATACAAATGTTGTTATAGACTCTT
1 ATACAAACGTCGCTAAAGACTCATACTTTAGTGACGTTTTTATACAAACGTTGCTATAGACTCTT
39273 AC-TTAGTGGCGTTTCT
66 ACTTTAGTGGCGTTTCT
* * * * *
39289 ATACAAATGTCTCTATAGACTCGTATTTTAGTGACGTTTTTATACAAACGTTGCTATAGACT-TG
1 ATACAAACGTCGCTAAAGACTCATACTTTAGTGACGTTTTTATACAAACGTTGCTATAGACTCT-
39353 TACTTTAGTG
65 TACTTTAGTG
39363 TTTACAATTT
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
80 1 0.02
81 57 0.89
82 6 0.09
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (82 bp):
ATACAAACGTCGCTAAAGACTCATACTTTAGTGACGTTTTTATACAAACGTTGCTATAGACTCTT
ACTTTAGTGGCGTTTCT
Found at i:40267 original size:4 final size:4
Alignment explanation
Indices: 40258--40316 Score: 118
Period size: 4 Copynumber: 14.8 Consensus size: 4
40248 TAAGCTGTGA
40258 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
40306 ATGT ATGT ATG
1 ATGT ATGT ATG
40317 AATGAGAGTG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:44042 original size:24 final size:24
Alignment explanation
Indices: 44010--44055 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
44000 GAGTTTTCCA
44010 TGAAGGATTTAGGGGAATTGTCCT
1 TGAAGGATTTAGGGGAATTGTCCT
44034 TGAAGGATTTAGGGGAATTGTC
1 TGAAGGATTTAGGGGAATTGTC
44056 TTACTTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.07, G:0.35, T:0.33
Consensus pattern (24 bp):
TGAAGGATTTAGGGGAATTGTCCT
Found at i:46325 original size:21 final size:22
Alignment explanation
Indices: 46287--46329 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
46277 ATTATCAGAG
46287 GGGAACCGATTCCCCTGCTACA
1 GGGAACCGATTCCCCTGCTACA
*
46309 GGGAACCGA-TGCCCTGCTACA
1 GGGAACCGATTCCCCTGCTACA
46330 ATACTGCTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.23, C:0.35, G:0.26, T:0.16
Consensus pattern (22 bp):
GGGAACCGATTCCCCTGCTACA
Found at i:48387 original size:6 final size:6
Alignment explanation
Indices: 48378--48415 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
48368 GAAGATACGG
48378 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GA
1 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GA
48416 AGAACAAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
GAGGAA
Found at i:48426 original size:18 final size:18
Alignment explanation
Indices: 48387--48437 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
48377 GGAGGAAGAG
* * *
48387 GAAGAGGAAGAGGAAGAG
1 GAAGAGGAAGAAGAACAA
48405 GAAGAGGAAGAAGAACAA
1 GAAGAGGAAGAAGAACAA
48423 GAAGAAGGAA-AAGAA
1 GAAG-AGGAAGAAGAA
48438 AGAGTTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 24 0.83
19 5 0.17
ACGTcount: A:0.59, C:0.02, G:0.39, T:0.00
Consensus pattern (18 bp):
GAAGAGGAAGAAGAACAA
Found at i:49546 original size:41 final size:44
Alignment explanation
Indices: 49496--49584 Score: 130
Period size: 42 Copynumber: 2.1 Consensus size: 44
49486 TTCACAAATG
49496 CCACTATATGAC-AAACATTTAGCGACG-TTTTGGGA-AAAACA
1 CCACTATATGACAAAACATTTAGCGACGTTTTTGGGACAAAACA
* **
49537 CCACTATATGTCAAAACATTTAGCGGTGTTTTTGGGACAAAACA
1 CCACTATATGACAAAACATTTAGCGACGTTTTTGGGACAAAACA
49581 CCAC
1 CCAC
49585 AAAAGAAAGA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
41 11 0.26
42 13 0.31
43 8 0.19
44 10 0.24
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (44 bp):
CCACTATATGACAAAACATTTAGCGACGTTTTTGGGACAAAACA
Found at i:53088 original size:23 final size:23
Alignment explanation
Indices: 53062--53123 Score: 124
Period size: 23 Copynumber: 2.7 Consensus size: 23
53052 TTCCCATGTG
53062 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCCTTCAAA
53085 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCCTTCAAA
53108 GGGGGAATCGGTTCCC
1 GGGGGAATCGGTTCCC
53124 TCATGGGAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.19, C:0.26, G:0.34, T:0.21
Consensus pattern (23 bp):
GGGGGAATCGGTTCCCCTTCAAA
Done.