Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000699.1 Hibiscus syriacus cultivar Beakdansim tig00001361_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: 49495
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Found at i:11934 original size:23 final size:23
Alignment explanation
Indices: 11904--11951 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
11894 TATATTTTTA
11904 TATTGAATC-ATTCAATACTATTT
1 TATTGAATCAATT-AATACTATTT
*
11927 TATTGAATCAATTAATATTATTT
1 TATTGAATCAATTAATACTATTT
11950 TA
1 TA
11952 CTAAATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (23 bp):
TATTGAATCAATTAATACTATTT
Found at i:12772 original size:32 final size:31
Alignment explanation
Indices: 12689--12772 Score: 87
Period size: 37 Copynumber: 2.5 Consensus size: 31
12679 GTATAATATT
12689 AAAAATTATAAAATATTTATATATTTTCTTTA
1 AAAAATTA-AAAATATTTATATATTTTCTTTA
*
12721 AAAAATTAAATTCATAATATTTATATAATTTTTTTTA
1 AAAAATT-AA---A-AATATTTATAT-ATTTTCTTTA
*
12758 CAAAATTAAAAATAT
1 AAAAATTAAAAATAT
12773 AAAAAAAGTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
32 13 0.30
33 2 0.05
35 1 0.02
36 13 0.30
37 15 0.34
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (31 bp):
AAAAATTAAAAATATTTATATATTTTCTTTA
Found at i:17071 original size:3 final size:3
Alignment explanation
Indices: 17011--17055 Score: 72
Period size: 3 Copynumber: 14.3 Consensus size: 3
17001 TTGTCTGTTT
17011 TTA TTA TTAA TTA TATA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TT-A TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
17056 CTTACAAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 34 0.85
4 6 0.15
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:17085 original size:15 final size:14
Alignment explanation
Indices: 17012--17095 Score: 67
Period size: 12 Copynumber: 6.4 Consensus size: 14
17002 TGTCTGTTTT
17012 TATTATTA-ATTATA
1 TATTATTATA-TATA
17026 TATTATTAT-TAT-
1 TATTATTATATATA
17038 TATTATTAT-TAT-
1 TATTATTATATATA
* *
17050 TATTATCT-TACAAA
1 TATTAT-TATATATA
17064 T-TTATTATATAATA
1 TATTATTATAT-ATA
17078 TATTATTATAT-TA
1 TATTATTATATATA
17091 TATTA
1 TATTA
17096 ATATTTACAA
Statistics
Matches: 59, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
12 20 0.34
13 18 0.31
14 12 0.20
15 9 0.15
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.58
Consensus pattern (14 bp):
TATTATTATATATA
Found at i:18106 original size:19 final size:22
Alignment explanation
Indices: 18065--18106 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
18055 TATCTCGAAA
*
18065 TCAGGTTCTTACATATTTCAAT
1 TCAGGTTCTCACATATTTCAAT
18087 TCAGGTT-TCACAT-TTT-AAT
1 TCAGGTTCTCACATATTTCAAT
18106 T
1 T
18107 ATTTTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 4 0.21
20 3 0.16
21 5 0.26
22 7 0.37
ACGTcount: A:0.26, C:0.17, G:0.10, T:0.48
Consensus pattern (22 bp):
TCAGGTTCTCACATATTTCAAT
Found at i:25867 original size:14 final size:13
Alignment explanation
Indices: 25848--25926 Score: 53
Period size: 13 Copynumber: 6.3 Consensus size: 13
25838 TGTCTGTTTT
25848 TATTATTAATTATA
1 TATTATT-ATTATA
25862 TATTATTATTATCA
1 TATTATTATTAT-A
* * *
25876 TCTTA-CA-TATT
1 TATTATTATTATA
*
25887 TATTA-TATAATA
1 TATTATTATTATA
25899 TATTATTA-TATTA
1 TATTATTATTA-TA
25912 TATTA-TATTAT-
1 TATTATTATTATA
25923 TATT
1 TATT
25927 TACAAATATT
Statistics
Matches: 52, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
11 9 0.17
12 14 0.27
13 17 0.33
14 12 0.23
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (13 bp):
TATTATTATTATA
Found at i:25904 original size:15 final size:17
Alignment explanation
Indices: 25848--25925 Score: 74
Period size: 18 Copynumber: 4.5 Consensus size: 17
25838 TGTCTGTTTT
25848 TATTATTA-ATTATATA
1 TATTATTATATTATATA
*
25864 TTATTATTATCATCT-TACA
1 -TATTATTAT-AT-TATATA
25883 TATTTATTATA-TA-ATA
1 TA-TTATTATATTATATA
25899 TATTATTATATTATATTA
1 TATTATTATATTATA-TA
25917 TATTATTAT
1 TATTATTAT
25926 TTACAAATAT
Statistics
Matches: 51, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
15 8 0.16
16 7 0.14
17 9 0.18
18 14 0.27
19 12 0.24
20 1 0.02
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTATTATATTATATA
Found at i:25910 original size:5 final size:5
Alignment explanation
Indices: 25882--25922 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
25872 ATCATCTTAC
*
25882 ATATT -TATT ATATA ATA-T ATTATT ATATT ATATT ATATT AT
1 ATATT ATATT ATATT ATATT A-TATT ATATT ATATT ATATT AT
25923 TATTTACAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
4 5 0.16
5 24 0.77
6 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:30083 original size:2 final size:2
Alignment explanation
Indices: 30076--30105 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
30066 ATCATGTAAG
30076 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
30106 TATTTCACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32292 original size:38 final size:38
Alignment explanation
Indices: 32250--32324 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 38
32240 ATATTATCTA
*
32250 ATCCTAACATTGAATACTAAGTTCTCTAACTAAGTCTC
1 ATCCTAACATTGAATACTAAGCTCTCTAACTAAGTCTC
** *
32288 ATCCTAACATTGGGTATTAAGCTCTCTAACTAAGTCT
1 ATCCTAACATTGAATACTAAGCTCTCTAACTAAGTCT
32325 TTAATGCCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.35
Consensus pattern (38 bp):
ATCCTAACATTGAATACTAAGCTCTCTAACTAAGTCTC
Found at i:36261 original size:18 final size:19
Alignment explanation
Indices: 36226--36262 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
36216 CACGGAATGT
36226 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
36246 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
36263 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:37780 original size:45 final size:42
Alignment explanation
Indices: 37731--37827 Score: 115
Period size: 42 Copynumber: 2.2 Consensus size: 42
37721 TTGGTTGCGG
37731 AAATTAAAATAAAAAGATTAGTTCTTTTTGATTATTAGACTG-TAA
1 AAATTAAAATAAAAAGATTAG-T-TTTTT-ATTATTAGACTGCT-A
* * **
37776 AAATTAAAATCAAATGATTAGTTTTTTATTATTAGGTTGCTA
1 AAATTAAAATAAAAAGATTAGTTTTTTATTATTAGACTGCTA
37818 AAATTAAAAT
1 AAATTAAAAT
37828 GATTAAATCT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
42 21 0.45
43 6 0.13
44 1 0.02
45 19 0.40
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.41
Consensus pattern (42 bp):
AAATTAAAATAAAAAGATTAGTTTTTTATTATTAGACTGCTA
Found at i:38107 original size:31 final size:31
Alignment explanation
Indices: 38023--38111 Score: 91
Period size: 31 Copynumber: 3.0 Consensus size: 31
38013 ATTTTTTAAA
38023 AAAG-AAATAAATTGTTAAATTTATTTTCTT
1 AAAGAAAATAAATTGTTAAATTTATTTTCTT
* * * *
38053 -GAGAATCATAAA-TG---ATTTTATTTTGTT
1 AAAGAA-AATAAATTGTTAAATTTATTTTCTT
38080 AAAGAAAATAAATTGTTAAATTTATTTTCTT
1 AAAGAAAATAAATTGTTAAATTTATTTTCTT
38111 A
1 A
38112 TGAAATTTTA
Statistics
Matches: 44, Mismatches: 8, Indels: 13
0.68 0.12 0.20
Matches are distributed among these distances:
27 16 0.36
28 6 0.14
29 2 0.05
30 3 0.07
31 17 0.39
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (31 bp):
AAAGAAAATAAATTGTTAAATTTATTTTCTT
Found at i:38108 original size:58 final size:58
Alignment explanation
Indices: 37985--38167 Score: 194
Period size: 58 Copynumber: 3.2 Consensus size: 58
37975 CGTAACGAGA
* * ** *
37985 TATTTTCTTGAAAATCGTGGATGATTTTATTTT-TTAAAAAAGAAATAAATTGTTAAATT
1 TATTTTCTTGAGAATCATAAATGATTTTATTTTGTT-AAAGA-AAATAAATTGTTAAATT
38044 TATTTTCTTGAGAATCATAAATGATTTTATTTTGTTAAAGAAAATAAATTGTTAAATT
1 TATTTTCTTGAGAATCATAAATGATTTTATTTTGTTAAAGAAAATAAATTGTTAAATT
* * * * * * *
38102 TATTTTCTT-ATGAAAT-TTTAATGTTTTTATTTTGTAAAAGGAAAT-AATCGTTAGATT
1 TATTTTCTTGA-G-AATCATAAATGATTTTATTTTGTTAAAGAAAATAAATTGTTAAATT
38159 TATTTTCTT
1 TATTTTCTT
38168 ATTTAAAAAA
Statistics
Matches: 109, Mismatches: 12, Indels: 8
0.84 0.09 0.06
Matches are distributed among these distances:
57 20 0.18
58 51 0.47
59 36 0.33
60 2 0.02
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (58 bp):
TATTTTCTTGAGAATCATAAATGATTTTATTTTGTTAAAGAAAATAAATTGTTAAATT
Found at i:38262 original size:39 final size:39
Alignment explanation
Indices: 38128--38318 Score: 211
Period size: 39 Copynumber: 5.0 Consensus size: 39
38118 TTTAATGTTT
*
38128 TTATTTTGTAAAAGGAAAT-AATCGTT-AGATTTATTTTC
1 TTATTTTGTAAAATGAAATAAATCGTTGA-ATTTATTTTC
** *
38166 TTA--TT-TAAAAAAAAATAAATCATTGAATTTA-TTT-
1 TTATTTTGTAAAATGAAATAAATCGTTGAATTTATTTTC
*
38200 TTATGTTT-TATAAATGAAATAAATGGTTGAATTTATTTTC
1 TTAT-TTTGTA-AAATGAAATAAATCGTTGAATTTATTTTC
*
38240 TTATTTTGTAAAATGAAATAAATGGTTGAATTTATTTTC
1 TTATTTTGTAAAATGAAATAAATCGTTGAATTTATTTTC
* *
38279 TTATTTTGTAAAA-GAAAATAAATCATTAAATTTATTTTC
1 TTATTTTGTAAAATG-AAATAAATCGTTGAATTTATTTTC
38318 T
1 T
38319 AAGAATCTCA
Statistics
Matches: 133, Mismatches: 10, Indels: 19
0.82 0.06 0.12
Matches are distributed among these distances:
34 3 0.02
35 12 0.09
36 13 0.10
37 5 0.04
38 24 0.18
39 70 0.53
40 6 0.05
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (39 bp):
TTATTTTGTAAAATGAAATAAATCGTTGAATTTATTTTC
Found at i:38269 original size:77 final size:75
Alignment explanation
Indices: 38128--38318 Score: 199
Period size: 77 Copynumber: 2.5 Consensus size: 75
38118 TTTAATGTTT
* * * *
38128 TTATTTTGTAAAAGGAAAT-AATCGTTAGATTTATTTTCTTATTTAAAAAAAAATAAATCATTGA
1 TTATTTTATAAAAGAAAATAAATCATTAAATTTATTTTCTTATTTAAAAAAAAATAAATCATTGA
38192 ATTTATTTT-
66 ATTTATTTTC
* * ** * ** **
38201 TATGTTTTATAAATG-AAATAAATGGTTGAATTTATTTTCTTATTTTGTAAAATGAAATAAATGG
1 T-TATTTTATAAAAGAAAATAAATCATTAAATTTATTTTCTTA--TT-TAAAAAAAAATAAATCA
38265 TTGAATTTATTTTC
62 TTGAATTTATTTTC
*
38279 TTATTTTGTAAAAGAAAATAAATCATTAAATTTATTTTCT
1 TTATTTTATAAAAGAAAATAAATCATTAAATTTATTTTCT
38319 AAGAATCTCA
Statistics
Matches: 95, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
73 5 0.05
74 29 0.31
76 2 0.02
77 36 0.38
78 23 0.24
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (75 bp):
TTATTTTATAAAAGAAAATAAATCATTAAATTTATTTTCTTATTTAAAAAAAAATAAATCATTGA
ATTTATTTTC
Found at i:40133 original size:19 final size:20
Alignment explanation
Indices: 40096--40133 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
40086 ATGAGTAGAA
*
40096 ATGAGTTTAAGAATGTGTAT
1 ATGAGTTTAAGAATATGTAT
*
40116 ATGAG-TTATGAATATGTA
1 ATGAGTTTAAGAATATGTA
40134 AAGGGATCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
ATGAGTTTAAGAATATGTAT
Found at i:47230 original size:17 final size:19
Alignment explanation
Indices: 47191--47233 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 19
47181 ATACCATAGG
*
47191 TATCGATACCTTAAGGGAGA
1 TATCGATACCTT-AGGGAAA
47211 TATCGATA-CTT-GGGAAA
1 TATCGATACCTTAGGGAAA
47228 TATCGA
1 TATCGA
47234 ATGTAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 11 0.50
19 3 0.14
20 8 0.36
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (19 bp):
TATCGATACCTTAGGGAAA
Found at i:47920 original size:18 final size:18
Alignment explanation
Indices: 47886--47937 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
47876 AGGGATTATC
47886 AGTGGTCCTTC-GGACAT
1 AGTGGTCCTTCGGGACAT
47903 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
47921 AGTGGTCCTTTGGGACA
1 AGTGGTCCTTCGGGACA
47938 AATATTCAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 11 0.33
18 22 0.67
ACGTcount: A:0.17, C:0.21, G:0.33, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Done.