Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004281.1 Hibiscus syriacus cultivar Beakdansim tig00009385_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: 51263
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:985 original size:58 final size:60
Alignment explanation
Indices: 823--998 Score: 177
Period size: 58 Copynumber: 3.0 Consensus size: 60
813 GGCTTAAACT
* *
823 AAAATAAACCCCTAAACTATACCCTTTATTTACTTTAAGTCCGT-AACTATTTTTTGGTC
1 AAAATAATCCCCTAAACTATACCCTTTATTTATTTTAAGTCCGTAAACTATTTTTTGGTC
* ** ** *
882 AAAATAAT--CCTTAACTATTA-TATTTAACTATTTTAAGT-AGCTAAACTATTTTTTGGTC
1 AAAATAATCCCCTAAACTA-TACCCTTTATTTATTTTAAGTCCG-TAAACTATTTTTTGGTC
* * *
940 -AAATAATCCCCTAAACTATGCCCTTT-TTTGTTTTAAGTCCGTAAACTATACTTTTGGTC
1 AAAATAATCCCCTAAACTATACCCTTTATTTATTTTAAGTCCGTAAACTAT-TTTTTGGTC
999 GAGACAAGTA
Statistics
Matches: 92, Mismatches: 17, Indels: 16
0.74 0.14 0.13
Matches are distributed among these distances:
56 1 0.01
57 29 0.32
58 35 0.38
59 27 0.29
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.41
Consensus pattern (60 bp):
AAAATAATCCCCTAAACTATACCCTTTATTTATTTTAAGTCCGTAAACTATTTTTTGGTC
Found at i:3876 original size:91 final size:91
Alignment explanation
Indices: 3738--3922 Score: 329
Period size: 93 Copynumber: 2.0 Consensus size: 91
3728 CTTTTTTTCC
3738 TAGAGTATTTTGGCCTTCAAACGCTGGTCGAAATTTCC-AAAATATATATGCCAAAATGATTGTC
1 TAGAGTATTTTGGCCTTCAAACGCTGGTCGAAATTTCCAAAAATATATATGCCAAAATGATTGTC
3802 TTGGTAAATATTGGGGGGTTAATTTTGA
66 TTGGTAAATATT-GGGGGTTAA-TTTGA
3830 TAGAGTA-TTTGGCCTTCAAACGCTGGTCGAAATGTTCCAAAAATATATATGCCAAAATGATTGT
1 TAGAGTATTTTGGCCTTCAAACGCTGGTCGAAAT-TTCCAAAAATATATATGCCAAAATGATTGT
3894 CTTGGTAAATATTGGGGGTTAATTTGA
65 CTTGGTAAATATTGGGGGTTAATTTGA
3921 TA
1 TA
3923 TTATACCAAA
Statistics
Matches: 91, Mismatches: 0, Indels: 5
0.95 0.00 0.05
Matches are distributed among these distances:
91 33 0.36
92 20 0.22
93 38 0.42
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.35
Consensus pattern (91 bp):
TAGAGTATTTTGGCCTTCAAACGCTGGTCGAAATTTCCAAAAATATATATGCCAAAATGATTGTC
TTGGTAAATATTGGGGGTTAATTTGA
Found at i:4254 original size:23 final size:23
Alignment explanation
Indices: 4228--4274 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
4218 AAATTAATAC
*
4228 AAAATA-AGTGTTTAAATATTTTT
1 AAAATATAGTATTTAAAT-TTTTT
4251 AAAATATTAGTATTTAAATTTTTT
1 AAAATA-TAGTATTTAAATTTTTT
4275 CGTTAAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 6 0.29
24 5 0.24
25 10 0.48
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (23 bp):
AAAATATAGTATTTAAATTTTTT
Found at i:7655 original size:15 final size:16
Alignment explanation
Indices: 7623--7653 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
7613 TTCGGTTTGA
7623 AAAAAACCGGTTTTTT
1 AAAAAACCGGTTTTTT
*
7639 AAAAAATCGGTTTTT
1 AAAAAACCGGTTTTT
7654 AATCCGGTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.39
Consensus pattern (16 bp):
AAAAAACCGGTTTTTT
Found at i:7725 original size:21 final size:20
Alignment explanation
Indices: 7680--7725 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
7670 CGGTCATCCA
*
7680 ATTTTTAAACCCCAGATCGG
1 ATTTTTAAACCCCAGAACGG
7700 ATTTTTAAACCCCAGAACGG
1 ATTTTTAAACCCCAGAACGG
7720 ATTTTT
1 ATTTTT
7726 TTTCTGGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (20 bp):
ATTTTTAAACCCCAGAACGG
Found at i:8327 original size:51 final size:52
Alignment explanation
Indices: 8257--8357 Score: 177
Period size: 52 Copynumber: 2.0 Consensus size: 52
8247 ACTCAATTTG
8257 ACTCAAAATAATATATTTA-TAAAAAATATTACTTTTATTCAATAAAAAAAT
1 ACTCAAAATAATATATTTATTAAAAAATATTACTTTTATTCAATAAAAAAAT
* *
8308 ACTCAAAATGATATTTTTATTAAAAAATATTACTTTTATTCAATAAAAAA
1 ACTCAAAATAATATATTTATTAAAAAATATTACTTTTATTCAATAAAAAA
8358 TAGAGATTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
51 17 0.36
52 30 0.64
ACGTcount: A:0.52, C:0.08, G:0.01, T:0.39
Consensus pattern (52 bp):
ACTCAAAATAATATATTTATTAAAAAATATTACTTTTATTCAATAAAAAAAT
Found at i:9027 original size:22 final size:21
Alignment explanation
Indices: 8984--9035 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
8974 TGTATAATTA
* *
8984 TAAATTAATTAAAAATTTAAGGG
1 TAAATT-ATTAAAAA-TAAAAGG
*
9007 TAAATTATTTAAAATAAAAGG
1 TAAATTATTAAAAATAAAAGG
9028 TAAATTAT
1 TAAATTAT
9036 ATCGTGACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 13 0.50
22 7 0.27
23 6 0.23
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.37
Consensus pattern (21 bp):
TAAATTATTAAAAATAAAAGG
Found at i:16325 original size:20 final size:21
Alignment explanation
Indices: 16300--16412 Score: 144
Period size: 20 Copynumber: 5.4 Consensus size: 21
16290 GCGATTCAGA
16300 AACGCGA-TCCAGAAAATCGC
1 AACGCGATTCCAGAAAATCGC
*
16320 AACGCGATCTTCCA-AGAATCGC
1 AACGCGA--TTCCAGAAAATCGC
*
16342 AACGCGATT-AAGAAAATCGC
1 AACGCGATTCCAGAAAATCGC
16362 AACGCGATTCCAAGAAAATCGC
1 AACGCGATTCC-AGAAAATCGC
*
16384 AACGCGATTCCA-AGAATCGC
1 AACGCGATTCCAGAAAATCGC
16404 AACGCGATT
1 AACGCGATT
16413 ATTGCATTTG
Statistics
Matches: 82, Mismatches: 5, Indels: 12
0.83 0.05 0.12
Matches are distributed among these distances:
19 1 0.01
20 41 0.50
21 1 0.01
22 35 0.43
23 4 0.05
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.15
Consensus pattern (21 bp):
AACGCGATTCCAGAAAATCGC
Found at i:16342 original size:22 final size:21
Alignment explanation
Indices: 16314--16412 Score: 123
Period size: 22 Copynumber: 4.7 Consensus size: 21
16304 CGATCCAGAA
16314 AATCGCAACGCGATCTTCCAAG
1 AATCGCAACGCGAT-TTCCAAG
***
16336 AATCGCAACGCGATTAAGAA-
1 AATCGCAACGCGATTTCCAAG
16356 AATCGCAACGCGA-TTCCAAG
1 AATCGCAACGCGATTTCCAAG
16376 AAAATCGCAACGCGA-TTCCAAG
1 --AATCGCAACGCGATTTCCAAG
16398 AATCGCAACGCGATT
1 AATCGCAACGCGATT
16413 ATTGCATTTG
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
19 3 0.04
20 26 0.39
21 4 0.06
22 34 0.51
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.16
Consensus pattern (21 bp):
AATCGCAACGCGATTTCCAAG
Found at i:16359 original size:42 final size:42
Alignment explanation
Indices: 16300--16412 Score: 144
Period size: 42 Copynumber: 2.7 Consensus size: 42
16290 GCGATTCAGA
**
16300 AACGCGATCCAGAAAATCGCAACGCGATCTTCCAAG-AATCGC
1 AACGCGATTAAGAAAATCGCAACGCGAT-TTCCAAGAAATCGC
16342 AACGCGATTAAGAAAATCGCAACGCGA-TTCCAAGAAAATCGC
1 AACGCGATTAAGAAAATCGCAACGCGATTTCCAAG-AAATCGC
16384 AACGCGATTCCAAG--AATCGCAACGCGATT
1 AACGCGATT--AAGAAAATCGCAACGCGATT
16413 ATTGCATTTG
Statistics
Matches: 64, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
40 7 0.11
42 53 0.83
43 1 0.02
44 3 0.05
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.15
Consensus pattern (42 bp):
AACGCGATTAAGAAAATCGCAACGCGATTTCCAAGAAATCGC
Found at i:16498 original size:6 final size:6
Alignment explanation
Indices: 16487--16566 Score: 153
Period size: 6 Copynumber: 13.5 Consensus size: 6
16477 GACACGTATT
16487 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
16535 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
16567 CGAGACGAGA
Statistics
Matches: 74, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.07
6 69 0.93
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:17104 original size:6 final size:6
Alignment explanation
Indices: 17063--17155 Score: 144
Period size: 6 Copynumber: 16.5 Consensus size: 6
17053 TCTCGTCTCG
17063 GGTCG- GGTCG- GGTCG- GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
17105 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
17153 GGT
1 GGT
17156 AATACGTGTC
Statistics
Matches: 87, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 30 0.34
6 57 0.66
ACGTcount: A:0.00, C:0.17, G:0.54, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:23907 original size:45 final size:46
Alignment explanation
Indices: 23858--23948 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
23848 AAACATCGAA
* *
23858 TGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
23903 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
23949 GTTTTTTCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
45 21 0.49
46 22 0.51
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.26
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
Found at i:31654 original size:21 final size:20
Alignment explanation
Indices: 31615--31652 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
31605 CAGAATGTCC
*
31615 GGGGGGTATCGATTCCCCTG
1 GGGGGGAATCGATTCCCCTG
31635 GGGGGGAATCGATTCCCC
1 GGGGGGAATCGATTCCCC
31653 CTAAAGGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.26, G:0.39, T:0.21
Consensus pattern (20 bp):
GGGGGGAATCGATTCCCCTG
Found at i:33621 original size:21 final size:21
Alignment explanation
Indices: 33579--33621 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
33569 TTTCTGGGCT
* *
33579 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
33600 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
33621 A
1 A
33622 ACGAACCAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:34868 original size:24 final size:24
Alignment explanation
Indices: 34819--34871 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
34809 TAAGTGAACC
*
34819 ATGTG-TTTATATGTATATGGGAT
1 ATGTGATTTATATGTATATGAGAT
*
34842 ATGTGATTTATATG-ATGATGAGCT
1 ATGTGATTTATATGTAT-ATGAGAT
34866 ATGTGA
1 ATGTGA
34872 AAGAACTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 7 0.27
24 19 0.73
ACGTcount: A:0.28, C:0.02, G:0.26, T:0.43
Consensus pattern (24 bp):
ATGTGATTTATATGTATATGAGAT
Found at i:35208 original size:103 final size:102
Alignment explanation
Indices: 34989--35200 Score: 352
Period size: 103 Copynumber: 2.1 Consensus size: 102
34979 AGGTTTACGC
*
34989 GGTCCTTCGGGACATATATGTATTCTTTGGAATATATGTGAAGCTGGTGAGACACATACTTGATC
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATATGTGAAGCTGGTGAGACACATACTTGATC
* *
35054 CTTGGCATATGTATATAATTCTTAAGGAATGATATGT
66 CCTAGCATATGTATATAATTCTTAAGGAATGATATGT
* *
35091 AGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATATGTGAAG-CTGGTGAGACACATACTTGAT
* *
35156 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
65 CCCTAGCATATGTATATAATTCTTAAGGAATGATATGT
35194 GGTCCTT
1 GGTCCTT
35201 ATGGACATTA
Statistics
Matches: 101, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
102 40 0.40
103 61 0.60
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (102 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACATATGTGAAGCTGGTGAGACACATACTTGATC
CCTAGCATATGTATATAATTCTTAAGGAATGATATGT
Found at i:35256 original size:23 final size:23
Alignment explanation
Indices: 35230--35284 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
35220 ACTACGGTAT
35230 AATTCTACGCGGCACTAT-GGTGC
1 AATTCTACGCGGCACT-TCGGTGC
* *
35253 AATTCTATGTGGCACTTCGGTGC
1 AATTCTACGCGGCACTTCGGTGC
*
35276 AATTATACG
1 AATTCTACG
35285 AGCTGTGGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.31
Consensus pattern (23 bp):
AATTCTACGCGGCACTTCGGTGC
Found at i:50446 original size:2 final size:2
Alignment explanation
Indices: 50439--50475 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
50429 ATAATAAGAA
50439 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
50476 TATTCCTAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Done.