Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003183.1 Hibiscus syriacus cultivar Beakdansim tig00006699_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: 62767
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:3890 original size:24 final size:24
Alignment explanation
Indices: 3858--3907 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
3848 GATGTGATTA
3858 CAAACTTCATGAATTCAATGGATG
1 CAAACTTCATGAATTCAATGGATG
3882 CAAACTTCATGAATTCAATGGATG
1 CAAACTTCATGAATTCAATGGATG
3906 CA
1 CA
3908 TCAGTCAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (24 bp):
CAAACTTCATGAATTCAATGGATG
Found at i:14520 original size:18 final size:19
Alignment explanation
Indices: 14485--14521 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
14475 TTCTGTATTG
14485 AATAGTATAGTCCAATCCC
1 AATAGTATAGTCCAATCCC
*
14504 AATAGTTTAGT-CAATCCC
1 AATAGTATAGTCCAATCCC
14522 TTCTTTTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.30
Consensus pattern (19 bp):
AATAGTATAGTCCAATCCC
Found at i:20597 original size:9 final size:9
Alignment explanation
Indices: 20585--20635 Score: 54
Period size: 9 Copynumber: 6.0 Consensus size: 9
20575 TAATATTTTA
20585 TATTTAATT
1 TATTTAATT
*
20594 TATTTAA-G
1 TATTTAATT
20602 TATTTAATT
1 TATTTAATT
20611 TATTTAA--
1 TATTTAATT
* *
20618 TATTTTACT
1 TATTTAATT
20627 TATTTAATT
1 TATTTAATT
20636 CTTTTGCAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 6 0.18
8 7 0.21
9 21 0.62
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
TATTTAATT
Found at i:20629 original size:16 final size:16
Alignment explanation
Indices: 20578--20634 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
20568 ATATTTTTAA
*
20578 TATTTTATATTTAATT
1 TATTTAATATTTAATT
20594 TATTTAAGTATTTAATT
1 TATTTAA-TATTTAATT
* *
20611 TATTTAATATTTTACT
1 TATTTAATATTTAATT
20627 TATTTAAT
1 TATTTAAT
20635 TCTTTTGCAG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
16 21 0.57
17 16 0.43
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (16 bp):
TATTTAATATTTAATT
Found at i:22328 original size:27 final size:27
Alignment explanation
Indices: 22298--22349 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
22288 GCCATCGCCT
* *
22298 TTCCATTACCATATGTCGCCGCCGCTA
1 TTCCATTACCAGATGCCGCCGCCGCTA
* *
22325 TTCCCTTACCCGATGCCGCCGCCGC
1 TTCCATTACCAGATGCCGCCGCCGC
22350 CATCATCACC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.13, C:0.44, G:0.17, T:0.25
Consensus pattern (27 bp):
TTCCATTACCAGATGCCGCCGCCGCTA
Found at i:28385 original size:18 final size:18
Alignment explanation
Indices: 28364--28427 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 18
28354 GGTTTTTTTC
*
28364 TTTTTTATTTCGTTTATT
1 TTTTTTATTTCATTTATT
* *
28382 TTTTTTTTTTAATTTATT
1 TTTTTTATTTCATTTATT
*
28400 ATTTATTTGATTTCTTTTATT
1 -TTT-TTT-ATTTCATTTATT
28421 TATTTTT
1 T-TTTTT
28428 TGTAATTCTA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
18 15 0.42
19 3 0.08
20 7 0.19
21 11 0.31
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.78
Consensus pattern (18 bp):
TTTTTTATTTCATTTATT
Found at i:28436 original size:22 final size:21
Alignment explanation
Indices: 28394--28436 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
28384 TTTTTTTTAA
*
28394 TTTATTATTTATTTGATTTCT
1 TTTATTATTTATTTGAATTCT
28415 TTTATTTATTT-TTTGTAATTCT
1 TTTA-TTATTTATTTG-AATTCT
28437 AAAATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.72
Consensus pattern (21 bp):
TTTATTATTTATTTGAATTCT
Found at i:28445 original size:39 final size:39
Alignment explanation
Indices: 28370--28446 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 39
28360 TTTCTTTTTT
* * * *
28370 ATTTCGTTTATTTTTTTTTTTTAATTTATTATTTATTTG
1 ATTTCGTTTATTTATTTTTTGTAATTTATAAATTATTTG
*
28409 ATTTCTTTTATTTATTTTTTGTAATTCTA-AAATTATTT
1 ATTTCGTTTATTTATTTTTTGTAATT-TATAAATTATTT
28447 TTGGTTTCCT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
39 30 0.94
40 2 0.06
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.70
Consensus pattern (39 bp):
ATTTCGTTTATTTATTTTTTGTAATTTATAAATTATTTG
Found at i:36597 original size:21 final size:21
Alignment explanation
Indices: 36572--36645 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
36562 TGAAACAAGA
36572 GGTTTCAAAACCTTTGATAGG
1 GGTTTCAAAACCTTTGATAGG
*
36593 GGTTTAAAAACCTTTGATAGG
1 GGTTTCAAAACCTTTGATAGG
* **
36614 GGTTTCGAAACCTTTGATAAA
1 GGTTTCAAAACCTTTGATAGG
36635 GGTTTCAAAAC
1 GGTTTCAAAAC
36646 ATGTAGGCCA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (21 bp):
GGTTTCAAAACCTTTGATAGG
Found at i:46821 original size:23 final size:21
Alignment explanation
Indices: 46795--46848 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 21
46785 TATAAAATAA
*
46795 TATTTATTCTAAATACTTTCAAT
1 TATTTATTATAAATAC-TT-AAT
*
46818 TATTTGATAATAAATACTTAAT
1 TATTT-ATTATAAATACTTAAT
46840 TAATTTATT
1 T-ATTTATT
46849 GTAATCGTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
22 6 0.23
23 11 0.42
24 9 0.35
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (21 bp):
TATTTATTATAAATACTTAAT
Found at i:47484 original size:23 final size:24
Alignment explanation
Indices: 47449--47493 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
47439 GGTTTCATTT
47449 TTTTCTTAATATTTATTATTAGGA
1 TTTTCTTAATATTTATTATTAGGA
47473 TTTT-TTAATATTTATTATTAG
1 TTTTCTTAATATTTATTATTAG
47494 TGGTCTATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.62
Consensus pattern (24 bp):
TTTTCTTAATATTTATTATTAGGA
Found at i:52652 original size:117 final size:116
Alignment explanation
Indices: 52486--52849 Score: 482
Period size: 117 Copynumber: 3.1 Consensus size: 116
52476 TAGCAAAAAG
* * * * * **
52486 AATGTTGATCCACCTCATTCTATGATAGATCTGAGAAAAATGTTGAACAAGTTCTTCTCATTATG
1 AATGTTAATCCACCTCATTCTGTGATAGATTTGAGCAAAAGGTCAAACAAGTTCTTCTCATTATG
*
52551 AACTTCTCCTCCCTTCGTGGTCGAGTTCTTCTCATTATGAACTCTCAATTGG
66 AACTTCTCCTCCCTTCGTGG-CGAGTTCTTCTCATTATGAACTCTCAATTGA
* * * *
52603 AATGTTAATACACCTCTTTCTGTGATGGATTTGAGCAAAAGGTCAAACAAGTTATTCTCATTATG
1 AATGTTAATCCACCTCATTCTGTGATAGATTTGAGCAAAAGGTCAAACAAGTTCTTCTCATTATG
* * * * *
52668 AACTTGTTCTCCCTCCGTGGACGTGTTCTTCTCATTATGAACTCTCCATTGA
66 AACTTCTCCTCCCTTCGTGG-CGAGTTCTTCTCATTATGAACTCTCAATTGA
* *
52720 AATGTTAATCCACCTCATTCTGTGATAGATTTGAGCAAAAGGTCAAACAAGTTCTTGTCATTATA
1 AATGTTAATCCACCTCATTCTGTGATAGATTTGAGCAAAAGGTCAAACAAGTTCTTCTCATTATG
* *
52785 AAATTCTCCT---TTCGTGGAGAGTTCTTCTCATTATGAACTCTCAATTGAA
66 AACTTCTCCTCCCTTCGTGGCGAGTTCTTCTCATTATGAACTCTCAATTG-A
*
52834 AATGTTGATCCACCTC
1 AATGTTAATCCACCTC
52850 CTTATTTGAT
Statistics
Matches: 214, Mismatches: 32, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
113 27 0.13
114 22 0.10
117 165 0.77
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.36
Consensus pattern (116 bp):
AATGTTAATCCACCTCATTCTGTGATAGATTTGAGCAAAAGGTCAAACAAGTTCTTCTCATTATG
AACTTCTCCTCCCTTCGTGGCGAGTTCTTCTCATTATGAACTCTCAATTGA
Found at i:52905 original size:45 final size:45
Alignment explanation
Indices: 52834--52998 Score: 143
Period size: 45 Copynumber: 3.7 Consensus size: 45
52824 CTCAATTGAA
* * *
52834 AATGTTGATCCACCTCCTTATTTGATGGAACCGAGCAAAAAAGAG
1 AATGTTGATCCACCTCCTTATGTGATGGAACCAAACAAAAAAGAG
* * ** *
52879 AATGTTGATCTACCTCCTTCTGTGATGGAACCAAACAAAATGGTG
1 AATGTTGATCCACCTCCTTATGTGATGGAACCAAACAAAAAAGAG
* * * * * * *
52924 -ATGTTGATCTAACTCCTTATATGATAGAATCTAACAAACAAAAAG
1 AATGTTGATCCACCTCCTTATGTGATGGAACCAAACAAA-AAAGAG
* * * *
52969 AATATTGATCCACCTCATTCTGTTATGGAA
1 AATGTTGATCCACCTCCTTATGTGATGGAA
52999 TAGAACAAAG
Statistics
Matches: 92, Mismatches: 26, Indels: 3
0.76 0.21 0.02
Matches are distributed among these distances:
44 32 0.35
45 39 0.42
46 21 0.23
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (45 bp):
AATGTTGATCCACCTCCTTATGTGATGGAACCAAACAAAAAAGAG
Found at i:52990 original size:90 final size:89
Alignment explanation
Indices: 52835--53037 Score: 212
Period size: 89 Copynumber: 2.3 Consensus size: 89
52825 TCAATTGAAA
* * * * * * * *
52835 ATGTTGATCCACCTCCTTATTTGATGGAACCGAGCAAAAAAGAGAATGTTGATCTACCTCCTTCT
1 ATGTTGATCCAACTCCTTATATGATAGAACCGAACAAAAAAAAGAATATTGATCCACCTCATTCT
52900 GTGATGGAACCAAACAAAATGGTG
66 GTGATGGAACCAAACAAAATGGTG
* * *
52924 ATGTTGATCTAACTCCTTATATGATAGAATCTAACAAACAAAAAGAATATTGATCCACCTCATTC
1 ATGTTGATCCAACTCCTTATATGATAGAACCGAACAAA-AAAAAGAATATTGATCCACCTCATTC
* * *
52989 TGTTATGGAA-TAGAAC-AAAGGGTG
65 TGTGATGGAACCA-AACAAAATGGTG
* * * *
53013 ATGCTGATTCAACTCATTATGTGAT
1 ATGTTGATCCAACTCCTTATATGAT
53038 GGAATCGAGC
Statistics
Matches: 93, Mismatches: 19, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
89 59 0.63
90 34 0.37
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30
Consensus pattern (89 bp):
ATGTTGATCCAACTCCTTATATGATAGAACCGAACAAAAAAAAGAATATTGATCCACCTCATTCT
GTGATGGAACCAAACAAAATGGTG
Found at i:53077 original size:44 final size:44
Alignment explanation
Indices: 52835--53095 Score: 175
Period size: 44 Copynumber: 5.9 Consensus size: 44
52825 TCAATTGAAA
* * * * * *
52835 ATGTTGATCCACCTCCTTATTTGATGGAACCGAGCAAAAAAGAG
1 ATGTTGATCCAACTCCTTATGTGATGGAATCGAACAAAAAGGTG
* * * * * *
52879 AATGTTGATCTACCTCCTTCTGTGATGGAACCAAACAAAATGGTG
1 -ATGTTGATCCAACTCCTTATGTGATGGAATCGAACAAAAAGGTG
* * * * ***
52924 ATGTTGATCTAACTCCTTATATGATAGAATCTAACAAACAAAAAG
1 ATGTTGATCCAACTCCTTATGTGATGGAATCGAACAAA-AAGGTG
* * * * * * *
52969 AATATTGATCCACCTCATTCTGTTATGGAATAGAAC-AAAGGGTG
1 -ATGTTGATCCAACTCCTTATGTGATGGAATCGAACAAAAAGGTG
* * * * * * *
53013 ATGCTGATTCAACTCATTATGTGATGGAATCGAGCGAAATGTTG
1 ATGTTGATCCAACTCCTTATGTGATGGAATCGAACAAAAAGGTG
*
53057 ATGTTGATCCAACTCCTTATGTGATGGAATC-AAGAAAAA
1 ATGTTGATCCAACTCCTTATGTGATGGAATCGAACAAAAA
53096 TATTGATATA
Statistics
Matches: 164, Mismatches: 49, Indels: 8
0.74 0.22 0.04
Matches are distributed among these distances:
43 31 0.19
44 68 0.41
45 40 0.24
46 25 0.15
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (44 bp):
ATGTTGATCCAACTCCTTATGTGATGGAATCGAACAAAAAGGTG
Found at i:53940 original size:13 final size:11
Alignment explanation
Indices: 53913--53958 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
53903 ATGACTAAGA
53913 ATAAATAAAAT
1 ATAAATAAAAT
53924 ATAAATATAAAT
1 ATAAATA-AAAT
53936 CAT-AATCAAAAT
1 -ATAAAT-AAAAT
53948 A-AAATAAAAT
1 ATAAATAAAAT
53958 A
1 A
53959 AACGTAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
10 6 0.19
11 11 0.35
12 11 0.35
13 3 0.10
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (11 bp):
ATAAATAAAAT
Found at i:57217 original size:20 final size:20
Alignment explanation
Indices: 57189--57229 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
57179 TTAGGCATTT
*
57189 TATAAGGGGAGTATCGATAC
1 TATAAGGGGAGCATCGATAC
*
57209 TATAGGGGGAGCATCGATAC
1 TATAAGGGGAGCATCGATAC
57229 T
1 T
57230 GCTACCCTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.32, C:0.12, G:0.32, T:0.24
Consensus pattern (20 bp):
TATAAGGGGAGCATCGATAC
Found at i:62493 original size:4 final size:4
Alignment explanation
Indices: 62486--62767 Score: 465
Period size: 4 Copynumber: 72.0 Consensus size: 4
62476 TATATATATA
62486 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
62534 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
62582 TAT- TATG TATG TATG TGATG TATG TA-G TATG T-TG TATG TATG TATG
1 TATG TATG TATG TATG T-ATG TATG TATG TATG TATG TATG TATG TATG
62628 TATG TATG TATG TATG TA-G TATG TATG TATG TATG TAT- TATG T-TG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
62673 TATG TATG TA-- TATG TATG TAT- TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
62718 TATT TATGG TATG TATG TATG TATG TATG TATG TATG TTATG TATG TATG
1 TATG TAT-G TATG TATG TATG TATG TATG TATG TATG -TATG TATG TATG
Statistics
Matches: 264, Mismatches: 2, Indels: 24
0.91 0.01 0.08
Matches are distributed among these distances:
2 2 0.01
3 21 0.08
4 230 0.87
5 11 0.04
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Done.