Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006838.1 Hibiscus syriacus cultivar Beakdansim tig00017385_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: 88847
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:9732 original size:20 final size:20
Alignment explanation
Indices: 9704--9746 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
9694 AATCCACCAC
9704 ATGCAACTAAATACTTCTAA
1 ATGCAACTAAATACTTCTAA
* * **
9724 ATGCCACTACATGGTTCTAA
1 ATGCAACTAAATACTTCTAA
9744 ATG
1 ATG
9747 AGCCTTTAGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATACTTCTAA
Found at i:12960 original size:17 final size:17
Alignment explanation
Indices: 12938--12972 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12928 AGTGTGTGTT
12938 TTATGT-TTTTGGTCGGG
1 TTATGTATTTTGGT-GGG
12955 TTATGTATTTTGGTGGG
1 TTATGTATTTTGGTGGG
12972 T
1 T
12973 ATTGTTTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.09, C:0.03, G:0.34, T:0.54
Consensus pattern (17 bp):
TTATGTATTTTGGTGGG
Found at i:25421 original size:2 final size:2
Alignment explanation
Indices: 25414--25438 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25404 TACAACCATT
25414 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
25439 TACTGAAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28498 original size:421 final size:424
Alignment explanation
Indices: 27763--28607 Score: 1642
Period size: 422 Copynumber: 2.0 Consensus size: 424
27753 CATCATAAAT
27763 GAGAAGACTTCTTTGAATTGTCTAAAATTTGGGTGTACACATCATATGCATGCATCCTTTTCGCA
1 GAGAAGACTTCTTTGAATTGTCTAAAATTTGGGTGTACACATCATATGCATGCATCCTTTTCGCA
*
27828 TTCTTAATTATATCTTGTTCTTTTTTACATGTTTTTTTACCCTATCTAGATTAGTCGATCAATAG
66 TTCTTAATTATATCTTGTTCTTTTTTACATGTTTTTTTACCATATCTAGATTAGTCGATCAATAG
27893 ATCAAAACCGGTGGTTATACCAAATAAATATGAAACTATTTAGGGTATTTTTATAAATACGAACC
131 ATCAAAACCGGTGGTTATACCAAATAAATATGAAACTATTTAGGGTATTTTTATAAATACGAACC
27958 AAATTGATATTAGCTAAGAATTGGTTTGGAGTTATTTTATGGATTTGGAAAATGAAATAAAAGAT
196 AAATTGATATTAGCTAAGAATTGGTTTGGAGTTATTTTATGGATTTGGAAAATGAAATAAAAGAT
28023 AAAAATGAAAAGAAGTAAAGGCATTAATGGTTATTTTTCTTATAATAGGAACCAAA-TTTTAAAA
261 AAAAATGAAAAGAAGTAAAGGCATTAATGGTTATTTTTCTTATAATAGGAACCAAATTTTTAAAA
28087 AAATATGAAAATGTTGGGAGTCTATTTTTATAATTATGGGTTAAATTAAT-AAATATATAAATAT
326 AAATATGAAAATGTTGGGAGTCTATTTTTATAATTATGGGTTAAATTAATAAAATATATAAATAT
28151 TGATGGTTAAATATGTTATTGTATCAATTATTTA
391 TGATGGTTAAATATGTTATTGTATCAATTATTTA
28185 GAGAAGACTTCTTTGAATTGTCTAAAATTTGGGTGTACACATCATATGCATGCATCCTTTTCGCA
1 GAGAAGACTTCTTTGAATTGTCTAAAATTTGGGTGTACACATCATATGCATGCATCCTTTTCGCA
*
28250 TTCTTAATTATATCTTGTTCTTTTTTACATGTTTTTTTACCATATCTGGATTAGTCGATCAATAG
66 TTCTTAATTATATCTTGTTCTTTTTTACATGTTTTTTTACCATATCTAGATTAGTCGATCAATAG
*
28315 ATCGAAACCGGTGGTTATACCAAATAAATATGAAACTATTTAGGGTA-TTTTATAAATACGAACC
131 ATCAAAACCGGTGGTTATACCAAATAAATATGAAACTATTTAGGGTATTTTTATAAATACGAACC
28379 AAATTGATATTAGCTAAGAATTGGTTTGGAGTTATTTTATGGATTTGGAAAATGAAATAAAAGAT
196 AAATTGATATTAGCTAAGAATTGGTTTGGAGTTATTTTATGGATTTGGAAAATGAAATAAAAGAT
28444 AAAAATGAAAAGAAGTAAAGGCATTAATGGTTATTTTTCTTATAATAGGAACCAAATTTTTAAAA
261 AAAAATGAAAAGAAGTAAAGGCATTAATGGTTATTTTTCTTATAATAGGAACCAAATTTTTAAAA
28509 AAATATGAAAATGTTGGGAGTCTATTTTTATAATTATGGGTTAAATTAATAAAATATATAAATAT
326 AAATATGAAAATGTTGGGAGTCTATTTTTATAATTATGGGTTAAATTAATAAAATATATAAATAT
28574 TGATGGTTAAATATGTTATTGTATCAATTATTTA
391 TGATGGTTAAATATGTTATTGTATCAATTATTTA
28608 ATGATCACGT
Statistics
Matches: 418, Mismatches: 3, Indels: 3
0.99 0.01 0.01
Matches are distributed among these distances:
421 138 0.33
422 232 0.56
423 48 0.11
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (424 bp):
GAGAAGACTTCTTTGAATTGTCTAAAATTTGGGTGTACACATCATATGCATGCATCCTTTTCGCA
TTCTTAATTATATCTTGTTCTTTTTTACATGTTTTTTTACCATATCTAGATTAGTCGATCAATAG
ATCAAAACCGGTGGTTATACCAAATAAATATGAAACTATTTAGGGTATTTTTATAAATACGAACC
AAATTGATATTAGCTAAGAATTGGTTTGGAGTTATTTTATGGATTTGGAAAATGAAATAAAAGAT
AAAAATGAAAAGAAGTAAAGGCATTAATGGTTATTTTTCTTATAATAGGAACCAAATTTTTAAAA
AAATATGAAAATGTTGGGAGTCTATTTTTATAATTATGGGTTAAATTAATAAAATATATAAATAT
TGATGGTTAAATATGTTATTGTATCAATTATTTA
Found at i:36881 original size:30 final size:30
Alignment explanation
Indices: 36842--36930 Score: 124
Period size: 30 Copynumber: 3.0 Consensus size: 30
36832 TCTATGGCTC
* * *
36842 CTCCACCGCTCCCTCCACCACCTACAGCTG
1 CTCCTCCGCTCCCTCAACCACCCACAGCTG
*
36872 CTCCTCCGCTCTCTCAACCACCCACAGCTG
1 CTCCTCCGCTCCCTCAACCACCCACAGCTG
* *
36902 TTCCTCCGCTCTCTCAACCACCCACAGCT
1 CTCCTCCGCTCCCTCAACCACCCACAGCT
36931 CCACCAACCC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.17, C:0.54, G:0.09, T:0.20
Consensus pattern (30 bp):
CTCCTCCGCTCCCTCAACCACCCACAGCTG
Found at i:37492 original size:2 final size:2
Alignment explanation
Indices: 37487--37517 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
37477 TAAACTAAAT
37487 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
37518 TAGAAAATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:50013 original size:22 final size:23
Alignment explanation
Indices: 49974--50020 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
49964 AACCCTAAAT
49974 AAGCCCAAAAATCATATCTGCTA
1 AAGCCCAAAAATCATATCTGCTA
* * *
49997 AAGCCC-AGAATCGTATCTTCTA
1 AAGCCCAAAAATCATATCTGCTA
50019 AA
1 AA
50021 CTCGCAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.40, C:0.26, G:0.11, T:0.23
Consensus pattern (23 bp):
AAGCCCAAAAATCATATCTGCTA
Found at i:53435 original size:18 final size:19
Alignment explanation
Indices: 53407--53454 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
53397 TAAAAGGAAA
*
53407 ATATATATAAAATCA-ATAT
1 ATATATTTAAAAT-ATATAT
53426 -TATATTTAAAAATATATAT
1 ATATATTT-AAAATATATAT
53445 ATATATTTAA
1 ATATATTTAA
53455 TAAAAACAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 7 0.28
19 11 0.44
20 7 0.28
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATATTTAAAATATATAT
Found at i:56895 original size:20 final size:20
Alignment explanation
Indices: 56872--56926 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
56862 TTCGCGTTGT
* *
56872 ATTTCGCGTTACGATTTTTC
1 ATTTCGCGTTGCGATTTTCC
56892 ATTTCGCGTTGCGATTTTCC
1 ATTTCGCGTTGCGATTTTCC
*
56912 AGTTCGCGTTGCGAT
1 ATTTCGCGTTGCGAT
56927 AGTCTACAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.44
Consensus pattern (20 bp):
ATTTCGCGTTGCGATTTTCC
Found at i:56944 original size:22 final size:22
Alignment explanation
Indices: 56911--56970 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
56901 TGCGATTTTC
*
56911 CAGTTCGCGTTGCGATAGTCTA
1 CAGTTCTCGTTGCGATAGTCTA
* *
56933 CAGTTGTTGTTGCGATAGTCTA
1 CAGTTCTCGTTGCGATAGTCTA
56955 CAGTTCTCGTTGCGAT
1 CAGTTCTCGTTGCGAT
56971 TTTCCAAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.17, C:0.20, G:0.27, T:0.37
Consensus pattern (22 bp):
CAGTTCTCGTTGCGATAGTCTA
Found at i:57750 original size:22 final size:22
Alignment explanation
Indices: 57725--57776 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
57715 AATTTGGAAA
57725 ATCGCAACAACAACTGTAGACT
1 ATCGCAACAACAACTGTAGACT
57747 ATCGCAACAACAACTGTAGACT
1 ATCGCAACAACAACTGTAGACT
57769 ATCGCAAC
1 ATCGCAAC
57777 GCGAAATGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.40, C:0.29, G:0.13, T:0.17
Consensus pattern (22 bp):
ATCGCAACAACAACTGTAGACT
Found at i:62670 original size:27 final size:27
Alignment explanation
Indices: 62636--62690 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
62626 AAATCAAAAC
62636 ACAATTGGTACAATAGATCCTACTCAA
1 ACAATTGGTACAATAGATCCTACTCAA
62663 ACAATTGGTACAATAGATCCTACTCAA
1 ACAATTGGTACAATAGATCCTACTCAA
62690 A
1 A
62691 TTACAACTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.25
Consensus pattern (27 bp):
ACAATTGGTACAATAGATCCTACTCAA
Found at i:64558 original size:30 final size:30
Alignment explanation
Indices: 64515--64580 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
64505 TTTTTTAGAC
* * * * *
64515 ATATGCTATATCACTCATAGTAGTGACTTA
1 ATATGTTAGATCACTCAAAATAATGACTTA
*
64545 ATATGTTAGATCACTCAAAATAATGATTTA
1 ATATGTTAGATCACTCAAAATAATGACTTA
64575 ATATGT
1 ATATGT
64581 GTCACATCAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (30 bp):
ATATGTTAGATCACTCAAAATAATGACTTA
Found at i:64914 original size:15 final size:14
Alignment explanation
Indices: 64891--64923 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
64881 TCATCAACAC
64891 AAAAAAATATTATT
1 AAAAAAATATTATT
64905 AAAAATAATATTATT
1 AAAAA-AATATTATT
64920 AAAA
1 AAAA
64924 CTATTCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAAAAATATTATT
Found at i:74737 original size:28 final size:28
Alignment explanation
Indices: 74706--74761 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
74696 AAAACTAAGA
74706 ACCAACCAAATACAGTAAAAGGCTTCTG
1 ACCAACCAAATACAGTAAAAGGCTTCTG
74734 ACCAACCAAATACAGTAAAAGGCTTCTG
1 ACCAACCAAATACAGTAAAAGGCTTCTG
74762 CCACTCTGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.25, G:0.14, T:0.18
Consensus pattern (28 bp):
ACCAACCAAATACAGTAAAAGGCTTCTG
Found at i:80256 original size:24 final size:23
Alignment explanation
Indices: 80224--80270 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
80214 ATCCTGCGTC
*
80224 TTTCCATCACCAGTGACGGTAGTT
1 TTTCCATCACCACTGAC-GTAGTT
80248 TTTCCATCACCACTGACGTAGTT
1 TTTCCATCACCACTGACGTAGTT
80271 AAATTTAAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (23 bp):
TTTCCATCACCACTGACGTAGTT
Found at i:85700 original size:41 final size:41
Alignment explanation
Indices: 85503--85693 Score: 217
Period size: 40 Copynumber: 4.7 Consensus size: 41
85493 CTATTTGGTG
* **
85503 GTTTATATATAAACGCCACTAAAGTACGAGTATTTCTCGGC
1 GTTTATATAAAAACGCCACTAAAGTACGAGTATTTAGCGGC
85544 GTTTATATAAAAACG-CACTAAAGTACGAGTATTTAGCGGC
1 GTTTATATAAAAACGCCACTAAAGTACGAGTATTTAGCGGC
* * * * *
85584 GGTTATATAAAAACGCCACTAAAATATGAGTATTTACCGAC
1 GTTTATATAAAAACGCCACTAAAGTACGAGTATTTAGCGGC
* * * * *
85625 GTTT-TTTAAAAAAAGCCACGAAAGTAC-AATATTTAGCGTC
1 GTTTATAT-AAAAACGCCACTAAAGTACGAGTATTTAGCGGC
* *
85665 GTTTAGATAAAAGCGCCACTAAAGTACGA
1 GTTTATATAAAAACGCCACTAAAGTACGA
85694 AAATTTACTG
Statistics
Matches: 124, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
40 69 0.56
41 55 0.44
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (41 bp):
GTTTATATAAAAACGCCACTAAAGTACGAGTATTTAGCGGC
Found at i:85700 original size:81 final size:81
Alignment explanation
Indices: 85503--85721 Score: 230
Period size: 81 Copynumber: 2.7 Consensus size: 81
85493 CTATTTGGTG
* * *
85503 GTTTATATATAAACGCCACTAAAGTACGAGTATTT-CTCGGCG-TTTATATAAAAACGCACTAAA
1 GTTTATATA-AAACGCCACTAAAGTACGAGTATTTAC-CGGCGTTTTTTAAAAAAACGCACGAAA
*
85566 GTACGAGTATTTAGCGGC
64 GTACGAATATTTAGCGGC
* * * *
85584 GGTTATATAAAAACGCCACTAAAATATGAGTATTTACCGACGTTTTTTAAAAAAA-GCCACGAAA
1 GTTTATAT-AAAACGCCACTAAAGTACGAGTATTTACCGGCGTTTTTTAAAAAAACG-CACGAAA
*
85648 GTAC-AATATTTAGCGTC
64 GTACGAATATTTAGCGGC
* ** * *
85665 GTTTAGATAAAAGCGCCACTAAAGTACGAAAATTTACTGGCGCTTTTTTAAGAAAAC
1 GTTTATATAAAA-CGCCACTAAAGTACGAGTATTTACCGGCG-TTTTTTAAAAAAAC
85722 CCGTATTTAT
Statistics
Matches: 113, Mismatches: 18, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
80 4 0.04
81 75 0.66
82 34 0.30
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (81 bp):
GTTTATATAAAACGCCACTAAAGTACGAGTATTTACCGGCGTTTTTTAAAAAAACGCACGAAAGT
ACGAATATTTAGCGGC
Done.