Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004527.1 Hibiscus syriacus cultivar Beakdansim tig00009990_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: 54328
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31
Found at i:656 original size:1 final size:1
Alignment explanation
Indices: 647--677 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
637 ACAAAAAAGC
*
647 AAAAGAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
678 GACTCAACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:757 original size:17 final size:17
Alignment explanation
Indices: 702--758 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
692 ATTGGAGTGC
*
702 AAAAAA-AAAAGAAGAAG
1 AAAAAAGAAAAG-TGAAG
* * *
719 AAAAGAAGAAAATTCAAC
1 AAAA-AAGAAAAGTGAAG
737 AAAAAAGAAAAGTGAAG
1 AAAAAAGAAAAGTGAAG
754 AAAAA
1 AAAAA
759 TGCAAAATAC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
17 19 0.61
18 8 0.26
19 4 0.13
ACGTcount: A:0.75, C:0.04, G:0.16, T:0.05
Consensus pattern (17 bp):
AAAAAAGAAAAGTGAAG
Found at i:5347 original size:11 final size:11
Alignment explanation
Indices: 5331--5362 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
5321 TTTTTTCTCT
5331 ATTTAGCTCCA
1 ATTTAGCTCCA
5342 ATTTAGCTCCA
1 ATTTAGCTCCA
5353 ATTTAGCTCC
1 ATTTAGCTCC
5363 CAAGTTGTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.25, C:0.28, G:0.09, T:0.38
Consensus pattern (11 bp):
ATTTAGCTCCA
Found at i:5547 original size:25 final size:23
Alignment explanation
Indices: 5519--5564 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
5509 ATAGCTATAG
*
5519 ATGTAATATGTATATGAATATAACT
1 ATGTAATA-GCATATGAA-ATAACT
*
5544 ATGTTATAGCATATGAAATAA
1 ATGTAATAGCATATGAAATAA
5565 AGCATCATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 8 0.42
25 7 0.37
ACGTcount: A:0.46, C:0.04, G:0.13, T:0.37
Consensus pattern (23 bp):
ATGTAATAGCATATGAAATAACT
Found at i:8473 original size:37 final size:37
Alignment explanation
Indices: 8432--8554 Score: 96
Period size: 38 Copynumber: 3.3 Consensus size: 37
8422 ATTTAGTCTT
8432 TCTTAAGA-TATTTCCCTAGAAACATCAATCTTGACTC
1 TCTTAAGACTATTTCCCTAGAAACATCAATCTT-ACTC
* * *
8469 TCTTAGGACT-TGTAT-CCTAGAAA-ACTAAAT-TTAGTC
1 TCTTAAGACTAT-T-TCCCTAGAAACA-TCAATCTTACTC
*
8505 ATCCTTAAGACTATTTCCCTATAAACATCAATCTTAACTC
1 -T-CTTAAGACTATTTCCCTAGAAACATCAATCTT-ACTC
8545 T-TTCAAGACT
1 TCTT-AAGACT
8555 TGACCCTAGA
Statistics
Matches: 67, Mismatches: 7, Indels: 23
0.69 0.07 0.24
Matches are distributed among these distances:
36 3 0.04
37 15 0.22
38 40 0.60
39 6 0.09
40 3 0.04
ACGTcount: A:0.33, C:0.23, G:0.08, T:0.36
Consensus pattern (37 bp):
TCTTAAGACTATTTCCCTAGAAACATCAATCTTACTC
Found at i:8513 original size:75 final size:75
Alignment explanation
Indices: 8421--8578 Score: 212
Period size: 75 Copynumber: 2.1 Consensus size: 75
8411 TCGAAAAATC
* * * * *
8421 AATTTAGTCTTTCTTAAGA-TATTTCCCTAGAAACATCAATCTTGACTCTCTT-AGGACTTGTAT
1 AATTTAGTCATCCTTAAGACTATTTCCCTAGAAACATCAATCTTAACTCT-TTCAAGACTTG-AC
8484 CCTAGAAAACTA
64 CCTAGAAAACTA
*
8496 AATTTAGTCATCCTTAAGACTATTTCCCTATAAACATCAATCTTAACTCTTTCAAGACTTGACCC
1 AATTTAGTCATCCTTAAGACTATTTCCCTAGAAACATCAATCTTAACTCTTTCAAGACTTGACCC
* *
8561 TAGAAAGCTC
66 TAGAAAACTA
8571 AATTTAGT
1 AATTTAGT
8579 TTACCTAGAA
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
75 38 0.52
76 35 0.48
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (75 bp):
AATTTAGTCATCCTTAAGACTATTTCCCTAGAAACATCAATCTTAACTCTTTCAAGACTTGACCC
TAGAAAACTA
Found at i:9255 original size:131 final size:128
Alignment explanation
Indices: 8900--9400 Score: 403
Period size: 131 Copynumber: 3.9 Consensus size: 128
8890 ATATTTGACC
* * * * * * * **
8900 TTCCTCAAGAGTAATAAAGAAAATCAATCTCGATTCAATCTTCCAT-AAAGAGTAGTGGTGTGAA
1 TTCCTGAAGAGTAGTGAAGCAAATCAACCTCTATTCAATCTTCCTTGAAA-AGTAGTGAAGTGAA
* * * * *
8964 CCAAAGTTTCCAGATGTAATATTTCCTGAAGAGTAGTAG-AGCATATCCC-ATTTCTAGATTTGA
65 TCAAAGTTTCCAGATCTGATA-TTCCTAAAGAGTAG-AGAAGCATATCCCTTTTTCTAGATTTGA
9027 T
128 T
* * *
9028 CTT-CTAGAAGAGTAGTGAAGCAAATCAACCTC-AGTTCAATCTTCTTTGAAGAGTAGTGAAATG
1 -TTCCT-GAAGAGTAGTGAAGCAAATCAACCTCTA-TTCAATCTTCCTTGAAAAGTAGTGAAGTG
* * *
9091 AATAAAAAATTTCCAGATCTGATTTTGCCTAAAGAGTAGAGAAGCATATCCCTTTTTCTAGATTT
63 AAT-CAAAGTTTCCAGATCTGATATT-CCTAAAGAGTAGAGAAGCATATCCCTTTTTCTAGATTT
9156 GAT
126 GAT
* *
9159 ATTCCTGAAGAGTAGTGAAGCAAATTAACCTCTATTCAATCTTCCCTGAAAAGTAGTGAAGTGAA
1 -TTCCTGAAGAGTAGTGAAGCAAATCAACCTCTATTCAATCTTCCTTGAAAAGTAGTGAAGTGAA
** * ** *
9224 TCAAAGTTTTTTAGATATGATATTCCTTAAAGAGTATCG-GAA--A-AAACTTATTTCTCTAGAT
65 TCAAAG-TTTCCAGATCTGATATTCC-TAAAGAGTA--GAGAAGCATATCCCT-TTT-TCTAGAT
9285 TTGACT
124 TTGA-T
** * * * *
9291 TTTTTAAAGAGT-GTCGAAGCAAATCAAACT-TGGTTCAATCTTCCTTGAAGAGTAGTGAAGTGA
1 TTCCTGAAGAGTAGT-GAAGCAAATCAACCTCT-ATTCAATCTTCCTTGAAAAGTAGTGAAGTGA
** * * *
9354 ATCAAAGTTTTTAGATCTGATCTTCCCTAAAGAGTAGTGAAACATAT
64 ATCAAAGTTTCCAGATCTGATATT-CCTAAAGAGTAGAGAAGCATAT
9401 ATTTTTCCAT
Statistics
Matches: 304, Mismatches: 45, Indels: 43
0.78 0.11 0.11
Matches are distributed among these distances:
128 4 0.01
129 55 0.18
130 74 0.24
131 162 0.53
132 8 0.03
133 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (128 bp):
TTCCTGAAGAGTAGTGAAGCAAATCAACCTCTATTCAATCTTCCTTGAAAAGTAGTGAAGTGAAT
CAAAGTTTCCAGATCTGATATTCCTAAAGAGTAGAGAAGCATATCCCTTTTTCTAGATTTGAT
Found at i:9468 original size:126 final size:126
Alignment explanation
Indices: 8920--9489 Score: 371
Period size: 131 Copynumber: 4.4 Consensus size: 126
8910 GTAATAAAGA
* * * *** * ** * *
8920 AAATCAATCTCGATTCAATCTTCCATAAAGAGTAGTGGTGTGAACCAAAGTTTCCAGATGTAATA
1 AAATCAACCTTGATTCAATCTTCCCTAAAGAGTAGTGAAATGAATCAAAGTTTTTAGATCTGATA
* * * *** * *
8985 TTTCCTGAAGAGTAGT-AGAGCATATCCCATTTCTAGATTTGATC-TTCTAGAAGAGTAGTGAAG
66 TTCCCTAAAGAGTAGTGA-AACATAT-ATTTTTCTAGATTTGA-CATTCTTG-A-AGTTGTGAAG
9048 C
126 C
* ** * * * **
9049 AAATCAACC-TCAGTTCAATCTTCTTTGAAGAGTAGTGAAATGAATAAAAAATTTCCAGATCTGA
1 AAATCAACCTTGA-TTCAATCTTCCCTAAAGAGTAGTGAAATGAAT-CAAAGTTTTTAGATCTGA
* * * * * * * *
9113 TTTTGCCTAAAGAGTAGAGAAGCATATCCCTTTTTCTAGATTTGATATTCCTGAAGAGTAGTGAA
64 TATTCCCTAAAGAGTAGTGAAACATAT--ATTTTTCTAGATTTGACATTCTTG-A-AGTTGTGAA
9178 GC
125 GC
* * *
9180 AAATTAACCTCT-ATTCAATCTTCCCTGAAA-AGTAGTGAAGTGAATCAAAGTTTTTTAGATATG
1 AAATCAACCT-TGATTCAATCTTCCCT-AAAGAGTAGTGAAATGAATCAAAG-TTTTTAGATCTG
* * * * * * *
9243 ATATTCCTTAAAGAGTA-TCGGAAA-AAACTTATTTCTCTAGATTTGACTTTTTTAAAGAGTGTC
63 ATATTCCCTAAAGAGTAGT--GAAACATA--TATTTTTCTAGATTTGACATTCTTGAAG-TTGT-
9306 GAAGC
122 GAAGC
* * * * * *
9311 AAATCAAACTTGGTTCAATCTTCCTTGAAGAGTAGTGAAGTGAATCAAAGTTTTTAGATCTGATC
1 AAATCAACCTTGATTCAATCTTCCCTAAAGAGTAGTGAAATGAATCAAAGTTTTTAGATCTGATA
* * * * *
9376 TTCCCTAAAGAGTAGTGAAACATATATTTTTCCATATTTCACCTTCTTGAAGTTGTGAAGA
66 TTCCCTAAAGAGTAGTGAAACATATATTTTTCTAGATTTGACATTCTTGAAGTTGTGAAGC
** * *
9437 AAATCAACCTTGATTCAATCTTATCTAAAGAGTGGTGAAATAAATCAAAGTTT
1 AAATCAACCTTGATTCAATCTTCCCTAAAGAGTAGTGAAATGAATCAAAGTTT
9490 CCCGATATGA
Statistics
Matches: 347, Mismatches: 75, Indels: 41
0.75 0.16 0.09
Matches are distributed among these distances:
126 48 0.14
127 3 0.01
128 22 0.06
129 39 0.11
130 72 0.21
131 155 0.45
132 6 0.02
133 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34
Consensus pattern (126 bp):
AAATCAACCTTGATTCAATCTTCCCTAAAGAGTAGTGAAATGAATCAAAGTTTTTAGATCTGATA
TTCCCTAAAGAGTAGTGAAACATATATTTTTCTAGATTTGACATTCTTGAAGTTGTGAAGC
Found at i:10884 original size:2 final size:2
Alignment explanation
Indices: 10877--10914 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
10867 TTGTTTGAGT
10877 TA TA TA TA TA T- 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 TA TA TA TA T
10915 TATTGCTTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:11060 original size:4 final size:4
Alignment explanation
Indices: 11053--11116 Score: 121
Period size: 4 Copynumber: 16.2 Consensus size: 4
11043 TGCGTGTGTG
11053 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA -GTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
11100 TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA T
11117 ATGTGTGTGA
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 3 0.05
4 56 0.95
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:15273 original size:22 final size:22
Alignment explanation
Indices: 15245--15296 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
15235 ATCTGACCCC
15245 GAGTATTGATACTCATTTAAAT
1 GAGTATTGATACTCATTTAAAT
15267 GAGTATTGATACTCATTTAAAT
1 GAGTATTGATACTCATTTAAAT
15289 GAGTATTG
1 GAGTATTG
15297 GTAATCTTAC
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:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (22 bp):
GAGTATTGATACTCATTTAAAT
Found at i:15405 original size:20 final size:20
Alignment explanation
Indices: 15345--15405 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
15335 ATCAATGCTA
* *
15345 TAAGAACAATATTGATATTG
1 TAAGAACAATATCGATACTG
15365 TGGAAGAACAATATC-AGTACTG
1 T--AAGAACAATATCGA-TACTG
15387 TAAGAACAATATCGATACT
1 TAAGAACAATATCGATACT
15406 AAATGCATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
22 16 0.46
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.28
Consensus pattern (20 bp):
TAAGAACAATATCGATACTG
Found at i:19398 original size:24 final size:24
Alignment explanation
Indices: 19345--19398 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
19335 AAAGAAGAAC
*
19345 ATTTTCATCTTTCAATTTTGAAAT
1 ATTTTTATCTTTCAATTTTGAAAT
19369 ATTTTTATCTTTCAATTTTGAAAT
1 ATTTTTATCTTTCAATTTTGAAAT
19393 ATTTTT
1 ATTTTT
19399 CTTATGCATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.28, C:0.09, G:0.04, T:0.59
Consensus pattern (24 bp):
ATTTTTATCTTTCAATTTTGAAAT
Found at i:21521 original size:24 final size:24
Alignment explanation
Indices: 21473--21521 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
21463 ATATTCGAAC
* *
21473 AATTAAATCGAATATAAACTTAAA
1 AATTAAATCGAAAATAAACTCAAA
* *
21497 AATTGAATCGAAAATAATCTCAAA
1 AATTAAATCGAAAATAAACTCAAA
21521 A
1 A
21522 TTTCTTTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.57, C:0.10, G:0.06, T:0.27
Consensus pattern (24 bp):
AATTAAATCGAAAATAAACTCAAA
Found at i:45383 original size:6 final size:6
Alignment explanation
Indices: 45372--45400 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
45362 CCCACTGGTA
45372 ATTTTT ATTTTT ATTTTT ATTTTT ATTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTT
45401 GAAAATAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:46198 original size:12 final size:10
Alignment explanation
Indices: 46157--46197 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
46147 TTTATCACAC
46157 CAAATTCTCT
1 CAAATTCTCT
46167 CAAATTCTCT
1 CAAATTCTCT
46177 -AAATTTCTCT
1 CAAA-TTCTCT
*
46187 CAAATACTCT
1 CAAATTCTCT
46197 C
1 C
46198 TTTTTAAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:46459 original size:111 final size:111
Alignment explanation
Indices: 46321--46542 Score: 363
Period size: 111 Copynumber: 2.0 Consensus size: 111
46311 TGAAAATCAT
* * *
46321 ATATCTCTACACTTTGCTGATACGGTAACATTTTAATATTTTAATTTAATTTAAATTATTAATAA
1 ATATCTCGACACTTTACTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAATAA
* * *
46386 TATTTAGTTGATTGATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAAAATTAA
* * *
46432 ATATCTCGACACTTTACTGATATGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAATAA
46497 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAAAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAAAATTAA
46543 TTTTTGTAGT
Statistics
Matches: 102, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
111 102 1.00
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTACTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAATAA
TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAAAATTAA
Found at i:48323 original size:15 final size:15
Alignment explanation
Indices: 48298--48341 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
48288 GCTTAGGACA
48298 ATGACGATGACGATG
1 ATGACGATGACGATG
* *
48313 ACGATGATGACGATG
1 ATGACGATGACGATG
* *
48328 GTGACGACGACGAT
1 ATGACGATGACGAT
48342 AACAATGATG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.32, C:0.16, G:0.34, T:0.18
Consensus pattern (15 bp):
ATGACGATGACGATG
Found at i:52312 original size:15 final size:15
Alignment explanation
Indices: 52289--52318 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52279 TAGCATATAA
52289 ATATAATATTAATAT
1 ATATAATATTAATAT
*
52304 ATATTATATTAATAT
1 ATATAATATTAATAT
52319 TTTTATTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATAATATTAATAT
Done.