Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008901.1 Hibiscus syriacus cultivar Beakdansim tig00112179_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: 58422
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Found at i:386 original size:18 final size:18
Alignment explanation
Indices: 363--404 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
353 AGCATTATCC
*
363 AATAAACTTCACATCCAT
1 AATAAACTTCAAATCCAT
*
381 AATAAACTTGAAATCCAT
1 AATAAACTTCAAATCCAT
399 AATAAA
1 AATAAA
405 AACTTGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.52, C:0.19, G:0.02, T:0.26
Consensus pattern (18 bp):
AATAAACTTCAAATCCAT
Found at i:409 original size:20 final size:20
Alignment explanation
Indices: 375--426 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
365 TAAACTTCAC
375 ATCCATAAT--AAACTTGAA
1 ATCCATAATAAAAACTTGAA
393 ATCCATAATAAAAACTTGAA
1 ATCCATAATAAAAACTTGAA
413 ATCCCAATAATAAA
1 AT-CC-ATAATAAA
427 TCAAAGTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.30
20 11 0.37
21 2 0.07
22 8 0.27
ACGTcount: A:0.54, C:0.17, G:0.04, T:0.25
Consensus pattern (20 bp):
ATCCATAATAAAAACTTGAA
Found at i:4511 original size:41 final size:40
Alignment explanation
Indices: 4449--4637 Score: 213
Period size: 41 Copynumber: 4.7 Consensus size: 40
4439 AATGCCATTA
* *
4449 TATGAGTCATATTA-CGGCGTTTATAGAAAAACGCTACTAAAG
1 TATGAGTC-T-TTAGCGGCGTTTGTATAAAAACGC-ACTAAAG
*
4491 TATGAGTCTTTAGCGGCGTTTGTCTAAAAACGCCACTAAAG
1 TATGAGTCTTTAGCGGCGTTTGTATAAAAACG-CACTAAAG
* * *
4532 TACGAGTCTTTAGC-GCCTTTGTCTAAAAACGCACTAAAG
1 TATGAGTCTTTAGCGGCGTTTGTATAAAAACGCACTAAAG
*
4571 TATGAGT-TTATAGCGGCGTTTGTACAAAAACGACACTAAAG
1 TATGAGTCTT-TAGCGGCGTTTGTATAAAAACG-CACTAAAG
* * *
4612 TACGAGTCTTTAGTGGCGTTTATATA
1 TATGAGTCTTTAGCGGCGTTTGTATA
4638 TAAAGTACAG
Statistics
Matches: 128, Mismatches: 13, Indels: 13
0.83 0.08 0.08
Matches are distributed among these distances:
38 2 0.02
39 18 0.14
40 33 0.26
41 64 0.50
42 11 0.09
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (40 bp):
TATGAGTCTTTAGCGGCGTTTGTATAAAAACGCACTAAAG
Found at i:4568 original size:80 final size:81
Alignment explanation
Indices: 4475--4624 Score: 252
Period size: 80 Copynumber: 1.9 Consensus size: 81
4465 GCGTTTATAG
*
4475 AAAAACGCTACTAAAGTATGAGTCTT-TAGCGGCGTTTGT-CTAAAAACGCCACTAAAGTACGAG
1 AAAAACGCTACTAAAGTATGAGT-TTATAGCGGCGTTTGTAC-AAAAACGACACTAAAGTACGAG
4538 TCTTTAGCGCCTTTGTCT
64 TCTTTAGCGCCTTTGTCT
4556 AAAAACGC-ACTAAAGTATGAGTTTATAGCGGCGTTTGTACAAAAACGACACTAAAGTACGAGTC
1 AAAAACGCTACTAAAGTATGAGTTTATAGCGGCGTTTGTACAAAAACGACACTAAAGTACGAGTC
4620 TTTAG
66 TTTAG
4625 TGGCGTTTAT
Statistics
Matches: 66, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
79 2 0.03
80 55 0.83
81 9 0.14
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (81 bp):
AAAAACGCTACTAAAGTATGAGTTTATAGCGGCGTTTGTACAAAAACGACACTAAAGTACGAGTC
TTTAGCGCCTTTGTCT
Found at i:11273 original size:13 final size:13
Alignment explanation
Indices: 11250--11288 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
11240 AATGACGCGC
*
11250 AATGAGCGTCATA
1 AATGCGCGTCATA
*
11263 AATGCGTGTCATA
1 AATGCGCGTCATA
11276 AATGCGCGTCATA
1 AATGCGCGTCATA
11289 GATTTATGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:11337 original size:99 final size:97
Alignment explanation
Indices: 11173--11349 Score: 228
Period size: 99 Copynumber: 1.8 Consensus size: 97
11163 CACAATGTAA
* ** * **
11173 GTCATAAATGCGTGTCATAAATTATGACACACAAATGTTTGTCTTCTTTATTTATGACGGGGGCT
1 GTCATAAATGCGCGTCATAAATTATGACACACAAATGCGTGTCATCTAGATTTATGACGGGGGCT
11238 TCAATGACGCGCAATGAGCGTCATAAATGCGT
66 TCAATGACGCGCAATGAGCGTCATAAATGCGT
* * * * *
11270 GTCATAAATGCGCGTCATAGATTTATGACGCACAATTGCGTGTCATCTGAGATTTATGTCGGTGG
1 GTCATAAATGCGCGTCATA-AATTATGACACACAAATGCGTGTCATCT-AGATTTATGACGGGGG
*
11335 CTTTAATGACGCGCA
64 CTTCAATGACGCGCA
11350 TTTGTGTGTC
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
97 18 0.27
98 22 0.33
99 26 0.39
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (97 bp):
GTCATAAATGCGCGTCATAAATTATGACACACAAATGCGTGTCATCTAGATTTATGACGGGGGCT
TCAATGACGCGCAATGAGCGTCATAAATGCGT
Found at i:12247 original size:19 final size:20
Alignment explanation
Indices: 12206--12247 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
12196 ATTAGTTTCA
* **
12206 ATTTAATATATATATAATGT
1 ATTTAATATATAAATAAAAT
12226 ATTTAA-ATATAAATAAAAT
1 ATTTAATATATAAATAAAAT
12245 ATT
1 ATT
12248 ATATTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
ATTTAATATATAAATAAAAT
Found at i:18647 original size:5 final size:5
Alignment explanation
Indices: 18637--18661 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
18627 ATAAGTAGAT
18637 GAAGA GAAGA GAAGA GAAGA GAAGA
1 GAAGA GAAGA GAAGA GAAGA GAAGA
18662 AGACAAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (5 bp):
GAAGA
Found at i:24971 original size:13 final size:13
Alignment explanation
Indices: 24953--24979 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
24943 TGGTTAAGGC
24953 AGTATCGATACTT
1 AGTATCGATACTT
24966 AGTATCGATACTT
1 AGTATCGATACTT
24979 A
1 A
24980 AGGATGAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (13 bp):
AGTATCGATACTT
Found at i:28666 original size:70 final size:70
Alignment explanation
Indices: 28575--28827 Score: 416
Period size: 70 Copynumber: 3.6 Consensus size: 70
28565 TTTTTTAAAA
* * *
28575 AAAACAATCCCACATGGCTAAGAAACATAGAAGAACATCCTAAAAGTTTAAAGAGTAAAAGTATG
1 AAAACAATCCCACATGGCTAAGAAACATAGAAGAGCATCCCAAAAGTTTAAAGAGTAAAAATATG
28640 AGAAC
66 AGAAC
* * *
28645 AAAACAATCACACATGACTAAGAAACATAGAAGAGCACCCCAAAAGTTTAAAGAGTAAAAATATG
1 AAAACAATCCCACATGGCTAAGAAACATAGAAGAGCATCCCAAAAGTTTAAAGAGTAAAAATATG
28710 AGAAC
66 AGAAC
**
28715 AAAACAATCCCACATGGCTAAGAAACATAGAAGAGCATCCCAAAAGTTTAAAGAACAAAAATATG
1 AAAACAATCCCACATGGCTAAGAAACATAGAAGAGCATCCCAAAAGTTTAAAGAGTAAAAATATG
28780 AGAAC
66 AGAAC
* *
28785 AAAACAATCTCAAATGGCTAAGAAACATAGAAGAGCATCCCAA
1 AAAACAATCCCACATGGCTAAGAAACATAGAAGAGCATCCCAA
28828 CTTACTTCTA
Statistics
Matches: 170, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 170 1.00
ACGTcount: A:0.53, C:0.18, G:0.15, T:0.15
Consensus pattern (70 bp):
AAAACAATCCCACATGGCTAAGAAACATAGAAGAGCATCCCAAAAGTTTAAAGAGTAAAAATATG
AGAAC
Found at i:29348 original size:3 final size:3
Alignment explanation
Indices: 29342--29367 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
29332 ATGAGAAGAG
29342 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
29368 AACCCAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:42365 original size:25 final size:25
Alignment explanation
Indices: 42331--42381 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
42321 GATCGGAAAG
42331 AATGAGCTTTACATAGTCGTTGATC
1 AATGAGCTTTACATAGTCGTTGATC
42356 AATGAGCTTTACATAGTCGTTGATC
1 AATGAGCTTTACATAGTCGTTGATC
42381 A
1 A
42382 CTTTAGGCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (25 bp):
AATGAGCTTTACATAGTCGTTGATC
Found at i:50091 original size:2 final size:2
Alignment explanation
Indices: 50084--50118 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
50074 AGATGCACAT
50084 TA TA 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 TA TA T
50119 GGGTATAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:54426 original size:35 final size:36
Alignment explanation
Indices: 54387--54454 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 36
54377 TAATAACGTA
* * *
54387 TATGGTTTTTTAACGATATGCACCTATA-ATATGTG
1 TATGGTTTTTGAACAACATGCACCTATATATATGTG
*
54422 TATGGTTTTTGAACAACATGCAGCTATATATAT
1 TATGGTTTTTGAACAACATGCACCTATATATAT
54455 ATATATATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 24 0.86
36 4 0.14
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (36 bp):
TATGGTTTTTGAACAACATGCACCTATATATATGTG
Found at i:54565 original size:20 final size:20
Alignment explanation
Indices: 54540--54589 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
54530 TCAGATGCAG
54540 ATGTCTGTATCCCCATAATC
1 ATGTCTGTATCCCCATAATC
54560 ATGTCTGTATCCCCATAATC
1 ATGTCTGTATCCCCATAATC
*
54580 TTGTCTGTAT
1 ATGTCTGTAT
54590 ATGCTGCGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.26, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTCTGTATCCCCATAATC
Found at i:56208 original size:22 final size:23
Alignment explanation
Indices: 56174--56231 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
56164 ATCAAGTACA
* *
56174 ATAACATATTAGGTA-CGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
56196 ATAATATAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
56219 ATAATAAAATAGG
1 ATAATATAATAGG
56232 CATTTAACCG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 13 0.41
23 19 0.59
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.33
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:56302 original size:84 final size:86
Alignment explanation
Indices: 56146--56304 Score: 218
Period size: 84 Copynumber: 1.9 Consensus size: 86
56136 TATGTTATAT
**
56146 CATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTACGCTTATATAATATAATAGGTA
1 CATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTACGCTTATATAATATAATACATA
*
56211 GCGCTTATATAATAAAATAGG
66 GCACTTATATAATAAAATAGG
* *
56232 CATTTAACC-GAAAATATTATC-A-TATAATAACATATTAGGTAGCGCTTATATAATGT-ATACA
1 CATTTAACCAG-AAATATTATCAAGTACAATAACATATTAGGTA-CGCTTATATAATATAATACA
*
56293 TATCACTTATAT
64 TAGCACTTATAT
56305 TTACCTATTT
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
84 31 0.48
85 15 0.23
86 19 0.29
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.34
Consensus pattern (86 bp):
CATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTACGCTTATATAATATAATACATA
GCACTTATATAATAAAATAGG
Done.