Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006757.1 Hibiscus syriacus cultivar Beakdansim tig00017044_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: 62008
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:2345 original size:46 final size:46
Alignment explanation
Indices: 2281--2528 Score: 154
Period size: 46 Copynumber: 5.4 Consensus size: 46
2271 ATTCATGTTT
* * *
2281 ATAATGCA-CCATTATGCATTTTCAATTATAGCAT-ACTTTTATGATG
1 ATAATGCACCCA-TATGCATTTTCAACTATAGCATCA-TTTCATGACG
* * * *
2327 ATAATGCACCCGTGTGCA-TTTCAACTATGGCATCATTTCATGCCG
1 ATAATGCACCCATATGCATTTTCAACTATAGCATCATTTCATGACG
* * * * * *
2372 ATAATGCACCCATATGCATTATT--ATTTTGTGCATCCTTTTATGCCG
1 ATAATGCACCCATATGCATT-TTCAACTAT-AGCATCATTTCATGACG
* * * * * *
2418 ATAATGCACCCATATGCATTATT--ATTTTGGTATCCTTTCATGCCG
1 ATAATGCACCCATATGCATT-TTCAACTATAGCATCATTTCATGACG
* * * * *
2463 ATAATGCACCCATATGCATTATT--ATTTTGGGCATCTTTTCATGTCG
1 ATAATGCACCCATATGCATT-TTCAACTAT-AGCATCATTTCATGACG
2509 ATAATGCACCCATATGCATT
1 ATAATGCACCCATATGCATT
2529 ATTATTTTGT
Statistics
Matches: 176, Mismatches: 20, Indels: 12
0.85 0.10 0.06
Matches are distributed among these distances:
45 81 0.46
46 91 0.52
47 4 0.02
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (46 bp):
ATAATGCACCCATATGCATTTTCAACTATAGCATCATTTCATGACG
Found at i:2376 original size:45 final size:45
Alignment explanation
Indices: 2354--2537 Score: 305
Period size: 46 Copynumber: 4.0 Consensus size: 45
2344 ATTTCAACTA
*
2354 TGGCATCATTTCATGCCGATAATGCACCCATATGCATTATTATTT
1 TGGCATCCTTTCATGCCGATAATGCACCCATATGCATTATTATTT
*
2399 TGTGCATCCTTTTATGCCGATAATGCACCCATATGCATTATTATTT
1 TG-GCATCCTTTCATGCCGATAATGCACCCATATGCATTATTATTT
*
2445 TGGTATCCTTTCATGCCGATAATGCACCCATATGCATTATTATTT
1 TGGCATCCTTTCATGCCGATAATGCACCCATATGCATTATTATTT
* *
2490 TGGGCATCTTTTCATGTCGATAATGCACCCATATGCATTATTATTT
1 T-GGCATCCTTTCATGCCGATAATGCACCCATATGCATTATTATTT
2536 TG
1 TG
2538 TTCATTCATT
Statistics
Matches: 130, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
45 45 0.35
46 85 0.65
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.40
Consensus pattern (45 bp):
TGGCATCCTTTCATGCCGATAATGCACCCATATGCATTATTATTT
Found at i:2411 original size:91 final size:89
Alignment explanation
Indices: 2311--2530 Score: 289
Period size: 91 Copynumber: 2.4 Consensus size: 89
2301 TTCAATTATA
* *
2311 GCATACTTTTATGATGATAATGCACCCGTGTGCATT-TCAACTATGGCATCATTTCATGCCGATA
1 GCAT-CTTTTATG-TGATAATGCACCCATATGCATTAT-AACTATGGCATCATTTCATGCCGATA
*
2375 ATGCACCCATATGCATTATTATTTTGT
63 ATGCACCCATATGCATTATTATTTTGG
* * * * * *
2402 GCATCCTTTTATGCCGATAATGCACCCATATGCATTATTATTTTGGTATCCTTTCATGCCGATAA
1 GCAT-CTTTTATG-TGATAATGCACCCATATGCATTATAACTATGGCATCATTTCATGCCGATAA
2467 TGCACCCATATGCATTATTATTTTGG
64 TGCACCCATATGCATTATTATTTTGG
2493 GCATCTTTTCATGTCGATAATGCACCCATATGCATTAT
1 GCATCTTTT-ATGT-GATAATGCACCCATATGCATTAT
2531 TATTTTGTTC
Statistics
Matches: 114, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
90 5 0.04
91 108 0.95
92 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (89 bp):
GCATCTTTTATGTGATAATGCACCCATATGCATTATAACTATGGCATCATTTCATGCCGATAATG
CACCCATATGCATTATTATTTTGG
Found at i:2531 original size:91 final size:91
Alignment explanation
Indices: 2362--2537 Score: 318
Period size: 91 Copynumber: 1.9 Consensus size: 91
2352 TATGGCATCA
*
2362 TTTCATGCCGATAATGCACCCATATGCATTATTATTTTGTGCATCCTTTTATGCCGATAATGCAC
1 TTTCATGCCGATAATGCACCCATATGCATTATTATTTTGGGCATCCTTTTATGCCGATAATGCAC
2427 CCATATGCATTATTATTTTGGTATCC
66 CCATATGCATTATTATTTTGGTATCC
*
2453 TTTCATGCCGATAATGCACCCATATGCATTATTATTTTGGGCAT-CTTTTCATGTCGATAATGCA
1 TTTCATGCCGATAATGCACCCATATGCATTATTATTTTGGGCATCCTTTT-ATGCCGATAATGCA
2517 CCCATATGCATTATTATTTTG
65 CCCATATGCATTATTATTTTG
2538 TTCATTCATT
Statistics
Matches: 82, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
90 5 0.06
91 77 0.94
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (91 bp):
TTTCATGCCGATAATGCACCCATATGCATTATTATTTTGGGCATCCTTTTATGCCGATAATGCAC
CCATATGCATTATTATTTTGGTATCC
Found at i:4679 original size:32 final size:31
Alignment explanation
Indices: 4628--4745 Score: 150
Period size: 32 Copynumber: 3.8 Consensus size: 31
4618 GTCCCTTAGA
4628 ACATAGGT-A-TCTGTCCATATGTCTCAAAAG
1 ACATAGGTAATTCTGTCCATATGTC-CAAAAG
* *
4658 ACATAGGTAATTCTGTACATATATCCTAAAAG
1 ACATAGGTAATTCTGTCCATATGTCC-AAAAG
* *
4690 ACATAGGTAATTCTGTCCATATCTCCCGAAAG
1 ACATAGGTAATTCTGTCCATATGT-CCAAAAG
*
4722 ACATAGGTAATTATGTCCATATGT
1 ACATAGGTAATTCTGTCCATATGT
4746 TCCGTAGAAC
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
30 8 0.10
31 2 0.03
32 65 0.84
33 2 0.03
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (31 bp):
ACATAGGTAATTCTGTCCATATGTCCAAAAG
Found at i:4758 original size:64 final size:61
Alignment explanation
Indices: 4624--4763 Score: 165
Period size: 64 Copynumber: 2.2 Consensus size: 61
4614 ATGTGTCCCT
* * *
4624 TAGAACATAGGT-ATCTGTCCATATGTCTCAAAAGACATAGGTAATTCTGTACATATATCC
1 TAGAACATAGGTAATCTGTCCATATCTCCCAAAAGACATAGGTAATTATGTACATATATCC
* * * *
4684 TAAAAGACATAGGTAATTCTGTCCATATCTCCCGAAAGACATAGGTAATTATGTCCATATGTTCC
1 T-AGA-ACATAGGTAA-TCTGTCCATATCTCCCAAAAGACATAGGTAATTATGTACATAT-ATCC
4749 GTAGAACATAGGTAA
1 -TAGAACATAGGTAA
4764 ACCCTCGACT
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
60 1 0.02
61 2 0.03
62 8 0.12
63 1 0.02
64 48 0.73
65 5 0.08
66 1 0.02
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (61 bp):
TAGAACATAGGTAATCTGTCCATATCTCCCAAAAGACATAGGTAATTATGTACATATATCC
Found at i:8332 original size:32 final size:32
Alignment explanation
Indices: 8218--8387 Score: 159
Period size: 32 Copynumber: 5.4 Consensus size: 32
8208 ACCTCGAAAG
* * *
8218 CTGTCCATAGGTCTCG-AAGAACCTAGGTAA-A
1 CTGTCCATATGTCTCGAAAG-ACATAGGTAATT
* *** *
8249 CGGTCCATATGT-TCCTTAGAACATAGGT-ATA
1 CTGTCCATATGTCTCGAAAG-ACATAGGTAATT
*
8280 CTGTCCATATGTCTCAAAAGACATAGGTAATT
1 CTGTCCATATGTCTCGAAAGACATAGGTAATT
* * * *
8312 TTGTCCATATATCTTGAAAGACATATGTAATT
1 CTGTCCATATGTCTCGAAAGACATAGGTAATT
*
8344 CTGTCCATATGTCCCGAAAGACATAGGTAATT
1 CTGTCCATATGTCTCGAAAGACATAGGTAATT
*
8376 CTGTTCATATGT
1 CTGTCCATATGT
8388 TCCGTAGAAC
Statistics
Matches: 114, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
30 3 0.03
31 40 0.35
32 71 0.62
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (32 bp):
CTGTCCATATGTCTCGAAAGACATAGGTAATT
Found at i:8400 original size:32 final size:32
Alignment explanation
Indices: 8251--8405 Score: 122
Period size: 32 Copynumber: 4.9 Consensus size: 32
8241 TAGGTAAACG
* *
8251 GTCCATATGTTCCTTAGAACATAGGT-ATACT
1 GTCCATATGTTCCGTAGAACATAGGTAATTCT
*** *
8282 GTCCATATGTCTCAAAAG-ACATAGGTAATTTT
1 GTCCATATGT-TCCGTAGAACATAGGTAATTCT
* * * *
8314 GTCCATAT-AT-CTTGAAAGACATATGTAATTCT
1 GTCCATATGTTCCGT-AGA-ACATAGGTAATTCT
* *
8346 GTCCATATGTCCCG-AAAGACATAGGTAATTCT
1 GTCCATATGTTCCGTAGA-ACATAGGTAATTCT
*
8378 GTTCATATGTTCCGTAGAACATAGGTAA
1 GTCCATATGTTCCGTAGAACATAGGTAA
8406 ACCCTCGACT
Statistics
Matches: 97, Mismatches: 19, Indels: 15
0.74 0.15 0.11
Matches are distributed among these distances:
30 2 0.02
31 18 0.19
32 74 0.76
33 2 0.02
34 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (32 bp):
GTCCATATGTTCCGTAGAACATAGGTAATTCT
Found at i:8400 original size:64 final size:64
Alignment explanation
Indices: 8251--8405 Score: 190
Period size: 64 Copynumber: 2.4 Consensus size: 64
8241 TAGGTAAACG
* *
8251 GTCCATATGTTCCTTAGAACATAGGT-ATACTGTCCATATGTCTCAAAAGACATAGGTAATTTT
1 GTCCATATGTTCCTTAGAACATAGGTAATACTGTCCATATGTCCCAAAAGACATAGGTAATTCT
* * * * *
8314 GTCCATAT-AT-CTTGAAAGACATATGTAATTCTGTCCATATGTCCCGAAAGACATAGGTAATTC
1 GTCCATATGTTCCTT-AGA-ACATAGGTAATACTGTCCATATGTCCCAAAAGACATAGGTAATTC
8377 T
64 T
* *
8378 GTTCATATGTTCCGTAGAACATAGGTAA
1 GTCCATATGTTCCTTAGAACATAGGTAA
8406 ACCCTCGACT
Statistics
Matches: 75, Mismatches: 12, Indels: 9
0.78 0.12 0.09
Matches are distributed among these distances:
61 3 0.04
62 3 0.04
63 15 0.20
64 49 0.65
65 3 0.04
66 2 0.03
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (64 bp):
GTCCATATGTTCCTTAGAACATAGGTAATACTGTCCATATGTCCCAAAAGACATAGGTAATTCT
Found at i:25630 original size:17 final size:17
Alignment explanation
Indices: 25593--25630 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
25583 TAAATAAACT
*
25593 AATTTAAATTTAAAAAT
1 AATTTAAATTTAAAAAA
25610 AATTTAAA-TTAAAGAAA
1 AATTTAAATTTAAA-AAA
25627 AATT
1 AATT
25631 AAACATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (17 bp):
AATTTAAATTTAAAAAA
Found at i:25705 original size:17 final size:17
Alignment explanation
Indices: 25685--25717 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
25675 TATATAGATT
25685 TAAAACTAAA-AAAACAG
1 TAAAA-TAAACAAAACAG
25702 TAAAATAAACAAAACA
1 TAAAATAAACAAAACA
25718 AAACAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.73, C:0.12, G:0.03, T:0.12
Consensus pattern (17 bp):
TAAAATAAACAAAACAG
Found at i:32425 original size:45 final size:45
Alignment explanation
Indices: 32361--32452 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
32351 GATAACAATT
32361 TTTCAGAGTCATTTAGGTGCTAGATATAAATCTATTATTTCATTG
1 TTTCAGAGTCATTTAGGTGCTAGATATAAATCTATTATTTCATTG
32406 TTTCAGAGTCATTTAGGTGCTAGATATAAATCTATTATTTCATTG
1 TTTCAGAGTCATTTAGGTGCTAGATATAAATCTATTATTTCATTG
32451 TT
1 TT
32453 GGAGGATATG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.46
Consensus pattern (45 bp):
TTTCAGAGTCATTTAGGTGCTAGATATAAATCTATTATTTCATTG
Found at i:36750 original size:21 final size:21
Alignment explanation
Indices: 36698--36750 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
36688 ATACGTGACC
* *
36698 ATTTAAATCCCATGCTGAATG
1 ATTTGAATCCTATGCTGAATG
* *
36719 ATTTGAATCCTATGTTGGATG
1 ATTTGAATCCTATGCTGAATG
36740 ATTTGAATCCT
1 ATTTGAATCCT
36751 GGAATTGTGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (21 bp):
ATTTGAATCCTATGCTGAATG
Found at i:38302 original size:45 final size:45
Alignment explanation
Indices: 38234--38337 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 45
38224 ATGCACATGA
*** * *
38234 AGTGTATCGATGCATTTCTTTAAAATAAAAACATCAAATGTCATT
1 AGTGTATCGATGCACCCCCTTAAAATAAAAACATCAAATGACATT
* * *
38279 AGTGTATCGATGCACCCCCTTAAAATACAAACATCGAATGAGATT
1 AGTGTATCGATGCACCCCCTTAAAATAAAAACATCAAATGACATT
38324 -GATGTATCGATGCA
1 AG-TGTATCGATGCA
38338 TAGATTGTGC
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
44 1 0.02
45 49 0.98
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (45 bp):
AGTGTATCGATGCACCCCCTTAAAATAAAAACATCAAATGACATT
Found at i:38353 original size:19 final size:20
Alignment explanation
Indices: 38319--38356 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
38309 ACATCGAATG
*
38319 AGATTGATGTATCGATGCAT
1 AGATTGATGCATCGATGCAT
38339 AGATTG-TGCATCGATGCA
1 AGATTGATGCATCGATGCA
38357 CCCGTCAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (20 bp):
AGATTGATGCATCGATGCAT
Found at i:42958 original size:40 final size:37
Alignment explanation
Indices: 42884--42974 Score: 112
Period size: 40 Copynumber: 2.4 Consensus size: 37
42874 AGTCAAATAT
* *
42884 TACACCGTAGTGTTGAGGTCGAGCCTTGCTCACCTAATAA
1 TACACCGTAGTGTTGAGGTCGAGCCATGCCCACCT--T-A
*
42924 TGCACCGTAGTGTTGAGGTC-AGGCCATGCCCACCTTA
1 TACACCGTAGTGTTGAGGTCGA-GCCATGCCCACCTTA
42961 TACACCGTAGTGTT
1 TACACCGTAGTGTT
42975 CTATATCGTG
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
37 14 0.30
38 1 0.02
39 1 0.02
40 30 0.65
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.27
Consensus pattern (37 bp):
TACACCGTAGTGTTGAGGTCGAGCCATGCCCACCTTA
Found at i:48551 original size:24 final size:22
Alignment explanation
Indices: 48510--48556 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 22
48500 ATGGGATATT
*
48510 TATTTTATTTTATTTTACTCGA
1 TATTTTATTTTATATTACTCGA
48532 TATTTTATGGTTTATATTACTCGA
1 TATTTTAT--TTTATATTACTCGA
48556 T
1 T
48557 TGAGATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.36
24 14 0.64
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.60
Consensus pattern (22 bp):
TATTTTATTTTATATTACTCGA
Found at i:49763 original size:20 final size:20
Alignment explanation
Indices: 49717--49755 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
49707 ATAAGTTTCC
*
49717 ATAGCTTTGGACTTCATTTG
1 ATAGCTTTAGACTTCATTTG
49737 ATAGCTTTAGACTTCATTT
1 ATAGCTTTAGACTTCATTT
49756 ACTAGCTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (20 bp):
ATAGCTTTAGACTTCATTTG
Found at i:54894 original size:23 final size:23
Alignment explanation
Indices: 54865--54936 Score: 90
Period size: 23 Copynumber: 3.0 Consensus size: 23
54855 GATAATTTAA
* *
54865 AAATAATTTTATTTCAAATAAAT
1 AAATAATATTATTTAAAATAAAT
*
54888 AATTAATATTATTTAAAATAAAT
1 AAATAATATTATTTAAAATAAAT
*
54911 AAATAATATGATTTTAAAAATAAAT
1 AAATAATATTA-TTT-AAAATAAAT
54936 A
1 A
54937 TTTTAAAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 29 0.69
24 3 0.07
25 10 0.24
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (23 bp):
AAATAATATTATTTAAAATAAAT
Found at i:54946 original size:14 final size:17
Alignment explanation
Indices: 54911--54944 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
54901 TAAAATAAAT
54911 AAATAATATGATTTTAA
1 AAATAATATGATTTTAA
54928 AAATAA-AT-ATTTTAA
1 AAATAATATGATTTTAA
54943 AA
1 AA
54945 TACTTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 2 0.12
17 6 0.35
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
AAATAATATGATTTTAA
Done.