Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004267.1 Hibiscus syriacus cultivar Beakdansim tig00009352_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: 92165
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:10492 original size:31 final size:31
Alignment explanation
Indices: 10454--10534 Score: 128
Period size: 31 Copynumber: 2.6 Consensus size: 31
10444 TAAGTATTAG
*
10454 AATGAAACAAAAA-TTAACGATGGTGTACTAA
1 AATGAAACAAAAAGTTAACGACGG-GTACTAA
10485 AATGAAACAAAAAGTTAACGACGGGTACTAA
1 AATGAAACAAAAAGTTAACGACGGGTACTAA
*
10516 AATGAAATAAAAAGTTAAC
1 AATGAAACAAAAAGTTAAC
10535 ATTAAGTATA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
31 38 0.81
32 9 0.19
ACGTcount: A:0.54, C:0.10, G:0.16, T:0.20
Consensus pattern (31 bp):
AATGAAACAAAAAGTTAACGACGGGTACTAA
Found at i:11859 original size:26 final size:26
Alignment explanation
Indices: 11823--11885 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
11813 AGGGATGGGC
11823 ATCCGACCCGAACCCGATGGGTTCTG
1 ATCCGACCCGAACCCGATGGGTTCTG
11849 ATCCGACCCGAACCCGATGGGTTCTG
1 ATCCGACCCGAACCCGATGGGTTCTG
*
11875 ATCCCACCCGA
1 ATCCGACCCGA
11886 TTGAGTCGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.21, C:0.38, G:0.24, T:0.17
Consensus pattern (26 bp):
ATCCGACCCGAACCCGATGGGTTCTG
Found at i:14767 original size:24 final size:25
Alignment explanation
Indices: 14740--14794 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
14730 AAATTATATA
14740 TATATATAGT-GATTTAA-TTTTTTC
1 TATAT-TAGTAGATTTAATTTTTTTC
* *
14764 TATATTTGTATATTTAATTTTTTTC
1 TATATTAGTAGATTTAATTTTTTTC
14789 TATATT
1 TATATT
14795 TAAAATTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 3 0.11
24 11 0.41
25 13 0.48
ACGTcount: A:0.27, C:0.04, G:0.05, T:0.64
Consensus pattern (25 bp):
TATATTAGTAGATTTAATTTTTTTC
Found at i:14802 original size:24 final size:24
Alignment explanation
Indices: 14751--14804 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
14741 ATATATAGTG
* *
14751 ATTTAATTTTTTCTATATTTGTAT
1 ATTTAATTTTTTCTATATTTGAAA
14775 ATTTAATTTTTTTCTATATTT-AAA
1 ATTTAA-TTTTTTCTATATTTGAAA
14799 ATTTAA
1 ATTTAA
14805 AATTTAGGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 13 0.48
25 14 0.52
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (24 bp):
ATTTAATTTTTTCTATATTTGAAA
Found at i:15182 original size:19 final size:19
Alignment explanation
Indices: 15154--15210 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 19
15144 AAATTATTAA
15154 TAATAA-TTAATATTATTT
1 TAATAATTTAATATTATTT
* * *
15172 TACTAATTTAATATTAATA
1 TAATAATTTAATATTATTT
* *
15191 TAATAGTTTAGTATTATTT
1 TAATAATTTAATATTATTT
15210 T
1 T
15211 GTTAAATTAT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
18 5 0.17
19 25 0.83
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (19 bp):
TAATAATTTAATATTATTT
Found at i:15258 original size:23 final size:22
Alignment explanation
Indices: 15212--15269 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
15202 TATTATTTTG
*
15212 TTAAATTATAATTATTAAAATA
1 TTAAAATATAATTATTAAAATA
* **
15234 TTTAAAATATATTTATTAATTTA
1 -TTAAAATATAATTATTAAAATA
15257 TTAATAATATAAT
1 TTAA-AATATAAT
15270 ATAATAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 4 0.14
23 25 0.86
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTAAAATATAATTATTAAAATA
Found at i:18418 original size:63 final size:62
Alignment explanation
Indices: 18317--18448 Score: 137
Period size: 63 Copynumber: 2.1 Consensus size: 62
18307 ATTCATATGC
* * * * *
18317 TTTAATTTCCACCTTTCAATTTTATTTCTTTTTCAATTT-AGTCTTCTATTTAACTTTT-TACAA
1 TTTAATTTCCACATTTCAATTTTAATTCTATTTAAATTTCAGTCCT-TATTT-A-TTTTGTACAA
*
18380 TTTAATTT-CAGCATTTCAATTTTACATT-TATTTAAATTTCAGTCCTTATTTATTTTGTATAA
1 TTTAATTTCCA-CATTTCAATTTTA-ATTCTATTTAAATTTCAGTCCTTATTTATTTTGTACAA
18442 TTTAATT
1 TTTAATT
18449 CTCCCTTTCA
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
61 4 0.07
62 14 0.24
63 34 0.58
64 7 0.12
ACGTcount: A:0.27, C:0.14, G:0.03, T:0.57
Consensus pattern (62 bp):
TTTAATTTCCACATTTCAATTTTAATTCTATTTAAATTTCAGTCCTTATTTATTTTGTACAA
Found at i:18528 original size:24 final size:24
Alignment explanation
Indices: 18498--18544 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
18488 CTCATAGTCT
18498 TATTTATAAATATTAT-TATAATAA
1 TATTTAT-AATATTATATATAATAA
18522 TATTTATAATATTATATATAATA
1 TATTTATAATATTATATATAATA
18545 CATGTGTGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TATTTATAATATTATATATAATAA
Found at i:18543 original size:12 final size:12
Alignment explanation
Indices: 18498--18544 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
18488 CTCATAGTCT
18498 TATT-TATA-AA
1 TATTATATATAA
18508 TATTAT-TATAA
1 TATTATATATAA
* *
18519 TAATATTTATAA
1 TATTATATATAA
18531 TATTATATATAA
1 TATTATATATAA
18543 TA
1 TA
18545 CATGTGTGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
10 6 0.19
11 8 0.26
12 17 0.55
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TATTATATATAA
Found at i:24343 original size:20 final size:20
Alignment explanation
Indices: 24318--24506 Score: 168
Period size: 20 Copynumber: 9.2 Consensus size: 20
24308 AATGACCAAC
*
24318 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* *
24338 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
24358 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
***
24378 AAAATCGCAACGCGATATTCC
1 AAAATCGCAACGCGAT-TAAG
*
24399 AAGAATCGCAATGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
* ***
24420 AGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
*
24441 AAGAATCGCAACGCGATTCAG
1 AA-AATCGCAACGCGATTAAG
*
24462 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTAAG
24482 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
24502 AAAAT
1 AAAAT
24507 GAGTAAATTC
Statistics
Matches: 139, Mismatches: 21, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
18 1 0.01
20 97 0.70
21 13 0.09
22 28 0.20
ACGTcount: A:0.42, C:0.22, G:0.20, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:24426 original size:42 final size:42
Alignment explanation
Indices: 24375--24506 Score: 189
Period size: 42 Copynumber: 3.2 Consensus size: 42
24365 CAACGGTCAA
*
24375 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATT
1 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAACGCGATT
* *
24417 AAGAGAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATT
1 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAACGCGATT
* *
24459 CAGAAAATCGCAACGCG--ATT-CAGAAAATCGCAACGCGATT
1 AAGAAAATCGCAACGCGATATTCCA-AGAATCGCAACGCGATT
24499 AAGAAAAT
1 AAGAAAAT
24507 GAGTAAATTC
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
39 2 0.02
40 25 0.31
42 54 0.67
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.17
Consensus pattern (42 bp):
AAGAAAATCGCAACGCGATATTCCAAGAATCGCAACGCGATT
Found at i:24610 original size:6 final size:6
Alignment explanation
Indices: 24599--24628 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
24589 GAAGACACGT
24599 ACGACC ACGACC ACGACC ACGACC ACGACC
1 ACGACC ACGACC ACGACC ACGACC ACGACC
24629 CGAGACGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
ACGACC
Found at i:25276 original size:20 final size:20
Alignment explanation
Indices: 25251--25347 Score: 151
Period size: 20 Copynumber: 4.8 Consensus size: 20
25241 CTCATTTTCT
25251 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
25271 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
25291 GAATCGCGTTGCGATTCTCT-
1 GAATCGCGTTGCGATTCT-TG
*
25311 TAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
25331 GAAGATCGCGTTGCGAT
1 G-A-ATCGCGTTGCGAT
25348 CTTCTTTTCA
Statistics
Matches: 71, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
19 1 0.01
20 55 0.77
21 2 0.03
22 13 0.18
ACGTcount: A:0.16, C:0.21, G:0.29, T:0.34
Consensus pattern (20 bp):
GAATCGCGTTGCGATTCTTG
Found at i:34208 original size:2 final size:2
Alignment explanation
Indices: 34201--34230 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
34191 CTTACTGAAA
34201 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34231 TCAAATTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38249 original size:15 final size:18
Alignment explanation
Indices: 38209--38254 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 18
38199 ATAGTCGGAG
*
38209 GAGAAGAAGAACGGCGAA
1 GAGAAGAGGAACGGCGAA
38227 GAGAAGAGGAACGGCGAGGA
1 GAGAAGAGGAACGGCGA--A
38247 GAGAAGAG
1 GAGAAGAG
38255 ATTGGGAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 16 0.64
20 9 0.36
ACGTcount: A:0.46, C:0.09, G:0.46, T:0.00
Consensus pattern (18 bp):
GAGAAGAGGAACGGCGAA
Found at i:40948 original size:30 final size:30
Alignment explanation
Indices: 40709--40931 Score: 410
Period size: 30 Copynumber: 7.4 Consensus size: 30
40699 TCCGAAGGAC
*
40709 CTATCCAGAGGTCATAAAGATCCTCGTTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
40739 CTGTCCAGAGGTCATAAAGATCCTCGATAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
40769 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
40799 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
40829 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
40859 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
40889 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
40919 CTATCCATAGGTC
1 CTATCCAGAGGTC
40932 CCGAAGAACC
Statistics
Matches: 188, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 188 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:40971 original size:31 final size:31
Alignment explanation
Indices: 40917--41009 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 31
40907 GATCCTCGGT
* *
40917 AACTATCCATAGGTCCCGAAGAACCTAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* **
40948 AACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* * *
40979 TACTGTCCATATGTCTCGACAG-ACATAGGTA
1 AACTATCCATATGTCCCGA-AGAACATAGGTA
41010 GTTCTTTGAC
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
31 48 0.96
32 2 0.04
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (31 bp):
AACTATCCATATGTCCCGAAGAACATAGGTA
Found at i:45966 original size:15 final size:18
Alignment explanation
Indices: 45926--45971 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 18
45916 ATAGTCGGAG
*
45926 GAGAAGAAGAACGGCGAA
1 GAGAAGAGGAACGGCGAA
45944 GAGAAGAGGAACGGCGAGGA
1 GAGAAGAGGAACGGCGA--A
45964 GAGAAGAG
1 GAGAAGAG
45972 ATTGGGAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 16 0.64
20 9 0.36
ACGTcount: A:0.46, C:0.09, G:0.46, T:0.00
Consensus pattern (18 bp):
GAGAAGAGGAACGGCGAA
Found at i:52791 original size:17 final size:17
Alignment explanation
Indices: 52769--52803 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
52759 AGAGTTGGTG
52769 GCGAAAATATGGGGTCT
1 GCGAAAATATGGGGTCT
52786 GCGAAAATATGGGGTCT
1 GCGAAAATATGGGGTCT
52803 G
1 G
52804 TCCCCTATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.37, T:0.23
Consensus pattern (17 bp):
GCGAAAATATGGGGTCT
Found at i:71180 original size:53 final size:53
Alignment explanation
Indices: 71089--71256 Score: 282
Period size: 53 Copynumber: 3.1 Consensus size: 53
71079 AACCAGTGTT
* * * *
71089 GCCTGCAGAAAGAAACTAGACTAATCAATATATATATATATATAACCAGCTTGCA
1 GCCTCCAGAAAAAAACTAGACTAA-CTA-ATATATATATGTATAACCAGCTTGCA
71144 GCCTCCAGAAAAAAACTAGACTAACTAATATATATATGTATAACCAGCTTGCA
1 GCCTCCAGAAAAAAACTAGACTAACTAATATATATATGTATAACCAGCTTGCA
71197 GCCTCCAGAAAAAAACTAGACTAACTAATATATATATGTATAACCAGCTTGCA
1 GCCTCCAGAAAAAAACTAGACTAACTAATATATATATGTATAACCAGCTTGCA
71250 GCCTCCA
1 GCCTCCA
71257 TCTCATATAC
Statistics
Matches: 109, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
53 85 0.78
54 2 0.02
55 22 0.20
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.24
Consensus pattern (53 bp):
GCCTCCAGAAAAAAACTAGACTAACTAATATATATATGTATAACCAGCTTGCA
Found at i:73561 original size:105 final size:105
Alignment explanation
Indices: 73376--73589 Score: 367
Period size: 105 Copynumber: 2.0 Consensus size: 105
73366 AATTGACAGG
*
73376 CAATTTCATAAAAAGATTTTACAGTTGAAAAATGAAAACTATACAACTATACTTGTTTTACAATT
1 CAATTTCATAAAAAGATTTTACAGTTGAAAAATGAAAACTATACAACTATAATTGTTTTACAATT
73441 TTTTAAAACATTTTTACTTTTTCTTAGACCCAAAGAGTGA
66 TTTTAAAACATTTTTACTTTTTCTTAGACCCAAAGAGTGA
* * *
73481 CAATTTCATAAAAAGATTTTACAGTTGAAAAATGAAAACTATACAATTATAATTGTTTATCCATT
1 CAATTTCATAAAAAGATTTTACAGTTGAAAAATGAAAACTATACAACTATAATTGTTT-TACAAT
*
73546 TTTTTAAAACA-TTTTACTTTTTCTTAGACCCAAAGAGTGG
65 TTTTTAAAACATTTTTACTTTTTCTTAGACCCAAAGAGTGA
73586 CAAT
1 CAAT
73590 ACCACAGCTC
Statistics
Matches: 103, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
105 88 0.85
106 15 0.15
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (105 bp):
CAATTTCATAAAAAGATTTTACAGTTGAAAAATGAAAACTATACAACTATAATTGTTTTACAATT
TTTTAAAACATTTTTACTTTTTCTTAGACCCAAAGAGTGA
Found at i:91100 original size:16 final size:16
Alignment explanation
Indices: 91076--91114 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
91066 CAGAGCTAAT
* *
91076 TCATACAGCCTCTGAA
1 TCATTCAGCATCTGAA
*
91092 TCATTCAGCATTTGAA
1 TCATTCAGCATCTGAA
91108 TCATTCA
1 TCATTCA
91115 ACGCTTAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (16 bp):
TCATTCAGCATCTGAA
Done.