Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000185.1 Hibiscus syriacus cultivar Beakdansim tig00000327_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: 76142
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1654 original size:26 final size:25
Alignment explanation
Indices: 1614--1694 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 25
1604 ATAAAATAGT
1614 AAGAAAAATAAATATAAAATAAAGAAA
1 AAGAAAAA-AAATATAAAATAAA-AAA
1641 AAGAAAAAAAATATATAAATAAAACAA
1 AAGAAAAAAAATATA-AAATAAAA-AA
*
1668 ATA-AAAAAATAATAAAAAAGTAAAAAA
1 A-AGAAAAAA-AATATAAAA-TAAAAAA
1695 TATATATAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
26 8 0.17
27 29 0.60
28 11 0.23
ACGTcount: A:0.79, C:0.01, G:0.05, T:0.15
Consensus pattern (25 bp):
AAGAAAAAAAATATAAAATAAAAAA
Found at i:1664 original size:17 final size:17
Alignment explanation
Indices: 1617--1715 Score: 67
Period size: 17 Copynumber: 5.6 Consensus size: 17
1607 AAATAGTAAG
1617 AAAAATAAATATAAAATAAA
1 AAAAATAAA-A-AAAAT-AA
* *
1637 GAAAAAGAAAAAAAATAT
1 -AAAAATAAAAAAAATAA
* *
1655 ATAAATAAAACAAATAA
1 AAAAATAAAAAAAATAA
1672 AAAAATAATAAAAAAGT-A
1 AAAAATAA-AAAAAA-TAA
* * *
1690 AAAAATATATATAAT-A
1 AAAAATAAAAAAAATAA
1706 AAAAATAAAA
1 AAAAATAAAA
1716 TAGTAAATAT
Statistics
Matches: 63, Mismatches: 13, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
16 10 0.16
17 24 0.38
18 14 0.22
19 6 0.10
20 1 0.02
21 8 0.13
ACGTcount: A:0.78, C:0.01, G:0.03, T:0.18
Consensus pattern (17 bp):
AAAAATAAAAAAAATAA
Found at i:1670 original size:43 final size:44
Alignment explanation
Indices: 1629--1715 Score: 119
Period size: 44 Copynumber: 2.0 Consensus size: 44
1619 AAATAAATAT
1629 AAAATAA-AGAAAAAGAAAAAAA-ATATATAAATAAAACAAATAAA
1 AAAATAATA-AAAAAGAAAAAAATATATAT-AATAAAACAAATAAA
*
1673 AAAATAATAAAAAAGTAAAAAATATATATAAT-AAA-AAATAAA
1 AAAATAATAAAAAAGAAAAAAATATATATAATAAAACAAATAAA
1715 A
1 A
1716 TAGTAAATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
42 8 0.20
43 3 0.08
44 22 0.55
45 7 0.17
ACGTcount: A:0.78, C:0.01, G:0.03, T:0.17
Consensus pattern (44 bp):
AAAATAATAAAAAAGAAAAAAATATATATAATAAAACAAATAAA
Found at i:1683 original size:20 final size:20
Alignment explanation
Indices: 1618--1715 Score: 74
Period size: 23 Copynumber: 4.6 Consensus size: 20
1608 AATAGTAAGA
* *
1618 AAAATAAATATAAAATA-AAG
1 AAAA-AAATAAAAAATATAAT
*
1638 AAAAAGAAAAAAAATATATAAAT
1 AAAAA-AATAAAAA-ATAT-AAT
1661 AAAACAAATAAAAAA-ATAAT
1 AAAA-AAATAAAAAATATAAT
*
1681 AAAAAAGTAAAAAATATATAT
1 AAAAAAATAAAAAATATA-AT
1702 AATAAAAAATAAAA
1 -A-AAAAAATAAAA
1716 TAGTAAATAT
Statistics
Matches: 63, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
19 10 0.16
20 20 0.32
21 7 0.11
22 2 0.03
23 23 0.37
24 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.03, T:0.18
Consensus pattern (20 bp):
AAAAAAATAAAAAATATAAT
Found at i:1703 original size:24 final size:23
Alignment explanation
Indices: 1646--1715 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 23
1636 AGAAAAAGAA
1646 AAAAAATATATA-AATAAAACAAAT
1 AAAAAATATATATAAT-AAA-AAAT
*
1670 AAAAAA-ATA-AT-A-AAAAAGT
1 AAAAAATATATATAATAAAAAAT
1689 AAAAAATATATATAATAAAAAAT
1 AAAAAATATATATAATAAAAAAT
1712 AAAA
1 AAAA
1716 TAGTAAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
19 9 0.23
20 6 0.15
21 2 0.05
22 3 0.08
23 13 0.33
24 6 0.15
ACGTcount: A:0.77, C:0.01, G:0.01, T:0.20
Consensus pattern (23 bp):
AAAAAATATATATAATAAAAAAT
Found at i:1717 original size:47 final size:44
Alignment explanation
Indices: 1617--1714 Score: 119
Period size: 45 Copynumber: 2.2 Consensus size: 44
1607 AAATAGTAAG
*
1617 AAAAATAAAT-ATAAAATAAAGAAAAAGAAAAAAAATATATAAA
1 AAAAATAAATAAAAAAATAAAGAAAAAGAAAAAAAATATATAAA
* * *
1660 TAAAACAAATAAAAAAATAATA-AAAAAGTAAAAAATATATATAATA
1 AAAAATAAATAAAAAAATAA-AGAAAAAG-AAAAAAAATATATAA-A
1706 AAAAATAAA
1 AAAAATAAA
1715 ATAGTAAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
43 8 0.18
44 14 0.31
45 15 0.33
46 8 0.18
ACGTcount: A:0.78, C:0.01, G:0.03, T:0.18
Consensus pattern (44 bp):
AAAAATAAATAAAAAAATAAAGAAAAAGAAAAAAAATATATAAA
Found at i:1725 original size:24 final size:24
Alignment explanation
Indices: 1617--1726 Score: 75
Period size: 24 Copynumber: 4.5 Consensus size: 24
1607 AAATAGTAAG
* *
1617 AAAAATAAATATAA-AATAAAGAA
1 AAAAATAAATATAATAAAAAAGTA
* * **
1640 AAAGAAAAAAAATATATAAATAAAACA
1 AAA-AATAAATATA-ATAAA-AAAGTA
1667 AATAAA-AAA-ATAATAAAAAAGTA
1 AA-AAATAAATATAATAAAAAAGTA
*
1690 AAAAATATATATAATAAAAAA-TA
1 AAAAATAAATATAATAAAAAAGTA
*
1713 AAATAGTAAATATA
1 AAA-AATAAATATA
1727 TATATATATA
Statistics
Matches: 69, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
22 3 0.04
23 16 0.23
24 32 0.46
25 4 0.06
26 5 0.07
27 8 0.12
28 1 0.01
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.20
Consensus pattern (24 bp):
AAAAATAAATATAATAAAAAAGTA
Found at i:1730 original size:30 final size:32
Alignment explanation
Indices: 1668--1800 Score: 103
Period size: 34 Copynumber: 4.0 Consensus size: 32
1658 AATAAAACAA
*
1668 ATAAAAAAATAATAAAAAAGTAAAAAATATAT
1 ATAATAAAATAATAAAAAAGTAAAAAATATAT
*
1700 ATAATAAAA-AATAAAATAGTAAATATATATATAT
1 ATAATAAAATAATAAAAAAGTAAA-A-A-ATATAT
* **
1734 ATAATATAATTAATAATGAA-TAAAATAATATAT
1 ATAATA-AAATAATAAAAAAGTAAAA-AATATAT
* *
1767 ATATATATATAAT-CTAAAAAAAT-AAAAATATAT
1 ATA-ATA-A-AATAATAAAAAAGTAAAAAATATAT
1800 A
1 A
1801 CTAAAGTAAA
Statistics
Matches: 83, Mismatches: 10, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
31 13 0.16
32 9 0.11
33 18 0.22
34 28 0.34
35 9 0.11
36 6 0.07
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (32 bp):
ATAATAAAATAATAAAAAAGTAAAAAATATAT
Found at i:1740 original size:43 final size:43
Alignment explanation
Indices: 1693--1777 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
1683 AAAAGTAAAA
*
1693 AATAT-ATATAATAAAAAATAAAATAGTAAATATATATATATAT
1 AATATAAT-TAATAAAAAATAAAATAATAAATATATATATATAT
** *
1736 AATATAATTAATAATGAATAAAATAATATATATATATATATA
1 AATATAATTAATAAAAAATAAAATAATAAATATATATATATA
1778 ATCTAAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 35 0.95
44 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (43 bp):
AATATAATTAATAAAAAATAAAATAATAAATATATATATATAT
Found at i:17491 original size:60 final size:58
Alignment explanation
Indices: 17363--17514 Score: 196
Period size: 60 Copynumber: 2.6 Consensus size: 58
17353 AAGCATAATG
* * * * *
17363 AATAGTCGAGTGACCATTTTGTAACTTTTAAAAGTCGAGACTCAACAAAGTAACTCCC
1 AATAGTTGAGGGACCATTTTGTAACTTTTAATAGTCGAGACTCAACAAAATAACTCCA
* *
17421 TATAGTTGAGGGACCATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAATAACTCTA
1 AATAGTTGAGGGACCATTTTGTAACTTTTAATAGTCGA--GACTCAACAAAATAACTCCA
* * *
17481 AATAGTTGAGGAACTATTTTGTAATTTTTAATAG
1 AATAGTTGAGGGACCATTTTGTAACTTTTAATAG
17515 GTGAGAGACT
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
58 34 0.42
60 47 0.58
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (58 bp):
AATAGTTGAGGGACCATTTTGTAACTTTTAATAGTCGAGACTCAACAAAATAACTCCA
Found at i:18748 original size:2 final size:2
Alignment explanation
Indices: 18741--18771 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
18731 TATCATTTAA
*
18741 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18772 ATTATAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:20741 original size:3 final size:3
Alignment explanation
Indices: 20733--20763 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
20723 CTTCCTCAAC
20733 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
20764 GCTTGTACTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:22176 original size:23 final size:24
Alignment explanation
Indices: 22125--22180 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 24
22115 CATTTAAATG
*
22125 ATAAACGAACACAAAAGAATGAAC
1 ATAAACGAAAACAAAAGAATGAAC
* *
22149 GTAAACGAAAACAATA-AATGAAC
1 ATAAACGAAAACAAAAGAATGAAC
22172 ATAAACGAA
1 ATAAACGAA
22181 TTTGCACAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 15 0.54
24 13 0.46
ACGTcount: A:0.62, C:0.14, G:0.12, T:0.11
Consensus pattern (24 bp):
ATAAACGAAAACAAAAGAATGAAC
Found at i:22215 original size:23 final size:23
Alignment explanation
Indices: 22186--22241 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
22176 ACGAATTTGC
22186 ACAAACATAACAAATGAACATAA
1 ACAAACATAACAAATGAACATAA
* * * *
22209 TCGAACATAATAAATGAACGTAA
1 ACAAACATAACAAATGAACATAA
22232 ACAAACATAA
1 ACAAACATAA
22242 ACAACAACAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.61, C:0.16, G:0.07, T:0.16
Consensus pattern (23 bp):
ACAAACATAACAAATGAACATAA
Found at i:22452 original size:14 final size:14
Alignment explanation
Indices: 22433--22465 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
22423 TGGGCTGAAT
22433 ATAAATGAACGAAC
1 ATAAATGAACGAAC
*
22447 ATAAATGAATGAAC
1 ATAAATGAACGAAC
22461 ATAAA
1 ATAAA
22466 CAAATGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.61, C:0.09, G:0.12, T:0.18
Consensus pattern (14 bp):
ATAAATGAACGAAC
Found at i:29598 original size:20 final size:19
Alignment explanation
Indices: 29573--29613 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
29563 TTAGTTCATT
*
29573 TTAATATTTAAACTATACAA
1 TTAATACTTAAACTAT-CAA
*
29593 TTAATACTTAAATTATCAA
1 TTAATACTTAAACTATCAA
29612 TT
1 TT
29614 TTGATTCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (19 bp):
TTAATACTTAAACTATCAA
Found at i:37384 original size:16 final size:16
Alignment explanation
Indices: 37365--37395 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
37355 TTTAGTGCGT
*
37365 TTTTATTTTATTTAAG
1 TTTTATGTTATTTAAG
37381 TTTTATGTTATTTAA
1 TTTTATGTTATTTAA
37396 TAATAATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (16 bp):
TTTTATGTTATTTAAG
Found at i:51846 original size:31 final size:31
Alignment explanation
Indices: 51805--51869 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
51795 CTTAAAATGA
*
51805 TCGGTCTAAATTAAGTCTGAGTTAATTTGAT
1 TCGGACTAAATTAAGTCTGAGTTAATTTGAT
51836 TCGGACTAAATTAAGTCTGAGTTAATTTGAT
1 TCGGACTAAATTAAGTCTGAGTTAATTTGAT
51867 TCG
1 TCG
51870 AATTAATCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (31 bp):
TCGGACTAAATTAAGTCTGAGTTAATTTGAT
Found at i:55342 original size:11 final size:13
Alignment explanation
Indices: 55328--55359 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
55318 ATAAATGGAG
55328 TTTAA-ATT-TTT
1 TTTAATATTATTT
55339 TTTAATATTATTT
1 TTTAATATTATTT
55352 TTTAATAT
1 TTTAATAT
55360 GATAAGTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 5 0.26
12 3 0.16
13 11 0.58
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTAATATTATTT
Found at i:55983 original size:12 final size:12
Alignment explanation
Indices: 55966--55996 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
55956 ATATATATAT
*
55966 ATACCCGGTCCG
1 ATACCCGGCCCG
55978 ATACCCGGCCCG
1 ATACCCGGCCCG
55990 ATACCCG
1 ATACCCG
55997 TTTAAATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.45, G:0.23, T:0.13
Consensus pattern (12 bp):
ATACCCGGCCCG
Found at i:64165 original size:30 final size:30
Alignment explanation
Indices: 64121--64197 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 30
64111 GTTTTTTAAC
* * *
64121 ATTTTCAGTCATTTTTTAACTCCTAGTAAT
1 ATTTTCAGTAATTTTTTAACGCCTAATAAT
*
64151 ATTTTCGGTAATTTTTTAACGCCTAATAAT
1 ATTTTCAGTAATTTTTTAACGCCTAATAAT
* * *
64181 GTTTCCAGTCATTTTTT
1 ATTTTCAGTAATTTTTT
64198 TAAAAATCTA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.25, C:0.16, G:0.09, T:0.51
Consensus pattern (30 bp):
ATTTTCAGTAATTTTTTAACGCCTAATAAT
Found at i:65084 original size:10 final size:10
Alignment explanation
Indices: 65069--65122 Score: 60
Period size: 10 Copynumber: 5.6 Consensus size: 10
65059 TATTTTTTTT
65069 AAAATAAATA
1 AAAATAAATA
65079 AAAATACAATA
1 AAAATA-AATA
65090 AAAAT---TA
1 AAAATAAATA
65097 AAAATAAATA
1 AAAATAAATA
* *
65107 AAAGTCAATA
1 AAAATAAATA
65117 AAAATA
1 AAAATA
65123 TGATGTAAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
7 7 0.19
10 20 0.56
11 9 0.25
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.20
Consensus pattern (10 bp):
AAAATAAATA
Found at i:65103 original size:28 final size:27
Alignment explanation
Indices: 65069--65121 Score: 88
Period size: 28 Copynumber: 1.9 Consensus size: 27
65059 TATTTTTTTT
65069 AAAATAAATAAAAATACAATAAAAATTA
1 AAAATAAATAAAAAT-CAATAAAAATTA
*
65097 AAAATAAATAAAAGTCAATAAAAAT
1 AAAATAAATAAAAATCAATAAAAAT
65122 ATGATGTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 10 0.42
28 14 0.58
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.21
Consensus pattern (27 bp):
AAAATAAATAAAAATCAATAAAAATTA
Found at i:65109 original size:27 final size:28
Alignment explanation
Indices: 65069--65121 Score: 83
Period size: 27 Copynumber: 1.9 Consensus size: 28
65059 TATTTTTTTT
65069 AAAATAAATAAAAA-TACAATAAAAATTA
1 AAAATAAATAAAAAGT-CAATAAAAATTA
65097 AAAATAAAT-AAAAGTCAATAAAAAT
1 AAAATAAATAAAAAGTCAATAAAAAT
65122 ATGATGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.21
Consensus pattern (28 bp):
AAAATAAATAAAAAGTCAATAAAAATTA
Found at i:66430 original size:11 final size:10
Alignment explanation
Indices: 66395--66436 Score: 50
Period size: 11 Copynumber: 4.0 Consensus size: 10
66385 TTAGTTTTAC
66395 ATTATATTTTT
1 ATTA-ATTTTT
66406 ATTGAA-TTTT
1 ATT-AATTTTT
66416 ATTAATTTTT
1 ATTAATTTTT
66426 AATTAATTTTT
1 -ATTAATTTTT
66437 TAAAAAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 2 0.07
10 11 0.39
11 14 0.50
12 1 0.04
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (10 bp):
ATTAATTTTT
Found at i:66436 original size:21 final size:21
Alignment explanation
Indices: 66395--66435 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
66385 TTAGTTTTAC
66395 ATTATATTTTTATTGAATTTT
1 ATTATATTTTTATTGAATTTT
66416 ATTA-ATTTTTAATT-AATTTT
1 ATTATATTTTT-ATTGAATTTT
66436 TTAAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (21 bp):
ATTATATTTTTATTGAATTTT
Done.