Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007326.1 Hibiscus syriacus cultivar Beakdansim tig00019571_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: 55923
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Found at i:9509 original size:26 final size:26
Alignment explanation
Indices: 9473--9525 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
9463 AAAGTATGTC
9473 CCTGCATTTGCCACTCTACTTTATTG
1 CCTGCATTTGCCACTCTACTTTATTG
9499 CCTGCATTTGCCACTCTACTTTATTG
1 CCTGCATTTGCCACTCTACTTTATTG
9525 C
1 C
9526 ATCTAGCAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.15, C:0.32, G:0.11, T:0.42
Consensus pattern (26 bp):
CCTGCATTTGCCACTCTACTTTATTG
Found at i:15488 original size:2 final size:2
Alignment explanation
Indices: 15476--15516 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
15466 ATAATAATGA
*
15476 AT AT A- AT AT AT AT AT AT AT AT AT AG AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15517 TATGTTTGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:16728 original size:60 final size:59
Alignment explanation
Indices: 16664--16776 Score: 136
Period size: 60 Copynumber: 1.9 Consensus size: 59
16654 TTAATATTTC
* * * ** * *
16664 AATTTTATCCTTAAACTGTGATTCTATTTCTAAATTAATCCTTAAACTTTTAAACAATCT
1 AATTTCATCCCTAAACTATGACCCTATTTCTAAATTAA-CCCTAAACTTCTAAACAATCT
* *
16724 AATTTCATCCCTAAATTATGACCCTCTTTCTAAATTAACCCTAAACTTCTAAA
1 AATTTCATCCCTAAACTATGACCCTATTTCTAAATTAACCCTAAACTTCTAAA
16777 TTTTCTAATT
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
59 13 0.30
60 31 0.70
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.41
Consensus pattern (59 bp):
AATTTCATCCCTAAACTATGACCCTATTTCTAAATTAACCCTAAACTTCTAAACAATCT
Found at i:17030 original size:60 final size:60
Alignment explanation
Indices: 16922--17045 Score: 162
Period size: 60 Copynumber: 2.1 Consensus size: 60
16912 GTATATACAT
* *
16922 ATAGTTTGGGATAAAATTGGAATGTTCAAAAAGTTCGAGGATCAATTTAGAATGA-AGATC
1 ATAGTTTGGGATAAAATTGAAATGTTCAAAAAGTTCGAGGATCAATTTAAAATGATA-ATC
* * **
16982 ATAGTTTGGGGATGAAATTTAAATGTTCAAAAAGTT-GAGGATTGATTTAAAATGATAATC
1 ATAGTTT-GGGATAAAATTGAAATGTTCAAAAAGTTCGAGGATCAATTTAAAATGATAATC
17042 ATAG
1 ATAG
17046 GTTAAGGATG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
60 30 0.54
61 26 0.46
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.32
Consensus pattern (60 bp):
ATAGTTTGGGATAAAATTGAAATGTTCAAAAAGTTCGAGGATCAATTTAAAATGATAATC
Found at i:17055 original size:60 final size:61
Alignment explanation
Indices: 16942--17058 Score: 157
Period size: 60 Copynumber: 1.9 Consensus size: 61
16932 ATAAAATTGG
* * **
16942 AATGTTCAAAAAGTTCGAGGATCAATTTAGAATGAAGATCATAGTTTGGGGATGAAATTTA
1 AATGTTCAAAAAGTTCGAGGATCAATTTAAAATGAAGATCATAGGTTAAGGATGAAATTTA
**
17003 AATGTTCAAAAAGTT-GAGGATTGATTTAAAATGATA-ATCATAGGTTAAGGATGAAA
1 AATGTTCAAAAAGTTCGAGGATCAATTTAAAATGA-AGATCATAGGTTAAGGATGAAA
17059 CTGGAACATT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
60 33 0.67
61 16 0.33
ACGTcount: A:0.42, C:0.05, G:0.22, T:0.31
Consensus pattern (61 bp):
AATGTTCAAAAAGTTCGAGGATCAATTTAAAATGAAGATCATAGGTTAAGGATGAAATTTA
Found at i:18222 original size:14 final size:14
Alignment explanation
Indices: 18203--18232 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
18193 CCATAACTTT
*
18203 TAAACCTTAAATCA
1 TAAACCCTAAATCA
18217 TAAACCCTAAATCA
1 TAAACCCTAAATCA
18231 TA
1 TA
18233 CCTTAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (14 bp):
TAAACCCTAAATCA
Found at i:20819 original size:37 final size:37
Alignment explanation
Indices: 20769--20844 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
20759 ATTGCAAATA
20769 ATGCAATGCTTTGTTAACAGTAAAACTTTATTTAACC
1 ATGCAATGCTTTGTTAACAGTAAAACTTTATTTAACC
20806 ATGCAATGCTTTGTTAACAGTAAAACTTTATTTAACC
1 ATGCAATGCTTTGTTAACAGTAAAACTTTATTTAACC
20843 AT
1 AT
20845 TCTAAAACCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (37 bp):
ATGCAATGCTTTGTTAACAGTAAAACTTTATTTAACC
Found at i:21377 original size:15 final size:15
Alignment explanation
Indices: 21357--21386 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
21347 AATTGAGTGG
21357 ACAAAACACAATCTC
1 ACAAAACACAATCTC
21372 ACAAAACACAATCTC
1 ACAAAACACAATCTC
21387 TAAAATCCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.33, G:0.00, T:0.13
Consensus pattern (15 bp):
ACAAAACACAATCTC
Found at i:27295 original size:3 final size:3
Alignment explanation
Indices: 27287--27352 Score: 64
Period size: 3 Copynumber: 22.0 Consensus size: 3
27277 TTGAGGAAAT
* *
27287 TGA TGA TGA T-A TTGA T-A TTGA AGA TGA AGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA -TGA TGA -TGA TGA TGA TGA TGA TGA TGA TGA TGA
* *
27332 TGA TGA TGA AGA TTA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA
27353 GGTTTGAACT
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
2 2 0.04
3 47 0.92
4 2 0.04
ACGTcount: A:0.38, C:0.00, G:0.29, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:29365 original size:72 final size:72
Alignment explanation
Indices: 29248--29396 Score: 298
Period size: 72 Copynumber: 2.1 Consensus size: 72
29238 ACGAAACTCT
29248 AGAATCGAGTTAGAGAAAAAAGCCATTGTTTTAATTATTTCTAGGTTTCCATATGCTCATTTGTT
1 AGAATCGAGTTAGAGAAAAAAGCCATTGTTTTAATTATTTCTAGGTTTCCATATGCTCATTTGTT
29313 TTGATTA
66 TTGATTA
29320 AGAATCGAGTTAGAGAAAAAAGCCATTGTTTTAATTATTTCTAGGTTTCCATATGCTCATTTGTT
1 AGAATCGAGTTAGAGAAAAAAGCCATTGTTTTAATTATTTCTAGGTTTCCATATGCTCATTTGTT
29385 TTGATTA
66 TTGATTA
29392 AGAAT
1 AGAAT
29397 GTAAGGATGT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 77 1.00
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.41
Consensus pattern (72 bp):
AGAATCGAGTTAGAGAAAAAAGCCATTGTTTTAATTATTTCTAGGTTTCCATATGCTCATTTGTT
TTGATTA
Found at i:31780 original size:60 final size:59
Alignment explanation
Indices: 31658--31791 Score: 155
Period size: 60 Copynumber: 2.2 Consensus size: 59
31648 GGCATAATTA
* *
31658 ATAGTCGGGTGACCATTCTGTAACTTTTAATAGTCGAGGGACTCAACAAAACAACTTTCT
1 ATAGTCGGG-GACCATTCTATAACTTTTAATAGTCAAGGGACTCAACAAAACAACTTTCT
* * * *
31718 ATAGTCGGGAGACCATTTTATGACTTTTAATAGTCAAGTGACTCAATAAAAC-A-TTGTGCT
1 ATAGTCGGG-GACCATTCTATAACTTTTAATAGTCAAGGGACTCAACAAAACAACTT-T-CT
31778 ATAGTCAGGGGACC
1 ATAGTC-GGGGACC
31792 GTTTGTGTAC
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
58 2 0.03
59 2 0.03
60 57 0.89
61 3 0.05
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (59 bp):
ATAGTCGGGGACCATTCTATAACTTTTAATAGTCAAGGGACTCAACAAAACAACTTTCT
Found at i:31804 original size:60 final size:60
Alignment explanation
Indices: 31658--31770 Score: 163
Period size: 60 Copynumber: 1.9 Consensus size: 60
31648 GGCATAATTA
* * * * *
31658 ATAGTCGGGTGACCATTCTGTAACTTTTAATAGTCGAGGGACTCAACAAAACAACTTTCT
1 ATAGTCGGGAGACCATTTTATGACTTTTAATAGTCAAGGGACTCAACAAAACAACTTTCT
* *
31718 ATAGTCGGGAGACCATTTTATGACTTTTAATAGTCAAGTGACTCAATAAAACA
1 ATAGTCGGGAGACCATTTTATGACTTTTAATAGTCAAGGGACTCAACAAAACA
31771 TTGTGCTATA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30
Consensus pattern (60 bp):
ATAGTCGGGAGACCATTTTATGACTTTTAATAGTCAAGGGACTCAACAAAACAACTTTCT
Found at i:36721 original size:27 final size:28
Alignment explanation
Indices: 36664--36721 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
36654 AGAGGTGCAC
36664 AAAAAATCCGAATATCCGATTTTGGGTAA
1 AAAAAATCCGAATATCCGATTTTGGG-AA
*
36693 AAAATATCCGAA-A-CCGGATTTT-GGAA
1 AAAAAATCCGAATATCC-GATTTTGGGAA
36719 AAA
1 AAA
36722 CCGGTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 5 0.19
27 4 0.15
28 7 0.26
29 11 0.41
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.24
Consensus pattern (28 bp):
AAAAAATCCGAATATCCGATTTTGGGAA
Found at i:36834 original size:26 final size:24
Alignment explanation
Indices: 36793--36877 Score: 116
Period size: 24 Copynumber: 3.5 Consensus size: 24
36783 AAATTGAATG
* * *
36793 ACCGATTTTTTTACCGGATTAAAA
1 ACCGGTTTTTTAACCGGATAAAAA
36817 ACCGGTTTTTTCAAACCGGATAAAAA
1 ACCGGTTTTTT--AACCGGATAAAAA
*
36843 ACCGGTTTTTTATCCGGATAAAAA
1 ACCGGTTTTTTAACCGGATAAAAA
36867 ACCGGTTTTTT
1 ACCGGTTTTTT
36878 TAAAAAACTG
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
24 33 0.60
26 22 0.40
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (24 bp):
ACCGGTTTTTTAACCGGATAAAAA
Found at i:36892 original size:16 final size:17
Alignment explanation
Indices: 36861--36934 Score: 76
Period size: 17 Copynumber: 4.0 Consensus size: 17
36851 TTTATCCGGA
36861 TAAAAAACCGGTTTTTT
1 TAAAAAACCGGTTTTTT
*
36878 TAAAAAACTGGTTTTTT
1 TAAAAAACCGGTTTTTT
36895 ATCCGAAAAAATCCGGTTTTTTT
1 -T---AAAAAA-CCGG-TTTTTT
*
36918 TTAAAAACCGGTTTTTT
1 TAAAAAACCGGTTTTTT
36935 GCAAACCGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
17 22 0.46
18 5 0.10
19 5 0.10
21 6 0.12
22 4 0.08
23 6 0.12
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (17 bp):
TAAAAAACCGGTTTTTT
Found at i:36916 original size:40 final size:41
Alignment explanation
Indices: 36837--36934 Score: 146
Period size: 40 Copynumber: 2.4 Consensus size: 41
36827 TCAAACCGGA
36837 TAAAAAACCGGTTTTTTATCCGGATAAAAAACCGGTTTTTT
1 TAAAAAACCGGTTTTTTATCCGGATAAAAAACCGGTTTTTT
* *
36878 TAAAAAACTGGTTTTTTATCC-GA-AAAAATCCGGTTTTTTT
1 TAAAAAACCGGTTTTTTATCCGGATAAAAAACCGG-TTTTTT
*
36918 TTAAAAACCGGTTTTTT
1 TAAAAAACCGGTTTTTT
36935 GCAAACCGAA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
39 9 0.17
40 23 0.44
41 20 0.38
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (41 bp):
TAAAAAACCGGTTTTTTATCCGGATAAAAAACCGGTTTTTT
Found at i:46135 original size:13 final size:13
Alignment explanation
Indices: 46117--46147 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
46107 TCTGATTAAT
46117 TTTTGCCTTAAAA
1 TTTTGCCTTAAAA
46130 TTTTGCCTTAAAA
1 TTTTGCCTTAAAA
46143 TTTTG
1 TTTTG
46148 GATTGAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.26, C:0.13, G:0.10, T:0.52
Consensus pattern (13 bp):
TTTTGCCTTAAAA
Found at i:47193 original size:11 final size:11
Alignment explanation
Indices: 47177--47202 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
47167 CTTTTTGTTC
47177 TTTTATTTTTA
1 TTTTATTTTTA
47188 TTTTATTTTTA
1 TTTTATTTTTA
47199 TTTT
1 TTTT
47203 GAAAATTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:47339 original size:20 final size:21
Alignment explanation
Indices: 47302--47340 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
47292 TTTGTTTTCC
*
47302 TTTATTTTTCTCTGGTTTTTT
1 TTTATTTTTCTCTAGTTTTTT
*
47323 TTTATTTTTTTC-AGTTTT
1 TTTATTTTTCTCTAGTTTT
47341 GAGGTTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.08, C:0.08, G:0.08, T:0.77
Consensus pattern (21 bp):
TTTATTTTTCTCTAGTTTTTT
Found at i:48087 original size:20 final size:20
Alignment explanation
Indices: 48064--48101 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
48054 CTGAAAAAAA
*
48064 CTAACTTAAAATCATAAATC
1 CTAACCTAAAATCATAAATC
*
48084 CTAACCTAAAATCCTAAA
1 CTAACCTAAAATCATAAA
48102 CCCCTAATCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (20 bp):
CTAACCTAAAATCATAAATC
Found at i:48110 original size:14 final size:14
Alignment explanation
Indices: 48100--48136 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
48090 TAAAATCCTA
48100 AACCCCTAATCTCT
1 AACCCCTAATCTCT
*
48114 AACCCCTAAACTCT
1 AACCCCTAATCTCT
*
48128 TACCCCTAA
1 AACCCCTAA
48137 CCCCTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.32, C:0.43, G:0.00, T:0.24
Consensus pattern (14 bp):
AACCCCTAATCTCT
Found at i:49566 original size:26 final size:27
Alignment explanation
Indices: 49530--49584 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
49520 ATATTTTTAA
49530 TTTTAATAATTATAAATATATATATTT
1 TTTTAATAATTATAAATATATATATTT
* * * *
49557 TTTTAA-AATTTTAATTTTTTATATTT
1 TTTTAATAATTATAAATATATATATTT
49583 TT
1 TT
49585 AAATATTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 18 0.75
27 6 0.25
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (27 bp):
TTTTAATAATTATAAATATATATATTT
Done.