Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000438.1 Hibiscus syriacus cultivar Beakdansim tig00000802_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: 69177
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:12016 original size:2 final size:2
Alignment explanation
Indices: 12009--12033 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11999 ATTGTTAATG
12009 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 T
12034 TAGTATATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27212 original size:15 final size:15
Alignment explanation
Indices: 27192--27224 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
27182 TTTTTCGAAC
27192 TTTTACGAGCTTCAA
1 TTTTACGAGCTTCAA
27207 TTTTACGAGCTTCAA
1 TTTTACGAGCTTCAA
27222 TTT
1 TTT
27225 ATGATTTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.45
Consensus pattern (15 bp):
TTTTACGAGCTTCAA
Found at i:28103 original size:2 final size:2
Alignment explanation
Indices: 28096--28135 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
28086 AAACATGTAT
28096 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28136 ATTCCCCCAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28270 original size:18 final size:18
Alignment explanation
Indices: 28249--28283 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28239 TTATTAAACC
28249 TTATTTCCAGATTAAGGT
1 TTATTTCCAGATTAAGGT
**
28267 TTATTTTTAGATTAAGG
1 TTATTTCCAGATTAAGG
28284 GCTACTAGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.17, T:0.49
Consensus pattern (18 bp):
TTATTTCCAGATTAAGGT
Found at i:32923 original size:28 final size:29
Alignment explanation
Indices: 32885--32964 Score: 137
Period size: 28 Copynumber: 2.8 Consensus size: 29
32875 TATATGATAT
32885 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
32915 GAG-AATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
32943 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
32965 ACATATAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
28 34 0.69
29 12 0.24
30 3 0.06
ACGTcount: A:0.44, C:0.16, G:0.23, T:0.17
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:33371 original size:22 final size:22
Alignment explanation
Indices: 33346--33401 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
33336 ATGGTAAGAA
33346 TGCATATTCATTAAAATATTGT
1 TGCATATTCATTAAAATATTGT
*
33368 TGCATATTCATGAAAATATTGT
1 TGCATATTCATTAAAATATTGT
33390 TGCATATTCATT
1 TGCATATTCATT
33402 TATTGCCTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.45
Consensus pattern (22 bp):
TGCATATTCATTAAAATATTGT
Found at i:35680 original size:23 final size:23
Alignment explanation
Indices: 35653--35702 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
35643 ACCTTTAGGG
*
35653 TGAAATGAAATAACTATTTTTCA
1 TGAAAAGAAATAACTATTTTTCA
** *
35676 TGAAAAGACTTAATTATTTTTCA
1 TGAAAAGAAATAACTATTTTTCA
35699 TGAA
1 TGAA
35703 TAGTCATGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (23 bp):
TGAAAAGAAATAACTATTTTTCA
Found at i:41146 original size:18 final size:19
Alignment explanation
Indices: 41111--41147 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
41101 CACGGAATGT
41111 AAGATTACTAGTGGGAATAA
1 AAGATTACTAG-GGGAATAA
41131 AAGATTACTA-GGGAATA
1 AAGATTACTAGGGGAATA
41148 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.05, G:0.24, T:0.24
Consensus pattern (19 bp):
AAGATTACTAGGGGAATAA
Found at i:41370 original size:37 final size:36
Alignment explanation
Indices: 41296--41370 Score: 105
Period size: 37 Copynumber: 2.1 Consensus size: 36
41286 CAAACTGTAA
**
41296 AATATTTATATATTTTCTTTAAAAAATTAAATTTAT
1 AATATTTATATATTTTCTTTAAAAAATTAAAAATAT
* *
41332 AATATTTATATAATTTTTTTTACAAAATTAAAAATAT
1 AATATTTATAT-ATTTTCTTTAAAAAATTAAAAATAT
41369 AA
1 AA
41371 AAAAGGTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
36 11 0.32
37 23 0.68
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (36 bp):
AATATTTATATATTTTCTTTAAAAAATTAAAAATAT
Found at i:41906 original size:2 final size:2
Alignment explanation
Indices: 41899--41930 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
41889 ATCTTCCATG
41899 AT 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 AT
41931 GGTTCATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46911 original size:25 final size:25
Alignment explanation
Indices: 46881--46931 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
46871 ATTATACTTC
46881 TATTGAATTTGTTCTATTTTGAGTA
1 TATTGAATTTGTTCTATTTTGAGTA
46906 TATTGAATTTGTTCTATTTTGAGTA
1 TATTGAATTTGTTCTATTTTGAGTA
46931 T
1 T
46932 CTTATTTTCA
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:0.24, C:0.04, G:0.16, T:0.57
Consensus pattern (25 bp):
TATTGAATTTGTTCTATTTTGAGTA
Found at i:50051 original size:20 final size:20
Alignment explanation
Indices: 50026--50074 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
50016 TCGATATTCG
50026 ACTCGAAAAGCTCGTGAGCA
1 ACTCGAAAAGCTCGTGAGCA
*
50046 ACTCGAAAAGCTCGTGAGTA
1 ACTCGAAAAGCTCGTGAGCA
*
50066 GCTCGAAAA
1 ACTCGAAAA
50075 AATATTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.16
Consensus pattern (20 bp):
ACTCGAAAAGCTCGTGAGCA
Found at i:50476 original size:14 final size:14
Alignment explanation
Indices: 50403--50467 Score: 55
Period size: 14 Copynumber: 4.6 Consensus size: 14
50393 AATTATGTGA
*
50403 TAAGGTTTAGGGTT
1 TAAGGTTTAGAGTT
50417 T-AGGATTTAGAGTT
1 TAAGG-TTTAGAGTT
* *
50431 T-ATGTGATAG-GATT
1 TAAGGT-TTAGAG-TT
50445 TAAGGTTTAGAGTT
1 TAAGGTTTAGAGTT
50459 TAAGGTTTA
1 TAAGGTTTA
50468 TGTGTTAAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
13 5 0.12
14 32 0.78
15 4 0.10
ACGTcount: A:0.28, C:0.00, G:0.29, T:0.43
Consensus pattern (14 bp):
TAAGGTTTAGAGTT
Found at i:50481 original size:21 final size:21
Alignment explanation
Indices: 50457--50504 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
50447 AGGTTTAGAG
*
50457 TTTAAGGTTTATGTGTTAAGA
1 TTTAAGGTTTATATGTTAAGA
* * *
50478 TTTAGGGTTTATATGTTAGGG
1 TTTAAGGTTTATATGTTAAGA
50499 TTTAAG
1 TTTAAG
50505 TTATGCCATG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.48
Consensus pattern (21 bp):
TTTAAGGTTTATATGTTAAGA
Found at i:50501 original size:35 final size:35
Alignment explanation
Indices: 50395--50502 Score: 121
Period size: 35 Copynumber: 3.1 Consensus size: 35
50385 TCATAACTAA
* *
50395 TTATGTGATAAGGTTTAGGGTTTAGGAT-TTAGAGT
1 TTATGTGATAAGATTTAGGGTTTA-GATGTTAGGGT
* * *
50430 TTATGTGATAGGATTTAAGGTTTAGA-GTTTAAGGT
1 TTATGTGATAAGATTTAGGGTTTAGATG-TTAGGGT
* *
50465 TTATGTGTTAAGATTTAGGGTTTATATGTTAGGGT
1 TTATGTGATAAGATTTAGGGTTTAGATGTTAGGGT
50500 TTA
1 TTA
50503 AGTTATGCCA
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
34 2 0.03
35 57 0.95
36 1 0.02
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.45
Consensus pattern (35 bp):
TTATGTGATAAGATTTAGGGTTTAGATGTTAGGGT
Found at i:52224 original size:26 final size:26
Alignment explanation
Indices: 52194--52270 Score: 136
Period size: 26 Copynumber: 3.0 Consensus size: 26
52184 GTTTTGGTGT
*
52194 TTGGTTCTCTGTCCCTTGTTTTTTGC
1 TTGGTGCTCTGTCCCTTGTTTTTTGC
*
52220 TTGGTGCTCTGTCCCTTGTTTTGTGC
1 TTGGTGCTCTGTCCCTTGTTTTTTGC
52246 TTGGTGCTCTGTCCCTTGTTTTTTG
1 TTGGTGCTCTGTCCCTTGTTTTTTG
52271 TGTCTGCAGG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.00, C:0.22, G:0.23, T:0.55
Consensus pattern (26 bp):
TTGGTGCTCTGTCCCTTGTTTTTTGC
Found at i:52663 original size:17 final size:17
Alignment explanation
Indices: 52641--52677 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
52631 ATTCGAGTTT
*
52641 GAGTTCGAGCTTTAATC
1 GAGTTCGAGCTTGAATC
52658 GAGTTCGAGCTTGAATC
1 GAGTTCGAGCTTGAATC
52675 GAG
1 GAG
52678 CTCAAAATCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (17 bp):
GAGTTCGAGCTTGAATC
Found at i:52676 original size:11 final size:11
Alignment explanation
Indices: 52662--52714 Score: 52
Period size: 12 Copynumber: 4.6 Consensus size: 11
52652 TTAATCGAGT
*
52662 TCGAGCTTGAA
1 TCGAGCTTAAA
*
52673 TCGAGCTCAAAA
1 TCGAGCT-TAAA
*
52685 TCGAGCTCAAAA
1 TCGAGCT-TAAA
*
52697 TCGAGCTTCAA
1 TCGAGCTTAAA
52708 TCGAGCT
1 TCGAGCT
52715 CGAGTCTCGA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
11 16 0.43
12 21 0.57
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.23
Consensus pattern (11 bp):
TCGAGCTTAAA
Found at i:52688 original size:12 final size:12
Alignment explanation
Indices: 52671--52715 Score: 67
Period size: 12 Copynumber: 3.8 Consensus size: 12
52661 TTCGAGCTTG
52671 AATCGAGCTCAA
1 AATCGAGCTCAA
52683 AATCGAGCTCAA
1 AATCGAGCTCAA
52695 AATCGAGCTTC--
1 AATCGAGC-TCAA
52706 AATCGAGCTC
1 AATCGAGCTC
52716 GAGTCTCGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 2 0.06
11 8 0.25
12 20 0.62
13 2 0.06
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.20
Consensus pattern (12 bp):
AATCGAGCTCAA
Found at i:53883 original size:19 final size:18
Alignment explanation
Indices: 53861--53907 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
53851 CATAAAAACG
*
53861 ATAAAAAAAATCAGCAAAA
1 ATAAAAAAAAACAG-AAAA
53880 ATAAAAACAAAACAGAAAA
1 ATAAAAA-AAAACAGAAAA
53899 A-AAAAAAAA
1 ATAAAAAAAA
53908 CAAAAAGGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 3 0.12
18 5 0.19
19 12 0.46
20 6 0.23
ACGTcount: A:0.81, C:0.09, G:0.04, T:0.06
Consensus pattern (18 bp):
ATAAAAAAAAACAGAAAA
Found at i:53901 original size:16 final size:15
Alignment explanation
Indices: 53875--53913 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 15
53865 AAAAAATCAG
53875 CAAAAATAAAAACAAAA
1 CAAAAA-AAAAA-AAAA
53892 CAGAAAAAAAAAAAAA
1 CA-AAAAAAAAAAAAA
53908 CAAAAA
1 CAAAAA
53914 GGGGAGGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 4 0.19
16 6 0.29
17 7 0.33
18 4 0.19
ACGTcount: A:0.85, C:0.10, G:0.03, T:0.03
Consensus pattern (15 bp):
CAAAAAAAAAAAAAA
Found at i:56454 original size:6 final size:6
Alignment explanation
Indices: 56443--56470 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
56433 ATCGAATTTT
56443 TTTTAA TTTTAA TTTTAA TTTTAA TTTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTT
56471 CTCAATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTAA
Found at i:59620 original size:74 final size:74
Alignment explanation
Indices: 59520--59704 Score: 235
Period size: 74 Copynumber: 2.5 Consensus size: 74
59510 TTAAATGACT
* * * * *
59520 AAGGGTATCGGTACCTCAAAGGGGGTATCGGTATCCGTTAGACATTTTGTTTTTCTCGGAGCCAA
1 AAGGGTATCGGTACCTCTATGAGGGTATCGGTACCCATTAGACATTTTGTTTTTCTCGGAGCCAA
59585 AATTGACAC
66 AATTGACAC
* *
59594 AAGGGTATCGGTACCTCTATGAGGGTATCGGTACCCATTGGGCATTTTGTTTTTCTCGGAGCCAA
1 AAGGGTATCGGTACCTCTATGAGGGTATCGGTACCCATTAGACATTTTGTTTTTCTCGGAGCCAA
* *
59659 AATTGGCAT
66 AATTGACAC
* * * *
59668 AGGGGTATCAGTACACCCTATGAGGGGTATCGATACC
1 AAGGGTATCGGTAC-CTCTATGA-GGGTATCGGTACC
59705 TCACTATTTA
Statistics
Matches: 96, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
74 77 0.80
75 7 0.07
76 12 0.12
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.29
Consensus pattern (74 bp):
AAGGGTATCGGTACCTCTATGAGGGTATCGGTACCCATTAGACATTTTGTTTTTCTCGGAGCCAA
AATTGACAC
Found at i:61861 original size:13 final size:13
Alignment explanation
Indices: 61838--61881 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
61828 ATCCTAATGG
61838 ACAAT-TTTGAAA
1 ACAATGTTTGAAA
*
61850 ACTATGTTTGAAA
1 ACAATGTTTGAAA
61863 ACAATGTTTGAAA
1 ACAATGTTTGAAA
61876 ATCAAT
1 A-CAAT
61882 ATGTAGTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 4 0.14
13 20 0.71
14 4 0.14
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.34
Consensus pattern (13 bp):
ACAATGTTTGAAA
Found at i:62416 original size:22 final size:23
Alignment explanation
Indices: 62351--62410 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
62341 GTACCCTTAT
*
62351 AGGGTATCGATACACATTCAAAG
1 AGGGTATCGATACACATTGAAAG
*
62374 AGGGTATCGATACACGTTGAAAG
1 AGGGTATCGATACACATTGAAAG
62397 -GGGTATCGATACAC
1 AGGGTATCGATACAC
62411 TCTGAACAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 14 0.40
23 21 0.60
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.22
Consensus pattern (23 bp):
AGGGTATCGATACACATTGAAAG
Found at i:68228 original size:74 final size:74
Alignment explanation
Indices: 68150--68334 Score: 244
Period size: 74 Copynumber: 2.5 Consensus size: 74
68140 TTAAATGACT
* * * * * *
68150 AAGGGTATCGGTACCTCAAAGGGGGTATCGGTACCCGTTAGACATTTTGTTTTTCTTGGAGCCAA
1 AAGGGTATCGGTACCTCTATGGGGGTATCGGTACCCATTAGACATTCTATTTTTCTCGGAGCCAA
68215 AATTGACAC
66 AATTGACAC
* *
68224 AAGGGTATCGATACCTCTATGGGGGTATCGGTACCCATTAGGCATTCTATTTTTCTCGGAGCCAA
1 AAGGGTATCGGTACCTCTATGGGGGTATCGGTACCCATTAGACATTCTATTTTTCTCGGAGCCAA
* *
68289 AATTGGCAT
66 AATTGACAC
* *
68298 AGGGGTATCGGTACACCCTATGAGGGGTATCGGTACC
1 AAGGGTATCGGTAC-CTCTATG-GGGGTATCGGTACC
68335 TCACTATTTA
Statistics
Matches: 96, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
74 76 0.79
75 6 0.06
76 14 0.15
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (74 bp):
AAGGGTATCGGTACCTCTATGGGGGTATCGGTACCCATTAGACATTCTATTTTTCTCGGAGCCAA
AATTGACAC
Done.