Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000816.1 Hibiscus syriacus cultivar Beakdansim tig00001580_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: 58127
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:4353 original size:64 final size:64
Alignment explanation
Indices: 4244--4407 Score: 185
Period size: 64 Copynumber: 2.5 Consensus size: 64
4234 TTTTCAAAGG
4244 GATGTACCGATGCACTAATGA-ATGCATCGATACAC-ACCTAATTTTATTG-AACATCAAATACT
1 GATGTACCGATGCAC--AT-ACATGCATCGATACACTACCTAATTTTA-TGAAACATCAAATACT
4306 TTT
62 TTT
* * *
4309 GATGTACCGATGCACATACCATGCATCGATTCACTA-C-AAGTTTTATGAAACATCGAATGCTTT
1 GATGTACCGATGCACATA-CATGCATCGATACACTACCTAA-TTTTATGAAACATCAAATACTTT
4372 T
64 T
* *
4373 GATGTACCGATGCACAGATCATGCATCGATGCACT
1 GATGTACCGATGCACATA-CATGCATCGATACACT
4408 CCTGGCTCTT
Statistics
Matches: 88, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
62 1 0.01
63 6 0.07
64 65 0.74
65 16 0.18
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (64 bp):
GATGTACCGATGCACATACATGCATCGATACACTACCTAATTTTATGAAACATCAAATACTTTT
Found at i:4452 original size:65 final size:64
Alignment explanation
Indices: 4309--4452 Score: 175
Period size: 64 Copynumber: 2.2 Consensus size: 64
4299 AAATACTTTT
* * * *
4309 GATGTACCGATGCACATACCATGCATCGATTCACTACAAGTTTTATGAAACATCGAATGCTTTT
1 GATGTACCGATGCACAGACCATGCATCGATGCACTACAAGTTTTATGAAACATCGAATGCATTA
* * **
4373 GATGTACCGATGCACAGATCATGCATCGATGCACTCCTGGCTCTTT-TGAAACATCGAATGCAAT
1 GATGTACCGATGCACAGACCATGCATCGATGCACTACAAG-T-TTTATGAAACATCGAATGC-AT
4437 TA
63 TA
4439 G-TGTACCGATGCAC
1 GATGTACCGATGCAC
4453 TAGGTCTTAT
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
64 34 0.49
65 29 0.42
66 6 0.09
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (64 bp):
GATGTACCGATGCACAGACCATGCATCGATGCACTACAAGTTTTATGAAACATCGAATGCATTA
Found at i:6682 original size:30 final size:30
Alignment explanation
Indices: 6615--6683 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
6605 AAAAACTGGC
* * *
6615 AAGAATTCAAGTTTAAATTTGTTACCACTA
1 AAGAATTTAAGTTTAAATTTGCTACCACCA
6645 AAGAATTTAAGTTT-AATTTCGCTACCACCA
1 AAGAATTTAAGTTTAAATTT-GCTACCACCA
6675 AAGAATTTA
1 AAGAATTTA
6684 TGTTGACAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 5 0.14
30 30 0.86
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (30 bp):
AAGAATTTAAGTTTAAATTTGCTACCACCA
Found at i:17050 original size:23 final size:21
Alignment explanation
Indices: 16995--17076 Score: 80
Period size: 23 Copynumber: 3.8 Consensus size: 21
16985 ATGCGCGCTA
16995 GGTATCGATACCCCCATTGAATG
1 GGTATCGATACCCCC-TTGAA-G
*
17018 GGCA-CTGATACCCTCCTTGAACG
1 GGTATC-GATACCC-CCTTGAA-G
17041 GGTATCGATACCCCC-TG-AG
1 GGTATCGATACCCCCTTGAAG
*
17060 GGTACCGATACCCCCTT
1 GGTATCGATACCCCCTT
17077 TGGGTTCTGG
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
19 15 0.29
20 2 0.04
21 2 0.04
22 3 0.06
23 26 0.51
24 3 0.06
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.23
Consensus pattern (21 bp):
GGTATCGATACCCCCTTGAAG
Found at i:18160 original size:15 final size:15
Alignment explanation
Indices: 18140--18169 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
18130 CTAATGCATT
18140 TGGATTAGATAATGA
1 TGGATTAGATAATGA
18155 TGGATTAGATAATGA
1 TGGATTAGATAATGA
18170 AAAAGAAACA
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:0.40, C:0.00, G:0.27, T:0.33
Consensus pattern (15 bp):
TGGATTAGATAATGA
Found at i:19309 original size:19 final size:18
Alignment explanation
Indices: 19285--19352 Score: 65
Period size: 18 Copynumber: 3.9 Consensus size: 18
19275 GGGAGTAATA
19285 ATTTTCAAAATTAATTTTG
1 ATTTTCAAAA-TAATTTTG
19304 ATTTTCAAAATAA-TTT-
1 ATTTTCAAAATAATTTTG
* *
19320 -TTCT-AAGAA-AATCTTG
1 ATTTTCAA-AATAATTTTG
19336 ATTTTCAAAATAATTTT
1 ATTTTCAAAATAATTTT
19353 TCTAAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
14 4 0.10
15 7 0.18
17 8 0.21
18 10 0.26
19 10 0.26
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (18 bp):
ATTTTCAAAATAATTTTG
Found at i:19337 original size:32 final size:32
Alignment explanation
Indices: 19301--19366 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
19291 AAAATTAATT
19301 TTGATTTTCAAAATAATTTTTCTAAGAAAATC
1 TTGATTTTCAAAATAATTTTTCTAAGAAAATC
19333 TTGATTTTCAAAATAATTTTTCTAAGAAAATC
1 TTGATTTTCAAAATAATTTTTCTAAGAAAATC
19365 TT
1 TT
19367 AAAATTACTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (32 bp):
TTGATTTTCAAAATAATTTTTCTAAGAAAATC
Found at i:22191 original size:27 final size:25
Alignment explanation
Indices: 22152--22204 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 25
22142 AAATTATAAT
*
22152 TAAAAATTAAAAATTGTTTTCTGAAAA
1 TAAAAATTAAAAA-TATTTTCT-AAAA
22179 TAAAAA-TAGAAAATATTTTCTAAAA
1 TAAAAATTA-AAAATATTTTCTAAAA
22204 T
1 T
22205 CAAACATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 5 0.21
26 9 0.38
27 10 0.42
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.36
Consensus pattern (25 bp):
TAAAAATTAAAAATATTTTCTAAAA
Found at i:22600 original size:21 final size:21
Alignment explanation
Indices: 22562--22601 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
22552 ATTTAAGAAC
**
22562 TCTAAACTCCAAGCTATAACA
1 TCTAAACTCCAAAATATAACA
*
22583 TCTAAACTCTAAAATATAA
1 TCTAAACTCCAAAATATAA
22602 ACCTTAAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.23, G:0.03, T:0.28
Consensus pattern (21 bp):
TCTAAACTCCAAAATATAACA
Found at i:38699 original size:16 final size:16
Alignment explanation
Indices: 38678--38713 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
38668 AAAGCAGGGA
38678 AGATTAATAAGATATC
1 AGATTAATAAGATATC
38694 AGATTAATAAGATATC
1 AGATTAATAAGATATC
38710 AGAT
1 AGAT
38714 AAGTGTCATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.50, C:0.06, G:0.14, T:0.31
Consensus pattern (16 bp):
AGATTAATAAGATATC
Found at i:38818 original size:13 final size:12
Alignment explanation
Indices: 38788--38812 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38778 CGGCCTGAGA
38788 ACAAAAAAACAT
1 ACAAAAAAACAT
38800 ACAAAAAAACAT
1 ACAAAAAAACAT
38812 A
1 A
38813 AGAAAACGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.16, G:0.00, T:0.08
Consensus pattern (12 bp):
ACAAAAAAACAT
Found at i:46146 original size:137 final size:137
Alignment explanation
Indices: 45927--46258 Score: 427
Period size: 137 Copynumber: 2.4 Consensus size: 137
45917 AGGTGCCGAA
* **
45927 TTAATTATTCGATAGTCCATAATTGATTAAAATTAATTAGGATTAATGCTAGAGCCTCCATCTTA
1 TTAATTATTCGA-AGTCAATAATT-ATTAAAATTAATTAGGATTAATATTAGAGCCTCCATCTTA
* * * *
45992 GGCCTAATTTTATATTTAATCCTTAAATTAGGTGAACTCTTAATTTGGTCATCGCTTTTACTTGA
64 GGCCTAATTTCACATTTAATCCTTAAATTAGGAGAACTCTTAATTTGGTCATCGCTTTTACTCGA
46057 GATTCCAA-T
129 GATT-CAACT
* *
46066 TTAATTATTCGAA-TCGATAATATATTAAAATTAATTAGGATTAATATTAAAGCCTCCATCTTAG
1 TTAATTATTCGAAGTCAATAAT-TATTAAAATTAATTAGGATTAATATTAGAGCCTCCATCTTAG
* * * * *
46130 GCTTAATTTCACATTTAGTCCTTAAATTAGGAGGATTCTTAATTTGGTCATCGCTTTTTCTCGAG
65 GCCTAATTTCACATTTAATCCTTAAATTAGGAGAACTCTTAATTTGGTCATCGCTTTTACTCGAG
*
46195 GTTCAACT
130 ATTCAACT
* * *
46203 TTAATTATTCGAATTGCAATAATGATTAAAATTAATTTAAG-TTAATATTAGAGCCT
1 TTAATTATTCGAAGT-CAATAATTATTAAAATTAA-TTAGGATTAATATTAGAGCCT
46259 ATATTTTTAG
Statistics
Matches: 170, Mismatches: 18, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
136 3 0.02
137 117 0.69
138 28 0.16
139 22 0.13
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.41
Consensus pattern (137 bp):
TTAATTATTCGAAGTCAATAATTATTAAAATTAATTAGGATTAATATTAGAGCCTCCATCTTAGG
CCTAATTTCACATTTAATCCTTAAATTAGGAGAACTCTTAATTTGGTCATCGCTTTTACTCGAGA
TTCAACT
Found at i:48672 original size:2 final size:2
Alignment explanation
Indices: 48665--48761 Score: 194
Period size: 2 Copynumber: 48.5 Consensus size: 2
48655 TGAGTTATTC
48665 TA 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 TA
48707 TA 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 TA
48749 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
48762 GTATGTACGT
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 95 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.