Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000826.1 Hibiscus syriacus cultivar Beakdansim tig00001598_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: 46329
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Found at i:1949 original size:22 final size:22
Alignment explanation
Indices: 1922--1966 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1912 TTGATCATTG
*
1922 TATATATGATTTTTATCATGAA
1 TATATATGATGTTTATCATGAA
*
1944 TATATATGATGTTTATTATGAA
1 TATATATGATGTTTATCATGAA
1966 T
1 T
1967 GTTACTTCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.51
Consensus pattern (22 bp):
TATATATGATGTTTATCATGAA
Found at i:2225 original size:61 final size:61
Alignment explanation
Indices: 2115--2318 Score: 223
Period size: 61 Copynumber: 3.3 Consensus size: 61
2105 GCATGTTTAT
* * **
2115 ATTAGCACTAGTGTGTAAGGACACTAGGTGTAGGTGGTGAGCACAACCTTATGTGTAATATTCAG
1 ATTAGCACTAGAGTGTAA--AC-CTA-GTGTAGGTGGTGGGCATGACCTTATGTGTAATATTCAG
* *
2180 ATTAGCACTAGAGTGTAAACCTAGTGTAGGTGGTGGGCATGACCTTATGTGTCATATTTAG
1 ATTAGCACTAGAGTGTAAACCTAGTGTAGGTGGTGGGCATGACCTTATGTGTAATATTCAG
* * * * * * *
2241 ATCAACACTATAGTGTAAACCTAATGTAGGTTGTGGGCCTGACCTTATGTTTAATA-TC-G
1 ATTAGCACTAGAGTGTAAACCTAGTGTAGGTGGTGGGCATGACCTTATGTGTAATATTCAG
*
2300 AATTAGCACTAGAGCGTAA
1 -ATTAGCACTAGAGTGTAA
2319 GCTTTGTGCA
Statistics
Matches: 119, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
59 1 0.01
60 15 0.13
61 81 0.68
62 3 0.03
63 2 0.02
65 17 0.14
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (61 bp):
ATTAGCACTAGAGTGTAAACCTAGTGTAGGTGGTGGGCATGACCTTATGTGTAATATTCAG
Found at i:4428 original size:4 final size:4
Alignment explanation
Indices: 4380--4445 Score: 50
Period size: 4 Copynumber: 16.8 Consensus size: 4
4370 TATACCCAAA
* **
4380 AAAT AAA- AAA- AAAT AGAAT AAA- ATAT AAATT AAAT ATCT -AAT AAAT
1 AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAA-T AAAT AAAT AAAT AAAT
4426 AAAT AAAT AAAT GAAAT AAA
1 AAAT AAAT AAAT -AAAT AAA
4446 ACAATTTAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
3 9 0.18
4 29 0.58
5 12 0.24
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:4478 original size:17 final size:18
Alignment explanation
Indices: 4419--4480 Score: 55
Period size: 17 Copynumber: 3.7 Consensus size: 18
4409 TTAAATATCT
4419 AATAAATAAATA-AA-TA
1 AATAAATAAATACAATTA
4435 AATGAAATAAA-ACAATTTA
1 AAT-AAATAAATACAA-TTA
*
4454 AA-AGA-AAATACAATTA
1 AATAAATAAATACAATTA
4470 AATAAA-AAATA
1 AATAAATAAATA
4481 ATGATAAAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
16 12 0.32
17 22 0.58
19 4 0.11
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (18 bp):
AATAAATAAATACAATTA
Found at i:13341 original size:4 final size:4
Alignment explanation
Indices: 13332--13492 Score: 322
Period size: 4 Copynumber: 40.2 Consensus size: 4
13322 AAGAACCATG
13332 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
13380 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
13428 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
13476 ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT A
13493 GGATTACCTA
Statistics
Matches: 157, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 157 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:17447 original size:30 final size:30
Alignment explanation
Indices: 17411--17505 Score: 86
Period size: 30 Copynumber: 3.1 Consensus size: 30
17401 ACCAATTTGT
*
17411 AACTTTTTAAA-ATTATCATTTTGGTC-CCTA
1 AACTTTTCAAAGATTAT-ATTTTGGTCACC-A
*
17441 AACTTTTCAAAGTTTATATTTTGGTCACCA
1 AACTTTTCAAAGATTATATTTTGGTCACCA
* ** * *
17471 AACTTTACAAATTCTTATAATTTGGTCACTA
1 AACTTTTCAAA-GATTATATTTTGGTCACCA
17502 AACT
1 AACT
17506 AAATCCATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
30 30 0.55
31 25 0.45
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (30 bp):
AACTTTTCAAAGATTATATTTTGGTCACCA
Found at i:17495 original size:31 final size:30
Alignment explanation
Indices: 17430--17505 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 30
17420 AAATTATCAT
* *
17430 TTTGGTC-CCTAAACTTTTCAAAGTTTATAT
1 TTTGGTCACC-AAACTTTACAAAGTTTATAA
*
17460 TTTGGTCACCAAACTTTACAAATTCTTATAA
1 TTTGGTCACCAAACTTTACAAAGT-TTATAA
*
17491 TTTGGTCACTAAACT
1 TTTGGTCACCAAACT
17506 AAATCCATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
30 19 0.47
31 21 0.52
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.42
Consensus pattern (30 bp):
TTTGGTCACCAAACTTTACAAAGTTTATAA
Found at i:22151 original size:35 final size:35
Alignment explanation
Indices: 22092--22159 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
22082 AACATAATCC
* *
22092 TCAATTTCATTCTAAAACTCAAATTCTAAAATAAT
1 TCAATTACATTATAAAACTCAAATTCTAAAATAAT
* *
22127 TCAATTACATTATAAACCTTAAATTCTAAAATA
1 TCAATTACATTATAAAACTCAAATTCTAAAATA
22160 CTTTAATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (35 bp):
TCAATTACATTATAAAACTCAAATTCTAAAATAAT
Found at i:25623 original size:37 final size:37
Alignment explanation
Indices: 25575--25873 Score: 332
Period size: 37 Copynumber: 8.6 Consensus size: 37
25565 AAAATAAAAC
* *
25575 ATATATTATATAGTTTTGAGAACATTTTTGAAAATAT
1 ATATAATATATAGTTTTGAAAACATTTTTGAAAATAT
* *
25612 ATATAATATATAGTTTTGAAAATATTTTTGAAAACAT
1 ATATAATATATAGTTTTGAAAACATTTTTGAAAATAT
*
25649 ATATAATATA-A-TTTT-AAAAC-GTTTTG-AAA-AT
1 ATATAATATATAGTTTTGAAAACATTTTTGAAAATAT
*
25680 ATATAATATATAGTTTTGAAAACATTTTTTTAAAATAT
1 ATATAATATATAGTTTTGAAAACA-TTTTTGAAAATAT
25718 ATATAATATATAGTTTTGAAAACATTTTTGAAAATAT
1 ATATAATATATAGTTTTGAAAACATTTTTGAAAATAT
*
25755 ATATAATATATAGTTTT-AAAAC-GTTTTG-AAA-AT
1 ATATAATATATAGTTTTGAAAACATTTTTGAAAATAT
*
25788 ATATAATATATAG-TTTG--GA-ATTTTT-----T-T
1 ATATAATATATAGTTTTGAAAACATTTTTGAAAATAT
* * * *
25815 TTAAAATATATAGTTTTGAAAACATTTTTGAATATGT
1 ATATAATATATAGTTTTGAAAACATTTTTGAAAATAT
*
25852 ATATAATATATAGTTTTTAAAA
1 ATATAATATATAGTTTTGAAAA
25874 AGGTTTTGTG
Statistics
Matches: 224, Mismatches: 18, Indels: 40
0.79 0.06 0.14
Matches are distributed among these distances:
27 12 0.05
28 4 0.02
30 1 0.00
31 23 0.10
32 7 0.03
33 24 0.11
34 12 0.05
35 9 0.04
36 11 0.05
37 95 0.42
38 26 0.12
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.45
Consensus pattern (37 bp):
ATATAATATATAGTTTTGAAAACATTTTTGAAAATAT
Found at i:25732 original size:106 final size:108
Alignment explanation
Indices: 25570--25873 Score: 420
Period size: 106 Copynumber: 2.9 Consensus size: 108
25560 TTTTAAAAAT
* * *
25570 AAAACATATATTATATAGTTTTGAGAACA-TTTTTGAAAATATATATAATATATAGTTTTGAAAA
1 AAAATATATAATATATAGTTTTGAGAACATTTTTTTAAAATATATATAATATATAGTTTTGAAAA
*
25634 TATTTTTGAAAACATATATAATATA-A-TTTTAAAACGTTTTG
66 CATTTTTGAAAACATATATAATATATAGTTTTAAAACGTTTTG
*
25675 AAAATATATAATATATAGTTTTGAAAACATTTTTTTAAAATATATATAATATATAGTTTTGAAAA
1 AAAATATATAATATATAGTTTTGAGAACATTTTTTTAAAATATATATAATATATAGTTTTGAAAA
*
25740 CATTTTTGAAAATATATATAATATATAGTTTTAAAACGTTTTG
66 CATTTTTGAAAACATATATAATATATAGTTTTAAAACGTTTTG
25783 AAAATATATAATATATAG-TTTG-G-A-ATTTTTTT----T-TA-A-AATATATAGTTTTGAAAA
1 AAAATATATAATATATAGTTTTGAGAACATTTTTTTAAAATATATATAATATATAGTTTTGAAAA
* **
25837 CATTTTTGAATATGTATATAATATATAGTTTTTAAAA
66 CATTTTTGAAAACATATATAATATATAG-TTTTAAAA
25874 AGGTTTTGTG
Statistics
Matches: 186, Mismatches: 9, Indels: 15
0.89 0.04 0.07
Matches are distributed among these distances:
97 44 0.24
98 9 0.05
99 2 0.01
100 1 0.01
104 8 0.04
105 27 0.15
106 57 0.31
107 5 0.03
108 33 0.18
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (108 bp):
AAAATATATAATATATAGTTTTGAGAACATTTTTTTAAAATATATATAATATATAGTTTTGAAAA
CATTTTTGAAAACATATATAATATATAGTTTTAAAACGTTTTG
Found at i:26247 original size:65 final size:64
Alignment explanation
Indices: 26178--26339 Score: 200
Period size: 65 Copynumber: 2.5 Consensus size: 64
26168 GAATAAATTG
* * * * *
26178 AACATCGAATGCAGTTTATGCA-CTGATGCACTCTCCATGCATCGATGCACTCAGGTTTTAATGA
1 AACATCGAATGCATTTTATGCATC-GATGCACACACCATGCATCGATGCACTCAGG-CTTAATCA
26242 A
64 A
* * * *
26243 AACATTGAATGCATTTTATGCATCGATGCACACACCATGCATTGATGCACTTAGGCTTATTCAA
1 AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTCAGGCTTAATCAA
* *
26307 AAAATCGAATGCATTTTATCCATCGATGCACAC
1 AACATCGAATGCATTTTATGCATCGATGCACAC
26340 TTAGTGTACC
Statistics
Matches: 84, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 36 0.43
65 47 0.56
66 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (64 bp):
AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTCAGGCTTAATCAA
Found at i:31269 original size:24 final size:24
Alignment explanation
Indices: 31242--31299 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
31232 AATCATGTCC
31242 TAAGGAATCACATTTACTAGTTGT
1 TAAGGAATCACATTTACTAGTTGT
31266 TAAGGAATCACATTTACTAGTTGT
1 TAAGGAATCACATTTACTAGTTGT
31290 TAAGAGAATC
1 TAAG-GAATC
31300 TTTAGGTACC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 28 0.85
25 5 0.15
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.34
Consensus pattern (24 bp):
TAAGGAATCACATTTACTAGTTGT
Found at i:37593 original size:6 final size:6
Alignment explanation
Indices: 37582--37609 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
37572 GTAAAGTTTG
37582 TTTTTA TTTTTA TTTTTA TTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTT
37610 GAAAATGTTA
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:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:42039 original size:14 final size:16
Alignment explanation
Indices: 42022--42070 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
42012 TCATAATATT
42022 ATATTTT-AAAG-AAA
1 ATATTTTGAAAGTAAA
*
42036 ATATTTTGAGAGTAAA
1 ATATTTTGAAAGTAAA
*
42052 ATATTTTGAGAGTATAA
1 ATATTTTGAAAGTA-AA
42069 AT
1 AT
42071 GATCAAGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
14 7 0.23
15 3 0.10
16 17 0.55
17 4 0.13
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39
Consensus pattern (16 bp):
ATATTTTGAAAGTAAA
Found at i:42054 original size:16 final size:16
Alignment explanation
Indices: 42033--42070 Score: 67
Period size: 16 Copynumber: 2.3 Consensus size: 16
42023 TATTTTAAAG
42033 AAAATATTTTGAGAGT
1 AAAATATTTTGAGAGT
42049 AAAATATTTTGAGAGT
1 AAAATATTTTGAGAGT
42065 ATAAAT
1 A-AAAT
42071 GATCAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.37
Consensus pattern (16 bp):
AAAATATTTTGAGAGT
Found at i:44344 original size:15 final size:16
Alignment explanation
Indices: 44324--44358 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
44314 ACAAAATGGC
44324 ATGACCCTC-TTTAAG
1 ATGACCCTCTTTTAAG
44339 ATGACCCTCTTTTAAG
1 ATGACCCTCTTTTAAG
44355 ATGA
1 ATGA
44359 TCCAAGTTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (16 bp):
ATGACCCTCTTTTAAG
Done.