Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003148.1 Hibiscus syriacus cultivar Beakdansim tig00006623_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: 62737
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1818 original size:15 final size:15
Alignment explanation
Indices: 1798--1826 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1788 TGGCCGACCG
1798 AACCGAATTAACCAT
1 AACCGAATTAACCAT
1813 AACCGAATTAACCA
1 AACCGAATTAACCA
1827 AACTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.28, G:0.07, T:0.17
Consensus pattern (15 bp):
AACCGAATTAACCAT
Found at i:2171 original size:176 final size:180
Alignment explanation
Indices: 1939--2318 Score: 569
Period size: 178 Copynumber: 2.1 Consensus size: 180
1929 AATTTTCTAA
* * * *
1939 TTTATATAAAAATTAAATA-TTTTTAATTCAAAAAAAGTTTATAATTAATTTAAAT-A-ATATAA
1 TTTATATATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATATAA
**
2001 TTATAAAATAAAAATTTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTT-AAAGTTAT
66 TTATAAAATAAAAAAATTAGAT-AATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
* *
2065 TGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTT-AGCCC-AT-
130 TGGATCTTAAATTATTAATTGAGTTTTAAATGATTTGGG-TTGAGCCCAATG
2114 TTTATATATATATTTAATATTTTTTAATT-AAAAAACAGTTTACAATTAATTTAAATAATATATA
1 TTTATATATATATTTAATATTTTTTAATTCAAAAAA-AGTTTACAATTAATTTAAATAATATATA
*
2178 ATTATAAAATAAAAAAATTATATAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
65 ATTATAAAATAAAAAAATTAGATAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
2243 TGGATCTTAAATTATTAATTGAGTTTTAAATGATTTGGGTTGAGCCCATATG
130 TGGATCTTAAATTATTAATTGAGTTTTAAATGATTTGGGTTGAGCCCA-ATG
2295 TTATATATAATATATTTAATATTT
1 TT-TATAT-ATATATTTAATATTT
2319 AAAATTTAAT
Statistics
Matches: 185, Mismatches: 9, Indels: 14
0.89 0.04 0.07
Matches are distributed among these distances:
175 22 0.12
176 28 0.15
177 36 0.19
178 75 0.41
180 2 0.01
181 2 0.01
182 5 0.03
183 15 0.08
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.46
Consensus pattern (180 bp):
TTTATATATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATATAA
TTATAAAATAAAAAAATTAGATAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
GGATCTTAAATTATTAATTGAGTTTTAAATGATTTGGGTTGAGCCCAATG
Found at i:4123 original size:3 final size:3
Alignment explanation
Indices: 4115--4143 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4105 TAAATACTAT
4115 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
4144 GAAATAGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:6636 original size:23 final size:23
Alignment explanation
Indices: 6607--6692 Score: 136
Period size: 23 Copynumber: 3.7 Consensus size: 23
6597 TGTACTTCTG
*
6607 TGCTGAATCATTCAGCACTGTTT
1 TGCTGAATCAGTCAGCACTGTTT
*
6630 TGTTGAATCAGTCAGCACTGTTT
1 TGCTGAATCAGTCAGCACTGTTT
* *
6653 TGCTGAATCAATCAGTACTGTTT
1 TGCTGAATCAGTCAGCACTGTTT
6676 TGCTGAATCAGTCAGCA
1 TGCTGAATCAGTCAGCA
6693 TTGAATCATT
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (23 bp):
TGCTGAATCAGTCAGCACTGTTT
Found at i:15170 original size:15 final size:15
Alignment explanation
Indices: 15132--15170 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
15122 TCCTATGGTA
* *
15132 GAAGAAGACTCAGAT
1 GAAGAAGAGTCAAAT
15147 GAAGAAGAGTCAAAT
1 GAAGAAGAGTCAAAT
15162 GAAGAAGAG
1 GAAGAAGAG
15171 GTTCAGACCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.51, C:0.08, G:0.31, T:0.10
Consensus pattern (15 bp):
GAAGAAGAGTCAAAT
Found at i:24625 original size:3 final size:3
Alignment explanation
Indices: 24617--24747 Score: 217
Period size: 3 Copynumber: 43.7 Consensus size: 3
24607 AATATATATT
* *
24617 TAA TAA TAA TAA TAA TGA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
24665 TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
24713 TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
24748 TGGATAAAAA
Statistics
Matches: 118, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 118 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:25128 original size:113 final size:112
Alignment explanation
Indices: 24997--25422 Score: 717
Period size: 113 Copynumber: 3.8 Consensus size: 112
24987 TCTTGATGAG
*
24997 TTCTTCTCATTATGAACTTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTG
1 TTCTTCTCATTATGAAC-TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTG
* * *
25062 GAAAAGATAATCCATCAATTGATGAATTCAGGTAAAAGGTTGAACAAA
65 GAAAAAATAATCCATCAAGTGATGAATTCAGATAAAAGGTTGAACAAA
25110 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTG
* *
25175 GAAAAAATAATCCATCCAGTGATGAATTCAGATTAAAGGTTGAACAAA
65 GAAAAAATAATCCATCAAGTGATGAATTCAGATAAAAGGTTGAACAAA
*
25223 TTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA-CTTCTCTG
* *
25288 GAAAAAATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAA
65 GAAAAAATAATCCATCAAGTGATGAATTCAGATAAAAGGTTGAACAAA
*
25336 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTCTGG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGG
* *
25401 AAAAGATAATCCATCAATTGAT
66 AAAAAATAATCCATCAAGTGAT
25423 AGATTTGAAT
Statistics
Matches: 296, Mismatches: 15, Indels: 5
0.94 0.05 0.02
Matches are distributed among these distances:
112 67 0.23
113 228 0.77
114 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (112 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGG
AAAAAATAATCCATCAAGTGATGAATTCAGATAAAAGGTTGAACAAA
Found at i:26309 original size:84 final size:84
Alignment explanation
Indices: 26160--26396 Score: 422
Period size: 84 Copynumber: 2.8 Consensus size: 84
26150 ACTGAATCAG
* *
26160 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATCG-GCAAATTCATCTTCTAAATTCAATG
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTCAATG
*
26224 ATTGGTTCTGTCAAACCAA
66 ATTGGTTCTGCCAAACCAA
*
26243 ATCAGATAACTCAAAGAACACCTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTCAATG
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTCAATG
*
26308 ATTGGTTCTGCCAAACCAG
66 ATTGGTTCTGCCAAACCAA
26327 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTCAATG
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTCAATG
26392 ATTGG
66 ATTGG
26397 ACTAAGATAT
Statistics
Matches: 147, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
83 37 0.25
84 110 0.75
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.27
Consensus pattern (84 bp):
ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTCAATG
ATTGGTTCTGCCAAACCAA
Found at i:27540 original size:19 final size:20
Alignment explanation
Indices: 27518--27561 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
27508 CTTGACCCCC
27518 CTTTTTCT-T-TTTTTCTTTT
1 CTTTTTCTATCTTTTT-TTTT
27537 C-TTTTCTATCTTTTTTTTT
1 CTTTTTCTATCTTTTTTTTT
27556 CTTTTT
1 CTTTTT
27562 TCTTCTCTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 6 0.27
19 7 0.32
20 9 0.41
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (20 bp):
CTTTTTCTATCTTTTTTTTT
Found at i:38190 original size:13 final size:15
Alignment explanation
Indices: 38168--38204 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
38158 TTTGACAGAA
38168 AAAT-AAATAC-TG-
1 AAATAAAATACTTGC
38180 AAATAAAATACTTGC
1 AAATAAAATACTTGC
38195 AAATAAAATA
1 AAATAAAATA
38205 AAACATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 6 0.27
14 2 0.09
15 10 0.45
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (15 bp):
AAATAAAATACTTGC
Found at i:38958 original size:20 final size:21
Alignment explanation
Indices: 38935--38975 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
38925 TATTATATGT
**
38935 ATATTTATGAATAT-ATAAAA
1 ATATTTAACAATATAATAAAA
38955 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
38976 TAAAAATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATTTAACAATATAATAAAA
Found at i:40368 original size:3 final size:3
Alignment explanation
Indices: 40360--40493 Score: 223
Period size: 3 Copynumber: 44.7 Consensus size: 3
40350 AATATATATT
* *
40360 TAA TAA TAA TAA TAA TGA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
40408 TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
40456 TAG TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
40494 TGGATAAAAA
Statistics
Matches: 121, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 121 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:47280 original size:16 final size:16
Alignment explanation
Indices: 47259--47292 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
47249 TTACTATTCA
*
47259 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
47275 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
47291 CG
1 CG
47293 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:48060 original size:15 final size:16
Alignment explanation
Indices: 48042--48074 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
48032 GTGGCAGATC
48042 AAAATCCAG-ACGGGA
1 AAAATCCAGAACGGGA
*
48057 AAAATCTAGAACGGGA
1 AAAATCCAGAACGGGA
48073 AA
1 AA
48075 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.15, G:0.24, T:0.09
Consensus pattern (16 bp):
AAAATCCAGAACGGGA
Found at i:53199 original size:28 final size:27
Alignment explanation
Indices: 53151--53216 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 27
53141 AATAAAAATG
* * * *
53151 ATAAATTATTAATATATTAAATTTTTA
1 ATAAATAATTAAAATACTAAATTATTA
53178 ATAAATAATTTAAAATACTAAATTATTA
1 ATAAATAA-TTAAAATACTAAATTATTA
* *
53206 ATTATTAATTA
1 ATAAATAATTA
53217 TTATTTTACT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
27 10 0.31
28 22 0.69
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (27 bp):
ATAAATAATTAAAATACTAAATTATTA
Found at i:55293 original size:18 final size:19
Alignment explanation
Indices: 55269--55313 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
55259 CCCAGTAATC
55269 ATATTCC-CTGGTAATCTT
1 ATATTCCACTGGTAATCTT
*
55287 TTATTCCCACTGGTAATCTT
1 ATATT-CCACTGGTAATCTT
55307 ATATTCC
1 ATATTCC
55314 GTGAACCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 15 0.65
ACGTcount: A:0.22, C:0.24, G:0.09, T:0.44
Consensus pattern (19 bp):
ATATTCCACTGGTAATCTT
Found at i:55301 original size:20 final size:20
Alignment explanation
Indices: 55276--55313 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
55266 ATCATATTCC
*
55276 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTATATTCCCA
55296 CTGGTAATCTTATATTCC
1 CTGGTAATCTTATATTCC
55314 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTATATTCCCA
Done.