Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001136.1 Hibiscus syriacus cultivar Beakdansim tig00002264_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: 41091
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4393 original size:22 final size:21
Alignment explanation
Indices: 4365--4427 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 21
4355 TTTTGGTGCA
*
4365 GAGGGAATCGATTCCTCCCCCT
1 GAGGGAACCGATTCC-CCCCCT
**
4387 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCCT
4408 GAAGGGAACCGATTCCCCCC
1 G-AGGGAACCGATTCCCCCC
4428 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.14
22 31 0.86
ACGTcount: A:0.21, C:0.37, G:0.24, T:0.19
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCCT
Found at i:4435 original size:21 final size:20
Alignment explanation
Indices: 4367--4448 Score: 56
Period size: 22 Copynumber: 3.9 Consensus size: 20
4357 TTGGTGCAGA
* *
4367 GGGAATCGATTCCTCCCCCTG
1 GGGAACCGATTCC-CCCCCAG
** *
4388 AGGGAACCGATTCCCCCTTTGAA
1 -GGGAACCGATTCCCCC--CCAG
4411 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCC-CAG
* *
4432 GGGAATCGATACCCCCC
1 GGGAACCGATTCCCCCC
4449 TGGGGATCTG
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
21 19 0.40
22 28 0.60
ACGTcount: A:0.22, C:0.38, G:0.23, T:0.17
Consensus pattern (20 bp):
GGGAACCGATTCCCCCCCAG
Found at i:4448 original size:44 final size:44
Alignment explanation
Indices: 4366--4449 Score: 100
Period size: 44 Copynumber: 1.9 Consensus size: 44
4356 TTTGGTGCAG
* * *
4366 AGGGAATCGATTCCTCCCCCTGAGGGAACCGATTCCCCCTTTGA
1 AGGGAACCGATTCCTCCCCCAGAGGGAACCGATCCCCCCTTTGA
*
4410 AGGGAACCGATTCC-CCCCACAG-GGGAATCGATACCCCCCT
1 AGGGAACCGATTCCTCCCC-CAGAGGGAACCGAT-CCCCCCT
4450 GGGGATCTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
43 13 0.38
44 21 0.62
ACGTcount: A:0.23, C:0.37, G:0.23, T:0.18
Consensus pattern (44 bp):
AGGGAACCGATTCCTCCCCCAGAGGGAACCGATCCCCCCTTTGA
Found at i:8490 original size:22 final size:22
Alignment explanation
Indices: 8465--8541 Score: 145
Period size: 22 Copynumber: 3.5 Consensus size: 22
8455 AATAAAGCTT
8465 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
8487 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
8509 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
8531 TCATCTTTGAA
1 TCATCTTTGAA
8542 GATTGTAGAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:13465 original size:7 final size:6
Alignment explanation
Indices: 13455--13558 Score: 65
Period size: 7 Copynumber: 16.5 Consensus size: 6
13445 CAATTTTCCT
*
13455 TTTTTC ATTTTTC -TTTTC TTTTTTC TTTTTC TTTCT- TTTTTC TTTCTTTC
1 TTTTTC -TTTTTC TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC -TT-TTTC
*
13505 TTTCTTTC TTTTT- TTTTTC TTTCTT- TCTTTC TTTTT- TTTCCTTC TTCTTTC
1 -TT-TTTC TTTTTC TTTTTC TTT-TTC TTTTTC TTTTTC TTT--TTC TT-TTTC
13556 TTT
1 TTT
13559 GCTGGATGAG
Statistics
Matches: 81, Mismatches: 4, Indels: 25
0.74 0.04 0.23
Matches are distributed among these distances:
5 19 0.23
6 23 0.28
7 24 0.30
8 14 0.17
9 1 0.01
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:13477 original size:19 final size:17
Alignment explanation
Indices: 13453--13554 Score: 107
Period size: 19 Copynumber: 5.6 Consensus size: 17
13443 TTCAATTTTC
13453 CTTTTTTCATTTTTCTTTT
1 CTTTTTTC-TTTTTC-TTT
13472 CTTTTTTCTTTTTCTTT
1 CTTTTTTCTTTTTCTTT
13489 CTTTTTTCTTTCTTTCTTT
1 CTTTTTTC-TT-TTTCTTT
*
13508 CTTTCTTTTTTTTTTCTTT
1 C-TT-TTTTCTTTTTCTTT
13527 CTTTCTTTCTTTTT-TTT
1 CTTT-TTTCTTTTTCTTT
* *
13544 CCTTCTTCTTT
1 CTTTTTTCTTT
13555 CTTTGCTGGA
Statistics
Matches: 74, Mismatches: 4, Indels: 13
0.81 0.04 0.14
Matches are distributed among these distances:
16 6 0.08
17 18 0.24
18 18 0.24
19 24 0.32
20 4 0.05
21 4 0.05
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (17 bp):
CTTTTTTCTTTTTCTTT
Found at i:13491 original size:4 final size:4
Alignment explanation
Indices: 13464--13558 Score: 103
Period size: 4 Copynumber: 24.8 Consensus size: 4
13454 TTTTTTCATT
13464 TTTC TTTTC TTT- TTTC -TT- TTTC TTTC TTT- TTTC TTTC TTTC TTTC
1 TTTC -TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
* * *
13509 TTTC TTT- TTTT TTTC TTTC TTTC TTTC TTTTT TTTC CTTC -TTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTTC TTTC TTTC TTTC TTTC
13556 TTT
1 TTT
13559 GCTGGATGAG
Statistics
Matches: 79, Mismatches: 4, Indels: 15
0.81 0.04 0.15
Matches are distributed among these distances:
3 16 0.20
4 56 0.71
5 7 0.09
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (4 bp):
TTTC
Found at i:13508 original size:23 final size:24
Alignment explanation
Indices: 13449--13538 Score: 87
Period size: 23 Copynumber: 3.8 Consensus size: 24
13439 TTGATTCAAT
* *
13449 TTTCCTTTTTTCATT-TTTCTTTTC
1 TTTCTTTTTTTCTTTCTTTC-TTTC
*
13473 TTTTTTCTTTTTCTTTCTTT-TTTC
1 TTTCTT-TTTTTCTTTCTTTCTTTC
* *
13497 TTTCTTTCTTTCTTTCTTT-TTTT
1 TTTCTTTTTTTCTTTCTTTCTTTC
*
13520 TTTCTTTCTTTCTTTCTTT
1 TTTCTTTTTTTCTTTCTTT
13539 TTTTTCCTTC
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
23 34 0.59
24 13 0.22
25 8 0.14
26 3 0.05
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.80
Consensus pattern (24 bp):
TTTCTTTTTTTCTTTCTTTCTTTC
Found at i:13539 original size:23 final size:22
Alignment explanation
Indices: 13464--13558 Score: 129
Period size: 23 Copynumber: 4.1 Consensus size: 22
13454 TTTTTTCATT
13464 TTTCTTTTCTTTTTTCTT-TTTC
1 TTTCTTTT-TTTTTTCTTCTTTC
*
13486 TTTCTTTTTTCTTTCTTTCTTTC
1 TTTCTTTTTTTTTTC-TTCTTTC
13509 TTTCTTTTTTTTTTCTTTCTTTC
1 TTTCTTTTTTTTTTC-TTCTTTC
13532 TTTCTTTTTTTTCCTTCTTCTTTC
1 TTTCTTTTTTTT--TTCTTCTTTC
13556 TTT
1 TTT
13559 GCTGGATGAG
Statistics
Matches: 67, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
21 6 0.09
22 10 0.15
23 38 0.57
24 10 0.15
25 3 0.04
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTCTTTTTTTTTTCTTCTTTC
Found at i:17307 original size:14 final size:14
Alignment explanation
Indices: 17273--17326 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
17263 ACATAAAATA
* *
17273 CAAATGCAAAGATG
1 CAAATGTAAATATG
17287 CCAAATGTAAATATG
1 -CAAATGTAAATATG
*
17302 CAAATGTAAAAATG
1 CAAATGTAAATATG
*
17316 TAAATGTAAAT
1 CAAATGTAAAT
17327 TCAAACGTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:18844 original size:18 final size:17
Alignment explanation
Indices: 18787--18845 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 17
18777 TACTTGAAAA
18787 ATAAAATAA-AACATTA-
1 ATAAAATAATAA-ATTAT
18803 ATAAAATAATATAAATTAT
1 ATAAAAT-A-ATAAATTAT
*
18822 -GAAAATAATGAAATTAT
1 ATAAAATAAT-AAATTAT
18839 ATAAAAT
1 ATAAAAT
18846 TTTTGAAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
16 9 0.26
17 9 0.26
18 15 0.43
19 2 0.06
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (17 bp):
ATAAAATAATAAATTAT
Found at i:19665 original size:3 final size:3
Alignment explanation
Indices: 19657--19706 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
19647 TTATATAAAA
* *
19657 AAT AAT AAT AAT GA- AAT AAT AAT TA- AAT CAAT AAT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
19700 AAT AAT A
1 AAT AAT A
19707 TTGCAAATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
2 4 0.10
3 32 0.82
4 3 0.08
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:21007 original size:3 final size:3
Alignment explanation
Indices: 20999--21062 Score: 75
Period size: 3 Copynumber: 23.0 Consensus size: 3
20989 GGCCTGTTTG
*
20999 TAA TAA TAA TAA TAA T-A TAA T-A TAA T-A TAA TAA TAA TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
21044 -AA CAA -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
21063 ATAAAACAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
2 10 0.19
3 44 0.81
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:21025 original size:19 final size:19
Alignment explanation
Indices: 21001--21058 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
20991 CCTGTTTGTA
21001 ATAATAATAATAAT-ATAAT
1 ATAAT-ATAATAATAATAAT
21020 ATAATATAATAATAATAAT
1 ATAATATAATAATAATAAT
* *
21039 ATTAAAACAA-AATAATAAT
1 A-TAATATAATAATAATAAT
21058 A
1 A
21059 ATAAATAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.23
19 21 0.60
20 6 0.17
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAATATAATAATAATAAT
Found at i:39173 original size:42 final size:41
Alignment explanation
Indices: 39081--39178 Score: 106
Period size: 42 Copynumber: 2.4 Consensus size: 41
39071 AGGTTTTATG
* * * *
39081 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTCACA
1 GATGGCCCGAAGGACTTAGCATCATGCTCGAAAGACTCACA
** * * *
39122 GATAACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
1 GATGGCCCGAAGGACTT-AGCATCATGCTCGAAAGACTCACA
39164 GATGGCCCGAAGGAC
1 GATGGCCCGAAGGAC
39179 ATATAAATTG
Statistics
Matches: 44, Mismatches: 12, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
41 14 0.32
42 30 0.68
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.21
Consensus pattern (41 bp):
GATGGCCCGAAGGACTTAGCATCATGCTCGAAAGACTCACA
Found at i:40088 original size:213 final size:214
Alignment explanation
Indices: 38917--40149 Score: 2023
Period size: 214 Copynumber: 5.8 Consensus size: 214
38907 AAATTAACCA
* * *
38917 AAGGATTTAAACACCATGCTCGAAAGACTTACTGATGTCCCGAAGGACTTATAAATTGTGAAATT
1 AAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAATT
** *
38982 TTGAAAATCATATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTCATTTTAAAA
66 TTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTCATTTTCAAA
*
39047 TTCTTGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTA
131 TTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTA
* *
39112 AAGGCTCACAGATAACCCG
196 AAGGCTTACAGATGACCCG
*
39131 AAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACATATAAATTGTGAAATT
1 AAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAATT
* *
39196 TTGAAAATCGCATTCTTCATTTTCAAAAATTTCATCTTCTTAAAACATCATTTTTTCATTTTCAA
66 TTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCA-TTTTTCATTTTCAA
*
39261 ATTCATGTG-AAACATCCTACTCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTTGCTCT
130 ATTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTTGCTCT
*
39325 -AA--CTTATAGATGACCCG
195 AAAGGCTTACAGATGACCCG
* *
39342 AAGAATTTAAGCATCATGCTCGAAAGACTTACTGATAGCCCGAAGGACTTATAAATTG-GAAATT
1 AAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAATT
* *
39406 TTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAGACATCATTTTCCATTTTCAAA
66 TTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTCATTTTCAAA
* * * *
39471 TTCATTTGAAAATATTCTACCCGAAGGTTTTATGGATGGCCCGAATGACTTATCATCTTGCTCTA
131 TTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTA
39536 AAGGCTTACAGATGACCCG
196 AAGGCTTACAGATGACCCG
* *
39555 AAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCTGAAGGACTTATAAATTGTGAAAAT
1 AAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAATT
*
39620 TTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTTCATTTCCAA
66 TTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCA-TTTTTCATTTTCAA
* * *
39685 ATTCATGTGAAAACGTCATACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCT
130 ATTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTTGCTCT
*
39750 AAAGGCTTACAGATAACCCG
195 AAAGGCTTACAGATGACCCG
*
39770 AAGGATTTAAGCATCATGCTCG-AAGACTTATTGATGGCCCGAAGGACTTATAAATTGTGAAATT
1 AAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAATT
*
39834 TTGAAAATCGCATTCTTCGTTTTC-AAAATTCCATCTTCTTAAAACATCATTTTTCATTTCCAAA
66 TTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTCATTTTCAAA
* * * *
39898 TTCATGTGAAAACATCTTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTACTCTG
131 TTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTA
39963 AAGGCTTACAGATGACCCG
196 AAGGCTTACAGATGACCCG
* * *
39982 AAGGATTTAAGCATCATGCTTGAAAGATTTACTGATGGCCCGAAGGACTTAT-AATCGTGAAATT
1 AAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAATT
* * *
40046 TTGAAAATCGTATTCTTCGTTTTTAAAAATTTCATCTTCTTAAAACATCATTTTTCATTTTCAAA
66 TTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTCATTTTCAAA
40111 TTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGG
131 TTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGG
40150 ATTTGCTTCA
Statistics
Matches: 950, Mismatches: 60, Indels: 19
0.92 0.06 0.02
Matches are distributed among these distances:
209 21 0.02
210 104 0.11
211 69 0.07
212 148 0.16
213 198 0.21
214 278 0.29
215 132 0.14
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.33
Consensus pattern (214 bp):
AAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAATT
TTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTCATTTTCAAA
TTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTA
AAGGCTTACAGATGACCCG
Found at i:40191 original size:34 final size:34
Alignment explanation
Indices: 40153--40358 Score: 241
Period size: 34 Copynumber: 5.9 Consensus size: 34
40143 TGGATGGATT
40153 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATGG
1 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATGG
* **
40187 TGCTTCACTACTCCTCTATGAAGGCTTAAGATGG
1 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATGG
* *
40221 TGCTTCACTACTCTTCTGTGAAGGCTTAAGATGAC
1 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATG-G
* ** * *
40256 TGCTTCACTATTCTTCTATGAAGGCTTAAGGTGAT
1 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATG-G
* *
40291 TACTTCACTACTCTCCGGTGAAGGCTTAAGATGG
1 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATGG
* * *
40325 TTTGTTTCACTCCTCTTTGGTGAAGGCTTAAGAT
1 --TGCTTCACTACTCTTCGGTGAAGGCTTAAGAT
40359 TGACTTTGCT
Statistics
Matches: 147, Mismatches: 22, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
34 62 0.42
35 58 0.39
36 27 0.18
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (34 bp):
TGCTTCACTACTCTTCGGTGAAGGCTTAAGATGG
Done.