Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004312.1 Hibiscus syriacus cultivar Beakdansim tig00009457_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: 41843
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:3208 original size:17 final size:17
Alignment explanation
Indices: 3186--3220 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3176 ATAAGTGAGG
*
3186 GGAAATAAGAAGGGTCA
1 GGAAATAAGAAAGGTCA
*
3203 GGAAATGAGAAAGGTCA
1 GGAAATAAGAAAGGTCA
3220 G
1 G
3221 ATTGGCTGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.06, G:0.37, T:0.11
Consensus pattern (17 bp):
GGAAATAAGAAAGGTCA
Found at i:3710 original size:8 final size:8
Alignment explanation
Indices: 3697--3724 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
3687 AGATCCTCCC
3697 ATATGTAT
1 ATATGTAT
3705 ATATGTAT
1 ATATGTAT
3713 ATATGTAT
1 ATATGTAT
3721 ATAT
1 ATAT
3725 ATCTTCTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (8 bp):
ATATGTAT
Found at i:7286 original size:29 final size:28
Alignment explanation
Indices: 7220--7287 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
7210 AATAAAAAAG
*
7220 AAAATGAAAAAAAATAATAAAAATGAGA
1 AAAATGAAAAAAAATAAGAAAAATGAGA
*
7248 AGAAA--AAAAAGAAGAAAAGAAAAATGAGA
1 A-AAATGAAAAA-AA-ATAAGAAAAATGAGA
7277 AAAATGAAAAA
1 AAAATGAAAAA
7288 TGATGGAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
27 5 0.15
28 6 0.18
29 17 0.52
30 5 0.15
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (28 bp):
AAAATGAAAAAAAATAAGAAAAATGAGA
Found at i:7300 original size:19 final size:19
Alignment explanation
Indices: 7256--7323 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 19
7246 GAAGAAAAAA
7256 AAGAAGAAAA-GAAAAAT-G
1 AAGAA-AAAATGAAAAATGG
7274 -AG-AAAAATGAAAAAT-G
1 AAGAAAAAATGAAAAATGG
* *
7290 ATGGAAAAAATGGAAAATGG
1 A-AGAAAAAATGAAAAATGG
7310 AAGAAAAAATGAAA
1 AAGAAAAAATGAAA
7324 GAGAAAAACA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
15 4 0.10
16 9 0.22
17 2 0.05
18 1 0.02
19 23 0.56
20 2 0.05
ACGTcount: A:0.68, C:0.00, G:0.22, T:0.10
Consensus pattern (19 bp):
AAGAAAAAATGAAAAATGG
Found at i:7317 original size:20 final size:19
Alignment explanation
Indices: 7256--7364 Score: 63
Period size: 19 Copynumber: 5.9 Consensus size: 19
7246 GAAGAAAAAA
*
7256 AAGAAGAAAA-GAAAAATG
1 AAGAAAAAAATGAAAAATG
7274 -AG--AAAAATGAAAAATG
1 AAGAAAAAAATGAAAAATG
* * *
7290 ATGGAAAAAATGGAAAATGG
1 AAGAAAAAAATGAAAAAT-G
*
7310 AAG-AAAAAATGAAAGA-G
1 AAGAAAAAAATGAAAAATG
* *
7327 AAAAACAAAAAGAGAAAAATG
1 AAGAA-AAAAA-TGAAAAATG
7348 AA-AAAATAAA-GAAAAAT
1 AAGAAAA-AAATGAAAAAT
7365 AAAAGGGGGT
Statistics
Matches: 72, Mismatches: 9, Indels: 20
0.71 0.09 0.20
Matches are distributed among these distances:
15 4 0.06
16 8 0.11
17 6 0.08
18 8 0.11
19 30 0.42
20 13 0.18
21 3 0.04
ACGTcount: A:0.71, C:0.01, G:0.19, T:0.09
Consensus pattern (19 bp):
AAGAAAAAAATGAAAAATG
Found at i:7351 original size:14 final size:14
Alignment explanation
Indices: 7238--7351 Score: 54
Period size: 14 Copynumber: 7.8 Consensus size: 14
7228 AAAAAATAAT
* *
7238 AAAAATGAGAAGAA
1 AAAAATGAAAAGAG
* *
7252 AAAAAAGAAGAAAAG
1 AAAAATGAA-AAGAG
*
7267 AAAAATGAGAAAAATG
1 AAAAATGA-AAAGA-G
**
7283 AAAAATG-ATGGA-
1 AAAAATGAAAAGAG
7295 AAAAATGGAAAATGGAAG
1 AAAAAT-GAAAA--G-AG
7313 AAAAAATG-AAAGAG
1 -AAAAATGAAAAGAG
**
7327 AAAAACAAAAAGAG
1 AAAAATGAAAAGAG
7341 AAAAATGAAAA
1 AAAAATGAAAA
7352 AATAAAGAAA
Statistics
Matches: 75, Mismatches: 14, Indels: 22
0.68 0.13 0.20
Matches are distributed among these distances:
12 6 0.08
13 6 0.08
14 27 0.36
15 15 0.20
16 10 0.13
17 4 0.05
18 1 0.01
19 6 0.08
ACGTcount: A:0.71, C:0.01, G:0.20, T:0.08
Consensus pattern (14 bp):
AAAAATGAAAAGAG
Found at i:7362 original size:65 final size:64
Alignment explanation
Indices: 7220--7363 Score: 154
Period size: 65 Copynumber: 2.2 Consensus size: 64
7210 AATAAAAAAG
* * *
7220 AAAATGAAAAAAAATAAT-AAAAATGAGAAGAAAAAAAAGAAGAAAAGAAAAATGAGAAAAATGA
1 AAAATGAAAGAAAA-AATGGAAAATGAGAAGAAAAAAAAGAAGAAAAGAAAAAAGAGAAAAATGA
**
7284 AAAATGATGGAAAAAATGGAAAATG-GAAGAAAAAATGAA-AGAGAAAA-ACAAAAAGAGAAAAA
1 AAAATGAAAGAAAAAATGGAAAATGAGAAGAAAAAA--AAGA-AGAAAAGA-AAAAAGAGAAAAA
7346 TGAA
62 TG-A
7350 AAAAT-AAAGAAAAA
1 AAAATGAAAGAAAAA
7364 TAAAAGGGGG
Statistics
Matches: 67, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
63 13 0.19
64 19 0.28
65 29 0.43
66 6 0.09
ACGTcount: A:0.73, C:0.01, G:0.17, T:0.09
Consensus pattern (64 bp):
AAAATGAAAGAAAAAATGGAAAATGAGAAGAAAAAAAAGAAGAAAAGAAAAAAGAGAAAAATGA
Found at i:8700 original size:37 final size:36
Alignment explanation
Indices: 8646--8717 Score: 126
Period size: 37 Copynumber: 2.0 Consensus size: 36
8636 AAACAGGTCA
8646 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAACC
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAACC
*
8682 ATCTGTAAGCCTTCACGGAAGATTAGTGAAGCAAAC
1 ATCT-TAAGCCTTCACGGAAGAGTAGTGAAGCAAAC
8718 TTATTTTATG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 4 0.12
37 30 0.88
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (36 bp):
ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAACC
Found at i:8968 original size:55 final size:55
Alignment explanation
Indices: 8732--9152 Score: 387
Period size: 55 Copynumber: 7.7 Consensus size: 55
8722 TTTATGAAGA
* * * * * *
8732 TCGAGTCATATACTCTCTAAAGGAATAGGGAGCGGACACGTTTGTTAAAGA---T
1 TCGAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACGTTTGATGAAGATTGT
* * * * *
8784 T-GAGTCCTATACTCTCTGAAAGAATAGGGAGCGGAC-CTGTTT-ATTGAAGATTTT
1 TCGAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACAC-GTTTGA-TGAAGATTGT
* * *
8838 TCGAGT-TCTATACTCTCTGAAGGAATAGAGAGCAAACTCGTTTTAATGAAGATTGT
1 TCGAGTCT-TATACTCTCTGAAGGAATAGAGAGCAGACACG-TTTGATGAAGATTGT
* * * *
8894 TCAAGTTTTATACTCTCTGAATGAATAGAGAGCAGACACGTTTGCTGAAGATTGT
1 TCGAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACGTTTGATGAAGATTGT
* * *
8949 TCGAGTCTTATACTCTCTGAAGGAATAGAGAGC-GAACCCATTTTTATGAAGATTGT
1 TCGAGTCTTATACTCTCTGAAGGAATAGAGAGCAG-ACAC-GTTTGATGAAGATTGT
* * *
9005 TCGAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGT
1 TCGAGTCT-TATACTCTCTGAAGGAATAGAGAGCAGACACGTTTGATGAAGATTGT
* * * *
9060 TCGAGTCTTATACTC-CTTGAATGAAAAGGGAGCAGACACGTTTGCTGAAGATTGGT
1 TCGAGTCTTATACTCTC-TGAAGGAATAGAGAGCAGACACGTTTGATGAAGATT-GT
* * * *
9116 T-GAGTCTTATACTCCCCTGAAGGGATAGGGAGAAGAC
1 TCGAGTCTTATACT-CTCTGAAGGAATAGAGAGCAGAC
9153 CCGTCATTCG
Statistics
Matches: 313, Mismatches: 36, Indels: 36
0.81 0.09 0.09
Matches are distributed among these distances:
50 1 0.00
51 41 0.13
52 1 0.00
54 4 0.01
55 146 0.47
56 116 0.37
57 4 0.01
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (55 bp):
TCGAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACGTTTGATGAAGATTGT
Found at i:9095 original size:166 final size:166
Alignment explanation
Indices: 8783--9143 Score: 514
Period size: 166 Copynumber: 2.2 Consensus size: 166
8773 TTGTTAAAGA
* * * * *
8783 TTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACCTGTTTATTGAAGATTTTTCGAGTTCTA
1 TTGAGTCTTATACTCTCTGAAGGAATAGAGAGCGAACCTGTTTATTGAAGATTGTTCGAGTTCTA
* *
8848 TACTCTCTGAAGGAATAGAGAGCAAACTCGTTTTAATGAAGATTGTTCAAGTTTTATACTCTCTG
66 TACTCTCTGAAGGAATAGAGAGCAAACCCGTTTTAATGAAGATTGTTCAAGTCTTATACTCTCTG
*
8913 AATGAATAGAGAGCAGACACGTTTGCTGAAGATT-G
131 AATGAAAAGAGAGCAGACACGTTTGCTGAAGATTGG
*
8948 TTCGAGTCTTATACTCTCTGAAGGAATAGAGAGCGAACCCATTTTTA-TGAAGATTGTTCGAGTT
1 TT-GAGTCTTATACTCTCTGAAGGAATAGAGAGCGAA-CC-TGTTTATTGAAGATTGTTCGAGTT
** *
9012 CTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTT-ATGAAGATTGTTCGAGTCTTATACTC-
63 CTATACTCTCTGAAGGAATAGAGAGCAAACCCGTTTTAATGAAGATTGTTCAAGTCTTATACTCT
*
9075 CTTGAATGAAAAGGGAGCAGACACGTTTGCTGAAGATTGG
128 C-TGAATGAAAAGAGAGCAGACACGTTTGCTGAAGATTGG
* *
9115 TTGAGTCTTATACTCCCCTGAAGGGATAG
1 TTGAGTCTTATACT-CTCTGAAGGAATAG
9144 GGAGAAGACC
Statistics
Matches: 175, Mismatches: 15, Indels: 10
0.88 0.08 0.05
Matches are distributed among these distances:
165 3 0.02
166 100 0.57
167 67 0.38
168 5 0.03
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.32
Consensus pattern (166 bp):
TTGAGTCTTATACTCTCTGAAGGAATAGAGAGCGAACCTGTTTATTGAAGATTGTTCGAGTTCTA
TACTCTCTGAAGGAATAGAGAGCAAACCCGTTTTAATGAAGATTGTTCAAGTCTTATACTCTCTG
AATGAAAAGAGAGCAGACACGTTTGCTGAAGATTGG
Found at i:9136 original size:111 final size:110
Alignment explanation
Indices: 8732--9143 Score: 394
Period size: 111 Copynumber: 3.8 Consensus size: 110
8722 TTTATGAAGA
* * * * ** * *
8732 TCGAGTCATATACTCTCTAAAGGAATAGGGAGCGGACACGTTTGTTAAAGA---TT-GAGTCCTA
1 TCGAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACGTTTAATGAAGATTGTTCGAGTCTTA
* * * *
8793 TACTCTCTGAAAGAATAGGGAGCGGACCTG-TTTATTGAAGATTTT
66 TACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTA-TGAAGATTGT
* * * *
8838 TCGAGT-TCTATACTCTCTGAAGGAATAGAGAGCAAACTCGTTTTAATGAAGATTGTTCAAGTTT
1 TCGAGTCT-TATACTCTCTGAAGGAATAGAGAGCAGACACG-TTTAATGAAGATTGTTCGAGTCT
* * * **
8902 TATACTCTCTGAATGAATAGAGAGCAGACACGTTTGCTGAAGATTGT
64 TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGT
* * *
8949 TCGAGTCTTATACTCTCTGAAGGAATAGAGAGC-GAACCCATTTTTATGAAGATTGTTCGAGT-T
1 TCGAGTCTTATACTCTCTGAAGGAATAGAGAGCAG-ACAC-GTTTAATGAAGATTGTTCGAGTCT
9012 CTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGT
64 -TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGT
* * * **
9060 TCGAGTCTTATACTC-CTTGAATGAAAAGGGAGCAGACACGTTTGCTGAAGATTGGTT-GAGTCT
1 TCGAGTCTTATACTCTC-TGAAGGAATAGAGAGCAGACACGTTTAATGAAGATT-GTTCGAGTCT
* *
9123 TATACTCCCCTGAAGGGATAG
64 TATACT-CTCTGAAGGAATAG
9144 GGAGAAGACC
Statistics
Matches: 251, Mismatches: 39, Indels: 27
0.79 0.12 0.09
Matches are distributed among these distances:
106 33 0.13
107 8 0.03
110 25 0.10
111 181 0.72
112 4 0.02
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.31
Consensus pattern (110 bp):
TCGAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACGTTTAATGAAGATTGTTCGAGTCTTA
TACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGT
Found at i:12352 original size:19 final size:19
Alignment explanation
Indices: 12320--12361 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
12310 GAATTCAAAC
12320 TTTTATAAATTA-TTAGTAA
1 TTTTATAAATTATTTA-TAA
12339 TTTTAT-AATATATTTATAA
1 TTTTATAAAT-TATTTATAA
12358 TTTT
1 TTTT
12362 TTTAAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 3 0.14
19 15 0.71
20 3 0.14
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTTATAAATTATTTATAA
Found at i:13293 original size:13 final size:13
Alignment explanation
Indices: 13275--13299 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13265 AATGATAAAA
13275 TATGAAAAATTAC
1 TATGAAAAATTAC
13288 TATGAAAAATTA
1 TATGAAAAATTA
13300 TAGTTAATCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.32
Consensus pattern (13 bp):
TATGAAAAATTAC
Found at i:28397 original size:3 final size:3
Alignment explanation
Indices: 28389--28430 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
28379 TTAGCTTGGC
28389 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28431 GAGAAAATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:28611 original size:21 final size:21
Alignment explanation
Indices: 28585--28650 Score: 114
Period size: 21 Copynumber: 3.1 Consensus size: 21
28575 TTCTCAACGT
28585 GAACTTCGACTATCGCAATGC
1 GAACTTCGACTATCGCAATGC
*
28606 GAACTTCGACTATCACAATGC
1 GAACTTCGACTATCGCAATGC
*
28627 GAACTTGGACTATCGCAATGC
1 GAACTTCGACTATCGCAATGC
28648 GAA
1 GAA
28651 TATGTAAATC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.23
Consensus pattern (21 bp):
GAACTTCGACTATCGCAATGC
Found at i:31337 original size:34 final size:34
Alignment explanation
Indices: 31282--31372 Score: 130
Period size: 34 Copynumber: 2.6 Consensus size: 34
31272 GATGTGTTAA
*
31282 AAAATTAATATAATAAT-AATAATATTTGGGTGACC
1 AAAA-TAAAATAA-AATCAATAATATTTGGGTGACC
31317 AAAATAAAATAAAATCAATAATATTTGGGTGACC
1 AAAATAAAATAAAATCAATAATATTTGGGTGACC
* *
31351 AAAATATAATAAAAGCAATAAT
1 AAAATAAAATAAAATCAATAAT
31373 TAGGATTCTA
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
33 3 0.06
34 45 0.87
35 4 0.08
ACGTcount: A:0.55, C:0.07, G:0.10, T:0.29
Consensus pattern (34 bp):
AAAATAAAATAAAATCAATAATATTTGGGTGACC
Found at i:32598 original size:35 final size:34
Alignment explanation
Indices: 32491--32622 Score: 119
Period size: 35 Copynumber: 3.8 Consensus size: 34
32481 GAGAAAAATT
* * *
32491 TCTCACTTACCCTTCATGTGACGCGCGCGA-AATT
1 TCTCATTTACCCTTCATGTGACGTG-GCGATAATC
*
32525 TCGT-ATTTACCCTTCATGTGACGT-GC-ACTCGAAAC
1 TC-TCATTTACCCTTCATGTGACGTGGCGA-T--AATC
*
32560 TCTCATGTACCCTTCATGTGACGTGGCGAGTAATC
1 TCTCATTTACCCTTCATGTGACGTGGCGA-TAATC
* *
32595 TCTCATTTACCATTCATGTTACGTGGCG
1 TCTCATTTACCCTTCATGTGACGTGGCG
32623 GGAAATCCAT
Statistics
Matches: 80, Mismatches: 10, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
31 1 0.01
32 2 0.03
34 21 0.26
35 52 0.65
36 2 0.03
37 2 0.03
ACGTcount: A:0.20, C:0.28, G:0.19, T:0.33
Consensus pattern (34 bp):
TCTCATTTACCCTTCATGTGACGTGGCGATAATC
Done.