Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002814.1 Hibiscus syriacus cultivar Beakdansim tig00005792_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: 59376
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:9214 original size:42 final size:42
Alignment explanation
Indices: 9167--9292 Score: 189
Period size: 42 Copynumber: 3.0 Consensus size: 42
9157 AATTTTTTTT
*
9167 AAGAAAATTACCATTATGGTCCCTAAATATTTCTAAATTTAG
1 AAGAAAATTACCATTCTGGTCCCTAAATATTTCTAAATTTAG
* * * *
9209 AAGAAAATTACCATTCTAGTCCCTGAATATTTCTAACTTTTG
1 AAGAAAATTACCATTCTGGTCCCTAAATATTTCTAAATTTAG
*
9251 AAGAAAATTACCATTCTGGTCTCTAAATATTTCTAAAATTTA
1 AAGAAAATTACCATTCTGGTCCCTAAATATTTCT-AAATTTA
9293 TACTTTACCA
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
42 68 0.93
43 5 0.07
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (42 bp):
AAGAAAATTACCATTCTGGTCCCTAAATATTTCTAAATTTAG
Found at i:16278 original size:23 final size:24
Alignment explanation
Indices: 16231--16281 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
16221 TTTAAATAAT
*
16231 AACACAACTGAACAAATATAAACG
1 AACACAACTAAACAAATATAAACG
* *
16255 AACACAA-TAAACGAATGTAAACG
1 AACACAACTAAACAAATATAAACG
16278 AACA
1 AACA
16282 TAAATGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.59, C:0.20, G:0.10, T:0.12
Consensus pattern (24 bp):
AACACAACTAAACAAATATAAACG
Found at i:16475 original size:14 final size:14
Alignment explanation
Indices: 16455--16516 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 14
16445 GATTGAGCTA
16455 AACATAAATGAACG
1 AACATAAATGAACG
*
16469 TACAT--A--AACG
1 AACATAAATGAACG
16479 AACATAAATGAACG
1 AACATAAATGAACG
*
16493 CACAT--A--AACG
1 AACATAAATGAACG
16503 AACATAAATGAACG
1 AACATAAATGAACG
16517 TACAAAAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 16
0.64 0.07 0.29
Matches are distributed among these distances:
10 16 0.44
12 4 0.11
14 16 0.44
ACGTcount: A:0.55, C:0.18, G:0.13, T:0.15
Consensus pattern (14 bp):
AACATAAATGAACG
Found at i:16487 original size:24 final size:24
Alignment explanation
Indices: 16455--16532 Score: 129
Period size: 24 Copynumber: 3.2 Consensus size: 24
16445 GATTGAGCTA
16455 AACATAAATGAACGTACATAAACG
1 AACATAAATGAACGTACATAAACG
*
16479 AACATAAATGAACGCACATAAACG
1 AACATAAATGAACGTACATAAACG
* *
16503 AACATAAATGAACGTACAAAAACA
1 AACATAAATGAACGTACATAAACG
16527 AACATA
1 AACATA
16533 TTACCGAACG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.58, C:0.18, G:0.10, T:0.14
Consensus pattern (24 bp):
AACATAAATGAACGTACATAAACG
Found at i:18163 original size:22 final size:22
Alignment explanation
Indices: 18138--18185 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
18128 ATTACCATAA
18138 TACAACATCATAAAATCATCCT
1 TACAACATCATAAAATCATCCT
* *
18160 TACATCATCATAACATCATCCT
1 TACAACATCATAAAATCATCCT
18182 TACA
1 TACA
18186 CTTTAATAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (22 bp):
TACAACATCATAAAATCATCCT
Found at i:18166 original size:11 final size:11
Alignment explanation
Indices: 18152--18185 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
18142 ACATCATAAA
18152 ATCATCCTTAC
1 ATCATCCTTAC
* *
18163 ATCATCATAAC
1 ATCATCCTTAC
18174 ATCATCCTTAC
1 ATCATCCTTAC
18185 A
1 A
18186 CTTTAATAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (11 bp):
ATCATCCTTAC
Found at i:19035 original size:16 final size:16
Alignment explanation
Indices: 19014--19046 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
19004 TAATAAATAA
19014 ACGAACATAAACAAAC
1 ACGAACATAAACAAAC
19030 ACGAACATAAACAAAC
1 ACGAACATAAACAAAC
19046 A
1 A
19047 ATTTTTTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.64, C:0.24, G:0.06, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACAAAC
Found at i:19132 original size:20 final size:20
Alignment explanation
Indices: 19107--19146 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
19097 ATTTAAATGA
*
19107 TAAACGAACATAAACGAACG
1 TAAACGAACACAAACGAACG
19127 TAAACGAACACAAACGAACG
1 TAAACGAACACAAACGAACG
19147 AACATAAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.55, C:0.23, G:0.15, T:0.07
Consensus pattern (20 bp):
TAAACGAACACAAACGAACG
Found at i:19148 original size:14 final size:14
Alignment explanation
Indices: 19129--19159 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
19119 AACGAACGTA
19129 AACGAACACAAACG
1 AACGAACACAAACG
*
19143 AACGAACATAAACG
1 AACGAACACAAACG
19157 AAC
1 AAC
19160 ATAATAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.26, G:0.13, T:0.03
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:19163 original size:10 final size:10
Alignment explanation
Indices: 19106--19145 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
19096 CATTTAAATG
19106 ATAAACGAAC
1 ATAAACGAAC
19116 ATAAACGAAC
1 ATAAACGAAC
*
19126 GTAAACGAAC
1 ATAAACGAAC
*
19136 ACAAACGAAC
1 ATAAACGAAC
19146 GAACATAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.07
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:19176 original size:23 final size:22
Alignment explanation
Indices: 19116--19208 Score: 98
Period size: 23 Copynumber: 4.0 Consensus size: 22
19106 ATAAACGAAC
*
19116 ATAAACGAACGTAAACGAACACA
1 ATAAACGAACATAAAC-AACACA
*
19139 A-ACGAACGAACATAAACGAACATA
1 ATA--AACGAACATAAAC-AACACA
*
19163 ATAAATGAACATAAACAAACACA
1 ATAAACGAACATAAAC-AACACA
*
19186 ATAAACAAACATAAACAACACA
1 ATAAACGAACATAAACAACACA
19208 A
1 A
19209 ACACAAAAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
22 8 0.13
23 32 0.53
24 19 0.32
25 1 0.02
ACGTcount: A:0.62, C:0.20, G:0.08, T:0.10
Consensus pattern (22 bp):
ATAAACGAACATAAACAACACA
Found at i:19210 original size:15 final size:13
Alignment explanation
Indices: 19175--19223 Score: 62
Period size: 13 Copynumber: 3.6 Consensus size: 13
19165 AAATGAACAT
*
19175 AAACAAACACAAT
1 AAACAAACACAAA
*
19188 AAACAAACATAAA
1 AAACAAACACAAA
19201 CAACACAAACACAAA
1 -AA-ACAAACACAAA
19216 AAACAAAC
1 AAACAAAC
19224 TTATTCGAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
13 17 0.55
14 4 0.13
15 10 0.32
ACGTcount: A:0.71, C:0.24, G:0.00, T:0.04
Consensus pattern (13 bp):
AAACAAACACAAA
Found at i:19241 original size:32 final size:28
Alignment explanation
Indices: 19167--19241 Score: 71
Period size: 28 Copynumber: 2.5 Consensus size: 28
19157 AACATAATAA
*
19167 ATGAACATAAACAAACACAATAAACAAAC
1 ATGAACAT-AACAAACACAAAAAACAAAC
*
19196 ATAAACA-ACACAAACACAAAAAACAAAC
1 ATGAACATA-ACAAACACAAAAAACAAAC
19224 TTATTCGAACATAACAAA
1 --A-T-GAACATAACAAA
19242 TGAATGTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
27 1 0.03
28 18 0.49
29 6 0.16
30 1 0.03
31 1 0.03
32 9 0.24
33 1 0.03
ACGTcount: A:0.64, C:0.21, G:0.03, T:0.12
Consensus pattern (28 bp):
ATGAACATAACAAACACAAAAAACAAAC
Found at i:19486 original size:14 final size:14
Alignment explanation
Indices: 19468--19523 Score: 85
Period size: 14 Copynumber: 4.0 Consensus size: 14
19458 CCCTCTGTTT
*
19468 GAACATAAATGAAT
1 GAACATAAATGAAC
19482 GAACATAAATGAAC
1 GAACATAAATGAAC
19496 GAACATAAATGAAC
1 GAACATAAATGAAC
* *
19510 AAACATAAACGAAC
1 GAACATAAATGAAC
19524 ATATAATCGA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 39 1.00
ACGTcount: A:0.59, C:0.14, G:0.12, T:0.14
Consensus pattern (14 bp):
GAACATAAATGAAC
Found at i:19506 original size:24 final size:25
Alignment explanation
Indices: 19479--19535 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 25
19469 AACATAAATG
*
19479 AATGAACATAA-ATGAACGAACATA-
1 AATGAACA-AACATAAACGAACATAT
19503 AATGAACAAACATAAACGAACATAT
1 AATGAACAAACATAAACGAACATAT
19528 AATCGAAC
1 AAT-GAAC
19536 GTTCACGAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 2 0.07
24 20 0.69
25 3 0.10
26 4 0.14
ACGTcount: A:0.58, C:0.16, G:0.11, T:0.16
Consensus pattern (25 bp):
AATGAACAAACATAAACGAACATAT
Found at i:24522 original size:288 final size:288
Alignment explanation
Indices: 24006--24584 Score: 1149
Period size: 288 Copynumber: 2.0 Consensus size: 288
23996 CAATAAAAGT
24006 AACATAATACTTAGATCCACCCAAAGACGATGTCGTGGAAGGCCCCCATACATCAGAATGCACAT
1 AACATAATACTTAGATCCACCCAAAGACGATGTCGTGGAAGGCCCCCATACATCAGAATGCACAT
24071 AATCAAGAATCTCTTCAGTTGTGTGCTTCCCAGTCTTGAAACGAACTTTAGTCTGTTTACCAAGA
66 AATCAAGAATCTCTTCAGTTGTGTGCTTCCCAGTCTTGAAACGAACTTTAGTCTGTTTACCAAGA
24136 ACACAATACTTGCAAAAATCGAGCTTACAACTTTTAACACCATGCAACATAATACTTTTATGTAA
131 ACACAATACTTGCAAAAATCGAGCTTACAACTTTTAACACCATGCAACATAATACTTTTATGTAA
24201 TTAAGCCATACCACGTTCACTAAGATGAGCAAGACGCATATGCCACAGTTTGGTAGTATCATCAC
196 TTAAGCCATACCACGTTCACTAAGATGAGCAAGACGCATATGCCACAGTTTGGTAGTATCATCAC
24266 AGAACTCAACATAATGAACTCCACATAC
261 AGAACTCAACATAATGAACTCCACATAC
24294 AACATAATACTTAGATCCACCCAAAGACGATGTCGTGGAAGGCCCCCATACATCAGAATGCACAT
1 AACATAATACTTAGATCCACCCAAAGACGATGTCGTGGAAGGCCCCCATACATCAGAATGCACAT
24359 AATCAAGAATCTCTTCAGTTGTGTGCTTCCCAGTCTTGAAACGAACTTTAGTCTGTTTACCAAGA
66 AATCAAGAATCTCTTCAGTTGTGTGCTTCCCAGTCTTGAAACGAACTTTAGTCTGTTTACCAAGA
24424 ACACAATACTTGCAAAAATCGAGCTTACAACTTTTAACACCATGCAACATAATACTTTTATGTAA
131 ACACAATACTTGCAAAAATCGAGCTTACAACTTTTAACACCATGCAACATAATACTTTTATGTAA
24489 TTAAGCCATACCACGTTCACTAAGATGAGCAAGACGCATATGCCACAGTTTGGTAGTATCATCAC
196 TTAAGCCATACCACGTTCACTAAGATGAGCAAGACGCATATGCCACAGTTTGGTAGTATCATCAC
*
24554 AGAACTCAACATAATGAACTCCACCTAC
261 AGAACTCAACATAATGAACTCCACATAC
24582 AAC
1 AAC
24585 GGTACTACCT
Statistics
Matches: 290, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
288 290 1.00
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.26
Consensus pattern (288 bp):
AACATAATACTTAGATCCACCCAAAGACGATGTCGTGGAAGGCCCCCATACATCAGAATGCACAT
AATCAAGAATCTCTTCAGTTGTGTGCTTCCCAGTCTTGAAACGAACTTTAGTCTGTTTACCAAGA
ACACAATACTTGCAAAAATCGAGCTTACAACTTTTAACACCATGCAACATAATACTTTTATGTAA
TTAAGCCATACCACGTTCACTAAGATGAGCAAGACGCATATGCCACAGTTTGGTAGTATCATCAC
AGAACTCAACATAATGAACTCCACATAC
Found at i:26385 original size:13 final size:15
Alignment explanation
Indices: 26356--26389 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
26346 CACAATAATA
26356 TTATTTAGTCTTTAT
1 TTATTTAGTCTTTAT
26371 TTATTTA-TC-TTAT
1 TTATTTAGTCTTTAT
26384 TTATTT
1 TTATTT
26390 CACCAGTCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.53
14 2 0.11
15 7 0.37
ACGTcount: A:0.21, C:0.06, G:0.03, T:0.71
Consensus pattern (15 bp):
TTATTTAGTCTTTAT
Found at i:27942 original size:27 final size:27
Alignment explanation
Indices: 27912--27974 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
27902 GAAAGTCAAT
27912 ATTCAAACCTCTTATCTTAGTTAAAGA
1 ATTCAAACCTCTTATCTTAGTTAAAGA
27939 ATTCAAACCTCTTATCTTAGTTAAAGA
1 ATTCAAACCTCTTATCTTAGTTAAAGA
*
27966 ATTCGAACC
1 ATTCAAACC
27975 CAATTTCCCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.35
Consensus pattern (27 bp):
ATTCAAACCTCTTATCTTAGTTAAAGA
Found at i:29919 original size:16 final size:16
Alignment explanation
Indices: 29898--29931 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
29888 GTAGATGAAA
29898 ATAAATTAT-TTTATTT
1 ATAAATTATATTT-TTT
29914 ATAAATTATATTTTTT
1 ATAAATTATATTTTTT
29930 AT
1 AT
29932 TAAAACCAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATAAATTATATTTTTT
Found at i:33049 original size:19 final size:20
Alignment explanation
Indices: 33008--33055 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
32998 AACTGAACTG
* * *
33008 AGTC-ATCTAGACTGAGTCG
1 AGTCGATCTGGACTGAGCCA
33027 AGTCG-TCTGGACTGAGCCA
1 AGTCGATCTGGACTGAGCCA
33046 AGTCGATCTG
1 AGTCGATCTG
33056 AGCAAAGTCG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (20 bp):
AGTCGATCTGGACTGAGCCA
Found at i:38865 original size:19 final size:18
Alignment explanation
Indices: 38841--38876 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
38831 ATATTCATAA
*
38841 ATATTTAATTTAATTTTAC
1 ATATTTAAATT-ATTTTAC
38860 ATATTTAAATTATTTTA
1 ATATTTAAATTATTTTA
38877 TGTTGTTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (18 bp):
ATATTTAAATTATTTTAC
Found at i:45513 original size:14 final size:14
Alignment explanation
Indices: 45494--45523 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
45484 TATTAGACAT
45494 TACGAGGTGGTCAA
1 TACGAGGTGGTCAA
45508 TACGAGGTGGTCAA
1 TACGAGGTGGTCAA
45522 TA
1 TA
45524 GGGTTGGTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.13, G:0.33, T:0.23
Consensus pattern (14 bp):
TACGAGGTGGTCAA
Found at i:51298 original size:27 final size:27
Alignment explanation
Indices: 51248--51299 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
51238 GCCATCACCC
*
51248 CTTTGAACTTGAAACTCCATAACATTA
1 CTTTGAACTTGAAACTCCACAACATTA
* *
51275 CTTTGAACTTGAAAGTCTACAACAT
1 CTTTGAACTTGAAACTCCACAACAT
51300 CAAGATCTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.33
Consensus pattern (27 bp):
CTTTGAACTTGAAACTCCACAACATTA
Found at i:51825 original size:29 final size:28
Alignment explanation
Indices: 51766--51831 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 28
51756 TTTTTAATTT
* *
51766 AACCTAAAATATTATGAATAATATAAATAA
1 AACC-AAAATATTATGAAAAAAATAAAT-A
**
51796 AACCAAAATATTATGAAAAAAATATGTA
1 AACCAAAATATTATGAAAAAAATAAATA
51824 AACCAAAA
1 AACCAAAA
51832 CTACTAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 9 0.28
29 19 0.59
30 4 0.12
ACGTcount: A:0.62, C:0.09, G:0.05, T:0.24
Consensus pattern (28 bp):
AACCAAAATATTATGAAAAAAATAAATA
Done.