Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005552.1 Hibiscus syriacus cultivar Beakdansim tig00012871_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: 76759
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:7269 original size:16 final size:16
Alignment explanation
Indices: 7248--7302 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
7238 CCGTTATGCA
7248 TGTGTATGTATACATG
1 TGTGTATGTATACATG
7264 TGTGTATGTATACATG
1 TGTGTATGTATACATG
* *
7280 TGTGTATATATATATG
1 TGTGTATGTATACATG
*
7296 TATGTAT
1 TGTGTAT
7303 CAATCATAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.27, C:0.04, G:0.22, T:0.47
Consensus pattern (16 bp):
TGTGTATGTATACATG
Found at i:10931 original size:18 final size:17
Alignment explanation
Indices: 10908--10953 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
10898 GTTTTTGAGA
*
10908 GAATTGGAATCTGTGAAG
1 GAATTGGAATCGGT-AAG
* *
10926 GAATTGAAATCGGTCAG
1 GAATTGGAATCGGTAAG
10943 GAATTGGAATC
1 GAATTGGAATC
10954 CAATTCCATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.35, C:0.09, G:0.30, T:0.26
Consensus pattern (17 bp):
GAATTGGAATCGGTAAG
Found at i:12056 original size:23 final size:23
Alignment explanation
Indices: 12030--12120 Score: 128
Period size: 23 Copynumber: 4.0 Consensus size: 23
12020 CACCACAGCT
* *
12030 CGTATAAATGCACCGAAGTACCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
12053 CGTAGAAATGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCG
*
12076 CGTAGAATTGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
*
12099 CGTAGAAATGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
12121 ATATAATGTC
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:19760 original size:21 final size:21
Alignment explanation
Indices: 19734--19773 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
19724 ATCATCACCT
19734 TCTTCTTCTT-CTCTATCTTTG
1 TCTTCTTCTTCCTCT-TCTTTG
19755 TCTTCTTCTTCCTCTTCTT
1 TCTTCTTCTTCCTCTTCTT
19774 CATCAAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.03, C:0.33, G:0.03, T:0.62
Consensus pattern (21 bp):
TCTTCTTCTTCCTCTTCTTTG
Found at i:28023 original size:7 final size:7
Alignment explanation
Indices: 28011--28038 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
28001 CAATAATTCA
28011 TTTCAAG
1 TTTCAAG
28018 TTTCAAG
1 TTTCAAG
28025 TTTCAAG
1 TTTCAAG
28032 TTTCAAG
1 TTTCAAG
28039 GCCTGATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (7 bp):
TTTCAAG
Found at i:31703 original size:15 final size:15
Alignment explanation
Indices: 31679--31723 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
31669 CTGTGAGAGC
31679 TTTT-GAGAGAATTA
1 TTTTAGAGAGAATTA
*
31693 TTTTAGAGAGAATTG
1 TTTTAGAGAGAATTA
*
31708 TTTTAGAGTGAATTA
1 TTTTAGAGAGAATTA
31723 T
1 T
31724 GTGAATCGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 4 0.15
15 23 0.85
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (15 bp):
TTTTAGAGAGAATTA
Found at i:32422 original size:40 final size:39
Alignment explanation
Indices: 32378--32466 Score: 124
Period size: 40 Copynumber: 2.3 Consensus size: 39
32368 GCATAGTTGA
* *
32378 CATCTTTGGTTGGTGGCTAACTTGTACACATTGGAAAATT
1 CATCTTTGGTAGGTGGCCAACTTGTACACA-TGGAAAATT
* * *
32418 CATCTTTGGTAGGTGGCCAACTTGTGCACATGGGAATTT
1 CATCTTTGGTAGGTGGCCAACTTGTACACATGGAAAATT
32457 CATCTTTGGT
1 CATCTTTGGT
32467 CCCTAAAATA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 17 0.39
40 27 0.61
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37
Consensus pattern (39 bp):
CATCTTTGGTAGGTGGCCAACTTGTACACATGGAAAATT
Found at i:36451 original size:8 final size:8
Alignment explanation
Indices: 36421--36450 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
36411 GTATAATGAG
36421 ATAAAAAA
1 ATAAAAAA
36429 ATAAAAAA
1 ATAAAAAA
36437 ATAAAATAA
1 ATAAAA-AA
36446 ATAAA
1 ATAAA
36451 TTGAGATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 14 0.67
9 7 0.33
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (8 bp):
ATAAAAAA
Found at i:37052 original size:19 final size:21
Alignment explanation
Indices: 37011--37053 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
37001 CAAATTCCTA
37011 AAAACATCTTAAATACTAATT
1 AAAACATCTTAAATACTAATT
*
37032 AAAACA-CTTAAA-ACTATTT
1 AAAACATCTTAAATACTAATT
37051 AAA
1 AAA
37054 CTAAAATACC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.43
20 6 0.29
21 6 0.29
ACGTcount: A:0.56, C:0.14, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAACATCTTAAATACTAATT
Found at i:37139 original size:71 final size:75
Alignment explanation
Indices: 37020--37210 Score: 246
Period size: 77 Copynumber: 2.6 Consensus size: 75
37010 AAAAACATCT
* * * * *
37020 TAAATACTAATTAAAACACTTAAAACTATTTAAACTAAAATACCT-A-AAAAAT-AATAT-TTAA
1 TAAATCCTAATTAAAATACTTAAACCTATTTAAACTAAAATACCTAACAAAAATAAAAATATAAA
*
37081 AATAATATTC
66 AATAATATCC
*
37091 TAAATCCTAATTAAAATACTTAAACCTATTTAAACTAAAATACTTAAAACAAAAATAAAAATATA
1 TAAATCCTAATTAAAATACTTAAACCTATTTAAACTAAAATACCT--AACAAAAATAAAAATATA
37156 AAAATAATATCC
64 AAAATAATATCC
* * *
37168 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATAC
1 TAAATCCTAATTAAAATACTTAAACCTATTTAAACTAAAATAC
37211 AAAGATAAAA
Statistics
Matches: 104, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
71 41 0.39
74 1 0.01
75 6 0.06
76 4 0.04
77 52 0.50
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (75 bp):
TAAATCCTAATTAAAATACTTAAACCTATTTAAACTAAAATACCTAACAAAAATAAAAATATAAA
AATAATATCC
Found at i:38200 original size:31 final size:31
Alignment explanation
Indices: 38158--38239 Score: 119
Period size: 31 Copynumber: 2.6 Consensus size: 31
38148 TAAATTTTTT
*
38158 TTTGTTTATGTTCGTTCATTAAGAAATATAA
1 TTTGTTCATGTTCGTTCATTAAGAAATATAA
* *
38189 TTTGTTCATGTTCGTTCATTAAGGAATATAG
1 TTTGTTCATGTTCGTTCATTAAGAAATATAA
* *
38220 CTTGTTCATATTCGTTCATT
1 TTTGTTCATGTTCGTTCATT
38240 TAAATGATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.49
Consensus pattern (31 bp):
TTTGTTCATGTTCGTTCATTAAGAAATATAA
Found at i:38270 original size:10 final size:10
Alignment explanation
Indices: 38246--38346 Score: 58
Period size: 10 Copynumber: 9.1 Consensus size: 10
38236 CATTTAAATG
*
38246 ATAAACGAAT
1 ATAAACGAAC
38256 ATAAACGAAC
1 ATAAACGAAC
* *
38266 GTAAACAAACAC
1 ATAAAC-GA-AC
*
38278 AAACGAACGAAC
1 ATA--AACGAAC
38290 ATAAACGAAC
1 ATAAACGAAC
*
38300 ATAATAAATGAAC
1 ---ATAAACGAAC
38313 ATAAACGAACAC
1 ATAAACG-A-AC
*
38325 AATAAACAAAC
1 -ATAAACGAAC
38336 ATAAACGAAC
1 ATAAACGAAC
38346 A
1 A
38347 ACACAAACAC
Statistics
Matches: 70, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
10 37 0.53
11 4 0.06
12 10 0.14
13 16 0.23
14 3 0.04
ACGTcount: A:0.61, C:0.19, G:0.09, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:38316 original size:23 final size:23
Alignment explanation
Indices: 38256--38346 Score: 112
Period size: 23 Copynumber: 3.9 Consensus size: 23
38246 ATAAACGAAT
* *
38256 ATAAACGAACGTAAACAAACACA
1 ATAAACGAACATAAACGAACACA
*
38279 A-ACGAACGAACATAAACGAACATA
1 ATA--AACGAACATAAACGAACACA
*
38303 ATAAATGAACATAAACGAACACA
1 ATAAACGAACATAAACGAACACA
*
38326 ATAAACAAACATAAACGAACA
1 ATAAACGAACATAAACGAACA
38347 ACACAAACAC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
22 1 0.02
23 38 0.66
24 18 0.31
25 1 0.02
ACGTcount: A:0.62, C:0.20, G:0.09, T:0.10
Consensus pattern (23 bp):
ATAAACGAACATAAACGAACACA
Found at i:38349 original size:13 final size:13
Alignment explanation
Indices: 38273--38354 Score: 54
Period size: 13 Copynumber: 6.7 Consensus size: 13
38263 AACGTAAACA
*
38273 AACACAAACGAAC
1 AACATAAACGAAC
38286 GAACATAAACGAAC
1 -AACATAAACGAAC
*
38300 ATA-ATAAATG---
1 A-ACATAAACGAAC
38310 AACATAAACGAAC
1 AACATAAACGAAC
38323 -ACAATAAAC--A-
1 AAC-ATAAACGAAC
38333 AACATAAACGAAC
1 AACATAAACGAAC
*
38346 AACACAAAC
1 AACATAAAC
38355 ACAAAAAATA
Statistics
Matches: 54, Mismatches: 4, Indels: 21
0.68 0.05 0.27
Matches are distributed among these distances:
9 1 0.02
10 13 0.24
11 3 0.06
12 3 0.06
13 21 0.39
14 13 0.24
ACGTcount: A:0.62, C:0.22, G:0.07, T:0.09
Consensus pattern (13 bp):
AACATAAACGAAC
Found at i:38354 original size:23 final size:23
Alignment explanation
Indices: 38287--38355 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
38277 CAAACGAACG
**
38287 AACATAAACGAACATA-ATAAATG
1 AACATAAACGAACA-ACATAAACA
38310 AACATAAACGAAC-ACAATAAACA
1 AACATAAACGAACAAC-ATAAACA
*
38333 AACATAAACGAACAACACAAACA
1 AACATAAACGAACAACATAAACA
38356 CAAAAAATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
21 1 0.03
23 37 0.93
24 2 0.05
ACGTcount: A:0.64, C:0.20, G:0.06, T:0.10
Consensus pattern (23 bp):
AACATAAACGAACAACATAAACA
Found at i:39597 original size:67 final size:69
Alignment explanation
Indices: 39475--39608 Score: 227
Period size: 67 Copynumber: 2.0 Consensus size: 69
39465 GGGATCTCTT
*
39475 TCTTTTTTTTATATATAAGAATTGAAGATTTCATTAAAAAAACTCTTCATGATTTAATGCACAGG
1 TCTTTTTTTTATATATAAGAATTGAAGATTTCATTAAAAAAACCCTTCATGATTTAATGCACAGG
39540 GAAC
66 GAAC
* *
39544 TCTTTTTTTT-TATATAAGAATTGAAGGTTTCATT-AAAAACCCCTTCATGATTTAATGCACAGG
1 TCTTTTTTTTATATATAAGAATTGAAGATTTCATTAAAAAAACCCTTCATGATTTAATGCACAGG
39607 GA
66 GA
39609 TCTCAAACCT
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
67 29 0.47
68 23 0.37
69 10 0.16
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (69 bp):
TCTTTTTTTTATATATAAGAATTGAAGATTTCATTAAAAAAACCCTTCATGATTTAATGCACAGG
GAAC
Found at i:52402 original size:30 final size:30
Alignment explanation
Indices: 52363--52421 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
52353 ATTTTTTTTA
52363 AAAGAGTTACAAAGGGTTGTGTGTCATGTT
1 AAAGAGTTACAAAGGGTTGTGTGTCATGTT
*
52393 AAAGGGTTACAAAGGGTTGTGTGTCATGT
1 AAAGAGTTACAAAGGGTTGTGTGTCATGT
52422 ATCATACCTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.29, C:0.07, G:0.32, T:0.32
Consensus pattern (30 bp):
AAAGAGTTACAAAGGGTTGTGTGTCATGTT
Found at i:53087 original size:139 final size:139
Alignment explanation
Indices: 52837--53117 Score: 508
Period size: 139 Copynumber: 2.0 Consensus size: 139
52827 GGTCACTATC
* *
52837 ATCATAGGGTCAATTCCACCTTTTTGTTCTTGATCTCCTTACATGGTTTTCTCAAAGGCAATAAA
1 ATCATAGGGTCAATTCCACCTTTTTGTTCTTGATCTCCTTACAGGGTTTTCTCAAAGACAATAAA
*
52902 AAAAGCTGTAGGAGTTAAAGTTAATTTTGTTCTGTAATATTCTATATGATTTTAGCATGTATGAG
66 AAAAGCTGTAGGAGTTAAAGTTAATTTTGTTCTATAATATTCTATATGATTTTAGCATGTATGAG
52967 GAAATGCAT
131 GAAATGCAT
* *
52976 ATCATAGGGTCACTTCCACCTTTTTGTTCTTGATCTCCTTACAGGGTTTTCTCAAAGATAATAAA
1 ATCATAGGGTCAATTCCACCTTTTTGTTCTTGATCTCCTTACAGGGTTTTCTCAAAGACAATAAA
53041 AAAAGCTGTAGGAGTTAAAGTTAATTTTGTTCTATAATATTCTATATGATTTTAGCATGTATGAG
66 AAAAGCTGTAGGAGTTAAAGTTAATTTTGTTCTATAATATTCTATATGATTTTAGCATGTATGAG
*
53106 GTAATGCAT
131 GAAATGCAT
53115 ATC
1 ATC
53118 TTTCAGCCGG
Statistics
Matches: 136, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
139 136 1.00
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (139 bp):
ATCATAGGGTCAATTCCACCTTTTTGTTCTTGATCTCCTTACAGGGTTTTCTCAAAGACAATAAA
AAAAGCTGTAGGAGTTAAAGTTAATTTTGTTCTATAATATTCTATATGATTTTAGCATGTATGAG
GAAATGCAT
Found at i:62276 original size:70 final size:72
Alignment explanation
Indices: 62145--62287 Score: 272
Period size: 70 Copynumber: 2.0 Consensus size: 72
62135 AATAGAAATC
62145 GTTGAAAGTAACAAATTTGTTACTAGTTTCTAACTAAATTATTTTTGGTGGAATAAACCAAAATT
1 GTTGAAAGTAACAAATTTGTTACTAGTTTCTAACTAAATTATTTTTGGTGGAATAAACCAAAATT
62210 AAATTTT
66 AAATTTT
62217 GTTGAAAGTAACAAATTT-TTACTAGTTTCTAACTAAATT-TTTTTGGTGGAATAAACCAAAATT
1 GTTGAAAGTAACAAATTTGTTACTAGTTTCTAACTAAATTATTTTTGGTGGAATAAACCAAAATT
62280 AAATTTT
66 AAATTTT
62287 G
1 G
62288 GTTTATTGTT
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
70 32 0.45
71 21 0.30
72 18 0.25
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (72 bp):
GTTGAAAGTAACAAATTTGTTACTAGTTTCTAACTAAATTATTTTTGGTGGAATAAACCAAAATT
AAATTTT
Found at i:64990 original size:23 final size:22
Alignment explanation
Indices: 64939--64990 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
64929 AACGTAATAT
64939 AATA-AATATAATTTATCATTA
1 AATAGAATATAATTTATCATTA
** *
64960 TCTTGAATATAATTTTATCATTA
1 AATAGAATATAA-TTTATCATTA
64983 AATAGAAT
1 AATAGAAT
64991 TTATTAAGTA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
21 1 0.04
22 7 0.30
23 15 0.65
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (22 bp):
AATAGAATATAATTTATCATTA
Done.