Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002025.1 Hibiscus syriacus cultivar Beakdansim tig00004136_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: 90868
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:259 original size:12 final size:13
Alignment explanation
Indices: 229--278 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
219 CTAATTTAAG
229 ATTAAAAATTATA
1 ATTAAAAATTATA
*
242 ATTAAAAATTGTA
1 ATTAAAAATTATA
255 A-TAAAAA--ATA
1 ATTAAAAATTATA
*
265 A-TAAAAATCATA
1 ATTAAAAATTATA
277 AT
1 AT
279 ATTTTAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 9 0.28
12 10 0.31
13 13 0.41
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (13 bp):
ATTAAAAATTATA
Found at i:2360 original size:4 final size:4
Alignment explanation
Indices: 2353--2397 Score: 51
Period size: 4 Copynumber: 11.8 Consensus size: 4
2343 TAACCAGAGA
*
2353 GAGG GAGG GAGG GA-- GAGG GAGAG G-GA GAGG GAGG GAGG GAGG GAG
1 GAGG GAGG GAGG GAGG GAGG GAG-G GAGG GAGG GAGG GAGG GAGG GAG
2398 AGAGAGAGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
2 2 0.06
3 1 0.03
4 30 0.86
5 2 0.06
ACGTcount: A:0.29, C:0.00, G:0.71, T:0.00
Consensus pattern (4 bp):
GAGG
Found at i:2380 original size:26 final size:26
Alignment explanation
Indices: 2349--2406 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 26
2339 TCGATAACCA
2349 GAGAGAGGGAGGGAGGGAGAGG-GAGA
1 GAGAGAGGGAGGGAGGGAG-GGAGAGA
*
2375 GGGAGAGGGAGGGAGGGAGGGAGAGA
1 GAGAGAGGGAGGGAGGGAGGGAGAGA
2401 GAGAGA
1 GAGAGA
2407 TTTAAGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 2 0.07
26 27 0.93
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (26 bp):
GAGAGAGGGAGGGAGGGAGGGAGAGA
Found at i:2387 original size:30 final size:30
Alignment explanation
Indices: 2348--2405 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
2338 TTCGATAACC
*
2348 AGAGAGAGGGAGGGAGGGAGAGGGAGAGGG
1 AGAGAGAGGGAGGGAGGGAGAGAGAGAGGG
*
2378 AGAGGGAGGGAGGGAGGGAGAGAGAGAG
1 AGAGAGAGGGAGGGAGGGAGAGAGAGAG
2406 ATTTAAGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (30 bp):
AGAGAGAGGGAGGGAGGGAGAGAGAGAGGG
Found at i:3922 original size:16 final size:16
Alignment explanation
Indices: 3909--3943 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3899 AAAACAACAT
3909 GAAACAAAATCAACTC
1 GAAACAAAATCAACTC
* *
3925 GAACCAAAATCAACCC
1 GAAACAAAATCAACTC
3941 GAA
1 GAA
3944 CCGAAAGCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.54, C:0.29, G:0.09, T:0.09
Consensus pattern (16 bp):
GAAACAAAATCAACTC
Found at i:3944 original size:16 final size:16
Alignment explanation
Indices: 3913--3956 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
3903 CAACATGAAA
*
3913 CAAAATCAACTCGAAC
1 CAAAATCAACCCGAAC
3929 CAAAATCAACCCGAAC
1 CAAAATCAACCCGAAC
* *
3945 CGAAAGCAACCC
1 CAAAATCAACCC
3957 AAATAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.48, C:0.36, G:0.09, T:0.07
Consensus pattern (16 bp):
CAAAATCAACCCGAAC
Found at i:8787 original size:19 final size:18
Alignment explanation
Indices: 8750--8789 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
8740 AAATTCAACG
8750 ATTAAATTTATTAATATA
1 ATTAAATTTATTAATATA
* *
8768 ATTATATTTTTTATATATA
1 ATTAAATTTATTA-ATATA
8787 ATT
1 ATT
8790 TTTTGAACCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTAAATTTATTAATATA
Found at i:9154 original size:19 final size:20
Alignment explanation
Indices: 9130--9172 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
9120 TCAGTAAGTG
9130 TTATAA-AATTTAATATA-TT
1 TTATAATAATTTAA-ATACTT
*
9149 TTATAATATTTTAAATACTT
1 TTATAATAATTTAAATACTT
9169 TTAT
1 TTAT
9173 TCACAGTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
TTATAATAATTTAAATACTT
Found at i:36626 original size:4 final size:4
Alignment explanation
Indices: 36619--36645 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
36609 GCATGCAAAC
36619 ATGT ATGT ATGT ATGT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATG
36646 ACATTGCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:38326 original size:15 final size:15
Alignment explanation
Indices: 38306--38335 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
38296 AACTGTTAAA
*
38306 ATAATATATTTTATT
1 ATAATATATTATATT
38321 ATAATATATTATATT
1 ATAATATATTATATT
38336 TTTAACAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATAATATATTATATT
Found at i:38348 original size:43 final size:42
Alignment explanation
Indices: 38232--38349 Score: 139
Period size: 43 Copynumber: 2.8 Consensus size: 42
38222 TCCGATCCAA
*
38232 ATTA-AATATATTAATATTTTAAAATAATTAAAATAATATATTT
1 ATTATAATATATT-ATATTTT-AAACAATTAAAATAATATATTT
* * * **
38275 ATAATTATTTATTATATTTTAAACTGTTAAAATAATATATTTT
1 ATTATAATATATTATATTTTAAACAATTAAAATAATATA-TTT
*
38318 ATTATAATATATTATATTTTTAACAATTAAAA
1 ATTATAATATATTATATTTTAAACAATTAAAA
38350 ACCTATTTTA
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
42 16 0.26
43 39 0.64
44 6 0.10
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (42 bp):
ATTATAATATATTATATTTTAAACAATTAAAATAATATATTT
Found at i:49648 original size:18 final size:18
Alignment explanation
Indices: 49616--49662 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
49606 GCCGCCGGAG
* *
49616 CAGCCTCTTTGGGTTTCT
1 CAGCTTCTTTCGGTTTCT
*
49634 CCGCTTCTTTCGGTTTCT
1 CAGCTTCTTTCGGTTTCT
*
49652 CAGCTTTTTTC
1 CAGCTTCTTTC
49663 TCCCCACCAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.04, C:0.30, G:0.17, T:0.49
Consensus pattern (18 bp):
CAGCTTCTTTCGGTTTCT
Found at i:49693 original size:18 final size:18
Alignment explanation
Indices: 49672--49708 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
49662 CTCCCCACCA
49672 TCTTTAGGCTTCTCAGCC
1 TCTTTAGGCTTCTCAGCC
* *
49690 TCTTTTGGTTTCTCAGCC
1 TCTTTAGGCTTCTCAGCC
49708 T
1 T
49709 TCTCCTCAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.08, C:0.30, G:0.16, T:0.46
Consensus pattern (18 bp):
TCTTTAGGCTTCTCAGCC
Found at i:49731 original size:48 final size:48
Alignment explanation
Indices: 49672--49783 Score: 125
Period size: 48 Copynumber: 2.3 Consensus size: 48
49662 CTCCCCACCA
* * *
49672 TCTTTAGGCTTCTCAGCCTCTTTTGGTTTCTCAGCCTTCTCCTCAGAT
1 TCTTTAGGCTTCTCAGCCTCTTTCGGCTTCTCAGCCTTCTCCTCAGAC
** * ** * *
49720 TCTTTAGGCTTCTTGGCCTCTTTCGGCTTCTCCGGTTTCTTCTCAGCC
1 TCTTTAGGCTTCTCAGCCTCTTTCGGCTTCTCAGCCTTCTCCTCAGAC
*
49768 TCTTTCGGCTTCTCAG
1 TCTTTAGGCTTCTCAG
49784 GTTTCTTCTG
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.07, C:0.32, G:0.17, T:0.44
Consensus pattern (48 bp):
TCTTTAGGCTTCTCAGCCTCTTTCGGCTTCTCAGCCTTCTCCTCAGAC
Found at i:49762 original size:30 final size:30
Alignment explanation
Indices: 49728--49865 Score: 186
Period size: 30 Copynumber: 4.6 Consensus size: 30
49718 ATTCTTTAGG
* *
49728 CTTCTTGGCCTCTTTCGGCTTCTCCGGTTT
1 CTTCTCGGCCTCTTTCGGCTTCTCGGGTTT
* *
49758 CTTCTCAGCCTCTTTCGGCTTCTCAGGTTT
1 CTTCTCGGCCTCTTTCGGCTTCTCGGGTTT
* * *
49788 CTTCTGGGCCTCCTTAGGCTTCTCGGGTTT
1 CTTCTCGGCCTCTTTCGGCTTCTCGGGTTT
* *
49818 CTTCTGGGCCTCTTTAGGCTTCTCGGGTTT
1 CTTCTCGGCCTCTTTCGGCTTCTCGGGTTT
*
49848 CTTCTCAGCCTCTTTCGG
1 CTTCTCGGCCTCTTTCGG
49866 TTTGTACGGT
Statistics
Matches: 96, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 96 1.00
ACGTcount: A:0.04, C:0.32, G:0.22, T:0.43
Consensus pattern (30 bp):
CTTCTCGGCCTCTTTCGGCTTCTCGGGTTT
Found at i:51939 original size:18 final size:17
Alignment explanation
Indices: 51918--51951 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
51908 TAGTTAGTTC
51918 TTATAAAATATATTTTTA
1 TTAT-AAATATATTTTTA
*
51936 TTATAATTATATTTTT
1 TTATAAATATATTTTT
51952 TATATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTATAAATATATTTTTA
Found at i:56266 original size:12 final size:12
Alignment explanation
Indices: 56251--56280 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
56241 TTAAAATATT
56251 ATTTAAATTTTA
1 ATTTAAATTTTA
*
56263 ATTTTAATTTTA
1 ATTTAAATTTTA
56275 ATTTAA
1 ATTTAA
56281 TATTCATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
ATTTAAATTTTA
Found at i:64405 original size:44 final size:44
Alignment explanation
Indices: 64357--64489 Score: 241
Period size: 44 Copynumber: 3.0 Consensus size: 44
64347 TAAAATAAAC
*
64357 TTTAATCTTTAGAGAAATTATCAATTACATTTTAAATAGACTTT
1 TTTAATCTTTAGAGAAATTATCAATTACTTTTTAAATAGACTTT
64401 TTTAATCTTTAGAGAAATTATCAATTACTTTTTAAATAGACTTT
1 TTTAATCTTTAGAGAAATTATCAATTACTTTTTAAATAGACTTT
*
64445 TTTAATCTTTAGAGAAATTATCAATTACTTTTTAAATTGA-TTT
1 TTTAATCTTTAGAGAAATTATCAATTACTTTTTAAATAGACTTT
64488 TT
1 TT
64490 AGTACAGTAA
Statistics
Matches: 87, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
43 5 0.06
44 82 0.94
ACGTcount: A:0.36, C:0.08, G:0.07, T:0.49
Consensus pattern (44 bp):
TTTAATCTTTAGAGAAATTATCAATTACTTTTTAAATAGACTTT
Found at i:71751 original size:39 final size:39
Alignment explanation
Indices: 71707--71781 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
71697 CATAAGTGAA
*
71707 TGGAATAATACTATTGTACATCAATGTCAACCTTTTTTT
1 TGGAATAATACTAGTGTACATCAATGTCAACCTTTTTTT
*
71746 TGGAATAATACTAGTGTACATCAATGTCGACCTTTT
1 TGGAATAATACTAGTGTACATCAATGTCAACCTTTT
71782 ATTCTTATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (39 bp):
TGGAATAATACTAGTGTACATCAATGTCAACCTTTTTTT
Found at i:78412 original size:2 final size:2
Alignment explanation
Indices: 78405--78448 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
78395 TCAAATTTGA
78405 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
78447 AT
1 AT
78449 TTAAAGTTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:79306 original size:23 final size:24
Alignment explanation
Indices: 79280--79337 Score: 64
Period size: 29 Copynumber: 2.2 Consensus size: 24
79270 CACCTAAATT
79280 AATTTA-ATGTCATTGCTTACATC
1 AATTTATATGTCATTGCTTACATC
79303 AATTTAGTTTTGATGTCATTGCTTACATC
1 AATTTA----T-ATGTCATTGCTTACATC
79332 AATTTA
1 AATTTA
79338 GTTAGGTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.21
29 23 0.79
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.47
Consensus pattern (24 bp):
AATTTATATGTCATTGCTTACATC
Found at i:83996 original size:29 final size:29
Alignment explanation
Indices: 83962--84020 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
83952 CCTAAATTAA
83962 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
83991 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
84020 T
1 T
84021 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Done.