Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005778.1 Hibiscus syriacus cultivar Beakdansim tig00013525_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: 69301
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:341 original size:173 final size:174
Alignment explanation
Indices: 31--374 Score: 463
Period size: 173 Copynumber: 2.0 Consensus size: 174
21 ATGTTAAATA
* * * *
31 TATATAAACATATGGACTCGGTCCAAACCATTTAAAACTCAATTAATAATTTAAGATCTAATAAT
1 TATATAAACATATGGACTCAGTCCAAACCATTTAAAACCCAATTAATAATTTAAGATCCAATAAC
96 TTTTAAACCTAAATAAATATTAATTAATTAAAAAATTATATAAATTTTTTATTTTATAATTATAT
66 TTTTAAACCTAAATAAATATTAATTAA-TAAAAAATTATATAAATTTTTTATTTTATAATTATAT
161 ATAAATTAATT-GTAAAC-TATTTTTTAATTAAAAAAATATTATATT
130 ATAAATTAATTAG-AAACGTATTTTTTAATT-AAAAAATATTATATT
* *
206 TATAT-AACATATGGGCTCAG-CCCAACCATTTAAAACCCAATTAATAATTTAAGATCCAATAAC
1 TATATAAACATATGGACTCAGTCCAAACCATTTAAAACCCAATTAATAATTTAAGATCCAATAAC
*
269 TTTTAAACCTAAATCAATAATTAATT-A-AAAAAATTATA-AAA-TTTTTA-TTTATAATTATAT
66 TTTTAAACCTAAATAAAT-ATTAATTAATAAAAAATTATATAAATTTTTTATTTTATAA-T-TAT
*
329 ATTATTTAAATTAATTAGAAACTGTTTTTTTTAATTAAAAAATATT
128 A-TA--TAAATTAATTAGAAAC-GTATTTTTTAATTAAAAAATATT
375 TAATTCGTTC
Statistics
Matches: 152, Mismatches: 8, Indels: 19
0.85 0.04 0.11
Matches are distributed among these distances:
168 7 0.05
169 7 0.05
170 7 0.05
171 13 0.09
173 71 0.47
174 31 0.20
175 16 0.11
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (174 bp):
TATATAAACATATGGACTCAGTCCAAACCATTTAAAACCCAATTAATAATTTAAGATCCAATAAC
TTTTAAACCTAAATAAATATTAATTAATAAAAAATTATATAAATTTTTTATTTTATAATTATATA
TAAATTAATTAGAAACGTATTTTTTAATTAAAAAATATTATATT
Found at i:11654 original size:22 final size:22
Alignment explanation
Indices: 11629--11672 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
11619 TGTATTTCAA
11629 TTATTATAT-ATTAAAATCATTT
1 TTATT-TATCATTAAAATCATTT
* *
11651 TTATTTTTCATTAAAATGATTT
1 TTATTTATCATTAAAATCATTT
11673 AAATTATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (22 bp):
TTATTTATCATTAAAATCATTT
Found at i:21936 original size:18 final size:18
Alignment explanation
Indices: 21913--21950 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
21903 GGGAACAGAT
21913 TGCAGATCCCAGACTTCA
1 TGCAGATCCCAGACTTCA
21931 TGCAGATCCCAGACTTCA
1 TGCAGATCCCAGACTTCA
21949 TG
1 TG
21951 GAAATTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (18 bp):
TGCAGATCCCAGACTTCA
Found at i:33924 original size:27 final size:28
Alignment explanation
Indices: 33874--33931 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
33864 AGGGGTGCAC
33874 AAAAAATCCGAATATCCGATTTTGCGAA
1 AAAAAATCCGAATATCCGATTTTGCGAA
* *
33902 AAAAATATCCGAA-ATCGGA-TTTGGGAA
1 AAAAA-ATCCGAATATCCGATTTTGCGAA
33929 AAA
1 AAA
33932 CCGGTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 10 0.37
28 10 0.37
29 7 0.26
ACGTcount: A:0.47, C:0.14, G:0.17, T:0.22
Consensus pattern (28 bp):
AAAAAATCCGAATATCCGATTTTGCGAA
Found at i:34029 original size:12 final size:12
Alignment explanation
Indices: 34014--34059 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
34004 CGATTTTTTT
*
34014 ACCGGATAAAAA
1 ACCGGTTAAAAA
34026 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
34041 ACCGGTTAAAAA
1 ACCGGTTAAAAA
34053 ACCGGTT
1 ACCGGTT
34060 TTTATCCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:34041 original size:15 final size:13
Alignment explanation
Indices: 34020--34060 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
34010 TTTTACCGGA
34020 TAAAAAACCGGTT
1 TAAAAAACCGGTT
34033 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
34047 TAAAAAACCGGTT
1 TAAAAAACCGGTT
34060 T
1 T
34061 TTATCCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:36380 original size:21 final size:21
Alignment explanation
Indices: 36356--36395 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
36346 TTTATTTTAT
36356 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
36377 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
36396 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:36443 original size:33 final size:33
Alignment explanation
Indices: 36390--36488 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
36380 TTTGTTTCAA
36390 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
36422 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
36455 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
36488 T
1 T
36489 ATGTTAAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:36517 original size:13 final size:13
Alignment explanation
Indices: 36474--36528 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
36464 TTGGAAGTAT
36474 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
36487 TTATGTTAAGTT-AA
1 TTAAG-T-ATTTCAA
36501 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
36514 TTAAGTATTTGAA
1 TTAAGTATTTCAA
36527 TT
1 TT
36529 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:36750 original size:21 final size:21
Alignment explanation
Indices: 36724--36780 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
36714 TGGAGCATGG
*
36724 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
36745 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
36766 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
36781 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:36974 original size:15 final size:15
Alignment explanation
Indices: 36954--37001 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
36944 TATTAAAATT
*
36954 GGTTTTTTTATAACC
1 GGTTTTTTTAAAACC
*
36969 GGTTTTTTAAAAAAACC
1 GGTTTTTT--TAAAACC
36986 GGTTTTTTTAAAACC
1 GGTTTTTTTAAAACC
37001 G
1 G
37002 AAACCGGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 15 0.54
17 13 0.46
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (15 bp):
GGTTTTTTTAAAACC
Found at i:37010 original size:21 final size:18
Alignment explanation
Indices: 36965--36998 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
36955 GTTTTTTTAT
36965 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
36982 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
36999 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:37118 original size:15 final size:17
Alignment explanation
Indices: 37092--37123 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
37082 TTCTATGGGA
37092 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
37108 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
37124 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:41797 original size:117 final size:115
Alignment explanation
Indices: 41554--41850 Score: 549
Period size: 117 Copynumber: 2.6 Consensus size: 115
41544 TTAGACTTTT
* * *
41554 ATGTTTAATTTTTGCGGTGGATAAATGGTTAACATATCGTGTTTTAGGTGTTAGAAATTAATAGT
1 ATGTTTAATTTTTGTGGTGGATAAATGGTTAACTTATCGTGTTTTAGGTGTTGGAAATTAATAGT
41619 ACTTCTTTCTAAGCTATTACATTAGACTTTTCAAACAAAACTTCAATGCC
66 ACTTCTTTCTAAGCTATTACATTAGACTTTTCAAACAAAACTTCAATGCC
41669 ATGTTTAATTTTTGTGGTGGATAAATGGTTAACTTATCGTGTTTTAGGTGTTGGAAATTAATAGT
1 ATGTTTAATTTTTGTGGTGGATAAATGGTTAACTTATCGTGTTTTAGGTGTTGGAAATTAATAGT
41734 ACTATTCTTTCTAAGCTATTACATTAGACTTTTCAAACAAAACTTCAATGCC
66 AC--TTCTTTCTAAGCTATTACATTAGACTTTTCAAACAAAACTTCAATGCC
41786 ATGTTTAATTTTTGTGGTGGATAAATGGTTAACTTATCGTGTTTTAGGTGTTGGAAATTAATAGT
1 ATGTTTAATTTTTGTGGTGGATAAATGGTTAACTTATCGTGTTTTAGGTGTTGGAAATTAATAGT
41851 TATACTGCAA
Statistics
Matches: 177, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
115 64 0.36
117 113 0.64
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.42
Consensus pattern (115 bp):
ATGTTTAATTTTTGTGGTGGATAAATGGTTAACTTATCGTGTTTTAGGTGTTGGAAATTAATAGT
ACTTCTTTCTAAGCTATTACATTAGACTTTTCAAACAAAACTTCAATGCC
Found at i:43169 original size:18 final size:19
Alignment explanation
Indices: 43141--43206 Score: 77
Period size: 18 Copynumber: 3.6 Consensus size: 19
43131 ACGTTCTACA
43141 ATCGATTCATCCTCCTTCG
1 ATCGATTCATCCTCCTTCG
*
43160 ATCG-TTCATCCTTCTTCTG
1 ATCGATTCATCCTCCTTC-G
43179 -TCG-TTCA-CCTCCTTCG
1 ATCGATTCATCCTCCTTCG
*
43195 GTCGATTCATCC
1 ATCGATTCATCC
43207 ACCGTAGAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
16 1 0.02
17 10 0.24
18 23 0.56
19 7 0.17
ACGTcount: A:0.12, C:0.36, G:0.12, T:0.39
Consensus pattern (19 bp):
ATCGATTCATCCTCCTTCG
Found at i:54314 original size:64 final size:63
Alignment explanation
Indices: 54229--54369 Score: 158
Period size: 64 Copynumber: 2.2 Consensus size: 63
54219 TTGTTTAAGG
* * * * *
54229 TGCATCGATGCACATGCAGTGCATCAATGCAT-GAATTTAAATAGAAAACATTGAACATGATTTA
1 TGCATCGATGCATAAGCAGTGCATCAATGCATCCAA-TTAAATA-AAAACATCGAACAGGATTTA
* * * * *
54293 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGCAGTGCATCAATGCAT-CCAATTAAATAAAAACATCGAACAGGATTTA
54357 TGCATCGATGCAT
1 TGCATCGATGCAT
54370 GGTGTAGTGC
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
64 57 0.88
65 7 0.11
66 1 0.02
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATAAGCAGTGCATCAATGCATCCAATTAAATAAAAACATCGAACAGGATTTA
Found at i:55821 original size:22 final size:22
Alignment explanation
Indices: 55764--55830 Score: 91
Period size: 22 Copynumber: 3.1 Consensus size: 22
55754 AGTCGAGGGT
*
55764 TTCACAGGTCAATCGGGAC-AA
1 TTCACAGGTCATTCGGGACAAA
* *
55785 CTCATAGGTCATTCGGGACAAA
1 TTCACAGGTCATTCGGGACAAA
*
55807 TTCACAGGTCCTTCGGGACAAA
1 TTCACAGGTCATTCGGGACAAA
55829 TT
1 TT
55831 TCATATGCCA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
21 16 0.41
22 23 0.59
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (22 bp):
TTCACAGGTCATTCGGGACAAA
Found at i:64217 original size:17 final size:19
Alignment explanation
Indices: 64191--64235 Score: 76
Period size: 18 Copynumber: 2.5 Consensus size: 19
64181 TTTATTAAAG
64191 TTTTATTTTTCTTTCATT-
1 TTTTATTTTTCTTTCATTA
64209 TTTTATTTTTCTTTCATTA
1 TTTTATTTTTCTTTCATTA
64228 TTTT-TTTT
1 TTTTATTTT
64236 CACACCGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 22 0.85
19 4 0.15
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTATTTTTCTTTCATTA
Found at i:64894 original size:21 final size:22
Alignment explanation
Indices: 64855--64895 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
64845 TTCTATTTTA
*
64855 TTTATTTAAATTGAGAATTATG
1 TTTATTTAAATTGACAATTATG
*
64877 TTTATTT-ATTTGACAATTA
1 TTTATTTAAATTGACAATTA
64896 CGACACTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.54
Consensus pattern (22 bp):
TTTATTTAAATTGACAATTATG
Done.