Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000220.1 Hibiscus syriacus cultivar Beakdansim tig00000389_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: 62828
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2934 original size:3 final size:3
Alignment explanation
Indices: 2926--2954 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2916 TTATCATGTC
2926 ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2955 TTTAAGAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:21449 original size:8 final size:7
Alignment explanation
Indices: 21421--21447 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
21411 ATTACGCCTA
21421 AAAAAAG
1 AAAAAAG
21428 AAAAAAG
1 AAAAAAG
21435 AAAAAAG
1 AAAAAAG
21442 AAAAAA
1 AAAAAA
21448 AGGAGAGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:22332 original size:44 final size:44
Alignment explanation
Indices: 22267--22990 Score: 351
Period size: 44 Copynumber: 16.4 Consensus size: 44
22257 TTAAATTTTT
* * *
22267 GCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGATATCTC
1 GCTCGATTCCATCACAGAAGGAGGTGGATCAGCATCGATATTTC
* * **
22311 GTTCGATTCCATCACAGAAGGAGGTGGATCAACAT-TTTATTTTC
1 GCTCGATTCCATCACAGAAGGAGGTGGATCAGCATCGATA-TTTC
* * * * * * *
22355 GCTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACT-TTTA
1 GCTCGATTCCATCACAGAAGGAGGTGGATCAGCATCGA-TATTTC
* * ** * *
22399 GCTCGATTCTATCACAGAATGAGGTAAATCAGCATCGACATCTC
1 GCTCGATTCCATCACAGAAGGAGGTGGATCAGCATCGATATTTC
* * * ***
22443 GTTCGATTCAATCACAGAAAGAGGTGGATC-GACATTTTTATTTTC
1 GCTCGATTCCATCACAGAAGGAGGTGGATCAG-CATCGATA-TTTC
* * ** * ** *
22488 GCTCAAATCCATCGTAGAAGGAGTTGGATCAGCATTAACT-TTTA
1 GCTCGATTCCATCACAGAAGGAGGTGGATCAGCATCGA-TATTTC
* * * *
22532 GCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTC
1 GCTCGATTCCATCACAGAAGGAGGTGGATCAGCATCGATATTTC
* * ***
22576 GTTCGATTCAATCACAGAAGGAGGTGGATC-GACATTTTTATTTTC
1 GCTCGATTCCATCACAGAAGGAGGTGGATCAG-CATCGATA-TTTC
* * * ** * * * *
22621 TCTCAAATCCATCGTAGAAGGAGTTGGATCAGCGTCAACT-TTTA
1 GCTCGATTCCATCACAGAAGGAGGTGGATCAGCATCGA-TATTTC
* * * *
22665 GCTCGATTCTATCACAGAATGAGAATGAGGTAGATCAGCATCGACATCTC
1 GCTCGATTCCATCACAG-A--AG---GAGGTGGATCAGCATCGATATTTC
* *
22715 GTTCGATTCAATCACAGAAGGAGGTGGATC-G-A-C-AT-TTTC
1 GCTCGATTCCATCACAGAAGGAGGTGGATCAGCATCGATATTTC
* * * * * * *
22754 GCTCAAATCCATCATAGAAGGAGTTGGATCAGCGTCAACT-TTTA
1 GCTCGATTCCATCACAGAAGGAGGTGGATCAGCATCGA-TATTTC
* * * * * * *
22798 GCTCGATTCTATCACAGAATGAGTTAGATCAGTATCGACATCTC
1 GCTCGATTCCATCACAGAAGGAGGTGGATCAGCATCGATATTTC
* *** *
22842 GTTCGATTCCATCACAGAAGGAGGTGGATC-GACATTTTTATTTTT
1 GCTCGATTCCATCACAGAAGGAGGTGGATCAG-CATCGATA-TTTC
* * * * * * * *
22887 GCTCAAATCCATCGCAGAAGGAGTTGGATCAACGTCAACT-TTTT
1 GCTCGATTCCATCACAGAAGGAGGTGGATCAGCATCGA-TATTTC
* * * * * *
22931 GCTCGATTCTATCACAGAAGGAGGTAGATCAACACCGACATCTC
1 GCTCGATTCCATCACAGAAGGAGGTGGATCAGCATCGATATTTC
* *
22975 GTTCAATTCCATCACA
1 GCTCGATTCCATCACA
22991 TATGGAGTTG
Statistics
Matches: 490, Mismatches: 159, Indels: 62
0.69 0.22 0.09
Matches are distributed among these distances:
39 27 0.06
40 2 0.00
41 1 0.00
42 2 0.00
43 7 0.01
44 323 0.66
45 86 0.18
46 6 0.01
47 4 0.01
49 1 0.00
50 31 0.06
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.29
Consensus pattern (44 bp):
GCTCGATTCCATCACAGAAGGAGGTGGATCAGCATCGATATTTC
Found at i:22549 original size:133 final size:133
Alignment explanation
Indices: 22262--22990 Score: 1139
Period size: 133 Copynumber: 5.5 Consensus size: 133
22252 CTTGTTTAAA
* * *
22262 TTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGATATCTCGTTCGATTCCATCACA
1 TTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGATTCAATCACA
* *
22327 GAAGGAGGTGGATCAACA-TTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTC
66 GAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGTAGAAGGAGTTGGATCAGCGTC
22391 AAC
131 AAC
* *
22394 TTTTAGCTCGATTCTATCACAGAATGAGGTAAATCAGCATCGACATCTCGTTCGATTCAATCACA
1 TTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGATTCAATCACA
* * *
22459 GAAAGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGTAGAAGGAGTTGGATCAGCATT
66 GAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGTAGAAGGAGTTGGATCAGCGTC
22524 AAC
131 AAC
22527 TTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGATTCAATCACA
1 TTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGATTCAATCACA
*
22592 GAAGGAGGTGGATCGACATTTTTATTTTCTCTCAAATCCATCGTAGAAGGAGTTGGATCAGCGTC
66 GAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGTAGAAGGAGTTGGATCAGCGTC
22657 AAC
131 AAC
22660 TTTTAGCTCGATTCTATCACAGAATGAGAATGAGGTAGATCAGCATCGACATCTCGTTCGATTCA
1 TTTTAGCTCGATTCTATCACAG-A--AG---GAGGTAGATCAGCATCGACATCTCGTTCGATTCA
*
22725 ATCACAGAAGGAGGTGGATCGAC------ATTTTCGCTCAAATCCATCATAGAAGGAGTTGGATC
60 ATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGTAGAAGGAGTTGGATC
22784 AGCGTCAAC
125 AGCGTCAAC
* * * *
22793 TTTTAGCTCGATTCTATCACAGAATGAGTTAGATCAGTATCGACATCTCGTTCGATTCCATCACA
1 TTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGATTCAATCACA
* * *
22858 GAAGGAGGTGGATCGACATTTTTATTTTTGCTCAAATCCATCGCAGAAGGAGTTGGATCAACGTC
66 GAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGTAGAAGGAGTTGGATCAGCGTC
22923 AAC
131 AAC
* * * * *
22926 TTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACACCGACATCTCGTTCAATTCCATCACA
1 TTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGATTCAATCACA
22991 TATGGAGTTG
Statistics
Matches: 551, Mismatches: 33, Indels: 25
0.90 0.05 0.04
Matches are distributed among these distances:
127 54 0.10
130 1 0.00
132 77 0.14
133 359 0.65
134 1 0.00
136 2 0.00
139 57 0.10
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (133 bp):
TTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGATTCAATCACA
GAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGTAGAAGGAGTTGGATCAGCGTC
AAC
Found at i:24190 original size:22 final size:22
Alignment explanation
Indices: 24121--24190 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 22
24111 TATTTCCTTG
*
24121 TATTTTA-GTCATTATTATTTTA
1 TATTTTATGTAATT-TTATTTTA
* ** *
24143 TA-TTTATGCAATTAGATCTT-
1 TATTTTATGTAATTTTATTTTA
*
24163 TATTTTATGTTATTTTATTTTA
1 TATTTTATGTAATTTTATTTTA
24185 TATTTT
1 TATTTT
24191 TAATGTTTTT
Statistics
Matches: 35, Mismatches: 10, Indels: 6
0.69 0.20 0.12
Matches are distributed among these distances:
20 2 0.06
21 21 0.60
22 12 0.34
ACGTcount: A:0.26, C:0.04, G:0.06, T:0.64
Consensus pattern (22 bp):
TATTTTATGTAATTTTATTTTA
Found at i:29111 original size:14 final size:14
Alignment explanation
Indices: 29072--29114 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
29062 ATATGTGTTT
29072 TTTAATATTAATTA
1 TTTAATATTAATTA
* *
29086 TTGT-TTAGTAATTA
1 TT-TAATATTAATTA
29100 TTTAATATTAATTA
1 TTTAATATTAATTA
29114 T
1 T
29115 GGTTTTGCAG
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
13 1 0.04
14 21 0.91
15 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (14 bp):
TTTAATATTAATTA
Found at i:30375 original size:14 final size:14
Alignment explanation
Indices: 30356--30385 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
30346 CAAATTTCTC
30356 ATCTTCCTAAGTTT
1 ATCTTCCTAAGTTT
30370 ATCTTCCTAAGTTT
1 ATCTTCCTAAGTTT
30384 AT
1 AT
30386 AAGCATGTTC
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:0.23, C:0.20, G:0.07, T:0.50
Consensus pattern (14 bp):
ATCTTCCTAAGTTT
Found at i:32964 original size:19 final size:19
Alignment explanation
Indices: 32936--32980 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
32926 AAAAGTAGTC
32936 AATATCACAGTTTACTATA
1 AATATCACAGTTTACTATA
*
32955 AATATTACAGTTTACTATA
1 AATATCACAGTTTACTATA
*
32974 AAAATCA
1 AATATCA
32981 AGGACATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.47, C:0.13, G:0.04, T:0.36
Consensus pattern (19 bp):
AATATCACAGTTTACTATA
Found at i:33242 original size:36 final size:38
Alignment explanation
Indices: 33201--33284 Score: 109
Period size: 36 Copynumber: 2.3 Consensus size: 38
33191 ATAAAAATTT
* *
33201 AAAATTTTAAATGATTCAACATA-TAAATTAA-TTATA
1 AAAATTTAAAAAGATTCAACATATTAAATTAATTTATA
* * *
33237 AAAATTTAAAAAGATTTAATATATTAATTTAATTTATA
1 AAAATTTAAAAAGATTCAACATATTAAATTAATTTATA
33275 AAAATTTAAA
1 AAAATTTAAA
33285 GGTAAATTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
36 19 0.46
37 7 0.17
38 15 0.37
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (38 bp):
AAAATTTAAAAAGATTCAACATATTAAATTAATTTATA
Found at i:35101 original size:3 final size:3
Alignment explanation
Indices: 35093--35125 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
35083 TTCAATAACT
*
35093 TTC TTC TTC TTC TTC TTC TTC TTC TTC CTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
35126 CTTTTTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:40066 original size:13 final size:13
Alignment explanation
Indices: 40048--40077 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
40038 GGGTATAATG
40048 CGAAAACCCGACT
1 CGAAAACCCGACT
*
40061 CGAAAACTCGACT
1 CGAAAACCCGACT
40074 CGAA
1 CGAA
40078 TTGCCCCCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.33, G:0.17, T:0.10
Consensus pattern (13 bp):
CGAAAACCCGACT
Found at i:41623 original size:91 final size:89
Alignment explanation
Indices: 41512--41871 Score: 497
Period size: 91 Copynumber: 4.0 Consensus size: 89
41502 AATCACCCAA
* * * *
41512 GTTGAACAAGTTCTTTTCATTATGAACTTATTCTCCCTCATTGGATGGGTTCTTCTCATTATGAA
1 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAA
* * *
41577 CTCATCGCTGGAAATGTTGATGCAAG
66 CTC-TCACTGGAAATCTTGA-ACAAG
* * *
41603 GTTGAACAAATTCTTCTCATTATGAACTTCTTTTTCCTCTTTTGGATGAGTTCTTCTCATTATGA
1 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTCCCTC-ATTGGATGAGTTCTTCTCATTATGA
41668 ACTCTCCACTGGAAATCTTGAACTAAG
65 ACTCT-CACTGGAAATCTTGAAC-AAG
* **
41695 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTGTTGGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAA
*
41760 CTCCCCACTGGAAATCTTGAACCAAG
66 CT-CTCACTGGAAATCTTGAA-CAAG
41786 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTCCCT-AGTTGGATGAGTTCTTCTCATTATGA
1 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTCCCTCA-TTGGATGAGTTCTTCTCATTATGA
*
41850 ACTCTCCACTAGAAATCTTGAA
65 ACTCT-CACTGGAAATCTTGAA
41872 TGGTTTATCT
Statistics
Matches: 242, Mismatches: 20, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
90 1 0.00
91 161 0.67
92 80 0.33
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (89 bp):
GTTGAACAAATTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAA
CTCTCACTGGAAATCTTGAACAAG
Found at i:50978 original size:14 final size:15
Alignment explanation
Indices: 50959--50988 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
50949 CCATGGGTAG
50959 CGGGTA-TGAACTGT
1 CGGGTACTGAACTGT
50973 CGGGTACTGAACTGT
1 CGGGTACTGAACTGT
50988 C
1 C
50989 TGAGTGCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.20, C:0.20, G:0.33, T:0.27
Consensus pattern (15 bp):
CGGGTACTGAACTGT
Found at i:53969 original size:18 final size:17
Alignment explanation
Indices: 53933--53995 Score: 54
Period size: 19 Copynumber: 3.5 Consensus size: 17
53923 ATTACAAAAT
* *
53933 AAATTAAATAAATACTA
1 AAATTAAAAAAATAATA
53950 AAATTAAACAAAATAATAA
1 AAATTAAA-AAAATAAT-A
* *
53969 AAATTACAAATAATAAAGA
1 AAATTA-AAAAAAT-AATA
53988 AAATTAAA
1 AAATTAAA
53996 GTACAAAGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
17 8 0.21
18 8 0.21
19 18 0.47
20 4 0.11
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.24
Consensus pattern (17 bp):
AAATTAAAAAAATAATA
Found at i:55177 original size:21 final size:20
Alignment explanation
Indices: 55149--55189 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
55139 ACGTGTTTAG
55149 TTGTAAAATAAAAAAAATAT
1 TTGTAAAATAAAAAAAATAT
**
55169 TTGTGAAAATATGAAAAATAT
1 TTGT-AAAATAAAAAAAATAT
55190 AAAAAAGATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.32
Consensus pattern (20 bp):
TTGTAAAATAAAAAAAATAT
Found at i:55447 original size:27 final size:30
Alignment explanation
Indices: 55394--55448 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
55384 TTATATTTTT
*
55394 ATATTTAATATATTAAATATCTTAATAATC
1 ATATTTAATATATTAAATATCTAAATAATC
*
55424 ATATTT-ATATTTTAAAT-T-TAAATAA
1 ATATTTAATATATTAAATATCTAAATAA
55449 ATTTAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 6 0.26
28 1 0.04
29 10 0.43
30 6 0.26
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (30 bp):
ATATTTAATATATTAAATATCTAAATAATC
Done.