Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002673.1 Hibiscus syriacus cultivar Beakdansim tig00005490_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: 61400
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:116 original size:29 final size:29
Alignment explanation
Indices: 74--154 Score: 121
Period size: 29 Copynumber: 2.8 Consensus size: 29
64 AAACTAAATT
74 GATGTCATTGCTTACATCATTTAAGTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
103 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
132 GA--TCATTGCTTACAATCAATTTA
1 GATGTCATTGCTTAC-ATC-ATTTA
155 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
27 11 0.22
28 3 0.06
29 35 0.71
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:2509 original size:2 final size:2
Alignment explanation
Indices: 2502--2567 Score: 102
Period size: 2 Copynumber: 34.5 Consensus size: 2
2492 ATAACAAAGT
*
2502 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TT TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2543 TA TA TA TA TA TA TA -A TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2568 TTTGGGTAGA
Statistics
Matches: 60, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
1 3 0.05
2 57 0.95
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:4470 original size:24 final size:24
Alignment explanation
Indices: 4443--4491 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
4433 ATAAAGAACC
*
4443 AAATAAA-CTTAAATATACCATTAA
1 AAATAAAGCTTAAACAT-CCATTAA
*
4467 AAATAAAGTTTAAACATCCATTAA
1 AAATAAAGCTTAAACATCCATTAA
4491 A
1 A
4492 CCAACCACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (24 bp):
AAATAAAGCTTAAACATCCATTAA
Found at i:6842 original size:14 final size:15
Alignment explanation
Indices: 6800--6837 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
6790 AAAATAATAT
* *
6800 TAAAATTAAAACTAA
1 TAAAAATAAAACAAA
6815 -AAAAATAAAACAAA
1 TAAAAATAAAACAAA
6829 TAAAAATAA
1 TAAAAATAA
6838 TCAAACAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.18
Consensus pattern (15 bp):
TAAAAATAAAACAAA
Found at i:6843 original size:18 final size:17
Alignment explanation
Indices: 6812--6848 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
6802 AAATTAAAAC
6812 TAAAAAAATAAAACAAA
1 TAAAAAAATAAAACAAA
*
6829 TAAAAATAATCAAACAAA
1 TAAAAA-AATAAAACAAA
6847 TA
1 TA
6849 CTCACGACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (17 bp):
TAAAAAAATAAAACAAA
Found at i:10091 original size:24 final size:24
Alignment explanation
Indices: 10046--10095 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
10036 ATAAAGAACC
*
10046 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
10070 AAAATAAAGTTTAAACAT-CCATTA
1 AAAATAAA-CTTAAACATACCATTA
10094 AA
1 AA
10096 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:12450 original size:15 final size:15
Alignment explanation
Indices: 12426--12459 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
12416 ATTTTATTTG
* *
12426 CTTTACAGCTTGATC
1 CTTTAAAGCTTGAGC
12441 CTTTAAAGCTTGAGC
1 CTTTAAAGCTTGAGC
12456 CTTT
1 CTTT
12460 GCTGTTTCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.41
Consensus pattern (15 bp):
CTTTAAAGCTTGAGC
Found at i:16151 original size:11 final size:12
Alignment explanation
Indices: 16125--16155 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
16115 ACATCAATTT
16125 AGTTAGGTGAAG
1 AGTTAGGTGAAG
16137 AGTTAGGTG-AG
1 AGTTAGGTGAAG
16148 AGTTAGGT
1 AGTTAGGT
16156 ATTTGTCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.29, C:0.00, G:0.42, T:0.29
Consensus pattern (12 bp):
AGTTAGGTGAAG
Found at i:21827 original size:17 final size:16
Alignment explanation
Indices: 21805--21836 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
21795 AGAAGAAAAA
21805 ATATA-AAAAAATGTT
1 ATATATAAAAAATGTT
21820 ATATATAAAAAATGTT
1 ATATATAAAAAATGTT
21836 A
1 A
21837 AAAGAAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.34
Consensus pattern (16 bp):
ATATATAAAAAATGTT
Found at i:21904 original size:21 final size:21
Alignment explanation
Indices: 21880--21919 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
21870 ATTTTAGAAG
*
21880 AAAAAAATAAACAAAATAAAC
1 AAAAAAATAAAAAAAATAAAC
21901 AAAAAAATAAAAAAAATAA
1 AAAAAAATAAAAAAAATAA
21920 TAAAAGAGAA
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:0.85, C:0.05, G:0.00, T:0.10
Consensus pattern (21 bp):
AAAAAAATAAAAAAAATAAAC
Found at i:21907 original size:12 final size:12
Alignment explanation
Indices: 21880--21923 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
21870 ATTTTAGAAG
21880 AAAAAAATAAAC
1 AAAAAAATAAAC
21892 ---AAAATAAAC
1 AAAAAAATAAAC
21901 AAAAAAATAAA-
1 AAAAAAATAAAC
21912 AAAAATAATAAA
1 AAAAA-AATAAA
21924 AGAGAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 9 0.32
11 5 0.18
12 14 0.50
ACGTcount: A:0.84, C:0.05, G:0.00, T:0.11
Consensus pattern (12 bp):
AAAAAAATAAAC
Found at i:21924 original size:12 final size:11
Alignment explanation
Indices: 21880--22008 Score: 57
Period size: 11 Copynumber: 11.0 Consensus size: 11
21870 ATTTTAGAAG
21880 AAAAAAAT--A
1 AAAAAAATAAA
*
21889 AACAAAATAAA
1 AAAAAAATAAA
21900 CAAAAAAATAAA
1 -AAAAAAATAAA
21912 AAAAATAATAAA
1 AAAAA-AATAAA
21924 AGAGAAAAATGTTAAAA
1 A-A-AAAAA---T-AAA
21941 GAGAAAAAATAATA
1 -A-AAAAAATAA-A
* *
21955 AACAAAACAAA
1 AAAAAAATAAA
* *
21966 ACAAAAATGAA
1 AAAAAAATAAA
* *
21977 ATAAAAA-AAG
1 AAAAAAATAAA
*
21987 TAAAAAATAAA
1 AAAAAAATAAA
*
21998 AATAAAATAAA
1 AAAAAAATAAA
22009 GGTTAGGAGA
Statistics
Matches: 91, Mismatches: 16, Indels: 24
0.69 0.12 0.18
Matches are distributed among these distances:
9 7 0.08
10 6 0.07
11 31 0.34
12 24 0.26
13 6 0.07
14 5 0.05
16 1 0.01
17 8 0.09
18 3 0.03
ACGTcount: A:0.78, C:0.04, G:0.05, T:0.12
Consensus pattern (11 bp):
AAAAAAATAAA
Found at i:21933 original size:16 final size:17
Alignment explanation
Indices: 21911--21956 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 17
21901 AAAAAAATAA
21911 AAAAAATAATAAAAGAG
1 AAAAAATAATAAAAGAG
**
21928 -AAAAATGTTAAAAGAG
1 AAAAAATAATAAAAGAG
21944 AAAAAATAATAAA
1 AAAAAATAATAAA
21957 CAAAACAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.15
Consensus pattern (17 bp):
AAAAAATAATAAAAGAG
Found at i:24405 original size:116 final size:115
Alignment explanation
Indices: 24280--24553 Score: 397
Period size: 116 Copynumber: 2.4 Consensus size: 115
24270 TAATCATAAA
24280 CAAATCTCAAGACTCAAATCACAATATTAAATCTAGAACAATAAAATTCATAAACAAACCACAAT
1 CAAATCTCAAGACTCAAATCACAATATTAAATCTAGAACAATAAAATTCATAAACAAACCACAAT
* * * *
24345 ATTAAGTCTAGAACAATAAAATTCATAAAACAAACCACAATATTAAAATATC
66 ATTAAGTCTAAAACAATAAAATTCAT-AAACAAACAACAATAGTAAAAT-GC
* ** *
24397 C-AATCTCAAGATTCAAATCACAATATTAACCCTAGAACAATAAAATTCATAAACAAACCATAAT
1 CAAATCTCAAGACTCAAATCACAATATTAAATCTAGAACAATAAAATTCATAAACAAACCACAAT
* * *
24461 ATTAAGTCTAAAATAATAAAATTCATAAACAAACAATAATAGTAAAGTGC
66 ATTAAGTCTAAAACAATAAAATTCATAAACAAACAACAATAGTAAAATGC
* * *
24511 CAAATCTCAAGACTCAAACCATAATATTAAGTCTAGAACAATA
1 CAAATCTCAAGACTCAAATCACAATATTAAATCTAGAACAATA
24554 TTAAACAACA
Statistics
Matches: 140, Mismatches: 16, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
114 2 0.01
115 54 0.39
116 83 0.59
117 1 0.01
ACGTcount: A:0.53, C:0.18, G:0.05, T:0.24
Consensus pattern (115 bp):
CAAATCTCAAGACTCAAATCACAATATTAAATCTAGAACAATAAAATTCATAAACAAACCACAAT
ATTAAGTCTAAAACAATAAAATTCATAAACAAACAACAATAGTAAAATGC
Found at i:24498 original size:20 final size:20
Alignment explanation
Indices: 24432--24499 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
24422 TTAACCCTAG
24432 AACAATAAAATTCATAAACA
1 AACAATAAAATTCATAAACA
* * * **
24452 AACCATAATATTAAGTCTA-A
1 AACAATAAAATTCA-TAAACA
*
24472 AATAATAAAATTCATAAACA
1 AACAATAAAATTCATAAACA
24492 AACAATAA
1 AACAATAA
24500 TAGTAAAGTG
Statistics
Matches: 34, Mismatches: 12, Indels: 4
0.68 0.24 0.08
Matches are distributed among these distances:
19 2 0.06
20 30 0.88
21 2 0.06
ACGTcount: A:0.62, C:0.13, G:0.01, T:0.24
Consensus pattern (20 bp):
AACAATAAAATTCATAAACA
Found at i:24501 original size:40 final size:40
Alignment explanation
Indices: 24294--24494 Score: 200
Period size: 40 Copynumber: 5.1 Consensus size: 40
24284 TCTCAAGACT
*
24294 CAAATCACAATATTAAATCTAGAACAATAAAATTCATAAA
1 CAAACCACAATATTAAATCTAGAACAATAAAATTCATAAA
*
24334 CAAACCACAATATTAAGTCTAGAACAATAAAATTCATAAAA
1 CAAACCACAATATTAAATCTAGAACAATAAAATTCAT-AAA
* ** * *
24375 CAAACCACAATATTAAA-ATA-TCCAAT----CTCA-AGATT
1 CAAACCACAATATTAAATCTAGAACAATAAAATTCATA-A-A
* **
24410 CAAATCACAATATTAACCCTAGAACAATAAAATTCATAAA
1 CAAACCACAATATTAAATCTAGAACAATAAAATTCATAAA
* * * *
24450 CAAACCATAATATTAAGTCTAAAATAATAAAATTCATAAA
1 CAAACCACAATATTAAATCTAGAACAATAAAATTCATAAA
24490 CAAAC
1 CAAAC
24495 AATAATAGTA
Statistics
Matches: 130, Mismatches: 21, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
33 1 0.01
34 1 0.01
35 18 0.14
36 2 0.02
37 4 0.03
39 4 0.03
40 76 0.58
41 23 0.18
42 1 0.01
ACGTcount: A:0.55, C:0.18, G:0.03, T:0.24
Consensus pattern (40 bp):
CAAACCACAATATTAAATCTAGAACAATAAAATTCATAAA
Found at i:37226 original size:19 final size:19
Alignment explanation
Indices: 37202--37239 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
37192 CATATTATGT
37202 CTTTT-GTTTTTCTTTTTTC
1 CTTTTAGTTTTT-TTTTTTC
37221 CTTTTGAGTTTTTTTTTTT
1 CTTTT-AGTTTTTTTTTTT
37240 TAATTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.03, C:0.11, G:0.08, T:0.79
Consensus pattern (19 bp):
CTTTTAGTTTTTTTTTTTC
Found at i:37246 original size:21 final size:21
Alignment explanation
Indices: 37207--37246 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
37197 TATGTCTTTT
**
37207 GTTTTTCTTTTTTCCTTTTGA
1 GTTTTTCTTTTTTAATTTTGA
*
37228 GTTTTTTTTTTTTAATTTT
1 GTTTTTCTTTTTTAATTTT
37247 AAATAAGAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.78
Consensus pattern (21 bp):
GTTTTTCTTTTTTAATTTTGA
Found at i:38450 original size:23 final size:23
Alignment explanation
Indices: 38424--38468 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
38414 TCGGTGCCCC
*
38424 CTTAGCCCCCTTAATTGACTTTT
1 CTTAACCCCCTTAATTGACTTTT
38447 CTTAACCCCCTTAATTGACTTT
1 CTTAACCCCCTTAATTGACTTT
38469 AAACAATCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.31, G:0.07, T:0.42
Consensus pattern (23 bp):
CTTAACCCCCTTAATTGACTTTT
Found at i:40296 original size:23 final size:23
Alignment explanation
Indices: 40265--40311 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
40255 TTTTTCAAAT
40265 TCTACTTTCTATAGCAAACGCAC
1 TCTACTTTCTATAGCAAACGCAC
*
40288 TCTATTTTCTATAGCAAACGCAC
1 TCTACTTTCTATAGCAAACGCAC
40311 T
1 T
40312 GATCAGTACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.34
Consensus pattern (23 bp):
TCTACTTTCTATAGCAAACGCAC
Found at i:53638 original size:19 final size:19
Alignment explanation
Indices: 53614--53651 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
53604 AACTAGTCCA
53614 AAATCAACATTTCAATATT
1 AAATCAACATTTCAATATT
* *
53633 AAATCAATATTTTAATATT
1 AAATCAACATTTCAATATT
53652 TGATTCCAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATCAACATTTCAATATT
Found at i:55522 original size:266 final size:266
Alignment explanation
Indices: 55048--55576 Score: 896
Period size: 266 Copynumber: 2.0 Consensus size: 266
55038 ATATTAATTT
* **
55048 AATACATAATTACAACTTTGTCCTTTAAAAATCATGATAATTACCATTTGCCTGAATAATATATT
1 AATACATAATTACAACTTTATCCTTTAAAAATCATGATAATTACCATTTGCCACAATAATATATT
* * * * *
55113 CCATTTTAATAATTAAAAGGTCAAACATGAATAAATATAATTCACTTTCCGCCTTTGCCTTTTGT
66 CCATTTTAATAATCAAAAAGTCAAACATAAACAAATATAATTCACTTTCCACCTTTGCCTTTTGT
* *
55178 AATTTTTGAAAATTACAATTTAGTCACTAAAATTTATAATTTCAACTTATCATGGAAAATCCATC
131 AATTTTTGAAAACTAAAATTTAGTCACTAAAATTTATAATTTCAACTTATCATGGAAAATCCATC
* *
55243 TAAATTACAAGGATCCATGTCAAATTTCATCATTCTAAAATATAGAAATAATATTTATAACTTTT
196 TAAATTACAAGGATCCATGTCAAATATCATCATTCTAAAATATAGAAATAATATTTATAACCTTT
55308 TTCTTA
261 TTCTTA
*
55314 AATACATAATTACAACTTTATCCTTTAAAAATCATGATAATTACCATTTGCCACAATAATATCTT
1 AATACATAATTACAACTTTATCCTTTAAAAATCATGATAATTACCATTTGCCACAATAATATATT
* * *
55379 TCATTTTAATAATCAAAAAGTCAAATATAAACAAATATAATTCACTTTCCACCTTTTCCTTTTGT
66 CCATTTTAATAATCAAAAAGTCAAACATAAACAAATATAATTCACTTTCCACCTTTGCCTTTTGT
55444 AATTTTTGAAAACTAAAATTTAGTCACTAAAATTTATAATTTCAACTTATCATGGAAAATCCATC
131 AATTTTTGAAAACTAAAATTTAGTCACTAAAATTTATAATTTCAACTTATCATGGAAAATCCATC
* *
55509 TAAATTCCAAGGATCCATGTCAAATATCTTCATTCTAAAATATAGAAATAATATTTATAACCTTT
196 TAAATTACAAGGATCCATGTCAAATATCATCATTCTAAAATATAGAAATAATATTTATAACCTTT
55574 TTC
261 TTC
55577 CATCATCCTT
Statistics
Matches: 245, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
266 245 1.00
ACGTcount: A:0.40, C:0.16, G:0.06, T:0.39
Consensus pattern (266 bp):
AATACATAATTACAACTTTATCCTTTAAAAATCATGATAATTACCATTTGCCACAATAATATATT
CCATTTTAATAATCAAAAAGTCAAACATAAACAAATATAATTCACTTTCCACCTTTGCCTTTTGT
AATTTTTGAAAACTAAAATTTAGTCACTAAAATTTATAATTTCAACTTATCATGGAAAATCCATC
TAAATTACAAGGATCCATGTCAAATATCATCATTCTAAAATATAGAAATAATATTTATAACCTTT
TTCTTA
Found at i:55906 original size:2 final size:2
Alignment explanation
Indices: 55899--55955 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
55889 GGTTAATAGA
55899 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
55941 A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
55956 TAATTAATTC
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.