Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007821.1 Hibiscus syriacus cultivar Beakdansim tig00110158_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: 29783
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30
Found at i:3014 original size:15 final size:15
Alignment explanation
Indices: 2994--3025 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2984 ATCAATACCT
2994 TTTTGCATACATACA
1 TTTTGCATACATACA
*
3009 TTTTGCATACATTCA
1 TTTTGCATACATACA
3024 TT
1 TT
3026 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATACA
Found at i:11426 original size:29 final size:29
Alignment explanation
Indices: 11393--11458 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 29
11383 AATCATTAAA
*
11393 TTTGGAAGATGAATGTGCTCATAGCATCT
1 TTTGGAAGATGAATATGCTCATAGCATCT
11422 TTTGGAAGATGAATATGCTCATAGCATCT
1 TTTGGAAGATGAATATGCTCATAGCATCT
*
11451 TCTGGAAG
1 TTTGGAAG
11459 TGTTCTTTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (29 bp):
TTTGGAAGATGAATATGCTCATAGCATCT
Found at i:11545 original size:123 final size:119
Alignment explanation
Indices: 11318--11552 Score: 398
Period size: 123 Copynumber: 1.9 Consensus size: 119
11308 AAGTGCCGTG
11318 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAGGGTATGAACCCCAAAAACC
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAGGGTATGAACCCCAAAAACC
* *
11383 AATCATTAAATTTGGAAGATGAATGTGCTCATAGCATCTTTTGGAAGATGAATA
66 AATCATTAAATTTGAAAGATGAATATGCTCATAGCATCTTTTGGAAGATGAATA
*
11437 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAA
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAG---GGTATGAACCCC-AAA
*
11502 AACCAATCATTTAATTTGAAAGATGAATATGCTCATAGCATCTTTTGGAAG
62 AACCAATCATTAAATTTGAAAGATGAATATGCTCATAGCATCTTTTGGAAG
11553 TGTTCTTTGA
Statistics
Matches: 108, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
119 45 0.42
122 12 0.11
123 51 0.47
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (119 bp):
TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAGGGTATGAACCCCAAAAACC
AATCATTAAATTTGAAAGATGAATATGCTCATAGCATCTTTTGGAAGATGAATA
Found at i:11588 original size:94 final size:93
Alignment explanation
Indices: 11422--11726 Score: 520
Period size: 94 Copynumber: 3.3 Consensus size: 93
11412 CATAGCATCT
*
11422 TTTGGAAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
1 TTTGAAAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
*
11487 GTATGAACCCCAAAAAACCAATCATTTAA
66 GTATGAACCAC-AAAAACCAATCATTTAA
*
11516 TTTGAAAGATGAATATGCTCATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
1 TTTGAAAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
* *
11581 GTATGAACCTCGAAAAGCCAATCATTTAA
66 GTATGAACCAC-AAAAACCAATCATTTAA
*
11610 TTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
1 TTTGAAAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
*
11675 GTATGAACCACAAAAACCAATCATTGAA
66 GTATGAACCACAAAAACCAATCATTTAA
*
11703 TTTGAAAGATGAATGTGCTCATAG
1 TTTGAAAGATGAATATGCTCATAG
11727 TAGAAATAAA
Statistics
Matches: 201, Mismatches: 10, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
93 39 0.19
94 162 0.81
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.35
Consensus pattern (93 bp):
TTTGAAAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
GTATGAACCACAAAAACCAATCATTTAA
Found at i:12964 original size:116 final size:112
Alignment explanation
Indices: 12507--13293 Score: 886
Period size: 108 Copynumber: 7.0 Consensus size: 112
12497 TAGCAAAGAT
* *
12507 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAA-TCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAG-GAGAGTTCATAATGAGAAGAACTCATCTGA
* *
12571 AGAAGGAAGAAGAAGTTCAAAATGAGAAGAATTTGTTCAACCTTTTGT
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * * * * *
12619 TTAAATTCATCATTTGATGGATTAAC-ATT-GAAGAAAGTTCATAATGAGAAGAACTCATCTGAA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGGAGAGTTCATAATGAGAAGAACTCATCTGAA
* * *
12682 GAAGGAAGAAGAAATTCATAATGAGAAGAATTTATTCAACCTTTCGC
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
12729 TCAAATCCATCATTTGA-AGATCAGCTTTTCC---AGAGTTCATAATGAGAAGAACTCATCTGAA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGGAGAGTTCATAATGAGAAGAACTCATCTGAA
*
12790 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * * *
12837 TTAAATTCATCATTTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATC
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGG-AGAGTTCATAATGAGAAGAA--C-TCATC
*
12902 TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
62 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* **
12953 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTTGAGTTCATAATGAGAAGAACTCATCTG-
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAG-GAGAGTTCATAATGAGAAGAACTCATCTGA
* *
13017 A-AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACTTTTTGC
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
13064 TCAAATCCATCACTTGATGGATCAGTTTTTCCA-GAGAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGGAG-AGTTCATAATGAGAAGAACTCATCTGA
* ** *
13128 AGAA-G-A-AA-AAGTTCACAATGAGAAGAGCTTATTCAACCTTTTGC
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * *
13172 AT-AATTCTATCACAGAAGCAGATAGATTAGCATCAGCTTTTCCAGAGAAAGTTCATAATGAGAA
1 -TCAA----ATC-C---ATCA-TTTGA-T-GGATCAGCTTTTCCAG-GAGAGTTCATAATGAGAA
* ** *
13236 GAACTCATCTGAAG-AGAAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTG
53 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
13294 AATGACTCTA
Statistics
Matches: 579, Mismatches: 63, Indels: 55
0.83 0.09 0.08
Matches are distributed among these distances:
108 119 0.21
109 38 0.07
110 96 0.17
111 79 0.14
112 28 0.05
113 28 0.05
114 1 0.00
115 1 0.00
116 103 0.18
117 3 0.01
118 1 0.00
119 14 0.02
120 29 0.05
121 3 0.01
122 2 0.00
123 34 0.06
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.29
Consensus pattern (112 bp):
TCAAATCCATCATTTGATGGATCAGCTTTTCCAGGAGAGTTCATAATGAGAAGAACTCATCTGAA
GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:13304 original size:123 final size:122
Alignment explanation
Indices: 13084--13381 Score: 385
Period size: 123 Copynumber: 2.5 Consensus size: 122
13074 CACTTGATGG
*
13084 ATCAGTTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTG-A-AG-AAGAAAAAGTTCACA
1 ATCAG-TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCACA
* * * * *
13145 ATGAGAAGAGCTTATTCAACCTTTTGCATAATTCTATCACAGAAGCAGATAGATTAGC
65 ATGAGAAGAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAGCAAATAGATCAAC
*
13203 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATA
1 ATCAG-TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCACA
* * *
13268 ATGAGAAGAGCTTATTCAACCTTTTGAATGACTCTATCACAGAAGGAAATAGGTCAAC
65 ATGAGAAGAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAGCAAATAGATCAAC
** * *
13326 ATCA--TCCCCAGCGAAAAGTTCATAATGAGAAGAACTCATCCGAAGA-AAGAGAAGAA
1 ATCAGTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAGAA-AGAAGAA
13382 TTTATTCAAC
Statistics
Matches: 158, Mismatches: 15, Indels: 10
0.86 0.08 0.05
Matches are distributed among these distances:
119 15 0.09
120 35 0.22
121 39 0.25
122 2 0.01
123 67 0.42
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.23
Consensus pattern (122 bp):
ATCAGTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCACAA
TGAGAAGAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAGCAAATAGATCAAC
Found at i:13533 original size:11 final size:12
Alignment explanation
Indices: 13518--13549 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
13508 TTACCCATTT
13518 TATTATTATATA
1 TATTATTATATA
13530 -ATTATTATATA
1 TATTATTATATA
13541 TATTATTAT
1 TATTATTAT
13550 TAAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TATTATTATATA
Found at i:13866 original size:19 final size:20
Alignment explanation
Indices: 13830--13871 Score: 77
Period size: 19 Copynumber: 2.1 Consensus size: 20
13820 CTGTTGTTGC
13830 CACGACACCAGCCTCGCCGA
1 CACGACACCAGCCTCGCCGA
13850 CACGACACCAG-CTCGCCGA
1 CACGACACCAGCCTCGCCGA
13869 CAC
1 CAC
13872 TCCAGAACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.26, C:0.50, G:0.19, T:0.05
Consensus pattern (20 bp):
CACGACACCAGCCTCGCCGA
Found at i:18389 original size:2 final size:2
Alignment explanation
Indices: 18382--18410 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
18372 TTAATATGAA
18382 AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18411 TGTTAGGGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18928 original size:2 final size:2
Alignment explanation
Indices: 18916--18992 Score: 145
Period size: 2 Copynumber: 38.5 Consensus size: 2
18906 GTACAATTGA
*
18916 AT AT CT 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
18958 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18993 AAATTTTACA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19539 original size:65 final size:64
Alignment explanation
Indices: 19406--19561 Score: 190
Period size: 65 Copynumber: 2.4 Consensus size: 64
19396 ACACCCCATT
* **
19406 TCGAATGCATTTTATGCATTGATGCACAGTCATGCATCGATGCACTCAGGATTTTTTTAAAACA
1 TCGAATGCATTTTATGCATTGATGCACAGTCATGCATCGATGCACTCAGGACTAGTTTAAAACA
* * *
19470 TCGAATTCATTTTATGCATTGATGCACA-TACCATGCATCGATGCACTCCATG-CTAGTTTGAAA
1 TCGAATGCATTTTATGCATTGATGCACAGT--CATGCATCGATGCACT-CAGGACTAGTTTAAAA
19533 CA
63 CA
* * *
19535 TCGAAAGCAATTTATGCATCGATGCAC
1 TCGAATGCATTTTATGCATTGATGCAC
19562 CCTTAGTGCA
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
63 1 0.01
64 27 0.34
65 48 0.61
66 3 0.04
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (64 bp):
TCGAATGCATTTTATGCATTGATGCACAGTCATGCATCGATGCACTCAGGACTAGTTTAAAACA
Found at i:19644 original size:21 final size:21
Alignment explanation
Indices: 19620--19675 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
19610 TTTACACTTG
*
19620 ATGCATCGATGCACTTTGACT
1 ATGCATCGATGCACCTTGACT
*
19641 ATGCATCGATTCACCTTGACT
1 ATGCATCGATGCACCTTGACT
19662 ATGCATC-ATGCACC
1 ATGCATCGATGCACC
19676 CACACTCCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 6 0.19
21 26 0.81
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.30
Consensus pattern (21 bp):
ATGCATCGATGCACCTTGACT
Found at i:25282 original size:44 final size:44
Alignment explanation
Indices: 25210--25304 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 44
25200 GTGCATAATG
*
25210 CATCGATACACTATGAAGATGCATCGATGCA-TCCCTATGAATGTA
1 CATCGATACACTATGAAGATGCACCGATGCACT-CCT-TGAATGTA
25255 CATCGATACA-TCAT-AAGATGCACCGATGCACTCCTTGAATGTA
1 CATCGATACACT-ATGAAGATGCACCGATGCACTCCTTGAATGTA
*
25298 TATCGAT
1 CATCGAT
25305 GCATTTAGCA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
43 14 0.30
44 19 0.41
45 13 0.28
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (44 bp):
CATCGATACACTATGAAGATGCACCGATGCACTCCTTGAATGTA
Found at i:27966 original size:63 final size:65
Alignment explanation
Indices: 27897--28051 Score: 244
Period size: 65 Copynumber: 2.4 Consensus size: 65
27887 CCACCCCATT
*
27897 TCGAATGCATTTTATGCATCGATGCACA-GTCATGCATCGATGCACT-CAAGATT-TATTAAAAC
1 TCGAATGCATTTTATGCATCGATGCACATATCATGCATCGATGCACTCCAAGATTGT-TTAAAAC
27959 A
65 A
* *
27960 TCGAATGCATTTTATGCATCGATGCACATATCATGCATCGATGCACTCCAAGCTTGTTTGAAACA
1 TCGAATGCATTTTATGCATCGATGCACATATCATGCATCGATGCACTCCAAGATTGTTTAAAACA
*
28025 TCGAATGCAATTTATGCATCGATGCAC
1 TCGAATGCATTTTATGCATCGATGCAC
28052 CCTTAGTGCA
Statistics
Matches: 85, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
63 28 0.33
64 17 0.20
65 39 0.46
66 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (65 bp):
TCGAATGCATTTTATGCATCGATGCACATATCATGCATCGATGCACTCCAAGATTGTTTAAAACA
Done.