Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002328.1 Hibiscus syriacus cultivar Beakdansim tig00004752_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: 48569
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:301 original size:37 final size:37
Alignment explanation
Indices: 225--301 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
215 TTTTTATATT
*
225 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
262 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
299 TTT
1 TTT
302 GTAATATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:6806 original size:35 final size:35
Alignment explanation
Indices: 6760--6835 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
6750 AAAACAGTCC
* *
6760 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* *
6795 TCAATTTCATTCTCAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
6830 TCAATT
1 TCAATT
6836 AAATTCAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.38, C:0.25, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:7389 original size:128 final size:128
Alignment explanation
Indices: 7232--7477 Score: 384
Period size: 128 Copynumber: 1.9 Consensus size: 128
7222 TATTTATAAA
* ** *
7232 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
* * * *
7297 TTAGCACATGATCATGACACGTGTCATTGGTGACGCATGTCACCATCTAATTATTTATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATGCT
*
7360 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCATGATCTGACATATG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
* * *
7425 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
7478 GAAGAAAATT
Statistics
Matches: 106, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
128 106 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (128 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATGCT
Found at i:7450 original size:23 final size:21
Alignment explanation
Indices: 7404--7450 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 21
7394 AATTAATCAT
7404 TTAACCATGATCTGACATATG
1 TTAACCATGATCTGACATATG
*
7425 TTAACACATGATCATGATATATG
1 TTAAC-CATGATC-TGACATATG
7448 TTA
1 TTA
7451 TTGGTGACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.22
22 7 0.30
23 11 0.48
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (21 bp):
TTAACCATGATCTGACATATG
Found at i:7964 original size:16 final size:18
Alignment explanation
Indices: 7943--7976 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
7933 ATTTCTTATT
7943 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
7959 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
7977 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:19640 original size:2 final size:2
Alignment explanation
Indices: 19628--19705 Score: 147
Period size: 2 Copynumber: 38.5 Consensus size: 2
19618 TCGGGTTTAA
19628 AT AT AT CAT 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
19671 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
19706 GATGTTTGGT
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 73 0.97
3 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20785 original size:34 final size:35
Alignment explanation
Indices: 20747--20813 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
20737 GGAAATTGAA
20747 TTCTGGAAAATAAATTACA-TTTCTGAAAAACGTT
1 TTCTGGAAAATAAATTACATTTTCTGAAAAACGTT
* *
20781 TTCTGTAAAATTAATTACATTTTTCTGAAAAAC
1 TTCTGGAAAATAAATTACA-TTTTCTGAAAAAC
20814 ATCTTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 17 0.59
36 12 0.41
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (35 bp):
TTCTGGAAAATAAATTACATTTTCTGAAAAACGTT
Found at i:21137 original size:23 final size:23
Alignment explanation
Indices: 21049--21125 Score: 68
Period size: 23 Copynumber: 3.2 Consensus size: 23
21039 AATAAAAATA
*
21049 TTAAAAATTAT-ATTAAT-TATT
1 TTAAAAATAATAATTAATATATT
* *
21070 TATTAAAGTAATAAGGTTATATTATATT
1 T-TAAAAATAATAA--TTA-A-TATATT
21098 TTAAAAATAATAATTAATATATT
1 TTAAAAATAATAATTAATATATT
21121 TTAAA
1 TTAAA
21126 TATCTTTATT
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
21 1 0.02
22 7 0.16
23 12 0.27
24 1 0.02
25 6 0.14
26 1 0.02
27 11 0.25
28 5 0.11
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (23 bp):
TTAAAAATAATAATTAATATATT
Found at i:21199 original size:19 final size:19
Alignment explanation
Indices: 21131--21211 Score: 64
Period size: 19 Copynumber: 4.3 Consensus size: 19
21121 TTAAATATCT
21131 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTA-A
21150 TTATTATATTAATATTA--AA
1 TTATTA-A-TAATATTATTAA
* *
21169 TATATAAATAATATTATTCA
1 T-TATTAATAATATTATTAA
*
21189 TTATTAATAAT-TTAATAA
1 TTATTAATAATATTATTAA
21207 -TATTA
1 TTATTA
21212 TTTCTATGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
17 5 0.10
18 13 0.25
19 18 0.35
20 8 0.16
22 7 0.14
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (19 bp):
TTATTAATAATATTATTAA
Found at i:22645 original size:37 final size:37
Alignment explanation
Indices: 22569--22645 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
22559 TTTTTATATT
*
22569 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
22606 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
22643 TTT
1 TTT
22646 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:29228 original size:35 final size:35
Alignment explanation
Indices: 29182--29257 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
29172 AAAACAGTCC
* *
29182 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* *
29217 TCAATTTCATTCTCAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
29252 TCAATT
1 TCAATT
29258 AAATTCAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.38, C:0.25, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:29813 original size:130 final size:130
Alignment explanation
Indices: 29654--29901 Score: 388
Period size: 130 Copynumber: 1.9 Consensus size: 130
29644 TATTTATAAA
* ** *
29654 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
* * * *
29719 TTAGCACATGATCATGACACGTGTCATTGGTGACGCATGTCACCATCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
*
29784 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCATGATCTGACATATG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
* * *
29849 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
29902 GAAGAAAATT
Statistics
Matches: 106, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
130 106 1.00
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:29874 original size:23 final size:21
Alignment explanation
Indices: 29828--29874 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 21
29818 AATTAATCAT
29828 TTAACCATGATCTGACATATG
1 TTAACCATGATCTGACATATG
*
29849 TTAACACATGATCATGATATATG
1 TTAAC-CATGATC-TGACATATG
29872 TTA
1 TTA
29875 TTGGTGACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.22
22 7 0.30
23 11 0.48
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (21 bp):
TTAACCATGATCTGACATATG
Found at i:29932 original size:130 final size:129
Alignment explanation
Indices: 29668--29932 Score: 273
Period size: 130 Copynumber: 2.0 Consensus size: 129
29658 ATTTGGTCCT
* ** * *
29668 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATGTTAACACATGATCA
* * * *** * * **** *
29733 TGACACGTGTCATTGGTGACGCATGTCACCATCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
*
29798 AAATTAAATAAAATTTAATAAATTAATCATTTAACCATGATCTGACATATGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATGTTAACACATGATCA
* * * *
29863 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
29927 -A
128 CA
29928 AAATT
1 AAATT
29933 TGGGTCTTGG
Statistics
Matches: 109, Mismatches: 23, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
130 96 0.88
132 8 0.07
133 5 0.05
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATGTTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:30258 original size:28 final size:28
Alignment explanation
Indices: 30226--30289 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
30216 TAGTTGATAC
30226 AATATTTTAAAAGAATAAATTTAAGATTT
1 AATATTTTAAAA-AATAAATTTAAGATTT
* * *
30255 ATATATTTT-TAAACTAAATTTAATATTT
1 A-ATATTTTAAAAAATAAATTTAAGATTT
30283 AATATTT
1 AATATTT
30290 ATATTTTTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 6 0.19
28 15 0.48
29 3 0.10
30 7 0.23
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (28 bp):
AATATTTTAAAAAATAAATTTAAGATTT
Found at i:30397 original size:16 final size:18
Alignment explanation
Indices: 30376--30409 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
30366 ATTTCTTATT
30376 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
30392 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
30410 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:42105 original size:2 final size:2
Alignment explanation
Indices: 42093--42166 Score: 139
Period size: 2 Copynumber: 36.5 Consensus size: 2
42083 TCGGGTTTAA
42093 AT AT AT CAT 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
42136 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 A
42167 GATGTTTGGT
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 69 0.97
3 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:43246 original size:34 final size:35
Alignment explanation
Indices: 43208--43274 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
43198 GGAAATTGAA
43208 TTCTGGAAAATAAATTACA-TTTCTGAAAAACGTT
1 TTCTGGAAAATAAATTACATTTTCTGAAAAACGTT
* *
43242 TTCTGTAAAATTAATTACATTTTTCTGAAAAAC
1 TTCTGGAAAATAAATTACA-TTTTCTGAAAAAC
43275 ATCTTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 17 0.59
36 12 0.41
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (35 bp):
TTCTGGAAAATAAATTACATTTTCTGAAAAACGTT
Found at i:43535 original size:33 final size:32
Alignment explanation
Indices: 43464--43528 Score: 82
Period size: 33 Copynumber: 2.1 Consensus size: 32
43454 TATTTTTATA
* *
43464 ATTTTATT--AATAAAAATATTAATATTGGTAT
1 ATTTTATTGAAATAAAAATATTAAAAAT-GTAT
43495 ATTTTATTGAAATAAAAATATTAAAAAT-TAT
1 ATTTTATTGAAATAAAAATATTAAAAATGTAT
43526 ATT
1 ATT
43529 AATTATTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 14 0.47
33 16 0.53
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (32 bp):
ATTTTATTGAAATAAAAATATTAAAAATGTAT
Found at i:43603 original size:23 final size:23
Alignment explanation
Indices: 43515--43591 Score: 68
Period size: 23 Copynumber: 3.2 Consensus size: 23
43505 AATAAAAATA
*
43515 TTAAAAATTAT-ATTAAT-TATT
1 TTAAAAATAATAATTAATATATT
* *
43536 TATTAAAGTAATAAGGTTATATTATATT
1 T-TAAAAATAATAA--TTA-A-TATATT
43564 TTAAAAATAATAATTAATATATT
1 TTAAAAATAATAATTAATATATT
43587 TTAAA
1 TTAAA
43592 TATCTTTATT
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
21 1 0.02
22 7 0.16
23 12 0.27
24 1 0.02
25 6 0.14
26 1 0.02
27 11 0.25
28 5 0.11
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (23 bp):
TTAAAAATAATAATTAATATATT
Found at i:43665 original size:19 final size:19
Alignment explanation
Indices: 43597--43677 Score: 64
Period size: 19 Copynumber: 4.3 Consensus size: 19
43587 TTAAATATCT
43597 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTA-A
43616 TTATTATATTAATATTA--AA
1 TTATTA-A-TAATATTATTAA
* *
43635 TATATAAATAATATTATTCA
1 T-TATTAATAATATTATTAA
*
43655 TTATTAATAAT-TTAATAA
1 TTATTAATAATATTATTAA
43673 -TATTA
1 TTATTA
43678 TTTCTATGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
17 5 0.10
18 13 0.25
19 18 0.35
20 8 0.16
22 7 0.14
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (19 bp):
TTATTAATAATATTATTAA
Found at i:43755 original size:23 final size:23
Alignment explanation
Indices: 43729--43781 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
43719 TTATTAATAA
43729 ATAATATAATAT-ATTATATTATT
1 ATAATATAAT-TGATTATATTATT
** *
43752 ATAATGGAATTGATTATTTTATT
1 ATAATATAATTGATTATATTATT
43775 ATAATAT
1 ATAATAT
43782 TTAAAATATA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (23 bp):
ATAATATAATTGATTATATTATT
Found at i:45118 original size:37 final size:37
Alignment explanation
Indices: 45042--45118 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
45032 TTTTTATATT
*
45042 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
45079 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
45116 TTT
1 TTT
45119 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Done.