Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005403.1 Hibiscus syriacus cultivar Beakdansim tig00012388_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: 63743
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:9574 original size:30 final size:30
Alignment explanation
Indices: 9534--9593 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
9524 TAATATAAAT
9534 ACTAAATATTTAATA-TAAATATTAT-TAAC
1 ACTAAATATTTAATATTAAA-ATTATATAAC
9563 ACTATAATATTTAATATTAAAATTATATAAC
1 ACTA-AATATTTAATATTAAAATTATATAAC
9594 TTAAATTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 4 0.14
30 16 0.57
31 8 0.29
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.42
Consensus pattern (30 bp):
ACTAAATATTTAATATTAAAATTATATAAC
Found at i:9620 original size:18 final size:18
Alignment explanation
Indices: 9597--9654 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
9587 ATATAACTTA
9597 AATTATCATAATATATAT
1 AATTATCATAATATATAT
9615 AATTAT-ACTAATAT-TAT
1 AATTATCA-TAATATATAT
* *
9632 AATTAATCTTAAAATA-AT
1 AATT-ATCATAATATATAT
9650 AATTA
1 AATTA
9655 ATGATGTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
17 9 0.26
18 25 0.74
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (18 bp):
AATTATCATAATATATAT
Found at i:15568 original size:51 final size:51
Alignment explanation
Indices: 15512--15609 Score: 196
Period size: 51 Copynumber: 1.9 Consensus size: 51
15502 ACGGCTAAAG
15512 TTAATGAGAGAGCATTTGAAAAATAGTATAATTGTCTTTTCATCATTGAAC
1 TTAATGAGAGAGCATTTGAAAAATAGTATAATTGTCTTTTCATCATTGAAC
15563 TTAATGAGAGAGCATTTGAAAAATAGTATAATTGTCTTTTCATCATT
1 TTAATGAGAGAGCATTTGAAAAATAGTATAATTGTCTTTTCATCATT
15610 ATAGGTTCAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (51 bp):
TTAATGAGAGAGCATTTGAAAAATAGTATAATTGTCTTTTCATCATTGAAC
Found at i:15620 original size:14 final size:14
Alignment explanation
Indices: 15601--15632 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
15591 TAATTGTCTT
15601 TTCATCATTATAGG
1 TTCATCATTATAGG
15615 TTCATCATTATAGG
1 TTCATCATTATAGG
15629 TTCA
1 TTCA
15633 ATACTTGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (14 bp):
TTCATCATTATAGG
Found at i:16716 original size:26 final size:27
Alignment explanation
Indices: 16687--16740 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
16677 GGTCTGACGT
*
16687 GGCAA-TTTCTAAAAGGTCCAGTCAGC
1 GGCAATTTTCTAAAAGATCCAGTCAGC
* *
16713 GGCAATTTTCTAGAAGATCTAGTCAGC
1 GGCAATTTTCTAAAAGATCCAGTCAGC
16740 G
1 G
16741 CACCTTCTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 5 0.21
27 19 0.79
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (27 bp):
GGCAATTTTCTAAAAGATCCAGTCAGC
Found at i:17604 original size:20 final size:20
Alignment explanation
Indices: 17581--17618 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
17571 AAAATTTTTT
*
17581 CTTTATTTTAATTTAAATCG
1 CTTTATTATAATTTAAATCG
*
17601 CTTTATTATCATTTAAAT
1 CTTTATTATAATTTAAAT
17619 ATCTTTTTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.11, G:0.03, T:0.55
Consensus pattern (20 bp):
CTTTATTATAATTTAAATCG
Found at i:17624 original size:20 final size:20
Alignment explanation
Indices: 17580--17624 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
17570 TAAAATTTTT
* *
17580 TCTTTATTTTAATTTAAATC
1 TCTTTATTATAATTTAAATA
* *
17600 GCTTTATTATCATTTAAATA
1 TCTTTATTATAATTTAAATA
17620 TCTTT
1 TCTTT
17625 TTACCAAAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.11, G:0.02, T:0.58
Consensus pattern (20 bp):
TCTTTATTATAATTTAAATA
Found at i:25709 original size:45 final size:42
Alignment explanation
Indices: 25660--25750 Score: 94
Period size: 45 Copynumber: 2.1 Consensus size: 42
25650 TTTTAATCAA
*
25660 CATAT-GATTCAATTAACCAAGCAATACAGACATCATCATATAAAT
1 CATATAGATT-AATTAA-CAAGAAATACAGACAT-A-CATATAAAT
* * *
25705 CATATCAGATTACTTAATAAGAAATACATACATACATATAAAT
1 CATAT-AGATTAATTAACAAGAAATACAGACATACATATAAAT
25748 CAT
1 CAT
25751 CATTAGTAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
43 12 0.30
44 1 0.03
45 18 0.45
46 5 0.12
47 4 0.10
ACGTcount: A:0.48, C:0.18, G:0.05, T:0.29
Consensus pattern (42 bp):
CATATAGATTAATTAACAAGAAATACAGACATACATATAAAT
Found at i:25998 original size:23 final size:23
Alignment explanation
Indices: 25967--26050 Score: 114
Period size: 23 Copynumber: 3.7 Consensus size: 23
25957 CTCGTAAAAA
*
25967 TGCACCGAAGTGCCAAGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
25990 TGCATCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* **
26013 TTCACCGAAGTGCTGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
26036 TACACCGAAGTGCCA
1 TGCACCGAAGTGCCA
26051 TATAAAATGT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:28181 original size:18 final size:18
Alignment explanation
Indices: 28158--28193 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
28148 TGTGTTATAT
28158 GTGGTCATTCGGGACATA
1 GTGGTCATTCGGGACATA
*
28176 GTGGTCCTTCGGGACATA
1 GTGGTCATTCGGGACATA
28194 TGTGTTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.19, G:0.33, T:0.28
Consensus pattern (18 bp):
GTGGTCATTCGGGACATA
Found at i:28191 original size:46 final size:46
Alignment explanation
Indices: 28124--28238 Score: 167
Period size: 46 Copynumber: 2.4 Consensus size: 46
28114 GGTCCTTTGA
* *
28124 GACATAGTCGTCCTTCGGGACATATGTGTTATATGTGGTCATTCGG
1 GACATAGTGGTCCTTCGGGACATATGTGTTATATGTGGTCATTCAG
*
28170 GACATAGTGGTCCTTCGGGACATATGTGTTATATGTGGTCTTTCAG
1 GACATAGTGGTCCTTCGGGACATATGTGTTATATGTGGTCATTCAG
*
28216 GATATCTACGTGGTCCTTCGGGA
1 GACA--TA-GTGGTCCTTCGGGA
28239 AAAATTCTAC
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
46 46 0.74
48 2 0.03
49 14 0.23
ACGTcount: A:0.19, C:0.17, G:0.29, T:0.35
Consensus pattern (46 bp):
GACATAGTGGTCCTTCGGGACATATGTGTTATATGTGGTCATTCAG
Found at i:28410 original size:7 final size:7
Alignment explanation
Indices: 28398--28424 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
28388 GTGAAATGGT
28398 ATATGTG
1 ATATGTG
28405 ATATGTG
1 ATATGTG
28412 ATATGTG
1 ATATGTG
28419 ATATGT
1 ATATGT
28425 AAAAGTAATA
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:0.30, C:0.00, G:0.26, T:0.44
Consensus pattern (7 bp):
ATATGTG
Found at i:30969 original size:10 final size:10
Alignment explanation
Indices: 30939--30972 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
30929 TCTTTGAGTG
30939 TTATATAAGC
1 TTATATAAGC
*
30949 TTAAATAAAGC
1 TTATAT-AAGC
30960 TTATATAAGC
1 TTATATAAGC
30970 TTA
1 TTA
30973 AAACACCAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (10 bp):
TTATATAAGC
Found at i:38175 original size:45 final size:42
Alignment explanation
Indices: 38126--38213 Score: 97
Period size: 45 Copynumber: 2.0 Consensus size: 42
38116 TTTTAATCAA
*
38126 CATAT-GATTCAATTAACCAAGCAATACATACATCATCATATAAAT
1 CATATAGATT-AATTAA-CAAGAAATACATACAT-A-CATATAAAT
* *
38171 CATATCAGATTACTTAATAAGAAATACATACATACATATAAAT
1 CATAT-AGATTAATTAACAAGAAATACATACATACATATAAAT
38214 AATCATTAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
43 9 0.24
44 1 0.03
45 19 0.50
46 5 0.13
47 4 0.11
ACGTcount: A:0.49, C:0.17, G:0.05, T:0.30
Consensus pattern (42 bp):
CATATAGATTAATTAACAAGAAATACATACATACATATAAAT
Found at i:38466 original size:23 final size:23
Alignment explanation
Indices: 38433--38536 Score: 154
Period size: 23 Copynumber: 4.5 Consensus size: 23
38423 CTCGTATAAA
* *
38433 TGCACAGAAGTGCCGTGTAGAAT
1 TGCACCGAAGTGCCGCGTAGAAT
*
38456 TGCACCAAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCGCGTAGAAT
*
38479 TGCACCGAAGTGTCGCGTAGAAT
1 TGCACCGAAGTGCCGCGTAGAAT
**
38502 TGCACCGAAGTGCCATGTAGAAT
1 TGCACCGAAGTGCCGCGTAGAAT
38525 TGCACCGAAGTG
1 TGCACCGAAGTG
38537 TCATATAAAA
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 73 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCGCGTAGAAT
Found at i:44256 original size:26 final size:26
Alignment explanation
Indices: 44227--44304 Score: 93
Period size: 26 Copynumber: 3.0 Consensus size: 26
44217 CGGTCTAACG
*
44227 TGGCAGTTTCTAGAAGGTCCATTCAA
1 TGGCAGTTTCTAGAAGGTCCAGTCAA
* *
44253 TGGCAGTTTCTAGAAGGTTCAGTCAG
1 TGGCAGTTTCTAGAAGGTCCAGTCAA
* * *
44279 CGGCAGTTTTCTAGAAGATCTAGTCA
1 TGGCAG-TTTCTAGAAGGTCCAGTCA
44305 GCGCGCCTTC
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
26 28 0.64
27 16 0.36
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (26 bp):
TGGCAGTTTCTAGAAGGTCCAGTCAA
Found at i:45196 original size:21 final size:21
Alignment explanation
Indices: 45153--45197 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
45143 AAATCTTTTC
*
45153 TTTATTTCACTTTAAATCGCT
1 TTTATTTCACTTTAAATAGCT
*
45174 TTTATTATCA-TTTAAATATCT
1 TTTATT-TCACTTTAAATAGCT
45195 TTT
1 TTT
45198 TATCAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.27, C:0.13, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTATTTCACTTTAAATAGCT
Found at i:54143 original size:15 final size:16
Alignment explanation
Indices: 54123--54153 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
54113 TAACGTTATT
54123 TTAAAATT-AAATTAA
1 TTAAAATTAAAATTAA
54138 TTAAAATTAAAATTAA
1 TTAAAATTAAAATTAA
54154 AATTTTCTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TTAAAATTAAAATTAA
Found at i:54735 original size:19 final size:20
Alignment explanation
Indices: 54691--54735 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
54681 TATTTGTTTT
*
54691 AATAAATTTTTATTTATGAA
1 AATAAATTTTTATTTATCAA
*
54711 ATTAAATTTTTATTT-TCAA
1 AATAAATTTTTATTTATCAA
54730 AATAAA
1 AATAAA
54736 ATATTAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (20 bp):
AATAAATTTTTATTTATCAA
Done.