Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003749.1 Hibiscus syriacus cultivar Beakdansim tig00008025_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: 69192
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:989 original size:15 final size:15
Alignment explanation
Indices: 965--998 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
955 CCGTAGGACC
965 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
*
980 ACTACGTCCCGAAGG
1 ACTACATCCCGAAGG
995 ACTA
1 ACTA
999 TTATACCCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.15
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:1123 original size:28 final size:28
Alignment explanation
Indices: 1081--1153 Score: 130
Period size: 28 Copynumber: 2.6 Consensus size: 28
1071 ATTTCATATG
1081 TCATGTA-CTCATGTCATTCTCTTGTGA
1 TCATGTAGCTCATGTCATTCTCTTGTGA
*
1108 TCATGTAGTTCATGTCATTCTCTTGTGA
1 TCATGTAGCTCATGTCATTCTCTTGTGA
1136 TCATGTAGCTCATGTCAT
1 TCATGTAGCTCATGTCAT
1154 GTTCTCATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
27 7 0.16
28 36 0.84
ACGTcount: A:0.19, C:0.21, G:0.16, T:0.44
Consensus pattern (28 bp):
TCATGTAGCTCATGTCATTCTCTTGTGA
Found at i:1175 original size:12 final size:12
Alignment explanation
Indices: 1158--1182 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1148 TGTCATGTTC
1158 TCATATCACATA
1 TCATATCACATA
1170 TCATATCACATA
1 TCATATCACATA
1182 T
1 T
1183 GTATTTGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (12 bp):
TCATATCACATA
Found at i:1632 original size:44 final size:44
Alignment explanation
Indices: 1540--1642 Score: 111
Period size: 44 Copynumber: 2.3 Consensus size: 44
1530 GCACTACTTG
* * * * *
1540 TGCATCGGTGCA-TAAAATGCATTCGATGTTTTATATTAATGGGA
1 TGCATCGATGCACT-AATTGCATTCGATCTTTTATATTAAAGAGA
* *
1584 TGCATTGATGCACTAATTGCATTCGATCTTTTATTTTAAA-AGA
1 TGCATCGATGCACTAATTGCATTCGATCTTTTATATTAAAGAGA
1627 GTGCATCGATGCACTA
1 -TGCATCGATGCACTA
1643 CCAGTGCATC
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
43 2 0.04
44 46 0.94
45 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (44 bp):
TGCATCGATGCACTAATTGCATTCGATCTTTTATATTAAAGAGA
Found at i:4744 original size:63 final size:63
Alignment explanation
Indices: 4696--4879 Score: 212
Period size: 63 Copynumber: 2.9 Consensus size: 63
4686 GATGACTCTT
4696 TTAA-AATAAAAGCATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCG
1 TTAATAATAAAA-CATCG-ATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCG
* ** *
4760 TTAATAATGAAACATCGATGCAATTGGTGCATCGATGCATAAGGAGTGCATCGATGCATCCCAG
1 TTAATAATAAAACATCGATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCC-G
* * ** * *
4824 -TAATAATAATACATCGAATACCTTTTATGCACCGATGCATCAA-TAGTGCATCGATG
1 TTAATAATAAAACATCG-ATGCAATTCATGCATCGATGCAT-AAGTAGTGCATCGATG
4880 TATACCTTCA
Statistics
Matches: 103, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
63 56 0.54
64 39 0.38
65 8 0.08
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.27
Consensus pattern (63 bp):
TTAATAATAAAACATCGATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCG
Found at i:5366 original size:29 final size:29
Alignment explanation
Indices: 5327--5407 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
5317 TATGTGATAT
5327 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
*
5357 GAGAAATGACATGAACTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
*
5386 GAGAAATGACATTAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
5408 ACATATAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
28 7 0.15
29 36 0.75
30 5 0.10
ACGTcount: A:0.46, C:0.16, G:0.20, T:0.19
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:10301 original size:29 final size:29
Alignment explanation
Indices: 10258--10367 Score: 186
Period size: 29 Copynumber: 3.8 Consensus size: 29
10248 TTTCATATGT
10258 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
10286 TCATGTAGTTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
10315 TCATGTAGCTCATGTAATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
10344 TCATGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
10368 ATATCACATA
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
28 7 0.09
29 64 0.84
30 5 0.07
ACGTcount: A:0.18, C:0.20, G:0.16, T:0.45
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:10830 original size:45 final size:45
Alignment explanation
Indices: 10763--10868 Score: 110
Period size: 45 Copynumber: 2.4 Consensus size: 45
10753 TGCACTACTT
* * *
10763 GTGCATCGGTGCA-TAAAATGCATTCGAT-GTTTTATTATT-AATGG
1 GTGCATCGATGCACT-AAATGCATTCGATCGTTTTATT-TTAAAAGA
* * *
10807 GATGCATCGATGCACTAATTGCATTTGATCTTTTTATTTTAAAAGA
1 G-TGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAGA
10853 GTGCATCGATGCACTA
1 GTGCATCGATGCACTA
10869 CCAGTGCATC
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
44 1 0.02
45 39 0.75
46 12 0.23
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (45 bp):
GTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAGA
Found at i:13131 original size:38 final size:38
Alignment explanation
Indices: 13080--13157 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
13070 CCCACCTCGG
13080 TACATATCGTAAGGAGTTGCGGATGAATGTCTCCACAT
1 TACATATCGTAAGGAGTTGCGGATGAATGTCTCCACAT
*
13118 TACATATCGTAAGGAGTTGCGGATGAATGTCTCCCCAT
1 TACATATCGTAAGGAGTTGCGGATGAATGTCTCCACAT
13156 TA
1 TA
13158 TGGCATTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.29
Consensus pattern (38 bp):
TACATATCGTAAGGAGTTGCGGATGAATGTCTCCACAT
Found at i:20434 original size:23 final size:23
Alignment explanation
Indices: 20405--20460 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
20395 AACTCAAGAC
*
20405 TCAAGCTCAATTTTGAGCTCGA-T
1 TCAAGCTCAACTTTGAGCTC-ATT
20428 TCAAGCTCAACTTTGAGCTCATT
1 TCAAGCTCAACTTTGAGCTCATT
*
20451 TGAAGCTCAA
1 TCAAGCTCAA
20461 AACGGGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 1 0.03
23 29 0.97
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (23 bp):
TCAAGCTCAACTTTGAGCTCATT
Found at i:22098 original size:21 final size:21
Alignment explanation
Indices: 22046--22099 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
22036 CAGATTTAGA
*
22046 TTTAAGGTTTAAGGTATATAG
1 TTTAAGGTTTATGGTATATAG
* * *
22067 TTTATGATTTATGGTTTATAG
1 TTTAAGGTTTATGGTATATAG
22088 TTTAAGGTTTAT
1 TTTAAGGTTTAT
22100 TGCAAAGACA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.20, T:0.52
Consensus pattern (21 bp):
TTTAAGGTTTATGGTATATAG
Found at i:33393 original size:14 final size:14
Alignment explanation
Indices: 33376--33427 Score: 58
Period size: 14 Copynumber: 4.0 Consensus size: 14
33366 TGAACGTTCG
33376 GTTATGTTCGTTTA
1 GTTATGTTCGTTTA
33390 GTTATGTTCG--T-
1 GTTATGTTCGTTTA
*
33401 -TTATGTTCGTTTG
1 GTTATGTTCGTTTA
*
33414 GTTATGTTTGTTTA
1 GTTATGTTCGTTTA
33428 TGTTCATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
10 9 0.28
12 2 0.06
14 21 0.66
ACGTcount: A:0.12, C:0.06, G:0.23, T:0.60
Consensus pattern (14 bp):
GTTATGTTCGTTTA
Found at i:33398 original size:24 final size:24
Alignment explanation
Indices: 33371--33445 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
33361 GTTCGTGAAC
*
33371 GTTCGGTTATGTTCGTTTAGTTAT
1 GTTCGTTTATGTTCGTTTAGTTAT
*
33395 GTTCGTTTATGTTCGTTTGGTTAT
1 GTTCGTTTATGTTCGTTTAGTTAT
* * *
33419 GTTTGTTTATGTTCATTTATTTAT
1 GTTCGTTTATGTTCGTTTAGTTAT
33443 GTT
1 GTT
33446 TAATCTAATC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.12, C:0.07, G:0.21, T:0.60
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTTAGTTAT
Found at i:34296 original size:16 final size:16
Alignment explanation
Indices: 34272--34306 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
34262 GGTCTCCAAC
34272 GTTTATGTTCGTTTAT
1 GTTTATGTTCGTTTAT
*
34288 GTTTGTGTTCGTTTAT
1 GTTTATGTTCGTTTAT
34304 GTT
1 GTT
34307 CGATTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.09, C:0.06, G:0.23, T:0.63
Consensus pattern (16 bp):
GTTTATGTTCGTTTAT
Found at i:34389 original size:85 final size:85
Alignment explanation
Indices: 34295--34477 Score: 303
Period size: 85 Copynumber: 2.2 Consensus size: 85
34285 TATGTTTGTG
34295 TTCGTTTATGTTCGATTATTTATTAAATAAACGAACATGAACAAGTTATATTCCTTAATAAACGA
1 TTCGTTTATGTTCGATTATTTATTAAATAAACGAACATGAACAAGTTATATTCCTTAATAAACGA
* *
34360 GCATGAACAAAAAAAAATTA
66 ACATAAACAAAAAAAAATTA
* * * *
34380 TTCGTTTATGTTCGTTTATTTATTAAATGAACGAATATGAACAAGTTATATTCTTTAATAAACGA
1 TTCGTTTATGTTCGATTATTTATTAAATAAACGAACATGAACAAGTTATATTCCTTAATAAACGA
*
34445 ACATAAATAAAAAAAAATTA
66 ACATAAACAAAAAAAAATTA
34465 TTCGTTTATGTTC
1 TTCGTTTATGTTC
34478 ATTTTCGTTT
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
85 91 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.37
Consensus pattern (85 bp):
TTCGTTTATGTTCGATTATTTATTAAATAAACGAACATGAACAAGTTATATTCCTTAATAAACGA
ACATAAACAAAAAAAAATTA
Found at i:36302 original size:40 final size:40
Alignment explanation
Indices: 36247--36342 Score: 156
Period size: 40 Copynumber: 2.4 Consensus size: 40
36237 GGATCTGGGT
* *
36247 TATGAATCTGGTTTGTCCATCGTCCAACTGTTTGAGCGGG
1 TATGAATCTGGTTTGTCCATCGTCCAACTGTTAGAGCGAG
* *
36287 TATGAATCTGGTTTGTCCATCGTCCAACTGTTAGGGCTAG
1 TATGAATCTGGTTTGTCCATCGTCCAACTGTTAGAGCGAG
36327 TATGAATCTGGTTTGT
1 TATGAATCTGGTTTGT
36343 GTTGCTTTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.38
Consensus pattern (40 bp):
TATGAATCTGGTTTGTCCATCGTCCAACTGTTAGAGCGAG
Found at i:50986 original size:23 final size:23
Alignment explanation
Indices: 50960--51005 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
50950 ATAATGGTCA
50960 TTATGACATACACGAGTGAATGC
1 TTATGACATACACGAGTGAATGC
50983 TTATGACATACACGAGTGAATGC
1 TTATGACATACACGAGTGAATGC
51006 GAGATTGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (23 bp):
TTATGACATACACGAGTGAATGC
Found at i:58047 original size:15 final size:15
Alignment explanation
Indices: 58012--58044 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
58002 CCATTACCCG
58012 ATTTATTATATATTT
1 ATTTATTATATATTT
*
58027 ATTTATTTTAT-TTT
1 ATTTATTATATATTT
58041 ATTT
1 ATTT
58045 TATATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
ATTTATTATATATTT
Found at i:58048 original size:25 final size:23
Alignment explanation
Indices: 58013--58062 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 23
58003 CATTACCCGA
*
58013 TTTATTATATATTTATTTATTTTAT
1 TTTATTATATA-TTAATT-TTTTAT
*
58038 TTTATTTTATATTAATTTTTTAT
1 TTTATTATATATTAATTTTTTAT
58061 TT
1 TT
58063 ACAATTCTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 8 0.35
24 5 0.22
25 10 0.43
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTATTATATATTAATTTTTTAT
Found at i:58278 original size:8 final size:8
Alignment explanation
Indices: 58265--58291 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
58255 ATTATAGACC
58265 TTTAAATT
1 TTTAAATT
58273 TTTAAATT
1 TTTAAATT
58281 TTTAAATT
1 TTTAAATT
58289 TTT
1 TTT
58292 CTATATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTAAATT
Found at i:59625 original size:24 final size:24
Alignment explanation
Indices: 59595--59655 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
59585 ATTGAATTAT
59595 AAATATTTGATTGAAAATTTATAA
1 AAATATTTGATTGAAAATTTATAA
*
59619 AAATATTTGAATGAAAATTTATAA
1 AAATATTTGATTGAAAATTTATAA
59643 AAATATTTTGATT
1 AAATA-TTTGATT
59656 ATTACACTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
24 28 0.82
25 6 0.18
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (24 bp):
AAATATTTGATTGAAAATTTATAA
Found at i:61507 original size:20 final size:20
Alignment explanation
Indices: 61468--61509 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
61458 CCTGACTTGT
*
61468 TTGGAAGACCTGTAAATCGG
1 TTGGAAGACCTGAAAATCGG
61488 TTGGAAGACCT-AAAATTCGG
1 TTGGAAGACCTGAAAA-TCGG
61508 TT
1 TT
61510 CATAATCCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (20 bp):
TTGGAAGACCTGAAAATCGG
Found at i:61711 original size:2 final size:2
Alignment explanation
Indices: 61704--61755 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
61694 ACTGGAAATG
61704 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
61746 AT AT AT AT AT
1 AT AT AT AT AT
61756 GATTGAATCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.