Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009389.1 Hibiscus syriacus cultivar Beakdansim tig00113284_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: 54332
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:1189 original size:27 final size:26
Alignment explanation
Indices: 1128--1200 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 26
1118 ATAAAAAGGT
* *
1128 AAGAAATAAATAAATAAAATTAAAATG
1 AAGAAA-AAATAAATAAAAATAAAATA
*
1155 AAGAAAAAATTAAATAAAAGATAAGATA
1 AAGAAAAAA-TAAATAAAA-ATAAAATA
1183 AAGAAAACAA-AAATAAAA
1 AAGAAAA-AATAAATAAAA
1201 TAGTAAGTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
26 3 0.08
27 23 0.57
28 12 0.30
29 2 0.05
ACGTcount: A:0.74, C:0.01, G:0.08, T:0.16
Consensus pattern (26 bp):
AAGAAAAAATAAATAAAAATAAAATA
Found at i:1227 original size:9 final size:9
Alignment explanation
Indices: 1209--1302 Score: 50
Period size: 9 Copynumber: 9.9 Consensus size: 9
1199 AATAGTAAGT
1209 AAAATAATAA
1 AAAAT-ATAA
1219 AAAATATAA
1 AAAATATAA
*
1228 AAAAAATATA
1 AAAATATA-A
*
1238 AAAATAAAGA
1 AAAATATA-A
*
1248 AAAAGA-AGA
1 AAAATATA-A
1257 AAAATAT-A
1 AAAATATAA
*
1265 TAAATA-AA
1 AAAATATAA
1273 ACAAATAATAA
1 A-AAAT-ATAA
*
1284 TAAAAAAGTAA
1 -AAAATA-TAA
1295 AAAATATA
1 AAAATATA
1303 TTATATATTA
Statistics
Matches: 66, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
8 7 0.11
9 25 0.38
10 25 0.38
11 8 0.12
12 1 0.02
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.18
Consensus pattern (9 bp):
AAAATATAA
Found at i:1233 original size:11 final size:11
Alignment explanation
Indices: 1212--1241 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
1202 AGTAAGTAAA
1212 ATAATAAAAAAT
1 ATAA-AAAAAAT
1224 ATAAAAAAAAT
1 ATAAAAAAAAT
1235 ATAAAAA
1 ATAAAAA
1242 TAAAGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (11 bp):
ATAAAAAAAAT
Found at i:1241 original size:29 final size:28
Alignment explanation
Indices: 1209--1300 Score: 89
Period size: 27 Copynumber: 3.2 Consensus size: 28
1199 AATAGTAAGT
1209 AAAATAATAAAAAATATAAAAAAAATATA
1 AAAATAA-AAAAAATATAAAAAAAATATA
* * *
1238 AAAATAAAGAAAA-AGAAGAAAAATATA
1 AAAATAAAAAAAATATAAAAAAAATATA
* *
1265 TAAATAAAACAAATAATAATAAAAAAGTA-A
1 AAAATAAAAAAAAT-ATAA-AAAAAA-TATA
1295 AAAATA
1 AAAATA
1301 TATTATATAT
Statistics
Matches: 50, Mismatches: 9, Indels: 7
0.76 0.14 0.11
Matches are distributed among these distances:
27 22 0.44
28 5 0.10
29 10 0.20
30 11 0.22
31 2 0.04
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.17
Consensus pattern (28 bp):
AAAATAAAAAAAATATAAAAAAAATATA
Found at i:1260 original size:38 final size:38
Alignment explanation
Indices: 1217--1303 Score: 97
Period size: 38 Copynumber: 2.3 Consensus size: 38
1207 GTAAAATAAT
* **
1217 AAAAAATATA-AAA-AAAATATAAAAATAAAGAAAAAGA
1 AAAAAATATATAAATAAAACA-AAAAATAATAAAAAAGA
* *
1254 AGAAAAATATATAAATAAAACAAATAATAATAAAAAAGT
1 A-AAAAATATATAAATAAAACAAAAAATAATAAAAAAGA
1293 AAAAAATATAT
1 AAAAAATATAT
1304 TATATATTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
37 1 0.02
38 19 0.45
39 17 0.40
40 5 0.12
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.18
Consensus pattern (38 bp):
AAAAAATATATAAATAAAACAAAAAATAATAAAAAAGA
Found at i:1325 original size:35 final size:34
Alignment explanation
Indices: 1277--1365 Score: 85
Period size: 36 Copynumber: 2.6 Consensus size: 34
1267 AATAAAACAA
* *
1277 ATAAT-AATAAAAAA-GTAAAAAATATATTATATATT
1 ATAATAAATAAAAAACATAAAAAA-ATAGTA-A-ATT
1312 ATAATAAAT-AAAAACATAAAAAAATAGTAAATT
1 ATAATAAATAAAAAACATAAAAAAATAGTAAATT
*
1345 ATATATAAATTAATAAACATA
1 ATA-ATAAA-TAAAAAACATA
1366 TAATAAAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
33 6 0.13
34 6 0.13
35 16 0.35
36 18 0.39
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (34 bp):
ATAATAAATAAAAAACATAAAAAAATAGTAAATT
Found at i:1335 original size:38 final size:37
Alignment explanation
Indices: 1292--1388 Score: 97
Period size: 38 Copynumber: 2.5 Consensus size: 37
1282 AATAAAAAAG
*
1292 TAAAAAATATATTATATATTATAATAAATAAAAACATAA
1 TAAAAAATAAATTATATA-TA-AATAAATAAAAACATAA
* * *
1331 -AAAAATAGTAAATTATATATAAATTAATAAACATATAA
1 TAAAAA-A-TAAATTATATATAAATAAATAAAAACATAA
*
1369 TAAAAAATAACAATATATAT
1 TAAAAAATAA-ATTATATAT
1389 GTAATCTAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
37 3 0.06
38 28 0.57
39 8 0.16
40 10 0.20
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (37 bp):
TAAAAAATAAATTATATATAAATAAATAAAAACATAA
Found at i:1997 original size:37 final size:37
Alignment explanation
Indices: 1943--2054 Score: 188
Period size: 37 Copynumber: 3.0 Consensus size: 37
1933 ATGCTTGTAG
* * *
1943 ATCCTATTTTTACGAGTTTGAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
*
1980 ATCCTATATTTAGGAGTTTGAATCCTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
2017 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
2054 A
1 A
2055 ACGTTATGTT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 70 1.00
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.39
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
Found at i:4701 original size:20 final size:20
Alignment explanation
Indices: 4660--4701 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
4650 TTTTTTTATT
*
4660 AAAACAACATAATTAAATCA
1 AAAACAACATAATTAAAACA
*
4680 AAAACAACA-ATTTAAAAACA
1 AAAACAACATAATT-AAAACA
4700 AA
1 AA
4702 TCATTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.69, C:0.14, G:0.00, T:0.17
Consensus pattern (20 bp):
AAAACAACATAATTAAAACA
Found at i:4752 original size:17 final size:17
Alignment explanation
Indices: 4730--4762 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4720 AATTTTAATT
4730 TTTTGA-GAAATCTTGTG
1 TTTTGATGAAAT-TTGTG
4747 TTTTGATGAAATTTGT
1 TTTTGATGAAATTTGT
4763 TGTAGATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.24, C:0.03, G:0.21, T:0.52
Consensus pattern (17 bp):
TTTTGATGAAATTTGTG
Found at i:7229 original size:12 final size:12
Alignment explanation
Indices: 7212--7236 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7202 ATGATCGTTC
7212 TCCAACGTCATG
1 TCCAACGTCATG
7224 TCCAACGTCATG
1 TCCAACGTCATG
7236 T
1 T
7237 GTATTTACAA
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:0.24, C:0.32, G:0.16, T:0.28
Consensus pattern (12 bp):
TCCAACGTCATG
Found at i:10008 original size:23 final size:23
Alignment explanation
Indices: 9981--10040 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
9971 ATTGCTCAGA
9981 GGGAACCGATTCCCTCCCATAGG
1 GGGAACCGATTCCCTCCCATAGG
10004 GGGAACCGATTCCCTCCCATAGG
1 GGGAACCGATTCCCTCCCATAGG
*
10027 GGGTACCGATTCCC
1 GGGAACCGATTCCC
10041 CCTGAATGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.20, C:0.35, G:0.27, T:0.18
Consensus pattern (23 bp):
GGGAACCGATTCCCTCCCATAGG
Found at i:15920 original size:21 final size:21
Alignment explanation
Indices: 15894--15933 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
15884 CCCCCTTTGA
*
15894 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
15915 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
15934 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:21630 original size:21 final size:20
Alignment explanation
Indices: 21601--21639 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
21591 TTGTCTTTCA
* *
21601 ATTTTGAAATATATTTTTTGT
1 ATTTCGAAA-ATAATTTTTGT
21622 ATTTCGAAAATAATTTTT
1 ATTTCGAAAATAATTTTT
21640 CATAATCCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.56
Consensus pattern (20 bp):
ATTTCGAAAATAATTTTTGT
Found at i:23170 original size:19 final size:18
Alignment explanation
Indices: 23142--23178 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
23132 CGTTGGTTGA
*
23142 CCTAGTGTATTGGTACAC
1 CCTAGTGTATCGGTACAC
23160 CCTAGGTGTATCGGTACAC
1 CCTA-GTGTATCGGTACAC
23179 TAATTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.30
Consensus pattern (18 bp):
CCTAGTGTATCGGTACAC
Found at i:25451 original size:40 final size:40
Alignment explanation
Indices: 25391--25468 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
25381 TCCTTTGTAG
25391 AAAGGCGCAACCCATGCATCGCGCCTTACGCCACGTGTTA
1 AAAGGCGCAACCCATGCATCGCGCCTTACGCCACGTGTTA
* * * *
25431 AAAGGCGCGACCCTTTCATCGCGCCTTATGCCACGTGT
1 AAAGGCGCAACCCATGCATCGCGCCTTACGCCACGTGT
25469 AAAGTCTGGG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.22, C:0.35, G:0.23, T:0.21
Consensus pattern (40 bp):
AAAGGCGCAACCCATGCATCGCGCCTTACGCCACGTGTTA
Found at i:32315 original size:18 final size:17
Alignment explanation
Indices: 32286--32322 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
32276 TAATCGAATT
*
32286 TAAAATTTAAAATTGAA
1 TAAAATTTAAAATTCAA
32303 TAAAATCTTAAAATTCAA
1 TAAAAT-TTAAAATTCAA
32321 TA
1 TA
32323 GTTCTTTATT
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:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (17 bp):
TAAAATTTAAAATTCAA
Found at i:34995 original size:31 final size:28
Alignment explanation
Indices: 34907--34974 Score: 136
Period size: 28 Copynumber: 2.4 Consensus size: 28
34897 ATTTTTCTTA
34907 ATTAATTTGAATAATAGCAGAATAAATG
1 ATTAATTTGAATAATAGCAGAATAAATG
34935 ATTAATTTGAATAATAGCAGAATAAATG
1 ATTAATTTGAATAATAGCAGAATAAATG
34963 ATTAATTTGAAT
1 ATTAATTTGAAT
34975 TATGTTGAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.49, C:0.03, G:0.13, T:0.35
Consensus pattern (28 bp):
ATTAATTTGAATAATAGCAGAATAAATG
Found at i:37800 original size:24 final size:24
Alignment explanation
Indices: 37773--37818 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
37763 GAGTCTACAC
37773 AATTATCCACTGAAGTACCTGAAT
1 AATTATCCACTGAAGTACCTGAAT
37797 AATTATCCACTGAAGTACCTGA
1 AATTATCCACTGAAGTACCTGA
37819 TTTTTTAGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (24 bp):
AATTATCCACTGAAGTACCTGAAT
Found at i:40849 original size:29 final size:30
Alignment explanation
Indices: 40788--40849 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
40778 GAAACTTTCA
* * *
40788 AAATTTTTGAAAATTTTAATTTAAATCTCT
1 AAATTTTTGAAAATTTTAAGTTAAACCCCT
*
40818 AAATTTTTTAAAATTTTAAGTT-AACCCCT
1 AAATTTTTGAAAATTTTAAGTTAAACCCCT
40847 AAA
1 AAA
40850 CTCTATCACC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 8 0.29
30 20 0.71
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (30 bp):
AAATTTTTGAAAATTTTAAGTTAAACCCCT
Found at i:41083 original size:14 final size:15
Alignment explanation
Indices: 41064--41092 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
41054 TTAAATGCAT
41064 TTATAAA-TATTAAA
1 TTATAAAGTATTAAA
41078 TTATAAAGTATTAAA
1 TTATAAAGTATTAAA
41093 CATATAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
TTATAAAGTATTAAA
Found at i:44643 original size:17 final size:18
Alignment explanation
Indices: 44623--44665 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
44613 TATGTTTAAG
44623 TTTATTTTA-TGTTGTTT
1 TTTATTTTACTGTTGTTT
*
44640 TTTATTTTACTGTTTTTT
1 TTTATTTTACTGTTGTTT
44658 TCTTATTT
1 T-TTATTT
44666 GATATTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.39
18 8 0.35
19 6 0.26
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.77
Consensus pattern (18 bp):
TTTATTTTACTGTTGTTT
Found at i:49855 original size:25 final size:25
Alignment explanation
Indices: 49826--49882 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
49816 GGTATAATCA
*
49826 AAATTGTGTAGCGAAGCAATCTGTC
1 AAATTGTGTAGCGAAACAATCTGTC
49851 AAATTGTGTAGCGAAACAATCTGTC
1 AAATTGTGTAGCGAAACAATCTGTC
49876 AAATTGT
1 AAATTGT
49883 TTGCTTCGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (25 bp):
AAATTGTGTAGCGAAACAATCTGTC
Found at i:52791 original size:30 final size:31
Alignment explanation
Indices: 52729--52802 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 31
52719 ATTTTTATGA
* *
52729 TATATCATCATCTAATTTATTAATTGTATAAAT
1 TATA-CATCAT-TAATTTATGAATTATATAAAT
52762 TATACATCATTAATTTATGAA-TATATAAAT
1 TATACATCATTAATTTATGAATTATATAAAT
*
52792 TAAACATCATT
1 TATACATCATT
52803 TAACGTGTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 18 0.47
31 10 0.26
32 6 0.16
33 4 0.11
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (31 bp):
TATACATCATTAATTTATGAATTATATAAAT
Done.