Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005792.1 Hibiscus syriacus cultivar Beakdansim tig00013580_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: 55125
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:4621 original size:17 final size:16
Alignment explanation
Indices: 4582--4615 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
4572 ACGAGTTATT
4582 AAAAAATATTTATGTAA
1 AAAAAATATTTA-GTAA
4599 AAAAAATATTTA-TAA
1 AAAAAATATTTAGTAA
4614 AA
1 AA
4616 TTAAAAAGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
17 12 0.71
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
AAAAAATATTTAGTAA
Found at i:5265 original size:19 final size:19
Alignment explanation
Indices: 5241--5285 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
5231 AATTCGAAGT
5241 AACGAGGGACTCTACCGAG
1 AACGAGGGACTCTACCGAG
5260 AACGAGGGACTCTACCGAG
1 AACGAGGGACTCTACCGAG
5279 AACGAGG
1 AACGAGG
5286 TTATTTTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.33, C:0.24, G:0.33, T:0.09
Consensus pattern (19 bp):
AACGAGGGACTCTACCGAG
Found at i:6111 original size:216 final size:214
Alignment explanation
Indices: 5713--6145 Score: 728
Period size: 216 Copynumber: 2.0 Consensus size: 214
5703 GGTGCCACAG
* *
5713 TAAATGATGTACGGATGAGGATCGACATCGCTGGTCGACATGCGATATACAATTTTCTTTTATTA
1 TAAATGATGTACGGATGAGGATCGACATCGCCGGTCGAAATGCGATATACAATTTTCTTTTATTA
*
5778 TTTTTTAAATTTTTTAAACTTTATATATATTAATTTTGATATTTATTATTTATAATTTTCTTTCC
66 TTTTTTAAATTTTTTAAACTTTATATATATTAACTTTGA-ATTTATTATTTATAATTTTCTTTCC
*
5843 TTCCGTATATGATGATGAGATCCACCGGTTATTGTCGCGTGATTGTTTTGAGGGGTCTGAGTTAT
130 TTCCGTATATGATGATGAGATCCACCGGTTATTGTCGCGGGATTGTTTTGA-GGGTCTGAGTTAT
5908 GGTGTGCCGTGACGCCGTTAC
194 GGTGTGCCGTGACGCCGTTAC
*
5929 TAAATGGTGTACGGATGAGGATCGACATCGCCGGTCGAAATGCGATATACAATTTTCTTTTATTA
1 TAAATGATGTACGGATGAGGATCGACATCGCCGGTCGAAATGCGATATACAATTTTCTTTTATTA
5994 TTTTTTTTAAAATTTTTTAAACTTTATATATATTAACTTTG-ATTTATTATTTATAATTTT-TTT
66 --TTTTTT-AAATTTTTTAAACTTTATATATATTAACTTTGAATTTATTATTTATAATTTTCTTT
*
6057 CCTTCCGTATATTGATGATGAGATCCATCGGTTATTGTCGCGGGATTG-TTTGAGGGTCTGAGTT
128 CCTTCCGTATA-TGATGATGAGATCCACCGGTTATTGTCGCGGGATTGTTTTGAGGGTCTGAGTT
*
6121 ATGGTGTGTCGTGACGCCGTTAC
192 ATGGTGTGCCGTGACGCCGTTAC
6144 TA
1 TA
6146 TATTTGCAAT
Statistics
Matches: 206, Mismatches: 7, Indels: 9
0.93 0.03 0.04
Matches are distributed among these distances:
215 35 0.17
216 81 0.39
217 53 0.26
218 6 0.03
219 31 0.15
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (214 bp):
TAAATGATGTACGGATGAGGATCGACATCGCCGGTCGAAATGCGATATACAATTTTCTTTTATTA
TTTTTTAAATTTTTTAAACTTTATATATATTAACTTTGAATTTATTATTTATAATTTTCTTTCCT
TCCGTATATGATGATGAGATCCACCGGTTATTGTCGCGGGATTGTTTTGAGGGTCTGAGTTATGG
TGTGCCGTGACGCCGTTAC
Found at i:6181 original size:33 final size:33
Alignment explanation
Indices: 6134--6208 Score: 132
Period size: 33 Copynumber: 2.3 Consensus size: 33
6124 GTGTGTCGTG
6134 ACGCCGTTACTATATTTGCAATTGTGGAGTGGT
1 ACGCCGTTACTATATTTGCAATTGTGGAGTGGT
*
6167 ACGCTGTTACTATATTTGCAATTGTGGAGTGGT
1 ACGCCGTTACTATATTTGCAATTGTGGAGTGGT
*
6200 ACGTCGTTA
1 ACGCCGTTA
6209 ATAGAGTGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.21, C:0.15, G:0.27, T:0.37
Consensus pattern (33 bp):
ACGCCGTTACTATATTTGCAATTGTGGAGTGGT
Found at i:10224 original size:23 final size:23
Alignment explanation
Indices: 10198--10243 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
10188 AATATAATGT
*
10198 AATATTAATATTAAATTTA-AATA
1 AATAATAAT-TTAAATTTAGAATA
*
10221 AATAATAATTTAACTTTAGAATA
1 AATAATAATTTAAATTTAGAATA
10244 TAGAGGTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
AATAATAATTTAAATTTAGAATA
Found at i:13146 original size:23 final size:22
Alignment explanation
Indices: 13110--13155 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
13100 CTAATGTCTT
*
13110 TATTATTAATAATTCATATATTA
1 TATTATTAATAATTAATAT-TTA
13133 TATT-TTAATAAATTAATATTTA
1 TATTATTAAT-AATTAATATTTA
13155 T
1 T
13156 GAATAAAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
TATTATTAATAATTAATATTTA
Found at i:13532 original size:31 final size:28
Alignment explanation
Indices: 13458--13519 Score: 124
Period size: 28 Copynumber: 2.2 Consensus size: 28
13448 ATGGTGGTAG
13458 CTCAATTGGCAATCCAACAGACGCAGCC
1 CTCAATTGGCAATCCAACAGACGCAGCC
13486 CTCAATTGGCAATCCAACAGACGCAGCC
1 CTCAATTGGCAATCCAACAGACGCAGCC
13514 CTCAAT
1 CTCAAT
13520 GATTGGCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.32, C:0.35, G:0.16, T:0.16
Consensus pattern (28 bp):
CTCAATTGGCAATCCAACAGACGCAGCC
Found at i:18266 original size:27 final size:27
Alignment explanation
Indices: 18228--18283 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
18218 AACCTCGGGT
18228 TGCCACACATTCAAAGATACCAAGGCC
1 TGCCACACATTCAAAGATACCAAGGCC
18255 TGCCACACATTCAAAGATACCAAGGCC
1 TGCCACACATTCAAAGATACCAAGGCC
18282 TG
1 TG
18284 TAAAATAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.36, C:0.32, G:0.16, T:0.16
Consensus pattern (27 bp):
TGCCACACATTCAAAGATACCAAGGCC
Found at i:18341 original size:29 final size:26
Alignment explanation
Indices: 18284--18341 Score: 62
Period size: 26 Copynumber: 2.1 Consensus size: 26
18274 CCAAGGCCTG
** *
18284 TAAAATAATTGTAATATATAAATTAA
1 TAAAATAATAATAATATATAAATAAA
18310 TAAAATAATAATAATAATATAATATAATA
1 TAAAATAATAATAAT-ATATAA-ATAA-A
18339 TAA
1 TAA
18342 TGTTTTTGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 13 0.50
27 6 0.23
28 3 0.12
29 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (26 bp):
TAAAATAATAATAATATATAAATAAA
Found at i:19734 original size:268 final size:267
Alignment explanation
Indices: 19170--20074 Score: 995
Period size: 269 Copynumber: 3.4 Consensus size: 267
19160 TGCTTCACCC
* * ** * ** ** **
19170 TCTGCCTTGGCTCTGTAAAAGATTCATCAGCAATATCCCTGCTGCCATCAGGCTTGAGCGACTTG
1 TCTGCCTTGGTTTTGTACTAGATTCATCAACAATATCCCCACTGCCATCAAACTTGAGTAAC-T-
* * ** * *
19235 TTCTCTTTCTCCGACTCATCAGAACTAGAAGTTTGTACTGTAGTTTCAGCTTCAGCT-ACCTGCA
64 CTCTCTTTCTCCGACTCATCAGAGCTAGAAGTTTGGCCTGTAGCTTCAGCTTCTG-TGACCTGCA
** * *
19299 -TCAAAGAATTGAAAGATATTGTTCACTTTCAGAAATGTACTTCAGTATATACTAATATTATACT
128 TTCAAATCATTGAAAGATATTGTTCAC-TTAATAAATGTAC-TCAGTATATACTAATATTATACT
* * * * *
19363 TTG-GCATTTGCCAAAACAAAATAGAA-G-ACGCATGTTAAACAGTGCGTTAAAAATTAGCTTTT
191 TTGAAC-TTTGCCAAAACAAAATGGAAGGTACACA-GTAAAACAGTGC--TAAAAATTAACTTTT
19425 CCTAGTTAATCAACCT
252 CCTAGTTAATCAACCT
*
19441 TCTGCCTTGATTTTGTACTAGATTCATCAACAATATCCCCACTGCCATCAAACTTGAGTAACTC-
1 TCTGCCTTGGTTTTGTACTAGATTCATCAACAATATCCCCACTGCCATCAAACTTGAGTAACTCT
* * * *
19505 CTCCTCCTCCAACTCATCAGAGCTAGAAGTTTGGCCTGTAGCTTCAGCTTCTGTGATCTGCATTC
66 CTCTTTCTCCGACTCATCAGAGCTAGAAGTTTGGCCTGTAGCTTCAGCTTCTGTGACCTGCATTC
*
19570 AAATCATTGAAAGACATTGTTCACTATAATAAATGTACTACAGTATATACTAATATTATACTTTG
131 AAATCATTGAAAGATATTGTTCACT-TAATAAATGTACT-CAGTATATACTAATATTATACTTTG
* * * * *
19635 AACTTTGCGAAAACAAAACGGAAGGTACACAGTAAACACAGTGCT-AAAATCATCTTGTCCTAGT
194 AACTTTGCCAAAACAAAATGGAAGGTACACAGTAAA-ACAGTGCTAAAAATTAACTTTTCCTAGT
*
19699 TAATCTACCT
258 TAATCAACCT
* * * *
19709 TCTGCCTTGGTTTTGAACAAGATTCATCAACAATATCCCCGCTGCCATCAAGCTTGAGTAACTCA
1 TCTGCCTTGGTTTTGTACTAGATTCATCAACAATATCCCCACTGCCATCAAACTTGAGTAACTC-
* * *
19774 TCTTCTTTCTCTGACTCATCAGAGCTAGAAGTTTGGCCCGCAGCTTCAGCTTCTGTGACCTGCAT
65 TC-TCTTTCTCCGACTCATCAGAGCTAGAAGTTTGGCCTGTAGCTTCAGCTTCTGTGACCTGCAT
* ** * * * *
19839 TCAAAATCATTGAAAGATATAGTTCACTTTTTGAAATATACTC-G-AGCATGCTAATATGATACT
129 TC-AAATCATTGAAAGATATTGTTCACTTAAT-AAATGTACTCAGTA-TATACTAATATTATACT
* * *
19902 TTGACCTCTGCCAAAACAAAATGGAAGGTACA-A-TAAATACAGCGCTAAAAATTAACTTTTCCT
191 TTGAACTTTGCCAAAACAAAATGGAAGGTACACAGTAAA-ACAGTGCTAAAAATTAACTTTTCCT
*
19965 AGTTAATCCACCT
255 AGTTAATCAACCT
* * * * *
19978 CCAGACTTGGTTTTGTACTAGATTCATCAGCAATATCCCCAGTGCCATCAAACTTGAGTAACTCA
1 TCTGCCTTGGTTTTGTACTAGATTCATCAACAATATCCCCACTGCCATCAAACTTGAGTAACTC-
*
20043 TTCTCTTTCTCTGACTCATCAGAGCTAGAAGT
65 -TCTCTTTCTCCGACTCATCAGAGCTAGAAGT
20075 CTCGTAAGAG
Statistics
Matches: 541, Mismatches: 77, Indels: 34
0.83 0.12 0.05
Matches are distributed among these distances:
267 1 0.00
268 148 0.27
269 187 0.35
270 53 0.10
271 121 0.22
272 31 0.06
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.32
Consensus pattern (267 bp):
TCTGCCTTGGTTTTGTACTAGATTCATCAACAATATCCCCACTGCCATCAAACTTGAGTAACTCT
CTCTTTCTCCGACTCATCAGAGCTAGAAGTTTGGCCTGTAGCTTCAGCTTCTGTGACCTGCATTC
AAATCATTGAAAGATATTGTTCACTTAATAAATGTACTCAGTATATACTAATATTATACTTTGAA
CTTTGCCAAAACAAAATGGAAGGTACACAGTAAAACAGTGCTAAAAATTAACTTTTCCTAGTTAA
TCAACCT
Found at i:20086 original size:18 final size:18
Alignment explanation
Indices: 20063--20110 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
20053 CTGACTCATC
*
20063 AGAGCTAGAAGTCTCGTA
1 AGAGCTAAAAGTCTCGTA
20081 AGAGCTAAAAGTCTCGTA
1 AGAGCTAAAAGTCTCGTA
20099 AGAGCTAAAAGT
1 AGAGCTAAAAGT
20111 TTGTCCTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.21
Consensus pattern (18 bp):
AGAGCTAAAAGTCTCGTA
Found at i:24417 original size:16 final size:17
Alignment explanation
Indices: 24388--24419 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
24378 CACTCAATTT
24388 TATTTTATTTTATTTTC
1 TATTTTATTTTATTTTC
24405 TATTTTA-TTTATTTT
1 TATTTTATTTTATTTT
24420 ACTTAATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (17 bp):
TATTTTATTTTATTTTC
Found at i:24772 original size:28 final size:29
Alignment explanation
Indices: 24724--24781 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
24714 ATGCAGTAAC
* *
24724 AAAAAAAATCAAATATATTAA-GTTCAAT
1 AAAAAAAATCAAATAGATTAACGTACAAT
24752 AAAAAAAAT-AAATAGATTTAACGTACAAT
1 AAAAAAAATCAAATAGA-TTAACGTACAAT
24781 A
1 A
24782 GGTGAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 6 0.23
28 13 0.50
29 7 0.27
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.26
Consensus pattern (29 bp):
AAAAAAAATCAAATAGATTAACGTACAAT
Found at i:34419 original size:21 final size:21
Alignment explanation
Indices: 34395--34438 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
34385 ACTTAACGCG
34395 TTTAGTACCTAAACCATCAGT
1 TTTAGTACCTAAACCATCAGT
**
34416 TTTAGTACCTAAACTTTCAGT
1 TTTAGTACCTAAACCATCAGT
34437 TT
1 TT
34439 GTTCAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (21 bp):
TTTAGTACCTAAACCATCAGT
Found at i:49090 original size:16 final size:18
Alignment explanation
Indices: 49050--49091 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
49040 CTGGATACAG
49050 ATGAAGAACTTGATGACAA
1 ATGAA-AACTTGATGACAA
*
49069 AAGAAAAC-TGATGAC-A
1 ATGAAAACTTGATGACAA
49085 ATGAAAA
1 ATGAAAA
49092 GAAAGAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 7 0.33
17 7 0.33
18 3 0.14
19 4 0.19
ACGTcount: A:0.55, C:0.10, G:0.19, T:0.17
Consensus pattern (18 bp):
ATGAAAACTTGATGACAA
Found at i:51611 original size:2 final size:2
Alignment explanation
Indices: 51604--51634 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
51594 AACAAGAAAT
51604 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
51635 GCATCTATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:51939 original size:2 final size:2
Alignment explanation
Indices: 51932--51967 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
51922 CTTTCAGATT
51932 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
51968 AAAACAACAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Done.