Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008980.1 Hibiscus syriacus cultivar Beakdansim tig00112342_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: 184855
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
File 2 of 2
Found at i:145311 original size:60 final size:58
Alignment explanation
Indices: 145193--145313 Score: 145
Period size: 60 Copynumber: 2.0 Consensus size: 58
145183 TTAACTTATT
*
145193 AAATATAATTTATTATTATCTTAACTCAAAAATATATTTTATTCTTATTTTAATTTTAAA
1 AAATATAATTTATTATTACCTTAACTCAAAAATATATTTTATTCTTA--TTAATTTTAAA
* * * *
145253 AAATATATTTTATTCTTACCTTAACTTAAAATTTTATATTTTATTCTTA-TAATATTTAAA
1 AAATATAATTTATTATTACCTTAACTCAAAA--ATATATTTTATTCTTATTAAT-TTTAAA
145313 A
1 A
145314 TTAAAATAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
59 4 0.08
60 34 0.64
62 15 0.28
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.52
Consensus pattern (58 bp):
AAATATAATTTATTATTACCTTAACTCAAAAATATATTTTATTCTTATTAATTTTAAA
Found at i:145367 original size:27 final size:27
Alignment explanation
Indices: 145305--145402 Score: 117
Period size: 26 Copynumber: 3.6 Consensus size: 27
145295 ATTCTTATAA
*
145305 TATTTAAAATTAAAATAAATATTTTT-
1 TATTTAAAATAAAAATAAATATTTTTG
* *
145331 TATTTCAAATAAAAATATATATTTTTG
1 TATTTAAAATAAAAATAAATATTTTTG
145358 TATTTAAAATAAAAATAAAATATATTTTG
1 TATTTAAAATAAAAAT-AAATAT-TTTTG
* * *
145387 TAATTAAGATATAAAT
1 TATTTAAAATAAAAAT
145403 TAAAATAAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
26 23 0.38
27 15 0.25
28 5 0.08
29 18 0.30
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (27 bp):
TATTTAAAATAAAAATAAATATTTTTG
Found at i:145405 original size:12 final size:10
Alignment explanation
Indices: 145397--145462 Score: 53
Period size: 11 Copynumber: 6.3 Consensus size: 10
145387 TAATTAAGAT
145397 ATAAATTAAA
1 ATAAATTAAA
145407 ATAAATTAAA
1 ATAAATTAAA
*
145417 ATAAGAATAAA
1 ATAA-ATTAAA
*
145428 ATATATATT-TA
1 ATA-A-ATTAAA
* *
145439 ATAAGTTAAT
1 ATAAATTAAA
145449 ATAAAATTAAA
1 AT-AAATTAAA
145460 ATA
1 ATA
145463 TATTTTTAGA
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
9 2 0.05
10 18 0.42
11 20 0.47
12 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (10 bp):
ATAAATTAAA
Found at i:145407 original size:30 final size:30
Alignment explanation
Indices: 145309--145469 Score: 87
Period size: 29 Copynumber: 5.7 Consensus size: 30
145299 TTATAATATT
* * *
145309 TAAAATTAAAATAAATATTTTT-TATTTCAAA
1 TAAAAATAAAAT--ATATTTTTGTAATTAAAA
*
145340 TAAAAAT---ATATATTTTTGTATTTAAAA
1 TAAAAATAAAATATATTTTTGTAATTAAAA
*
145367 TAAAAATAAAATATA-TTTTGTAATTAAGA
1 TAAAAATAAAATATATTTTTGTAATTAAAA
* *
145396 TATAAATTAAA-ATA-------AATTAAAA
1 TAAAAATAAAATATATTTTTGTAATTAAAA
* ** *
145418 TAAGAATAAAATATATATTTAATAAGTTAATA
1 TAAAAATAAAATATAT-TTTTGTAA-TTAAAA
*
145450 TAAAATTAAAATATATTTTT
1 TAAAAATAAAATATATTTTT
145470 AGAAGTTAAG
Statistics
Matches: 102, Mismatches: 14, Indels: 28
0.71 0.10 0.19
Matches are distributed among these distances:
22 15 0.15
23 3 0.03
26 8 0.08
27 15 0.15
28 5 0.05
29 21 0.21
30 5 0.05
31 11 0.11
32 19 0.19
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.42
Consensus pattern (30 bp):
TAAAAATAAAATATATTTTTGTAATTAAAA
Found at i:145426 original size:51 final size:53
Alignment explanation
Indices: 145361--145462 Score: 147
Period size: 51 Copynumber: 2.0 Consensus size: 53
145351 ATTTTTGTAT
*
145361 TTAAAATAAAAATAAAATATAT-TTT-GTAA-TTAAGATATAAATTAAAATAAA
1 TTAAAATAAAAATAAAATATATATTTAATAAGTTAAGATA-AAATTAAAATAAA
* *
145412 TTAAAATAAGAATAAAATATATATTTAATAAGTTAATATAAAATTAAAATA
1 TTAAAATAAAAATAAAATATATATTTAATAAGTTAAGATAAAATTAAAATA
145463 TATTTTTAGA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
51 21 0.47
52 3 0.07
53 14 0.31
54 7 0.16
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (53 bp):
TTAAAATAAAAATAAAATATATATTTAATAAGTTAAGATAAAATTAAAATAAA
Found at i:148307 original size:97 final size:97
Alignment explanation
Indices: 148154--148333 Score: 315
Period size: 97 Copynumber: 1.9 Consensus size: 97
148144 CAATAGATTT
*
148154 CATGATCCATAAATCAATAACGATCATATTTTCCAGTGAAAACAGGAAACCCGATAACACATTTC
1 CATGATCCATAAATCAATAACGATCATATTTCCCAGTGAAAACAGGAAACCCGATAACACATTTC
*
148219 AGGTAACCATAGTTCATAAAACCAGTAGGTTC
66 AAGTAACCATAGTTCATAAAACCAGTAGGTTC
* * *
148251 CATGATCCATAAATCAGTAACGATCATATTTCCCAGTGAAAACAGGATACCTGATAACACATTTC
1 CATGATCCATAAATCAATAACGATCATATTTCCCAGTGAAAACAGGAAACCCGATAACACATTTC
148316 AAGTAACCATAGTTCATA
66 AAGTAACCATAGTTCATA
148334 TACTAGGAAA
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
97 78 1.00
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.26
Consensus pattern (97 bp):
CATGATCCATAAATCAATAACGATCATATTTCCCAGTGAAAACAGGAAACCCGATAACACATTTC
AAGTAACCATAGTTCATAAAACCAGTAGGTTC
Found at i:153858 original size:131 final size:131
Alignment explanation
Indices: 153615--153983 Score: 499
Period size: 131 Copynumber: 2.8 Consensus size: 131
153605 ATAATTTTAA
* * * * *
153615 GAGAGAAAACGATACTATCTAATTATTTCTAATCGGGT-ATAAATAACTTCTCATGCCTTAAAGC
1 GAGAGAAAACGATAATATCTAATTATTTCCAATC-GATAATAAATGACCTCTCATGCCTTAAAGC
* * * **
153679 AGACATTTATTACTCCAATTGAAACGAAGAGATATCACTATTTTGTCTTA-AAATTCAATATTGA
65 AGTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTCCGTCTTAGAAA-TCAATATTGA
153743 TCT
129 TCT
* * * *
153746 GAGTGAAAAAGATAATATCTAATGATTTCCAATCGATAATAAATGACCTCTTATGCCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGATAATAAATGACCTCTCATGCCTTAAAGCA
*
153811 GTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTCCGTCTTAGAAATCAATATTGATT
66 GTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTCCGTCTTAGAAATCAATATTGATC
153876 T
131 T
* * * *
153877 GAGAGAAAACGATAATGTCTAATTATTTCCAATCGAAAATAAATGACCTCTCATGCCTTAATGAA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGATAATAAATGACCTCTCATGCCTTAAAGCA
* * * *
153942 GTTATTCATTACTCCAATCGAAATGAAAAGATATTACTATTC
66 GTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTC
153984 TCAATACCGA
Statistics
Matches: 209, Mismatches: 27, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
130 2 0.01
131 204 0.98
132 3 0.01
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.33
Consensus pattern (131 bp):
GAGAGAAAACGATAATATCTAATTATTTCCAATCGATAATAAATGACCTCTCATGCCTTAAAGCA
GTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTCCGTCTTAGAAATCAATATTGATC
T
Found at i:164979 original size:3 final size:3
Alignment explanation
Indices: 164971--165045 Score: 150
Period size: 3 Copynumber: 25.0 Consensus size: 3
164961 GACCTGTATA
164971 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
165019 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
165046 TGTAGCGTCG
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:166606 original size:2 final size:2
Alignment explanation
Indices: 166562--166589 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
166552 ACTTAAAGTA
166562 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
166590 TCACGTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:168711 original size:16 final size:16
Alignment explanation
Indices: 168686--168723 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
168676 ATATTCTATT
*
168686 AAGTGATCAAAATGTA
1 AAGTGTTCAAAATGTA
*
168702 AAGTGTTCAAAATGTG
1 AAGTGTTCAAAATGTA
168718 AAGTGT
1 AAGTGT
168724 ATAAGTTATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.42, C:0.05, G:0.24, T:0.29
Consensus pattern (16 bp):
AAGTGTTCAAAATGTA
Found at i:171707 original size:28 final size:28
Alignment explanation
Indices: 171657--171734 Score: 66
Period size: 28 Copynumber: 2.7 Consensus size: 28
171647 GAAGACACTA
* * * *
171657 GTTTTTTTTTTTATTTTTTATTTCATTT
1 GTTTTATTTATTATTATTAATTTCATTT
**
171685 GTTTTATTTATTATTATTAATTTGTTTT
1 GTTTTATTTATTATTATTAATTTCATTT
*
171713 ATTATTATTATATATATTATTA
1 GTT-TTATT-TAT-TATTATTA
171735 TTATGAAATA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
28 24 0.60
29 5 0.12
30 3 0.08
31 8 0.20
ACGTcount: A:0.23, C:0.01, G:0.04, T:0.72
Consensus pattern (28 bp):
GTTTTATTTATTATTATTAATTTCATTT
Found at i:173216 original size:16 final size:17
Alignment explanation
Indices: 173190--173221 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
173180 GATGTTTGTA
173190 TCTTAACTTTATTTTTT
1 TCTTAACTTTATTTTTT
173207 TCTT-ACTTTATTTTT
1 TCTTAACTTTATTTTT
173222 CTTTGCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (17 bp):
TCTTAACTTTATTTTTT
Found at i:174181 original size:20 final size:20
Alignment explanation
Indices: 174158--174197 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
174148 AGAAATTAAA
174158 AATTCATATATTTAATTTTT
1 AATTCATATATTTAATTTTT
* * *
174178 AATTCTTTTCTTTAATTTTT
1 AATTCATATATTTAATTTTT
174198 TTACTTATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (20 bp):
AATTCATATATTTAATTTTT
Found at i:174211 original size:13 final size:12
Alignment explanation
Indices: 174195--174246 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 12
174185 TTCTTTAATT
174195 TTTTTACTTATTA
1 TTTTTA-TTATTA
174208 TTTTTATATATTA
1 TTTTTAT-TATTA
174221 TTATTTATTATT-
1 TT-TTTATTATTA
174233 TTATTTATT-TTA
1 TT-TTTATTATTA
174245 TT
1 TT
174247 CAAGAATTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.06
12 12 0.33
13 17 0.47
14 5 0.14
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTTATTATTA
Found at i:175885 original size:14 final size:14
Alignment explanation
Indices: 175847--175900 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
175837 ATTTTAAATA
*
175847 ATTTACATTTACA-
1 ATTTACATTTGCAT
175860 ATTTTACATTTGCAT
1 A-TTTACATTTGCAT
175875 ATTTACATTTGGCAT
1 ATTTACATTT-GCAT
* *
175890 CTTTGCATTTG
1 ATTTACATTTG
175901 TATTGCACAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
13 1 0.03
14 21 0.60
15 13 0.37
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:175889 original size:15 final size:15
Alignment explanation
Indices: 175862--175900 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
175852 CATTTACAAT
175862 TTTACATTT-GCATA
1 TTTACATTTGGCATA
*
175876 TTTACATTTGGCATC
1 TTTACATTTGGCATA
*
175891 TTTGCATTTG
1 TTTACATTTG
175901 TATTGCACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.21, C:0.15, G:0.13, T:0.51
Consensus pattern (15 bp):
TTTACATTTGGCATA
Found at i:179082 original size:23 final size:23
Alignment explanation
Indices: 179055--179099 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
179045 TTGAAGTATT
179055 ATCCAGCAAAGAAAGAAAAAAAA
1 ATCCAGCAAAGAAAGAAAAAAAA
*
179078 ATCCAGCAAAGAAAGGAAAAAA
1 ATCCAGCAAAGAAAGAAAAAAA
179100 GAAAAGAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.67, C:0.13, G:0.16, T:0.04
Consensus pattern (23 bp):
ATCCAGCAAAGAAAGAAAAAAAA
Found at i:181446 original size:83 final size:83
Alignment explanation
Indices: 181302--181809 Score: 837
Period size: 83 Copynumber: 6.1 Consensus size: 83
181292 AAATGTAATG
181302 TGCTCCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCAT
1 TGCT-CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCAT
* *
181367 TGAATTTGGAAGATGAATG
65 TGAATTTAGAAGATGAATT
*
181386 TGCTCATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATT
*
181451 TAATTTAGAAGATGAATT
66 GAATTTAGAAGATGAATT
*
181469 TGC-CAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCAT
1 TGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCAT
181533 TGAATTTAGAAGATGAATT
65 TGAATTTAGAAGATGAATT
181552 TGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCAT
1 TGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCAT
* *
181616 TGAATTTGGAAGATGAATG
65 TGAATTTAGAAGATGAATT
*
181635 TGCTCATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGAACCAATCAT
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAACCAATCAT
181699 TGAATTTAGAAGATGAATT
65 TGAATTTAGAAGATGAATT
*
181718 TGC-CAATATCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGG-CAGAACCAATCAT
1 TGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCAT
*
181781 TGAATTTGGAAGATGAATTT
65 TGAATTTAGAAGATGAA-TT
181801 TGCTCATAG
1 TGCTCATAG
181810 TAGAAATAAG
Statistics
Matches: 401, Mismatches: 17, Indels: 13
0.93 0.04 0.03
Matches are distributed among these distances:
82 35 0.09
83 356 0.89
84 10 0.02
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.36
Consensus pattern (83 bp):
TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATT
GAATTTAGAAGATGAATT
Found at i:184312 original size:22 final size:22
Alignment explanation
Indices: 184247--184323 Score: 91
Period size: 22 Copynumber: 3.5 Consensus size: 22
184237 ATCTACACTC
* *
184247 TTTAAAGATGATAGATTCTCTC
1 TTTAAAGATGATAAATTCTCTT
* *
184269 TTCAAAGATGATATATTCTCTT
1 TTTAAAGATGATAAATTCTCTT
*
184291 TTTAAAGATTATAAATTCTCTT
1 TTTAAAGATGATAAATTCTCTT
* *
184313 TTCAAATATGA
1 TTTAAAGATGA
184324 AGCTTTATTG
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (22 bp):
TTTAAAGATGATAAATTCTCTT
Done.