Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007097.1 Hibiscus syriacus cultivar Beakdansim tig00018545_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: 272671
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
File 2 of 2
Found at i:225197 original size:3 final size:3
Alignment explanation
Indices: 225153--225180 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
225143 GCTTAAAATA
225153 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
225181 TCTAGTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:227101 original size:2 final size:2
Alignment explanation
Indices: 227094--227159 Score: 123
Period size: 2 Copynumber: 33.0 Consensus size: 2
227084 TAGAAAATAG
227094 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
*
227136 AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
227160 TCACATGTGC
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:228070 original size:28 final size:29
Alignment explanation
Indices: 228038--228092 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
228028 GTGAAACATC
* * *
228038 TGTTTTTATTATATGTAAGTT-TAATGCA
1 TGTTTTCATTATAAGTAAATTATAATGCA
228066 TGTTTTCATTATAAGTAAATTATAATG
1 TGTTTTCATTATAAGTAAATTATAATG
228093 TTTATAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.51
Consensus pattern (29 bp):
TGTTTTCATTATAAGTAAATTATAATGCA
Found at i:230263 original size:15 final size:14
Alignment explanation
Indices: 230243--230284 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
230233 TTAGCATTTA
230243 ATTATTGATATTAAT
1 ATTATT-ATATTAAT
230258 ATTATTATATTTAAT
1 ATTATTATA-TTAAT
*
230273 AGTATTATATTA
1 ATTATTATATTA
230285 CCTTATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 6 0.24
15 19 0.76
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (14 bp):
ATTATTATATTAAT
Found at i:231114 original size:20 final size:20
Alignment explanation
Indices: 231089--231131 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
231079 CATTTAAAAG
231089 TTTTTATTGAATTTGAAATA
1 TTTTTATTGAATTTGAAATA
231109 TTTTTATTGAATTTGAAATA
1 TTTTTATTGAATTTGAAATA
231129 TTT
1 TTT
231132 AAAAAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (20 bp):
TTTTTATTGAATTTGAAATA
Found at i:244393 original size:36 final size:36
Alignment explanation
Indices: 244339--244411 Score: 112
Period size: 36 Copynumber: 2.0 Consensus size: 36
244329 TGGCAACCAA
*
244339 CTTTGGAAAATGTTTTTTTCAAAGTTTGGTAAATATTT
1 CTTTGAAAAATG-TTTTTTCAAAGTTTGGTAAA-ATTT
244377 CTTTGAAAAATG-TTTTTCAAAGTTTGGTAAAATTT
1 CTTTGAAAAATGTTTTTTCAAAGTTTGGTAAAATTT
244412 TGGTAGATGT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 4 0.12
36 19 0.56
38 11 0.32
ACGTcount: A:0.32, C:0.05, G:0.15, T:0.48
Consensus pattern (36 bp):
CTTTGAAAAATGTTTTTTCAAAGTTTGGTAAAATTT
Found at i:249479 original size:18 final size:18
Alignment explanation
Indices: 249422--249479 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
249412 TTCATTTGGG
249422 GTTATCATGATTCAAGAT
1 GTTATCATGATTCAAGAT
* *
249440 GTTACTATATGCGTTC-AG--
1 GTTA-T-CATG-ATTCAAGAT
249458 GTTATCATGATTCAAGAT
1 GTTATCATGATTCAAGAT
249476 GTTA
1 GTTA
249480 CCAGATTCCC
Statistics
Matches: 30, Mismatches: 4, Indels: 12
0.65 0.09 0.26
Matches are distributed among these distances:
15 3 0.10
16 5 0.17
17 1 0.03
18 12 0.40
19 1 0.03
20 5 0.17
21 3 0.10
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (18 bp):
GTTATCATGATTCAAGAT
Found at i:251528 original size:115 final size:114
Alignment explanation
Indices: 251350--251830 Score: 364
Period size: 117 Copynumber: 4.1 Consensus size: 114
251340 TTTGGACAAG
* * * * * * *
251350 TTCTCAATATGAACT-CTCATTGAAAATGTTGATCCACCTACTTCTGTGATAGGTTTGAACAAAA
1 TTCTCATTATGAACTCCCCATTGAAAATGTTGGTCCACCTATTTCTATGATAGATTTGAGCAAAA
* * ** *
251414 GGTCGAACAAATTTTTCTCAGAATGAACTTCTCCCTCTTTGGACGAGTTT
66 GGTCAAACAAATTCTTCTCATTATGAACTTCTCCCTCTTTGGATGAG-TT
* * * *
251464 TTCTCATTATTAACTCCCCATTGAAAATGTTGGTCCACCTATTTTTATGATTGACTTGAGCAAAA
1 TTCTCATTATGAACTCCCCATTGAAAATGTTGGTCCACCTATTTCTATGATAGATTTGAGC-AAA
* **
251529 AGGTCAAACAAGTTCTTCTCATTATGAGTTTTTTCTCCCTCTTTGGATGAG--
65 AGGTCAAACAAATTCTTCTCATTATGA---ACTTCTCCCTCTTTGGATGAGTT
* * * * * *
251580 TTCTCATTATGAACTCTCCATTGAAAATGTTTGTCCTCCTCTTTCTATGATGGATTTAAGCAAAA
1 TTCTCATTATGAACTCCCCATTGAAAATGTTGGTCCACCTATTTCTATGATAGATTTGAGCAAAA
** * *
251645 AATCAAACTAGA-TCTTCTTATTATGAACTTTTTCTCCCTCTTTGGATGAGTT
66 GGTCAAAC-AAATTCTTCTCATTATGAAC---TTCTCCCTCTTTGGATGAGTT
* * * * * * **
251697 CTTCCCATTATGAACTCTCCATTG-AAATGTTAGTCCACTTCA-TTCTGTG-TTGAATTTGATAA
1 -TTCTCATTATGAACTCCCCATTGAAAATGTTGGTCCACCT-ATTTCTATGATAG-ATTTGAGCA
* * * * * * *
251759 AAATGTCGAACAAGTTCTTCTCATTTTGAACTTTTTCTCTCTCTTTAGATGAATT
63 AAAGGTCAAACAAATTCTTCTCATTATGAAC---TTCTCCCTCTTTGGATGAGTT
*
251814 CTTCTCATTTTGAACTC
1 -TTCTCATTATGAACTC
251831 TCTTTGAAAA
Statistics
Matches: 295, Mismatches: 57, Indels: 27
0.78 0.15 0.07
Matches are distributed among these distances:
114 13 0.04
115 78 0.26
116 81 0.27
117 83 0.28
118 22 0.07
119 18 0.06
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.40
Consensus pattern (114 bp):
TTCTCATTATGAACTCCCCATTGAAAATGTTGGTCCACCTATTTCTATGATAGATTTGAGCAAAA
GGTCAAACAAATTCTTCTCATTATGAACTTCTCCCTCTTTGGATGAGTT
Found at i:251587 original size:116 final size:115
Alignment explanation
Indices: 251307--251815 Score: 455
Period size: 116 Copynumber: 4.4 Consensus size: 115
251297 TCTAAAGTTG
* * * * ** *
251307 AACAAGCTCTTCT-A-TATGAACTTTTTCTTCTTTTTTGGACAAGTTCTCAATATGAACTCT-CA
1 AACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCTTTGGATGAGTTCTCATTATGAACTCTCCA
* * * * * * *
251369 TTGAAAATGTT-GATCCACCTACTTCTGTGATAGGTTTGAACAAAAGGTCG
66 TTGAAAATGTTAG-TCCACCTATTTCTATGATTGATTTGAGCAAAAAGTCA
* * ** * * *
251419 AACAAATTTTTCTCAGAATGAAC---TTCTCCCTCTTTGGACGAGTTTTTCTCATTATTAACTCC
1 AACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCTTTGGATGAG---TTCTCATTATGAACTCT
* * *
251481 CCATTGAAAATGTTGGTCCACCTATTTTTATGATTGACTTGAGCAAAAAGGTCA
63 CCATTGAAAATGTTAGTCCACCTATTTCTATGATTGATTTGAGCAAAAA-GTCA
**
251535 AACAAGTTCTTCTCATTATGAGTTTTTTCTCCCTCTTTGGATGAGTTCTCATTATGAACTCTCCA
1 AACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCTTTGGATGAGTTCTCATTATGAACTCTCCA
* * * * * *
251600 TTGAAAATGTTTGTCCTCCTCTTTCTATGATGGATTTAAGCAAAAAATCA
66 TTGAAAATGTTAGTCCACCTATTTCTATGATTGATTTGAGCAAAAAGTCA
* * *
251650 AACTAGATCTTCTTATTATGAACTTTTTCTCCCTCTTTGGATGAGTTCTTCCCATTATGAACTCT
1 AACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCTTTGGATGAGTTC-T--CATTATGAACTCT
* * * *
251715 CCATTG-AAATGTTAGTCCACTTCA-TTCTGTG-TTGAATTTGA-TAAAAATGTCG
63 CCATTGAAAATGTTAGTCCACCT-ATTTCTATGATTG-ATTTGAGCAAAAA-GTCA
* * * *
251767 AACAAGTTCTTCTCATTTTGAACTTTTTCTCTCTCTTTAGATGAATTCT
1 AACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCTTTGGATGAGTTCT
251816 TCTCATTTTG
Statistics
Matches: 321, Mismatches: 59, Indels: 30
0.78 0.14 0.07
Matches are distributed among these distances:
111 15 0.05
112 10 0.03
113 1 0.00
114 20 0.06
115 84 0.26
116 87 0.27
117 67 0.21
118 19 0.06
119 18 0.06
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (115 bp):
AACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCTTTGGATGAGTTCTCATTATGAACTCTCCA
TTGAAAATGTTAGTCCACCTATTTCTATGATTGATTTGAGCAAAAAGTCA
Found at i:251872 original size:117 final size:117
Alignment explanation
Indices: 251525--251872 Score: 294
Period size: 117 Copynumber: 3.0 Consensus size: 117
251515 TGACTTGAGC
* * ** * *
251525 AAAAAGGTCAAACAAGTTCTTCTCATTATGAGTTTTTTCTCCCTCTTTGGATGAGTTC-T--CAT
1 AAAAATGTCGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCTTTAGATGAATTCTTCCCAT
* * ** * * * * * *
251587 TATGAACTCTCCATTGAAAATGTTTGTCCTCCTCTTTCTATGATGGATTTAAGC
66 TATGAACTCTCCATTG-AAAGGTTAGTCAACCTCATTCTGTGAAGAATTTGA-T
* * * * * * *
251641 AAAAA-ATCAAACTAGATCTTCTTATTATGAACTTTTTCTCCCTCTTTGGATGAGTTCTTCCCAT
1 AAAAATGTCGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCTTTAGATGAATTCTTCCCAT
* * * **
251705 TATGAACTCTCCATTGAAATGTTAGTCCACTTCATTCTGTGTTGAATTTGAT
66 TATGAACTCTCCATTGAAAGGTTAGTCAACCTCATTCTGTGAAGAATTTGAT
* * *
251757 AAAAATGTCGAACAAGTTCTTCTCATTTTGAACTTTTTCTCTCTCTTTAGATGAATTCTTCTCAT
1 AAAAATGTCGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCTTTAGATGAATTCTTCCCAT
* * * * *
251822 TTTGAACTCT-CTTTGAAAAGGATTGGTCAACCTC-TTCTTTGAAGACTTTGA
66 TATGAACTCTCCATTG-AAAGG-TTAGTCAACCTCATTCTGTGAAGAATTTGA
251873 ACTTGTAAAA
Statistics
Matches: 191, Mismatches: 35, Indels: 11
0.81 0.15 0.05
Matches are distributed among these distances:
115 46 0.24
116 15 0.08
117 102 0.53
118 28 0.15
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (117 bp):
AAAAATGTCGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCTTTAGATGAATTCTTCCCAT
TATGAACTCTCCATTGAAAGGTTAGTCAACCTCATTCTGTGAAGAATTTGAT
Found at i:254211 original size:16 final size:17
Alignment explanation
Indices: 254159--254212 Score: 60
Period size: 16 Copynumber: 3.2 Consensus size: 17
254149 TGAACCTCGT
*
254159 TTTTCTTTTATTTCTTC
1 TTTTCTTTTCTTTCTTC
254176 ATTTTC--TTCTTTCTTCC
1 -TTTTCTTTTCTTTCTT-C
254193 TTTTCTTTTCTTT-TTC
1 TTTTCTTTTCTTTCTTC
254209 TTTT
1 TTTT
254213 TTTATTTTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
16 18 0.56
17 3 0.09
18 11 0.34
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTCTTTTCTTTCTTC
Found at i:256084 original size:94 final size:94
Alignment explanation
Indices: 255967--256180 Score: 238
Period size: 94 Copynumber: 2.3 Consensus size: 94
255957 ATCGAACCTG
*
255967 GGAAAATTGATGATTTGT-TCCACCGTCTCTTTC-TAGAGAACAAATCTAGAAAGATGATAATTC
1 GGAAAATTGATGATTT-TCTCCACCATCT-TTTCATAGAGAACAAATCTAGAAAGATGATAATTC
* * *
256030 AC-TCAAATGTCTCTTTGA-GAAGGATGAATAT
64 ACTTC-AATGTCGC-TTCATGAAGCATGAATAT
* * * * * *
256061 GGAAAATTGATGATTTTCTCCACCATCTTTTCATGGGGATCAAATTTGGAAAGATGATGATTCAC
1 GGAAAATTGATGATTTTCTCCACCATCTTTTCATAGAGAACAAATCTAGAAAGATGATAATTCAC
* * *
256126 TTCATTGTCGCTTCATGAATCATGAATCT
66 TTCAATGTCGCTTCATGAAGCATGAATAT
*
256155 AGAAAATTGATGATTTTCTCCACCAT
1 GGAAAATTGATGATTTTCTCCACCAT
256181 TTCTTCGTGA
Statistics
Matches: 102, Mismatches: 14, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
93 8 0.08
94 92 0.90
95 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Consensus pattern (94 bp):
GGAAAATTGATGATTTTCTCCACCATCTTTTCATAGAGAACAAATCTAGAAAGATGATAATTCAC
TTCAATGTCGCTTCATGAAGCATGAATAT
Found at i:261106 original size:20 final size:20
Alignment explanation
Indices: 261062--261106 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
261052 GGGGTGATAT
*
261062 TGATACTGCTAAGACAGCAC
1 TGATAATGCTAAGACAGCAC
* *
261082 CGATAATGCTAAGACAGTAC
1 TGATAATGCTAAGACAGCAC
261102 TGATA
1 TGATA
261107 CTGCCTGTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (20 bp):
TGATAATGCTAAGACAGCAC
Found at i:262694 original size:21 final size:20
Alignment explanation
Indices: 262665--262705 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
262655 AAATTATGGT
*
262665 GAAGGAAGAAGAAGAACAAGA
1 GAAGAAAGAAGAAGAA-AAGA
*
262686 GAAGAAAGATGAAGAAAAGA
1 GAAGAAAGAAGAAGAAAAGA
262706 ATGAAATGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.63, C:0.02, G:0.32, T:0.02
Consensus pattern (20 bp):
GAAGAAAGAAGAAGAAAAGA
Found at i:270346 original size:15 final size:15
Alignment explanation
Indices: 270305--270339 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
270295 TCTCGAGAGG
*
270305 ATCTTGAGTTTCCTC
1 ATCTTGCGTTTCCTC
270320 ATCTTGCGTTTCCTC
1 ATCTTGCGTTTCCTC
270335 ATCTT
1 ATCTT
270340 TTGTTTCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.11, C:0.29, G:0.11, T:0.49
Consensus pattern (15 bp):
ATCTTGCGTTTCCTC
Done.