Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003157.1 Hibiscus syriacus cultivar Beakdansim tig00006641_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: 217688
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
File 2 of 2
Found at i:181864 original size:19 final size:19
Alignment explanation
Indices: 181837--181877 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
181827 TTTCCTAACT
*
181837 TTTGAGAAAGTTTTGAAAC
1 TTTGAGAAAGTATTGAAAC
*
181856 TTTGTGAAAGTATTGAAAC
1 TTTGAGAAAGTATTGAAAC
181875 TTT
1 TTT
181878 TAAACACACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.34, C:0.05, G:0.20, T:0.41
Consensus pattern (19 bp):
TTTGAGAAAGTATTGAAAC
Found at i:182711 original size:20 final size:20
Alignment explanation
Indices: 182686--182726 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
182676 GTTTATTTGA
182686 TATTTGG-TACTTGAATGTTT
1 TATTTGGTTACTTGAAT-TTT
*
182706 TATTTGGTTATTTGAATTTT
1 TATTTGGTTACTTGAATTTT
182726 T
1 T
182727 GTTATTACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.20, C:0.02, G:0.17, T:0.61
Consensus pattern (20 bp):
TATTTGGTTACTTGAATTTT
Found at i:187059 original size:20 final size:21
Alignment explanation
Indices: 187015--187068 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
187005 AAACTAGTCG
***
187015 TGCATCGATGCACAGCCTTGA
1 TGCATCGATGCACAGCAAGGA
187036 TGCATCGATGCACAG-AAGGA
1 TGCATCGATGCACAGCAAGGA
187056 TGCATCGATGCAC
1 TGCATCGATGCAC
187069 TAATTGCATT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (21 bp):
TGCATCGATGCACAGCAAGGA
Found at i:187136 original size:22 final size:23
Alignment explanation
Indices: 187103--187145 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
187093 ATGGATGCAC
187103 TGCATGGTGCATCGATGCACTAG
1 TGCATGGTGCATCGATGCACTAG
*
187126 TGCA-GGTGCATGGATGCACT
1 TGCATGGTGCATCGATGCACT
187146 GCAGGGATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.26
Consensus pattern (23 bp):
TGCATGGTGCATCGATGCACTAG
Found at i:187158 original size:21 final size:20
Alignment explanation
Indices: 187092--187187 Score: 122
Period size: 21 Copynumber: 4.6 Consensus size: 20
187082 TGTTTGAGTA
*
187092 CATGGATGCACTGCATGGTG
1 CATGGATGCACTGCAGGGTG
*
187112 CATCGATGCACTAGTGCA-GGTG
1 CATGGATGCAC---TGCAGGGTG
187134 CATGGATGCACTGCAGGGATG
1 CATGGATGCACTGCAGGG-TG
187155 CATGGATGCACTGCAGGGGTG
1 CATGGATGCACTGCA-GGGTG
187176 CATGGATGCACT
1 CATGGATGCACT
187188 TTGACACCCT
Statistics
Matches: 68, Mismatches: 2, Indels: 11
0.84 0.02 0.14
Matches are distributed among these distances:
19 4 0.06
20 12 0.18
21 31 0.46
22 17 0.25
23 4 0.06
ACGTcount: A:0.22, C:0.21, G:0.35, T:0.22
Consensus pattern (20 bp):
CATGGATGCACTGCAGGGTG
Found at i:187288 original size:29 final size:29
Alignment explanation
Indices: 187267--187324 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
187257 AAACTTTGAA
187267 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
187296 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
187325 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:187314 original size:30 final size:30
Alignment explanation
Indices: 187267--187326 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
187257 AAACTTTGAA
187267 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
187296 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
187327 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:189047 original size:22 final size:21
Alignment explanation
Indices: 189022--189062 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
189012 TATAAAAAAT
189022 TATTTTTATTAAATATTTTTGA
1 TATTTTTATTAAAT-TTTTTGA
*
189044 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
189063 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGA
Found at i:189182 original size:17 final size:17
Alignment explanation
Indices: 189141--189182 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
189131 GGTAGCATGG
*
189141 CCGGTTCGCTAACCGGT
1 CCGGTTCTCTAACCGGT
*
189158 CCGGTTCTCTAACTGGT
1 CCGGTTCTCTAACCGGT
189175 CCGGTTCT
1 CCGGTTCT
189183 GAAAACCATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.10, C:0.33, G:0.26, T:0.31
Consensus pattern (17 bp):
CCGGTTCTCTAACCGGT
Found at i:192502 original size:20 final size:20
Alignment explanation
Indices: 192477--192515 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
192467 AACCAGACTA
192477 TTGACCTAACTGTTGACTTT
1 TTGACCTAACTGTTGACTTT
*
192497 TTGACCTGACTGTTGACTT
1 TTGACCTAACTGTTGACTT
192516 GACTTTGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.44
Consensus pattern (20 bp):
TTGACCTAACTGTTGACTTT
Found at i:199529 original size:16 final size:16
Alignment explanation
Indices: 199489--199531 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
199479 ATTTCTCTAA
*
199489 TGAACTTTAATAAGTCC
1 TGAA-TTTAATAAGTAC
199506 TG-ATTTAATAAGTAC
1 TGAATTTAATAAGTAC
199521 TGAATTTAATA
1 TGAATTTAATA
199532 TCCTCCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 13 0.54
16 9 0.38
17 2 0.08
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.40
Consensus pattern (16 bp):
TGAATTTAATAAGTAC
Found at i:202864 original size:18 final size:18
Alignment explanation
Indices: 202839--202903 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 18
202829 ATGATAAACA
202839 ATATCATACATAATAGTC
1 ATATCATACATAATAGTC
* * **
202857 AGATCATAGCCATGATAAAC
1 ATATCATA--CATAATAGTC
202877 AATATCATACATAATAGTC
1 -ATATCATACATAATAGTC
202896 ATATCATA
1 ATATCATA
202904 TTCTTTTTCA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
18 15 0.42
19 7 0.19
20 7 0.19
21 7 0.19
ACGTcount: A:0.46, C:0.17, G:0.08, T:0.29
Consensus pattern (18 bp):
ATATCATACATAATAGTC
Found at i:202870 original size:39 final size:39
Alignment explanation
Indices: 202827--202903 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
202817 TTTATCTAAA
202827 CCATGATAAACAATATCATACATAATAGTCAGATCATAG
1 CCATGATAAACAATATCATACATAATAGTCAGATCATAG
*
202866 CCATGATAAACAATATCATACATAATAGTCATATCATA
1 CCATGATAAACAATATCATACATAATAGTCAGATCATA
202904 TTCTTTTTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.47, C:0.18, G:0.08, T:0.27
Consensus pattern (39 bp):
CCATGATAAACAATATCATACATAATAGTCAGATCATAG
Found at i:204872 original size:30 final size:31
Alignment explanation
Indices: 204811--204872 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
204801 TACACATCAT
**
204811 CCCATAACTTTTCAAAATTGTTAAATAGGTC
1 CCCATAACTTTTCAAAATTGACAAATAGGTC
*
204842 CCCAT-ACTTTTTCAAAATT-ACAAATTGGTC
1 CCCATAAC-TTTTCAAAATTGACAAATAGGTC
204872 C
1 C
204873 AAATAGCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.34, C:0.23, G:0.08, T:0.35
Consensus pattern (31 bp):
CCCATAACTTTTCAAAATTGACAAATAGGTC
Found at i:209546 original size:39 final size:40
Alignment explanation
Indices: 209503--209579 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
209493 CTCATTATTT
*
209503 TATCAAAACCATGAT-AAACAATATCATACATAATAGTCA
1 TATCAAAACCATGATAAAAAAATATCATACATAATAGTCA
* *
209542 TATCATAGCCATGATAAAAAAATATCATACATAATAGT
1 TATCAAAACCATGATAAAAAAATATCATACATAATAGT
209580 AACACCATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
39 13 0.38
40 21 0.62
ACGTcount: A:0.51, C:0.16, G:0.06, T:0.27
Consensus pattern (40 bp):
TATCAAAACCATGATAAAAAAATATCATACATAATAGTCA
Found at i:209636 original size:13 final size:13
Alignment explanation
Indices: 209618--209663 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
209608 AATACAAGAC
*
209618 TTTCATATCTCAT
1 TTTCATATTTCAT
* *
209631 TTTCATCTTTCAC
1 TTTCATATTTCAT
209644 TTTCATATTTCAT
1 TTTCATATTTCAT
209657 TTTCATA
1 TTTCATA
209664 ATCCATACTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTCATATTTCAT
Found at i:209704 original size:19 final size:18
Alignment explanation
Indices: 209680--209768 Score: 70
Period size: 19 Copynumber: 4.8 Consensus size: 18
209670 ACTTTCACAT
*
209680 TTCAGAACTTATTCTCATA
1 TTCAGAACTTATT-TCAGA
* *
209699 TTCAGAACTTGTTTTCGGA
1 TTCAGAACTT-ATTTCAGA
* *
209718 CTCATAACTTATTTCAGA
1 TTCAGAACTTATTTCAGA
* *
209736 TTCATAACTTAATTTCATA
1 TTCAGAACTT-ATTTCAGA
* *
209755 TTCATATCTTATTT
1 TTCAGAACTTATTT
209769 TTAAGTTCAT
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
18 19 0.33
19 37 0.64
20 2 0.03
ACGTcount: A:0.29, C:0.18, G:0.07, T:0.46
Consensus pattern (18 bp):
TTCAGAACTTATTTCAGA
Found at i:213610 original size:47 final size:47
Alignment explanation
Indices: 213516--213611 Score: 174
Period size: 47 Copynumber: 2.0 Consensus size: 47
213506 TAGAGAAGTT
**
213516 CAATATAAAAAGACTTGGTTGACTCGTAAGATCTTTAGGAATTAACA
1 CAATATAAAAAGACTTGGTTGACTCGTAAGATCTTTAGGAAGCAACA
213563 CAATATAAAAAGACTTGGTTGACTCGTAAGATCTTTAGGAAGCAACA
1 CAATATAAAAAGACTTGGTTGACTCGTAAGATCTTTAGGAAGCAACA
213610 CA
1 CA
213612 GATAGTGTCT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.27
Consensus pattern (47 bp):
CAATATAAAAAGACTTGGTTGACTCGTAAGATCTTTAGGAAGCAACA
Done.