Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002923.1 Hibiscus syriacus cultivar Beakdansim tig00006041_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: 190927
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:182167 original size:19 final size:18
Alignment explanation
Indices: 182145--182225 Score: 90
Period size: 19 Copynumber: 4.3 Consensus size: 18
182135 AAATCGCAAC
*
182145 GCGAATTTAGTTTCGCGTT
1 GCGATTTTA-TTTCGCGTT
182164 GCGATTTTATTTTCGCGTT
1 GCGATTTTA-TTTCGCGTT
*
182183 GCGATTTTCATTTCTCGTT
1 GCGATTTT-ATTTCGCGTT
* *
182202 GCGATTTTCATTTAGCATT
1 GCGATTTT-ATTTCGCGTT
182221 GCGAT
1 GCGAT
182226 AGTCATTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
19 54 0.98
20 1 0.02
ACGTcount: A:0.15, C:0.17, G:0.21, T:0.47
Consensus pattern (18 bp):
GCGATTTTATTTCGCGTT
Found at i:182232 original size:38 final size:38
Alignment explanation
Indices: 182155--182233 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 38
182145 GCGAATTTAG
* * **
182155 TTTCGCGTTGCGATTTTATTTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTATTTTAGCATTGCGATAGTCA
*
182193 TTTCTCGTTGCGATTTTCA-TTTAGCATTGCGATAGTCA
1 TTTCGCGTTGCGATTTT-ATTTTAGCATTGCGATAGTCA
182231 TTT
1 TTT
182234 TTGCCTTCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
38 34 0.97
39 1 0.03
ACGTcount: A:0.14, C:0.18, G:0.19, T:0.49
Consensus pattern (38 bp):
TTTCGCGTTGCGATTTTATTTTAGCATTGCGATAGTCA
Found at i:182351 original size:14 final size:14
Alignment explanation
Indices: 182332--182368 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
182322 CATCAATTAA
182332 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
182346 ACAAATCATCTTTT
1 ACAAATCAACTTTT
182360 ACAAATCAA
1 ACAAATCAA
182369 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:184263 original size:19 final size:19
Alignment explanation
Indices: 184215--184332 Score: 76
Period size: 19 Copynumber: 6.6 Consensus size: 19
184205 TCTGGAACTT
*
184215 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG-AAAA-G
**
184236 ACTATCGCAACGCGAAAAG
1 AAAATCGCAACGCGAAAAG
184255 AAAATCGCAA--CG---AG
1 AAAATCGCAACGCGAAAAG
* *
184269 AGAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAAAG
184288 AAAATCGCAA--CG---AG
1 AAAATCGCAACGCGAAAAG
* * *
184302 AGAATCGCAATGCGAAATG
1 AAAATCGCAACGCGAAAAG
184321 AAAATCGCAACG
1 AAAATCGCAACG
184333 TGATTATAGT
Statistics
Matches: 74, Mismatches: 13, Indels: 22
0.68 0.12 0.20
Matches are distributed among these distances:
14 21 0.28
16 4 0.05
17 4 0.05
19 30 0.41
20 4 0.05
21 11 0.15
ACGTcount: A:0.47, C:0.20, G:0.22, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAAAG
Found at i:184276 original size:14 final size:14
Alignment explanation
Indices: 184257--184311 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
184247 GCGAAAAGAA
184257 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
184271 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
184290 AATCGCAACGAGAG
1 AATCGCAACGAGAG
184304 AATCGCAA
1 AATCGCAA
184312 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.22, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:184281 original size:33 final size:33
Alignment explanation
Indices: 184239--184332 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
184229 AAAAATGACT
*
184239 ATCGCAACGCGAAAAGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
184272 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
184305 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAACGCGAAATGAAAATCGCAACG
184333 TGATTATAGT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:184386 original size:14 final size:14
Alignment explanation
Indices: 184362--184407 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
184352 CGATTTTTGG
*
184362 TTTCGCGTTGCGAT
1 TTTCTCGTTGCGAT
*
184376 TTTGTCGTTGCGAT
1 TTTCTCGTTGCGAT
*
184390 TCTCTCGTTGCGAT
1 TTTCTCGTTGCGAT
184404 TTTC
1 TTTC
184408 ATTTCGCGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.07, C:0.22, G:0.24, T:0.48
Consensus pattern (14 bp):
TTTCTCGTTGCGAT
Found at i:184419 original size:19 final size:20
Alignment explanation
Indices: 184395--184462 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
184385 GCGATTCTCT
184395 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTTCATTTTCG
** *
184414 CGTTGCGATAGTCATTTTTCA
1 CGTTGCGATTTTCA-TTTTCG
* *
184435 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCATTTTCG
*
184455 TGTTGCGA
1 CGTTGCGA
184463 AAGTAAACTA
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
19 12 0.32
20 11 0.29
21 15 0.39
ACGTcount: A:0.15, C:0.18, G:0.24, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCG
Found at i:184660 original size:95 final size:91
Alignment explanation
Indices: 184513--184787 Score: 370
Period size: 95 Copynumber: 3.1 Consensus size: 91
184503 ATGGATTGCA
* *
184513 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGTT
1 TTACTTCAACCAAAAGA-AAAACAAAGA-AAATACTAACTTCACAGTGTTAAAGAATACACAGTT
*
184578 TAGCAGAATTGGCAGCAACCGAACAAAT
64 TAGCAGAATTGGCAGCAACCGAATAAAT
184606 TTACTTTCAACCAAAAAGATAAAACAAAGATAAATACTAACTTCACAGTGTTAAAGAATACACAG
1 TTAC-TTCAACC-AAAAGA-AAAACAAAGA-AAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
184671 TTTAGCAGAATCGACAGCAACCGAATAAAT
62 TTTAGCAGAATTGGCAGCAACCGAATAAAT
*
184701 TTACTTCAACCAAAAG----AC-----AAATACTAACTTCACAGTGTTAAAGAATAAACAGTTTA
1 TTACTTCAACCAAAAGAAAAACAAAGAAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTA
*
184757 GCAGTATTGGCAGCAACCGAATAAAT
66 GCAGAATTGGCAGCAACCGAATAAAT
184783 TTACT
1 TTACT
184788 AAGCAATCTA
Statistics
Matches: 169, Mismatches: 11, Indels: 15
0.87 0.06 0.08
Matches are distributed among these distances:
82 65 0.38
88 2 0.01
93 9 0.05
94 14 0.08
95 79 0.47
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.23
Consensus pattern (91 bp):
TTACTTCAACCAAAAGAAAAACAAAGAAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTA
GCAGAATTGGCAGCAACCGAATAAAT
Found at i:184771 original size:82 final size:82
Alignment explanation
Indices: 184631--184787 Score: 269
Period size: 82 Copynumber: 1.9 Consensus size: 82
184621 AAGATAAAAC
* *
184631 AAAGATAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATCGACAGCAACCGAA
1 AAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGTTTAGCAGAATCGACAGCAACCGAA
184696 TAAATTTACTTCAACCA
66 TAAATTTACTTCAACCA
* * *
184713 AAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGTTTAGCAGTATTGGCAGCAACCGAA
1 AAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGTTTAGCAGAATCGACAGCAACCGAA
184778 TAAATTTACT
66 TAAATTTACT
184788 AAGCAATCTA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 70 1.00
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.24
Consensus pattern (82 bp):
AAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGTTTAGCAGAATCGACAGCAACCGAA
TAAATTTACTTCAACCA
Found at i:186557 original size:14 final size:14
Alignment explanation
Indices: 186540--186596 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
186530 TTTGGTTTTG
186540 CGTTGCGATTATCT
1 CGTTGCGATTATCT
*
186554 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TT-A--TCT
*
186573 CGTTGCGATTCTCT
1 CGTTGCGATTATCT
186587 CGTTGCGATT
1 CGTTGCGATT
186597 TTCATTTATC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 2 0.06
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTATCT
Found at i:186576 original size:33 final size:33
Alignment explanation
Indices: 186524--186603 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
186514 AAAATCGCAA
** *
186524 TGCGATTTTGGTTTTGCGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
*
186557 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
186590 TGCGATTTTCATTT
1 TGCGATTTTCATTT
186604 ATCTCGTTGC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.10, C:0.19, G:0.23, T:0.49
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
Found at i:186610 original size:21 final size:20
Alignment explanation
Indices: 186588--186659 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
186578 CGATTCTCTC
186588 GTTGCGATTTTCATTTATC-T
1 GTTGCGATTTTCATTT-TCAT
** *
186608 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCAT
*
186629 GTTGCGATTTTCACTTTCAT
1 GTTGCGATTTTCATTTTCAT
186649 GTTGCGATTTT
1 GTTGCGATTTT
186660 ACGTTTAGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
20 29 0.66
21 15 0.34
ACGTcount: A:0.14, C:0.17, G:0.19, T:0.50
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:187384 original size:20 final size:20
Alignment explanation
Indices: 187356--187441 Score: 118
Period size: 20 Copynumber: 4.2 Consensus size: 20
187346 AAATTTGCTT
187356 TGCGATTACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAA
* *
187376 CGTGATTACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAA
* *
187396 TGCGAATTAGGAAAATCGCAA
1 TGCG-ATTACGTAAATCGCAA
*
187417 TGCGAATACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAA
187437 TGCGA
1 TGCGA
187442 ATCTGACTAT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
20 38 0.68
21 18 0.32
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (20 bp):
TGCGATTACGTAAATCGCAA
Found at i:188019 original size:20 final size:20
Alignment explanation
Indices: 187994--188083 Score: 77
Period size: 20 Copynumber: 4.8 Consensus size: 20
187984 TTCTAAACTT
*
187994 AAAATCGCAACATGAAAATG
1 AAAATCGCAACACGAAAATG
188014 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
**
188034 ACTATCGC-A-ACG---A-G
1 AAAATCGCAACACGAAAATG
* *
188048 AGAATCGCAACGC-AAAATG
1 AAAATCGCAACACGAAAATG
*
188067 AAAATCGCAACGCGAAA
1 AAAATCGCAACACGAAA
188084 CCAAAATCGC
Statistics
Matches: 56, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
14 7 0.12
15 2 0.04
16 1 0.02
18 4 0.07
19 14 0.25
20 28 0.50
ACGTcount: A:0.50, C:0.21, G:0.18, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:188072 original size:19 final size:19
Alignment explanation
Indices: 187994--188094 Score: 70
Period size: 20 Copynumber: 5.5 Consensus size: 19
187984 TTCTAAACTT
187994 AAAATCGCAACATG-AAAATG
1 AAAATCGCAAC--GCAAAATG
*
188014 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGC-AAAATG
**
188034 ACTATCGCAACG----A-G
1 AAAATCGCAACGCAAAATG
*
188048 AGAATCGCAACGCAAAATG
1 AAAATCGCAACGCAAAATG
* **
188067 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCAAAATG
188086 AAAATCGCA
1 AAAATCGCA
188095 TTGCGATTTT
Statistics
Matches: 64, Mismatches: 10, Indels: 15
0.72 0.11 0.17
Matches are distributed among these distances:
14 11 0.17
15 1 0.02
18 1 0.02
19 25 0.39
20 26 0.41
ACGTcount: A:0.50, C:0.23, G:0.17, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCAAAATG
Found at i:188131 original size:14 final size:14
Alignment explanation
Indices: 188112--188148 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
188102 TTTCATTTCG
188112 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
188126 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
188140 CGTTGCGAT
1 CGTTGCGAT
188149 AGTCATTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.08, C:0.27, G:0.24, T:0.41
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:188174 original size:20 final size:21
Alignment explanation
Indices: 188134--188197 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 21
188124 CTCGTTGCGA
* **
188134 TTCTCTCGTTGCGATAGTCAT
1 TTCTCGCGTTGCGATTTTCAT
188155 TTC-CGCGTTGCGATTTTCA-
1 TTCTCGCGTTGCGATTTTCAT
* *
188174 TTCTCTCGATGCGATTTTCAT
1 TTCTCGCGTTGCGATTTTCAT
188195 TTC
1 TTC
188198 AACCAAAAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 3 0.08
20 27 0.75
21 6 0.17
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.45
Consensus pattern (21 bp):
TTCTCGCGTTGCGATTTTCAT
Found at i:189957 original size:12 final size:13
Alignment explanation
Indices: 189934--189962 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
189924 CATTGTGAAG
189934 TTTGTATTTGTCT
1 TTTGTATTTGTCT
189947 TTTGT-TTTGTCT
1 TTTGTATTTGTCT
189959 TTTG
1 TTTG
189963 GTTGAAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.03, C:0.07, G:0.17, T:0.72
Consensus pattern (13 bp):
TTTGTATTTGTCT
Found at i:190062 original size:91 final size:91
Alignment explanation
Indices: 189877--190155 Score: 431
Period size: 92 Copynumber: 3.1 Consensus size: 91
189867 TTAGATGCTT
* * * *
189877 AGTAAATTTATCGGTTGCTGCC-A-TATGCTAAACTGTTTATTCTTTAACATTGTGAAGTTTGTA
1 AGTAAATTTTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACA-TGTGAAGTTAGTA
189940 TTTGTCTTTTGTTTTGTCTTTTGGTTGA
65 TTTGTC-TTTGTTTTGTCTTTTGGTTGA
189968 AGTAAATTTTTCGGTTGCTGCCAATTCTGCTAAACTGTGTA-TCTTTAACACTGTGAAGTTAGTA
1 AGTAAATTTTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACA-TGTGAAGTTAGTA
190032 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
65 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
* *
190059 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATATATGAAGTTAGTA
1 AGTAAATTT-TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACATGTGAAGTTAGTA
190124 TTTGTCTTTGTTTTGTCTTTTGGTTGA
65 TTTGTCTTTGTTTTGTCTTTTGGTTGA
190151 AGTAA
1 AGTAA
190156 TATACCATTC
Statistics
Matches: 175, Mismatches: 7, Indels: 11
0.91 0.04 0.06
Matches are distributed among these distances:
90 15 0.09
91 35 0.20
92 88 0.50
93 37 0.21
ACGTcount: A:0.21, C:0.11, G:0.19, T:0.48
Consensus pattern (91 bp):
AGTAAATTTTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACATGTGAAGTTAGTAT
TTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:190369 original size:19 final size:19
Alignment explanation
Indices: 190295--190375 Score: 70
Period size: 19 Copynumber: 4.7 Consensus size: 19
190285 CGAAACTATA
190295 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
190314 TCACATTGCGA--TT-ATT
1 TCGCGTTGCGATTTTCATT
*
190330 TTGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
190344 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
190363 TCGCGTTGCGATT
1 TCGCGTTGCGATT
190376 CTCTCGTTCG
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
14 9 0.19
16 16 0.33
17 2 0.04
19 21 0.44
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Done.