Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003940.1 Hibiscus syriacus cultivar Beakdansim tig00008513_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: 168851
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:160395 original size:21 final size:21
Alignment explanation
Indices: 160369--160468 Score: 146
Period size: 21 Copynumber: 4.7 Consensus size: 21
160359 CTAGTGCAGG
160369 TGCATGGATGCACTACAGGGA
1 TGCATGGATGCACTACAGGGA
*
160390 TGCATGGATGCACTGCAGAGAGA
1 TGCATGGATGCACTACAG-G-GA
160413 TGCATGGATGCACTACAGGGA
1 TGCATGGATGCACTACAGGGA
* * *
160434 TGCATGGATGTACTGCAGGGG
1 TGCATGGATGCACTACAGGGA
160455 TGCATGGATGCACT
1 TGCATGGATGCACT
160469 TTGACACCCT
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
21 50 0.70
22 2 0.03
23 19 0.27
ACGTcount: A:0.26, C:0.18, G:0.35, T:0.21
Consensus pattern (21 bp):
TGCATGGATGCACTACAGGGA
Found at i:160425 original size:44 final size:42
Alignment explanation
Indices: 160369--160468 Score: 164
Period size: 44 Copynumber: 2.3 Consensus size: 42
160359 CTAGTGCAGG
160369 TGCATGGATGCACTACAGGGATGCATGGATGCACTGCAGAGAGA
1 TGCATGGATGCACTACAGGGATGCATGGATGCACTGCAG-G-GA
* *
160413 TGCATGGATGCACTACAGGGATGCATGGATGTACTGCAGGGG
1 TGCATGGATGCACTACAGGGATGCATGGATGCACTGCAGGGA
160455 TGCATGGATGCACT
1 TGCATGGATGCACT
160469 TTGACACCCT
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
42 15 0.28
43 1 0.02
44 38 0.70
ACGTcount: A:0.26, C:0.18, G:0.35, T:0.21
Consensus pattern (42 bp):
TGCATGGATGCACTACAGGGATGCATGGATGCACTGCAGGGA
Found at i:160582 original size:30 final size:31
Alignment explanation
Indices: 160548--160608 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
160538 AAACTTTGAA
160548 TAAATTCAATT-AA-TCCCAAAAAACATTTTG
1 TAAATTCAATTCAAGT-CCAAAAAACATTTTG
*
160578 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAAACATTTTG
160609 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 11 0.39
31 16 0.57
32 1 0.04
ACGTcount: A:0.44, C:0.18, G:0.05, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAAACATTTTG
Found at i:161919 original size:19 final size:20
Alignment explanation
Indices: 161876--161923 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
161866 TCTAAATCCT
*
161876 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
161896 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
161915 TTTTCAAAA
1 TTTTCAAAA
161924 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:163163 original size:21 final size:21
Alignment explanation
Indices: 163133--163180 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
163123 CATAACATGG
*
163133 TGCATTAGTGCACTATCAAGC
1 TGCATCAGTGCACTATCAAGC
* *
163154 TGCATCAGTGCACTGTCAAGG
1 TGCATCAGTGCACTATCAAGC
163175 TGCATC
1 TGCATC
163181 GATACCCCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (21 bp):
TGCATCAGTGCACTATCAAGC
Found at i:163278 original size:41 final size:41
Alignment explanation
Indices: 163219--163297 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
163209 TAGTTGTTGC
* **
163219 AGCCTTCATGCATGGATGCACATCAGGATGCATCGATGCAT
1 AGCCTTCATGCATCGATGCACAGAAGGATGCATCGATGCAT
*
163260 AGCCTTGATGCATCGATGCACAGAAGGATGCATCGATG
1 AGCCTTCATGCATCGATGCACAGAAGGATGCATCGATG
163298 TACTAATTGC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.23
Consensus pattern (41 bp):
AGCCTTCATGCATCGATGCACAGAAGGATGCATCGATGCAT
Found at i:163291 original size:20 final size:20
Alignment explanation
Indices: 163226--163297 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
163216 TGCAGCCTTC
* *
163226 ATGCATGGATGCACATCAGG
1 ATGCATCGATGCACAGCAGG
* **
163246 ATGCATCGATGCATAGCCTTG
1 ATGCATCGATGCACAG-CAGG
*
163267 ATGCATCGATGCACAGAAGG
1 ATGCATCGATGCACAGCAGG
163287 ATGCATCGATG
1 ATGCATCGATG
163298 TACTAATTGC
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 25 0.60
21 17 0.40
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (20 bp):
ATGCATCGATGCACAGCAGG
Found at i:163368 original size:22 final size:23
Alignment explanation
Indices: 163335--163378 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
163325 ATAAATGCAC
163335 TGCATGGTGCATCGATGCACTAG
1 TGCATGGTGCATCGATGCACTAG
*
163358 TGCA-GGTGCATGGATGCACTA
1 TGCATGGTGCATCGATGCACTA
163379 CAGGGATGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (23 bp):
TGCATGGTGCATCGATGCACTAG
Found at i:163390 original size:21 final size:21
Alignment explanation
Indices: 163364--163461 Score: 144
Period size: 21 Copynumber: 4.7 Consensus size: 21
163354 CTAGTGCAGG
163364 TGCATGGATGCACTACAGGGA
1 TGCATGGATGCACTACAGGGA
* *
163385 TGCATGGATGCACTGCAGAGA
1 TGCATGGATGCACTACAGGGA
*
163406 TGCATGGATGCACTATAGGGA
1 TGCATGGATGCACTACAGGGA
*
163427 TGCATGGATGCACTGCAAGGG-
1 TGCATGGATGCACTAC-AGGGA
163448 TGCATGGATGCACT
1 TGCATGGATGCACT
163462 TTGACACCCT
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
21 65 0.94
22 4 0.06
ACGTcount: A:0.27, C:0.18, G:0.34, T:0.21
Consensus pattern (21 bp):
TGCATGGATGCACTACAGGGA
Found at i:163396 original size:63 final size:63
Alignment explanation
Indices: 163329--163461 Score: 168
Period size: 63 Copynumber: 2.1 Consensus size: 63
163319 GAGTGCATAA
163329 ATGCACTGCATG-G-TGCATCGATGCACTAGT-GCAGG-TGCATGGATGCACTAC-AGGGATGCA
1 ATGCACTGCA-GAGATGCATCGATGCACTA-TAG--GGATGCATGGATGCACTACAAGGG-TGCA
163389 TGG
61 TGG
* *
163392 ATGCACTGCAGAGATGCATGGATGCACTATAGGGATGCATGGATGCACTGCAAGGGTGCATGG
1 ATGCACTGCAGAGATGCATCGATGCACTATAGGGATGCATGGATGCACTACAAGGGTGCATGG
163455 ATGCACT
1 ATGCACT
163462 TTGACACCCT
Statistics
Matches: 63, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
62 3 0.05
63 41 0.65
64 19 0.30
ACGTcount: A:0.26, C:0.20, G:0.33, T:0.22
Consensus pattern (63 bp):
ATGCACTGCAGAGATGCATCGATGCACTATAGGGATGCATGGATGCACTACAAGGGTGCATGG
Found at i:163410 original size:42 final size:42
Alignment explanation
Indices: 163364--163461 Score: 162
Period size: 42 Copynumber: 2.3 Consensus size: 42
163354 CTAGTGCAGG
163364 TGCATGGATGCACTACAGGGATGCATGGATGCACTGC-AGAGA
1 TGCATGGATGCACTACAGGGATGCATGGATGCACTGCAAG-GA
* *
163406 TGCATGGATGCACTATAGGGATGCATGGATGCACTGCAAGGG
1 TGCATGGATGCACTACAGGGATGCATGGATGCACTGCAAGGA
163448 TGCATGGATGCACT
1 TGCATGGATGCACT
163462 TTGACACCCT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
42 51 0.96
43 2 0.04
ACGTcount: A:0.27, C:0.18, G:0.34, T:0.21
Consensus pattern (42 bp):
TGCATGGATGCACTACAGGGATGCATGGATGCACTGCAAGGA
Found at i:163562 original size:29 final size:29
Alignment explanation
Indices: 163541--163598 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
163531 AAACTTTGAA
163541 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
163570 TAAATTCAATTCAAGTCCAAAAATCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
163599 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:0.16, G:0.05, T:0.34
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:163588 original size:30 final size:30
Alignment explanation
Indices: 163541--163600 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
163531 AAACTTTGAA
163541 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAATCATTTTG
163570 TAAATTCAATTCAAGTCCAAAAATCATTTTG
1 TAAATTCAATT-AAGTCCAAAAATCATTTTG
163601 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:0.15, G:0.07, T:0.35
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAATCATTTTG
Found at i:165834 original size:34 final size:32
Alignment explanation
Indices: 165772--165841 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
165762 CCTTACAAAC
* *
165772 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTGCCGGGATAAACTAGAACCTT
*
165804 TCCCTAGCTTTTGCACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTGC-CGGGATAAACTAGAACCTT
165838 TCCC
1 TCCC
165842 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.21, C:0.30, G:0.17, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTGCCGGGATAAACTAGAACCTT
Found at i:166155 original size:21 final size:21
Alignment explanation
Indices: 166125--166172 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
166115 CATAACATGG
166125 TGCATCAGTGCACTATCAAGC
1 TGCATCAGTGCACTATCAAGC
* *
166146 TGCATTAGTGCACTATCAAGG
1 TGCATCAGTGCACTATCAAGC
166167 TGCATC
1 TGCATC
166173 GATACCCCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (21 bp):
TGCATCAGTGCACTATCAAGC
Found at i:166248 original size:20 final size:20
Alignment explanation
Indices: 166219--166289 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
166209 GCAGCCTTCG
* *
166219 TGCATGGATGCACATCAGGA
1 TGCATCGATGCACACCAGGA
**
166239 TGCATCGATGCACAGCCTTGA
1 TGCATCGATGCACA-CCAGGA
**
166260 TGCATCGATGCACAGAAGGA
1 TGCATCGATGCACACCAGGA
166280 TGCATCGATG
1 TGCATCGATG
166290 TACTAATTGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 25 0.60
21 17 0.40
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (20 bp):
TGCATCGATGCACACCAGGA
Found at i:166270 original size:41 final size:41
Alignment explanation
Indices: 166210--166289 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 41
166200 CTAGTTGTTG
* **
166210 CAGCCTTCGTGCATGGATGCACATCAGGATGCATCGATGCA
1 CAGCCTTCGTGCATCGATGCACAGAAGGATGCATCGATGCA
166251 CAGCCTT-GATGCATCGATGCACAGAAGGATGCATCGATG
1 CAGCCTTCG-TGCATCGATGCACAGAAGGATGCATCGATG
166290 TACTAATTGC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
40 1 0.03
41 34 0.97
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.21
Consensus pattern (41 bp):
CAGCCTTCGTGCATCGATGCACAGAAGGATGCATCGATGCA
Found at i:166385 original size:21 final size:21
Alignment explanation
Indices: 166311--166411 Score: 89
Period size: 21 Copynumber: 4.8 Consensus size: 21
166301 TTTGGTGTTT
* * *
166311 GAGTGCATGAATGCACTGCAT
1 GAGTGCATGGATGCACTACAG
* **
166332 G-GTGCATCGATGCACTAGTG
1 GAGTGCATGGATGCACTACAG
* *
166352 CAGGTGTATGGATGCACTACAG
1 GA-GTGCATGGATGCACTACAG
*
166374 G-GATGCATGGATGCACTGCAG
1 GAG-TGCATGGATGCACTACAG
166395 GAGTGCATGGATGCACT
1 GAGTGCATGGATGCACT
166412 TTGACACCCT
Statistics
Matches: 62, Mismatches: 14, Indels: 8
0.74 0.17 0.10
Matches are distributed among these distances:
20 14 0.23
21 32 0.52
22 16 0.26
ACGTcount: A:0.25, C:0.19, G:0.34, T:0.23
Consensus pattern (21 bp):
GAGTGCATGGATGCACTACAG
Found at i:166405 original size:42 final size:40
Alignment explanation
Indices: 166310--166411 Score: 107
Period size: 42 Copynumber: 2.5 Consensus size: 40
166300 ATTTGGTGTT
* * *
166310 TGAGTGCATGAATGCACTGCATGGTGCATCGATGCACTAG
1 TGAGTGCATGGATGCACTACAGGGTGCATCGATGCACTAG
* *
166350 TGCAGGTGTATGGATGCACTACAGGGATGCATGGATGCACTGCAG
1 TG-A-GTGCATGGATGCACTACAGGG-TGCATCGATGCACT--AG
166395 -GAGTGCATGGATGCACT
1 TGAGTGCATGGATGCACT
166412 TTGACACCCT
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
40 2 0.04
41 1 0.02
42 31 0.61
43 14 0.27
44 1 0.02
45 2 0.04
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.24
Consensus pattern (40 bp):
TGAGTGCATGGATGCACTACAGGGTGCATCGATGCACTAG
Found at i:166512 original size:29 final size:29
Alignment explanation
Indices: 166491--166548 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
166481 AAACTTTGAA
166491 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
166520 TAAATTCAATTCAAGTCCAAAAATCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
166549 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:0.16, G:0.05, T:0.34
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:166538 original size:30 final size:30
Alignment explanation
Indices: 166491--166550 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
166481 AAACTTTGAA
166491 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAATCATTTTG
166520 TAAATTCAATTCAAGTCCAAAAATCATTTTG
1 TAAATTCAATT-AAGTCCAAAAATCATTTTG
166551 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:0.15, G:0.07, T:0.35
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAATCATTTTG
Found at i:167025 original size:25 final size:26
Alignment explanation
Indices: 166997--167048 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
166987 ACTAAAATAC
*
166997 TTTAT-GCAATACCAATTGTTGAAAT
1 TTTATAGCAATACCAATTGTTAAAAT
* *
167022 TTTATATCAATACCATTTGTTAAAAT
1 TTTATAGCAATACCAATTGTTAAAAT
167048 T
1 T
167049 AAGTGCATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.44
Consensus pattern (26 bp):
TTTATAGCAATACCAATTGTTAAAAT
Done.