Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005717.1 Hibiscus syriacus cultivar Beakdansim tig00013368_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: 63766
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1505 original size:104 final size:103
Alignment explanation
Indices: 1326--1532 Score: 360
Period size: 104 Copynumber: 2.0 Consensus size: 103
1316 TGTGGTAGAG
* *
1326 TTGAGTTACTAATGTGTAACCTTGGATTTCTAAGCGTTGGAAGCACCTCAAAATCACCCTAGCAC
1 TTGAGTTACAAATGTGTAACCTTGGATTTCTAAGCATTGGAAGCACCTCAAAATCACCCTAGCAC
1391 AAGCATCTCCTTGTTCTTGCTCTTGGAGATTTCACCCA
66 AAGCATCTCCTTGTTCTTGCTCTTGGAGATTTCACCCA
*
1429 TTGAGTTAGAAATGTGTAACCTTGGATTTCTAAGCTATTGGAAGCACCTCAAAATCACCCTAGCA
1 TTGAGTTACAAATGTGTAACCTTGGATTTCTAAGC-ATTGGAAGCACCTCAAAATCACCCTAGCA
* *
1494 CAAGCTTCTCCTTTTTCTTGCTCTTGGAGATTTCACCCA
65 CAAGCATCTCCTTGTTCTTGCTCTTGGAGATTTCACCCA
1533 CTTCTCTCAC
Statistics
Matches: 98, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
103 33 0.34
104 65 0.66
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.33
Consensus pattern (103 bp):
TTGAGTTACAAATGTGTAACCTTGGATTTCTAAGCATTGGAAGCACCTCAAAATCACCCTAGCAC
AAGCATCTCCTTGTTCTTGCTCTTGGAGATTTCACCCA
Found at i:2300 original size:19 final size:17
Alignment explanation
Indices: 2239--2314 Score: 53
Period size: 19 Copynumber: 4.1 Consensus size: 17
2229 ATTTTTAAAA
* *
2239 AAATTTCAATTAAATTT
1 AAATTTAAATTAATTTT
*
2256 AAATTTTTAAATTAATTAAGT
1 AAA--TTTAAATTAATT--TT
*
2277 CAATTTAAATTCATATTTT
1 AAATTTAAATT-A-ATTTT
*
2296 AAATTTTAATTAATTTT
1 AAATTTAAATTAATTTT
2313 AA
1 AA
2315 TAAAAATAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
17 10 0.22
18 1 0.02
19 28 0.61
20 1 0.02
21 6 0.13
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.50
Consensus pattern (17 bp):
AAATTTAAATTAATTTT
Found at i:2418 original size:5 final size:5
Alignment explanation
Indices: 2410--2435 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2400 TATAATTTAA
2410 TTATT TTATT TTATT TTATT TTATT T
1 TTATT TTATT TTATT TTATT TTATT T
2436 AATCTTATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:2443 original size:15 final size:15
Alignment explanation
Indices: 2410--2443 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2400 TATAATTTAA
* *
2410 TTATTTTATTTTATT
1 TTATTTTATTTAATC
2425 TTATTTTATTTAATC
1 TTATTTTATTTAATC
2440 TTAT
1 TTAT
2444 GGCTAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (15 bp):
TTATTTTATTTAATC
Found at i:7140 original size:20 final size:20
Alignment explanation
Indices: 7081--7141 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
7071 ACCTTAGGCA
* * *
7081 AAGGTAGTACTGATACCATC
1 AAGGTAGTACCGATACTACC
7101 AAGGTAGTACCGATACTACC
1 AAGGTAGTACCGATACTACC
*
7121 AAGGTAGTACCGATAATACC
1 AAGGTAGTACCGATACTACC
7141 A
1 A
7142 TGAAGGATCA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (20 bp):
AAGGTAGTACCGATACTACC
Found at i:7147 original size:23 final size:22
Alignment explanation
Indices: 7093--7147 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 22
7083 GGTAGTACTG
7093 ATACCATCAAGGTAGTACCGATA
1 ATACCAT-AAGGTAGTACCGATA
*
7116 CTACC--AAGGTAGTACCGATA
1 ATACCATAAGGTAGTACCGATA
7136 ATACCATGAAGG
1 ATACCAT-AAGG
7148 ATCAAAACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 19 0.70
23 8 0.30
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (22 bp):
ATACCATAAGGTAGTACCGATA
Found at i:10133 original size:13 final size:14
Alignment explanation
Indices: 10113--10148 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
10103 GGGGGAGCTT
10113 TGATTTTTTTCAAA
1 TGATTTTTTTCAAA
10127 TGATTTTTTTCAAA
1 TGATTTTTTTCAAA
10141 TGATTTTT
1 TGATTTTT
10149 AATGTCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.25, C:0.06, G:0.08, T:0.61
Consensus pattern (14 bp):
TGATTTTTTTCAAA
Found at i:30302 original size:11 final size:10
Alignment explanation
Indices: 30251--30302 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
30241 TTTTGAATTC
*
30251 TTTTCTTTTC
1 TTTTCTTTTT
30261 TTTTCTTCTTT
1 TTTTCTT-TTT
*
30272 TCTTCTTCTTT
1 TTTTCTT-TTT
*
30283 TTGTCTTTTT
1 TTTTCTTTTT
*
30293 CTTTCTTTTT
1 TTTTCTTTTT
30303 GCACTCCAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 18 0.51
11 17 0.49
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:30303 original size:18 final size:18
Alignment explanation
Indices: 30249--30303 Score: 69
Period size: 18 Copynumber: 3.0 Consensus size: 18
30239 CTTTTTGAAT
30249 TCTTTTCTTTTCTTTTCT-
1 TCTTTTCTTTTCTTTT-TG
30267 TCTTTTCTTCTTCTTTTTG
1 TCTTTTCTT-TTCTTTTTG
30286 TCTTTT-TCTTTCTTTTTG
1 TCTTTTCT-TTTCTTTTTG
30304 CACTCCAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
18 20 0.59
19 14 0.41
ACGTcount: A:0.00, C:0.20, G:0.04, T:0.76
Consensus pattern (18 bp):
TCTTTTCTTTTCTTTTTG
Found at i:33437 original size:31 final size:31
Alignment explanation
Indices: 33400--33465 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
33390 AATTCAAACC
* *
33400 TGACCATACTGTGCATTATTTGAATATACCA
1 TGACCATACTGTGCATTATATGAATACACCA
** *
33431 TGACCATGTTGTGCATTATATGAATGCACCA
1 TGACCATACTGTGCATTATATGAATACACCA
33462 TGAC
1 TGAC
33466 TAGGATATAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (31 bp):
TGACCATACTGTGCATTATATGAATACACCA
Found at i:33994 original size:13 final size:13
Alignment explanation
Indices: 33976--34000 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33966 GAAGGCTTAT
33976 TTGTTTGTTATTG
1 TTGTTTGTTATTG
33989 TTGTTTGTTATT
1 TTGTTTGTTATT
34001 AAACTGATCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.20, T:0.72
Consensus pattern (13 bp):
TTGTTTGTTATTG
Found at i:35864 original size:13 final size:13
Alignment explanation
Indices: 35846--35872 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35836 TCGAATATAA
35846 AATCTTAAAATTC
1 AATCTTAAAATTC
35859 AATCTTAAAATTC
1 AATCTTAAAATTC
35872 A
1 A
35873 TTAACACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (13 bp):
AATCTTAAAATTC
Found at i:41938 original size:21 final size:21
Alignment explanation
Indices: 41897--41939 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
41887 TGAAAGAAGC
*
41897 TTTAAGATCATCAATTTCTTT
1 TTTAAGATCATCAATTACTTT
*
41918 TTTATGATCATC-ATATACTTT
1 TTTAAGATCATCAAT-TACTTT
41939 T
1 T
41940 GAAAGTAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.28, C:0.14, G:0.05, T:0.53
Consensus pattern (21 bp):
TTTAAGATCATCAATTACTTT
Found at i:48206 original size:14 final size:14
Alignment explanation
Indices: 48187--48216 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
48177 ACACATAATT
48187 TAAAATAAAAATAA
1 TAAAATAAAAATAA
48201 TAAAATAAAAATAA
1 TAAAATAAAAATAA
48215 TA
1 TA
48217 TTAACTCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAAATAAAAATAA
Found at i:55339 original size:25 final size:25
Alignment explanation
Indices: 55305--55362 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
55295 GTAAATGATC
55305 ATCAAAGAAAAGATGGAAAGTGCTT
1 ATCAAAGAAAAGATGGAAAGTGCTT
55330 ATCAAAGAAAAGATGGAAAGTGCTT
1 ATCAAAGAAAAGATGGAAAGTGCTT
*
55355 GTCAAAGA
1 ATCAAAGA
55363 TAGATCAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.48, C:0.09, G:0.24, T:0.19
Consensus pattern (25 bp):
ATCAAAGAAAAGATGGAAAGTGCTT
Found at i:58992 original size:25 final size:25
Alignment explanation
Indices: 58941--58992 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
58931 TATTATGAAC
* *
58941 ATGGAATATGAAAATGAATATGTGA
1 ATGGAATATGAAAATGAAAATGAGA
*
58966 ATGG-ATATGAAAGTGGAAAATGAGA
1 ATGGAATATGAAAAT-GAAAATGAGA
58991 AT
1 AT
58993 AAAATAAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.48, C:0.00, G:0.27, T:0.25
Consensus pattern (25 bp):
ATGGAATATGAAAATGAAAATGAGA
Found at i:62742 original size:18 final size:18
Alignment explanation
Indices: 62711--62756 Score: 83
Period size: 18 Copynumber: 2.5 Consensus size: 18
62701 CGGCCAAGAG
62711 CATGTATCTTCATTAAAAT
1 CATGTAT-TTCATTAAAAT
62730 CATGTATTTCATTAAAAT
1 CATGTATTTCATTAAAAT
62748 CATGTATTT
1 CATGTATTT
62757 TCAAAGGGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 20 0.74
19 7 0.26
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.46
Consensus pattern (18 bp):
CATGTATTTCATTAAAAT
Done.