Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007399.1 Hibiscus syriacus cultivar Beakdansim tig00019968_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: 56336
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:10758 original size:22 final size:22
Alignment explanation
Indices: 10716--10758 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
10706 TCCATAAACA
**
10716 TGTTCATTTAGCATTTGTTTAG
1 TGTTCATTTAGCATTCATTTAG
*
10738 TGTTCATTTAGTATTCATTTA
1 TGTTCATTTAGCATTCATTTA
10759 TATGTTTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.09, G:0.14, T:0.56
Consensus pattern (22 bp):
TGTTCATTTAGCATTCATTTAG
Found at i:11336 original size:34 final size:34
Alignment explanation
Indices: 11253--11356 Score: 102
Period size: 34 Copynumber: 3.1 Consensus size: 34
11243 AAGGTGTGAT
* * **
11253 AAACATCATAACTTTTGGAGGCATATTTTGGATG
1 AAACATCATGACTTTTGGAGGAACCTTTTGGATG
* * * *
11287 AAAAAACATGCCTTTTGGAGGAACCTTTTTGATG
1 AAACATCATGACTTTTGGAGGAACCTTTTGGATG
* *
11321 AAACGTCATGACTTTT-GAAGACACCTTTTGGATG
1 AAACATCATGACTTTTGGAGGA-ACCTTTTGGATG
11355 AA
1 AA
11357 GAATTGTGTC
Statistics
Matches: 55, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
33 4 0.07
34 51 0.93
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (34 bp):
AAACATCATGACTTTTGGAGGAACCTTTTGGATG
Found at i:13294 original size:27 final size:29
Alignment explanation
Indices: 13244--13307 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 29
13234 TTCAAATTGC
13244 TATTTTAGAAGTTTTTAAGTAATAATAAATT
1 TATTTTAGAAGTTTTTAAG-AATAAT-AATT
*
13275 T-TTTTAGAA-TTTTTTA-AATAATAATT
1 TATTTTAGAAGTTTTTAAGAATAATAATT
13301 TATTTTA
1 TATTTTA
13308 TATGATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
26 5 0.16
27 11 0.35
29 6 0.19
30 8 0.26
31 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (29 bp):
TATTTTAGAAGTTTTTAAGAATAATAATT
Found at i:27185 original size:12 final size:12
Alignment explanation
Indices: 27170--27220 Score: 59
Period size: 12 Copynumber: 4.1 Consensus size: 12
27160 CCTGAAAAAG
27170 ACAAGTAAAATA
1 ACAAGTAAAATA
27182 ACAAGTAAAACTA
1 ACAAGTAAAA-TA
*
27195 TACAA-AAAAATGA
1 -ACAAGTAAAAT-A
27208 ACAAGTAAAATA
1 ACAAGTAAAATA
27220 A
1 A
27221 AAATGCTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
12 17 0.52
13 12 0.36
14 4 0.12
ACGTcount: A:0.67, C:0.10, G:0.08, T:0.16
Consensus pattern (12 bp):
ACAAGTAAAATA
Found at i:30086 original size:13 final size:13
Alignment explanation
Indices: 30068--30097 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
30058 ACTTGGGAAA
30068 GAGATAAGGACAT
1 GAGATAAGGACAT
*
30081 GAGATAAGGGCAT
1 GAGATAAGGACAT
30094 GAGA
1 GAGA
30098 AAGCAGTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.37, T:0.13
Consensus pattern (13 bp):
GAGATAAGGACAT
Found at i:33915 original size:18 final size:19
Alignment explanation
Indices: 33892--33938 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
33882 TTCATTGAAA
33892 AACCGAAAAA-CCGAACCG
1 AACCGAAAAACCCGAACCG
33910 AACCGAAAAACCCGAACCG
1 AACCGAAAAACCCGAACCG
33929 AACCGAAAAA
1 AACCGAAAAA
33939 ACCGGATTCG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 10 0.36
19 18 0.64
ACGTcount: A:0.53, C:0.32, G:0.15, T:0.00
Consensus pattern (19 bp):
AACCGAAAAACCCGAACCG
Found at i:34810 original size:28 final size:29
Alignment explanation
Indices: 34756--34812 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
34746 ACCAATATTG
34756 ACATAGTATTTTGAAAAACACTCTAATAT
1 ACATAGTATTTTGAAAAACACTCTAATAT
34785 ACATAGTATTTTGAAAAA-ACTCTAATAT
1 ACATAGTATTTTGAAAAACACTCTAATAT
34813 GCTATCTCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 10 0.36
29 18 0.64
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.35
Consensus pattern (29 bp):
ACATAGTATTTTGAAAAACACTCTAATAT
Found at i:35220 original size:43 final size:42
Alignment explanation
Indices: 35170--35397 Score: 221
Period size: 42 Copynumber: 5.4 Consensus size: 42
35160 AAATGCTGCA
*
35170 AAAGGTCGGGATCTATAGCGGCGTTTTTTAAACAAACGCCGC-
1 AAAGGTC-AGATCTATAGCGGCGTTTTTTAAACAAACGCCGCT
* ** *
35212 AAACGGTCGAGATCTGTAGCGGCG-TTTTTGGACAAACGGCGCT
1 AAA-GGTC-AGATCTATAGCGGCGTTTTTTAAACAAACGCCGCT
* * * * *
35255 AAAGTTAAAGATCTATAGCTGCG-TTTTTGAATAAACGCCGCT
1 AAAGGT-CAGATCTATAGCGGCGTTTTTTAAACAAACGCCGCT
* *
35297 AAAGGGCAGATCTATAGCGGCGTTTTTTGTAACAAACGCCGCT
1 AAAGGTCAGATCTATAGCGGCGTTTTTT-AAACAAACGCCGCT
* * * *
35340 AAAGTTCAGATCTATAGCGGTGTTTTTCAAACAAACGCTG-T
1 AAAGGTCAGATCTATAGCGGCGTTTTTTAAACAAACGCCGCT
*
35381 AAAAGGTCAGACCTATA
1 -AAAGGTCAGATCTATA
35398 TCGATATTTT
Statistics
Matches: 154, Mismatches: 26, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
41 15 0.10
42 82 0.53
43 57 0.37
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.26
Consensus pattern (42 bp):
AAAGGTCAGATCTATAGCGGCGTTTTTTAAACAAACGCCGCT
Found at i:35332 original size:85 final size:83
Alignment explanation
Indices: 35179--35377 Score: 249
Period size: 84 Copynumber: 2.3 Consensus size: 83
35169 AAAAGGTCGG
* * *
35179 GATCTATAGCGGCGTTTTTTAAACAAACGCCGCAAACGGTCGAGATCTGTAGCGGCGTTTTTGGA
1 GATCTATAGCGGCG-TTTTTAAACAAACGCCGCAAACGGGCGAGATCTATAGCGGCGTTTTTGAA
*
35244 CAAACGGCGCTAAAGTTAAA
65 CAAACGCCGCTAAAGTT-AA
* * *
35264 GATCTATAGCTGCGTTTTTGAATAAACGCCGCTAAA-GGGC-AGATCTATAGCGGCGTTTTTTGT
1 GATCTATAGCGGCGTTTTTAAACAAACGCCGC-AAACGGGCGAGATCTATAGCGGCG-TTTTTG-
*
35327 AACAAACGCCGCTAAAGTTCA
63 AACAAACGCCGCTAAAGTTAA
*
35348 GATCTATAGCGGTGTTTTTCAAACAAACGC
1 GATCTATAGCGGCGTTTTT-AAACAAACGC
35378 TGTAAAAGGT
Statistics
Matches: 98, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
83 14 0.14
84 43 0.44
85 41 0.42
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (83 bp):
GATCTATAGCGGCGTTTTTAAACAAACGCCGCAAACGGGCGAGATCTATAGCGGCGTTTTTGAAC
AAACGCCGCTAAAGTTAA
Found at i:35386 original size:85 final size:85
Alignment explanation
Indices: 35179--35427 Score: 263
Period size: 85 Copynumber: 2.9 Consensus size: 85
35169 AAAAGGTCGG
* * *
35179 GATCTATAGCGGCGTTTTTTAAACAAACGCCGCAAACGGTCGAGATCTGTAGCGGCG-TTTTTG-
1 GATCTATAGCGGCG-TTTTTAAACAAACGCCGTAAAAGGTC-AGATCTATAGCGGCGTTTTTTGT
* *
35242 GACAAACGGCGCTAAAGTTAAA
64 AACAAACGCCGCTAAAGTTAAA
* * * *
35264 GATCTATAGCTGCGTTTTTGAATAAACGCCGCT-AAAGGGCAGATCTATAGCGGCGTTTTTTGTA
1 GATCTATAGCGGCGTTTTTAAACAAACGCCG-TAAAAGGTCAGATCTATAGCGGCGTTTTTTGTA
*
35328 ACAAACGCCGCTAAAGTT-CA
65 ACAAACGCCGCTAAAGTTAAA
* * * * *** *
35348 GATCTATAGCGGTGTTTTTCAAACAAACGCTGTAAAAGGTCAGACCTATATCGATATTTTTTCTA
1 GATCTATAGCGGCGTTTTT-AAACAAACGCCGTAAAAGGTCAGATCTATAGCGGCGTTTTTTGTA
35413 TACAAACGCCGCTAA
65 -ACAAACGCCGCTAA
35428 TTACCTTTCA
Statistics
Matches: 136, Mismatches: 22, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
83 14 0.10
84 45 0.33
85 63 0.46
86 14 0.10
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (85 bp):
GATCTATAGCGGCGTTTTTAAACAAACGCCGTAAAAGGTCAGATCTATAGCGGCGTTTTTTGTAA
CAAACGCCGCTAAAGTTAAA
Found at i:35408 original size:42 final size:42
Alignment explanation
Indices: 35287--35427 Score: 115
Period size: 42 Copynumber: 3.3 Consensus size: 42
35277 GTTTTTGAAT
* * * **
35287 AAACGCCGCTAAAGGGCAGATCTATAGCGGCGT-TTTTTGTAAC
1 AAACGCCGCTAAAGGTCAGACCTATAGC-G-ATATTTTTCAAAC
* * * *
35330 AAACGCCGCTAAAGTTCAGATCTATAGCGGTGTTTTTCAAAC
1 AAACGCCGCTAAAGGTCAGACCTATAGCGATATTTTTCAAAC
* * *
35372 AAACGCTG-TAAAAGGTCAGACCTATATCGATATTTTTTCTATAC
1 AAACGCCGCT-AAAGGTCAGACCTATAGCGATA-TTTTTC-AAAC
35416 AAACGCCGCTAA
1 AAACGCCGCTAA
35428 TTACCTTTCA
Statistics
Matches: 81, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
41 3 0.04
42 33 0.41
43 32 0.40
44 12 0.15
45 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (42 bp):
AAACGCCGCTAAAGGTCAGACCTATAGCGATATTTTTCAAAC
Found at i:35506 original size:27 final size:27
Alignment explanation
Indices: 35464--35527 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
35454 GATTTTGCAT
*
35464 ATTTAATTTCTACTCTACAACACCTAA
1 ATTTAATATCTACTCTACAACACCTAA
*
35491 ATTTAATATCTGCTCTACAACACCTAA
1 ATTTAATATCTACTCTACAACACCTAA
35518 ATTTAATATC
1 ATTTAATATC
35528 ATTTAGCTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.38
Consensus pattern (27 bp):
ATTTAATATCTACTCTACAACACCTAA
Found at i:35595 original size:21 final size:21
Alignment explanation
Indices: 35571--35673 Score: 188
Period size: 21 Copynumber: 4.9 Consensus size: 21
35561 TAATTAAGAC
*
35571 ACAAACTTGAAATCCATAATA
1 ACAAACTTGAAATCCATAACA
35592 ACAAACTTGAAATCCATAACA
1 ACAAACTTGAAATCCATAACA
*
35613 GCAAACTTGAAATCCATAACA
1 ACAAACTTGAAATCCATAACA
35634 ACAAACTTGAAATCCATAACA
1 ACAAACTTGAAATCCATAACA
35655 ACAAACTTGAAATCCATAA
1 ACAAACTTGAAATCCATAA
35674 TAATAAATCA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 79 1.00
ACGTcount: A:0.51, C:0.22, G:0.06, T:0.20
Consensus pattern (21 bp):
ACAAACTTGAAATCCATAACA
Found at i:47958 original size:9 final size:9
Alignment explanation
Indices: 47944--47993 Score: 59
Period size: 10 Copynumber: 5.6 Consensus size: 9
47934 TCATTTTTTT
47944 ATTTTTTCAA
1 ATTTTTTC-A
47954 ATTTTTTCA
1 ATTTTTTCA
47963 ATTTTTTTC-
1 A-TTTTTTCA
47972 ATTTTTTCA
1 ATTTTTTCA
*
47981 TTTTTTTC-
1 ATTTTTTCA
47989 ATTTT
1 ATTTT
47994 AGTGGGTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
8 11 0.31
9 10 0.28
10 15 0.42
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (9 bp):
ATTTTTTCA
Found at i:47959 original size:18 final size:16
Alignment explanation
Indices: 47933--47993 Score: 59
Period size: 18 Copynumber: 3.5 Consensus size: 16
47923 TATTCATAAC
*
47933 TTCATTTTTTTATTTT
1 TTCATTTTTTAATTTT
47949 TTCAAATTTTTTCAATTTTT
1 TTC--ATTTTTT-AA-TTTT
*
47969 TTCATTTTTTCATTTTT
1 TTCATTTTTT-AATTTT
47986 TTCATTTT
1 TTCATTTT
47994 AGTGGGTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
16 3 0.08
17 12 0.31
18 16 0.41
19 1 0.03
20 7 0.18
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.74
Consensus pattern (16 bp):
TTCATTTTTTAATTTT
Found at i:47976 original size:7 final size:8
Alignment explanation
Indices: 47933--47993 Score: 68
Period size: 8 Copynumber: 7.0 Consensus size: 8
47923 TATTCATAAC
47933 TTCATTTT
1 TTCATTTT
*
47941 TTTATTTT
1 TTCATTTT
47949 TTCAAATTTT
1 TTC--ATTTT
47959 TTCAATTTTT
1 TTC-A-TTTT
47969 TTCATTTT
1 TTCATTTT
47977 TTCATTTTT
1 TTCA-TTTT
47986 TTCATTTT
1 TTCATTTT
47994 AGTGGGTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
8 21 0.45
9 11 0.23
10 15 0.32
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.74
Consensus pattern (8 bp):
TTCATTTT
Done.