Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005642.1 Hibiscus syriacus cultivar Beakdansim tig00013155_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: 55147
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:7655 original size:2 final size:2
Alignment explanation
Indices: 7648--7679 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
7638 TTTGGTGAGT
7648 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7680 AACAATGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11720 original size:2 final size:2
Alignment explanation
Indices: 11713--11792 Score: 50
Period size: 2 Copynumber: 44.0 Consensus size: 2
11703 CCGCCCCAAT
* * *
11713 TA TA TA TA TA TA TA TA TA TA TA T- TT TA TA T- TT TT TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
11752 TA -A T- TA TA TA TA TA -A TA TT TA TA TT TT TA T- TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11789 TA TA
1 TA TA
11793 AAATATTTTC
Statistics
Matches: 64, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
1 8 0.12
2 56 0.88
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (2 bp):
TA
Found at i:11786 original size:33 final size:31
Alignment explanation
Indices: 11712--11800 Score: 103
Period size: 33 Copynumber: 2.8 Consensus size: 31
11702 CCCGCCCCAA
11712 TTATATATATATATATATATATATTTTATATTTT
1 TTATAT-TATATATATATA-ATA-TTTATATTTT
11746 TTATATTAATTATATATATAATATTTATA-TTT
1 TTATATT-A-TATATATATAATATTTATATTTT
11778 TTATTATTATATATA-A-AATATTT
1 TTA-TATTATATATATATAATATTT
11801 TCGGGTTCGG
Statistics
Matches: 52, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
29 7 0.13
30 1 0.02
31 6 0.12
32 7 0.13
33 11 0.21
34 10 0.19
35 10 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (31 bp):
TTATATTATATATATATAATATTTATATTTT
Found at i:12944 original size:3 final size:3
Alignment explanation
Indices: 12924--12976 Score: 63
Period size: 3 Copynumber: 17.3 Consensus size: 3
12914 GTTCCTGTAA
* *
12924 AAT AAT AAA AAT ATT AAT AAT -AT AAT AAAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT
12969 AAAT AAT A
1 -AAT AAT A
12977 TTTTTAAATC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
2 2 0.05
3 35 0.81
4 6 0.14
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:12963 original size:27 final size:26
Alignment explanation
Indices: 12923--12976 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
12913 GGTTCCTGTA
*
12923 AAATAATAAAAATATTAATAATATAAT
1 AAATAATAAAAATAATAATAA-ATAAT
*
12950 AAATAATAATAATAATAATAAATAAT
1 AAATAATAAAAATAATAATAAATAAT
12976 A
1 A
12977 TTTTTAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 6 0.24
27 19 0.76
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (26 bp):
AAATAATAAAAATAATAATAAATAAT
Found at i:17606 original size:23 final size:22
Alignment explanation
Indices: 17533--17611 Score: 61
Period size: 23 Copynumber: 3.5 Consensus size: 22
17523 CACAACATAG
*
17533 TGCATCGATGCACATTCAAGGA
1 TGCATCGATACACATTCAAGGA
* * * * *
17555 GTACATCGGTGCACCTTCATGG-
1 -TGCATCGATACACATTCAAGGA
*
17577 TGTATCGATACACATTCAAGGGA
1 TGCATCGATACACATTCAA-GGA
*
17600 TGCATCGGTACA
1 TGCATCGATACA
17612 TAGTCTAGTG
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
21 13 0.31
22 2 0.05
23 27 0.64
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (22 bp):
TGCATCGATACACATTCAAGGA
Found at i:19686 original size:15 final size:15
Alignment explanation
Indices: 19666--19694 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
19656 ACATCATCAT
19666 TCACACAAGAATCCC
1 TCACACAAGAATCCC
19681 TCACACAAGAATCC
1 TCACACAAGAATCC
19695 TTCCTCGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.38, G:0.07, T:0.14
Consensus pattern (15 bp):
TCACACAAGAATCCC
Found at i:21314 original size:20 final size:21
Alignment explanation
Indices: 21275--21314 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
21265 GAAGCTTTAA
* *
21275 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTTACTCTTGAT
21296 GATCATC-ATTTACTCTTGA
1 GATCATCAATTTACTCTTGA
21315 AAGTAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (21 bp):
GATCATCAATTTACTCTTGAT
Found at i:21856 original size:6 final size:6
Alignment explanation
Indices: 21845--21876 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
21835 TGACATTTCC
*
21845 TCGTCA TCGTCA TCGTCA TCGTCA TCTTCA TC
1 TCGTCA TCGTCA TCGTCA TCGTCA TCGTCA TC
21877 CAAATCACTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.34, G:0.12, T:0.38
Consensus pattern (6 bp):
TCGTCA
Found at i:25881 original size:22 final size:22
Alignment explanation
Indices: 25832--25894 Score: 81
Period size: 23 Copynumber: 2.8 Consensus size: 22
25822 CAATTCGCTC
*
25832 CAAGGGGGAATCGATTCCCCTT
1 CAAGGGGGAATCGATTCCCCTA
* *
25854 CAAAGGGGGAATTGGTTCCCCTA
1 C-AAGGGGGAATCGATTCCCCTA
*
25877 CAAGGGGGTATCGATTCC
1 CAAGGGGGAATCGATTCC
25895 TCCTGCACTA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 15 0.44
23 19 0.56
ACGTcount: A:0.24, C:0.24, G:0.30, T:0.22
Consensus pattern (22 bp):
CAAGGGGGAATCGATTCCCCTA
Found at i:28787 original size:19 final size:19
Alignment explanation
Indices: 28763--28813 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
28753 GAAAATATTC
28763 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
28782 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
28801 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
28814 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:28805 original size:65 final size:65
Alignment explanation
Indices: 28656--28815 Score: 180
Period size: 65 Copynumber: 2.5 Consensus size: 65
28646 TGTACCAAGT
* ***
28656 GTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTGGTGCATCAATGCATGGCTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGGTGCATCAATGCATGGAGA
* * * * ** *
28720 GTGTATCGATACATCAAATGCGTTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATGGAG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAG-GTGCATCAATGCATGGAG
28784 A
65 A
* *
28785 GTGCATCGGTGCATGGAATGCATTCGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
28816 CAATTAATTC
Statistics
Matches: 77, Mismatches: 17, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
64 33 0.43
65 44 0.57
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGGTGCATCAATGCATGGAGA
Found at i:29883 original size:21 final size:21
Alignment explanation
Indices: 29845--29888 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
29835 CTGGAGGAGG
*
29845 AGGAGGAGCACGAAAAGAACT
1 AGGAGCAGCACGAAAAGAACT
* *
29866 AGGAGCAGCTCGAGAAGAACT
1 AGGAGCAGCACGAAAAGAACT
29887 AG
1 AG
29889 CTCCCGGAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.16, G:0.34, T:0.07
Consensus pattern (21 bp):
AGGAGCAGCACGAAAAGAACT
Found at i:30747 original size:21 final size:21
Alignment explanation
Indices: 30691--30754 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
30681 TCAATAAGCC
* *
30691 ATTAGGA-GCTTGAGGATCAGG
1 ATTAGGATG-TTGAGGAACGGG
* **
30712 ATTAGGTTGAGGAGGAACGGG
1 ATTAGGATGTTGAGGAACGGG
30733 ATTAGGATGTTGAGGAACGGG
1 ATTAGGATGTTGAGGAACGGG
30754 A
1 A
30755 GGACGGTTTT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
21 33 0.97
22 1 0.03
ACGTcount: A:0.30, C:0.06, G:0.42, T:0.22
Consensus pattern (21 bp):
ATTAGGATGTTGAGGAACGGG
Found at i:35360 original size:22 final size:21
Alignment explanation
Indices: 35318--35357 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
35308 GAGTTTGTTT
*
35318 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
35339 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
35358 ACAGTTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:37323 original size:18 final size:17
Alignment explanation
Indices: 37298--37332 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
37288 GCACCAAGTG
37298 TGCATCGATGCTTGAAA
1 TGCATCGATGCTTGAAA
*
37315 TGCATTCGATGTTTGAAA
1 TGCA-TCGATGCTTGAAA
37333 AATAGCCTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (17 bp):
TGCATCGATGCTTGAAA
Found at i:37368 original size:64 final size:64
Alignment explanation
Indices: 37294--37456 Score: 211
Period size: 65 Copynumber: 2.5 Consensus size: 64
37284 TCGGGCACCA
* *
37294 AGTGTGCATCGATGCTTGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAGTGCATCGATGCATGG
** * **
37358 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
* * *
37423 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
37457 CAATTAATTC
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
64 38 0.45
65 46 0.55
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:37428 original size:19 final size:19
Alignment explanation
Indices: 37404--37454 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
37394 GAAAATATTC
37404 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
37423 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
37442 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
37455 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:37496 original size:65 final size:65
Alignment explanation
Indices: 37298--37504 Score: 187
Period size: 65 Copynumber: 3.2 Consensus size: 65
37288 GCACCAAGTG
* * * * ** *
37298 TGCATCGATGCTTGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG-CTT
1 TGCATCGGTGCATCAAATGCATTCGATGTTT-CAAAATATTCAGAGTGCATCGATGCATGGAC-T
37361 G-
64 GA
* *
37362 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGA--G
1 TGCATCGGTGCATCAAATGCATTCGATG-TTTCAAAATATTCAGAGTGCATCGATGCATGGACTG
37425 A
65 A
** *
37426 GTGCATCGGTGCATGGAATGCATTCGATG-TTC-AATTAATTCATCGA-TGCATCGATGCATGGA
1 -TGCATCGGTGCATCAAATGCATTCGATGTTTCAAAAT-ATTCA--GAGTGCATCGATGCATGGA
37488 CTGA
62 CTGA
37492 TGCATCGGTGCAT
1 TGCATCGGTGCAT
37505 ACCTTTGAAT
Statistics
Matches: 122, Mismatches: 11, Indels: 19
0.80 0.07 0.12
Matches are distributed among these distances:
62 3 0.02
63 8 0.07
64 50 0.41
65 59 0.48
66 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (65 bp):
TGCATCGGTGCATCAAATGCATTCGATGTTTCAAAATATTCAGAGTGCATCGATGCATGGACTGA
Found at i:45828 original size:24 final size:24
Alignment explanation
Indices: 45801--45856 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
45791 CTATTATTTC
45801 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
45825 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
45849 GCTTCAAT
1 GCTTCAAT
45857 CGAACTTCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:46145 original size:30 final size:30
Alignment explanation
Indices: 46081--46176 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 30
46071 AGTGAATCAG
** * *
46081 CGGTTCAAACCGGTTTTGCCAGTTTTCATC
1 CGGTTCACCCCGGTTTTCCCGGTTTTCATC
*
46111 CGGTTTACCCCGGTTTTCCCGGTTTTCAGT-
1 CGGTTCACCCCGGTTTTCCCGGTTTTCA-TC
** *
46141 CGGTTCACCCAAGTTTTCCCGGTTTTCTTC
1 CGGTTCACCCCGGTTTTCCCGGTTTTCATC
*
46171 AGGTTC
1 CGGTTC
46177 TTTACTGATT
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
29 1 0.02
30 52 0.96
31 1 0.02
ACGTcount: A:0.11, C:0.29, G:0.21, T:0.39
Consensus pattern (30 bp):
CGGTTCACCCCGGTTTTCCCGGTTTTCATC
Done.