Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003215.1 Hibiscus syriacus cultivar Beakdansim tig00006769_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: 45928
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2126 original size:37 final size:37
Alignment explanation
Indices: 2070--2186 Score: 161
Period size: 35 Copynumber: 3.2 Consensus size: 37
2060 CCCATTATCA
* * * *
2070 TTTTC-AACAAACATCTACCAAAATTTGAAAAACTAT
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAAACCAT
2106 TTTTCAAAGAAACATTTACCAAACTTTG-AAAACCA-
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAAACCAT
2141 TTTTCAAAGAAACATTTACCAAACTTT-AAAAACCATT
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAAACCA-T
2178 TTTTCAAAG
1 TTTTCAAAG
2187 TTGGTTACCA
Statistics
Matches: 73, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
35 34 0.47
36 11 0.15
37 28 0.38
ACGTcount: A:0.45, C:0.19, G:0.04, T:0.32
Consensus pattern (37 bp):
TTTTCAAAGAAACATTTACCAAACTTTGAAAAACCAT
Found at i:2142 original size:21 final size:21
Alignment explanation
Indices: 2118--2178 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2108 TTCAAAGAAA
2118 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
2139 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
*
2153 CATTTACCAAACTTTAAAAAC
1 CATTTACCAAACTTTGAAAAC
2174 CATTT
1 CATTT
2179 TTTCAAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
14 5 0.17
15 7 0.23
16 1 0.03
20 7 0.23
21 10 0.33
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:6700 original size:36 final size:36
Alignment explanation
Indices: 6629--6783 Score: 226
Period size: 35 Copynumber: 4.3 Consensus size: 36
6619 ATCCCATTAT
* * *
6629 CATTTTTC-AACAAACATCTACCAAAATTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
6665 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
*
6701 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAT
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
6736 C-TTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
6771 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
6784 TTGGTTACCA
Statistics
Matches: 108, Mismatches: 7, Indels: 7
0.89 0.06 0.06
Matches are distributed among these distances:
35 66 0.61
36 13 0.12
37 29 0.27
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:6792 original size:70 final size:70
Alignment explanation
Indices: 6647--6810 Score: 208
Period size: 70 Copynumber: 2.3 Consensus size: 70
6637 AACAAACATC
*
6647 TACCAAAATTTGAAAAACTATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCATTTTCAAAG
1 TACCAAACTTTG-AAAACTATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCATTTTCAAAG
*
6712 AAACATT
65 -AACAGT
*
6719 TACCAAACTTTGAAAA-TCTTTTTCAAAGAAACATTTACCAAACTTTGAAAACCATTTTTTCAAA
1 TACCAAACTTTGAAAACTATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA--TTTTCAAA
***
6783 G-TTGGT
64 GAACAGT
*
6789 TACCAAAC-TTGAAAACCATTTT
1 TACCAAACTTTGAAAACTATTTT
6811 AACAACCATC
Statistics
Matches: 81, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
69 7 0.09
70 50 0.62
71 4 0.05
72 20 0.25
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.33
Consensus pattern (70 bp):
TACCAAACTTTGAAAACTATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCATTTTCAAAGA
ACAGT
Found at i:13947 original size:16 final size:16
Alignment explanation
Indices: 13926--13958 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
13916 TAGCCTTATG
13926 CTATTGGAATAGTGAC
1 CTATTGGAATAGTGAC
13942 CTATTGGAATAGTGAC
1 CTATTGGAATAGTGAC
13958 C
1 C
13959 CTTATATAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (16 bp):
CTATTGGAATAGTGAC
Found at i:14898 original size:27 final size:27
Alignment explanation
Indices: 14838--14899 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
14828 TTATTTATAT
* *
14838 TATTATAATTATTATAATAATAATAAT
1 TATTATTATTATTATAATAATAATAAA
* * *
14865 TATTATTATTATTTTATTATTAATAAA
1 TATTATTATTATTATAATAATAATAAA
14892 TATTATTA
1 TATTATTA
14900 CAGGCCCAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TATTATTATTATTATAATAATAATAAA
Found at i:14899 original size:3 final size:3
Alignment explanation
Indices: 14826--14886 Score: 54
Period size: 3 Copynumber: 20.7 Consensus size: 3
14816 TTCATTTAAA
* * * * *
14826 TAT TAT T-T ATAT TAT TAT AAT TAT TAT AAT AAT AAT AAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
14871 TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TA
14887 ATAAATATTA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
2 3 0.06
3 47 0.92
4 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:17117 original size:26 final size:27
Alignment explanation
Indices: 17065--17122 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
17055 TAATTCTTTC
*
17065 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATAC-TATTA
* *
17093 TTTTCATAATATTTATATGTA-TATTA
1 TTTTCAAAATATTTATATATACTATTA
17119 TTTT
1 TTTT
17123 ATTAATGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 9 0.33
28 18 0.67
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATACTATTA
Found at i:27815 original size:11 final size:10
Alignment explanation
Indices: 27798--27825 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
27788 TATTATGCTT
27798 GAAAAAAAAA
1 GAAAAAAAAA
27808 GAAAAAAAAA
1 GAAAAAAAAA
27818 GAAAAAAA
1 GAAAAAAA
27826 GAGAGAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:27824 original size:18 final size:18
Alignment explanation
Indices: 27801--27841 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
27791 TATGCTTGAA
27801 AAAAAAAGAAAAAAAAAG
1 AAAAAAAGAAAAAAAAAG
* * *
27819 AAAAAAAGAGAGAGAAAG
1 AAAAAAAGAAAAAAAAAG
27837 AAAAA
1 AAAAA
27842 GAGGGGGTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAAAAGAAAAAAAAAG
Found at i:28721 original size:115 final size:114
Alignment explanation
Indices: 28519--28858 Score: 520
Period size: 115 Copynumber: 3.0 Consensus size: 114
28509 GTGCCACGTT
*
28519 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTAATCTGATCTG
1 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTG
*
28584 ATTTGGTATGAACCCTAAAATCAATCATTGAATTTTAAAAGATGAATTTG
66 ATTTGGTATGAACCCCAAAATCAATCATTGAA-TTTAAAAGATGAATTTG
*
28634 CTCATAGTAGAAATAAGAAGACCCAATAACATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTG
* *
28699 ATTTGGTATGAACCCCAAAATCAATCATTTGCATTTGAAAGATGAATTTG
66 ATTTGGTATGAACCCCAAAATCAATCA-TTGAATTTAAAAGATGAATTTG
* *
28749 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGATATCTGATCTG
1 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTG
* * * * * * *
28814 GTTCGGTAGGAATCACAGAACCAATCATTGGAA-TTAAAAGATGAA
66 ATTTGGTATGAACCCCAAAATCAATCATT-GAATTTAAAAGATGAA
28859 CTGCATGATC
Statistics
Matches: 206, Mismatches: 17, Indels: 5
0.90 0.07 0.02
Matches are distributed among these distances:
114 13 0.06
115 189 0.92
116 4 0.02
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (114 bp):
CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTG
ATTTGGTATGAACCCCAAAATCAATCATTGAATTTAAAAGATGAATTTG
Found at i:29780 original size:116 final size:112
Alignment explanation
Indices: 29563--30120 Score: 650
Period size: 116 Copynumber: 5.0 Consensus size: 112
29553 GCAAAGATTT
* ** * *
29563 AAATCCATCATTTAATGGATCAACATTTTTAGTTAGAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCATTTGATGGATCAACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
29628 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
66 AA-GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * *
29676 GAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTG
1 AAATCCATCATTTGATGGATCAACATTTCCAGGTAGAGTTCATAATGAGAAGAA--C-TCATCTG
29741 AAGAAGAAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
63 AAGAAG-AAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * * *
29792 AAATCCATCACTTGATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTAAA
1 AAATCCATCATTTGATGGATCAACATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAA
* * * *
29856 GAAGGAAGAAGAAGTTTATAATGAGAAGAATTTGTTCAACCTTTT-TTT
65 GAA-GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * * **
29904 GAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCAT-CT
1 AAATCCATCATTTGATGGATCAACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATC-TGAA
29968 GAAG-A-AA-AAATTCATAATGAGAAGAATTTGTTCAAACCTTTTGCTC
65 GAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTC-AACCTTTTGCTC
* * * *
30014 AAATCCATCACTTGATGGATTAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCCATCATTTGATGGATCAACATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAA
* * **
30078 GAAGAAGAAG---TTCACAGTGAGAAGAGCTTGTTCAACCTTTTGC
65 GAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
30121 ATAATTCTAT
Statistics
Matches: 379, Mismatches: 51, Indels: 34
0.82 0.11 0.07
Matches are distributed among these distances:
108 24 0.06
109 21 0.06
110 75 0.20
111 4 0.01
112 56 0.15
113 96 0.25
114 2 0.01
115 2 0.01
116 98 0.26
117 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.30
Consensus pattern (112 bp):
AAATCCATCATTTGATGGATCAACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:30217 original size:17 final size:17
Alignment explanation
Indices: 30169--30219 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
30159 TTTCCCGAGA
30169 AAGTTCATAATGAGAAG
1 AAGTTCATAATGAGAAG
* *
30186 AA-CTCAT-CTGAAGAAG
1 AAGTTCATAATG-AGAAG
30202 AAGTTCATAATGAGAAG
1 AAGTTCATAATGAGAAG
30219 A
1 A
30220 GCTTATTCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
15 2 0.07
16 11 0.41
17 12 0.44
18 2 0.07
ACGTcount: A:0.47, C:0.10, G:0.22, T:0.22
Consensus pattern (17 bp):
AAGTTCATAATGAGAAG
Found at i:30249 original size:117 final size:117
Alignment explanation
Indices: 30039--30315 Score: 362
Period size: 117 Copynumber: 2.4 Consensus size: 117
30029 TGGATTAACT
* *
30039 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAGTGAGAAGAG
1 TTTCCCGAGAAAGTTCATAATGAGAAGAACTCATCT---GAAGAAGAAGTTCACAATGAGAAGAG
* * * * * *
30104 CTTGTTCAACCTTTTGCATAATTCTATCACAGAAGGAGATAGATTAGCATCAACC
63 CTTATTCAACCTTTTGAATAACTCTATCACAGAAGGAAATAGATCAACATCAACC
*
30159 TTTCCCGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGTTCATAATGAGAAGAGCTT
1 TTTCCCGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGTTCACAATGAGAAGAGCTT
* * * *
30224 ATTCAACCTTTTGAATGACTCTATCACATAAGGAAATAGGTCAACATCATCC
66 ATTCAACCTTTTGAATAACTCTATCACAGAAGGAAATAGATCAACATCAACC
* *
30276 --TCAGCGA-AAAGTTCATAATGAGAAGAACTCATTTGAAGAA
1 TTTC-CCGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA
30316 ATAGAAGAAT
Statistics
Matches: 141, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
115 34 0.24
116 3 0.02
117 69 0.49
120 35 0.25
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (117 bp):
TTTCCCGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGTTCACAATGAGAAGAGCTT
ATTCAACCTTTTGAATAACTCTATCACAGAAGGAAATAGATCAACATCAACC
Found at i:30513 original size:3 final size:3
Alignment explanation
Indices: 30461--30500 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
30451 TTCATTTAAA
30461 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT T-T TAT TA
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
30501 ATAAATATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 3 0.09
3 30 0.88
4 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:36711 original size:32 final size:31
Alignment explanation
Indices: 36674--36750 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
36664 TGGAGACATG
* * *
36674 GGGCCTACCTAAGAATACATCTTAGGGTCGTA
1 GGGCCTACCTAAGAAT-CATCTCAGGGCCGCA
** *
36706 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAATCATCTCAGGGCCGCA
*
36737 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
36751 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 22 0.61
32 14 0.39
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (31 bp):
GGGCCTACCTAAGAATCATCTCAGGGCCGCA
Done.