Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000935.1 Hibiscus syriacus cultivar Beakdansim tig00001869_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: 730910
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:727473 original size:16 final size:17
Alignment explanation
Indices: 727447--727480 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
727437 ATAAAAAAAG
727447 AGAAAGAAAAAAAGAAA
1 AGAAAGAAAAAAAGAAA
727464 AGAAAG-AAAAAAGAAA
1 AGAAAGAAAAAAAGAAA
727480 A
1 A
727481 AGAGGGGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AGAAAGAAAAAAAGAAA
Found at i:727481 original size:17 final size:16
Alignment explanation
Indices: 727439--727483 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
727429 AAATAATAAT
*
727439 AAAAAAAGAGAAAGAA
1 AAAAAAAAAGAAAGAA
727455 AAAAAGAAAAGAAAGAA
1 AAAAA-AAAAGAAAGAA
727472 AAAAGAAAAAGA
1 AAAA-AAAAAGA
727484 GGGGTCAAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 5 0.19
17 20 0.77
18 1 0.04
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAGAAAGAA
Found at i:728752 original size:83 final size:83
Alignment explanation
Indices: 728613--729078 Score: 721
Period size: 83 Copynumber: 5.7 Consensus size: 83
728603 ACATTAGCTG
* *
728613 GAAAGATGAATGTGCTCATAGCATCTTCTGAAAGTGTCCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
*
728678 AAACCAATCAATGAATTT
66 AAACCAATCATTGAATTT
728696 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
*
728761 AAACCAATCAATGAATTT
66 AAACCAATCATTGAATTT
728779 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGTA
1 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
*
728843 AAACTAATCATTGAATTT
66 AAACCAATCATTGAATTT
* * *
728861 G-GAGAGGAATGTGCTCATAGCAT-TTCTGGAAGTGTCCTTTGAGTTATCTGATC-GGTTTGGTA
1 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
*
728923 AAACTAATCATTGAATTT
66 AAACCAATCATTGAATTT
* * *
728941 GGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCCGATCTGGTTTGGTA
1 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
729006 AAACCAATCATTGAA-TT
66 AAACCAATCATTGAATTT
* * * *
729023 GAAA-AT-AAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCT
1 GAAAGATGAATGTG-CTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
729079 AATTGGTTTG
Statistics
Matches: 359, Mismatches: 18, Indels: 13
0.92 0.05 0.03
Matches are distributed among these distances:
79 2 0.01
80 58 0.16
81 44 0.12
82 93 0.26
83 162 0.45
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (83 bp):
GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
AAACCAATCATTGAATTT
Found at i:728974 original size:162 final size:166
Alignment explanation
Indices: 728613--729078 Score: 703
Period size: 162 Copynumber: 2.8 Consensus size: 166
728603 ACATTAGCTG
* *
728613 GAAAGATGAATGTGCTCATAGCATCTTCTGAAAGTGTCCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
* * *
728678 AAACCAATCAATGAATTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTT
66 AAACCAATCATTGAATTTGAAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTCCTTTGAGTT
728743 ATCTGATCTGGTTTGGTAAAACCAATCAATGAATTT
131 ATCTGATCTGGTTTGGTAAAACCAATCAATGAATTT
728779 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGTA
1 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
* *
728843 AAACTAATCATTGAATTTG-GAGAGGAATGTGCTCATAGCAT-TTCTGGAAGTGTCCTTTGAGTT
66 AAACCAATCATTGAATTTGAAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTCCTTTGAGTT
* *
728906 ATCTGATC-GGTTTGGTAAAACTAATCATTGAATTT
131 ATCTGATCTGGTTTGGTAAAACCAATCAATGAATTT
* * *
728941 GGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCCGATCTGGTTTGGTA
1 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
* * * * * *
729006 AAACCAATCATTGAA-TTGAAA-A-TAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAA
66 AAACCAATCATTGAATTTGAAAGAGGAATGTG-CTC-ATAGCATCTTCTGGAAGTGTCCTTTGAG
729068 TTATCTGATCT
129 TTATCTGATCT
729079 AATTGGTTTG
Statistics
Matches: 274, Mismatches: 20, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
161 4 0.01
162 86 0.31
163 57 0.21
164 48 0.18
165 23 0.08
166 56 0.20
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (166 bp):
GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
AAACCAATCATTGAATTTGAAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTCCTTTGAGTT
ATCTGATCTGGTTTGGTAAAACCAATCAATGAATTT
Found at i:729954 original size:110 final size:111
Alignment explanation
Indices: 729792--730774 Score: 1260
Period size: 113 Copynumber: 9.0 Consensus size: 111
729782 GCAAAGATTT
* *
729792 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAGA
1 AAATCCATCACTTGATGGATTATCTTTTCCAGA-GAAGTTCATAATGAGAAGAACTCATCTGAGA
*
729857 AGGATGAAGAAGTTCAT-ATGAGAAGAATTTTGTTCAACCTTTTGCTC
65 AGGAAGAAGAAGTTCATAATGAGAAGAA-TTTGTTCAACCTTTTGCTC
* * *
729904 AAATCTATCACTTGATGGA-TATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATTTAAAGA
1 AAATCCATCACTTGATGGATTATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCT-GAGA
729968 AGGAAGAAGAAG-TCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
65 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* *
730014 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCG-AGTTCATAAT--GAAGAACTCATCT---
1 AAATCCATCACTTGATGGATTATCTTTTCCAG--AGAAGTTCATAATGAGAAGAACTCATCTGAG
730073 ------GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
64 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* **
730115 AAATCTATCACTTGATGGATTATCTTTTCCATTTCG-AGTTCATAATGAGAAG-ACTCATCTGAA
1 AAATCCATCACTTGATGGATTATCTTTTCCA--GAGAAGTTCATAATGAGAAGAACTCATCTG-A
*
730178 GAAGGAAGAACAAGTTCATAATGAGAAGAATTTGTTCAAACC-TTTGCTC
63 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC-AACCTTTTGCTC
*
730227 AAATCCATCACTTGATGGATTATCTTTTCCAGTTCG-AGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCCATCACTTGATGGATTATCTTTTCCAG--AGAAGTTCATAATGAGAAGAACTCATCTG-A
*
730291 GAAGGAAGAAGAATTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
63 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
730340 AAATCCATCACTTGATGGATTATCTTTTCCAGTTCG-AGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCCATCACTTGATGGATTATCTTTTCCAG--AGAAGTTCATAATGAGAAGAACTCATCTG-A
730404 GAAGGAAGAAGAAGTTC---ATGAGAAGAATTTGTTCAA-C-TTTGCTC
63 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* *
730448 AAATCCATCACTTGATGGATTAGCTTTTCCAGAAGAAGTTCATAATGAGAAGAACTC-T-TAAAG
1 AAATCCATCACTTGATGGATTATCTTTTCCAG-AGAAGTTCATAATGAGAAGAACTCATCT-GAG
* *
730511 AA-GAAGAAGAAGTTCATAATGAG-AGAATTTGTTCAGCTTTTTGCTC
64 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * *
730557 AAATCCATCACTTGATGGATCAACATTTCTAGAGAAAGTTCATAATGAGAAGAAACTCATCTGAA
1 AAATCCATCACTTGATGGATTATCTTTTCCAGAG-AAGTTCATAATGAGAAG-AACTCATCTG-A
* *
730622 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAGCTTTTTGCTC
63 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * *
730671 AAATCCATCAC-TGATGGGTCAGT-TTTTCCAGAGAAGTTCATAATGAGAAGAACTCATC--AGG
1 AAATCCATCACTTGATGGATTA-TCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAGA
** *
730732 A-GAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTG
65 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
730775 AATGACTCTA
Statistics
Matches: 795, Mismatches: 36, Indels: 85
0.87 0.04 0.09
Matches are distributed among these distances:
100 7 0.01
101 77 0.10
102 8 0.01
103 4 0.01
105 13 0.02
106 5 0.01
107 51 0.06
108 69 0.09
109 53 0.07
110 104 0.13
111 56 0.07
112 138 0.17
113 176 0.22
114 34 0.04
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.31
Consensus pattern (111 bp):
AAATCCATCACTTGATGGATTATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAGAA
GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:730500 original size:17 final size:17
Alignment explanation
Indices: 730478--730534 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
730468 TAGCTTTTCC
730478 AGAAGAAGTTCATAATG
1 AGAAGAAGTTCATAATG
* * * *
730495 AGAAGAACTCTTAAAGAAG
1 AGAAGAAGT-TCATA-ATG
730514 AAGAAGAAGTTCATAATG
1 -AGAAGAAGTTCATAATG
730532 AGA
1 AGA
730535 GAATTTGTTC
Statistics
Matches: 29, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
17 11 0.38
18 5 0.17
19 5 0.17
20 8 0.28
ACGTcount: A:0.51, C:0.07, G:0.23, T:0.19
Consensus pattern (17 bp):
AGAAGAAGTTCATAATG
Found at i:730635 original size:221 final size:219
Alignment explanation
Indices: 729792--730774 Score: 1261
Period size: 221 Copynumber: 4.5 Consensus size: 219
729782 GCAAAGATTT
* *
729792 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAGA
1 AAATCCATCACTTGATGGATTAGCTTTTCCAGA-GAAGTTCATAATGAGAAGAACTC-T-TAAGA
* *
729857 AGGATGAAGAAGTTCAT-ATGAGAAGAATTTTGTTCAACCTTTTGCTCAAATCTATCACTTGATG
63 A-GAAGAAGAAGTTCATAATGAGAAGAA-TTTGTTCAACCTTTTGCTCAAATCCATCACTTGATG
* * *
729921 GA-TATCTTTTCCAG--AGAAGTTCATAATGAGAAGAACTCATTTAAAGAAGGAAGAAGAAG-TC
126 GATTATCTTTTCCAGTTCG-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
729982 ATAATGAGAAGAATTTGTTCAACCTTTTGCTC
190 ATAATGAGAAGAATTTGTTCAA-C-TTTGCTC
* * *
730014 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCG-AGTTCATAAT--GAAGAACTC------A
1 AAATCCATCACTTGATGGATTAGCTTTTCCAG--AGAAGTTCATAATGAGAAGAACTCTTAAGAA
*** *
730070 TCTGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTATCACTTGATGGAT
64 GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGAT
* *
730135 TATCTTTTCCATTTCGAGTTCATAATGAGAAG-ACTCATCTGAAGAAGGAAGAACAAGTTCATAA
129 TATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
730199 TGAGAAGAATTTGTTCAAACCTTTGCTC
194 TGAGAAGAATTTGTTC-AA-CTTTGCTC
* *
730227 AAATCCATCACTTGATGGATTATCTTTTCCAGTTCG-AGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCCATCACTTGATGGATTAGCTTTTCCAG--AGAAGTTCATAATGAGAAGAACTC-T-T-AA
*
730291 GAAGGAAGAAGAATTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGAT
61 GAA-GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGAT
730356 GGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
125 GGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
730421 ---ATGAGAAGAATTTGTTCAACTTTGCTC
190 ATAATGAGAAGAATTTGTTCAACTTTGCTC
730448 AAATCCATCACTTGATGGATTAGCTTTTCCAGAAGAAGTTCATAATGAGAAGAACTCTTAAAGAA
1 AAATCCATCACTTGATGGATTAGCTTTTCCAG-AGAAGTTCATAATGAGAAGAACTCTT-AAGAA
* *
730513 GAAGAAGAAGTTCATAATGAG-AGAATTTGTTCAGCTTTTTGCTCAAATCCATCACTTGATGGAT
64 GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGAT
* * * * ****
730577 CAACATTTCTAGAGAAAGTTCATAATGAGAAGAAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
129 TATCTTTTCCAGTTCGAGTTCATAATGAGAAG-AACTCATCTGAAGAAGGAAGAAGAAGTTCATA
*
730642 ATGAGAAGAATTTGTTCAGCTTTTTGCTC
193 ATGAGAAGAATTTGTTCAAC--TTTGCTC
* * * * * *
730671 AAATCCATCAC-TGATGGGTCAGTTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCAGGAGA
1 AAATCCATCACTTGATGGATTAGCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCTTAAGAAGA
** *
730735 AGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTG
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
730775 AATGACTCTA
Statistics
Matches: 686, Mismatches: 46, Indels: 59
0.87 0.06 0.07
Matches are distributed among these distances:
211 51 0.07
212 44 0.06
213 90 0.13
214 5 0.01
215 9 0.01
217 65 0.09
218 49 0.07
219 6 0.01
220 35 0.05
221 119 0.17
222 58 0.08
223 36 0.05
224 1 0.00
225 91 0.13
226 27 0.04
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.31
Consensus pattern (219 bp):
AAATCCATCACTTGATGGATTAGCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCTTAAGAAGA
AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATTA
TCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
AGAAGAATTTGTTCAACTTTGCTC
Found at i:730757 original size:17 final size:17
Alignment explanation
Indices: 730702--730757 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
730692 GTTTTTCCAG
730702 AGAAGTTCATAATGAGA
1 AGAAGTTCATAATGAGA
*
730719 AGAA-CTCATCAGGA-GAAGA
1 AGAAGTTCAT-A--ATG-AGA
730738 AGAAGTTCATAATGAGA
1 AGAAGTTCATAATGAGA
730755 AGA
1 AGA
730758 GCTTATTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
16 4 0.13
17 12 0.39
18 2 0.06
19 9 0.29
20 4 0.13
ACGTcount: A:0.48, C:0.09, G:0.25, T:0.18
Consensus pattern (17 bp):
AGAAGTTCATAATGAGA
Done.