Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001357.1 Hibiscus syriacus cultivar Beakdansim tig00002642_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: 89002
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:895 original size:13 final size:14
Alignment explanation
Indices: 877--909 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
867 TTGGGTTTTG
877 GATTTAGA-TTTAT
1 GATTTAGAGTTTAT
890 GATTTA-AGTTTAT
1 GATTTAGAGTTTAT
903 GATTTAG
1 GATTTAG
910 GGGATTGTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.06
13 17 0.94
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.52
Consensus pattern (14 bp):
GATTTAGAGTTTAT
Found at i:7794 original size:22 final size:22
Alignment explanation
Indices: 7766--7814 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
7756 ATTCTGTAAG
7766 GATGATAAATTCTCTTTCCAAA
1 GATGATAAATTCTCTTTCCAAA
* *
7788 GATGATAGATTCTCTTTTCAAA
1 GATGATAAATTCTCTTTCCAAA
7810 GATGA
1 GATGA
7815 AAACTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (22 bp):
GATGATAAATTCTCTTTCCAAA
Found at i:13205 original size:23 final size:22
Alignment explanation
Indices: 13174--13246 Score: 85
Period size: 23 Copynumber: 3.3 Consensus size: 22
13164 CGATGGGTGT
13174 ATCGATGCACATTCAAGGAATGC
1 ATCGATGCACATTCAAGG-ATGC
* * * *
13197 ATCGGTGCACCTTCATGG-TGT
1 ATCGATGCACATTCAAGGATGC
13218 ATCGATGCACATTCAAGGGATGC
1 ATCGATGCACATTCAA-GGATGC
13241 ATCGAT
1 ATCGAT
13247 ACACTCTAGT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
21 15 0.38
22 2 0.05
23 23 0.57
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.26
Consensus pattern (22 bp):
ATCGATGCACATTCAAGGATGC
Found at i:13226 original size:21 final size:21
Alignment explanation
Indices: 13169--13235 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
13159 AAACCCGATG
13169 GGTGTATCGATGCACATTCAA
1 GGTGTATCGATGCACATTCAA
* * * *
13190 GGAATGCATCGGTGCACCTTCAT
1 GG--TGTATCGATGCACATTCAA
13213 GGTGTATCGATGCACATTCAA
1 GGTGTATCGATGCACATTCAA
13234 GG
1 GG
13236 GATGCATCGA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
21 19 0.53
23 17 0.47
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (21 bp):
GGTGTATCGATGCACATTCAA
Found at i:17077 original size:23 final size:21
Alignment explanation
Indices: 17035--17078 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
17025 GAGATTATTT
*
17035 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTCAAATA
*
17056 TCATTTTTTATATTTTACAAATA
1 TCATTTTTCA-ATTTT-CAAATA
17079 ATTTATCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
22 5 0.26
23 5 0.26
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTCAAATA
Found at i:18877 original size:21 final size:21
Alignment explanation
Indices: 18849--18900 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
18839 TTGGGAGTGT
*
18849 GTGTGCATTGGTACACCATCAG
1 GTGTGCATCGGTACACCATC-G
18871 G-GTGCATCGGTACACCATCG
1 GTGTGCATCGGTACACCATCG
18891 GTGTGCATCG
1 GTGTGCATCG
18901 AAACCCTATG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 2 0.07
21 25 0.89
22 1 0.04
ACGTcount: A:0.19, C:0.25, G:0.31, T:0.25
Consensus pattern (21 bp):
GTGTGCATCGGTACACCATCG
Found at i:19893 original size:20 final size:20
Alignment explanation
Indices: 19868--19961 Score: 154
Period size: 20 Copynumber: 4.8 Consensus size: 20
19858 ATTTCTCATG
*
19868 AATTTGTAAAACCTTCGGGT
1 AATTTGTAAAGCCTTCGGGT
19888 AATTTGTAAAGCCTTCGGGT
1 AATTTGTAAAGCCTTCGGGT
19908 AA-TTGTAAAGCCTTCGGGT
1 AATTTGTAAAGCCTTCGGGT
* *
19927 AATTTGTAAAACCTTCGGAT
1 AATTTGTAAAGCCTTCGGGT
19947 AATTTGTAAAGCCTT
1 AATTTGTAAAGCCTT
19962 TGAGTCATCT
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.28
20 50 0.72
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (20 bp):
AATTTGTAAAGCCTTCGGGT
Found at i:19914 original size:39 final size:40
Alignment explanation
Indices: 19868--19961 Score: 154
Period size: 39 Copynumber: 2.4 Consensus size: 40
19858 ATTTCTCATG
* * *
19868 AATTTGTAAAACCTTCGGGTAATTTGTAAAGCCTTCGGGT
1 AATTTGTAAAGCCTTCGGGTAATTTGTAAAACCTTCGGAT
19908 AA-TTGTAAAGCCTTCGGGTAATTTGTAAAACCTTCGGAT
1 AATTTGTAAAGCCTTCGGGTAATTTGTAAAACCTTCGGAT
19947 AATTTGTAAAGCCTT
1 AATTTGTAAAGCCTT
19962 TGAGTCATCT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
39 36 0.72
40 14 0.28
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (40 bp):
AATTTGTAAAGCCTTCGGGTAATTTGTAAAACCTTCGGAT
Found at i:20722 original size:16 final size:17
Alignment explanation
Indices: 20691--20725 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
20681 CATATATAAT
20691 AATAATATTATATTATA
1 AATAATATTATATTATA
*
20708 AATATTATTAT-TTATA
1 AATAATATTATATTATA
20724 AA
1 AA
20726 GCCCGAAGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AATAATATTATATTATA
Found at i:24054 original size:27 final size:27
Alignment explanation
Indices: 24024--24080 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
24014 AGTTTATATT
24024 TCAGACTATTAAAGATCATATCGTCTA
1 TCAGACTATTAAAGATCATATCGTCTA
24051 TCAGACTATTAAAGATCATATCGTCTA
1 TCAGACTATTAAAGATCATATCGTCTA
24078 TCA
1 TCA
24081 ATTGAAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (27 bp):
TCAGACTATTAAAGATCATATCGTCTA
Found at i:31856 original size:29 final size:29
Alignment explanation
Indices: 31823--31916 Score: 82
Period size: 29 Copynumber: 3.1 Consensus size: 29
31813 TCTTAAATTG
31823 ATCCTTAAAATTTTGAATATTCCAATTTC
1 ATCCTTAAAATTTTGAATATTCCAATTTC
* * * * * *
31852 ATCCTCATAACTATGATTCTCATTCTAAATTT-
1 ATCCTTAAAATTTTGA--AT-ATTC-CAATTTC
*
31884 GTCCTTAAAATTTTGAATATTCCAATTTC
1 ATCCTTAAAATTTTGAATATTCCAATTTC
31913 ATCC
1 ATCC
31917 CCAAATCCAT
Statistics
Matches: 46, Mismatches: 14, Indels: 10
0.66 0.20 0.14
Matches are distributed among these distances:
28 5 0.11
29 19 0.41
30 1 0.02
31 1 0.02
32 15 0.33
33 5 0.11
ACGTcount: A:0.32, C:0.20, G:0.04, T:0.44
Consensus pattern (29 bp):
ATCCTTAAAATTTTGAATATTCCAATTTC
Found at i:32212 original size:60 final size:59
Alignment explanation
Indices: 32038--32214 Score: 173
Period size: 60 Copynumber: 3.0 Consensus size: 59
32028 AGTATATACG
**
32038 TATAGTTTGGGATGAAATCAGAATGTTAAAAAATTTTGGGGA-TCAATTTAGAATGAATAT
1 TATAGTTTGGGATGAAATCAGAATGTTAAAAAA-TTTAAGGACT-AATTTAGAATGAATAT
* * * * *
32098 CATAGTTTGGGGATAAAATCA-CATGTTCAAAAGTTTGAA-GACTAATTTAGAATG-ATAAT
1 TATAGTTT-GGGATGAAATCAGAATGTTAAAAAATTT-AAGGACTAATTTAGAATGAAT-AT
* * * *
32157 TATAGTTTAGGGATGAAATTAGAATATTTAAAAATTTAAGGACTAATTTAAAATGAAT
1 TATAGTTT-GGGATGAAATCAGAATGTTAAAAAATTTAAGGACTAATTTAGAATGAAT
32215 GTCATACTTT
Statistics
Matches: 94, Mismatches: 16, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
58 2 0.02
59 37 0.39
60 42 0.45
61 13 0.14
ACGTcount: A:0.42, C:0.05, G:0.19, T:0.34
Consensus pattern (59 bp):
TATAGTTTGGGATGAAATCAGAATGTTAAAAAATTTAAGGACTAATTTAGAATGAATAT
Found at i:33725 original size:21 final size:23
Alignment explanation
Indices: 33700--33745 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
33690 ACTTATTTAT
* *
33700 TTATTTTAATTAT-TTAAT-GTA
1 TTATTTGAATCATATTAATAGTA
33721 TTATTTGAATCATATTAATAGTA
1 TTATTTGAATCATATTAATAGTA
33744 TT
1 TT
33746 CACTGCCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.52
22 5 0.24
23 5 0.24
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.57
Consensus pattern (23 bp):
TTATTTGAATCATATTAATAGTA
Found at i:34276 original size:22 final size:22
Alignment explanation
Indices: 34251--34293 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
34241 ATATAAATTC
34251 TAAATAATTT-TTTCAGATTTTA
1 TAAA-AATTTATTTCAGATTTTA
* *
34273 TAAAGATTTATTTGAGATTTT
1 TAAAAATTTATTTCAGATTTT
34294 TCATATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.53
Consensus pattern (22 bp):
TAAAAATTTATTTCAGATTTTA
Found at i:41232 original size:21 final size:21
Alignment explanation
Indices: 41206--41248 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
41196 ATCCACATTC
41206 ATACCTTAAACTTAATAATAT
1 ATACCTTAAACTTAATAATAT
*
41227 ATACCTTAACCTTAATAATAT
1 ATACCTTAAACTTAATAATAT
41248 A
1 A
41249 CTGAGCTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (21 bp):
ATACCTTAAACTTAATAATAT
Found at i:43626 original size:2 final size:2
Alignment explanation
Indices: 43619--43649 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
43609 GCACTTTATT
43619 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
43650 GAGGTTAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53427 original size:2 final size:2
Alignment explanation
Indices: 53420--53444 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
53410 CAATTTTGTA
53420 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
53445 AATTTTATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55145 original size:19 final size:19
Alignment explanation
Indices: 55121--55159 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
55111 ATTAAGAGAA
55121 AAATATTTACAATTAAAAT
1 AAATATTTACAATTAAAAT
* *
55140 AAATATTTATAATTATAAT
1 AAATATTTACAATTAAAAT
55159 A
1 A
55160 GGAAATTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
AAATATTTACAATTAAAAT
Found at i:56769 original size:21 final size:20
Alignment explanation
Indices: 56728--56776 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
56718 TTAGGGTTTA
* *
56728 AAGGTTATAGGGTTATGATTT
1 AAGGTT-TAGGATTATAATTT
56749 AAGGTTTAGGATTATCAATTT
1 AAGGTTTAGGATTAT-AATTT
*
56770 AGGGTTT
1 AAGGTTT
56777 TAAGTTATGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.29, C:0.02, G:0.27, T:0.43
Consensus pattern (20 bp):
AAGGTTTAGGATTATAATTT
Found at i:58452 original size:3 final size:3
Alignment explanation
Indices: 58444--58476 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
58434 TATGTAACCG
58444 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
58477 AGTTTAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:63858 original size:34 final size:34
Alignment explanation
Indices: 63819--63904 Score: 113
Period size: 34 Copynumber: 2.5 Consensus size: 34
63809 GGCTACATGG
63819 TATGTGTTCTCTGATTAT-GATTTTCACTGAAAAA
1 TATGTGTTCTCTGATT-TCGATTTTCACTGAAAAA
* *
63853 TATGTGTTCTCTAATTTCGGTTTTCACTGAAAAA
1 TATGTGTTCTCTGATTTCGATTTTCACTGAAAAA
63887 TATGATTGTTC-CTGATTT
1 TATG--TGTTCTCTGATTT
63905 ATGGAATCGT
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
33 1 0.02
34 34 0.74
35 6 0.13
36 5 0.11
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.47
Consensus pattern (34 bp):
TATGTGTTCTCTGATTTCGATTTTCACTGAAAAA
Found at i:67054 original size:13 final size:14
Alignment explanation
Indices: 67011--67041 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
67001 AGTCAACTTA
67011 TTGACTTTGATCCG
1 TTGACTTTGATCCG
67025 TTGACTTTGAT-CG
1 TTGACTTTGATCCG
67038 TTGA
1 TTGA
67042 TCGTTGACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.16, C:0.16, G:0.23, T:0.45
Consensus pattern (14 bp):
TTGACTTTGATCCG
Found at i:69089 original size:34 final size:33
Alignment explanation
Indices: 69046--69117 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 33
69036 GGCTACATGG
69046 TATGTGTTCTCTGA-TTACGATTTTCACTGAAAAA
1 TATGTGTTCTCTGATTTA-G-TTTTCACTGAAAAA
69080 TATGTGTTCTCTGATTTTAGTTTTCACTGAAAAA
1 TATGTGTTCTCTGA-TTTAGTTTTCACTGAAAAA
69114 TATG
1 TATG
69118 ATTGTTCATG
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
34 32 0.89
35 1 0.03
36 3 0.08
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.44
Consensus pattern (33 bp):
TATGTGTTCTCTGATTTAGTTTTCACTGAAAAA
Found at i:69623 original size:32 final size:30
Alignment explanation
Indices: 69522--69626 Score: 111
Period size: 31 Copynumber: 3.4 Consensus size: 30
69512 TAAGGTGACC
* * *
69522 CTTGGGTAGACTCCGAGGCCCCGAGATCTTA
1 CTTGGGTAGGCCCCGA-GCCCCGAGATCTTT
* * *
69553 CTTGGGTTGGCCCTGCAGCCCCGAGATCCTT
1 CTTGGGTAGGCCCCG-AGCCCCGAGATCTTT
*
69584 CTTGGGTAGGCCCCGTAGCCCCGAGTAACTTT
1 CTTGGGTAGGCCCCG-AGCCCCGAG-ATCTTT
69616 CTTGGGTAGGC
1 CTTGGGTAGGC
69627 TCTCAGGCCC
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
31 45 0.74
32 16 0.26
ACGTcount: A:0.14, C:0.30, G:0.30, T:0.25
Consensus pattern (30 bp):
CTTGGGTAGGCCCCGAGCCCCGAGATCTTT
Found at i:78470 original size:19 final size:20
Alignment explanation
Indices: 78441--78480 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
78431 AGAAGTGTAA
78441 GTGTGTTTAAAATGATAAAT
1 GTGTGTTTAAAATGATAAAT
78461 GTGT-TTTAAAATGATAAAT
1 GTGTGTTTAAAATGATAAAT
78480 G
1 G
78481 AGAGAAGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (20 bp):
GTGTGTTTAAAATGATAAAT
Done.