Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_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: 21326069
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 89 of 89
Found at i:21316733 original size:16 final size:16
Alignment explanation
Indices: 21316712--21316744 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
21316702 AAAAAAATTT
21316712 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
21316728 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
21316744 T
1 T
21316745 CTATTTATTA
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:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:21318185 original size:21 final size:22
Alignment explanation
Indices: 21318155--21318337 Score: 129
Period size: 21 Copynumber: 8.6 Consensus size: 22
21318145 GATTTACATA
* *
21318155 TTCGCATTGCGA-TAGTCCAAG
1 TTCGCGTTGCGATTATTCCAAG
21318176 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA-TTATTCCAAG
*
21318199 TT--CGTTGCGA-TAGTT-GAAG
1 TTCGCGTTGCGATTA-TTCCAAG
* *
21318218 TTCGCGTTGCGATTTATTCTAAA
1 TTCGCGTTGCGA-TTATTCCAAG
*
21318241 TT--CGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA-TTATTCCAAG
* * *
21318262 TT--TGTTGCGA-TAGTCGAAG
1 TTCGCGTTGCGATTATTCCAAG
*
21318281 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA-TTATTCCAAG
*
21318304 TTCGCGTTGCGATTTATTCTAAG
1 TTCGCGTTGCGA-TTATTCCAAG
21318327 TT--CGTTGCGAT
1 TTCGCGTTGCGAT
21318338 AGTTCAAAAT
Statistics
Matches: 134, Mismatches: 16, Indels: 25
0.77 0.09 0.14
Matches are distributed among these distances:
19 15 0.11
20 3 0.02
21 69 0.51
22 2 0.01
23 45 0.34
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.39
Consensus pattern (22 bp):
TTCGCGTTGCGATTATTCCAAG
Found at i:21318212 original size:42 final size:42
Alignment explanation
Indices: 21318161--21318350 Score: 181
Period size: 42 Copynumber: 4.5 Consensus size: 42
21318151 CATATTCGCA
* *
21318161 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAATTCGCGTTGCGATTTATTCTAAGTTCG
** * *
21318203 TTGCGATAGTTGAAGTTCGCGTTGCGATTTATTCTAAATTCG
1 TTGCGATAGTCCAAATTCGCGTTGCGATTTATTCTAAGTTCG
* * * *
21318245 TTGCGATTTATTCCAAATT--TGTTGCGA--TAGTCGAAGTTCGCG
1 TTGCGA--TAGTCCAAATTCGCGTTGCGATTTATTCTAAGTT--CG
*
21318287 TTGCGATTTATTCCAAATTCGCGTTGCGATTTATTCTAAGTTCG
1 TTGCGA--TAGTCCAAATTCGCGTTGCGATTTATTCTAAGTTCG
* *
21318331 TTGCGATAGTTCAAAATCGC
1 TTGCGATAGTCCAAATTCGC
21318351 AACGACGGTA
Statistics
Matches: 122, Mismatches: 18, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
40 8 0.07
42 83 0.68
44 22 0.18
46 9 0.07
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (42 bp):
TTGCGATAGTCCAAATTCGCGTTGCGATTTATTCTAAGTTCG
Found at i:21318230 original size:63 final size:64
Alignment explanation
Indices: 21318155--21318341 Score: 263
Period size: 63 Copynumber: 2.9 Consensus size: 64
21318145 GATTTACATA
* * *
21318155 TTCGCATTGCGA-TAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTTGAAG
1 TTCGCGTTGCGATTATTCCAAATTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTTGAAG
* * * *
21318218 TTCGCGTTGCGATTTATTCTAAATT--CGTTGCGATTTATTCCAAATTTGTTGCGATAGTCGAAG
1 TTCGCGTTGCGA-TTATTCCAAATTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTTGAAG
*
21318281 TTCGCGTTGCGATTTATTCCAAATTCGCGTTGCGATTTATTCTAAGTTCGTTGCGATAGTT
1 TTCGCGTTGCGA-TTATTCCAAATTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTT
21318342 CAAAATCGCA
Statistics
Matches: 108, Mismatches: 12, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
63 70 0.65
65 38 0.35
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40
Consensus pattern (64 bp):
TTCGCGTTGCGATTATTCCAAATTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTTGAAG
Found at i:21318461 original size:10 final size:11
Alignment explanation
Indices: 21318430--21318463 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
21318420 GACACGTATT
21318430 ACCACGACCACG
1 ACCACGACC-CG
21318442 ACCACGACCCG
1 ACCACGACCCG
21318453 ACC-CGACCCG
1 ACCACGACCCG
21318463 A
1 A
21318464 GACGAGACGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.36
11 5 0.23
12 9 0.41
ACGTcount: A:0.29, C:0.53, G:0.18, T:0.00
Consensus pattern (11 bp):
ACCACGACCCG
Found at i:21319068 original size:21 final size:20
Alignment explanation
Indices: 21319044--21319199 Score: 174
Period size: 21 Copynumber: 7.6 Consensus size: 20
21319034 AATTTACATA
21319044 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGT-CAAG
21319065 TTCGCATTGCGATAGTC-AG
1 TTCGCATTGCGATAGTCAAG
* *
21319084 TTCGCATTGCGATAGTCGAC
1 TTCGCATTGCGATAGTCAAG
*
21319104 TATCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGT-CA-AG
*
21319125 TTCGCATTACGATAGTCCAAG
1 TTCGCATTGCGATAGT-CAAG
*
21319146 TTCGCATTACGATAGTTCAAG
1 TTCGCATTGCGATAG-TCAAG
21319167 TTCGCATTGCGATAGTCAATG
1 TTCGCATTGCGATAGTCAA-G
*
21319188 TTCGCGTTGCGA
1 TTCGCATTGCGA
21319200 ATCTGGAAAC
Statistics
Matches: 119, Mismatches: 8, Indels: 16
0.83 0.06 0.11
Matches are distributed among these distances:
19 19 0.16
20 20 0.17
21 78 0.66
22 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (20 bp):
TTCGCATTGCGATAGTCAAG
Found at i:21319160 original size:62 final size:60
Alignment explanation
Indices: 21319065--21319179 Score: 160
Period size: 62 Copynumber: 1.9 Consensus size: 60
21319055 ATAGTCCAAG
* * *
21319065 TTCGCATTGCGATAGTCAGTTCGCATTGCGATAG-TCGACTATCGCATTGCGATTTACATA
1 TTCGCATTACGATAGTCAGTTCGCATTACGATAGTTCAACT-TCGCATTGCGATTTACATA
*
21319125 TTCGCATTACGATAGTCCAAGTTCGCATTACGATAGTTCAAGTTCGCATTGCGAT
1 TTCGCATTACGATAGT-C-AGTTCGCATTACGATAGTTCAACTTCGCATTGCGAT
21319180 AGTCAATGTT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
60 15 0.31
61 1 0.02
62 28 0.58
63 4 0.08
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (60 bp):
TTCGCATTACGATAGTCAGTTCGCATTACGATAGTTCAACTTCGCATTGCGATTTACATA
Found at i:21323133 original size:29 final size:29
Alignment explanation
Indices: 21323096--21323243 Score: 255
Period size: 29 Copynumber: 5.1 Consensus size: 29
21323086 AAATACAGAA
*
21323096 AAAT-TAAATACTGGAAATTAAAAGACTG
1 AAATGTAAATAATGGAAATTAAAAGACTG
21323124 AAATGTAAATAATGGAAATTAAAAGACTG
1 AAATGTAAATAATGGAAATTAAAAGACTG
21323153 AAATGTAAATAATGGAAATTAAAAGACTG
1 AAATGTAAATAATGGAAATTAAAAGACTG
21323182 AAATGTAAATAATGGAAATTAAAAGACTG
1 AAATGTAAATAATGGAAATTAAAAGACTG
*
21323211 AAATGTAAATAATAGAAATT-AAAGAACTG
1 AAATGTAAATAATGGAAATTAAAAG-ACTG
21323240 AAAT
1 AAAT
21323244 TTATATACTA
Statistics
Matches: 116, Mismatches: 2, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
28 8 0.07
29 108 0.93
ACGTcount: A:0.56, C:0.04, G:0.16, T:0.24
Consensus pattern (29 bp):
AAATGTAAATAATGGAAATTAAAAGACTG
Found at i:21323228 original size:15 final size:13
Alignment explanation
Indices: 21323096--21323244 Score: 90
Period size: 14 Copynumber: 10.4 Consensus size: 13
21323086 AAATACAGAA
*
21323096 AAATTAAATACTGG
1 AAATTAAATAAT-G
21323110 AAATTAAA-AGACTG
1 AAATTAAATA-A-TG
21323124 AAATGTAAATAATGG
1 AAAT-TAAATAAT-G
21323139 AAATTAAA-AGACTG
1 AAATTAAATA-A-TG
21323153 AAATGTAAATAATGG
1 AAAT-TAAATAAT-G
21323168 AAATTAAA-AGACTG
1 AAATTAAATA-A-TG
21323182 AAATGTAAATAATGG
1 AAAT-TAAATAAT-G
21323197 AAATTAAA-AGACTG
1 AAATTAAATA-A-TG
21323211 AAATGTAAATAATAG
1 AAAT-TAAATAAT-G
*
21323226 AAATTAAAGAACTG
1 AAATTAAATAA-TG
21323240 AAATT
1 AAATT
21323245 TATATACTAA
Statistics
Matches: 112, Mismatches: 2, Indels: 42
0.72 0.01 0.27
Matches are distributed among these distances:
13 4 0.04
14 59 0.53
15 45 0.40
16 4 0.04
ACGTcount: A:0.56, C:0.04, G:0.15, T:0.25
Consensus pattern (13 bp):
AAATTAAATAATG
Found at i:21323262 original size:29 final size:28
Alignment explanation
Indices: 21323116--21323262 Score: 132
Period size: 29 Copynumber: 5.1 Consensus size: 28
21323106 CTGGAAATTA
** *
21323116 AAAGACTGAAATGTAAATAATGGAAATT
1 AAAGACTGAAATGTAAATAATAAAAAAT
** *
21323144 AAAAGACTGAAATGTAAATAATGGAAATT
1 -AAAGACTGAAATGTAAATAATAAAAAAT
** *
21323173 AAAAGACTGAAATGTAAATAATGGAAATT
1 -AAAGACTGAAATGTAAATAATAAAAAAT
* *
21323202 AAAAGACTGAAATGTAAATAATAGAAATT
1 -AAAGACTGAAATGTAAATAATAAAAAAT
* * *
21323231 AAAGAACTGAAATTTATATACTAAAAAAT
1 AAAG-ACTGAAATGTAAATAATAAAAAAT
21323260 AAA
1 AAA
21323263 TGGCATAAAT
Statistics
Matches: 111, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
28 4 0.04
29 107 0.96
ACGTcount: A:0.57, C:0.04, G:0.14, T:0.24
Consensus pattern (28 bp):
AAAGACTGAAATGTAAATAATAAAAAAT
Found at i:21323280 original size:87 final size:86
Alignment explanation
Indices: 21323096--21323262 Score: 237
Period size: 87 Copynumber: 1.9 Consensus size: 86
21323086 AAATACAGAA
* *
21323096 AAATTAAATACTGGAAATTAAAAGACTGAAATGTAAATAATGGAAATTAAAAGACTGAAATGTAA
1 AAATTAAATAATGGAAATTAAAAGACTGAAATGTAAATAATAGAAATTAAAAGACTGAAATGTAA
** *
21323161 ATAATGGAAATTAAAAGACTG
66 ATAATAAAAAATAAAAGACTG
*
21323182 AAATGTAAATAATGGAAATTAAAAGACTGAAATGTAAATAATAGAAATT-AAAGAACTGAAATTT
1 AAAT-TAAATAATGGAAATTAAAAGACTGAAATGTAAATAATAGAAATTAAAAG-ACTGAAATGT
* *
21323246 ATATACTAAAAAATAAA
64 AAATAATAAAAAATAAA
21323263 TGGCATAAAT
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
86 8 0.11
87 63 0.89
ACGTcount: A:0.57, C:0.04, G:0.14, T:0.25
Consensus pattern (86 bp):
AAATTAAATAATGGAAATTAAAAGACTGAAATGTAAATAATAGAAATTAAAAGACTGAAATGTAA
ATAATAAAAAATAAAAGACTG
Found at i:21323292 original size:87 final size:87
Alignment explanation
Indices: 21323109--21323292 Score: 201
Period size: 87 Copynumber: 2.1 Consensus size: 87
21323099 TTAAATACTG
* * ** *
21323109 GAAATTAAAAGACTGAAATGTAAATAATGGAAATTAAAAGACTGAAATGTAAATAATGGAAATTA
1 GAAAATAAAAGACTGAAATGTAAATAATAGAAATTAAAAGACTGAAATGTAAATAATAAAAAATA
* **
21323174 AAAGACTGAAATGTAAATAATG
66 AAAGACTGAAATATAAATAACA
* * * *
21323196 GAAATTAAAAGACTGAAATGTAAATAATAGAAATT-AAAGAACTGAAATTTATATACTAAAAAAT
1 GAAAATAAAAGACTGAAATGTAAATAATAGAAATTAAAAG-ACTGAAATGTAAATAATAAAAAAT
* *
21323260 AAATGGCAT-AAATATAAATAACA
65 AAAAGAC-TGAAATATAAATAACA
*
21323283 TAAAATAAAA
1 GAAAATAAAA
21323293 AATCGAATAA
Statistics
Matches: 81, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
86 4 0.05
87 76 0.94
88 1 0.01
ACGTcount: A:0.58, C:0.04, G:0.13, T:0.24
Consensus pattern (87 bp):
GAAAATAAAAGACTGAAATGTAAATAATAGAAATTAAAAGACTGAAATGTAAATAATAAAAAATA
AAAGACTGAAATATAAATAACA
Found at i:21325529 original size:17 final size:18
Alignment explanation
Indices: 21325507--21325549 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
21325497 TTGTTGGGGA
**
21325507 ATTTGGG-TTTTGATCAT
1 ATTTGGGATTTTGAGAAT
21325524 ATTTGGGGATTTTGAGAAT
1 ATTT-GGGATTTTGAGAAT
21325543 ATTTGGG
1 ATTTGGG
21325550 GGGTTTGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 4 0.18
18 6 0.27
19 12 0.55
ACGTcount: A:0.21, C:0.02, G:0.30, T:0.47
Consensus pattern (18 bp):
ATTTGGGATTTTGAGAAT
Done.