Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000118.1 Hibiscus syriacus cultivar Beakdansim tig00000213_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: 59370
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1387 original size:20 final size:20
Alignment explanation
Indices: 1349--1387 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1339 TTTTGGAGGG
*
1349 CATGCACCGATGCACCAATC
1 CATGCACCGATACACCAATC
* *
1369 CATGCATCGATACATCAAT
1 CATGCACCGATACACCAAT
1388 TAATTTTTTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.33, G:0.13, T:0.21
Consensus pattern (20 bp):
CATGCACCGATACACCAATC
Found at i:1456 original size:45 final size:46
Alignment explanation
Indices: 1407--1494 Score: 133
Period size: 45 Copynumber: 1.9 Consensus size: 46
1397 GAACATCGAA
* *
1407 TGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTCAT
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAT
* *
1452 TGCATTTGATGCATCGATGCACAAGACTATGTATCGATGCACT
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACT
1495 TAGGCTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
45 21 0.55
46 17 0.45
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAT
Found at i:9005 original size:21 final size:21
Alignment explanation
Indices: 8963--9006 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
8953 ACTCCGGGAG
* *
8963 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
8984 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
9005 CT
1 CT
9007 CCTCCGGCTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:10117 original size:26 final size:26
Alignment explanation
Indices: 10088--10145 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
10078 CCATGCACCG
10088 ATGCACTCATTGCATTTGATGCATCA
1 ATGCACTCATTGCATTTGATGCATCA
10114 ATGCACTCATTGCATTTGATGCATCA
1 ATGCACTCATTGCATTTGATGCATCA
10140 ATGCAC
1 ATGCAC
10146 AAGACTATGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.33
Consensus pattern (26 bp):
ATGCACTCATTGCATTTGATGCATCA
Found at i:10396 original size:160 final size:160
Alignment explanation
Indices: 10212--10534 Score: 610
Period size: 160 Copynumber: 2.0 Consensus size: 160
10202 ACTCTTAGTG
*
10212 CACCGATGCACCGATGCACTCTTAGTGCACCGATGCACTAAGGGTCCAACGGTCAAAATATTTGA
1 CACCGATGCACCAATGCACTCTTAGTGCACCGATGCACTAAGGGTCCAACGGTCAAAATATTTGA
10277 ATTTTACATTGATGCACCATGGGTATGCATCGATGCACTGATGCTCCCAACTGATTTTATTAATT
66 ATTTTACATTGATGCACCATGGGTATGCATCGATGCACTGATGCTCCCAACTGATTTTATTAATT
10342 ATTTTCACACTTAAACGGCTATATTGACTC
131 ATTTTCACACTTAAACGGCTATATTGACTC
* *
10372 CACCGATGCATCAATGCACTCTTAGTGCACCGATGCACTAAGGGTCTAACGGTCAAAATATTTGA
1 CACCGATGCACCAATGCACTCTTAGTGCACCGATGCACTAAGGGTCCAACGGTCAAAATATTTGA
*
10437 ATTTTACATTGATGCACCATGGGTATGCATCGTTGCACTGATGCTCCCAACTGATTTTATTAATT
66 ATTTTACATTGATGCACCATGGGTATGCATCGATGCACTGATGCTCCCAACTGATTTTATTAATT
10502 ATTTTCACACTTAAACGGCTATATTGACTC
131 ATTTTCACACTTAAACGGCTATATTGACTC
10532 CAC
1 CAC
10535 TAAGCATCCC
Statistics
Matches: 159, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
160 159 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (160 bp):
CACCGATGCACCAATGCACTCTTAGTGCACCGATGCACTAAGGGTCCAACGGTCAAAATATTTGA
ATTTTACATTGATGCACCATGGGTATGCATCGATGCACTGATGCTCCCAACTGATTTTATTAATT
ATTTTCACACTTAAACGGCTATATTGACTC
Found at i:13737 original size:19 final size:19
Alignment explanation
Indices: 13713--13767 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
13703 GACTGTTTCC
13713 TACAGTCTATTTTCTACTA
1 TACAGTCTATTTTCTACTA
* *
13732 TACAGTCTGTTTTCTTTCTA
1 TACAGTCTATTTTC-TACTA
13752 T--AGTCTGATTTTCTAC
1 TACAGTCT-ATTTTCTAC
13768 ATGGTATCAG
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
18 7 0.23
19 18 0.60
20 5 0.17
ACGTcount: A:0.20, C:0.20, G:0.09, T:0.51
Consensus pattern (19 bp):
TACAGTCTATTTTCTACTA
Found at i:15814 original size:36 final size:36
Alignment explanation
Indices: 15767--15838 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
15757 CCTAGCATTT
** *
15767 GCCAAGAACCAGATTCTGATCCTGTTGCCTCTGAAA
1 GCCAAGAACCAGATTCAAATCCTGTTGCATCTGAAA
*
15803 GCCAAGAACCAGATTCAAATCTTGTTGCATCTGAAA
1 GCCAAGAACCAGATTCAAATCCTGTTGCATCTGAAA
15839 CAGAAGGTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (36 bp):
GCCAAGAACCAGATTCAAATCCTGTTGCATCTGAAA
Found at i:27220 original size:53 final size:55
Alignment explanation
Indices: 27156--27317 Score: 161
Period size: 62 Copynumber: 2.9 Consensus size: 55
27146 TGTCTTTGGT
27156 ATTTAAAGATTTATATAGTATTTTAGTCTTATAAAATTTACATT-ATTTT-AAAA
1 ATTTAAAGATTTATATAGTATTTTAGTCTTATAAAATTTACATTCATTTTAAAAA
* * * *
27209 ATTTAAAGATTTATATAGTATTTCATTTACAATGTATCAAATTATTC-TTCATTTTAAAAAAA
1 ATTTAAAGATTTATATAGTATTTTA-GT-C--T-TATAAAATT-TACATTCATTTT--AAAAA
* **
27271 ATTAAAAGATTTATATAACATTTTAGTCTTATAAAATTTACA-TCATT
1 ATTTAAAGATTTATATAGTATTTTAGTCTTATAAAATTTACATTCATT
27318 ATCACTTTGG
Statistics
Matches: 87, Mismatches: 11, Indels: 19
0.74 0.09 0.16
Matches are distributed among these distances:
53 24 0.28
54 1 0.01
55 1 0.01
56 7 0.08
57 9 0.10
58 11 0.13
59 7 0.08
60 1 0.01
61 1 0.01
62 25 0.29
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (55 bp):
ATTTAAAGATTTATATAGTATTTTAGTCTTATAAAATTTACATTCATTTTAAAAA
Found at i:31444 original size:10 final size:9
Alignment explanation
Indices: 31417--31449 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
31407 AGATAATATT
31417 ATTTAAATA
1 ATTTAAATA
31426 ATTTAAATA
1 ATTTAAATA
31435 ATTATAAAT-
1 ATT-TAAATA
31444 ATTTAA
1 ATTTAA
31450 TCGAGTATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 3 0.13
9 15 0.65
10 5 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
ATTTAAATA
Found at i:35703 original size:8 final size:8
Alignment explanation
Indices: 35690--35730 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
35680 CTCATTTTCA
35690 GAGAATTT
1 GAGAATTT
35698 GAGAATTT
1 GAGAATTT
*
35706 -AGAGTTT
1 GAGAATTT
*
35713 GGGAATTT
1 GAGAATTT
35721 GAGAATTT
1 GAGAATTT
35729 GA
1 GA
35731 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:36029 original size:128 final size:128
Alignment explanation
Indices: 35801--36173 Score: 631
Period size: 128 Copynumber: 2.9 Consensus size: 128
35791 TAATCGGAGT
35801 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
35866 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
35929 ACTATTCACATGAAGGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
35994 CATTGCCCTATTATGTCACTCATGTCCCTCAGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *** * * *
36057 TC-AGGAGACATGAAGACGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTA
1 ACTA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
*
36121 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTA
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
36174 AATCAGGTAA
Statistics
Matches: 230, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
127 1 0.00
128 229 1.00
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.32
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:36635 original size:33 final size:34
Alignment explanation
Indices: 36574--36673 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
36564 AAATTTAATG
*
36574 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
36608 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
36641 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
36674 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:37223 original size:21 final size:20
Alignment explanation
Indices: 37196--37286 Score: 110
Period size: 21 Copynumber: 4.3 Consensus size: 20
37186 GATATAAAAC
*
37196 CCTGCGGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
37216 CCTGGCGGGCTAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
* *
37237 CCCTGTGGGCTCGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
*
37258 CCATGCGGGCTCGGAATGTAA
1 CC-TGCGGGCTAGGAATGTAA
37279 CCCTGCGG
1 -CCTGCGG
37287 AGATGGCATA
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
20 5 0.08
21 53 0.84
22 5 0.08
ACGTcount: A:0.20, C:0.25, G:0.35, T:0.20
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:37256 original size:42 final size:42
Alignment explanation
Indices: 37193--37286 Score: 136
Period size: 42 Copynumber: 2.2 Consensus size: 42
37183 TATGATATAA
*
37193 AACCCTGCGGGCTAGGCATGTAACC-TGGCGGGCTAGGAATGT
1 AACCCTGCGGGCTAGGAATGTAACCAT-GCGGGCTAGGAATGT
* * *
37235 AACCCTGTGGGCTCGGAATGTAACCATGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGTAACCATGCGGGCTAGGAATGT
37277 AACCCTGCGG
1 AACCCTGCGG
37287 AGATGGCATA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 45 0.98
43 1 0.02
ACGTcount: A:0.21, C:0.26, G:0.34, T:0.19
Consensus pattern (42 bp):
AACCCTGCGGGCTAGGAATGTAACCATGCGGGCTAGGAATGT
Found at i:37316 original size:21 final size:21
Alignment explanation
Indices: 37290--37337 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
37280 CCTGCGGAGA
*
37290 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
*
37311 TGGCATATAAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
37332 GGGCAT
1 TGGCAT
37338 GTACCCCTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.25, C:0.12, G:0.38, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:39123 original size:30 final size:34
Alignment explanation
Indices: 39059--39137 Score: 101
Period size: 33 Copynumber: 2.4 Consensus size: 34
39049 TTAATAATTC
* *
39059 TAAATAAATAATAATTATATAAATATTATTTTA-A
1 TAAA-AAATAATAATTACATAAATATTATTTAATA
*
39093 TAAAAAATAATATTTACATAAATA-TA-TTAATA
1 TAAAAAATAATAATTACATAAATATTATTTAATA
39125 TAAAAAATAATAA
1 TAAAAAATAATAA
39138 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
31 3 0.08
32 15 0.38
33 18 0.45
34 4 0.10
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (34 bp):
TAAAAAATAATAATTACATAAATATTATTTAATA
Found at i:42379 original size:22 final size:22
Alignment explanation
Indices: 42354--42395 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
42344 CAATTCATTT
42354 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
42376 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
42396 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:47082 original size:22 final size:21
Alignment explanation
Indices: 47046--47086 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
47036 CAATTCATTT
47046 ATCTTTTCTTATCTTGTTTTA
1 ATCTTTTCTTATCTTGTTTTA
*
47067 ATCTTATTTTTATCTTGTTT
1 ATCTT-TTCTTATCTTGTTT
47087 CCAGCACCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.15, C:0.12, G:0.05, T:0.68
Consensus pattern (21 bp):
ATCTTTTCTTATCTTGTTTTA
Found at i:51725 original size:2 final size:2
Alignment explanation
Indices: 51718--51780 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
51708 TTCTTTCTGT
51718 TA TA TA TA TA 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 TA TA TA TA TA
51760 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
51781 TAAAAATAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.