Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000209.1 Hibiscus syriacus cultivar Beakdansim tig00000372_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: 54979
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:193 original size:13 final size:14
Alignment explanation
Indices: 177--210 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
167 AATGTTGTTG
*
177 GAAAAAAAAGAGA-
1 GAAAAAAAAGACAT
190 GAAAAAAAAGACAT
1 GAAAAAAAAGACAT
204 GAAAAAA
1 GAAAAAA
211 TGGAAAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (14 bp):
GAAAAAAAAGACAT
Found at i:1915 original size:18 final size:17
Alignment explanation
Indices: 1884--1922 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1874 CTTATTTTTA
* *
1884 ATTTAGTTGCTTTTATTT
1 ATTTAATTGATTTTA-TT
1902 ATTTAATTGATTTTATT
1 ATTTAATTGATTTTATT
1919 ATTT
1 ATTT
1923 TAATATCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.23, C:0.03, G:0.08, T:0.67
Consensus pattern (17 bp):
ATTTAATTGATTTTATT
Found at i:2290 original size:10 final size:10
Alignment explanation
Indices: 2277--2310 Score: 68
Period size: 10 Copynumber: 3.4 Consensus size: 10
2267 ATTCACACTC
2277 ACTCACGCCG
1 ACTCACGCCG
2287 ACTCACGCCG
1 ACTCACGCCG
2297 ACTCACGCCG
1 ACTCACGCCG
2307 ACTC
1 ACTC
2311 CACCCCCTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.21, C:0.50, G:0.18, T:0.12
Consensus pattern (10 bp):
ACTCACGCCG
Found at i:2477 original size:2 final size:2
Alignment explanation
Indices: 2472--2499 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2462 ACACAAACAC
2472 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2500 TTCTCTCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20492 original size:2 final size:2
Alignment explanation
Indices: 20485--20529 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
20475 AATTCAAATT
20485 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
20527 TA T
1 TA T
20530 TCATTTTTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22723 original size:23 final size:25
Alignment explanation
Indices: 22697--22748 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 25
22687 TAGTTGAAGT
*
22697 ATTTTTTTATTGT-ATATTTC-TAA
1 ATTTTTTTATTGTCACATTTCTTAA
*
22720 ATTTTTTTATTTTCACATTTCTTAA
1 ATTTTTTTATTGTCACATTTCTTAA
22745 ATTT
1 ATTT
22749 ATAATATAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 12 0.48
24 6 0.24
25 7 0.28
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.65
Consensus pattern (25 bp):
ATTTTTTTATTGTCACATTTCTTAA
Found at i:23291 original size:25 final size:25
Alignment explanation
Indices: 23236--23291 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
23226 CCCGTAGTTG
23236 GTTTGACTAATTGATTTTATTAACT
1 GTTTGACTAATTGATTTTATTAACT
*
23261 GATTTGA-TAATTG-TTTATATATAAGT
1 G-TTTGACTAATTGATTT-TAT-TAACT
23287 GTTTG
1 GTTTG
23292 GTAAAATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 3 0.11
25 14 0.52
26 10 0.37
ACGTcount: A:0.29, C:0.04, G:0.16, T:0.52
Consensus pattern (25 bp):
GTTTGACTAATTGATTTTATTAACT
Found at i:26196 original size:2 final size:2
Alignment explanation
Indices: 26189--26216 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
26179 ATATTTCTTC
26189 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26217 TTATTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26221 original size:4 final size:4
Alignment explanation
Indices: 26214--26238 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
26204 TATATATATA
26214 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
26239 TTATCATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:26251 original size:23 final size:24
Alignment explanation
Indices: 26224--26276 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
26214 TATTTATTTA
26224 TTTATTTATTTATT-TTTATCATT
1 TTTATTTATTTATTCTTTATCATT
* *
26247 TTTA-TTATTTTTTCTTTATCCTT
1 TTTATTTATTTATTCTTTATCATT
26270 TTTATTT
1 TTTATTT
26277 TCTTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 8 0.31
23 16 0.62
24 2 0.08
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTATTTATTTATTCTTTATCATT
Found at i:26282 original size:23 final size:23
Alignment explanation
Indices: 26224--26291 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
26214 TATTTATTTA
*
26224 TTTATTTATTTATT-TTTATCATT
1 TTTA-TTATTTTTTCTTTATCATT
*
26247 TTTATTATTTTTTCTTTATCCTT
1 TTTATTATTTTTTCTTTATCATT
*
26270 TTTATT-TTCTTTT-TTTTTCATT
1 TTTATTATT-TTTTCTTTATCATT
26292 CATATTTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
22 17 0.44
23 22 0.56
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTATTATTTTTTCTTTATCATT
Found at i:26406 original size:29 final size:33
Alignment explanation
Indices: 26337--26406 Score: 78
Period size: 33 Copynumber: 2.2 Consensus size: 33
26327 TTTCGTTTCA
* *
26337 TATTTTATTTTTTTAGTACTTTATGTTGTTTTCT
1 TATTTTATTTTGTTA-TACTTTATGTTGTTTACT
26371 TA-TTTATTTTGTT-TAC-TT-TGTT-TTTACT
1 TATTTTATTTTGTTATACTTTATGTTGTTTACT
26399 TATTTTAT
1 TATTTTAT
26407 CTTTTTGCAC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
28 7 0.21
29 9 0.27
30 2 0.06
31 3 0.09
33 10 0.30
34 2 0.06
ACGTcount: A:0.16, C:0.06, G:0.07, T:0.71
Consensus pattern (33 bp):
TATTTTATTTTGTTATACTTTATGTTGTTTACT
Found at i:36670 original size:16 final size:14
Alignment explanation
Indices: 36634--36687 Score: 65
Period size: 14 Copynumber: 3.8 Consensus size: 14
36624 TAAGTCGAAG
*
36634 AAAG-AAAAAGAAA
1 AAAGAAAAAACAAA
*
36647 AAGGAAAAAACAAA
1 AAAGAAAAAACAAA
36661 AAAGAAAAAACGAAA
1 AAAGAAAAAAC-AAA
36676 AAGAGAAAAAAC
1 AA-AGAAAAAAC
36688 GTTTAGGGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
13 3 0.09
14 18 0.51
15 5 0.14
16 9 0.26
ACGTcount: A:0.80, C:0.06, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAGAAAAAACAAA
Found at i:36676 original size:21 final size:21
Alignment explanation
Indices: 36638--36686 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
36628 TCGAAGAAAG
*
36638 AAAAAGAAAAAGGAAAAAACA
1 AAAAAGAAAAACGAAAAAACA
*
36659 AAAAAGAAAAAACGAAAAAGAGA
1 AAAAAG-AAAAACGAAAAA-ACA
36682 AAAAA
1 AAAAA
36687 CGTTTAGGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 6 0.25
22 11 0.46
23 7 0.29
ACGTcount: A:0.82, C:0.04, G:0.14, T:0.00
Consensus pattern (21 bp):
AAAAAGAAAAACGAAAAAACA
Found at i:36737 original size:9 final size:9
Alignment explanation
Indices: 36723--36779 Score: 50
Period size: 9 Copynumber: 6.7 Consensus size: 9
36713 GCCCTAAATT
36723 GAAAAAAGA
1 GAAAAAAGA
36732 GAAAAAAGA
1 GAAAAAAGA
36741 G--AAAA-A
1 GAAAAAAGA
*
36747 GAACAAA-A
1 GAAAAAAGA
*
36755 GAAAAAGGA
1 GAAAAAAGA
*
36764 GAAAGAAAAA
1 GAAA-AAAGA
36774 GAAAAA
1 GAAAAA
36780 TAAGATGGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
6 2 0.05
7 4 0.10
8 9 0.23
9 17 0.44
10 7 0.18
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (9 bp):
GAAAAAAGA
Found at i:36784 original size:9 final size:8
Alignment explanation
Indices: 36724--36784 Score: 50
Period size: 8 Copynumber: 7.0 Consensus size: 8
36714 CCCTAAATTG
36724 AAAAAAGA
1 AAAAAAGA
36732 GAAAAAAGA
1 -AAAAAAGA
*
36741 GAAAAAGA
1 AAAAAAGA
*
36749 ACAAAAGA
1 AAAAAAGA
*
36757 AAAAGGAGAA
1 AAAA-AAG-A
36767 AGAAAAAGA
1 A-AAAAAGA
36776 AAAATAAGA
1 AAAA-AAGA
36785 TGGGTTTAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
8 19 0.45
9 16 0.38
10 4 0.10
11 3 0.07
ACGTcount: A:0.77, C:0.02, G:0.20, T:0.02
Consensus pattern (8 bp):
AAAAAAGA
Found at i:37988 original size:111 final size:111
Alignment explanation
Indices: 37791--37998 Score: 339
Period size: 111 Copynumber: 1.9 Consensus size: 111
37781 GCTTCCCAGT
*
37791 TTCAGAGCTAATTTTAACTTCACAGCGAAGGATATTGAACTCAAGACAGCACAAGCTCAACTTCA
1 TTCAGAGCTAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAGCACAAGCTCAACTTCA
37856 CAGCGAAGGGGCGACTAACTGTCAACAAACAACTTCTTCAGTTTCA
66 CAGCGAAGGGGCGACTAACTGTCAACAAACAACTTCTTCAGTTTCA
*
37902 TTCAGAG-TATATTTCAACTTCACAGCGAAGGATATT-ATACTCAAGACATCACAAGCTCAACTT
1 TTCAGAGCTA-ATTTCAACTTCACAGCGAAGGATATTGA-ACTCAAGACAGCACAAGCTCAACTT
* * *
37965 CATAGCGAAGGGGCGGCTGACTGTCAACAAACAA
64 CACAGCGAAGGGGCGACTAACTGTCAACAAACAA
37999 TTTCCCAGTT
Statistics
Matches: 90, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
110 3 0.03
111 87 0.97
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.23
Consensus pattern (111 bp):
TTCAGAGCTAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAGCACAAGCTCAACTTCA
CAGCGAAGGGGCGACTAACTGTCAACAAACAACTTCTTCAGTTTCA
Found at i:46287 original size:20 final size:21
Alignment explanation
Indices: 46262--46315 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
46252 AAATTATCCG
*
46262 TTAGTATCGATACTGGGACA-
1 TTAGTATCGATACTGAGACAC
*
46282 TTAGTATCGATACTGAGCCAC
1 TTAGTATCGATACTGAGACAC
*
46303 TTGGTATCGATAC
1 TTAGTATCGATAC
46316 CCACTGACTG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (21 bp):
TTAGTATCGATACTGAGACAC
Found at i:47240 original size:19 final size:19
Alignment explanation
Indices: 47216--47261 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
47206 CTTGAGAGAG
*
47216 GAAGAAGAAATGGGTTGAA
1 GAAGAAGAAACGGGTTGAA
47235 GAAGAAGAAACGGGTTGAA
1 GAAGAAGAAACGGGTTGAA
47254 GAAGAAGA
1 GAAGAAGA
47262 GAAGATGACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.50, C:0.02, G:0.37, T:0.11
Consensus pattern (19 bp):
GAAGAAGAAACGGGTTGAA
Found at i:53917 original size:30 final size:28
Alignment explanation
Indices: 53860--53948 Score: 101
Period size: 29 Copynumber: 3.0 Consensus size: 28
53850 AAGAGTCGAG
53860 GTTACCTATGTCTTTCGAGAC--ATGGATA
1 GTTACCTATGTC-TTCG-GACATATGGATA
53888 GTTTACCTATGTCATTCGGACATATGGATA
1 G-TTACCTATGTC-TTCGGACATATGGATA
*
53918 GTTACCTATGTTCTTTGGAACATATGGATA
1 GTTACCTATG-TCTTCGG-ACATATGGATA
53948 G
1 G
53949 ATCCTTCGGG
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
28 4 0.07
29 28 0.52
30 22 0.41
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (28 bp):
GTTACCTATGTCTTCGGACATATGGATA
Done.