Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001008.1 Hibiscus syriacus cultivar Beakdansim tig00002011_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: 58369
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4279 original size:19 final size:19
Alignment explanation
Indices: 4255--4293 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
4245 AATATCAATT
*
4255 AAAATATATT-ATTTTATTA
1 AAAATAT-TTAATTATATTA
4274 AAAATATTTAATTATATTA
1 AAAATATTTAATTATATTA
4293 A
1 A
4294 TTTTTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AAAATATTTAATTATATTA
Found at i:11300 original size:6 final size:6
Alignment explanation
Indices: 11289--11321 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
11279 GCTTTGATCT
11289 GTGGCA GTGGCA GTGGCA GTGGCA GTGGCA GTG
1 GTGGCA GTGGCA GTGGCA GTGGCA GTGGCA GTG
11322 AAGTGTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.15, G:0.52, T:0.18
Consensus pattern (6 bp):
GTGGCA
Found at i:13086 original size:36 final size:36
Alignment explanation
Indices: 13004--13086 Score: 96
Period size: 36 Copynumber: 2.2 Consensus size: 36
12994 TTTTGATTGT
*
13004 AACATAAATTATAAAATATTATAAAAAAATATATTTAT
1 AACAT-AATTATAAAATATTAT-AAAAAATATATTTAA
* *
13042 AACGTAATTCATAAAATATTAT-AAAAGTATATTTAA
1 AACATAATT-ATAAAATATTATAAAAAATATATTTAA
*
13078 AATATAATT
1 AACATAATT
13087 TATATTACAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
36 19 0.49
37 4 0.10
38 16 0.41
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (36 bp):
AACATAATTATAAAATATTATAAAAAATATATTTAA
Found at i:13541 original size:15 final size:15
Alignment explanation
Indices: 13521--13558 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
13511 GTGAAAAATA
13521 TTTGACTCGAGTTGG
1 TTTGACTCGAGTTGG
13536 TTTGACTCGAGTTGG
1 TTTGACTCGAGTTGG
13551 TTTGACTC
1 TTTGACTC
13559 AAACTCGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.13, C:0.16, G:0.29, T:0.42
Consensus pattern (15 bp):
TTTGACTCGAGTTGG
Found at i:13727 original size:37 final size:38
Alignment explanation
Indices: 13672--13762 Score: 100
Period size: 37 Copynumber: 2.4 Consensus size: 38
13662 TTACTTCAAA
* *
13672 ATTATTTTATTCAA-AAAAACA-AATCTAAATAATAA-TT
1 ATTAATTTATT-AATAAAAAAATAAT-TAAATAATAACTT
*
13709 ATTAATTTATTAATAAAAAAATAATTAACTAATAACTT
1 ATTAATTTATTAATAAAAAAATAATTAAATAATAACTT
*
13747 ATT-ATTTTTTAATAAA
1 ATTAATTTATTAATAAA
13763 TAATAAAATG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
36 2 0.04
37 37 0.79
38 8 0.17
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (38 bp):
ATTAATTTATTAATAAAAAAATAATTAAATAATAACTT
Found at i:15667 original size:124 final size:125
Alignment explanation
Indices: 15442--15695 Score: 377
Period size: 124 Copynumber: 2.0 Consensus size: 125
15432 TGAGAGTTCT
*
15442 GTGAGAACACTTTATGAACTAATGCTAGAACATCAATTCTTGATTCTTTTCTGTTCTAATTTTCC
1 GTGAGAACACTTTATGAACTAATGCTAGAACATCAATTCTTGATTC--TTCTATTCTAATTTTCC
*
15507 CCTTCTATTCTATGCCCTATGGCTCTTTTTAATTTGGCCTAGTAGTATGTGTATCTGAACTG
64 CCTTCTATTCTATGCCCTATGGCTCTTTTTAATTTGGCCTAGTAGTACGTGTATCTGAACTG
* * *
15569 GTGAGAACACTTTATGAGCTAAT-CATAGAGCATCAATTCTTGATTC-TCTATTCTAATTTTTCC
1 GTGAGAACACTTTATGAACTAATGC-TAGAACATCAATTCTTGATTCTTCTATTCTAATTTTCCC
* * * * *
15632 CTTCTTTTCTATGCCCTGTGGCTCTTTTTAGTTTGGCCTATTAGTACGTGTATCTGAATTG
65 CTTCTATTCTATGCCCTATGGCTCTTTTTAATTTGGCCTAGTAGTACGTGTATCTGAACTG
15693 GTG
1 GTG
15696 TACTTGTGCT
Statistics
Matches: 116, Mismatches: 10, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
124 73 0.63
126 1 0.01
127 42 0.36
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.43
Consensus pattern (125 bp):
GTGAGAACACTTTATGAACTAATGCTAGAACATCAATTCTTGATTCTTCTATTCTAATTTTCCCC
TTCTATTCTATGCCCTATGGCTCTTTTTAATTTGGCCTAGTAGTACGTGTATCTGAACTG
Found at i:19028 original size:14 final size:14
Alignment explanation
Indices: 19011--19039 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
19001 GAACACAAGT
19011 AGCTTATGAGCACA
1 AGCTTATGAGCACA
19025 AGCTTATGAGCACA
1 AGCTTATGAGCACA
19039 A
1 A
19040 ATGTCTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (14 bp):
AGCTTATGAGCACA
Found at i:21919 original size:83 final size:83
Alignment explanation
Indices: 21780--21945 Score: 314
Period size: 83 Copynumber: 2.0 Consensus size: 83
21770 ATGCACCTTT
*
21780 ATATTTAGGGTAAATTATACTATTGATTATCTAATTATTACCTCTTTTCACTTTGACTATCAATC
1 ATATTTAGGGTAAATTATACTATTGATTATCTAATTATTACCTCTTTTCACTTTGACTATCAATA
21845 TTCTAATTTTTTCAATTA
66 TTCTAATTTTTTCAATTA
*
21863 ATATTTAGGGTAAATTATACTATTGATTATCTAATTATTTCCTCTTTTCACTTTGACTATCAATA
1 ATATTTAGGGTAAATTATACTATTGATTATCTAATTATTACCTCTTTTCACTTTGACTATCAATA
21928 TTCTAATTTTTTCAATTA
66 TTCTAATTTTTTCAATTA
21946 GTTCACTTAA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.30, C:0.14, G:0.06, T:0.50
Consensus pattern (83 bp):
ATATTTAGGGTAAATTATACTATTGATTATCTAATTATTACCTCTTTTCACTTTGACTATCAATA
TTCTAATTTTTTCAATTA
Found at i:27692 original size:24 final size:24
Alignment explanation
Indices: 27655--27719 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
27645 ATCATTTTAA
*
27655 TAAAA-ATATATATTATTAATATT
1 TAAAATATATATATTAATAATATT
* *
27678 TAAAATATATTTATTAATAATCTT
1 TAAAATATATATATTAATAATATT
27702 TAATAATATA-ATA-TAATA
1 TAA-AATATATATATTAATA
27720 TTTTTATTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
23 10 0.28
24 20 0.56
25 6 0.17
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
TAAAATATATATATTAATAATATT
Found at i:27880 original size:25 final size:23
Alignment explanation
Indices: 27852--27906 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 23
27842 TTATTTTAAT
*
27852 AAATATATTAACTATTAAAATATTA
1 AAATATATTAACTAAT-AAAT-TTA
* *
27877 AAATATATTTATTAATAAATTTA
1 AAATATATTAACTAATAAATTTA
27900 AAATATA
1 AAATATA
27907 ATATAATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 10 0.37
24 4 0.15
25 13 0.48
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
AAATATATTAACTAATAAATTTA
Found at i:32436 original size:20 final size:20
Alignment explanation
Indices: 32413--32455 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
32403 TAAAATTTTA
32413 AAATAAAAAATTTAATTGAG
1 AAATAAAAAATTTAATTGAG
32433 AAATAAAAAATTTAATTGAG
1 AAATAAAAAATTTAATTGAG
32453 AAA
1 AAA
32456 AACAAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (20 bp):
AAATAAAAAATTTAATTGAG
Found at i:44449 original size:14 final size:15
Alignment explanation
Indices: 44420--44455 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
44410 TTAGATCGAT
44420 TATATTATTATTTAA
1 TATATTATTATTTAA
*
44435 TTTATTATT-TTTAA
1 TATATTATTATTTAA
44449 TATATTA
1 TATATTA
44456 ATAATTATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TATATTATTATTTAA
Found at i:54413 original size:13 final size:13
Alignment explanation
Indices: 54389--54421 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
54379 TATATTTAAA
54389 TTATTATTATTATT
1 TTATT-TTATTATT
54403 TTATTTTATTATT
1 TTATTTTATTATT
54416 TTATTT
1 TTATTT
54422 AAAAAAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTATTTTATTATT
Done.