Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004385.1 Hibiscus syriacus cultivar Beakdansim tig00009616_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: 59550
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:4963 original size:133 final size:133
Alignment explanation
Indices: 4548--5123 Score: 714
Period size: 133 Copynumber: 4.3 Consensus size: 133
4538 AATTGAACTG
* *
4548 GATTCAATCTTGCCTGAAGAACAGTGGAATGAATCAACATTTCCAAATCTGATTTTCCCTCAAGA
1 GATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCAAGA
* * * * * * * **
4613 AGCAGCGGAACATATCCCTCTTTTTCTCAGATTTGATCTTTCCTGAGGAACGGTGGAACAAGTCT
66 AGAAGC-GAACATATACCTCTCTTTC-AAGATTTGATATTCCCTGAGTAACAATGGAACAAGTCT
4678 GTCTC
129 GTCTC
** *
4683 GATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTTTAGATCCGATTTTCCCTCAAGA
1 GATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCAAGA
* * * * *
4748 AGCAA-CGAA-ATAGATCTCTTTCTTTCAAGATTTGATATTCCCTAAGAAACAGTGGAACAAGTC
66 AG-AAGCGAACATATA-C-CTCTCTTTCAAGATTTGATATTCCCTGAGTAACAATGGAACAAGTC
4811 T-TCCTC
128 TGT-CTC
* * *
4817 GATTCAACCTTCCCTGAAGAACAGTGCAATGAATCAATATTTCCAGATCTGATTTTCCCTCAAGA
1 GATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCAAGA
* * *
4882 AGAAGCAAACATATAACTCTCTTTCAAGACTTGATATTCCCTGAGTAACAATGGAACAAGTCTGT
66 AGAAGCGAACATATACCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAATGGAACAAGTCTGT
4947 CTC
131 CTC
* *
4950 GATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAATATTTCCAGATCTGATTTTCCCTTAAGA
1 GATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCAAGA
* * * * * *
5015 AG-TG-GAACAAAT-CCATCTCTTTCAAGATTTGATATTCCATGAGTAGCAATTGAACAAGCCTG
66 AGAAGCGAACATATACC-TCTCTTTCAAGATTTGATATTCCCTGAGTAACAATGGAACAAGTCTG
* *
5077 CCTT
130 TCTC
* *
5081 GATTCAATCTTCCCTGAAGAACAGTAGAATGAATCAACGTTTC
1 GATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTC
5124 TCAATATGAT
Statistics
Matches: 386, Mismatches: 47, Indels: 20
0.85 0.10 0.04
Matches are distributed among these distances:
130 1 0.00
131 90 0.23
132 1 0.00
133 115 0.30
134 104 0.27
135 74 0.19
136 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (133 bp):
GATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCAAGA
AGAAGCGAACATATACCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAATGGAACAAGTCTGT
CTC
Found at i:5302 original size:13 final size:12
Alignment explanation
Indices: 5284--5315 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
5274 CTCGATGTTT
5284 TTATTTTTATTAA
1 TTATTTTTATT-A
5297 TTATTTTTATTA
1 TTATTTTTATTA
5309 TTATTTT
1 TTATTTT
5316 ATTTTTGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (12 bp):
TTATTTTTATTA
Found at i:5305 original size:19 final size:17
Alignment explanation
Indices: 5281--5321 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
5271 CGTCTCGATG
*
5281 TTTTTATTTTTATTAATTA
1 TTTTTATTATTATT--TTA
5300 TTTTTATTATTATTTTA
1 TTTTTATTATTATTTTA
5317 TTTTT
1 TTTTT
5322 GGTTACAGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.38
19 13 0.62
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTATTATTATTTTA
Found at i:7549 original size:130 final size:129
Alignment explanation
Indices: 7393--7889 Score: 523
Period size: 131 Copynumber: 3.8 Consensus size: 129
7383 TCGATATTAA
* * * **
7393 GAATAGTAATATCTTTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATAAGAGGTCAT
1 GAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGACATAAGAAATCAT
* *
7458 TTATTCTCGATTGAAAATAATTAGATATTACCGTTTTCTCGCGAATCAATATTGATTTTAAGATG
66 TTATTCTCGATTGAAAATAATTAGATATTACCATTTTCTC-CGAATCAATATTGATTTTAAGACG
* * * * * * *
7523 GAATAATGATATCTCTTTATTTCGATTGAAGTAATAAATGAATGCTTTAAGGCATGAGAAGTCAT
1 GAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGACATAAGAAATCAT
* * *
7588 TTATTCTCGATT-AGAAATAATTCGATATTACTATTTTCTCCTTAATCAATATTGATTTTTAAGA
66 TTATTCTCGATTGA-AAATAATTAGATATTACCATTTTCTCC-GAATCAATATTGA-TTTTAAGA
*
7652 CA
128 CG
* * * * * * *
7654 GAATTGTGATATCTCTTCATTTCGATTGGAGCAATAAATAACTGTTTTAAGATATGATAAATCAT
1 GAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGACATAAGAAATCAT
* * * * * * *
7719 TTATTCTCAAATGAAAA-ACATTAGATATTATCATTTTCACTCGAATCGATATTAAACTTTAAGA
66 TTATTCTCGATTGAAAATA-ATTAGATATTACCATTTTCTC-CGAATCAATATT-GATTTTAAGA
7783 CG
128 CG
* * * * *
7785 AAATAGTCATATCTCTTCATTTTGATTGTAGTAATAAATGATTGCTTTAAGACATAA-AAGATCA
1 GAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGACATAAGAA-ATCA
* * * * *
7849 TTTATTATCGATTAAAAATAATTAAATATTATCGTTTTCTC
65 TTTATTCTCGATTGAAAATAATTAGATATTACCATTTTCTC
7890 TCTTAAAATT
Statistics
Matches: 303, Mismatches: 55, Indels: 17
0.81 0.15 0.05
Matches are distributed among these distances:
129 2 0.01
130 107 0.35
131 190 0.63
132 4 0.01
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (129 bp):
GAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGACATAAGAAATCAT
TTATTCTCGATTGAAAATAATTAGATATTACCATTTTCTCCGAATCAATATTGATTTTAAGACG
Found at i:24632 original size:10 final size:10
Alignment explanation
Indices: 24619--24664 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
24609 AAATTTTGGC
24619 TTTTTTGTTT
1 TTTTTTGTTT
*
24629 TTTTTTGCCTT
1 TTTTTTG-TTT
24640 TTTTTTG--T
1 TTTTTTGTTT
24648 TTTTTTGTTT
1 TTTTTTGTTT
24658 TTTTTTG
1 TTTTTTG
24665 AAAAAAATAG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
8 8 0.25
10 15 0.47
11 9 0.28
ACGTcount: A:0.00, C:0.04, G:0.11, T:0.85
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:24634 original size:19 final size:19
Alignment explanation
Indices: 24612--24664 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
24602 TTTTTTAAAA
*
24612 TTTTGGCTTTTTTGTT-TTT
1 TTTTGCCTTTTTT-TTGTTT
24631 TTTTGCCTTTTTTTTGTTT
1 TTTTGCCTTTTTTTTGTTT
*
24650 TTTTG-TTTTTTTTTG
1 TTTTGCCTTTTTTTTG
24665 AAAAAAATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 11 0.35
19 20 0.65
ACGTcount: A:0.00, C:0.06, G:0.13, T:0.81
Consensus pattern (19 bp):
TTTTGCCTTTTTTTTGTTT
Found at i:26694 original size:23 final size:22
Alignment explanation
Indices: 26629--26702 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 22
26619 GACAGTGTAC
* *
26629 CGATGCATCCCTTGAATATTCAT
1 CGATGCAT-CCTTGAATGTGCAT
* *
26652 CGATACA-CCATGAA-GATGCAT
1 CGATGCATCCTTGAATG-TGCAT
26673 CGATGCATTCCTTGAATGTGCAT
1 CGATGCA-TCCTTGAATGTGCAT
26696 CGATGCA
1 CGATGCA
26703 CTCTGCCGTG
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
21 16 0.39
23 24 0.59
24 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (22 bp):
CGATGCATCCTTGAATGTGCAT
Found at i:27324 original size:25 final size:25
Alignment explanation
Indices: 27296--27345 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
27286 ATATTGAAGA
27296 CTCTTTTGAGTTTTGGGATTGATTG
1 CTCTTTTGAGTTTTGGGATTGATTG
27321 CTCTTTTGAGTTTTGGGATTGATTG
1 CTCTTTTGAGTTTTGGGATTGATTG
27346 AAATTGCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.12, C:0.08, G:0.28, T:0.52
Consensus pattern (25 bp):
CTCTTTTGAGTTTTGGGATTGATTG
Found at i:29200 original size:65 final size:64
Alignment explanation
Indices: 29119--29274 Score: 213
Period size: 65 Copynumber: 2.4 Consensus size: 64
29109 GCAACCCATT
* ** *
29119 TCGAATGCATTTTGTGTACCGATGCACAAGCCATGCATCGATGCACTTTTGAATATTTTGAAACA
1 TCGAATGCATTTTGTGTACCGATGCACAAACCATGCATCGATGCACTCCTGAAT-CTTTGAAACA
* * *
29184 TCGAATGCATTTTGTGTACGGATGCACAAACCATGCATCGATGCACTCCTGACTCTTTGGAACA
1 TCGAATGCATTTTGTGTACCGATGCACAAACCATGCATCGATGCACTCCTGAATCTTTGAAACA
* * *
29248 TCGAATGTAATTAGTGTACCGATGCAC
1 TCGAATGCATTTTGTGTACCGATGCAC
29275 TAAGTCTTAT
Statistics
Matches: 80, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
64 31 0.39
65 49 0.61
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (64 bp):
TCGAATGCATTTTGTGTACCGATGCACAAACCATGCATCGATGCACTCCTGAATCTTTGAAACA
Found at i:30930 original size:45 final size:45
Alignment explanation
Indices: 30858--31204 Score: 473
Period size: 45 Copynumber: 7.7 Consensus size: 45
30848 AATGCACAAT
* * * * *
30858 TATGCATTTTCATTTATGACATTCTTTCATGCCAATAATGTACCCA
1 TATGCA-TTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCA
30904 TATGCATTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCA
1 TATGCATTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCA
* * * *
30949 TATGTATTTCAATTATGGCATCATTTCATTCCGATAATGCAACCA
1 TATGCATTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCA
* *
30994 TATGCATTTCAATTATGACATCCTTTCATGTCGATAATGCACCCA
1 TATGCATTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCA
* *
31039 TATCCATTTCAATTATGGCCTCCTTTCATGCCGATAATGCACCCA
1 TATGCATTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCA
* * *
31084 TATGCATTTC-ATTAATGGCATCCTTTTATGGC-ATTAATACACCCA
1 TATGCATTTCAATT-ATGGCATCCTTTCATGCCGA-TAATGCACCCA
* *
31129 TATACATTTCATTTATGGCATCCTTTCATGCCGATAATGCACCCA
1 TATGCATTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCA
* *
31174 TATGTATTTCATTTATGGCATCCTTTCATGC
1 TATGCATTTCAATTATGGCATCCTTTCATGC
31205 TTTTTTATTC
Statistics
Matches: 266, Mismatches: 31, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
44 4 0.02
45 253 0.95
46 9 0.03
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.37
Consensus pattern (45 bp):
TATGCATTTCAATTATGGCATCCTTTCATGCCGATAATGCACCCA
Found at i:31506 original size:68 final size:68
Alignment explanation
Indices: 31397--31788 Score: 603
Period size: 68 Copynumber: 5.8 Consensus size: 68
31387 ATGTATTTAA
*
31397 CCTTTCATCTAACT-GCATAATTGACACATTTCTGTCAAATGCACAACTAGGCCTCAAAGGCACT
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCTCAAAGGCACT
31461 TAG
66 TAG
* * *
31464 CCTTTCATCTAACTGGCATAATTGACACCTTTGTATCAAATGCACAACTAGGCCTCAAAGGCAAT
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCTCAAAGGCACT
31529 TAG
66 TAG
** * * *
31532 ATTTTCATCTAACTGGCATAATTGACAACTTTCTTTCAAATGCATAACTAGGCCTCAAAGGCACT
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCTCAAAGGCACT
31597 TAG
66 TAG
*
31600 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCCTCAAAGGCACT
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCTCAAAGGCACT
31665 TAG
66 TAG
* * *
31668 CCTTTCATCTAACTTGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCCTCAAAGGCA-T
1 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCTCAAAGGCACT
31732 TAG
66 TAG
* *
31735 CCTTTCATCTAACTGGAATAATTAACACCCTTT-TGTCAAA-GCCACAACTAGGCC
1 CCTTTCATCTAACTGGCATAATTGACA-CCTTTCTGTCAAATG-CACAACTAGGCC
31789 ATTAATCTTT
Statistics
Matches: 298, Mismatches: 24, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
66 1 0.00
67 60 0.20
68 237 0.80
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (68 bp):
CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCTCAAAGGCACT
TAG
Found at i:33035 original size:46 final size:46
Alignment explanation
Indices: 32911--33088 Score: 167
Period size: 46 Copynumber: 3.8 Consensus size: 46
32901 GTGATTGGAC
* ** * * * * *
32911 ATTACCATCCTACGAGGATCCACCAACCTATAATTCGGTAATTGAA
1 ATTACCATCCGATAAGGATGCACCAGCCTGTAATTCAGTAATTAAA
* * * *
32957 ATTACCTTCCGATAAGGGTGCACCATCCTGTAAATCAGTAATTAAA
1 ATTACCATCCGATAAGGATGCACCAGCCTGTAATTCAGTAATTAAA
* * * * * *
33003 ATTATCATCCGATAAGGATGCACCCGCATGTAATTTAGTTATTATA
1 ATTACCATCCGATAAGGATGCACCAGCCTGTAATTCAGTAATTAAA
* *
33049 TTTAGCCATCCGATGAGGATGCACCAGCCTGTAATTCAGT
1 ATTA-CCATCCGATAAGGATGCACCAGCCTGTAATTCAGT
33089 TATCCTTCCT
Statistics
Matches: 104, Mismatches: 27, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
46 74 0.71
47 30 0.29
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.29
Consensus pattern (46 bp):
ATTACCATCCGATAAGGATGCACCAGCCTGTAATTCAGTAATTAAA
Found at i:40471 original size:12 final size:12
Alignment explanation
Indices: 40443--40476 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
40433 ATGTCTTAAA
40443 AAAGTCAACAATC
1 AAAGTCAA-AATC
*
40456 AAAGTCAAATTC
1 AAAGTCAAAATC
40468 AAAGTCAAA
1 AAAGTCAAA
40477 GTTAACAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.56, C:0.18, G:0.09, T:0.18
Consensus pattern (12 bp):
AAAGTCAAAATC
Found at i:52922 original size:108 final size:108
Alignment explanation
Indices: 52645--53016 Score: 442
Period size: 108 Copynumber: 3.4 Consensus size: 108
52635 ACTACAGTCA
* * * * * * *
52645 TTCATAAACATATTATAAATTTTGTGGGTTACACACATAGTGCCTAAATGATTGTTCATTAACAT
1 TTCATTAACATATAATGAATTTTGTGGGTTGCACACATAGTGCCAAAATGATTGTTCATCAACTT
* * *
52710 ATAATGAATTCCGTGGTTTGCACACATATAGTGCCAAAACGGTTG
66 ATGATGAATTCCGTGGGTTGCACAC--ATAGTGCCTAAACGGTTG
* * * * *
52755 TTCATCAACTTATGATGAATTTCGTGGGTTGCACACATAGTGCCAAAGTGATTGTTCATCAACTT
1 TTCATTAACATATAATGAATTTTGTGGGTTGCACACATAGTGCCAAAATGATTGTTCATCAACTT
* * * *
52820 AGGATGAATTCCGTGGGTTGCAGACATAGTTCTTAAACGGTTG
66 ATGATGAATTCCGTGGGTTGCACACATAGTGCCTAAACGGTTG
* * * * * *
52863 TTGATTAACATATAATGAATTCTGTGGTTTGCGCACACAGTGCCAAAATGGTTGTTCATCAACTT
1 TTCATTAACATATAATGAATTTTGTGGGTTGCACACATAGTGCCAAAATGATTGTTCATCAACTT
* *
52928 ATGATGAATTCCATGGGTTGCACACATAGTGCCTAAATGGTTG
66 ATGATGAATTCCGTGGGTTGCACACATAGTGCCTAAACGGTTG
* * *
52971 TTCATTAAC-T-TAATGAATTTTGTGGTTTGCATACAAAGTGCCAAAA
1 TTCATTAACATATAATGAATTTTGTGGGTTGCACACATAGTGCCAAAA
53017 GTACACATAG
Statistics
Matches: 223, Mismatches: 39, Indels: 4
0.84 0.15 0.02
Matches are distributed among these distances:
106 32 0.14
107 1 0.00
108 114 0.51
110 76 0.34
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (108 bp):
TTCATTAACATATAATGAATTTTGTGGGTTGCACACATAGTGCCAAAATGATTGTTCATCAACTT
ATGATGAATTCCGTGGGTTGCACACATAGTGCCTAAACGGTTG
Found at i:52953 original size:162 final size:161
Alignment explanation
Indices: 52668--52989 Score: 459
Period size: 162 Copynumber: 2.0 Consensus size: 161
52658 TATAAATTTT
*
52668 GTGGGTTACACACATAGTGCCTAAATGATTGTTCATTAACATATAATGAATTCCGTGGTTTGCAC
1 GTGGGTTACACACATAGTGCCTAAACGATTGTTCATTAACATATAATGAATTCCGTGGTTTGCAC
* * *
52733 ACATATAGTGCCAAAACGGTTGTTCATCAACTTATGATGAATTTCGTGGGTTGCACACATAGTGC
66 ACA-ACAGTGCCAAAACGGTTGTTCATCAACTTATGATGAATTCCATGGGTTGCACACATAGTGC
52798 C-AAAGTGATTGTTCATCAACTTAGGATGAATTCC
130 CTAAA-TGATTGTTCATCAACTTA--ATGAATTCC
* * * * * * * *
52832 GTGGGTTGCAGACATAGTTCTTAAACGGTTGTTGATTAACATATAATGAATTCTGTGGTTTGCGC
1 GTGGGTTACACACATAGTGCCTAAACGATTGTTCATTAACATATAATGAATTCCGTGGTTTGCAC
*
52897 AC-ACAGTGCCAAAATGGTTGTTCATCAACTTATGATGAATTCCATGGGTTGCACACATAGTGCC
66 ACAACAGTGCCAAAACGGTTGTTCATCAACTTATGATGAATTCCATGGGTTGCACACATAGTGCC
* *
52961 TAAATGGTTGTTCATTAACTTAATGAATT
131 TAAATGATTGTTCATCAACTTAATGAATT
52990 TTGTGGTTTG
Statistics
Matches: 142, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
160 7 0.05
162 74 0.52
163 3 0.02
164 58 0.41
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (161 bp):
GTGGGTTACACACATAGTGCCTAAACGATTGTTCATTAACATATAATGAATTCCGTGGTTTGCAC
ACAACAGTGCCAAAACGGTTGTTCATCAACTTATGATGAATTCCATGGGTTGCACACATAGTGCC
TAAATGATTGTTCATCAACTTAATGAATTCC
Found at i:52981 original size:54 final size:54
Alignment explanation
Indices: 52668--53012 Score: 363
Period size: 54 Copynumber: 6.4 Consensus size: 54
52658 TATAAATTTT
* * * * *
52668 GTGGGTTACACACATAGTGCCTAAATGATTGTTCATTAACATATAATGAATTCC
1 GTGGGTTGCACACATAGTGCCTAAATGGTTGTTCATCAACTTATGATGAATTCC
* * * *
52722 GTGGTTTGCACACATATAGTGCCAAAACGGTTGTTCATCAACTTATGATGAATTTC
1 GTGGGTTGCACAC--ATAGTGCCTAAATGGTTGTTCATCAACTTATGATGAATTCC
* *
52778 GTGGGTTGCACACATAGTGCC-AAAGTGATTGTTCATCAACTTAGGATGAATTCC
1 GTGGGTTGCACACATAGTGCCTAAA-TGGTTGTTCATCAACTTATGATGAATTCC
* * * * * * * * *
52832 GTGGGTTGCAGACATAGTTCTTAAACGGTTGTTGATTAACATATAATGAATTCT
1 GTGGGTTGCACACATAGTGCCTAAATGGTTGTTCATCAACTTATGATGAATTCC
* * * *
52886 GTGGTTTGCGCACACAGTGCCAAAATGGTTGTTCATCAACTTATGATGAATTCC
1 GTGGGTTGCACACATAGTGCCTAAATGGTTGTTCATCAACTTATGATGAATTCC
* * **
52940 ATGGGTTGCACACATAGTGCCTAAATGGTTGTTCATTAACTTA--ATGAATTTT
1 GTGGGTTGCACACATAGTGCCTAAATGGTTGTTCATCAACTTATGATGAATTCC
* * *
52992 GTGGTTTGCATACAAAGTGCC
1 GTGGGTTGCACACATAGTGCC
53013 AAAAGTACAC
Statistics
Matches: 237, Mismatches: 50, Indels: 10
0.80 0.17 0.03
Matches are distributed among these distances:
52 24 0.10
53 3 0.01
54 161 0.68
55 3 0.01
56 46 0.19
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.34
Consensus pattern (54 bp):
GTGGGTTGCACACATAGTGCCTAAATGGTTGTTCATCAACTTATGATGAATTCC
Found at i:59524 original size:54 final size:53
Alignment explanation
Indices: 59372--59550 Score: 206
Period size: 54 Copynumber: 3.4 Consensus size: 53
59362 ACTACGATCA
* * * * *
59372 TTCATAAACATATTATGAATTTTGTGGGTTGCACACATAGTGTCTAAACGGTTG
1 TTCATCAACTTATGATGAA-TTTGTGGGTTGCACACATAGTGCCAAAACGGTTG
* * *
59426 TTC-T-TA--TATAATGAATTTGTGGATTGCACACATATAGTGCCAAAACGGTTG
1 TTCATCAACTTATGATGAATTTGTGGGTTGCACAC--ATAGTGCCAAAACGGTTG
*
59477 TTCATCAACTTATGATGAATTTCGTGGGTTGCACACATAGTGCCAAAACAGTTG
1 TTCATCAACTTATGATGAATTT-GTGGGTTGCACACATAGTGCCAAAACGGTTG
59531 TTCATCAACTT-TGATGAATT
1 TTCATCAACTTATGATGAATT
Statistics
Matches: 109, Mismatches: 9, Indels: 15
0.82 0.07 0.11
Matches are distributed among these distances:
49 15 0.14
50 8 0.07
51 19 0.17
52 2 0.02
53 11 0.10
54 31 0.28
55 11 0.10
56 12 0.11
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (53 bp):
TTCATCAACTTATGATGAATTTGTGGGTTGCACACATAGTGCCAAAACGGTTG
Done.