Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006810.1 Hibiscus syriacus cultivar Beakdansim tig00017284_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: 50310
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:4644 original size:22 final size:23
Alignment explanation
Indices: 4616--4666 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
4606 CTTCCAGTGT
* *
4616 TATTTTC-AGTTTCTTACCCATG
1 TATTTTCAAATTTCTTACCCATA
4638 TATTTTCATAATTTCTTACCCATA
1 TATTTTCA-AATTTCTTACCCATA
4662 TATTT
1 TATTT
4667 ATGACAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 7 0.28
24 18 0.72
ACGTcount: A:0.24, C:0.20, G:0.04, T:0.53
Consensus pattern (23 bp):
TATTTTCAAATTTCTTACCCATA
Found at i:7288 original size:22 final size:24
Alignment explanation
Indices: 7256--7303 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
7246 ATATCAAGAC
*
7256 TTAAAAA-TTT-TGTACACTTTTT
1 TTAAAAATTTTCTGCACACTTTTT
*
7278 TTAAAACTTTTCTGCACACTTTTT
1 TTAAAAATTTTCTGCACACTTTTT
7302 TT
1 TT
7304 TTTTAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 6 0.27
23 3 0.14
24 13 0.59
ACGTcount: A:0.27, C:0.15, G:0.04, T:0.54
Consensus pattern (24 bp):
TTAAAAATTTTCTGCACACTTTTT
Found at i:14286 original size:29 final size:26
Alignment explanation
Indices: 14244--14321 Score: 102
Period size: 29 Copynumber: 2.8 Consensus size: 26
14234 TAAAATTTAC
*
14244 TTTTTTTTAGTATTTGCTATTAGAGACT
1 TTTTTTTTAATATTTG-TATTAGAGA-T
14272 TATTTTTTTAATATTTGTCATTAGAGAT
1 T-TTTTTTTAATATTTGT-ATTAGAGAT
14300 TTTTTTTTAATATTTGTTATTA
1 TTTTTTTTAATATTTG-TATTA
14322 TGAAGTTGCC
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
27 19 0.41
28 5 0.11
29 22 0.48
ACGTcount: A:0.24, C:0.04, G:0.10, T:0.62
Consensus pattern (26 bp):
TTTTTTTTAATATTTGTATTAGAGAT
Found at i:16108 original size:25 final size:24
Alignment explanation
Indices: 16080--16127 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
16070 AATTCGACTT
* *
16080 AATTTGAAAAATTAATTTTTTTTTA
1 AATTTAAAAAATT-ATTATTTTTTA
16105 AATTTAAAAAATTATTATTTTTT
1 AATTTAAAAAATTATTATTTTTT
16128 CAACATGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
AATTTAAAAAATTATTATTTTTTA
Found at i:16138 original size:24 final size:25
Alignment explanation
Indices: 16084--16139 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
16074 CGACTTAATT
* **
16084 TGAAAAATTAATTTTTTTTTAAATT
1 TGAAAAATTAATTATTTTTTAAACA
* *
16109 TAAAAAATT-ATTATTTTTTCAACA
1 TGAAAAATTAATTATTTTTTAAACA
16133 TGAAAAA
1 TGAAAAA
16140 AATTTAATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
24 17 0.68
25 8 0.32
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (25 bp):
TGAAAAATTAATTATTTTTTAAACA
Found at i:17216 original size:28 final size:28
Alignment explanation
Indices: 17155--17241 Score: 122
Period size: 28 Copynumber: 3.1 Consensus size: 28
17145 AAATAAAACA
17155 AAAACTAAAAATTAGATATG-TTTTTTT
1 AAAACTAAAAATTAGATATGATTTTTTT
* * *
17182 AATACTAAAGATTAGATATGATTTTTTG
1 AAAACTAAAAATTAGATATGATTTTTTT
* *
17210 AAAACTAAATATTATATATGATTTTTTT
1 AAAACTAAAAATTAGATATGATTTTTTT
17238 AAAA
1 AAAA
17242 ATTAAGAGTT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
27 18 0.35
28 34 0.65
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (28 bp):
AAAACTAAAAATTAGATATGATTTTTTT
Found at i:18320 original size:33 final size:33
Alignment explanation
Indices: 18278--18348 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
18268 GAATAGACTT
*
18278 GGTTTTGAAGAATCAAACCAGTGGCGGGAACTC
1 GGTTTTGAAGAATCAAACCAGTGGCGGGAACAC
*
18311 GGTTTTGAAGAGTCAAACCAGTGGCGGGAACAC
1 GGTTTTGAAGAATCAAACCAGTGGCGGGAACAC
18344 GGTTT
1 GGTTT
18349 CTGATGCTGG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.28, C:0.17, G:0.32, T:0.23
Consensus pattern (33 bp):
GGTTTTGAAGAATCAAACCAGTGGCGGGAACAC
Found at i:22956 original size:114 final size:114
Alignment explanation
Indices: 22756--22984 Score: 458
Period size: 114 Copynumber: 2.0 Consensus size: 114
22746 AGGAAAAGAA
22756 TATCAGTAAAAAATATATACTATACATACTCATCCATATATGGGAACATATATGCATTATGCATC
1 TATCAGTAAAAAATATATACTATACATACTCATCCATATATGGGAACATATATGCATTATGCATC
22821 TCTACACTTATTTTTCTTGTCTATCCAGCTTCTTATATGGCTTATGCAT
66 TCTACACTTATTTTTCTTGTCTATCCAGCTTCTTATATGGCTTATGCAT
22870 TATCAGTAAAAAATATATACTATACATACTCATCCATATATGGGAACATATATGCATTATGCATC
1 TATCAGTAAAAAATATATACTATACATACTCATCCATATATGGGAACATATATGCATTATGCATC
22935 TCTACACTTATTTTTCTTGTCTATCCAGCTTCTTATATGGCTTATGCAT
66 TCTACACTTATTTTTCTTGTCTATCCAGCTTCTTATATGGCTTATGCAT
22984 T
1 T
22985 CTGCATCTCT
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 115 1.00
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (114 bp):
TATCAGTAAAAAATATATACTATACATACTCATCCATATATGGGAACATATATGCATTATGCATC
TCTACACTTATTTTTCTTGTCTATCCAGCTTCTTATATGGCTTATGCAT
Found at i:23042 original size:57 final size:57
Alignment explanation
Indices: 22920--23044 Score: 232
Period size: 57 Copynumber: 2.2 Consensus size: 57
22910 TGGGAACATA
*
22920 TATGCATTATGCATCTCTACACTTATTTTTCTTGTCTATCCAGCTTCTTATATGGCT
1 TATGCATTCTGCATCTCTACACTTATTTTTCTTGTCTATCCAGCTTCTTATATGGCT
*
22977 TATGCATTCTGCATCTCTACACTTATTTTTCTTGTCTATCCTGCTTCTTATATGGCT
1 TATGCATTCTGCATCTCTACACTTATTTTTCTTGTCTATCCAGCTTCTTATATGGCT
23034 TATGCATTCTG
1 TATGCATTCTG
23045 AGAAGTCATC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 66 1.00
ACGTcount: A:0.18, C:0.23, G:0.11, T:0.48
Consensus pattern (57 bp):
TATGCATTCTGCATCTCTACACTTATTTTTCTTGTCTATCCAGCTTCTTATATGGCT
Found at i:29291 original size:17 final size:17
Alignment explanation
Indices: 29269--29333 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
29259 CGTATAAATG
29269 TCCCGAAGGACCTATCA
1 TCCCGAAGGACCTATCA
** *
29286 TCCCGAAGGATGTCATCTGTG
1 TCCCGAAGGACCT-ATC---A
*
29307 TCCCGAAGGACCTGTCA
1 TCCCGAAGGACCTATCA
29324 TCCCGAAGGA
1 TCCCGAAGGA
29334 TGTAATCTGT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
17 21 0.57
18 3 0.08
20 2 0.05
21 11 0.30
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.20
Consensus pattern (17 bp):
TCCCGAAGGACCTATCA
Found at i:29312 original size:21 final size:21
Alignment explanation
Indices: 29286--29349 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
29276 GGACCTATCA
29286 TCCCGAAGGATGTCATCTGTG
1 TCCCGAAGGATGTCATCTGTG
*
29307 TCCCGAAGGA---C--CTGTCA
1 TCCCGAAGGATGTCATCTGT-G
*
29324 TCCCGAAGGATGTAATCTGTG
1 TCCCGAAGGATGTCATCTGTG
29345 TCCCG
1 TCCCG
29350 TATGACCTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 12
0.69 0.06 0.24
Matches are distributed among these distances:
16 4 0.12
17 10 0.29
18 1 0.03
21 15 0.44
22 4 0.12
ACGTcount: A:0.20, C:0.28, G:0.27, T:0.25
Consensus pattern (21 bp):
TCCCGAAGGATGTCATCTGTG
Found at i:29318 original size:38 final size:38
Alignment explanation
Indices: 29267--29362 Score: 156
Period size: 38 Copynumber: 2.5 Consensus size: 38
29257 CTCGTATAAA
*
29267 TGTCCCGAAGGACCTATCATCCCGAAGGATGTCATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
*
29305 TGTCCCGAAGGACCTGTCATCCCGAAGGATGTAATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
* *
29343 TGTCCCGTATGACCTATCAT
1 TGTCCCGAAGGACCTATCAT
29363 ATGTCTTATA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 53 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (38 bp):
TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
Found at i:32591 original size:48 final size:48
Alignment explanation
Indices: 32520--32619 Score: 137
Period size: 48 Copynumber: 2.1 Consensus size: 48
32510 CATACTTTGT
*
32520 GTATGATGGTCATCGATCGATTTTATTTAATGCATAGGTTGCATTTTC
1 GTATGATGGTCATCGATCAATTTTATTTAATGCATAGGTTGCATTTTC
* * * * **
32568 GTATGATGGTTATCGATTAATTTTGTTTAATGCCTATTTTGCATTTTC
1 GTATGATGGTCATCGATCAATTTTATTTAATGCATAGGTTGCATTTTC
32616 GTAT
1 GTAT
32620 CAGTATTATG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.22, C:0.11, G:0.19, T:0.48
Consensus pattern (48 bp):
GTATGATGGTCATCGATCAATTTTATTTAATGCATAGGTTGCATTTTC
Found at i:32754 original size:56 final size:55
Alignment explanation
Indices: 32644--32824 Score: 190
Period size: 56 Copynumber: 3.3 Consensus size: 55
32634 CTTTCGGCAC
* * * * * *
32644 TATGTGTGCAACACATGAAATTCATAATGAGTTTGTGAATTATCGTATCAACACTA
1 TATGTGTGCAACTCATG-AATTCATAATGAGTTTATGAATTACCATTTCGACACTA
* * *
32700 TATGTGTGCAACCCATGACATTCATAATGAGTTTATAAATGACCATTTCGACACTA
1 TATGTGTGCAACTCATGA-ATTCATAATGAGTTTATGAATTACCATTTCGACACTA
* * * *
32756 CATGTGTGC-ATTAATGGAATTCATAATGAGTTTATGGATTACCATTTCGACACT-
1 TATGTGTGCAACTCAT-GAATTCATAATGAGTTTATGAATTACCATTTCGACACTA
32810 TA-G-GTGCAACTCATG
1 TATGTGTGCAACTCATG
32825 TACCTTGTAT
Statistics
Matches: 104, Mismatches: 18, Indels: 10
0.79 0.14 0.08
Matches are distributed among these distances:
52 5 0.05
53 5 0.05
54 1 0.01
55 37 0.36
56 56 0.54
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (55 bp):
TATGTGTGCAACTCATGAATTCATAATGAGTTTATGAATTACCATTTCGACACTA
Found at i:36905 original size:131 final size:132
Alignment explanation
Indices: 36671--37198 Score: 637
Period size: 131 Copynumber: 4.0 Consensus size: 132
36661 AACCTTTCAC
* *
36671 GAGGAGGTGGAAAATCATAGAAAAGGAGGGTTTTT-CTGAAATGGGTTTCTCTTGATTTTGAGAA
1 GAGGAGGTGGAAAATCATAGAAAAGGAGGGTTTTTAAT-AAATGGGTTTCTCTTGATTTTGAGGA
* *
36735 GTTTTTATTAATGAATAAACTGCTCCAGTTAGAGGGAATGGGGGTTTTT-CCGTCTTGAAATTGG
65 GTTTTTATTAATGAATAAACTGCTCCAATTAGAGGGAATGGGGGTTTTTCCCGTCTTGAAATGGG
36799 AAG
130 AAG
36802 GAGGAGGTGGAAAATCATAGAAAAGGAGGGTTTTTAATAAATGGGTTTCTCTTGATTTTGAGGAG
1 GAGGAGGTGGAAAATCATAGAAAAGGAGGGTTTTTAATAAATGGGTTTCTCTTGATTTTGAGGAG
* * * *
36867 TTTTTTTTAATGAATAAACTTCTGCAATTAGAGGGAATGGGGTTTTTTCCCGTCTTGAAATGGGA
66 TTTTTATTAATGAATAAACTGCTCCAATTAGAGGGAATGGGGGTTTTTCCCGTCTTGAAATGGGA
36932 A-
131 AG
* * * * * * * * * ****
36933 GTGTAGAT-GAAGAT-AGT-G--AAGGA--ATTAATTGGAGGAGGAGGAGGAGGAGGATCTTGAT
1 GAGGAGGTGGAAAATCA-TAGAAAAGGAGGGTT--TT-TA--A-TA-AATG-GGTTTCTCTTGAT
*
36991 TTTGAGGAGTTTTTATTAATGAATAAACTGCTCCAGTTAGAGGGAATGGGGGTTTTT-CCGTCTT
57 TTTGAGGAGTTTTTATTAATGAATAAACTGCTCCAATTAGAGGGAATGGGGGTTTTTCCCGTCTT
*
37055 GAAATTGGAAG
122 GAAATGGGAAG
37066 GAGGAGGTGGAAAATCATAGAAAAGGAGGGTTTTTTAATAAATGGGTTTCTCTTGATTTTGAGGA
1 GAGGAGGTGGAAAATCATAGAAAAGGAGGG-TTTTTAATAAATGGGTTTCTCTTGATTTTGAGGA
* * * *
37131 GTTTTTTTTAATGAATAAACTTCTGCAATTAGAGGGAATGGGGTTTTTTCCCGTCTTGAAATGGG
65 GTTTTTATTAATGAATAAACTGCTCCAATTAGAGGGAATGGGGGTTTTTCCCGTCTTGAAATGGG
37196 AAG
130 AAG
37199 TGAAATGGGA
Statistics
Matches: 330, Mismatches: 46, Indels: 40
0.79 0.11 0.10
Matches are distributed among these distances:
125 2 0.01
127 7 0.02
128 1 0.00
129 2 0.01
130 7 0.02
131 110 0.33
132 96 0.29
133 85 0.26
134 7 0.02
135 3 0.01
137 6 0.02
138 2 0.01
140 2 0.01
ACGTcount: A:0.30, C:0.07, G:0.30, T:0.34
Consensus pattern (132 bp):
GAGGAGGTGGAAAATCATAGAAAAGGAGGGTTTTTAATAAATGGGTTTCTCTTGATTTTGAGGAG
TTTTTATTAATGAATAAACTGCTCCAATTAGAGGGAATGGGGGTTTTTCCCGTCTTGAAATGGGA
AG
Found at i:37017 original size:133 final size:133
Alignment explanation
Indices: 36851--37260 Score: 397
Period size: 132 Copynumber: 3.0 Consensus size: 133
36841 AATGGGTTTC
36851 TCTTGATTTTGAGGAGTTTTTTTTAATGAATAAACTTCTGCAATTAGAGGGAATGGGGTTTTTTC
1 TCTTGATTTTGAGGAGTTTTTTTTAATGAATAAACTTCTGCAATTAGAGGGAATGGGGTTTTTTC
36916 CCGTCTTGAAATGGGAAGTGTAGATGAAGATAGTGAAGGAATTAATTGGAGGAGGAGGAGGAGGA
66 CCGTCTTGAAATGGGAAGTGTAGATGAAGATAGTGAAGGAATTAATTGGAGGAGGAGGAGGAGGA
36981 GGA
131 GGA
* * * * *
36984 TCTTGATTTTGAGGAGTTTTTATTAATGAATAAACTGCTCCAGTTAGAGGGAATGGGGGTTTTT-
1 TCTTGATTTTGAGGAGTTTTTTTTAATGAATAAACTTCTGCAATTAGAGGGAATGGGGTTTTTTC
* * * * * * ** *
37048 CCGTCTTGAAATTGGAAGGAGGAGGTGGAAAATCA-TAGAAAAGGAGGGTT--TTTTA--A-TA-
66 CCGTCTTGAAATGGGAA-GTGTAGAT-GAAGAT-AGT-G--AAGGA--ATTAATTGGAGGAGGAG
* * ****
37106 AATG-GGTTTC
123 GAGGAGGAGGA
37116 TCTTGATTTTGAGGAGTTTTTTTTAATGAATAAACTTCTGCAATTAGAGGGAATGGGGTTTTTTC
1 TCTTGATTTTGAGGAGTTTTTTTTAATGAATAAACTTCTGCAATTAGAGGGAATGGGGTTTTTTC
37181 CCGTCTTGAAATGGGAAGTGAAATGGGAAGTGTAGATGAAGATAGTGAAGGAATTAATTGGAGGA
66 CCGTC------T------TGAAATGGGAAGTGTAGATGAAGATAGTGAAGGAATTAATTGGAGGA
37246 GGAGGAGGAGGAGGA
119 GGAGGAGGAGGAGGA
37261 GGAGGAGGAG
Statistics
Matches: 208, Mismatches: 40, Indels: 46
0.71 0.14 0.16
Matches are distributed among these distances:
132 77 0.37
133 71 0.34
134 7 0.03
135 3 0.01
137 8 0.04
138 2 0.01
139 3 0.01
140 8 0.04
142 3 0.01
143 7 0.03
144 7 0.03
145 12 0.06
ACGTcount: A:0.30, C:0.06, G:0.31, T:0.32
Consensus pattern (133 bp):
TCTTGATTTTGAGGAGTTTTTTTTAATGAATAAACTTCTGCAATTAGAGGGAATGGGGTTTTTTC
CCGTCTTGAAATGGGAAGTGTAGATGAAGATAGTGAAGGAATTAATTGGAGGAGGAGGAGGAGGA
GGA
Found at i:37204 original size:12 final size:12
Alignment explanation
Indices: 37187--37212 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
37177 TTTCCCGTCT
37187 TGAAATGGGAAG
1 TGAAATGGGAAG
37199 TGAAATGGGAAG
1 TGAAATGGGAAG
37211 TG
1 TG
37213 TAGATGAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.42, T:0.19
Consensus pattern (12 bp):
TGAAATGGGAAG
Found at i:37248 original size:3 final size:3
Alignment explanation
Indices: 37240--37556 Score: 634
Period size: 3 Copynumber: 105.7 Consensus size: 3
37230 GGAATTAATT
37240 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
37288 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
37336 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
37384 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
37432 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
37480 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
37528 GGA GGA GGA GGA GGA GGA GGA GGA GGA GG
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GG
37557 TAATTAAGTG
Statistics
Matches: 314, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 314 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:41191 original size:48 final size:48
Alignment explanation
Indices: 41115--41209 Score: 145
Period size: 48 Copynumber: 2.0 Consensus size: 48
41105 ATACTTTGTG
41115 TATGATGGTCATCGATCGATTTTATTTAATGCATAAGTTGCATTTTCA
1 TATGATGGTCATCGATCGATTTTATTTAATGCATAAGTTGCATTTTCA
* * * * *
41163 TATGATGGTTATTGATCGATTTTGTTTAATGCCTATGTTGCATTTTC
1 TATGATGGTCATCGATCGATTTTATTTAATGCATAAGTTGCATTTTC
41210 GTATCAGTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.23, C:0.12, G:0.18, T:0.47
Consensus pattern (48 bp):
TATGATGGTCATCGATCGATTTTATTTAATGCATAAGTTGCATTTTCA
Found at i:41346 original size:54 final size:54
Alignment explanation
Indices: 41229--41401 Score: 179
Period size: 54 Copynumber: 3.2 Consensus size: 54
41219 TTATGTGTAC
* * * * *
41229 TTTCTGCACTATGTGTGCAACACACGAAATTCATAATGAGTTTGTGAATTACCG
1 TTTCGGCACTATGTGTGCAACACATGGAATTCATAATGAGTTTATGAATTACCA
* * * * *
41283 TATT-AGCACTATGTGTGCAACCCATGGTATTCATAATGAGATTATGAATGACCA
1 T-TTCGGCACTATGTGTGCAACACATGGAATTCATAATGAGTTTATGAATTACCA
** *
41337 TTTCGGCACTACATGTGTGCATTA-ATGGAATTCATAATGAGTTTATGGATTACCA
1 TTTCGGCACT--ATGTGTGCAACACATGGAATTCATAATGAGTTTATGAATTACCA
*
41392 TTTCGACACT
1 TTTCGGCACT
41402 TAGGTGCAAA
Statistics
Matches: 97, Mismatches: 18, Indels: 7
0.80 0.15 0.06
Matches are distributed among these distances:
53 2 0.02
54 48 0.49
55 38 0.39
56 9 0.09
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (54 bp):
TTTCGGCACTATGTGTGCAACACATGGAATTCATAATGAGTTTATGAATTACCA
Found at i:48395 original size:20 final size:20
Alignment explanation
Indices: 48370--48505 Score: 114
Period size: 20 Copynumber: 6.7 Consensus size: 20
48360 CTGGATGAAA
*
48370 TGGTATCAATACCAGAGTGT
1 TGGTATCCATACCAGAGTGT
*
48390 TGGTATCCATACCAGA-TGAAC
1 TGGTATCCATACCAGAGTG--T
* * *
48411 TAGTATCCATAACAGTGTGT
1 TGGTATCCATACCAGAGTGT
* *
48431 TGGTATCGATACCGGAGTGT
1 TGGTATCCATACCAGAGTGT
* *
48451 TGGTATCCATACCGGA-TGAAC
1 TGGTATCCATACCAGAGTG--T
***
48472 TGGTATCCATATTGGAGTGT
1 TGGTATCCATACCAGAGTGT
48492 TGGTATCCATACCA
1 TGGTATCCATACCA
48506 AATGAATAAT
Statistics
Matches: 91, Mismatches: 19, Indels: 12
0.75 0.16 0.10
Matches are distributed among these distances:
19 4 0.04
20 56 0.62
21 27 0.30
22 4 0.04
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.30
Consensus pattern (20 bp):
TGGTATCCATACCAGAGTGT
Found at i:48431 original size:41 final size:41
Alignment explanation
Indices: 48363--48443 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
48353 ATCAATACTG
* *
48363 GATGAAATGGTATCAATACCAGAGTGTTGGTATCCATACCA
1 GATGAAATAGTATCAATAACAGAGTGTTGGTATCCATACCA
* * * *
48404 GATGAACTAGTATCCATAACAGTGTGTTGGTATCGATACC
1 GATGAAATAGTATCAATAACAGAGTGTTGGTATCCATACC
48444 GGAGTGTTGG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.28
Consensus pattern (41 bp):
GATGAAATAGTATCAATAACAGAGTGTTGGTATCCATACCA
Found at i:48492 original size:61 final size:61
Alignment explanation
Indices: 48370--48505 Score: 191
Period size: 61 Copynumber: 2.2 Consensus size: 61
48360 CTGGATGAAA
*
48370 TGGTATCAATACCAGAGTGTTGGTATCCATACCAGATGAACTAGTATCCATAACAGTGTGT
1 TGGTATCAATACCAGAGTGTTGGTATCCATACCAGATGAACTAGTATCCATAACAGAGTGT
* * * * ***
48431 TGGTATCGATACCGGAGTGTTGGTATCCATACCGGATGAACTGGTATCCATATTGGAGTGT
1 TGGTATCAATACCAGAGTGTTGGTATCCATACCAGATGAACTAGTATCCATAACAGAGTGT
*
48492 TGGTATCCATACCA
1 TGGTATCAATACCA
48506 AATGAATAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.30
Consensus pattern (61 bp):
TGGTATCAATACCAGAGTGTTGGTATCCATACCAGATGAACTAGTATCCATAACAGAGTGT
Found at i:49132 original size:32 final size:32
Alignment explanation
Indices: 49095--49244 Score: 124
Period size: 32 Copynumber: 4.7 Consensus size: 32
49085 ATCTGCTACC
* *
49095 CATTATCTAAATGTTATACTGACACTCTTATG
1 CATTATCTGAATGTTATACTGACTCTCTTATG
*** * * * *
49127 CATTATCTGAATACAACATTAACTCTGTTATG
1 CATTATCTGAATGTTATACTGACTCTCTTATG
* *
49159 CATTATTTGAATGTTATACTGACTCTAC-TGTG
1 CATTATCTGAATGTTATACTGACTCT-CTTATG
* *
49191 CATTATATGAATGTTATACTGACTCTAC-TGTG
1 CATTATCTGAATGTTATACTGACTCT-CTTATG
* **
49223 AATTATCTGAATGCAATACTGA
1 CATTATCTGAATGTTATACTGA
49245 AACTATTATA
Statistics
Matches: 94, Mismatches: 23, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
32 94 1.00
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (32 bp):
CATTATCTGAATGTTATACTGACTCTCTTATG
Done.