Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004019.1 Hibiscus syriacus cultivar Beakdansim tig00008779_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: 225756
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:171083 original size:97 final size:97
Alignment explanation
Indices: 170994--171191 Score: 226
Period size: 85 Copynumber: 2.2 Consensus size: 97
170984 TTTTAATATT
* * *
170994 ATGATTTAATAATGATTTAGTAATAATCA-TT-ATAATAATGATTTAATAATGACTTTAATATTT
1 ATGATTTAATAAT-AATGA-TAATAATCATTTAATAATAATGATTTAATAATGAATTTAATATTT
171057 AATGATTTGATGATTTAGTAATGATTTTATAATA
64 AATGATTTGATGATTTAGTAATGATTTTATAATA
* *
171091 ATGATTTAATAATAATGATAATAATGATTTAATAATAATCA-TT-ATAAT-AA--T-A-ATTTAA
1 ATGATTTAATAATAATGATAATAATCATTTAATAATAATGATTTAATAATGAATTTAATATTTAA
171149 T-A---G-TGATTTAGTAATGATTTTATAATA
66 TGATTTGATGATTTAGTAATGATTTTATAATA
*
171176 ATTATTTAATAATAAT
1 ATGATTTAATAATAAT
171192 TATTTAATAA
Statistics
Matches: 93, Mismatches: 6, Indels: 16
0.81 0.05 0.14
Matches are distributed among these distances:
85 39 0.42
86 1 0.01
89 1 0.01
90 7 0.08
91 1 0.01
92 1 0.01
94 1 0.01
95 13 0.14
96 7 0.08
97 22 0.24
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (97 bp):
ATGATTTAATAATAATGATAATAATCATTTAATAATAATGATTTAATAATGAATTTAATATTTAA
TGATTTGATGATTTAGTAATGATTTTATAATA
Found at i:171148 original size:26 final size:23
Alignment explanation
Indices: 170969--171180 Score: 133
Period size: 23 Copynumber: 8.8 Consensus size: 23
170959 TAATGATTTG
* * *
170969 ATGATTTAGTAATGATTTTAATA
1 ATGATTTAATAATAATTATAATA
*
170992 TTATGATTTAATAATGATTTAGTAATA
1 --ATGATTTAATAAT-AATTA-TAATA
* *
171019 ATCATTATAATAATGATT-TAATA
1 ATGATT-TAATAATAATTATAATA
* * * *
171042 ATGACTTTAATATTTAATGAT-TTG
1 ATGA-TTTAATA-ATAATTATAATA
* *
171066 ATGATTTAGTAATGATTTTATAATA
1 ATGATTTAATAAT-A-ATTATAATA
*
171091 ATGATTTAATAATAATGATAATA
1 ATGATTTAATAATAATTATAATA
171114 ATGATTTAATAATAATCATTATAATA
1 ATGATTTAATAAT-A--ATTATAATA
* * * *
171140 ATAATTTAATAGTGATT-TAGTA
1 ATGATTTAATAATAATTATAATA
*
171162 ATGATTTTATAATAATTAT
1 ATGATTTAATAATAATTAT
171181 TTAATAATAA
Statistics
Matches: 143, Mismatches: 31, Indels: 28
0.71 0.15 0.14
Matches are distributed among these distances:
22 18 0.13
23 44 0.31
24 15 0.10
25 33 0.23
26 28 0.20
27 5 0.03
ACGTcount: A:0.43, C:0.01, G:0.09, T:0.46
Consensus pattern (23 bp):
ATGATTTAATAATAATTATAATA
Found at i:171212 original size:10 final size:11
Alignment explanation
Indices: 171086--171218 Score: 59
Period size: 11 Copynumber: 10.9 Consensus size: 11
171076 AATGATTTTA
*
171086 TAATAATGATT
1 TAATAATTATT
* *
171097 TAATAATAATGA
1 TAATAATTAT-T
*
171109 TAATAATGATT
1 TAATAATTATT
171120 TAATAATAATCATT
1 TAATAAT--T-ATT
*
171134 ATAATAATAATT
1 -TAATAATTATT
* *
171146 TAATAGTGATT
1 TAATAATTATT
* *
171157 TAGTAATGATTTT
1 TAATAAT--TATT
171170 ATAATAATTATTT
1 -TAATAATTA-TT
171183 AATAATAATTATT
1 --TAATAATTATT
*
171196 TAATAATTTTT
1 TAATAATTATT
171207 ACTAATAATTAT
1 --TAATAATTAT
171219 GGAATAATAA
Statistics
Matches: 94, Mismatches: 16, Indels: 22
0.71 0.12 0.17
Matches are distributed among these distances:
11 40 0.43
12 13 0.14
13 15 0.16
14 19 0.20
15 7 0.07
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (11 bp):
TAATAATTATT
Found at i:171245 original size:85 final size:85
Alignment explanation
Indices: 171067--171238 Score: 215
Period size: 85 Copynumber: 2.0 Consensus size: 85
171057 AATGATTTGA
171067 TGATTTAGTAATGATTTTATAATAATGATTTAATAATAATGATAATAATGATTTAATAATAATCA
1 TGATTTAGTAATGATTTTATAATAATGATTTAATAATAATGATAATAATGATTTAATAATAATCA
* **
171132 TTATAATAATAATTTAATAG
66 TTAGAATAATAATCAAATAG
* * * *
171152 TGATTTAGTAATGATTTTATAATAATTATTTAATAATAATTATTTAATAAT-TTTTACTAATAAT
1 TGATTTAGTAATGATTTTATAATAATGATTTAATAATAATGA--TAATAATGATTTAATAATAAT
* *
171216 TA-TGGAATAATAA-CAAATGAG
64 CATTAGAATAATAATCAAAT-AG
171237 TG
1 TG
171239 TATTAGTGTG
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
84 3 0.04
85 53 0.71
86 12 0.16
87 7 0.09
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.44
Consensus pattern (85 bp):
TGATTTAGTAATGATTTTATAATAATGATTTAATAATAATGATAATAATGATTTAATAATAATCA
TTAGAATAATAATCAAATAG
Found at i:171367 original size:24 final size:24
Alignment explanation
Indices: 171319--171363 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
171309 TATTTGATAC
*
171319 TAATGATTTACTAATTATTATTAA
1 TAATGATTTACTAATTAATATTAA
*
171343 TAATGATTTA-TTATTAATATT
1 TAATGATTTACTAATTAATATT
171364 TAATTATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (24 bp):
TAATGATTTACTAATTAATATTAA
Found at i:171370 original size:17 final size:17
Alignment explanation
Indices: 171330--171371 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
171320 AATGATTTAC
171330 TAATTATTATTAATAAT
1 TAATTATTATTAATAAT
* * *
171347 GATTTATTATTAATATT
1 TAATTATTATTAATAAT
171364 TAATTATT
1 TAATTATT
171372 TGATACTAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TAATTATTATTAATAAT
Found at i:171405 original size:59 final size:56
Alignment explanation
Indices: 171287--171413 Score: 157
Period size: 59 Copynumber: 2.2 Consensus size: 56
171277 TCGAATTTAT
* *
171287 TAATGATTTTTAAATATTTAATTATTTGATACTAATGATTTACTAATTATTATTAA
1 TAATGATTTTTAAATATTTAATTATTTGATACTAATGATTTACTAATGATAATTAA
*
171343 TAATGATTTATTATTAATATTTAATTATTTGATACTAATGATTACTAGTAATGA-AATTATAA
1 TAATGATTT-TTA--AATATTTAATTATTTGATACTAATGATT--TACTAATGATAA-T-TAA
171405 TAATGATTT
1 TAATGATTT
171414 GATACTAAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
56 9 0.15
57 3 0.05
59 28 0.46
60 1 0.02
61 8 0.13
62 12 0.20
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (56 bp):
TAATGATTTTTAAATATTTAATTATTTGATACTAATGATTTACTAATGATAATTAA
Found at i:175866 original size:106 final size:106
Alignment explanation
Indices: 175689--176114 Score: 690
Period size: 106 Copynumber: 4.0 Consensus size: 106
175679 TGTATTGTTC
* * * * * * *
175689 CGAGTCCAATATTCTCCGCCGTGAAGTTAAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * *
175754 ACCAGCCGTCCCTTCTTTGTGAAGTTGAACTTCTATTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
*
175795 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* *
175860 ACCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGCTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
**
175901 CGAGTCCAATGCCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
175966 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
176007 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
176072 ACTAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
176113 CG
1 CG
176115 GGTGGTGCGA
Statistics
Matches: 299, Mismatches: 21, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
106 299 1.00
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:176977 original size:36 final size:37
Alignment explanation
Indices: 176927--177002 Score: 136
Period size: 36 Copynumber: 2.1 Consensus size: 37
176917 GAAACAATTT
*
176927 CAAAGGTTTTTTTCAAGGGAAACTGTCTCAAGAGAGA
1 CAAAGGTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
176964 CAAA-GTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
1 CAAAGGTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
177000 CAA
1 CAA
177003 TGGTGAGCAC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 34 0.89
37 4 0.11
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (37 bp):
CAAAGGTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
Found at i:183172 original size:9 final size:9
Alignment explanation
Indices: 183127--183220 Score: 50
Period size: 9 Copynumber: 10.0 Consensus size: 9
183117 TAAAAGGAAT
183127 ATAAA-AAA
1 ATAAATAAA
* *
183135 ATAAAGACA
1 ATAAATAAA
*
183144 ATGAAATAAG
1 AT-AAATAAA
183154 ATAAAT-AA
1 ATAAATAAA
183162 ATAAATAAA
1 ATAAATAAA
*
183171 ATAGGA-AAA
1 ATA-AATAAA
*
183180 ATGAATCAATGA
1 ATAAAT-AA--A
*
183192 ATAAAGAAA
1 ATAAATAAA
183201 ATAAAAATAAA
1 AT--AAATAAA
183212 ATAAATAAA
1 ATAAATAAA
183221 CAAAACGTAG
Statistics
Matches: 65, Mismatches: 11, Indels: 19
0.68 0.12 0.20
Matches are distributed among these distances:
8 13 0.20
9 28 0.43
10 9 0.14
11 10 0.15
12 5 0.08
ACGTcount: A:0.71, C:0.02, G:0.09, T:0.18
Consensus pattern (9 bp):
ATAAATAAA
Found at i:184195 original size:21 final size:22
Alignment explanation
Indices: 184169--184216 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
184159 GTTAAACGTA
184169 AACTATT-TTTAATATAACTTT
1 AACTATTCTTTAATATAACTTT
184190 AACTATTCTTTAATATAACTTT
1 AACTATTCTTTAATATAACTTT
184212 AACTA
1 AACTA
184217 ATAAACTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 7 0.27
22 19 0.73
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (22 bp):
AACTATTCTTTAATATAACTTT
Found at i:184200 original size:11 final size:12
Alignment explanation
Indices: 184176--184216 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 12
184166 GTAAACTATT
184176 TTTAA-TATAAC
1 TTTAACTATAAC
*
184187 TTTAACTAT-TC
1 TTTAACTATAAC
184198 TTTAA-TATAAC
1 TTTAACTATAAC
184209 TTTAACTA
1 TTTAACTA
184217 ATAAACTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
10 3 0.12
11 17 0.68
12 5 0.20
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (12 bp):
TTTAACTATAAC
Found at i:184224 original size:30 final size:29
Alignment explanation
Indices: 184190--184285 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 29
184180 ATATAACTTT
184190 AACTATTCTTTAATATAACTTTAACTAATA
1 AACTATTCTTTAATATAA-TTTAACTAATA
*
184220 AACTATTCTTTAATATAAATTAAACTAATA
1 AACTATTCTTTAATAT-AATTTAACTAATA
*
184250 AACGT-TT-TTTAATTATAATTTACTACTAAAA
1 AAC-TATTCTTTAA-TATAATTTA--ACTAATA
184281 AACTA
1 AACTA
184286 ATTAACTAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 11
0.80 0.04 0.15
Matches are distributed among these distances:
29 10 0.18
30 35 0.61
31 12 0.21
ACGTcount: A:0.46, C:0.11, G:0.01, T:0.42
Consensus pattern (29 bp):
AACTATTCTTTAATATAATTTAACTAATA
Found at i:184233 original size:15 final size:16
Alignment explanation
Indices: 184189--184237 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 16
184179 AATATAACTT
184189 TAACTATTCTTTAATA
1 TAACTATTCTTTAATA
***
184205 TAACT-TTAACTAATA
1 TAACTATTCTTTAATA
184220 -AACTATTCTTTAATA
1 TAACTATTCTTTAATA
184235 TAA
1 TAA
184238 ATTAAACTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
14 4 0.16
15 14 0.56
16 7 0.28
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (16 bp):
TAACTATTCTTTAATA
Found at i:184262 original size:29 final size:30
Alignment explanation
Indices: 184190--184252 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
184180 ATATAACTTT
* *
184190 AACTATTCTTTAATATAACTTTAACTAATA
1 AACTATTCTTTAATATAAATTAAACTAATA
184220 AACTATTCTTTAATATAAATTAAACTAATA
1 AACTATTCTTTAATATAAATTAAACTAATA
184250 AAC
1 AAC
184253 GTTTTTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.40
Consensus pattern (30 bp):
AACTATTCTTTAATATAAATTAAACTAATA
Found at i:184397 original size:41 final size:37
Alignment explanation
Indices: 184342--184455 Score: 97
Period size: 41 Copynumber: 2.9 Consensus size: 37
184332 CTTAACTATT
184342 TAACTAAC--ACAAACTAATTACATATTTTTTTATATA
1 TAACTAACAAACAAACTAATTA-ATATTTTTTTATATA
* *
184378 TAACTAACGACTAACAAACTAACTAATTATTTTTATTAATATG
1 TAACTAAC-A--AACAAACTAATTAA-TATTTTT-TT-ATATA
* * *
184421 TAACTATCAAACATACTAATTAAATAATTTTTTAT
1 TAACTAACAAACAAACTAATT-AATATTTTTTTAT
184456 TTCTATATGA
Statistics
Matches: 63, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
36 8 0.13
38 2 0.03
39 2 0.03
40 17 0.27
41 20 0.32
42 3 0.05
43 11 0.17
ACGTcount: A:0.45, C:0.13, G:0.02, T:0.40
Consensus pattern (37 bp):
TAACTAACAAACAAACTAATTAATATTTTTTTATATA
Found at i:184489 original size:21 final size:21
Alignment explanation
Indices: 184465--184504 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
184455 TTTCTATATG
184465 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
*
184486 ATATAATTTAAACTAACAA
1 ATATAACTTAAACTAACAA
184505 ACTCATTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.30
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:184585 original size:18 final size:18
Alignment explanation
Indices: 184532--184586 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
184522 TTGTTTTACC
*
184532 CTAATTTATAATAATAAA
1 CTAATTTATAACAATAAA
184550 CTAA--T-TAAC--T-AA
1 CTAATTTATAACAATAAA
184562 -TAATTTATAACAATAAA
1 CTAATTTATAACAATAAA
184579 CTAATTTA
1 CTAATTTA
184587 AATAATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 3 0.10
12 2 0.07
13 2 0.07
14 4 0.14
15 3 0.10
16 2 0.07
17 2 0.07
18 11 0.38
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (18 bp):
CTAATTTATAACAATAAA
Found at i:184752 original size:27 final size:29
Alignment explanation
Indices: 184717--184781 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
184707 TATATATAAC
*
184717 TTAACTATTTA-ACTAACT-ACAAACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
184744 TTAAATA-TTAGACTAACTAACACACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
184772 TTAATTATTT
1 TTAAATATTT
184782 TTTAATATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 3 0.09
27 13 0.41
28 14 0.44
29 2 0.06
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (29 bp):
TTAAATATTTAGACTAACTAACAAACTAA
Found at i:185055 original size:23 final size:22
Alignment explanation
Indices: 185015--185059 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
185005 TGTTGTGCTA
*
185015 TCCCTTTCTTCTTCCTCCTCTTT
1 TCCCTTGCTTCTTCCTCC-CTTT
185038 TCCCTTGCTCTCTT-CTCCCTTT
1 TCCCTTGCT-TCTTCCTCCCTTT
185060 CTTTCTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 12 0.60
24 4 0.20
ACGTcount: A:0.00, C:0.44, G:0.02, T:0.53
Consensus pattern (22 bp):
TCCCTTGCTTCTTCCTCCCTTT
Found at i:185187 original size:11 final size:11
Alignment explanation
Indices: 185171--185228 Score: 62
Period size: 11 Copynumber: 5.1 Consensus size: 11
185161 TGAAGGACTA
185171 CAATAATGCAG
1 CAATAATGCAG
* *
185182 CAATAAGGGCTG
1 CAATAA-TGCAG
185194 CAATAATGCAG
1 CAATAATGCAG
**
185205 CAATAAGTGCTT
1 CAATAA-TGCAG
185217 CAATAATGCAG
1 CAATAATGCAG
185228 C
1 C
185229 TGAATTCACG
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
11 19 0.51
12 18 0.49
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.21
Consensus pattern (11 bp):
CAATAATGCAG
Found at i:185197 original size:23 final size:23
Alignment explanation
Indices: 185171--185228 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
185161 TGAAGGACTA
185171 CAATAATGCAGCAATAAGGGCTG
1 CAATAATGCAGCAATAAGGGCTG
* *
185194 CAATAATGCAGCAATAAGTGCTT
1 CAATAATGCAGCAATAAGGGCTG
185217 CAATAATGCAGC
1 CAATAATGCAGC
185229 TGAATTCACG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.21
Consensus pattern (23 bp):
CAATAATGCAGCAATAAGGGCTG
Found at i:185198 original size:12 final size:12
Alignment explanation
Indices: 185171--185222 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 12
185161 TGAAGGACTA
*
185171 CAATAA-TGCAG
1 CAATAAGTGCTG
*
185182 CAATAAGGGCTG
1 CAATAAGTGCTG
*
185194 CAATAA-TGCAG
1 CAATAAGTGCTG
*
185205 CAATAAGTGCTT
1 CAATAAGTGCTG
185217 CAATAA
1 CAATAA
185223 TGCAGCTGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
11 15 0.45
12 18 0.55
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.21
Consensus pattern (12 bp):
CAATAAGTGCTG
Found at i:185410 original size:29 final size:29
Alignment explanation
Indices: 185367--185449 Score: 103
Period size: 29 Copynumber: 2.9 Consensus size: 29
185357 TCACAACGTT
* *
185367 GGTCGTCGGGCGTGCATGGCGACCTACAA
1 GGTCGTTGGGAGTGCATGGCGACCTACAA
***
185396 GGTCGTTGGGAGTGCATGGCGACCTTGTA
1 GGTCGTTGGGAGTGCATGGCGACCTACAA
**
185425 GGTCACTGGGAGTGCATGGCGACCT
1 GGTCGTTGGGAGTGCATGGCGACCT
185450 GTGTTGGAGA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.16, C:0.23, G:0.40, T:0.22
Consensus pattern (29 bp):
GGTCGTTGGGAGTGCATGGCGACCTACAA
Found at i:186514 original size:15 final size:15
Alignment explanation
Indices: 186494--186522 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
186484 TACACTATTT
186494 TAGGTTTATTTTATG
1 TAGGTTTATTTTATG
186509 TAGGTTTATTTTAT
1 TAGGTTTATTTTAT
186523 ATAATATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.17, T:0.62
Consensus pattern (15 bp):
TAGGTTTATTTTATG
Found at i:188512 original size:33 final size:34
Alignment explanation
Indices: 188474--188545 Score: 83
Period size: 38 Copynumber: 2.0 Consensus size: 34
188464 AAGAAACAGT
*
188474 GAAGTT-TCGGTGTGGACCAAGGGACGGGAGAAG
1 GAAGTTATCAGTGTGGACCAAGGGACGGGAGAAG
*
188507 GAAGTTCAGAATCAGTGTGGAGCAAGGGACGGGAGAAG
1 GAAGTT----ATCAGTGTGGACCAAGGGACGGGAGAAG
188545 G
1 G
188546 TGGAAAATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
33 6 0.19
38 26 0.81
ACGTcount: A:0.31, C:0.11, G:0.44, T:0.14
Consensus pattern (34 bp):
GAAGTTATCAGTGTGGACCAAGGGACGGGAGAAG
Found at i:188592 original size:20 final size:20
Alignment explanation
Indices: 188567--188608 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
188557 TTACGGATTT
188567 CCAAACGGTAAGTCATTTTA
1 CCAAACGGTAAGTCATTTTA
188587 CCAAACGGTAAGTCATTTTA
1 CCAAACGGTAAGTCATTTTA
188607 CC
1 CC
188609 GTGTTTTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (20 bp):
CCAAACGGTAAGTCATTTTA
Found at i:192689 original size:32 final size:31
Alignment explanation
Indices: 192648--192807 Score: 202
Period size: 32 Copynumber: 5.1 Consensus size: 31
192638 GAGTCGAGGG
*
192648 TTACCTATGTCTTTCGGGACATATGTACAGGA
1 TTACCTATGTCTTTCGGGACATATGGACA-GA
192680 TTACCTATGT-TCTTCGGGACATATGGACAAGA
1 TTACCTATGTCT-TTCGGGACATATGGAC-AGA
* *
192712 TTACCTATGT-TATTCGGGATATATGGACATA
1 TTACCTATGTCT-TTCGGGACATATGGACAGA
*
192743 TTACCTATGTCATTCGGGACATATGGACA-A
1 TTACCTATGTCTTTCGGGACATATGGACAGA
192773 TTTACCTATGTTCTTT-GGGACATATGGACAGA
1 -TTACCTATG-TCTTTCGGGACATATGGACAGA
192805 TTA
1 TTA
192808 TTATACGAGC
Statistics
Matches: 115, Mismatches: 7, Indels: 13
0.85 0.05 0.10
Matches are distributed among these distances:
30 1 0.01
31 55 0.48
32 58 0.50
33 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.35
Consensus pattern (31 bp):
TTACCTATGTCTTTCGGGACATATGGACAGA
Found at i:192749 original size:31 final size:31
Alignment explanation
Indices: 192648--192807 Score: 207
Period size: 31 Copynumber: 5.1 Consensus size: 31
192638 GAGTCGAGGG
*
192648 TTACCTATGTCT-TTCGGGACATATGTACAGGA
1 TTACCTATGT-TATTCGGGACATATGGACA-GA
*
192680 TTACCTATGTTCTTCGGGACATATGGACAAGA
1 TTACCTATGTTATTCGGGACATATGGAC-AGA
* *
192712 TTACCTATGTTATTCGGGATATATGGACATA
1 TTACCTATGTTATTCGGGACATATGGACAGA
*
192743 TTACCTATGTCATTCGGGACATATGGACA-A
1 TTACCTATGTTATTCGGGACATATGGACAGA
* *
192773 TTTACCTATGTTCTTTGGGACATATGGACAGA
1 -TTACCTATGTTATTCGGGACATATGGACAGA
192805 TTA
1 TTA
192808 TTATACGAGC
Statistics
Matches: 115, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
30 1 0.01
31 59 0.51
32 54 0.47
33 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.35
Consensus pattern (31 bp):
TTACCTATGTTATTCGGGACATATGGACAGA
Found at i:193545 original size:19 final size:19
Alignment explanation
Indices: 193509--193557 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
193499 TTGTTCACAG
*
193509 TACTGTTCTTACAGTATAA
1 TACTGTTCATACAGTATAA
*
193528 TACTGTTCATACCA-TATAT
1 TACTGTTCATA-CAGTATAA
*
193547 TACTATTCATA
1 TACTGTTCATA
193558 AAAACGTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 24 0.92
20 2 0.08
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.43
Consensus pattern (19 bp):
TACTGTTCATACAGTATAA
Found at i:195442 original size:11 final size:11
Alignment explanation
Indices: 195426--195453 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
195416 GCTTAAAGTT
195426 ATTAATAATGA
1 ATTAATAATGA
195437 ATTAATAATGA
1 ATTAATAATGA
195448 ATTAAT
1 ATTAAT
195454 TGGTCCCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (11 bp):
ATTAATAATGA
Found at i:198514 original size:2 final size:2
Alignment explanation
Indices: 198507--198531 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
198497 GGTATGTCTG
198507 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
198532 GTGTGCGTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:198554 original size:2 final size:2
Alignment explanation
Indices: 198549--198577 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
198539 TGCGTGTGTG
198549 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
198578 GAAAATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:203395 original size:18 final size:18
Alignment explanation
Indices: 203372--203414 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
203362 TTTACTGGTT
203372 CAATGACTACTGATGCTG
1 CAATGACTACTGATGCTG
203390 CAATGACTACTGATGCTG
1 CAATGACTACTGATGCTG
203408 CAATGAC
1 CAATGAC
203415 AAAGGCACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (18 bp):
CAATGACTACTGATGCTG
Found at i:209172 original size:32 final size:31
Alignment explanation
Indices: 209060--209172 Score: 97
Period size: 32 Copynumber: 3.5 Consensus size: 31
209050 TGACCCAAAT
*
209060 AAAAAATCAACCGATCTGATATTGACTCAATCC
1 AAAAAATCAACCGATCTGATATTGAC-CCA-CC
209093 AAAAGAA--AACCGATCTGATATTGACCTCA-C
1 AAAA-AATCAACCGATCTGATATTGACC-CACC
* ** * *
209123 ATAAAATCTAATTGATCTGGTATTAACCCGACC
1 AAAAAATC-AACCGATCTGATATTGACCC-ACC
209156 AAAAAATCAACCGATCT
1 AAAAAATCAACCGATCT
209173 CATAGTTACC
Statistics
Matches: 64, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
29 2 0.03
30 4 0.06
31 2 0.03
32 42 0.66
33 12 0.19
34 2 0.03
ACGTcount: A:0.42, C:0.23, G:0.11, T:0.24
Consensus pattern (31 bp):
AAAAAATCAACCGATCTGATATTGACCCACC
Found at i:209763 original size:19 final size:21
Alignment explanation
Indices: 209733--209771 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
209723 TGATTTTAAG
209733 ATTTTATCTTTA-GTTATTTC
1 ATTTTATCTTTAGGTTATTTC
209753 ATTTT-TCTTTAGGTTATTT
1 ATTTTATCTTTAGGTTATTT
209772 GAAAGCTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.18, C:0.08, G:0.08, T:0.67
Consensus pattern (21 bp):
ATTTTATCTTTAGGTTATTTC
Done.