Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004739.1 Hibiscus syriacus cultivar Beakdansim tig00010699_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: 46601
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:12366 original size:74 final size:75
Alignment explanation
Indices: 12243--12405 Score: 222
Period size: 74 Copynumber: 2.2 Consensus size: 75
12233 TAAGTAAGGA
* * *
12243 GGTACCGATACCCCTCACAGGGTGTACCGATACCCCTAAGCCAATTTTGGCTCCAAGAAAAACAG
1 GGTACCGATA-CCCTCACAAGGTGTACCAATACCCCTAAGCAAATTTTGGCTCCAAGAAAAACAG
*
12308 ATTGCCCAATG
65 AATGCCCAATG
* * *
12319 GGTACCGATACCCT-ACATAGG-GTACCAATACCCCTATGCAAATTTTGGCTCCGAGAAAAATAG
1 GGTACCGATACCCTCACA-AGGTGTACCAATACCCCTAAGCAAATTTTGGCTCCAAGAAAAACAG
*
12382 AATGCCCTATG
65 AATGCCCAATG
12393 GGTACCGATACCC
1 GGTACCGATACCC
12406 CCTTAAAGGT
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
74 62 0.79
75 6 0.08
76 10 0.13
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.21
Consensus pattern (75 bp):
GGTACCGATACCCTCACAAGGTGTACCAATACCCCTAAGCAAATTTTGGCTCCAAGAAAAACAGA
ATGCCCAATG
Found at i:12417 original size:74 final size:74
Alignment explanation
Indices: 12266--12428 Score: 220
Period size: 74 Copynumber: 2.2 Consensus size: 74
12256 CTCACAGGGT
* *
12266 GTACCGATACCCCTAAGCCAATTTTGGCTCCAAGAAAAACAGATTGCCCAATGGGTACCGATACC
1 GTACCGATACCCCTAAGCAAATTTTGGCTCCAAGAAAAACAGAATGCCCAATGGGTACCGATACC
*
12331 CTACATAGG
66 CTACATAAG
* * * * *
12340 GTACCAATACCCCTATGCAAATTTTGGCTCCGAGAAAAATAGAATGCCCTATGGGTACCGATACC
1 GTACCGATACCCCTAAGCAAATTTTGGCTCCAAGAAAAACAGAATGCCCAATGGGTACCGATACC
* *
12405 C-CCTTAAAG
66 CTACAT-AAG
12414 GTACCGATACCCCTA
1 GTACCGATACCCCTA
12429 GTCATTTAAC
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
73 2 0.03
74 75 0.97
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (74 bp):
GTACCGATACCCCTAAGCAAATTTTGGCTCCAAGAAAAACAGAATGCCCAATGGGTACCGATACC
CTACATAAG
Found at i:12493 original size:21 final size:21
Alignment explanation
Indices: 12467--12516 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
12457 TTACACTGTA
*
12467 GGTACCGAGACTGATTGAAGG
1 GGTACCGAGACTCATTGAAGG
12488 GGTACCGAGACTCATTGAAGG
1 GGTACCGAGACTCATTGAAGG
12509 GGTACCGA
1 GGTACCGA
12517 TACCCCACGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.18, G:0.36, T:0.18
Consensus pattern (21 bp):
GGTACCGAGACTCATTGAAGG
Found at i:15138 original size:7 final size:7
Alignment explanation
Indices: 15074--15203 Score: 80
Period size: 7 Copynumber: 19.0 Consensus size: 7
15064 ATATATATAT
15074 TAAATAA
1 TAAATAA
15081 T-AATAA
1 TAAATAA
15087 T-AATAA
1 TAAATAA
15093 TAAAT-A
1 TAAATAA
*
15099 TAAGTAA
1 TAAATAA
15106 TAAAATAA
1 T-AAATAA
15114 -AAA-AGA
1 TAAATA-A
15120 TAAA-ATA
1 TAAATA-A
*
15127 CAAATAA
1 TAAATAA
*
15134 TAAATAT
1 TAAATAA
15141 TAATTATAA
1 TAA--ATAA
15150 -AAATAA
1 TAAATAA
*
15156 TAAATTA
1 TAAATAA
*
15163 TAAATTA
1 TAAATAA
*
15170 TAATTAA
1 TAAATAA
15177 T-AATAA
1 TAAATAA
*
15183 TTAAGTAA
1 -TAAATAA
15191 TAAA-AA
1 TAAATAA
15197 TAAATAA
1 TAAATAA
15204 ATAATTATAA
Statistics
Matches: 98, Mismatches: 13, Indels: 24
0.73 0.10 0.18
Matches are distributed among these distances:
5 1 0.01
6 35 0.36
7 47 0.48
8 12 0.12
9 3 0.03
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (7 bp):
TAAATAA
Found at i:15184 original size:39 final size:39
Alignment explanation
Indices: 15130--15233 Score: 103
Period size: 39 Copynumber: 2.7 Consensus size: 39
15120 TAAAATACAA
* *
15130 ATAATAAATATTAATTA-TAAAAATAATAAAT-TATAAATT
1 ATAAT-AATAATAATTAGTAAAAATAATAAATAAAT-AATT
15169 ATAATTAATAATAATTAAGTAATAAA-AATAAATAAATAATT
1 ATAA-TAATAATAATT-AGTAA-AAATAATAAATAAATAATT
15210 ATAA-AATAAT-ATTAGT-AAAATAAT
1 ATAATAATAATAATTAGTAAAAATAAT
15234 GATAGGGTAT
Statistics
Matches: 57, Mismatches: 2, Indels: 15
0.77 0.03 0.20
Matches are distributed among these distances:
35 3 0.05
36 4 0.07
37 3 0.05
38 3 0.05
39 19 0.33
40 2 0.04
41 18 0.32
42 5 0.09
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (39 bp):
ATAATAATAATAATTAGTAAAAATAATAAATAAATAATT
Found at i:15220 original size:14 final size:14
Alignment explanation
Indices: 15077--15233 Score: 65
Period size: 14 Copynumber: 10.7 Consensus size: 14
15067 TATATATTAA
*
15077 ATAATAATAATAATA
1 ATAA-AATAATAATT
*
15092 AT-AAAT-ATAAGTA
1 ATAAAATAATAA-TT
* **
15105 ATAAAATAAAAAAG
1 ATAAAATAATAATT
*
15119 ATAAAATACA-AATA
1 ATAAAATA-ATAATT
*
15133 AT-AAATATTAATT
1 ATAAAATAATAATT
15146 ATAAAAATAATAAATT
1 AT-AAAATAAT-AATT
*
15162 AT-AAATTATAATT
1 ATAAAATAATAATT
*
15175 AATAATAATTAAGTAATAA
1 -ATAA-AA-TAA-TAAT-T
*
15194 AAATAAATAAATAATT
1 ATA-AAAT-AATAATT
15210 ATAAAATAAT-ATT
1 ATAAAATAATAATT
15223 AGTAAAATAAT
1 A-TAAAATAAT
15234 GATAGGGTAT
Statistics
Matches: 111, Mismatches: 14, Indels: 35
0.69 0.09 0.22
Matches are distributed among these distances:
12 4 0.04
13 25 0.23
14 37 0.33
15 17 0.15
16 10 0.09
17 7 0.06
18 10 0.09
19 1 0.01
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.32
Consensus pattern (14 bp):
ATAAAATAATAATT
Found at i:15440 original size:2 final size:2
Alignment explanation
Indices: 15433--15459 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
15423 TGCAACCCAT
15433 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 T
15460 GGAGTAAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15840 original size:17 final size:19
Alignment explanation
Indices: 15804--15840 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
15794 ACATTTCAAT
15804 TTCATTCTCAAACTATGGCC
1 TTCATTCTCAAAC-ATGGCC
15824 TTCATTCT-AAA-ATGGCC
1 TTCATTCTCAAACATGGCC
15841 CCCAACCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.35
19 3 0.18
20 8 0.47
ACGTcount: A:0.27, C:0.27, G:0.11, T:0.35
Consensus pattern (19 bp):
TTCATTCTCAAACATGGCC
Found at i:16112 original size:60 final size:60
Alignment explanation
Indices: 16048--16178 Score: 192
Period size: 60 Copynumber: 2.2 Consensus size: 60
16038 TAGAAAGGGG
* *
16048 GTCATAGTTTAGGGATAAAATTAGAATATTCAAAAATTTAAAGA-CTAATTTATAATGAGA
1 GTCATAGTTTAGGGATAAAATTAAAATATTCAAAAATTTAAAGATC-AATTTAAAATGAGA
* *
16108 GTCATAGTTTAGTGATAAAATTAAAATATTTAAAAATTTAAAGATCAATTTAAAATGAGA
1 GTCATAGTTTAGGGATAAAATTAAAATATTCAAAAATTTAAAGATCAATTTAAAATGAGA
**
16168 GTTGTAGTTTA
1 GTCATAGTTTA
16179 AATTTTGTCG
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
60 63 0.98
61 1 0.02
ACGTcount: A:0.46, C:0.04, G:0.15, T:0.36
Consensus pattern (60 bp):
GTCATAGTTTAGGGATAAAATTAAAATATTCAAAAATTTAAAGATCAATTTAAAATGAGA
Found at i:16417 original size:6 final size:6
Alignment explanation
Indices: 16406--16437 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
16396 TTATTATAAG
16406 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TT
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TT
16438 TGAAATTCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
TTAAAA
Found at i:18318 original size:22 final size:22
Alignment explanation
Indices: 18286--18347 Score: 108
Period size: 22 Copynumber: 2.9 Consensus size: 22
18276 CGGTACCGTA
18286 ATAG-AGTATTGATACCATAGT
1 ATAGTAGTATTGATACCATAGT
18307 ATAGTAGTATTGATACCATAGT
1 ATAGTAGTATTGATACCATAGT
*
18329 ATAGTAGTATCGATACCAT
1 ATAGTAGTATTGATACCAT
18348 GATGGGAGTA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
21 4 0.10
22 35 0.90
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (22 bp):
ATAGTAGTATTGATACCATAGT
Found at i:18746 original size:54 final size:54
Alignment explanation
Indices: 18688--18790 Score: 179
Period size: 54 Copynumber: 1.9 Consensus size: 54
18678 TTACCAAATA
*
18688 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTC
1 GGCACTAAGTGTGCATTTCAAGGAATTCATCCTATGTGGATGAATAACCATTTC
* *
18742 GGCACTAAGTGTGTATTTCAAGGAATTCATCCTATGTTGATGAATAACC
1 GGCACTAAGTGTGCATTTCAAGGAATTCATCCTATGTGGATGAATAACC
18791 GTACAGACAC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.32
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCAAGGAATTCATCCTATGTGGATGAATAACCATTTC
Found at i:18837 original size:55 final size:55
Alignment explanation
Indices: 18763--19245 Score: 737
Period size: 55 Copynumber: 8.9 Consensus size: 55
18753 TGTATTTCAA
* * *
18763 GGAATTCATCCT-ATGTTGATGAATAACCGTACAGACACTATGTGTTCAAATCCAC
1 GGAATTCATCATGA-GTTGATGAATAACCGTACAGGCACTATGTGTGCAAATCCAC
**
18818 GGAATTCATCATGAGTTGATGAATAACCGTACATACACTATGTGTGCAAATCCAC
1 GGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAATCCAC
* *
18873 GTAATTCATCATGAGTTGATGAATAACCGTACATGCACTATGTGTGCAAAT-C-C
1 GGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAATCCAC
*
18926 --AATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTTCAAATCCAC
1 GGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAATCCAC
* * *
18979 GGAATTCATCATGAGTTGATGAATAATCGTACAGACACTATGTGTACAAATCCAC
1 GGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAATCCAC
19034 GGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAATCCAC
1 GGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAATCCAC
*
19089 GGAATTCATCACGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAATCCAC
1 GGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAATCCAC
* * * *
19144 GAAATTCATCATAAGTTGATGAATAACCGTACAGGCACGATGTGTGC-AACCCAC
1 GGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAATCCAC
* *
19198 GGAATTCATCATGAGTTGATGAACT-ACCGTATAGGCACTACGTGTGCA
1 GGAATTCATCATGAGTTGATGAA-TAACCGTACAGGCACTATGTGTGCA
19246 TCTTAATAAA
Statistics
Matches: 397, Mismatches: 24, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
51 47 0.12
52 1 0.00
53 2 0.01
54 47 0.12
55 299 0.75
56 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (55 bp):
GGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAATCCAC
Found at i:18979 original size:161 final size:164
Alignment explanation
Indices: 18764--19245 Score: 751
Period size: 161 Copynumber: 3.0 Consensus size: 164
18754 GTATTTCAAG
* *
18764 GAATTCATC-CTATGTTGATGAATAACCGTACAGACACTATGTGTTCAAATCCACGGAATTCATC
1 GAATTCATCACGA-GTTGATGAATAACCGTACAGGCACTATGTGTTCAAATCCACGGAATTCATC
* *
18828 ATGAGTTGATGAATAACCGTACATACACTATGTGTGCAAATCCACGTAATTCATCATGAGTTGAT
65 ATGAGTTGATGAATAACCGTACAGACACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGAT
*
18893 GAATAACCGTACATGCACTATGTGTGCAAAT-C-C
130 GAATAACCGTACAGGCACTATGTGTGCAAATCCAC
*
18926 -AATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTTCAAATCCACGGAATTCATCA
1 GAATTCATCACGAGTTGATGAATAACCGTACAGGCACTATGTGTTCAAATCCACGGAATTCATCA
* *
18990 TGAGTTGATGAATAATCGTACAGACACTATGTGTACAAATCCACGGAATTCATCATGAGTTGATG
66 TGAGTTGATGAATAACCGTACAGACACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATG
19055 AATAACCGTACAGGCACTATGTGTGCAAATCCAC
131 AATAACCGTACAGGCACTATGTGTGCAAATCCAC
* *
19089 GGAATTCATCACGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAATCCACGAAATTCATC
1 -GAATTCATCACGAGTTGATGAATAACCGTACAGGCACTATGTGTTCAAATCCACGGAATTCATC
* * * *
19154 ATAAGTTGATGAATAACCGTACAGGCACGATGTGTGC-AACCCACGGAATTCATCATGAGTTGAT
65 ATGAGTTGATGAATAACCGTACAGACACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGAT
* *
19218 GAACT-ACCGTATAGGCACTACGTGTGCA
130 GAA-TAACCGTACAGGCACTATGTGTGCA
19246 TCTTAATAAA
Statistics
Matches: 295, Mismatches: 19, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
161 149 0.51
162 2 0.01
163 1 0.00
164 50 0.17
165 93 0.32
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (164 bp):
GAATTCATCACGAGTTGATGAATAACCGTACAGGCACTATGTGTTCAAATCCACGGAATTCATCA
TGAGTTGATGAATAACCGTACAGACACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATG
AATAACCGTACAGGCACTATGTGTGCAAATCCAC
Found at i:19084 original size:216 final size:218
Alignment explanation
Indices: 18763--19242 Score: 754
Period size: 216 Copynumber: 2.2 Consensus size: 218
18753 TGTATTTCAA
* *
18763 GGAATTCATCCT-ATGTTGATGAATAACCGTACAGACACTATGTGTTCAAATCCACGGAATTCAT
1 GGAATTCATCATGA-GTTGATGAATAACCGTACAGACACTATGTGTACAAATCCACGGAATTCAT
* * *
18827 CATGAGTTGATGAATAACCGTACATACACTATGTGTGCAAATCCACGTAATTCATCATGAGTTGA
65 CATGAGTTGATGAATAACCGTACAGACACTATGTGTGCAAATCCACGGAATTCATCACGAGTTGA
* *
18892 TGAATAACCGTACATGCACTATGTGTGCAAAT-C-C-AATTCATCATGAGTTGATGAATAACCGT
130 TGAATAACCGTACAGGCACTATGTGTGCAAATCCACAAATTCATCATAAGTTGATGAATAACCGT
* * *
18954 ACAGGCACTATGTGTTCAAATCCAC
195 ACAGGCACGATGTGTGC-AACCCAC
*
18979 GGAATTCATCATGAGTTGATGAATAATCGTACAGACACTATGTGTACAAATCCACGGAATTCATC
1 GGAATTCATCATGAGTTGATGAATAACCGTACAGACACTATGTGTACAAATCCACGGAATTCATC
*
19044 ATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAATCCACGGAATTCATCACGAGTTGAT
66 ATGAGTTGATGAATAACCGTACAGACACTATGTGTGCAAATCCACGGAATTCATCACGAGTTGAT
19109 GAATAACCGTACAGGCACTATGTGTGCAAATCCACGAAATTCATCATAAGTTGATGAATAACCGT
131 GAATAACCGTACAGGCACTATGTGTGCAAATCCAC-AAATTCATCATAAGTTGATGAATAACCGT
19174 ACAGGCACGATGTGTGCAACCCAC
195 ACAGGCACGATGTGTGCAACCCAC
* * *
19198 GGAATTCATCATGAGTTGATGAACT-ACCGTATAGGCACTACGTGT
1 GGAATTCATCATGAGTTGATGAA-TAACCGTACAGACACTATGTGT
19243 GCATCTTAAT
Statistics
Matches: 242, Mismatches: 16, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
216 151 0.62
217 2 0.01
218 1 0.00
219 45 0.19
220 43 0.18
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (218 bp):
GGAATTCATCATGAGTTGATGAATAACCGTACAGACACTATGTGTACAAATCCACGGAATTCATC
ATGAGTTGATGAATAACCGTACAGACACTATGTGTGCAAATCCACGGAATTCATCACGAGTTGAT
GAATAACCGTACAGGCACTATGTGTGCAAATCCACAAATTCATCATAAGTTGATGAATAACCGTA
CAGGCACGATGTGTGCAACCCAC
Found at i:19763 original size:44 final size:45
Alignment explanation
Indices: 19687--19819 Score: 128
Period size: 44 Copynumber: 3.0 Consensus size: 45
19677 TGTATAGAAT
* * *
19687 GGCATGAAAGGATGCCATAAATAAAATGCATATGGGTGCATTAAC
1 GGCATGAAAAGATGACATAAATAAAATGCATATGAGTGCATTAAC
* * * **
19732 GGCATGAAAAGAT-ACATAATTGAAATTCATATGAGTGCATTATT
1 GGCATGAAAAGATGACATAAATAAAATGCATATGAGTGCATTAAC
* *
19776 GGCAAG-AAAGAATGTCATAAATGAAAATGCATAATG-GTGCATTA
1 GGCATGAAAAG-ATGACATAAAT-AAAATGCAT-ATGAGTGCATTA
19820 TAAGTACGAA
Statistics
Matches: 71, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
43 4 0.06
44 31 0.44
45 18 0.25
46 15 0.21
47 3 0.04
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.26
Consensus pattern (45 bp):
GGCATGAAAAGATGACATAAATAAAATGCATATGAGTGCATTAAC
Found at i:22185 original size:3 final size:3
Alignment explanation
Indices: 22142--22171 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
22132 TGATGATGAT
22142 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
22172 ATAGAGGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:28047 original size:17 final size:18
Alignment explanation
Indices: 28013--28052 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
28003 ATATTTCACT
* *
28013 AATAGAGGAAATATTACA
1 AATAGAGGAAAGAATACA
28031 AATAGA-GAAAGAATACA
1 AATAGAGGAAAGAATACA
28048 AATAG
1 AATAG
28053 CCTTTAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.60, C:0.05, G:0.17, T:0.17
Consensus pattern (18 bp):
AATAGAGGAAAGAATACA
Found at i:34928 original size:182 final size:182
Alignment explanation
Indices: 34628--35103 Score: 710
Period size: 182 Copynumber: 2.6 Consensus size: 182
34618 CGATCCAAAT
* * *
34628 TAAAAATGTATCGATCCATATCAATATAACAGGTAAAAATATCGATAAAACCGGTCA-CGAAA-A
1 TAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATAT-GATAAAACCGGT-ATCGAAATA
* * ** * *
34691 GACAATACCGGTAAA-TCCTTACCGGATATATTGAACGTGTCGATACTTTAATATAA-TGATCGA
64 -ATAAAACCGGTAAAGAGC-TACCGGATATATTTAAAGTGTCGATACTTTAATATAAGT-ATCGA
*
34754 TACTTTGTGAATTTAAAAGAGAAGCA-TTTTTAACGCCTATAAAGTGTCGATACTTTA
126 CACTTTGTGAATTTAAAAGAGAAGCAGTTTTT-ACGCCTATAAAGTGTCGATACTTTA
*
34811 TAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCGGTATCGAAATAAT
1 TAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCGAAATAAT
*
34876 AAAACCGGTAAAGAGCTACCGAATATATTTAAAGTGTCGATACTTTAATATAAGTATCGACACTT
66 AAAACCGGTAAAGAGCTACCGGATATATTTAAAGTGTCGATACTTTAATATAAGTATCGACACTT
*
34941 TGTGAATTTAAAATAGAAGCAGTTTTTACGCCTATAAAGTGTCGATACTTTA
131 TGTGAATTTAAAAGAGAAGCAGTTTTTACGCCTATAAAGTGTCGATACTTTA
* *
34993 TAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
1 TAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCGAAATAAT
* *
35058 AAAACCGATAAAGCGCTACCGGATATATTTAAAGTGTCGATACTTT
66 AAAACCGGTAAAGAGCTACCGGATATATTTAAAGTGTCGATACTTT
35104 CATAAGTACG
Statistics
Matches: 269, Mismatches: 19, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
181 1 0.00
182 221 0.82
183 47 0.17
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (182 bp):
TAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCGAAATAAT
AAAACCGGTAAAGAGCTACCGGATATATTTAAAGTGTCGATACTTTAATATAAGTATCGACACTT
TGTGAATTTAAAAGAGAAGCAGTTTTTACGCCTATAAAGTGTCGATACTTTA
Found at i:35047 original size:20 final size:19
Alignment explanation
Indices: 35024--35069 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
35014 CGATATAACA
35024 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
35044 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
*
35064 GATAAA
1 GGTAAA
35070 GCGCTACCGG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.05
20 18 0.82
21 3 0.14
ACGTcount: A:0.54, C:0.11, G:0.15, T:0.20
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:37208 original size:15 final size:15
Alignment explanation
Indices: 37188--37220 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
37178 TGGTTGTATT
*
37188 GGGGGATGATGGTGA
1 GGGGGATGACGGTGA
37203 GGGGGATGACGGTGA
1 GGGGGATGACGGTGA
37218 GGG
1 GGG
37221 AAAACAGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.03, G:0.64, T:0.15
Consensus pattern (15 bp):
GGGGGATGACGGTGA
Found at i:37331 original size:21 final size:21
Alignment explanation
Indices: 37307--37346 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
37297 CAATCAAGAG
*
37307 TCGAATAGAAACTTGAGAGAA
1 TCGAAGAGAAACTTGAGAGAA
* *
37328 TCGAAGATACACTTGAGAG
1 TCGAAGAGAAACTTGAGAG
37347 GCATAAGGGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.12, G:0.25, T:0.20
Consensus pattern (21 bp):
TCGAAGAGAAACTTGAGAGAA
Found at i:37422 original size:33 final size:33
Alignment explanation
Indices: 37380--37445 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
37370 AAATAGATGG
*
37380 AGTGGTGAAAAAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAAAAGTAGAGGTGTTAAGGGGTGA
* *
37413 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
1 AGTGGTGAAAAAAGTAGAGGTGTTAAGGGGTGA
37446 TCTTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.32, C:0.00, G:0.45, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAAAAGTAGAGGTGTTAAGGGGTGA
Found at i:39276 original size:19 final size:19
Alignment explanation
Indices: 39249--39294 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
39239 TAAGGTTAAT
*
39249 TTTTTTATAAGATTTATAA
1 TTTTGTATAAGATTTATAA
39268 TTTTGTATAAGATTTATAA
1 TTTTGTATAAGATTTATAA
*
39287 ATTTGTAT
1 TTTTGTAT
39295 GTGAATGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.57
Consensus pattern (19 bp):
TTTTGTATAAGATTTATAA
Found at i:39885 original size:190 final size:191
Alignment explanation
Indices: 39559--40288 Score: 819
Period size: 202 Copynumber: 3.7 Consensus size: 191
39549 GTAAAATTTA
* * * * *
39559 TCGATCCCAGAAACATATG-CATCCATAAGTATAATGTAATAGGTAAATTTTCAATATAACCGGT
1 TCGATCCCAGAAACAT-CGAAACCCATAATTATAATGTAATAGGTAAATTTTCAATGTAACCGG-
39623 ATAAAATATACTGGTTTTATGAGAGAATA-GTCTACAACATGTATCGACAC-TTTTTTAATTTTG
64 -----ATATA---G-TTTATGAGAGAATAGGTCTACAACATGTATCGACACGTTTTTTAATTTTG
* * * *
39686 TTTCGATACTTTTGGTCCAAAATGGATACCAAAAAGGGTGAACACATAAAGTATCGATACATTTT
120 TGTCGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAAC-CATAAAGTGTCGATACATTTT
39751 GAAAAAGTG
184 -AAAAAGTG
*
39760 TCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACCGG-T
1 TCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTTCAATGTAACCGGAT
* *
39824 ATA-TTTATGAGAGAATAGGTCTACAACATGTATCGATAC-TTTTTTAATTTTATGTCGATACTT
66 ATAGTTTATGAGAGAATAGGTCTACAACATGTATCGACACGTTTTTTAATTTTGTGTCGATACTT
* * *
39887 TTGGTCCAGAATTGATGCCAAAAAGGGTGAACGCATAAAGTGTCGTTACATTTCCAAAAAGTG
131 TTGGTCCAGAATGGATGCCAAAAAGGGTGAAC-CATAAAGTGTCGATACATTT-TAAAAAGTG
* *
39950 TCGATCCCAAAAACATCGAAACCCGTAATTATAATGTAATAGGTAAATTTTCAATGTAACCGGTA
1 TCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTTCAATGTAACCGG--
* * * *
40015 TAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCAATACTTTTTTTAATTTTGTT
64 ---ATATA---G-TTTATGAGAGAATAGGTCTACAACATGTATCGACACGTTTTTTAATTTTGTG
** *
40080 TCGATACTTTTGGTCTTGAATGAATGCCAAAAAGGGTGCAACCATAAAGTGTCGATACATTTATA
122 TCGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTG-AACCATAAAGTGTCGATACATTT-TA
*
40145 AAAAGTA
185 AAAAGTG
* * * *
40152 TCGATCCCAGAAACATATG-CATCCATAAGTATAATGTAATAGGTAAATTTTCAATGTAACCGGT
1 TCGATCCCAGAAACAT-CGAAACCCATAATTATAATGTAATAGGTAAATTTTCAATGTAACCGG-
40216 ATAAATATATCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACGTTTTTT-ATTTTGT
64 ----ATATA---G-TTTATGAGAGAATAGGTCTACAACATGTATCGACACGTTTTTTAATTTTGT
40280 GTCGATACT
121 GTCGATACT
40289 AATTTAAATA
Statistics
Matches: 471, Mismatches: 41, Indels: 34
0.86 0.08 0.06
Matches are distributed among these distances:
189 14 0.03
190 157 0.33
194 4 0.01
196 4 0.01
200 1 0.00
201 105 0.22
202 182 0.39
203 4 0.01
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (191 bp):
TCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTTCAATGTAACCGGAT
ATAGTTTATGAGAGAATAGGTCTACAACATGTATCGACACGTTTTTTAATTTTGTGTCGATACTT
TTGGTCCAGAATGGATGCCAAAAAGGGTGAACCATAAAGTGTCGATACATTTTAAAAAGTG
Found at i:45537 original size:196 final size:190
Alignment explanation
Indices: 45067--45753 Score: 611
Period size: 196 Copynumber: 3.5 Consensus size: 190
45057 ACCTAAATAT
* * * *
45067 TGTCGATACATTT-TATACAAGTATCGACCCAAAAAACATCAAAACCAATAATTATAATGT-ATA
1 TGTCGATACATTTATA-AAAAGTATCGATCC-AAAAA-ATCGAAACCGATAATTATAATGTAATA
** * * *
45130 GAAAAATTAACAATGTAACCGATATAAATACCGGTTAATTA-GAAAACT--GTCAACATAATGTA
63 GGTAAATTTACAATGTAACCGATATAAATATCGGTT--TTATGAAAAATAGGTC-ACATAA-GTA
* * * * *
45192 TCGACACTTGTGTAATTTGTGTCGATACTTATTGTCCAGGATGAATGCACAAACGAGGT-GCACA
124 TCGACACTTG-CTAATTTGTGTCGATACTT-TTGTCCAGAATGAATAC-CAAA-AAGGTGGAAC-
45256 CATAAAG
184 CATAAAG
* * *
45263 TGTCGATACATTTATTAAAAGTATCGATCCCAAAAATCGAAACCGATAATTA-AATGTATTAGGT
1 TGTCGATACATTTATAAAAAGTATCGATCCAAAAAATCGAAACCGATAATTATAATGTAATAGGT
*
45327 AAAATTACAATGTAACCGATATAAATATCGGTTTTATGATAAAATAGGTCAGCATCAAGTATCGA
66 AAATTTACAATGTAACCGATATAAATATCGGTTTTATGA-AAAATAGGTCA-CAT-AAGTATCGA
45392 CACTTGCTAATTTGTGTCGATACTTTTGGTCCAGAATGAATACCAAAAAGGTGGAACCATAAAG
128 CACTTGCTAATTTGTGTCGATACTTTT-GTCCAGAATGAATACCAAAAAGGTGGAACCATAAAG
* * *
45456 TGTCGATACATTTATAAAAAATATCGATTCCGAAAATATCGAAAGCC-ATAAGTATAATGTAATA
1 TGTCGATACATTTATAAAAAGTATCGA-TCC-AAAAAATCGAAA-CCGATAATTATAATGTAATA
* * * * * *
45520 GGTAAATTTTCAATGTAACTGGT-TAAATATACCGGTTTTATGAGAGAATAGGTCTAAATATGTA
63 GGTAAATTTACAATGTAACCGATATAAATAT--CGGTTTTATGA-AAAATAGGTC-ACATAAGTA
* * * * **
45584 TCGACACGTTGTTAGTTTGTTTCGATACTTTTTTTCCAGAATGAATATGAATGTCCAACCAGGTG
124 TCGACAC-TTGCTAATTTGTGTCGATAC-TTTTGTCCAGAATG-A-AT--A---CCAAAAAGGTG
* *
45649 CAAGCATAAAG
180 GAACCATAAAG
** * * *
45660 TGTCGATACATTTA-AAATTGTATCGATCTAAAAAACATCGTAACCGATAATAATAATGTAATAG
1 TGTCGATACATTTATAAAAAGTATCGATC-CAAAAA-ATCGAAACCGATAATTATAATGTAATAG
* * *
45724 GTAAATTTGCAATGTTACCGGTATAAATAT
64 GTAAATTTACAATGTAACCGATATAAATAT
45754 ATCGATTTAC
Statistics
Matches: 410, Mismatches: 51, Indels: 52
0.80 0.10 0.10
Matches are distributed among these distances:
192 3 0.01
193 43 0.10
194 64 0.16
195 59 0.14
196 84 0.20
197 51 0.12
198 6 0.01
199 2 0.00
201 1 0.00
202 8 0.02
203 50 0.12
204 39 0.10
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (190 bp):
TGTCGATACATTTATAAAAAGTATCGATCCAAAAAATCGAAACCGATAATTATAATGTAATAGGT
AAATTTACAATGTAACCGATATAAATATCGGTTTTATGAAAAATAGGTCACATAAGTATCGACAC
TTGCTAATTTGTGTCGATACTTTTGTCCAGAATGAATACCAAAAAGGTGGAACCATAAAG
Found at i:46058 original size:15 final size:14
Alignment explanation
Indices: 46038--46072 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
46028 ATAATTTAAA
46038 TTTTATTTGAAATTT
1 TTTTATTTG-AATTT
46053 TTTTATTTGAATTT
1 TTTTATTTGAATTT
*
46067 GTTTAT
1 TTTTAT
46073 AAAATTTGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.69
Consensus pattern (14 bp):
TTTTATTTGAATTT
Found at i:46201 original size:30 final size:29
Alignment explanation
Indices: 46165--46222 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 29
46155 ATATTATACA
*
46165 TATTTGATAGACTTGACTCAAACATTAAAC
1 TATTTGATAGACTTGACTAAAAC-TTAAAC
*
46195 TATTTGATGGACTTGACTAAAACTTAAA
1 TATTTGATAGACTTGACTAAAACTTAAA
46223 AACTATCACT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 5 0.19
30 21 0.81
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (29 bp):
TATTTGATAGACTTGACTAAAACTTAAAC
Done.