Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004190.1 Hibiscus syriacus cultivar Beakdansim tig00009168_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: 53148
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:5255 original size:7 final size:7
Alignment explanation
Indices: 5239--5321 Score: 54
Period size: 7 Copynumber: 12.4 Consensus size: 7
5229 ATTATGCTTG
*
5239 AAGAAAA
1 AAGAAGA
5246 AAGAAGA
1 AAGAAGA
*
5253 AAGAAGG
1 AAGAAGA
5260 AA-AA-A
1 AAGAAGA
5265 AAGAA-A
1 AAGAAGA
5271 AAGAAAAGA
1 AAG--AAGA
5280 AA-AAGA
1 AAGAAGA
*
5286 AAAAAGA
1 AAGAAGA
*
5293 AAGAAAA
1 AAGAAGA
5300 AAG-AGAA
1 AAGAAG-A
5307 AAGAA-A
1 AAGAAGA
5313 AAGAA-A
1 AAGAAGA
5319 AAG
1 AAG
5322 GGGGTCAGAT
Statistics
Matches: 63, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
5 2 0.03
6 25 0.40
7 30 0.48
8 3 0.05
9 3 0.05
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (7 bp):
AAGAAGA
Found at i:5279 original size:11 final size:11
Alignment explanation
Indices: 5263--5319 Score: 75
Period size: 11 Copynumber: 5.4 Consensus size: 11
5253 AAGAAGGAAA
5263 AAAAGAAAAAG
1 AAAAGAAAAAG
5274 AAAAGAAAAAG
1 AAAAGAAAAAG
5285 AAAA-AAGAAAG
1 AAAAGAA-AAAG
*
5296 -AAA-AAAGAG
1 AAAAGAAAAAG
5305 AAAAGAAAAAG
1 AAAAGAAAAAG
5316 AAAA
1 AAAA
5320 AGGGGGTCAG
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
9 3 0.07
10 10 0.24
11 28 0.68
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:5286 original size:36 final size:37
Alignment explanation
Indices: 5243--5321 Score: 117
Period size: 36 Copynumber: 2.2 Consensus size: 37
5233 TGCTTGAAGA
* *
5243 AAAAAGAAGAAAGAAGGAAAAAA-AGAAAA-AGAAAAG
1 AAAAAGAAAAAAGAAAGAAAAAAGAGAAAAGA-AAAAG
5279 AAAAAGAAAAAAGAAAGAAAAAAGAGAAAAGAAAAAG
1 AAAAAGAAAAAAGAAAGAAAAAAGAGAAAAGAAAAAG
5316 AAAAAG
1 AAAAAG
5322 GGGGTCAGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
36 21 0.54
37 17 0.44
38 1 0.03
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (37 bp):
AAAAAGAAAAAAGAAAGAAAAAAGAGAAAAGAAAAAG
Found at i:5308 original size:18 final size:18
Alignment explanation
Indices: 5239--5312 Score: 82
Period size: 18 Copynumber: 4.1 Consensus size: 18
5229 ATTATGCTTG
5239 AAGAAAAAAGA-AGAAAGA
1 AAGAAAAAAGAGA-AAAGA
*
5257 AGGAAAAAA-AGAAAAAGA
1 AAGAAAAAAGAG-AAAAGA
*
5275 AA-AGAAAAAGAAAAAAGA
1 AAGA-AAAAAGAGAAAAGA
5293 AAGAAAAAAGAGAAAAGA
1 AAGAAAAAAGAGAAAAGA
5311 AA
1 AA
5313 AAGAAAAAGG
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
17 2 0.04
18 42 0.89
19 3 0.06
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (18 bp):
AAGAAAAAAGAGAAAAGA
Found at i:5319 original size:18 final size:17
Alignment explanation
Indices: 5243--5321 Score: 81
Period size: 19 Copynumber: 4.4 Consensus size: 17
5233 TGCTTGAAGA
5243 AAAAAGAAGAAAGAAGGAA-
1 AAAAAGAA-AAAGAA--AAG
5262 AAAAAGAAAAAGAAAAG
1 AAAAAGAAAAAGAAAAG
5279 AAAAAGAAAAA-AGAAAG
1 AAAAAGAAAAAGA-AAAG
5296 AAAAAAGAGAAAAGAAAAAG
1 -AAAAAGA-AAAAG-AAAAG
5316 AAAAAG
1 AAAAAG
5322 GGGGTCAGAT
Statistics
Matches: 54, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
16 3 0.06
17 15 0.28
18 13 0.24
19 18 0.33
20 4 0.07
21 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAAGAAAAG
Found at i:6782 original size:91 final size:92
Alignment explanation
Indices: 6547--7073 Score: 910
Period size: 91 Copynumber: 5.8 Consensus size: 92
6537 AGAAGACCCA
*
6547 ATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAAT
6612 CATTGAATTTGGAAGATAAA--TG-TC
66 CATTGAATTTGGAAGATAAATGTGCTC
*
6636 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGTACCACAGAACCAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAAT
6701 CATTG-ATTTGGAAGATAAATGTGCTC
66 CATTGAATTTGGAAGATAAATGTGCTC
*
6727 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGAATGAACCACAGAACCAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAAT
6792 CATTG-ATTTGGAAGAT-AATGTGCTC
66 CATTGAATTTGGAAGATAAATGTGCTC
*
6817 ATAGCATCTTCTGGAAGTGGTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAAT
6882 CATTGAATTTGGAAGATAAATGTGCTC
66 CATTGAATTTGGAAGATAAATGTGCTC
6909 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAAT
6974 CATTGAATTTGGAAGAT-AATGTGCTC
66 CATTGAATTTGGAAGATAAATGTGCTC
* * *
7000 ATAGCATCTTCTGGAAGTGTTCTTT-ATATTATCTGATCTGGTTCGGTA-GGACCACAGAACCAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGA-GTTATCTGATCTGGTTTGGTATGAACCACAGAACCAA
7063 TCATTGGAATT
65 TCATT-GAATT
7074 AAAAGATGAA
Statistics
Matches: 421, Mismatches: 10, Indels: 12
0.95 0.02 0.03
Matches are distributed among these distances:
88 14 0.03
89 68 0.16
90 99 0.24
91 150 0.36
92 90 0.21
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (92 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAAT
CATTGAATTTGGAAGATAAATGTGCTC
Found at i:7957 original size:24 final size:23
Alignment explanation
Indices: 7914--7958 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
7904 GTTCATAATG
*
7914 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
7937 AGAAGAAATTCATAATG-AGAAG
1 AGAAG-AATTCAT-ATGAAGAAG
7959 AATTTGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 12 0.63
25 2 0.11
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:8069 original size:23 final size:23
Alignment explanation
Indices: 8027--8070 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
8017 GTTCATAATG
*
8027 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
8050 AGAAGAATTCATAATG-AGAAG
1 AGAAGAATTCAT-ATGAAGAAG
8071 AATTTGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.50, C:0.07, G:0.25, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:8181 original size:24 final size:23
Alignment explanation
Indices: 8138--8182 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
8128 GTTCATAATG
*
8138 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
8161 AGAAGAAATTCATAATG-AGAAG
1 AGAAG-AATTCAT-ATGAAGAAG
8183 AATTGTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 12 0.63
25 2 0.11
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:8200 original size:111 final size:113
Alignment explanation
Indices: 7754--8733 Score: 1518
Period size: 111 Copynumber: 8.8 Consensus size: 113
7744 TAGCAAAGAT
* * *
7754 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAA-TATTCATCTGA
1 TCAAATTCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
*
7818 AGAAGGAAGAAG-AATTCATAATGAGAAGAATTTGTTTAACCATTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
*
7865 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
1 TCAAATTCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
*
7930 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGT
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
*
7978 TCAAATTCATCACTTGATGGATCAGTTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
1 TCAAATTCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
8043 AGAAGGAAGAAG-AATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
8090 TCAAATTCATCACTTGATGGATCAGCTTTT-CAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
1 TCAAATTCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
8154 AGAAGGAAGAAGAAATTCATAATGAGAAGAA-TTGTTTAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
*
8201 TC-AATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
1 TCAAATTCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
* *
8265 A-AA--AGGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGT
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
* *
8310 TCAAATTCATCACTTGATGGATCAGTTTTTTCCAGTTCGAGTTCATAAT--GAAGAATTCATCTA
1 TCAAATTCATCACTTGATGGATCAG-CTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTG
8373 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
*
8422 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAG-TCATAATGAGAAGAATTCATCTGA
1 TCAAATTCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
*
8486 AGAA-G--GAAGAAATTCATAATGA-AAGAATTTGTTTAACCTTTTGT
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
*
8530 TCAAATTCATCACTTGATGGATCAGCTTTTCCAGTTCAAGTTCATAAT--GAAGAATTCATCTGA
1 TCAAATTCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
* **
8593 AGAAGGAAGAA-AAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTAT
66 AGAAGGAAGAAGAAA-TTCATAATGAGAAGAATTTGTTTAACCTTTTGC
* * * **** *
8641 TCATATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAAT-AAAAGAACTT-ATCTG
1 TCAAATTCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAA-TTCATCTG
* * *
8704 AAG-AGAAAGAAGAAGTTCACAATGAGAAGA
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGA
8734 CCTGTTCAAC
Statistics
Matches: 814, Mismatches: 34, Indels: 42
0.91 0.04 0.05
Matches are distributed among these distances:
107 19 0.02
108 84 0.10
109 59 0.07
110 71 0.09
111 271 0.33
112 200 0.25
113 110 0.14
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (113 bp):
TCAAATTCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
Found at i:8410 original size:332 final size:334
Alignment explanation
Indices: 7754--8733 Score: 1540
Period size: 332 Copynumber: 2.9 Consensus size: 334
7744 TAGCAAAGAT
* *
7754 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAA-TATTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
*
7818 AGAAGGAAGAAG-AATTCATAATGAGAAGAATTTGTTTAACCATTTGCTCAAATCCATCACTTGA
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGCTCAAATCCATCACTTGA
*
7882 TGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAATT
131 TGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGAA-AA--AGGAAGAAATT
7947 CATAATGAGAAGAATTTGTTTAACCTTTTGTTCAAATTCATCACTTGATGGATCAGTTTTTCCAG
193 CATAATGAGAAGAATTTGTTTAACCTTTTGTTCAAATTCATCACTTGATGGATCAGTTTTTCCAG
*
8012 TTCGAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAATTCATAATGAGAAGAATTTG
258 TTCGAGTTCATAAT-AGAAGAATTCATCTAAAGAAGGAAGAAGAATTCATAATGAGAAGAATTTG
8077 TTTAACCTTTTGC
322 TTTAACCTTTTGC
*
8090 TCAAATTCATCACTTGATGGATCAGCTTTT-CAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
8154 AGAAGGAAGAAGAAATTCATAATGAGAAGAA-TTGTTTAACCTTTTGCTC-AATCCATCACTTGA
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGCTCAAATCCATCACTTGA
8217 TGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGAAAAAGGAAGAAATTCAT
131 TGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGAAAAAGGAAGAAATTCAT
8282 AATGAGAAGAATTTGTTTAACCTTTTGTTCAAATTCATCACTTGATGGATCAGTTTTTTCCAGTT
196 AATGAGAAGAATTTGTTTAACCTTTTGTTCAAATTCATCACTTGATGGATCAG-TTTTTCCAGTT
8347 CGAGTTCATAAT-GAAGAATTCATCTAAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
260 CGAGTTCATAATAGAAGAATTCATCTAAAGAAGGAAGAAG-AATTCATAATGAGAAGAATTTGTT
8411 TAACCTTTTGC
324 TAACCTTTTGC
8422 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAG-TCATAATGAGAAGAATTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
* *
8486 AGAA-G--GAAGAAATTCATAATGA-AAGAATTTGTTTAACCTTTTGTTCAAATTCATCACTTGA
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGCTCAAATCCATCACTTGA
* *
8547 TGGATCAGCTTTTCCAGTTCAAGTTCATAAT--GAAGAATTCATCTGAAGAAGGAAGAAAAAGTT
131 TGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGAAAAAGGAAG--AAA-TT
* * * ***
8610 CATAATGAGAAGAACTTGTTTAACCTTTTATTCATATTCATCACTTGATGGATCAACATTTCCAG
193 CATAATGAGAAGAATTTGTTTAACCTTTTGTTCAAATTCATCACTTGATGGATCAGTTTTTCCAG
**** * * * *
8675 AGAAAGTTCATAATAAAAGAACTT-ATCTGAAG-AGAAAGAAGAAGTTCACAATGAGAAGA
258 TTCGAGTTCATAATAGAAGAA-TTCATCTAAAGAAGGAAGAAGAA-TTCATAATGAGAAGA
8734 CCTGTTCAAC
Statistics
Matches: 606, Mismatches: 25, Indels: 32
0.91 0.04 0.05
Matches are distributed among these distances:
328 28 0.05
329 36 0.06
330 85 0.14
331 93 0.15
332 160 0.26
333 32 0.05
334 2 0.00
335 85 0.14
336 67 0.11
337 18 0.03
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (334 bp):
TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGCTCAAATCCATCACTTGA
TGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGAAAAAGGAAGAAATTCAT
AATGAGAAGAATTTGTTTAACCTTTTGTTCAAATTCATCACTTGATGGATCAGTTTTTCCAGTTC
GAGTTCATAATAGAAGAATTCATCTAAAGAAGGAAGAAGAATTCATAATGAGAAGAATTTGTTTA
ACCTTTTGC
Found at i:9099 original size:3 final size:3
Alignment explanation
Indices: 9093--9143 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
9083 TTACTCATTT
*
9093 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
9141 TTA
1 TTA
9144 AAAAATAATT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:12833 original size:27 final size:27
Alignment explanation
Indices: 12780--12833 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
12770 AAATCGAGTG
*
12780 GAGTTAAACATTTTTATTTATTTATTT
1 GAGTTAAACATTTTTATTTATTAATTT
12807 GAGTTGAAA-ATTTTTATTT-TATAATTT
1 GAGTT-AAACATTTTTATTTAT-TAATTT
12834 AAATTTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 1 0.04
27 20 0.83
28 3 0.12
ACGTcount: A:0.31, C:0.02, G:0.09, T:0.57
Consensus pattern (27 bp):
GAGTTAAACATTTTTATTTATTAATTT
Found at i:13973 original size:49 final size:49
Alignment explanation
Indices: 13901--14011 Score: 204
Period size: 49 Copynumber: 2.3 Consensus size: 49
13891 GTCATATAAA
13901 GAAAGGCGCAGATGGCGATATGCACTTTCGCAGGGTTTCTGACACGTAC
1 GAAAGGCGCAGATGGCGATATGCACTTTCGCAGGGTTTCTGACACGTAC
*
13950 GAAAGGCGCAGATGGCTATATGCACTTTCGCAGGGTTTCTGACACGTAC
1 GAAAGGCGCAGATGGCGATATGCACTTTCGCAGGGTTTCTGACACGTAC
*
13999 GGAAGGCGCAGAT
1 GAAAGGCGCAGAT
14012 AATGATCCGC
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 60 1.00
ACGTcount: A:0.25, C:0.22, G:0.32, T:0.22
Consensus pattern (49 bp):
GAAAGGCGCAGATGGCGATATGCACTTTCGCAGGGTTTCTGACACGTAC
Found at i:17534 original size:17 final size:18
Alignment explanation
Indices: 17501--17549 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
17491 AGAAAACAAT
17501 ACAACTCAAACAATAAAA
1 ACAACTCAAACAATAAAA
*
17519 ACAACT-AAATAATAAAA
1 ACAACTCAAACAATAAAA
* *
17536 ACAATTCGAACAAT
1 ACAACTCAAACAAT
17550 TAAATAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.63, C:0.18, G:0.02, T:0.16
Consensus pattern (18 bp):
ACAACTCAAACAATAAAA
Found at i:17537 original size:26 final size:26
Alignment explanation
Indices: 17508--17584 Score: 82
Period size: 26 Copynumber: 2.9 Consensus size: 26
17498 AATACAACTC
*
17508 AAACAATAAAAACAACTAAATAATAA
1 AAACAATAAAAACAAATAAATAATAA
*** *
17534 AAACAATTCGAACAATTAAATAATAA
1 AAACAATAAAAACAAATAAATAATAA
*
17560 AAACATTAACAAACCAAATAAATAA
1 AAACAATAA-AAA-CAAATAAATAA
17585 AAAGTTCATA
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
26 28 0.70
27 2 0.05
28 10 0.25
ACGTcount: A:0.68, C:0.13, G:0.01, T:0.18
Consensus pattern (26 bp):
AAACAATAAAAACAAATAAATAATAA
Found at i:18473 original size:77 final size:77
Alignment explanation
Indices: 18346--18506 Score: 313
Period size: 77 Copynumber: 2.1 Consensus size: 77
18336 TTGAACCACT
*
18346 CATAATAATAATCCACAACCTAGTAATGATCCACATAAATAGGCTTTGTACGGGGAATACACCCA
1 CATAACAATAATCCACAACCTAGTAATGATCCACATAAATAGGCTTTGTACGGGGAATACACCCA
18411 TGTCGATCCTCC
66 TGTCGATCCTCC
18423 CATAACAATAATCCACAACCTAGTAATGATCCACATAAATAGGCTTTGTACGGGGAATACACCCA
1 CATAACAATAATCCACAACCTAGTAATGATCCACATAAATAGGCTTTGTACGGGGAATACACCCA
18488 TGTCGATCCTCC
66 TGTCGATCCTCC
18500 CATAACA
1 CATAACA
18507 TTACCCACTC
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 83 1.00
ACGTcount: A:0.36, C:0.27, G:0.14, T:0.24
Consensus pattern (77 bp):
CATAACAATAATCCACAACCTAGTAATGATCCACATAAATAGGCTTTGTACGGGGAATACACCCA
TGTCGATCCTCC
Found at i:18783 original size:2 final size:2
Alignment explanation
Indices: 18776--18802 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
18766 ACTAAAACAA
18776 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
18803 ATTCTTATCA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22222 original size:64 final size:65
Alignment explanation
Indices: 22151--22309 Score: 227
Period size: 64 Copynumber: 2.5 Consensus size: 65
22141 TGATAAATTG
*
22151 AACATCGAATGCATTTTATGCATCGATGCACAAACCATGCATCAATGCACTCA-G-T-TTTTATG
1 AACATCGAATGCATTTTATGCATCGATGCACAAACCATGCATCAATACACTCAGGCTATTTTA--
22213 AA
64 AA
* *
22215 AACATCGAATGCATTTTATGCATCGATGCACAAGCCATGCATCGATACACTCAGGCTATTTTAAA
1 AACATCGAATGCATTTTATGCATCGATGCACAAACCATGCATCAATACACTCAGGCTATTTTAAA
* *
22280 AA-ATCGAATACATTTTATGCATCAATGCAC
1 AACATCGAATGCATTTTATGCATCGATGCAC
22310 TCTTAGTGCA
Statistics
Matches: 87, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
64 76 0.87
65 5 0.06
66 1 0.01
67 5 0.06
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (65 bp):
AACATCGAATGCATTTTATGCATCGATGCACAAACCATGCATCAATACACTCAGGCTATTTTAAA
Found at i:27024 original size:55 final size:54
Alignment explanation
Indices: 26934--27298 Score: 437
Period size: 55 Copynumber: 6.8 Consensus size: 54
26924 TGGGTTCGCT
* *
26934 CCCTATTTCTTC--AGAGTATAAGACTTGAATC-ATCTTCAACAAATTTGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAA-CAATCTTCAAC-AATTCGTCTGCC
*
26987 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATT-CGTCTGCC
* * * *
27042 CCCTATTTCTTC--AGAGTATAAGAC-C-CATAATCTTCATC-A-TCGCATATGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATTCG--TCTGCC
* *
27092 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGTGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATT-CGTCTGCC
* * * * *
27147 CCCTATTTCTTCAGAGAGTAAAAGAC-C-CACAATCTTCATCAATCGCGTTTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAT-TCGTCTGCC
* *
27200 CCCTATTTCTTCAGAGAGTATAAGACCCGAACAATCTTCAACGATTGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATT-CGTCTGCC
27255 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAA
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAA
27299 ATGGGTTCGC
Statistics
Matches: 268, Mismatches: 27, Indels: 32
0.82 0.08 0.10
Matches are distributed among these distances:
48 2 0.01
49 1 0.00
50 18 0.07
51 10 0.04
52 13 0.05
53 69 0.26
54 16 0.06
55 137 0.51
56 1 0.00
57 1 0.00
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (54 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATTCGTCTGCC
Found at i:27243 original size:108 final size:107
Alignment explanation
Indices: 26983--27294 Score: 520
Period size: 108 Copynumber: 2.9 Consensus size: 107
26973 CAAATTTGTC
26983 TGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTAT
1 TGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTAT
*
27048 TTCTTC--AGAGTATAAGACCCATAATCTTCATCATCGCATA
66 TTCTTCAGAGAGTATAAGACCCACAATCTTCATCATCGCATA
*
27088 TGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGTGTCTGCCCCCTAT
1 TGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTAT
* * *
27153 TTCTTCAGAGAGTAAAAGACCCACAATCTTCATCAATCGCGTT
66 TTCTTCAGAGAGTATAAGACCCACAATCTTCATC-ATCGCATA
*
27196 TGCCCCCTATTTCTTCAGAGAGTATAAGACCCGAACAATCTTCAACGATTGCGTCTGCCCCCTAT
1 TGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTAT
*
27261 TTCTTCAGAGAGTATAAGACTCGAACAATCTTCA
66 TTCTTCAGAGAGTATAAGAC-C-CACAATCTTCA
27295 ACAAATGGGT
Statistics
Matches: 193, Mismatches: 9, Indels: 5
0.93 0.04 0.02
Matches are distributed among these distances:
105 70 0.36
107 24 0.12
108 88 0.46
109 1 0.01
110 10 0.05
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.29
Consensus pattern (107 bp):
TGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTAT
TTCTTCAGAGAGTATAAGACCCACAATCTTCATCATCGCATA
Found at i:27314 original size:55 final size:55
Alignment explanation
Indices: 26910--27351 Score: 391
Period size: 55 Copynumber: 8.2 Consensus size: 55
26900 GAATTCAATA
* * *
26910 AATCTTCAGAAAAATGGGTTCGCTCCCTATTTCTTC--AGAGTATAAGACTTGAATC
1 AATCTTCA-ACAAATGGGTTCGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAA-C
**
26965 -ATCTTCAACAAATTTG-TCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACAAATGGGTTC-GCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * * * *
27019 AATCTTCAACGATTGCG-TCTGCCCCCTATTTCTTC--AGAGTATAAGAC-C-CAT
1 AATCTTCAACAAATGGGTTC-GCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* **
27070 AATCTTCATC--ATCGCATAT-GCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACAAAT-GGGT-TCGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * * * *
27124 AATCTTCAACGATTGTG-TCTGCCCCCTATTTCTTCAGAGAGTAAAAGAC-C-CAC
1 AATCTTCAACAAATGGGTTC-GCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * * *
27177 AATCTTCATC-AATCGCGTTTGCCCCCTATTTCTTCAGAGAGTATAAGACCCGAAC
1 AATCTTCAACAAAT-GGGTTCGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * *
27232 AATCTTCAACGATTGCG-TCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACAAATGGGTTC-GCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* *
27287 AATCTTCAACAAATGGGTTCGCTCCCTATTTC-TCTAGGGAGTAT-AGAACTCGAAC
1 AATCTTCAACAAATGGGTTCGCCCCCTATTTCTTC-AGAGAGTATAAG-ACTCGAAC
*
27342 ATCTCTTCAA
1 A-ATCTTCAA
27352 ACGGGTTCGC
Statistics
Matches: 324, Mismatches: 38, Indels: 49
0.79 0.09 0.12
Matches are distributed among these distances:
49 1 0.00
50 17 0.05
51 10 0.03
52 18 0.06
53 75 0.23
54 26 0.08
55 165 0.51
56 12 0.04
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (55 bp):
AATCTTCAACAAATGGGTTCGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
Found at i:27442 original size:51 final size:51
Alignment explanation
Indices: 27270--27690 Score: 490
Period size: 51 Copynumber: 8.3 Consensus size: 51
27260 TTTCTTCAGA
* * * * *
27270 GAGTATA-AGACTCGAACAATCTTCAACAAATGGGTTCGCTCCCTATTTCTCTAGG
1 GAGTATAGA-ACTCGAAC-ATCTT---CAAACGGGTTCGCTCCTTCTTTCTTTAAG
*
27325 GAGTATAGAACTCGAACATCTCTTCAAACGGGTTCGCTCATTC-TTCTTTAAG
1 GAGTATAGAACTCGAACA--TCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
27377 GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
1 GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
*
27428 GAGTATAGAACTCGAACATCTTCAAAC-GGTTCGCTCCCTCTTTC-TT-AG
1 GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
** *
27476 GAGTATAGAACTCGAACATC-TCTTTACGGGTTCGCTCC-TCTTTCTCT-AG
1 GAGTATAGAACTCGAACATCTTC-AAACGGGTTCGCTCCTTCTTTCTTTAAG
* * *
27525 G-GTATGGAACTCGAACATCTTC-AACTGGGTTCGCTCCCTCTTTCTCT-AG
1 GAGTATAGAACTCGAACATCTTCAAAC-GGGTTCGCTCCTTCTTTCTTTAAG
* *
27574 GA-TATGGAACT-TAGACATCTCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
1 GAGTATAGAACTCGA-ACA--TCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
* *
27626 GAGTATGGACCTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
1 GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
27677 GAGTATAGAACTCG
1 GAGTATAGAACTCG
27691 CATATTTTCA
Statistics
Matches: 328, Mismatches: 20, Indels: 40
0.85 0.05 0.10
Matches are distributed among these distances:
47 4 0.01
48 59 0.18
49 42 0.13
50 38 0.12
51 105 0.32
52 32 0.10
53 26 0.08
54 2 0.01
55 15 0.05
56 5 0.02
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.33
Consensus pattern (51 bp):
GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
Found at i:27616 original size:198 final size:204
Alignment explanation
Indices: 27301--27690 Score: 559
Period size: 198 Copynumber: 1.9 Consensus size: 204
27291 TTCAACAAAT
*
27301 GGGTTCGCTCCCTATTTCTCTAGGGAGTATAGAACTCGAACATCTCTTCAAACGGGTTCGCTCAT
1 GGGTTCGCTCCCTATTTCTCTAGGGAGTATAGAACTCGAACA-CTCTTCAAACGGGTTCGCTCAC
* *
27366 TCTTCTTTAAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAG
65 TCTTCTCTAAGGAGTATAGAACTAGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAG
27431 TATAGAACTCGAACATCTTCAAAC-GGTTCGCTCCCTCTTTC-TT-AGGAGTATAGAACTCGAAC
130 TATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTTTAAGGAGTATAGAACTCGAAC
27493 ATCTCTTTAC
195 ATCTCTTTAC
* * *
27503 GGGTTCGCT-CCTCTTTCTCTA-GG-GTATGGAACTCGAACA-TCTTC-AACTGGGTTCGCTCCC
1 GGGTTCGCTCCCTATTTCTCTAGGGAGTATAGAACTCGAACACTCTTCAAAC-GGGTTCGCTCAC
*
27563 TCTTTCTCT-AGGA-TATGGAACTTAG-ACATCTCTTCAAACGGGTTCGCTCCTTCTTTCTTTAA
65 TC-TTCTCTAAGGAGTATAGAAC-TAGAACA--TCTTCAAACGGGTTCGCTCCTTCTTTCTTTAA
* * *
27625 GGAGTATGGACCTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTC
126 GGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTTTAAGGAGTATAGAACTC
27690 G
191 G
27691 CATATTTTCA
Statistics
Matches: 170, Mismatches: 10, Indels: 17
0.86 0.05 0.09
Matches are distributed among these distances:
196 13 0.08
197 23 0.14
198 63 0.37
199 31 0.18
200 4 0.02
201 27 0.16
202 9 0.05
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (204 bp):
GGGTTCGCTCCCTATTTCTCTAGGGAGTATAGAACTCGAACACTCTTCAAACGGGTTCGCTCACT
CTTCTCTAAGGAGTATAGAACTAGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGT
ATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTTTAAGGAGTATAGAACTCGAACA
TCTCTTTAC
Found at i:28126 original size:36 final size:36
Alignment explanation
Indices: 28069--28295 Score: 232
Period size: 36 Copynumber: 6.4 Consensus size: 36
28059 ACTCTTCTGA
* **
28069 GAAGGCTTAA-ATGGATCTGCTTCACTACTTTTTGGT
1 GAAGGCTTAAGATGG-TTTGCTTCACTACTTTCCGGT
* * *
28105 GAAGACTTAAGATGGTTTGCTTCACTACTCTCTGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTACTTTCCGGT
* * *
28141 GAAGACTTATGATTGTTTGCTTCACTA-TTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTACTT-TCCGGT
* * *
28177 GAAGGCTTCAGATTGATTGCTTCACTA-TTCTCC-GT
1 GAAGGCTTAAGATGGTTTGCTTCACTACTT-TCCGGT
* *
28212 GAAGGCTTCAGATGGTTTGCTTCACTACTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTACTTTCCGGT
* *
28248 GAAGGCTTAGGATGGTTTGCTTCACTTCTCTT-C-GT
1 GAAGGCTTAAGATGGTTTGCTTCACTACT-TTCCGGT
28283 GAAGGCTTAAGAT
1 GAAGGCTTAAGAT
28296 TGACTTGCTC
Statistics
Matches: 166, Mismatches: 20, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
35 45 0.27
36 116 0.70
37 5 0.03
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (36 bp):
GAAGGCTTAAGATGGTTTGCTTCACTACTTTCCGGT
Found at i:28237 original size:107 final size:107
Alignment explanation
Indices: 28069--28304 Score: 300
Period size: 107 Copynumber: 2.2 Consensus size: 107
28059 ACTCTTCTGA
* * **
28069 GAAGGCTTAA-ATGGA-TCTGCTTCACTACTTTTTGGTGAAGACTTAAGATGGTTTGCTTCACTA
1 GAAGGCTTAAGATTGACT-TGCTTCACTA-TTCTCCGTGAAGACTTAAGATGGTTTGCTTCACTA
* * *
28132 CTCTCTGGTGAAGACTTATGATTGTTTGCTTCACTAT-TCTCCGGT
64 CTCTCCGGTGAAGACTTAGGATGGTTTGCTTCACT-TCTCTCC-GT
* * *
28177 GAAGGCTTCAGATTGA-TTGCTTCACTATTCTCCGTGAAGGCTTCAGATGGTTTGCTTCACTACT
1 GAAGGCTTAAGATTGACTTGCTTCACTATTCTCCGTGAAGACTTAAGATGGTTTGCTTCACTACT
* *
28241 CTCCGGTGAAGGCTTAGGATGGTTTGCTTCACTTCTCTTCGT
66 CTCCGGTGAAGACTTAGGATGGTTTGCTTCACTTCTCTCCGT
28283 GAAGGCTTAAGATTGACTTGCT
1 GAAGGCTTAAGATTGACTTGCT
28305 CCAATCTCAT
Statistics
Matches: 112, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
106 18 0.16
107 70 0.62
108 19 0.17
109 5 0.04
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (107 bp):
GAAGGCTTAAGATTGACTTGCTTCACTATTCTCCGTGAAGACTTAAGATGGTTTGCTTCACTACT
CTCCGGTGAAGACTTAGGATGGTTTGCTTCACTTCTCTCCGT
Found at i:28244 original size:71 final size:69
Alignment explanation
Indices: 28069--28291 Score: 241
Period size: 71 Copynumber: 3.1 Consensus size: 69
28059 ACTCTTCTGA
* * * ** * *
28069 GAAGGCTTAAATGGATCTGCTTCACTACTTTTTGGTGAAGACTTAAGATGGTTTGCTTCACTACT
1 GAAGGCTTAGATGG-TTTGCTTCACTACTCTCCGGTGAAGGCTT-AGATGGTTTGCTTCACTATT
*
28134 CTCTGGT
64 CTC-CGT
* * * * *
28141 GAAGACTTATGATTGTTTGCTTCACTATTCTCCGGTGAAGGCTTCAGATTGATTGCTTCACTATT
1 GAAGGCTTA-GATGGTTTGCTTCACTACTCTCCGGTGAAGGCTT-AGATGGTTTGCTTCACTATT
28206 CTCCGT
64 CTCCGT
28212 GAAGGCTTCAGATGGTTTGCTTCACTACTCTCCGGTGAAGGCTTAGGATGGTTTGCTTCACT-TC
1 GAAGGCTT-AGATGGTTTGCTTCACTACTCTCCGGTGAAGGCTTA-GATGGTTTGCTTCACTAT-
*
28276 TCTTCGT
63 TCTCCGT
28283 GAAGGCTTA
1 GAAGGCTTA
28292 AGATTGACTT
Statistics
Matches: 127, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
70 3 0.02
71 69 0.54
72 52 0.41
73 3 0.02
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (69 bp):
GAAGGCTTAGATGGTTTGCTTCACTACTCTCCGGTGAAGGCTTAGATGGTTTGCTTCACTATTCT
CCGT
Found at i:29703 original size:125 final size:124
Alignment explanation
Indices: 29480--29786 Score: 393
Period size: 125 Copynumber: 2.5 Consensus size: 124
29470 ACTGATGTCG
* * * * * *
29480 CAACATTATTTTATTCTGGTACGGGCCTTCAGAATGCCTCAAT-ATCTCAAATTATAAGGCTCAT
1 CAACATTATCTTATACTGGTACGGGCCTTCAAAATGCC-CCATCACCTCAAATTGTAAGGCTCAT
** * *
29544 TCTCAATGCCTTCTTGGTCTGAATCTTGTAATTTCATCATGATGTGGGTTCATTCGCGCCC
65 TCTCAATGCCTTCTTGGTCTGAATCTTGTAATTTCAAAATGAT-AGGGTTCAATCGCGCCC
*
29605 CAACATTATCTCATACTGGTACGGGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCTCATT
1 CAACATTATCTTATACTGGTACGGGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCTCATT
** * * *
29670 CTTGATGCCTTCTTTGTCTGAATCTTGTCATTTCAAAATGATAGGGTTCAATCGTGCCC
66 CTCAATGCCTTCTTGGTCTGAATCTTGTAATTTCAAAATGATAGGGTTCAATCGCGCCC
** * * *
29729 CAACATTATCTTATAAAGGTACGGGTCTTCAAAATACCCCAACACCTCAAA-TGTAAGG
1 CAACATTATCTTATACTGGTACGGGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGG
29787 GATGGGCTAC
Statistics
Matches: 159, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
123 7 0.04
124 62 0.39
125 90 0.57
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (124 bp):
CAACATTATCTTATACTGGTACGGGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCTCATT
CTCAATGCCTTCTTGGTCTGAATCTTGTAATTTCAAAATGATAGGGTTCAATCGCGCCC
Found at i:30519 original size:175 final size:175
Alignment explanation
Indices: 30170--30529 Score: 679
Period size: 175 Copynumber: 2.1 Consensus size: 175
30160 TTTAGGTTGG
30170 CTTCCTATTTTCTAAGGCTTCGACCACCAAAATACCATCTCTTTCTTGATCGTTGTGACCATCAC
1 CTTCC-ATTTTCTAAGGCTTCGACCACCAAAATACCATCTCTTTCTTGATCGTTGTGACCATCAC
30235 AACATGCCCTTCTTTCTTGGCTTGGTATTTTAATCGATGCGGACAAAATGACGCAATAGTATACT
65 AACATGCCCTTCTTTCTTGGCTTGGTATTTTAATCGATGCGGACAAAATGACGCAATAGTATACT
30300 CCATTACTAGACTTTCCAGAACACTTCCATTTCAGTTCTCTGAAAT
130 CCATTACTAGACTTTCCAGAACACTTCCATTTCAGTTCTCTGAAAT
30346 CTTCCATTTTCTAAGGCTTCGACCACCAAAATACCATCTCTTTCTTGATCGTTGTGACCATCACA
1 CTTCCATTTTCTAAGGCTTCGACCACCAAAATACCATCTCTTTCTTGATCGTTGTGACCATCACA
30411 ACATGCCCTTCTTTCTTGGCTTGGTATTTTAATCGGATGCGGACAAAATGACGCAAATAGTATAC
66 ACATGCCCTTCTTTCTTGGCTTGGTATTTTAATC-GATGCGGACAAAATGACGC-AATAGTATAC
30476 TCCATTACTAGACTTTCCAGAACACTTCCATTTCAG-T-TCTGAAAT
129 TCCATTACTAGACTTTCCAGAACACTTCCATTTCAGTTCTCTGAAAT
30521 CTTCCATTT
1 CTTCCATTT
30530 GTTCAAGCTT
Statistics
Matches: 182, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
175 111 0.61
176 25 0.14
177 46 0.25
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.35
Consensus pattern (175 bp):
CTTCCATTTTCTAAGGCTTCGACCACCAAAATACCATCTCTTTCTTGATCGTTGTGACCATCACA
ACATGCCCTTCTTTCTTGGCTTGGTATTTTAATCGATGCGGACAAAATGACGCAATAGTATACTC
CATTACTAGACTTTCCAGAACACTTCCATTTCAGTTCTCTGAAAT
Found at i:33322 original size:13 final size:12
Alignment explanation
Indices: 33304--33346 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 12
33294 AAATTAATAC
33304 ATGCAATGCGAAA
1 ATGCAATGC-AAA
33317 ATGCAAATGCAAA
1 ATGC-AATGCAAA
33330 ATGCAAATGC-AA
1 ATGC-AATGCAAA
33342 ATGCA
1 ATGCA
33347 CGAGGTGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 1 0.03
12 6 0.21
13 17 0.59
14 5 0.17
ACGTcount: A:0.49, C:0.16, G:0.19, T:0.16
Consensus pattern (12 bp):
ATGCAATGCAAA
Found at i:33326 original size:6 final size:6
Alignment explanation
Indices: 33315--33346 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
33305 TGCAATGCGA
33315 AAATGC AAATGC AAAATGC AAATGC AAATGC A
1 AAATGC AAATGC -AAATGC AAATGC AAATGC A
33347 CGAGGTGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.53, C:0.16, G:0.16, T:0.16
Consensus pattern (6 bp):
AAATGC
Found at i:33328 original size:19 final size:17
Alignment explanation
Indices: 33304--33346 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 17
33294 AAATTAATAC
33304 ATGCAATGCGAAAATGCAA
1 ATGCAATGC--AAATGCAA
33323 ATGCAAAATGCAAATGCAA
1 ATGC--AATGCAAATGCAA
33342 ATGCA
1 ATGCA
33347 CGAGGTGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 1 0.05
19 16 0.73
21 5 0.23
ACGTcount: A:0.49, C:0.16, G:0.19, T:0.16
Consensus pattern (17 bp):
ATGCAATGCAAATGCAA
Found at i:33611 original size:21 final size:21
Alignment explanation
Indices: 33586--33745 Score: 200
Period size: 21 Copynumber: 7.6 Consensus size: 21
33576 CCATGCGATG
*
33586 TGGTCTTCTCGTCTTTATGAA
1 TGGTCTTCTCGTCTTGATGAA
*
33607 GGGTCTTCTCGTCTTGATGAA
1 TGGTCTTCTCGTCTTGATGAA
*
33628 TGG-CATTCTCCTCTTGATGAA
1 TGGTC-TTCTCGTCTTGATGAA
*
33649 TGCTCTTCTCGTCTTGATGAA
1 TGGTCTTCTCGTCTTGATGAA
*
33670 TGGCCTTCTCGTCTTGATGAA
1 TGGTCTTCTCGTCTTGATGAA
*
33691 TGG-CATTCTTGTCTTGATGAA
1 TGGTC-TTCTCGTCTTGATGAA
*
33712 T-GACATTCTCGTCTTGATGAA
1 TGGTC-TTCTCGTCTTGATGAA
*
33733 TGCTCTTCTCGTC
1 TGGTCTTCTCGTC
33746 CTTGGTACAA
Statistics
Matches: 122, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
20 3 0.02
21 117 0.96
22 2 0.02
ACGTcount: A:0.16, C:0.22, G:0.21, T:0.41
Consensus pattern (21 bp):
TGGTCTTCTCGTCTTGATGAA
Found at i:33648 original size:42 final size:42
Alignment explanation
Indices: 33591--33745 Score: 222
Period size: 42 Copynumber: 3.7 Consensus size: 42
33581 CGATGTGGTC
* * *
33591 TTCTCGTCTTTATGAAGGGTCTTCTCGTCTTGATGAATGGCA
1 TTCTCGTCTTGATGAATGCTCTTCTCGTCTTGATGAATGGCA
* *
33633 TTCTCCTCTTGATGAATGCTCTTCTCGTCTTGATGAATGGCC
1 TTCTCGTCTTGATGAATGCTCTTCTCGTCTTGATGAATGGCA
* * *
33675 TTCTCGTCTTGATGAATGGC-ATTCTTGTCTTGATGAATGACA
1 TTCTCGTCTTGATGAAT-GCTCTTCTCGTCTTGATGAATGGCA
33717 TTCTCGTCTTGATGAATGCTCTTCTCGTC
1 TTCTCGTCTTGATGAATGCTCTTCTCGTC
33746 CTTGGTACAA
Statistics
Matches: 99, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
41 2 0.02
42 95 0.96
43 2 0.02
ACGTcount: A:0.16, C:0.22, G:0.21, T:0.41
Consensus pattern (42 bp):
TTCTCGTCTTGATGAATGCTCTTCTCGTCTTGATGAATGGCA
Found at i:33657 original size:63 final size:64
Alignment explanation
Indices: 33589--33745 Score: 237
Period size: 63 Copynumber: 2.5 Consensus size: 64
33579 TGCGATGTGG
* *
33589 TCTTCTCGTCTTTATGAAGGGTCTTCTCGTCTTGATGAATGGCATTCTCCTCTTGATGAATG-C
1 TCTTCTCGTCTTGATGAATGGTCTTCTCGTCTTGATGAATGGCATTCTCCTCTTGATGAATGAC
* **
33652 TCTTCTCGTCTTGATGAATGGCCTTCTCGTCTTGATGAATGGCATTCTTGTCTTGATGAATGAC
1 TCTTCTCGTCTTGATGAATGGTCTTCTCGTCTTGATGAATGGCATTCTCCTCTTGATGAATGAC
* *
33716 -ATTCTCGTCTTGATGAATGCTCTTCTCGTC
1 TCTTCTCGTCTTGATGAATGGTCTTCTCGTC
33746 CTTGGTACAA
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
63 84 0.99
64 1 0.01
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.41
Consensus pattern (64 bp):
TCTTCTCGTCTTGATGAATGGTCTTCTCGTCTTGATGAATGGCATTCTCCTCTTGATGAATGAC
Found at i:45635 original size:15 final size:15
Alignment explanation
Indices: 45617--45651 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
45607 ATACTCCCAA
45617 TATTGGTACTCATAG
1 TATTGGTACTCATAG
*
45632 TATTGGTACTCGTAG
1 TATTGGTACTCATAG
45647 TATTG
1 TATTG
45652 ATATTGCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.43
Consensus pattern (15 bp):
TATTGGTACTCATAG
Found at i:46258 original size:17 final size:14
Alignment explanation
Indices: 46225--46271 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 14
46215 GGTTACTTAG
46225 AGAAGATGAAG-GA
1 AGAAGATGAAGAGA
46238 AGAAGAAATGAAGAAGA
1 AGAAG--ATGAAG-AGA
46255 AGAAGATGAAGAGA
1 AGAAGATGAAGAGA
46269 AGA
1 AGA
46272 TAAATGGGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 5 0.17
14 6 0.20
15 12 0.40
17 7 0.23
ACGTcount: A:0.60, C:0.00, G:0.34, T:0.06
Consensus pattern (14 bp):
AGAAGATGAAGAGA
Found at i:48831 original size:162 final size:163
Alignment explanation
Indices: 48630--48949 Score: 432
Period size: 162 Copynumber: 2.0 Consensus size: 163
48620 TAAATTTTAC
** *
48630 CAAATTTGAACCACATGCTTTTAAACCATAGTAGAATACACTGTGCACTTTCAATTCCT-TTCTT
1 CAAATTTGAACCACATGCTCCTAAACCATAGTAGAATACA-TGTGCACTTTCAATTCCTCTT-TA
* * **
48694 TGATAAC-AACTTTTTTATTTTTCAATTTAGTCTTTCAA-TTTTTCATAATCTCCTTATTTGTTC
64 TGATAACAAACTTTTTTATTTTTCAATTTAGTCCTTCAATTTTTTCATAATCTCATTATTCCTTC
*
48757 -AATTCGTCATTTATTTTAAGTCCATTTTTTTATAT
129 AAATT-ATCATTTATTTTAAGTCCATTTTTTTATAT
* * * *
48792 CAAATTTGAGCCTCATGCTCCTAAACTATAGTAGAATACATGTGTACTTTCAATTCCTCTTTATG
1 CAAATTTGAACCACATGCTCCTAAACCATAGTAGAATACATGTGCACTTTCAATTCCTCTTTATG
* *
48857 ATAACAAATTTTTTTATTTTTTAATTTAGTCCTTCAATTTTTTCATAATCTCATTATTCCTTCAA
66 ATAACAAACTTTTTTATTTTTCAATTTAGTCCTTCAATTTTTTCATAATCTCATTATTCCTTC-A
* *
48922 AATTATGATTTATTTTAAGTCTATTTTT
130 AATTATCATTTATTTTAAGTCCATTTTT
48950 ACCAAATTTA
Statistics
Matches: 137, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
161 25 0.18
162 65 0.47
163 22 0.16
164 21 0.15
165 4 0.03
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (163 bp):
CAAATTTGAACCACATGCTCCTAAACCATAGTAGAATACATGTGCACTTTCAATTCCTCTTTATG
ATAACAAACTTTTTTATTTTTCAATTTAGTCCTTCAATTTTTTCATAATCTCATTATTCCTTCAA
ATTATCATTTATTTTAAGTCCATTTTTTTATAT
Found at i:50178 original size:19 final size:18
Alignment explanation
Indices: 50156--50213 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 18
50146 AAATAATACA
50156 ACATTCCTATAATAATGAT
1 ACATTCC-ATAATAATGAT
50175 ACATT-C-TAATAAT-AT
1 ACATTCCATAATAATGAT
* *
50190 -TATTCCCATAATAATGTT
1 ACATT-CCATAATAATGAT
50208 ACATTC
1 ACATTC
50214 TAATATCGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 11
0.69 0.07 0.24
Matches are distributed among these distances:
14 3 0.10
15 2 0.06
16 8 0.26
17 7 0.23
18 3 0.10
19 8 0.26
ACGTcount: A:0.40, C:0.17, G:0.03, T:0.40
Consensus pattern (18 bp):
ACATTCCATAATAATGAT
Found at i:50218 original size:30 final size:31
Alignment explanation
Indices: 50158--50219 Score: 81
Period size: 33 Copynumber: 2.0 Consensus size: 31
50148 ATAATACAAC
*
50158 ATTCCTATAATAATGATACATTCTAATAATATT
1 ATTCCCATAATAATGATACATTC--ATAATATT
*
50191 ATTCCCATAATAATGTTACATTC-TAATAT
1 ATTCCCATAATAATGATACATTCATAATAT
50220 CGTTATTCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 6 0.22
33 21 0.78
ACGTcount: A:0.40, C:0.15, G:0.03, T:0.42
Consensus pattern (31 bp):
ATTCCCATAATAATGATACATTCATAATATT
Found at i:50453 original size:2 final size:2
Alignment explanation
Indices: 50446--50480 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
50436 AGACAATCAG
50446 TA TA TA 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 TA TA TA T
50481 TTGTTTGTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.