Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008464.1 Hibiscus syriacus cultivar Beakdansim tig00111277_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: 593006
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:4775 original size:21 final size:21
Alignment explanation
Indices: 4757--4851 Score: 113
Period size: 21 Copynumber: 4.6 Consensus size: 21
4747 ATGAAGCAAG
*
4757 GGAAACAGAGAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
**
4778 GGAAGCAGCTAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
*
4799 GGAAGCAGAGAGAGAAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* *
4820 GGCAGCAGAGAG-GCAGCGGC
1 GGAAGCAGAGAGAGCAGCAGC
*
4840 AGAA-CAGAGAGA
1 GGAAGCAGAGAGA
4852 AGTAATGTAT
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
19 7 0.11
20 8 0.13
21 47 0.76
ACGTcount: A:0.39, C:0.19, G:0.41, T:0.01
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAGC
Found at i:4835 original size:17 final size:17
Alignment explanation
Indices: 4809--4841 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4799 GGAAGCAGAG
4809 AGAGAAGCAGCGGCAGC
1 AGAGAAGCAGCGGCAGC
*
4826 AGAGAGGCAGCGGCAG
1 AGAGAAGCAGCGGCAG
4842 AACAGAGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.21, G:0.45, T:0.00
Consensus pattern (17 bp):
AGAGAAGCAGCGGCAGC
Found at i:4848 original size:17 final size:17
Alignment explanation
Indices: 4815--4848 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4805 AGAGAGAGAA
* *
4815 GCAGCGGCAGCAGAGAG
1 GCAGCGGCAGAACAGAG
4832 GCAGCGGCAGAACAGAG
1 GCAGCGGCAGAACAGAG
4849 AGAAGTAATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.24, G:0.44, T:0.00
Consensus pattern (17 bp):
GCAGCGGCAGAACAGAG
Found at i:6995 original size:81 final size:82
Alignment explanation
Indices: 6888--7246 Score: 368
Period size: 82 Copynumber: 4.4 Consensus size: 82
6878 AAATTATTGC
* ** * * *
6888 GGCGTTTGTA-AAATAACACCGCTAAAGTACTACTCTGTGGCAACG-TTCTTGAAAAATGCCGCT
1 GGCGTTTGTATAAA-AACACCACTAAAGTACTACTCTGTCACAACGTTTGTTGAAAAACGCCACT
*
6951 ATGAATGAACCCTATTAT
65 ATGGATGAACCCTATTAT
* * * * * * *
6969 GGCATTTGTATAAAAATACCATTAAAGTACTACTCTGTCACGACATTTGTTGAAAAAAGCTACTA
1 GGCGTTTGTATAAAAACACCACTAAAGTACTACTCTGTCACAACGTTTGTTGAAAAACGCCACTA
* **
7034 TGGATGAACCGTATTGC
66 TGGATGAACCCTATTAT
* * ** * * * *
7051 AGCGTTTGTATAAAAACGCTGCTAAAGTACTACTCTGTCGCGACGTTTGTTGAAAAACACAACTA
1 GGCGTTTGTATAAAAACACCACTAAAGTACTACTCTGTCACAACGTTTGTTGAAAAACGCCACTA
7116 TGGATGAACCCTATTAT
66 TGGATGAACCCTATTAT
* * * * *
7133 GACGTTTATAT-AAAATACCGCTAAAGTACTACTCTGTCACAATGTTTGTTGAAAAACGCCACTA
1 GGCGTTTGTATAAAAACACCACTAAAGTACTACTCTGTCACAACGTTTGTTGAAAAACGCCACTA
*
7197 TGGATGAA-TCTATT-T
66 TGGATGAACCCTATTAT
* *
7212 CGGCGTTTGTATAAAAACGCCACTAAAGTATTACT
1 -GGCGTTTGTATAAAAACACCACTAAAGTACTACT
7247 TTATCGCAGA
Statistics
Matches: 225, Mismatches: 49, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
79 1 0.00
80 14 0.06
81 104 0.46
82 106 0.47
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (82 bp):
GGCGTTTGTATAAAAACACCACTAAAGTACTACTCTGTCACAACGTTTGTTGAAAAACGCCACTA
TGGATGAACCCTATTAT
Found at i:7059 original size:82 final size:80
Alignment explanation
Indices: 6889--7246 Score: 314
Period size: 81 Copynumber: 4.4 Consensus size: 80
6879 AATTATTGCG
* ** * * * **
6889 GCGTTTGTA-AAATAACACCGCTAAAGTACTACTCTGTGGCAACG-TTCTTGAAAAATGCCGCTA
1 GCGTTTGTATAAA-AACACCACTAAAGTACTACTCTGTCACGACGTTTGTTGAAAAAAGCAACTA
*
6952 TGAATGAACCCTATT-A
65 TGGATGAA-CCTATTCA
* * * * *
6968 TGGCATTTGTATAAAAATACCATTAAAGTACTACTCTGTCACGACATTTGTTGAAAAAAGCTACT
1 --GCGTTTGTATAAAAACACCACTAAAGTACTACTCTGTCACGACGTTTGTTGAAAAAAGCAACT
7033 ATGGATGAACCGTATTGCA
64 ATGGATGAACC-TATT-CA
* ** *
7052 GCGTTTGTATAAAAACGCTGCTAAAGTACTACTCTGTCGCGACGTTTGTTGAAAAACA-CAACTA
1 GCGTTTGTATAAAAACACCACTAAAGTACTACTCTGTCACGACGTTTGTTGAAAAA-AGCAACTA
7116 TGGATGAACCCTATT-A
65 TGGATGAA-CCTATTCA
* * * * * * *
7132 TGACGTTTATAT-AAAATACCGCTAAAGTACTACTCTGTCACAATGTTTGTTGAAAAACGCCACT
1 -G-CGTTTGTATAAAAACACCACTAAAGTACTACTCTGTCACGACGTTTGTTGAAAAAAGCAACT
* *
7196 ATGGATGAATCTATTTCG
64 ATGGATGAACCTA-TTCA
* *
7214 GCGTTTGTATAAAAACGCCACTAAAGTATTACT
1 GCGTTTGTATAAAAACACCACTAAAGTACTACT
7247 TTATCGCAGA
Statistics
Matches: 226, Mismatches: 38, Indels: 26
0.78 0.13 0.09
Matches are distributed among these distances:
80 12 0.05
81 108 0.48
82 102 0.45
83 3 0.01
84 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (80 bp):
GCGTTTGTATAAAAACACCACTAAAGTACTACTCTGTCACGACGTTTGTTGAAAAAAGCAACTAT
GGATGAACCTATTCA
Found at i:7160 original size:163 final size:162
Alignment explanation
Indices: 6882--7246 Score: 464
Period size: 163 Copynumber: 2.2 Consensus size: 162
6872 CATATCAAAT
* * **
6882 TATTGCGGCGTTTGTA-AAATAACACCGCTAAAGTACTACTCTGTGGCAACGTTCTTGAAAAATG
1 TATTGCGGCGTTTGTATAAA-AACGCCGCTAAAGTACTACTCTGTCGCAACGTTCTTGAAAAACA
** * * * *
6946 CCGCTATGAATGAACCCTATTATGGCATTTGTATAAAAATACCATTAAAGTACTACTCTGTCACG
65 CAACTATGAATGAACCCTATTATGACATTTATATAAAAATACCACTAAAGTACTACTCTGTCACA
*
7011 ACATTTGTTGAAAAAAGCTACTATGGATGAACC
130 ACATTTGTTGAAAAAAGCCACTATGGATGAACC
* * * *
7044 GTATTGCAGCGTTTGTATAAAAACGCTGCTAAAGTACTACTCTGTCGCGACGTTTGTTGAAAAAC
1 -TATTGCGGCGTTTGTATAAAAACGCCGCTAAAGTACTACTCTGTCGCAACG-TTCTTGAAAAAC
* * *
7109 ACAACTATGGATGAACCCTATTATGACGTTTATAT-AAAATACCGCTAAAGTACTACTCTGTCAC
64 ACAACTATGAATGAACCCTATTATGACATTTATATAAAAATACCACTAAAGTACTACTCTGTCAC
** * *
7173 AATGTTTGTTGAAAAACGCCACTATGGATGAATC
129 AACATTTGTTGAAAAAAGCCACTATGGATGAACC
* * *
7207 TATTTCGGCGTTTGTATAAAAACGCCACTAAAGTATTACT
1 TATTGCGGCGTTTGTATAAAAACGCCGCTAAAGTACTACT
7247 TTATCGCAGA
Statistics
Matches: 173, Mismatches: 27, Indels: 5
0.84 0.13 0.02
Matches are distributed among these distances:
162 35 0.20
163 97 0.56
164 41 0.24
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (162 bp):
TATTGCGGCGTTTGTATAAAAACGCCGCTAAAGTACTACTCTGTCGCAACGTTCTTGAAAAACAC
AACTATGAATGAACCCTATTATGACATTTATATAAAAATACCACTAAAGTACTACTCTGTCACAA
CATTTGTTGAAAAAAGCCACTATGGATGAACC
Found at i:7524 original size:16 final size:16
Alignment explanation
Indices: 7503--7542 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
7493 GAAGCCGGTT
7503 GGGAAATAGTAAGAAG
1 GGGAAATAGTAAGAAG
7519 GGGAAATAGTAAGAAG
1 GGGAAATAGTAAGAAG
7535 GGGAAATA
1 GGGAAATA
7543 ATGCCAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.38, T:0.12
Consensus pattern (16 bp):
GGGAAATAGTAAGAAG
Found at i:7914 original size:18 final size:18
Alignment explanation
Indices: 7891--7926 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
7881 CATTAAATTT
7891 TAAGTGATGTATCGTTTG
1 TAAGTGATGTATCGTTTG
7909 TAAGTGATGTATCGTTTG
1 TAAGTGATGTATCGTTTG
7927 CATTATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.06, G:0.28, T:0.44
Consensus pattern (18 bp):
TAAGTGATGTATCGTTTG
Found at i:9414 original size:23 final size:24
Alignment explanation
Indices: 9382--9427 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
9372 AGCCTTATGT
*
9382 TTTTCTAACATGATAAATATAATA
1 TTTTCTAACATGAAAAATATAATA
9406 TTTT-TAACATGAAAAATATAAT
1 TTTTCTAACATGAAAAATATAAT
9428 CAATTAAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (24 bp):
TTTTCTAACATGAAAAATATAATA
Found at i:16946 original size:22 final size:22
Alignment explanation
Indices: 16918--16961 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
16908 ATTCTGCAAG
*
16918 GATGATAGATT-ATCTTTTCAAA
1 GATGATAAATTCA-CTTTTCAAA
16940 GATGATAAATTCACTTTTCAAA
1 GATGATAAATTCACTTTTCAAA
16962 AACGAAAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (22 bp):
GATGATAAATTCACTTTTCAAA
Found at i:17313 original size:13 final size:13
Alignment explanation
Indices: 17297--17321 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17287 TGCATTCATC
17297 ATGCATTTCATTA
1 ATGCATTTCATTA
17310 ATGCATTTCATT
1 ATGCATTTCATT
17322 GCATTTGCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (13 bp):
ATGCATTTCATTA
Found at i:17753 original size:95 final size:96
Alignment explanation
Indices: 17589--17812 Score: 353
Period size: 95 Copynumber: 2.4 Consensus size: 96
17579 TTCAAGTCAA
* * * *
17589 ATCAAACTTCACGGAAGAGTAGCGAAGTAGAAAGCACGAACTAGAATAAAATTCAGTTTCCACAA
1 ATCAAACTTCACGGAAGAGTAGTGAAGCAGAAAGCAAGAACCAGAATAAAATTCAGTTTCCACAA
17654 AAGAGTAGTGGAACGGA-TTTTCAGCAAAGT
66 AAGAGTAGTGGAACGGATTTTTCAGCAAAGT
* * **
17684 ATCAAACTTCACGGAAGAGTAGTGAAGCAGAAAGCAAGAACCAGAATAAAATTTAGTTTTCACGG
1 ATCAAACTTCACGGAAGAGTAGTGAAGCAGAAAGCAAGAACCAGAATAAAATTCAGTTTCCACAA
17749 AAGAGTAGTGGAACGGATTTTTCAGCAAAGT
66 AAGAGTAGTGGAACGGATTTTTCAGCAAAGT
*
17780 ATCAAACTTCACAGAAGAGTAGTGAAGCA-AAAG
1 ATCAAACTTCACGGAAGAGTAGTGAAGCAGAAAG
17813 ACCAAAATCT
Statistics
Matches: 119, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
95 78 0.66
96 41 0.34
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (96 bp):
ATCAAACTTCACGGAAGAGTAGTGAAGCAGAAAGCAAGAACCAGAATAAAATTCAGTTTCCACAA
AAGAGTAGTGGAACGGATTTTTCAGCAAAGT
Found at i:24494 original size:17 final size:18
Alignment explanation
Indices: 24461--24494 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
24451 CGATTGTTGT
*
24461 AAAGAAATAAGACTAAGG
1 AAAGAAAGAAGACTAAGG
24479 AAAGAAAGAA-ACTAAG
1 AAAGAAAGAAGACTAAG
24495 ATGTTGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.65, C:0.06, G:0.21, T:0.09
Consensus pattern (18 bp):
AAAGAAAGAAGACTAAGG
Found at i:27863 original size:11 final size:11
Alignment explanation
Indices: 27847--27876 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
27837 ATACATGCTT
27847 GAATCAAGTGA
1 GAATCAAGTGA
27858 GAATCAAGTGA
1 GAATCAAGTGA
*
27869 AAATCAAG
1 GAATCAAG
27877 AACCCTAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.50, C:0.10, G:0.23, T:0.17
Consensus pattern (11 bp):
GAATCAAGTGA
Found at i:29967 original size:19 final size:18
Alignment explanation
Indices: 29929--30002 Score: 87
Period size: 19 Copynumber: 4.1 Consensus size: 18
29919 TATGTATTGG
29929 GCTATGAAT-TGAAATAA
1 GCTATGAATCTGAAATAA
*
29946 GCTATGAATCTGACAGTAA
1 GCTATGAATCTGA-AATAA
* *
29965 GCTATGAGTTTGAAATAA
1 GCTATGAATCTGAAATAA
*
29983 GTTATGAATCTGGAAATAA
1 GCTATGAATCT-GAAATAA
30002 G
1 G
30003 TTCTGATTCA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
17 9 0.19
18 15 0.32
19 23 0.49
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (18 bp):
GCTATGAATCTGAAATAA
Found at i:33556 original size:17 final size:17
Alignment explanation
Indices: 33534--33568 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
33524 ATCTTGATGT
33534 TGATTATCGATCGTTGG
1 TGATTATCGATCGTTGG
33551 TGATTATCGATCGTTGG
1 TGATTATCGATCGTTGG
33568 T
1 T
33569 TATCTTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.11, G:0.29, T:0.43
Consensus pattern (17 bp):
TGATTATCGATCGTTGG
Found at i:35403 original size:21 final size:22
Alignment explanation
Indices: 35367--35407 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
35357 TTAAATATTA
35367 TAAAGGTAGTAACGATACTCAT
1 TAAAGGTAGTAACGATACTCAT
*
35389 TAAAGG-AGTACCGATACTC
1 TAAAGGTAGTAACGATACTC
35408 CCTGTTCTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (22 bp):
TAAAGGTAGTAACGATACTCAT
Found at i:38266 original size:21 final size:22
Alignment explanation
Indices: 38230--38270 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
38220 TTAAATATTA
38230 TAAAGGTAGTACCGATACTCAT
1 TAAAGGTAGTACCGATACTCAT
*
38252 TAAAGG-AGTATCGATACTC
1 TAAAGGTAGTACCGATACTC
38271 CCTGTTATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (22 bp):
TAAAGGTAGTACCGATACTCAT
Found at i:41439 original size:24 final size:24
Alignment explanation
Indices: 41412--41458 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
41402 CCGAATTCTA
*
41412 TTATGATATCTGAAATGGATTATG
1 TTATGATATATGAAATGGATTATG
**
41436 TTATGATATATGATCTGGATTAT
1 TTATGATATATGAAATGGATTAT
41459 ATTCTAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.32, C:0.04, G:0.19, T:0.45
Consensus pattern (24 bp):
TTATGATATATGAAATGGATTATG
Found at i:45170 original size:12 final size:12
Alignment explanation
Indices: 45153--45245 Score: 57
Period size: 12 Copynumber: 7.8 Consensus size: 12
45143 ATGTTTTATC
45153 TGATTTCTGTTA
1 TGATTTCTGTTA
* *
45165 TGATTTCTGATC
1 TGATTTCTGTTA
*
45177 TGGA-TTCTATTA
1 T-GATTTCTGTTA
* *
45189 TGATATCTGATA
1 TGATTTCTGTTA
*
45201 TGGA-TTCTGTTC
1 T-GATTTCTGTTA
* * *
45213 TGATATCTGATC
1 TGATTTCTGTTA
45225 TGAATTT-TGTTA
1 TG-ATTTCTGTTA
45237 TGATTTCTG
1 TGATTTCTG
45246 ATTTTTGTTT
Statistics
Matches: 59, Mismatches: 16, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
11 8 0.14
12 44 0.75
13 7 0.12
ACGTcount: A:0.20, C:0.11, G:0.18, T:0.51
Consensus pattern (12 bp):
TGATTTCTGTTA
Found at i:45177 original size:24 final size:24
Alignment explanation
Indices: 45157--45247 Score: 119
Period size: 24 Copynumber: 3.8 Consensus size: 24
45147 TTTATCTGAT
*
45157 TTCTGTTATGATTTCTGATCTGGA
1 TTCTGTTATGATATCTGATCTGGA
* *
45181 TTCTATTATGATATCTGATATGGA
1 TTCTGTTATGATATCTGATCTGGA
* *
45205 TTCTGTTCTGATATCTGATCTGAA
1 TTCTGTTATGATATCTGATCTGGA
* *
45229 TTTTGTTATGATTTCTGAT
1 TTCTGTTATGATATCTGAT
45248 TTTTGTTTAC
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.51
Consensus pattern (24 bp):
TTCTGTTATGATATCTGATCTGGA
Found at i:45469 original size:31 final size:29
Alignment explanation
Indices: 45387--45469 Score: 94
Period size: 31 Copynumber: 2.7 Consensus size: 29
45377 TAAGGTGACC
*
45387 CTTGGGTAGGCTCTGCGGCCCTGAGATTTT
1 CTTGGGTAGGCTC-GCTGCCCTGAGATTTT
* *
45417 CTTGGGTAAGCCTCCGTTGCCCTGAGAATTTT
1 CTTGGGT-AGGCT-CGCTGCCCTGAG-ATTTT
45449 CTTGGGTAGGCTCGCATGCCC
1 CTTGGGTAGGCTCGC-TGCCC
45470 CAAGGTACTC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
30 9 0.20
31 22 0.50
32 13 0.30
ACGTcount: A:0.12, C:0.27, G:0.30, T:0.31
Consensus pattern (29 bp):
CTTGGGTAGGCTCGCTGCCCTGAGATTTT
Found at i:46491 original size:58 final size:58
Alignment explanation
Indices: 46415--46671 Score: 295
Period size: 58 Copynumber: 4.4 Consensus size: 58
46405 TTGTGTTAAC
46415 TCTAACTTTATAAGGAAAATAGATTGTTGAATTTATTTCCTTGAGAATATTAAATGAT
1 TCTAACTTTATAAGGAAAATAGATTGTTGAATTTATTTCCTTGAGAATATTAAATGAT
* * * * * * *
46473 GCTAACTTTGTAAGGAAAATATATTGTTTAATTT-TTTCCTTGATAATCTTTAATGAT
1 TCTAACTTTATAAGGAAAATAGATTGTTGAATTTATTTCCTTGAGAATATTAAATGAT
* * * *
46530 TCTAACTTTTTAAGGAAAATAGATTGTTTAATTTATTTCCTTTAGAATCTTAAATGAT
1 TCTAACTTTATAAGGAAAATAGATTGTTGAATTTATTTCCTTGAGAATATTAAATGAT
* ** * * *
46588 TCTAACTTTATAATGAGCATAAATTGTTGAATTTATTTCCTTG-GAAAATTGAATGAT
1 TCTAACTTTATAAGGAAAATAGATTGTTGAATTTATTTCCTTGAGAATATTAAATGAT
* * *
46645 T-TGAACTTTTTTAAGAAAAATAAATTG
1 TCT-AAC-TTTATAAGGAAAATAGATTG
46672 CAATACCCCA
Statistics
Matches: 168, Mismatches: 28, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
56 1 0.01
57 66 0.39
58 101 0.60
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (58 bp):
TCTAACTTTATAAGGAAAATAGATTGTTGAATTTATTTCCTTGAGAATATTAAATGAT
Found at i:46538 original size:57 final size:58
Alignment explanation
Indices: 46415--46630 Score: 299
Period size: 58 Copynumber: 3.7 Consensus size: 58
46405 TTGTGTTAAC
*
46415 TCTAACTTTATAAGGAAAATAGATTGTTGAATTTATTTCCTTGAGAATATTAAATGAT
1 TCTAACTTTATAAGGAAAATAGATTGTTGAATTTATTTCCTTGAGAATCTTAAATGAT
* * * * * *
46473 GCTAACTTTGTAAGGAAAATATATTGTTTAATTT-TTTCCTTGATAATCTTTAATGAT
1 TCTAACTTTATAAGGAAAATAGATTGTTGAATTTATTTCCTTGAGAATCTTAAATGAT
* * *
46530 TCTAACTTTTTAAGGAAAATAGATTGTTTAATTTATTTCCTTTAGAATCTTAAATGAT
1 TCTAACTTTATAAGGAAAATAGATTGTTGAATTTATTTCCTTGAGAATCTTAAATGAT
* ** *
46588 TCTAACTTTATAATGAGCATAAATTGTTGAATTTATTTCCTTG
1 TCTAACTTTATAAGGAAAATAGATTGTTGAATTTATTTCCTTG
46631 GAAAATTGAA
Statistics
Matches: 137, Mismatches: 20, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
57 51 0.37
58 86 0.63
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.45
Consensus pattern (58 bp):
TCTAACTTTATAAGGAAAATAGATTGTTGAATTTATTTCCTTGAGAATCTTAAATGAT
Found at i:46621 original size:115 final size:116
Alignment explanation
Indices: 46415--46630 Score: 326
Period size: 115 Copynumber: 1.9 Consensus size: 116
46405 TTGTGTTAAC
46415 TCTAACTTTATAAGGAAAATAGATTGTTGAATTTATTTCCTTGAGAATATTAAATGATGCTAACT
1 TCTAACTTTATAAGGAAAATAGATTGTTGAATTTATTTCCTTGAGAATATTAAATGATGCTAACT
* * *
46480 TTGTAAGGAAAATATATTGTTTAATTT-TTTCCTTGATAATCTTTAATGAT
66 TTATAAGGAAAATAAATTGTTGAATTTATTTCCTTGATAATCTTTAATGAT
* * * * *
46530 TCTAACTTTTTAAGGAAAATAGATTGTTTAATTTATTTCCTTTAGAATCTTAAATGATTCTAACT
1 TCTAACTTTATAAGGAAAATAGATTGTTGAATTTATTTCCTTGAGAATATTAAATGATGCTAACT
* **
46595 TTATAATGAGCATAAATTGTTGAATTTATTTCCTTG
66 TTATAAGGAAAATAAATTGTTGAATTTATTTCCTTG
46631 GAAAATTGAA
Statistics
Matches: 89, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
115 81 0.91
116 8 0.09
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.45
Consensus pattern (116 bp):
TCTAACTTTATAAGGAAAATAGATTGTTGAATTTATTTCCTTGAGAATATTAAATGATGCTAACT
TTATAAGGAAAATAAATTGTTGAATTTATTTCCTTGATAATCTTTAATGAT
Found at i:46643 original size:115 final size:115
Alignment explanation
Indices: 46415--46671 Score: 322
Period size: 115 Copynumber: 2.2 Consensus size: 115
46405 TTGTGTTAAC
*
46415 TCTAACTTTATAAGGAAAATAGATTGTTGAATTTATTTCCTTGAGAATATTAAATGATGCTAACT
1 TCTAACTTTTTAAGGAAAATAGATTGTTGAATTTATTTCCTTGAGAATATTAAATGATGCTAACT
* * * * *
46480 TTGTAAGGAAAATATATTGTTTAATTTTTTCCTTGATAATCTTTAATGAT
66 TTATAAGGAAAATAAATTGTTGAATTTTTTCCTTGATAATATTGAATGAT
* * * *
46530 TCTAACTTTTTAAGGAAAATAGATTGTTTAATTTATTTCCTTTAGAATCTTAAATGATTCTAACT
1 TCTAACTTTTTAAGGAAAATAGATTGTTGAATTTATTTCCTTGAGAATATTAAATGATGCTAACT
* **
46595 TTATAATGAGCATAAATTGTTGAATTTATTTCCTTGGA-AA-ATTGAATGAT
66 TTATAAGGAAAATAAATTGTTGAATTT-TTTCCTT-GATAATATTGAATGAT
* *
46645 T-TGAACTTTTTTAAGAAAAATAAATTG
1 TCT-AAC-TTTTTAAGGAAAATAGATTG
46672 CAATACCCCA
Statistics
Matches: 123, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
114 1 0.01
115 93 0.76
116 27 0.22
117 2 0.02
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (115 bp):
TCTAACTTTTTAAGGAAAATAGATTGTTGAATTTATTTCCTTGAGAATATTAAATGATGCTAACT
TTATAAGGAAAATAAATTGTTGAATTTTTTCCTTGATAATATTGAATGAT
Found at i:47200 original size:30 final size:30
Alignment explanation
Indices: 47132--47240 Score: 101
Period size: 30 Copynumber: 3.5 Consensus size: 30
47122 TAGCACTATG
* * *
47132 GTGTGTAAGGACACTTAGTTCATATGGTACTATA
1 GTGTGTAAGGACACTTAG-T-ACAT--CACTGTA
47166 GTGTGTAAGGACACTTAGTACATCACTGTA
1 GTGTGTAAGGACACTTAGTACATCACTGTA
* * * * *
47196 GTGTGTAAGGACGCTCAGTGCAACACTGTG
1 GTGTGTAAGGACACTTAGTACATCACTGTA
*
47226 GTGTGTAATGACACT
1 GTGTGTAAGGACACT
47241 CTGTGCATAT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
30 43 0.66
32 3 0.05
33 1 0.02
34 18 0.28
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.30
Consensus pattern (30 bp):
GTGTGTAAGGACACTTAGTACATCACTGTA
Found at i:48213 original size:97 final size:96
Alignment explanation
Indices: 48090--48368 Score: 301
Period size: 97 Copynumber: 2.9 Consensus size: 96
48080 ATTTTCTTAT
* * * *
48090 ATGATTCT-AT-TTTAAAAGGAAATAAATCATTGGATTTATTTTCTTGTTTTGTAAAATGAAATA
1 ATGATTCTGATATGTAAAAGGAAATAAATCATTGGATTTATTTTCCTATTTTG-AAAAAGAAATA
* * *
48153 AATTATTGAATTTATTTTCCTGAGAATCTCAC
65 AATCATTGAATTTACTTTCCTAAGAATCTCAC
* * * * * *
48185 ATGATTCTTATCTGTCAAAGGAAATAAATCATAGAATTTATTTTCCTACTTTGAAAAAGAAAATA
1 ATGATTCTGATATGTAAAAGGAAATAAATCATTGGATTTATTTTCCTATTTTGAAAAAG-AAATA
** * ***
48250 AATCGGTAAATTTACTTTCCTAAGAATCTTGT
65 AATCATTGAATTTACTTTCCTAAGAATCTCAC
* *
48282 ATGATTCTGATATGTAAAAGGAAATAAGTCGTTGGATTTATTTTCCTATTTTGAAAAAAGGAAAT
1 ATGATTCTGATATGTAAAAGGAAATAAATCATTGGATTTATTTTCCTATTTTG-AAAAA-GAAAT
* *
48347 AAATCATAGAATTTAGTTTCCT
64 AAATCATTGAATTTACTTTCCT
48369 TATTTGTAAA
Statistics
Matches: 149, Mismatches: 30, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
95 8 0.05
96 7 0.05
97 107 0.72
98 26 0.17
99 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.40
Consensus pattern (96 bp):
ATGATTCTGATATGTAAAAGGAAATAAATCATTGGATTTATTTTCCTATTTTGAAAAAGAAATAA
ATCATTGAATTTACTTTCCTAAGAATCTCAC
Found at i:48400 original size:39 final size:40
Alignment explanation
Indices: 48294--48430 Score: 172
Period size: 39 Copynumber: 3.5 Consensus size: 40
48284 GATTCTGATA
* * *
48294 TGTAAAAGGAAATAAGTCGTTGGATTTATTTTCC-TATTT
1 TGTAAAAAGAAATAAATCGTTGGATTTAGTTTCCTTATTT
* * * *
48333 TGAAAAAAGGAAATAAATCATAGAATTTAGTTTCCTTA-TT
1 TGTAAAAA-GAAATAAATCGTTGGATTTAGTTTCCTTATTT
48373 TGTAAAAAGAAATAAATCGTTGGATTTAGTTT-CTTATTT
1 TGTAAAAAGAAATAAATCGTTGGATTTAGTTTCCTTATTT
*
48412 TGTAAAAGGAAATAAATCG
1 TGTAAAAAGAAATAAATCG
48431 AAACAAATCG
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
38 4 0.05
39 47 0.57
40 30 0.36
41 2 0.02
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.38
Consensus pattern (40 bp):
TGTAAAAAGAAATAAATCGTTGGATTTAGTTTCCTTATTT
Found at i:48451 original size:79 final size:83
Alignment explanation
Indices: 48294--48518 Score: 219
Period size: 88 Copynumber: 2.7 Consensus size: 83
48284 GATTCTGATA
* * * * * *
48294 TGTAAAAGGAAATAAGTCGTTGGATTTATTTTCCTATTTTGAAAAAAGGAAATAAATCATAGAAT
1 TGTAAAAAGAAATAAATCGTTGGATTTATTTTCTTATTTTG-TAAAAGGAAATAAATCAAACAAT
* *
48359 TTAG-TT-T-CCT-TA-TT
65 ATAGTTTATATCTATATTT
*
48373 TGTAAAAAGAAATAAATCGTTGGATTTAGTTTCTTATTTTGTAAAAGGAAATAAATCGAAACAA-
1 TGTAAAAAGAAATAAATCGTTGGATTTATTTTCTTATTTTGTAAAAGGAAATAAATC-AAACAAT
* *
48437 ATCGTTTAATTTATTTTCATATTT
65 ATAGTTT-A--TA-TCT-ATATTT
* * *
48461 TGTAGAAATAAATAAATCGTTGGATTTATTTTCTTATTTTTTAAAAGGAAATAAATCA
1 TGTAAAAAGAAATAAATCGTTGGATTTATTTTCTTATTTTGTAAAAGGAAATAAATCA
48519 TTGGATTTTT
Statistics
Matches: 120, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
78 17 0.14
79 43 0.36
83 1 0.01
85 1 0.01
87 3 0.03
88 55 0.46
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (83 bp):
TGTAAAAAGAAATAAATCGTTGGATTTATTTTCTTATTTTGTAAAAGGAAATAAATCAAACAATA
TAGTTTATATCTATATTT
Found at i:48460 original size:49 final size:49
Alignment explanation
Indices: 48381--48479 Score: 128
Period size: 49 Copynumber: 2.0 Consensus size: 49
48371 TTTGTAAAAA
* * *
48381 GAAATAAATCGTTGGATTTAGTTTCTTATTTTGTA-AAAGGAAATAAATC
1 GAAACAAATCGTTGAATTTAGTTTCATATTTTGTAGAAA-GAAATAAATC
* * *
48430 GAAACAAATCGTTTAATTTATTTTCATATTTTGTAGAAATAAATAAATC
1 GAAACAAATCGTTGAATTTAGTTTCATATTTTGTAGAAAGAAATAAATC
48479 G
1 G
48480 TTGGATTTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
49 40 0.93
50 3 0.07
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.39
Consensus pattern (49 bp):
GAAACAAATCGTTGAATTTAGTTTCATATTTTGTAGAAAGAAATAAATC
Found at i:48480 original size:39 final size:39
Alignment explanation
Indices: 48430--48530 Score: 107
Period size: 39 Copynumber: 2.6 Consensus size: 39
48420 GAAATAAATC
* *
48430 GAAACAAATCGTTTAATTTATTTTCATATTTTGTAGAAA-
1 GAAATAAATCGTTGAATTTATTTTCATATTTTGTA-AAAG
* * * *
48469 TAAATAAATCGTTGGATTTATTTTCTTATTTTTTAAAAG
1 GAAATAAATCGTTGAATTTATTTTCATATTTTGTAAAAG
* *
48508 GAAATAAATCATTGGATTT-TTTT
1 GAAATAAATCGTTGAATTTATTTT
48531 GGGAATCTTG
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
38 7 0.13
39 46 0.87
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.48
Consensus pattern (39 bp):
GAAATAAATCGTTGAATTTATTTTCATATTTTGTAAAAG
Found at i:53788 original size:20 final size:19
Alignment explanation
Indices: 53765--53816 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
53755 GAAAGCCAAT
53765 TTCGCAACACAGTTTCCGAA
1 TTCGCAACACAGTTT-CGAA
* * * *
53785 TTCGCCACTCGAATTTGGAA
1 TTCGCAACAC-AGTTTCGAA
53805 TTCGCAACACAG
1 TTCGCAACACAG
53817 AAGTAGAATT
Statistics
Matches: 24, Mismatches: 7, Indels: 3
0.71 0.21 0.09
Matches are distributed among these distances:
19 1 0.04
20 19 0.79
21 4 0.17
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (19 bp):
TTCGCAACACAGTTTCGAA
Found at i:53872 original size:20 final size:20
Alignment explanation
Indices: 53823--53933 Score: 82
Period size: 20 Copynumber: 5.5 Consensus size: 20
53813 ACAGAAGTAG
* *
53823 AATTCGCAACTCGAATTTGA
1 AATTCGCAACTCGATTTTTA
*
53843 CATTTTCGCAACTCGATTTTTA
1 -A-ATTCGCAACTCGATTTTTA
* * *
53865 AATTCGCAACACGAGTTTCA
1 AATTCGCAACTCGATTTTTA
** *
53885 TTTTCGCAACTCAATTTTCT-
1 AATTCGCAACTCGATTTT-TA
*
53905 AATTCGCAACTTGATTTTCT-
1 AATTCGCAACTCGATTTT-TA
53925 AATTCGCAA
1 AATTCGCAA
53934 TGCGAGTTTC
Statistics
Matches: 71, Mismatches: 17, Indels: 5
0.76 0.18 0.05
Matches are distributed among these distances:
20 53 0.75
21 2 0.03
22 16 0.23
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.38
Consensus pattern (20 bp):
AATTCGCAACTCGATTTTTA
Found at i:53896 original size:40 final size:41
Alignment explanation
Indices: 53823--53914 Score: 125
Period size: 40 Copynumber: 2.2 Consensus size: 41
53813 ACAGAAGTAG
* *
53823 AATTCGCAACTCGAATTTGACATTTTCGCAACTCGATTTT-T
1 AATTCGCAACACGAATTT-ACATTTTCGCAACTCAATTTTCT
*
53864 AAATTCGCAACACGAGTTT-CATTTTCGCAACTCAATTTTCT
1 -AATTCGCAACACGAATTTACATTTTCGCAACTCAATTTTCT
53905 AATTCGCAAC
1 AATTCGCAAC
53915 TTGATTTTCT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
40 29 0.63
41 1 0.02
42 16 0.35
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (41 bp):
AATTCGCAACACGAATTTACATTTTCGCAACTCAATTTTCT
Found at i:53943 original size:20 final size:20
Alignment explanation
Indices: 53847--53947 Score: 84
Period size: 20 Copynumber: 5.1 Consensus size: 20
53837 ATTTGACATT
*
53847 TTCGCAACTCGA-TTTTTAAA
1 TTCGCAACTCGAGTTTCT-AA
* *
53867 TTCGCAACACGAGTTTC-ATT
1 TTCGCAACTCGAGTTTCTA-A
* *
53887 TTCGCAACTCAATTTTCTAA
1 TTCGCAACTCGAGTTTCTAA
* *
53907 TTCGCAACTTGATTTTCTAA
1 TTCGCAACTCGAGTTTCTAA
53927 TTCGCAA-TGCGAGTTTC-AA
1 TTCGCAACT-CGAGTTTCTAA
53946 TT
1 TT
53948 TTACAACGCA
Statistics
Matches: 66, Mismatches: 11, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
19 6 0.09
20 56 0.85
21 4 0.06
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.40
Consensus pattern (20 bp):
TTCGCAACTCGAGTTTCTAA
Found at i:53971 original size:60 final size:61
Alignment explanation
Indices: 53846--53996 Score: 159
Period size: 60 Copynumber: 2.5 Consensus size: 61
53836 AATTTGACAT
* * * *
53846 TTTCGCAACTCGATTTTTAAATTCGCAACACGAGTTTCATTTTCGCAACTCAATTTTCTAA
1 TTTCGCAACTCGATTTTTAAATTCGCAACACGAGTTTCATTTTCACAACGCAAATTTCAAA
* **
53907 -TTCGCAACTTGATTTTCT-AATTCGCAATGCGAGTTTCAATTTT-ACAACGCAAATTT-AAA
1 TTTCGCAACTCGATTTT-TAAATTCGCAACACGAGTTTC-ATTTTCACAACGCAAATTTCAAA
* *
53966 TTTCGCAACTC-AGCTTTTAATTTCGCAACAC
1 TTTCGCAACTCGA-TTTTTAAATTCGCAACAC
53997 AAATGTTTTG
Statistics
Matches: 73, Mismatches: 12, Indels: 11
0.76 0.12 0.11
Matches are distributed among these distances:
59 4 0.05
60 63 0.86
61 6 0.08
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.38
Consensus pattern (61 bp):
TTTCGCAACTCGATTTTTAAATTCGCAACACGAGTTTCATTTTCACAACGCAAATTTCAAA
Found at i:53974 original size:20 final size:20
Alignment explanation
Indices: 53951--54000 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
53941 TTCAATTTTA
*
53951 CAACGCAAATTTAAATTTCG
1 CAACACAAATTTAAATTTCG
* ** *
53971 CAACTCAGCTTTTAATTTCG
1 CAACACAAATTTAAATTTCG
53991 CAACACAAAT
1 CAACACAAAT
54001 GTTTTGGGTA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.38, C:0.24, G:0.08, T:0.30
Consensus pattern (20 bp):
CAACACAAATTTAAATTTCG
Found at i:54765 original size:12 final size:12
Alignment explanation
Indices: 54744--54777 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
54734 ACCACATTTC
*
54744 CAATACCAAACA
1 CAATATCAAACA
54756 CAATATCAAACA
1 CAATATCAAACA
*
54768 CAATCTCAAA
1 CAATATCAAA
54778 ATCCACAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:54916 original size:24 final size:24
Alignment explanation
Indices: 54897--54946 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
54887 TAGTCAGTAT
54897 TCGAAATTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
* *
54921 TCGGACTTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
54945 TC
1 TC
54947 AGATTTTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (24 bp):
TCGAAATTTGATCTTGGTCAATAC
Found at i:54954 original size:24 final size:24
Alignment explanation
Indices: 54903--54956 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
54893 GTATTCGAAA
*
54903 TTTGATCTTGGTCAATACTCGGAC
1 TTTGATCTTGGTCAATACTCAGAC
*
54927 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACTCAGAC
54951 TTTGAT
1 TTTGAT
54957 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACTCAGAC
Found at i:56799 original size:42 final size:42
Alignment explanation
Indices: 56734--56885 Score: 209
Period size: 42 Copynumber: 3.6 Consensus size: 42
56724 TCTCACGTAG
*
56734 AGCACCT-CCTCATCACGTAAAACACCATTGTCATCACGTAA
1 AGCACCTACCTCATCACGTAAAACACCATTGTCATCACATAA
* *
56775 ACCACCTACCTCGTCACGTAAAACACCATTGTCATCACATAA
1 AGCACCTACCTCATCACGTAAAACACCATTGTCATCACATAA
* * **
56817 AGCACTTACCTCATCACGTAAAGCACC-TACCTCATCACATAA
1 AGCACCTACCTCATCACGTAAAACACCAT-TGTCATCACATAA
*
56859 AGCACCGACCTCATCACGTAAAACACC
1 AGCACCTACCTCATCACGTAAAACACC
56886 TAACTTATCA
Statistics
Matches: 97, Mismatches: 12, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
41 7 0.07
42 90 0.93
ACGTcount: A:0.36, C:0.36, G:0.09, T:0.20
Consensus pattern (42 bp):
AGCACCTACCTCATCACGTAAAACACCATTGTCATCACATAA
Found at i:56897 original size:21 final size:21
Alignment explanation
Indices: 56726--56898 Score: 154
Period size: 21 Copynumber: 8.3 Consensus size: 21
56716 TGAAATAATC
* *
56726 TCACGTAGAGCACCT-CCTCA
1 TCACGTAAAACACCTACCTCA
**
56746 TCACGTAAAACACC-ATTGTCA
1 TCACGTAAAACACCTA-CCTCA
* *
56767 TCACGTAAACCACCTACCTCG
1 TCACGTAAAACACCTACCTCA
**
56788 TCACGTAAAACACC-ATTGTCA
1 TCACGTAAAACACCTA-CCTCA
* * *
56809 TCACATAAAGCACTTACCTCA
1 TCACGTAAAACACCTACCTCA
*
56830 TCACGTAAAGCACCTACCTCA
1 TCACGTAAAACACCTACCTCA
* * *
56851 TCACATAAAGCACCGACCTCA
1 TCACGTAAAACACCTACCTCA
* *
56872 TCACGTAAAACACCTAACTTA
1 TCACGTAAAACACCTACCTCA
56893 TCACGT
1 TCACGT
56899 GGAGGTGAAG
Statistics
Matches: 122, Mismatches: 26, Indels: 9
0.78 0.17 0.06
Matches are distributed among these distances:
20 13 0.11
21 107 0.88
22 2 0.02
ACGTcount: A:0.35, C:0.35, G:0.09, T:0.21
Consensus pattern (21 bp):
TCACGTAAAACACCTACCTCA
Found at i:57097 original size:42 final size:42
Alignment explanation
Indices: 57049--57179 Score: 208
Period size: 42 Copynumber: 3.1 Consensus size: 42
57039 GAATCGGCTT
* *
57049 GATGAGGTGATGGATCTCGGTGTCAAAGTGGAGAATCAACTT
1 GATGAGGTGATGGATCTCGGTGTCGAAGTGGAGAATCAACTC
* **
57091 GATGAGGTGATGGATCTCGGCGTCGAAGTGGAGAATCGGCTC
1 GATGAGGTGATGGATCTCGGTGTCGAAGTGGAGAATCAACTC
*
57133 GATGAGGTGATGGATCTCGGTGTCGAAGTAGAGAATCAACTC
1 GATGAGGTGATGGATCTCGGTGTCGAAGTGGAGAATCAACTC
57175 GATGA
1 GATGA
57180 AAAAGTGGGG
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 80 1.00
ACGTcount: A:0.27, C:0.14, G:0.36, T:0.24
Consensus pattern (42 bp):
GATGAGGTGATGGATCTCGGTGTCGAAGTGGAGAATCAACTC
Found at i:59903 original size:20 final size:20
Alignment explanation
Indices: 59817--59987 Score: 105
Period size: 20 Copynumber: 8.4 Consensus size: 20
59807 AAAACATTTG
**
59817 GTTGCGAAATT-AAAAGCTGA
1 GTTGCGAAATTGAAATTC-GA
* * *
59837 GTTGCGAAATTTAAATTGGC
1 GTTGCGAAATTGAAATTCGA
*
59857 GTTGC-AAATTCGAAAATTCGC
1 GTTGCGAAATT-G-AAATTCGA
*
59878 GTTGCGAAATTGAAACTCGA
1 GTTGCGAAATTGAAATTCGA
** * *
59898 GTTGCGAAAACGAAACTCGT
1 GTTGCGAAATTGAAATTCGA
* * *
59918 GTTACGAATTTAAAAATT-GA
1 GTTGCGAAATT-GAAATTCGA
** *
59938 GTTGCGAAACAGAAATTCGT
1 GTTGCGAAATTGAAATTCGA
*
59958 GTTGCGAAAATGTCAAATTCGA
1 GTTGCG-AAAT-TGAAATTCGA
59980 GTTGCGAA
1 GTTGCGAA
59988 TTCGAAAACT
Statistics
Matches: 115, Mismatches: 28, Indels: 15
0.73 0.18 0.09
Matches are distributed among these distances:
19 10 0.09
20 62 0.54
21 25 0.22
22 18 0.16
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.27
Consensus pattern (20 bp):
GTTGCGAAATTGAAATTCGA
Found at i:61069 original size:23 final size:23
Alignment explanation
Indices: 61043--61087 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
61033 ACCAAAATGT
*
61043 AGAGATAAACGTGCCACAAAGAC
1 AGAGACAAACGTGCCACAAAGAC
* *
61066 AGAGACAAATGTGTCACAAAGA
1 AGAGACAAACGTGCCACAAAGA
61088 AAAAATTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.49, C:0.18, G:0.22, T:0.11
Consensus pattern (23 bp):
AGAGACAAACGTGCCACAAAGAC
Found at i:63159 original size:24 final size:24
Alignment explanation
Indices: 63132--63177 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
63122 AATGAAGAAT
*
63132 AAAAATAAGTAAAAAAACAAAAGG
1 AAAAATAAATAAAAAAACAAAAGG
* *
63156 AAAAATAAATAAATAAATAAAA
1 AAAAATAAATAAAAAAACAAAA
63178 TATTAATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.78, C:0.02, G:0.07, T:0.13
Consensus pattern (24 bp):
AAAAATAAATAAAAAAACAAAAGG
Found at i:63274 original size:14 final size:16
Alignment explanation
Indices: 63239--63271 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
63229 TCATAACAAT
63239 AATAATAGTAATATGAA
1 AATAATAGTAATAT-AA
63256 AATAATA-TAATATAA
1 AATAATAGTAATATAA
63271 A
1 A
63272 TAAAAAAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 6 0.38
17 7 0.44
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (16 bp):
AATAATAGTAATATAA
Found at i:63292 original size:20 final size:20
Alignment explanation
Indices: 63269--63317 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
63259 AATATAATAT
63269 AAATAAAAAAACCA-AAACCA
1 AAATAAAAAAA-CATAAACCA
* *
63289 AAATAAATAAATATAAACCA
1 AAATAAAAAAACATAAACCA
63309 AATATAAAA
1 AA-ATAAAA
63318 GTATACATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 18 0.75
21 5 0.21
ACGTcount: A:0.73, C:0.12, G:0.00, T:0.14
Consensus pattern (20 bp):
AAATAAAAAAACATAAACCA
Found at i:63603 original size:66 final size:64
Alignment explanation
Indices: 63452--63624 Score: 172
Period size: 64 Copynumber: 2.6 Consensus size: 64
63442 GCTTATAAGT
*
63452 AAAATATTTAAAAAATTTATATATATATATATATATAAATAATAAATATAGTATTAAAAAACCAA
1 AAAATATTTAAAAAA---ATATATATATATATATAT-AATAATAAATATAGTATAAAAAAACCAA
63517 ATG
62 ATG
** * * * *
63520 AATAA-AAAT-AAATAATATATATATATATATATAATAATAATATATAGTGTAAAAAAATCAATT
1 AA-AATATTTAAAAAAATATATATATATATATATAATAATAA-ATATAGTATAAAAAAACCAAAT
63583 G
64 G
*
63584 AAAATCATTTAAAAAAATATACGTATATATATTTAT-ATAAT
1 AAAAT-ATTTAAAAAAATATA--TATATATATATATAATAAT
63625 GACAATAATG
Statistics
Matches: 87, Mismatches: 11, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
63 10 0.11
64 39 0.45
65 2 0.02
66 9 0.10
67 9 0.10
68 16 0.18
69 2 0.02
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (64 bp):
AAAATATTTAAAAAAATATATATATATATATATAATAATAAATATAGTATAAAAAAACCAAATG
Found at i:64078 original size:37 final size:37
Alignment explanation
Indices: 64037--64141 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
64027 GTGCTTGTGG
* * *
64037 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTTT
* * *
64074 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTTT
64111 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
64142 GACGAAAAGG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTTT
Found at i:65220 original size:30 final size:29
Alignment explanation
Indices: 65145--65263 Score: 114
Period size: 30 Copynumber: 3.9 Consensus size: 29
65135 AGAGTCGAGG
* ** *
65145 GTTACCTATGTCTTTCAAGACATATGGATA
1 GTTACC-ATGTCCTTCGGGACATATGGACA
65175 GTTTACCTATGTCCTTCGGGACATATGGACA
1 G-TTACC-ATGTCCTTCGGGACATATGGACA
*
65206 GGATTACC-TGTCCTTCGGGACATATGGGCA
1 -G-TTACCATGTCCTTCGGGACATATGGACA
* *
65236 GTTACCTATGTTCTTCGGAACATATGGA
1 GTTACC-ATGTCCTTCGGGACATATGGA
65264 TAGGTCCTTC
Statistics
Matches: 76, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
28 5 0.07
29 1 0.01
30 39 0.51
31 25 0.33
32 6 0.08
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (29 bp):
GTTACCATGTCCTTCGGGACATATGGACA
Found at i:66565 original size:71 final size:71
Alignment explanation
Indices: 66435--66566 Score: 194
Period size: 71 Copynumber: 1.9 Consensus size: 71
66425 GCATCAAATC
* * *
66435 AAAATATAAATAAGTATGGACCATTTTCATATACAAATATAATTTTAATGACTAGATTGAAGTAA
1 AAAATATAAATAAATATGGACCATTTTCATATACAAATATAATTTTAAGGACTAAATTGAAGTAA
66500 ATCACA
66 ATCACA
** *
66506 AAAATATAAATAAATATGTTCCGA-TTTCATATACAAATATAATTTTAAGGATTAAATTGAA
1 AAAATATAAATAAATATGGACC-ATTTTCATATACAAATATAATTTTAAGGACTAAATTGAA
66567 CAAATATGAA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
71 53 0.98
72 1 0.02
ACGTcount: A:0.48, C:0.08, G:0.09, T:0.34
Consensus pattern (71 bp):
AAAATATAAATAAATATGGACCATTTTCATATACAAATATAATTTTAAGGACTAAATTGAAGTAA
ATCACA
Found at i:66728 original size:2 final size:2
Alignment explanation
Indices: 66721--66754 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
66711 ATCAATTTTA
*
66721 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
66755 ATGAATGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:66825 original size:2 final size:2
Alignment explanation
Indices: 66818--67162 Score: 149
Period size: 2 Copynumber: 175.5 Consensus size: 2
66808 ATATTATAAG
* * *
66818 TA TA TA TA TA TA TA TA -A TG T- TA TG CA TA TA T- TA TA -A GTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* *
66857 TA TA CT- TA TA TA AA TA TA TA -A TA TA TA TA TA -A CTA TA CA T-
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * *
66897 TA TA CTA -A TA -A GTA TA TA TA TA TT TA TA CA TA TG TA TA CT-
1 TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
** * * * * * *
66937 TA TA CC TA TA TA TA TA -A T- TA CA CA CA CA TA TA -A AA GTA TC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* ** * * *
66977 CA TA TA TA GG TA TG TA TA TA AA TA TA TA TA -A GTA TA AA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA
*
67020 -A TA TA TA -A GTA TG TA TA TA TA -A GTA TA TA TA -A GTA TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA
* * * *
67059 TG TA TGA TG TA TA TA -A GTA TA TA CA TA -A GTA TA TA TA TA CA
1 TA TA T-A TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA
67100 TA -A GTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
67142 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
67163 CATTGAACAT
Statistics
Matches: 259, Mismatches: 46, Indels: 76
0.68 0.12 0.20
Matches are distributed among these distances:
1 22 0.08
2 219 0.85
3 18 0.07
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (2 bp):
TA
Found at i:66866 original size:19 final size:18
Alignment explanation
Indices: 66806--66920 Score: 82
Period size: 19 Copynumber: 6.4 Consensus size: 18
66796 TACACTACAC
66806 TTATATTATAAGTATATA
1 TTATATTATAAGTATATA
66824 -TATATATATAATGT-TATGCA
1 TTATAT-TATAA-GTATAT--A
66844 -TATATTATAAGTATATA
1 TTATATTATAAGTATATA
66861 CTTATA-TA-AA-TATATA
1 -TTATATTATAAGTATATA
* * *
66877 ATATATATATAACTATACA
1 TTATAT-TATAAGTATATA
*
66896 TTATACTAATAAGTATATA
1 TTATA-TTATAAGTATATA
66915 -TATATT
1 TTATATT
66921 TATACATATG
Statistics
Matches: 78, Mismatches: 7, Indels: 25
0.71 0.06 0.23
Matches are distributed among these distances:
15 4 0.05
16 6 0.08
17 11 0.14
18 18 0.23
19 32 0.41
20 7 0.09
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.45
Consensus pattern (18 bp):
TTATATTATAAGTATATA
Found at i:67527 original size:40 final size:39
Alignment explanation
Indices: 67470--67554 Score: 89
Period size: 40 Copynumber: 2.2 Consensus size: 39
67460 CAACATTTGT
* * * **
67470 CAAAAAAATAAAATTTCCTTCTTTCCTTTTCTAAATTCC
1 CAAAAAAATAAAATTTCCCTATTCCCTCGTCTAAATTCC
** *
67509 CAAAAAAATCAATTTTTCCCTATTCCCTCGTCTAAATTCT
1 CAAAAAAAT-AAAATTTCCCTATTCCCTCGTCTAAATTCC
67549 CAAAAA
1 CAAAAA
67555 GTCAAAATTT
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
39 9 0.24
40 28 0.76
ACGTcount: A:0.38, C:0.25, G:0.01, T:0.36
Consensus pattern (39 bp):
CAAAAAAATAAAATTTCCCTATTCCCTCGTCTAAATTCC
Found at i:67950 original size:14 final size:13
Alignment explanation
Indices: 67924--67961 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
67914 TTAATTTATT
67924 GATTATAATTAA-
1 GATTATAATTAAG
67936 GATTTATAATATAAG
1 GA-TTATAAT-TAAG
67951 GATTATAATTA
1 GATTATAATTA
67962 TTATAGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 2 0.09
13 9 0.39
14 10 0.43
15 2 0.09
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (13 bp):
GATTATAATTAAG
Found at i:68030 original size:40 final size:37
Alignment explanation
Indices: 67986--68111 Score: 98
Period size: 37 Copynumber: 3.3 Consensus size: 37
67976 TTTATTATTT
*
67986 TAATTATCCTAACTAACAATTTATATTAACTTTTAAAGA
1 TAATTATCATAACTAACAATTTAT-TTAACTTTTAAA-A
* * *
68025 GTAATTAT-ATTAATTATCATAGTTTATTTAA-TTGTCAAAA
1 -TAATTATCA-TAACTAACA-A-TTTATTTAACTT-TTAAAA
*
68065 -AATTATCATAACTAACAATTTGTTTTAACTTTTAAAA
1 TAATTATCATAACTAACAATTT-ATTTAACTTTTAAAA
*
68102 -AATAATCATA
1 TAATTATCATA
68112 TTTATTATAA
Statistics
Matches: 70, Mismatches: 9, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
36 3 0.04
37 20 0.29
38 15 0.21
39 1 0.01
40 17 0.24
41 9 0.13
42 5 0.07
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.43
Consensus pattern (37 bp):
TAATTATCATAACTAACAATTTATTTAACTTTTAAAA
Found at i:74632 original size:16 final size:15
Alignment explanation
Indices: 74591--74643 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
74581 TTTTCATCTC
*
74591 ATAAAATTATAAAAT
1 ATAAAAATATAAAAT
* * *
74606 AATTAATATATTAAAT
1 -ATAAAAATATAAAAT
74622 ATTAAAAATATAAAAT
1 A-TAAAAATATAAAAT
74638 ATAAAA
1 ATAAAA
74644 TAATTTTAAC
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
15 6 0.21
16 23 0.79
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
ATAAAAATATAAAAT
Found at i:87050 original size:16 final size:16
Alignment explanation
Indices: 87021--87060 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
87011 TGTTCATTTA
87021 ATAAAT-AA-ACGAAC
1 ATAAATGAACACGAAC
87035 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
*
87051 ATAAACGAAC
1 ATAAATGAAC
87061 CAATTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.26
15 2 0.09
16 15 0.65
ACGTcount: A:0.60, C:0.17, G:0.10, T:0.12
Consensus pattern (16 bp):
ATAAATGAACACGAAC
Found at i:87465 original size:10 final size:10
Alignment explanation
Indices: 87447--87480 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
87437 CCCTCTGTTC
87447 GAACATAAAT
1 GAACATAAAT
*
87457 GAGCATAAAT
1 GAACATAAAT
*
87467 GAACAAAAAT
1 GAACATAAAT
87477 GAAC
1 GAAC
87481 GAACATAAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.59, C:0.12, G:0.15, T:0.15
Consensus pattern (10 bp):
GAACATAAAT
Found at i:88234 original size:21 final size:21
Alignment explanation
Indices: 88210--88261 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
88200 AATTATGATG
**
88210 TTAATGTGATTGTTCACAATA
1 TTAATGTGATAATTCACAATA
* *
88231 TTAAAGTGATAATTCACGATA
1 TTAATGTGATAATTCACAATA
88252 TTAATGTGAT
1 TTAATGTGAT
88262 CCATGATGAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (21 bp):
TTAATGTGATAATTCACAATA
Found at i:88455 original size:25 final size:24
Alignment explanation
Indices: 88427--88498 Score: 62
Period size: 25 Copynumber: 3.0 Consensus size: 24
88417 TAAAGTATAT
88427 ATATTAAATTACTAAAAAT-ATTCAA
1 ATATTAAATTA-TAAAAATAATT-AA
88452 ATATCATAAATTAT-AAAATAATTAA
1 ATAT--TAAATTATAAAAATAATTAA
*
88477 TTATT-AATTATTAAAAA-AATTA
1 ATATTAAATTA-TAAAAATAATTA
88499 GAAATCATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
22 5 0.12
23 7 0.17
24 4 0.10
25 14 0.34
26 4 0.10
27 7 0.17
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (24 bp):
ATATTAAATTATAAAAATAATTAA
Found at i:95734 original size:23 final size:23
Alignment explanation
Indices: 95707--95757 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
95697 TGCATCTTTG
95707 GCAAACAAAAGAAAGTCAGTTTT
1 GCAAACAAAAGAAAGTCAGTTTT
*
95730 GCAAACAAAATAAAGTCAGTTTT
1 GCAAACAAAAGAAAGTCAGTTTT
95753 GCAAA
1 GCAAA
95758 GATTGGCAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.49, C:0.14, G:0.16, T:0.22
Consensus pattern (23 bp):
GCAAACAAAAGAAAGTCAGTTTT
Found at i:102491 original size:32 final size:31
Alignment explanation
Indices: 102423--102528 Score: 90
Period size: 32 Copynumber: 3.4 Consensus size: 31
102413 TTGGGGTCTT
* *
102423 AGAGCCCACCCAAGGAACACCTTAGGGCCTT
1 AGAGCCTACCCAAGGAACACCTTAGGGCCTG
* *
102454 AGAGCCTACCCAATGAAGCA-CTTTGGGACCTG
1 AGAGCCTACCCAAGGAA-CACCTTAGGG-CCTG
* * * *
102486 AGAGCCTACCAAAGGGAACAAC-TCGAGGCCTA
1 AGAGCCTACCCAA-GGAACACCTTAG-GGCCTG
102518 AGAGCCTACCC
1 AGAGCCTACCC
102529 GAGGGTCACA
Statistics
Matches: 61, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
31 21 0.34
32 34 0.56
33 6 0.10
ACGTcount: A:0.31, C:0.32, G:0.24, T:0.13
Consensus pattern (31 bp):
AGAGCCTACCCAAGGAACACCTTAGGGCCTG
Found at i:104363 original size:197 final size:195
Alignment explanation
Indices: 104030--104424 Score: 736
Period size: 197 Copynumber: 2.0 Consensus size: 195
104020 ATATCCAGTT
*
104030 GTTGATCTCCTGCATAATCAGCATCACAATAACCACTAACTTGCAGTCTTCACCTTTCTTATACA
1 GTTGATCTCCTGCATAATCAGCATCACAATAACCACTAACTTGCAATCTTCACCTTTCTTATACA
*
104095 AAGACCATAGTCAATTGTATTCTTCACATATCTCAGTATTCGTCGAACTGCTTCCAAATGAGGCT
66 AAGACCATAGTCAATTGTATTATTCACATATCTCAGTATTCGTCGAACTGCTTCCAAATGAGGCT
104160 TCTTTGGATTTTACATATACCGACTCATCACACCAACTGCATAAGAAATGTCAGGTCGGGTCAAG
131 TCTTTGGATTTTACATATACCGACTCATCACACCAACTGCATAAGAAATGTCAGGTCGGGTCAAG
*
104225 GTTGATCTCCTGCATAATCAGCATCACAATAACCAACTAACTTGCAATCTTCACCTTTCTTGTAC
1 GTTGATCTCCTGCATAATCAGCATCACAATAACC-ACTAACTTGCAATCTTCACCTTTCTTATAC
104290 AAAAGACCATAGTCAATTGTATTATTCACATATCTCAGTATTCGTCGAACTGCTTCCAAATGAGG
65 -AAAGACCATAGTCAATTGTATTATTCACATATCTCAGTATTCGTCGAACTGCTTCCAAATGAGG
*
104355 CTTCTTTGGATTTTGCATATACCGACTCATCACACCAACTGCATAAGAAATGTCAGGTCGGGTCA
129 CTTCTTTGGATTTTACATATACCGACTCATCACACCAACTGCATAAGAAATGTCAGGTCGGGTCA
104420 AG
194 AG
104422 GTT
1 GTT
104425 AAGTAGATCA
Statistics
Matches: 194, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
195 34 0.18
196 28 0.14
197 132 0.68
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.31
Consensus pattern (195 bp):
GTTGATCTCCTGCATAATCAGCATCACAATAACCACTAACTTGCAATCTTCACCTTTCTTATACA
AAGACCATAGTCAATTGTATTATTCACATATCTCAGTATTCGTCGAACTGCTTCCAAATGAGGCT
TCTTTGGATTTTACATATACCGACTCATCACACCAACTGCATAAGAAATGTCAGGTCGGGTCAAG
Found at i:116204 original size:30 final size:31
Alignment explanation
Indices: 116170--116249 Score: 90
Period size: 32 Copynumber: 2.6 Consensus size: 31
116160 TAATAGTCGG
* * * *
116170 GGACTCAATTAAGAAACA-TCTCTAATCGAA
1 GGACTCAATAAAGAAACACCCTATAATCAAA
*
116200 GGACTCAATAAAAATAACACCCTATAATCAAA
1 GGACTCAATAAAGA-AACACCCTATAATCAAA
*
116232 GGACTCAATAAAGTAACA
1 GGACTCAATAAAGAAACA
116250 ACTTATAGTC
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
30 12 0.29
31 8 0.20
32 21 0.51
ACGTcount: A:0.49, C:0.20, G:0.11, T:0.20
Consensus pattern (31 bp):
GGACTCAATAAAGAAACACCCTATAATCAAA
Found at i:118928 original size:45 final size:45
Alignment explanation
Indices: 118877--118968 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
118867 CTGGCAGTAG
*
118877 CACCGGCATAACCCCACCAACTGGGATTCCGACCACCGGGCCAAA
1 CACCGGCATAACCCCACCAACTGGGATTCCGACCACCGGACCAAA
118922 CACCGGCATAACCCCACCAACTGGGATTCCGACCACCGGACCAAA
1 CACCGGCATAACCCCACCAACTGGGATTCCGACCACCGGACCAAA
118967 CA
1 CA
118969 TTGGAACCCC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.30, C:0.42, G:0.18, T:0.09
Consensus pattern (45 bp):
CACCGGCATAACCCCACCAACTGGGATTCCGACCACCGGACCAAA
Found at i:121176 original size:187 final size:190
Alignment explanation
Indices: 120861--121238 Score: 719
Period size: 187 Copynumber: 2.0 Consensus size: 190
120851 GAAACATAAG
120861 TAGAAAAGTTTGAATGAATATAATTTGACTTTGATCATTGGAGTAACGTATTTGACAAGTAAAGC
1 TAGAAAAGTTTGAATGAATATAATTTGACTTTGATCATTGGAGTAACGTATTTGACAAGTAAAGC
120926 ATAAAGCTTTTGGCGCTTTTCAGATCATAACGTCTGAACTATCTACGGATTACAAGCGCGTTG-A
66 ATAAAGCTTTTGGCGCTTTTCAGATCATAACGTCTGAACTATCTACGGATTACAAGCGCGTTGAA
120990 AAGAGA-GAGAGGAGAGCCGAGGTTTAGAAAAAATAATACTA-TATA-GCTTACTTGGTCT
131 AAGAGAGGAGA-GAGAGCCGAGGTTTAGAAAAAATAATACTACTATATGCTTACTTGGTCT
121048 TAGAAAAGTTTGAATGAATATAATTTGACTTTGATCATTGGAGTAACGTATTTGACAAGTAAAGC
1 TAGAAAAGTTTGAATGAATATAATTTGACTTTGATCATTGGAGTAACGTATTTGACAAGTAAAGC
121113 ATAAAGCTTTTGGCGCTTTTCAGATCATAACGTCTGAACTATCTACGGATTACAAGCGCGTTGAA
66 ATAAAGCTTTTGGCGCTTTTCAGATCATAACGTCTGAACTATCTACGGATTACAAGCGCGTTGAA
121178 AAGAGAGGAGAGAGAGCCGAGGTTTAGAAAAAATAATACTACTATATGCTTACTTGGTCT
131 AAGAGAGGAGAGAGAGCCGAGGTTTAGAAAAAATAATACTACTATATGCTTACTTGGTCT
121238 T
1 T
121239 GTAATTTTTA
Statistics
Matches: 187, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
187 128 0.68
188 37 0.20
189 8 0.04
190 14 0.07
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (190 bp):
TAGAAAAGTTTGAATGAATATAATTTGACTTTGATCATTGGAGTAACGTATTTGACAAGTAAAGC
ATAAAGCTTTTGGCGCTTTTCAGATCATAACGTCTGAACTATCTACGGATTACAAGCGCGTTGAA
AAGAGAGGAGAGAGAGCCGAGGTTTAGAAAAAATAATACTACTATATGCTTACTTGGTCT
Found at i:121971 original size:2 final size:2
Alignment explanation
Indices: 121960--121996 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
121950 TATTAATTTA
121960 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
121997 TTCAAATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:122440 original size:17 final size:18
Alignment explanation
Indices: 122404--122441 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
122394 GGATGATTTC
122404 ATTAAACGACATAGTTTT
1 ATTAAACGACATAGTTTT
* *
122422 ATTAAATGAC-TATTTTT
1 ATTAAACGACATAGTTTT
122439 ATT
1 ATT
122442 CTCTAAATGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (18 bp):
ATTAAACGACATAGTTTT
Found at i:124090 original size:24 final size:23
Alignment explanation
Indices: 124063--124111 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
124053 TTAGTCACTG
124063 TTTTATTTATGATTTT-TTATTGTT
1 TTTTATTTAT-ATTTTATTA-TGTT
*
124087 TTTTTTTTATATTTTATTATGTT
1 TTTTATTTATATTTTATTATGTT
124110 TT
1 TT
124112 AATCCTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78
Consensus pattern (23 bp):
TTTTATTTATATTTTATTATGTT
Found at i:124322 original size:15 final size:15
Alignment explanation
Indices: 124302--124331 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
124292 TAATTTCAAT
124302 CTTTTAATTTTTTTA
1 CTTTTAATTTTTTTA
124317 CTTTTAATTTTTTTA
1 CTTTTAATTTTTTTA
124332 TTATTGTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (15 bp):
CTTTTAATTTTTTTA
Found at i:125150 original size:25 final size:25
Alignment explanation
Indices: 125113--125160 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
125103 CAAAAGAAAA
*
125113 CCCCCAAGTCGTACTAAGTTTTTTT
1 CCCCCAAGCCGTACTAAGTTTTTTT
*
125138 CCCCCGAGCCGTACTAAGTTTTT
1 CCCCCAAGCCGTACTAAGTTTTT
125161 CCCCCGCCCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.19, C:0.31, G:0.15, T:0.35
Consensus pattern (25 bp):
CCCCCAAGCCGTACTAAGTTTTTTT
Found at i:125163 original size:23 final size:24
Alignment explanation
Indices: 125113--125166 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
125103 CAAAAGAAAA
* *
125113 CCCCCAAGTCGTACTAAGTTTTTTT
1 CCCCCGAGCCGTACTAAG-TTTTTT
125138 CCCCCGAGCCGTACTAAG-TTTTT
1 CCCCCGAGCCGTACTAAGTTTTTT
125161 CCCCCG
1 CCCCCG
125167 CCCGAGCGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 11 0.41
25 16 0.59
ACGTcount: A:0.17, C:0.37, G:0.15, T:0.31
Consensus pattern (24 bp):
CCCCCGAGCCGTACTAAGTTTTTT
Found at i:125334 original size:18 final size:19
Alignment explanation
Indices: 125311--125349 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
125301 ATTTCTTTCA
125311 ATTCTTTTATTAT-TTTTT
1 ATTCTTTTATTATATTTTT
*
125329 ATTCTTTTATTTTATTTTT
1 ATTCTTTTATTATATTTTT
125348 AT
1 AT
125350 ATCCTTGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (19 bp):
ATTCTTTTATTATATTTTT
Found at i:126829 original size:20 final size:20
Alignment explanation
Indices: 126804--126842 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
126794 ATTTATATTT
*
126804 TGCATCTTTGCATTTGCATG
1 TGCATCTTTGCATTAGCATG
126824 TGCATCTTTGCATTAGCAT
1 TGCATCTTTGCATTAGCAT
126843 TTATACGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.44
Consensus pattern (20 bp):
TGCATCTTTGCATTAGCATG
Found at i:128187 original size:8 final size:8
Alignment explanation
Indices: 128174--128247 Score: 60
Period size: 8 Copynumber: 8.8 Consensus size: 8
128164 AAACACACAC
128174 AAAAAAGA
1 AAAAAAGA
128182 AAAAAAGA
1 AAAAAAGA
* *
128190 TAGAAAGA
1 AAAAAAGA
128198 AAAAACAGGA
1 AAAAA-A-GA
128208 AAACAAA-A
1 AAA-AAAGA
*
128216 AAAAATAAA
1 AAAAA-AGA
*
128225 AAAAAATA
1 AAAAAAGA
128233 AAAAAAGA
1 AAAAAAGA
128241 AGAAAAA
1 A-AAAAA
128248 AATAAAAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
7 2 0.04
8 32 0.59
9 12 0.22
10 6 0.11
11 2 0.04
ACGTcount: A:0.82, C:0.03, G:0.11, T:0.04
Consensus pattern (8 bp):
AAAAAAGA
Found at i:128216 original size:1 final size:1
Alignment explanation
Indices: 128207--128258 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
128197 AAAAAACAGG
* * * * * *
128207 AAAACAAAAAAAAATAAAAAAAAATAAAAAAAGAAGAAAAAAATAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
128259 GGAAGAAGAA
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.88, C:0.02, G:0.04, T:0.06
Consensus pattern (1 bp):
A
Found at i:128220 original size:10 final size:10
Alignment explanation
Indices: 128207--128258 Score: 70
Period size: 10 Copynumber: 5.3 Consensus size: 10
128197 AAAAAACAGG
*
128207 AAAACAAAAA
1 AAAATAAAAA
128217 AAAATAAAAA
1 AAAATAAAAA
128227 AAAATAAAAA
1 AAAATAAAAA
* *
128237 AAGA-AGAAA
1 AAAATAAAAA
128246 AAAATAAAAA
1 AAAATAAAAA
128256 AAA
1 AAA
128259 GGAAGAAGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
9 7 0.19
10 29 0.81
ACGTcount: A:0.88, C:0.02, G:0.04, T:0.06
Consensus pattern (10 bp):
AAAATAAAAA
Found at i:128229 original size:19 final size:18
Alignment explanation
Indices: 128213--128258 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
128203 CAGGAAAACA
128213 AAAAAAAATAAAAAAAAAT
1 AAAAAAAA-AAAAAAAAAT
*
128232 AAAAAAAGAAGAAAAAAAT
1 AAAAAAA-AAAAAAAAAAT
128251 AAAAAAAA
1 AAAAAAAA
128259 GGAAGAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 1 0.04
19 23 0.92
20 1 0.04
ACGTcount: A:0.89, C:0.00, G:0.04, T:0.07
Consensus pattern (18 bp):
AAAAAAAAAAAAAAAAAT
Found at i:128263 original size:21 final size:20
Alignment explanation
Indices: 128174--128272 Score: 80
Period size: 21 Copynumber: 5.0 Consensus size: 20
128164 AAACACACAC
*
128174 AAAAAAGAA-AAAAAGATAGA
1 AAAAAAGAAGAAAAAAATA-A
* * *
128194 AAGAAAAAACAGGAAAACA-AA
1 AA-AAAAGA-AGAAAAAAATAA
*
128215 AAAAAATAA-AAAAAAAT-A
1 AAAAAAGAAGAAAAAAATAA
128233 AAAAAAGAAGAAAAAAATAA
1 AAAAAAGAAGAAAAAAATAA
*
128253 AAAAAAGGAAGAAGAAAATA
1 AAAAAA-GAAGAAAAAAATA
128273 GATAGATCCA
Statistics
Matches: 64, Mismatches: 8, Indels: 13
0.75 0.09 0.15
Matches are distributed among these distances:
18 14 0.22
19 9 0.14
20 14 0.22
21 20 0.31
22 2 0.03
23 5 0.08
ACGTcount: A:0.81, C:0.02, G:0.12, T:0.05
Consensus pattern (20 bp):
AAAAAAGAAGAAAAAAATAA
Found at i:135597 original size:2 final size:2
Alignment explanation
Indices: 135590--135684 Score: 190
Period size: 2 Copynumber: 47.5 Consensus size: 2
135580 ATTTAAGTGA
135590 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
135632 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
135674 AC AC AC AC AC A
1 AC AC AC AC AC A
135685 TATTTCCCAG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 93 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:135910 original size:54 final size:53
Alignment explanation
Indices: 135844--136152 Score: 277
Period size: 54 Copynumber: 5.8 Consensus size: 53
135834 GCTAATGAGT
* * * * * *
135844 TTTTAAATAAACTAAGTCTAATTTTCAGAAGTTTCTTGACGATTTTTAAATGAG
1 TTTTAAAGAAACTAAGCCTAATTTTCAGGAGTTTCTTGATG-TTTTCAAATGAA
* * ** * *
135898 TTTTAAAGAAACTAAGTCTGATTTTCAAAAGTTTCTTGATGATTTTTAAAAGAA
1 TTTTAAAGAAACTAAGCCTAATTTTCAGGAGTTTCTTGATG-TTTTCAAATGAA
* * * *
135952 CTTTCAAAGAAATTAAGCCTAATTTAT-AGGGGTTTCTTGATGTTTTCAAATAAA
1 -TTTTAAAGAAACTAAGCCTAATTT-TCAGGAGTTTCTTGATGTTTTCAAATGAA
* * * *
136006 TTTGAAAGAAGCTAAACCTGATTTTCAGGAGTTTCTTGATG-TTTCAAATGAA
1 TTTTAAAGAAACTAAGCCTAATTTTCAGGAGTTTCTTGATGTTTTCAAATGAA
* *
136058 TTTCAAAGAAA-TCAAGCCTAAATTTT-AGGGGTTTCTTGATGTTTTCAAATGAA
1 TTTTAAAGAAACT-AAGCCT-AATTTTCAGGAGTTTCTTGATGTTTTCAAATGAA
* * * *
136111 TTTTTAAA-AAAGCTAAGCATAATTTTTAGGGGTTTATTGATG
1 -TTTTAAAGAAA-CTAAGCCTAATTTTCAGGAGTTTCTTGATG
136153 ATAACTGTAA
Statistics
Matches: 214, Mismatches: 31, Indels: 20
0.81 0.12 0.08
Matches are distributed among these distances:
51 1 0.00
52 39 0.18
53 58 0.27
54 82 0.38
55 33 0.15
56 1 0.00
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (53 bp):
TTTTAAAGAAACTAAGCCTAATTTTCAGGAGTTTCTTGATGTTTTCAAATGAA
Found at i:136090 original size:105 final size:107
Alignment explanation
Indices: 135874--136113 Score: 315
Period size: 105 Copynumber: 2.2 Consensus size: 107
135864 ATTTTCAGAA
* * * * **
135874 GTTTCTTGACGATTTTTAAATGAGTTTTAAAGAAACTAAGTCTGATTTTCAAAAGTTTCTTGATG
1 GTTTCTTGATG-TTTTCAAATGAATTTGAAAGAAACTAAACCTGATTTTCAAAAGTTTCTTGATG
* *
135939 ATTTTTAAAAGAACTTTCAAAGAAATTAAGCCTAATTTATAGGG
65 A-TTTCAAAAGAACTTTCAAAGAAATCAAGCCTAATTTATAGGG
* * **
135983 GTTTCTTGATGTTTTCAAATAAATTTGAAAGAAGCTAAACCTGATTTTCAGGAGTTTCTTGATG-
1 GTTTCTTGATGTTTTCAAATGAATTTGAAAGAAACTAAACCTGATTTTCAAAAGTTTCTTGATGA
*
136047 TTTCAAATGAA-TTTCAAAGAAATCAAGCCTAAATTT-TAGGG
66 TTTCAAAAGAACTTTCAAAGAAATCAAGCCT-AATTTATAGGG
136088 GTTTCTTGATGTTTTCAAATGAATTT
1 GTTTCTTGATGTTTTCAAATGAATTT
136114 TTAAAAAAGC
Statistics
Matches: 116, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
105 48 0.41
106 14 0.12
108 44 0.38
109 10 0.09
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (107 bp):
GTTTCTTGATGTTTTCAAATGAATTTGAAAGAAACTAAACCTGATTTTCAAAAGTTTCTTGATGA
TTTCAAAAGAACTTTCAAAGAAATCAAGCCTAATTTATAGGG
Found at i:136092 original size:52 final size:54
Alignment explanation
Indices: 135928--136152 Score: 239
Period size: 53 Copynumber: 4.2 Consensus size: 54
135918 ATTTTCAAAA
* * *
135928 GTTTCTTGATGATTTTTAAAAGAACTTTCAAAGAAA-TTAAGCCTAATTTATAGGG
1 GTTTCTTGATG-TTTTCAAATGAACTTTCAAAGAAAGCTAAGCCTAATTT-TAGGG
* * * * *
135983 GTTTCTTGATGTTTTCAAAT-AAATTTGAAAG-AAGCTAAACCTGATTTTCAGGA
1 GTTTCTTGATGTTTTCAAATGAACTTTCAAAGAAAGCTAAGCCTAATTTT-AGGG
*
136036 GTTTCTTGATG-TTTCAAATGAA-TTTCAAAGAAATC-AAGCCTAAATTTTAGGG
1 GTTTCTTGATGTTTTCAAATGAACTTTCAAAGAAAGCTAAGCCT-AATTTTAGGG
* * *
136088 GTTTCTTGATGTTTTCAAATGAATTTTTAAA-AAAGCTAAGCATAATTTTTAGGG
1 GTTTCTTGATGTTTTCAAATGAACTTTCAAAGAAAGCTAAGCCTAA-TTTTAGGG
*
136142 GTTTATTGATG
1 GTTTCTTGATG
136153 ATAACTGTAA
Statistics
Matches: 144, Mismatches: 17, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
52 37 0.26
53 60 0.42
54 36 0.25
55 11 0.08
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (54 bp):
GTTTCTTGATGTTTTCAAATGAACTTTCAAAGAAAGCTAAGCCTAATTTTAGGG
Found at i:137368 original size:18 final size:19
Alignment explanation
Indices: 137345--137386 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
137335 GTAAGAAAAT
*
137345 ATTAAAATAA-TAAAAGCG
1 ATTAAAATAAGTAAAAGCA
137363 ATT-AAATAAGTAAAAGCA
1 ATTAAAATAAGTAAAAGCA
137381 ATTAAA
1 ATTAAA
137387 GTAAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 6 0.29
18 13 0.62
19 2 0.10
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.24
Consensus pattern (19 bp):
ATTAAAATAAGTAAAAGCA
Found at i:146567 original size:45 final size:45
Alignment explanation
Indices: 146470--146627 Score: 122
Period size: 56 Copynumber: 3.3 Consensus size: 45
146460 CACATTCAAT
* * * * ** *
146470 GTGTATCGATGCA-CTCTTTAAAGAAG-AAACATCGAATGCAATTA
1 GTGTATCGATGCACCCCCTTAAA-ATGAAAACATCGAAGGTGATTG
*
146514 GTGCATCGATGCACCCCCTTAAAATGAAAACATCGAAGGTGATTG
1 GTGTATCGATGCACCCCCTTAAAATGAAAACATCGAAGGTGATTG
146559 GTGTATCGATGCAAATGTTATGCACCCCCTTAAAATGAAAACATCGAAGGTGATTG
1 GTG--T--AT-C----G--ATGCACCCCCTTAAAATGAAAACATCGAAGGTGATTG
146615 GTGTATCGATGCA
1 GTGTATCGATGCA
146628 TGGGTAGTGC
Statistics
Matches: 92, Mismatches: 9, Indels: 25
0.73 0.07 0.20
Matches are distributed among these distances:
44 14 0.15
45 29 0.32
47 1 0.01
49 2 0.02
50 1 0.01
51 1 0.01
52 2 0.02
54 2 0.02
56 40 0.43
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (45 bp):
GTGTATCGATGCACCCCCTTAAAATGAAAACATCGAAGGTGATTG
Found at i:146608 original size:56 final size:56
Alignment explanation
Indices: 146522--146627 Score: 212
Period size: 56 Copynumber: 1.9 Consensus size: 56
146512 TAGTGCATCG
146522 ATGCACCCCCTTAAAATGAAAACATCGAAGGTGATTGGTGTATCGATGCAAATGTT
1 ATGCACCCCCTTAAAATGAAAACATCGAAGGTGATTGGTGTATCGATGCAAATGTT
146578 ATGCACCCCCTTAAAATGAAAACATCGAAGGTGATTGGTGTATCGATGCA
1 ATGCACCCCCTTAAAATGAAAACATCGAAGGTGATTGGTGTATCGATGCA
146628 TGGGTAGTGC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 50 1.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (56 bp):
ATGCACCCCCTTAAAATGAAAACATCGAAGGTGATTGGTGTATCGATGCAAATGTT
Found at i:146680 original size:20 final size:22
Alignment explanation
Indices: 146635--146692 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
146625 GCATGGGTAG
146635 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
146659 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
146679 TGTATCGATGCACT
1 TGCATCGATGCACT
146693 TCAAAGGAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:148276 original size:23 final size:23
Alignment explanation
Indices: 148250--148313 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
148240 GGACATTATA
**
148250 TGGCACTACGGTGCATTTCTACG
1 TGGCACTTTGGTGCATTTCTACG
148273 TGGCACTTTGGTGCATTTCTACG
1 TGGCACTTTGGTGCATTTCTACG
* *
148296 CGCCACTTTGGTGCATTT
1 TGGCACTTTGGTGCATTT
148314 ACATGAGCTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.14, C:0.25, G:0.25, T:0.36
Consensus pattern (23 bp):
TGGCACTTTGGTGCATTTCTACG
Found at i:150582 original size:64 final size:63
Alignment explanation
Indices: 150507--150627 Score: 179
Period size: 64 Copynumber: 1.9 Consensus size: 63
150497 ATTATTCAAG
* * * *
150507 GTGTATCGATGCACATGAAGTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATTA
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTT-AAATAAAAACATCGAATGCCATTA
* *
150571 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAATACAAACATCGAATG
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAATAAAAACATCGAATG
150628 GAATTTATGC
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
63 17 0.33
64 34 0.67
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (63 bp):
GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAATAAAAACATCGAATGCCATTA
Found at i:150646 original size:63 final size:64
Alignment explanation
Indices: 150513--150668 Score: 165
Period size: 63 Copynumber: 2.5 Consensus size: 64
150503 CAAGGTGTAT
* * * * * * * *
150513 CGATGCACATGAAGTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATTAGTGTAT
1 CGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCAATTAGTGCAC
* *
150577 CGATGCACAAGTAGTGCATCGATGCACCCCCTT-AAATACAAACATCGAATGGAATTTA-TGCAC
1 CGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCAA-TTAGTGCAC
* *
150640 CGATGCA-TAGATAGTGCATCAATGCACCC
1 CGATGCACAAG-TAGTGCATCGATGCACCC
150669 GTCAAGGGAT
Statistics
Matches: 78, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
62 2 0.03
63 45 0.58
64 31 0.40
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (64 bp):
CGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCAATTAGTGCAC
Found at i:151333 original size:2 final size:2
Alignment explanation
Indices: 151326--151376 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
151316 TAGCATAAAC
151326 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
151368 TA TA TA TA T
1 TA TA TA TA T
151377 GTGTGTGTGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:152327 original size:23 final size:23
Alignment explanation
Indices: 152301--152357 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
152291 GGTACATTTA
*
152301 TACGTGACACTACGGTGTAATTC
1 TACGTGGCACTACGGTGTAATTC
*
152324 TACGCGGCACTACGGTGTAATTC
1 TACGTGGCACTACGGTGTAATTC
152347 TACGTGGCACT
1 TACGTGGCACT
152358 TCAGTGCATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.28
Consensus pattern (23 bp):
TACGTGGCACTACGGTGTAATTC
Found at i:154644 original size:23 final size:23
Alignment explanation
Indices: 154618--154686 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
154608 CACCACAGCT
* *
154618 CGTATAAATACACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * * *
154641 CGTAGAATTGTACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
154664 CATAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
154687 TATAAGATTG
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:157219 original size:2 final size:2
Alignment explanation
Indices: 157212--157246 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
157202 TAGAGTAAAC
157212 TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
157247 GGGTAAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:159056 original size:20 final size:22
Alignment explanation
Indices: 159011--159068 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
159001 GCATGGGTAG
159011 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
159035 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
159055 TGTATCGATGCACT
1 TGCATCGATGCACT
159069 TCAAAGGGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:160648 original size:23 final size:23
Alignment explanation
Indices: 160622--160685 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
160612 GAACATTATA
*
160622 TGGCACTACGGTGCATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
*
160645 TGGCACTTCGGTGCATTTCTATG
1 TGGCACTTCGGTGCATTTCTACG
*
160668 CGGCACTTCGGTGCATTT
1 TGGCACTTCGGTGCATTT
160686 ACATGAGCTG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.14, C:0.25, G:0.27, T:0.34
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:163589 original size:136 final size:137
Alignment explanation
Indices: 163374--163700 Score: 378
Period size: 136 Copynumber: 2.4 Consensus size: 137
163364 TAGCTCGATT
* * * * *
163374 CGAACTCATCCGACAAAGGGAGAATAAGTTCATAATGAGAATAGCTTGTTCGACCTATCACTTGA
1 CGAACTCATCCGATAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTTCA
*** * ** * *
163439 TTCATGGCATTTCGAATCAGTGACGCCTCACTTAAGGGAATGACATTT-CAGATGGAGAGTTCAT
66 TTCACAACACTTCGAATCAGCAACACCTCACTTAAGGGAATAACATTTCCAG-TGGAGAGTTCAT
163503 AATGA-AA
130 AATGAGAA
* *
163510 CGAACTCATCTGATAGAGAGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTATTC-C-TC
1 CGAACTCATCCGATAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTA-TCACTTC
* * * * *
163573 ATTTCACAACACTTCGAATCAGCAACACCTCGCTTGAGGGATTAACATTTCCAGTGTAGAGTTCG
65 A-TTCACAACACTTCGAATCAGCAACACCTCACTTAAGGGAATAACATTTCCAGTGGAGAGTTCA
163638 TAATGAGAA
129 TAATGAGAA
* * *
163647 -GAACTCATCCGAT-GAGGGATAAGAAGTTCATAATGAGAAGAACTTGTTCAACCT
1 CGAACTCATCCGATAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCT
163701 TAGCTTGTTT
Statistics
Matches: 162, Mismatches: 25, Indels: 9
0.83 0.13 0.05
Matches are distributed among these distances:
135 39 0.24
136 116 0.72
137 7 0.04
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (137 bp):
CGAACTCATCCGATAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTTCA
TTCACAACACTTCGAATCAGCAACACCTCACTTAAGGGAATAACATTTCCAGTGGAGAGTTCATA
ATGAGAA
Found at i:163810 original size:42 final size:41
Alignment explanation
Indices: 163710--163821 Score: 127
Period size: 42 Copynumber: 2.7 Consensus size: 41
163700 TTAGCTTGTT
* * * * *
163710 TCCATCATATAAGGAGTTGGAACAACACCGACTTTTGTTCG
1 TCCATCACATAAGGAGTTGGATCAACACCGACTTTCGCTCA
*
163751 TCCATCACATAAGGAGTTGGATCAACATC-ATCATTTCGCTCA
1 TCCATCACATAAGGAGTTGGATCAACACCGA-C-TTTCGCTCA
* *
163793 TCCATCACATAAGGAGTTAGATCAGCACC
1 TCCATCACATAAGGAGTTGGATCAACACC
163822 ACCTTCAATC
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
40 1 0.02
41 27 0.45
42 32 0.53
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (41 bp):
TCCATCACATAAGGAGTTGGATCAACACCGACTTTCGCTCA
Found at i:168959 original size:190 final size:190
Alignment explanation
Indices: 168591--168960 Score: 476
Period size: 190 Copynumber: 1.9 Consensus size: 190
168581 AGATAAATTT
* * **
168591 TAATTTGAATATTAGTAGGATAATTACTCTTTTAATAAATCAACTTAAAAATGTATTTATTATTT
1 TAATTTGAATATTAGTAGGATAATTAATCTTTAAATAAATCAACTTAAAAATGTATTTATTACCT
* ** *
168656 TTTTAATTTTAAATATTAAAAGATAATTATATACTTTTGTATATTTCAAATTAAAATAATATTTG
66 TTTTAACTTTAAATATTAAAAGATAATTATATACTTTTAAATATTTCAAATTAAAATAATATTTA
* * * *
168721 TTTAAATTTGAATAGTAATAGGAGTTTACATTTTGACCATTGTAAATTAAGTATATTATC
131 TTTAAATTTGAATAGTAAAAAGAGTTTACATTATGAACATTGTAAATTAAGTATATTATC
** * *
168781 TAATTTGAATATTAGTAGGATAATTAATCTTTAAATATGTCAA-TTTAAAATGGTATTTGTTACC
1 TAATTTGAATATTAGTAGGATAATTAATCTTTAAATAAATCAACTTAAAAAT-GTATTTATTACC
* * *
168845 TTTTTAACTTTGAATATT-AAAGATAGTTATATACTTTTAAATATTTTAAATTAAAATAATATTT
65 TTTTTAACTTTAAATATTAAAAGATAATTATATACTTTTAAATATTTCAAATTAAAATAATATTT
* * * * *
168909 ATTTAAGTTTGAATGGTAAAAATAGTTTTATC-TTATGAATATTTTAAATTAA
130 ATTTAAATTTGAATAGTAAAAAGAG-TTTA-CATTATGAACATTGTAAATTAA
168961 AAGATATTAT
Statistics
Matches: 153, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
189 68 0.44
190 84 0.55
191 1 0.01
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (190 bp):
TAATTTGAATATTAGTAGGATAATTAATCTTTAAATAAATCAACTTAAAAATGTATTTATTACCT
TTTTAACTTTAAATATTAAAAGATAATTATATACTTTTAAATATTTCAAATTAAAATAATATTTA
TTTAAATTTGAATAGTAAAAAGAGTTTACATTATGAACATTGTAAATTAAGTATATTATC
Found at i:179241 original size:3 final size:3
Alignment explanation
Indices: 179233--179296 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
179223 GCAAAAATTG
* **
179233 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
179277 TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA
179297 CGGAAAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 5 0.10
3 43 0.84
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:179288 original size:32 final size:32
Alignment explanation
Indices: 179235--179298 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
179225 AAAAATTGTA
*
179235 ATAATAAATAATAATAAAATAATAAGATAACG
1 ATAATAAATAATAATAAAATAATAAAATAACG
179267 ATAAT-AATAATAATAATAATAATAAAATAACG
1 ATAATAAATAATAATAA-AATAATAAAATAACG
179299 GAAAAAAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 11 0.37
32 19 0.63
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.27
Consensus pattern (32 bp):
ATAATAAATAATAATAAAATAATAAAATAACG
Found at i:179665 original size:46 final size:45
Alignment explanation
Indices: 179465--179870 Score: 268
Period size: 40 Copynumber: 9.4 Consensus size: 45
179455 ACACTGTTCA
* * ** * **
179465 TACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGATTCC
1 TACGTGATGAGGAGATCTGGTTATCT-AAGGTGATGACACGGCTCC
* * *
179511 TACGTGATGAGGACG-GCTGATTATCT-AGG-G-TGACACGGCTCA
1 TACGTGATGAGGA-GATCTGGTTATCTAAGGTGATGACACGGCTCC
* *
179553 TACGTGATGAGGAGATCTGG---TC--AGCTGATGACACGGCTCA
1 TACGTGATGAGGAGATCTGGTTATCTAAGGTGATGACACGGCTCC
* * ** * *
179593 TACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCC
1 TACGTGATGAGGAGATCTGGTTATCT-AAGGTGATGACACGGCTCC
* *
179639 TACGTGATGAGGACG-GCTGGTTATCTATGGT--TGACACGGCTCC
1 TACGTGATGAGGA-GATCTGGTTATCTAAGGTGATGACACGGCTCC
* *
179682 TACGTGATGAGGAGATCTGG---TC--AGCTGATGACACGGCTCA
1 TACGTGATGAGGAGATCTGGTTATCTAAGGTGATGACACGGCTCC
* * ** * * *
179722 TACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCT
1 TACGTGATGAGGAGATCTGGTTATCT-AAGGTGATGACACGGCTCC
* *
179768 TACGTGATGAGGACG-GCTGGTTATCTATGGT--TGACACGGCTCC
1 TACGTGATGAGGA-GATCTGGTTATCTAAGGTGATGACACGGCTCC
* *
179811 TACGTGATGAGGAGATCTGG---TC--AGCTGATGACACGGCTCA
1 TACGTGATGAGGAGATCTGGTTATCTAAGGTGATGACACGGCTCC
* *
179851 TACGTGATGAAGAGTTCTGG
1 TACGTGATGAGGAGATCTGG
179871 CCATCTAAAG
Statistics
Matches: 287, Mismatches: 49, Indels: 54
0.74 0.13 0.14
Matches are distributed among these distances:
38 6 0.02
39 3 0.01
40 92 0.32
41 1 0.00
42 26 0.09
43 58 0.20
44 3 0.01
45 8 0.03
46 87 0.30
47 3 0.01
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (45 bp):
TACGTGATGAGGAGATCTGGTTATCTAAGGTGATGACACGGCTCC
Found at i:179744 original size:129 final size:129
Alignment explanation
Indices: 179462--179881 Score: 788
Period size: 129 Copynumber: 3.3 Consensus size: 129
179452 ACGACACTGT
*
179462 TCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGATTCCTACGTGATGAGGACGG
1 TCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
* * *
179527 CTGATTATCTA-GGGTGACACGGCTCATACGTGATGAGGAGATCTGGTCAGCTGATGACACGGC
66 CTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGCTGATGACACGGC
179590 TCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
1 TCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
179655 CTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGCTGATGACACGGC
66 CTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGCTGATGACACGGC
*
179719 TCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCTTACGTGATGAGGACGG
1 TCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
179784 CTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGCTGATGACACGGC
66 CTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGCTGATGACACGGC
179848 TCATACGTGATGAAGAGTTCTGGCCATCTAAAGG
1 TCATACGTGATGAAGAGTTCTGGCCATCTAAAGG
179882 ATTTATGGTT
Statistics
Matches: 286, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
128 74 0.26
129 212 0.74
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (129 bp):
TCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
CTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGCTGATGACACGGC
Found at i:179939 original size:28 final size:28
Alignment explanation
Indices: 179889--179942 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
179879 AGGATTTATG
* *
179889 GTTTCAAGAGAAACCAAATCAAAGATTT
1 GTTTCAAAAGAAACCAAACCAAAGATTT
179917 GTTTCAAAAGAAA-CAAACCCAAAGAT
1 GTTTCAAAAGAAACCAAA-CCAAAGAT
179943 GATATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.20
Consensus pattern (28 bp):
GTTTCAAAAGAAACCAAACCAAAGATTT
Found at i:180361 original size:15 final size:15
Alignment explanation
Indices: 180337--180371 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
180327 AAGATGATCT
*
180337 TGTTTTAAGAGAAAA
1 TGTTTCAAGAGAAAA
180352 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
180367 TGTTT
1 TGTTT
180372 TTAATTGTAA
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:0.40, C:0.03, G:0.20, T:0.37
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:180610 original size:62 final size:63
Alignment explanation
Indices: 180539--180662 Score: 178
Period size: 63 Copynumber: 2.0 Consensus size: 63
180529 AAGGTTGGTA
* * * *
180539 TTTTCAAAAGAAGTTGTC-TCGAGAGACAAAATTTTGTTTCAAAGGAAACAAACTCACAGATT
1 TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATT
* * *
180601 TTTTCAAAAGAAATTGTCTTTAAGAGATAAAATTTTGTTTCAAAAGAAACATACTCAAAGAT
1 TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT
180663 GAATCACATC
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
62 17 0.31
63 37 0.69
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (63 bp):
TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATT
Found at i:180962 original size:64 final size:64
Alignment explanation
Indices: 180882--181176 Score: 509
Period size: 64 Copynumber: 4.5 Consensus size: 64
180872 TCATTTTAAG
* *
180882 AGAAACAGATTCAAAGATTTTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAA
1 AGAAACAAACTCAAAGATTTTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAA
180946 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAAACTCAAAGA--TTT-TTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
181011 AA
63 AA
181013 AGAAACAAACTCAAAGATTTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTC
1 AGAAACAAACTCAAAGA---TTT-TTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTC
181078 CAA
62 CAA
181081 AGAAACAAACTCAAAGATTTTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAA
1 AGAAACAAACTCAAAGATTTTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAA
181145 AGAAACAAACTCAAAGATTTTTTCAAAAGAAA
1 AGAAACAAACTCAAAGATTTTTTCAAAAGAAA
181177 CATCTCAAAG
Statistics
Matches: 225, Mismatches: 2, Indels: 8
0.96 0.01 0.03
Matches are distributed among these distances:
64 91 0.40
65 3 0.01
66 3 0.01
67 61 0.27
68 67 0.30
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.30
Consensus pattern (64 bp):
AGAAACAAACTCAAAGATTTTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAA
Found at i:181183 original size:26 final size:27
Alignment explanation
Indices: 181138--181193 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
181128 CAAAATTTTG
*
181138 TTTCCAAAGAAACAAACTCAAAGATTT
1 TTTCAAAAGAAACAAACTCAAAGATTT
*
181165 TTTCAAAAGAAAC-ATCTCAAAGATTT
1 TTTCAAAAGAAACAAACTCAAAGATTT
181191 TTT
1 TTT
181194 TTTCACAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.32
Consensus pattern (27 bp):
TTTCAAAAGAAACAAACTCAAAGATTT
Found at i:181194 original size:27 final size:28
Alignment explanation
Indices: 181128--181194 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 28
181118 TTAAGAGAGA
*
181128 CAAA-ATTTTGTTTCCAAAGAAACAAACT
1 CAAAGATTTT-TTTCAAAAGAAACAAACT
*
181156 CAAAGA-TTTTTTCAAAAGAAAC-ATCT
1 CAAAGATTTTTTTCAAAAGAAACAAACT
181182 CAAAGATTTTTTT
1 CAAAGATTTTTTT
181195 TTCACAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 9 0.26
27 18 0.51
28 7 0.20
29 1 0.03
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.34
Consensus pattern (28 bp):
CAAAGATTTTTTTCAAAAGAAACAAACT
Found at i:181422 original size:138 final size:141
Alignment explanation
Indices: 181109--181477 Score: 559
Period size: 138 Copynumber: 2.6 Consensus size: 141
181099 TTTTTCAAAA
* * * * * * *
181109 GAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTTCAAAAG
1 GAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGACTCAAAGA-TTTTTCAAAAG
181174 AAAC-ATCTCAAAGATTTTTTTTTCACAAAATTGTCTCAAGAAAGACAAAACTTTGTTTCAGACT
65 AAACAATCTCAAAGA--TTTTTTTCACAAAATTGTCTCAAGAAAGACAAAACTTTGTTTCAGACT
* *
181238 CAAGGATTTTTCAC
128 CAAAGACTTTTCAC
*
181252 GAAATTGTCTCAAGAGAAACAAAACTTTGTTTCAAAATAAATAGACTCAAAGATTTTTCAAAAGA
1 GAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGACTCAAAGATTTTTCAAAAGA
*
181317 AACAATCTCAAAGATTTTTTTCACAAAATTGTCTCAAGAGAGAC-AAAC-TTGTTTCAGACTCAA
66 AACAATCTCAAAGATTTTTTTCACAAAATTGTCTCAAGAAAGACAAAACTTTGTTTCAGACTCAA
181380 AG-CTTTTCAC
131 AGACTTTTCAC
181390 GAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGACTCAAAGATTTTTCAAAAGA
1 GAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGACTCAAAGATTTTTCAAAAGA
*
181455 AACAA-CTCAAAGATATTTATTCA
66 AACAATCTCAAAGAT-TTTTTTCA
181478 AAAGGAACAA
Statistics
Matches: 211, Mismatches: 13, Indels: 9
0.91 0.06 0.04
Matches are distributed among these distances:
137 9 0.04
138 83 0.39
139 16 0.08
140 4 0.02
141 29 0.14
142 15 0.07
143 55 0.26
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.30
Consensus pattern (141 bp):
GAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGACTCAAAGATTTTTCAAAAGA
AACAATCTCAAAGATTTTTTTCACAAAATTGTCTCAAGAAAGACAAAACTTTGTTTCAGACTCAA
AGACTTTTCAC
Found at i:181448 original size:26 final size:25
Alignment explanation
Indices: 181419--181566 Score: 111
Period size: 28 Copynumber: 5.5 Consensus size: 25
181409 CAAAACTTTG
* *
181419 TTTCAAAATAAATAGACTCAAAGATT
1 TTTCAAAAGAAACA-ACTCAAAGATT
181445 TTTCAAAAGAAACAACTCAAAGATATT
1 TTTCAAAAGAAACAACTCAAAG--ATT
* *
181472 TATTCAAAAGGAACAAACTCCAAGATTTT
1 T-TTCAAAAGAAAC-AACTCAAAGA--TT
181501 TATTCAAAATG-AACAAACTCAAAGATTT
1 T-TTCAAAA-GAAAC-AACTCAAAGA-TT
* *
181529 TTTCCAAGAGAAACAAACTCAAATATT
1 TTT-CAAAAGAAAC-AACTCAAAGATT
181556 TTT-AAAAGAAA
1 TTTCAAAAGAAA
181567 TTGTCTTTAA
Statistics
Matches: 105, Mismatches: 8, Indels: 19
0.80 0.06 0.14
Matches are distributed among these distances:
25 15 0.14
26 12 0.11
27 13 0.12
28 32 0.30
29 32 0.30
30 1 0.01
ACGTcount: A:0.50, C:0.14, G:0.08, T:0.28
Consensus pattern (25 bp):
TTTCAAAAGAAACAACTCAAAGATT
Found at i:181502 original size:29 final size:29
Alignment explanation
Indices: 181420--181559 Score: 148
Period size: 29 Copynumber: 5.0 Consensus size: 29
181410 AAAACTTTGT
* * *
181420 TTCAAAATAAATAGACTCAAAGA--TTT-
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
*
181446 TTCAAAAGAAAC-AACTCAAAGATATTTA
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
* *
181474 TTCAAAAGGAACAAACTCCAAGATTTTTA
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
181503 TTCAAAATG-AACAAACTCAAAGATTTTT-
1 TTCAAAA-GAAACAAACTCAAAGATTTTTA
* * *
181531 TCCAAGAGAAACAAACTCAAATATTTTTA
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
181560 AAAGAAATTG
Statistics
Matches: 97, Mismatches: 10, Indels: 11
0.82 0.08 0.09
Matches are distributed among these distances:
25 9 0.09
26 10 0.10
27 4 0.04
28 34 0.35
29 39 0.40
30 1 0.01
ACGTcount: A:0.49, C:0.15, G:0.08, T:0.29
Consensus pattern (29 bp):
TTCAAAAGAAACAAACTCAAAGATTTTTA
Found at i:181544 original size:57 final size:57
Alignment explanation
Indices: 181420--181559 Score: 148
Period size: 57 Copynumber: 2.5 Consensus size: 57
181410 AAAACTTTGT
* * *
181420 TTCAAAATAAATAGACTCAAAGA--TTT-TTCAAAAGAAACAACTCAAAGATATTTA
1 TTCAAAAGAAACAAACTCAAAGATTTTTATTCAAAAGAAACAACTCAAAGATATTTA
* *
181474 TTCAAAAGGAACAAACTCCAAGATTTTTATTCAAAATG-AACAAACTCAAAGAT-TTT-
1 TTCAAAAGAAACAAACTCAAAGATTTTTATTCAAAA-GAAAC-AACTCAAAGATATTTA
* *
181530 TTCCAAGAGAAACAAACTCAAATATTTTTA
1 TT-CAAAAGAAACAAACTCAAAGATTTTTA
181560 AAAGAAATTG
Statistics
Matches: 71, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
54 18 0.25
56 5 0.07
57 36 0.51
58 12 0.17
ACGTcount: A:0.49, C:0.15, G:0.08, T:0.29
Consensus pattern (57 bp):
TTCAAAAGAAACAAACTCAAAGATTTTTATTCAAAAGAAACAACTCAAAGATATTTA
Found at i:181891 original size:36 final size:36
Alignment explanation
Indices: 181807--181910 Score: 124
Period size: 36 Copynumber: 3.0 Consensus size: 36
181797 GAGAAAATGA
* * *
181807 TGTCTCAAGCGAGACGAAATTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
* **
181841 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
*
181877 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAA
181911 ACGATCTCAA
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 19 0.33
35 10 0.17
36 29 0.50
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
Found at i:181938 original size:36 final size:36
Alignment explanation
Indices: 181808--181926 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 36
181798 AGAAAATGAT
* * * *
181808 GTCTCAAGCGAGACGAAATTTG-CTTTA-AGATATA-
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGA-AAAC
* **
181842 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
* *
181878 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
181913 GATCTCAAGTGAGA
1 G-TCTCAAGTGAGA
181927 TCAACTTTGT
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
34 19 0.28
35 12 0.17
36 38 0.55
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (36 bp):
GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
Found at i:182057 original size:105 final size:102
Alignment explanation
Indices: 181878--182111 Score: 276
Period size: 105 Copynumber: 2.3 Consensus size: 102
181868 TAGAGAAATT
* *
181878 GTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAATG
1 GTCTCAAGCGAGACAAAATTTG-TTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATG
* *
181943 TGAAACAAATTCGAAATTTGGATCTCAAAGG-GAAAAG
65 TGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAAG
* * *
181980 GTCTCAAGCGAGCCAAAATTTGTTTTGAAAGAAACAACAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACAAAATTTGTTTTG--AG-AA-AACAATCTCAA-GTGAGATCAACTTTG-TT
* * *
182044 TAA-GTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAAT
60 TAATGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAAG
**
182086 GTCTCAAGCGAGACGCAATTTGTTTT
1 GTCTCAAGCGAGACAAAATTTGTTTT
182112 AAAATTCTCA
Statistics
Matches: 112, Mismatches: 13, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
101 5 0.04
102 20 0.18
103 2 0.02
104 4 0.04
105 49 0.44
106 32 0.29
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (102 bp):
GTCTCAAGCGAGACAAAATTTGTTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATGT
GAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAAG
Done.