Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 146 of 208
Found at i:44456072 original size:45 final size:45
Alignment explanation
Indices: 44455887--44456074 Score: 220
Period size: 45 Copynumber: 4.2 Consensus size: 45
44455877 AATAATAACA
* * * *
44455887 GATACACAGTGG-ATCAGCACATAGC-ACCACCCTTATAGTCAAT
1 GATACCCAGTGGAATCAGCACACAGCAACCACCTTTATAATCAAT
* * * * * *
44455930 GATACTCGGTGGAATCAACACATAGCAACCACCTTCATAATTAAT
1 GATACCCAGTGGAATCAGCACACAGCAACCACCTTTATAATCAAT
* *
44455975 -AGTACCCGGTGGAATCAGCACACAACAACCACCTTTATAATCAAT
1 GA-TACCCAGTGGAATCAGCACACAGCAACCACCTTTATAATCAAT
*
44456020 CATACCCAGTGGAATCAGCACACAGCAACCACCTTTATAATCAAT
1 GATACCCAGTGGAATCAGCACACAGCAACCACCTTTATAATCAAT
*
44456065 GGTACCCAGT
1 GATACCCAGT
44456075 ACACGTAGTA
Statistics
Matches: 124, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
43 10 0.08
44 13 0.10
45 100 0.81
46 1 0.01
ACGTcount: A:0.36, C:0.28, G:0.14, T:0.21
Consensus pattern (45 bp):
GATACCCAGTGGAATCAGCACACAGCAACCACCTTTATAATCAAT
Found at i:44460825 original size:18 final size:18
Alignment explanation
Indices: 44460802--44460839 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
44460792 TTAAGATGAG
44460802 AAATGAAAAGAAATTTTC
1 AAATGAAAAGAAATTTTC
44460820 AAATGAAAAGAAATTTTC
1 AAATGAAAAGAAATTTTC
44460838 AA
1 AA
44460840 GTGATTATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.58, C:0.05, G:0.11, T:0.26
Consensus pattern (18 bp):
AAATGAAAAGAAATTTTC
Found at i:44471242 original size:11 final size:11
Alignment explanation
Indices: 44471220--44471255 Score: 63
Period size: 11 Copynumber: 3.2 Consensus size: 11
44471210 AACAAATCCT
44471220 CTCTCAAATTTC
1 CTCTC-AATTTC
44471232 CTCTCAATTTC
1 CTCTCAATTTC
44471243 CTCTCAATTTC
1 CTCTCAATTTC
44471254 CT
1 CT
44471256 TCCAAATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 19 0.79
12 5 0.21
ACGTcount: A:0.19, C:0.36, G:0.00, T:0.44
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:44471272 original size:11 final size:11
Alignment explanation
Indices: 44471219--44471274 Score: 55
Period size: 11 Copynumber: 5.0 Consensus size: 11
44471209 AAACAAATCC
44471219 TCTCTCAAATT
1 TCTCTCAAATT
44471230 TCCTCTC-AATT
1 T-CTCTCAAATT
44471241 TCCTCTC-AATT
1 T-CTCTCAAATT
44471252 TC-CTTCCAAATT
1 TCTC-T-CAAATT
44471264 TCTCTCAAATT
1 TCTCTCAAATT
44471275 CGTATTTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
9 1 0.03
10 2 0.05
11 24 0.60
12 12 0.30
13 1 0.03
ACGTcount: A:0.23, C:0.32, G:0.00, T:0.45
Consensus pattern (11 bp):
TCTCTCAAATT
Found at i:44471274 original size:23 final size:22
Alignment explanation
Indices: 44471219--44471274 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
44471209 AAACAAATCC
44471219 TCTCTCAAATTTCCTCTCAATT
1 TCTCTCAAATTTCCTCTCAATT
44471241 TCCTCTC-AATTTCCT-TCCAAATT
1 T-CTCTCAAATTTCCTCT-C-AATT
44471264 TCTCTCAAATT
1 TCTCTCAAATT
44471275 CGTATTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
21 1 0.03
22 15 0.50
23 14 0.47
ACGTcount: A:0.23, C:0.32, G:0.00, T:0.45
Consensus pattern (22 bp):
TCTCTCAAATTTCCTCTCAATT
Found at i:44474230 original size:9 final size:9
Alignment explanation
Indices: 44474215--44474245 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
44474205 AACATCATTA
44474215 TCCTCATCG
1 TCCTCATCG
*
44474224 TCTTCATCG
1 TCCTCATCG
44474233 TCCTCATCG
1 TCCTCATCG
44474242 TCCT
1 TCCT
44474246 TTTTGCAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.10, C:0.42, G:0.10, T:0.39
Consensus pattern (9 bp):
TCCTCATCG
Found at i:44476508 original size:13 final size:13
Alignment explanation
Indices: 44476485--44476525 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
44476475 AGATAAATAC
44476485 AAATGTAAGAAAG
1 AAATGTAAGAAAG
*
44476498 AAAT-TACAGAAAT
1 AAATGTA-AGAAAG
44476511 AAATGTAAGAAAG
1 AAATGTAAGAAAG
44476524 AA
1 AA
44476526 TGCCTATGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 2 0.08
13 20 0.83
14 2 0.08
ACGTcount: A:0.63, C:0.02, G:0.17, T:0.17
Consensus pattern (13 bp):
AAATGTAAGAAAG
Found at i:44477633 original size:20 final size:20
Alignment explanation
Indices: 44477608--44477645 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
44477598 CACTACTGGG
44477608 ATATCAGAGAAAGAAAAAAT
1 ATATCAGAGAAAGAAAAAAT
44477628 ATATCAGAGAAAGAAAAA
1 ATATCAGAGAAAGAAAAA
44477646 TAAAACAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.66, C:0.05, G:0.16, T:0.13
Consensus pattern (20 bp):
ATATCAGAGAAAGAAAAAAT
Found at i:44478394 original size:21 final size:21
Alignment explanation
Indices: 44478370--44478416 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
44478360 ATGCCCTATT
*
44478370 GGAAGAACCAGAATCCCCACC
1 GGAAGAACCACAATCCCCACC
* *
44478391 GGAAGAACCACAATCGCCGCC
1 GGAAGAACCACAATCCCCACC
44478412 GGAAG
1 GGAAG
44478417 CTGGACAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.34, G:0.26, T:0.04
Consensus pattern (21 bp):
GGAAGAACCACAATCCCCACC
Found at i:44478715 original size:14 final size:15
Alignment explanation
Indices: 44478696--44478757 Score: 53
Period size: 14 Copynumber: 4.3 Consensus size: 15
44478686 CCCTAATCAT
*
44478696 AACCCTTAACT-TAA
1 AACCCTAAACTCTAA
44478710 AACCCTAAACTCT-A
1 AACCCTAAACTCTAA
*
44478724 AA-CCTAAAAAC-CTTA
1 AACCCT--AAACTCTAA
44478739 AACCCTAAAC-CTAA
1 AACCCTAAACTCTAA
44478753 AACCC
1 AACCC
44478758 CCAAAACCTA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
13 3 0.07
14 27 0.66
15 8 0.20
16 3 0.07
ACGTcount: A:0.47, C:0.34, G:0.00, T:0.19
Consensus pattern (15 bp):
AACCCTAAACTCTAA
Found at i:44478734 original size:22 final size:22
Alignment explanation
Indices: 44478708--44478902 Score: 180
Period size: 22 Copynumber: 8.6 Consensus size: 22
44478698 CCCTTAACTT
*
44478708 AAAACCCTAAACTCTAAACCTA
1 AAAACCCTAAACCCTAAACCTA
*
44478730 AAAACCTTAAACCCTAAACCTA
1 AAAACCCTAAACCCTAAACCTA
* * *
44478752 AAACCCCCAAAACCTAAACCTA
1 AAAACCCTAAACCCTAAACCTA
* *
44478774 AAAACCCTAAACACTAAACTTA
1 AAAACCCTAAACCCTAAACCTA
*
44478796 AAAACTCC-AAACCCTAATAATTAACTTA
1 AAAAC-CCTAAACCC---T-A--AACCTA
44478824 AAAACCAC-AAACCCTAAACCTA
1 AAAACC-CTAAACCCTAAACCTA
* * *
44478846 AAAACCATAAACCCTTAACTTA
1 AAAACCCTAAACCCTAAACCTA
*
44478868 AAAACCAC-AAACCCTAAACTTA
1 AAAACC-CTAAACCCTAAACCTA
44478890 AAAACCCTAAACC
1 AAAACCCTAAACC
44478903 GTTAATACTG
Statistics
Matches: 144, Mismatches: 18, Indels: 22
0.78 0.10 0.12
Matches are distributed among these distances:
21 1 0.01
22 118 0.82
23 2 0.01
24 1 0.01
25 2 0.01
26 1 0.01
27 1 0.01
28 18 0.12
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (22 bp):
AAAACCCTAAACCCTAAACCTA
Found at i:44478769 original size:29 final size:29
Alignment explanation
Indices: 44478709--44478775 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
44478699 CCTTAACTTA
*
44478709 AAACCCTAAACTCTAAACCTAAAAACCTT
1 AAACCCTAAACTCTAAACCCAAAAACCTT
*
44478738 AAACCCTAAAC-CTAAAACCCCCAAAACC-T
1 AAACCCTAAACTCT-AAA-CCCAAAAACCTT
44478767 AAA-CCTAAA
1 AAACCCTAAA
44478776 AACCCTAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 8 0.24
29 18 0.53
30 8 0.24
ACGTcount: A:0.51, C:0.34, G:0.00, T:0.15
Consensus pattern (29 bp):
AAACCCTAAACTCTAAACCCAAAAACCTT
Found at i:44478842 original size:94 final size:94
Alignment explanation
Indices: 44478728--44478902 Score: 237
Period size: 94 Copynumber: 1.9 Consensus size: 94
44478718 ACTCTAAACC
** * *
44478728 TAAAAACCTTAAACCCTAAACCTAAAACCCCCAAAACCTAAACCTAAAAACC-CTAAACACTAAA
1 TAAAAACCACAAACCCTAAACCTAAAAACCACAAAACCTAAACCTAAAAACCAC-AAACACTAAA
44478792 CTTAAAAACTCC-AAACCCTAATAATTAACT
65 CTTAAAAAC-CCTAAACCCTAATAATTAACT
* * * * *
44478822 TAAAAACCACAAACCCTAAACCTAAAAACCATAAACCCTTAACTTAAAAACCACAAACCCTAAAC
1 TAAAAACCACAAACCCTAAACCTAAAAACCACAAAACCTAAACCTAAAAACCACAAACACTAAAC
44478887 TTAAAAACCCTAAACC
66 TTAAAAACCCTAAACC
44478903 GTTAATACTG
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
93 2 0.03
94 67 0.96
95 1 0.01
ACGTcount: A:0.52, C:0.31, G:0.00, T:0.17
Consensus pattern (94 bp):
TAAAAACCACAAACCCTAAACCTAAAAACCACAAAACCTAAACCTAAAAACCACAAACACTAAAC
TTAAAAACCCTAAACCCTAATAATTAACT
Found at i:44478866 original size:72 final size:72
Alignment explanation
Indices: 44478750--44478884 Score: 200
Period size: 72 Copynumber: 1.9 Consensus size: 72
44478740 ACCCTAAACC
* * *
44478750 TAAAACCCCCAAAACCTAAACCTAAAAACCCTAAACACTAAACTTAAAAACTC-CAAACCCTAAT
1 TAAAAACCACAAAACCTAAACCTAAAAACCATAAACACTAAACTTAAAAAC-CACAAACCCTAAT
44478814 AATTAACT
65 AATTAACT
* * *
44478822 TAAAAACCACAAACCCTAAACCTAAAAACCATAAACCCTTAACTTAAAAACCACAAACCCTAA
1 TAAAAACCACAAAACCTAAACCTAAAAACCATAAACACTAAACTTAAAAACCACAAACCCTAA
44478885 ACTTAAAAAC
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
71 1 0.02
72 55 0.98
ACGTcount: A:0.53, C:0.31, G:0.00, T:0.16
Consensus pattern (72 bp):
TAAAAACCACAAAACCTAAACCTAAAAACCATAAACACTAAACTTAAAAACCACAAACCCTAATA
ATTAACT
Found at i:44480617 original size:251 final size:250
Alignment explanation
Indices: 44480174--44480738 Score: 862
Period size: 251 Copynumber: 2.3 Consensus size: 250
44480164 CCCAAACATG
*
44480174 CTATTGTAGCAAAAGCGCGTCCACGTGGGCGTGATTTCACAAATTCTTCTCATAAAGCATCCTGG
1 CTATTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGG
*
44480239 TAGAAGCGATTTTGTACTATTTGCTCCAAAACATCAACTCGAAATTATTTCTTCCAGGACCAACT
66 TAGAAGCGATTTTATACTATTTGCTCCAAAACATCAACTCGAAATTATTTCTTCCAGGACCAACT
* * * *
44480304 GTAGAAAAAGCGCGTCCACGAGGGCACGATTTCAGAAATTCTTCTCAAATAGCATCCTGCTTGAA
131 GTAGAAAAAGCGCGTCCACGAGGGCACGACTTCACAAATACTTCGCAAATAGCATCCTGCTTGAA
* **
44480369 GCTTTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATAATTTTTTTAGGAC
196 GC-ATTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATAATTTTTCCAGGAC
*
44480425 CTATTGTAGCAAAAGCACGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGG
1 CTATTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGG
* **
44480490 TAGAAGCGATTTTATATTATTTGCT-CAGAAATGTCAACTCGAAATTATTTCTTCCAGGACCAAC
66 TAGAAGCGATTTTATACTATTTGCTCCA-AAACATCAACTCGAAATTATTTCTTCCAGGACCAAC
* * ** *
44480554 TGTAGCAAAAGCGCGTCCAGGAGGGTGCGACTTCACAAATACTTCGCATATAGCATCCTGCTTGA
130 TGTAGAAAAAGCGCGTCCACGAGGGCACGACTTCACAAATACTTCGCAAATAGCATCCTGCTTGA
*
44480619 AGCATTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
195 AGCATTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATAATTTTTCCAGGAC
* * * * * * * *
44480675 CTACTGTAGCAAAAGCGCGTACACGTGGGCGCGACTGCAAAAATCCTTCTGATAAATCATCCTG
1 CTATTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTG
44480739 CTTTGATTTT
Statistics
Matches: 285, Mismatches: 28, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
250 106 0.37
251 179 0.63
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (250 bp):
CTATTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGG
TAGAAGCGATTTTATACTATTTGCTCCAAAACATCAACTCGAAATTATTTCTTCCAGGACCAACT
GTAGAAAAAGCGCGTCCACGAGGGCACGACTTCACAAATACTTCGCAAATAGCATCCTGCTTGAA
GCATTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATAATTTTTCCAGGAC
Found at i:44480741 original size:125 final size:125
Alignment explanation
Indices: 44480178--44480741 Score: 715
Period size: 125 Copynumber: 4.5 Consensus size: 125
44480168 AACATGCTAT
* * *
44480178 TGTAGCAAAAGCGCGTCCACGTGGGCGTGATTTCACAAATTCTTCTCATAAAGCATCCTGGTAGA
1 TGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGA
* *
44480243 AGCGATTTTGTACTATTTGCTCCA-AAACATCAACTCGAAATTATTTCTTCCAGGACCAAC
66 AGCGATTTTATACTATTTGCT-CAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCAAC
* * * *
44480303 TGTAGAAAAAGCGCGTCCACGAGGGCACGATTTCAGAAATTCTTCTCA-AATAGCATCCTGCTTG
1 TGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTGCTTG
** * ** * *
44480367 AAGCTTTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATAATTT-TTTTAGGACCTAT
65 AAGC--GATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCAAC
* * *
44480429 TGTAGCAAAAGCACGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGGTAGA
1 TGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGA
* *
44480494 AGCGATTTTATATTATTTGCTCAGAAATGTCAACTCGAAATTATTTCTTCCAGGACCAAC
66 AGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCAAC
* * * * * * *
44480554 TGTAGCAAAAGCGCGTCCAGGAGGGTGCGACTTCACAAATACTTCGCATATAGCATCCTGCTTGA
1 TGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGA
*
44480619 AGC-ATTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TTCCAGGACCTAC
66 AGCGA--TTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCAAC
* * * * * * *
44480679 TGTAGCAAAAGCGCGTACACGTGGGCGCGACTGCAAAAATCCTTCTGATAAATCATCCTGCTT
1 TGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTT
44480742 TGATTTTATC
Statistics
Matches: 375, Mismatches: 56, Indels: 16
0.84 0.13 0.04
Matches are distributed among these distances:
124 41 0.11
125 189 0.50
126 108 0.29
127 37 0.10
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (125 bp):
TGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGA
AGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCAAC
Found at i:44482199 original size:28 final size:28
Alignment explanation
Indices: 44482137--44482200 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
44482127 TTAATATAAA
44482137 TATAA-ATATAAATATATAATTATTATT
1 TATAACATATAAATATATAATTATTATT
* *
44482164 TA-ATACATATAATTAATATAA-TATTTTT
1 TATA-ACATATAAAT-ATATAATTATTATT
44482192 TATAACATA
1 TATAACATA
44482201 ATATATTCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
26 1 0.03
27 3 0.10
28 20 0.65
29 7 0.23
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (28 bp):
TATAACATATAAATATATAATTATTATT
Found at i:44488083 original size:50 final size:50
Alignment explanation
Indices: 44487946--44488143 Score: 236
Period size: 50 Copynumber: 3.8 Consensus size: 50
44487936 ATTTGGGTAA
44487946 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAG---ATG
* *
44488002 AGAGGTCCC-TGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * * *
44488051 AGAGGTCCCCTGTAAGACTATGTCTTGGACATGGCATGGGCACCGATATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
44488101 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
44488144 TGTTATGATC
Statistics
Matches: 126, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
49 12 0.10
50 37 0.29
51 33 0.26
52 3 0.02
54 2 0.02
55 31 0.25
56 8 0.06
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.23
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:44495529 original size:50 final size:50
Alignment explanation
Indices: 44495421--44495669 Score: 300
Period size: 50 Copynumber: 4.8 Consensus size: 50
44495411 ATTTGGGTAA
*
44495421 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAG---ATG
* *
44495477 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
44495527 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
44495577 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*** * * *
44495627 AGAACACCCCATTTAAGACCATGTTTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
44495670 TGTTATGATC
Statistics
Matches: 172, Mismatches: 20, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
50 97 0.56
51 31 0.18
53 3 0.02
55 1 0.01
56 40 0.23
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:44497795 original size:23 final size:23
Alignment explanation
Indices: 44497750--44497796 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
44497740 TTAATTAATT
*
44497750 AAAAATTAAACAAGTATATAAAC
1 AAAAATTAAACAAATATATAAAC
*
44497773 AAAAATTAAAAGAAATATA-AAAC
1 AAAAATT-AAACAAATATATAAAC
44497796 A
1 A
44497797 TTTTTCCTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.70, C:0.06, G:0.04, T:0.19
Consensus pattern (23 bp):
AAAAATTAAACAAATATATAAAC
Found at i:44508544 original size:11 final size:13
Alignment explanation
Indices: 44508519--44508550 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
44508509 TAGTTTATTA
44508519 ATATTTTAAATTG
1 ATATTTTAAATTG
44508532 AT-TTTTAAA-TG
1 ATATTTTAAATTG
44508543 ATATTTTA
1 ATATTTTA
44508551 TTATTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.22
12 12 0.67
13 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (13 bp):
ATATTTTAAATTG
Found at i:44510559 original size:40 final size:41
Alignment explanation
Indices: 44510450--44510594 Score: 213
Period size: 41 Copynumber: 3.6 Consensus size: 41
44510440 AAAAATAATG
44510450 TTGAATTGCACATACGTGCCCCTGTTTGTACTTCGATACCC
1 TTGAATTGCACATACGTGCCCCTGTTTGTACTTCGATACCC
* * * *
44510491 CTGAATTTCACATACGTGCCCCTATTTGTATTTC-AGTACCC
1 TTGAATTGCACATACGTGCCCCTGTTTGTACTTCGA-TACCC
* *
44510532 TTGAA-TGCACATAAGTGCCTCTGTTTGTACTTCGATACCC
1 TTGAATTGCACATACGTGCCCCTGTTTGTACTTCGATACCC
44510572 TTGAATTGCACATACGTGCCCCT
1 TTGAATTGCACATACGTGCCCCT
44510595 ATCTATACTT
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
40 34 0.38
41 55 0.62
ACGTcount: A:0.21, C:0.28, G:0.16, T:0.34
Consensus pattern (41 bp):
TTGAATTGCACATACGTGCCCCTGTTTGTACTTCGATACCC
Found at i:44511452 original size:59 final size:59
Alignment explanation
Indices: 44511360--44511478 Score: 184
Period size: 59 Copynumber: 2.0 Consensus size: 59
44511350 GACACGAGCG
* * *
44511360 TCTGACTCAGCCGTGTGTGACACACGGCCAGGCGACACGACCGTGTGTCCCTTGTAGGT
1 TCTGACTCAGCCGTGTGTCACACACGGCCAGGCGACACGACCGTGTCTCCCCTGTAGGT
* * *
44511419 TCTGACTCAGCTGTGTGTCACACACGGCTAGGCGACATGACCGTGTCTCCCCTGTAGGT
1 TCTGACTCAGCCGTGTGTCACACACGGCCAGGCGACACGACCGTGTCTCCCCTGTAGGT
44511478 T
1 T
44511479 TAATGTATGC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.17, C:0.30, G:0.29, T:0.24
Consensus pattern (59 bp):
TCTGACTCAGCCGTGTGTCACACACGGCCAGGCGACACGACCGTGTCTCCCCTGTAGGT
Found at i:44525361 original size:22 final size:22
Alignment explanation
Indices: 44525336--44525387 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
44525326 CCCTAACCGA
*
44525336 AAAATTCAAAACTTTTAACCCC
1 AAAATTCAAAACTTCTAACCCC
* *
44525358 AAAAGTCAAAACTTCTAACCCT
1 AAAATTCAAAACTTCTAACCCC
44525380 AAAATTCA
1 AAAATTCA
44525388 GGGTGTTACA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.48, C:0.25, G:0.02, T:0.25
Consensus pattern (22 bp):
AAAATTCAAAACTTCTAACCCC
Found at i:44534083 original size:40 final size:40
Alignment explanation
Indices: 44534028--44534108 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
44534018 GCCTATTTAT
44534028 AGACTTGAGGTAGTCGTTGTCCTTAACCCTAGGTTAACTA
1 AGACTTGAGGTAGTCGTTGTCCTTAACCCTAGGTTAACTA
*
44534068 AGACTTGAGGTAGTCGTTGTCCTTAACCTTAGGTTAACTA
1 AGACTTGAGGTAGTCGTTGTCCTTAACCCTAGGTTAACTA
44534108 A
1 A
44534109 CACTCTCGAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (40 bp):
AGACTTGAGGTAGTCGTTGTCCTTAACCCTAGGTTAACTA
Found at i:44537796 original size:29 final size:29
Alignment explanation
Indices: 44537733--44537838 Score: 113
Period size: 29 Copynumber: 3.6 Consensus size: 29
44537723 GTCATTAAGG
* * *
44537733 TTTATCAGGCACTATGTGTTAGTGATTATA
1 TTTATCAGGTACTATGTATCAGTG-TTATA
* *
44537763 TTTATCAGGTACTTTGTATCGGTGTTATA
1 TTTATCAGGTACTATGTATCAGTGTTATA
* * * * *
44537792 GTTATCAAGCACTATGTTTCAGTTTTATA
1 TTTATCAGGTACTATGTATCAGTGTTATA
44537821 TTTATCAGGTACTATGTA
1 TTTATCAGGTACTATGTA
44537839 CCGATGGTGG
Statistics
Matches: 60, Mismatches: 16, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
29 41 0.68
30 19 0.32
ACGTcount: A:0.25, C:0.11, G:0.18, T:0.45
Consensus pattern (29 bp):
TTTATCAGGTACTATGTATCAGTGTTATA
Found at i:44539709 original size:68 final size:68
Alignment explanation
Indices: 44539449--44539710 Score: 337
Period size: 68 Copynumber: 3.9 Consensus size: 68
44539439 TATCTGGCAC
* * * **
44539449 CATAGCCCAACTATGGTCTTACA-ATGTATGAACCCATGTTTAATGTTTTGGTAGACTCCATATG
1 CATAGCCTAGCTATGGTCTTACACAT-TATGAACCCATGTTTAATGTCTTGGCGGACTCCATATG
*
44539513 TTGC
65 TTGT
* * * * *
44539517 CATAGCCTAGGTATGGTCTTACACAGTATGAACCCATGTTTAATGTCCTAGCGAACTCCATATGT
1 CATAGCCTAGCTATGGTCTTACACATTATGAACCCATGTTTAATGTCTTGGCGGACTCCATATGT
44539582 TGT
66 TGT
* * * * * *
44539585 CATAGCCTAGCTATGGTCATACACATTATAAACTCATGTTTAATGTCTTGGAGGACTTCATATAT
1 CATAGCCTAGCTATGGTCTTACACATTATGAACCCATGTTTAATGTCTTGGCGGACTCCATATGT
44539650 TGT
66 TGT
* *
44539653 CATATCCTAGCTATGGTCTTACACATTATGAATCCATGTTTAATGTCTTGGCGGACTC
1 CATAGCCTAGCTATGGTCTTACACATTATGAACCCATGTTTAATGTCTTGGCGGACTC
44539711 TTAATTTCGA
Statistics
Matches: 164, Mismatches: 29, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
68 163 0.99
69 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.35
Consensus pattern (68 bp):
CATAGCCTAGCTATGGTCTTACACATTATGAACCCATGTTTAATGTCTTGGCGGACTCCATATGT
TGT
Found at i:44542054 original size:14 final size:14
Alignment explanation
Indices: 44542035--44542072 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 14
44542025 TCATGTCATC
44542035 AAATATTTAAAAAA
1 AAATATTTAAAAAA
44542049 AAATATTTCTAAAAAA
1 AAATA-TT-TAAAAAA
44542065 AAATATTT
1 AAATATTT
44542073 TTTTATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 6 0.27
15 4 0.18
16 12 0.55
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (14 bp):
AAATATTTAAAAAA
Found at i:44542063 original size:16 final size:16
Alignment explanation
Indices: 44542042--44542072 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
44542032 ATCAAATATT
44542042 TAAAAAAAAATATTTC
1 TAAAAAAAAATATTTC
44542058 TAAAAAAAAATATTT
1 TAAAAAAAAATATTT
44542073 TTTTATTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (16 bp):
TAAAAAAAAATATTTC
Found at i:44561545 original size:106 final size:106
Alignment explanation
Indices: 44561379--44561958 Score: 838
Period size: 106 Copynumber: 5.5 Consensus size: 106
44561369 AGGAACAAAT
* * *
44561379 TCAAATAAACTTAGGTTGTGATTTTAAATCAGCTAACCTTTATCATATCAGCTGTGAACGTAGGT
1 TCAAAGAAACTTAGGTTGTGATCTTAAATCAGCTAACCTTTATAATATCAGCTGTGAACGTAGGT
** * *
44561444 CAGCGAGCTGTTTTAGGAGTTGCAATCTCAAATCAGCTAAC
66 CATTGAGCTGTTTTAGGAGTTGCGATCTTAAATCAGCTAAC
* *
44561485 TCAAAGAAACTTAGGTTGTGATCTTAAATCAGCTAACCTTTATAATATTAGCTGTAAACGTAGGT
1 TCAAAGAAACTTAGGTTGTGATCTTAAATCAGCTAACCTTTATAATATCAGCTGTGAACGTAGGT
* * * *
44561550 CATTGAGCTATTTTAGGAGTTGCAATATTAAATTAGCTAAC
66 CATTGAGCTGTTTTAGGAGTTGCGATCTTAAATCAGCTAAC
*
44561591 TCAAAGAAGCTTAGGTTGTGATCTTAAATCAGCTAACCTTTATAATATCAGCTGTGAACGTAGGT
1 TCAAAGAAACTTAGGTTGTGATCTTAAATCAGCTAACCTTTATAATATCAGCTGTGAACGTAGGT
* * *
44561656 CAGTGAGATGTTTTAGGAGTTGCGATCTCAAATCAGCTAAC
66 CATTGAGCTGTTTTAGGAGTTGCGATCTTAAATCAGCTAAC
* * * *
44561697 TCAAAAAAACTTAGGTTG-CAGTCTTAAATCAACTAACCTTTATAATATCAGCTATGAACGTAGG
1 TCAAAGAAACTTAGGTTGTGA-TCTTAAATCAGCTAACCTTTATAATATCAGCTGTGAACGTAGG
* * *
44561761 TCATTGAGCTATTTTAGGAGTTCCGGTCTTAAATCAGCTAAC
65 TCATTGAGCTGTTTTAGGAGTTGCGATCTTAAATCAGCTAAC
*
44561803 TCAAAGAAACTTAGGTTGTGATCGTAAATCAGCTAACCTTTATAATATCAGCTGTGAACGTAGGT
1 TCAAAGAAACTTAGGTTGTGATCTTAAATCAGCTAACCTTTATAATATCAGCTGTGAACGTAGGT
** * * *
44561868 CATCAAGCTGTTTTAGGAGTTGTGATCTTAAATAAACTAAC
66 CATTGAGCTGTTTTAGGAGTTGCGATCTTAAATCAGCTAAC
* * * *
44561909 TCAAAGAAACTTAGATTGCGATATTAAATCAGCTAACCTTTATCATATCA
1 TCAAAGAAACTTAGGTTGTGATCTTAAATCAGCTAACCTTTATAATATCA
44561959 TCACTTGTAA
Statistics
Matches: 422, Mismatches: 50, Indels: 4
0.89 0.11 0.01
Matches are distributed among these distances:
105 1 0.00
106 420 1.00
107 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (106 bp):
TCAAAGAAACTTAGGTTGTGATCTTAAATCAGCTAACCTTTATAATATCAGCTGTGAACGTAGGT
CATTGAGCTGTTTTAGGAGTTGCGATCTTAAATCAGCTAAC
Found at i:44572305 original size:5 final size:5
Alignment explanation
Indices: 44572295--44572331 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
44572285 TGCAAAGCCC
44572295 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAA-A AAA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAA
44572332 CGCTCCAAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:44572505 original size:17 final size:17
Alignment explanation
Indices: 44572480--44572519 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
44572470 GATAAGTATA
*
44572480 TATTATCATTACATTTT
1 TATTTTCATTACATTTT
44572497 TATTTTCATTACATTTT
1 TATTTTCATTACATTTT
*
44572514 CATTTT
1 TATTTT
44572520 AGTGCATTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.25, C:0.12, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTTTCATTACATTTT
Found at i:44589128 original size:19 final size:20
Alignment explanation
Indices: 44589085--44589129 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
44589075 TGCCTCTTTT
*
44589085 TGCATT-CATTTCATTCATC
1 TGCATTACATTTCATTCATA
*
44589104 TACATTACATTTCA-TCATA
1 TGCATTACATTTCATTCATA
44589123 TGCATTA
1 TGCATTA
44589130 AGTTTCATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.29, C:0.22, G:0.04, T:0.44
Consensus pattern (20 bp):
TGCATTACATTTCATTCATA
Found at i:44593116 original size:13 final size:13
Alignment explanation
Indices: 44593098--44593124 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
44593088 CTGTAATCTG
44593098 TTCTGTTTCAATT
1 TTCTGTTTCAATT
44593111 TTCTGTTTCAATT
1 TTCTGTTTCAATT
44593124 T
1 T
44593125 CACTCATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.07, T:0.63
Consensus pattern (13 bp):
TTCTGTTTCAATT
Found at i:44593392 original size:50 final size:50
Alignment explanation
Indices: 44593331--44593515 Score: 228
Period size: 51 Copynumber: 3.7 Consensus size: 50
44593321 TATCACTCGA
*
44593331 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAACTTTCCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAACTTTCCGG
* *
44593381 TTCACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAAACCTTCCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACC-AAACTTTCCGG
** * * * * *
44593432 TACATATAGTAGCTTGCACATAGTACTACACATGTGACCATTATCTAT-CGA
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA--AACTTTCCGG
* *
44593483 TACACGTAGTTGCCTGCACTTAGTACTACACAC
1 TACACGTAGTAGCCTGCACATAGTACTACACAC
44593516 TTGTTTATAG
Statistics
Matches: 114, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
50 38 0.33
51 73 0.64
52 3 0.03
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (50 bp):
TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAACTTTCCGG
Found at i:44601022 original size:6 final size:6
Alignment explanation
Indices: 44601011--44601055 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
44601001 GTTAATAAGA
* * *
44601011 TTCACC TTCACC TTCACT TTCACC TTCACA TTCA-C TTCACA TTCA
1 TTCACC TTCACC TTCACC TTCACC TTCACC TTCACC TTCACC TTCA
44601056 TCCTACCAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
5 4 0.12
6 29 0.88
ACGTcount: A:0.22, C:0.40, G:0.00, T:0.38
Consensus pattern (6 bp):
TTCACC
Found at i:44601032 original size:12 final size:12
Alignment explanation
Indices: 44601011--44601055 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
44601001 GTTAATAAGA
*
44601011 TTCACCTTCACC
1 TTCACATTCACC
*
44601023 TTCACTTTCACC
1 TTCACATTCACC
44601035 TTCACATTCA-C
1 TTCACATTCACC
44601046 TTCACATTCA
1 TTCACATTCA
44601056 TCCTACCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 11 0.35
12 20 0.65
ACGTcount: A:0.22, C:0.40, G:0.00, T:0.38
Consensus pattern (12 bp):
TTCACATTCACC
Found at i:44601034 original size:18 final size:18
Alignment explanation
Indices: 44601011--44601047 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
44601001 GTTAATAAGA
*
44601011 TTCACCTTCACCTTCACT
1 TTCACCTTCACATTCACT
44601029 TTCACCTTCACATTCACT
1 TTCACCTTCACATTCACT
44601047 T
1 T
44601048 CACATTCATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.19, C:0.41, G:0.00, T:0.41
Consensus pattern (18 bp):
TTCACCTTCACATTCACT
Found at i:44610455 original size:32 final size:31
Alignment explanation
Indices: 44610402--44610604 Score: 230
Period size: 32 Copynumber: 6.4 Consensus size: 31
44610392 AAATGGCTAC
* *
44610402 AAGCCATAAGT-ACAGTAATATGATTGGAACA
1 AAGCCATCAGTAAC-GTAATATGATTGGCACA
*
44610433 AAGCCATCAGTAACAGTGATATGATTGGCACA
1 AAGCCATCAGTAAC-GTAATATGATTGGCACA
* *
44610465 CAGCCATCAGTAACGATAATATGACAT-GCACA
1 AAGCCATCAGTAACG-TAATATGA-TTGGCACA
*
44610497 AAGCCATCAGTAACGGTAATATGATAGGCACA
1 AAGCCATCAGTAAC-GTAATATGATTGGCACA
* * *
44610529 AAGCCATCAGAAACGGTAAAATGATCGGCACA
1 AAGCCATCAGTAAC-GTAATATGATTGGCACA
* *
44610561 AAGCCATCAGTAACGATAAAATGATCGGCACA
1 AAGCCATCAGTAACG-TAATATGATTGGCACA
44610593 AAGCCATCAGTA
1 AAGCCATCAGTA
44610605 GCATTGCAGC
Statistics
Matches: 153, Mismatches: 13, Indels: 11
0.86 0.07 0.06
Matches are distributed among these distances:
31 12 0.08
32 139 0.91
33 2 0.01
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (31 bp):
AAGCCATCAGTAACGTAATATGATTGGCACA
Found at i:44610592 original size:96 final size:96
Alignment explanation
Indices: 44610402--44610604 Score: 275
Period size: 96 Copynumber: 2.1 Consensus size: 96
44610392 AAATGGCTAC
* * * * * * *
44610402 AAGCCATAAGT-ACAGTAATATGATTGGAACAAAGCCATCAGTAACAGTGATATGATTGGCACAC
1 AAGCCATCAGTAACAGTAATATGATAGGAACAAAGCCATCAGAAACAGTAAAATGATCGGCACAA
* *
44610466 AGCCATCAGTAACGATAATATGACATGCACA
66 AGCCATCAGTAACGATAAAATGACAGGCACA
* * *
44610497 AAGCCATCAGTAACGGTAATATGATAGGCACAAAGCCATCAGAAACGGTAAAATGATCGGCACAA
1 AAGCCATCAGTAACAGTAATATGATAGGAACAAAGCCATCAGAAACAGTAAAATGATCGGCACAA
44610562 AGCCATCAGTAACGATAAAATGATC-GGCACA
66 AGCCATCAGTAACGATAAAATGA-CAGGCACA
44610593 AAGCCATCAGTA
1 AAGCCATCAGTA
44610605 GCATTGCAGC
Statistics
Matches: 94, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
95 10 0.11
96 83 0.88
97 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (96 bp):
AAGCCATCAGTAACAGTAATATGATAGGAACAAAGCCATCAGAAACAGTAAAATGATCGGCACAA
AGCCATCAGTAACGATAAAATGACAGGCACA
Found at i:44610773 original size:24 final size:24
Alignment explanation
Indices: 44610746--44610792 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
44610736 GGCTCAGAAT
*
44610746 CAGTGATACAAATCACAGACAAAG
1 CAGTCATACAAATCACAGACAAAG
*
44610770 CAGTCATACCAATCACAGACAAA
1 CAGTCATACAAATCACAGACAAA
44610793 TCAATCATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.49, C:0.26, G:0.13, T:0.13
Consensus pattern (24 bp):
CAGTCATACAAATCACAGACAAAG
Found at i:44610800 original size:24 final size:24
Alignment explanation
Indices: 44610751--44610800 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
44610741 AGAATCAGTG
*
44610751 ATACAAATCACAGACAAAGCAGTC
1 ATACAAATCACAGACAAAGCAATC
* *
44610775 ATACCAATCACAGACAAATCAATC
1 ATACAAATCACAGACAAAGCAATC
44610799 AT
1 AT
44610801 TTACCCTCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.26, G:0.08, T:0.16
Consensus pattern (24 bp):
ATACAAATCACAGACAAAGCAATC
Found at i:44610820 original size:27 final size:26
Alignment explanation
Indices: 44610790--44610840 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
44610780 AATCACAGAC
*
44610790 AAATCAATCATTTACCCTCGAGGGGGA
1 AAAT-AATCATTTACCCTCCAGGGGGA
*
44610817 AAATAGTCATTTACCCTCCAGGGG
1 AAATAATCATTTACCCTCCAGGGG
44610841 CATTACGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.24
Consensus pattern (26 bp):
AAATAATCATTTACCCTCCAGGGGGA
Found at i:44615815 original size:26 final size:26
Alignment explanation
Indices: 44615786--44615855 Score: 95
Period size: 26 Copynumber: 2.7 Consensus size: 26
44615776 CATTCTGACC
*
44615786 CACAACTTGTGTAAGCAAACCCATTT
1 CACAGCTTGTGTAAGCAAACCCATTT
* * *
44615812 CACAGCTTGTGTGAGCATACCTATTT
1 CACAGCTTGTGTAAGCAAACCCATTT
*
44615838 CACAGCTCGTGTAAGCAA
1 CACAGCTTGTGTAAGCAA
44615856 CTATATATAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (26 bp):
CACAGCTTGTGTAAGCAAACCCATTT
Found at i:44617346 original size:4 final size:4
Alignment explanation
Indices: 44617337--44617362 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
44617327 TAGGGTAAAC
44617337 AAGT AAGT AAGT AAGT AAGT AAGT AA
1 AAGT AAGT AAGT AAGT AAGT AAGT AA
44617363 AGAAGAAGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (4 bp):
AAGT
Found at i:44633612 original size:26 final size:27
Alignment explanation
Indices: 44633539--44633614 Score: 68
Period size: 26 Copynumber: 2.9 Consensus size: 27
44633529 TGGAGGAAGT
**
44633539 ATACTATTACTGGCAG-CTT-TCCTAC
1 ATACTATTACTGGCAGCCTTGTTGTAC
* * * *
44633564 GATACTGTTACTAGTAGCTTTGTTGTA-
1 -ATACTATTACTGGCAGCCTTGTTGTAC
44633591 ATACTATTACTGGCAGCCTTGTTG
1 ATACTATTACTGGCAGCCTTGTTG
44633615 CGATATTGGT
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
26 33 0.87
27 2 0.05
28 3 0.08
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.39
Consensus pattern (27 bp):
ATACTATTACTGGCAGCCTTGTTGTAC
Found at i:44633791 original size:28 final size:29
Alignment explanation
Indices: 44633731--44633792 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 29
44633721 TACTGATATT
* * *
44633731 TTATTGGGCTAAGGCCTACATTATTACTG
1 TTATTGGGCTAAGGCCCACACTAGTACTG
44633760 -TATTGGGCTAAGGCCCACACT-GTACTG
1 TTATTGGGCTAAGGCCCACACTAGTACTG
44633787 TTATTG
1 TTATTG
44633793 AATAGGGCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 5 0.17
28 24 0.83
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (29 bp):
TTATTGGGCTAAGGCCCACACTAGTACTG
Found at i:44637428 original size:14 final size:15
Alignment explanation
Indices: 44637394--44637432 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
44637384 TCAGTAGAGC
44637394 TTCA-TATCTTGGAT
1 TTCATTATCTTGGAT
44637408 TTCATTATCTTGG-T
1 TTCATTATCTTGGAT
*
44637422 TTTATTATCTT
1 TTCATTATCTT
44637433 TCTTATTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 15 0.65
15 8 0.35
ACGTcount: A:0.18, C:0.13, G:0.10, T:0.59
Consensus pattern (15 bp):
TTCATTATCTTGGAT
Found at i:44643632 original size:24 final size:24
Alignment explanation
Indices: 44643600--44643651 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
44643590 TTTTCTTTAG
* *
44643600 GATCTTCTTCTAGGTCATCCTCCA
1 GATCTTCTTCAAAGTCATCCTCCA
* *
44643624 GATCTTCTTCAAAGTCTTCCTCTA
1 GATCTTCTTCAAAGTCATCCTCCA
44643648 GATC
1 GATC
44643652 CTCCTCTTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.19, C:0.31, G:0.12, T:0.38
Consensus pattern (24 bp):
GATCTTCTTCAAAGTCATCCTCCA
Found at i:44659635 original size:21 final size:24
Alignment explanation
Indices: 44659588--44659635 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
44659578 TTGAATTAAA
* *
44659588 TTATAATAATTTATACTAATTTTT
1 TTATAATAATCTATACTAATTTAT
44659612 TTATAA-AATCTATACT-A-TTAT
1 TTATAATAATCTATACTAATTTAT
44659633 TTA
1 TTA
44659636 AACTCTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 6 0.27
22 1 0.05
23 9 0.41
24 6 0.27
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (24 bp):
TTATAATAATCTATACTAATTTAT
Found at i:44663175 original size:2 final size:2
Alignment explanation
Indices: 44663168--44663196 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
44663158 CCAGACACAA
44663168 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44663197 TCATTACCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44664677 original size:11 final size:13
Alignment explanation
Indices: 44664657--44664688 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
44664647 AATAAATTAA
44664657 TAAAATATCAT-T
1 TAAAATATCATAT
44664669 TAAAA-ATCATAT
1 TAAAATATCATAT
44664681 TAAAATAT
1 TAAAATAT
44664689 TAATAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATATCATAT
Found at i:44668676 original size:50 final size:50
Alignment explanation
Indices: 44668458--44668800 Score: 316
Period size: 51 Copynumber: 6.8 Consensus size: 50
44668448 TATCGATAAA
* * *
44668458 CACGTGTGTAGTACTGTGTGAAGGCTACTATGTGTACCGATAAATA-ATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCG-TAAA-ACTTGGT
* * * * *
44668509 CACATGTGCAGTACTAAGTGAAGGCTACTATGTGTACCG-AGAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGTA-AAAC-TTGGT
* * * ***
44668560 CACGTGTGTAGTACTGTGTGAAGGCTACTACTTGTACTGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCG-TAAAACTTGGT
* * *
44668611 CACGTGTGTAGTACTATGTAAAGGCTACTACGTGAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGTAAAACTTGGT
* * * **
44668661 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGTAAAATTTAAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGTAAAACTTGGT
* * *
44668711 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGAAA-TT-GT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA-CCG-T-AAAACTTGGT
* * * * *
44668762 CACATGTGTAGTACTACGTGCAGGCTACTATGTGAACCG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCG
44668801 GTTACCATTG
Statistics
Matches: 244, Mismatches: 40, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
49 1 0.00
50 91 0.37
51 143 0.59
52 5 0.02
53 4 0.02
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGTAAAACTTGGT
Found at i:44668942 original size:75 final size:75
Alignment explanation
Indices: 44668819--44668995 Score: 261
Period size: 75 Copynumber: 2.4 Consensus size: 75
44668809 TGACTATAAA
*
44668819 GGTGGTTGCTACGTGCTGATTCCACCGTAATTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCC
1 GGTGGTTGCTAAGTGCTGATTCCACCGTAATTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCC
44668884 CCGAATCATT
66 CCGAATCATT
*
44668894 GGTGGTTGCTAAGTGCTGA-TCTCACAC-T-ATCTTAAATGTGAAAGGGGTTGCTAAGTGTTGAT
1 GGTGGTTGCTAAGTGCTGATTC-CAC-CGTAAT-TTAAATGTGAAAGGGGTTGCTAAGTGCTGAT
*
44668956 TCCCCGATTCATT
63 TCCCCGAATCATT
* *
44668969 GGTAGTTGCTAAGTGCTGAATCCACCG
1 GGTGGTTGCTAAGTGCTGATTCCACCG
44668996 ATAACGGATA
Statistics
Matches: 93, Mismatches: 4, Indels: 10
0.87 0.04 0.09
Matches are distributed among these distances:
74 5 0.05
75 85 0.91
76 3 0.03
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.32
Consensus pattern (75 bp):
GGTGGTTGCTAAGTGCTGATTCCACCGTAATTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCC
CCGAATCATT
Found at i:44669918 original size:49 final size:50
Alignment explanation
Indices: 44669828--44669924 Score: 128
Period size: 49 Copynumber: 2.0 Consensus size: 50
44669818 ACATGTGAAC
*
44669828 ATGTGATTATGTGATTCTGTGTAAGACCATAACTGAGCTATGGCATCGGT
1 ATGTGATTATGTGATTCTGTGTAAGACCATAACTGAGCTATGACATCGGT
**
44669878 ATGTGATT-TGTGATTAC-GTGTAAGACCATAGTTG-GACTATGACATCG
1 ATGTGATTATGTGATT-CTGTGTAAGACCATAACTGAG-CTATGACATCG
44669925 AGAAAACGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
48 1 0.02
49 32 0.76
50 9 0.21
ACGTcount: A:0.27, C:0.13, G:0.26, T:0.34
Consensus pattern (50 bp):
ATGTGATTATGTGATTCTGTGTAAGACCATAACTGAGCTATGACATCGGT
Found at i:44675388 original size:23 final size:22
Alignment explanation
Indices: 44675362--44675407 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
44675352 TGAATTGATA
44675362 AGTTA-TGAAACTAGAAAAAAATT
1 AGTTACTG-AACTA-AAAAAAATT
*
44675385 AGTTACTGAATTAAAAAAAATT
1 AGTTACTGAACTAAAAAAAATT
44675407 A
1 A
44675408 CATCAACAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 10 0.48
23 9 0.43
24 2 0.10
ACGTcount: A:0.57, C:0.04, G:0.11, T:0.28
Consensus pattern (22 bp):
AGTTACTGAACTAAAAAAAATT
Found at i:44677348 original size:3 final size:3
Alignment explanation
Indices: 44677331--44677412 Score: 50
Period size: 3 Copynumber: 28.7 Consensus size: 3
44677321 ACTATAAAAC
* * * *
44677331 AAT AAT ATT AGT AAT AAT AAC AAT AA- AAA AAT AA- AAT AAAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
* *
44677374 AAT AA- AAA AGAT AAT ATT AA- AAT AAT AA- AAT AAT AAT AA
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
44677413 CAAATGAATA
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
2 12 0.19
3 45 0.73
4 5 0.08
ACGTcount: A:0.71, C:0.01, G:0.02, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:44677375 original size:14 final size:14
Alignment explanation
Indices: 44677346--44677412 Score: 68
Period size: 14 Copynumber: 4.7 Consensus size: 14
44677336 TATTAGTAAT
44677346 AATAACAATAAA-AA
1 AATAA-AATAAATAA
44677360 AATAAAATAAATAA
1 AATAAAATAAATAA
44677374 AATAAAA-AAGATAA
1 AATAAAATAA-ATAA
*
44677388 TATTAAAAT-AATAA
1 -AATAAAATAAATAA
44677402 AATAATAATAA
1 AATAA-AATAA
44677413 CAAATGAATA
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
13 12 0.27
14 25 0.56
15 8 0.18
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.22
Consensus pattern (14 bp):
AATAAAATAAATAA
Found at i:44677394 original size:20 final size:19
Alignment explanation
Indices: 44677342--44677408 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 19
44677332 ATAATATTAG
*
44677342 TAATAATAACAATAAAAAAA
1 TAATATTAA-AATAAAAAAA
*
44677362 TAAAATAAATAAAATAAAAAAGA
1 T--AAT-ATTAAAATAAAAAA-A
*
44677385 TAATATTAAAATAATAAAA
1 TAATATTAAAATAAAAAAA
44677404 TAATA
1 TAATA
44677409 ATAACAAATG
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
19 6 0.15
20 13 0.32
21 3 0.07
22 12 0.29
23 7 0.17
ACGTcount: A:0.73, C:0.01, G:0.01, T:0.24
Consensus pattern (19 bp):
TAATATTAAAATAAAAAAA
Found at i:44677407 original size:8 final size:8
Alignment explanation
Indices: 44677342--44677409 Score: 55
Period size: 8 Copynumber: 7.8 Consensus size: 8
44677332 ATAATATTAG
44677342 TAATAATAA
1 TAATAA-AA
*
44677351 CAATAAAA
1 TAATAAAA
*
44677359 AAATAAAA
1 TAATAAAA
44677367 TAAATAAAA
1 T-AATAAAA
*
44677376 TAAAAAAGA
1 TAATAAA-A
44677385 TAATATTAAAA
1 T-A-A-TAAAA
44677396 TAATAAAA
1 TAATAAAA
44677404 TAATAA
1 TAATAA
44677410 TAACAAATGA
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
8 25 0.51
9 16 0.33
10 2 0.04
11 3 0.06
12 3 0.06
ACGTcount: A:0.74, C:0.01, G:0.01, T:0.24
Consensus pattern (8 bp):
TAATAAAA
Found at i:44678310 original size:30 final size:30
Alignment explanation
Indices: 44678274--44678350 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 30
44678264 TGACTCGCCA
* *
44678274 GTGTGTCTAGGCTGTGTATCATACACGACC
1 GTGTGTCTAGGCTGTGTATCACACACAACC
* * **
44678304 GTGTGTCCAGGCCGTGTATCACACACAATT
1 GTGTGTCTAGGCTGTGTATCACACACAACC
*
44678334 GTGTCTCTAGGCTGTGT
1 GTGTGTCTAGGCTGTGT
44678351 GATTCACCCC
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.18, C:0.23, G:0.27, T:0.31
Consensus pattern (30 bp):
GTGTGTCTAGGCTGTGTATCACACACAACC
Found at i:44680368 original size:28 final size:27
Alignment explanation
Indices: 44680290--44680456 Score: 239
Period size: 27 Copynumber: 6.1 Consensus size: 27
44680280 TATAATAGTC
* * *
44680290 TTTTACCTTATGGGGGTATTTTGGTCA
1 TTTTACCCTATGGGGGTATTTCGATCA
44680317 TTTTACCCTATGGGGGTATTTCGATCA
1 TTTTACCCTATGGGGGTATTTCGATCA
*
44680344 TTTTACCCTATAGGGGGCATTTCGATCA
1 TTTTACCCTAT-GGGGGTATTTCGATCA
44680372 TTTTACCCTATGGGGGGTATTTC-AGTCA
1 TTTTACCCTAT-GGGGGTATTTCGA-TCA
*
44680400 TTTTACCCTATGGGGGTATTTCAATCA
1 TTTTACCCTATGGGGGTATTTCGATCA
44680427 TTTTACCCTATGGGGGTATTTC-AGTCA
1 TTTTACCCTATGGGGGTATTTCGA-TCA
44680454 TTT
1 TTT
44680457 ATTGACCTCT
Statistics
Matches: 130, Mismatches: 6, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
26 1 0.01
27 78 0.60
28 51 0.39
ACGTcount: A:0.19, C:0.17, G:0.22, T:0.42
Consensus pattern (27 bp):
TTTTACCCTATGGGGGTATTTCGATCA
Found at i:44680373 original size:55 final size:54
Alignment explanation
Indices: 44680286--44680456 Score: 256
Period size: 55 Copynumber: 3.1 Consensus size: 54
44680276 GGGGTATAAT
* * *
44680286 AGTC-TTTTACCTTATGGGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTC
1 AGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTC
*
44680339 -GATCATTTTACCCTATAGGGGGCATTTCGATCATTTTACCCTATGGGGGGTATTTC
1 AG-TCATTTTACCCTAT-GGGGGTATTTCGATCATTTTACCCTAT-GGGGGTATTTC
*
44680395 AGTCATTTTACCCTATGGGGGTATTTCAATCATTTTACCCTATGGGGGTATTTC
1 AGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTC
44680449 AGTCATTT
1 AGTCATTT
44680457 ATTGACCTCT
Statistics
Matches: 107, Mismatches: 6, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
52 1 0.01
53 2 0.02
54 29 0.27
55 49 0.46
56 25 0.23
57 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.42
Consensus pattern (54 bp):
AGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTC
Found at i:44697186 original size:24 final size:24
Alignment explanation
Indices: 44697154--44697202 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
44697144 ACAGTCCTCG
44697154 AGCACTCCAAAGCCTATAATTGAA
1 AGCACTCCAAAGCCTATAATTGAA
44697178 AGCACTCCAAAGCCTATAATTGAA
1 AGCACTCCAAAGCCTATAATTGAA
44697202 A
1 A
44697203 AAATAACACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.24, G:0.12, T:0.20
Consensus pattern (24 bp):
AGCACTCCAAAGCCTATAATTGAA
Found at i:44698656 original size:14 final size:15
Alignment explanation
Indices: 44698635--44698668 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
44698625 ATTAGAATGT
44698635 AAAA-ATTAAA-TAA
1 AAAATATTAAATTAA
44698648 AAAATATTAAATTAA
1 AAAATATTAAATTAA
44698663 AAAATA
1 AAAATA
44698669 AATATGGCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.21
14 6 0.32
15 9 0.47
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAATATTAAATTAA
Found at i:44698659 original size:19 final size:19
Alignment explanation
Indices: 44698637--44698673 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
44698627 TAGAATGTAA
44698637 AAATTAAATAAA-AAATATT
1 AAATTAAA-AAATAAATATT
44698656 AAATTAAAAAATAAATAT
1 AAATTAAAAAATAAATAT
44698674 GGCTAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AAATTAAAAAATAAATATT
Found at i:44698663 original size:26 final size:27
Alignment explanation
Indices: 44698619--44698672 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 27
44698609 TCAAACAAAC
*
44698619 AAAAAAATTAGAATGTAAAAATTAAAT
1 AAAAAAATTAGAATGTAAAAAATAAAT
44698646 AAAAAATATTA-AAT-TAAAAAATAAAT
1 AAAAAA-ATTAGAATGTAAAAAATAAAT
44698672 A
1 A
44698673 TGGCTAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 12 0.48
27 9 0.36
28 4 0.16
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (27 bp):
AAAAAAATTAGAATGTAAAAAATAAAT
Found at i:44700769 original size:35 final size:35
Alignment explanation
Indices: 44700723--44700794 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
44700713 TACGATGTTA
44700723 GACCATAGATGAAAGATGCTATGACAACAAGGTAT
1 GACCATAGATGAAAGATGCTATGACAACAAGGTAT
*
44700758 GACCATAGATGAAAGATTCTATGACAACAAGGTAT
1 GACCATAGATGAAAGATGCTATGACAACAAGGTAT
44700793 GA
1 GA
44700795 TGAGTAAGAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.21
Consensus pattern (35 bp):
GACCATAGATGAAAGATGCTATGACAACAAGGTAT
Found at i:44701033 original size:33 final size:33
Alignment explanation
Indices: 44700974--44701037 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
44700964 TATTTCACCA
* *
44700974 GGACAGTAAACACAAAACAGAGATAGTCCATTG
1 GGACAGTAAACACAAAACAAACATAGTCCATTG
* *
44701007 GGACAGTAAACACAGAATAAACATAGTCCAT
1 GGACAGTAAACACAAAACAAACATAGTCCAT
44701038 AAAGATAGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.16
Consensus pattern (33 bp):
GGACAGTAAACACAAAACAAACATAGTCCATTG
Found at i:44714902 original size:17 final size:16
Alignment explanation
Indices: 44714874--44714926 Score: 97
Period size: 16 Copynumber: 3.2 Consensus size: 16
44714864 TTTGGTTCGC
44714874 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
44714890 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
44714907 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
44714923 TGTA
1 TGTA
44714927 ATAGCTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:44714991 original size:44 final size:45
Alignment explanation
Indices: 44714907--44714997 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
44714897 GGATTAGAGG
* * *
44714907 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
44714952 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
44714996 TG
1 TG
44714998 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:44715451 original size:122 final size:121
Alignment explanation
Indices: 44715145--44715728 Score: 1019
Period size: 121 Copynumber: 4.8 Consensus size: 121
44715135 ATCATATTTA
* *
44715145 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAAAAAAAATTCTTAATAATTA
1 AACATAATTATTATTAAATAAATTTTAATTAAACTATATAATTT-AAAAAAATTCTTAATAATTA
*
44715210 ATATTC-TTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
65 ATATTCTTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
44715266 AACATAATTATTATTAAATAAATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATAAATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
*
44715331 TATTCTTTATATTAATTTACTCACATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
44715387 AACATAATTTATTATTAAATAAATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTA
1 AACATAA-TTATTATTAAATAAATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTA
*
44715452 ATATTCTTTATATTAATTTACTCACATCATAATATATGATACTGTAAAATATAAATT
65 ATATTCTTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
44715509 AACATAATTATTATTAAATAAATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATAAATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
*
44715574 TATTCTTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
* * * * *
44715630 AACATAATATATGATTAAATATATTTTAATTGAACAATATAATTTAATAAAATTCTTAATAATTA
1 AACATAAT-TATTATTAAATAAATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTA
44715695 ATATTC-TTATATTAATTTACTCAAATCATAATAT
65 ATATTCTTTATATTAATTTACTCAAATCATAATAT
44715729 TCTTAATAAT
Statistics
Matches: 446, Mismatches: 14, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
120 25 0.06
121 244 0.55
122 177 0.40
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (121 bp):
AACATAATTATTATTAAATAAATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
TATTCTTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:44715572 original size:243 final size:242
Alignment explanation
Indices: 44715145--44715728 Score: 1035
Period size: 243 Copynumber: 2.4 Consensus size: 242
44715135 ATCATATTTA
*
44715145 AACATAA-TTATTATTAAATATATTTTAATTAAAATATATAATTTAAAAAAAATTCTTAATAATT
1 AACATAATTTATTATTAAATATATTTTAATTAAACTATATAATTT-AAAAAAATTCTTAATAATT
*
44715209 AATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATTAACATAAT
65 AATATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAAT
*
44715274 TATTATTAAATAAATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAATATTCTTT
130 TATTATTAAATAAATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAATATTCTTT
*
44715339 ATATTAATTTACTCACATCATAATATATGATACTGTAAAATATAAATT
195 ATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
44715387 AACATAATTTATTATTAAATAAATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTA
1 AACATAATTTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTA
*
44715452 ATATTCTTTATATTAATTTACTCACATCATAATATATGATACTGTAAAATATAAATTAACATAAT
66 ATATTC-TTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAAT
44715517 TATTATTAAATAAATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAATATTCTTT
130 TATTATTAAATAAATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAATATTCTTT
*
44715582 ATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
195 ATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
* * * * *
44715630 AACATAATATATGATTAAATATATTTTAATTGAACAATATAATTTAATAAAATTCTTAATAATTA
1 AACATAATTTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTA
44715695 ATATTCTTATATTAATTTACTCAAATCATAATAT
66 ATATTCTTATATTAATTTACTCAAATCATAATAT
44715729 TCTTAATAAT
Statistics
Matches: 326, Mismatches: 14, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
242 60 0.18
243 266 0.82
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (242 bp):
AACATAATTTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTA
ATATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATT
ATTATTAAATAAATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAATATTCTTTA
TATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:44715702 original size:16 final size:16
Alignment explanation
Indices: 44715681--44715749 Score: 65
Period size: 16 Copynumber: 4.4 Consensus size: 16
44715671 ATTTAATAAA
44715681 ATTCTTAATAATTAAT
1 ATTCTTAATAATTAAT
44715697 ATTCTT-AT-ATTAAT
1 ATTCTTAATAATTAAT
* *
44715711 -TTACTCAAATCA-TAAT
1 ATT-CT-TAATAATTAAT
*
44715727 ATTCTTAATAATTCAT
1 ATTCTTAATAATTAAT
44715743 ATTCTTA
1 ATTCTTA
44715750 TATTAACTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
13 2 0.05
14 8 0.19
15 6 0.14
16 24 0.56
17 3 0.07
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTCTTAATAATTAAT
Found at i:44719218 original size:43 final size:43
Alignment explanation
Indices: 44719166--44719326 Score: 322
Period size: 43 Copynumber: 3.7 Consensus size: 43
44719156 TATATTAAAG
44719166 ATTATATAATCAAAATGATTTTAATTATATTTCAATTAAAAAT
1 ATTATATAATCAAAATGATTTTAATTATATTTCAATTAAAAAT
44719209 ATTATATAATCAAAATGATTTTAATTATATTTCAATTAAAAAT
1 ATTATATAATCAAAATGATTTTAATTATATTTCAATTAAAAAT
44719252 ATTATATAATCAAAATGATTTTAATTATATTTCAATTAAAAAT
1 ATTATATAATCAAAATGATTTTAATTATATTTCAATTAAAAAT
44719295 ATTATATAATCAAAATGATTTTAATTATATTT
1 ATTATATAATCAAAATGATTTTAATTATATTT
44719327 TAATATACCT
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 118 1.00
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.45
Consensus pattern (43 bp):
ATTATATAATCAAAATGATTTTAATTATATTTCAATTAAAAAT
Found at i:44720391 original size:21 final size:21
Alignment explanation
Indices: 44720348--44720403 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
44720338 AAGCAGATGG
* *
44720348 AGCCGCTGCAAATTAATTATAT
1 AGCCACTGCAAA-CAATTATAT
*
44720370 AGCCACTGCAAACAATTGTAT
1 AGCCACTGCAAACAATTATAT
*
44720391 AGCCATTGCAAAC
1 AGCCACTGCAAAC
44720404 GGGGGAAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 19 0.63
22 11 0.37
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (21 bp):
AGCCACTGCAAACAATTATAT
Found at i:44738882 original size:51 final size:51
Alignment explanation
Indices: 44738806--44738905 Score: 173
Period size: 51 Copynumber: 2.0 Consensus size: 51
44738796 ACTTCTGAGC
* * *
44738806 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATTAGTGACA
1 AGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTAATCAGTGACA
44738857 AGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTAATCAGTGA
1 AGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTAATCAGTGA
44738906 TGAGTGGTAG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTAATCAGTGACA
Found at i:44738917 original size:37 final size:37
Alignment explanation
Indices: 44738864--44738949 Score: 136
Period size: 37 Copynumber: 2.3 Consensus size: 37
44738854 ACAAGTGACA
44738864 AGTGATAAGTGATAGCTTTAGCTACACTTATCTAATC
1 AGTGATAAGTGATAGCTTTAGCTACACTTATCTAATC
* * *
44738901 AGTGATGAGTGGTAGCTTTAGCTACACTTATCTGATC
1 AGTGATAAGTGATAGCTTTAGCTACACTTATCTAATC
*
44738938 AGTGACAAGTGA
1 AGTGATAAGTGA
44738950 CAAGTGATGA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (37 bp):
AGTGATAAGTGATAGCTTTAGCTACACTTATCTAATC
Found at i:44738987 original size:51 final size:51
Alignment explanation
Indices: 44738901--44739008 Score: 164
Period size: 51 Copynumber: 2.1 Consensus size: 51
44738891 TTATCTAATC
*
44738901 AGTGATGAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACA
1 AGTGATGAGTGGTAGCTTTAGCTACACTTATCTGATCAGGGACAAGTGACA
* * *
44738952 AGTGATGAGTGGTAGTTTTAGCTACCCTT-TCCTGATCAGGGACAAGTGGCA
1 AGTGATGAGTGGTAGCTTTAGCTACACTTAT-CTGATCAGGGACAAGTGACA
44739003 AGTGAT
1 AGTGAT
44739009 AAATGTGATC
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
50 1 0.02
51 51 0.98
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.30
Consensus pattern (51 bp):
AGTGATGAGTGGTAGCTTTAGCTACACTTATCTGATCAGGGACAAGTGACA
Found at i:44738990 original size:88 final size:88
Alignment explanation
Indices: 44738813--44738976 Score: 283
Period size: 88 Copynumber: 1.9 Consensus size: 88
44738803 AGCAGTGACA
*
44738813 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATTAGTGACAAGTGACAAGTGATAAGTGATA
1 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATAAGTGATA
44738878 GCTTTAGCTACACTTATCTAATC
66 GCTTTAGCTACACTTATCTAATC
* * *
44738901 AGTGATGAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATGAGTGGTA
1 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATAAGTGATA
*
44738966 GTTTTAGCTAC
66 GCTTTAGCTAC
44738977 CCTTTCCTGA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 71 1.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (88 bp):
AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATAAGTGATA
GCTTTAGCTACACTTATCTAATC
Found at i:44739000 original size:88 final size:88
Alignment explanation
Indices: 44738819--44739000 Score: 267
Period size: 88 Copynumber: 2.1 Consensus size: 88
44738809 GACAAGTGAT
*
44738819 AAGTGGTAGCTTTAGCTACACTTATCTGATTAGTGACAAGTGACAAGTGATAAGTGATAGCTTTA
1 AAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATAAGTGATAGCTTTA
* *
44738884 GCTACACTTATCTAATCAGTGAT
66 GCTACACTTATCTAATCAGGGAC
* * * *
44738907 GAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATGAGTGGTAGTTTTA
1 AAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATAAGTGATAGCTTTA
* *
44738972 GCTACCCTT-TCCTGATCAGGGAC
66 GCTACACTTAT-CTAATCAGGGAC
44738995 AAGTGG
1 AAGTGG
44739001 CAAGTGATAA
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
87 1 0.01
88 82 0.99
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (88 bp):
AAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATAAGTGATAGCTTTA
GCTACACTTATCTAATCAGGGAC
Found at i:44740465 original size:49 final size:48
Alignment explanation
Indices: 44740296--44740485 Score: 192
Period size: 47 Copynumber: 4.0 Consensus size: 48
44740286 CATGTGAAAA
* *
44740296 TGTGATTATGTGATTTCTATGTAAGACCATATCTGGGATATGGCATCGG
1 TGTGA-TATGTGATTACTATGTAAGACCATAGCTGGGATATGGCATCGG
* * * * * *
44740345 TGTGATATGTG-CTACTGTGTAAGACCACATCTAGGATATGGCATCAG
1 TGTGATATGTGATTACTATGTAAGACCATAGCTGGGATATGGCATCGG
* * *
44740392 CGTGATATGTGATTCCGTA-G-AAGACCATAGCTGGGCTATGGCATCGG
1 TGTGATATGTGATTAC-TATGTAAGACCATAGCTGGGATATGGCATCGG
*
44740439 TATGTGATATGTGATTAC-ATGTAAGACCATAG-TTGGATTATGGCATC
1 --TGTGATATGTGATTACTATGTAAGACCATAGCTGGGA-TATGGCATC
44740486 AAGAAAATGA
Statistics
Matches: 115, Mismatches: 19, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
47 63 0.55
48 13 0.11
49 39 0.34
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (48 bp):
TGTGATATGTGATTACTATGTAAGACCATAGCTGGGATATGGCATCGG
Found at i:44744380 original size:51 final size:51
Alignment explanation
Indices: 44744304--44744471 Score: 266
Period size: 51 Copynumber: 3.3 Consensus size: 51
44744294 ACTTCTGAGC
44744304 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
*
44744355 AGTGACAAGTGATAAGTGGAAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
* * * * *
44744406 AGTGAGAAGTGATGAGTGGTAGCTTTAGCTACCCTT-TCCTGATTAGGGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTAT-CTGATCAGTGACA
44744457 AGTGACAAGTGATAA
1 AGTGACAAGTGATAA
44744472 ATGTGATCCA
Statistics
Matches: 107, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
50 1 0.01
51 106 0.99
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.28
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
Found at i:44749238 original size:17 final size:17
Alignment explanation
Indices: 44749216--44749250 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
44749206 AAGTAAAAGT
44749216 TGACGAAATTTGTTTTA
1 TGACGAAATTTGTTTTA
44749233 TGACGAAATTTGTTTTA
1 TGACGAAATTTGTTTTA
44749250 T
1 T
44749251 AATTACTATC
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:0.29, C:0.06, G:0.17, T:0.49
Consensus pattern (17 bp):
TGACGAAATTTGTTTTA
Found at i:44749567 original size:16 final size:16
Alignment explanation
Indices: 44749546--44749577 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
44749536 AAATAAATAA
44749546 TTAAAAAATAAAAATT
1 TTAAAAAATAAAAATT
*
44749562 TTAAAAAATTAAAATT
1 TTAAAAAATAAAAATT
44749578 CTAATTCAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TTAAAAAATAAAAATT
Found at i:44761254 original size:16 final size:16
Alignment explanation
Indices: 44761230--44761263 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
44761220 TTTTGGCGGC
*
44761230 ATAGCGTGAATGGTGT
1 ATAGAGTGAATGGTGT
44761246 ATAGAGTGAATGGTGT
1 ATAGAGTGAATGGTGT
44761262 AT
1 AT
44761264 GGTCTAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (16 bp):
ATAGAGTGAATGGTGT
Found at i:44769525 original size:101 final size:101
Alignment explanation
Indices: 44769349--44769551 Score: 352
Period size: 101 Copynumber: 2.0 Consensus size: 101
44769339 TTTATATTTA
* *
44769349 TAACTTAAATCTATTCATTGTCTCTACTTTTGTGATATATTAGATATTTTTGGCGTCACTCATAA
1 TAACTTAAATCTATTCATTGTCTCTACTTGTGTGATATATTAGATATTGTTGGCGTCACTCATAA
44769414 TCTTCGATGATCCTTACCACCATGTTCAATTTTTTG
66 TCTTCGATGATCCTTACCACCATGTTCAATTTTTTG
*
44769450 TAACTTAAATCTATTCATTGTCTCTACTTGTGTGATATATTAGATATTGTTGGCGTCATTCATAA
1 TAACTTAAATCTATTCATTGTCTCTACTTGTGTGATATATTAGATATTGTTGGCGTCACTCATAA
* **
44769515 TCTTCTATGATCCTTACCACCATGTTTGATTTTTTG
66 TCTTCGATGATCCTTACCACCATGTTCAATTTTTTG
44769551 T
1 T
44769552 TTATCAAGAT
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
101 96 1.00
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.46
Consensus pattern (101 bp):
TAACTTAAATCTATTCATTGTCTCTACTTGTGTGATATATTAGATATTGTTGGCGTCACTCATAA
TCTTCGATGATCCTTACCACCATGTTCAATTTTTTG
Found at i:44775530 original size:13 final size:15
Alignment explanation
Indices: 44775499--44775533 Score: 56
Period size: 13 Copynumber: 2.5 Consensus size: 15
44775489 ATGAAACGAA
44775499 TTAAAATAAATCAAT
1 TTAAAATAAATCAAT
44775514 TTAAAA-AAATC-AT
1 TTAAAATAAATCAAT
44775527 TTAAAAT
1 TTAAAAT
44775534 TACATGTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 8 0.42
14 5 0.26
15 6 0.32
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (15 bp):
TTAAAATAAATCAAT
Found at i:44775861 original size:19 final size:20
Alignment explanation
Indices: 44775821--44775862 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
44775811 ATACATCATA
* *
44775821 AATTTAAAAAAATTGATGAT
1 AATTTAAAAAAATTAATAAT
44775841 AATTTAAAAAAA-TAATAAT
1 AATTTAAAAAAATTAATAAT
44775860 AAT
1 AAT
44775863 ACGTGATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (20 bp):
AATTTAAAAAAATTAATAAT
Found at i:44777842 original size:181 final size:180
Alignment explanation
Indices: 44777612--44778042 Score: 521
Period size: 181 Copynumber: 2.4 Consensus size: 180
44777602 ATTTTAATTC
* *
44777612 ACTCCACTGCAACTTCAGGGAGATAGGA-TTGGTTTA-TTCAATCTGCTCCACTACAACTTTATG
1 ACTCCACTGCAACTTCAGGGAGATAAGACTT-G--TACTTCAATCTGCTCCACTACAACTTCATG
* *
44777675 GAGATAAGGTTTGATATGATCTACTCTACTACAACTTTAAAGAGATAAAATCTATAATTTATAGC
63 GAGATAAGGTTTGATATGATCTACTCTACTACAACTTCAAAGAGATAAAATCTACAATTTATAGC
* *
44777740 T-TCAATCAGTTCCACTGCAACTTCAGAGAAATAAGATTCGCTATCTTCAGTCT
128 TCT-AACCAGTTCCACTGCAACTTCAGAGAAATAACATTCGCTATCTTCAGTCT
* * * *
44777793 GCTCTACTGCAACTTTAGGGAGATAAGACTTGTAACTTCAA-CTTGCTCCACTACAACTTCAGGG
1 ACTCCACTGCAACTTCAGGGAGATAAGACTTGT-ACTTCAATC-TGCTCCACTACAACTTCATGG
* * * * * *
44777857 AGATAAGGTTTGCTATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGCAATTTATAGCT
64 AGATAAGGTTTGATATGATCTACTCTACTACAACTTCAAAGAGATAAAATCTACAATTTATAGCT
* * * * * * *
44777922 CTAACCTGTTCCGCTGCCACTTCAGGGGAATGACATTTGCTATCTTCAGTCT
129 CTAACCAGTTCCACTGCAACTTCAGAGAAATAACATTCGCTATCTTCAGTCT
* * * * *
44777974 ATTCCACTGCAACTTCAGGAAGATAAAACTT-TACTTCAATCCGCTCCACTGCAACTTCATGGAG
1 ACTCCACTGCAACTTCAGGGAGATAAGACTTGTACTTCAATCTGCTCCACTACAACTTCATGGAG
44778038 ATAAG
66 ATAAG
44778043 ATTATTGGCT
Statistics
Matches: 212, Mismatches: 32, Indels: 14
0.82 0.12 0.05
Matches are distributed among these distances:
179 33 0.16
180 4 0.02
181 172 0.81
182 3 0.01
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (180 bp):
ACTCCACTGCAACTTCAGGGAGATAAGACTTGTACTTCAATCTGCTCCACTACAACTTCATGGAG
ATAAGGTTTGATATGATCTACTCTACTACAACTTCAAAGAGATAAAATCTACAATTTATAGCTCT
AACCAGTTCCACTGCAACTTCAGAGAAATAACATTCGCTATCTTCAGTCT
Found at i:44777893 original size:41 final size:42
Alignment explanation
Indices: 44777753--44777905 Score: 123
Period size: 44 Copynumber: 3.5 Consensus size: 42
44777743 AATCAGTTCC
* * *
44777753 ACTGCAACTTCAGAGAAATAAGA-TTCGCTATCTTCAGTCTGCTCT
1 ACTGCAACTTCAGGGAGATAAGACTT-G-TAAC-TCA-TCTGCTCT
* * *
44777798 ACTGCAACTTTAGGGAGATAAGACTTGTAACTTCAACTTGCTCC
1 ACTGCAACTTCAGGGAGATAAGACTTGTAAC-TCATC-TGCTCT
* ** *
44777842 ACTACAACTTCAGGGAGATAAGGTTTGCT-A-TGATCTGCTCT
1 ACTGCAACTTCAGGGAGATAAGACTTG-TAACTCATCTGCTCT
*
44777883 ACTGCAACTTCAGAGAGATAAGA
1 ACTGCAACTTCAGGGAGATAAGA
44777906 TCTGCAATTT
Statistics
Matches: 89, Mismatches: 16, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
41 25 0.28
42 3 0.03
43 1 0.01
44 36 0.40
45 22 0.25
46 2 0.02
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.29
Consensus pattern (42 bp):
ACTGCAACTTCAGGGAGATAAGACTTGTAACTCATCTGCTCT
Found at i:44778074 original size:44 final size:42
Alignment explanation
Indices: 44777965--44778125 Score: 144
Period size: 44 Copynumber: 3.6 Consensus size: 42
44777955 CATTTGCTAT
*
44777965 CTTCAGTCTATTCCACTGCAACTTCAGGAAGATAAAACTTTA
1 CTTCAATCTATTCCACTGCAACTTCAGGAAGATAAAACTTTA
*** * * *
44778007 CTTCAATCCGCTCCACTGCAACTTCATGG-AGATAAGATTATTGG
1 CTTCAATCTATTCCACTGCAACTTCA-GGAAGATAAAACT-TT-A
* * *
44778051 CTTTAATCTATTCCACTGCAACTTCAGGAAGATAATATTTGTCA
1 CTTCAATCTATTCCACTGCAACTTCAGGAAGATAAAACTT-T-A
44778095 TCTTTTTCAATCTATTCCACTGCAACTTCAG
1 -C---TTCAATCTATTCCACTGCAACTTCAG
44778126 TGGTATAGGA
Statistics
Matches: 95, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
42 30 0.32
43 7 0.07
44 32 0.34
45 1 0.01
48 25 0.26
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.34
Consensus pattern (42 bp):
CTTCAATCTATTCCACTGCAACTTCAGGAAGATAAAACTTTA
Found at i:44787929 original size:3 final size:3
Alignment explanation
Indices: 44787923--44787991 Score: 68
Period size: 3 Copynumber: 22.3 Consensus size: 3
44787913 AGTTTTTTTA
* * *
44787923 TAT TAT TAA TAT TGT TAT TGCAT CAT TAT TAT TA- TAT TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT T--AT TAT TAT TAT TAT TAT TAT TA-T TAT
*
44787970 TAT TAT TAT TAT CAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
44787992 TCTATACACA
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
2 2 0.04
3 47 0.87
4 3 0.06
5 2 0.04
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:44800459 original size:45 final size:45
Alignment explanation
Indices: 44800402--44800840 Score: 592
Period size: 45 Copynumber: 9.8 Consensus size: 45
44800392 AAAATAGCAA
* * * *
44800402 ATCTTGTCTTCCTATATTGGCAACAAAGTAGATCAAAGATAGCAG
1 ATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCAAAGATAACAG
*
44800447 ATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAACAG
1 ATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCAAAGATAACAG
* * * * *
44800492 TTCTTTTCTTCCTATATTGGCAGTGAAGTAGATCAAAGATAGCAG
1 ATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCAAAGATAACAG
* *
44800537 ATCTTGTCTTCCTATATTGGTAGCAAAGTAGATCGAAGATAACAG
1 ATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCAAAGATAACAG
* * * *
44800582 ATCTTTTCTTCCTGTATCT-GCAGCGAAGTAGATCAAAGATAGCAG
1 ATCTTGTCTTCCTATAT-TGGTAGCGAAGTAGATCAAAGATAACAG
*
44800627 ATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAACAG
1 ATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCAAAGATAACAG
* * * *
44800672 ATCTTGTCTTCCTATACTAGTAGCGAAGTAGATCAAAAATACCAG
1 ATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCAAAGATAACAG
* *
44800717 ATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGATAACAT
1 ATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCAAAGATAACAG
* * * * *
44800762 ATCTTGTTTTCCTGTATTGGCAGTGAAGTAGATCAAATATAACAG
1 ATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCAAAGATAACAG
* *
44800807 ATCTTATCTTCCTATATTGGTATCGAAGTAGATC
1 ATCTTGTCTTCCTATATTGGTAGCGAAGTAGATC
44800841 GAGGATAGCA
Statistics
Matches: 339, Mismatches: 53, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
44 1 0.00
45 337 0.99
46 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (45 bp):
ATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCAAAGATAACAG
Found at i:44800566 original size:90 final size:90
Alignment explanation
Indices: 44800402--44800847 Score: 671
Period size: 90 Copynumber: 5.0 Consensus size: 90
44800392 AAAATAGCAA
* * *
44800402 ATCTTGTCTTCCTATATTGGCAACAAAGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGG
1 ATCTTTTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGG
44800467 TAGCGAAGTAGATCGAAGATAACAG
66 TAGCGAAGTAGATCGAAGATAACAG
* *
44800492 TTCTTTTCTTCCTATATTGGCAGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGG
1 ATCTTTTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGG
*
44800557 TAGCAAAGTAGATCGAAGATAACAG
66 TAGCGAAGTAGATCGAAGATAACAG
*
44800582 ATCTTTTCTTCCTGTATCT-GCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTG
1 ATCTTTTCTTCCTATAT-TGGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTG
44800646 GTAGCGAAGTAGATCGAAGATAACAG
65 GTAGCGAAGTAGATCGAAGATAACAG
* * * * * *
44800672 ATCTTGTCTTCCTATACTAGTAGCGAAGTAGATCAAAAATACCAGATCTTGTCTTCCTATATTGG
1 ATCTTTTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGG
*
44800737 TAGCGAAGTAGATCGAAGATAACAT
66 TAGCGAAGTAGATCGAAGATAACAG
* * * * *
44800762 ATCTTGTT-TTCCTGTATTGGCAGTGAAGTAGATCAAATATAACAGATCTTATCTTCCTATATTG
1 ATCTT-TTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTG
* *
44800826 GTATCGAAGTAGATCGAGGATA
65 GTAGCGAAGTAGATCGAAGATA
44800848 GCAGCCTTAT
Statistics
Matches: 325, Mismatches: 28, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
89 1 0.00
90 322 0.99
91 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (90 bp):
ATCTTTTCTTCCTATATTGGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGG
TAGCGAAGTAGATCGAAGATAACAG
Found at i:44802596 original size:3 final size:3
Alignment explanation
Indices: 44802590--44802660 Score: 72
Period size: 3 Copynumber: 23.3 Consensus size: 3
44802580 TGTTTTTTTA
* * * *
44802590 TAT TAT TAA TAT TGT TAT TA- CAT CAT TAT TAT TAT ATATT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TA-T TAT TAT
*
44802636 TAT TAT TAT TAT TAT CAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
44802661 TCTATACACA
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
2 1 0.02
3 51 0.89
4 4 0.07
5 1 0.02
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:44802717 original size:23 final size:21
Alignment explanation
Indices: 44802676--44802715 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
44802666 ACACACGCAT
44802676 ATTTTTTTATAATATATATGC
1 ATTTTTTTATAATATATATGC
44802697 ATTTTTTTATAATATATAT
1 ATTTTTTTATAATATATAT
44802716 ATACTCATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (21 bp):
ATTTTTTTATAATATATATGC
Found at i:44807718 original size:16 final size:15
Alignment explanation
Indices: 44807694--44807727 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
44807684 GAAACGAATT
*
44807694 AAAATAAATCAATTTA
1 AAAAAAAATC-ATTTA
44807710 AAAAAAAATCATTTA
1 AAAAAAAATCATTTA
44807725 AAA
1 AAA
44807728 TTACATGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAAAAAATCATTTA
Found at i:44808222 original size:17 final size:17
Alignment explanation
Indices: 44808202--44808234 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
44808192 GTATTGATAA
44808202 TAAACTTAAAAATAAAT
1 TAAACTTAAAAATAAAT
*
44808219 TAAACTTAAACATAAA
1 TAAACTTAAAAATAAA
44808235 AAGAATGTTA
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:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAACTTAAAAATAAAT
Found at i:44815840 original size:20 final size:18
Alignment explanation
Indices: 44815824--44815877 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 18
44815814 CTAATAATTC
44815824 TATTTTAAAATTAATAAAAT
1 TATTTTAAAATTAAT--AAT
*
44815844 T-TTTTAATTAATAAATAAT
1 TATTTTAA--AATTAATAAT
44815863 TATTTTAAAATTAAT
1 TATTTTAAAATTAAT
44815878 TTAATAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
18 6 0.21
19 10 0.34
20 7 0.24
21 6 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTTTAAAATTAATAAT
Found at i:44815845 original size:17 final size:17
Alignment explanation
Indices: 44815825--44815858 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
44815815 TAATAATTCT
44815825 ATTTTAAAATTAATAAA
1 ATTTTAAAATTAATAAA
**
44815842 ATTTTTTAATTAATAAA
1 ATTTTAAAATTAATAAA
44815859 TAATTATTTT
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTTTAAAATTAATAAA
Found at i:44830291 original size:99 final size:99
Alignment explanation
Indices: 44830116--44830314 Score: 344
Period size: 99 Copynumber: 2.0 Consensus size: 99
44830106 GGTGCTGCCC
* * *
44830116 AGTCAAAAACATTCTTTAACGTAGCGCTAACCACAAGATATAATAGCAACATCGTCAAAATGACT
1 AGTCAAAAACATTCTTTAACGCAGCCCCAACCACAAGATATAATAGCAACATCGTCAAAATGACT
44830181 TTCAGTATGGAGCAATGATTCTTGTTTAAAGATA
66 TTCAGTATGGAGCAATGATTCTTGTTTAAAGATA
44830215 AGTCAAAAACATTCTTTAACGCAGCCCCAACCACAAGATATAATAGCAACATCGTCAAAATGACT
1 AGTCAAAAACATTCTTTAACGCAGCCCCAACCACAAGATATAATAGCAACATCGTCAAAATGACT
* * *
44830280 TTCTGTTTGGAGTAATGATTCTTGTTTAAAGATA
66 TTCAGTATGGAGCAATGATTCTTGTTTAAAGATA
44830314 A
1 A
44830315 AACATATATG
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
99 94 1.00
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.29
Consensus pattern (99 bp):
AGTCAAAAACATTCTTTAACGCAGCCCCAACCACAAGATATAATAGCAACATCGTCAAAATGACT
TTCAGTATGGAGCAATGATTCTTGTTTAAAGATA
Found at i:44835050 original size:12 final size:13
Alignment explanation
Indices: 44835026--44835054 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
44835016 GGGCTATAGC
44835026 TATTGCATTTATT
1 TATTGCATTTATT
44835039 TATTGC-TTTATT
1 TATTGCATTTATT
44835051 TATT
1 TATT
44835055 CATGTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:44838209 original size:15 final size:15
Alignment explanation
Indices: 44838191--44838230 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
44838181 CGCCTGGCCG
44838191 TGTGTCACACACAGT
1 TGTGTCACACACAGT
44838206 TGTGTCACACACAGT
1 TGTGTCACACACAGT
*
44838221 TGAGTCACAC
1 TGTGTCACAC
44838231 TGTAACACCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (15 bp):
TGTGTCACACACAGT
Found at i:44838370 original size:33 final size:33
Alignment explanation
Indices: 44838333--44838398 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
44838323 CACTAAACAT
44838333 AGCATAATCAATTCATATTCATGCATGTCGTCC
1 AGCATAATCAATTCATATTCATGCATGTCGTCC
44838366 AGCATAATCAATTCATATTCATGCATGTCGTCC
1 AGCATAATCAATTCATATTCATGCATGTCGTCC
44838399 CTTATTCAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.33
Consensus pattern (33 bp):
AGCATAATCAATTCATATTCATGCATGTCGTCC
Found at i:44841969 original size:41 final size:41
Alignment explanation
Indices: 44841904--44842147 Score: 213
Period size: 41 Copynumber: 6.0 Consensus size: 41
44841894 GTACATCTAG
* * * *
44841904 GGGTA-CGTAAGTAGAAACTGGGGCATGTCTGTGCAATTCAA
1 GGGTACCG-AAGTACAAACAGGGGCACGTATGTGCAATTCAA
* * * * * * *
44841945 GGGTATCGAAGTACAAATAAGGGCATGTATGTGTAATTTAG
1 GGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATTCAA
* * * * * * *
44841986 GGGTACCAAAGTACAAATAGGGGCACATCTATGAAATT-TA
1 GGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATTCAA
* * * * *
44842026 GGGGACCGAAGTACAAAGAAGGGCATGTATGTGCAACTCAA
1 GGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATTCAA
* *
44842067 GGGTACCGAAGTACAAACAGGGGCACATATGTGCAATTCAG
1 GGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATTCAA
* * *
44842108 GGGTATCGAAATATAAACAGGGGCACGTATGTGCAATTCA
1 GGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATTCA
44842148 TCATTATTCT
Statistics
Matches: 161, Mismatches: 40, Indels: 4
0.79 0.20 0.02
Matches are distributed among these distances:
40 28 0.17
41 131 0.81
42 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.29, T:0.22
Consensus pattern (41 bp):
GGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATTCAA
Found at i:44842110 original size:81 final size:81
Alignment explanation
Indices: 44841933--44842143 Score: 242
Period size: 81 Copynumber: 2.6 Consensus size: 81
44841923 GGGGCATGTC
* * * * * *
44841933 TGTGCAATTCAAGGGTATCGAAGTACAAATAAGGGCATGTATGTGTAATTTAGGGGTACCAAAGT
1 TGTGCAATTC-AGGGGATCGAAGTACAAACAAGGGCATGTATGTGCAACTCAAGGGTACCAAAGT
* *
44841998 ACAAATAGGGGCACATC
65 ACAAACAGGGGCACATA
* * * * * *
44842015 TATGAAATTTAGGGGACCGAAGTACAAAGAAGGGCATGTATGTGCAACTCAAGGGTACCGAAGTA
1 TGTGCAATTCAGGGGATCGAAGTACAAACAAGGGCATGTATGTGCAACTCAAGGGTACCAAAGTA
44842080 CAAACAGGGGCACATA
66 CAAACAGGGGCACATA
* * * *
44842096 TGTGCAATTCAGGGGTATCGAAATATAAACAGGGGCACGTATGTGCAA
1 TGTGCAATTCAGGGG-ATCGAAGTACAAACAAGGGCATGTATGTGCAA
44842144 TTCATCATTA
Statistics
Matches: 106, Mismatches: 22, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
81 73 0.69
82 33 0.31
ACGTcount: A:0.36, C:0.15, G:0.28, T:0.21
Consensus pattern (81 bp):
TGTGCAATTCAGGGGATCGAAGTACAAACAAGGGCATGTATGTGCAACTCAAGGGTACCAAAGTA
CAAACAGGGGCACATA
Found at i:44849352 original size:20 final size:20
Alignment explanation
Indices: 44849329--44849475 Score: 61
Period size: 20 Copynumber: 7.2 Consensus size: 20
44849319 AAGTATATCT
44849329 AGGGGTACCGAAGTACAAAC
1 AGGGGTACCGAAGTACAAAC
* *
44849349 AGGGGCA-CGCATGTA-AAATTC
1 AGGGGTACCG-AAGTACAAA--C
*
44849370 AGGGGTACTGAAGTACAAAC
1 AGGGGTACCGAAGTACAAAC
** ** * *
44849390 ACAGGTA-CGTCTGTGCAATTC
1 AGGGGTACCG-AAGTACAA-AC
** *
44849411 AAAGGTACCGAAATACAAAC
1 AGGGGTACCGAAGTACAAAC
* * *
44849431 AGGGG--CAGATATGTGCAATC
1 AGGGGTACCGA-A-GTACAAAC
44849451 AGGGGTACCGAAGTACAAAC
1 AGGGGTACCGAAGTACAAAC
44849471 AGGGG
1 AGGGG
44849476 CACGTATGTG
Statistics
Matches: 88, Mismatches: 27, Indels: 24
0.63 0.19 0.17
Matches are distributed among these distances:
18 3 0.03
19 7 0.08
20 46 0.52
21 23 0.26
22 9 0.10
ACGTcount: A:0.37, C:0.18, G:0.29, T:0.16
Consensus pattern (20 bp):
AGGGGTACCGAAGTACAAAC
Found at i:44849377 original size:41 final size:42
Alignment explanation
Indices: 44849329--44849488 Score: 177
Period size: 41 Copynumber: 3.9 Consensus size: 42
44849319 AAGTATATCT
**
44849329 AGGGGTACCGAAGTACAAACAGGGGCACG-CATGTAAAATTC
1 AGGGGTACCGAAGTACAAACAGGGGCACGACATGTGCAATTC
* ** * *
44849370 AGGGGTACTGAAGTACAAACACAGGTACGTC-TGTGCAATTC
1 AGGGGTACCGAAGTACAAACAGGGGCACGACATGTGCAATTC
** * *
44849411 AAAGGTACCGAAATACAAACAGGGGCA-GATATGTGCAA-TC
1 AGGGGTACCGAAGTACAAACAGGGGCACGACATGTGCAATTC
*
44849451 AGGGGTACCGAAGTACAAACAGGGGCACG-TATGTGCAA
1 AGGGGTACCGAAGTACAAACAGGGGCACGACATGTGCAA
44849489 CTTATCATTA
Statistics
Matches: 98, Mismatches: 18, Indels: 7
0.80 0.15 0.06
Matches are distributed among these distances:
40 36 0.37
41 61 0.62
42 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.29, T:0.16
Consensus pattern (42 bp):
AGGGGTACCGAAGTACAAACAGGGGCACGACATGTGCAATTC
Found at i:44849486 original size:81 final size:82
Alignment explanation
Indices: 44849332--44849488 Score: 210
Period size: 81 Copynumber: 1.9 Consensus size: 82
44849322 TATATCTAGG
* * *
44849332 GGTACCGAAGTACAAACAGGGGCACGCATGTAAAATTCAGGGGTACTGAAGTACAAACACAGGTA
1 GGTACCGAAATACAAACAGGGGCACGCATGTAAAATTCAGGGGTACCGAAGTACAAACACAGGCA
*
44849397 CGTCTGTGCAATTCAAA
66 CGTATGTGCAATTCAAA
* ** **
44849414 GGTACCGAAATACAAACAGGGGCA-GATATGTGCAA-TCAGGGGTACCGAAGTACAAACAGGGGC
1 GGTACCGAAATACAAACAGGGGCACG-CATGTAAAATTCAGGGGTACCGAAGTACAAACACAGGC
44849477 ACGTATGTGCAA
65 ACGTATGTGCAA
44849489 CTTATCATTA
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
81 36 0.55
82 29 0.45
ACGTcount: A:0.36, C:0.19, G:0.28, T:0.17
Consensus pattern (82 bp):
GGTACCGAAATACAAACAGGGGCACGCATGTAAAATTCAGGGGTACCGAAGTACAAACACAGGCA
CGTATGTGCAATTCAAA
Found at i:44858567 original size:50 final size:50
Alignment explanation
Indices: 44858485--44858586 Score: 159
Period size: 50 Copynumber: 2.0 Consensus size: 50
44858475 TAAAAGTAGA
* * *
44858485 ATAACTTTAGTAGCAGTGCAAGTAAATCTGTAGTAGGGTTCTTTTAATGC
1 ATAACTTCAATAGCAATGCAAGTAAATCTGTAGTAGGGTTCTTTTAATGC
* *
44858535 ATAACTTCAATAGCAATGCAAGTAAGTTTGTAGTAGGGTTCTTTTAATGC
1 ATAACTTCAATAGCAATGCAAGTAAATCTGTAGTAGGGTTCTTTTAATGC
44858585 AT
1 AT
44858587 TTAGAATTTC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (50 bp):
ATAACTTCAATAGCAATGCAAGTAAATCTGTAGTAGGGTTCTTTTAATGC
Found at i:44863253 original size:64 final size:64
Alignment explanation
Indices: 44863152--44863291 Score: 253
Period size: 64 Copynumber: 2.2 Consensus size: 64
44863142 AAATAAACTC
44863152 TGAATTTGTCAAAGGCAAATACCACAGCCAATAGCTCCTTCTCAATGGTGGTATAATTTAGCTG
1 TGAATTTGTCAAAGGCAAATACCACAGCCAATAGCTCCTTCTCAATGGTGGTATAATTTAGCTG
* * *
44863216 TGAATTTGTCAAAGGCAAATACCACAGCTAATAGCTCCTTCTCAATGGTGTTATAATTTTGCTG
1 TGAATTTGTCAAAGGCAAATACCACAGCCAATAGCTCCTTCTCAATGGTGGTATAATTTAGCTG
44863280 TGAATTTGTCAA
1 TGAATTTGTCAA
44863292 CGTACGACTT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 73 1.00
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Consensus pattern (64 bp):
TGAATTTGTCAAAGGCAAATACCACAGCCAATAGCTCCTTCTCAATGGTGGTATAATTTAGCTG
Found at i:44869861 original size:54 final size:54
Alignment explanation
Indices: 44869793--44869900 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 54
44869783 ATTTAAGCTC
*
44869793 CCATCTTCTATTTGTTTCCTTGCAAGATTTGTTACATGGCTTTAAGAATGGATG
1 CCATCTTCTATTTGTTTCCTTGCAAGATTCGTTACATGGCTTTAAGAATGGATG
*
44869847 CCATCTTCTATTTGTTTCCTTGCAAGCTTCGTTACATGGCTTTAAGAATGGATG
1 CCATCTTCTATTTGTTTCCTTGCAAGATTCGTTACATGGCTTTAAGAATGGATG
44869901 TCGCCCCCTC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.42
Consensus pattern (54 bp):
CCATCTTCTATTTGTTTCCTTGCAAGATTCGTTACATGGCTTTAAGAATGGATG
Found at i:44871325 original size:56 final size:55
Alignment explanation
Indices: 44871214--44871347 Score: 137
Period size: 57 Copynumber: 2.3 Consensus size: 55
44871204 TATATTATTA
* *
44871214 TATATTATGATTTTAGTAAATTCATATAAGAATAATTATATTAAGAATTTTATTAAAT
1 TATA-TAT-ATTTTA-TAAATTCATATAAGAATAATTATATTAAGAATATGATTAAAT
* *
44871272 TATATATATTTTATTAAATT-ATATTTAATAATAATTATGTTAA-AATATGATTAAAT
1 TATATATATTTTA-TAAATTCATA--TAAGAATAATTATATTAAGAATATGATTAAAT
*
44871328 TATTTATTATTTGTATAAAT
1 TATATA-TATTT-TATAAAT
44871348 AATCTTATTA
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
55 3 0.05
56 28 0.42
57 29 0.44
58 6 0.09
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.50
Consensus pattern (55 bp):
TATATATATTTTATAAATTCATATAAGAATAATTATATTAAGAATATGATTAAAT
Found at i:44871537 original size:45 final size:44
Alignment explanation
Indices: 44871455--44871547 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
44871445 ATTACAACAT
44871455 CATTCCATTCAACCAAAGACAAGAATACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAAGACAAGAATACTATTACAGTTCTATTC
*
44871499 CATTCCATTCAA-CGAA-ACAATTGAATTACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAAGACAA--GAA-TACTATTACAGTTCTATTC
44871544 CATT
1 CATT
44871548 ACAGCTCTAT
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
42 4 0.09
43 3 0.07
44 15 0.33
45 23 0.51
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.33
Consensus pattern (44 bp):
CATTCCATTCAACCAAAGACAAGAATACTATTACAGTTCTATTC
Found at i:44871550 original size:16 final size:16
Alignment explanation
Indices: 44871529--44871584 Score: 76
Period size: 16 Copynumber: 3.5 Consensus size: 16
44871519 TTGAATTACT
*
44871529 ATTACAGTTCTATTCC
1 ATTACAGCTCTATTCC
**
44871545 ATTACAGCTCTATTTA
1 ATTACAGCTCTATTCC
*
44871561 ATTACAACTCTATTCC
1 ATTACAGCTCTATTCC
44871577 ATTACAGC
1 ATTACAGC
44871585 GAACCAAACG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.39
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:44879357 original size:21 final size:21
Alignment explanation
Indices: 44879313--44879358 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
44879303 CTACAACTTA
*
44879313 AAGCAGATGCAGCAACAAGGG
1 AAGCAGATGCAGCAACAAGAG
* *
44879334 AAGCAGATGCAGCAGCGAGAG
1 AAGCAGATGCAGCAACAAGAG
44879355 AAGC
1 AAGC
44879359 TGAGGTTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.20, G:0.35, T:0.04
Consensus pattern (21 bp):
AAGCAGATGCAGCAACAAGAG
Found at i:44879437 original size:87 final size:87
Alignment explanation
Indices: 44879247--44879443 Score: 243
Period size: 87 Copynumber: 2.3 Consensus size: 87
44879237 ACTCAAATTA
* ** *
44879247 AAACAGAGGTAGCATTGAGAGAAGCTGAGGTCCGAAGAAAATATAAAGAACTCCAACTACAACTT
1 AAACAGAGGCAGCAGCGAGAGAAGCTGAGGTCCAAAGAAAATATAAAGAACTCCAACTACAACTT
*
44879312 AAAGCAGATGCAGCAACAAGGG
66 AAAGCAGATGCAGCAACAAGAG
* * * * *
44879334 AAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAAAGAAAATATGAAGAACTCCAGCTACAACTT
1 AAACAGAGGCAGCAGCGAGAGAAGCTGAGGTCCAAAGAAAATATAAAGAACTCCAACTACAACTT
* * ***
44879399 AAATCTGATGCAGCAGTGAGAG
66 AAAGCAGATGCAGCAACAAGAG
44879421 AAACAGAGGCTA-CAGCGAGAGAA
1 AAACAGAGGC-AGCAGCGAGAGAA
44879444 CCAGAACAGA
Statistics
Matches: 92, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
87 91 0.99
88 1 0.01
ACGTcount: A:0.43, C:0.17, G:0.26, T:0.14
Consensus pattern (87 bp):
AAACAGAGGCAGCAGCGAGAGAAGCTGAGGTCCAAAGAAAATATAAAGAACTCCAACTACAACTT
AAAGCAGATGCAGCAACAAGAG
Found at i:44879810 original size:43 final size:43
Alignment explanation
Indices: 44879761--44879957 Score: 243
Period size: 43 Copynumber: 4.6 Consensus size: 43
44879751 TTTTAAAAAT
* * *
44879761 GCCGCTAAAGGTCATTACCTATAGCGGATTTTGTGGGAAAAGC
1 GCCGCTAAAGGTCATGATCTATAGCGGAGTTTGTGGGAAAAGC
* * *
44879804 ACCGCTAAAGGTCATGATCTATAGCGGCGTTTGTGGGAAAAGT
1 GCCGCTAAAGGTCATGATCTATAGCGGAGTTTGTGGGAAAAGC
* * * *
44879847 GCCGCTAAAGGTCATGATCAATAGCGGCGTTTGTGGTAAAAGT
1 GCCGCTAAAGGTCATGATCTATAGCGGAGTTTGTGGGAAAAGC
* * *
44879890 GCCGCTAAAGGTCATAATTTATAACGGCA-TTTGTGGGAAAAGC
1 GCCGCTAAAGGTCATGATCTATAGCGG-AGTTTGTGGGAAAAGC
* *
44879933 GCTGCTAAAGGTCCTGATCTATAGC
1 GCCGCTAAAGGTCATGATCTATAGC
44879958 AGCGCTTTTA
Statistics
Matches: 132, Mismatches: 21, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
43 132 1.00
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (43 bp):
GCCGCTAAAGGTCATGATCTATAGCGGAGTTTGTGGGAAAAGC
Found at i:44881115 original size:48 final size:48
Alignment explanation
Indices: 44881047--44881221 Score: 188
Period size: 48 Copynumber: 3.6 Consensus size: 48
44881037 TCTCGATGGT
* * * * * * * *
44881047 CTGCACACAGTCCATACCACCATTGTGTAATAGCAGATTTTCGGTGGC
1 CTGCACACAGTCCGTGCCACCCTTGTATCATAACAGAATATCGGTGGC
* * * * *
44881095 CTGCACATAGTCCGTGCCACCCTTATATCATAATATAATATCAGTGGC
1 CTGCACACAGTCCGTGCCACCCTTGTATCATAACAGAATATCGGTGGC
* *
44881143 TTGCACACAGTTCGTGCCACCCTTGTATCATAACAGAATATCGGTGGC
1 CTGCACACAGTCCGTGCCACCCTTGTATCATAACAGAATATCGGTGGC
* * *
44881191 CTGCACACAGTCTGTGCCACTCTTGTGTCAT
1 CTGCACACAGTCCGTGCCACCCTTGTATCAT
44881222 GATAGAACAT
Statistics
Matches: 102, Mismatches: 25, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
48 102 1.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.29
Consensus pattern (48 bp):
CTGCACACAGTCCGTGCCACCCTTGTATCATAACAGAATATCGGTGGC
Done.