Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2351
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: 521823
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
File 2 of 4
Found at i:149506 original size:95 final size:95
Alignment explanation
Indices: 149022--149581 Score: 370
Period size: 95 Copynumber: 5.8 Consensus size: 95
149012 GATGCCATGG
* * *
149022 AGTTGTGGAC-TTAAAAAGAAAAAGGGTGCCAC-GAAGTTGTGGGCTTAAAAAGAAAAGGTGCCA
1 AGTTGTGGGCTTTGAAAAGAAAAA-GGTGCCACAG-AGTTGTGGACTTAAAAAG---A-GTGCCA
* * * * * *
149085 CGGAATTGTGGGCTTTGAAAAGAAAAAAGGTGCCATAG
60 CGGAGTTGTAGAC-TTAAAAAGAAAAAA-GTGCCACAA
* * * * **
149123 AGTTGTGGGCTTTGAAAATAAAGAGGTGCCACAGAGTTGTGGATTTACAAGAAAAAAAGGTGTTA
1 AGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACAGAGTTGTGGACTT-----AAAAAGA-GTGCCA
149188 CGGAGTTGT-GAGCTT-AAAAG----AA-TGCCACAA
60 CGGAGTTGTAGA-CTTAAAAAGAAAAAAGTGCCACAA
* ** * * * *
149218 AGTTGTGAGCTTT-AAAA-AAAAAGGTGCCATGGAGTTATGGGCTTAAAAGAAAAAGGTGCCATG
1 AGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACAGAGTTGTGGACTT--AA-AAAGA-GTGCCACG
* *
149281 GAGTTGTAGGCTT------AAAAAAGTGCCACAG
62 GAGTTGTAGACTTAAAAAGAAAAAAGTGCCACAA
* * * *
149309 AGCTGTGGGCTTTG-AAAGAAAAAAGTGCCACAGAGTTGTAGG-CTTAAAAGAAAAATGTGCCAT
1 AGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACAGAGTTGT-GGACTT--AA-AAAGA-GTGCCAC
** * * *
149372 GGAGTTGTAAGTTTTGAAAAGAAAAATGTGCCACGA
61 GGAGTTGT-AGACTTAAAAAGAAAAAAGTGCCACAA
* *
149408 AGTTGTGGGCTTTGAAAAGAAAGAGGTGCCACAGAGTTGTGGACTTAAAAAGAGTGCCA-GCAGT
1 AGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACAGAGTTGTGGACTTAAAAAGAGTGCCACGGAGT
*
149472 TGTAGACTTAAAAAGAAAAAAGGTGCCATAA
66 TGTAGACTTAAAAAGAAAAAA-GTGCCACAA
* * *
149503 AGTTGTGGACTTTGAAAAGAAAAAGGTTCCATAGAGTTGTGGACTT-AAAAGAGTGCCACGGAGT
1 AGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACAGAGTTGTGGACTTAAAAAGAGTGCCACGGAGT
* *
149567 TATGGACTTAAAAAG
66 TGTAGACTTAAAAAG
149582 GTGCTACGAA
Statistics
Matches: 374, Mismatches: 56, Indels: 64
0.76 0.11 0.13
Matches are distributed among these distances:
90 5 0.01
91 42 0.11
92 46 0.12
93 27 0.07
94 30 0.08
95 91 0.24
96 6 0.02
97 6 0.02
98 2 0.01
99 27 0.07
100 26 0.07
101 32 0.09
102 14 0.04
103 15 0.04
106 5 0.01
ACGTcount: A:0.38, C:0.11, G:0.29, T:0.23
Consensus pattern (95 bp):
AGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACAGAGTTGTGGACTTAAAAAGAGTGCCACGGAGT
TGTAGACTTAAAAAGAAAAAAGTGCCACAA
Found at i:149566 original size:27 final size:28
Alignment explanation
Indices: 149522--149763 Score: 115
Period size: 27 Copynumber: 8.2 Consensus size: 28
149512 CTTTGAAAAG
* *
149522 AAAA-AGGTTCCATAGAGTTGTGGACTT
1 AAAAGAGGTGCCACAGAGTTGTGGACTT
* *
149549 AAAAGA-GTGCCACGGAGTTATGGACTT
1 AAAAGAGGTGCCACAGAGTTGTGGACTT
* *
149576 AAAA-AGGTGCTAC-GAAGTTAT-GAGCTT
1 AAAAGAGGTGCCACAG-AGTTGTGGA-CTT
* *
149603 AAAACGAAAAAGGGTGCCACGGAGTTATGGACTTT
1 AAAA-G----A-GGTGCCACAGAGTTGTGGAC-TT
* *
149638 GGAAAGAAAAAGGTGCCATAGAGTTGTGGACTT
1 ----A-AAAGAGGTGCCACAGAGTTGTGGACTT
149671 AAAA-AGGTGCCACAGAGTTGTGGA-TT
1 AAAAGAGGTGCCACAGAGTTGTGGACTT
* *
149697 CAAAAGGAAAAATGTGCCACTA-AGTTGTGGACTC
1 -AAAA-G----AGGTGCCAC-AGAGTTGTGGACTT
*
149731 AAAA-TGGTGCCACAGAGTTGTGGACTT
1 AAAAGAGGTGCCACAGAGTTGTGGACTT
149758 AAAAGA
1 AAAAGA
149764 AAAAAAGGTG
Statistics
Matches: 168, Mismatches: 17, Indels: 59
0.69 0.07 0.24
Matches are distributed among these distances:
26 7 0.04
27 89 0.53
28 4 0.02
29 1 0.01
33 24 0.14
34 33 0.20
35 6 0.04
39 1 0.01
40 3 0.02
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.23
Consensus pattern (28 bp):
AAAAGAGGTGCCACAGAGTTGTGGACTT
Found at i:149573 original size:61 final size:60
Alignment explanation
Indices: 149489--149767 Score: 201
Period size: 60 Copynumber: 4.6 Consensus size: 60
149479 TTAAAAAGAA
* * *
149489 AAAAG-GTGCCATAAAGTTGTGGACTTTGAAAAGAAAAAGGTTCCATAGAGTTGTGGACTT
1 AAAAGAGTGCCACAGAGTTGTGGAC-TTGAAAAGAAAAAGGTGCCATAGAGTTGTGGACTT
* * *
149549 AAAAGAGTGCCACGGAGTTATGGACTT------AAAAAGGTG-C-TACGAAGTTAT-GAGCTT
1 AAAAGAGTGCCACAGAGTTGTGGACTTGAAAAGAAAAAGGTGCCATA-G-AGTTGTGGA-CTT
* * *
149603 AAAACGAAAAAGGGTGCCACGGAGTTATGGACTTTGGAAAGAAAAAGGTGCCATAGAGTTGTGGA
1 AAAA-G----A--GTGCCACAGAGTTGTGGAC-TTGAAAAGAAAAAGGTGCCATAGAGTTGTGGA
149668 CTT
58 CTT
* * *
149671 AAAA-AGGTGCCACAGAGTTGTGGA-TTCAAAAGGAAAAATGTGCCACTA-AGTTGTGGACTC
1 AAAAGA-GTGCCACAGAGTTGTGGACTTGAAAA-GAAAAAGGTGCCA-TAGAGTTGTGGACTT
149731 AAAATG-GTGCCACAGAGTTGTGGACTT-AAAAGAAAAA
1 AAAA-GAGTGCCACAGAGTTGTGGACTTGAAAAGAAAAA
149768 AAGGTGCTAC
Statistics
Matches: 180, Mismatches: 13, Indels: 53
0.73 0.05 0.22
Matches are distributed among these distances:
52 2 0.01
53 4 0.02
54 20 0.11
55 1 0.01
59 12 0.07
60 56 0.31
61 55 0.31
62 3 0.02
68 21 0.12
69 4 0.02
70 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.28, T:0.23
Consensus pattern (60 bp):
AAAAGAGTGCCACAGAGTTGTGGACTTGAAAAGAAAAAGGTGCCATAGAGTTGTGGACTT
Found at i:149573 original size:122 final size:123
Alignment explanation
Indices: 148912--149703 Score: 426
Period size: 122 Copynumber: 6.3 Consensus size: 123
148902 CTTAAAAAAG
* * * * * * *
148912 AAAA-AGGTGTCACGGAGTTGTGCACTTAAAAGGGTGCCATGAACTTATG-GACTT-AAAAGGAA
1 AAAAGAGGTGCCACAGAGTTGTGGACTTAAAAAGGTGCCACGAAGTTATGAG-CTTAAAAAGAAA
* ** * * *
148974 AAAGGATACCACGGAGTTATGAACTTTGAAAAGAAAAAGATGCCATGGAGTTGTGGACTT
65 AAAGG-TGCCACAAAGTTATGGACTTTGAAAAGAAAAAGGTGCCATAGAGTTGTGGACTT
* * *
149034 AAAAAGAAAAAGGGTGCCAC-GAAGTTGTGGGCTTAAAAAGAAAAGGTGCCACGGAA-TTGTGGG
1 -AAAAG----A-GGTGCCACAG-AGTTGTGGACTT----A-AAAAGGTGCCAC-GAAGTTATGAG
* * * * * * * *
149097 CTTTGAAAAGAAAAAAGGTGCCATAGAGTTGTGGGCTTTGAAAATAAAGAGGTGCCACAGAGTTG
53 C-TTAAAAAGAAAAAAGGTGCCACAAAGTTATGGACTTTGAAAAGAAAAAGGTGCCATAGAGTTG
*
149162 TGGATTT
117 TGGACTT
* ** * * * * *
149169 ACAAGAAAAAAAGGTGTTACGGAGTTGT-GAGCTT-AAAAGAATGCCACAAAGTTGTGAGCTT-T
1 ------AAAAGAGGTGCCACAGAGTTGTGGA-CTTAAAAAG-GTGCCACGAAGTTATGAGCTTAA
*** * *
149231 AAA-AAAAAAGGTGCCATGGAGTTATGGGC-TT-AAAAGAAAAAGGTGCCATGGAGTTGTAGG-C
58 AAAGAAAAAAGGTGCCACAAAGTTATGGACTTTGAAAAGAAAAAGGTGCCATAGAGTTGT-GGAC
149292 TT
122 TT
* * * * *
149294 AAAA-AAGTGCCACAGAGCTGTGGGCTTTGAAAGAAAAAAGTGCCAC-AGAGTTGT-AGGCTT-A
1 AAAAGAGGTGCCACAGAGTTGTGGAC-TT-----AAAAAGGTGCCACGA-AGTTATGA-GCTTAA
* *** * * * * * *
149355 AAAG-AAAAATGTGCCATGGAGTTGT-AAGTTTTGAAAAGAAAAATGTGCCA-CGAAGTTGTGGG
58 AAAGAAAAAAGGTGCCACAAAGTTATGGA-CTTTGAAAAGAAAAAGGTGCCATAG-AGTTGTGGA
149417 CTTT
121 C-TT
* *
149421 GAAAAGAAAGAGGTGCCACAGAGTTGTGGACTTAAAAAGAGTGCCA-GCAGTTGT-AGACTTAAA
1 ----A-AAAGAGGTGCCACAGAGTTGTGGACTTAAAAAG-GTGCCACGAAGTTATGAG-CTTAAA
* * *
149484 AAGAAAAAAGGTGCCATAAAGTTGTGGACTTTGAAAAGAAAAAGGTTCCATAGAGTTGTGGACTT
59 AAGAAAAAAGGTGCCACAAAGTTATGGACTTTGAAAAGAAAAAGGTGCCATAGAGTTGTGGACTT
* * * *
149549 AAAAGA-GTGCCACGGAGTTATGGACTTAAAAAGGTGCTACGAAGTTATGAGCTTAAAACGAAAA
1 AAAAGAGGTGCCACAGAGTTGTGGACTTAAAAAGGTGCCACGAAGTTATGAGCTTAAAAAGAAAA
* ** *
149613 AGGGTGCCACGGAGTTATGGACTTTGGAAAGAAAAAGGTGCCATAGAGTTGTGGACTT
66 AAGGTGCCACAAAGTTATGGACTTTGAAAAGAAAAAGGTGCCATAGAGTTGTGGACTT
*
149671 AAAA-AGGTGCCACAGAGTTGTGGA-TTCAAAAGG
1 AAAAGAGGTGCCACAGAGTTGTGGACTTAAAAAGG
149704 AAAAATGTGC
Statistics
Matches: 530, Mismatches: 80, Indels: 120
0.73 0.11 0.16
Matches are distributed among these distances:
118 13 0.02
119 7 0.01
121 14 0.03
122 114 0.22
123 13 0.02
124 39 0.07
125 33 0.06
126 28 0.05
127 41 0.08
128 18 0.03
129 72 0.14
130 15 0.03
131 1 0.00
132 5 0.01
133 19 0.04
134 16 0.03
135 63 0.12
136 14 0.03
140 5 0.01
ACGTcount: A:0.38, C:0.11, G:0.29, T:0.22
Consensus pattern (123 bp):
AAAAGAGGTGCCACAGAGTTGTGGACTTAAAAAGGTGCCACGAAGTTATGAGCTTAAAAAGAAAA
AAGGTGCCACAAAGTTATGGACTTTGAAAAGAAAAAGGTGCCATAGAGTTGTGGACTT
Found at i:149714 original size:33 final size:33
Alignment explanation
Indices: 149671--149734 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
149661 TTGTGGACTT
*
149671 AAAAAGGTGCCAC-AGAGTTGTGGATTCAAAAGG
1 AAAAAGGTGCCACTA-AGTTGTGGACTCAAAAGG
*
149704 AAAAATGTGCCACTAAGTTGTGGACTCAAAA
1 AAAAAGGTGCCACTAAGTTGTGGACTCAAAA
149735 TGGTGCCACA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.20
Consensus pattern (33 bp):
AAAAAGGTGCCACTAAGTTGTGGACTCAAAAGG
Found at i:149811 original size:35 final size:35
Alignment explanation
Indices: 149764--149844 Score: 117
Period size: 35 Copynumber: 2.3 Consensus size: 35
149754 ACTTAAAAGA
*
149764 AAAAAAGGTGCTACGAAGTCGTGGGCTTTTGGAAG
1 AAAAAAGATGCTACGAAGTCGTGGGCTTTTGGAAG
* * * *
149799 AAAAATGATGCTATGGAGTTGTGGGCTTTTGGAAG
1 AAAAAAGATGCTACGAAGTCGTGGGCTTTTGGAAG
149834 AAAAAAGATGC
1 AAAAAAGATGC
149845 CACTGAGTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.35, C:0.09, G:0.32, T:0.25
Consensus pattern (35 bp):
AAAAAAGATGCTACGAAGTCGTGGGCTTTTGGAAG
Found at i:149853 original size:35 final size:35
Alignment explanation
Indices: 149784--149857 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
149774 CTACGAAGTC
* *
149784 GTGGGCTTTTGGAAGAAAAATGATGCTATGGAGTT
1 GTGGGCTTTTGGAAGAAAAAAGATGCCATGGAGTT
149819 GTGGGCTTTTGGAAGAAAAAAGATGCCACT-GAGTT
1 GTGGGCTTTTGGAAGAAAAAAGATGCCA-TGGAGTT
149854 GTGG
1 GTGG
149858 ACTTAAAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 35 0.97
36 1 0.03
ACGTcount: A:0.28, C:0.08, G:0.35, T:0.28
Consensus pattern (35 bp):
GTGGGCTTTTGGAAGAAAAAAGATGCCATGGAGTT
Found at i:155835 original size:33 final size:33
Alignment explanation
Indices: 155798--155864 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
155788 TTCAACGATT
155798 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
155831 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
155864 T
1 T
155865 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:155836 original size:13 final size:13
Alignment explanation
Indices: 155818--155842 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
155808 CATAAAATGT
155818 TGTATCGATACAA
1 TGTATCGATACAA
155831 TGTATCGATACA
1 TGTATCGATACA
155843 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:155923 original size:13 final size:13
Alignment explanation
Indices: 155905--155929 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
155895 ATTACTCAAA
155905 TGTATCGATACAT
1 TGTATCGATACAT
155918 TGTATCGATACA
1 TGTATCGATACA
155930 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:156031 original size:52 final size:52
Alignment explanation
Indices: 155938--156061 Score: 207
Period size: 52 Copynumber: 2.4 Consensus size: 52
155928 CACTGATCTT
*
155938 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATT-AAA
155989 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
*
156041 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
156062 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
51 19 0.28
52 47 0.68
53 3 0.04
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:162437 original size:19 final size:20
Alignment explanation
Indices: 162410--162447 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
162400 ATTTAACGTG
*
162410 ACTT-AAAAATTAAAAAAAA
1 ACTTAAAAAAATAAAAAAAA
*
162429 ACTTTAAAAAATAAAAAAA
1 ACTTAAAAAAATAAAAAAA
162448 TAACAAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (20 bp):
ACTTAAAAAAATAAAAAAAA
Found at i:163867 original size:7 final size:7
Alignment explanation
Indices: 163855--163889 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
163845 GCCAAAACAC
163855 AATAATT
1 AATAATT
163862 AATAATT
1 AATAATT
*
163869 AATATTT
1 AATAATT
*
163876 AATATTT
1 AATAATT
163883 AATAATT
1 AATAATT
163890 TTAAAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (7 bp):
AATAATT
Found at i:164391 original size:6 final size:6
Alignment explanation
Indices: 164372--164406 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
164362 AATCATATAA
*
164372 TATATT TATGTT TATATT TATATT TATATT TATAT
1 TATATT TATATT TATATT TATATT TATATT TATAT
164407 AATTTTTACC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (6 bp):
TATATT
Found at i:164879 original size:16 final size:19
Alignment explanation
Indices: 164839--164881 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
164829 ATAAGTTAAT
164839 TTATATTTAAAATATTAAAA
1 TTATATTTAAAATA-TAAAA
164859 TTATATTT-AAATA-AAAA
1 TTATATTTAAAATATAAAA
164876 -TATATT
1 TTATATT
164882 ATCTATGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 6 0.26
17 4 0.17
19 5 0.22
20 8 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTATATTTAAAATATAAAA
Found at i:167302 original size:29 final size:29
Alignment explanation
Indices: 167233--167304 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 29
167223 AAATCTAGTA
*
167233 TTAATTTT-T-AAA-TAAATTATAAATTT
1 TTAATTTTATAAAATTATATTATAAATTT
*
167259 TTAATTTTATCAAATTATATTATTAAATTT
1 TTAATTTTATAAAATTATATTA-TAAATTT
167289 TT-ATTATTA-AAAATTA
1 TTAATT-TTATAAAATTA
167305 AATAACTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
26 8 0.21
27 1 0.03
28 3 0.08
29 15 0.38
30 12 0.31
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (29 bp):
TTAATTTTATAAAATTATATTATAAATTT
Found at i:168900 original size:226 final size:226
Alignment explanation
Indices: 168500--168953 Score: 820
Period size: 226 Copynumber: 2.0 Consensus size: 226
168490 TCTAAAGTTG
* *
168500 GACCTATAACTAATTCTTTTTGTATTAGATGCTTAACATATATGAACACAATATATTTAATATAT
1 GACCTATAACCAATTCTTTTTGTATTAGATGCTTAACATATATGAACACAACATATTTAATATAT
*
168565 GCAAAGATAATATAATAAACACAATTTATACAATATATTTAATATACTTGTATATTTATATTTTG
66 ACAAAGATAATATAATAAACACAATTTATACAATATATTTAATATACTTGTATATTTATATTTTG
168630 AATTTTTATATATTTAATAATTTATAATTTATTTATAATTACGTGACATTAAAAAATATGAAACA
131 AATTTTTATATATTTAATAATTTATAATTTATTTATAATTACGTGACATTAAAAAATATGAAACA
* *
168695 CAACATGCATCTATAATGATAAAATCTAATT
196 CAACAAGCATCGATAATGATAAAATCTAATT
168726 GACCTATAACCAA-TCGTTTTTGTATTAGATGCTTAACATATATGAACACAACATATTTAATATA
1 GACCTATAACCAATTC-TTTTTGTATTAGATGCTTAACATATATGAACACAACATATTTAATATA
*
168790 TACAAAGATAATATAATAAACACAATTTATACAATATATTTAGTATACTTGTATATTTATATTTT
65 TACAAAGATAATATAATAAACACAATTTATACAATATATTTAATATACTTGTATATTTATATTTT
*
168855 GAATTTTTATATATTTAATAATTTATAATTTATTTATACTTACGTGACATTAAAAAATATGAAAC
130 GAATTTTTATATATTTAATAATTTATAATTTATTTATAATTACGTGACATTAAAAAATATGAAAC
*
168920 ACAATAAGCATCGATAATGATAAAATCTAATT
195 ACAACAAGCATCGATAATGATAAAATCTAATT
168952 GA
1 GA
168954 ATATAATCTA
Statistics
Matches: 219, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
225 2 0.01
226 217 0.99
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (226 bp):
GACCTATAACCAATTCTTTTTGTATTAGATGCTTAACATATATGAACACAACATATTTAATATAT
ACAAAGATAATATAATAAACACAATTTATACAATATATTTAATATACTTGTATATTTATATTTTG
AATTTTTATATATTTAATAATTTATAATTTATTTATAATTACGTGACATTAAAAAATATGAAACA
CAACAAGCATCGATAATGATAAAATCTAATT
Found at i:169503 original size:111 final size:107
Alignment explanation
Indices: 169322--169519 Score: 263
Period size: 111 Copynumber: 1.8 Consensus size: 107
169312 TCTTATTTAA
* *
169322 ATATGTAATTTAAATAATTTATTTAAATTTAAATTAATAAATATTTAAAAATAGAACCCATATGA
1 ATATGTAATTTAAATAATTTATTTAAATTTAAATCAATAAATATTTAAAAATAGAACCCATATAA
*
169387 TATT-AAGTTACTTTTAAATTAATAAATTTATTTTATTTATATAT
66 AATTAAAG-TAC-TTT-AATTAATAAATTTATTTTATTTATATAT
*** * **
169431 ATATGTAATTTTTTTAATTTTATTTAAATTTAAATCAATTAAATATTTAAAAATATAGTCCATAT
1 ATATGTAATTTAAATAA-TTTATTTAAATTTAAATCAA-TAAATATTTAAAAATAGAACCCATAT
169496 AAAATTAAAGTACTTTAATTAATA
64 AAAATTAAAGTACTTTAATTAATA
169520 TATAGAGTGT
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
109 22 0.29
110 22 0.29
111 30 0.39
112 3 0.04
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (107 bp):
ATATGTAATTTAAATAATTTATTTAAATTTAAATCAATAAATATTTAAAAATAGAACCCATATAA
AATTAAAGTACTTTAATTAATAAATTTATTTTATTTATATAT
Found at i:169679 original size:2 final size:2
Alignment explanation
Indices: 169651--169697 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
169641 TCCTATCAGA
* * *
169651 AT AT AT -T AA AT AT AC AT AT AA AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
169692 AT AT AT
1 AT AT AT
169698 GATGGGGACA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:176087 original size:19 final size:20
Alignment explanation
Indices: 176060--176098 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
176050 ATTTAAATTT
176060 AAATGATTTTAAATGTTAAA
1 AAATGATTTTAAATGTTAAA
*
176080 AAAT-ATTTTTAATGTTAAA
1 AAATGATTTTAAATGTTAAA
176099 CAAGTAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.44
Consensus pattern (20 bp):
AAATGATTTTAAATGTTAAA
Found at i:176617 original size:19 final size:19
Alignment explanation
Indices: 176595--176631 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
176585 TGCAAAATGC
* *
176595 ATAATTTTTTTAAGAATAA
1 ATAAGTTTTTTAAAAATAA
176614 ATAAGTTTTTTAAAAATA
1 ATAAGTTTTTTAAAAATA
176632 TATTTACATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (19 bp):
ATAAGTTTTTTAAAAATAA
Found at i:177715 original size:22 final size:22
Alignment explanation
Indices: 177690--177741 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
177680 ATGATAAGAT
*
177690 ATTATTATAATATAACATACAA
1 ATTATTATAATAAAACATACAA
* *
177712 ATTATTATAATAAAATATACAT
1 ATTATTATAATAAAACATACAA
177734 ATTATTAT
1 ATTATTAT
177742 TAACAGCCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (22 bp):
ATTATTATAATAAAACATACAA
Found at i:178276 original size:16 final size:16
Alignment explanation
Indices: 178235--178279 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
178225 TGAATTATCT
*
178235 TTGAATTTGAATTAAA
1 TTGAATTTGGATTAAA
*
178251 TTAAATTTGGATTAAA
1 TTGAATTTGGATTAAA
178267 TTGAATTTGGATT
1 TTGAATTTGGATT
178280 GTTGATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.47
Consensus pattern (16 bp):
TTGAATTTGGATTAAA
Found at i:182495 original size:28 final size:28
Alignment explanation
Indices: 182447--182527 Score: 96
Period size: 28 Copynumber: 3.0 Consensus size: 28
182437 GACAAACAAT
* *
182447 AAACCACCATTTTTTAC--ATACAAA-A
1 AAACCACCATATTTGACAAATACAAAGA
*
182472 ATAACTACCATATTTGACAAATACAAAGA
1 A-AACCACCATATTTGACAAATACAAAGA
*
182501 AAACCATCATATTTGACAAATACAAAG
1 AAACCACCATATTTGACAAATACAAAG
182528 GGTGGCATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
25 1 0.02
26 13 0.28
28 31 0.66
29 2 0.04
ACGTcount: A:0.51, C:0.20, G:0.05, T:0.25
Consensus pattern (28 bp):
AAACCACCATATTTGACAAATACAAAGA
Found at i:188446 original size:15 final size:15
Alignment explanation
Indices: 188426--188470 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
188416 GTTGTGTTTA
188426 TTTTATTTTTATATT
1 TTTTATTTTTATATT
*
188441 TTTTATGTTTA-ATT
1 TTTTATTTTTATATT
188455 ATTTT-TTTTTATATT
1 -TTTTATTTTTATATT
188470 T
1 T
188471 ATGTTGTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 9 0.35
15 17 0.65
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (15 bp):
TTTTATTTTTATATT
Found at i:188482 original size:29 final size:30
Alignment explanation
Indices: 188423--188495 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 30
188413 TGTGTTGTGT
* *
188423 TTATTTTATTTTTATATTTTTTATGTTTAA
1 TTATTTTATTTTTATATTTTGTATGTATAA
188453 TTATTTT-TTTTTATATTTATGT-TGTATAA
1 TTATTTTATTTTTATATTT-TGTATGTATAA
* *
188482 TTATATTATGTTTA
1 TTATTTTATTTTTA
188496 AAATTATTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 23 0.62
30 14 0.38
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (30 bp):
TTATTTTATTTTTATATTTTGTATGTATAA
Found at i:188502 original size:17 final size:19
Alignment explanation
Indices: 188463--188502 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
188453 TTATTTTTTT
*
188463 TTATATTTATGTTGTATAA
1 TTATATTTATGTTGTAAAA
188482 TTATA-TTATGTT-TAAAA
1 TTATATTTATGTTGTAAAA
188499 TTAT
1 TTAT
188503 TAAATTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 7 0.35
19 5 0.25
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (19 bp):
TTATATTTATGTTGTAAAA
Found at i:188920 original size:57 final size:58
Alignment explanation
Indices: 188832--188941 Score: 136
Period size: 56 Copynumber: 1.9 Consensus size: 58
188822 TATAGTATTT
* *
188832 TTTTAAATATTAATTTTATAATTATAAATATAAT-ATAAAT-TATTAAAATATCAAAA
1 TTTTAAATATAAATTATATAATTATAAATATAATGATAAATATATTAAAATATCAAAA
* * *
188888 TTTTAAATATAAA-TATATATATATATACATATAATGATAATTATATTTAAATAT
1 TTTTAAATATAAATTATATA-AT-TATAAATATAATGATAAATATATTAAAATAT
188942 ATTATATTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
55 5 0.11
56 14 0.31
57 11 0.24
58 5 0.11
59 10 0.22
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (58 bp):
TTTTAAATATAAATTATATAATTATAAATATAATGATAAATATATTAAAATATCAAAA
Found at i:188964 original size:14 final size:14
Alignment explanation
Indices: 188941--188971 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
188931 TATTTAAATA
*
188941 TATTATATTATTTT
1 TATTACATTATTTT
188955 TATTACATTATTTT
1 TATTACATTATTTT
188969 TAT
1 TAT
188972 ATTTATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTACATTATTTT
Found at i:192120 original size:2 final size:2
Alignment explanation
Indices: 192113--192141 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
192103 GACTTTATTT
192113 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
192142 CTTTTTGGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:192321 original size:2 final size:2
Alignment explanation
Indices: 192314--192352 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
192304 TTAATCGATG
192314 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
192353 GAAAATAACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:192911 original size:30 final size:31
Alignment explanation
Indices: 192843--192909 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
192833 TCGATTAGGC
* *
192843 TTTTTGAACGTTTAATTTGTACTTATATAAA
1 TTTTTTAACGTTTAATTTGTACTTAAATAAA
*
192874 TTTTTTAACTTTTAATTTGTA-TCTAAATAAA
1 TTTTTTAACGTTTAATTTGTACT-TAAATAAA
192905 TTTTT
1 TTTTT
192910 AATTTACACT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 1 0.03
31 31 0.97
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (31 bp):
TTTTTTAACGTTTAATTTGTACTTAAATAAA
Found at i:194936 original size:13 final size:13
Alignment explanation
Indices: 194920--194953 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
194910 AGGGATATAA
*
194920 GAGAGGGATGCTT
1 GAGAGGGACGCTT
*
194933 GAGAGGGACGTTT
1 GAGAGGGACGCTT
194946 GAGAGGGA
1 GAGAGGGA
194954 GGAGGGAGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.26, C:0.06, G:0.50, T:0.18
Consensus pattern (13 bp):
GAGAGGGACGCTT
Found at i:195062 original size:27 final size:27
Alignment explanation
Indices: 195032--195107 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
195022 CAAACAATAT
* * * *
195032 ACCATCATTTTTTATAAATAAAAAGAA
1 ACCACCATTTTTGACAAACAAAAAGAA
* *
195059 ACCACCATTTTTGACAAACACAAAGTA
1 ACCACCATTTTTGACAAACAAAAAGAA
*
195086 ACCACCATTTTTGACAACCAAA
1 ACCACCATTTTTGACAAACAAA
195108 GGGTGGCTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.46, C:0.22, G:0.05, T:0.26
Consensus pattern (27 bp):
ACCACCATTTTTGACAAACAAAAAGAA
Found at i:199511 original size:13 final size:13
Alignment explanation
Indices: 199495--199528 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
199485 AGGGATACAA
199495 GAGAGGGATGCTT
1 GAGAGGGATGCTT
*
199508 GAGAAGGATGCTT
1 GAGAGGGATGCTT
199521 GAGAGGGA
1 GAGAGGGA
199529 AGAGGGAGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.29, C:0.06, G:0.47, T:0.18
Consensus pattern (13 bp):
GAGAGGGATGCTT
Found at i:199650 original size:27 final size:27
Alignment explanation
Indices: 199612--199682 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
199602 AACATGCCAT
* *
199612 CATTTTTGACAAATAAAAAGAAACTAC
1 CATTTTTGACAAACAAAAAGAAACCAC
* *
199639 CATTTTTGACAAACATAAAGTAACCAC
1 CATTTTTGACAAACAAAAAGAAACCAC
*
199666 CATTTTTGACAACCAAA
1 CATTTTTGACAAACAAA
199683 GCGTGGCTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.46, C:0.20, G:0.07, T:0.27
Consensus pattern (27 bp):
CATTTTTGACAAACAAAAAGAAACCAC
Found at i:203355 original size:29 final size:29
Alignment explanation
Indices: 203274--203355 Score: 75
Period size: 29 Copynumber: 3.0 Consensus size: 29
203264 AATTGTGTAT
* *
203274 TGATAATAATAATAATTTTTAATAAATAT
1 TGATTATAATAATAATTTTTAATAAATAA
* *
203303 TAAGTTA-AAAAATAA-TTTT--T-AATAA
1 TGA-TTATAATAATAATTTTTAATAAATAA
*
203328 TGATTATAATGATAATTTTTAATAAATA
1 TGATTATAATAATAATTTTTAATAAATA
203356 TAAAGTAGAT
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
24 3 0.08
25 12 0.30
26 5 0.12
28 5 0.12
29 13 0.32
30 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (29 bp):
TGATTATAATAATAATTTTTAATAAATAA
Found at i:203824 original size:2 final size:2
Alignment explanation
Indices: 203817--203864 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
203807 AATTGGGATG
203817 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
203858 AT AT AT A
1 AT AT AT A
203865 GAGAGAGAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:205978 original size:30 final size:30
Alignment explanation
Indices: 205944--206001 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
205934 ATTTAAGCAT
*
205944 TTAACCTTTAATTTATACTTAAATATGCCC
1 TTAACCTTTAATTTATACTCAAATATGCCC
* *
205974 TTAACTTTTAATTTGTACTCAAATATGC
1 TTAACCTTTAATTTATACTCAAATATGC
206002 TTCTAGTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.17, G:0.05, T:0.45
Consensus pattern (30 bp):
TTAACCTTTAATTTATACTCAAATATGCCC
Found at i:206449 original size:2 final size:2
Alignment explanation
Indices: 206442--206471 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
206432 CCAAATAAGC
206442 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
206472 GAGGCAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:206525 original size:18 final size:17
Alignment explanation
Indices: 206498--206536 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
206488 TTTTATATAT
*
206498 AAATATAAAACCAAAGAA
1 AAATAGAAAA-CAAAGAA
*
206516 AAATAGAAAAGAAAGAA
1 AAATAGAAAACAAAGAA
206533 AAAT
1 AAAT
206537 GACTCAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.74, C:0.05, G:0.10, T:0.10
Consensus pattern (17 bp):
AAATAGAAAACAAAGAA
Found at i:207482 original size:30 final size:29
Alignment explanation
Indices: 207428--207524 Score: 113
Period size: 29 Copynumber: 3.2 Consensus size: 29
207418 TTTTTATATC
207428 TAAATAACTCTTTAACCTTTTAACTTATAAT
1 TAAATAACTC-TTAACC-TTTAACTTATAAT
* *
207459 TAAATATACTCTAAACCTTTAACTTAGAAT
1 TAAATA-ACTCTTAACCTTTAACTTATAAT
* * * *
207489 TAAATAAATCTTAACTTTTAAATTATATT
1 TAAATAACTCTTAACCTTTAACTTATAAT
207518 TAAATAA
1 TAAATAA
207525 ACCCTTATAA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
29 24 0.42
30 18 0.32
31 11 0.19
32 4 0.07
ACGTcount: A:0.44, C:0.12, G:0.01, T:0.42
Consensus pattern (29 bp):
TAAATAACTCTTAACCTTTAACTTATAAT
Found at i:209165 original size:21 final size:20
Alignment explanation
Indices: 209133--209171 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
209123 CATATTTTTG
*
209133 TCTAAATGTATCGATACATT
1 TCTAAATATATCGATACATT
209153 TCTAGAATATATCGATACA
1 TCTA-AATATATCGATACA
209172 AAGTCCCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.36
Consensus pattern (20 bp):
TCTAAATATATCGATACATT
Found at i:209349 original size:33 final size:33
Alignment explanation
Indices: 209292--209391 Score: 91
Period size: 33 Copynumber: 3.1 Consensus size: 33
209282 GCCAAGGAAA
*
209292 TGTATCGATACATTACTCAATGTATTGATACAT
1 TGTATCGATACATTACTCAATGTATCGATACAT
**
209325 TGTATCGATACATTGA-TCTTTGTATCGATACAT
1 TGTATCGATACATT-ACTCAATGTATCGATACAT
* * *
209358 T-TA-GGA-ACTTTTACCCAGATGTATCGATACAT
1 TGTATCGATAC-ATTACTCA-ATGTATCGATACAT
209390 TG
1 TG
209392 AATAATGTAT
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
30 3 0.06
31 5 0.09
32 16 0.30
33 29 0.54
34 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATTACTCAATGTATCGATACAT
Found at i:211561 original size:27 final size:27
Alignment explanation
Indices: 211531--211599 Score: 138
Period size: 27 Copynumber: 2.6 Consensus size: 27
211521 TTTATTCATC
211531 GGGGACACTCCAACCACATTCCTCCGA
1 GGGGACACTCCAACCACATTCCTCCGA
211558 GGGGACACTCCAACCACATTCCTCCGA
1 GGGGACACTCCAACCACATTCCTCCGA
211585 GGGGACACTCCAACC
1 GGGGACACTCCAACC
211600 CCGTTTTCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.26, C:0.41, G:0.20, T:0.13
Consensus pattern (27 bp):
GGGGACACTCCAACCACATTCCTCCGA
Found at i:213138 original size:26 final size:27
Alignment explanation
Indices: 213093--213154 Score: 92
Period size: 26 Copynumber: 2.3 Consensus size: 27
213083 TTTGTGTTTG
213093 TCAAAAATGGTAGTTCCTTTTTATTTA
1 TCAAAAATGGTAGTTCCTTTTTATTTA
*
213120 TCAAAAATGGT-GATT-CTTTTTGTTTA
1 TCAAAAATGGTAG-TTCCTTTTTATTTA
213146 TCAAAAATG
1 TCAAAAATG
213155 ATAGCTTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
26 20 0.61
27 13 0.39
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (27 bp):
TCAAAAATGGTAGTTCCTTTTTATTTA
Found at i:213173 original size:24 final size:24
Alignment explanation
Indices: 213116--213202 Score: 68
Period size: 24 Copynumber: 3.5 Consensus size: 24
213106 TTCCTTTTTA
* * *
213116 TTTATCAAAAATGGTGATTCTTTTTG
1 TTTATCAAAAATGAT-A-GCTTATTG
213142 TTTATCAAAAATGATAGCTTATTG
1 TTTATCAAAAATGATAGCTTATTG
* * * *
213166 TTTGTCAAAATTGGTAGCTAATT-
1 TTTATCAAAAATGATAGCTTATTG
*
213189 TTTATTAGAAAATG
1 TTTATCA-AAAATG
213203 GGAGAGGATA
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
23 5 0.10
24 30 0.60
25 1 0.02
26 14 0.28
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (24 bp):
TTTATCAAAAATGATAGCTTATTG
Found at i:213890 original size:209 final size:210
Alignment explanation
Indices: 213506--213927 Score: 704
Period size: 209 Copynumber: 2.0 Consensus size: 210
213496 TTGTATTGGC
* *
213506 AAGCTCTTGAAGAATTTGTGATTCCAAAATGAGTTTAACATCAGCTGCATTAACATCTTCATCAG
1 AAGCTATTGAAGAATTTGTGATTCCAAAATGAGTTTAACATCAGCTGCATCAACATCTTCATCAG
* * *
213571 CACCCATTTGGGCTAAGACTACTGTGACAAATGGAAAATTGGCTGTGGCGATTTTTGATGGTACG
66 CACCCATTTGGGCTAAGACTACTGTGACAAATGAAAAATTGGCTGTGGAGATTTTTGATGGTACA
* *
213636 GGTCATTTTGGCATGTGGCAGAGTGAAGTTTTAGATGCTCTCTAGACTATCTATCTAGAGAGCAG
131 AGTCATTTTGGCATGTGGCAGAGTGAAGTTCTAGATGCTCTCTAGACTATCTATCTAGAGAGCAG
*
213701 AGATATGCCTTTTCT
196 AGATAGGCCTTTTCT
* *
213716 AAGCTATTGAAGAATTTGTGATT-CAAAATGAGTTTGATATCAGCTGCATCAACATCTTCATCAG
1 AAGCTATTGAAGAATTTGTGATTCCAAAATGAGTTTAACATCAGCTGCATCAACATCTTCATCAG
* *
213780 CACCCATTTGGGCT-AGAACTGCTGTGACAAATGAAAAATTGGCTGTGGAGATTTTTGATGGTAT
66 CACCCATTTGGGCTAAG-ACTACTGTGACAAATGAAAAATTGGCTGTGGAGATTTTTGATGGTAC
*
213844 AAGTCATTTTGGCATGTGGTAGAGTGAAGTTCTAGATGCTCTCTAGACTATCTATCTAGAGAGCA
130 AAGTCATTTTGGCATGTGGCAGAGTGAAGTTCTAGATGCTCTCTAGACTATCTATCTAGAGAGCA
213909 GAGATAGGCCTTTTCT
195 GAGATAGGCCTTTTCT
213925 AAG
1 AAG
213928 GAGACTTCTG
Statistics
Matches: 198, Mismatches: 13, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
208 2 0.01
209 174 0.88
210 22 0.11
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (210 bp):
AAGCTATTGAAGAATTTGTGATTCCAAAATGAGTTTAACATCAGCTGCATCAACATCTTCATCAG
CACCCATTTGGGCTAAGACTACTGTGACAAATGAAAAATTGGCTGTGGAGATTTTTGATGGTACA
AGTCATTTTGGCATGTGGCAGAGTGAAGTTCTAGATGCTCTCTAGACTATCTATCTAGAGAGCAG
AGATAGGCCTTTTCT
Found at i:215846 original size:21 final size:22
Alignment explanation
Indices: 215815--215857 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
215805 CTGTTTAGAC
* *
215815 AAGTAGTACTCCACAGCAGGTG
1 AAGTAGTACTCCAAAACAGGTG
215837 AAGTA-TACTCCAAAACAGGTG
1 AAGTAGTACTCCAAAACAGGTG
215858 GAGTTTCAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19
Consensus pattern (22 bp):
AAGTAGTACTCCAAAACAGGTG
Found at i:217802 original size:24 final size:25
Alignment explanation
Indices: 217750--217803 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
217740 TGTGTTTACG
*
217750 AAAAATGGTAGTTCTTTTTATTTGTC
1 AAAAATGGTAG-TCTTGTTATTTGTC
*
217776 AAAAATGGTAG-CTTGTTGTTTGTC
1 AAAAATGGTAGTCTTGTTATTTGTC
217800 AAAA
1 AAAA
217804 TTAATGGCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 15 0.58
26 11 0.42
ACGTcount: A:0.31, C:0.07, G:0.19, T:0.43
Consensus pattern (25 bp):
AAAAATGGTAGTCTTGTTATTTGTC
Found at i:220064 original size:7 final size:7
Alignment explanation
Indices: 220052--220077 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
220042 AAAATTTTAA
220052 TTTATAT
1 TTTATAT
220059 TTTATAT
1 TTTATAT
220066 TTTATAT
1 TTTATAT
220073 TTTAT
1 TTTAT
220078 TATAATAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTATAT
Found at i:220753 original size:18 final size:17
Alignment explanation
Indices: 220703--220754 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
220693 ATTTGTATTT
220703 TTAAAATGTTATATT-TA
1 TTAAAAT-TTATATTATA
* *
220720 TTTAAATTT-TAATATA
1 TTAAAATTTATATTATA
220736 TTAATAATTTATATTATA
1 TTAA-AATTTATATTATA
220754 T
1 T
220755 ATTTTTATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
15 3 0.11
16 7 0.25
17 11 0.39
18 7 0.25
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TTAAAATTTATATTATA
Found at i:220795 original size:19 final size:20
Alignment explanation
Indices: 220754--220798 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
220744 TTATATTATA
* * *
220754 TATTTTTATTATTTTTATTT
1 TATTTTTAATATTTGTATCT
220774 TATTTTTAATA-TTGTATCT
1 TATTTTTAATATTTGTATCT
220793 TATTTT
1 TATTTT
220799 AATTATTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (20 bp):
TATTTTTAATATTTGTATCT
Found at i:220805 original size:19 final size:19
Alignment explanation
Indices: 220754--220805 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
220744 TTATATTATA
* * *
220754 TATTTTTATTATTTTTATTT
1 TATTTTAATTA-TTGTATCT
220774 TATTTTTAA-TATTGTATCT
1 TA-TTTTAATTATTGTATCT
220793 TATTTTAATTATT
1 TATTTTAATTATT
220806 ATTTTATGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 6 0.22
19 12 0.44
20 4 0.15
21 5 0.19
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (19 bp):
TATTTTAATTATTGTATCT
Found at i:222305 original size:13 final size:12
Alignment explanation
Indices: 222268--222310 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
222258 AATAATAAAA
222268 AAAATTATTTTT
1 AAAATTATTTTT
*
222280 AATAATCAATTTTT
1 AA-AAT-TATTTTT
222294 AAAATTATTTTTT
1 AAAATTA-TTTTT
222307 AAAA
1 AAAA
222311 AAATTTATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 3 0.12
13 15 0.58
14 8 0.31
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (12 bp):
AAAATTATTTTT
Found at i:228564 original size:25 final size:26
Alignment explanation
Indices: 228536--228584 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 26
228526 TCAATCCACA
228536 TTTTTTTTAATTGGG-TTTT-GTTTC
1 TTTTTTTTAATTGGGCTTTTAGTTTC
228560 TTTTTTTTAATTGGGCTTTTAGTTT
1 TTTTTTTTAATTGGGCTTTTAGTTT
228585 AGATTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 15 0.65
25 4 0.17
26 4 0.17
ACGTcount: A:0.10, C:0.04, G:0.16, T:0.69
Consensus pattern (26 bp):
TTTTTTTTAATTGGGCTTTTAGTTTC
Found at i:228597 original size:23 final size:23
Alignment explanation
Indices: 228565--228617 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
228555 GTTTCTTTTT
*
228565 TTTAATTGGGCTTTTAGTTTAGA
1 TTTAAATGGGCTTTTAGTTTAGA
*
228588 TTTAAATGGGTTTTTAGTTTAGA
1 TTTAAATGGGCTTTTAGTTTAGA
228611 TTTAAAT
1 TTTAAAT
228618 AAGTTTAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.26, C:0.02, G:0.19, T:0.53
Consensus pattern (23 bp):
TTTAAATGGGCTTTTAGTTTAGA
Found at i:228623 original size:23 final size:22
Alignment explanation
Indices: 228576--228636 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
228566 TTAATTGGGC
**
228576 TTTTAGTTTAGATTTAAATGGG
1 TTTTAGTTTAGATTTAAATAAG
228598 TTTTTAGTTTAGATTTAAATAAG
1 -TTTTAGTTTAGATTTAAATAAG
* *
228621 TTTAAGTTTAAATTTA
1 TTTTAGTTTAGATTTA
228637 TATTTTATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 14 0.41
23 20 0.59
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (22 bp):
TTTTAGTTTAGATTTAAATAAG
Found at i:229582 original size:26 final size:26
Alignment explanation
Indices: 229526--229584 Score: 77
Period size: 24 Copynumber: 2.3 Consensus size: 26
229516 TTTATTTATA
229526 AATTATAATATTTTTTAGATAAAAAAT
1 AATT-TAATATTTTTTAGATAAAAAAT
*
229553 -ATTTAATA-TTTTTAGCTAAAAAAT
1 AATTTAATATTTTTTAGATAAAAAAT
229577 CAATTTAA
1 -AATTTAA
229585 ATTGGACCTG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 15 0.52
25 5 0.17
26 9 0.31
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.44
Consensus pattern (26 bp):
AATTTAATATTTTTTAGATAAAAAAT
Found at i:229693 original size:39 final size:40
Alignment explanation
Indices: 229643--229731 Score: 121
Period size: 39 Copynumber: 2.2 Consensus size: 40
229633 CATATTTATA
229643 TTATTATATA-TTTATATAAATTTA-ATATATTA-ATAATTT
1 TTATTATATATTTTA-ATAAATTTATATAT-TTATATAATTT
*
229682 TTATTATATATTTTAATAAATTTATATATTTATATTATTT
1 TTATTATATATTTTAATAAATTTATATATTTATATAATTT
229722 TATATTATAT
1 T-TATTATAT
229732 TATATTTTAA
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
39 22 0.49
40 15 0.33
41 8 0.18
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (40 bp):
TTATTATATATTTTAATAAATTTATATATTTATATAATTT
Found at i:229697 original size:22 final size:21
Alignment explanation
Indices: 229643--229753 Score: 67
Period size: 21 Copynumber: 5.4 Consensus size: 21
229633 CATATTTATA
*
229643 TTATTATATATTTATATAA-AT
1 TTATTATATATTT-TATAATTT
*
229664 TTA--ATATA-TTAATAATTT
1 TTATTATATATTTTATAATTT
*
229682 TTATTATATATTTTAATAA-AT
1 TTATTATATATTTT-ATAATTT
* *
229703 TTA-TATAT-TTATATTATTT
1 TTATTATATATTTTATAATTT
229722 TATATTATATTATATTT-TAATTT
1 T-TATTATA-TAT-TTTATAATTT
*
229745 TTTTTATAT
1 TTATTATAT
229754 CGTAAAAACA
Statistics
Matches: 69, Mismatches: 10, Indels: 22
0.68 0.10 0.22
Matches are distributed among these distances:
17 4 0.06
18 9 0.13
19 10 0.14
20 12 0.17
21 14 0.20
22 11 0.16
23 7 0.10
24 2 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTATTATATATTTTATAATTT
Found at i:229706 original size:18 final size:18
Alignment explanation
Indices: 229646--229712 Score: 57
Period size: 18 Copynumber: 3.6 Consensus size: 18
229636 ATTTATATTA
229646 TTATATA-TTTATATAAAT
1 TTATATATTTTA-ATAAAT
* *
229664 TTA-ATATATTAATAATTTTT
1 TTATATATTTTAATAA---AT
229684 ATTATATATTTTAATAAAT
1 -TTATATATTTTAATAAAT
229703 TTATATATTT
1 TTATATATTT
229713 ATATTATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
17 7 0.18
18 16 0.41
19 1 0.03
20 1 0.03
21 3 0.08
22 11 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTATATATTTTAATAAAT
Found at i:229732 original size:39 final size:41
Alignment explanation
Indices: 229634--229732 Score: 116
Period size: 39 Copynumber: 2.4 Consensus size: 41
229624 TGTCATACTC
229634 ATATTTATATTATTATATATTTATATAAATTTAATATATTAATA
1 ATATTT-TA-TATTATAT-TTTATATAAATTTAATATATTAATA
*
229678 AT-TTTTAT-TATATATTTTA-ATAAATTT-ATATATTTATA
1 ATATTTTATAT-TATATTTTATATAAATTTAATATATTAATA
*
229716 TTATTTTATATTATATT
1 ATATTTTATATTATATT
229733 ATATTTTAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
38 11 0.22
39 20 0.40
40 6 0.12
41 6 0.12
42 2 0.04
43 3 0.06
44 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (41 bp):
ATATTTTATATTATATTTTATATAAATTTAATATATTAATA
Found at i:229734 original size:10 final size:9
Alignment explanation
Indices: 229635--229737 Score: 56
Period size: 10 Copynumber: 11.1 Consensus size: 9
229625 GTCATACTCA
229635 TATTTATAT
1 TATTTATAT
229644 TA-TTATA-
1 TATTTATAT
229651 TATTTATAT
1 TATTTATAT
*
229660 AAATTTA-AT
1 -TATTTATAT
*
229669 ATATTAATAAT
1 -TATTTAT-AT
229680 T-TTTATTAT
1 TATTTA-TAT
229689 ATATTT-TAAT
1 -TATTTAT-AT
*
229699 AAATTTATA-
1 -TATTTATAT
229708 TATTTATAT
1 TATTTATAT
229717 TATTTTATAT
1 TA-TTTATAT
229727 TATATTATAT
1 TAT-TTATAT
229737 T
1 T
229738 TTAATTTTTT
Statistics
Matches: 75, Mismatches: 6, Indels: 25
0.71 0.06 0.24
Matches are distributed among these distances:
7 2 0.03
8 17 0.23
9 18 0.24
10 32 0.43
11 6 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TATTTATAT
Found at i:229736 original size:20 final size:18
Alignment explanation
Indices: 229634--229737 Score: 79
Period size: 19 Copynumber: 5.6 Consensus size: 18
229624 TGTCATACTC
229634 ATATTTATATTA--TTAT
1 ATATTTATATTATTTTAT
* *
229650 ATATTTATATAAATTTAAT
1 ATATTTATAT-TATTTTAT
* *
229669 ATATTAATAATTTTTATTAT
1 ATATTTAT-ATTATT-TTAT
* *
229689 ATATTT-TAATAAATTTAT
1 ATATTTAT-ATTATTTTAT
229707 ATATTTATATTATTTTAT
1 ATATTTATATTATTTTAT
229725 ATTATATTATATT
1 A-TAT-TTATATT
229738 TTAATTTTTT
Statistics
Matches: 68, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
16 10 0.15
17 1 0.01
18 19 0.28
19 21 0.31
20 17 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATATTTATATTATTTTAT
Found at i:237991 original size:2 final size:2
Alignment explanation
Indices: 237980--238014 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
237970 ATCCAAACAG
237980 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
238015 TTATTAGAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:238434 original size:19 final size:18
Alignment explanation
Indices: 238409--238450 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
238399 AATTTTCTTA
238409 AAAATATATTTAAAAATT
1 AAAATATATTTAAAAATT
*
238427 ATAAATATATTTTAAAATT
1 A-AAATATATTTAAAAATT
238446 AAAAT
1 AAAAT
238451 TAAATATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAATATATTTAAAAATT
Found at i:240337 original size:19 final size:21
Alignment explanation
Indices: 240313--240359 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
240303 CCTACTTAAA
240313 TTTAAATTATTTATT-C-TTT
1 TTTAAATTATTTATTACATTT
* *
240332 TTTAAAATATTTTTTACATTT
1 TTTAAATTATTTATTACATTT
240353 TTTAAAT
1 TTTAAAT
240360 AAACCATCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 13 0.57
20 1 0.04
21 9 0.39
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTAAATTATTTATTACATTT
Found at i:251553 original size:19 final size:19
Alignment explanation
Indices: 251531--251569 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
251521 AATAATAGAG
251531 AAAGAAAATAAATATAACA
1 AAAGAAAATAAATATAACA
251550 AAAGAAAATAAATATAACA
1 AAAGAAAATAAATATAACA
251569 A
1 A
251570 TGAGTAAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.15
Consensus pattern (19 bp):
AAAGAAAATAAATATAACA
Found at i:252279 original size:29 final size:29
Alignment explanation
Indices: 252240--252300 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
252230 ACATTTTCCC
* *
252240 AAAATCTTATCGCACATGCACAAGTTAAA
1 AAAATCTTATCACACATACACAAGTTAAA
*
252269 AAAATCTTATCACACGTACACAAGTTAAA
1 AAAATCTTATCACACATACACAAGTTAAA
252298 AAA
1 AAA
252301 GTAAAAATGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.49, C:0.20, G:0.08, T:0.23
Consensus pattern (29 bp):
AAAATCTTATCACACATACACAAGTTAAA
Found at i:254928 original size:37 final size:37
Alignment explanation
Indices: 254878--254970 Score: 95
Period size: 37 Copynumber: 2.5 Consensus size: 37
254868 TTTAAATTAA
*
254878 ATTAAAT-TAAATTATTATTTATTAAT-TAAAAATTTT
1 ATTAAATAT-AATTATTATTTATTAATATAAAAATATT
**
254914 ATTTAAATATAATTA-TAAATATTAATATAAAAATATT
1 A-TTAAATATAATTATTATTTATTAATATAAAAATATT
*
254951 ATTAATTATTAA-TATTATTT
1 ATTAAATA-TAATTATTATTT
254971 TAAATAGTGA
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
36 18 0.39
37 27 0.59
38 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (37 bp):
ATTAAATATAATTATTATTTATTAATATAAAAATATT
Found at i:254947 original size:14 final size:13
Alignment explanation
Indices: 254897--254955 Score: 54
Period size: 12 Copynumber: 4.8 Consensus size: 13
254887 AATTATTATT
254897 TATTAATTAAAAA
1 TATTAATTAAAAA
* *
254910 T-TTTATT-TAAA
1 TATTAATTAAAAA
*
254921 TA-TAATTATAAA
1 TATTAATTAAAAA
254933 TATTAATATAAAAA
1 TATTAAT-TAAAAA
254947 TATT-ATTAA
1 TATTAATTAA
254956 TTATTAATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
11 8 0.21
12 14 0.37
13 7 0.18
14 9 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TATTAATTAAAAA
Found at i:255838 original size:6 final size:7
Alignment explanation
Indices: 255820--255849 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
255810 ATAAAGTTTA
255820 ATTTTTT
1 ATTTTTT
255827 ATTTTTT
1 ATTTTTT
255834 ATTTTTT
1 ATTTTTT
255841 ATTTTTT
1 ATTTTTT
255848 AT
1 AT
255850 ATTCTTGGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (7 bp):
ATTTTTT
Found at i:257778 original size:37 final size:38
Alignment explanation
Indices: 257698--257778 Score: 112
Period size: 37 Copynumber: 2.2 Consensus size: 38
257688 AATTCAAATC
* * *
257698 ATTTCATATTTAGATTATTTAAGTTTGTGTTGTTTGTCG
1 ATTT-ATATTTAGATTATTTAAATTTGTGCTGTTTATCG
257737 -TTTATATTTAGATTATTTAAATTTGTGCTGTTTAT-G
1 ATTTATATTTAGATTATTTAAATTTGTGCTGTTTATCG
257773 ATTTAT
1 ATTTAT
257779 GTTTTTCGAC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 1 0.03
37 34 0.89
38 3 0.08
ACGTcount: A:0.23, C:0.04, G:0.15, T:0.58
Consensus pattern (38 bp):
ATTTATATTTAGATTATTTAAATTTGTGCTGTTTATCG
Found at i:258191 original size:14 final size:16
Alignment explanation
Indices: 258144--258208 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 16
258134 AAATAAAGAC
*
258144 ATTTAATTTTATAAAAAA
1 ATTT-ATTTTAT-AATAA
258162 ATATT-TTTT-TAATAA
1 AT-TTATTTTATAATAA
258177 ATTTA-TTTA-AATAA
1 ATTTATTTTATAATAA
*
258191 AATTATTTTATAATAA
1 ATTTATTTTATAATAA
258207 AT
1 AT
258209 AAAAGGACTT
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
14 14 0.36
15 10 0.26
16 7 0.18
17 4 0.10
18 2 0.05
19 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTATTTTATAATAA
Found at i:258341 original size:132 final size:132
Alignment explanation
Indices: 258193--258449 Score: 351
Period size: 132 Copynumber: 1.9 Consensus size: 132
258183 TTAAATAAAA
* * * * * * *
258193 TTATTTTATAATAAAT-AAAAGGACTTAAAGTTTATATTAAATTGCTTTTATTT-TCAAA-TTGT
1 TTATTTTATAATAAATAAAAAAGAATTAAAATTTACATTAAATT-ATTTTATTTGT-AAAGGTCT
* *
258255 AATTTTTTAAAAAAGTAAACAAATTTATTTACTAAATTCT-AACTTGCTATTGTAAATTTTTTTA
64 AA-TTTTTAAAAAAATAAACAAATTTATTTAATAAATTCTGAA-TTGCTATTGTAAATTTTTTTA
258319 ATGGCT
127 ATGGCT
*
258325 TTATTTTATAATAAATAAAAAATAATTAAAATTTACATTAAATTATTTTATTTGTAAAGGTCTAA
1 TTATTTTATAATAAATAAAAAAGAATTAAAATTTACATTAAATTATTTTATTTGTAAAGGTCTAA
*
258390 TTTTTAAAAAAATAAATAAATTTATTTAATAAATTCTGAATTGCTATTGTAAATTTTTTT
66 TTTTTAAAAAAATAAACAAATTTATTTAATAAATTCTGAATTGCTATTGTAAATTTTTTT
258450 TACTATTAAT
Statistics
Matches: 110, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
132 81 0.74
133 29 0.26
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (132 bp):
TTATTTTATAATAAATAAAAAAGAATTAAAATTTACATTAAATTATTTTATTTGTAAAGGTCTAA
TTTTTAAAAAAATAAACAAATTTATTTAATAAATTCTGAATTGCTATTGTAAATTTTTTTAATGG
CT
Found at i:259885 original size:24 final size:24
Alignment explanation
Indices: 259853--259919 Score: 116
Period size: 24 Copynumber: 2.8 Consensus size: 24
259843 CATCTCATTG
259853 AGTTTATATTTTATAAATTTATTT
1 AGTTTATATTTTATAAATTTATTT
*
259877 AGTTTATATTTTATAATTTTATTT
1 AGTTTATATTTTATAAATTTATTT
*
259901 AATTTATATTTTATAAATT
1 AGTTTATATTTTATAAATT
259920 CACTGTCAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (24 bp):
AGTTTATATTTTATAAATTTATTT
Found at i:260716 original size:3 final size:3
Alignment explanation
Indices: 260710--260744 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
260700 GGGTAATGTC
260710 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
260745 AACTGAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:265488 original size:22 final size:21
Alignment explanation
Indices: 265440--265491 Score: 79
Period size: 22 Copynumber: 2.5 Consensus size: 21
265430 ATATATTAGT
265440 AAAAGTT-AAAAGGAAAAATA
1 AAAAGTTAAAAAGGAAAAATA
*
265460 AATAGTTAAAAAGGAAAGAATA
1 AAAAGTTAAAAAGGAAA-AATA
265482 AAAAGTTAAA
1 AAAAGTTAAA
265492 GTAGATCTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 6 0.21
21 9 0.32
22 13 0.46
ACGTcount: A:0.67, C:0.00, G:0.15, T:0.17
Consensus pattern (21 bp):
AAAAGTTAAAAAGGAAAAATA
Found at i:266098 original size:43 final size:42
Alignment explanation
Indices: 265991--266126 Score: 136
Period size: 43 Copynumber: 3.3 Consensus size: 42
265981 TTTTCAGGGA
* * *
265991 AAACGCCGCTAACTACTTAAATTTAGCGGCGTTT-TTCTT-T
1 AAACGCCGCTAAATACTTAAATTTAGTGGCGTTTATTTTTAT
* * * *
266031 AAATGCTGTTAATTACTTAAATTTAGTGGCGTTTATTTTTAGT
1 AAACGCCGCTAAATACTTAAATTTAGTGGCGTTTATTTTTA-T
* *
266074 AAACGCCGCTAAATA-TTCAAATTTAGTGACGTTTATATTTA-
1 AAACGCCGCTAAATACTT-AAATTTAGTGGCGTTTATTTTTAT
*
266115 AAATGCCGCTAA
1 AAACGCCGCTAA
266127 TTTAATGAAT
Statistics
Matches: 79, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
40 29 0.37
41 15 0.19
42 2 0.03
43 33 0.42
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (42 bp):
AAACGCCGCTAAATACTTAAATTTAGTGGCGTTTATTTTTAT
Found at i:272199 original size:18 final size:18
Alignment explanation
Indices: 272145--272202 Score: 55
Period size: 18 Copynumber: 3.0 Consensus size: 18
272135 TAAAAAGTGT
272145 AAATAAAAA-AATAATATA
1 AAATAAAAATAATAA-ATA
*
272163 ACATAAATATATAACATAAATA
1 AAATAAA-A-AT-A-ATAAATA
272185 AAATAAAAATAATAAATA
1 AAATAAAAATAATAAATA
272203 TTCAGATCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
18 13 0.39
19 2 0.06
20 3 0.09
21 1 0.03
22 10 0.30
23 4 0.12
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.24
Consensus pattern (18 bp):
AAATAAAAATAATAAATA
Found at i:272923 original size:18 final size:18
Alignment explanation
Indices: 272900--272938 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
272890 TTGGTGTGAG
272900 ATTATTATATATTGCTAA
1 ATTATTATATATTGCTAA
272918 ATTATTATATATTGCTAA
1 ATTATTATATATTGCTAA
272936 ATT
1 ATT
272939 GGAGATGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.51
Consensus pattern (18 bp):
ATTATTATATATTGCTAA
Found at i:273557 original size:15 final size:15
Alignment explanation
Indices: 273524--273558 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
273514 TACATCGCAT
*
273524 AAAAGCAAATAAGGA
1 AAAAGCAAATAAAGA
273539 AAAAGACAAATAAAGA
1 AAAAG-CAAATAAAGA
273555 AAAA
1 AAAA
273559 TAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.74, C:0.06, G:0.14, T:0.06
Consensus pattern (15 bp):
AAAAGCAAATAAAGA
Found at i:275156 original size:13 final size:14
Alignment explanation
Indices: 275128--275156 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
275118 TAAATTGAGG
275128 CAGAAAGTGCTTTT
1 CAGAAAGTGCTTTT
275142 CAGAAAGTG-TTTT
1 CAGAAAGTGCTTTT
275155 CA
1 CA
275157 ACAATTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (14 bp):
CAGAAAGTGCTTTT
Found at i:277114 original size:22 final size:21
Alignment explanation
Indices: 277082--277166 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 21
277072 AAACTAGTAG
*
277082 GATTTTTAATTAAATATTTTAA
1 GATTTTAAATTAAAT-TTTTAA
277104 GATTTTAAATTAAACTTTTATTATA
1 GATTTTAAATTAAA--TTT-TTA-A
* *
277129 GGATTTTCAATTAAATTTTTTA
1 -GATTTTAAATTAAATTTTTAA
*
277151 GAATTTT-ATTTAAATT
1 G-ATTTTAAATTAAATT
277167 ACAAATAATA
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
21 9 0.17
22 19 0.36
23 4 0.08
24 7 0.13
25 1 0.02
26 13 0.25
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (21 bp):
GATTTTAAATTAAATTTTTAA
Found at i:277125 original size:26 final size:26
Alignment explanation
Indices: 277096--277148 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
277086 TTTAATTAAA
*
277096 TATTTTAAGATTTTAAATTAAACTTT
1 TATTATAAGATTTTAAATTAAACTTT
* * *
277122 TATTATAGGATTTTCAATTAAATTTT
1 TATTATAAGATTTTAAATTAAACTTT
277148 T
1 T
277149 TAGAATTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.55
Consensus pattern (26 bp):
TATTATAAGATTTTAAATTAAACTTT
Found at i:287170 original size:20 final size:20
Alignment explanation
Indices: 287142--287216 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
287132 TCATACCCTG
287142 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
287162 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
287182 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
287202 ATGTATCGATACATT
1 ATGTATCGATACATT
287217 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:287209 original size:40 final size:39
Alignment explanation
Indices: 287142--287219 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
287132 TCATACCCTG
* *
287142 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
287182 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
287220 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:298986 original size:16 final size:17
Alignment explanation
Indices: 298965--298997 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
298955 TATTTGTCAA
298965 ACCCGCCAGTG-TTGGT
1 ACCCGCCAGTGCTTGGT
*
298981 ACCCGCCGGTGCTTGGT
1 ACCCGCCAGTGCTTGGT
298998 CGTCCTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.09, C:0.33, G:0.33, T:0.24
Consensus pattern (17 bp):
ACCCGCCAGTGCTTGGT
Found at i:301247 original size:11 final size:11
Alignment explanation
Indices: 301231--301271 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
301221 CCTTTACACC
*
301231 AAAAAAAATAA
1 AAAAAAAACAA
301242 AAAAAAAACAA
1 AAAAAAAACAA
301253 AAGAAAAAACAA
1 AA-AAAAAACAA
*
301265 GAAAAAA
1 AAAAAAA
301272 TAGCAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.88, C:0.05, G:0.05, T:0.02
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:302543 original size:29 final size:28
Alignment explanation
Indices: 302499--303566 Score: 957
Period size: 29 Copynumber: 35.4 Consensus size: 28
302489 GAAAGTTCAT
*
302499 CCCTTTCAAAGACCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
302527 CTCCTTTCAAAGCCCACAAATCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
*
302556 CTCTTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
302585 CCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
302613 CTCCTTTCAAAGCCTACAAGTTAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* *
302642 CTCTTTTCAAAGCCCACAAATCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* *
302671 CTCTTTTTAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
302700 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
*
302729 CTCCTTTCAAAGCCCACAAATCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
302758 CTCTTTTCAAAGCCTACAAGTTAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* *
302787 CTCTTTTCAAAGCCCACAAATCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* *
302816 CTCTTTTTAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
302845 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
*
302874 CTCCTTTCAAAGCCCACAAATCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
*
302903 CTCTTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* *
302932 CCCTTTCAAAGCCCACAACTCATTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
302960 TCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
302988 CTCCTTTCAAAGCCCACAAGCCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
303017 CTCTTTTCAGAGCCCACAAGTTAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* *
303046 CCCTTTCAGAGCCCACAAGTCGGTGGCAA
1 CCCTTTCAAAGCCCACAAGTCAGTGGC-A
* *
303075 CCCATTTTAAAGCCCACACAAGTCGGTGGCAA
1 CCC-TTTCAAAG-CC-CACAAGTCAGTGGC-A
* *
303107 CCCATTCCAAAGCCCACACAAGTCGGTGGCAA
1 CCC-TTTCAAAG-CC-CACAAGTCAGTGGC-A
* *
303139 CCCATTCCAAAGCCCACACAAGTCGGTGGCAA
1 CCC-TTTCAAAG-CC-CACAAGTCAGTGGC-A
*
303171 CCCATTTCAAAGCCCACACAAGTCGGTGGCAA
1 CCC-TTTCAAAG-CC-CACAAGTCAGTGGC-A
*
303203 CCCATTTCAAAGCCCACACAAGTCGGTGGCAA
1 CCC-TTTCAAAG-CC-CACAAGTCAGTGGC-A
* *
303235 CCCATTCCAAAGCCCACACAAGTCGGTGGCAA
1 CCC-TTTCAAAG-CC-CACAAGTCAGTGGC-A
* *
303267 CCCATTCCAAAGCCCACACAAGTCGGTGGCAA
1 CCC-TTTCAAAG-CC-CACAAGTCAGTGGC-A
* *
303299 CCCATTCCAAAGCCCACACAAGTCGGTGGCAA
1 CCC-TTTCAAAG-CC-CACAAGTCAGTGGC-A
*
303331 CCCATTTCAAAGCCCACACAAGTCGGTGGCAA
1 CCC-TTTCAAAG-CC-CACAAGTCAGTGGC-A
*
303363 CCCATTTCAAAGCCCACATAAGTCGGTGGCAA
1 CCC-TTTCAAAGCCCAC--AAGTCAGTGGC-A
* *
303395 CCCATTTCAAAGCCCACACAAGTCGGTAGCAAA
1 CCC-TTTCAAAG-CC-CACAAGTCAGTGGC--A
* *
303428 CCCATTTCAAAACCCACACAAGTCGGTGGCAA
1 CCC-TTTC-AAAGCC-CACAAGTCAGTGGC-A
* *
303460 CCCATTCCAAAGCCCACACAAGTCGGTGGCAA
1 CCC-TTTCAAAG-CC-CACAAGTCAGTGGC-A
* *
303492 CTCATTTCAAAGCCCACACAAGTCGGTGGCAA
1 C-CCTTTCAAAG-CC-CACAAGTCAGTGGC-A
*
303524 CCCATTTAAAAGCCCATGCAAGTCAGTGGCAA
1 CCC-TTTCAAAGCCCA--CAAGTCAGTGGC-A
303556 CCCTTTTCAAA
1 CCC-TTTCAAA
303567 TCACCATATT
Statistics
Matches: 958, Mismatches: 64, Indels: 32
0.91 0.06 0.03
Matches are distributed among these distances:
28 100 0.10
29 402 0.42
30 11 0.01
31 10 0.01
32 400 0.42
33 29 0.03
34 6 0.01
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.19
Consensus pattern (28 bp):
CCCTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:303098 original size:32 final size:30
Alignment explanation
Indices: 302499--303566 Score: 965
Period size: 32 Copynumber: 35.3 Consensus size: 30
302489 GAAAGTTCAT
*
302499 CCCTTTCAAAG-AC-CACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACACAAGTCAGTGGCA
302527 CTCCTTTCAAAGCCCACA-AA-TCAGTGGCA
1 C-CCTTTCAAAGCCCACACAAGTCAGTGGCA
*
302556 CTCTTTTCAAAG-CC-CACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACACAAGTCAGTGGCA
302585 CCCTTTCAAAG-CC-CACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACACAAGTCAGTGGCA
* *
302613 CTCCTTTCAAAG-CC-TACAAGTTAGTGGCA
1 C-CCTTTCAAAGCCCACACAAGTCAGTGGCA
*
302642 CTCTTTTCAAAGCCCACA-AA-TCAGTGGCA
1 C-CCTTTCAAAGCCCACACAAGTCAGTGGCA
* *
302671 CTCTTTTTAAAG-CC-CACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACACAAGTCAGTGGCA
302700 CTCCTTTCAAAG-CC-CACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACACAAGTCAGTGGCA
302729 CTCCTTTCAAAGCCCACA-AA-TCAGTGGCA
1 C-CCTTTCAAAGCCCACACAAGTCAGTGGCA
* * *
302758 CTCTTTTCAAAG-CC-TACAAGTTAGTGGCA
1 C-CCTTTCAAAGCCCACACAAGTCAGTGGCA
*
302787 CTCTTTTCAAAGCCCACA-AA-TCAGTGGCA
1 C-CCTTTCAAAGCCCACACAAGTCAGTGGCA
* *
302816 CTCTTTTTAAAG-CC-CACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACACAAGTCAGTGGCA
302845 CTCCTTTCAAAG-CC-CACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACACAAGTCAGTGGCA
302874 CTCCTTTCAAAGCCCACA-AA-TCAGTGGCA
1 C-CCTTTCAAAGCCCACACAAGTCAGTGGCA
*
302903 CTCTTTTCAAAG-CC-CACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACACAAGTCAGTGGCA
* *
302932 CCCTTTCAAAG-CC-CACAACTCATTGGCA
1 CCCTTTCAAAGCCCACACAAGTCAGTGGCA
*
302960 TCCTTTCAAAG-CC-CACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACACAAGTCAGTGGCA
*
302988 CTCCTTTCAAAG-CC-CACAAGCCAGTGGCA
1 C-CCTTTCAAAGCCCACACAAGTCAGTGGCA
* * *
303017 CTCTTTTCAGAG-CC-CACAAGTTAGTGGCA
1 C-CCTTTCAAAGCCCACACAAGTCAGTGGCA
* *
303046 CCCTTTCAGAG-CC-CACAAGTCGGTGGCAA
1 CCCTTTCAAAGCCCACACAAGTCAGTGGC-A
* *
303075 CCCATTTTAAAGCCCACACAAGTCGGTGGCAA
1 CCC-TTTCAAAGCCCACACAAGTCAGTGGC-A
* *
303107 CCCATTCCAAAGCCCACACAAGTCGGTGGCAA
1 CCC-TTTCAAAGCCCACACAAGTCAGTGGC-A
* *
303139 CCCATTCCAAAGCCCACACAAGTCGGTGGCAA
1 CCC-TTTCAAAGCCCACACAAGTCAGTGGC-A
*
303171 CCCATTTCAAAGCCCACACAAGTCGGTGGCAA
1 CCC-TTTCAAAGCCCACACAAGTCAGTGGC-A
*
303203 CCCATTTCAAAGCCCACACAAGTCGGTGGCAA
1 CCC-TTTCAAAGCCCACACAAGTCAGTGGC-A
* *
303235 CCCATTCCAAAGCCCACACAAGTCGGTGGCAA
1 CCC-TTTCAAAGCCCACACAAGTCAGTGGC-A
* *
303267 CCCATTCCAAAGCCCACACAAGTCGGTGGCAA
1 CCC-TTTCAAAGCCCACACAAGTCAGTGGC-A
* *
303299 CCCATTCCAAAGCCCACACAAGTCGGTGGCAA
1 CCC-TTTCAAAGCCCACACAAGTCAGTGGC-A
*
303331 CCCATTTCAAAGCCCACACAAGTCGGTGGCAA
1 CCC-TTTCAAAGCCCACACAAGTCAGTGGC-A
* *
303363 CCCATTTCAAAGCCCACATAAGTCGGTGGCAA
1 CCC-TTTCAAAGCCCACACAAGTCAGTGGC-A
* *
303395 CCCATTTCAAAGCCCACACAAGTCGGTAGCAAA
1 CCC-TTTCAAAGCCCACACAAGTCAGTGGC--A
* *
303428 CCCATTTCAAAACCCACACAAGTCGGTGGCAA
1 CCC-TTTCAAAGCCCACACAAGTCAGTGGC-A
* *
303460 CCCATTCCAAAGCCCACACAAGTCGGTGGCAA
1 CCC-TTTCAAAGCCCACACAAGTCAGTGGC-A
* *
303492 CTCATTTCAAAGCCCACACAAGTCGGTGGCAA
1 C-CCTTTCAAAGCCCACACAAGTCAGTGGC-A
* **
303524 CCCATTTAAAAGCCCATGCAAGTCAGTGGCAA
1 CCC-TTTCAAAGCCCACACAAGTCAGTGGC-A
303556 CCCTTTTCAAA
1 CCC-TTTCAAA
303567 TCACCATATT
Statistics
Matches: 952, Mismatches: 58, Indels: 56
0.89 0.05 0.05
Matches are distributed among these distances:
27 9 0.01
28 120 0.13
29 336 0.35
30 25 0.03
31 11 0.01
32 420 0.44
33 31 0.03
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.19
Consensus pattern (30 bp):
CCCTTTCAAAGCCCACACAAGTCAGTGGCA
Found at i:303765 original size:49 final size:49
Alignment explanation
Indices: 303636--303754 Score: 220
Period size: 49 Copynumber: 2.4 Consensus size: 49
303626 ATTTATGACC
*
303636 CCAATGTCGTTGGCCTTGAATCAGCACATTGGTCCACTTTTCCCTTAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGTCCACTTTTCCCTTAGT
303685 CCAATGTCGCTGGCCTTGAATCAGCACATTGGTCCACTTTTCCCTTAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGTCCACTTTTCCCTTAGT
*
303734 CCAATGTCGCTGGTCTTGAAT
1 CCAATGTCGCTGGCCTTGAAT
303755 TGGCATATTG
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 68 1.00
ACGTcount: A:0.18, C:0.29, G:0.19, T:0.34
Consensus pattern (49 bp):
CCAATGTCGCTGGCCTTGAATCAGCACATTGGTCCACTTTTCCCTTAGT
Found at i:304171 original size:20 final size:20
Alignment explanation
Indices: 304143--304217 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
304133 TCATACCCTG
304143 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
304163 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
304183 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
304203 ATGTATCGATACATT
1 ATGTATCGATACATT
304218 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:304210 original size:40 final size:39
Alignment explanation
Indices: 304143--304220 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
304133 TCATACCCTG
* *
304143 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
304183 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
304221 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:307752 original size:20 final size:21
Alignment explanation
Indices: 307716--307754 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
307706 AAGTTGATTT
307716 TAATTTTTGGATATTTAAATG
1 TAATTTTTGGATATTTAAATG
*
307737 TAATTTTTGTAT-TTTAAA
1 TAATTTTTGGATATTTAAA
307755 AATTATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.56
Consensus pattern (21 bp):
TAATTTTTGGATATTTAAATG
Found at i:311191 original size:28 final size:28
Alignment explanation
Indices: 311153--311220 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
311143 TGTTAAAAAG
* *
311153 AATATAGATAAGCTTG-TCTTAATAAGAC
1 AATATAAATAAGCATGTTC-TAATAAGAC
*
311181 AATATAAATAACCATGTTCTAATAAGAC
1 AATATAAATAAGCATGTTCTAATAAGAC
*
311209 AATATGAATAAG
1 AATATAAATAAG
311221 GTTATTTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 32 0.94
29 2 0.06
ACGTcount: A:0.49, C:0.10, G:0.12, T:0.29
Consensus pattern (28 bp):
AATATAAATAAGCATGTTCTAATAAGAC
Found at i:312441 original size:37 final size:37
Alignment explanation
Indices: 312379--312502 Score: 115
Period size: 37 Copynumber: 3.4 Consensus size: 37
312369 AATTTAAATA
* * *
312379 TTATTATATT-ATTTATTATTTAATGATAAAATTGAT
1 TTATTATATTAAATTATTATATAATGATAAAATTAAT
* * * *
312415 TTATCATATTAAATTATTATATAATGATTAAACTAAC
1 TTATTATATTAAATTATTATATAATGATAAAATTAAT
* ** * * *
312452 TTATTATTTTATTTTATTATAAAATAATAAAATTTAT
1 TTATTATATTAAATTATTATATAATGATAAAATTAAT
*
312489 TTGTTATATTAAAT
1 TTATTATATTAAAT
312503 CAAATAAAAT
Statistics
Matches: 66, Mismatches: 21, Indels: 1
0.75 0.24 0.01
Matches are distributed among these distances:
36 9 0.14
37 57 0.86
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.52
Consensus pattern (37 bp):
TTATTATATTAAATTATTATATAATGATAAAATTAAT
Found at i:313858 original size:17 final size:17
Alignment explanation
Indices: 313824--313863 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
313814 TTAATTAATT
313824 AATTATAAAATTTATAA
1 AATTATAAAATTTATAA
* *
313841 AATT-TAAATTTTATTA
1 AATTATAAAATTTATAA
313857 AATTATA
1 AATTATA
313864 TATACTGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTATAAAATTTATAA
Found at i:313961 original size:24 final size:24
Alignment explanation
Indices: 313930--313976 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
313920 TATAATATTT
* *
313930 TAATTATTAAAATTAAATTTATAA
1 TAATTATTAAAATAAAATATATAA
*
313954 TAATTATTTAAATAAAATATATA
1 TAATTATTAAAATAAAATATATA
313977 TTTTAAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TAATTATTAAAATAAAATATATAA
Found at i:316001 original size:9 final size:9
Alignment explanation
Indices: 315962--316008 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
315952 AAAAATTCAG
315962 TAATAAAAT
1 TAATAAAAT
315971 TAATTAAAA-
1 TAA-TAAAAT
*
315980 CAA-AAAAT
1 TAATAAAAT
*
315988 AAATAAAAT
1 TAATAAAAT
315997 TAATAAAAT
1 TAATAAAAT
316006 TAA
1 TAA
316009 GATATTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
7 4 0.12
8 2 0.06
9 21 0.66
10 5 0.16
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (9 bp):
TAATAAAAT
Found at i:316981 original size:8 final size:7
Alignment explanation
Indices: 316945--316983 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
316935 AATGAAAGAA
*
316945 TTAAATT
1 TTAATTT
*
316952 TTAAATT
1 TTAATTT
*
316959 TTGATTT
1 TTAATTT
316966 TTAATTT
1 TTAATTT
316973 TTAATTT
1 TTAATTT
316980 TTAA
1 TTAA
316984 AAAATAGTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (7 bp):
TTAATTT
Found at i:319903 original size:2 final size:2
Alignment explanation
Indices: 319896--319934 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
319886 AGTTCAGTCA
319896 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
319935 AGCAGTAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:328410 original size:2 final size:2
Alignment explanation
Indices: 328377--328439 Score: 76
Period size: 2 Copynumber: 32.5 Consensus size: 2
328367 CCATGTCATC
* * **
328377 AT AT AC AT AT AC AT AT A- AT AT GC AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
328417 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
328440 AAGCTATTCA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
1 2 0.04
2 49 0.96
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:333933 original size:27 final size:29
Alignment explanation
Indices: 333902--333974 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 29
333892 ATTATAACAC
333902 AAATAAATTATAATTTTT-AAAA-TTTAA
1 AAATAAATTATAATTTTTAAAAATTTTAA
* *
333929 AAATAATTTAATATTTTTTAAAAATTTTAA
1 AAATAAATT-ATAATTTTTAAAAATTTTAA
* *
333959 ATATAAAATAT-ATTTT
1 AAATAAATTATAATTTT
333975 ATCTTTTAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
27 8 0.22
28 12 0.32
29 6 0.16
30 11 0.30
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
AAATAAATTATAATTTTTAAAAATTTTAA
Found at i:334504 original size:24 final size:23
Alignment explanation
Indices: 334456--334506 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
334446 TCAATAAATT
* *
334456 TTTAAATAATAGTAATTAATCAA
1 TTTAAATAATAATAATTAATAAA
*
334479 TTTAAATAATAATATTTTAATAAA
1 TTTAAATAATAATA-ATTAATAAA
334503 TTTA
1 TTTA
334507 TTTCAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
TTTAAATAATAATAATTAATAAA
Found at i:334616 original size:22 final size:22
Alignment explanation
Indices: 334566--334616 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
334556 TATACACTTA
*
334566 AATTAAAATATAATTTAATAAT
1 AATTAAAATATAATTTAAGAAT
* *
334588 AACTAAAA-ATAATTTTAAGATT
1 AATTAAAATATAA-TTTAAGAAT
334610 AATTAAA
1 AATTAAA
334617 TCTTCATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (22 bp):
AATTAAAATATAATTTAAGAAT
Found at i:334655 original size:15 final size:17
Alignment explanation
Indices: 334624--334656 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
334614 AAATCTTCAT
334624 TATTTTGTAATTAAAAA
1 TATTTTGTAATTAAAAA
334641 TATTTT-TAA-TAAAAA
1 TATTTTGTAATTAAAAA
334656 T
1 T
334657 GATACAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 3 0.19
17 6 0.38
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TATTTTGTAATTAAAAA
Found at i:334828 original size:30 final size:29
Alignment explanation
Indices: 334729--334834 Score: 83
Period size: 30 Copynumber: 3.6 Consensus size: 29
334719 AATAATAATA
* *
334729 ATTTAAAAAATAAATATATTTTTGATCAA-
1 ATTTAAAAAATAAATAGATTTTT-ATAAAG
* *
334758 ATCTTAAAAGAAAAAATAGATATTTTTTAAACG
1 AT-TTAAAA-AATAAATAGAT-TTTTATAAA-G
* *
334791 -TTAAAAAAATTAATAGATTTTTCATAAAG
1 ATTTAAAAAATAAATAGATTTTT-ATAAAG
334820 ATTT-AAAAATAAATA
1 ATTTAAAAAATAAATA
334835 ACATTTATTT
Statistics
Matches: 60, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
29 17 0.28
30 21 0.35
31 17 0.28
32 5 0.08
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.37
Consensus pattern (29 bp):
ATTTAAAAAATAAATAGATTTTTATAAAG
Found at i:334844 original size:21 final size:20
Alignment explanation
Indices: 334820--334878 Score: 50
Period size: 18 Copynumber: 3.0 Consensus size: 20
334810 TTTCATAAAG
334820 ATTTAAAAATAAATAACATTT
1 ATTT-AAAATAAATAACATTT
* *
334841 ATTTTGATATAAAT-A-ATTT
1 A-TTTAAAATAAATAACATTT
* *
334860 ATTTTAAACAAATAACATT
1 ATTTAAAATAAATAACATT
334879 GATTAAATCG
Statistics
Matches: 30, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
18 9 0.30
19 6 0.20
20 4 0.13
21 8 0.27
22 3 0.10
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (20 bp):
ATTTAAAATAAATAACATTT
Found at i:334874 original size:18 final size:19
Alignment explanation
Indices: 334837--334874 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
334827 AATAAATAAC
* *
334837 ATTTATTTTGATATAAATA
1 ATTTATTTTGAAACAAATA
334856 ATTTATTTT-AAACAAATA
1 ATTTATTTTGAAACAAATA
334874 A
1 A
334875 CATTGATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (19 bp):
ATTTATTTTGAAACAAATA
Found at i:335393 original size:21 final size:20
Alignment explanation
Indices: 335338--335400 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 20
335328 TTGAAATTTT
*
335338 TTTAAAAAAATTAATATTAA
1 TTTAAAAAAATTTATATTAA
* ***
335358 TATTAATATTTTTTATAATTAA
1 T-TTAAAAAAATTTAT-ATTAA
335380 TTTAAAAAAATTTATTATTAA
1 TTTAAAAAAATTTA-TATTAA
335401 ATAATAATTT
Statistics
Matches: 31, Mismatches: 9, Indels: 5
0.69 0.20 0.11
Matches are distributed among these distances:
20 1 0.03
21 23 0.74
22 7 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTAAAAAAATTTATATTAA
Found at i:337040 original size:16 final size:18
Alignment explanation
Indices: 337014--337098 Score: 72
Period size: 17 Copynumber: 4.7 Consensus size: 18
337004 ACTATATTTC
*
337014 TAAATTATTATTATA-AA
1 TAAATTTTTATTATATAA
337031 T-AATTTTTATTA-ATAA
1 TAAATTTTTATTATATAA
337047 TAAATTTTTATTAT-TAA
1 TAAATTTTTATTATATAA
337064 TCAAATTTATTTAATT-TATAA
1 T-AAA-TT-TTT-ATTATATAA
*
337085 GTAATTTTTTATTA
1 -TAAATTTTTATTA
337099 ATTAAATTTA
Statistics
Matches: 56, Mismatches: 2, Indels: 18
0.74 0.03 0.24
Matches are distributed among these distances:
15 1 0.02
16 13 0.23
17 16 0.29
18 6 0.11
19 5 0.09
20 6 0.11
21 8 0.14
22 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (18 bp):
TAAATTTTTATTATATAA
Found at i:337051 original size:20 final size:20
Alignment explanation
Indices: 337017--337064 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
337007 ATATTTCTAA
*
337017 ATTATT-ATTATAAATAATTT
1 ATTATTAATAATAAAT-ATTT
*
337037 -TTATTAATAATAAATTTTT
1 ATTATTAATAATAAATATTT
337056 ATTATTAAT
1 ATTATTAAT
337065 CAAATTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTATTAATAATAAATATTT
Found at i:337135 original size:45 final size:46
Alignment explanation
Indices: 337086--337173 Score: 117
Period size: 46 Copynumber: 1.9 Consensus size: 46
337076 AATTTATAAG
* *
337086 TAATTTTTTATT-AAT-TAAATTTACTTAATTTATAAATAAAAAATT
1 TAATTTATTATTAAATATAAATTTACTTAA-TGATAAATAAAAAATT
* *
337131 TAATTTATTATTAAATATATATTTATTTAATGATAAATAAAAA
1 TAATTTATTATTAAATATAAATTTACTTAATGATAAATAAAAA
337174 GTATTAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
45 11 0.30
46 15 0.41
47 11 0.30
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (46 bp):
TAATTTATTATTAAATATAAATTTACTTAATGATAAATAAAAAATT
Found at i:337407 original size:2 final size:2
Alignment explanation
Indices: 337402--337426 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
337392 CATGTATTGC
337402 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
337427 GCATAAAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:338966 original size:14 final size:15
Alignment explanation
Indices: 338940--338976 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
338930 ATTTTTATCG
338940 TAAATTCAAAAATA-T
1 TAAATT-AAAAATATT
338955 TAAATTAAAAATATT
1 TAAATTAAAAATATT
338970 TAAATTA
1 TAAATTA
338977 GTTGATGTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAATTAAAAATATT
Found at i:340054 original size:13 final size:14
Alignment explanation
Indices: 340030--340058 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
340020 CTTTATTTTC
340030 TTTATATTTTATAA
1 TTTATATTTTATAA
340044 TTTAT-TTTTATAA
1 TTTATATTTTATAA
340057 TT
1 TT
340059 AATGTGATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTATATTTTATAA
Found at i:342949 original size:14 final size:14
Alignment explanation
Indices: 342923--342958 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
342913 AATTTGAAAA
342923 AAAATTATAAATATT
1 AAAATT-TAAATATT
342938 AAAATTTAAATATT
1 AAAATTTAAATATT
342952 -AAATTTA
1 AAAATTTA
342959 CAAAATATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 7 0.33
14 8 0.38
15 6 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AAAATTTAAATATT
Found at i:343353 original size:14 final size:14
Alignment explanation
Indices: 343327--343362 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
343317 AATTTGAAAA
343327 AAAATTATAAATATT
1 AAAATT-TAAATATT
343342 AAAATTTAAATATT
1 AAAATTTAAATATT
343356 -AAATTTA
1 AAAATTTA
343363 CAAAATATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 7 0.33
14 8 0.38
15 6 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AAAATTTAAATATT
Done.