Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold494
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: 556777
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:212783 original size:94 final size:93
Alignment explanation
Indices: 212558--213122 Score: 627
Period size: 94 Copynumber: 6.1 Consensus size: 93
212548 TTAGTGGCAT
* * * * *
212558 CTTTTCAAAGTCCACACAAGTTGGTGGCATCC-TTTCAAAGCCCACA-AA-TCAGTGGCA-TCCT
1 CTTTTCAAAGCCCACACAAGTCGGTGGCAACCATTTCAAAGCCCACACAAGTCGGTGGCACT-AT
*
212619 TTCAAAG-CC-CACAAGTCAGTGGC-A-C
65 TTCAAAGCCCACACAAGTCGGTGGCAACC
* * * *
212644 CATTTCAAAG-CC-CATAAGTCAGTGGCAA-CATTTCAAAGCCCACACAAATCGGTGGCACTATT
1 CTTTTCAAAGCCCACACAAGTCGGTGGCAACCATTTCAAAGCCCACACAAGTCGGTGGCACTATT
212706 TCAAAGCCCACACAAGTCGGTGGCAACC
66 TCAAAGCCCACACAAGTCGGTGGCAACC
* * * *
212734 CATTTCAAAGCCGACACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCAGTGGCACTAT
1 CTTTTCAAAGCCCACACAAGTCGGTGGCAA-CCATTTCAAAGCCCACACAAGTCGGTGGCACTAT
212799 TTCAAAGCCCACACAAGTCGGTGGCAACC
65 TTCAAAGCCCACACAAGTCGGTGGCAACC
* *
212828 CTTTTCAAAGCCCACACAAGTCGGTGGC-ACTATTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 CTTTTCAAAGCCCACACAAGTCGGTGGCAACCATTTCAAAGCCCACACAAGTCGGTGGC-A-CTA
212892 TTTCAAAGCCCACACAAGTCGGTGGCAACC
64 TTTCAAAGCCCACACAAGTCGGTGGCAACC
* * * * *
212922 CTTTTCAAAGCCCACACAAGTTGATGGCAACCCATTTCAAAGCCCACATAAGTCGGTGGTAACCC
1 CTTTTCAAAGCCCACACAAGTCGGTGGCAA-CCATTTCAAAGCCCACACAAGTCGGTGG-CA-CT
212987 ATTTCAAAGCCCACACAAGTCGGTGGCAACC
63 ATTTCAAAGCCCACACAAGTCGGTGGCAACC
* * * * * ** *
213018 CTTTTCAAAGCCCACACAAGTTGATGGGAACCTCTTTCAAAAGTCCACAC-TTTCGGTGGAAACC
1 CTTTTCAAAGCCCACACAAGTCGGTGGCAACC-ATTTC-AAAGCCCACACAAGTCGGTGG---CA
* * * *
213082 CT-TTTAAAAACCCACGCAAGTCAGTGGCAACC
61 CTATTTCAAAGCCCACACAAGTCGGTGGCAACC
213114 CTTTTCAAA
1 CTTTTCAAA
213123 TCACCATTTT
Statistics
Matches: 419, Mismatches: 39, Indels: 32
0.86 0.08 0.07
Matches are distributed among these distances:
83 1 0.00
84 26 0.06
85 4 0.01
86 25 0.06
87 3 0.01
88 13 0.03
89 1 0.00
90 11 0.03
91 1 0.00
92 40 0.10
93 2 0.00
94 143 0.34
95 3 0.01
96 136 0.32
97 10 0.02
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.21
Consensus pattern (93 bp):
CTTTTCAAAGCCCACACAAGTCGGTGGCAACCATTTCAAAGCCCACACAAGTCGGTGGCACTATT
TCAAAGCCCACACAAGTCGGTGGCAACC
Found at i:214394 original size:20 final size:20
Alignment explanation
Indices: 214351--214397 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
214341 GGTAAGAAAG
* * * *
214351 AAAGAAAGAAGATGAAGAAG
1 AAAGAAAGAACAAGAAAAAA
214371 AAAGAAAGAACAAGAAAAAA
1 AAAGAAAGAACAAGAAAAAA
214391 AAAGAAA
1 AAAGAAA
214398 AAAATATGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.74, C:0.02, G:0.21, T:0.02
Consensus pattern (20 bp):
AAAGAAAGAACAAGAAAAAA
Found at i:217243 original size:16 final size:15
Alignment explanation
Indices: 217210--217239 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
217200 TTTTTTAATA
217210 AAATTAAAAAAATTT
1 AAATTAAAAAAATTT
*
217225 AAATTAAATAAATTT
1 AAATTAAAAAAATTT
217240 TAAAAAATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATTAAAAAAATTT
Found at i:217876 original size:71 final size:72
Alignment explanation
Indices: 217774--218044 Score: 252
Period size: 71 Copynumber: 3.8 Consensus size: 72
217764 TATAGTTATG
*
217774 AGTTTAAA-ATTTTAAAG-TATAATTTATTTTTATTTGTAAAAATTTAAATTTATTTTTTGGTTT
1 AGTTTAAATA-TTT-AAGTTATTATTTATTTTTATTTGTAAAAATTTAAATTTATTTTTTGGTTT
*
217837 GATTAGACA
64 GATTATACA
* * * * * **
217846 AGTTTAAATATTT-AGTTATTATTTATTTTTATTCGTGAAAGTTTAAATTTGTTTTTTAAG-AAG
1 AGTTTAAATATTTAAGTTATTATTTATTTTTATTTGTAAAAATTTAAATTTATTTTTT-GGTTTG
217909 ATTATACA
65 ATTATACA
* * * * * * * *
217917 AGTTTAAATTTTTTAAAG-TATAATATA-TTTTATTTATAGAAGTTTAAATCT-GTTTTTGGTTT
1 AGTTTAAA-TATTT-AAGTTATTATTTATTTTTATTTGTAAAAATTTAAATTTATTTTTTGGTTT
*
217979 AATTATA-A
64 GATTATACA
* *
217987 GAATTTAAATATTTAAGTTATTATTTATTTTTATTTGTAAAAATTTTAATTTATTTTT
1 -AGTTTAAATATTTAAGTTATTATTTATTTTTATTTGTAAAAATTTAAATTTATTTTT
218045 ATTTATAAAA
Statistics
Matches: 156, Mismatches: 32, Indels: 22
0.74 0.15 0.10
Matches are distributed among these distances:
69 3 0.02
70 15 0.10
71 89 0.57
72 39 0.25
73 8 0.05
74 2 0.01
ACGTcount: A:0.35, C:0.01, G:0.09, T:0.54
Consensus pattern (72 bp):
AGTTTAAATATTTAAGTTATTATTTATTTTTATTTGTAAAAATTTAAATTTATTTTTTGGTTTGA
TTATACA
Found at i:217964 original size:143 final size:143
Alignment explanation
Indices: 217774--218044 Score: 359
Period size: 143 Copynumber: 1.9 Consensus size: 143
217764 TATAGTTATG
* * * * *
217774 AGTTTAAAATTTTAAAGTATAATTTATTTTTATTTGTAAAAATTTAAATTTATTTTTTGGTTTGA
1 AGTTTAAAATTTTAAAGTATAATATATTTTTATTTATAAAAATTTAAATCT-GTTTTTGGTTTAA
* * * *
217839 TTAGACA-AGTTTAAATATTT-AGTTATTATTTATTTTTATTCGTGAAAGTTTAAATTTGTTTTT
65 TTAGA-AGAATTTAAATATTTAAGTTATTATTTATTTTTATTCGTAAAAATTTAAATTTATTTTT
217902 TAAGAAGATTATACA
129 TAAGAAGATTATACA
* * *
217917 AGTTTAAATTTTTTAAAGTATAATATA-TTTTATTTATAGAAGTTTAAATCTGTTTTTGGTTTAA
1 AGTTTAAA-ATTTTAAAGTATAATATATTTTTATTTATAAAAATTTAAATCTGTTTTTGGTTTAA
* * *
217981 TTATAAGAATTTAAATATTTAAGTTATTATTTATTTTTATTTGTAAAAATTTTAATTTATTTTT
65 TTAGAAGAATTTAAATATTTAAGTTATTATTTATTTTTATTCGTAAAAATTTAAATTTATTTTT
218045 ATTTATAAAA
Statistics
Matches: 110, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
141 1 0.01
142 27 0.25
143 66 0.60
144 16 0.15
ACGTcount: A:0.35, C:0.01, G:0.09, T:0.54
Consensus pattern (143 bp):
AGTTTAAAATTTTAAAGTATAATATATTTTTATTTATAAAAATTTAAATCTGTTTTTGGTTTAAT
TAGAAGAATTTAAATATTTAAGTTATTATTTATTTTTATTCGTAAAAATTTAAATTTATTTTTTA
AGAAGATTATACA
Found at i:218261 original size:80 final size:80
Alignment explanation
Indices: 218064--218247 Score: 209
Period size: 80 Copynumber: 2.4 Consensus size: 80
218054 ATCACACCAG
* * * * * *
218064 AAAACAAATTTAAAGTTATACAAGTAAAAAT-AAAAT-CATAT-C-TT-GAAAATTTTAAACTCA
1 AAAACAAATTTAAACTTTTACAAATAAAAATAAAAATAAAAATACTTTAAAAAATTTTAAACTCA
** **
218124 TATAATAATTCCTAA
66 TATAATAAAACAAAA
*
218139 AAAATAAATTTAAACTTTTACAAATAAAAATAAAAATAAAAATACTTTAAAAAATTTTAAACTTC
1 AAAACAAATTTAAACTTTTACAAATAAAAATAAAAATAAAAATACTTTAAAAAATTTTAAAC-TC
218204 -TATAATAAAACAAAA
65 ATATAATAAAACAAAA
*
218219 AAAACAAATTTAAAGTTTTACAAATAAAA
1 AAAACAAATTTAAACTTTTACAAATAAAA
218248 TCATATCTTA
Statistics
Matches: 90, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
75 27 0.30
76 5 0.06
77 3 0.03
78 1 0.01
79 2 0.02
80 50 0.56
81 2 0.02
ACGTcount: A:0.59, C:0.09, G:0.02, T:0.30
Consensus pattern (80 bp):
AAAACAAATTTAAACTTTTACAAATAAAAATAAAAATAAAAATACTTTAAAAAATTTTAAACTCA
TATAATAAAACAAAA
Found at i:218399 original size:72 final size:71
Alignment explanation
Indices: 218064--219122 Score: 791
Period size: 72 Copynumber: 14.7 Consensus size: 71
218054 ATCACACCAG
* * * * * * *
218064 AAAACAAATTTAAAGTTATACAAGTAAAAATAAAATCATATCTTGAAAATTTTAAACTCATATAA
1 AAAACAAATTTAAACTTCTACAAATAAAAAT-AAATAATACCTT-AAAAATTTAAACTCGTATAA
* *
218129 TAATTCCTAA
64 TCA-TAC-AA
* * *
218139 AAAATAAATTTAAACTTTTACAAATAAAAATAAAAATAAAAATACTTTAAAAAATTTTAAACTTC
1 AAAACAAATTTAAACTTCTACAAATAAAAAT--AAAT---AATACCTT-AAAAA-TTTAAAC-TC
* *
218204 -TATAATAAAACAAAA
58 GTATAATCATAC--AA
* * *
218219 AAAACAAATTTAAAGTTTTACAAAT-AAAAT-CAT-AT--CTT-AAAATTTAAAACTCGTATAAT
1 AAAACAAATTTAAACTTCTACAAATAAAAATAAATAATACCTTAAAAATTT-AAACTCGTATAAT
218278 CATACCAA
65 CATA-CAA
* * *** * * *
218286 AGAAACGAATTTAAACTTTTATGGATAGAAATAAGTTATACCTTAAAAAATTTAAACTCGTATAA
1 A-AAACAAATTTAAACTTCTACAAATAAAAATAAATAATACCTT-AAAAATTTAAACTCGTATAA
*
218351 TCATACAC
64 TCATACAA
* * * * *
218359 AAAAGAAATTTAAACTTTTACAAATAAAGATAAACAATACCTTAAAAATTTAAACTCGTATAATT
1 AAAACAAATTTAAACTTCTACAAATAAAAATAAATAATACCTTAAAAATTTAAACTCGTATAATC
*
218424 AAACCAA
66 ATA-CAA
* * *
218431 AGAACAAATTTAAACTT-TAACAAA-AAAAATAAATTATACCTTAAAAATTTAAA-TTGTATAAT
1 AAAACAAATTTAAACTTCT-ACAAATAAAAATAAATAATACCTTAAAAATTTAAACTCGTATAAT
*
218493 CATATTGAA
65 CATA--CAA
* *** *
218502 AAAAGAAATTTAAACTTCTACAAATAAAAATAAA-AATGTTTTAAAAAATTTAAACTCGTCTAAT
1 AAAACAAATTTAAACTTCTACAAATAAAAATAAATAATACCTT-AAAAATTTAAACTCGTATAAT
218566 CGA-ATCAA
65 C-ATA-CAA
** * * * *
218574 AAAACAAATTTAATGTTTTACAAATAAAAATAAATCATACTTTAAAAATTTAAACTCGTATTATC
1 AAAACAAATTTAAACTTCTACAAATAAAAATAAATAATACCTTAAAAATTTAAACTCGTATAATC
218639 ATACTCAA
66 ATA--CAA
* *
218647 AAAATAAATTTAAACTTCTACAAATAAAAATAAA-AATACCTTTTAAAAAATTAAA-TACGTATA
1 AAAACAAATTTAAACTTCTACAAATAAAAATAAATAATACC--TTAAAAATTTAAACT-CGTATA
* *
218710 ATCAAACTAG
63 ATCATAC-AA
* ** * ** *
218720 GAAACAAATTTAATGTTCTACAAATAAAAATAAATTATTTCTTAAAAATTTAAACTCATATAATC
1 AAAACAAATTTAAACTTCTACAAATAAAAATAAATAATACCTTAAAAATTTAAACTCGTATAATC
*
218785 GTACTAA
66 ATAC-AA
* * * * * *
218792 AAAATAAATTTAAACTTATACAAAT---AATCAATAATATCTTAAAAATTTAAACTCGTTTAATA
1 AAAACAAATTTAAACTTCTACAAATAAAAATAAATAATACCTTAAAAATTTAAACTCGTATAATC
*
218854 ATACCTA
66 ATA-CAA
* ** * * * * * *
218861 AAAA-AAATTCAATGTTCTACAAATAAAAATAAATTATATCTTAAAAATTTTATCTTGTATAATT
1 AAAACAAATTTAAACTTCTACAAATAAAAATAAATAATACCTTAAAAATTTAAACTCGTATAATC
218925 ATAC--
66 ATACAA
* * ** **
218929 AAAA-AAATTTAAACTTCTA-TAATAGAAATAAATTGTACCTTAAAAAATTTAAACTTATATAAT
1 AAAACAAATTTAAACTTCTACAAATAAAAATAAATAATACCTT-AAAAATTTAAACTCGTATAAT
*
218992 TATACCCAA
65 CATA--CAA
* * * *
219001 AAAACAAATTTAAACTTCTACAAACAAAGATCAATAATA-CTTAAAAATTTAAACTTGTATAATC
1 AAAACAAATTTAAACTTCTACAAATAAAAATAAATAATACCTTAAAAATTTAAACTCGTATAATC
*
219065 AAATC-A
66 ATA-CAA
* *
219071 AAAACTAAATTTAAACTT-TAACAAACAAAAATAAATTATACCTTAAAAATTT
1 AAAAC-AAATTTAAACTTCT-ACAAATAAAAATAAATAATACCTTAAAAATTT
219123 TACTTTTATT
Statistics
Matches: 797, Mismatches: 138, Indels: 101
0.77 0.13 0.10
Matches are distributed among these distances:
67 26 0.03
68 89 0.11
69 43 0.05
70 23 0.03
71 142 0.18
72 217 0.27
73 105 0.13
74 54 0.07
75 34 0.04
76 7 0.01
79 15 0.02
80 40 0.05
81 2 0.00
ACGTcount: A:0.54, C:0.11, G:0.03, T:0.32
Consensus pattern (71 bp):
AAAACAAATTTAAACTTCTACAAATAAAAATAAATAATACCTTAAAAATTTAAACTCGTATAATC
ATACAA
Found at i:218430 original size:145 final size:142
Alignment explanation
Indices: 218064--219122 Score: 820
Period size: 143 Copynumber: 7.4 Consensus size: 142
218054 ATCACACCAG
* * * * * * * *
218064 AAAACAAATTTAAAGTTATACAAGTAAAAATAAAATCATATCTTGAAAATTTTAAACTCATATAA
1 AAAATAAATTTAAACTTCTACAAAT-AAAAT-AAATAATACCTT-AAAAATTTAAACTCGTATAA
* * * *
218129 T-AATTCCTAAAAAATAAATTTAAACTTTTACAAATAAAAATAAAAATAAAAATACTTTAAAAAA
63 TCAA-ACC-AAAAAACAAATTTAAACTTCTACAAATAAAAAT--AAAT---TATAC-TT-AAAAA
* *
218193 TTTTAAACTTC-TATAAT-AAAACAAAA
119 -TTTAAAC-TCGTATAATCATATC--AA
* * * *
218219 AAAACAAATTTAAAGTTTTACAAATAAAAT-CAT-AT--CTT-AAAATTTAAAACTCGTATAATC
1 AAAATAAATTTAAACTTCTACAAATAAAATAAATAATACCTTAAAAATTT-AAACTCGTATAATC
* * * *** * *
218279 ATACCAAAGAAACGAATTTAAACTTTTATGGATAGAAATAAGTTATACCTTAAAAAATTTAAACT
65 AAACCAAA-AAACAAATTTAAACTTCTACAAATAAAAATAAATTATA-CTT-AAAAATTTAAACT
*
218344 CGTATAATCATA-CAC
127 CGTATAATCATATCAA
* * * *
218359 AAAAGAAATTTAAACTTTTACAAATAAAGATAAACAATACCTTAAAAATTTAAACTCGTATAATT
1 AAAATAAATTTAAACTTCTACAAATAAA-ATAAATAATACCTTAAAAATTTAAACTCGTATAATC
* *
218424 AAACCAAAGAACAAATTTAAACTT-TAACAAA-AAAAATAAATTATACCTTAAAAATTTAAA-TT
65 AAACCAAAAAACAAATTTAAACTTCT-ACAAATAAAAATAAATTATA-CTTAAAAATTTAAACTC
*
218486 GTATAATCATATTGAA
128 GTATAATCATA-TCAA
* *** *
218502 AAAAGAAATTTAAACTTCTACAAATAAAAATAAA-AATGTTTTAAAAAATTTAAACTCGTCTAAT
1 AAAATAAATTTAAACTTCTACAAAT-AAAATAAATAATACCTT-AAAAATTTAAACTCGTATAAT
* * ** * *
218566 CGAATCAAAAAACAAATTTAATGTTTTACAAATAAAAATAAATCATACTTTAAAAATTTAAACTC
64 CAAACCAAAAAACAAATTTAAACTTCTACAAATAAAAATAAATTATAC-TTAAAAATTTAAACTC
*
218631 GTATTATCATACTCAA
128 GTATAATCATA-TCAA
*
218647 AAAATAAATTTAAACTTCTACAAATAAAAATAAA-AATACCTTTTAAAAAATTAAA-TACGTATA
1 AAAATAAATTTAAACTTCTACAAAT-AAAATAAATAATACC--TTAAAAATTTAAACT-CGTATA
* ** ** *
218710 ATCAAACTAGGAAACAAATTTAATGTTCTACAAATAAAAATAAATTATTTCTTAAAAATTTAAAC
62 ATCAAACCAAAAAACAAATTTAAACTTCTACAAATAAAAATAAATTA-TACTTAAAAATTTAAAC
* *
218775 TCATATAATCGTA-CTAA
126 TCGTATAATCATATC-AA
* * * *
218792 AAAATAAATTTAAACTTATACAAAT--AATCAATAATATCTTAAAAATTTAAACTCGTTTAAT-A
1 AAAATAAATTTAAACTTCTACAAATAAAATAAATAATACCTTAAAAATTTAAACTCGTATAATCA
* * ** * * *
218854 ATACCTAAAAA-AAATTCAATGTTCTACAAATAAAAATAAATTATATCTTAAAAATTTTATCTTG
66 A-ACCAAAAAACAAATTTAAACTTCTACAAATAAAAATAAATTATA-CTTAAAAATTTAAACTCG
*
218918 TATAAT--TAT-AC
129 TATAATCATATCAA
* ** **
218929 AAAA-AAATTTAAACTTCTA-TAATAGAAATAAATTGTACCTTAAAAAATTTAAACTTATATAAT
1 AAAATAAATTTAAACTTCTACAAATA-AAATAAATAATACCTT-AAAAATTTAAACTCGTATAAT
* * * * * * *
218992 TATACCCAAAAAACAAATTTAAACTTCTACAAACAAAGATCAATAATACTTAAAAATTTAAACTT
64 CA-AACCAAAAAACAAATTTAAACTTCTACAAATAAAAATAAATTATACTTAAAAATTTAAACTC
*
219057 GTATAATCAAATCAA
128 GTATAATCATATCAA
* * *
219072 AAACTAAATTTAAACTT-TAACAAACAAAAATAAATTATACCTTAAAAATTT
1 AAAATAAATTTAAACTTCT-ACAAA-TAAAATAAATAATACCTTAAAAATTT
219123 TACTTTTATT
Statistics
Matches: 751, Mismatches: 108, Indels: 101
0.78 0.11 0.11
Matches are distributed among these distances:
135 3 0.00
136 14 0.02
137 5 0.01
138 13 0.02
139 19 0.03
140 110 0.15
141 68 0.09
142 39 0.05
143 117 0.16
144 69 0.09
145 117 0.16
146 90 0.12
147 13 0.02
148 38 0.05
149 4 0.01
151 2 0.00
152 2 0.00
154 5 0.01
155 23 0.03
ACGTcount: A:0.54, C:0.11, G:0.03, T:0.32
Consensus pattern (142 bp):
AAAATAAATTTAAACTTCTACAAATAAAATAAATAATACCTTAAAAATTTAAACTCGTATAATCA
AACCAAAAAACAAATTTAAACTTCTACAAATAAAAATAAATTATACTTAAAAATTTAAACTCGTA
TAATCATATCAA
Found at i:219049 original size:39 final size:37
Alignment explanation
Indices: 219006--219122 Score: 102
Period size: 39 Copynumber: 3.2 Consensus size: 37
218996 CCCAAAAAAC
219006 AAATTTAAACTTCTACAAACAAAGATCAATAATACTTAA
1 AAATTTAAACTT-TACAAACAAA-ATCAATAATACTTAA
* *
219045 AAATTTAAACTTGTATAATC-AAATCAA-AA-AC-T--
1 AAATTTAAACTT-TACAAACAAAATCAATAATACTTAA
* *
219077 AAATTTAAACTTTAACAAACAAAAATAAATTATACCTTAA
1 AAATTTAAACTTT-ACAAAC-AAAATCAATAATA-CTTAA
219117 AAATTT
1 AAATTT
219123 TACTTTTATT
Statistics
Matches: 62, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
31 1 0.02
32 16 0.26
34 7 0.11
35 3 0.05
36 3 0.05
37 6 0.10
38 3 0.05
39 17 0.27
40 6 0.10
ACGTcount: A:0.55, C:0.13, G:0.02, T:0.31
Consensus pattern (37 bp):
AAATTTAAACTTTACAAACAAAATCAATAATACTTAA
Found at i:219594 original size:71 final size:72
Alignment explanation
Indices: 219497--219747 Score: 262
Period size: 71 Copynumber: 3.5 Consensus size: 72
219487 TTTTATGAGT
* * * *
219497 AAAAATAAACTTAAATTTTTATAAATAAAAATAAATAATAACTTAAATATTTAAAC-AATTATAA
1 AAAAATAAATTTAAACTTTTACAAATAAAAATAAATAATAACTTAAATATTTAAACTTA-TATAA
*
219561 TCAAACCA
65 TCAAACTA
* * * *
219569 AAAAACATACTT-AACTTTTACAAAT-AAAATAAACT-AT-ACTTTAAAAAATTTAAACTTATAT
1 AAAAATAAATTTAAACTTTTACAAATAAAAATAAA-TAATAAC-TT-AAATATTTAAACTTATAT
*
219630 AATCATACTTA
63 AATCAAAC-TA
* ** * * *
219641 AAAAATAAATTTAAACTTTCATGAATAAAAACAAATAATAAC-TAAATATTTAAACTTGTCTAAT
1 AAAAATAAATTTAAACTTTTACAAATAAAAATAAATAATAACTTAAATATTTAAACTTATATAAT
219705 CAAACTA
66 CAAACTA
*
219712 AAAAATAAATTTAAACTTCTACAAATAAAAATAAAT
1 AAAAATAAATTTAAACTTTTACAAATAAAAATAAAT
219748 TATACTTTAA
Statistics
Matches: 146, Mismatches: 24, Indels: 19
0.77 0.13 0.10
Matches are distributed among these distances:
69 2 0.01
70 12 0.08
71 66 0.45
72 43 0.29
73 12 0.08
74 9 0.06
75 2 0.01
ACGTcount: A:0.57, C:0.10, G:0.01, T:0.32
Consensus pattern (72 bp):
AAAAATAAATTTAAACTTTTACAAATAAAAATAAATAATAACTTAAATATTTAAACTTATATAAT
CAAACTA
Found at i:219729 original size:144 final size:144
Alignment explanation
Indices: 219497--219768 Score: 370
Period size: 144 Copynumber: 1.9 Consensus size: 144
219487 TTTTATGAGT
* * *
219497 AAAAATAAACTTAAATTTTTATAAATAAAAATAAATAATAACTTAAATATTTAAACAATTATAAT
1 AAAAATAAACTTAAACTTTCATAAATAAAAACAAATAATAACTTAAATATTTAAACAATTATAAT
* * *
219562 CAAACCAAAAAACATACTTAACTTTTACAAAT-AAAATAAACTATACTTTAAAAAATTTAAACTT
66 CAAACCAAAAAACAAACTTAACTTCTACAAATAAAAATAAACTATACTTT-AAAAATTCAAACTT
219626 ATATAATCATACTTA
130 ATATAATCATACTTA
* * * *
219641 AAAAATAAATTTAAACTTTCATGAATAAAAACAAATAATAAC-TAAATATTTAAAC-TTGTCTAA
1 AAAAATAAACTTAAACTTTCATAAATAAAAACAAATAATAACTTAAATATTTAAACAAT-TATAA
* * * *
219704 TCAAACTAAAAAATAAATTTAAACTTCTACAAATAAAAATAAATTATACTTTAAAAATTCAAACT
65 TCAAACCAAAAAACAAACTT-AACTTCTACAAATAAAAATAAACTATACTTTAAAAATTCAAACT
219769 CATAACAATA
Statistics
Matches: 111, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
142 1 0.01
143 33 0.30
144 61 0.55
145 16 0.14
ACGTcount: A:0.56, C:0.11, G:0.01, T:0.32
Consensus pattern (144 bp):
AAAAATAAACTTAAACTTTCATAAATAAAAACAAATAATAACTTAAATATTTAAACAATTATAAT
CAAACCAAAAAACAAACTTAACTTCTACAAATAAAAATAAACTATACTTTAAAAATTCAAACTTA
TATAATCATACTTA
Found at i:220054 original size:73 final size:73
Alignment explanation
Indices: 219964--220558 Score: 357
Period size: 73 Copynumber: 8.3 Consensus size: 73
219954 AAACTTTTAC
* * * * * *
219964 AAATAAA-AATACTTTAAAAAAATTAAACTTATATAATCAAATC-AGAAAACAAATTCAAAGTTT
1 AAATAAATAATACCTTAAAAAAATTAAACTCATATAATCAAACCTAAAAAATAAATT-AAACTTT
220027 TACAAATAA
65 TACAAATAA
* * * * * * *
220036 AAAGAAATAATACCTT-AAAAATTTAAACTCGTATCATCATACCTAAAAAATAAAATTACACTTC
1 AAATAAATAATACCTTAAAAAAATTAAACTCATATAATCAAACCTAAAAAAT-AAATTAAACTTT
220100 TACAAATAA
65 TACAAATAA
** * * *
220109 AAAT-AA-AATACCTTAAAAAAATTTAAACAAATATAATCAAA-CTAGAAAATAAGTTTAA-TTT
1 AAATAAATAATACCTTAAAAAAA-TTAAACTCATATAATCAAACCTAAAAAATAAATTAAACTTT
220170 TCGACAAATAA
65 T--ACAAATAA
* * * * * * *
220181 AAATAAATTATATCTTAAAAATA-TAAACTCGTATAATCATACCCAAAAAATAAATTTAAACTTA
1 AAATAAATAATACCTTAAAAAAATTAAACTCATATAATCAAACCTAAAAAATAAA-TTAAACTTT
220245 TACAAATAA
65 TACAAATAA
* * * * * **
220254 AGATCAATAATATCTT-AAAAATTTAAACTCTTATAAT-AATACCTAAAAAATAAATTTAATGTT
1 AAATAAATAATACCTTAAAAAAATTAAACTCATATAATCAA-ACCTAAAAAATAAA-TTAAACTT
*
220317 TTACAAAGAA
64 TTACAAATAA
* * * * * * * ** * *
220327 ATATAAATTATATCTT-ATAAATTTTACCTCGCATAATC--A--TACAAAA-AAATTAAACTTCT
1 AAATAAATAATACCTTAAAAAAATTAAACTCATATAATCAAACCTAAAAAATAAATTAAACTTTT
*
220386 A-TAATAA
66 ACAAATAA
* * * * * * *
220393 AAATAAATTATA-TTTTAAAAATTTAAACTCGTATAATCATACCCAAAAAATAAATTTAAACTTT
1 AAATAAATAATACCTTAAAAAAATTAAACTCATATAATCAAACCTAAAAAATAAA-TTAAACTTT
* * *
220457 CATAAACAA
65 TACAAATAA
* * * * * ** * * *
220466 AGATCAATAATATCTT-AAAAATTTATACTTGTGTAATCAAATC-AAAAAATAAATTTAAATTTT
1 AAATAAATAATACCTTAAAAAAATTAAACTCATATAATCAAACCTAAAAAATAAA-TTAAACTTT
220529 TACAAATAA
65 TACAAATAA
* *
220538 AAATAAATTATACCTCAAAAA
1 AAATAAATAATACCTTAAAAA
220559 TTTTACTTTT
Statistics
Matches: 405, Mismatches: 93, Indels: 49
0.74 0.17 0.09
Matches are distributed among these distances:
65 2 0.00
66 33 0.08
67 8 0.02
68 4 0.01
69 6 0.01
70 8 0.02
71 17 0.04
72 118 0.29
73 183 0.45
74 23 0.06
75 3 0.01
ACGTcount: A:0.54, C:0.12, G:0.03, T:0.31
Consensus pattern (73 bp):
AAATAAATAATACCTTAAAAAAATTAAACTCATATAATCAAACCTAAAAAATAAATTAAACTTTT
ACAAATAA
Found at i:220289 original size:145 final size:144
Alignment explanation
Indices: 219964--220561 Score: 522
Period size: 145 Copynumber: 4.2 Consensus size: 144
219954 AAACTTTTAC
* * * * * *
219964 AAATAAA-AATACTTTAAAAAAATTAAACTTATATAATCAAA-TCAGAAAACAAATTCAAAGTTT
1 AAATAAATAATACCTT-AAAAATTTAAACTCATATAATCAAACT-AAAAAATAAATT-TAA-TTT
* * * * *
220027 T-ACAAATAAAAAGAAATAATACCTTAAAAATTTAAACTCGTATCATCATACCTAAAAAATAAAA
62 TCACAAATAAAAATAAATAATATCTTAAAAATTTAAACTCGTATAATCATACCCAAAAAATAAAT
*
220091 TTACACTTCTACAAATAA
127 TTAAACTTCTACAAATAA
** * *
220109 AAAT-AA-AATACCTTAAAAAAATTTAAACAAATATAATCAAACTAGAAAATAAGTTTAATTTTC
1 AAATAAATAATACCTT--AAAAATTTAAACTCATATAATCAAACTAAAAAATAAATTTAATTTTC
* *
220172 GACAAATAAAAATAAATTATATCTTAAAAATATAAACTCGTATAATCATACCCAAAAAATAAATT
64 -ACAAATAAAAATAAATAATATCTTAAAAATTTAAACTCGTATAATCATACCCAAAAAATAAATT
*
220237 TAAACTTATACAAATAA
128 TAAACTTCTACAAATAA
* * * *
220254 AGATCAATAATATCTTAAAAATTTAAACTCTTATAAT-AATACCTAAAAAATAAATTTAATGTTT
1 AAATAAATAATACCTTAAAAATTTAAACTCATATAATCAA-A-CTAAAAAATAAATTTAAT-TTT
* * * * * * * *
220318 TACAAAGAAATATAAATTATATCTTATAAATTTTACCTCGCATAATCATA--C--AAAA-AAA-T
63 CACAAATAAAAATAAATAATATCTTAAAAATTTAAACTCGTATAATCATACCCAAAAAATAAATT
*
220377 TAAACTTCTA-TAATAA
128 TAAACTTCTACAAATAA
* ** * * * *
220393 AAATAAATTATATTTTAAAAATTTAAACTCGTATAATCATACCCAAAAAATAAATTTAAACTTTC
1 AAATAAATAATACCTTAAAAATTTAAACTCATATAATCA-AACTAAAAAATAAATTT-AATTTTC
* * * * * * * **
220458 ATAAACAAAGATCAATAATATCTTAAAAATTTATACTTGTGTAATCA-AATCAAAAAATAAATTT
64 ACAAATAAAAATAAATAATATCTTAAAAATTTAAACTCGTATAATCATACCCAAAAAATAAATTT
* *
220522 AAATTTTTACAAATAA
129 AAACTTCTACAAATAA
* *
220538 AAATAAATTATACCTCAAAAATTT
1 AAATAAATAATACCTTAAAAATTT
220562 TACTTTTATT
Statistics
Matches: 374, Mismatches: 60, Indels: 38
0.79 0.13 0.08
Matches are distributed among these distances:
138 1 0.00
139 89 0.24
140 14 0.04
141 4 0.01
142 8 0.02
143 7 0.02
144 23 0.06
145 157 0.42
146 61 0.16
147 10 0.03
ACGTcount: A:0.54, C:0.12, G:0.03, T:0.32
Consensus pattern (144 bp):
AAATAAATAATACCTTAAAAATTTAAACTCATATAATCAAACTAAAAAATAAATTTAATTTTCAC
AAATAAAAATAAATAATATCTTAAAAATTTAAACTCGTATAATCATACCCAAAAAATAAATTTAA
ACTTCTACAAATAA
Found at i:220453 original size:212 final size:211
Alignment explanation
Indices: 220176--220564 Score: 597
Period size: 212 Copynumber: 1.8 Consensus size: 211
220166 ATTTTCGACA
220176 AATAAAAATAAATTATATCTTAAAAATATAAACTCGTATAATCATACCCAAAAAATAAATTTAAA
1 AATAAAAATAAATTATATCTTAAAAATATAAACTCGTATAATCATACCCAAAAAATAAATTTAAA
*
220241 CTTAT-ACAAATAAAGATCAATAATATCTTAAAAATTTAAACTCT-TATAAT-AATACCTAAAAA
66 CTT-TCACAAACAAAGATCAATAATATCTTAAAAATTTAAACT-TGTATAATCAA-ACC-AAAAA
* * * *
220303 ATAAATTT-AATGTTTTACAAAGAAATATAAATTATATCTTATAAATTTTACCTCGCATAATCAT
127 ATAAATTTAAAT-TTTTACAAAGAAAAATAAATTATACCTCAAAAATTTTACCTCGCATAATCAT
220367 ACAAAAAAATTAAACTTCTAT
191 ACAAAAAAATTAAACTTCTAT
* *
220388 AATAAAAATAAATTATATTTTAAAAATTTAAACTCGTATAATCATACCCAAAAAATAAATTTAAA
1 AATAAAAATAAATTATATCTTAAAAATATAAACTCGTATAATCATACCCAAAAAATAAATTTAAA
* * * *
220453 CTTTCATAAACAAAGATCAATAATATCTTAAAAATTTATACTTGTGTAATCAAATCAAAAAATAA
66 CTTTCACAAACAAAGATCAATAATATCTTAAAAATTTAAACTTGTATAATCAAACCAAAAAATAA
*
220518 ATTTAAATTTTTACAAATAAAAATAAATTATACCTCAAAAATTTTAC
131 ATTTAAATTTTTACAAAGAAAAATAAATTATACCTCAAAAATTTTAC
220565 TTTTATTACA
Statistics
Matches: 161, Mismatches: 12, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
211 49 0.30
212 110 0.68
213 2 0.01
ACGTcount: A:0.53, C:0.11, G:0.02, T:0.34
Consensus pattern (211 bp):
AATAAAAATAAATTATATCTTAAAAATATAAACTCGTATAATCATACCCAAAAAATAAATTTAAA
CTTTCACAAACAAAGATCAATAATATCTTAAAAATTTAAACTTGTATAATCAAACCAAAAAATAA
ATTTAAATTTTTACAAAGAAAAATAAATTATACCTCAAAAATTTTACCTCGCATAATCATACAAA
AAAATTAAACTTCTAT
Found at i:220628 original size:108 final size:106
Alignment explanation
Indices: 220510--220820 Score: 295
Period size: 108 Copynumber: 2.9 Consensus size: 106
220500 AATCAAATCA
*
220510 AAAAATAAATTTAAATTTTTACAAATAAAAATAAATTATACCT-CAA-AAATTTTACTTTTATTA
1 AAAAATAAATTTAAATTTTTAC--AT--AAATAAATTATACCTGAAATAAATTTTACTTTTATTA
* * *
220573 CATTAATGCAATCAAACTATATTTTACTTTTGTTTCTTAAACTAC
62 CATTAATGCAATCAAACTATATTTTACATTTATTTCTTAAACAAC
** * * ** * *** *
220618 AAAAATAAATTTTACTTTTATTGCATTAATGTATTGTTGTTGAAATAAATTTTACTTTTATTGCA
1 AAAAATAAA-TTTAAATTT-TTACATAAATAAATTATACCTGAAATAAATTTTACTTTTATTACA
*
220683 TTAATGCAATCAAACTATATTTTACATTTATTTCTTAAACAAT
64 TTAATGCAATCAAACTATATTTTACATTTATTTCTTAAACAAC
* * * ** * * *
220726 AAAAATAAATTTTAATTTTATTGCATTAATGTATTGTTA-TTGAAATAAATTTTACTTTTATTGC
1 AAAAATAAA-TTTAAATTT-TTACATAAATAAATT-ATACCTGAAATAAATTTTACTTTTATTAC
*
220790 ATTAATGCAATCAAACTATATTTTTCATTTA
63 ATTAATGCAATCAAACTATATTTTACATTTA
220821 GTTATGTTAA
Statistics
Matches: 178, Mismatches: 20, Indels: 10
0.86 0.10 0.05
Matches are distributed among these distances:
106 8 0.04
107 2 0.01
108 157 0.88
109 8 0.04
110 3 0.02
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.46
Consensus pattern (106 bp):
AAAAATAAATTTAAATTTTTACATAAATAAATTATACCTGAAATAAATTTTACTTTTATTACATT
AATGCAATCAAACTATATTTTACATTTATTTCTTAAACAAC
Found at i:220746 original size:33 final size:35
Alignment explanation
Indices: 220660--220755 Score: 108
Period size: 33 Copynumber: 2.8 Consensus size: 35
220650 ATTGTTGTTG
* * *
220660 AAATAAATTTTACTTTTATTGCATTAATGCAATCA
1 AAATAAATTTTAATTTTATTGCATTAATACAATAA
* * *
220695 AACTATATTTTACA-TTTATTTC-TTAA-ACAATAA
1 AAATAAATTTTA-ATTTTATTGCATTAATACAATAA
220728 AAATAAATTTTAATTTTATTGCATTAAT
1 AAATAAATTTTAATTTTATTGCATTAAT
220756 GTATTGTTAT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
32 1 0.02
33 22 0.46
34 8 0.17
35 17 0.35
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.46
Consensus pattern (35 bp):
AAATAAATTTTAATTTTATTGCATTAATACAATAA
Found at i:220851 original size:108 final size:108
Alignment explanation
Indices: 220556--220820 Score: 440
Period size: 108 Copynumber: 2.5 Consensus size: 108
220546 TATACCTCAA
* * * * *
220556 AAATTTTACTTTTATTACATTAATGCAATCAAACTATATTTTACTTTTGTTTCTTAAACTACAAA
1 AAATTTTACTTTTATTGCATTAATGCAATCAAACTATATTTTACATTTATTTCTTAAACAATAAA
* * *
220621 AATAAATTTTACTTTTATTGCATTAATGTATTGTTGTTGAAAT
66 AATAAATTTGAATTTTATTGCATTAATGTATTGTTATTGAAAT
220664 AAATTTTACTTTTATTGCATTAATGCAATCAAACTATATTTTACATTTATTTCTTAAACAATAAA
1 AAATTTTACTTTTATTGCATTAATGCAATCAAACTATATTTTACATTTATTTCTTAAACAATAAA
*
220729 AATAAATTTTAATTTTATTGCATTAATGTATTGTTATTGAAAT
66 AATAAATTTGAATTTTATTGCATTAATGTATTGTTATTGAAAT
*
220772 AAATTTTACTTTTATTGCATTAATGCAATCAAACTATATTTTTCATTTA
1 AAATTTTACTTTTATTGCATTAATGCAATCAAACTATATTTTACATTTA
220821 GTTATGTTAA
Statistics
Matches: 149, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
108 149 1.00
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.48
Consensus pattern (108 bp):
AAATTTTACTTTTATTGCATTAATGCAATCAAACTATATTTTACATTTATTTCTTAAACAATAAA
AATAAATTTGAATTTTATTGCATTAATGTATTGTTATTGAAAT
Found at i:221321 original size:71 final size:71
Alignment explanation
Indices: 221158--221353 Score: 227
Period size: 72 Copynumber: 2.7 Consensus size: 71
221148 TTTTATGAGT
* * * **
221158 AAAAATAAATTTAAACTTTTAAAAATAAAAATAAATAATAACTT-AAATATTTAAATGCTTATAA
1 AAAAATAAATTTAAACTTTTACAAAT-AAAATAAATTAT-ACTTAAAAAATTTAAATGAGTATAA
221222 TTAAACCA
64 TTAAACCA
* * *
221230 AAAAACAGATTTAAACTTTTACAAATAAAATAAATTATACTTTAAAAAATTTAAATTAGTATAAT
1 AAAAATAAATTTAAACTTTTACAAATAAAATAAATTATAC-TTAAAAAATTTAAATGAGTATAAT
*
221295 TAAATCA
65 TAAACCA
* *
221302 AAAAATAAATTTAAA-TTTTAACAAA-AATATAAATTATACCTTAAAAATTTTA
1 AAAAATAAATTTAAACTTTT-ACAAATAAAATAAATTATA-CTTAAAAAATTTA
221354 CTTTTATTAC
Statistics
Matches: 107, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
70 2 0.02
71 40 0.37
72 65 0.61
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.35
Consensus pattern (71 bp):
AAAAATAAATTTAAACTTTTACAAATAAAATAAATTATACTTAAAAAATTTAAATGAGTATAATT
AAACCA
Found at i:221389 original size:35 final size:34
Alignment explanation
Indices: 221346--221504 Score: 108
Period size: 35 Copynumber: 4.5 Consensus size: 34
221336 TATACCTTAA
221346 AAATTTTACTTTTATTACAATAATGCAATCAAACT
1 AAATTTTACTTTTATTACAATAATGCAATCAAA-T
* * * *
221381 ATATTTTACTTTTATTTCTTAA-ACTACAA--AAAT
1 AAATTTTACTTTTATTAC--AATAATGCAATCAAAT
* * * *
221414 AAATTTTACTTTTATTATAATAATGTATTGTTGTTGAAAT
1 AAATTTTACTTTTATTACAATAATGCA------ATCAAAT
* *
221454 AAATTTTACTTTTATTGCATTAATGCAATCAAATT
1 AAATTTTACTTTTATTACAATAATGCAATCAAA-T
*
221489 ATATTTTACTTTTATT
1 AAATTTTACTTTTATT
221505 TATTTTAATA
Statistics
Matches: 94, Mismatches: 18, Indels: 24
0.69 0.13 0.18
Matches are distributed among these distances:
31 2 0.02
32 3 0.03
33 16 0.17
34 7 0.07
35 32 0.34
36 5 0.05
37 2 0.02
40 27 0.29
ACGTcount: A:0.37, C:0.09, G:0.04, T:0.49
Consensus pattern (34 bp):
AAATTTTACTTTTATTACAATAATGCAATCAAAT
Found at i:221956 original size:72 final size:72
Alignment explanation
Indices: 221839--222913 Score: 343
Period size: 73 Copynumber: 14.7 Consensus size: 72
221829 TTTTATGAGT
* * * *
221839 AAAAATAAATTTTAAA-TTTTATGAATAAAAATAAA-TATAACTTAAATATTGAAACGCT-TATA
1 AAAAATAAA-TTTAAACTTTTATAAATAAAAATAAATTATAACTTAAAAATTTAAAC-TTGTATA
*
221901 ATCAAACAAA
64 ATCAAAC-TA
*
221911 AAAAATAAATTTAAA-TATTTACAAAT-AAAATAAATTAT-ACTTTAAAAAATTTAAACTTGTAT
1 AAAAATAAATTTAAACT-TTTATAAATAAAAATAAATTATAAC-TT-AAAAATTTAAACTTGTAT
**
221973 AATCACATTTA
63 AATCA-AACTA
* * * *
221984 AAAAATAAATTTAAACTTTTGTAAATAAAAATAAATAATAAC-TAAATATTTAAACTTGTCTAAT
1 AAAAATAAATTTAAACTTTTATAAATAAAAATAAATTATAACTTAAAAATTTAAACTTGTATAAT
*
222048 TAAACTA
66 CAAACTA
* * * * **
222055 AAAAATAAATTTAAAGTTATAAAAATAAAAATAAATTA-GACTTTAAAAATTTAAACTCATCACT
1 AAAAATAAATTTAAACTTTTATAAATAAAAATAAATTATAAC-TTAAAAATTTAAACTTGT-A-T
*
222119 ATTTCATAAC--
63 A-ATCA-AACTA
**** * * * * * * * * * ** *
222129 ACTTTTACAAATAAAAATATTATCATTTAAAATACTAATTAT--C-T-AATATTTCAACAAGAAT
1 AAAAATA-AATTTAAACTTTTATAAATAAAAATA--AATTATAACTTAAAAATTTAAACTTGTAT
222190 ACA-CTAATAC-A
63 A-ATC-AA-ACTA
* * * * *
222201 ATCAAACTATATTTTATCTTATT-TAGATAAAATATCCCAAGAATTAAAATAATCTTACAAACAA
1 A--AAAATAAATTTAAACTT-TTATAAATAAAA-AT----A-AATT---ATAA-CTT---AA-AA
** * *
222265 AAATAAA--T-TATACTTTAAA--A
49 ATTTAAACTTGTATA-ATCAAACTA
* * * * * *
222285 TAAAACAAATTAAAACTTTTACAAATAAAAATAAA-AAT-ACTTTAAAAAATTTAAA-TTCATAT
1 AAAAATAAATTTAAACTTTTATAAATAAAAATAAATTATAAC-TT-AAAAATTTAAACTT-GTAT
*
222347 AATTAAA-TCA
63 AATCAAACT-A
* * * * * * *
222357 GAAAACAAATTTAAAATTTTATAGATAAAAATAAATAATACCTTAAAAATTTAAACTTGTATTAT
1 AAAAATAAATTTAAACTTTTATAAATAAAAATAAATTATAACTTAAAAATTTAAACTTGTATAAT
* *
222422 CATATCCA
66 CA-AACTA
* * * * * *
222430 AAAATTAAATTTAAACTTCTACAAATAAAAATAAA-AATACCTTAAAAAAATTTAAA-TACGTAT
1 AAAAATAAATTTAAACTTTTATAAATAAAAATAAATTATAACTT--AAAAATTTAAACT-TGTAT
*
222493 AATTAAACTA
63 AATCAAACTA
* * ** ** * * * * * ** * *
222503 GAGAATAGTTTTAATGTTCTACAAATAAAAATAAACTATATCTTAAAAATATAAACTCCTACAAC
1 AAAAATAAATTTAAACTTTTATAAATAAAAATAAATTATAACTTAAAAATTTAAACTTGTATAAT
* *
222568 CATACCCA
66 CA-AACTA
** * * * * * * *
222576 AAAAATAAATTTAAACTTCGACAAATTAAAGTCAATAATATCTTAAAAATTTAAACTCGTATAAT
1 AAAAATAAATTTAAACTTTTATAAATAAAAATAAATTATAACTTAAAAATTTAAACTTGTATAAT
222641 -AATACCTA
66 CAA-A-CTA
** * * * * * *
222649 AAAAATAAATTTAATGTTTTACAAATAAAAATAAATTATATCTTATAAATTTTATCTCGTATAAT
1 AAAAATAAATTTAAACTTTTATAAATAAAAATAAATTATAACTTAAAAATTTAAACTTGTATAAT
222714 C--A-TA
66 CAAACTA
* * * * * * **
222718 GCAAAA-GAATTTAAACTTCTCT-CATAGAAATAAATTAT-ACTTTAAAAATTTAAACTCATATA
1 -AAAAATAAATTTAAACTTTTATAAATAAAAATAAATTATAAC-TTAAAAATTTAAACTTGTATA
*
222780 AT-AATCCTTA
64 ATCAA-AC-TA
* * * * * *
222790 AAAAATAAATTTAAACTTCTATAAATAAAGATCAATAATATCTTAAAAATTTAAATTTGTATAAT
1 AAAAATAAATTTAAACTTTTATAAATAAAAATAAATTATAACTTAAAAATTTAAACTTGTATAAT
222855 CAAA-TCA
66 CAAACT-A
* * *
222862 AAAAATAAATTTAAATTTTTACAAATAAAAATAAATTATACCTTAAAAATTT
1 AAAAATAAATTTAAACTTTTATAAATAAAAATAAATTATAACTTAAAAATTT
222914 TACTTTTATT
Statistics
Matches: 738, Mismatches: 189, Indels: 152
0.68 0.18 0.14
Matches are distributed among these distances:
67 1 0.00
68 40 0.05
69 16 0.02
70 14 0.02
71 72 0.10
72 195 0.26
73 269 0.36
74 53 0.07
75 21 0.03
76 6 0.01
77 10 0.01
78 1 0.00
80 2 0.00
81 4 0.01
82 18 0.02
83 1 0.00
84 2 0.00
85 1 0.00
86 6 0.01
88 1 0.00
89 5 0.01
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.34
Consensus pattern (72 bp):
AAAAATAAATTTAAACTTTTATAAATAAAAATAAATTATAACTTAAAAATTTAAACTTGTATAAT
CAAACTA
Found at i:221989 original size:682 final size:683
Alignment explanation
Indices: 220664--222003 Score: 2070
Period size: 682 Copynumber: 2.0 Consensus size: 683
220654 TTGTTGAAAT
* * *
220664 AAATTTTACTTTTATTGCATTAATGCAATCAAACTATATTTTACATTTATTTCTTAAACAATAAA
1 AAATTTTACTTTTATTACAATAATGCAATCAAACTATATTTTACATTTATTTCTTAAACAACAAA
* *
220729 AATAAATTTTAATTTTATTGCATTAATGTATTGTTATTGAAATAAATTTTACTTTTATTGCATTA
66 AATAAATTTTAATTTTATTACAATAATGTATTGTTATTGAAATAAATTTTACTTTTATTGCATTA
*
220794 ATGCAATCAAACTATATTTTTCATTTAGTTATGTTAATAGTTTTTCTAATTTGAATTTGTAGATA
131 ATGCAATCAAACTATATTTTACATTTAGTTATGTTAATAGTTTTTCTAATTTGAATTTGTAGATA
** *** *
220859 GCAATAAATTTAAATTTTTACAAATAAAAATGGGTTGTTTATTATTGTTGTTGAAATAAGTATTA
196 AAAATAAATTTAAATTTTTACAAATAAAAATAAATAGTTTATTATTGTTGTTGAAATAAGTATTA
*
220924 TTTATATAATTTACCTTTTAAATTTTACTTTTATTGTTGTTGAAATAAGTTATTATTTATTTATT
261 TTTATATAATCTACCTTTTAAATTTTACTTTTATTGTTGTTGAAATAAGTTATTATTTATTTATT
* *
220989 ACATTAATGCGTTTTATTTTTATTGCAATCAAACTATTAAAATAAATTTTGCATTTATTGCATTA
326 ACATTAATGCATTTTACTTTTATTGCAATCAAACTATTAAAATAAATTTTGCATTTATTGCATTA
221054 ATATATTGTTGTTGAAATAAATTTTACTTTTATTACATTAATGCAACCAAACTATATTTTATATT
391 ATATATTGTTGTTGAAATAAATTTTACTTTTATTACATTAATGCAACCAAACTATATTTTATATT
* * *
221119 TATTTCTTAAAATAGTTTTTTTGGTTTGATTTTATGAGTAAAAATAAATTTAAACTTTTAAAAAT
456 TACTTCTTAAAATAGTTTTTCTGGTTTAATTTTATGAGTAAAAATAAATTTAAACTTTTAAAAAT
* * * * *
221184 AAAAATAAATAATAACTTAAATATTTAAATGCTTATAATTAAACCAAAAAACAGATTTAAACTTT
521 AAAAATAAATAATAACTTAAATATTGAAACGCTTATAATCAAACAAAAAAACAAATTTAAACTTT
*
221249 TACAAATAAAATAAATTATACTTTAAAAAATTTAAATTAGTATAATTAAATCAAAAAATAAATTT
586 TACAAATAAAATAAATTATACTTTAAAAAATTTAAATTAGTATAATCAAATCAAAAAATAAATTT
221314 AAA-TTTTAACAAAAATATAAATTATACCTTAA
651 AAACTTTTAACAAAAATATAAATTATACCTTAA
* *
221346 AAATTTTACTTTTATTACAATAATGCAATCAAACTATATTTTACTTTTATTTCTTAAACTACAAA
1 AAATTTTACTTTTATTACAATAATGCAATCAAACTATATTTTACATTTATTTCTTAAACAACAAA
* * *
221411 AATAAATTTTACTTTTATTATAATAATGTATTGTTGTTGAAATAAATTTTACTTTTATTGCATTA
66 AATAAATTTTAATTTTATTACAATAATGTATTGTTATTGAAATAAATTTTACTTTTATTGCATTA
* * * * * *
221476 ATGCAATCAAATTATATTTTACTTTTATTTATTTTAATAGTTTTTCTGATTT-CATTT-TATGAA
131 ATGCAATCAAACTATATTTTACATTTAGTTATGTTAATAGTTTTTCTAATTTGAATTTGTA-G-A
** *
221539 TAAAAATAAATTTAAATTTTTATGAATAAAAATAAATAGTTTATTATTGTTGTTGAAATATGTTA
194 TAAAAATAAATTTAAATTTTTACAAATAAAAATAAATAGTTTATTATTGTTGTTGAAATAAG-TA
221604 TTATTTATATAATCTACCTTTTAAATTTTACTTTTATTGTTGTTGAAATAAGTTATTATTTATTT
258 TTATTTATATAATCTACCTTTTAAATTTTACTTTTATTGTTGTTGAAATAAGTTATTATTTATTT
* *
221669 ATTGCATTAATGTATTTTACTTTTATTGCAATCAAACTATTAAAATAAA-TTTGCATTTATTGCA
323 ATTACATTAATGCATTTTACTTTTATTGCAATCAAACTATTAAAATAAATTTTGCATTTATTGCA
* * * * *
221733 TTAATGTATTGTTGTTGAAATAAATTTTACTTTTATTGCATTAATGTAATCAAACTATATTTTGC
388 TTAATATATTGTTGTTGAAATAAATTTTACTTTTATTACATTAATGCAACCAAACTATATTTT-A
*
221798 T-TTTACTTCTTACAATAG-TTTTCTGGTTTAATTTTATGAGTAAAAATAAATTTTAAA-TTTTA
452 TATTTACTTCTTAAAATAGTTTTTCTGGTTTAATTTTATGAGTAAAAATAAA-TTTAAACTTTTA
** *
221860 TGAATAAAAATAAAT-ATAACTTAAATATTGAAACGCTTATAATCAAACAAAAAAAATAAATTTA
516 AAAATAAAAATAAATAATAACTTAAATATTGAAACGCTTATAATCAAAC-AAAAAAACAAATTTA
* *
221924 AA-TATTTACAAATAAAATAAATTATACTTTAAAAAATTTAAACTT-GTATAATCACATTTAAAA
580 AACT-TTTACAAATAAAATAAATTATACTTTAAAAAATTTAAA-TTAGTATAATCA-AATCAAAA
221987 AATAAATTTAAACTTTT
642 AATAAATTTAAACTTTT
222004 GTAAATAAAA
Statistics
Matches: 597, Mismatches: 51, Indels: 19
0.90 0.08 0.03
Matches are distributed among these distances:
680 33 0.06
681 113 0.19
682 335 0.56
683 116 0.19
ACGTcount: A:0.40, C:0.07, G:0.06, T:0.46
Consensus pattern (683 bp):
AAATTTTACTTTTATTACAATAATGCAATCAAACTATATTTTACATTTATTTCTTAAACAACAAA
AATAAATTTTAATTTTATTACAATAATGTATTGTTATTGAAATAAATTTTACTTTTATTGCATTA
ATGCAATCAAACTATATTTTACATTTAGTTATGTTAATAGTTTTTCTAATTTGAATTTGTAGATA
AAAATAAATTTAAATTTTTACAAATAAAAATAAATAGTTTATTATTGTTGTTGAAATAAGTATTA
TTTATATAATCTACCTTTTAAATTTTACTTTTATTGTTGTTGAAATAAGTTATTATTTATTTATT
ACATTAATGCATTTTACTTTTATTGCAATCAAACTATTAAAATAAATTTTGCATTTATTGCATTA
ATATATTGTTGTTGAAATAAATTTTACTTTTATTACATTAATGCAACCAAACTATATTTTATATT
TACTTCTTAAAATAGTTTTTCTGGTTTAATTTTATGAGTAAAAATAAATTTAAACTTTTAAAAAT
AAAAATAAATAATAACTTAAATATTGAAACGCTTATAATCAAACAAAAAAACAAATTTAAACTTT
TACAAATAAAATAAATTATACTTTAAAAAATTTAAATTAGTATAATCAAATCAAAAAATAAATTT
AAACTTTTAACAAAAATATAAATTATACCTTAA
Found at i:222030 original size:145 final size:144
Alignment explanation
Indices: 221839--222111 Score: 367
Period size: 145 Copynumber: 1.9 Consensus size: 144
221829 TTTTATGAGT
*
221839 AAAAATAAATTTTAAATTTTATGAATAAAAATAAATATAACTTAAATATTGAAACGCT-TATAAT
1 AAAAATAAATTTTAAATTTTATAAATAAAAATAAATATAACTTAAATATTGAAAC-CTGTATAAT
* * *
221903 CAAACAAAAAAAATAAATTTAAA-TATTTACAAAT-AAAATAAATTATACTTTAAAAAATTTAAA
65 CAAAC-AAAAAAATAAATTTAAAGT-TATAAAAATAAAAATAAATTAGACTTT-AAAAATTTAAA
221966 CTTGTATAATCACATTTA
127 CTTGTATAATCACATTTA
* * * *
221984 AAAAATAAA-TTTAAACTTTTGTAAATAAAAATAAATAATAAC-TAAATATTTAAACTTGTCTAA
1 AAAAATAAATTTTAAA-TTTTATAAATAAAAATAAAT-ATAACTTAAATATTGAAACCTGTATAA
* *
222047 TTAAACTAAAAAATAAATTTAAAGTTATAAAAATAAAAATAAATTAGACTTTAAAAATTTAAACT
64 TCAAACAAAAAAATAAATTTAAAGTTATAAAAATAAAAATAAATTAGACTTTAAAAATTTAAACT
222112 CATCACTATT
Statistics
Matches: 113, Mismatches: 10, Indels: 11
0.84 0.07 0.08
Matches are distributed among these distances:
144 43 0.38
145 65 0.58
146 5 0.04
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.34
Consensus pattern (144 bp):
AAAAATAAATTTTAAATTTTATAAATAAAAATAAATATAACTTAAATATTGAAACCTGTATAATC
AAACAAAAAAATAAATTTAAAGTTATAAAAATAAAAATAAATTAGACTTTAAAAATTTAAACTTG
TATAATCACATTTA
Found at i:222081 original size:71 final size:70
Alignment explanation
Indices: 221839--222111 Score: 268
Period size: 71 Copynumber: 3.8 Consensus size: 70
221829 TTTTATGAGT
* * *
221839 AAAAATAAATTTTAAATTTTATGAATAAAAATAAATATAACTTAAATATTGAAACGCT-TATAAT
1 AAAAATAAA-TTTAAATTTTATAAATAAAAATAAATATAACTTAAATATTTAAAC-TTGTATAAT
*
221903 CAAACAAA
64 CAAAC-TA
* *
221911 AAAAATAAATTTAAATATTTACAAAT-AAAATAAAT-TATACTTTAAAAAATTTAAACTTGTATA
1 AAAAATAAATTTAAAT-TTTATAAATAAAAATAAATATA-AC-TT-AAATATTTAAACTTGTATA
**
221974 ATCACATTTA
62 ATCA-AACTA
* *
221984 AAAAATAAATTTAAACTTTTGTAAATAAAAATAAATAATAAC-TAAATATTTAAACTTGTCTAAT
1 AAAAATAAATTTAAA-TTTTATAAATAAAAATAAAT-ATAACTTAAATATTTAAACTTGTATAAT
*
222048 TAAACTA
64 CAAACTA
* * *
222055 AAAAATAAATTTAAAGTTATAAAAATAAAAATAAAT-TAGACTTTAAAAATTTAAACT
1 AAAAATAAATTTAAA-TTTTATAAATAAAAATAAATATA-AC-TTAAATATTTAAACT
222112 CATCACTATT
Statistics
Matches: 168, Mismatches: 20, Indels: 26
0.79 0.09 0.12
Matches are distributed among these distances:
69 2 0.01
70 4 0.02
71 53 0.32
72 52 0.31
73 42 0.25
74 11 0.07
75 2 0.01
76 2 0.01
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.34
Consensus pattern (70 bp):
AAAAATAAATTTAAATTTTATAAATAAAAATAAATATAACTTAAATATTTAAACTTGTATAATCA
AACTA
Found at i:222109 original size:26 final size:26
Alignment explanation
Indices: 222055--222104 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
222045 AATTAAACTA
*
222055 AAAAATAAATTTAAAGTTATAAAAAT
1 AAAAATAAATTTAAACTTATAAAAAT
*
222081 AAAAATAAA-TTAGACTT-TAAAAAT
1 AAAAATAAATTTAAACTTATAAAAAT
222105 TTAAACTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 6 0.27
26 9 0.41
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (26 bp):
AAAAATAAATTTAAACTTATAAAAAT
Found at i:222217 original size:682 final size:678
Alignment explanation
Indices: 220861--222217 Score: 1509
Period size: 682 Copynumber: 2.0 Consensus size: 678
220851 TGTAGATAGC
*** *
220861 AATAAATTTAAATTTTTACAAATAAAAATGGGTTGTTTATTATTGTTGTTGAAATAAGTATTATT
1 AATAAATTTAAATTTTTACAAATAAAAATAAATAGTTTATTATTGTTGTTGAAATAAGTATTATT
*
220926 TATATAATTTACCTTTTAAATTTTACTTTTATTGTTGTTGAAATAAGTTATTATTTATTTATTAC
66 TATATAATCTACCTTTTAAATTTTACTTTTATTGTTGTTGAAATAAGTTATTATTTATTTATTAC
* *
220991 ATTAATGCGTTTTATTTTTATTGCAATCAAACTATTAAAATAAATTTTGCATTTATTGCATTAAT
131 ATTAATGCATTTTACTTTTATTGCAATCAAACTATTAAAATAAATTTTGCATTTATTGCATTAAT
221056 ATATTGTTGTTGAAATAAATTTTACTTTTATTACATTAATGCAACCAAACTATATTTTATATTTA
196 ATATTGTTGTTGAAATAAATTTTACTTTTATTACATTAATGCAACCAAACTATATTTTATATTTA
* * *
221121 TTTCTTAAAATAGTTTTTTTGGTTTGATTTTATGAGTAAAAATAAATTTAAACTTTTAAAAATAA
261 CTTCTTAAAATAGTTTTTCTGGTTTAATTTTATGAGTAAAAATAAATTTAAACTTTTAAAAATAA
* * * * *
221186 AAATAAATAATAACTTAAATATTTAAATGCTTATAATTAAACCAAAAAACAGATTTAAACTTTTA
326 AAATAAATAATAACTTAAATATTGAAACGCTTATAATCAAACAAAAAAACAAATTTAAACTTTTA
*
221251 CAAATAAAATAAATTATACTTTAAAAAATTTAAATTAGTATAATTAAATCAAAAAATAAATTTAA
391 CAAATAAAATAAATTATACTTTAAAAAATTTAAATTAGTATAATCAAATCAAAAAATAAATTTAA
* * * * * * *
221316 ATTTTAACAAAAATATAAATTATACCTTAAAAATTTTACTTTTATTACAATAATGCAATCAAACT
456 ATTTTAACAAAAATATAAATAATAACTTAAAAATTTAACTTGTACTACAATAATACAA-CAAAAT
* * * * * ** * ** ** ***
221381 ATATTTTACTTTTATTTCTTAAACTACAAAAATAAATTTTACTTTTATTATAATAATGTATTGTT
520 ATAATTTA---TAAGTTCATAAACAACAAAAATAAATTAGACTTTAAAAATAATAAACTATCACT
* *** *** * * *** ***
221446 GTTGAAATAAATTTTACTTTTATTGCATTAATGCAATCAAATTATATTTTACTTTTATTTATTTT
582 ATTGAAATAAATTTTACAAATATAAAATTAATGCAATCAAAATATATTTTAATTTTAACAAGAAT
* *** ** *
221511 AATAGTTTTTCTGATTTCATTTTATGAATAAA
647 AATAATCAATCAAATATCATTTTATGAATAAA
** *
221543 AATAAATTTAAATTTTTATGAATAAAAATAAATAGTTTATTATTGTTGTTGAAATATGTTATTAT
1 AATAAATTTAAATTTTTACAAATAAAAATAAATAGTTTATTATTGTTGTTGAAATAAG-TATTAT
*
221608 TTATATAATCTACCTTTTAAATTTTACTTTTATTGTTGTTGAAATAAGTTATTATTTATTTATTG
65 TTATATAATCTACCTTTTAAATTTTACTTTTATTGTTGTTGAAATAAGTTATTATTTATTTATTA
*
221673 CATTAATGTATTTTACTTTTATTGCAATCAAACTATTAAAATAAA-TTTGCATTTATTGCATTAA
130 CATTAATGCATTTTACTTTTATTGCAATCAAACTATTAAAATAAATTTTGCATTTATTGCATTAA
* * * * *
221737 TGTATTGTTGTTGAAATAAATTTTACTTTTATTGCATTAATGTAATCAAACTATATTTTGCT-TT
195 TATATTGTTGTTGAAATAAATTTTACTTTTATTACATTAATGCAACCAAACTATATTTT-ATATT
* **
221801 TACTTCTTACAATAG-TTTTCTGGTTTAATTTTATGAGTAAAAATAAATTTTAAA-TTTTATGAA
259 TACTTCTTAAAATAGTTTTTCTGGTTTAATTTTATGAGTAAAAATAAA-TTTAAACTTTTAAAAA
*
221864 TAAAAATAAAT-ATAACTTAAATATTGAAACGCTTATAATCAAACAAAAAAAATAAATTTAAA-T
323 TAAAAATAAATAATAACTTAAATATTGAAACGCTTATAATCAAAC-AAAAAAACAAATTTAAACT
* *
221927 ATTTACAAATAAAATAAATTATACTTTAAAAAATTTAAACTT-GTATAATCACATTTAAAAAATA
387 -TTTACAAATAAAATAAATTATACTTTAAAAAATTTAAA-TTAGTATAATCA-AATCAAAAAATA
* *
221991 AATTTAAACTTTTGTAA-ATAAAA-ATAAATAATAAC-TAAATATTTAAACTTGT-CTA-ATTAA
449 AATTTAAA--TTT-TAACA-AAAATATAAATAATAACTTAAAAATTT-AACTTGTACTACAATAA
* *
222051 -ACTAA-AAAATA-AATTTA-AAGTT-ATAAA-AATAAAAATAAATTAGACTTTAAAAAT-TTAA
509 TAC-AACAAAATATAATTTATAAGTTCATAAACAACAAAAATAAATTAGACTTTAAAAATAATAA
** * * *
222109 ACTCATCACTATT-TCATAACACTTTTACAAATA-AAAATATTAT-CATTTAAAATACTAATTAT
573 ACT-ATCACTATTGAAATAA-A-TTTTACAAATATAAAAT-TAATGCAATCAAAATA-T-ATT-T
222171 CTAATATTTCAACAAGAATACACTAATACAATCAAACTAT-ATTTTAT
631 -TAAT-TTT-AACAAGAATA-A-TAAT-CAATCAAA-TATCATTTTAT
222218 CTTATTTAGA
Statistics
Matches: 563, Mismatches: 85, Indels: 54
0.80 0.12 0.08
Matches are distributed among these distances:
672 8 0.01
673 36 0.06
674 16 0.03
675 6 0.01
676 1 0.00
677 3 0.01
678 3 0.01
679 9 0.02
680 37 0.07
681 112 0.20
682 182 0.32
683 124 0.22
684 19 0.03
685 7 0.01
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.44
Consensus pattern (678 bp):
AATAAATTTAAATTTTTACAAATAAAAATAAATAGTTTATTATTGTTGTTGAAATAAGTATTATT
TATATAATCTACCTTTTAAATTTTACTTTTATTGTTGTTGAAATAAGTTATTATTTATTTATTAC
ATTAATGCATTTTACTTTTATTGCAATCAAACTATTAAAATAAATTTTGCATTTATTGCATTAAT
ATATTGTTGTTGAAATAAATTTTACTTTTATTACATTAATGCAACCAAACTATATTTTATATTTA
CTTCTTAAAATAGTTTTTCTGGTTTAATTTTATGAGTAAAAATAAATTTAAACTTTTAAAAATAA
AAATAAATAATAACTTAAATATTGAAACGCTTATAATCAAACAAAAAAACAAATTTAAACTTTTA
CAAATAAAATAAATTATACTTTAAAAAATTTAAATTAGTATAATCAAATCAAAAAATAAATTTAA
ATTTTAACAAAAATATAAATAATAACTTAAAAATTTAACTTGTACTACAATAATACAACAAAATA
TAATTTATAAGTTCATAAACAACAAAAATAAATTAGACTTTAAAAATAATAAACTATCACTATTG
AAATAAATTTTACAAATATAAAATTAATGCAATCAAAATATATTTTAATTTTAACAAGAATAATA
ATCAATCAAATATCATTTTATGAATAAA
Found at i:222289 original size:22 final size:23
Alignment explanation
Indices: 222263--222331 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 23
222253 TCTTACAAAC
222263 AAAAATAAATTATACTTTAAAAT
1 AAAAATAAATTATACTTTAAAAT
* *
222286 -AAAACAAATTAAAACTTTTACAAAT
1 AAAAATAAATT-ATAC-TTTA-AAAT
*
222311 AAAAATAAA-AATACTTTAAAA
1 AAAAATAAATTATACTTTAAAA
222332 AATTTAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
22 12 0.32
23 7 0.19
24 7 0.19
25 4 0.11
26 7 0.19
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (23 bp):
AAAAATAAATTATACTTTAAAAT
Found at i:222535 original size:146 final size:144
Alignment explanation
Indices: 222286--222915 Score: 546
Period size: 146 Copynumber: 4.4 Consensus size: 144
222276 ACTTTAAAAT
* * * *
222286 AAAACAAATTAAAACTTTTACAAATAAAAATAAAAATACTTTAAAAAATTTAAATTCATATAATT
1 AAAATAAATTTAAACTTCTACAAATAAAAATAAAAATAC-TTAAAAAATTTAAACTCATATAA-T
* * * * * * *
222351 AA-A-TCAGAAAACAAATTTAAAATTTTATAGATAAAAATAAATAATACCTTAAAAATTTAAACT
64 AATACT-AAAAAATAAATTTAAAGTTCTACAAATAAAAATAAATAATATCTTAAAAATTTAAACT
* *
222414 TGTATTATCATATCCAA
128 CGTATAATCATATCCAA
* *
222431 AAATTAAATTTAAACTTCTACAAATAAAAATAAAAATACCTTAAAAAAATTTAAA-TACGTATAA
1 AAAATAAATTTAAACTTCTACAAATAAAAATAAAAATA-CTT-AAAAAATTTAAACT-CATATAA
* * ** * *
222495 TTAA-ACTAGAGAATAGTTTTAATGTTCTACAAATAAAAATAAACT-ATATCTTAAAAATATAAA
63 -TAATACTAAAAAATAAATTTAAAGTTCTACAAATAAAAATAAA-TAATATCTTAAAAATTTAAA
* * * *
222558 CTCCTACAACCATACCCAA
126 CTCGTATAATCATATCCAA
* * * * *
222577 AAAATAAATTTAAACTTCGACAAATTAAAGTCAATAATATCTT-AAAAATTTAAACTCGTATAAT
1 AAAATAAATTTAAACTTCTACAAATAAAAAT-AAAAATA-CTTAAAAAATTTAAACTCATATAAT
* * * * * *
222641 AATACCTAAAAAATAAATTTAATGTTTTACAAATAAAAATAAATTATATCTTATAAATTTTATCT
64 AATA-CTAAAAAATAAATTTAAAGTTCTACAAATAAAAATAAATAATATCTTAAAAATTTAAACT
*
222706 CGTATAATCATA-GC--
128 CGTATAATCATATCCAA
* ** * * *
222720 AAAA-GAATTTAAACTTCT-CTCATAGAAATAAATTATACTTTAAAAATTTAAACTCATATAATA
1 AAAATAAATTTAAACTTCTACAAATAAAAATAAA-AATACTTAAAAAATTTAAACTCATATAATA
* * * * * * *
222783 ATCCTTAAAAAATAAATTTAAACTTCTATAAATAAAGATCAATAATATCTTAAAAATTTAAATTT
65 ATAC-TAAAAAATAAATTTAAAGTTCTACAAATAAAAATAAATAATATCTTAAAAATTTAAACTC
*
222848 GTATAATCAAAT-CAA
129 GTATAATCATATCCAA
* * * *
222863 AAAATAAATTTAAATTTTTACAAATAAAAATAAATTATACCTTAAAAATTTTA
1 AAAATAAATTTAAACTTCTACAAATAAAAATAAA-AATA-CTTAAAAAATTTA
222916 CTTTTATTGT
Statistics
Matches: 393, Mismatches: 73, Indels: 37
0.78 0.15 0.07
Matches are distributed among these distances:
140 6 0.02
141 91 0.23
142 12 0.03
143 8 0.02
144 14 0.04
145 74 0.19
146 177 0.45
147 11 0.03
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.33
Consensus pattern (144 bp):
AAAATAAATTTAAACTTCTACAAATAAAAATAAAAATACTTAAAAAATTTAAACTCATATAATAA
TACTAAAAAATAAATTTAAAGTTCTACAAATAAAAATAAATAATATCTTAAAAATTTAAACTCGT
ATAATCATATCCAA
Found at i:223064 original size:35 final size:34
Alignment explanation
Indices: 222908--223066 Score: 108
Period size: 35 Copynumber: 4.5 Consensus size: 34
222898 TATACCTTAA
* *
222908 AAATTTTACTTTTATTGTATTAATGCAACCAAACT
1 AAATTTTACTTTTATTGCATTAATGCAATCAAA-T
* * *
222943 ATATTTTACTTTTATTTC-TTAAACTACAA--AAAT
1 AAATTTTACTTTTATTGCATT-AA-TGCAATCAAAT
* * * * *
222976 AAATTTTGCTTTTATTGCGTTAATGTATTGTTGTTGAAAT
1 AAATTTTACTTTTATTGCATTAATGCA------ATCAAAT
223016 AAATTTTACTTTTATTGCATTAATGCAATCAAACT
1 AAATTTTACTTTTATTGCATTAATGCAATCAAA-T
*
223051 ATATTTTACTTTTATT
1 AAATTTTACTTTTATT
223067 TTTTTAATAG
Statistics
Matches: 96, Mismatches: 16, Indels: 24
0.71 0.12 0.18
Matches are distributed among these distances:
32 2 0.02
33 18 0.19
34 11 0.11
35 33 0.34
36 4 0.04
40 28 0.29
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.49
Consensus pattern (34 bp):
AAATTTTACTTTTATTGCATTAATGCAATCAAAT
Found at i:223540 original size:72 final size:71
Alignment explanation
Indices: 223373--223609 Score: 236
Period size: 72 Copynumber: 3.3 Consensus size: 71
223363 TGAATAAAAA
* *
223373 AATAACTTAAATATTGAAACGCT-TATAATCAAAC-TAAAAAATAAATTTAAACATTTACAAAT-
1 AATAACTTAAATATTTAAAC-TTGTATAATC-AACTTAAAAAATAAATTTAAAC-TTTACAAATA
223435 AAAATAAAT
63 AAAATAAAT
* * *
223444 TAT-ACTTTAAAAAATTTAAACTTGTATAATCATACTTAAAAAATAAATTTAAACTTCTGCAAAT
1 AATAAC-TT-AAATATTTAAACTTGTATAATCA-ACTTAAAAAATAAATTTAAACTT-TACAAAT
223508 AAAAATAAAT
62 AAAAATAAAT
* * * * *
223518 AATAAC-TAAATATTTAAACTTGTCTAATTAAATTAAAAAATAAATTTAAAGTTATACTAATAAA
1 AATAACTTAAATATTTAAACTTGTATAATCAACTTAAAAAATAAATTTAAACTT-TACAAATAAA
223582 AATAAAT
65 AATAAAT
*
223589 --TACACTTTAAAAATTTAAACT
1 AATA-AC-TTAAATATTTAAACT
223610 CATCACTATA
Statistics
Matches: 140, Mismatches: 15, Indels: 21
0.80 0.09 0.12
Matches are distributed among these distances:
69 2 0.01
70 4 0.03
71 42 0.30
72 54 0.39
73 25 0.18
74 11 0.08
75 2 0.01
ACGTcount: A:0.55, C:0.09, G:0.03, T:0.34
Consensus pattern (71 bp):
AATAACTTAAATATTTAAACTTGTATAATCAACTTAAAAAATAAATTTAAACTTTACAAATAAAA
ATAAAT
Found at i:223580 original size:71 final size:71
Alignment explanation
Indices: 223342--223609 Score: 234
Period size: 72 Copynumber: 3.8 Consensus size: 71
223332 TTTTATGTGT
* * * *
223342 AAAAATAAATTTAAAGTTT---TATGAATAA-AAA-AATAACTTAAATATTGAAACGCT-TATAA
1 AAAAATAAATTTAAAGTTTACAAAT-AAAAATAAATAATAACTTAAATATTTAAAC-TTGTATAA
*
223401 TCAAACTA
64 TCAAATTA
* * *
223409 AAAAATAAATTTAAACATTTACAAAT-AAAATAAATTAT-ACTTTAAAAAATTTAAACTTGTATA
1 AAAAATAAATTTAAA-GTTTACAAATAAAAATAAATAATAAC-TT-AAATATTTAAACTTGTATA
*
223472 ATCATACTTA
63 ATCA-AATTA
* * *
223482 AAAAATAAATTTAAACTTCTGCAAATAAAAATAAATAATAAC-TAAATATTTAAACTTGTCTAAT
1 AAAAATAAATTTAAAGTT-TACAAATAAAAATAAATAATAACTTAAATATTTAAACTTGTATAAT
*
223546 TAAATTA
65 CAAATTA
* *
223553 AAAAATAAATTTAAAGTTATACTAATAAAAATAAAT--TACACTTTAAAAATTTAAACT
1 AAAAATAAATTTAAAGTT-TACAAATAAAAATAAATAATA-AC-TTAAATATTTAAACT
223610 CATCACTATA
Statistics
Matches: 164, Mismatches: 21, Indels: 27
0.77 0.10 0.13
Matches are distributed among these distances:
67 15 0.09
68 3 0.02
69 5 0.03
70 7 0.04
71 43 0.26
72 53 0.32
73 25 0.15
74 11 0.07
75 2 0.01
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.34
Consensus pattern (71 bp):
AAAAATAAATTTAAAGTTTACAAATAAAAATAAATAATAACTTAAATATTTAAACTTGTATAATC
AAATTA
Found at i:224014 original size:146 final size:145
Alignment explanation
Indices: 223789--224058 Score: 328
Period size: 146 Copynumber: 1.9 Consensus size: 145
223779 AAAATAAAAC
* * * *
223789 AAATTAAAACTTTTATATATAAAAATAAAAATGCTTTAAAAAATTTAAATTCATATAATTAAATC
1 AAATTAAAACTTTTACAAATAAAAATAAAAATGCTTTAAAAAATTTAAATACATATAATCAAATC
* * *
223854 AGAAAACAAATTTAAAATTTTATAAATAAAAATAAATAATACCTTAAAAATTTAAACTCGCATTA
66 AGAAAACAAATTTAAAATTCTACAAATAAAAATAAATAATACCTTAAAAATATAAACTCGCATTA
223919 TCATATCCAAAAATT
131 TCATATCCAAAAATT
* * * *
223934 AAATTTAAATTTTTACAAATAAAAATAAAAAT-ATCTTAAAAAACTTTAAATACATATAGTCAAA
1 AAATTAAAACTTTTACAAATAAAAATAAAAATGCT-TTAAAAAA-TTTAAATACATATAATCAAA
* * ** ** * *
223998 -CTAGAGAATAGGTTTAATGTTCTACAAATAAAAATAAATTATATCTTAAAAATATAAACTC
64 TC-AGAAAACAAATTTAAAATTCTACAAATAAAAATAAATAATACCTTAAAAATATAAACTC
224059 CTATAACCAT
Statistics
Matches: 103, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
144 1 0.01
145 37 0.36
146 65 0.63
ACGTcount: A:0.54, C:0.09, G:0.03, T:0.33
Consensus pattern (145 bp):
AAATTAAAACTTTTACAAATAAAAATAAAAATGCTTTAAAAAATTTAAATACATATAATCAAATC
AGAAAACAAATTTAAAATTCTACAAATAAAAATAAATAATACCTTAAAAATATAAACTCGCATTA
TCATATCCAAAAATT
Found at i:224196 original size:24 final size:26
Alignment explanation
Indices: 224151--224200 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 26
224141 ATAATACTTA
*
224151 AAAAATAAATTTAATATTTTATAAAT
1 AAAAATAAATTTAATATCTTATAAAT
224177 AAAAATAAA-TT-ATATCTTATAAAT
1 AAAAATAAATTTAATATCTTATAAAT
224201 TTTATCTCGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.52
25 2 0.09
26 9 0.39
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (26 bp):
AAAAATAAATTTAATATCTTATAAAT
Found at i:224201 original size:73 final size:72
Alignment explanation
Indices: 223856--224411 Score: 249
Period size: 73 Copynumber: 7.7 Consensus size: 72
223846 ATTAAATCAG
* * * * ** *
223856 AAAACAAATTTAAAATTTTATAAATAAAAATAAATAATACCTTAAAAATTTAAACTCGCATTATC
1 AAAATAAATTT-AAATTTTACAAATAAAAATAAATAATATCTTAAAAATTTAAACTCGTAAAATA
*
223921 ATA-TCCAA
65 ATACT-TAA
* * *
223929 AAATTAAATTTAAATTTTTACAAATAAAAATAAA-AATATCTTAAAAAACTTTAAA-TACATATA
1 AAAATAAATTTAAA-TTTTACAAATAAAAATAAATAATATCTT-AAAAA-TTTAAACT-CGTAAA
* *
223992 GTCAA-AC-TAG
62 AT-AATACTTAA
* ** * * *
224002 AGAATAGGTTT-AATGTTCTACAAATAAAAATAAATTATATCTTAAAAATATAAACTCCTATAAC
1 AAAATAAATTTAAAT-TT-TACAAATAAAAATAAATAATATCTTAAAAATTTAAACTCGTA-AA-
** ***
224066 CATACCAAAAAA
62 -ATAATACTTAA
* * * ** *
224078 AAAACAAAAATTAAACTTTGACAAATAAAGGTCAATAATATCTTAAAAATTTAAACTCGTAAAAT
1 AAAA-TAAATTTAAA-TTTTACAAATAAAAATAAATAATATCTTAAAAATTTAAACTCGTAAAAT
224143 AATACTTAA
64 AATACTTAA
* * * * *
224152 AAAATAAATTTAATATTTTATAAATAAAAATAAATTATATCTTATAAATTTTATCTCGT---ATA
1 AAAATAAATTTAA-ATTTTACAAATAAAAATAAATAATATCTTAAAAATTTAAACTCGTAAAATA
* * *
224214 GT-CATAGC
65 ATACTTA-A
* * * * * * *
224222 AAAA-GAATTTAAGCTTCT-CTAATAGAAATAAATTATA-CTTTAAAAAATTAAACTCGTATAAA
1 AAAATAAATTTAA-ATTTTACAAATAAAAATAAATAATATC-TTAAAAATTTAAACTCGTA-AAA
* **
224284 T-ATCCCCAA
63 TAATACTTAA
* * *
224293 AAAGA-AAATTTAAACTTCTATA-AAATAAAGATCAATAATATCTTAAAAATTTAAACTTGT---
1 AAA-ATAAATTTAAA-TT-T-TACAAATAAAAATAAATAATATCTTAAAAATTTAAACTCGTAAA
224353 AT-A-A-TTAA
62 ATAATACTTAA
* *
224361 ATAAA-AAATTTAAATTTTTACAAATAAAAATAAATTATATTTTAAAAATTT
1 A-AAATAAATTTAAA-TTTTACAAATAAAAATAAATAATATCTTAAAAATTT
224412 TACTTTTATT
Statistics
Matches: 361, Mismatches: 88, Indels: 74
0.69 0.17 0.14
Matches are distributed among these distances:
66 2 0.01
67 28 0.08
68 45 0.12
69 15 0.04
70 11 0.03
71 5 0.01
72 36 0.10
73 106 0.29
74 60 0.17
75 4 0.01
76 6 0.02
77 38 0.11
78 4 0.01
79 1 0.00
ACGTcount: A:0.53, C:0.10, G:0.04, T:0.33
Consensus pattern (72 bp):
AAAATAAATTTAAATTTTACAAATAAAAATAAATAATATCTTAAAAATTTAAACTCGTAAAATAA
TACTTAA
Found at i:224388 original size:27 final size:26
Alignment explanation
Indices: 224337--224396 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
224327 ATAATATCTT
* *
224337 AAAAATTTAAACTTGTATAATTAAATA
1 AAAAATTTAAACTTGTACAAATAAA-A
* *
224364 AAAAATTTAAATTTTTACAAATAAAA
1 AAAAATTTAAACTTGTACAAATAAAA
*
224390 ATAAATT
1 AAAAATT
224397 ATATTTTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (26 bp):
AAAAATTTAAACTTGTACAAATAAAA
Found at i:224487 original size:33 final size:35
Alignment explanation
Indices: 224406--224497 Score: 98
Period size: 33 Copynumber: 2.7 Consensus size: 35
224396 TATATTTTAA
* * *
224406 AAATTTTACTTTTATTGTATTAATGCAACCAAACT
1 AAATTTTACTTTTATTGTATTAATACAACAAAAAT
* * * *
224441 ATATTTTAGTTTTATT-TCTTAA-ACTACAAAAAT
1 AAATTTTACTTTTATTGTATTAATACAACAAAAAT
*
224474 AAATTTTACTTTTATTGCATTAAT
1 AAATTTTACTTTTATTGTATTAAT
224498 GTATTGTTGT
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
33 21 0.48
34 9 0.20
35 14 0.32
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.48
Consensus pattern (35 bp):
AAATTTTACTTTTATTGTATTAATACAACAAAAAT
Found at i:224549 original size:35 final size:35
Alignment explanation
Indices: 224406--224564 Score: 119
Period size: 35 Copynumber: 4.5 Consensus size: 35
224396 TATATTTTAA
* * *
224406 AAATTTTACTTTTATTGTATTAATGCAACCAAACT
1 AAATTTTACTTTTATTGCATTAATGCAATCAAATT
* * * *
224441 ATATTTTAGTTTTATTTC-TTAAACTACAA--AAA-T
1 AAATTTTACTTTTATTGCATT-AA-TGCAATCAAATT
* * **
224474 AAATTTTACTTTTATTGCATTAATGTATTGTTGTTGAATT
1 AAATTTTACTTTTATTGCATTAATGCA-----ATCAAATT
224514 AAATTTTACTTTTATTGCATTAATGCAATCAAATT
1 AAATTTTACTTTTATTGCATTAATGCAATCAAATT
*
224549 ATATTTTACTTTTATT
1 AAATTTTACTTTTATT
224565 TATTTTATTA
Statistics
Matches: 96, Mismatches: 17, Indels: 22
0.71 0.13 0.16
Matches are distributed among these distances:
32 2 0.02
33 18 0.19
34 7 0.07
35 36 0.38
36 4 0.04
39 2 0.02
40 27 0.28
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.50
Consensus pattern (35 bp):
AAATTTTACTTTTATTGCATTAATGCAATCAAATT
Found at i:224979 original size:72 final size:72
Alignment explanation
Indices: 224897--225166 Score: 239
Period size: 72 Copynumber: 3.8 Consensus size: 72
224887 TTTTATGAGT
* *
224897 AAAAATAAATTTAAACTTTTACGAATAAAAATAAATAATAACTTAAATATTTAAACACTTATAAT
1 AAAAATAAATTTAAACTTTTACAAATAAAAATAAATAATAACTTAAAAATTTAAACACTTATAAT
*
224962 AAAACCA
66 AAAATCA
* * ** **
224969 AAAAACAAATTTAAACTTTTACAAAT-AAAATAAATTATATTTTAAAAAATTTAAACTTTTATAA
1 AAAAATAAATTTAAACTTTTACAAATAAAAATAAATAATAACTT-AAAAATTTAAACACTTATAA
**** *
225033 TCTTTTTTA
65 T-AAAATCA
* * * *
225042 AAAAATAAATTTAAACTTTCAC-GA-AAAAACAAATAATAAC-TAAATATTT-AA-ACTTATCTA
1 AAAAATAAATTTAAACTTTTACAAATAAAAATAAATAATAACTTAAAAATTTAAACACTTA--TA
*
225102 ATCAAATCA
64 ATAAAATCA
* * * *
225111 AAAAATAAATTCAAACTTCTACAAATAAAAGTAAATTAT-ACTTTAAAAATTTAAAC
1 AAAAATAAATTTAAACTTTTACAAATAAAAATAAATAATAAC-TTAAAAATTTAAAC
225167 TCCTAACTAT
Statistics
Matches: 150, Mismatches: 37, Indels: 20
0.72 0.18 0.10
Matches are distributed among these distances:
68 3 0.02
69 23 0.15
70 14 0.09
71 25 0.17
72 62 0.41
73 23 0.15
ACGTcount: A:0.56, C:0.10, G:0.01, T:0.33
Consensus pattern (72 bp):
AAAAATAAATTTAAACTTTTACAAATAAAAATAAATAATAACTTAAAAATTTAAACACTTATAAT
AAAATCA
Found at i:225127 original size:142 final size:145
Alignment explanation
Indices: 224897--225167 Score: 401
Period size: 142 Copynumber: 1.9 Consensus size: 145
224887 TTTTATGAGT
* *
224897 AAAAATAAATTTAAACTTTTACGAATAAAAATAAATAATAACTTAAATATTTAAACACTTATAAT
1 AAAAATAAATTTAAACTTTCACGAATAAAAACAAATAATAACTTAAATATTTAAACACTTATAAT
* * *
224962 AAAACCAAAAAACAAATTTAAACTTTTACAAATAAAA-TAAATTATATTTTAAAAAATTTAAACT
66 AAAACCAAAAAACAAATTCAAACTTCTACAAATAAAAGTAAATTATACTTT-AAAAATTTAAACT
225026 TTTATAATCTTTTTTA
130 TTTATAATCTTTTTTA
225042 AAAAATAAATTTAAACTTTCACG-A-AAAAACAAATAATAAC-TAAATATTT-AA-ACTTATCTA
1 AAAAATAAATTTAAACTTTCACGAATAAAAACAAATAATAACTTAAATATTTAAACACTTA--TA
* * *
225102 ATCAAATCAAAAAATAAATTCAAACTTCTACAAATAAAAGTAAATTATACTTTAAAAATTTAAAC
64 ATAAAACCAAAAAACAAATTCAAACTTCTACAAATAAAAGTAAATTATACTTTAAAAATTTAAAC
225167 T
129 T
225168 CCTAACTATA
Statistics
Matches: 115, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
140 5 0.04
141 2 0.02
142 58 0.50
143 27 0.23
144 1 0.01
145 22 0.19
ACGTcount: A:0.55, C:0.10, G:0.01, T:0.34
Consensus pattern (145 bp):
AAAAATAAATTTAAACTTTCACGAATAAAAACAAATAATAACTTAAATATTTAAACACTTATAAT
AAAACCAAAAAACAAATTCAAACTTCTACAAATAAAAGTAAATTATACTTTAAAAATTTAAACTT
TTATAATCTTTTTTA
Found at i:225464 original size:72 final size:73
Alignment explanation
Indices: 225343--225971 Score: 463
Period size: 72 Copynumber: 8.7 Consensus size: 73
225333 ACTTTAAAAT
* * * *
225343 AAAATAAATTTACACTTCTATAAATAAAAATAAA-AATA-CTTTAATAAATTTGAACTCATATAA
1 AAAATAAATTTAAACTTCTACAAATAAAAATAAATAATATC-TTAA-AAATTTAAACTCGTATAA
*
225406 TCAAATC-AG
64 TCAAATCTAA
* * * * *
225415 AAAATAAATTTAAAGTTTTACAAATAAAAATAAATCATGTCTTAAAAATTTAAACTTGTATTAAT
1 AAAATAAATTTAAACTTCTACAAATAAAAATAAATAATATCTTAAAAATTTAAACTCGTA-TAAT
*
225480 -ATA-C-AA
65 CAAATCTAA
* * * * *
225486 AAAAAATAATTTAAATTTTTCCAAAAAAATAAAAATAAA-AATAACTTAAAAAAATTTAAA-TAC
1 AAAATA-AATTTAAA--CTT-C-TACAAATAAAAATAAATAATATCTT--AAAAATTTAAACT-C
*
225549 GTATAATCAAA-CTAG
58 GTATAATCAAATCTAA
* * *** * * * * *
225564 AAAACAAGTTTATTGTTCCAAAAATAAAGATAAATTATATCTTAAAAATTTAAACTCGTATAATT
1 AAAATAAATTTAAACTTCTACAAATAAAAATAAATAATATCTTAAAAATTTAAACTCGTATAATC
* *
225629 ATACCT-A
66 AAATCTAA
* *** * * *
225636 AAAATAAATTTAAACTTATACAAATAGTGATTAATAATATCTTAAACATTTAAACTCGTATAATA
1 AAAATAAATTTAAACTTCTACAAATAAAAATAAATAATATCTTAAAAATTTAAACTCGTATAATC
*
225701 AAACCTAA
66 AAATCTAA
** ** * * *
225709 AAAGCAAATTTAATGTTCTACAAATAAAAATAAATTATATCTTAAAAATTTTATCTCGTATAATC
1 AAAATAAATTTAAACTTCTACAAATAAAAATAAATAATATCTTAAAAATTTAAACTCGTATAATC
*
225774 --A--TAC
66 AAATCTAA
* * * * *
225778 AAAA-AAATTTAAACTTTTA-TAATAGAAATAAATTATA-CTTCAAAAAATTAAACTCGTATAAT
1 AAAATAAATTTAAACTTCTACAAATAAAAATAAATAATATCTT-AAAAATTTAAACTCGTATAAT
*
225840 CATATCTAA
65 CAAATCTAA
* * *
225849 AAAATAAATTTAAACTTCTACAAATAAAGATTAATAATATCTTAAAAATTTAAACTTGTATAATC
1 AAAATAAATTTAAACTTCTACAAATAAAAATAAATAATATCTTAAAAATTTAAACTCGTATAATC
225914 AAA--TAA
66 AAATCTAA
* * * *
225920 AAAATATATTTAAACTTTTA-ACAA-AAAAATAAATTATACCTTAAAATATTTA
1 AAAATAAATTTAAACTTCTACA-AATAAAAATAAATAATATCTTAAAA-ATTTA
225972 CTTTTATTGC
Statistics
Matches: 441, Mismatches: 89, Indels: 55
0.75 0.15 0.09
Matches are distributed among these distances:
66 3 0.01
67 35 0.08
68 12 0.03
69 6 0.01
70 19 0.04
71 42 0.10
72 143 0.32
73 114 0.26
74 13 0.03
75 7 0.02
76 19 0.04
77 22 0.05
78 6 0.01
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.34
Consensus pattern (73 bp):
AAAATAAATTTAAACTTCTACAAATAAAAATAAATAATATCTTAAAAATTTAAACTCGTATAATC
AAATCTAA
Found at i:226115 original size:35 final size:34
Alignment explanation
Indices: 226072--226162 Score: 105
Period size: 33 Copynumber: 2.7 Consensus size: 34
226062 CTGTTGAAAT
* *
226072 AAATTTTACTTTTATTGCATTAACGCAATCA-AAC
1 AAATTTTACTTTTATTGCATTAA-ACAATAACAAC
* **
226106 TATATTTTACTTTTATT-TTTTAAACAATAACAAC
1 -AAATTTTACTTTTATTGCATTAAACAATAACAAC
226140 AAATTTTACTTTTATTGCATTAA
1 AAATTTTACTTTTATTGCATTAA
226163 TGTATTGTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
33 20 0.43
34 11 0.24
35 15 0.33
ACGTcount: A:0.37, C:0.13, G:0.03, T:0.46
Consensus pattern (34 bp):
AAATTTTACTTTTATTGCATTAAACAATAACAAC
Found at i:226219 original size:108 final size:108
Alignment explanation
Indices: 225963--226231 Score: 378
Period size: 108 Copynumber: 2.5 Consensus size: 108
225953 TTATACCTTA
* * * *
225963 AAATATTTACTTTTATTGCATTAATGTAATTAAACTATATATTACTTTTATTTCTTAAACTATAA
1 AAAT-TTTACTTTTATTGCATTAATGCAATCAAACTATATTTTACTTTTATTTCTTAAACAATAA
*
226028 AAATAAAATTTTCTTTTATTGAATTAATGTATTGCTGTTGAAAT
65 AAATAAAATTTTCTTTTATTGAATTAATGTATTGCTATTGAAAT
* * *
226072 AAATTTTACTTTTATTGCATTAACGCAATCAAACTATATTTTACTTTTATTTTTTAAACAATAAC
1 AAATTTTACTTTTATTGCATTAATGCAATCAAACTATATTTTACTTTTATTTCTTAAACAATAAA
* * *
226137 AA-CAAATTTTACTTTTATTGCATTAATGTATTGTTATTGAAAT
66 AATAAAATTTT-CTTTTATTGAATTAATGTATTGCTATTGAAAT
* * * *
226180 AAATTTTACTTTTATTGTATTAATGCAATCAAACAATATTTTCCATTTATTT
1 AAATTTTACTTTTATTGCATTAATGCAATCAAACTATATTTTACTTTTATTT
226232 ATTTTAATAG
Statistics
Matches: 143, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
107 7 0.05
108 132 0.92
109 4 0.03
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.48
Consensus pattern (108 bp):
AAATTTTACTTTTATTGCATTAATGCAATCAAACTATATTTTACTTTTATTTCTTAAACAATAAA
AATAAAATTTTCTTTTATTGAATTAATGTATTGCTATTGAAAT
Found at i:226828 original size:25 final size:27
Alignment explanation
Indices: 226751--226828 Score: 63
Period size: 25 Copynumber: 2.8 Consensus size: 27
226741 ATAACTAAAT
226751 ATTTAAACTTATCTAATCAAATTATAAAATAA
1 ATTTAAAC-T-TCTAA--AAATTA-AAAATAA
* *
226783 ATTTAAACTTCTACAAA-TAAAAGTAA
1 ATTTAAACTTCTAAAAATTAAAAATAA
*
226809 A-TTATACTT-TAAAAATTAAA
1 ATTTAAACTTCTAAAAATTAAA
226829 CTCATAACTA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
24 5 0.12
25 11 0.27
26 7 0.17
27 2 0.05
28 3 0.07
30 4 0.10
31 1 0.02
32 8 0.20
ACGTcount: A:0.54, C:0.09, G:0.01, T:0.36
Consensus pattern (27 bp):
ATTTAAACTTCTAAAAATTAAAAATAA
Found at i:229063 original size:3 final size:3
Alignment explanation
Indices: 229055--229103 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
229045 TGAGATACTA
* * *
229055 CCT CCT CCT CCT CCT CCT CCT CCT CCT CC- CCT CCA CCA CCT CCA CCT
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT
229102 CC
1 CC
229104 ACCACCCCCA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.06, C:0.69, G:0.00, T:0.24
Consensus pattern (3 bp):
CCT
Found at i:229104 original size:6 final size:6
Alignment explanation
Indices: 229054--229130 Score: 54
Period size: 6 Copynumber: 13.5 Consensus size: 6
229044 TTGAGATACT
* * * *
229054 ACCTCC TCCTCC TCCTCC TCCTCC TCCTCC -CCTCC A---CC ACCTCC
1 ACCTCC ACCTCC ACCTCC ACCTCC ACCTCC ACCTCC ACCTCC ACCTCC
* * * *
229098 ACCTCC ACCACC CCCACC ACCACC ACCTCC ACC
1 ACCTCC ACCTCC ACCTCC ACCTCC ACCTCC ACC
229131 ATCTCTAGTT
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
3 3 0.05
5 5 0.08
6 54 0.87
ACGTcount: A:0.14, C:0.69, G:0.00, T:0.17
Consensus pattern (6 bp):
ACCTCC
Found at i:229131 original size:15 final size:15
Alignment explanation
Indices: 229087--229131 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
229077 CTCCTCCCCT
*
229087 CCACCACCTCCACCT
1 CCACCACCTCCACCA
*
229102 CCACCACCCCCACCA
1 CCACCACCTCCACCA
229117 CCACCACCTCCACCA
1 CCACCACCTCCACCA
229132 TCTCTAGTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.24, C:0.69, G:0.00, T:0.07
Consensus pattern (15 bp):
CCACCACCTCCACCA
Found at i:232741 original size:72 final size:70
Alignment explanation
Indices: 232606--232873 Score: 260
Period size: 72 Copynumber: 3.8 Consensus size: 70
232596 TTTTATGAGT
* * * * *
232606 AAAAATAAATTTAAACTTTTACGAATAAAAATAAATAATAACTTAAATATTTAGACGCTTATAAT
1 AAAAATAAATTTAAACTTTTACAAATAAAAATAAATTAT-ACTTAAAAATTTAAAC-TTTATAAT
*
232671 TAAACCA
64 CAAACCA
* * *
232678 AAAAACAGATTTAAACTTTTACAAAT-AAAATAAATTATACTTTAAAAAATTTCAACTTGTATAA
1 AAAAATAAATTTAAACTTTTACAAATAAAAATAAATTATAC-TT-AAAAATTTAAACTT-TATAA
** *
232742 TCATTCTTA
63 TCAAAC-CA
* * * *
232751 AAAAATAAATTTAAAGTTTTACAAA-AAAAAT-AA-TA-AC-TAAATATTGAAACTTATCTAATC
1 AAAAATAAATTTAAACTTTTACAAATAAAAATAAATTATACTTAAAAATTTAAACTT-TATAATC
232811 AAACCA
65 AAACCA
* *
232817 TAAAATAAATTTAAACTTCTACAAATAAAAATAAATTATACTTTAAAAATTTAAACT
1 AAAAATAAATTTAAACTTTTACAAATAAAAATAAATTATAC-TTAAAAATTTAAACT
232874 CATAACTATA
Statistics
Matches: 157, Mismatches: 28, Indels: 22
0.76 0.14 0.11
Matches are distributed among these distances:
66 23 0.15
67 25 0.16
68 3 0.02
69 2 0.01
70 6 0.04
71 16 0.10
72 54 0.34
73 28 0.18
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (70 bp):
AAAAATAAATTTAAACTTTTACAAATAAAAATAAATTATACTTAAAAATTTAAACTTTATAATCA
AACCA
Found at i:232840 original size:139 final size:142
Alignment explanation
Indices: 232606--232873 Score: 359
Period size: 139 Copynumber: 1.9 Consensus size: 142
232596 TTTTATGAGT
**
232606 AAAAATAAATTTAAACTTTTACGAATAAAAATAAATAATAACTTAAATATTTAGACGCTTATAAT
1 AAAAATAAATTTAAACTTTTAC--A-AAAAATAAATAATAACTTAAATATTTAGAAACTTATAAT
* * * *
232671 TAAACCAAAAAACAGATTTAAACTTTTACAAAT-AAAATAAATTATACTTTAAAAAATTTCAACT
63 CAAACCAAAAAACAAATTTAAACTTCTACAAATAAAAATAAATTATACTTT-AAAAATTTAAACT
232735 TGTATAATCATTCTTA
127 TGTATAATCATTCTTA
*
232751 AAAAATAAATTTAAAGTTTTAC-AAAAA-AAATAATAAC-TAAATA-TT-GAAACTTATCTAATC
1 AAAAATAAATTTAAACTTTTACAAAAAATAAATAATAACTTAAATATTTAGAAACTTA--TAATC
* *
232811 AAACCATAAAATAAATTTAAACTTCTACAAATAAAAATAAATTATACTTTAAAAATTTAAACT
64 AAACCAAAAAACAAATTTAAACTTCTACAAATAAAAATAAATTATACTTTAAAAATTTAAACT
232874 CATAACTATA
Statistics
Matches: 111, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
137 6 0.05
138 2 0.02
139 50 0.45
140 27 0.24
141 5 0.05
145 21 0.19
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (142 bp):
AAAAATAAATTTAAACTTTTACAAAAAATAAATAATAACTTAAATATTTAGAAACTTATAATCAA
ACCAAAAAACAAATTTAAACTTCTACAAATAAAAATAAATTATACTTTAAAAATTTAAACTTGTA
TAATCATTCTTA
Found at i:233429 original size:15 final size:15
Alignment explanation
Indices: 233409--233438 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
233399 CTATTTTTTA
233409 AAATTTATTTAATTT
1 AAATTTATTTAATTT
233424 AAATTTATTTAATTT
1 AAATTTATTTAATTT
233439 TATTAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
AAATTTATTTAATTT
Found at i:233440 original size:16 final size:16
Alignment explanation
Indices: 233404--233440 Score: 58
Period size: 15 Copynumber: 2.3 Consensus size: 16
233394 TAGCTCTATT
233404 TTTTAAAATTTATTTAA
1 TTTT-AAATTTATTTAA
233421 -TTTAAATTTATTTAA
1 TTTTAAATTTATTTAA
233436 TTTTA
1 TTTTA
233441 TTAAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTAAATTTATTTAA
Found at i:234834 original size:16 final size:16
Alignment explanation
Indices: 234813--234844 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
234803 GTGTTTTATG
234813 CTTGTCTTTGTGTAGC
1 CTTGTCTTTGTGTAGC
234829 CTTGTCTTTGTGTAGC
1 CTTGTCTTTGTGTAGC
234845 TTCATATGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.19, G:0.25, T:0.50
Consensus pattern (16 bp):
CTTGTCTTTGTGTAGC
Found at i:235179 original size:12 final size:12
Alignment explanation
Indices: 235173--235199 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
235163 TCCACCACCT
235173 CCACCACCTCCA
1 CCACCACCTCCA
235185 CCACCACCTCCA
1 CCACCACCTCCA
235197 CCA
1 CCA
235200 TCTCTAGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.67, G:0.00, T:0.07
Consensus pattern (12 bp):
CCACCACCTCCA
Found at i:235199 original size:9 final size:9
Alignment explanation
Indices: 235151--235189 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
235141 TTGAGATACT
*
235151 ACCTCCTCC
1 ACCTCCACC
*
235160 TCCTCCACC
1 ACCTCCACC
235169 ACCTCCACC
1 ACCTCCACC
235178 ACCTCCACC
1 ACCTCCACC
235187 ACC
1 ACC
235190 ACCTCCACCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.18, C:0.67, G:0.00, T:0.15
Consensus pattern (9 bp):
ACCTCCACC
Found at i:239022 original size:8 final size:8
Alignment explanation
Indices: 239011--239040 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
239001 TTTTAAAAGG
239011 TAAAAAAA
1 TAAAAAAA
239019 T-AAAAAA
1 TAAAAAAA
239026 TAAAAAAA
1 TAAAAAAA
239034 TAAAAAA
1 TAAAAAA
239041 TAATCATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (8 bp):
TAAAAAAA
Found at i:239029 original size:15 final size:15
Alignment explanation
Indices: 239011--239043 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
239001 TTTTAAAAGG
239011 TAAAAAAATAAAAAA
1 TAAAAAAATAAAAAA
239026 TAAAAAAATAAAAAA
1 TAAAAAAATAAAAAA
239041 TAA
1 TAA
239044 TCATAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (15 bp):
TAAAAAAATAAAAAA
Found at i:239030 original size:6 final size:7
Alignment explanation
Indices: 239013--239043 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
239003 TTAAAAGGTA
239013 AAAAAAT
1 AAAAAAT
239020 AAAAAAT
1 AAAAAAT
239027 AAAAAAAT
1 -AAAAAAT
239035 AAAAAAT
1 AAAAAAT
239042 AA
1 AA
239044 TCATAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAAAAT
Found at i:239055 original size:21 final size:21
Alignment explanation
Indices: 239031--239097 Score: 56
Period size: 21 Copynumber: 3.4 Consensus size: 21
239021 AAAAATAAAA
239031 AAATAAAAAATAATCATAATT
1 AAATAAAAAATAATCATAATT
* *
239052 AAATAATATATATAT-ATAATGT
1 AAATAAAAAATA-ATCATAAT-T
239074 -AAT-AAAAA-AATCA-AATT
1 AAATAAAAAATAATCATAATT
239091 AAA-AAAA
1 AAATAAAA
239098 GACGAATTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 13
0.69 0.07 0.24
Matches are distributed among these distances:
17 1 0.03
18 10 0.27
19 2 0.05
20 3 0.08
21 18 0.49
22 3 0.08
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.28
Consensus pattern (21 bp):
AAATAAAAAATAATCATAATT
Found at i:239606 original size:27 final size:27
Alignment explanation
Indices: 239568--239672 Score: 97
Period size: 27 Copynumber: 3.8 Consensus size: 27
239558 CAAGTAACAA
239568 CAGCTGCAATGAAGAGAGAAACTGATG
1 CAGCTGCAATGAAGAGAGAAACTGATG
239595 CAGCTGCAATG-AGAAGAGAAA-TCGATG
1 CAGCTGCAATGAAG-AGAGAAACT-GATG
* * * *
239622 CAACTACAATGAGGAAAGAAAACTGATG
1 CAGCTGCAATGAAGAGAG-AAACTGATG
** *
239650 TTGCTGCAATAAAGAGAAGAAAC
1 CAGCTGCAATGAAGAG-AGAAAC
239673 GGCAGCAATG
Statistics
Matches: 61, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
26 3 0.05
27 34 0.56
28 21 0.34
29 3 0.05
ACGTcount: A:0.45, C:0.14, G:0.26, T:0.15
Consensus pattern (27 bp):
CAGCTGCAATGAAGAGAGAAACTGATG
Found at i:240957 original size:20 final size:20
Alignment explanation
Indices: 240932--241008 Score: 118
Period size: 20 Copynumber: 3.9 Consensus size: 20
240922 TACTGCCAGT
240932 TTTATGTATCGATACAATTC
1 TTTATGTATCGATACAATTC
**
240952 TTTATGTATCGATACAAAGC
1 TTTATGTATCGATACAATTC
**
240972 AATATGTATCGATACAATTC
1 TTTATGTATCGATACAATTC
240992 TTTATGTATCGATACAA
1 TTTATGTATCGATACAA
241009 AGCAATATGT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (20 bp):
TTTATGTATCGATACAATTC
Found at i:240986 original size:40 final size:40
Alignment explanation
Indices: 240934--241023 Score: 180
Period size: 40 Copynumber: 2.2 Consensus size: 40
240924 CTGCCAGTTT
240934 TATGTATCGATACAATTCTTTATGTATCGATACAAAGCAA
1 TATGTATCGATACAATTCTTTATGTATCGATACAAAGCAA
240974 TATGTATCGATACAATTCTTTATGTATCGATACAAAGCAA
1 TATGTATCGATACAATTCTTTATGTATCGATACAAAGCAA
241014 TATGTATCGA
1 TATGTATCGA
241024 CACTTCGGGC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (40 bp):
TATGTATCGATACAATTCTTTATGTATCGATACAAAGCAA
Found at i:241017 original size:20 final size:20
Alignment explanation
Indices: 240934--241023 Score: 108
Period size: 20 Copynumber: 4.5 Consensus size: 20
240924 CTGCCAGTTT
** **
240934 TATGTATCGATACAATTCTT
1 TATGTATCGATACAAAGCAA
240954 TATGTATCGATACAAAGCAA
1 TATGTATCGATACAAAGCAA
** **
240974 TATGTATCGATACAATTCTT
1 TATGTATCGATACAAAGCAA
240994 TATGTATCGATACAAAGCAA
1 TATGTATCGATACAAAGCAA
241014 TATGTATCGA
1 TATGTATCGA
241024 CACTTCGGGC
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (20 bp):
TATGTATCGATACAAAGCAA
Found at i:245805 original size:13 final size:13
Alignment explanation
Indices: 245787--245814 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
245777 CATTATTCAA
245787 TGTATCGATACAT
1 TGTATCGATACAT
245800 TGTATCGATACAT
1 TGTATCGATACAT
245813 TG
1 TG
245815 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:245809 original size:33 final size:33
Alignment explanation
Indices: 245767--245833 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
245757 GCCAAGGAAA
245767 TGTATCGATACATT-ATTCAATGTATCGATACAT
1 TGTATCGATACATTGA-TCAATGTATCGATACAT
**
245800 TGTATCGATACATTGATCTTTGTATCGATACAT
1 TGTATCGATACATTGATCAATGTATCGATACAT
245833 T
1 T
245834 TGGGAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATTGATCAATGTATCGATACAT
Found at i:257739 original size:21 final size:21
Alignment explanation
Indices: 257713--257769 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
257703 AAATTATCCA
257713 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
257734 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
257755 AATGTATCGATACAT
1 AATGTATCGATACAT
257770 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:257916 original size:13 final size:13
Alignment explanation
Indices: 257898--257924 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
257888 TACGTTTTTT
257898 TTGTATCGATACA
1 TTGTATCGATACA
257911 TTGTATCGATACA
1 TTGTATCGATACA
257924 T
1 T
257925 GGATCTTTGT
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:260345 original size:51 final size:53
Alignment explanation
Indices: 260281--260411 Score: 160
Period size: 51 Copynumber: 2.5 Consensus size: 53
260271 AGTTTCTCAA
* * * * *
260281 TTCTCCACAATCGGGGATATTCCAACTCTGATTTTATTTTC-AAAACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
260332 TT-TTCTATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
260386 TTCTTCACAATCGGGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
260412 CCCGTTATTT
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
50 2 0.03
51 32 0.48
53 9 0.14
54 20 0.30
55 3 0.05
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.34
Consensus pattern (53 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
Found at i:260481 original size:80 final size:81
Alignment explanation
Indices: 260344--260495 Score: 211
Period size: 80 Copynumber: 1.9 Consensus size: 81
260334 TTCTATAATC
*
260344 GGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCC
1 GGGGATACTCCAACTCCGATTTTA-TTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCC
260409 AACCCCGTTATTTTCGA
65 AACCCCGTTATTTTCGA
* * *
260426 GGGGATACTCCAACTCCGGTTTTA-TCGC-TAAAACACTAATTT-TTCCACAATCGGGGATACTC
1 GGGGATACTCCAACTCCGATTTTATTC-CAAAAAACACCAATTTCTT-CACAATCGGGGATACTC
*
260488 CAATCCCG
64 CAACCCCG
260496 GTTTTATTTT
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
79 2 0.03
80 38 0.60
81 1 0.02
82 22 0.35
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (81 bp):
GGGGATACTCCAACTCCGATTTTATTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCA
ACCCCGTTATTTTCGA
Found at i:260511 original size:52 final size:53
Alignment explanation
Indices: 260426--260592 Score: 175
Period size: 52 Copynumber: 3.2 Consensus size: 53
260416 TTATTTTCGA
* *
260426 GGGGATACTCCAACTCCGGTTTTA--TCGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACTCCGGTTTTATTTC-CAAAAACACCAATTTTTCCACAATC
* * **
260478 GGGGATACTCCAA-TCCCGGTTTTATTTTC-AAAACGCCAA-TTTTCCTTTAATC
1 GGGGATACTCCAACT-CCGGTTTTATTTCCAAAAACACCAATTTTTCC-ACAATC
* * *
260530 GGGGATACTCCAACTCTGATTTTATTTCCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAACTCCGGTTTTATTTCCAAAAACACCAATTTTTCCACAATC
*
260582 GAGGATACTCC
1 GGGGATACTCC
260593 TACCTCGTTA
Statistics
Matches: 95, Mismatches: 13, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
51 7 0.07
52 72 0.76
53 11 0.12
54 5 0.05
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (53 bp):
GGGGATACTCCAACTCCGGTTTTATTTCCAAAAACACCAATTTTTCCACAATC
Found at i:260615 original size:28 final size:28
Alignment explanation
Indices: 260579--260650 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
260569 ATTTTTCACA
* * * *
260579 ATCGAGGATACTCCTACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
260607 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
*
260635 -TAAGGGGATACTCCAA
1 AT-CGGGGATACTCCAA
260651 TCTCGATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
27 1 0.03
28 37 0.97
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:264025 original size:13 final size:13
Alignment explanation
Indices: 264003--264061 Score: 75
Period size: 13 Copynumber: 4.5 Consensus size: 13
263993 CATCCTCCGC
264003 AAAA-AAAAAAAA
1 AAAACAAAAAAAA
264015 AAAACAAAAAACAA
1 AAAACAAAAAA-AA
*
264029 AACACAAAAAAAA
1 AAAACAAAAAAAA
*
264042 AAAACAAAAATAA
1 AAAACAAAAAAAA
*
264055 ACAACAA
1 AAAACAA
264062 CAACAAAAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
12 4 0.10
13 25 0.61
14 12 0.29
ACGTcount: A:0.86, C:0.12, G:0.00, T:0.02
Consensus pattern (13 bp):
AAAACAAAAAAAA
Found at i:264045 original size:33 final size:32
Alignment explanation
Indices: 264003--264070 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
263993 CATCCTCCGC
264003 AAAAAAAAAAAAAAAACAAAAAACAAAACACAA
1 AAAAAAAAAAAAAAAACAAAAAACAAAA-ACAA
* * * *
264036 AAAAAAAAAACAAAAATAAACAACAACAACAA
1 AAAAAAAAAAAAAAAACAAAAAACAAAAACAA
264068 AAA
1 AAA
264071 GGGTCCGGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 7 0.23
33 24 0.77
ACGTcount: A:0.85, C:0.13, G:0.00, T:0.01
Consensus pattern (32 bp):
AAAAAAAAAAAAAAAACAAAAAACAAAAACAA
Found at i:264070 original size:1 final size:1
Alignment explanation
Indices: 264003--264051 Score: 53
Period size: 1 Copynumber: 49.0 Consensus size: 1
263993 CATCCTCCGC
* * * * *
264003 AAAAAAAAAAAAAAAACAAAAAACAAAACACAAAAAAAAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
264052 TAAACAACAA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:265536 original size:29 final size:29
Alignment explanation
Indices: 265492--265726 Score: 255
Period size: 29 Copynumber: 8.1 Consensus size: 29
265482 CATTCCTCAC
* *
265492 TTTCCAAAGCCTACAAGTCAGTGGCATCT
1 TTTCAAAAGCCCACAAGTCAGTGGCATCT
* *
265521 TTTCAAAAGCCCACAAGTTAGTGGCAAC-
1 TTTCAAAAGCCCACAAGTCAGTGGCATCT
* *
265549 CTTCAAAAGCCCACAAGTCAGTGGCACCCT
1 TTTCAAAAGCCCACAAGTCAGTGGCA-TCT
*
265579 TTTC-AAAGCCTACAAGTCAGTGGCATCT
1 TTTCAAAAGCCCACAAGTCAGTGGCATCT
* *
265607 TTTCAAAAGCCCACTAGTTAGTGGCA-CT
1 TTTCAAAAGCCCACAAGTCAGTGGCATCT
* * *
265635 TTCTC-AAAGCCTACAAGTCAGTGGTAAC-
1 TT-TCAAAAGCCCACAAGTCAGTGGCATCT
*
265663 CTTCAAAAAGCCCACAAGTCAGTGGCATCT
1 TTTC-AAAAGCCCACAAGTCAGTGGCATCT
**
265693 TTTCAAAAGCCCACATAAGTTGGTGGCATCT
1 TTTCAAAAGCCCAC--AAGTCAGTGGCATCT
265724 TTT
1 TTT
265727 TCTAAGTCCA
Statistics
Matches: 172, Mismatches: 24, Indels: 18
0.80 0.11 0.08
Matches are distributed among these distances:
27 2 0.01
28 52 0.30
29 96 0.56
30 6 0.03
31 16 0.09
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (29 bp):
TTTCAAAAGCCCACAAGTCAGTGGCATCT
Found at i:265587 original size:57 final size:57
Alignment explanation
Indices: 265497--265707 Score: 275
Period size: 57 Copynumber: 3.7 Consensus size: 57
265487 CTCACTTTCC
* *
265497 AAAGCCTACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTTAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTCA
* * * *
265554 AAAGCCCACAAGTCAGTGGCACCCTTTTC-AAAGCCTACAAGTCAGTGGCATCTTTTCA
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTCAAAAGCCCACAAGTCAGTGGCAAC-CTTCA
* * * *
265612 AAAGCCCACTAGTTAGTGGCA-CTTTCTC-AAAGCCTACAAGTCAGTGGTAACCTTCAA
1 AAAGCCCACAAGTCAGTGGCATCTTT-TCAAAAGCCCACAAGTCAGTGGCAACCTTC-A
265669 AAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACA
265708 TAAGTTGGTG
Statistics
Matches: 134, Mismatches: 14, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
56 7 0.05
57 85 0.63
58 42 0.31
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (57 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTCA
Found at i:265644 original size:86 final size:85
Alignment explanation
Indices: 265491--265725 Score: 317
Period size: 86 Copynumber: 2.7 Consensus size: 85
265481 ACATTCCTCA
* * *
265491 CTTTCCAAAGCCTACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTTAGTGGCAACCTTCAAA
1 CTTTACAAAGCCTACAAGTCAGTGGCATCTTTTCAAAAGCCCACTAGTTAGTGGC-ACTTTCAAA
*
265556 AGCCCACAAGTCAGTGGCACC
65 AGCCCACAAGTCAGTGGCAAC
* *
265577 CTTTTCAAAGCCTACAAGTCAGTGGCATCTTTTCAAAAGCCCACTAGTTAGTGGCACTTTCTCAA
1 CTTTACAAAGCCTACAAGTCAGTGGCATCTTTTCAAAAGCCCACTAGTTAGTGGCACTTTC-AAA
* *
265642 AGCCTACAAGTCAGTGGTAAC
65 AGCCCACAAGTCAGTGGCAAC
* * * *
265663 CTTCAAAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACATAAGTTGGTGGCATCTTT
1 CTTTACAAAGCCTACAAGTCAGTGGCATCTTTTCAAAAGCCCAC-T-AGTTAGTGGCA-CTTT
265726 TTCTAAGTCC
Statistics
Matches: 133, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
85 5 0.04
86 113 0.85
87 1 0.01
88 10 0.08
89 4 0.03
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.25
Consensus pattern (85 bp):
CTTTACAAAGCCTACAAGTCAGTGGCATCTTTTCAAAAGCCCACTAGTTAGTGGCACTTTCAAAA
GCCCACAAGTCAGTGGCAAC
Found at i:265892 original size:49 final size:48
Alignment explanation
Indices: 265729--266205 Score: 331
Period size: 49 Copynumber: 9.8 Consensus size: 48
265719 CATCTTTTTC
* *
265729 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA---C--CTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTCATCTT
* * * * * **
265772 TAAGTCCAATATCACTAGCCTTAAATCAGCATATTGGCACCTTGTCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTCATCTT
* *
265820 TAAGACCAATGTCGCTGGCCTTGAATCAACACATTGGCACGCTCATCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC-CTCATCTT
* * * * ***
265869 TAAGTCCGATATCGTTGGTCTTGAATCAGTGTATTGGCACCTTCATCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-TCATCTT
* * * * *
265918 TAAGACCGATGTCGTTGGCCTAGAATCAGCACATTGGCACCTTAACCATTTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-T---CATCTT
* * *
265970 TAAGTCCAATGTCACTGGCCTTGAATCAGTACATTGGCATCTTCATCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CCTCATCTT
* * *
266019 TAAGTCCAATGTTGCTGACCTTGAATCAGCACATTGGCACGTTCATCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC-CTCATCTT
* * * * * * * * * *
266068 TAAGTTCGATATCGCTAGCCTTGAATTAGCATATTGCCATCTTTAACATT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CCTCATC-TT
* ** * * *
266118 CCTAAG-CCTAATGTCGCTAGCCTTGTCTCAGCATATTGGCA-TTCTTCTT
1 --TAAGTCC-AATGTCGCTGGCCTTGAATCAGCACATTGGCACCTCATCTT
* * * *
266167 CAAGTCTAATGTCGCT-GACTATGAATTAGCACATTGGCA
1 TAAGTCCAATGTCGCTGGCCT-TGAATCAGCACATTGGCA
266206 TTCTTTATAT
Statistics
Matches: 345, Mismatches: 70, Indels: 34
0.77 0.16 0.08
Matches are distributed among these distances:
43 36 0.10
46 3 0.01
47 26 0.08
48 39 0.11
49 164 0.48
50 6 0.02
51 1 0.00
52 69 0.20
53 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.33
Consensus pattern (48 bp):
TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTCATCTT
Found at i:266131 original size:150 final size:148
Alignment explanation
Indices: 265820--266205 Score: 382
Period size: 150 Copynumber: 2.6 Consensus size: 148
265810 ACCTTGTCTT
* * * * * *
265820 TAAGACCAATGTCGCTGGCCTTGAATCAACACATTGGCACGCTCATCTTTAAGTCCGATATCGTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC-TTCATCTTTAAGTCCAATGTCGCT
* *** * * *
265885 GGTCTTGAATCAGTGTATTGGCACCTTCATCTTTAAGACCGATGTCGTTGGCCTAGAATCAGCAC
65 -GACTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCGATATCGCTAGCCTAGAATCAGCAC
* **
265950 ATTGGCACCTTAACCATTTT
129 ATTGCCACCTTAACCATTCC
* * *
265970 TAAGTCCAATGTCACTGGCCTTGAATCAGTACATTGGCATCTTCATCTTTAAGTCCAATGTTGCT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTTTAAGTCCAATGTCGCT
* ** * * *
266035 GACCTTGAATCAGCACATTGGCACGTTCATCTTTAAGTTCGATATCGCTAGCCTTGAATTAGCAT
65 GA-CTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCGATATCGCTAGCCTAGAATCAGCAC
*
266100 ATTGCCATCTTTAA-CATTCC
129 ATTGCCA-CCTTAACCATTCC
* ** * * * *
266120 TAAG-CCTAATGTCGCTAGCCTTGTCTCAGCATATTGGCA-TTCTTCTTCAAGTCTAATGTCGCT
1 TAAGTCC-AATGTCGCTGGCCTTGAATCAGCACATTGGCACTTCATCTTTAAGTCCAATGTCGCT
*
266183 GACTATGAATTAGCACATTGGCA
65 GACT-TGAATCAGCACATTGGCA
266206 TTCTTTATAT
Statistics
Matches: 194, Mismatches: 37, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
147 2 0.01
148 39 0.20
149 3 0.02
150 144 0.74
151 6 0.03
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (148 bp):
TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTCATCTTTAAGTCCAATGTCGCTG
ACTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCGATATCGCTAGCCTAGAATCAGCACAT
TGCCACCTTAACCATTCC
Found at i:266142 original size:101 final size:98
Alignment explanation
Indices: 265729--266110 Score: 391
Period size: 101 Copynumber: 3.9 Consensus size: 98
265719 CATCTTTTTC
* * * * *
265729 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA----C--CTTTAAGTCCAATATCACT
1 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACGTTCATCTTTAAGTCCGATATCGCT
* * * * *
265788 AGCCTTAAATCAGCATATTGGCACCTT-GTCTT
66 GGCCTTGAATCAGTATATTGGCATCTTCATCTT
* * *
265820 TAAGACCAATGTCGCTGGCCTTGAATCAACACATTGGCACGCTCATCTTTAAGTCCGATATCGTT
1 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACGTTCATCTTTAAGTCCGATATCGCT
* * *
265885 GGTCTTGAATCAGTGTATTGGCACCTTCATCTT
66 GGCCTTGAATCAGTATATTGGCATCTTCATCTT
* * * * * * *
265918 TAAGACCGATGTCGTTGGCCTAGAATCAGCACATTGGCACCTTAACCATTTTTAAGTCCAATGTC
1 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACGTT---CATCTTTAAGTCCGATATC
* *
265983 ACTGGCCTTGAATCAGTACATTGGCATCTTCATCTT
63 GCTGGCCTTGAATCAGTATATTGGCATCTTCATCTT
* * * *
266019 TAAGTCCAATGTTGCTGACCTTGAATCAGCACATTGGCACGTTCATCTTTAAGTTCGATATCGCT
1 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACGTTCATCTTTAAGTCCGATATCGCT
* * * *
266084 AGCCTTGAATTAGCATATTGCCATCTT
66 GGCCTTGAATCAGTATATTGGCATCTT
266111 TAACATTCCT
Statistics
Matches: 236, Mismatches: 45, Indels: 13
0.80 0.15 0.04
Matches are distributed among these distances:
91 35 0.15
95 1 0.00
97 38 0.16
98 80 0.34
101 82 0.35
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (98 bp):
TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACGTTCATCTTTAAGTCCGATATCGCT
GGCCTTGAATCAGTATATTGGCATCTTCATCTT
Found at i:274473 original size:43 final size:43
Alignment explanation
Indices: 274425--274523 Score: 198
Period size: 43 Copynumber: 2.3 Consensus size: 43
274415 TACTTTTCAT
274425 AATGTATCGATACATACATTTGAAATTTATAGTCGTTAGGCAC
1 AATGTATCGATACATACATTTGAAATTTATAGTCGTTAGGCAC
274468 AATGTATCGATACATACATTTGAAATTTATAGTCGTTAGGCAC
1 AATGTATCGATACATACATTTGAAATTTATAGTCGTTAGGCAC
274511 AATGTATCGATAC
1 AATGTATCGATAC
274524 TTTTTACTAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.34
Consensus pattern (43 bp):
AATGTATCGATACATACATTTGAAATTTATAGTCGTTAGGCAC
Found at i:274550 original size:13 final size:13
Alignment explanation
Indices: 274532--274561 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
274522 ACTTTTTACT
*
274532 ATGTATCGATACA
1 ATGTATCAATACA
274545 ATGTATCAATACA
1 ATGTATCAATACA
274558 ATGT
1 ATGT
274562 CCCATGTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (13 bp):
ATGTATCAATACA
Found at i:277045 original size:13 final size:13
Alignment explanation
Indices: 277027--277051 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
277017 CATAAAATGT
277027 TGTATCGATACAA
1 TGTATCGATACAA
277040 TGTATCGATACA
1 TGTATCGATACA
277052 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:277049 original size:33 final size:33
Alignment explanation
Indices: 277007--277076 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
276997 TTCAACGATT
277007 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
277040 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
277073 TGTA
1 TGTA
277077 AGCTACTGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:277207 original size:52 final size:52
Alignment explanation
Indices: 277151--277269 Score: 202
Period size: 52 Copynumber: 2.3 Consensus size: 52
277141 CTGATCTTTA
*
277151 TATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACATTATAAAATG
1 TATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATAAAATG
* *
277203 TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAATG
1 TATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATAAAATG
*
277255 TATCGATACTTGCAG
1 TATCGATACATGCAG
277270 TAACTTTTCA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 63 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.29
Consensus pattern (52 bp):
TATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATAAAATG
Found at i:282103 original size:28 final size:28
Alignment explanation
Indices: 282065--282120 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
282055 CGCGATGCCT
282065 AAAATCGGTACCTTCTAACTATGTCTTA
1 AAAATCGGTACCTTCTAACTATGTCTTA
* *
282093 AAAATTGGTACCTTTTAACTATGTCTTA
1 AAAATCGGTACCTTCTAACTATGTCTTA
282121 CTTAAATCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (28 bp):
AAAATCGGTACCTTCTAACTATGTCTTA
Found at i:282909 original size:51 final size:51
Alignment explanation
Indices: 282849--282964 Score: 144
Period size: 51 Copynumber: 2.3 Consensus size: 51
282839 TAAGGCCGAG
* * * * *
282849 GTTGAAGTATCCCTGATTAT-GAGAAATCAATATTTTGAAAATAAAATTGGA
1 GTTGGAGTATCCCCGACTATGGA-AAATCAATATTTTAAAAATAAAATCGGA
* * *
282900 GTTGGAGTATCCCCGACTGTGGAAAATTAGTATTTTAAAAATAAAATCGGA
1 GTTGGAGTATCCCCGACTATGGAAAATCAATATTTTAAAAATAAAATCGGA
282951 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
282965 TCGGAAATAA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
51 54 0.96
52 2 0.04
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGACTATGGAAAATCAATATTTTAAAAATAAAATCGGA
Found at i:282999 original size:28 final size:28
Alignment explanation
Indices: 282952--283023 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 28
282942 AAAATCGGAG
***
282952 TTGGAGTATCCCCTCGGAAATAACAGGA
1 TTGGAGTATCCCCGATGAAATAACAGGA
** *
282980 TTGGAGTATCCCCGATGAAATAATGGGG
1 TTGGAGTATCCCCGATGAAATAACAGGA
*
283008 TTGGAGTACCCCCGAT
1 TTGGAGTATCCCCGAT
283024 TATGAAAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (28 bp):
TTGGAGTATCCCCGATGAAATAACAGGA
Found at i:283177 original size:51 final size:51
Alignment explanation
Indices: 283115--283259 Score: 182
Period size: 51 Copynumber: 2.8 Consensus size: 51
283105 AAATAACGGG
* * * * *
283115 GTTGGAATATCCCCAATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGAGAAAAATTGATGTTTTGGAAATAAAATCGAA
* * * * *
283166 GTTGGAGTATCCCCGATTGCGATAAATCGATGCTTTAGAAATAAAATCGAA
1 GTTGGAGTATCCCCGATTGAGAAAAATTGATGTTTTGGAAATAAAATCGAA
* *
283217 GTTGGAGTATCCCTGATTAAGAAAAATTGATGTTTTGGAAATA
1 GTTGGAGTATCCCCGATTGAGAAAAATTGATGTTTTGGAAATA
283260 GAACCGGGAT
Statistics
Matches: 78, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 78 1.00
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGAGAAAAATTGATGTTTTGGAAATAAAATCGAA
Found at i:285451 original size:16 final size:16
Alignment explanation
Indices: 285430--285462 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
285420 ATCTTAAAAC
285430 ATGTTTAAATTCCATT
1 ATGTTTAAATTCCATT
285446 ATGTTTAAATTCCATT
1 ATGTTTAAATTCCATT
285462 A
1 A
285463 CGACCCCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.48
Consensus pattern (16 bp):
ATGTTTAAATTCCATT
Found at i:285612 original size:20 final size:19
Alignment explanation
Indices: 285587--285692 Score: 98
Period size: 20 Copynumber: 5.7 Consensus size: 19
285577 AAATGCCTGC
*
285587 ATGTATCGATACAATGAGCA
1 ATGTATCGATACAATGA-AA
285607 ATGTATCGATAC----AAA
1 ATGTATCGATACAATGAAA
* *
285622 A--TATCGATACAATTAGCA
1 ATGTATCGATACAATGA-AA
285640 ATGTATCGATACAATGCAAA
1 ATGTATCGATACAATG-AAA
*
285660 ATGTATTGATACAATGCAAA
1 ATGTATCGATACAATG-AAA
285680 ATGTATCGATACA
1 ATGTATCGATACA
285693 TTTGGGTAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 16
0.77 0.06 0.17
Matches are distributed among these distances:
13 9 0.12
15 2 0.03
16 1 0.01
17 1 0.01
18 2 0.03
20 56 0.78
21 1 0.01
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.27
Consensus pattern (19 bp):
ATGTATCGATACAATGAAA
Found at i:285632 original size:33 final size:33
Alignment explanation
Indices: 285590--285653 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
285580 TGCCTGCATG
285590 TATCGATACAATGAGCAATGTATCGATACAAAA
1 TATCGATACAATGAGCAATGTATCGATACAAAA
*
285623 TATCGATACAATTAGCAATGTATCGATACAA
1 TATCGATACAATGAGCAATGTATCGATACAA
285654 TGCAAAATGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.27
Consensus pattern (33 bp):
TATCGATACAATGAGCAATGTATCGATACAAAA
Found at i:285755 original size:13 final size:13
Alignment explanation
Indices: 285708--285737 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
285698 GTAAACCTAG
285708 AATGTATCGATAC
1 AATGTATCGATAC
*
285721 AATGTATTGATAC
1 AATGTATCGATAC
285734 AATG
1 AATG
285738 AACAATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:286525 original size:49 final size:48
Alignment explanation
Indices: 286453--286589 Score: 160
Period size: 49 Copynumber: 2.9 Consensus size: 48
286443 GACAAAGGAA
* *
286453 AAAAAGGAAAACGAAA-TGTGTCCTGCTCTTTGAGGA-TAAAGGAAAAAGG
1 AAAAAGGAAAA-TAAAGTGCGTCCTGCTCTTTGAGGACTAAAGG-AAAA-G
*
286502 AAAAAGGAAAATAAAGTGCGTCCTGCTCTTTGAGAACTAGAAGGAAAAG
1 AAAAAGGAAAATAAAGTGCGTCCTGCTCTTTGAGGACTA-AAGGAAAAG
*
286551 ---AAGG-AAATGAAGTGCGTCCTGCTCTTTGAGGACTAAAGG
1 AAAAAGGAAAATAAAGTGCGTCCTGCTCTTTGAGGACTAAAGG
286590 GTGCCACCAA
Statistics
Matches: 80, Mismatches: 5, Indels: 11
0.83 0.05 0.11
Matches are distributed among these distances:
44 4 0.05
45 29 0.36
46 4 0.05
48 3 0.04
49 30 0.38
50 6 0.08
51 4 0.05
ACGTcount: A:0.41, C:0.12, G:0.27, T:0.20
Consensus pattern (48 bp):
AAAAAGGAAAATAAAGTGCGTCCTGCTCTTTGAGGACTAAAGGAAAAG
Found at i:286574 original size:45 final size:43
Alignment explanation
Indices: 286497--286589 Score: 134
Period size: 45 Copynumber: 2.1 Consensus size: 43
286487 GATAAAGGAA
286497 AAAGGAAAAAGGAAAATAAAGTGCGTCCTGCTCTTTGAGAACT
1 AAAGGAAAAAGGAAAATAAAGTGCGTCCTGCTCTTTGAGAACT
* *
286540 AGAAGGAAAAGAAGG-AAATGAAGTGCGTCCTGCTCTTTGAGGACT
1 A-AAGG-AAA-AAGGAAAATAAAGTGCGTCCTGCTCTTTGAGAACT
286585 AAAGG
1 AAAGG
286590 GTGCCACCAA
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
43 1 0.02
44 8 0.18
45 32 0.71
46 4 0.09
ACGTcount: A:0.40, C:0.13, G:0.28, T:0.19
Consensus pattern (43 bp):
AAAGGAAAAAGGAAAATAAAGTGCGTCCTGCTCTTTGAGAACT
Found at i:286714 original size:123 final size:123
Alignment explanation
Indices: 286564--287876 Score: 1505
Period size: 123 Copynumber: 10.7 Consensus size: 123
286554 GAAATGAAGT
286564 GCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGT
1 GCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGT
** * ** * *
286629 TTTTCTCTTTGAGGACTAAAGGTTTCACCAACTTATGTGGGCTTTAAAAAGAAAAAAT
66 CCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAG
** * * * * *
286687 ATGTCTTGTTCTTTGAGGACTGAAGGGTGCCACCAACTTGTGTGGGCTTT-GAAGGAGAAGGCAG
1 GCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC-G
* * * *
286751 TCCTGCTCTTTGCGGACTAAAGGGTGCCACCAACTTGTGTGCGCTTT-AAAAG-GACAAG
65 TCCTGCTCTTTGAGGACTAAA-GGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAG
* * * *
286809 GCGTCCTGCTTTTTGAGGACTAAA-GGTGCCACCAACTTATGTGGGCTTTAAAAAGAAAAAAGGT
1 GCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTT-AAAAG-GAAAAGGC
* ** * * *
286873 GTCCTGCTCTTTGAGGACTGAAGGGTGCCACCAACTCATGTGGGCTTT--GAAG-GAGAAG
64 GTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAG
* *
286931 ACGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCAT
1 GCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGT
* *
286996 CCTGCTCTTTGAGGACTCAAGGTGCCACCAACTTGTATGGGCTTTAAAAAGAAAAAAG
66 CCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAG
* ** * * * *
287054 GCGTCCTGCTCTCTGAGGACTGGAGGGTGCCACCAACTCGAGTGGGCTTT-GAAGGAGAAGGCGT
1 GCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGT
** *
287118 CCTGCTCTTTGAAAACTAAAGGGTGCCACCAACTTGTGTGGGCTTT-AAAAG-GAAAAG
66 CCTGCTCTTTGAGGACTAAA-GGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAG
* * *
287175 GCATCCTGCTCTTTGAGGACTAAA-GGTGCCACCAACTTGGGTGGGCTTTAAAAAGAAAAAAGGC
1 GCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTT-AAAAG-GAAAAGGC
* * * * * * * * *
287239 ATCCTGCTCTTTGAGGACTGGAGGGTGTCACCAACTCGAGTGGGCTTT--GAAG-GAGAAG
64 GTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAG
* * * *
287297 GCGTCCTGCTTTTTAAGGACTAAAGGGTGCCACCAACTTATGTGAGCTTTAAAAGGAAAAGGCGT
1 GCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGT
* *
287362 CCTGCTTTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTATAAAGAAAAAAG
66 CCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAG
* ** * ** * *
287420 GCATCCTATTCTTTGAGGACTAGAGGGTGCCACCAACTCATGTGGGCTTT-GAAGGAGAAGGCGT
1 GCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGT
* * *
287484 CCTGCTTTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGC-TT-AATAG-GAAAAG
66 CCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAG
* * * *
287540 GCATCCTGCTCTTTGAAGACTAAAGGG-GCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGGTG
1 GCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGGCG
* * * * * *
287604 TCTTGCTCTTTGAGGACTGGAGGGTGCCACCAAGTCGTGTGGGCTTTGAAAAGAAAAAAG
65 TCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAG
* * *
287664 GCATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCAT
1 GCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGT
* * *
287729 CCTGCTTTTTGAGGACTAAAGGCGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAAG
66 CCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAG
* * * * *
287787 GCGTCCTGCTCTTTGAGGATTGGAA-GGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAAGA
1 GCGTCCTGCTCTTTGAGGACT-AAAGGGTGCCACCAACTTGTGTGGGCTTT-AAAAG-GAAAAGG
*
287851 CGTGCTGCTCTTTGAGGACTAGAAGG
63 CGTCCTGCTCTTTGAGGACTA-AAGG
287877 GCTAAAAGAG
Statistics
Matches: 1007, Mismatches: 153, Indels: 57
0.83 0.13 0.05
Matches are distributed among these distances:
119 20 0.02
120 97 0.10
121 146 0.14
122 175 0.17
123 427 0.42
124 93 0.09
125 45 0.04
126 4 0.00
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (123 bp):
GCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGT
CCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAG
Found at i:287024 original size:183 final size:183
Alignment explanation
Indices: 286559--287877 Score: 1894
Period size: 183 Copynumber: 7.2 Consensus size: 183
286549 AGAAGGAAAT
286559 GAAGTGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA
1 GAAG-GCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA
* ** * ** * ***
286624 GGCGTTTTTCTCTTTGAGGACTAAAGGTTTCACCAACTTATGTGGGCTTTAAAAAGAAAAAATAT
65 GGCATCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAGGC
* * **
286689 GTCTTGTTCTTTGAGGACTGAAGGGTGCCACCAACTTGTGTGGGCTTTGAAGGA
130 GTCCTGCTCTTTGAGGACTGAAGGGTGCCACCAACTCATGTGGGCTTTGAAGGA
* * *
286743 GAAGGCAGTCCTGCTCTTTGCGGACTAAAGGGTGCCACCAACTTGTGTGCGCTTTAAAAGGACAA
1 GAAGGC-GTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA
* * * *
286808 GGCGTCCTGCTTTTTGAGGACTAAAGGTGCCACCAACTTATGTGGGCTTTAAAAAGAAAAAAGGT
65 GGCATCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAGGC
286873 GTCCTGCTCTTTGAGGACTGAAGGGTGCCACCAACTCATGTGGGCTTTGAAGGA
130 GTCCTGCTCTTTGAGGACTGAAGGGTGCCACCAACTCATGTGGGCTTTGAAGGA
*
286927 GAAGACGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
1 GAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
* *
286992 GCATCCTGCTCTTTGAGGACTCAAGGTGCCACCAACTTGTATGGGCTTTAAAAAGAAAAAAGGCG
66 GCATCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAGGCG
* *
287057 TCCTGCTCTCTGAGGACTGGAGGGTGCCACCAACTCGA-GTGGGCTTTGAAGGA
131 TCCTGCTCTTTGAGGACTGAAGGGTGCCACCAACTC-ATGTGGGCTTTGAAGGA
**
287110 GAAGGCGTCCTGCTCTTTGAAAACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
1 GAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
* *
287175 GCATCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGGGTGGGCTTTAAAAAGAAAAAAGGCA
66 GCATCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAGGCG
* *
287240 TCCTGCTCTTTGAGGACTGGAGGGTGTCACCAACTCGA-GTGGGCTTTGAAGGA
131 TCCTGCTCTTTGAGGACTGAAGGGTGCCACCAACTC-ATGTGGGCTTTGAAGGA
* * * *
287293 GAAGGCGTCCTGCTTTTTAAGGACTAAAGGGTGCCACCAACTTATGTGAGCTTTAAAAGGAAAAG
1 GAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
* * * *
287358 GCGTCCTGCTTTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTATAAAGAAAAAAGGCA
66 GCATCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAGGCG
**
287423 TCCTATTCTTTGAGGACT-AGAGGGTGCCACCAACTCATGTGGGCTTTGAAGGA
131 TCCTGCTCTTTGAGGACTGA-AGGGTGCCACCAACTCATGTGGGCTTTGAAGGA
* * *
287476 GAAGGCGTCCTGCTTTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGC-TTAATAGGAAAAG
1 GAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
* * *
287540 GCATCCTGCTCTTTGAAGACTAAAGGGGCCACCAACTTGTGTGGGCTTTAAAAAG-AAAAAGGTG
66 GCATCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAGGCG
* * * * *
287604 TCTTGCTCTTTGAGGACTGGAGGGTGCCACCAAGTCGTGTGGGCTTTGAAAAGAAA
131 TCCTGCTCTTTGAGGACTGAAGGGTGCCACCAACTCATGTGGGCTTTG--AAG-GA
* * *
287660 AAAGGCATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
1 GAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
* * *
287725 GCATCCTGCTTTTTGAGGACTAAAGGCGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAAGGCG
66 GCATCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAGGCG
* * *
287790 TCCTGCTCTTTGAGGATTGGAA-GGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAA
131 TCCTGCTCTTTGAGGACT-GAAGGGTGCCACCAACTCATGTGGGCTTTG--AAG-GA
* * *
287846 AAAGACGTGCTGCTCTTTGAGGACTAGAAGGG
1 GAAGGCGTCCTGCTCTTTGAGGACTA-AAGGG
287878 CTAAAAGAGG
Statistics
Matches: 1037, Mismatches: 86, Indels: 21
0.91 0.08 0.02
Matches are distributed among these distances:
181 48 0.05
182 63 0.06
183 556 0.54
184 221 0.21
185 63 0.06
186 80 0.08
187 6 0.01
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (183 bp):
GAAGGCGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
GCATCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAGGCG
TCCTGCTCTTTGAGGACTGAAGGGTGCCACCAACTCATGTGGGCTTTGAAGGA
Found at i:291469 original size:2 final size:2
Alignment explanation
Indices: 291462--291488 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
291452 TTTATGTATG
291462 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
291489 CTTCAAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:297856 original size:10 final size:10
Alignment explanation
Indices: 297837--297870 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
297827 CACCAATCCT
297837 AAAA-AAAAA
1 AAAACAAAAA
297846 AAAACAAAAA
1 AAAACAAAAA
297856 AAAACAAAAA
1 AAAACAAAAA
297866 AAAAC
1 AAAAC
297871 CTTTTCACCC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.17
10 20 0.83
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAACAAAAA
Found at i:299191 original size:78 final size:77
Alignment explanation
Indices: 299059--299252 Score: 194
Period size: 78 Copynumber: 2.5 Consensus size: 77
299049 AATAACGGGG
* * * ** * *
299059 TTGGAGTATCCTCTTGAAAATAACAGGGTTGGAGTATCCCCGGTTGTGAAAAATCGATGA-TTAG
1 TTGGAGTATCCCCTCG-AAATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCAAT-ATTTAG
**
299123 GAAATAAAATC-GAGA
64 G-AATAAAGCCAG-GA
* *
299138 TTGGAGTATCCCCTCGAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTTGG
1 TTGGAGTATCCCCTCGAAATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCAATA-TTTAGG
*
299203 AATAAAGCCAGGG
65 AATAAAGCCAGGA
**
299216 TTGGAGTATCCCCTCGGAGGTAACGGGGTTGGAGTAT
1 TTGGAGTATCCCCTC-GAAATAACGGGGTTGGAGTAT
299253 TCCCGATGAA
Statistics
Matches: 97, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
77 1 0.01
78 58 0.60
79 38 0.39
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (77 bp):
TTGGAGTATCCCCTCGAAATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCAATATTTAGGA
ATAAAGCCAGGA
Found at i:299361 original size:51 final size:51
Alignment explanation
Indices: 299304--299655 Score: 214
Period size: 51 Copynumber: 6.7 Consensus size: 51
299294 AAAATGGTAT
*
299304 TTTTGAAAATAAAATCGGAGTTGGAGTATCCCCAATTAAAGAAAATTGGTG
1 TTTTGAAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAATTGGTG
** *
299355 TTTTGAAAATAAAATCAGG-GTTGGAGTATCCCCGATT-GTGAAAAATTAGTG
1 TTTTGAAAATAAAATC-GGAGTTGGAGTATCCCCGATTAAAG-AAAATTGGTG
* * * * *** *
299406 TTTT-AGAAATAAAACCGGGGTTGGAGTATCCCCTCGGAGGTAACG-GGGTTGGAG
1 TTTTGA-AAATAAAATCGGAGTTGGAGTAT-CCC-C-GA-TTAAAGAAAATTGGTG
* ***** * * ** *
299460 TATCCCCGATGAAATAAC-GAGGTTGGAGTATCCTCGATT-GTGAAAAATTGGTAT
1 TTTTGAAAAT-AAA-ATCGGA-GTTGGAGTATCCCCGATTAAAG-AAAATTGGT-G
* *
299514 TTTTGAAAATAAAATCGGAGTTGAAGTATTCCCGATTAAAGGAAAATTGGTG
1 TTTTGAAAATAAAATCGGAGTTGGAGTATCCCCGATTAAA-GAAAATTGGTG
* * * ** *
299566 TTTTGAAAATAAAATTGGGGTTAGGAGTATCCCTGATTATGGAAAATTAGTG
1 TTTTGAAAATAAAATCGGAGTT-GGAGTATCCCCGATTAAAGAAAATTGGTG
* * *
299618 TTTT-AGAAATAAAACCGGGGTTAGAGTATCCCCGATTA
1 TTTTGA-AAATAAAATCGGAGTTGGAGTATCCCCGATTA
299656 TGAGAAATCA
Statistics
Matches: 226, Mismatches: 54, Indels: 42
0.70 0.17 0.13
Matches are distributed among these distances:
50 4 0.02
51 81 0.36
52 71 0.31
53 34 0.15
54 16 0.07
55 7 0.03
56 13 0.06
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.30
Consensus pattern (51 bp):
TTTTGAAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAATTGGTG
Found at i:299445 original size:210 final size:211
Alignment explanation
Indices: 299162--299650 Score: 764
Period size: 210 Copynumber: 2.3 Consensus size: 211
299152 CGAAATAACG
* * * * * * * * *
299162 GGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTTGGAATAAAGCCAGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCC
* * *
299227 CCTCGGAGGTAACGGGGTTGGAGTATTCCCGATGAAATGATGAGGTTGGAGTATCCTCGATTGTG
66 CCTCGGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGTG
*
299292 AAAAAATGGTATTTTTGAAAATAAAATCGGAGTTGGAGTATCCCCAATTAAA-GAAAATTGGTGT
131 AAAAAATGGTATTTTTGAAAATAAAATCGGAGTTGAAGTATCCCCAATTAAAGGAAAATTGGTGT
299356 TTTGAAAATAAAATCA
196 TTTGAAAATAAAATCA
*
299372 GGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCC
299437 CCTCGGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGTG
66 CCTCGGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGTG
* * *
299502 AAAAATTGGTATTTTTGAAAATAAAATCGGAGTTGAAGTATTCCCGATTAAAGGAAAATTGGTGT
131 AAAAAATGGTATTTTTGAAAATAAAATCGGAGTTGAAGTATCCCCAATTAAAGGAAAATTGGTGT
**
299567 TTTGAAAATAAAATTG
196 TTTGAAAATAAAATCA
* * *
299583 GGGTTAGGAGTATCCCTGATTATGGAAAATTAGTGTTTTAGAAATAAAACCGGGGTTAGAGTATC
1 GGGTT-GGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACCGGGGTTGGAGTATC
299648 CCC
65 CCC
299651 GATTATGAGA
Statistics
Matches: 254, Mismatches: 23, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
210 165 0.65
211 31 0.12
212 58 0.23
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (211 bp):
GGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCC
CCTCGGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGTG
AAAAAATGGTATTTTTGAAAATAAAATCGGAGTTGAAGTATCCCCAATTAAAGGAAAATTGGTGT
TTTGAAAATAAAATCA
Found at i:299477 original size:28 final size:28
Alignment explanation
Indices: 299421--299497 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 28
299411 GAAATAAAAC
*** **
299421 CGGGGTTGGAGTATCCCCTCGGAGGTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
299449 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* *
299477 CGAGGTTGGAGTATCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
299498 TGTGAAAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:299550 original size:52 final size:50
Alignment explanation
Indices: 299480--299663 Score: 156
Period size: 52 Copynumber: 3.5 Consensus size: 50
299470 GAAATAACGA
* *
299480 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGAAAATAAAATCGG
1 GGTTGAAGTATCC-CGATTATGAAAAATTGGT-TTTTTGAAAATAAAATCGG
* * * * *
299532 AGTTGAAGTATTCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAATTGG
1 GGTTGAAGTA-TCCCGATT-ATGAAAAATTGGTTTTTTGAAAATAAAATCGG
* * * * *
299584 GGTTAGGAGTATCCCTGATTATGGAAAATTAGTGTTTT-AGAAATAAAACCGG
1 GGTT-GAAGTATCCC-GATTATGAAAAATTGGTTTTTTGA-AAATAAAATCGG
*
299636 GGTT-AGAGTATCCCCGATTATGAGAAAT
1 GGTTGA-AGTAT-CCCGATTATGAAAAAT
299664 CAATATTTTG
Statistics
Matches: 109, Mismatches: 16, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
51 17 0.16
52 70 0.64
53 22 0.20
ACGTcount: A:0.35, C:0.09, G:0.24, T:0.32
Consensus pattern (50 bp):
GGTTGAAGTATCCCGATTATGAAAAATTGGTTTTTTGAAAATAAAATCGG
Found at i:299651 original size:263 final size:263
Alignment explanation
Indices: 299304--299869 Score: 857
Period size: 264 Copynumber: 2.2 Consensus size: 263
299294 AAAATGGTAT
* * ** *
299304 TTTTGAAAATAAAATCGGAGTTGGAGTATCCCCAATTAAAGAAAATTGGTGTTTTGAAAATAAAA
1 TTTTGAAAATAAAATCGGGGTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTGAAAATAAAA
* * * * * *
299369 TCAGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCGGGGTTGGAGTA
66 CCAGGGTTAGAGTATCCCCGATTATGAAAAATCAATATTTTAGAAATAAAACCGGGGTTGGAGTA
299434 TCCCCTC-GGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGAT
131 TCCCCTCAGGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGAT
* *
299498 TGTGAAAAATTGGTATTTTTGAAAATAAAATCGGAGTTGAAGTATTCCCGATTAAAGGAAAATTG
196 TGTGAAAAATTAGTATTTTTGAAAATAAAATCGGAGTCGAAGTATTCCCGATTAAAGGAAAATTG
299563 GTG
261 GTG
* *
299566 TTTTGAAAATAAAATTGGGGTTAGGAGTATCCCTGATTATGGAAAATTAGTGTTTT-AGAAATAA
1 TTTTGAAAATAAAATCGGGGTT-GGAGTATCCCCGATTATGGAAAATTAGTGTTTTGA-AAATAA
* * * * *
299630 AACCGGGGTTAGAGTATCCCCGATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAG
64 AACCAGGGTTAGAGTATCCCCGATTATGAAAAATCAATATTTTAGAAATAAAACCGGGGTTGGAG
* * *
299695 TATCCCTTCAGGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCTTTG
129 TATCCCCTCAGGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCG
* * * *
299760 ATTGTGAAAAATTAGTGTTTTTGGAAATAAAATCGGAGTCGGAGTATTCCTGATTAAAGGAAAAT
194 ATTGTGAAAAATTAGTATTTTTGAAAATAAAATCGGAGTCGAAGTATTCCCGATTAAAGGAAAAT
299825 TGGTG
259 TGGTG
299830 TTTTGAAAATAAAATCGGGGTTGGAGTATCCCCGATTATG
1 TTTTGAAAATAAAATCGGGGTTGGAGTATCCCCGATTATG
299870 AACAATTGGG
Statistics
Matches: 272, Mismatches: 29, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
262 21 0.08
263 113 0.42
264 138 0.51
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (263 bp):
TTTTGAAAATAAAATCGGGGTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTGAAAATAAAA
CCAGGGTTAGAGTATCCCCGATTATGAAAAATCAATATTTTAGAAATAAAACCGGGGTTGGAGTA
TCCCCTCAGGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGAT
TGTGAAAAATTAGTATTTTTGAAAATAAAATCGGAGTCGAAGTATTCCCGATTAAAGGAAAATTG
GTG
Found at i:299680 original size:51 final size:51
Alignment explanation
Indices: 299572--299700 Score: 143
Period size: 51 Copynumber: 2.5 Consensus size: 51
299562 GGTGTTTTGA
** * * * *
299572 AAATAAAATTGGGGTTAGGAGTATCCCTGATTATGGAAAATTAGTGTTTTAG
1 AAATAAAACCGGGGTTA-GAGTATCCCCGATTATGGAAAATCAATATTTTAG
*
299624 AAATAAAACCGGGGTTAGAGTATCCCCGATTAT-GAGAAATCAATATTTTGG
1 AAATAAAACCGGGGTTAGAGTATCCCCGATTATGGA-AAATCAATATTTTAG
* * *
299675 GAATAAAGCCGGGGTTGGAGTATCCC
1 AAATAAAACCGGGGTTAGAGTATCCC
299701 TTCAGGAGGT
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
50 2 0.03
51 49 0.74
52 15 0.23
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
AAATAAAACCGGGGTTAGAGTATCCCCGATTATGGAAAATCAATATTTTAG
Found at i:299814 original size:52 final size:51
Alignment explanation
Indices: 299748--299876 Score: 132
Period size: 52 Copynumber: 2.5 Consensus size: 51
299738 TAACGAGGTT
** * *
299748 GGAGTATCTTTGATTGTGAAAAATTAGTGTTTTTGGAAATAAAATCGGAGTC
1 GGAGTATCCCTGATTATGAAAAATTAGTG-TTTTGAAAATAAAATCGGAGTC
* * * * * *
299800 GGAGTATTCCTGATTAAAGGAAAATTGGTGTTTTGAAAATAAAATCGGGGTT
1 GGAGTATCCCTGATT-ATGAAAAATTAGTGTTTTGAAAATAAAATCGGAGTC
* *
299852 GGAGTATCCCCGATTATGAACAATT
1 GGAGTATCCCTGATTATGAAAAATT
299877 GGGAAACTTA
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
51 7 0.11
52 44 0.72
53 10 0.16
ACGTcount: A:0.33, C:0.09, G:0.25, T:0.33
Consensus pattern (51 bp):
GGAGTATCCCTGATTATGAAAAATTAGTGTTTTGAAAATAAAATCGGAGTC
Found at i:299832 original size:53 final size:52
Alignment explanation
Indices: 299767--299867 Score: 139
Period size: 52 Copynumber: 1.9 Consensus size: 52
299757 TTGATTGTGA
* * *
299767 AAAATTAGTGTTTTTGGAAATAAAATCGGAGTCGGAGTATTCCTGATTAAAGG
1 AAAATTAGTG-TTTTGAAAATAAAATCGGAGTCGGAGTATCCCCGATTAAAGG
* * *
299820 AAAATTGGTGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCCGATTA
1 AAAATTAGTGTTTTGAAAATAAAATCGGAGTCGGAGTATCCCCGATTA
299868 TGAACAATTG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
52 33 0.79
53 9 0.21
ACGTcount: A:0.35, C:0.09, G:0.25, T:0.32
Consensus pattern (52 bp):
AAAATTAGTGTTTTGAAAATAAAATCGGAGTCGGAGTATCCCCGATTAAAGG
Found at i:302278 original size:21 final size:21
Alignment explanation
Indices: 302254--302295 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
302244 GTATTGATAC
302254 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
302275 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
302296 GGTAGTAGCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.43
Consensus pattern (21 bp):
AATGTATCGATACATTTCCTT
Found at i:302330 original size:13 final size:13
Alignment explanation
Indices: 302312--302363 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
302302 AGCGTCGTAG
302312 CGATACATTGTAT
1 CGATACATTGTAT
302325 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
302344 CGATACATTGTAT
1 CGATACATTGTAT
302357 CGATACA
1 CGATACA
302364 ACACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 17 0.52
15 2 0.06
16 2 0.06
17 2 0.06
19 10 0.30
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:302344 original size:19 final size:18
Alignment explanation
Indices: 302320--302382 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
302310 AGCGATACAT
302320 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
302339 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
302352 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
302371 TGTATCGATACA
1 TGTATCGATACA
302383 TTTTCTGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:302353 original size:32 final size:32
Alignment explanation
Indices: 302312--302384 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
302302 AGCGTCGTAG
302312 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
302344 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
302376 CGATACATT
1 CGATACATT
302385 TTCTGTTTGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:302411 original size:19 final size:19
Alignment explanation
Indices: 302351--302412 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
302341 TATCGATACA
302351 TTGTATCGATACAACACT-T
1 TTGTATCGATACAA-ACTGT
* **
302370 ATGTATCGATACATTTTCTGT
1 TTGTATCGATACA--AACTGT
302391 TTGTATCGATACAAACTGT
1 TTGTATCGATACAAACTGT
302410 TTG
1 TTG
302413 AAATTCAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
19 19 0.56
20 2 0.06
21 13 0.38
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (19 bp):
TTGTATCGATACAAACTGT
Found at i:303589 original size:27 final size:27
Alignment explanation
Indices: 303550--303744 Score: 275
Period size: 27 Copynumber: 7.1 Consensus size: 27
303540 TGGCATTTCT
*
303550 TTTTAAAGTCCACAACTCCGTGGCATCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
** *
303578 TTTTAAGTCCACAACTTTGTGGCATCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
303605 TTTTAAAGTCCACAACTCCAG-GGCACCC
1 TTTT-AAGTCCACAACTCC-GTGGCACCC
* *
303633 TATTAAAGTCCACAACTCTGTGGCACCC
1 T-TTTAAGTCCACAACTCCGTGGCACCC
303661 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
303688 TTTTAAGTCCACAACTCAGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
303715 TTTTAAGTCCACAACTCAGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
303742 TTT
1 TTT
303745 GAAAGCCCAT
Statistics
Matches: 153, Mismatches: 10, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
27 106 0.69
28 44 0.29
29 3 0.02
ACGTcount: A:0.25, C:0.32, G:0.14, T:0.28
Consensus pattern (27 bp):
TTTTAAGTCCACAACTCCGTGGCACCC
Found at i:303691 original size:83 final size:81
Alignment explanation
Indices: 303551--303744 Score: 291
Period size: 83 Copynumber: 2.4 Consensus size: 81
303541 GGCATTTCTT
* * ** *
303551 TTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTTTGTGGCATCCTTTTAAAGTCC
1 TTTAAAGTCCACAACTCAGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCC
303616 ACAACTCCAG-GGCACCC
65 ACAACT-CAGTGGCACCC
*
303633 TATTAAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 T-TTAAAGTCCACAACTCAGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
303698 ACAACTCAGTGGCACCC
65 ACAACTCAGTGGCACCC
*
303715 TTTTAAGTCCACAACTCAGTGGCACCCTTT
1 TTTAAAGTCCACAACTCAGTGGCACCCTTT
303745 GAAAGCCCAT
Statistics
Matches: 103, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
81 30 0.29
82 21 0.20
83 52 0.50
ACGTcount: A:0.25, C:0.32, G:0.14, T:0.28
Consensus pattern (81 bp):
TTTAAAGTCCACAACTCAGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
CAACTCAGTGGCACCC
Found at i:303783 original size:32 final size:32
Alignment explanation
Indices: 303724--304511 Score: 732
Period size: 32 Copynumber: 26.1 Consensus size: 32
303714 CTTTTAAGTC
* * *
303724 CACAACTCAGTGGC-ACCC-TTTGAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
303754 TACAAGTTGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * * *
303786 CGCAAGTCAGTGGCAACTCATTTGAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
303818 CACAAGTTGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
303850 CACAAGTTGGTGGCAACCCATTTCAAAGCCTA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
303882 CACAAGTCTGTGGTAACCCATTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
303912 CACAAGTCGGTGGC-A-TCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
303942 CACAAGTTGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
303974 CACAAGTTGGTGGCAACCCATTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
304004 CACAAGTCAGTGG-TACCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** * *
304032 CACAAGTCAATGGC-ATCC-TTTCAAAG-TC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
304060 TACAAGTCGGTGGC-A-TCTTTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
304088 CATAAGTCAGTGGC-ACCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
304116 CACAAGTCAGTGGC-ATCC-TTTCAAAG-TC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
304144 CACAAGTCGGTGGC-A-TCTTTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
304172 CACAAGTCGGTGGC-A-TCTTTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * **
304200 CACAAGTCGGTGGC-A-TCTTTTCAAAGCTGA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
304230 CACAAGTCGGTGGC-ACCCATTT-AAGGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
304260 CACAAGTCGGTGGCAACTCATTTGAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
304292 CACAAGTCGGTGGTAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
304324 CACAAGTTGGTTGCAACCTATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
304356 CACAAGTTGGTGGCAACCCATTTGAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
304388 CACAAGTCAGTGGCAACTCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
304420 CACAAGTTGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
304452 CACAAGTCAGTGGC-A-TCTTTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** *
304480 CACAAGTCAATGGC-ATCC-TTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
304510 CA
1 CA
304512 AGTCAGTGGC
Statistics
Matches: 659, Mismatches: 81, Indels: 36
0.85 0.10 0.05
Matches are distributed among these distances:
27 2 0.00
28 210 0.32
29 13 0.02
30 91 0.14
31 20 0.03
32 323 0.49
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:303936 original size:28 final size:28
Alignment explanation
Indices: 303772--304599 Score: 578
Period size: 28 Copynumber: 27.7 Consensus size: 28
303762 GGTGGCAACC
*
303772 CATTTCAAAGCCCACGCAAGTCAGTGGCAACT
1 CATTTCAAAGCCCA--CAAGTCGGTGGC-A-T
* * *
303804 CATTTGAAAGCCCACACAAGTTGGTGGCAACC
1 CATTTCAAAG-CC-CACAAGTCGGTGGC-A-T
* *
303836 CATTTCAAAGCCCACACAAGTTGGTGGCAACC
1 CATTTCAAAG-CC-CACAAGTCGGTGGC-A-T
* * *
303868 CATTTCAAAGCCTACACAAGTCTGTGGTAACC
1 CATTTCAAAGCC--CACAAGTCGGTGG-CA-T
303900 CATTTCAAAGCCCACAAGTCGGTGGCAT
1 CATTTCAAAGCCCACAAGTCGGTGGCAT
* * *
303928 CATTCCAAAGCCCACACAAGTTGGTGGCAACC
1 CATTTCAAAG-CC-CACAAGTCGGTGGC-A-T
* *
303960 CATTTCAAAGCCCACACAAGTTGGTGGCAACC
1 CATTTCAAAG-CC-CACAAGTCGGTGGC-A-T
* * *
303992 CATTTCAAAGCCCACAAGTCAGTGGTAC
1 CATTTCAAAGCCCACAAGTCGGTGGCAT
* **
304020 CCTTTCAAAGCCCACAAGTCAATGGCAT
1 CATTTCAAAGCCCACAAGTCGGTGGCAT
* * *
304048 CCTTTCAAAGTCTACAAGTCGGTGGCAT
1 CATTTCAAAGCCCACAAGTCGGTGGCAT
* * * *
304076 CTTTTCAAAGCCCATAAGTCAGTGGCAC
1 CATTTCAAAGCCCACAAGTCGGTGGCAT
* *
304104 CCTTTCAAAGCCCACAAGTCAGTGGCAT
1 CATTTCAAAGCCCACAAGTCGGTGGCAT
* *
304132 CCTTTCAAAGTCCACAAGTCGGTGGCAT
1 CATTTCAAAGCCCACAAGTCGGTGGCAT
*
304160 CTTTTCAAAGCCCACAAGTCGGTGGCAT
1 CATTTCAAAGCCCACAAGTCGGTGGCAT
*
304188 CTTTTCAAAGCCCACAAGTCGGTGGCAT
1 CATTTCAAAGCCCACAAGTCGGTGGCAT
* * *
304216 CTTTTCAAAGCTGACACAAGTCGGTGGCACC
1 CATTTCAAAGC--CCACAAGTCGGTGGCA-T
*
304247 CATTT-AAGGCCCACACAAGTCGGTGGCAACT
1 CATTTCAAAG-CC-CACAAGTCGGTGGC-A-T
* * *
304278 CATTTGAAAGCCCACACAAGTCGGTGGTAACC
1 CATTTCAAAG-CC-CACAAGTCGGTGG-CA-T
* * *
304310 CATTTCAAAGCCCACACAAGTTGGTTGCAAC
1 CATTTCAAAG-CC-CACAAGTCGGTGGC-AT
* *
304341 CTATTTCAAAGCCCACACAAGTTGGTGGCAACC
1 C-ATTTCAAAG-CC-CACAAGTCGGTGGC-A-T
* *
304374 CATTTGAAAGCCCACACAAGTCAGTGGCAACT
1 CATTTCAAAG-CC-CACAAGTCGGTGGC-A-T
* *
304406 CATTTCAAAGCCCACACAAGTTGGTGGCAACC
1 CATTTCAAAG-CC-CACAAGTCGGTGGC-A-T
*
304438 CATTTCAAAGCCCACACAAGTCAGTGGCAT
1 CATTTCAAAG-CC-CACAAGTCGGTGGCAT
* **
304468 CTTTTCAAAGCCCACAAGTCAATGGCAT
1 CATTTCAAAGCCCACAAGTCGGTGGCAT
* *
304496 CCTTTCAAAGCCCACAAGTCAGTGGCAT
1 CATTTCAAAGCCCACAAGTCGGTGGCAT
* * * *
304524 CCTTTCAATGTCCACAAGTCAGTGGCAT
1 CATTTCAAAGCCCACAAGTCGGTGGCAT
* * * **
304552 CCTTTCAATGTCCACAAGTCAATGGCAT
1 CATTTCAAAGCCCACAAGTCGGTGGCAT
* *
304580 CTTTTCCAAGCCCACAAGTC
1 CATTTCAAAGCCCACAAGTC
304600 CATGACTCGA
Statistics
Matches: 702, Mismatches: 75, Indels: 42
0.86 0.09 0.05
Matches are distributed among these distances:
28 306 0.44
29 6 0.01
30 77 0.11
31 20 0.03
32 287 0.41
33 4 0.01
34 2 0.00
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.22
Consensus pattern (28 bp):
CATTTCAAAGCCCACAAGTCGGTGGCAT
Found at i:304066 original size:56 final size:57
Alignment explanation
Indices: 303554--304599 Score: 702
Period size: 56 Copynumber: 17.7 Consensus size: 57
303544 ATTTCTTTTT
* * * * * * ** * *
303554 AAAGTCCACAACTCCGTGGCATCCTTT-TAAGTCCACAACTTTGTGGCATCC-TTTT
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCGGTGGCACCCATTTC
* * * * * *
303609 AAAGTCCACAACTCCAG-GGCACCCTATT-AAAGTCCACAACTCTGTGGCACCC-TTT-
1 AAAGCCCACAAGT-CAGTGGCATCCT-TTCAAAGCCCACAAGTCGGTGGCACCCATTTC
* * * * * * * * *
303664 TAAGTCCACAACTCCGTGGCACCCTTT-TAAGTCCACAACTCAGTGGCACCC-TTT-
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCGGTGGCACCCATTTC
* * * * * *
303718 TAAGTCCACAACTCAGTGGCACCCTTTGAAAGCCCATACAAGTTGGTGGCAACCCATTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCC--ACAAGTCGGTGGC-ACCCATTTC
* * *
303778 AAAGCCCACGCAAGTCAGTGGCAACTCATTTGAAAGCCCACACAAGTTGGTGGCAACCCATTTC
1 AAAGCCCA--CAAGTCAGTGGC-A-TCCTTTCAAAG-CC-CACAAGTCGGTGGC-ACCCATTTC
** * * *
303842 AAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCTACACAAGTCTGTGGTAACCCATTTC
1 AAAG-CC-CACAAGTCAGTGGC-ATCC-TTTCAAAGCC--CACAAGTCGGTGG-CACCCATTTC
* * * *
303906 AAAGCCCACAAGTCGGTGGCATCATTCCAAAGCCCACACAAGTTGGTGGCAACCCATTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAG-CC-CACAAGTCGGTGGC-ACCCATTTC
** * * *
303966 AAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCACAAGTCAGTGGTACCC-TTTC
1 AAAG-CC-CACAAGTCAGTGGC-ATCC-TTTCAAAGCCCACAAGTCGGTGGCACCCATTTC
* * * * *
304026 AAAGCCCACAAGTCAATGGCATCCTTTCAAAGTCTACAAGTCGGTGGCA-TCTTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCGGTGGCACCCATTTC
* * * *
304082 AAAGCCCATAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCC-TTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCGGTGGCACCCATTTC
* * * * *
304138 AAAGTCCACAAGTCGGTGGCATCTTTTCAAAGCCCACAAGTCGGTGGCA-TCTTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCGGTGGCACCCATTTC
* * *
304194 AAAGCCCACAAGTCGGTGGCATCTTTTCAAAGCTGACACAAGTCGGTGGCACCCATTT-
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC--CCACAAGTCGGTGGCACCCATTTC
* * * * *
304252 AAGGCCCACACAAGTCGGTGGCAACTCATTTGAAAGCCCACACAAGTCGGTGGTAACCCATTTC
1 AAAG-CC-CACAAGTCAGTGGC-A-TCCTTTCAAAG-CC-CACAAGTCGGTGG-CACCCATTTC
** * * * *
304316 AAAGCCCACACAAGTTGGTTGCAACCTATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTG
1 AAAG-CC-CACAAGTCAGTGGCATCC--TTTCAAAG-CC-CACAAGTCGGTGGC-ACCCATTTC
* *
304380 AAAGCCCACACAAGTCAGTGGCAACTCATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTC
1 AAAG-CC-CACAAGTCAGTGGC-A-TCCTTTCAAAG-CC-CACAAGTCGGTGGC-ACCCATTTC
* ** *
304444 AAAGCCCACACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAATGGCATCC-TTTC
1 AAAG-CC-CACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCGGTGGCACCCATTTC
* * * *
304502 AAAGCCCACAAGTCAGTGGCATCCTTTCAATGTCCACAAGTCAGTGGCATCC-TTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCGGTGGCACCCATTTC
* * * * *
304558 AATGTCCACAAGTCAATGGCATCTTTTCCAAGCCCACAAGTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTC
304600 CATGACTCGA
Statistics
Matches: 841, Mismatches: 105, Indels: 89
0.81 0.10 0.09
Matches are distributed among these distances:
54 55 0.07
55 47 0.06
56 260 0.31
57 16 0.02
58 41 0.05
59 14 0.02
60 71 0.08
61 13 0.02
62 81 0.10
63 21 0.02
64 213 0.25
65 5 0.01
66 4 0.00
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (57 bp):
AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCGGTGGCACCCATTTC
Found at i:304095 original size:84 final size:84
Alignment explanation
Indices: 303596--304599 Score: 638
Period size: 84 Copynumber: 11.3 Consensus size: 84
303586 CCACAACTTT
* * * * * * * *
303596 GTGGCATCCTTTTAAAGTCCACAACTCCAG-GGCACCCTATT-AAAGTCCACAACTCTGTGGCAC
1 GTGGCATCCTTTCAAAGCCCACAAGT-CGGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGCAC
* * * *
303659 CCTTT-TAAGTCCACAACTCC
64 CCTTTCAAAGCCCACAAGTCA
* * * * * * *
303679 GTGGCACCCTTT-TAAGTCCACAACTCAGTGGCACCCTTTT--AAGTCCACAACTCAGTGGCACC
1 GTGGCATCCTTTCAAAGCCCACAAGTCGGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGCACC
* **
303741 CTTTGAAAGCCCATACAAGTTG
65 CTTTCAAAGCCC--ACAAGTCA
* * * * **
303763 GTGGCAACCCATTTCAAAGCCCACGCAAGTCAGTGGCAACTCATTTGAAAGCCCACACAAGTTGG
1 GTGGC-ATCC-TTTCAAAGCCCA--CAAGTCGGTGGC-AC-CTTTTCAAAG-CC-CACAAGTCAG
**
303828 TGGCAACCCATTTCAAAGCCCACACAAGTTG
58 TGGC-ACCC-TTTCAAAG-CC-CACAAGTCA
* * * * *
303859 GTGGCAACCCATTTCAAAGCCTACACAAGTCTGTGGTAACCCATTTCAAAGCCCACAAGTCGGTG
1 GTGGC-ATCC-TTTCAAAGCC--CACAAGTCGGTGG-CA-CCTTTTCAAAGCCCACAAGTCAGTG
* * * **
303924 GCATCATTCCAAAGCCCACACAAGTTG
60 GCACCCTTTCAAAG-CC-CACAAGTCA
* * *
303951 GTGGCAACCCATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCACAAGTCAGTG
1 GTGGC-ATCC-TTTCAAAG-CC-CACAAGTCGGTGGC-A-CCTTTTCAAAGCCCACAAGTCAGTG
*
304016 GTACCCTTTCAAAGCCCACAAGTCA
60 GCACCCTTTCAAAGCCCACAAGTCA
* * * * *
304041 ATGGCATCCTTTCAAAGTCTACAAGTCGGTGGCATCTTTTCAAAGCCCATAAGTCAGTGGCACCC
1 GTGGCATCCTTTCAAAGCCCACAAGTCGGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACCC
304106 TTTCAAAGCCCACAAGTCA
66 TTTCAAAGCCCACAAGTCA
* * * * *
304125 GTGGCATCCTTTCAAAGTCCACAAGTCGGTGGCATCTTTTCAAAGCCCACAAGTCGGTGGCATCT
1 GTGGCATCCTTTCAAAGCCCACAAGTCGGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACCC
*
304190 TTTCAAAGCCCACAAGTCG
66 TTTCAAAGCCCACAAGTCA
* * * * *
304209 GTGGCATCTTTTCAAAGCTGACACAAGTCGGTGGCACCCATTT-AAGGCCCACACAAGTCGGTGG
1 GTGGCATCCTTTCAAAGC--CCACAAGTCGGTGGCA-CCTTTTCAAAG-CC-CACAAGTCAGTGG
* * *
304273 CAACTCATTTGAAAGCCCACACAAGTCG
61 C-AC-CCTTTCAAAG-CC-CACAAGTCA
* * * * **
304301 GTGGTAACCCATTTCAAAGCCCACACAAGTTGGTTGCAACCTATTTCAAAGCCCACACAAGTTGG
1 GTGG-CATCC-TTTCAAAG-CC-CACAAGTCGGTGGC-ACCT-TTTCAAAG-CC-CACAAGTCAG
*
304366 TGGCAACCCATTTGAAAGCCCACACAAGTCA
58 TGGC-ACCC-TTTCAAAG-CC-CACAAGTCA
* * *
304397 GTGGCAACTCATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCACACAAGTCAG
1 GTGGC-A-TCCTTTCAAAG-CC-CACAAGTCGGTGGC-A-CCTTTTCAAAG-CC-CACAAGTCAG
* *
304462 TGGCATCTTTTCAAAGCCCACAAGTCA
58 TGGCACCCTTTCAAAGCCCACAAGTCA
* * * * *
304489 ATGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCC-TTTCAATGTCCACAAGTCAGTGGCATC
1 GTGGCATCCTTTCAAAGCCCACAAGTCGGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGCACC
* *
304553 CTTTCAATGTCCACAAGTCA
65 CTTTCAAAGCCCACAAGTCA
* * *
304573 ATGGCATCTTTTCCAAGCCCACAAGTC
1 GTGGCATCCTTTCAAAGCCCACAAGTC
304600 CATGACTCGA
Statistics
Matches: 783, Mismatches: 93, Indels: 89
0.81 0.10 0.09
Matches are distributed among these distances:
81 28 0.04
82 27 0.03
83 11 0.01
84 208 0.27
85 6 0.01
86 40 0.05
87 16 0.02
88 34 0.04
89 18 0.02
90 34 0.04
91 5 0.01
92 116 0.15
93 9 0.01
94 53 0.07
95 14 0.02
96 155 0.20
97 6 0.01
98 3 0.00
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.22
Consensus pattern (84 bp):
GTGGCATCCTTTCAAAGCCCACAAGTCGGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACCC
TTTCAAAGCCCACAAGTCA
Found at i:310535 original size:79 final size:78
Alignment explanation
Indices: 310371--310557 Score: 209
Period size: 79 Copynumber: 2.4 Consensus size: 78
310361 TCGATGTTCC
* *
310371 AGAAATAAAACCGGGGTTGGAGTATCCCCTCAGAAATAACAGGGTTGGAGTATCCTTGATTATAG
1 AGAAATAAAATCGGGGTTGGAGTATCCCCTCAGAAATAACAGGGTTGGAGTATCCTCGATTATAG
**
310436 AAAATCGGTATTT
66 AAAATCAATATTT
* * *
310449 TGAAAATAAAATCGGGGTTGGAGTATCCCCTC-GAAAATAA-TGAGGTTGGAGTATCCTCGATTG
1 AG-AAATAAAATCGGGGTTGGAGTATCCCCTCAG-AAATAACAG-GGTTGGAGTATCCTCGATTA
*
310512 T-GAAAAATTAATGATTT
63 TAG-AAAATCAAT-ATTT
** *
310529 AGAAATAAGGTCGGGGTTGAAGTATCCCC
1 AGAAATAAAATCGGGGTTGGAGTATCCCC
310558 GATTATGAGA
Statistics
Matches: 92, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
78 4 0.04
79 83 0.90
80 5 0.05
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.27
Consensus pattern (78 bp):
AGAAATAAAATCGGGGTTGGAGTATCCCCTCAGAAATAACAGGGTTGGAGTATCCTCGATTATAG
AAAATCAATATTT
Found at i:310561 original size:51 final size:50
Alignment explanation
Indices: 310492--310658 Score: 208
Period size: 51 Copynumber: 3.3 Consensus size: 50
310482 AAAATAATGA
* **
310492 GGTTGGAGTATCCTCGATTGTGAAAAATTAATGATTTAGAAATAAGGTCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTAAT-ATTTAGAAATAAAATCGG
* * * *
310543 GGTTGAAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAATCGA
1 GGTTGGAGTATCCCCGATTGTGAAAAATTAATA-TTTAGAAATAAAATCGG
* ** *
310594 AGTTGGAGTATCCCCGATTGTGAAAAATTGGTCTTTTAGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTAAT-ATTTAGAAATAAAATCGG
310645 GGTTGGAGTATCCC
1 GGTTGGAGTATCCC
310659 TCCGAAAATA
Statistics
Matches: 98, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
50 1 0.01
51 97 0.99
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.31
Consensus pattern (50 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTAATATTTAGAAATAAAATCGG
Found at i:310695 original size:28 final size:27
Alignment explanation
Indices: 310647--310710 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 27
310637 AAAATCGGGG
310647 TTGGAGTATCCCTCCGAAAATAACAGGA
1 TTGGAGTATCCCT-CGAAAATAACAGGA
* *
310675 TTGGAGTATCCCT-GATGAAATAACGGGG
1 TTGGAGTATCCCTCGA--AAATAACAGGA
310703 TTGGAGTA
1 TTGGAGTA
310711 CCCCCGATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 2 0.06
28 30 0.94
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (27 bp):
TTGGAGTATCCCTCGAAAATAACAGGA
Found at i:310788 original size:109 final size:107
Alignment explanation
Indices: 310595--310875 Score: 314
Period size: 109 Copynumber: 2.6 Consensus size: 107
310585 TAAAATCGAA
* * *** * *
310595 GTTGGAGTATCCCCGATTGTGAAAAATTGGTCTTTTAGAAATAAAATCGGGGTTGGAGTATCCCT
1 GTTGGAGTACCCCCGATTATGAAAAATCAATCTTTTAGAAATAAAACCAGGGTTGGAGTATCCCT
*
310660 CCGAAAATAACAGGATTGGAGTATCCCTGATGAAATAACGGG
66 CCGAAAATAACAGGATTGGAGTATCCCCGATGAAATAACGGG
* *
310702 GTTGGAGTACCCCCGATTATGAAAAAATCAATACTTTTAGATATAAAGCCAGGGTTGGAGTATCT
1 GTTGGAGTACCCCCGATTATG-AAAAATCAAT-CTTTTAGAAATAAAACCAGGGTTGGAGTATC-
* *
310767 CCT-CGGAAATAACAGGGTTGGAGTATCCCCGATGAAATAACGGG
63 CCTCCGAAAATAACAGGATTGGAGTATCCCCGATGAAATAACGGG
* * * * *** * * *
310811 GTTGGAGTATCTCCAATTGTGAAAAATTGGTGTTTTGGAAATAAAATC-GGAGTTGGAGTATCCC
1 GTTGGAGTACCCCCGATTATGAAAAATCAATCTTTTAGAAATAAAACCAGG-GTTGGAGTATCCC
310875 T
65 T
310876 GATTGCGATA
Statistics
Matches: 146, Mismatches: 24, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
106 5 0.03
107 42 0.29
108 14 0.10
109 82 0.56
110 3 0.02
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.28
Consensus pattern (107 bp):
GTTGGAGTACCCCCGATTATGAAAAATCAATCTTTTAGAAATAAAACCAGGGTTGGAGTATCCCT
CCGAAAATAACAGGATTGGAGTATCCCCGATGAAATAACGGG
Done.