Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 37 of 126
Found at i:11138817 original size:14 final size:15
Alignment explanation
Indices: 11138785--11138821 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
11138775 TTCATGATTT
11138785 GTAT-TTTATTTTTC
1 GTATATTTATTTTTC
*
11138799 TTATATTTA-TTTTC
1 GTATATTTATTTTTC
11138813 GTATATTTA
1 GTATATTTA
11138822 CTCATTCGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (15 bp):
GTATATTTATTTTTC
Found at i:11155133 original size:15 final size:15
Alignment explanation
Indices: 11155113--11155149 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
11155103 CTAGCAGAAG
*
11155113 GAGAAGGAAGAACAA
1 GAGAAGGAAGAAAAA
11155128 GAGAAGGAAGAAAAA
1 GAGAAGGAAGAAAAA
11155143 GAAGAAG
1 G-AGAAG
11155150 AGAATGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.62, C:0.03, G:0.35, T:0.00
Consensus pattern (15 bp):
GAGAAGGAAGAAAAA
Found at i:11156246 original size:17 final size:17
Alignment explanation
Indices: 11156224--11156274 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
11156214 TCAATCACTT
*
11156224 GAAAAAGAAAAAAATGA
1 GAAAAAGAAAAAAAAGA
11156241 GAAAAAGAAAGAGAAAAGA
1 GAAAAAGAAA-A-AAAAGA
11156260 -AAAGAAGAAAAAAAA
1 GAAA-AAGAAAAAAAA
11156275 TTTTATTACT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
17 14 0.47
18 5 0.17
19 11 0.37
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (17 bp):
GAAAAAGAAAAAAAAGA
Found at i:11156274 original size:12 final size:11
Alignment explanation
Indices: 11156225--11156274 Score: 57
Period size: 12 Copynumber: 4.4 Consensus size: 11
11156215 CAATCACTTG
11156225 AAAA-AGAAAA
1 AAAAGAGAAAA
*
11156235 AAATGAGAAAA
1 AAAAGAGAAAA
11156246 AGAAAGAGAAAA
1 A-AAAGAGAAAA
11156258 GAAAAGAAGAAAA
1 -AAAAG-AGAAAA
11156271 AAAA
1 AAAA
11156275 TTTTATTACT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 3 0.09
11 7 0.21
12 17 0.50
13 7 0.21
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (11 bp):
AAAAGAGAAAA
Found at i:11164807 original size:24 final size:24
Alignment explanation
Indices: 11164756--11164810 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
11164746 TCTTCCAGCT
*
11164756 AAACTCTATTTATTTGTTTCAATT
1 AAACTCTATTTATTTGTTTCAATC
* * *
11164780 AAACTCTGTTTATTTGTTTTAGTC
1 AAACTCTATTTATTTGTTTCAATC
11164804 AAACTCT
1 AAACTCT
11164811 TATTAGTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.51
Consensus pattern (24 bp):
AAACTCTATTTATTTGTTTCAATC
Found at i:11166410 original size:16 final size:16
Alignment explanation
Indices: 11166379--11166408 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11166369 TTACTCAACC
11166379 AAATAAAATATAAAAT
1 AAATAAAATATAAAAT
11166395 AAATAAAAT-TAAAA
1 AAATAAAATATAAAA
11166409 ATTCCATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AAATAAAATATAAAAT
Found at i:11167649 original size:30 final size:30
Alignment explanation
Indices: 11167614--11167670 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
11167604 CACTCTATTT
11167614 TTTTAATTT-ATACCTTTAATTTATTTACAA
1 TTTTAATTTAAT-CCTTTAATTTATTTACAA
*
11167644 TTTTAATTTAATCCTTTTATTTATTTA
1 TTTTAATTTAATCCTTTAATTTATTTA
11167671 TTTCAGTCCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (30 bp):
TTTTAATTTAATCCTTTAATTTATTTACAA
Found at i:11167774 original size:12 final size:11
Alignment explanation
Indices: 11167739--11167793 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 11
11167729 TTTACCCTCT
*
11167739 TTTATTATTTA
1 TTTATTTTTTA
11167750 TTCTATTGCTTTTA
1 TT-TATT--TTTTA
11167764 TTGTATTTTTTA
1 TT-TATTTTTTA
11167776 TTTA--TTTTA
1 TTTATTTTTTA
11167785 TTTATTTTT
1 TTTATTTTT
11167794 AATGCTTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
9 9 0.24
11 7 0.19
12 11 0.30
14 10 0.27
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.75
Consensus pattern (11 bp):
TTTATTTTTTA
Found at i:11167777 original size:21 final size:20
Alignment explanation
Indices: 11167737--11167806 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 20
11167727 CCTTTACCCT
11167737 CTTTTA-TTATTTATTCTATTG
1 CTTTTATTTATTT-TT-TATTG
*
11167758 CTTTTATTGTATTTTTTATTT
1 CTTTTATT-TATTTTTTATTG
* *
11167779 ATTTTATTTA-TTTTTAATG
1 CTTTTATTTATTTTTTATTG
11167798 CTTTTATTT
1 CTTTTATTT
11167807 CACGCTATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
19 15 0.36
20 2 0.05
21 17 0.40
22 3 0.07
23 5 0.12
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.71
Consensus pattern (20 bp):
CTTTTATTTATTTTTTATTG
Found at i:11171870 original size:16 final size:16
Alignment explanation
Indices: 11171849--11171879 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11171839 CGTTAACAAA
11171849 TAAAATGCAATGACAG
1 TAAAATGCAATGACAG
*
11171865 TAAAATGTAATGACA
1 TAAAATGCAATGACA
11171880 ACTACATGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.10, G:0.16, T:0.23
Consensus pattern (16 bp):
TAAAATGCAATGACAG
Found at i:11179137 original size:41 final size:41
Alignment explanation
Indices: 11179028--11179254 Score: 260
Period size: 41 Copynumber: 5.5 Consensus size: 41
11179018 ACTTGATGTA
* *
11179028 TAAATGGAAGACTCATGTCTCGAGATGAGCATGAGATTATA-
1 TAAA-GGAAGACTCATGACTCGAAATGAGCATGAGATTATAT
* * * *
11179069 TAAAGGAAGACTCATGTCT-TAAGATAAGCATGAGATTAAAT
1 TAAAGGAAGACTCATGACTCGAA-ATGAGCATGAGATTATAT
* *
11179110 TAAAGGAAGACTCGTGACTCGAAATAAGCATGAGATTATAT
1 TAAAGGAAGACTCATGACTCGAAATGAGCATGAGATTATAT
* *
11179151 TAAAAGAAGACTCATGACTCAAAATGAGCATGAGATTATAT
1 TAAAGGAAGACTCATGACTCGAAATGAGCATGAGATTATAT
** * ** *
11179192 TAAAGGAAGACTTGTGAGTCGGGATGAGTATGAGATTATATT
1 TAAAGGAAGACTCATGACTCGAAATGAGCATGAGATTATA-T
*
11179234 TAAAGGAAGACTTATGACTCG
1 TAAAGGAAGACTCATGACTCG
11179255 GTAGAGCATA
Statistics
Matches: 160, Mismatches: 22, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
39 1 0.01
40 30 0.19
41 107 0.67
42 22 0.14
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.26
Consensus pattern (41 bp):
TAAAGGAAGACTCATGACTCGAAATGAGCATGAGATTATAT
Found at i:11179195 original size:82 final size:82
Alignment explanation
Indices: 11179028--11179253 Score: 292
Period size: 82 Copynumber: 2.7 Consensus size: 82
11179018 ACTTGATGTA
* * * * *
11179028 TAAATGGAAGACTCATGTCTCGAGATGAGCATGAGATTATA-TAAAGGAAGACTCATGTCTTAAG
1 TAAA-GGAAGACTCGTGACTCGAGATGAGCATGAGATTATATTAAAGGAAGACTCATGACTCAAA
11179092 ATAAGCATGAGATTAAAT
65 ATAAGCATGAGATTAAAT
* * *
11179110 TAAAGGAAGACTCGTGACTCGAAATAAGCATGAGATTATATTAAAAGAAGACTCATGACTCAAAA
1 TAAAGGAAGACTCGTGACTCGAGATGAGCATGAGATTATATTAAAGGAAGACTCATGACTCAAAA
* *
11179175 TGAGCATGAGATTATAT
66 TAAGCATGAGATTAAAT
* * * * *
11179192 TAAAGGAAGACTTGTGAGTCGGGATGAGTATGAGATTATATTTAAAGGAAGACTTATGACTC
1 TAAAGGAAGACTCGTGACTCGAGATGAGCATGAGATTATA-TTAAAGGAAGACTCATGACTC
11179254 GGTAGAGCAT
Statistics
Matches: 124, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
81 32 0.26
82 73 0.59
83 19 0.15
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.27
Consensus pattern (82 bp):
TAAAGGAAGACTCGTGACTCGAGATGAGCATGAGATTATATTAAAGGAAGACTCATGACTCAAAA
TAAGCATGAGATTAAAT
Found at i:11179262 original size:82 final size:81
Alignment explanation
Indices: 11179028--11179283 Score: 275
Period size: 82 Copynumber: 3.1 Consensus size: 81
11179018 ACTTGATGTA
* * * *
11179028 TAAATGGAAGACTCATGTCTCGAGATGAGCATGAGATTATA-TAAAGGAAGACTCATGTCTTAAG
1 TAAA-GGAAGACTCGTGACTCGAGATGAGCATGAGATTATATTAAAGGAAGACTCATGAC-T-CG
*
11179092 ATA-AGCATGAGATTAAAT
63 ATAGAGCATGAGATTATAT
* * * * *
11179110 TAAAGGAAGACTCGTGACTCGAAATAAGCATGAGATTATATTAAAAGAAGACTCATGACTCAAAA
1 TAAAGGAAGACTCGTGACTCGAGATGAGCATGAGATTATATTAAAGGAAGACTCATGACTCGATA
11179175 TGAGCATGAGATTATAT
66 -GAGCATGAGATTATAT
* * * * * *
11179192 TAAAGGAAGACTTGTGAGTCGGGATGAGTATGAGATTATATTTAAAGGAAGACTTATGACTCGGT
1 TAAAGGAAGACTCGTGACTCGAGATGAGCATGAGATTATA-TTAAAGGAAGACTCATGACTCGAT
* *
11179257 AGAGCATAAGATTGT-T
65 AGAGCATGAGATTATAT
11179273 TAAAAGGAAGA
1 T-AAAGGAAGA
11179284 TCTACGACTC
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
80 2 0.01
81 35 0.24
82 89 0.61
83 20 0.14
ACGTcount: A:0.41, C:0.10, G:0.23, T:0.26
Consensus pattern (81 bp):
TAAAGGAAGACTCGTGACTCGAGATGAGCATGAGATTATATTAAAGGAAGACTCATGACTCGATA
GAGCATGAGATTATAT
Found at i:11179269 original size:41 final size:41
Alignment explanation
Indices: 11179028--11179283 Score: 248
Period size: 41 Copynumber: 6.2 Consensus size: 41
11179018 ACTTGATGTA
* *
11179028 TAAATGGAAGACTCATGTCTCGAGATGAGCATGAGATTATA-
1 TAAA-GGAAGACTCATGACTCGATATGAGCATGAGATTATAT
* ** * * *
11179069 TAAAGGAAGACTCATGTCTTAAGATAAGCATGAGATTAAAT
1 TAAAGGAAGACTCATGACTCGATATGAGCATGAGATTATAT
* * *
11179110 TAAAGGAAGACTCGTGACTCGAAATAAGCATGAGATTATAT
1 TAAAGGAAGACTCATGACTCGATATGAGCATGAGATTATAT
* * *
11179151 TAAAAGAAGACTCATGACTCAAAATGAGCATGAGATTATAT
1 TAAAGGAAGACTCATGACTCGATATGAGCATGAGATTATAT
** * ** *
11179192 TAAAGGAAGACTTGTGAGTCGGGATGAGTATGAGATTATATT
1 TAAAGGAAGACTCATGACTCGATATGAGCATGAGATTATA-T
* * * *
11179234 TAAAGGAAGACTTATGACTCGGTA-GAGCATAAGATTGT-T
1 TAAAGGAAGACTCATGACTCGATATGAGCATGAGATTATAT
11179273 TAAAAGGAAGA
1 T-AAAGGAAGA
11179284 TCTACGACTC
Statistics
Matches: 184, Mismatches: 28, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
39 2 0.01
40 41 0.22
41 119 0.65
42 22 0.12
ACGTcount: A:0.41, C:0.10, G:0.23, T:0.26
Consensus pattern (41 bp):
TAAAGGAAGACTCATGACTCGATATGAGCATGAGATTATAT
Found at i:11179269 original size:123 final size:121
Alignment explanation
Indices: 11179028--11179283 Score: 282
Period size: 123 Copynumber: 2.1 Consensus size: 121
11179018 ACTTGATGTA
* * * * * *
11179028 TAAATGGAAGACTCATGTCTCGAGATGAGCATGAGATTATATAAAGGAAGACTCATGTCTTAAGA
1 TAAAAGGAAGACTCATGACTCAAAATGAGCATGAGATTATATAAAGGAAGACTCATGACTCAAGA
* *
11179093 TAAGCATGAGATTAAATTAAAGGAAGACTCGTGACTCGAAATAAGCATGAGATTATAT
66 TAAGCATGAGATTAAATTAAAGGAAGACTCATGACTCG-AATAAGCATAAGATTAT-T
** * **
11179151 TAAAA-GAAGACTCATGACTCAAAATGAGCATGAGATTATATTAAAGGAAGACTTGTGAGTCGGG
1 TAAAAGGAAGACTCATGACTCAAAATGAGCATGAGATTATA-TAAAGGAAGACTCATGACTCAAG
* * * * * *
11179215 ATGAGTATGAGATTATATTTAAAGGAAGACTTATGACTCG-GTAGAGCATAAGATTGTT
65 ATAAGCATGAGATTA-AATTAAAGGAAGACTCATGACTCGAATA-AGCATAAGATTATT
11179273 TAAAAGGAAGA
1 TAAAAGGAAGA
11179284 TCTACGACTC
Statistics
Matches: 110, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
122 40 0.36
123 49 0.45
124 21 0.19
ACGTcount: A:0.41, C:0.10, G:0.23, T:0.26
Consensus pattern (121 bp):
TAAAAGGAAGACTCATGACTCAAAATGAGCATGAGATTATATAAAGGAAGACTCATGACTCAAGA
TAAGCATGAGATTAAATTAAAGGAAGACTCATGACTCGAATAAGCATAAGATTATT
Found at i:11194662 original size:18 final size:19
Alignment explanation
Indices: 11194636--11194674 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
11194626 ATTACTTTAT
*
11194636 AATTGTAAAATATAA-AAC
1 AATTATAAAATATAATAAC
11194654 AATTATAAAATATAATAAC
1 AATTATAAAATATAATAAC
11194673 AA
1 AA
11194675 ATAATAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (19 bp):
AATTATAAAATATAATAAC
Found at i:11194685 original size:19 final size:18
Alignment explanation
Indices: 11194641--11194682 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 18
11194631 TTTATAATTG
*
11194641 TAAAATATAAAACAATTA
1 TAAAATATAAAACAATAA
11194659 TAAAATATAATAACAAATAA
1 TAAAATATAA-AAC-AATAA
11194679 TAAA
1 TAAA
11194683 TATTTTATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.48
19 3 0.14
20 8 0.38
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (18 bp):
TAAAATATAAAACAATAA
Found at i:11197294 original size:21 final size:21
Alignment explanation
Indices: 11197268--11197307 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
11197258 TTCATTAAGT
11197268 TTTCATTT-AACTTTCATTTGG
1 TTTCATTTGAA-TTTCATTTGG
11197289 TTTCATTTGAATTTCATTT
1 TTTCATTTGAATTTCATTT
11197308 CGTGACACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.20, C:0.12, G:0.07, T:0.60
Consensus pattern (21 bp):
TTTCATTTGAATTTCATTTGG
Found at i:11202034 original size:26 final size:25
Alignment explanation
Indices: 11202005--11202075 Score: 65
Period size: 26 Copynumber: 2.7 Consensus size: 25
11201995 TGAAAAGCAT
*
11202005 TTTTTTCATAAATTTTGGAATTAT-AA
1 TTTTTT-ATAAATTTT-AAATTATGAA
*
11202031 TTTTATT-TATAATTTATAAATTTTGAA
1 TTTT-TTATA-AATTT-TAAATTATGAA
11202058 TTTTTTATAAATTTTAAA
1 TTTTTTATAAATTTTAAA
11202076 ATATTCCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
25 6 0.16
26 21 0.55
27 11 0.29
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (25 bp):
TTTTTTATAAATTTTAAATTATGAA
Found at i:11214779 original size:21 final size:23
Alignment explanation
Indices: 11214746--11214811 Score: 73
Period size: 21 Copynumber: 2.9 Consensus size: 23
11214736 AATATGTATC
11214746 TTTAATAATATTAAAATTATAATA-
1 TTTAA-AA-ATTAAAATTATAATAT
* * *
11214770 TTT-GAAATTAATATTTTAATAT
1 TTTAAAAATTAAAATTATAATAT
11214792 TTTAAAAATTAAAATTATAA
1 TTTAAAAATTAAAATTATAA
11214812 ATATATTATA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
21 13 0.38
22 5 0.15
23 13 0.38
24 3 0.09
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
TTTAAAAATTAAAATTATAATAT
Found at i:11215329 original size:23 final size:23
Alignment explanation
Indices: 11215294--11215355 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
11215284 AAAGGAGATT
* * *
11215294 AAGAGAAGGGGGAGAGAGAGGAG
1 AAGAGGAGAGGGAGAGAAAGGAG
11215317 AAGAGGAGAGGGAGAGGGAAAGGAG
1 AAGAGGAGAGGGAGA--GAAAGGAG
11215342 -AG-GGAGAGGGAGAG
1 AAGAGGAGAGGGAGAG
11215356 GGGGGAGAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 1 0.03
23 24 0.71
24 2 0.06
25 7 0.21
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (23 bp):
AAGAGGAGAGGGAGAGAAAGGAG
Found at i:11215332 original size:6 final size:6
Alignment explanation
Indices: 11215307--11215357 Score: 59
Period size: 6 Copynumber: 8.2 Consensus size: 6
11215297 AGAAGGGGGA
*
11215307 GAGAGAG GAGAAGAG GAGAGG GAGAGG GA-AAG GAGAGG GAGAGG GAGAGG
1 GAGAG-G GAG-AG-G GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG
11215357 G
1 G
11215358 GGGAGAGGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
5 4 0.10
6 24 0.60
7 5 0.12
8 7 0.17
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:11215344 original size:17 final size:17
Alignment explanation
Indices: 11215309--11215365 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
11215299 AAGGGGGAGA
11215309 GAGAGGAGAAGAGGAGAGG
1 GAGAGG-GAA-AGGAGAGG
11215328 GAGAGGGAAAGGAGAGG
1 GAGAGGGAAAGGAGAGG
*
11215345 GAGAGGGAGAGG-G-GG
1 GAGAGGGAAAGGAGAGG
11215360 GAGAGG
1 GAGAGG
11215366 AACAAAGGGA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
15 8 0.22
16 1 0.03
17 19 0.51
18 3 0.08
19 6 0.16
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (17 bp):
GAGAGGGAAAGGAGAGG
Found at i:11216619 original size:61 final size:61
Alignment explanation
Indices: 11216523--11216644 Score: 199
Period size: 61 Copynumber: 2.0 Consensus size: 61
11216513 CAGTGTTCAT
* * **
11216523 CTTTCTCTTGCTTTTTCCTCTTTGAGGATTGTGAAATAATTTACTTCTTCCTTTAAGACAA
1 CTTTCTCTTGCTTTTTCCTCTTTGAGAATTATGAAATAACATACTTCTTCCTTTAAGACAA
*
11216584 CTTTCTCTTGCTTTTTCCTCTTTGAGAATTATGAAATAGCATACTTCTTCCTTTAAGACAA
1 CTTTCTCTTGCTTTTTCCTCTTTGAGAATTATGAAATAACATACTTCTTCCTTTAAGACAA
11216645 ATAGCTAATG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 56 1.00
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.46
Consensus pattern (61 bp):
CTTTCTCTTGCTTTTTCCTCTTTGAGAATTATGAAATAACATACTTCTTCCTTTAAGACAA
Found at i:11218014 original size:5 final size:5
Alignment explanation
Indices: 11218004--11218028 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
11217994 AAGTTTCTAA
11218004 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
11218029 TTATACCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:11218639 original size:25 final size:25
Alignment explanation
Indices: 11218596--11218644 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
11218586 TTAATTTTTT
*
11218596 TAAAAAAAAAAACTTAAGTATCAAAA
1 TAAAAAAAAAAACTCAAGT-TCAAAA
*
11218622 TAAAAAAAAATA-TCAAGTTCAAA
1 TAAAAAAAAAAACTCAAGTTCAAA
11218645 TACCAAATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.24
25 5 0.24
26 11 0.52
ACGTcount: A:0.67, C:0.08, G:0.04, T:0.20
Consensus pattern (25 bp):
TAAAAAAAAAAACTCAAGTTCAAAA
Found at i:11218754 original size:56 final size:57
Alignment explanation
Indices: 11218600--11218766 Score: 187
Period size: 56 Copynumber: 2.9 Consensus size: 57
11218590 TTTTTTTAAA
* * *
11218600 AAAAAAAACTTAAGTATCAAAATAAAAAAAAATATCAAGTTCAAATACCAAATTGAGT
1 AAAAAAAATTTAAGTATC-AAATTAAAAAAAATATCAAATTCAAATACCAAATTGAGT
* * * * ** *
11218658 CAAAAAAAATTT-TGATATCAAATTAAAAAAAATGTAAAATTTAGGTGCCAAATTG-G-
1 -AAAAAAAATTTAAG-TATCAAATTAAAAAAAATATCAAATTCAAATACCAAATTGAGT
11218714 ATAAAAAAATTTAAGTATCAAATTAAAAAAAATATCAAATTCAAATACCAAAT
1 A-AAAAAAATTTAAGTATCAAATTAAAAAAAATATCAAATTCAAATACCAAAT
11218767 GTTATATTAA
Statistics
Matches: 88, Mismatches: 17, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
55 1 0.01
56 42 0.48
57 2 0.02
58 29 0.33
59 14 0.16
ACGTcount: A:0.58, C:0.09, G:0.07, T:0.26
Consensus pattern (57 bp):
AAAAAAAATTTAAGTATCAAATTAAAAAAAATATCAAATTCAAATACCAAATTGAGT
Found at i:11229103 original size:14 final size:16
Alignment explanation
Indices: 11229084--11229115 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
11229074 GGTTTTTTAT
11229084 AAAAA-TAA-TACAAA
1 AAAAATTAAGTACAAA
11229098 AAAAATTAAGTACAAA
1 AAAAATTAAGTACAAA
11229114 AA
1 AA
11229116 TGGTATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 3 0.19
16 8 0.50
ACGTcount: A:0.75, C:0.06, G:0.03, T:0.16
Consensus pattern (16 bp):
AAAAATTAAGTACAAA
Found at i:11234802 original size:27 final size:27
Alignment explanation
Indices: 11234772--11234829 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
11234762 TTTCCATTTA
11234772 ATATCAACTGTCTGTTCAGATAATATT
1 ATATCAACTGTCTGTTCAGATAATATT
11234799 ATATCAACTGTCTGTTCAGATAATATT
1 ATATCAACTGTCTGTTCAGATAATATT
11234826 ATAT
1 ATAT
11234830 GTATATATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.41
Consensus pattern (27 bp):
ATATCAACTGTCTGTTCAGATAATATT
Found at i:11240269 original size:304 final size:305
Alignment explanation
Indices: 11239705--11240289 Score: 754
Period size: 304 Copynumber: 1.9 Consensus size: 305
11239695 GAGGGGACTT
* *** *
11239705 TGAAAATGAAATGGATGTGTGAGGGTTGAAGGATTGAACCAACCCCATTTTATAAAAAGAAATAT
1 TGAAAATGAAATGGATGTATGAGGGTTGAAGGACCAAACCAACCCCATTTTATAAAAAGAAATAA
* *
11239770 TATTTTTATTAAATCTTTTTTAAATCTGAACAGATGGGTCACGTCCGATCAAAGGGGTTGTGGAT
66 TATTTTTATTAAATCTTTTTTAAATCTGAACAGATGGGTCACATCCGATCAAAGGGGTTGGGGA-
* *
11239835 TTATTTTTTTTATAAGCTGAAAAGTAAAAAAAAAAATTAGTGTCTTAAATTCTTTTCGAGTACGA
130 TTATTTTTTTTATAAGCTGAAAAGTAAAAAAAAAAACTAGTGTCTTAAATTCTCTTCGAGTACGA
* * * * * *
11239900 AAACACAGGCTCGTGATCAACGGGTTACATTTGCGTCAACCGTCAGGCTAGTGCCTTCGATGTGT
195 AAACACAGGCCCGTGATCAACGGGTCACATCTGCGTCAACCGTCAAGCTAGTGCCTCCAATGTGT
** *
11239965 CAGGAAGAGAAGGAAGGAAACCTGCCTTGCTGGGGTGAAAGGACCC
260 CAAAAAGAGAAGGAAGAAAACCTGCCTTGCTGGGGTGAAAGGACCC
* * *
11240011 TGAAAATGAATTGGATGTATGAGGGTTG-AGGACCAAACCAATCCCTTTTTATAGTAAAA-AAAT
1 TGAAAATGAAATGGATGTATGAGGGTTGAAGGACCAAACCAACCCCATTTTATA--AAAAGAAAT
* * *
11240074 AATA-TTTTGTTAAATC-TTTTTAAAGT-TGAACAGATGGGTCACATCCGGTCAAGGGGGTTGGG
64 AATATTTTTATTAAATCTTTTTTAAA-TCTGAACAGATGGGTCACATCCGATCAAAGGGGTTGGG
*
11240136 GA-TATTTATTTTT-TAAGCTGAAAAGTAAAAAAAATAATACTAGTGTTTTAAATTCTCTTCGAG
128 GATTATTT-TTTTTATAAGCTGAAAAGTAAAAAAAA-AA-ACTAGTGTCTTAAATTCTCTTCGAG
* ** * * * *
11240199 TATGAAAACAC-GAGCCCGTGATTGACGGGTCATATCTGTGTCAGCCGTCAAGCTGGTGCCTCCA
190 TACGAAAACACAG-GCCCGTGATCAACGGGTCACATCTGCGTCAACCGTCAAGCTAGTGCCTCCA
11240263 ATGTGTCAAAAAGAGAAGGAAGAAAAC
254 ATGTGTCAAAAAGAGAAGGAAGAAAAC
11240290 AATATTAAAC
Statistics
Matches: 240, Mismatches: 32, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
302 26 0.11
303 8 0.03
304 137 0.57
305 32 0.13
306 33 0.14
307 4 0.02
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (305 bp):
TGAAAATGAAATGGATGTATGAGGGTTGAAGGACCAAACCAACCCCATTTTATAAAAAGAAATAA
TATTTTTATTAAATCTTTTTTAAATCTGAACAGATGGGTCACATCCGATCAAAGGGGTTGGGGAT
TATTTTTTTTATAAGCTGAAAAGTAAAAAAAAAAACTAGTGTCTTAAATTCTCTTCGAGTACGAA
AACACAGGCCCGTGATCAACGGGTCACATCTGCGTCAACCGTCAAGCTAGTGCCTCCAATGTGTC
AAAAAGAGAAGGAAGAAAACCTGCCTTGCTGGGGTGAAAGGACCC
Found at i:11240670 original size:378 final size:370
Alignment explanation
Indices: 11240057--11240730 Score: 927
Period size: 378 Copynumber: 1.8 Consensus size: 370
11240047 ACCAATCCCT
* * * * * * *
11240057 TTTTATAGTAAAAAAATAATATTTTGTTAAATCTTTTTAAAGTTGAACAGATGGGTCACATCCGG
1 TTTTATAATAAAAAAACAATATTTTATTAAATCTTTTTAAAGCTGAACAAATGGATCACATCCGA
** *
11240122 TCAAGGGGGTTGGGGATATTTATTTTTTAAGCTGAAAAGTAAAAAAAATAATACTAGTGTTTTAA
66 TCAAAAGGGTTGGGGATATTTATTTTTTAAGCTGAAAAGTAAAAAAAATAAAACTAGTGTTTTAA
* * * * * * * *
11240187 ATTCTCTTCGAGTATGAAAACACGAGCCCGTGATTGACGGGTCATATCTGTGTCAGCCGTCAAGC
131 ATTCTCTTCGAGTACGAAAACACGAGCCCGTGATCGACAGATCACATCCGCGTCAACCGTCAAGC
* * * * *
11240252 TGGTGCCTCCAATGTGTCAAAAAGAGAAGGAAGAAAACAATATTAAACTAACTACTATTAATAAT
196 TGGTACCTCCAATGTATCAAAAAGAAAAGAAAGAAAACAATATTAAACTAACTACTATTAACAAT
11240317 ATTAATTTAAAAAAACAAAGGAAGAGAAGGAAAGAAACCTATCTTACTGGGGAAGAGGGGACTTT
261 ATTAA-TTAAAAAAACAAAGGAAGAGAAGGAAAGAAACCTATCTTACTGGGGAAGAGGGGACTTT
11240382 GAAAATGAAATTGGAGTATAGGGGTCGGGGGATCAAATCGACCTCC
325 GAAAATGAAATTGGAGTATAGGGGTCGGGGGATCAAATCGACCTCC
* *
11240428 TTTTATAATAAAAAAACAATGTCTTTATTAAATCTTTTTTAAAGCTGAACAAATGGATCGCATCC
1 TTTTATAATAAAAAAACAATAT-TTTATTAAATC-TTTTTAAAGCTGAACAAATGGATCACATCC
* *
11240493 GATCAAAAGGGTTGGGGATTTTTTTTTTAATTTTTTAAGTTGAAAAGT-AAAAAAATAAAACTAG
64 GATCAAAAGGGTTGGGGA-----TATTT-ATTTTTTAAGCTGAAAAGTAAAAAAAATAAAACTAG
* * *
11240557 TGTTTTAAATTCTTTTTGGGTACGAAAACACGAGCCCGTGATCGACAGATCACATCCGCGTCAAC
123 TGTTTTAAATTCTCTTCGAGTACGAAAACACGAGCCCGTGATCGACAGATCACATCCGCGTCAAC
* * ** * *
11240622 CGTCAGGCTGGTACCTCTAATGTATCAGGAAGAAAAGAAAGGAAACAATATTAAACTAACTATTA
188 CGTCAAGCTGGTACCTCCAATGTATCAAAAAGAAAAGAAAGAAAACAATATTAAACTAACTACTA
*
11240687 TTAACAATATTAATTAAAAAAACAAAGGAAGAGAAGGAAGGAAA
253 TTAACAATATTAATTAAAAAAACAAAGGAAGAGAAGGAAAGAAA
11240731 TCTCCCTTGC
Statistics
Matches: 258, Mismatches: 37, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
371 19 0.07
372 10 0.04
373 41 0.16
377 30 0.12
378 140 0.54
379 18 0.07
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (370 bp):
TTTTATAATAAAAAAACAATATTTTATTAAATCTTTTTAAAGCTGAACAAATGGATCACATCCGA
TCAAAAGGGTTGGGGATATTTATTTTTTAAGCTGAAAAGTAAAAAAAATAAAACTAGTGTTTTAA
ATTCTCTTCGAGTACGAAAACACGAGCCCGTGATCGACAGATCACATCCGCGTCAACCGTCAAGC
TGGTACCTCCAATGTATCAAAAAGAAAAGAAAGAAAACAATATTAAACTAACTACTATTAACAAT
ATTAATTAAAAAAACAAAGGAAGAGAAGGAAAGAAACCTATCTTACTGGGGAAGAGGGGACTTTG
AAAATGAAATTGGAGTATAGGGGTCGGGGGATCAAATCGACCTCC
Found at i:11242338 original size:22 final size:23
Alignment explanation
Indices: 11242310--11242353 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
11242300 AGATACATGG
11242310 ATTTAATTATGTT-ATTGTGTTA
1 ATTTAATTATGTTGATTGTGTTA
* *
11242332 ATTTAATTGTGTTGATTTTGTT
1 ATTTAATTATGTTGATTGTGTT
11242354 TATGCGTGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.23, C:0.00, G:0.16, T:0.61
Consensus pattern (23 bp):
ATTTAATTATGTTGATTGTGTTA
Found at i:11242604 original size:3 final size:3
Alignment explanation
Indices: 11242596--11242621 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
11242586 ATATATTGTA
11242596 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
11242622 ATTTAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:11243646 original size:16 final size:16
Alignment explanation
Indices: 11243622--11243657 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
11243612 TTTTGTTAGT
*
11243622 TGTTGCTTCTCATGAC
1 TGTTACTTCTCATGAC
*
11243638 TGTTACTTCTCATGGC
1 TGTTACTTCTCATGAC
11243654 TGTT
1 TGTT
11243658 GGTTTGGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.19, T:0.47
Consensus pattern (16 bp):
TGTTACTTCTCATGAC
Found at i:11243727 original size:19 final size:19
Alignment explanation
Indices: 11243703--11243744 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
11243693 AATGGTTACC
*
11243703 TTATGCAACTCTTGTGTGA
1 TTATGCAACTCTTGAGTGA
11243722 TTATGCAACTCTTGAGTGA
1 TTATGCAACTCTTGAGTGA
11243741 TTAT
1 TTAT
11243745 ACCAGTTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.24, C:0.14, G:0.19, T:0.43
Consensus pattern (19 bp):
TTATGCAACTCTTGAGTGA
Found at i:11245171 original size:11 final size:11
Alignment explanation
Indices: 11245135--11245180 Score: 58
Period size: 11 Copynumber: 4.1 Consensus size: 11
11245125 AGCATCCAAT
11245135 ATAAAGTCAAC
1 ATAAAGTCAAC
11245146 ATTAAAG-CAGAC
1 A-TAAAGTCA-AC
*
11245158 ATAAAGTCATC
1 ATAAAGTCAAC
11245169 ATAAAGTCAAC
1 ATAAAGTCAAC
11245180 A
1 A
11245181 AAACACAGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
11 20 0.67
12 10 0.33
ACGTcount: A:0.52, C:0.17, G:0.11, T:0.20
Consensus pattern (11 bp):
ATAAAGTCAAC
Found at i:11245260 original size:14 final size:14
Alignment explanation
Indices: 11245218--11245260 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
11245208 TTAGGGTATT
11245218 AAAAACAACATAC-
1 AAAAACAACATACA
* *
11245231 -AAAACAAAATAAA
1 AAAAACAACATACA
11245244 AAAAACAACATACA
1 AAAAACAACATACA
11245258 AAA
1 AAA
11245261 TAATATTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
12 10 0.42
14 14 0.58
ACGTcount: A:0.77, C:0.16, G:0.00, T:0.07
Consensus pattern (14 bp):
AAAAACAACATACA
Found at i:11247565 original size:12 final size:12
Alignment explanation
Indices: 11247536--11247574 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
11247526 CAAAAACCCT
*
11247536 AAATCAAAAATAA
1 AAATC-AAAATTA
*
11247549 AAATCAATATTA
1 AAATCAAAATTA
11247561 AAATCAAAATTA
1 AAATCAAAATTA
11247573 AA
1 AA
11247575 TAAACCCTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 18 0.78
13 5 0.22
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATCAAAATTA
Found at i:11247953 original size:21 final size:22
Alignment explanation
Indices: 11247917--11247963 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 22
11247907 GTTTGACCCT
*
11247917 TCAGCTAGTATTAACTTGTCACG
1 TCAGCTAG-ATTAACTTGCCACG
11247940 TCAGCTAG-TTAACTTGCCACG
1 TCAGCTAGATTAACTTGCCACG
11247961 TCA
1 TCA
11247964 TCATGCTCGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 15 0.65
23 8 0.35
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.32
Consensus pattern (22 bp):
TCAGCTAGATTAACTTGCCACG
Found at i:11256248 original size:6 final size:7
Alignment explanation
Indices: 11256231--11256257 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
11256221 AGACTATAAT
11256231 TTTTTTA
1 TTTTTTA
11256238 TTTTTTA
1 TTTTTTA
11256245 TTTTTTA
1 TTTTTTA
11256252 TTTTTT
1 TTTTTT
11256258 GAATATACTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTA
Found at i:11257150 original size:30 final size:29
Alignment explanation
Indices: 11257114--11257188 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 29
11257104 TTAAATTAAT
11257114 AATAATAAAATTACATTTTAATTCTTCAAA
1 AATAATAAAATTACATTTTAATT-TTCAAA
*
11257144 AATAATAAAAAATTA-A-TTTAATTTTTAAA
1 AATAAT--AAAATTACATTTTAATTTTCAAA
* *
11257173 AATTATAAAAATACAT
1 AATAATAAAATTACAT
11257189 ACTATAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
27 6 0.16
28 1 0.03
29 10 0.26
30 13 0.34
31 1 0.03
32 7 0.18
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (29 bp):
AATAATAAAATTACATTTTAATTTTCAAA
Found at i:11257508 original size:29 final size:27
Alignment explanation
Indices: 11257474--11257530 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
11257464 TATGGTTTTC
*
11257474 TATTTTCAAATATTAAACAATAAAAAAAT
1 TATTTTCAAA-AGTAAA-AATAAAAAAAT
**
11257503 TATTTTTTAAAGTAAAAATAAAAAAAT
1 TATTTTCAAAAGTAAAAATAAAAAAAT
11257530 T
1 T
11257531 TAAATCAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 12 0.48
28 5 0.20
29 8 0.32
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.37
Consensus pattern (27 bp):
TATTTTCAAAAGTAAAAATAAAAAAAT
Found at i:11259704 original size:17 final size:17
Alignment explanation
Indices: 11259684--11259735 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
11259674 ATTAATAATC
11259684 ACATTATAATAATTGAA
1 ACATTATAATAATTGAA
* *
11259701 ACA-T-TAATGA-T--C
1 ACATTATAATAATTGAA
11259713 ACATTATAATAATTGAA
1 ACATTATAATAATTGAA
11259730 ACATTA
1 ACATTA
11259736 ATTATCAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 10
0.65 0.10 0.25
Matches are distributed among these distances:
12 3 0.12
13 1 0.04
14 6 0.23
15 6 0.23
16 1 0.04
17 9 0.35
ACGTcount: A:0.50, C:0.10, G:0.06, T:0.35
Consensus pattern (17 bp):
ACATTATAATAATTGAA
Found at i:11259713 original size:29 final size:29
Alignment explanation
Indices: 11259646--11259742 Score: 140
Period size: 29 Copynumber: 3.3 Consensus size: 29
11259636 ATAACATCTC
* *
11259646 AATAATCAAATTATTATAAATTGACAACATT
1 AATAATCACATTATAAT-AATTGA-AACATT
11259677 AATAATCACATTATAATAATTGAAACATT
1 AATAATCACATTATAATAATTGAAACATT
*
11259706 AATGATCACATTATAATAATTGAAACATT
1 AATAATCACATTATAATAATTGAAACATT
*
11259735 AATTATCA
1 AATAATCA
11259743 AAACGAAAAC
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
29 41 0.66
30 6 0.10
31 15 0.24
ACGTcount: A:0.51, C:0.10, G:0.04, T:0.35
Consensus pattern (29 bp):
AATAATCACATTATAATAATTGAAACATT
Found at i:11259943 original size:18 final size:18
Alignment explanation
Indices: 11259922--11259958 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
11259912 AAATCGAATT
11259922 AATTCGGTTAATCGATCG
1 AATTCGGTTAATCGATCG
* *
11259940 AATTTGGTTAATTGATCG
1 AATTCGGTTAATCGATCG
11259958 A
1 A
11259959 TTAATTGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.38
Consensus pattern (18 bp):
AATTCGGTTAATCGATCG
Found at i:11268772 original size:20 final size:20
Alignment explanation
Indices: 11268747--11268798 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
11268737 GAACTCGTAA
11268747 CAAAATTTTTAAC-ATAAAAT
1 CAAAATTTTTAACGA-AAAAT
* *
11268767 CAAAATTTCTAACGAAATAT
1 CAAAATTTTTAACGAAAAAT
*
11268787 CAATATTTTTAA
1 CAAAATTTTTAA
11268799 TGATTATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.50, C:0.12, G:0.02, T:0.37
Consensus pattern (20 bp):
CAAAATTTTTAACGAAAAAT
Found at i:11269383 original size:21 final size:21
Alignment explanation
Indices: 11269343--11269383 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
11269333 TTTCTAATGC
* * *
11269343 AATACCAATATTTTTTATAAG
1 AATACCAAAATTTGTAATAAG
11269364 AATACCAAAATTTGTAATAA
1 AATACCAAAATTTGTAATAA
11269384 TAGCAAAATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.37
Consensus pattern (21 bp):
AATACCAAAATTTGTAATAAG
Found at i:11269390 original size:18 final size:18
Alignment explanation
Indices: 11269364--11269398 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11269354 TTTTTATAAG
*
11269364 AATACCAAAATTTGTAAT
1 AATACCAAAATCTGTAAT
*
11269382 AATAGCAAAATCTGTAA
1 AATACCAAAATCTGTAA
11269399 CGCCATACCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (18 bp):
AATACCAAAATCTGTAAT
Found at i:11269426 original size:20 final size:20
Alignment explanation
Indices: 11269332--11269426 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
11269322 TTATATCAAT
*
11269332 ATTTCTAATGCAATACCAATA
1 ATTTGTAATGCAATACCAA-A
* * *
11269353 TTTTTTATAAG-AATACCAAA
1 ATTTGTA-ATGCAATACCAAA
*
11269373 ATTTGTAAT--AATAGCAAA
1 ATTTGTAATGCAATACCAAA
* * *
11269391 ATCTGTAACGCCATACCAAA
1 ATTTGTAATGCAATACCAAA
11269411 ATTTGTAATGCAATAC
1 ATTTGTAATGCAATAC
11269427 GTTTATATTT
Statistics
Matches: 57, Mismatches: 14, Indels: 7
0.73 0.18 0.09
Matches are distributed among these distances:
18 15 0.26
19 1 0.02
20 26 0.46
21 13 0.23
22 2 0.04
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.33
Consensus pattern (20 bp):
ATTTGTAATGCAATACCAAA
Found at i:11274173 original size:11 final size:10
Alignment explanation
Indices: 11274158--11274200 Score: 50
Period size: 11 Copynumber: 4.0 Consensus size: 10
11274148 GTATTTTCGC
11274158 ATTTTTTTAT
1 ATTTTTTTAT
*
11274168 ATTTTTTCAT
1 ATTTTTTTAT
11274178 GATTTTTTTAT
1 -ATTTTTTTAT
11274189 ACTTTCTTTTAT
1 A-TTT-TTTTAT
11274201 TTCTAGTATG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 10 0.36
11 12 0.43
12 6 0.21
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.72
Consensus pattern (10 bp):
ATTTTTTTAT
Found at i:11274291 original size:22 final size:22
Alignment explanation
Indices: 11274266--11274316 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
11274256 CATTTTTTTA
*
11274266 ATATTCTCTCGC-AATTTTTGGT
1 ATATTCTCTC-CTAACTTTTGGT
*
11274288 ATATCCTCTCCTAACTTTTGGT
1 ATATTCTCTCCTAACTTTTGGT
*
11274310 ATTTTCT
1 ATATTCT
11274317 AGAATTTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.18, C:0.22, G:0.10, T:0.51
Consensus pattern (22 bp):
ATATTCTCTCCTAACTTTTGGT
Found at i:11274463 original size:20 final size:20
Alignment explanation
Indices: 11274438--11274480 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
11274428 TTTTTTTTAC
*
11274438 ATTCTCTC-ATAATTTATGGT
1 ATTCTCTCAAAAATTT-TGGT
11274458 ATTCTCTCAAAAATTTTGGT
1 ATTCTCTCAAAAATTTTGGT
11274478 ATT
1 ATT
11274481 TCCTTATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.28, C:0.14, G:0.09, T:0.49
Consensus pattern (20 bp):
ATTCTCTCAAAAATTTTGGT
Found at i:11274494 original size:20 final size:20
Alignment explanation
Indices: 11274448--11274519 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
11274438 ATTCTCTCAT
* *
11274448 AATTTATGGTATT-CTCTCAA
1 AATTTTTGGTATTAC-CTTAA
* * *
11274468 AAATTTTGGTATTTCCTTAT
1 AATTTTTGGTATTACCTTAA
**
11274488 AATTTTTTATATTACCTTAA
1 AATTTTTGGTATTACCTTAA
11274508 AATTTTTGGTAT
1 AATTTTTGGTAT
11274520 AGTTTCAAAA
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 39 0.98
21 1 0.03
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.53
Consensus pattern (20 bp):
AATTTTTGGTATTACCTTAA
Found at i:11274776 original size:20 final size:20
Alignment explanation
Indices: 11274721--11274779 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
11274711 AACTAATTTA
*
11274721 GTACACCTTCATAATTTTTG
1 GTACACTTTCATAATTTTTG
*** * *
11274741 GTATTTTTTTAAAATTTTTG
1 GTACACTTTCATAATTTTTG
11274761 GTACACTTTCATAATTTTT
1 GTACACTTTCATAATTTTT
11274780 TGTGTAGTCC
Statistics
Matches: 28, Mismatches: 11, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.08, T:0.54
Consensus pattern (20 bp):
GTACACTTTCATAATTTTTG
Found at i:11280011 original size:12 final size:13
Alignment explanation
Indices: 11279980--11280012 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
11279970 AACTCTATTT
11279980 TTTAGGATTAATA
1 TTTAGGATTAATA
*
11279993 TTTAGGATTATTA
1 TTTAGGATTAATA
11280006 -TTAGGAT
1 TTTAGGAT
11280013 ATTGTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.48
Consensus pattern (13 bp):
TTTAGGATTAATA
Found at i:11287320 original size:21 final size:21
Alignment explanation
Indices: 11287296--11287335 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
11287286 ATGATAACAA
*
11287296 TTTTGTTGAAAGTCTTTACTT
1 TTTTCTTGAAAGTCTTTACTT
*
11287317 TTTTCTTGAATGTCTTTAC
1 TTTTCTTGAAAGTCTTTAC
11287336 AAGGTCGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.12, G:0.12, T:0.57
Consensus pattern (21 bp):
TTTTCTTGAAAGTCTTTACTT
Found at i:11290434 original size:54 final size:54
Alignment explanation
Indices: 11290376--11290489 Score: 192
Period size: 54 Copynumber: 2.1 Consensus size: 54
11290366 AACACCAGTG
*
11290376 CAAAAACCACCGAAACAAGAGGAATCACCCGTAATAAGGGAACGATCTCCACCA
1 CAAAAACCACCGAAACAAGAGGAATCACCCGTAACAAGGGAACGATCTCCACCA
* *
11290430 CAAAAACCACCGGAACAAGAGGAATCACCTGTAACAAGGGAACGATCTCCACCA
1 CAAAAACCACCGAAACAAGAGGAATCACCCGTAACAAGGGAACGATCTCCACCA
*
11290484 CCAAAA
1 CAAAAA
11290490 TTGCCACCAC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.45, C:0.30, G:0.17, T:0.09
Consensus pattern (54 bp):
CAAAAACCACCGAAACAAGAGGAATCACCCGTAACAAGGGAACGATCTCCACCA
Found at i:11290515 original size:75 final size:75
Alignment explanation
Indices: 11290434--11290572 Score: 260
Period size: 75 Copynumber: 1.9 Consensus size: 75
11290424 CCACCACAAA
*
11290434 AACCACCGGAACAAGAGGAATCACCTGTAACAAGGGAACGATCTCCACCACCAAAATTGCCACCA
1 AACCACCGAAACAAGAGGAATCACCTGTAACAAGGGAACGATCTCCACCACCAAAATTGCCACCA
11290499 CCAGTGCCAG
66 CCAGTGCCAG
*
11290509 AACCACCGAAACAAGAGGAATCACCTGTAACAAGGGAACGATCTCCGCCACCAAAATTGCCACC
1 AACCACCGAAACAAGAGGAATCACCTGTAACAAGGGAACGATCTCCACCACCAAAATTGCCACC
11290573 CTAGTTGTTA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 62 1.00
ACGTcount: A:0.38, C:0.33, G:0.18, T:0.11
Consensus pattern (75 bp):
AACCACCGAAACAAGAGGAATCACCTGTAACAAGGGAACGATCTCCACCACCAAAATTGCCACCA
CCAGTGCCAG
Found at i:11290641 original size:24 final size:24
Alignment explanation
Indices: 11290609--11290688 Score: 99
Period size: 24 Copynumber: 3.3 Consensus size: 24
11290599 GGTCAATTCT
11290609 CCACCACCTCCGATTCATTCTCCA
1 CCACCACCTCCGATTCATTCTCCA
* *
11290633 CCACCACCTCCGGTTCATTCCCCA
1 CCACCACCTCCGATTCATTCTCCA
* * *
11290657 CCACCACCACC-AGTCCACTCTCCA
1 CCACCACCTCCGA-TTCATTCTCCA
11290681 CCACCACC
1 CCACCACC
11290689 ACCACCACCA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.21, C:0.56, G:0.05, T:0.17
Consensus pattern (24 bp):
CCACCACCTCCGATTCATTCTCCA
Found at i:11290666 original size:30 final size:29
Alignment explanation
Indices: 11290630--11290785 Score: 151
Period size: 30 Copynumber: 5.4 Consensus size: 29
11290620 GATTCATTCT
* *
11290630 CCACCACCACCTCCGGTTCATTCCCCACCA
1 CCACCACCACCTCCAGTCCA-TCCCCACCA
* *
11290660 CCACCACCA-GTCCACT-C-TCCACCACCA
1 CCACCACCACCTCCAGTCCATCC-CCACCA
* * *
11290687 CCACCACCACCACCAGTCCA--CTCTCCA
1 CCACCACCACCTCCAGTCCATCCCCACCA
* *
11290714 CCACCACCACTTCCAGTCCATTCTCCACCA
1 CCACCACCACCTCCAGTCCA-TCCCCACCA
*
11290744 CCACCACCACCTCCAGTCCACTCTCCACCA
1 CCACCACCACCTCCAGTCCA-TCCCCACCA
11290774 CCACCACCACCT
1 CCACCACCACCT
11290786 ATTCACTCTC
Statistics
Matches: 104, Mismatches: 15, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
26 3 0.03
27 37 0.36
28 6 0.06
29 5 0.05
30 53 0.51
ACGTcount: A:0.24, C:0.58, G:0.04, T:0.14
Consensus pattern (29 bp):
CCACCACCACCTCCAGTCCATCCCCACCA
Found at i:11290792 original size:27 final size:27
Alignment explanation
Indices: 11290630--11290806 Score: 164
Period size: 27 Copynumber: 6.3 Consensus size: 27
11290620 GATTCATTCT
* * *
11290630 CCACCACCACCTCCGGTTCA-T-TCC-
1 CCACCACCACCACCAGTCCACTCTCCA
11290654 CCACCACCACCACCAGTCCACTCTCCACCACCA
1 CCACCACCACCACCAGTCCACTCT------CCA
11290687 CCACCACCACCACCAGTCCACTCTCCA
1 CCACCACCACCACCAGTCCACTCTCCA
** *
11290714 CCACCACCACTTCCAGTCCATTCTCCA
1 CCACCACCACCACCAGTCCACTCTCCA
11290741 CCACCACCACCACCTCCAGTCCACTCTCCA
1 CCACCACCACCA---CCAGTCCACTCTCCA
* *
11290771 CCACCACCACCACCTA-TTCACTCTCCT
1 CCACCACCACCACC-AGTCCACTCTCCA
11290798 CCACCACCA
1 CCACCACCA
11290807 GTGCATTCTC
Statistics
Matches: 129, Mismatches: 11, Indels: 23
0.79 0.07 0.14
Matches are distributed among these distances:
24 17 0.13
25 1 0.01
26 1 0.01
27 57 0.44
28 1 0.01
30 26 0.20
32 2 0.02
33 24 0.19
ACGTcount: A:0.24, C:0.58, G:0.03, T:0.15
Consensus pattern (27 bp):
CCACCACCACCACCAGTCCACTCTCCA
Found at i:11290796 original size:57 final size:57
Alignment explanation
Indices: 11290630--11290806 Score: 218
Period size: 57 Copynumber: 3.1 Consensus size: 57
11290620 GATTCATTCT
* *
11290630 CCACCACCACCTCCGGTTCA-T-TCC-CCACCACCACCACCAGTCCACTCTCCACCACCA
1 CCACCACCACCTCCAGTCCACTCTCCACCACCACCACCACCAGTCCACTCT---CCACCA
* ** *
11290687 CCACCACCACCACCAGTCCACTCTCCACCACCACCACTTCCAGTCCATTCTCCACCA
1 CCACCACCACCTCCAGTCCACTCTCCACCACCACCACCACCAGTCCACTCTCCACCA
* *
11290744 CCACCACCACCTCCAGTCCACTCTCCACCACCACCACCACCTA-TTCACTCTCCTCCA
1 CCACCACCACCTCCAGTCCACTCTCCACCACCACCACCACC-AGTCCACTCTCCACCA
11290801 CCACCA
1 CCACCA
11290807 GTGCATTCTC
Statistics
Matches: 104, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
57 78 0.75
58 2 0.02
59 3 0.03
60 21 0.20
ACGTcount: A:0.24, C:0.58, G:0.03, T:0.15
Consensus pattern (57 bp):
CCACCACCACCTCCAGTCCACTCTCCACCACCACCACCACCAGTCCACTCTCCACCA
Found at i:11290800 original size:30 final size:29
Alignment explanation
Indices: 11290654--11290806 Score: 143
Period size: 30 Copynumber: 5.2 Consensus size: 29
11290644 GGTTCATTCC
*
11290654 CCACCACCACCACCAGTCCACTCTCCACCA
1 CCACCACCACCACCA-TCCACTCTCCTCCA
* *
11290684 CCACCACCACCACCA-CCAGTCCACTCTCCA
1 CCACCACCACCACCATCCACT-CTC-CTCCA
** * *
11290714 CCACCACCACTTCCAGTCCATTCTCCACCA
1 CCACCACCACCACCA-TCCACTCTCCTCCA
*
11290744 CCACCACCACCTCCAGTCCA--CT-CTCCA
1 CCACCACCACCACCA-TCCACTCTCCTCCA
*
11290771 CCACCACCACCACCTATTCACTCTCCTCCA
1 CCACCACCACCACC-ATCCACTCTCCTCCA
11290801 CCACCA
1 CCACCA
11290807 GTGCATTCTC
Statistics
Matches: 103, Mismatches: 12, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
27 20 0.19
28 7 0.07
29 4 0.04
30 66 0.64
31 2 0.02
32 4 0.04
ACGTcount: A:0.25, C:0.58, G:0.03, T:0.14
Consensus pattern (29 bp):
CCACCACCACCACCATCCACTCTCCTCCA
Found at i:11290804 original size:3 final size:3
Alignment explanation
Indices: 11290654--11290784 Score: 82
Period size: 3 Copynumber: 39.7 Consensus size: 3
11290644 GGTTCATTCC
*
11290654 CCA CCA CCA CCA CCA GTCCA CTCT CCA CCA CCA CCA CCA CCA CCA CCA
1 CCA CCA CCA CCA CCA --CCA C-CA CCA CCA CCA CCA CCA CCA CCA CCA
* ** * *
11290702 GTCCA CTCT CCA CCA CCA CCA CTT CCA GTCCA TTCT CCA CCA CCA CCA
1 --CCA C-CA CCA CCA CCA CCA CCA CCA --CCA -CCA CCA CCA CCA CCA
* *
11290750 CCA CCT CCA GTCCA CTCT CCA CCA CCA CCA CCA CC
1 CCA CCA CCA --CCA C-CA CCA CCA CCA CCA CCA CC
11290785 TATTCACTCT
Statistics
Matches: 101, Mismatches: 16, Indels: 22
0.73 0.12 0.16
Matches are distributed among these distances:
3 81 0.80
4 8 0.08
5 12 0.12
ACGTcount: A:0.25, C:0.60, G:0.03, T:0.12
Consensus pattern (3 bp):
CCA
Found at i:11292236 original size:18 final size:18
Alignment explanation
Indices: 11292213--11292248 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
11292203 AACGTACACA
*
11292213 CACCTTGCACACACAGGT
1 CACCTTGAACACACAGGT
11292231 CACCTTGAACACACAGGT
1 CACCTTGAACACACAGGT
11292249 GCTCGAACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.36, G:0.17, T:0.17
Consensus pattern (18 bp):
CACCTTGAACACACAGGT
Found at i:11293551 original size:26 final size:26
Alignment explanation
Indices: 11293517--11293578 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
11293507 AATAATACCA
*
11293517 TAAATATAATAAATATTTTATTATTT
1 TAAATATAATAAATATTTTATTATAT
* *
11293543 TAAAAATAATAAATATTTTATTGTAT
1 TAAATATAATAAATATTTTATTATAT
11293569 TAAATATAAT
1 TAAATATAAT
11293579 TTTAAAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (26 bp):
TAAATATAATAAATATTTTATTATAT
Found at i:11301945 original size:16 final size:16
Alignment explanation
Indices: 11301924--11301966 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
11301914 GTGAAAATTA
11301924 AATATTTTATTAAAAT
1 AATATTTTATTAAAAT
*
11301940 AATATTTTAATTAAGAT
1 AATATTTT-ATTAAAAT
*
11301957 CAT-TTTTATT
1 AATATTTTATT
11301967 TAATAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 3 0.12
16 12 0.50
17 9 0.38
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (16 bp):
AATATTTTATTAAAAT
Found at i:11319161 original size:52 final size:52
Alignment explanation
Indices: 11319047--11319147 Score: 141
Period size: 52 Copynumber: 1.9 Consensus size: 52
11319037 TAATAATCTG
* * *
11319047 AACAACATAATAACTAACTATTTAAAATTAAATAACTTAATAATATTTTCTT
1 AACATCATAATAACTAACGAATTAAAATTAAATAACTTAATAATATTTTCTT
* *
11319099 AACATCATAATAATTAACGAATTAAAATTAAATTA-TTAAATAATATTTT
1 AACATCATAATAACTAACGAATTAAAATTAAATAACTT-AATAATATTTT
11319148 TTACCATTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
51 2 0.05
52 41 0.95
ACGTcount: A:0.51, C:0.09, G:0.01, T:0.39
Consensus pattern (52 bp):
AACATCATAATAACTAACGAATTAAAATTAAATAACTTAATAATATTTTCTT
Found at i:11320443 original size:30 final size:31
Alignment explanation
Indices: 11320365--11320484 Score: 199
Period size: 31 Copynumber: 3.9 Consensus size: 31
11320355 TACTCAAATT
11320365 TGACACTTTTTTCTAATTTGATACCTAAACA
1 TGACACTTTTTTCTAATTTGATACCTAAACA
11320396 TGACACTTTTTTCTAATTTGATACCTAAACA
1 TGACACTTTTTTCTAATTTGATACCTAAACA
* *
11320427 TGATACTTTTTT-TAATTTGATACCTAAACT
1 TGACACTTTTTTCTAATTTGATACCTAAACA
11320457 TGACAC-TTTTTCTTAATTTGATACCTAA
1 TGACACTTTTTTC-TAATTTGATACCTAA
11320485 TATGTTTTTG
Statistics
Matches: 84, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
29 5 0.06
30 22 0.26
31 57 0.68
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.45
Consensus pattern (31 bp):
TGACACTTTTTTCTAATTTGATACCTAAACA
Found at i:11320449 original size:61 final size:62
Alignment explanation
Indices: 11320369--11320484 Score: 200
Period size: 61 Copynumber: 1.9 Consensus size: 62
11320359 CAAATTTGAC
11320369 ACTTTTTTCTAATTTGATACCTAAACATGACACTTTTT-TCTAATTTGATACCTAAACATGAT
1 ACTTTTTTCTAATTTGATACCTAAACATGACACTTTTTCT-TAATTTGATACCTAAACATGAT
*
11320431 ACTTTTTT-TAATTTGATACCTAAACTTGACACTTTTTCTTAATTTGATACCTAA
1 ACTTTTTTCTAATTTGATACCTAAACATGACACTTTTTCTTAATTTGATACCTAA
11320485 TATGTTTTTG
Statistics
Matches: 52, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
61 43 0.83
62 9 0.17
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.46
Consensus pattern (62 bp):
ACTTTTTTCTAATTTGATACCTAAACATGACACTTTTTCTTAATTTGATACCTAAACATGAT
Found at i:11320614 original size:89 final size:90
Alignment explanation
Indices: 11320431--11320624 Score: 227
Period size: 89 Copynumber: 2.2 Consensus size: 90
11320421 TAAACATGAT
* *
11320431 ACTTTTT-TTAATTTGATACCTAAACTTGACACTTTTTCTTAATTTGATACCTAATATGTTTTTG
1 ACTTTTTCCTAATTTGATACCTAAACTTGACACTTTTTCTTAAGTTGATACCTAATATGTTTTTG
*
11320495 GTCCAATTTAGTACTCAAATTTGAG
66 GTCCAATTTAGTACTCAAATTTGAC
* * * *
11320520 ACTTTTTCCTAATTTGATGCCTAAACTTGATACTTTTT-TTAAGTTGGTACTTAA-AT-TTTTTG
1 ACTTTTTCCTAATTTGATACCTAAACTTGACACTTTTTCTTAAGTTGATACCTAATATGTTTTT-
* *
11320582 GGATCCAATTTGGTAC-CTGAATTTGAC
65 GG-TCCAATTTAGTACTC-AAATTTGAC
* *
11320609 TCTTTTTTCTAATTTG
1 ACTTTTTCCTAATTTG
11320625 GTATCTAATC
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
87 5 0.06
88 5 0.06
89 53 0.59
90 27 0.30
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.48
Consensus pattern (90 bp):
ACTTTTTCCTAATTTGATACCTAAACTTGACACTTTTTCTTAAGTTGATACCTAATATGTTTTTG
GTCCAATTTAGTACTCAAATTTGAC
Found at i:11322541 original size:22 final size:25
Alignment explanation
Indices: 11322507--11322555 Score: 59
Period size: 22 Copynumber: 2.1 Consensus size: 25
11322497 AATAAAACAT
*
11322507 AAAATATGTATTATATTA-AAATAA
1 AAAATATGTATTAAATTATAAATAA
*
11322531 AAAATA-G-ATTAAATTATAAGTAA
1 AAAATATGTATTAAATTATAAATAA
11322554 AA
1 AA
11322556 TGGAATTAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 8 0.36
23 8 0.36
24 6 0.27
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (25 bp):
AAAATATGTATTAAATTATAAATAA
Found at i:11324870 original size:31 final size:31
Alignment explanation
Indices: 11324835--11324896 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
11324825 ATATATATGA
11324835 TAAAATTTAAACTTTTAATGTTACACATAAT
1 TAAAATTTAAACTTTTAATGTTACACATAAT
11324866 TAAAATTTAAACTTTTAATGTTACACATAAT
1 TAAAATTTAAACTTTTAATGTTACACATAAT
11324897 GTTTCAACCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (31 bp):
TAAAATTTAAACTTTTAATGTTACACATAAT
Found at i:11328175 original size:39 final size:39
Alignment explanation
Indices: 11328132--11328278 Score: 195
Period size: 39 Copynumber: 3.8 Consensus size: 39
11328122 ATTTCTTTGC
** * * *
11328132 AGTGTTTTTAGTGTCACTACTAGTTCAGTAGCATCTTGT
1 AGTGTTTACAGTGTCACTGCTAGTTCAGTAGCGTATTGT
* * *
11328171 AGTGTTTACAGTGCCACTGCCAGTTCAGTAGCGTATTGC
1 AGTGTTTACAGTGTCACTGCTAGTTCAGTAGCGTATTGT
*
11328210 AGTGTTTACAGTGTCACTGCTAGTTTAGTAGCGTATTGT
1 AGTGTTTACAGTGTCACTGCTAGTTCAGTAGCGTATTGT
* *
11328249 AGTGTTTACAGTGTCACTGCCAGTTTAGTA
1 AGTGTTTACAGTGTCACTGCTAGTTCAGTA
11328279 AATTGATAAC
Statistics
Matches: 95, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 95 1.00
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (39 bp):
AGTGTTTACAGTGTCACTGCTAGTTCAGTAGCGTATTGT
Found at i:11328211 original size:78 final size:78
Alignment explanation
Indices: 11328128--11328278 Score: 230
Period size: 78 Copynumber: 1.9 Consensus size: 78
11328118 CAGTATTTCT
** *
11328128 TTGCAGTGTTTTTAGTGTCACTACTAGTTCAGTAGCATCTTGTAGTGTTTACAGTGCCACTGCCA
1 TTGCAGTGTTTACAGTGTCACTACTAGTTCAGTAGCATATTGTAGTGTTTACAGTGCCACTGCCA
11328193 GTTCAGTAGCGTA
66 GTTCAGTAGCGTA
* * * *
11328206 TTGCAGTGTTTACAGTGTCACTGCTAGTTTAGTAGCGTATTGTAGTGTTTACAGTGTCACTGCCA
1 TTGCAGTGTTTACAGTGTCACTACTAGTTCAGTAGCATATTGTAGTGTTTACAGTGCCACTGCCA
*
11328271 GTTTAGTA
66 GTTCAGTA
11328279 AATTGATAAC
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
78 65 1.00
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (78 bp):
TTGCAGTGTTTACAGTGTCACTACTAGTTCAGTAGCATATTGTAGTGTTTACAGTGCCACTGCCA
GTTCAGTAGCGTA
Found at i:11328502 original size:73 final size:71
Alignment explanation
Indices: 11328368--11328564 Score: 218
Period size: 73 Copynumber: 2.7 Consensus size: 71
11328358 TCGTGTGTGT
* * *
11328368 CACACGATCTGGCACACGCCTGTGTGTCCAGGCTGTGTAACTCACTGTTTTTGTTCACACAAA-A
1 CACACGGTCT-GCACACGCCTGTGTGTCCAGGCCGTGTAACTCACTGTTTCTGTTCACACAAACA
* *
11328432 TGGTATGGG
65 --GAATGGC
* * * *
11328441 CACACGGTCTGCCACACGCCCGTGTGTCCAGCCCATGTAACTCACTGTTTCTGATT-TCACAAAC
1 CACACGGTCTG-CACACGCCTGTGTGTCCAGGCCGTGTAACTCACTGTTTCTG-TTCACACAAAC
*
11328505 AGAATGTC
64 AGAATGGC
* *
11328513 CACACGGTCCAGCACACGCCTGTGTGTCCAGGCCGTGTAACTCATTGTTTCT
1 CACACGGT-CTGCACACGCCTGTGTGTCCAGGCCGTGTAACTCACTGTTTCT
11328565 ATACTTTCAA
Statistics
Matches: 105, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
72 49 0.47
73 53 0.50
74 3 0.03
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.27
Consensus pattern (71 bp):
CACACGGTCTGCACACGCCTGTGTGTCCAGGCCGTGTAACTCACTGTTTCTGTTCACACAAACAG
AATGGC
Found at i:11328552 original size:72 final size:71
Alignment explanation
Indices: 11328379--11328564 Score: 214
Period size: 72 Copynumber: 2.6 Consensus size: 71
11328369 ACACGATCTG
* * * *
11328379 GCACACGCCTGTGTGTCCAGGCTGTGTAACTCACTGTTTTTGTTCACACAAAATGGTATGGGCAC
1 GCACACGCCTGTGTGTCCAGGCCGTGTAACTCACTGTTTCTGTTCACACAAAA-GGAATGGCCAC
*
11328444 ACGGTCT
65 ACGGTCA
* * * * *
11328451 GCCACACGCCCGTGTGTCCAGCCCATGTAACTCACTGTTTCTGATTTCACA-AACA-GAATGTCC
1 G-CACACGCCTGTGTGTCCAGGCCGTGTAACTCACTGTTTCTG--TTCACACAAAAGGAATGGCC
11328514 ACACGGTCCA
63 ACACGGT-CA
*
11328524 GCACACGCCTGTGTGTCCAGGCCGTGTAACTCATTGTTTCT
1 GCACACGCCTGTGTGTCCAGGCCGTGTAACTCACTGTTTCT
11328565 ATACTTTCAA
Statistics
Matches: 96, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
72 49 0.51
73 38 0.40
74 3 0.03
75 6 0.06
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.27
Consensus pattern (71 bp):
GCACACGCCTGTGTGTCCAGGCCGTGTAACTCACTGTTTCTGTTCACACAAAAGGAATGGCCACA
CGGTCA
Found at i:11339805 original size:12 final size:12
Alignment explanation
Indices: 11339784--11339812 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
11339774 GATATGAAGG
11339784 TTTT-GGAGTGT
1 TTTTGGGAGTGT
11339795 TTTTGGGAGTGT
1 TTTTGGGAGTGT
11339807 TTTTGG
1 TTTTGG
11339813 ATGCATGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.07, C:0.00, G:0.38, T:0.55
Consensus pattern (12 bp):
TTTTGGGAGTGT
Found at i:11346495 original size:20 final size:20
Alignment explanation
Indices: 11346470--11346508 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
11346460 CAGATACACT
11346470 ACTCCACCTCTCGATGCGAA
1 ACTCCACCTCTCGATGCGAA
11346490 ACTCCACCTCTCGATGCGA
1 ACTCCACCTCTCGATGCGA
11346509 GCAATGATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.41, G:0.15, T:0.21
Consensus pattern (20 bp):
ACTCCACCTCTCGATGCGAA
Found at i:11370135 original size:17 final size:16
Alignment explanation
Indices: 11370095--11370135 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
11370085 AAAATAGGGT
11370095 TTTATTTATTTTTCAA
1 TTTATTTATTTTTCAA
* *
11370111 TTTTTTTATTTTGTGAA
1 TTTATTTATTTT-TCAA
11370128 TTTATTTA
1 TTTATTTA
11370136 ATATGGTGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (16 bp):
TTTATTTATTTTTCAA
Found at i:11371250 original size:30 final size:30
Alignment explanation
Indices: 11371213--11371360 Score: 140
Period size: 30 Copynumber: 4.9 Consensus size: 30
11371203 CATTAAAATT
* *
11371213 GGGTCAAATTTGAATTTTTGGAAAGTTTAA
1 GGGTCAAATTTAAATTTTTAGAAAGTTTAA
* ** *
11371243 GGATCAAATCAAAATTTTTAGAAAG-TTAGG
1 GGGTCAAATTTAAATTTTTAGAAAGTTTA-A
* *
11371273 GGGTCAAATTCAAATTTTT-GAAAAGTTCAA
1 GGGTCAAATTTAAATTTTTAG-AAAGTTTAA
* *
11371303 GGGTTAAATTTGAATTTTTAGAAAGTTTAA
1 GGGTCAAATTTAAATTTTTAGAAAGTTTAA
**
11371333 GGGTCAAA-ACATAATTTTTAGAAAGTTT
1 GGGTCAAATTTA-AATTTTTAGAAAGTTT
11371361 GGAGTTAAAA
Statistics
Matches: 94, Mismatches: 19, Indels: 10
0.76 0.15 0.08
Matches are distributed among these distances:
29 4 0.04
30 87 0.93
31 3 0.03
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (30 bp):
GGGTCAAATTTAAATTTTTAGAAAGTTTAA
Found at i:11371289 original size:60 final size:60
Alignment explanation
Indices: 11371213--11371360 Score: 156
Period size: 60 Copynumber: 2.5 Consensus size: 60
11371203 CATTAAAATT
** *
11371213 GGGTCAAATTTGAATTTTTGGAAAGTTTAAGGATCAAATCAAAATTTTTAGAAAG-TTAGG
1 GGGTCAAATTCAAATTTTTGGAAAGTTTAAGGATCAAATCAAAATTTTTAGAAAGTTTA-A
* * * * ***
11371273 GGGTCAAATTCAAATTTTTGAAAAGTTCAAGGGTTAAATTTGAATTTTTAGAAAGTTTAA
1 GGGTCAAATTCAAATTTTTGGAAAGTTTAAGGATCAAATCAAAATTTTTAGAAAGTTTAA
* *
11371333 GGGTCAAA-ACATAATTTTTAGAAAGTTT
1 GGGTCAAATTCA-AATTTTTGGAAAGTTT
11371361 GGAGTTAAAA
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
59 2 0.03
60 67 0.93
61 3 0.04
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (60 bp):
GGGTCAAATTCAAATTTTTGGAAAGTTTAAGGATCAAATCAAAATTTTTAGAAAGTTTAA
Found at i:11371376 original size:29 final size:29
Alignment explanation
Indices: 11371315--11371379 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
11371305 GTTAAATTTG
*
11371315 AATTTTTAGAAAGTTTAAGGGTCAAAACAT
1 AATTTTTAGAAAGTTT-AGGGTAAAAACAT
11371345 AATTTTTAGAAAGTTT-GGAGTTAAAAAC-T
1 AATTTTTAGAAAGTTTAGG-G-TAAAAACAT
11371374 AATTTT
1 AATTTT
11371380 AAAATAAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
28 2 0.06
29 8 0.25
30 22 0.69
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.38
Consensus pattern (29 bp):
AATTTTTAGAAAGTTTAGGGTAAAAACAT
Found at i:11371657 original size:59 final size:59
Alignment explanation
Indices: 11371593--11371748 Score: 181
Period size: 59 Copynumber: 2.6 Consensus size: 59
11371583 CATTAAAATC
**
11371593 GGGTCAAATTTGAATATTTGAAAAGTTTAGGGATCAAATCAAAATTTTTAGAAAG-TTAG
1 GGGTCAAATTCAAATATTTGAAAAGTTTAGGG-TCAAATCAAAATTTTTAGAAAGTTTAG
* * ***
11371652 GGGTCAAATTCAAATTTTTGGAAAGTTTAGGGTCAAATTTGAATTTTTAGAAAGTTTAG
1 GGGTCAAATTCAAATATTTGAAAAGTTTAGGGTCAAATCAAAATTTTTAGAAAGTTTAG
* * *
11371711 GGGTCAAA-ACATAATTTTTGGAAAGTTTAGAGGTCAAA
1 GGGTCAAATTCA-AATATTTGAAAAGTTTAG-GGTCAAA
11371749 AAATAATTTT
Statistics
Matches: 86, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
58 21 0.24
59 58 0.67
60 7 0.08
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.35
Consensus pattern (59 bp):
GGGTCAAATTCAAATATTTGAAAAGTTTAGGGTCAAATCAAAATTTTTAGAAAGTTTAG
Found at i:11371660 original size:29 final size:30
Alignment explanation
Indices: 11371614--11371748 Score: 159
Period size: 29 Copynumber: 4.6 Consensus size: 30
11371604 GAATATTTGA
*
11371614 AAAGTTTAGGGATCAAATCAAAATTTTTAG
1 AAAGTTTAGGGGTCAAATCAAAATTTTTAG
*
11371644 AAAG-TTAGGGGTCAAATTC-AAATTTTTGG
1 AAAGTTTAGGGGTCAAA-TCAAAATTTTTAG
***
11371673 AAAGTTTA-GGGTCAAATTTGAATTTTTAG
1 AAAGTTTAGGGGTCAAATCAAAATTTTTAG
* * *
11371702 AAAGTTTAGGGGTCAAAACATAATTTTTGG
1 AAAGTTTAGGGGTCAAATCAAAATTTTTAG
*
11371732 AAAGTTTAGAGGTCAAA
1 AAAGTTTAGGGGTCAAA
11371749 AAATAATTTT
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
28 1 0.01
29 48 0.53
30 41 0.46
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.34
Consensus pattern (30 bp):
AAAGTTTAGGGGTCAAATCAAAATTTTTAG
Found at i:11371749 original size:30 final size:29
Alignment explanation
Indices: 11371609--11371758 Score: 144
Period size: 30 Copynumber: 5.1 Consensus size: 29
11371599 AATTTGAATA
* * *
11371609 TTTGAAAAGTTTAGGGATCAAATCAAAATT
1 TTTGGAAAGTTTAGGG-TCAAAACATAATT
* *
11371639 TTTAGAAAG-TTAGGGGTCAAATTCA-AATT
1 TTTGGAAAGTTTA-GGGTCAAA-ACATAATT
**
11371668 TTTGGAAAGTTTAGGGTC-AAATTTGAATT
1 TTTGGAAAGTTTAGGGTCAAAACAT-AATT
*
11371697 TTTAGAAAGTTTAGGGGTCAAAACATAATT
1 TTTGGAAAGTTTA-GGGTCAAAACATAATT
*
11371727 TTTGGAAAGTTTAGAGGTCAAAAAATAATT
1 TTTGGAAAGTTTAG-GGTCAAAACATAATT
11371757 TT
1 TT
11371759 AAAATAAAAC
Statistics
Matches: 101, Mismatches: 11, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
28 2 0.02
29 42 0.42
30 53 0.52
31 4 0.04
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (29 bp):
TTTGGAAAGTTTAGGGTCAAAACATAATT
Found at i:11371878 original size:379 final size:380
Alignment explanation
Indices: 11371155--11371909 Score: 1174
Period size: 379 Copynumber: 2.0 Consensus size: 380
11371145 CAAACAAATA
* * * *
11371155 AAATAATATACATATGCATATGCATATAAAAGGGATTTTAAAAAATTACATTAAAATTGGGTCAA
1 AAATAAAATACATATACATATGCATATAAAAGAGATTTTAAAAAATTACATTAAAATCGGGTCAA
* *
11371220 ATTTGAATTTTTGGAAAGTTTAAGGATCAAATCAAAATTTTTAGAAAGTTAGGGGGTCAAATTCA
66 ATTTGAATATTTGAAAAGTTTAAGGATCAAATCAAAATTTTTAGAAAGTTAGGGGGTCAAATTCA
*
11371285 AATTTTTGAAAAGTTCAAGGGTTAAATTTGAATTTTTAGAAAGTTTAAGGGTCAAAACATAATTT
131 AATTTTTGAAAAGTTCAAGGGTCAAATTTGAATTTTTAGAAAGTTTAAGGGTCAAAACATAATTT
* * * * *
11371350 TTAGAAAGTTTGGAGTTAAAAACTAATTTTAAAATAAAACAAGGGCTTCGTGGGCAATAAACCCA
196 TTAGAAAGTTTAGAGTCAAAAAATAATTTTAAAATAAAACAAGAGCTTCATGGGCAATAAACCCA
* * * * ** * *
11371415 AAAATCTTGATACGTGGTAGCCTCAGGGACACTTTTGGGTCAAGGACCAAATTGAAAATCGAGTG
261 AAAATCTTGACACATGGCAGCCTAAAAGACACTTTTGGGTCAAGGACCAAATTGAAAACCGAATG
* * *
11371480 AAATTATAGGGCCAAATTAAACATAACAAAAAATGGGGCAAAAGGATCTAATTGAC
326 AAATTATAGGACCAAATTAAAAATAACAAAAAA-GGGACAAAAGGATCTAATTGAC
11371536 AAATAAAATA-ATATACATATGCATATAAAAGAGATTTTAAAAAATTACATTAAAATCGGGTCAA
1 AAATAAAATACATATACATATGCATATAAAAGAGATTTTAAAAAATTACATTAAAATCGGGTCAA
*
11371600 ATTTGAATATTTGAAAAGTTTAGGGATCAAATCAAAATTTTTAGAAAGTTA-GGGGTCAAATTCA
66 ATTTGAATATTTGAAAAGTTTAAGGATCAAATCAAAATTTTTAGAAAGTTAGGGGGTCAAATTCA
* * *
11371664 AATTTTTGGAAAGTT-TAGGGTCAAATTTGAATTTTTAGAAAGTTTAGGGGTCAAAACATAATTT
131 AATTTTTGAAAAGTTCAAGGGTCAAATTTGAATTTTTAGAAAGTTTAAGGGTCAAAACATAATTT
* * *
11371728 TTGGAAAGTTTAGAGGTCAAAAAATAATTTTAAAATAAAACAAGAGCTTCATGGGTAATAAACCT
196 TTAGAAAGTTTAGA-GTCAAAAAATAATTTTAAAATAAAACAAGAGCTTCATGGGCAATAAACCC
* *
11371793 AAAAATCTTGACATATGGCAGCCTAAAAGACACTTTTGGGTCAAGGATCAAATTGAAAACCGAAT
260 AAAAATCTTGACACATGGCAGCCTAAAAGACACTTTTGGGTCAAGGACCAAATTGAAAACCGAAT
*
11371858 GAAATTATAGGACTAAATTAAAAATAACAAAAAAGGGACAAAAGGATCTAAT
325 GAAATTATAGGACCAAATTAAAAATAACAAAAAAGGGACAAAAGGATCTAAT
11371910 AGAAAAAAAT
Statistics
Matches: 340, Mismatches: 33, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
378 75 0.22
379 157 0.46
380 99 0.29
381 9 0.03
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.29
Consensus pattern (380 bp):
AAATAAAATACATATACATATGCATATAAAAGAGATTTTAAAAAATTACATTAAAATCGGGTCAA
ATTTGAATATTTGAAAAGTTTAAGGATCAAATCAAAATTTTTAGAAAGTTAGGGGGTCAAATTCA
AATTTTTGAAAAGTTCAAGGGTCAAATTTGAATTTTTAGAAAGTTTAAGGGTCAAAACATAATTT
TTAGAAAGTTTAGAGTCAAAAAATAATTTTAAAATAAAACAAGAGCTTCATGGGCAATAAACCCA
AAAATCTTGACACATGGCAGCCTAAAAGACACTTTTGGGTCAAGGACCAAATTGAAAACCGAATG
AAATTATAGGACCAAATTAAAAATAACAAAAAAGGGACAAAAGGATCTAATTGAC
Found at i:11372629 original size:14 final size:15
Alignment explanation
Indices: 11372602--11372635 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
11372592 TAGATTTTAA
*
11372602 GGTTTTGTTTTTTTG
1 GGTTTTGTTCTTTTG
11372617 GGTTTT-TTCTTTTG
1 GGTTTTGTTCTTTTG
11372631 GGTTT
1 GGTTT
11372636 GGGTTTGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.00, C:0.03, G:0.26, T:0.71
Consensus pattern (15 bp):
GGTTTTGTTCTTTTG
Found at i:11376893 original size:29 final size:28
Alignment explanation
Indices: 11376852--11376981 Score: 106
Period size: 29 Copynumber: 4.5 Consensus size: 28
11376842 CACAAATACA
*
11376852 TTCCTTTATCAGAGATCGTCATGAAGTTAT
1 TTCCTTTA-CAGAGATTGTCATGAAG-TAT
11376882 TTCCTTTACAGAGATTGTCAT-AGAG-AT
1 TTCCTTTACAGAGATTGTCATGA-AGTAT
* * ** *
11376909 TT-CTTTAACAGAGATAGCCACAAAAGTGT
1 TTCCTTT-ACAGAGATTGTCA-TGAAGTAT
*
11376938 TTCCTTGACAGAGATTGTCATAGAAGTAT
1 TTCCTTTACAGAGATTGTCAT-GAAGTAT
11376967 TT-CTTTAACAGAGAT
1 TTCCTTT-ACAGAGAT
11376982 AGCCACAAAG
Statistics
Matches: 80, Mismatches: 12, Indels: 17
0.73 0.11 0.16
Matches are distributed among these distances:
26 4 0.05
27 15 0.19
28 6 0.08
29 44 0.55
30 11 0.14
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (28 bp):
TTCCTTTACAGAGATTGTCATGAAGTAT
Found at i:11377039 original size:29 final size:30
Alignment explanation
Indices: 11376965--11377119 Score: 122
Period size: 29 Copynumber: 5.3 Consensus size: 30
11376955 TCATAGAAGT
* *
11376965 ATTT-CTTTAACAGAGATAGCCACAAAGGC
1 ATTTCCTTTAACAAAGATTGCCACAAAGGC
* * * * *
11376994 GTTTACTTT-GCAGAGATTGCCACAGAGGC
1 ATTTCCTTTAACAAAGATTGCCACAAAGGC
* * * *
11377023 CTTT-CTTTAACAAAGATTGCTATAAAGGT
1 ATTTCCTTTAACAAAGATTGCCACAAAGGC
* * * * *
11377052 GTTTCCTTT-ACAAACATTACCATAGAGGC
1 ATTTCCTTTAACAAAGATTGCCACAAAGGC
*
11377081 ATTT-CTTTAACAAAGATCGCCACAAAGGC
1 ATTTCCTTTAACAAAGATTGCCACAAAGGC
11377110 ATTTCCTTTA
1 ATTTCCTTTA
11377120 CATTCAGTAC
Statistics
Matches: 98, Mismatches: 23, Indels: 9
0.75 0.18 0.07
Matches are distributed among these distances:
28 8 0.08
29 77 0.79
30 13 0.13
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (30 bp):
ATTTCCTTTAACAAAGATTGCCACAAAGGC
Found at i:11377118 original size:58 final size:58
Alignment explanation
Indices: 11376881--11377121 Score: 270
Period size: 58 Copynumber: 4.2 Consensus size: 58
11376871 CATGAAGTTA
* * * *
11376881 TTTCCTTTACAGAGATTGTCATAGA-G-ATTTCTTTAACAGAGATAGCCACAAAAGTG
1 TTTCCTTTACAGAGATTGCCATAGAGGCATTTCTTTAACAAAGATAGCCACAAAGGCG
* * * * *
11376937 TTTCCTTGACAGAGATTGTCATAGAAGTATTTCTTTAACAGAGATAGCCACAAAGGCG
1 TTTCCTTTACAGAGATTGCCATAGAGGCATTTCTTTAACAAAGATAGCCACAAAGGCG
* * * * * * * *
11376995 TTTACTTTGCAGAGATTGCCACAGAGGCCTTTCTTTAACAAAGATTGCTATAAAGGTG
1 TTTCCTTTACAGAGATTGCCATAGAGGCATTTCTTTAACAAAGATAGCCACAAAGGCG
* * * * *
11377053 TTTCCTTTACAAACATTACCATAGAGGCATTTCTTTAACAAAGATCGCCACAAAGGCA
1 TTTCCTTTACAGAGATTGCCATAGAGGCATTTCTTTAACAAAGATAGCCACAAAGGCG
11377111 TTTCCTTTACA
1 TTTCCTTTACA
11377122 TTCAGTACTT
Statistics
Matches: 155, Mismatches: 28, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
56 24 0.15
57 1 0.01
58 130 0.84
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (58 bp):
TTTCCTTTACAGAGATTGCCATAGAGGCATTTCTTTAACAAAGATAGCCACAAAGGCG
Found at i:11377347 original size:87 final size:85
Alignment explanation
Indices: 11377173--11377351 Score: 191
Period size: 87 Copynumber: 2.1 Consensus size: 85
11377163 ACAAAAGCAT
* * *
11377173 TCTTTAAAAGGTTCACCATAAAAGCTTACATTTCTAGAGTTTTGCCACAAAGGCGTTTCCTAAAT
1 TCTTTAAAAGGTTCACCACAAAAGCTTACATTTCTAGAGTTTTGCCAAAAAGGCG-TTCCTAAAC
* * *
11377238 AGAGATCGCCACACAGATTTA
65 AAAAATCGCCACACAGACTTA
* * * *
11377259 TCATTTAAGAGGTTCACCACAAAGGCTTACCTTTCTAGAGTTTTGCCAAAAAGGTC-TTCCTTGA
1 TC-TTTAAAAGGTTCACCACAAAAGCTTACATTTCTAGAGTTTTGCCAAAAAGG-CGTTCC-TAA
* *
11377323 ACAAAAATCGTCACATA-ACCTTA
63 ACAAAAATCGCCACACAGA-CTTA
11377346 TCTTTA
1 TCTTTA
11377352 TTGATGTCTT
Statistics
Matches: 77, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
86 11 0.14
87 65 0.84
88 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (85 bp):
TCTTTAAAAGGTTCACCACAAAAGCTTACATTTCTAGAGTTTTGCCAAAAAGGCGTTCCTAAACA
AAAATCGCCACACAGACTTA
Found at i:11378929 original size:132 final size:133
Alignment explanation
Indices: 11378573--11378973 Score: 652
Period size: 132 Copynumber: 3.0 Consensus size: 133
11378563 TAAATATAAC
* *
11378573 ATATATAT-ATAT--ATATATA-TGGTTGGAAATAAATAAATAAATGCTTTTT-TCCATGTGAAT
1 ATATATATGATATGCATATTTAGTGGCTGGAAATAAATAAATAAATGCTTTTTGT-CATGTGAAT
11378633 TATATTGAACATTTTGGATTGTTGAAATGAGTTGAATACAAAGGATTAATGAAAGATTTGAATTT
65 TATATTGAACATTTTGGATTGTTGAAATGAGTTGAATACAAAGGATTAATGAAAGATTTGAA-TT
*
11378698 ATATAT
129 GT-TAT
* * * *
11378704 ATATATATTATATGCATATTTGGTGGCTGGAAATAAATAAATAAATTCTTTTTGCCATGTGAATT
1 ATATATATGATATGCATATTTAGTGGCTGGAAATAAATAAATAAATGCTTTTTGTCATGTGAATT
*
11378769 ATATTGAACATTTTGGATTGTTGAAATGAGTTGAATACAAAAGATTAATGAAAGATTTGAATTGT
66 ATATTGAACATTTTGGATTGTTGAAATGAGTTGAATACAAAGGATTAATGAAAGATTTGAATTGT
11378834 TAT
131 TAT
11378837 ATATAT-TGATATGCATATTTAGTGGCTGGAAATAAATAAATAAATGCTTTTTGTCATGTGAATT
1 ATATATATGATATGCATATTTAGTGGCTGGAAATAAATAAATAAATGCTTTTTGTCATGTGAATT
*
11378901 ATATTGAACATTTTGGATTGTTGAAATGAGTTGAATACAAAGGATTAATAAAAGATTTGAATTGT
66 ATATTGAACATTTTGGATTGTTGAAATGAGTTGAATACAAAGGATTAATGAAAGATTTGAATTGT
11378966 TAT
131 TAT
11378969 ATATA
1 ATATA
11378974 GAGAGAGCAA
Statistics
Matches: 252, Mismatches: 13, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
131 8 0.03
132 129 0.51
133 9 0.04
134 8 0.03
135 98 0.39
ACGTcount: A:0.39, C:0.04, G:0.17, T:0.40
Consensus pattern (133 bp):
ATATATATGATATGCATATTTAGTGGCTGGAAATAAATAAATAAATGCTTTTTGTCATGTGAATT
ATATTGAACATTTTGGATTGTTGAAATGAGTTGAATACAAAGGATTAATGAAAGATTTGAATTGT
TAT
Found at i:11379608 original size:102 final size:102
Alignment explanation
Indices: 11379349--11379618 Score: 319
Period size: 102 Copynumber: 2.6 Consensus size: 102
11379339 ACGGATTATT
* * * *
11379349 CGTTGGTTAATCCAACTAGAGTTGGGATCACATAACGCGGTTTATCCGCTAGGCACTGGGTGTCA
1 CGTTGGTTAATCCAACTAGAGCTGGGCTCACATAACGCGGTTTATCTGCTAGGCACTGGGTGCCA
* * *
11379414 TAACCGTCGGTTTATCCGACTAGCGTTGGGCACAAAC
66 TAACCATCAGTTTATCCAACTAGCGTTGGGCACAAAC
* * * **
11379451 CGTAGGTTAATCCAA-TCAGAGCTAGGCTCACATATCGTTGTTTATCTGCTAGGCACTGGGTGCC
1 CGTTGGTTAATCCAACT-AGAGCTGGGCTCACATAACGCGGTTTATCTGCTAGGCACTGGGTGCC
* *
11379515 ATAACCATCAGTTTATTCAACTAGC-TCTGGGCGCAAAC
65 ATAACCATCAGTTTATCCAACTAGCGT-TGGGCACAAAC
* * * * * **
11379553 CGTTGGATAATCCAACTAGAGCTGGGCTCACATACCGCGGTATATTTGCTTGGCACCAGGTGCCA
1 CGTTGGTTAATCCAACTAGAGCTGGGCTCACATAACGCGGTTTATCTGCTAGGCACTGGGTGCCA
11379618 T
66 T
11379619 GAATTAACGG
Statistics
Matches: 140, Mismatches: 25, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
101 2 0.01
102 137 0.98
103 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (102 bp):
CGTTGGTTAATCCAACTAGAGCTGGGCTCACATAACGCGGTTTATCTGCTAGGCACTGGGTGCCA
TAACCATCAGTTTATCCAACTAGCGTTGGGCACAAAC
Found at i:11389261 original size:20 final size:21
Alignment explanation
Indices: 11389224--11389262 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
11389214 AATTCATTTG
* *
11389224 ATATTTGTAAATATATATTAA
1 ATATTTGTAAAAACATATTAA
11389245 ATATTT-TAAAAACATATT
1 ATATTTGTAAAAACATATT
11389263 GATAAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (21 bp):
ATATTTGTAAAAACATATTAA
Found at i:11390326 original size:26 final size:26
Alignment explanation
Indices: 11390297--11390391 Score: 95
Period size: 26 Copynumber: 3.5 Consensus size: 26
11390287 TAAATTATAT
11390297 ATTATTTTATTAAATTATATTTAATA
1 ATTATTTTATTAAATTATATTTAATA
* * * *
11390323 ATTATGTTAATATATAATTA-AATTATTT
1 ATTAT-TTTAT-TA-AATTATATTTAATA
11390351 ATTATTTTTATTAAATTATATTTAATA
1 ATTA-TTTTATTAAATTATATTTAATA
11390378 A-TATTATTATTAAA
1 ATTATT-TTATTAAA
11390392 ATTTAATAAC
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
25 2 0.04
26 20 0.36
27 12 0.22
28 15 0.27
29 6 0.11
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (26 bp):
ATTATTTTATTAAATTATATTTAATA
Found at i:11392587 original size:17 final size:18
Alignment explanation
Indices: 11392556--11392589 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
11392546 AACAAATAAC
*
11392556 TTAAAAACTATAAAATAT
1 TTAAAAACTAAAAAATAT
11392574 TTAAAAA-TAAAAAATA
1 TTAAAAACTAAAAAATA
11392590 AGACATAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
TTAAAAACTAAAAAATAT
Found at i:11392822 original size:16 final size:18
Alignment explanation
Indices: 11392791--11392826 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
11392781 TATATATTTA
11392791 AATTTATTACATTTTTTG
1 AATTTATTACATTTTTTG
11392809 AATTT-TTA-ATTTTTTG
1 AATTTATTACATTTTTTG
11392825 AA
1 AA
11392827 ATATTGTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 3 0.17
18 5 0.28
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.61
Consensus pattern (18 bp):
AATTTATTACATTTTTTG
Found at i:11393318 original size:37 final size:37
Alignment explanation
Indices: 11393258--11393338 Score: 126
Period size: 37 Copynumber: 2.2 Consensus size: 37
11393248 ATTCTGTAGA
* *
11393258 GTCTGTGGCTAGATCCCGGATTGACTGCTGATGGTCAT
1 GTCT-TGGCAAGATCCCGGATTGACTGCTGACGGTCAT
*
11393296 GTCTTGGCAAGATCTCGGATTGACTGCTGACGGTCAT
1 GTCTTGGCAAGATCCCGGATTGACTGCTGACGGTCAT
11393333 GTCTTG
1 GTCTTG
11393339 TTGATCGAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
37 36 0.90
38 4 0.10
ACGTcount: A:0.16, C:0.21, G:0.31, T:0.32
Consensus pattern (37 bp):
GTCTTGGCAAGATCCCGGATTGACTGCTGACGGTCAT
Found at i:11397189 original size:14 final size:14
Alignment explanation
Indices: 11397170--11397214 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
11397160 CAGTAAATAA
11397170 TTTTAAAATTATTT
1 TTTTAAAATTATTT
**
11397184 TTTTAAAATATAAAAT
1 TTTTAAAAT-T-ATTT
11397200 TTTTAAAATTATTT
1 TTTTAAAATTATTT
11397214 T
1 T
11397215 AATATTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 2 0.08
16 11 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTTAAAATTATTT
Found at i:11397975 original size:99 final size:98
Alignment explanation
Indices: 11397811--11398004 Score: 289
Period size: 99 Copynumber: 2.0 Consensus size: 98
11397801 TTCCTAAGAA
* * * * **
11397811 ATGAGATTGAAATAGAGAACCTTGAAGGTTAAGAGAATGATGGAAGAAGAATAAGTGATGGTTTG
1 ATGAGATTAAAATAGAGAACCTTGAAGGTTAAGAGAACGATGGAAGAAAAAGAAGCCATGGTTTG
*
11397876 ATTCAAAATCCAAGTGGAGAAGTAACCATGATT
66 ATTCAAAATCCAAGTAGAGAAGTAACCATGATT
**
11397909 ATGAGATTAAAATAGAGAACCTTGAAAGGTTGGGAGAACGATGGAAGAAAAAGAAGCCATGGTTT
1 ATGAGATTAAAATAGAGAACCTTG-AAGGTTAAGAGAACGATGGAAGAAAAAGAAGCCATGGTTT
*
11397974 GATTCAAAATCCAAGTAGAGAAGTAGCCATG
65 GATTCAAAATCCAAGTAGAGAAGTAACCATG
11398005 GTTTGGTTCA
Statistics
Matches: 85, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
98 23 0.27
99 62 0.73
ACGTcount: A:0.42, C:0.09, G:0.27, T:0.22
Consensus pattern (98 bp):
ATGAGATTAAAATAGAGAACCTTGAAGGTTAAGAGAACGATGGAAGAAAAAGAAGCCATGGTTTG
ATTCAAAATCCAAGTAGAGAAGTAACCATGATT
Found at i:11398158 original size:11 final size:10
Alignment explanation
Indices: 11398127--11398171 Score: 58
Period size: 9 Copynumber: 4.6 Consensus size: 10
11398117 ATTAAAATTA
11398127 TTTAAA-AAT
1 TTTAAATAAT
*
11398136 TTTAATTAAT
1 TTTAAATAAT
11398146 TTTAAAATAAT
1 TTT-AAATAAT
11398157 TTT-AATAAT
1 TTTAAATAAT
11398166 TTTAAA
1 TTTAAA
11398172 ATCATTTGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
9 14 0.45
10 8 0.26
11 9 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
TTTAAATAAT
Found at i:11398167 original size:20 final size:21
Alignment explanation
Indices: 11398133--11398178 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
11398123 ATTATTTAAA
11398133 AATTTTAATTAATTTTAAAAT
1 AATTTTAATTAATTTTAAAAT
11398154 AATTTTAA-TAATTTTAAAAT
1 AATTTTAATTAATTTTAAAAT
*
11398174 CATTT
1 AATTT
11398179 GTTGACATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
AATTTTAATTAATTTTAAAAT
Found at i:11398178 original size:11 final size:11
Alignment explanation
Indices: 11398133--11398178 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
11398123 ATTATTTAAA
*
11398133 AATTTT-AATT
1 AATTTTAAAAT
11398143 AATTTTAAAAT
1 AATTTTAAAAT
11398154 AATTTT--AAT
1 AATTTTAAAAT
11398163 AATTTTAAAAT
1 AATTTTAAAAT
*
11398174 CATTT
1 AATTT
11398179 GTTGACATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
9 9 0.29
10 6 0.19
11 16 0.52
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (11 bp):
AATTTTAAAAT
Found at i:11401198 original size:42 final size:42
Alignment explanation
Indices: 11401152--11401265 Score: 122
Period size: 42 Copynumber: 2.7 Consensus size: 42
11401142 ACGCGCATAA
* * * * *
11401152 TGCATCATTGGATAAATCGAAA-CAATCATACTGACATGTAAG
1 TGCATCATTGGATAAA-CCAAAGAAAACATACTAACACGTAAG
* **
11401194 TGCATCATCGGATGTACCAAAGAAAACATACTAACACGTAAG
1 TGCATCATTGGATAAACCAAAGAAAACATACTAACACGTAAG
* *
11401236 TGCATCATTGGATATACCAAAAAAAACATA
1 TGCATCATTGGATAAACCAAAGAAAACATA
11401266 TTGGCACGTA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 4 0.07
42 56 0.93
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.23
Consensus pattern (42 bp):
TGCATCATTGGATAAACCAAAGAAAACATACTAACACGTAAG
Found at i:11401274 original size:42 final size:42
Alignment explanation
Indices: 11401178--11401295 Score: 146
Period size: 42 Copynumber: 2.8 Consensus size: 42
11401168 TCGAAACAAT
* * *
11401178 CATACTGACATGTAAGTGCATCATCGGATGTACCAAAGAAAA
1 CATACTGACACGTAAGTGCATCATCGGATATACCAAAAAAAA
* *
11401220 CATACTAACACGTAAGTGCATCATTGGATATACCAAAAAAAA
1 CATACTGACACGTAAGTGCATCATCGGATATACCAAAAAAAA
* * * * *
11401262 CATATTGGCACGTAACTACATCATCAGATATACC
1 CATACTGACACGTAAGTGCATCATCGGATATACC
11401296 GAAACAATAC
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.42, C:0.21, G:0.14, T:0.23
Consensus pattern (42 bp):
CATACTGACACGTAAGTGCATCATCGGATATACCAAAAAAAA
Found at i:11401324 original size:42 final size:42
Alignment explanation
Indices: 11401178--11401324 Score: 143
Period size: 42 Copynumber: 3.5 Consensus size: 42
11401168 TCGAAACAAT
* * * * *
11401178 CATACTGACATGTAAGTGCATCATCGGATGTACCAAAGAAAA
1 CATACTAACACGTAAGTACATCATCGGATATACCAAAAAAAA
* *
11401220 CATACTAACACGTAAGTGCATCATTGGATATACCAAAAAAAA
1 CATACTAACACGTAAGTACATCATCGGATATACCAAAAAAAA
* ** * * * *
11401262 CATATTGGCACGTAACTACATCATCAGATATACCGAAACAATA
1 CATACTAACACGTAAGTACATCATCGGATATACC-AAAAAAAA
*
11401305 C-TACTAACACATAAGTACAT
1 CATACTAACACGTAAGTACAT
11401325 TATTGGCTAA
Statistics
Matches: 85, Mismatches: 19, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
42 78 0.92
43 7 0.08
ACGTcount: A:0.44, C:0.21, G:0.13, T:0.22
Consensus pattern (42 bp):
CATACTAACACGTAAGTACATCATCGGATATACCAAAAAAAA
Found at i:11407282 original size:22 final size:21
Alignment explanation
Indices: 11407257--11407305 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
11407247 TTTATATTGT
11407257 AATATATGAAATATAAATTTTA
1 AATATATGAAAT-TAAATTTTA
* *
11407279 AATATTTTTAAATTAAATTTTA
1 AATA-TATGAAATTAAATTTTA
11407301 AATAT
1 AATAT
11407306 TTTTAAGCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 17 0.71
23 6 0.25
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
AATATATGAAATTAAATTTTA
Found at i:11407309 original size:23 final size:23
Alignment explanation
Indices: 11407265--11407311 Score: 87
Period size: 22 Copynumber: 2.1 Consensus size: 23
11407255 GTAATATATG
11407265 AAATATAAATTTTAAATATTTTT
1 AAATATAAATTTTAAATATTTTT
11407288 AAAT-TAAATTTTAAATATTTTT
1 AAATATAAATTTTAAATATTTTT
11407310 AA
1 AA
11407312 GCAATTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AAATATAAATTTTAAATATTTTT
Found at i:11414776 original size:15 final size:15
Alignment explanation
Indices: 11414734--11414776 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
11414724 CATGTTAACT
*
11414734 TAAATGATTAAAATA
1 TAAATAATTAAAATA
* *
11414749 T-AATATTTTAAATA
1 TAAATAATTAAAATA
11414763 TAAATAATTAAAAT
1 TAAATAATTAAAAT
11414777 GTAACTTGAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
TAAATAATTAAAATA
Found at i:11417938 original size:2 final size:2
Alignment explanation
Indices: 11417931--11417999 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
11417921 ATGATTTGAT
11417931 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
11417973 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
11418000 GTTCCCACAC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:11419949 original size:21 final size:23
Alignment explanation
Indices: 11419925--11419966 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
11419915 TTGTTCAAAC
11419925 TCTTTC-TTTTTT-CTTTTTTTT
1 TCTTTCTTTTTTTGCTTTTTTTT
11419946 TCTTTCTTTTTTTGCTTTTTT
1 TCTTTCTTTTTTTGCTTTTTT
11419967 AACTCTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.32
22 6 0.32
23 7 0.37
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.83
Consensus pattern (23 bp):
TCTTTCTTTTTTTGCTTTTTTTT
Found at i:11426253 original size:64 final size:64
Alignment explanation
Indices: 11426177--11426305 Score: 258
Period size: 64 Copynumber: 2.0 Consensus size: 64
11426167 CAATCATGCA
11426177 TACTTACTAATCAATCATCCCCTTACTTAACTTATGCTTGTCCTCACGCATATTTTATAAGAAC
1 TACTTACTAATCAATCATCCCCTTACTTAACTTATGCTTGTCCTCACGCATATTTTATAAGAAC
11426241 TACTTACTAATCAATCATCCCCTTACTTAACTTATGCTTGTCCTCACGCATATTTTATAAGAAC
1 TACTTACTAATCAATCATCCCCTTACTTAACTTATGCTTGTCCTCACGCATATTTTATAAGAAC
11426305 T
1 T
11426306 GAAGTACAGT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.38
Consensus pattern (64 bp):
TACTTACTAATCAATCATCCCCTTACTTAACTTATGCTTGTCCTCACGCATATTTTATAAGAAC
Found at i:11433697 original size:25 final size:25
Alignment explanation
Indices: 11433663--11433754 Score: 121
Period size: 25 Copynumber: 3.7 Consensus size: 25
11433653 ATAGAGTTTA
* *
11433663 GCTCTTACGAGTCAGTCAAAACATC
1 GCTCTTACGAGCCAGTCAAAATATC
* * *
11433688 GCTCTTACGAGCTAGACAAATTATC
1 GCTCTTACGAGCCAGTCAAAATATC
* *
11433713 GCTCTTACGAGCCAGGCAGAATATC
1 GCTCTTACGAGCCAGTCAAAATATC
11433738 GCTCTTACGAGCCAGTC
1 GCTCTTACGAGCCAGTC
11433755 TTCAGTTAAT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 57 1.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (25 bp):
GCTCTTACGAGCCAGTCAAAATATC
Found at i:11439778 original size:17 final size:17
Alignment explanation
Indices: 11439737--11439793 Score: 50
Period size: 16 Copynumber: 3.5 Consensus size: 17
11439727 AAGAAAAAAA
11439737 AATATTTTTCATCCTTCT
1 AATA-TTTTCATCCTTCT
*
11439755 AGT-TTTTCATCCCTTC-
1 AATATTTTCAT-CCTTCT
*
11439771 AATATTTT-ATTCTTCT
1 AATATTTTCATCCTTCT
11439787 AAT-TTTT
1 AATATTTT
11439794 TTTTCACTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
15 8 0.24
16 14 0.42
17 9 0.27
18 2 0.06
ACGTcount: A:0.21, C:0.19, G:0.02, T:0.58
Consensus pattern (17 bp):
AATATTTTCATCCTTCT
Found at i:11440932 original size:16 final size:15
Alignment explanation
Indices: 11440907--11440944 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
11440897 AATTTTATAT
11440907 TTTATA-TTAAATTTA
1 TTTATATTTAAA-TTA
11440922 TTTATATTTAAATTA
1 TTTATATTTAAATTA
11440937 -TTATATTT
1 TTTATATTT
11440945 CTATTAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.36
15 9 0.41
16 5 0.23
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTATATTTAAATTA
Found at i:11447227 original size:57 final size:57
Alignment explanation
Indices: 11447157--11447517 Score: 422
Period size: 57 Copynumber: 6.4 Consensus size: 57
11447147 ACAAGTGGAT
* * * *
11447157 AAGTCCATCTTAAAGAGGTGTGACTATCAATTTTGCCTTAAAGAGGTAAACTGTATA
1 AAGTCCATCTTAAAGAGGTGTGACTATCAACTTTGCCTTAAAGAGGTGAATTATATA
* * ** ** *
11447214 AAGTCCATATTAAAGAGGTGTGATTATCAGTTTTGCCGCAAAGAGATGAATTATATA
1 AAGTCCATCTTAAAGAGGTGTGACTATCAACTTTGCCTTAAAGAGGTGAATTATATA
* * * * *
11447271 AAGTCCATCTTAAGGAGGTATGACTATCAACTTCGCCTTAAAGACGTGAATAATATA
1 AAGTCCATCTTAAAGAGGTGTGACTATCAACTTTGCCTTAAAGAGGTGAATTATATA
* * ** *
11447328 AAGTCCATCTTAAGGAGGTGTGATTATCAACTTTAACTT-AA-AGGTGAACTATATA
1 AAGTCCATCTTAAAGAGGTGTGACTATCAACTTTGCCTTAAAGAGGTGAATTATATA
* ** *
11447383 AAGTCCATCTTAAAAAGGTGTGACTATCAACTTCACCTTAAAGAGGCGAATTATATA
1 AAGTCCATCTTAAAGAGGTGTGACTATCAACTTTGCCTTAAAGAGGTGAATTATATA
* * * *
11447440 ACG-CCTATGTTAAAGAGGTGTGACTATTAACTTTGCCTTAAAGAGGTTAATTATATA
1 AAGTCC-ATCTTAAAGAGGTGTGACTATCAACTTTGCCTTAAAGAGGTGAATTATATA
*
11447497 AAGTCCATCTTAAGGAGGTGT
1 AAGTCCATCTTAAAGAGGTGT
11447518 AACATCATTT
Statistics
Matches: 253, Mismatches: 47, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
55 45 0.18
56 6 0.02
57 200 0.79
58 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (57 bp):
AAGTCCATCTTAAAGAGGTGTGACTATCAACTTTGCCTTAAAGAGGTGAATTATATA
Found at i:11447438 original size:169 final size:171
Alignment explanation
Indices: 11447157--11447545 Score: 455
Period size: 169 Copynumber: 2.3 Consensus size: 171
11447147 ACAAGTGGAT
* * ** *
11447157 AAGTCCATCTTAAAGAGGTGTGACTATCAATTTTGCCTTAAAGAGGTAAACTGTATAAAGTCCAT
1 AAGTCCATCTTAAGGAGGTGTGACTATCAACTTTAACTTAAAGAGGTAAACTATATAAAGTCCAT
* * ** ** * *
11447222 ATTAAAGAGGTGTGATTATCAGTTTTGCCGCAAAGAGATGAATTATATAAAGTCC-ATCTTAAGG
66 ATTAAAAAGGTGTGACTATCAACTTCACCGCAAAGAGACGAATTATATAAAG-CCTATCTTAAAG
11447286 AGGTATGACTATCAACTTCGCCTTAAAGACGTGAATAATATA
130 AGGTATGACTATCAACTTCGCCTTAAAGACGTGAATAATATA
* *
11447328 AAGTCCATCTTAAGGAGGTGTGATTATCAACTTTAACTT-AA-AGGTGAACTATATAAAGTCCAT
1 AAGTCCATCTTAAGGAGGTGTGACTATCAACTTTAACTTAAAGAGGTAAACTATATAAAGTCCAT
* ** * * *
11447391 CTTAAAAAGGTGTGACTATCAACTTCACCTTAAAGAGGCGAATTATATAACGCCTATGTTAAAGA
66 ATTAAAAAGGTGTGACTATCAACTTCACCGCAAAGAGACGAATTATATAAAGCCTATCTTAAAGA
* * * * * *
11447456 GGTGTGACTATTAACTTTGCCTTAAAGAGGTTAATTATATA
131 GGTATGACTATCAACTTCGCCTTAAAGACGTGAATAATATA
* * *
11447497 AAGTCCATCTTAAGGAGGTGTAAC-ATC-ATTTTCATCTTAAAGAGGTAAA
1 AAGTCCATCTTAAGGAGGTGTGACTATCAACTTT-AACTTAAAGAGGTAAA
11447546 TCATCTTAGT
Statistics
Matches: 182, Mismatches: 32, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
167 4 0.02
168 9 0.05
169 127 0.70
170 8 0.04
171 34 0.19
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (171 bp):
AAGTCCATCTTAAGGAGGTGTGACTATCAACTTTAACTTAAAGAGGTAAACTATATAAAGTCCAT
ATTAAAAAGGTGTGACTATCAACTTCACCGCAAAGAGACGAATTATATAAAGCCTATCTTAAAGA
GGTATGACTATCAACTTCGCCTTAAAGACGTGAATAATATA
Found at i:11450340 original size:28 final size:28
Alignment explanation
Indices: 11450283--11450359 Score: 66
Period size: 28 Copynumber: 2.8 Consensus size: 28
11450273 TCACCAAAAA
* * * *
11450283 TTAAGGGGGCAGTCCGCCAAGTACTCTC
1 TTAAGAGGGAAGTCCGTCAAGTACTATC
11450311 TTAAGAGGGAAGTCCGTCAA-TGACTATC
1 TTAAGAGGGAAGTCCGTCAAGT-ACTATC
** * *
11450339 TTGGGTGGAAAGTCCGTCAAG
1 TTAAGAGGGAAGTCCGTCAAG
11450360 AATTAACAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
27 1 0.03
28 38 0.97
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (28 bp):
TTAAGAGGGAAGTCCGTCAAGTACTATC
Found at i:11451443 original size:16 final size:16
Alignment explanation
Indices: 11451418--11451450 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
11451408 CATTGTGTGG
11451418 TAGATATGGATTAAGT
1 TAGATATGGATTAAGT
*
11451434 TAGATGTGGATTAAGT
1 TAGATATGGATTAAGT
11451450 T
1 T
11451451 TTAACAAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.27, T:0.39
Consensus pattern (16 bp):
TAGATATGGATTAAGT
Done.