Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold98
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: 1546936
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 25 characters in sequence are not A, C, G, or T
File 4 of 13
Found at i:414709 original size:13 final size:13
Alignment explanation
Indices: 414691--414716 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
414681 CAATTTTTTG
414691 TGTATCGATACAT
1 TGTATCGATACAT
414704 TGTATCGATACAT
1 TGTATCGATACAT
414717 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:417226 original size:13 final size:13
Alignment explanation
Indices: 417208--417246 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
417198 ATAATCACCC
*
417208 TGTATCGATACAG
1 TGTATCGATACAA
417221 TGTATCGATACAA
1 TGTATCGATACAA
417234 TGTATCGATACAA
1 TGTATCGATACAA
417247 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:417257 original size:20 final size:20
Alignment explanation
Indices: 417232--417310 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
417222 GTATCGATAC
417232 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
417252 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
417277 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
417297 CATGTATCGATACA
1 AATGTATCGATACA
417311 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:423424 original size:13 final size:13
Alignment explanation
Indices: 423406--423431 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
423396 CAATTTTTTG
423406 TGTATCGATACAT
1 TGTATCGATACAT
423419 TGTATCGATACAT
1 TGTATCGATACAT
423432 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:426835 original size:6 final size:6
Alignment explanation
Indices: 426818--426854 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
426808 CCTCAAAAGT
* *
426818 ACAAAC ACAAAA AAAAAA ACAAAA ACAAAA ACAAAA A
1 ACAAAA ACAAAA ACAAAA ACAAAA ACAAAA ACAAAA A
426855 AAAGAGAGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (6 bp):
ACAAAA
Found at i:428230 original size:62 final size:61
Alignment explanation
Indices: 428146--428613 Score: 509
Period size: 62 Copynumber: 7.5 Consensus size: 61
428136 ATCTCTCTTC
* *
428146 TCAAAGTCCACGACTCAATGGCATCTCTTTTCTAAGTCCACGACTCAATGGCATCATTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTCTTTTCAAAGTCCACGACTCAATGGCATC-TTTTCT
* * *
428208 TCAAAGTCCATGACTTAGTGGCATCTCTTTTCAAAGTCCACGACTCAGTGGCATCCTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTCTTTTCAAAGTCCACGACTCAATGGCAT-CTTTTCT
*
428270 TCAAAGTCCACGACTCAGTGGCATCTTTTTCTTCAAAGTCCACGACTCAATGGCATCTCTTTC-
1 TCAAAGTCCACGACTCAGTGGCATC-TCTT-TTCAAAGTCCACGACTCAATGGCATCT-TTTCT
* * *
428333 CCAAAGTCCACGACTCAGTGGCATCTCTTTCCCAAAGTCCATGACTCAATGGCATCTCTTTC-
1 TCAAAGTCCACGACTCAGTGGCATCTCTTT-TCAAAGTCCACGACTCAATGGCATCT-TTTCT
* * * ** *
428395 CCAAAATCCATGACTCAGTGGCATCTCTTCCCAAGGTCCACGACTCAATGGCATCTTTTGCT
1 TCAAAGTCCACGACTCAGTGGCATCTCTTTTCAAAGTCCACGACTCAATGGCATCTTTT-CT
* * *
428457 TCAAAGTCCACAAC-CTAGTGGCATCTCTTTCCCAAAGTCCACGACTCAGTGGCATCTTTTTTCT
1 TCAAAGTCCACGACTC-AGTGGCATCTCTTT-TCAAAGTCCACGACTCAATGGCATC--TTTTCT
* * * *
428521 CCAAAGTCCACGACTCAGTGGCATCTTTTTTCTTCAATA-TCCACGACTCAGTAGCATCTTTTC-
1 TCAAAGTCCACGACTCAGTGGCATC--TCTT-TTCAA-AGTCCACGACTCAATGGCATCTTTTCT
* * *
428584 -CAAAAGCCCACAACTCCGTGGCA-CTCTTTT
1 TC-AAAGTCCACGACTCAGTGGCATCTCTTTT
428614 TCCTTTTAAG
Statistics
Matches: 355, Mismatches: 34, Indels: 37
0.83 0.08 0.09
Matches are distributed among these distances:
59 2 0.01
60 6 0.02
61 27 0.08
62 162 0.46
63 71 0.20
64 56 0.16
65 5 0.01
66 24 0.07
67 2 0.01
ACGTcount: A:0.24, C:0.31, G:0.14, T:0.31
Consensus pattern (61 bp):
TCAAAGTCCACGACTCAGTGGCATCTCTTTTCAAAGTCCACGACTCAATGGCATCTTTTCT
Found at i:428338 original size:31 final size:31
Alignment explanation
Indices: 428136--428612 Score: 517
Period size: 32 Copynumber: 15.3 Consensus size: 31
428126 AATTCTTCAA
*
428136 ATCTCTCTTCTCAAAGTCCACGACTCAATGGC
1 ATCTCT-TTCTCAAAGTCCACGACTCAGTGGC
* *
428168 ATCTCTTT-TCTAAGTCCACGACTCAATGGC
1 ATCTCTTTCTCAAAGTCCACGACTCAGTGGC
* *
428198 ATCAT-TTTCTTCAAAGTCCATGACTTAGTGGC
1 ATC-TCTTTC-TCAAAGTCCACGACTCAGTGGC
428230 ATCTCTTT-TCAAAGTCCACGACTCAGTGGC
1 ATCTCTTTCTCAAAGTCCACGACTCAGTGGC
428260 ATC-CTTTTCTTCAAAGTCCACGACTCAGTGGC
1 ATCTC-TTTC-TCAAAGTCCACGACTCAGTGGC
* *
428292 ATCTTTTTCTTCAAAGTCCACGACTCAATGGC
1 ATCTCTTTC-TCAAAGTCCACGACTCAGTGGC
*
428324 ATCTCTTTCCCAAAGTCCACGACTCAGTGGC
1 ATCTCTTTCTCAAAGTCCACGACTCAGTGGC
* * *
428355 ATCTCTTTCCCAAAGTCCATGACTCAATGGC
1 ATCTCTTTCTCAAAGTCCACGACTCAGTGGC
* * *
428386 ATCTCTTTCCCAAAATCCATGACTCAGTGGC
1 ATCTCTTTCTCAAAGTCCACGACTCAGTGGC
* * *
428417 ATCTC-TTCCCAAGGTCCACGACTCAATGGC
1 ATCTCTTTCTCAAAGTCCACGACTCAGTGGC
*
428447 ATCT-TTTGCTTCAAAGTCCACAAC-CTAGTGGC
1 ATCTCTTT-C-TCAAAGTCCACGACTC-AGTGGC
*
428479 ATCTCTTTCCCAAAGTCCACGACTCAGTGGC
1 ATCTCTTTCTCAAAGTCCACGACTCAGTGGC
*
428510 ATCTTTTTTCTCCAAAGTCCACGACTCAGTGGC
1 ATC-TCTTTCT-CAAAGTCCACGACTCAGTGGC
* *
428543 ATCTTTTTTCTTCAATA-TCCACGACTCAGTAGC
1 ATC-TCTTTC-TCAA-AGTCCACGACTCAGTGGC
* * *
428576 ATCT-TTTC-CAAAAGCCCACAACTCCGTGGC
1 ATCTCTTTCTC-AAAGTCCACGACTCAGTGGC
428606 A-CTCTTT
1 ATCTCTTT
428613 TTCCTTTTAA
Statistics
Matches: 391, Mismatches: 33, Indels: 44
0.84 0.07 0.09
Matches are distributed among these distances:
29 5 0.01
30 98 0.25
31 114 0.29
32 117 0.30
33 55 0.14
34 2 0.01
ACGTcount: A:0.24, C:0.31, G:0.14, T:0.31
Consensus pattern (31 bp):
ATCTCTTTCTCAAAGTCCACGACTCAGTGGC
Found at i:428462 original size:187 final size:186
Alignment explanation
Indices: 428136--428546 Score: 569
Period size: 187 Copynumber: 2.2 Consensus size: 186
428126 AATTCTTCAA
* * * *
428136 ATCTCTCTTCTCAAAGTCCACGACTCAATGGCATCTCTTTTCTAAGTCCACGACTCAATGGCATC
1 ATCTCT-TTCCCAAAGTCCACGACTCAGTGGCATCTCTTTCCAAAGTCCACGACTCAATGGCATC
* * * ** *
428201 ATTTTCTTCAAAGTCCATGACTTAGTGGCATCTCTTTTCAAAGTCCACGACTCAGTGGCATCCTT
65 ATTTTCTCCAAAATCCATGACTCAGTGGCATCTCTTCCCAAAGTCCACGACTCAATGGCATCCTT
* * *
428266 TTCTTCAAAGTCCACGA-CTCAGTGGCATCTTTTTCTTCAAAGTCCACGACTCAATGGC
130 TTCTTCAAAGTCCACAACCT-AGTGGCATCTCTTTC-CCAAAGTCCACGACTCAATGGC
*
428324 ATCTCTTTCCCAAAGTCCACGACTCAGTGGCATCTCTTTCCCAAAGTCCATGACTCAATGGCATC
1 ATCTCTTTCCCAAAGTCCACGACTCAGTGGCATCTCTTT-CCAAAGTCCACGACTCAATGGCATC
*
428389 -TCTTTC-CCAAAATCCATGACTCAGTGGCATCTCTTCCCAAGGTCCACGACTCAATGGCAT-CT
65 AT-TTTCTCCAAAATCCATGACTCAGTGGCATCTCTTCCCAAAGTCCACGACTCAATGGCATCCT
*
428451 TTTGCTTCAAAGTCCACAACCTAGTGGCATCTCTTTCCCAAAGTCCACGACTCAGTGGC
129 TTT-CTTCAAAGTCCACAACCTAGTGGCATCTCTTTCCCAAAGTCCACGACTCAATGGC
*
428510 ATCTTTTTTCTCCAAAGTCCACGACTCAGTGGCATCT
1 ATC-TCTTTC-CCAAAGTCCACGACTCAGTGGCATCT
428547 TTTTTCTTCA
Statistics
Matches: 200, Mismatches: 17, Indels: 12
0.87 0.07 0.05
Matches are distributed among these distances:
186 28 0.14
187 112 0.56
188 60 0.30
ACGTcount: A:0.24, C:0.31, G:0.15, T:0.30
Consensus pattern (186 bp):
ATCTCTTTCCCAAAGTCCACGACTCAGTGGCATCTCTTTCCAAAGTCCACGACTCAATGGCATCA
TTTTCTCCAAAATCCATGACTCAGTGGCATCTCTTCCCAAAGTCCACGACTCAATGGCATCCTTT
TCTTCAAAGTCCACAACCTAGTGGCATCTCTTTCCCAAAGTCCACGACTCAATGGC
Found at i:428630 original size:34 final size:33
Alignment explanation
Indices: 428591--428947 Score: 331
Period size: 34 Copynumber: 11.2 Consensus size: 33
428581 TTCCAAAAGC
428591 CCACAACTCCGTGGCACTCTTTTTCCTTTTAAGT
1 CCACAACTCCGTGGCAC-CTTTTTCCTTTTAAGT
* *
428625 CCACAACTTCGTGGCA-C-----CCATTTAAGT
1 CCACAACTCCGTGGCACCTTTTTCCTTTTAAGT
* *
428652 CCACAACTCCGTGGCACCTTTTTCTTTTTAAAGC
1 CCACAACTCCGTGGCACCTTTTTCCTTTT-AAGT
*
428686 CCACAACTCTGTGGCACTCTTTTTCCTTTTAAGT
1 CCACAACTCCGTGGCAC-CTTTTTCCTTTTAAGT
*
428720 CCACAACTCTGTGGCA-C-----CCTTTTAAGT
1 CCACAACTCCGTGGCACCTTTTTCCTTTTAAGT
*
428747 CCACAACTCCGTGGCA-C-----CCTTTTAAGC
1 CCACAACTCCGTGGCACCTTTTTCCTTTTAAGT
* *
428774 CCACAACTTCGTGGCATTCTTTTTCCTTTTAAGT
1 CCACAACTCCGTGGCA-CCTTTTTCCTTTTAAGT
* *
428808 CCATAACTCCATGGCACCTTTTT-CTTTTGAAAG-
1 CCACAACTCCGTGGCACCTTTTTCCTTTT--AAGT
* *
428841 CTCATAACTCCGTGGCACTCTTTTTCCTTTTGAGT
1 C-CACAACTCCGTGGCAC-CTTTTTCCTTTTAAGT
* * *
428876 CCACAACTCTGTGGCGCCTTGTTCCTTTTAAGT
1 CCACAACTCCGTGGCACCTTTTTCCTTTTAAGT
* * *
428909 CCACAACTCCGTGGCATCTTTCTCCTTTTAAGC
1 CCACAACTCCGTGGCACCTTTTTCCTTTTAAGT
428942 CCACAA
1 CCACAA
428948 GTTAGTGGCA
Statistics
Matches: 272, Mismatches: 30, Indels: 43
0.79 0.09 0.12
Matches are distributed among these distances:
27 74 0.27
28 1 0.00
29 1 0.00
32 7 0.03
33 58 0.21
34 108 0.40
35 18 0.07
36 5 0.02
ACGTcount: A:0.20, C:0.32, G:0.13, T:0.35
Consensus pattern (33 bp):
CCACAACTCCGTGGCACCTTTTTCCTTTTAAGT
Found at i:428639 original size:97 final size:96
Alignment explanation
Indices: 428224--428640 Score: 287
Period size: 93 Copynumber: 4.4 Consensus size: 96
428214 TCCATGACTT
* * *
428224 AGTGGCATCTCTTT--T-CAAAGTCCACGACTCAGTGGCATCCTTTT-CTTCAAAGTCCACGA-C
1 AGTGGCATCTTTTTCCTCCAAAGTCCACAACTCAGTGGCAT-CTTTTGCTTCAAAGTCCACAACC
* * * *
428284 TCAGTGGCATCTTTTTCTTC-AAAGTCCACGACTC
65 T-AGTAGCATCTCTTTC--CAAAAGCCCACAACTC
* * * * **
428318 AATGGCATCTCTTT-C-CCAAAGTCCACGACTCAGTGGCATCTCTTT-C-CCAAAGTCCATGA-C
1 AGTGGCATCTTTTTCCTCCAAAGTCCACAACTCAGTGGCATCT-TTTGCTTCAAAGTCCACAACC
* * * **
428378 TCAATGGCATCTCTTTCCCAAAA-TCCATGACTC
65 T-AGTAGCATCTCTTT-CCAAAAGCCCACAACTC
* * * *
428411 AGTGGCATC-TCTT-C-CCAAGGTCCACGACTCAATGGCATCTTTTGCTTCAAAGTCCACAACCT
1 AGTGGCATCTTTTTCCTCCAAAGTCCACAACTCAGTGGCATCTTTTGCTTCAAAGTCCACAACCT
* * * *
428473 AGTGGCATCTCTTTCCCAAAGTCCACGACTC
66 AGTAGCATCTCTTTCCAAAAGCCCACAACTC
* * * *
428504 AGTGGCATCTTTTTTCTCCAAAGTCCACGACTCAGTGGCATCTTTTTTCTTCAATA-TCCACGA-
1 AGTGGCATCTTTTTCCTCCAAAGTCCACAACTCAGTGGCATC-TTTTGCTTCAA-AGTCCACAAC
428567 CTCAGTAGCATCT-TTTCCAAAAGCCCACAACTC
64 CT-AGTAGCATCTCTTTCCAAAAGCCCACAACTC
* ***
428600 CGTGGCACTCTTTTTCCTTTTAAGTCCACAACTTC-GTGGCA
1 AGTGGCA-TCTTTTTCCTCCAAAGTCCACAAC-TCAGTGGCA
428641 CCCATTTAAG
Statistics
Matches: 274, Mismatches: 32, Indels: 31
0.81 0.09 0.09
Matches are distributed among these distances:
91 3 0.01
92 33 0.12
93 59 0.22
94 49 0.18
95 29 0.11
96 48 0.18
97 50 0.18
98 3 0.01
ACGTcount: A:0.24, C:0.31, G:0.15, T:0.30
Consensus pattern (96 bp):
AGTGGCATCTTTTTCCTCCAAAGTCCACAACTCAGTGGCATCTTTTGCTTCAAAGTCCACAACCT
AGTAGCATCTCTTTCCAAAAGCCCACAACTC
Found at i:428656 original size:27 final size:27
Alignment explanation
Indices: 428615--428789 Score: 147
Period size: 27 Copynumber: 6.0 Consensus size: 27
428605 CACTCTTTTT
428615 CCTTTTAAGTCCACAACTTCGTGGCAC
1 CCTTTTAAGTCCACAACTTCGTGGCAC
* *
428642 CCATTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTTCGTGGCAC
*
428669 CTTTTTCTTTTTAAAGCCCACAAC-TCTGTGGCACTC
1 C-----C-TTTT-AAGTCCACAACTTC-GTGGCA--C
428705 TTTTTCCTTTTAAGTCCACAAC-TCTGTGGCAC
1 -----CCTTTTAAGTCCACAACTTC-GTGGCAC
*
428737 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTTCGTGGCAC
*
428764 CCTTTTAAGCCCACAACTTCGTGGCA
1 CCTTTTAAGTCCACAACTTCGTGGCA
428790 TTCTTTTTCC
Statistics
Matches: 123, Mismatches: 9, Indels: 32
0.75 0.05 0.20
Matches are distributed among these distances:
27 74 0.60
28 1 0.01
32 2 0.02
33 4 0.03
34 35 0.28
35 4 0.03
36 2 0.02
41 1 0.01
ACGTcount: A:0.22, C:0.33, G:0.14, T:0.31
Consensus pattern (27 bp):
CCTTTTAAGTCCACAACTTCGTGGCAC
Found at i:428708 original size:95 final size:93
Alignment explanation
Indices: 428587--428924 Score: 395
Period size: 95 Copynumber: 3.6 Consensus size: 93
428577 TCTTTTCCAA
* * *
428587 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTTCGTGGCACCCATTTAAGT
1 AAGCCCACAACTCTGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGT
428652 CCACAACTCCGTGGCACCTTTTTCTTTTT
66 CCACAACTCCGTGGCACCTTTTTC-TTTT
*
428681 AAAGCCCACAACTCTGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAG
1 -AAGCCCACAACTCTGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAG
428746 TCCACAACTCCGTGGCACC-----CTTTT
65 TCCACAACTCCGTGGCACCTTTTTCTTTT
* * *
428770 AAGCCCACAACT-TCGTGGCATTCTTTTTCCTTTTAAGTCCATAACTCCATGGCACCTTTTTCTT
1 AAGCCCACAACTCT-GTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACC-----CTT
*
428834 TTGAAAG-CTCATAACTCCGTGGCACTCTTTTTCCTTTT
60 TT--AAGTC-CACAACTCCGTGGCAC-CTTTTT-CTTTT
* * * *
428872 GAGTCCACAACTCTGTGGCGC-CTTGTTCCTTTTAAGTCCACAACTCCGTGGCA
1 AAGCCCACAACTCTGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCA
428925 TCTTTCTCCT
Statistics
Matches: 210, Mismatches: 16, Indels: 28
0.83 0.06 0.11
Matches are distributed among these distances:
87 1 0.00
88 50 0.24
89 4 0.02
90 1 0.00
93 5 0.02
94 1 0.00
95 97 0.46
96 1 0.00
101 29 0.14
102 20 0.10
103 1 0.00
ACGTcount: A:0.20, C:0.32, G:0.14, T:0.34
Consensus pattern (93 bp):
AAGCCCACAACTCTGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGT
CCACAACTCCGTGGCACCTTTTTCTTTT
Found at i:428728 original size:68 final size:66
Alignment explanation
Indices: 428591--428947 Score: 331
Period size: 61 Copynumber: 5.6 Consensus size: 66
428581 TTCCAAAAGC
* *
428591 CCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTTCGTGGCA-C-----CCATTTAA
1 CCACAACTCCGTGGCAC-CTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCCTTTTAA
428650 GT
65 GT
* * *
428652 CCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCTTTTA
1 CCACAACTCCGTGGCACCTTTTTCCTTTT-AAGTCCACAACTCCGTGGCAC-CTTTTTCCTTTTA
428717 AGT
64 AGT
*
428720 CCACAACTCTGTGGCA-C-----CCTTTTAAGTCCACAACTCCGTGGCA-C-----CCTTTTAAG
1 CCACAACTCCGTGGCACCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCCTTTTAAG
*
428773 C
66 T
* * * *
428774 CCACAACTTCGTGGCATTCTTTTTCCTTTTAAGTCCATAACTCCATGGCACCTTTTT-CTTTTGA
1 CCACAACTCCGTGGCA-CCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCCTTTT--
428838 AAG-
63 AAGT
* * * * *
428841 CTCATAACTCCGTGGCACTCTTTTTCCTTTTGAGTCCACAACTCTGTGGCGCCTTGTTCCTTTTA
1 C-CACAACTCCGTGGCAC-CTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCCTTTTA
428906 AGT
64 AGT
* * *
428909 CCACAACTCCGTGGCATCTTTCTCCTTTTAAGCCCACAA
1 CCACAACTCCGTGGCACCTTTTTCCTTTTAAGTCCACAA
428948 GTTAGTGGCA
Statistics
Matches: 241, Mismatches: 28, Indels: 49
0.76 0.09 0.15
Matches are distributed among these distances:
54 23 0.10
56 1 0.00
59 1 0.00
60 11 0.05
61 76 0.32
62 6 0.02
63 1 0.00
66 24 0.10
67 19 0.08
68 74 0.31
69 5 0.02
ACGTcount: A:0.20, C:0.32, G:0.13, T:0.35
Consensus pattern (66 bp):
CCACAACTCCGTGGCACCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCCTTTTAAG
T
Found at i:428759 original size:156 final size:156
Alignment explanation
Indices: 428591--428960 Score: 457
Period size: 156 Copynumber: 2.3 Consensus size: 156
428581 TTCCAAAAGC
*
428591 CCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTTCGTGGCACCCATTTAAGTCCAC
1 CCACAACTCCGTGGCA-TC-TTTTCCTTTTAAGCCCACAACTTCGTGGCACCCATTTAAGTCCAC
* * *
428656 AACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCTTTTAAGTC
64 AACTCCATGGCACCTTTTTCTTTTGAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTC
428721 CACAACTCTGTGGC-AC-CCTTTTAAGT
129 CACAACTCTGTGGCGACTCCTTTTAAGT
*
428747 CCACAACTCCGTGGCA-C----CCTTTTAAGCCCACAACTTCGTGGCATTCTTTTTCCTTTTAAG
1 CCACAACTCCGTGGCATCTTTTCCTTTTAAGCCCACAACTTCGTGGCA--C-----CCATTTAAG
* * *
428807 TCCATAACTCCATGGCACCTTTTTCTTTTGAAAGCTCATAACTCCGTGGCACTCTTTTTCCTTTT
59 TCCACAACTCCATGGCACCTTTTTCTTTTGAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
* *
428872 GAGTCCACAACTCTGTGGCGCCTTGTTCCTTTTAAGT
124 AAGTCCACAACTCTGTGGCGAC----TCCTTTTAAGT
* *
428909 CCACAACTCCGTGGCATCTTTCTCCTTTTAAGCCCACAAGTTAGTGGCACCC
1 CCACAACTCCGTGGCATCTTT-TCCTTTTAAGCCCACAACTTCGTGGCACCC
428961 TTTCCAAAAG
Statistics
Matches: 183, Mismatches: 12, Indels: 33
0.80 0.05 0.14
Matches are distributed among these distances:
149 25 0.14
151 1 0.01
154 1 0.01
156 101 0.55
157 1 0.01
161 2 0.01
162 26 0.14
163 1 0.01
166 1 0.01
168 24 0.13
ACGTcount: A:0.20, C:0.32, G:0.14, T:0.35
Consensus pattern (156 bp):
CCACAACTCCGTGGCATCTTTTCCTTTTAAGCCCACAACTTCGTGGCACCCATTTAAGTCCACAA
CTCCATGGCACCTTTTTCTTTTGAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCA
CAACTCTGTGGCGACTCCTTTTAAGT
Found at i:429009 original size:29 final size:29
Alignment explanation
Indices: 428938--429062 Score: 139
Period size: 29 Copynumber: 4.3 Consensus size: 29
428928 TTCTCCTTTT
*
428938 AAGCCCACAAGTTAGTGGCACCCTTTCCAA
1 AAGCCCACAAGTCAGTGGCACCCTTT-CAA
*
428968 AAGCCCACAAGTCGGTGGCACCCCTTTC-A
1 AAGCCCACAAGTCAGTGGCA-CCCTTTCAA
*
428997 AAGCCCACAAGTCAGTGGCAACC-TTCAA
1 AAGCCCACAAGTCAGTGGCACCCTTTCAA
* * **
429025 AGGCACACAAGTTGGT-GCAACCCTTTCAA
1 AAGCCCACAAGTCAGTGGC-ACCCTTTCAA
429054 AAGCCCACA
1 AAGCCCACA
429063 CAAGTTGGTG
Statistics
Matches: 80, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
27 5 0.06
28 18 0.22
29 32 0.40
30 19 0.24
31 6 0.08
ACGTcount: A:0.31, C:0.34, G:0.18, T:0.17
Consensus pattern (29 bp):
AAGCCCACAAGTCAGTGGCACCCTTTCAA
Found at i:429196 original size:48 final size:48
Alignment explanation
Indices: 429079--429567 Score: 442
Period size: 48 Copynumber: 10.9 Consensus size: 48
429069 GGTGATGTCT
* * * * **
429079 TCTTCTAAGTCCAATGTCGTTGGCCTTGAATCAACACATTGGTACCTTCA
1 TCTT-TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CTTTG
* * *
429129 TCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTG
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTTG
* *
429177 TCTTTAAGACCAATGTCGCTAGCTTTGAATCAGCACATTGGCA-----
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTTG
* * * *
429220 -C---AAGCCCAATATCGCTGGCCTTGAATCAGTATATTGGCACTTTG
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTTG
*
429264 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCAAATTGGCA-----
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTTG
* * * *
429307 -C---AAGCCCAATATCGCTGGCCTTGAATCAGTATATTGGCACTTTG
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTTG
429351 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-----
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTTG
* *
429394 -C---AAG-CCTAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTG
1 TCTTTAAGACC-AATGTCGCTGGCCTTGAATCAGCACATTGGCACTTTG
*
429438 TCTTTAAGACCAATGTCGCTGGCCTTGAATTAGCACATTGGCA-----
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTTG
* * *
429481 -C---AAG-CCAATATCGCTGGCCTTGAATCAGTATATTGGCACTTTG
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTTG
*
429524 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTAGCAC
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
429568 AAGCCCAATA
Statistics
Matches: 356, Mismatches: 44, Indels: 80
0.74 0.09 0.17
Matches are distributed among these distances:
38 32 0.09
39 102 0.29
42 4 0.01
44 1 0.00
45 3 0.01
47 3 0.01
48 172 0.48
49 35 0.10
50 4 0.01
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.30
Consensus pattern (48 bp):
TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTTG
Found at i:429244 original size:39 final size:39
Alignment explanation
Indices: 429186--430060 Score: 600
Period size: 39 Copynumber: 20.8 Consensus size: 39
429176 GTCTTTAAGA
* * *
429186 CCAATGTCGCTAGCTTTGAATCAGCACATTGGCACAAGC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACAAGC
* * *
429225 CCAATATCGCTGGCCTTGAATCAGTATATTGGCACTTTGTCTTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCA------C---AAGC
* *
429273 CCAATGTCGCTGGCCTTGAATCAGCAAATTGGCACAAGC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACAAGC
* * *
429312 CCAATATCGCTGGCCTTGAATCAGTATATTGGCACTTTGTCTTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCA------C---AAGC
*
429360 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACAAGC
* * *
429399 CTAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTGTCTTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCA------C---AAGC
* *
429447 CCAATGTCGCTGGCCTTGAATTAGCACATTGGCACAAG-
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACAAGC
* * *
429485 CCAATATCGCTGGCCTTGAATCAGTATATTGGCACTTTGTCTTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCA------C---AAGC
* *
429533 CCAATGTCGCTGGCCTTGAATCAGCACATTAGCACAAGC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACAAGC
*
429572 CCAATATCACTGGCC-T---T--G-A-A-TGGCACAAGC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACAAGC
* *
429602 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTGTCTTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCA------C---AAGC
*
429650 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACAAGC
*
429689 CCAATATCGTTGGCCTTGAATCAGCACATTGGCACAAGC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACAAGC
*
429728 CCAATATCGCTGGCCTTGAATCAGCACATTGGCAGAAGC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACAAGC
* * *
429767 CCAATATCGCTGGTCTTGAATCAGCATATTGGCACTTTGTCTTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCA------C---AAGC
*
429815 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACAAGC
* ** * * *
429854 CTAATATCATTGGCCTTGAATCAGCATATTAGCACTTTGTCTTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCA------C---AAGC
* *
429902 CCAATGTCGCTAGCCTTGAATCAGCACATTGGCACAAGC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACAAGC
* * *
429941 CCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTGTCTTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCA------C---AAGC
* * *
429989 CCAATGTTGCTGGCCTTGAATCAGCACATTGGCACAAGT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACAAGC
* *
430028 CCAATATCGCTGGCCTTGAATCAACATATTGGC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGC
430061 GCCTTTGTCA
Statistics
Matches: 670, Mismatches: 84, Indels: 164
0.73 0.09 0.18
Matches are distributed among these distances:
30 23 0.03
31 2 0.00
32 1 0.00
33 1 0.00
34 1 0.00
35 1 0.00
36 1 0.00
37 1 0.00
38 32 0.05
39 326 0.49
42 8 0.01
44 1 0.00
45 6 0.01
47 3 0.00
48 263 0.39
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.28
Consensus pattern (39 bp):
CCAATATCGCTGGCCTTGAATCAGCACATTGGCACAAGC
Found at i:429280 original size:87 final size:87
Alignment explanation
Indices: 429134--429592 Score: 830
Period size: 87 Copynumber: 5.3 Consensus size: 87
429124 CTTCATCTTT
* *
429134 AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTGTCTTTAAGACCAATGTCGCTAG
1 AAGCCCAATATCGCTGGCCTTGAATCAGTATATTGGCACTTTGTCTTTAAGACCAATGTCGCTGG
*
429199 CTTTGAATCAGCACATTGGCAC
66 CCTTGAATCAGCACATTGGCAC
429221 AAGCCCAATATCGCTGGCCTTGAATCAGTATATTGGCACTTTGTCTTTAAGACCAATGTCGCTGG
1 AAGCCCAATATCGCTGGCCTTGAATCAGTATATTGGCACTTTGTCTTTAAGACCAATGTCGCTGG
*
429286 CCTTGAATCAGCAAATTGGCAC
66 CCTTGAATCAGCACATTGGCAC
429308 AAGCCCAATATCGCTGGCCTTGAATCAGTATATTGGCACTTTGTCTTTAAGACCAATGTCGCTGG
1 AAGCCCAATATCGCTGGCCTTGAATCAGTATATTGGCACTTTGTCTTTAAGACCAATGTCGCTGG
429373 CCTTGAATCAGCACATTGGCAC
66 CCTTGAATCAGCACATTGGCAC
* *
429395 AAGCCTAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTGTCTTTAAGACCAATGTCGCTGG
1 AAGCCCAATATCGCTGGCCTTGAATCAGTATATTGGCACTTTGTCTTTAAGACCAATGTCGCTGG
*
429460 CCTTGAATTAGCACATTGGCAC
66 CCTTGAATCAGCACATTGGCAC
429482 AAG-CCAATATCGCTGGCCTTGAATCAGTATATTGGCACTTTGTCTTTAAGACCAATGTCGCTGG
1 AAGCCCAATATCGCTGGCCTTGAATCAGTATATTGGCACTTTGTCTTTAAGACCAATGTCGCTGG
*
429546 CCTTGAATCAGCACATTAGCAC
66 CCTTGAATCAGCACATTGGCAC
*
429568 AAGCCCAATATCACTGGCCTTGAAT
1 AAGCCCAATATCGCTGGCCTTGAAT
429593 GGCACAAGCC
Statistics
Matches: 358, Mismatches: 13, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
86 82 0.23
87 276 0.77
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (87 bp):
AAGCCCAATATCGCTGGCCTTGAATCAGTATATTGGCACTTTGTCTTTAAGACCAATGTCGCTGG
CCTTGAATCAGCACATTGGCAC
Found at i:429600 original size:30 final size:30
Alignment explanation
Indices: 429564--429622 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
429554 CAGCACATTA
429564 GCACAAGCCCAATATCACTGGCCTTGAATG
1 GCACAAGCCCAATATCACTGGCCTTGAATG
*
429594 GCACAAGCCCAATATCGCTGGCCTTGAAT
1 GCACAAGCCCAATATCACTGGCCTTGAAT
429623 CAGCATATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (30 bp):
GCACAAGCCCAATATCACTGGCCTTGAATG
Found at i:429630 original size:203 final size:195
Alignment explanation
Indices: 429389--429787 Score: 611
Period size: 203 Copynumber: 2.0 Consensus size: 195
429379 ATCAGCACAT
*
429389 TGGCACAAGCCTAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTGTCTTTAAGACCAATGT
1 TGGCACAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTGTCTTTAAGACCAATGT
* * *
429454 CGCTGGCCTTGAATTAGCACATTGGCACAAG-CCAATATCGCTGGCCTTGAATCAGTATATTGGC
66 CGCTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGC
*
429518 ACTTTGTCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTAGCACAAGCCCAATATCACT
131 A------C---AAGACCAATATCGCTGGCCTTGAATCAGCACATTAGCACAAGCCCAATATCACT
429583 GGCCTTGAA
187 GGCCTTGAA
429592 TGGCACAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTGTCTTTAAGACCAATGT
1 TGGCACAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTGTCTTTAAGACCAATGT
*
429657 CGCTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGTTGGCCTTGAATCAGCACATTGGC
66 CGCTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGC
* * * * *
429722 ACAAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCAGAAGCCCAATATCGCTGGTCTTGAA
131 ACAAGACCAATATCGCTGGCCTTGAATCAGCACATTAGCACAAGCCCAATATCACTGGCCTTGAA
429787 T
1 T
429788 CAGCATATTG
Statistics
Matches: 184, Mismatches: 11, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
195 58 0.32
198 1 0.01
203 94 0.51
204 31 0.17
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.27
Consensus pattern (195 bp):
TGGCACAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTGTCTTTAAGACCAATGT
CGCTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGC
ACAAGACCAATATCGCTGGCCTTGAATCAGCACATTAGCACAAGCCCAATATCACTGGCCTTGAA
Found at i:429874 original size:87 final size:86
Alignment explanation
Indices: 429728--430214 Score: 596
Period size: 87 Copynumber: 5.4 Consensus size: 86
429718 TGGCACAAGC
* * *
429728 CCAATATCGCTGGCCTTGAATCAGCACATTGGCAGAAGCCCAATATCGCTGGTCTTGAATCAGCA
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAG-CCAATATCGCTGGCCTTGAATCAGCA
429793 TATTGGCACTTTGTCTTTAAGA
65 TATTGGCACTTTGTCTTTAAGA
**
429815 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGCCTAATATCATTGGCCTTGAATCAGCA
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGCC-AATATCGCTGGCCTTGAATCAGCA
*
429880 TATTAGCACTTTGTCTTTAAGA
65 TATTGGCACTTTGTCTTTAAGA
* *
429902 CCAATGTCGCTAGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTAAATCAGCA
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAG-CCAATATCGCTGGCCTTGAATCAGCA
*
429967 TATTGGCACCTTGTCTTTAAGA
65 TATTGGCACTTTGTCTTTAAGA
* *
429989 CCAATGTTGCTGGCCTTGAATCAGCACATTGGCACAAGTCCAATATCGCTGGCCTTGAATCAACA
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAG-CCAATATCGCTGGCCTTGAATCAGCA
* *
430054 TATTGGCGCCTTTGTCATCTTCAAGT
65 TATTGGC-ACTTTGTC-T-TT-AAGA
* *
430080 CCAATGTCGCTCGCCTTGAATCAGTACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGG------CA-C---AAG-CCAATATCGCTGGCCT
* *
430145 TGAATCAGCATATTGGCTCCTTCGTCATCTTTAAGA
55 TGAATCAGCATATTGGC-ACTT--T-GTCTTTAAGA
* *
430181 CCAATGTCACTGGCCTTGAATCAGCACAATGGCA
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
430215 TCTTCAGCTT
Statistics
Matches: 350, Mismatches: 31, Indels: 30
0.85 0.08 0.07
Matches are distributed among these distances:
86 2 0.01
87 223 0.64
88 8 0.02
89 1 0.00
90 2 0.01
91 32 0.09
95 2 0.01
97 2 0.01
98 1 0.00
101 71 0.20
102 2 0.01
103 2 0.01
104 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (86 bp):
CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGCCAATATCGCTGGCCTTGAATCAGCAT
ATTGGCACTTTGTCTTTAAGA
Found at i:430145 original size:49 final size:51
Alignment explanation
Indices: 430024--430360 Score: 255
Period size: 49 Copynumber: 6.7 Consensus size: 51
430014 ACATTGGCAC
* * * *
430024 AAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCGCCTTTGTCATCTTC
1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC-TTGTCATCTTT
* * *
430076 AAGTCCAATGTCGCTCGCCTTGAATCAGTACATTGGCACC-T-TCATCTTT
1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTGTCATCTTT
* *
430125 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCTCCTTCGTCATCTTT
1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT-GTCATCTTT
* * * * * *
430177 AAGACCAATGTCACTGGCCTTGAATCAGCACAATGGCATC-T-TCAGCTTT
1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTGTCATCTTT
* * * * * * * *
430226 AAGTCCGATATTGTTGACCTTGAATCAACATATTGGCATCTT-TAACATTCCTT
1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTGT--CA-TCTTT
* * * * *
430279 AAGCCCAATGTCGTTGGCCTT--ATCTTAGCACATTGGCA---T-TCTTCTTC
1 AAGTCCAATATCGCTGGCCTTGAATC--AGCACATTGGCACCTTGTCATCTTT
* * *
430326 AAGTCTAATGTCGCTGGCCATGAATCAGCACATTG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTG
430361 TCATTCTTCG
Statistics
Matches: 228, Mismatches: 46, Indels: 27
0.76 0.15 0.09
Matches are distributed among these distances:
47 29 0.13
48 1 0.00
49 82 0.36
50 6 0.03
51 4 0.02
52 77 0.34
53 29 0.13
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (51 bp):
AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTGTCATCTTT
Found at i:430199 original size:101 final size:101
Alignment explanation
Indices: 430024--430262 Score: 343
Period size: 101 Copynumber: 2.4 Consensus size: 101
430014 ACATTGGCAC
* * *
430024 AAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCGCCTTTGTCATCTTCAAGTCCAATGTCG
1 AAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCGCCTTCGTCATCTTCAAGACCAATGTCA
* * *
430089 CTCGCCTTGAATCAGTACATTGGCACCTTCATCTTT
66 CTCGCCTTGAATCAGCACAATGGCACCTTCAGCTTT
* * *
430125 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCTCCTTCGTCATCTTTAAGACCAATGTCA
1 AAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCGCCTTCGTCATCTTCAAGACCAATGTCA
* *
430190 CTGGCCTTGAATCAGCACAATGGCATCTTCAGCTTT
66 CTCGCCTTGAATCAGCACAATGGCACCTTCAGCTTT
* * * *
430226 AAGTCCGATATTGTTGACCTTGAATCAACATATTGGC
1 AAGTCCAATATCGCTGGCCTTGAATCAACATATTGGC
430263 ATCTTTAACA
Statistics
Matches: 122, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
101 122 1.00
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (101 bp):
AAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCGCCTTCGTCATCTTCAAGACCAATGTCA
CTCGCCTTGAATCAGCACAATGGCACCTTCAGCTTT
Found at i:441249 original size:19 final size:20
Alignment explanation
Indices: 441206--441257 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
441196 CACACCCAGA
* *
441206 TGTATCGATACATTATGCTT
1 TGTATCGATACATGATGCAT
*
441226 TGTATCGATACATGCT-CAT
1 TGTATCGATACATGATGCAT
441245 TGTATCGATACAT
1 TGTATCGATACAT
441258 ACCCAATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATGATGCAT
Found at i:441268 original size:20 final size:19
Alignment explanation
Indices: 441187--441275 Score: 79
Period size: 20 Copynumber: 4.5 Consensus size: 19
441177 ACCTTTGAAA
* *
441187 GTATCGATACACACCCAGAT
1 GTATCGATACATACCCA-TT
** *
441207 GTATCGATACATTATGCTTT
1 GTATCGATACA-TACCCATT
* *
441227 GTATCGATACATGCTCATT
1 GTATCGATACATACCCATT
441246 GTATCGATACATACCCAATT
1 GTATCGATACATACCC-ATT
*
441266 GTATTGATAC
1 GTATCGATAC
441276 GTGAAACTGG
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
19 18 0.33
20 35 0.64
21 2 0.04
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (19 bp):
GTATCGATACATACCCATT
Found at i:441345 original size:13 final size:13
Alignment explanation
Indices: 441327--441352 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
441317 CATAGGACAA
441327 TGTATCGATACAT
1 TGTATCGATACAT
441340 TGTATCGATACAT
1 TGTATCGATACAT
441353 GAAGAATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:441351 original size:33 final size:33
Alignment explanation
Indices: 441309--441376 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
441299 AAGTGAAATA
*
441309 TATCGATACAT-AGGACAATGTATCGATACATTG
1 TATCGATACATGAAGA-AATGTATCGATACATTG
* *
441342 TATCGATACATGAAGAATTGTATTGATACATTG
1 TATCGATACATGAAGAAATGTATCGATACATTG
441375 TA
1 TA
441377 CCCAACGACT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
33 28 0.90
34 3 0.10
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.34
Consensus pattern (33 bp):
TATCGATACATGAAGAAATGTATCGATACATTG
Found at i:443755 original size:17 final size:17
Alignment explanation
Indices: 443733--443766 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
443723 TTACATATAG
443733 TATAAAAGTATAAATAA
1 TATAAAAGTATAAATAA
443750 TATAAAAGTATAAATAA
1 TATAAAAGTATAAATAA
443767 CTAGAGACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (17 bp):
TATAAAAGTATAAATAA
Found at i:447797 original size:80 final size:79
Alignment explanation
Indices: 447597--447942 Score: 378
Period size: 79 Copynumber: 4.4 Consensus size: 79
447587 AGATAACAAT
* * * * *
447597 GGGGCTGGAGTATCTCCGATTATGAAAAATTGGTGTTCT-GAAAATAAAATCGGGGTTGGAGTAT
1 GGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAG-AAATAAAACCGGGGTTGGAGTAT
*
447661 CCCCGT-GAAAATAAT
65 CCCC-TCGAAAATAAC
* * ** * ** *
447676 GGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAGGCCGGGGTTGAAGTATC
1 GGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATC
447741 CCCAAT-G-AAATAATC
66 CCC--TCGAAAATAA-C
* * * * *
447756 GGAGTTGGAGTATCCCCGATTATGGAGAATTGGTGTTTTAGAAATAAAATCGGGGTTGGAGTATC
1 GGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATC
* *
447821 CCCTTGGAAATAAC
66 CCCTCGAAAATAAC
* * *
447835 GGGATTGGAGTATTCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTCGAGTATC
1 GGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATC
447900 CCCTCGAAAATAAC
66 CCCTCGAAAATAAC
* *
447914 GGGGTTGGAGTATCCTCGA-GATGAAAAAT
1 GGGGTTGGAGTATCCCCGATTATGAAAAAT
447943 CTAGAAATTT
Statistics
Matches: 220, Mismatches: 42, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
78 10 0.05
79 146 0.66
80 64 0.29
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (79 bp):
GGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATC
CCCTCGAAAATAAC
Found at i:447891 original size:159 final size:158
Alignment explanation
Indices: 447602--447942 Score: 431
Period size: 159 Copynumber: 2.2 Consensus size: 158
447592 ACAATGGGGC
*
447602 TGGAGTATCTCCGATTATGAAAAATTGGTGTTCTGAAAATAAAATCGGGGTTGGAGTATCCCCGT
1 TGGAGTATCCCCGATTATGAAAAATTGGTGTTCTGAAAATAAAATCGGGGTTGGAGTATCCCCGT
* * * * **
447667 GAAAATAATGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAGGCCGGGGT
66 GAAAATAACGGGATTGGAGTATCCCCGATTATGAAAAATCAATATTTTAGAAATAAAACCGGGGT
447732 T-GAAGTATCCCCAAT-G-AAATAATCGGAGT
131 TCG-AGTATCCCC--TCGAAAATAA-CGGAGT
* * * *
447761 TGGAGTATCCCCGATTATGGAGAATTGGTGTT-TTAGAAATAAAATCGGGGTTGGAGTATCCCCT
1 TGGAGTATCCCCGATTATGAAAAATTGGTGTTCTGA-AAATAAAATCGGGGTTGGAGTATCCCCG
* * ** *
447825 TGGAAATAACGGGATTGGAGTATTCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGG
65 TGAAAATAACGGGATTGGAGTATCCCCGATTATGAAAAATCAATATTTTAGAAATAAAACCGGGG
*
447890 TTCGAGTATCCCCTCGAAAATAACGGGGT
130 TTCGAGTATCCCCTCGAAAATAACGGAGT
* *
447919 TGGAGTATCCTCGA-GATGAAAAAT
1 TGGAGTATCCCCGATTATGAAAAAT
447943 CTAGAAATTT
Statistics
Matches: 157, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
157 8 0.05
158 21 0.13
159 127 0.81
160 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.28
Consensus pattern (158 bp):
TGGAGTATCCCCGATTATGAAAAATTGGTGTTCTGAAAATAAAATCGGGGTTGGAGTATCCCCGT
GAAAATAACGGGATTGGAGTATCCCCGATTATGAAAAATCAATATTTTAGAAATAAAACCGGGGT
TCGAGTATCCCCTCGAAAATAACGGAGT
Found at i:450327 original size:21 final size:21
Alignment explanation
Indices: 450303--450344 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
450293 ACAAAAGATC
450303 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
*
450324 AATGTATCGATATATTTCCTT
1 AATGTATCGATACATTTCCTT
450345 GGCAGTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.45
Consensus pattern (21 bp):
AATGTATCGATACATTTCCTT
Found at i:450393 original size:19 final size:19
Alignment explanation
Indices: 450369--450441 Score: 83
Period size: 19 Copynumber: 3.7 Consensus size: 19
450359 AGCGATACAT
*
450369 TGTATCGATATAAAACTTA
1 TGTATCGATACAAAACTTA
*
450388 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
** *
450407 TGTATCGATACATTTACTATT
1 TGTATCGATACA-AAACT-TA
450428 TGTATCGATACAAA
1 TGTATCGATACAAA
450442 TTGTTTGAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
19 29 0.64
20 3 0.07
21 13 0.29
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:453336 original size:2 final size:2
Alignment explanation
Indices: 453329--453357 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
453319 TTACAGAGTA
453329 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
453358 CTGTAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:454935 original size:2 final size:2
Alignment explanation
Indices: 454928--454958 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
454918 TTCAAACTTT
454928 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
454959 GTCATCTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:455005 original size:4 final size:4
Alignment explanation
Indices: 454998--455024 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
454988 ACATACATTC
454998 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
455025 TAACCTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:455942 original size:28 final size:29
Alignment explanation
Indices: 455911--455966 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
455901 ACTTTGTTTT
* *
455911 AAAGTCGACACATTAATTTCAT-TAAAGC
1 AAAGTAGACACACTAATTTCATCTAAAGC
*
455939 AAAGTAGACACACTAATTTGATCTAAAG
1 AAAGTAGACACACTAATTTCATCTAAAG
455967 TCGATCCATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.27
Consensus pattern (29 bp):
AAAGTAGACACACTAATTTCATCTAAAGC
Found at i:456629 original size:15 final size:15
Alignment explanation
Indices: 456594--456629 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
456584 ATTATTATTA
*
456594 AAAAAAGTTTCAGTT
1 AAAAAAGTTTAAGTT
*
456609 AGAAAAGTTTAAGTT
1 AAAAAAGTTTAAGTT
456624 AAAAAA
1 AAAAAA
456630 AATGTGTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.56, C:0.03, G:0.14, T:0.28
Consensus pattern (15 bp):
AAAAAAGTTTAAGTT
Found at i:463337 original size:21 final size:21
Alignment explanation
Indices: 463296--463339 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
463286 CTCCCCTTTA
* *
463296 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
463317 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
463338 TC
1 TC
463340 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:463519 original size:22 final size:24
Alignment explanation
Indices: 463491--463539 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
463481 AACACTAGAT
463491 ACAAGGTCAA-AG-TACAATAAAC
1 ACAAGGTCAACAGATACAATAAAC
463513 ACAAGGTCAAGCAGATACAATAAAC
1 ACAAGGTCAA-CAGATACAATAAAC
463538 AC
1 AC
463540 TAGATATACT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 10 0.42
24 2 0.08
25 12 0.50
ACGTcount: A:0.53, C:0.20, G:0.14, T:0.12
Consensus pattern (24 bp):
ACAAGGTCAACAGATACAATAAAC
Found at i:467255 original size:15 final size:15
Alignment explanation
Indices: 467235--467265 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
467225 ATTTCGTTTG
*
467235 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
467250 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
467265 G
1 G
467266 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:469098 original size:21 final size:21
Alignment explanation
Indices: 469069--469113 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
469059 AAGTTTTCAT
*
469069 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
469089 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
469111 TTT
1 TTT
469114 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:470638 original size:33 final size:33
Alignment explanation
Indices: 470601--470667 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
470591 TTCAACGATT
470601 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
470634 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
470667 T
1 T
470668 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:470639 original size:13 final size:13
Alignment explanation
Indices: 470621--470645 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
470611 CATAAAATGT
470621 TGTATCGATACAA
1 TGTATCGATACAA
470634 TGTATCGATACA
1 TGTATCGATACA
470646 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:470798 original size:52 final size:52
Alignment explanation
Indices: 470742--470862 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
470732 CACCGATCTT
*
470742 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
470794 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
470846 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
470863 ATAAATTTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:474994 original size:20 final size:21
Alignment explanation
Indices: 474969--475021 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
474959 TACAAGCCAA
**
474969 TGTATCGATACAATTTTTTG-
1 TGTATCGATACAATTACTTGC
474989 TGTATCGATAC-ATTACTTGC
1 TGTATCGATACAATTACTTGC
475009 TGTATCGATACAA
1 TGTATCGATACAA
475022 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 6 0.21
20 22 0.76
21 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (21 bp):
TGTATCGATACAATTACTTGC
Found at i:476209 original size:52 final size:52
Alignment explanation
Indices: 476060--476188 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
476050 CAAAATATGA
* *
476060 AAATTTGGCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
* *
476112 AAATTTGCCTGTATGTATCGATACATTTTATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
476164 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
476189 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
Found at i:476275 original size:32 final size:32
Alignment explanation
Indices: 476232--476334 Score: 179
Period size: 32 Copynumber: 3.2 Consensus size: 32
476222 AGCTTCGTAG
* *
476232 CGATACATTGTATCGAAACAAAACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
*
476264 CAATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
476296 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
476328 CGATACA
1 CGATACA
476335 AATCGTTGAA
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 67 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:476296 original size:19 final size:19
Alignment explanation
Indices: 476272--476335 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
476262 ATCAATACAT
476272 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
476291 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
476304 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
476323 TGTATCGATACAA
1 TGTATCGATACAA
476336 ATCGTTGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 9 0.23
14 1 0.03
16 6 0.15
18 1 0.03
19 22 0.56
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:476309 original size:13 final size:13
Alignment explanation
Indices: 476259--476315 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
476249 ACAAAACTTA
*
476259 TGTATCAATACAT
1 TGTATCGATACAT
476272 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
476290 ATGTATCGATACAT
1 -TGTATCGATACAT
476304 TGTATCGATACA
1 TGTATCGATACA
476316 ACACTTATGT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 20 0.54
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:479406 original size:3 final size:3
Alignment explanation
Indices: 479398--479433 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
479388 ATCAAAGATA
479398 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
479434 CTCGGATGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:486407 original size:21 final size:21
Alignment explanation
Indices: 486358--486409 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
486348 AATATCAAAG
**
486358 ATGTTTTAAAGTTAAGTATAA
1 ATGTTTTTCAGTTAAGTATAA
486379 ATGTTTTTCAGTTAAGTATAA
1 ATGTTTTTCAGTTAAGTATAA
486400 ATGTTTTTCA
1 ATGTTTTTCA
486410 AGCTATAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.48
Consensus pattern (21 bp):
ATGTTTTTCAGTTAAGTATAA
Found at i:486576 original size:13 final size:13
Alignment explanation
Indices: 486558--486584 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
486548 ACATATTACT
486558 TTGTATCGATACA
1 TTGTATCGATACA
486571 TTGTATCGATACA
1 TTGTATCGATACA
486584 T
1 T
486585 ATTCTTGGTA
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:491091 original size:20 final size:20
Alignment explanation
Indices: 491066--491120 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
491056 TTCTGGAAAA
491066 ATTGTATCGATACATTATTC
1 ATTGTATCGATACATTATTC
* *
491086 ATTGTATCGATACATTCTTT
1 ATTGTATCGATACATTATTC
* *
491106 AATATATCGATACAT
1 ATTGTATCGATACAT
491121 GCAGGCAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.44
Consensus pattern (20 bp):
ATTGTATCGATACATTATTC
Found at i:495462 original size:20 final size:20
Alignment explanation
Indices: 495398--495469 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
495388 AGCCAGTTTC
** *
495398 ATGTATCGATACAATTCACT
1 ATGTATCGATACAAAGCAAT
* ** *
495418 GTGTATCGATACCGAG-AAC
1 ATGTATCGATACAAAGCAAT
495437 ATGTATCGATACAAAGCAAT
1 ATGTATCGATACAAAGCAAT
495457 ATGTATCGATACA
1 ATGTATCGATACA
495470 TCTGGGTATG
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
19 14 0.35
20 26 0.65
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.28
Consensus pattern (20 bp):
ATGTATCGATACAAAGCAAT
Found at i:500026 original size:19 final size:18
Alignment explanation
Indices: 499967--500064 Score: 72
Period size: 19 Copynumber: 5.8 Consensus size: 18
499957 ATTTCAACGA
499967 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
*
499986 TGTTATATCGATAC--AA-
1 T-TTGTATCGATACATAAG
500002 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
*
500018 TGTTGTATCGGTAC--AA-
1 T-TTGTATCGATACATAAG
500034 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
500050 TTTTGTATCGATACA
1 -TTTGTATCGATACA
500065 ATGTAAGCTA
Statistics
Matches: 62, Mismatches: 4, Indels: 26
0.67 0.04 0.28
Matches are distributed among these distances:
13 20 0.32
15 4 0.06
17 4 0.06
19 23 0.37
20 11 0.18
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:500027 original size:32 final size:32
Alignment explanation
Indices: 499969--500069 Score: 166
Period size: 32 Copynumber: 3.1 Consensus size: 32
499959 TTCAACGATT
*
499969 TGTATCGATACATAAAGTGTTATATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
*
500002 TGTATCGATACATAAGTGTTGTATCGGTACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
500034 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
500066 TGTA
1 TGTA
500070 AGCTACTGCC
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 51 0.80
33 13 0.20
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:500184 original size:52 final size:52
Alignment explanation
Indices: 500140--500424 Score: 498
Period size: 52 Copynumber: 5.5 Consensus size: 52
500130 CACTGATCTT
* * *
500140 TGTATCGATACATGCAGGCAAGTTTGCCCAGATGTATCAATACACTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
500192 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
500244 TGTATCGATACATGCAGGCAAGTTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
500296 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* * *
500348 TGTCTCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
500400 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
500425 TCATATTTTG
Statistics
Matches: 221, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 221 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:508907 original size:20 final size:21
Alignment explanation
Indices: 508881--508936 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
508871 TACAAACAGC
*
508881 AAATGTATCGATACATGAGT-
1 AAATGTATCGATACATGACTA
* *
508901 GAATGTATCGATACATGCCTA
1 AAATGTATCGATACATGACTA
508922 AAATGTATCGATACA
1 AAATGTATCGATACA
508937 AAACTACCCT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 17 0.55
21 14 0.45
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (21 bp):
AAATGTATCGATACATGACTA
Found at i:514999 original size:166 final size:164
Alignment explanation
Indices: 514604--515009 Score: 449
Period size: 166 Copynumber: 2.4 Consensus size: 164
514594 TTTCATCAGA
* * *
514604 TTAAAATTTTTAAAATTCATCGAATATTATTATCTAATTACTATTTAATCAGTTTTGAAAAATTC
1 TTAAAATTTTTAAAATTCATCAAATATTATCAT-TAATT-CTATTAAATCAGTTTTGAAAAATTC
* * * *
514669 ATTTATTTGCATAAGTTTTTCATTTTTTCCTTAAAATTCTCGTATTTTCAAAAAATCGAGTTTTC
64 ATTTATTTGCATAAGTTTTTCATTTTTTCCTTAAAATTCTCCTATTTCCAAAAAATCAAATTTTC
*
514734 TATTTCATAAATGTTTTCAGGGGAGTTTTTCTTGGT
129 TATTTCATAAATGTTTTCAGGGGAGCTTTTCTTGGT
* * ** * * ** *
514770 TCAAAATGTTTATTATTCATCAAATATCATCATTTAAATCATAGAAAATCAATTTTGAAAAATTC
1 TTAAAATTTTTAAAATTCATCAAATATTATCA-TTAATTC-TATTAAATCAGTTTTGAAAAATTC
* * * * *
514835 TTTTTTTTGCATGAGTTTTTCA-TTTTTCCTTTGAAATTTTCCTATTTCCAAAAAA-CTAAATTT
64 ATTTATTTGCATAAGTTTTTCATTTTTTCC-TTAAAATTCTCCTATTTCCAAAAAATC-AAATTT
*
514898 TCTATTTCATAAATGTTTT-TGGGGAGACTTTTCTTGGT
127 TCTATTTCATAAATGTTTTCAGGGGAG-CTTTTCTTGGT
* * **
514936 TTAAAATTTTTAAAATTCATCTAATATTGTCATTGAATTCTCATTAAATCAGTTTAAAAAAATTT
1 TTAAAATTTTTAAAATTCATCAAATATTATCATT-AATTCT-ATTAAATCAGTTTTGAAAAA-TT
*
515001 AATTTATTT
63 CATTTATTT
515010 TATGAGTTTT
Statistics
Matches: 193, Mismatches: 39, Indels: 15
0.78 0.16 0.06
Matches are distributed among these distances:
165 18 0.09
166 166 0.86
167 9 0.05
ACGTcount: A:0.33, C:0.11, G:0.08, T:0.48
Consensus pattern (164 bp):
TTAAAATTTTTAAAATTCATCAAATATTATCATTAATTCTATTAAATCAGTTTTGAAAAATTCAT
TTATTTGCATAAGTTTTTCATTTTTTCCTTAAAATTCTCCTATTTCCAAAAAATCAAATTTTCTA
TTTCATAAATGTTTTCAGGGGAGCTTTTCTTGGT
Found at i:515486 original size:6 final size:6
Alignment explanation
Indices: 515471--515531 Score: 65
Period size: 6 Copynumber: 10.3 Consensus size: 6
515461 GAGCTTTGGT
*
515471 AAAGAG AAAGAA AAAGAGA GAAAGAA AAA-AA AAAGAA AAAG-A AAAGAA
1 AAAGAA AAAGAA AAAGA-A -AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
*
515519 AAA-AA AGAGAA AA
1 AAAGAA AAAGAA AA
515532 TAAGAAAATA
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
5 14 0.30
6 26 0.55
7 2 0.04
8 5 0.11
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:515492 original size:14 final size:14
Alignment explanation
Indices: 515473--515528 Score: 66
Period size: 14 Copynumber: 4.2 Consensus size: 14
515463 GCTTTGGTAA
515473 AGAGAAAGAAAAAG
1 AGAGAAAGAAAAAG
515487 AGAGAAAGAAAAA-
1 AGAGAAAGAAAAAG
515500 A-A-AAAGAAAAAG
1 AGAGAAAGAAAAAG
*
515512 AAAAGAAA-AAAAAG
1 -AGAGAAAGAAAAAG
515526 AGA
1 AGA
515529 AAATAAGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
11 9 0.24
12 1 0.03
13 4 0.11
14 20 0.54
15 3 0.08
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AGAGAAAGAAAAAG
Found at i:515507 original size:11 final size:11
Alignment explanation
Indices: 515477--515531 Score: 65
Period size: 11 Copynumber: 4.7 Consensus size: 11
515467 TGGTAAAGAG
515477 AAAGAAAAAGAGA
1 AAAGAAAAA-A-A
515490 GAAAGAAAAAAA
1 -AAAGAAAAAAA
*
515502 AAAGAAAAAGA
1 AAAGAAAAAAA
515513 AAAGAAAAAAA
1 AAAGAAAAAAA
*
515524 AGAGAAAA
1 AAAGAAAA
515532 TAAGAAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
11 27 0.71
12 1 0.03
13 1 0.03
14 9 0.24
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:515519 original size:22 final size:24
Alignment explanation
Indices: 515477--515531 Score: 78
Period size: 22 Copynumber: 2.3 Consensus size: 24
515467 TGGTAAAGAG
515477 AAAGAAAAAGAGAGAAAGAAAAAAA
1 AAAG-AAAAGAGAGAAAGAAAAAAA
515502 AAAGAAAA-AGA-AAAGAAAAAAA
1 AAAGAAAAGAGAGAAAGAAAAAAA
*
515524 AGAGAAAA
1 AAAGAAAA
515532 TAAGAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 18 0.62
23 3 0.10
24 4 0.14
25 4 0.14
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (24 bp):
AAAGAAAAGAGAGAAAGAAAAAAA
Found at i:515536 original size:10 final size:9
Alignment explanation
Indices: 515475--515539 Score: 51
Period size: 10 Copynumber: 6.7 Consensus size: 9
515465 TTTGGTAAAG
515475 AGAAAGAAAA
1 AGAAA-AAAA
*
515485 AGAGAGAAAGA
1 AGA-A-AAAAA
515496 A-AAAAAAA
1 AGAAAAAAA
515504 AGAAAAAGAAA
1 AG-AAAA-AAA
515515 AGAAAAAAA
1 AGAAAAAAA
*
515524 AGAGAAAATA
1 AGA-AAAAAA
515534 AGAAAA
1 AGAAAA
515540 TACATGCTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
8 5 0.11
9 10 0.22
10 20 0.43
11 10 0.22
12 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (9 bp):
AGAAAAAAA
Found at i:515539 original size:16 final size:14
Alignment explanation
Indices: 515471--515539 Score: 59
Period size: 14 Copynumber: 4.6 Consensus size: 14
515461 GAGCTTTGGT
*
515471 AAAGAGAAAGAAAA
1 AAAGAAAAAGAAAA
*
515485 AGAGAGAAAGAAAAAAA
1 A-A-AGAAA-AAGAAAA
515502 AAAGAAAAAGAAAA
1 AAAGAAAAAGAAAA
515516 GAAA-AAAAAGAGAAA
1 -AAAGAAAAAGA-AAA
515531 ATAAGAAAA
1 A-AAGAAAA
515540 TACATGCTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
14 15 0.33
15 14 0.31
16 9 0.20
17 7 0.16
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (14 bp):
AAAGAAAAAGAAAA
Found at i:518729 original size:20 final size:20
Alignment explanation
Indices: 518684--518737 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
518674 GTTACAAGCA
*
518684 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTCACC
*
518704 ACGTATCGATACAATGT-ACC
1 ATGTATCGATACAAT-TCACC
*
518724 ATGTATCAATACAA
1 ATGTATCGATACAA
518738 ACAGTGGTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACAATTCACC
Found at i:518805 original size:13 final size:13
Alignment explanation
Indices: 518787--518811 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
518777 ACAATGATCA
518787 TGTATCGATACAG
1 TGTATCGATACAG
518800 TGTATCGATACA
1 TGTATCGATACA
518812 AAGCATAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:518828 original size:33 final size:32
Alignment explanation
Indices: 518768--518830 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
518758 GCCAGTTTCA
* *
518768 TGTATCGATACAATGATCATGTATCGATACAG
1 TGTATCGATACAAAGATAATGTATCGATACAG
518800 TGTATCGATACAAAGCATAATGTATCGATAC
1 TGTATCGATACAAAG-ATAATGTATCGATAC
518831 TTCTGGGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (32 bp):
TGTATCGATACAAAGATAATGTATCGATACAG
Found at i:525680 original size:13 final size:13
Alignment explanation
Indices: 525664--525691 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
525654 TACAAAAGAT
525664 CAATGTATCGATA
1 CAATGTATCGATA
525677 CAATGTATCGATA
1 CAATGTATCGATA
525690 CA
1 CA
525692 TTTGAGTAAT
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:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:527570 original size:27 final size:28
Alignment explanation
Indices: 527530--527582 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
527520 CAAAATTTTA
527530 TTCGACGGAGACACTCCAACCCCATTCC
1 TTCGACGGAGACACTCCAACCCCATTCC
*
527558 TTCGA-GGGGACACTCCAACCCCATT
1 TTCGACGGAGACACTCCAACCCCATT
527583 TTCAACCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 19 0.79
28 5 0.21
ACGTcount: A:0.25, C:0.40, G:0.17, T:0.19
Consensus pattern (28 bp):
TTCGACGGAGACACTCCAACCCCATTCC
Found at i:533409 original size:52 final size:52
Alignment explanation
Indices: 533225--533620 Score: 287
Period size: 53 Copynumber: 7.5 Consensus size: 52
533215 GCTAAGATGT
* * * * *
533225 TGATTCAAGGCTAGCGACATTGGACTTAAAGATGGT-AAGAATGCCAATTGGGC
1 TGATTCAAGGCCAGCGACATCGGACTTAAAGATGATAAAG-GTGCCAA-TGTGC
* * * * * * * *
533278 TGATTAAAGGTCAGTG-CTATTGGACTTAGAGATGAT-AAGAATGCTGAATGTGT
1 TGATTCAAGGCCAGCGAC-ATCGGACTTAAAGATGATAAAG-GTGC-CAATGTGC
* * * *
533331 TGATTCAAGGCCAGCGGCATTGGACTTAAAGATGATAAAGGTGCTAATATGC
1 TGATTCAAGGCCAGCGACATCGGACTTAAAGATGATAAAGGTGCCAATGTGC
* * * * *
533383 TGATTCAAGGCCAGCAATATCAGACTTAAAGATGATAAGGGTGCCAATGTGA
1 TGATTCAAGGCCAGCGACATCGGACTTAAAGATGATAAAGGTGCCAATGTGC
* * * * ** * * * *
533435 TGATTTAAGGCTAGCAACATTGGGTTTAAAAAATGACAAAAGTGCCTATGTGC
1 TGATTCAAGGCCAGCGACATCGGACTT-AAAGATGATAAAGGTGCCAATGTGC
* *
533488 TAATTCAAGGCCAGCGACATCGGACTTAGAAAGAT-ATAAAGGTGCCAATATGC
1 TGATTCAAGGCCAGCGACATCGGACTT--AAAGATGATAAAGGTGCCAATGTGC
* * * * * * *
533541 TGATTCAACGCTAGTGATATCAGATTTAAAGATGACAAAGGTGCCAATGTGC
1 TGATTCAAGGCCAGCGACATCGGACTTAAAGATGATAAAGGTGCCAATGTGC
* ** *
533593 CGATTCAAGGCCAATGACATTGGACTTA
1 TGATTCAAGGCCAGCGACATCGGACTTA
533621 GAAAGAGATG
Statistics
Matches: 267, Mismatches: 69, Indels: 15
0.76 0.20 0.04
Matches are distributed among these distances:
51 6 0.02
52 105 0.39
53 145 0.54
54 11 0.04
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (52 bp):
TGATTCAAGGCCAGCGACATCGGACTTAAAGATGATAAAGGTGCCAATGTGC
Found at i:533577 original size:105 final size:106
Alignment explanation
Indices: 533356--533626 Score: 280
Period size: 105 Copynumber: 2.6 Consensus size: 106
533346 GGCATTGGAC
* * * * *
533356 TTAAAGATGATAAAGGTG-CTAATATGCTGATTCAAGGCCAGCAATATCAGACTT--AAAGATGA
1 TTAAAGATGACAAAGGTGCCT-ATGTGCTGATTCAAGGCCAGCGACATCGGACTTAGAAAGATGA
* * * * ** *
533418 TAAGGGTGCCAATGTGATGATTTAAGGCTAGCAACATTGGGT
65 TAAAGGTGCCAATATGATGATTCAACGCTAGCAACATCAGAT
* * *
533460 TTAAAAAATGACAAAAGTGCCTATGTGCTAATTCAAGGCCAGCGACATCGGACTTAGAAAGAT-A
1 TT-AAAGATGACAAAGGTGCCTATGTGCTGATTCAAGGCCAGCGACATCGGACTTAGAAAGATGA
* ** *
533524 TAAAGGTGCCAATATGCTGATTCAACGCTAGTGATATCAGAT
65 TAAAGGTGCCAATATGATGATTCAACGCTAGCAACATCAGAT
* * ** *
533566 TTAAAGATGACAAAGGTGCCAATGTGCCGATTCAAGGCCAATGACATTGGACTTAGAAAGA
1 TTAAAGATGACAAAGGTGCCTATGTGCTGATTCAAGGCCAGCGACATCGGACTTAGAAAGA
533627 GATGGTTTGA
Statistics
Matches: 136, Mismatches: 27, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
104 2 0.01
105 92 0.68
106 36 0.26
107 6 0.04
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (106 bp):
TTAAAGATGACAAAGGTGCCTATGTGCTGATTCAAGGCCAGCGACATCGGACTTAGAAAGATGAT
AAAGGTGCCAATATGATGATTCAACGCTAGCAACATCAGAT
Found at i:533765 original size:33 final size:32
Alignment explanation
Indices: 533672--533992 Score: 311
Period size: 31 Copynumber: 10.1 Consensus size: 32
533662 CCAACAACAT
* **
533672 TGGGC-TTAG-AAGGAGATGCCACTGTCTTGTG
1 TGGGCTTTAGAAAGG-GTTGCCACTAACTTGTG
*
533703 TGGGCTTTTA-AAAGGGTTGCCA-TCGACTTGTG
1 TGGGC-TTTAGAAAGGGTTGCCACT-AACTTGTG
533735 TGGGCTTTAGAAAGGGGTTGCCACTAACTTGTG
1 TGGGCTTTAGAAA-GGGTTGCCACTAACTTGTG
* * *
533768 TGGGCTTTAGAAAAAGGTTGCCACTGACTTATG
1 TGGGCTTTAG-AAAGGGTTGCCACTAACTTGTG
* * *
533801 TGGGATTTAGAAAAGGGTTGCCACTGACTTATG
1 TGGGCTTTAG-AAAGGGTTGCCACTAACTTGTG
* **
533834 CGGGCTTTCA-AAA-GGTTGCCACCGACTTGTG
1 TGGGCTTT-AGAAAGGGTTGCCACTAACTTGTG
* *
533865 TGGGCTTTAG-AAGAGG-TGCCACAAATTTGTG
1 TGGGCTTTAGAAAG-GGTTGCCACTAACTTGTG
* *
533896 TGGGCTTTAGAAAGGGGTGCCACCAACTTGTG
1 TGGGCTTTAGAAAGGGTTGCCACTAACTTGTG
* *
533928 TGGGCTTTAG-AAGGGTTGCCATTAACTTGTA
1 TGGGCTTTAGAAAGGGTTGCCACTAACTTGTG
* *
533959 TGGGCTTTA-AAAGGGTTACCACCAACTTGTG
1 TGGGCTTTAGAAAGGGTTGCCACTAACTTGTG
533990 TGG
1 TGG
533993 AGTTTTAAAA
Statistics
Matches: 249, Mismatches: 26, Indels: 30
0.82 0.09 0.10
Matches are distributed among these distances:
30 3 0.01
31 103 0.41
32 52 0.21
33 86 0.35
34 5 0.02
ACGTcount: A:0.23, C:0.16, G:0.31, T:0.30
Consensus pattern (32 bp):
TGGGCTTTAGAAAGGGTTGCCACTAACTTGTG
Found at i:534130 original size:62 final size:60
Alignment explanation
Indices: 534033--534532 Score: 394
Period size: 60 Copynumber: 8.3 Consensus size: 60
534023 ACTTTGAAAG
* *
534033 GTGCCACAGGGTTGTGTACTTAAAAGAGGTGCCACAGAGTTATGGACTTAAAAGGAAAAAAA
1 GTGCCACAGAGTTGTGGACTTAAAAG-GGTGCCACAGAGTTATGGACTTAAAAGG-AAAAAA
* * * * *
534095 GTGCCATAGAGTTGTGGACTTAAAAAGGGTGCCACAAAGTTGTGGACTTAAAAAGAAAAAGG
1 GTGCCACAGAGTTGTGGACTT-AAAAGGGTGCCACAGAGTTATGGACTTAAAAGGAAAAA-A
* * * * *
534157 GTGCTACGGAGTTGTGGACTTTAAAAAGGTGCCATAGAGTTATGGACTT------AAAAAG
1 GTGCCACAGAGTTGTGGAC-TTAAAAGGGTGCCACAGAGTTATGGACTTAAAAGGAAAAAA
* * ** ** *
534212 GTGCCACAAAGTTGTGGGCTTAAAAGGGCACCATGGAGTTATGGACTTAAAAGGAAAAAG
1 GTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTATGGACTTAAAAGGAAAAAA
* * * *
534272 GTGCCATAAAGTTATGGACTTAAAAGGGTGCCACGGAGTTATGGACTTAAAAGGAAAAAA
1 GTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTATGGACTTAAAAGGAAAAAA
* * ** * * ** * *
534332 TTTCCATGGTGTTGTGGACGTAAAAGGGTGCCATGGAGTTGTGGACTTTAAAGG-AAAAA
1 GTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTATGGACTTAAAAGGAAAAAA
* * * ** **
534391 GTGTCAC-GAAGTTGTGGACTTAAAAGGGTGTCAC-GAAGTTGTGGACTTAAAAATAGAAATG
1 GTGCCACAG-AGTTGTGGACTTAAAAGGGTGCCACAG-AGTTATGGACTTAAAAGGA-AAAAA
* *
534452 GTGCCACGGAGTTGTGGACTTAAAAAGAAAAGGGTGCCACAGAGTTATGGACTT---AGAAAAAA
1 GTGCCACAGAGTTGTGGACTT------AAAAGGGTGCCACAGAGTTATGGACTTAAAAGGAAAAA
534514 A
60 A
**
534515 GTGCCATGGAGTTGTGGA
1 GTGCCACAGAGTTGTGGA
534533 ATTTGAGAAG
Statistics
Matches: 357, Mismatches: 60, Indels: 41
0.78 0.13 0.09
Matches are distributed among these distances:
54 25 0.07
55 16 0.04
56 5 0.01
58 2 0.01
59 44 0.12
60 103 0.29
61 26 0.07
62 83 0.23
63 27 0.08
64 2 0.01
67 23 0.06
68 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.30, T:0.23
Consensus pattern (60 bp):
GTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTATGGACTTAAAAGGAAAAAA
Found at i:534155 original size:34 final size:34
Alignment explanation
Indices: 534054--534184 Score: 130
Period size: 34 Copynumber: 4.0 Consensus size: 34
534044 TTGTGTACTT
* *
534054 AAAAGAGGTGCCACAGAGTTATGGACTTAAAAGGA
1 AAAAG-GGTGCCACAGAGTTGTGGACTTAAAAAGA
** *
534089 AAAAAAGTGCCATAGAGTTGTGGACTT------A
1 AAAAGGGTGCCACAGAGTTGTGGACTTAAAAAGA
*
534117 AAAAGGGTGCCACAAAGTTGTGGACTTAAAAAGA
1 AAAAGGGTGCCACAGAGTTGTGGACTTAAAAAGA
* *
534151 AAAAGGGTGCTACGGAGTTGTGGACTTTAAAAAG
1 AAAAGGGTGCCACAGAGTTGTGGAC-TTAAAAAG
534185 GTGCCATAGA
Statistics
Matches: 78, Mismatches: 11, Indels: 14
0.76 0.11 0.14
Matches are distributed among these distances:
28 24 0.31
34 42 0.54
35 12 0.15
ACGTcount: A:0.40, C:0.11, G:0.28, T:0.21
Consensus pattern (34 bp):
AAAAGGGTGCCACAGAGTTGTGGACTTAAAAAGA
Found at i:534527 original size:30 final size:32
Alignment explanation
Indices: 534029--534532 Score: 215
Period size: 27 Copynumber: 16.7 Consensus size: 32
534019 GTGGACTTTG
*
534029 AAAGGTGCCACAGG-GTTGTGTACTT-AAAAG-
1 AAAGGTGCCAC-GGAGTTGTGGACTTAAAAAGA
* * *
534059 --AGGTGCCACAGAGTTATGGACTTAAAAGGAAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAA--AGA
* **
534091 AAAAGTGCCATAGAGTTGTGGACTTAAAAAG-
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAAGA
**
534122 ---GGTGCCACAAAGTTGTGGACTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAAG-A
* *
534152 AAAGGGTGCTACGGAGTTGTGGACTT---TA-A
1 AAA-GGTGCCACGGAGTTGTGGACTTAAAAAGA
** *
534181 AAAGGTGCCATAGAGTTATGGACTT----A-A
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAAGA
** *
534208 AAAGGTGCCACAAAGTTGTGGGCTT-AAAAG-
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAAGA
** * * *
534238 ---GGCACCATGGAGTTATGGACTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAAG-A
*** *
534268 AAAGGTGCCATAAAGTTATGGACTT-AAAAG-
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAAGA
* *
534298 ---GGTGCCACGGAGTTATGGACTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAAG-A
** * * * *
534328 AAAATTTCCATGGTGTTGTGGACGT-AAAAG-
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAAGA
* * *
534358 ---GGTGCCATGGAGTTGTGGACTTTAAAGGA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAAGA
* * *
534387 AAAAGTGTCACGAAGTTGTGGACTT-AAAAG-
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAAGA
* *
534417 ---GGTGTCACGAAGTTGTGGACTTAAAAATAGA
1 AAAGGTGCCACGGAGTTGTGGACTT-AAAA-AGA
*
534448 AATGGTGCCACGGAGTTGTGGACTTAAAAAGA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAAGA
* * *
534480 AAAGGGTGCCACAGAGTTATGGACTTAGAAA-A
1 AAA-GGTGCCACGGAGTTGTGGACTTAAAAAGA
*
534512 AAA-GTGCCATGGAGTTGTGGA
1 AAAGGTGCCACGGAGTTGTGGA
534533 ATTTGAGAAG
Statistics
Matches: 363, Mismatches: 69, Indels: 84
0.70 0.13 0.16
Matches are distributed among these distances:
27 96 0.26
28 73 0.20
29 10 0.03
30 18 0.05
31 6 0.02
32 36 0.10
33 61 0.17
34 63 0.17
ACGTcount: A:0.36, C:0.12, G:0.30, T:0.23
Consensus pattern (32 bp):
AAAGGTGCCACGGAGTTGTGGACTTAAAAAGA
Found at i:534583 original size:29 final size:30
Alignment explanation
Indices: 534529--534595 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 30
534519 CATGGAGTTG
*
534529 TGGAATTTGAGAAGAGATGCCACTAAGTCA
1 TGGACTTTGAGAAGAGATGCCACTAAGTCA
* **
534559 TGGACTTTGAGAAG-GGTGCCACTAAGTGG
1 TGGACTTTGAGAAGAGATGCCACTAAGTCA
534588 TGGACTTT
1 TGGACTTT
534596 TGGAAAAAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
29 20 0.61
30 13 0.39
ACGTcount: A:0.28, C:0.13, G:0.31, T:0.27
Consensus pattern (30 bp):
TGGACTTTGAGAAGAGATGCCACTAAGTCA
Found at i:540856 original size:19 final size:20
Alignment explanation
Indices: 540832--540885 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
540822 ACATTATGCT
**
540832 TTGTATCGATACATG-TTAA
1 TTGTATCGATACATGCACAA
*
540851 TTGTATCGATGCATGCACAA
1 TTGTATCGATACATGCACAA
540871 TTGTATCGATACATG
1 TTGTATCGATACATG
540886 AAATTGGCAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGCACAA
Found at i:544748 original size:13 final size:13
Alignment explanation
Indices: 544730--544755 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
544720 TACACCAAGC
544730 ATGTATCGATACA
1 ATGTATCGATACA
544743 ATGTATCGATACA
1 ATGTATCGATACA
544756 CCAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:544753 original size:32 final size:33
Alignment explanation
Indices: 544712--544775 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
544702 TAGCCAAACT
**
544712 TGTATCGATACACCAAGCA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
544744 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
544776 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:545267 original size:34 final size:35
Alignment explanation
Indices: 545204--545270 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
545194 CTAAGTGATT
545204 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
545240 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
545271 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:548119 original size:19 final size:19
Alignment explanation
Indices: 548083--548121 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
548073 CTTAAATGGA
* *
548083 TTTTTATTCAATTTTTGAT
1 TTTTTATTCAAATATTGAT
*
548102 TTTTTTTTCAAATATTGAT
1 TTTTTATTCAAATATTGAT
548121 T
1 T
548122 AATCTTGATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (19 bp):
TTTTTATTCAAATATTGAT
Found at i:548447 original size:13 final size:13
Alignment explanation
Indices: 548429--548453 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
548419 TTTTCCAAAT
548429 TGTATCGATACAA
1 TGTATCGATACAA
548442 TGTATCGATACA
1 TGTATCGATACA
548454 TTGCTTCAGT
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:549458 original size:124 final size:124
Alignment explanation
Indices: 549307--549554 Score: 478
Period size: 124 Copynumber: 2.0 Consensus size: 124
549297 ATTGCATAAA
549307 CCTTTGGTATTAAGAAGGGGAGAGAATAGATTTGGCCTAATAGAAAAGGGGAGATATTTTAGTAA
1 CCTTTGGTATTAAGAAGGGGAGAGAATAGATTTGGCCTAATAGAAAAGGGGAGATATTTTAGTAA
549372 GGGGAAGAAAATGTTTATTTGTTATAAAGGAAGAAATTGATAATATTGAAGAATATTGG
66 GGGGAAGAAAATGTTTATTTGTTATAAAGGAAGAAATTGATAATATTGAAGAATATTGG
*
549431 CCTTTGGTATTAAGAAGGGGAGAGAATAGATTTGGCCTAATAGAAAGGGGGAGATATTTTAGTAA
1 CCTTTGGTATTAAGAAGGGGAGAGAATAGATTTGGCCTAATAGAAAAGGGGAGATATTTTAGTAA
*
549496 GGGGACGAAAATGTTTATTTGTTATAAAGGAAGAAATTGATAATATTGAAGAATATTGG
66 GGGGAAGAAAATGTTTATTTGTTATAAAGGAAGAAATTGATAATATTGAAGAATATTGG
549555 TATAAAATTT
Statistics
Matches: 122, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
124 122 1.00
ACGTcount: A:0.39, C:0.04, G:0.28, T:0.30
Consensus pattern (124 bp):
CCTTTGGTATTAAGAAGGGGAGAGAATAGATTTGGCCTAATAGAAAAGGGGAGATATTTTAGTAA
GGGGAAGAAAATGTTTATTTGTTATAAAGGAAGAAATTGATAATATTGAAGAATATTGG
Found at i:550450 original size:20 final size:20
Alignment explanation
Indices: 550396--550451 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
550386 AAAACCCTTA
** *
550396 AAAGTATCGATACACATTTC
1 AAAGTATCGATACATGTTGC
550416 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTTGC
*
550436 AATGTATCGATACATG
1 AAAGTATCGATACATG
550452 AAAAATATGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (20 bp):
AAAGTATCGATACATGTTGC
Found at i:550539 original size:13 final size:13
Alignment explanation
Indices: 550521--550546 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
550511 TACACCAAGT
550521 ATGTATCGATACA
1 ATGTATCGATACA
550534 ATGTATCGATACA
1 ATGTATCGATACA
550547 CCAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:550544 original size:32 final size:33
Alignment explanation
Indices: 550503--550566 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
550493 TAGCCAAACT
**
550503 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
550535 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
550567 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:551058 original size:34 final size:35
Alignment explanation
Indices: 550995--551061 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
550985 CTAAGTGATT
550995 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
551031 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
551062 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:554181 original size:20 final size:21
Alignment explanation
Indices: 554143--554182 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
554133 TTTCAAATTT
*
554143 CTTCATTTTCACTTCAAAATA
1 CTTCATTTTCACATCAAAATA
554164 CTTCATTTT-ACATCAAAAT
1 CTTCATTTTCACATCAAAAT
554183 TATCAACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (21 bp):
CTTCATTTTCACATCAAAATA
Found at i:555765 original size:22 final size:22
Alignment explanation
Indices: 555738--555789 Score: 86
Period size: 22 Copynumber: 2.3 Consensus size: 22
555728 TCAAACGAGA
555738 TAAAAAAGATTTAATTTTTTGGT
1 TAAAAAAGATTTAA-TTTTTGGT
555761 TAAAAAAGATTTAATTTTTGGT
1 TAAAAAAGATTTAATTTTTGGT
*
555783 TGAAAAA
1 TAAAAAA
555790 TGGGATGGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.42
Consensus pattern (22 bp):
TAAAAAAGATTTAATTTTTGGT
Found at i:557214 original size:20 final size:22
Alignment explanation
Indices: 557179--557219 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
557169 TGGACATGTT
557179 AAAATGCAAGGAACAT-GGCTC
1 AAAATGCAAGGAACATAGGCTC
*
557200 AAAATGC-ATGAACATAGGCT
1 AAAATGCAAGGAACATAGGCT
557220 GTTTAAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.17
Consensus pattern (22 bp):
AAAATGCAAGGAACATAGGCTC
Found at i:558284 original size:20 final size:21
Alignment explanation
Indices: 558261--558299 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
558251 GATACATTCA
558261 CTTA-TGTATCAATACAAAGC
1 CTTATTGTATCAATACAAAGC
*
558281 CTTATTGTCTCAATACAAA
1 CTTATTGTATCAATACAAA
558300 TTGTTGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (21 bp):
CTTATTGTATCAATACAAAGC
Found at i:562831 original size:52 final size:52
Alignment explanation
Indices: 562753--562883 Score: 199
Period size: 52 Copynumber: 2.5 Consensus size: 52
562743 CCCGAAATAT
* *
562753 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTTCACAGTGTATCGATACATCTCG
* *
562805 GAAAATTTGCCTGCATGTATCGATACATTTTACAGTGTATTGATACATCTCG
1 GAAAATTTGCCTGCATGTATCGATACATTTCACAGTGTATCGATACATCTCG
* * *
562857 GCAAATTTGTCTGTATGTATCGATACA
1 GAAAATTTGCCTGCATGTATCGATACA
562884 AAGATTAGTG
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (52 bp):
GAAAATTTGCCTGCATGTATCGATACATTTCACAGTGTATCGATACATCTCG
Found at i:562894 original size:52 final size:50
Alignment explanation
Indices: 562753--562903 Score: 167
Period size: 52 Copynumber: 2.9 Consensus size: 50
562743 CCCGAAATAT
** *
562753 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACAGAT--TAGTGTATCGATACATCTCG
** *
562805 GAAAATTTGCCTGCATGTATCGATACATTTTACAGTGTATTGATACATCTCG
1 GAAAATTTGCCTGCATGTATCGATACAGATT--AGTGTATCGATACATCTCG
* * *
562857 GCAAATTTGTCTGTATGTATCGATACAAAGATTAGTGTATCGATACA
1 GAAAATTTGCCTGCATGTATCGATAC--AGATTAGTGTATCGATACA
562904 ATGTATCGAT
Statistics
Matches: 87, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
50 1 0.01
52 83 0.95
54 3 0.03
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (50 bp):
GAAAATTTGCCTGCATGTATCGATACAGATTAGTGTATCGATACATCTCG
Found at i:562910 original size:13 final size:13
Alignment explanation
Indices: 562892--562916 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
562882 CAAAGATTAG
562892 TGTATCGATACAA
1 TGTATCGATACAA
562905 TGTATCGATACA
1 TGTATCGATACA
562917 TTTAAGTAAT
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:562983 original size:19 final size:19
Alignment explanation
Indices: 562959--563023 Score: 61
Period size: 19 Copynumber: 3.7 Consensus size: 19
562949 TAGCTTACAT
562959 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
562978 TGTATCAATAC---A--T-
1 TGTATCGATACAAAACTTA
*
562991 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
*
563010 TGTATTGATACAAA
1 TGTATCGATACAAA
563024 TCGTTCAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
13 10 0.28
14 1 0.03
16 2 0.06
18 1 0.03
19 22 0.61
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:563021 original size:32 final size:32
Alignment explanation
Indices: 562954--563014 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
562944 GGCAGTAGCT
562954 TACATTGTATCGATACAAAACTTATGTATCAA
1 TACATTGTATCGATACAAAACTTATGTATCAA
*
562986 TACATTGTATCGATACAACACTTATGTAT
1 TACATTGTATCGATACAAAACTTATGTAT
563015 TGATACAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (32 bp):
TACATTGTATCGATACAAAACTTATGTATCAA
Found at i:563908 original size:67 final size:68
Alignment explanation
Indices: 563795--563921 Score: 195
Period size: 67 Copynumber: 1.9 Consensus size: 68
563785 ATTGGGTTTT
*
563795 AAAGATGATAAAGGTGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
563860 AGA
66 AGA
* * *
563863 AAAG-TGATAAAGATGCCAATATGTTGATTCACA-GCCAACGATATTGGGCTTAAAGATGA
1 AAAGATGATAAAGATGCCAATATGCTGATTCA-AGGCCAACAATATTGGACTTAAAGATGA
563922 GAAAAAGGAT
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
67 49 0.91
68 5 0.09
ACGTcount: A:0.41, C:0.13, G:0.23, T:0.24
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
AGA
Found at i:563971 original size:55 final size:52
Alignment explanation
Indices: 563871--564761 Score: 290
Period size: 49 Copynumber: 18.9 Consensus size: 52
563861 GAAAAGTGAT
* * * * * **
563871 AAAGATGCCAATATGTTGATTCACAGCCAA-CGATATTGGGCTTAAAGATGAGAA
1 AAAGGTGCCAATATGCTGATTCA-AGGCAAGCTACATTGAACTTAAAGATG-G-A
* * *
563925 AAAGGATGTCAATGTGCTGATTTAAGGCCAA-CTACATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGG-CAAGCTACATTGAACTTAAAGATGGA
* *
563978 AAAGGTGCCAATATGCTGATTCAAGGCAAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCAAGCTACATTGAACTTAAAGATGGA
* * * *
564021 AAAGGTGCCAATGTGCTGATTCAAGTCCAGCTACATTGGACTTAAAGA---A
1 AAAGGTGCCAATATGCTGATTCAAGGCAAGCTACATTGAACTTAAAGATGGA
* * * *
564070 GAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCAAGCTACATTGAACTTAAAGATGGA
* * *
564113 AAAGGTGCCAATAGTGCTGATTCAAAGCCAGCTACATTGGACTTAAAGA---A
1 AAAGGTGCCAATA-TGCTGATTCAAGGCAAGCTACATTGAACTTAAAGATGGA
* * * * * *
564163 GAAGGTTCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCAAGCTACATTGAACTTAAAGATGGA
* * *
564207 -AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---A
1 AAAGGTGCCAATATGCTGATTCAAGGCAAGCTACATTGAACTTAAAGATGGA
* * * * * *
564255 AAAGATGCCAATATGCTAATTCAAGGCCAGCGATATTGGAC-T-----T-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCAAGCTACATTGAACTTAAAGATGGA
* * * *
564299 -AAGGTGCCAATGTGCTAATTCAAGGCCAGCTACATTGGACTTAAAGA---A
1 AAAGGTGCCAATATGCTGATTCAAGGCAAGCTACATTGAACTTAAAGATGGA
* * * * *
564347 AAAGATACCAATATACTGATTCAAGGC---C-A-A-TGATA-TT--GGACTTG-
1 AAAGGTGCCAATATGCTGATTCAAGGCAAGCTACATTGA-ACTTAAAGA-TGGA
* * *
564391 -AAGGTGCCAATGTGCTGATTCAAGGCTAGCTACATTGGACTTAAAGA---A
1 AAAGGTGCCAATATGCTGATTCAAGGCAAGCTACATTGAACTTAAAGATGGA
* * * * * *
564439 GAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCAAGCTACATTGAACTTAAAGATGGA
* * *
564482 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCAAGCTACATTGAACTTAAAGATGGA
* * * *
564532 -AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCAAGCTACATTGAACTTAAAGATGGA
* * * * *
564574 AAAGGTGCCGATGTGCTGATTCAAGGCCAGCTACATTGCACTTAAAGA---C
1 AAAGGTGCCAATATGCTGATTCAAGGCAAGCTACATTGAACTTAAAGATGGA
* * *
564623 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCAAGCTACATTGAACTTAAAGATGGA
* * * * *
564666 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTAAATTGGACTTAAAGA---C
1 AAAGGTGCCAATATGCTGATTCAAGGCAAGCTACATTGAACTTAAAGATGGA
* * * *
564715 AAAGGTGCCAATATGTTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 AAAGGTGCCAATATGCTGATTCAAGGCAAGCTACATTGAACTTAAAG
564762 GAAGATGCCA
Statistics
Matches: 674, Mismatches: 84, Indels: 163
0.73 0.09 0.18
Matches are distributed among these distances:
41 2 0.00
43 258 0.38
44 34 0.05
45 2 0.00
46 3 0.00
47 1 0.00
48 8 0.01
49 276 0.41
50 11 0.02
51 6 0.01
52 27 0.04
53 6 0.01
54 7 0.01
55 33 0.05
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCAAGCTACATTGAACTTAAAGATGGA
Found at i:564102 original size:92 final size:92
Alignment explanation
Indices: 563925--564762 Score: 1295
Period size: 92 Copynumber: 9.1 Consensus size: 92
563915 AAGATGAGAA
* * * * *
563925 AAAGGATGTCAATGTGCTGATTTAAGGCCAACTACATTGAACTTAAAGATGGAAAAGGTGCCAAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---AGAAGGTGCCAAT
*
563990 ATGCTGATTCAAGGCAAGCTATATTGGACTT
62 ATGCTGATTCAAGGCCAGCTATATTGGACTT
*
564021 AAAGGTGCCAATGTGCTGATTCAAGTCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
564086 TGATTCAAGGCCAGCTATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
* *
564113 AAAGGTGCCAATAGTGCTGATTCAAAGCCAGCTACATTGGACTTAAAGAAGAAGGTTCCAATATG
1 AAAGGTGCCAAT-GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATG
*
564178 CTGATTCAAGGCCAGCGATATTGGACTT
65 CTGATTCAAGGCCAGCTATATTGGACTT
* * *
564206 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGATGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
* *
564271 TAATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
* * * * * *
564298 GAAGGTGCCAATGTGCTAATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGATACCAATATAC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
*
564363 TGATTCAAGGCCA-ATGATATTGGACTT
66 TGATTCAAGGCCAGCT-ATATTGGACTT
* * *
564390 GAAGGTGCCAATGTGCTGATTCAAGGCTAGCTACATTGGACTTAAAGAAGAAGATGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
*
564455 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
*
564482 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
*
564547 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
* *
564574 AAAGGTGCCGATGTGCTGATTCAAGGCCAGCTACATTGCACTTAAAGACA-AAGGTGCCAATATG
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-AGAAGGTGCCAATATG
564638 CTGATTCAAGGCCAGCTATATTGGACTT
65 CTGATTCAAGGCCAGCTATATTGGACTT
*
564666 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTAAATTGGACTTAAAGACA-AAGGTGCCAATATG
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-AGAAGGTGCCAATATG
*
564730 TTGATTCAAGGCCAGCTATATTGGACTT
65 CTGATTCAAGGCCAGCTATATTGGACTT
564758 AAAGG
1 AAAGG
564763 AAGATGCCAC
Statistics
Matches: 696, Mismatches: 42, Indels: 12
0.93 0.06 0.02
Matches are distributed among these distances:
92 566 0.81
93 87 0.12
95 38 0.05
96 5 0.01
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
TGATTCAAGGCCAGCTATATTGGACTT
Found at i:564927 original size:34 final size:34
Alignment explanation
Indices: 564867--565231 Score: 317
Period size: 33 Copynumber: 10.9 Consensus size: 34
564857 TTAAAAAGAT
* *
564867 GGTG-CACGGAGTCGTGGAC-TTAAAAGGTACAA
1 GGTGCCACGGAGTTGTGGACTTTAAAAGGAACAA
* * *
564899 GGTGCCATGGGGTTGTGGACTTTAAAAGGGAAAAA
1 GGTGCCACGGAGTTGTGGACTTTAAAA-GGAACAA
* * *
564934 TAGTGCCACGGAGTTGTGGGCTTGGAAAA-G---AA
1 -GGTGCCACGGAGTTGTGGACTT-TAAAAGGAACAA
* *
564966 GGTGCCATGGAGTCGTGGAC-TTAAAAGGAACAA
1 GGTGCCACGGAGTTGTGGACTTTAAAAGGAACAA
* * * *
564999 GGTGCCATGGGGTTGTAGACTTTAAAAGTGAAAAA
1 GGTGCCACGGAGTTGTGGACTTTAAAAG-GAACAA
*
565034 GAGTGCCACGGAGTTGTGGGCTTTGAAAA-GAACAA
1 G-GTGCCACGGAGTTGTGGACTTT-AAAAGGAACAA
* * *
565069 GGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA
1 GGTGCCACGGAGTTGTGGACTTTAAAAGGAACAA
* *
565103 GGTGCCACAGAGTTGTGGAC-TTAAAAGGAAGAA
1 GGTGCCACGGAGTTGTGGACTTTAAAAGGAACAA
* * *
565136 GATGCCACGGGGTCGTGGAC-TTAAAAGGAACAAA
1 GGTGCCACGGAGTTGTGGACTTTAAAAGGAAC-AA
*
565170 GAGTGCCACGGAGTTGTGGGCTTTGAAAA-G---AA
1 G-GTGCCACGGAGTTGTGGACTTT-AAAAGGAACAA
*
565202 GGTGCCACAGAGTTGTGGACTTTAAGAAGG
1 GGTGCCACGGAGTTGTGGACTTTAA-AAGG
565232 TATTTGAAGA
Statistics
Matches: 273, Mismatches: 40, Indels: 40
0.77 0.11 0.11
Matches are distributed among these distances:
29 4 0.01
30 4 0.01
31 38 0.14
32 10 0.04
33 72 0.26
34 61 0.22
35 33 0.12
36 39 0.14
37 12 0.04
ACGTcount: A:0.32, C:0.13, G:0.35, T:0.21
Consensus pattern (34 bp):
GGTGCCACGGAGTTGTGGACTTTAAAAGGAACAA
Found at i:565021 original size:100 final size:100
Alignment explanation
Indices: 564819--565145 Score: 410
Period size: 100 Copynumber: 3.3 Consensus size: 100
564809 CTTTTATGGG
* ** * *
564819 CTTTAGAAGGGAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAAAGATGGTG-CACGGAGTCGTG
1 CTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTG
* *
564883 GACTTAAAAGGTACAAGGTGCCATGGGGTTGTGGA
66 GACTTAAAAGGAACAAGGTGCCATGGGGTTGTAGA
* * *
564918 CTTTAAAAGGGAAAAATAGTGCCACGGAGTTGTGGGCTTGGAAAAGAAGGTGCCATGGAGTCGTG
1 CTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTG
564983 GACTTAAAAGGAACAAGGTGCCATGGGGTTGTAGA
66 GACTTAAAAGGAACAAGGTGCCATGGGGTTGTAGA
* *
565018 CTTTAAAAGTGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAACAAGGTGCCACGGAGTT
1 CTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAG---AAGGTGCCACGGAGTC
* * * ** * *
565083 GTGGGCTTTAAAAAGAAAAAGGTGCCACAGAGTTGTGGA
63 GTGGAC-TTAAAAGGAACAAGGTGCCATGGGGTTGTAGA
*
565122 C-TTAAAA-GGAAGAAGA-TGCCACGG
1 CTTTAAAAGGGAAAAAGAGTGCCACGG
565146 GGTCGTGGAC
Statistics
Matches: 199, Mismatches: 24, Indels: 8
0.86 0.10 0.03
Matches are distributed among these distances:
99 45 0.23
100 87 0.44
101 8 0.04
102 7 0.04
103 25 0.13
104 27 0.14
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.21
Consensus pattern (100 bp):
CTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTG
GACTTAAAAGGAACAAGGTGCCATGGGGTTGTAGA
Found at i:565051 original size:136 final size:135
Alignment explanation
Indices: 564871--565199 Score: 400
Period size: 136 Copynumber: 2.4 Consensus size: 135
564861 AAAGATGGTG
* * * * * *
564871 CACGGAGTCGTGGACTTAAAAGGTAC-AAG-GTGCCATGGGGTTGTGGACTTT-AAAAGGGAAAA
1 CACGGGGTCGTAGACTTAAAAGGAACAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAA-GGAAAA
* **
564933 ATAGTGCCACGGAGTTGTGGGCTTGGAAAAG-AAGGTGCCATGGAGTCGTGGACTTAAAAGGAAC
65 A-AGTGCCACGGAGTTGTGGGCTTGAAAAAGAAAGGTGCCACAGAGTCGTGGACTTAAAAGGAAC
*
564997 AAGGTGC
129 AAGATGC
* * *
565004 CATGGGGTTGTAGACTTTAAAAGTGAA-AAAGAGTGCCACGGAGTTGTGGGCTTTGAAAA-GAAC
1 CACGGGGTCGTAGAC-TTAAAAG-GAACAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
* * *
565067 AAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGA
64 AAAGTGCCACGGAGTTGTGGGCTTGAAAAAG--AAAGGTGCCACAGAGTCGTGGACTTAAAAGGA
*
565132 AGAAGATGC
127 ACAAGATGC
*
565141 CACGGGGTCGTGGACTTAAAAGGAACAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAG
1 CACGGGGTCGTAGACTTAAAAGGAACAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAG
565200 AAGGTGCCAC
Statistics
Matches: 166, Mismatches: 20, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
133 11 0.07
134 33 0.20
135 13 0.08
136 58 0.35
137 51 0.31
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (135 bp):
CACGGGGTCGTAGACTTAAAAGGAACAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAA
AGTGCCACGGAGTTGTGGGCTTGAAAAAGAAAGGTGCCACAGAGTCGTGGACTTAAAAGGAACAA
GATGC
Found at i:566185 original size:1 final size:1
Alignment explanation
Indices: 566181--566226 Score: 65
Period size: 1 Copynumber: 46.0 Consensus size: 1
566171 TTTTCCTCTC
* * *
566181 TTTTTTTTTTTTTTTGTTTTTTTTTGTTTTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
566227 GGAAAAGAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (1 bp):
T
Found at i:566194 original size:10 final size:10
Alignment explanation
Indices: 566181--566225 Score: 83
Period size: 10 Copynumber: 4.6 Consensus size: 10
566171 TTTTCCTCTC
566181 TTTTTT-TTT
1 TTTTTTGTTT
566190 TTTTTTGTTT
1 TTTTTTGTTT
566200 TTTTTTGTTT
1 TTTTTTGTTT
566210 TTTTTTGTTT
1 TTTTTTGTTT
566220 TTTTTT
1 TTTTTT
566226 TGGAAAAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
9 6 0.17
10 29 0.83
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:566487 original size:18 final size:16
Alignment explanation
Indices: 566464--566518 Score: 58
Period size: 17 Copynumber: 3.4 Consensus size: 16
566454 GGCTTTACAC
*
566464 TTTTTTGTGTGTTTTT
1 TTTTTTTTGTGTTTTT
*
566480 TGTTTTTTTGT-ATTTT
1 T-TTTTTTTGTGTTTTT
*
566496 TTTTTGTTGCTGTTTTT
1 TTTTTTTTG-TGTTTTT
566513 TTTTTT
1 TTTTTT
566519 ATTTTTAAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
15 7 0.23
16 7 0.23
17 17 0.55
ACGTcount: A:0.02, C:0.02, G:0.15, T:0.82
Consensus pattern (16 bp):
TTTTTTTTGTGTTTTT
Found at i:566500 original size:15 final size:16
Alignment explanation
Indices: 566476--566518 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
566466 TTTTGTGTGT
566476 TTTTTGTTTTTTTG-TA
1 TTTTT-TTTTTTTGCTA
* *
566492 TTTTTTTTTGTTGCTG
1 TTTTTTTTTTTTGCTA
566508 TTTTTTTTTTT
1 TTTTTTTTTTT
566519 ATTTTTAAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.02, C:0.02, G:0.12, T:0.84
Consensus pattern (16 bp):
TTTTTTTTTTTTGCTA
Found at i:578567 original size:21 final size:21
Alignment explanation
Indices: 578534--578574 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
578524 CTAAGTAAAA
578534 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
578555 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
578575 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:578640 original size:21 final size:20
Alignment explanation
Indices: 578611--578667 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
578601 AAAACCCTGA
**
578611 AAAGTATCGATACACATTTT
1 AAAGTATCGATACACATTGC
*
578631 AAATGTATCGATACAGATTGC
1 AAA-GTATCGATACACATTGC
*
578652 ATAGTATCGATACACA
1 AAAGTATCGATACACA
578668 CAAATATGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (20 bp):
AAAGTATCGATACACATTGC
Found at i:578738 original size:53 final size:53
Alignment explanation
Indices: 578655--578791 Score: 213
Period size: 53 Copynumber: 2.6 Consensus size: 53
578645 AGATTGCATA
* * *
578655 GTATCGATACACACAAATATGTATCGATACAGGAT-ATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGG-TCACTGCCAATAGCCAAATTT
578709 GTATCGATACACACAATATGTATCGATACAGGTCACTGCCAATAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAGGTCACTGCCAATAGCCAAATTT
*
578762 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
578792 TTGGTAGTAG
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
52 1 0.01
53 63 0.81
54 14 0.18
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGTCACTGCCAATAGCCAAATTT
Found at i:578834 original size:10 final size:10
Alignment explanation
Indices: 578815--578845 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
578805 AATCTCATTT
578815 TCACTGTTCA
1 TCACTGTTCA
*
578825 TCACTATTCA
1 TCACTGTTCA
578835 TCACTGTTCA
1 TCACTGTTCA
578845 T
1 T
578846 GTATTGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:580445 original size:84 final size:84
Alignment explanation
Indices: 580285--580445 Score: 186
Period size: 84 Copynumber: 1.9 Consensus size: 84
580275 ACTCAAAGAA
* * * *
580285 GAAAATAAATCAATAAGTGTAGAGAATCATATTCTTGAAAAGAAATTAAGTGAATTAGAGAAGAG
1 GAAAATAAATCAATAAGTGTAGAAAATCATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAG
* *
580350 TATGAAAGAGTTACAAAAT
66 AAAGAAAGAGTTACAAAAT
* *
580369 GAAAATAAATCAATGAGTTTAGAAAAT-A-ATTCTTTTAAAAAGAAAATAAATGAATT--AGAAG
1 GAAAATAAATCAATAAGTGTAGAAAATCATATTC--TTAAAAAGAAAATAAATGAATTAGAGAAG
580430 AGAAAAGAAATGAGTT
64 AG-AAAGAAA-GAGTT
580446 GCAAGTCGAA
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
82 11 0.17
83 6 0.09
84 48 0.74
ACGTcount: A:0.53, C:0.04, G:0.17, T:0.25
Consensus pattern (84 bp):
GAAAATAAATCAATAAGTGTAGAAAATCATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAG
AAAGAAAGAGTTACAAAAT
Found at i:581782 original size:92 final size:91
Alignment explanation
Indices: 581643--581953 Score: 347
Period size: 92 Copynumber: 3.4 Consensus size: 91
581633 ACTCCTTACG
* * *
581643 GCAAGGACATCCTGACCACACATTCCTAATCATATCCCTTTCATCCAACCACTAGATGGTATTGA
1 GCAAAGACATCCCGACCACACATTCCCAATCATAT-CCTTTCATCCAACCACTAGATGGTATTGA
* * * *
581708 TGTATCACAAAGCTTGATTTA-TTAGG
65 TGCATCACAAAGCCTGATTTACTAAGA
* * *
581734 GACAAAGACATCCCGGCCATACATTCCCAATCATATCTCTTTCATCCAACCACCAGATGGTATTG
1 G-CAAAGACATCCCGACCACACATTCCCAATCATATC-CTTTCATCCAACCACTAGATGGTATTG
* *
581799 ATGCATCAAAAAGCCTGATTTCCTAAGA
64 ATGCATCACAAAGCCTGATTTACTAAGA
** * * *
581827 GCATGGACATCCCGACCACATATTCCCAATTATATCCTTTTCATCCAACCACTAGATAGTATTGA
1 GCAAAGACATCCCGACCACACATTCCCAATCATATCC-TTTCATCCAACCACTAGATGGTATTGA
* ** *
581892 TGCATCACAAAGCCT-AGTTTCCTTGGG
65 TGCATCACAAAGCCTGA-TTTACTAAGA
* * *
581919 GCAAGGATATCCTGACCACACATTCCCAATCATAT
1 GCAAAGACATCCCGACCACACATTCCCAATCATAT
581954 TTCTTCTTTT
Statistics
Matches: 186, Mismatches: 29, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
91 4 0.02
92 178 0.96
93 4 0.02
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.27
Consensus pattern (91 bp):
GCAAAGACATCCCGACCACACATTCCCAATCATATCCTTTCATCCAACCACTAGATGGTATTGAT
GCATCACAAAGCCTGATTTACTAAGA
Found at i:582615 original size:45 final size:45
Alignment explanation
Indices: 582558--582664 Score: 142
Period size: 45 Copynumber: 2.4 Consensus size: 45
582548 TTGACTGTAT
* *
582558 CTAGTCAAACTCTTTTCACTACTGTTTGACATGATGGTTTTTGCC
1 CTAGTCAAACTCTTTTCACTACTATTTGACATGATGGTTCTTGCC
* * * *
582603 TTAGTTAAACTCTTTTCATTATTATTTGACATGATGGTTCTTGCC
1 CTAGTCAAACTCTTTTCACTACTATTTGACATGATGGTTCTTGCC
*
582648 CTAGTCACAAATCTTTT
1 CTAGTCA-AACTCTTTT
582665 TATTATCGTT
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
45 44 0.85
46 8 0.15
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.45
Consensus pattern (45 bp):
CTAGTCAAACTCTTTTCACTACTATTTGACATGATGGTTCTTGCC
Found at i:582941 original size:45 final size:45
Alignment explanation
Indices: 582864--582952 Score: 106
Period size: 45 Copynumber: 2.0 Consensus size: 45
582854 ACTGTATCTG
* * * *
582864 GTCAAACTTTTTTCACTACTGTTTAACATGATGGTTCTCGCCCTT
1 GTCAAACTCTTTTCACTACTATTTAACATGATGATTCTAGCCCTT
* * **
582909 GTCAAACTCTTTTCATTACTATTTGATGTGATGATTCTAGCCCT
1 GTCAAACTCTTTTCACTACTATTTAACATGATGATTCTAGCCCT
582953 GTTATCGCGA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.21, C:0.22, G:0.13, T:0.43
Consensus pattern (45 bp):
GTCAAACTCTTTTCACTACTATTTAACATGATGATTCTAGCCCTT
Found at i:586476 original size:20 final size:20
Alignment explanation
Indices: 586453--586507 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
586443 CATTTCAAAC
*
586453 ATGTATTGATACATTCACTT
1 ATGTATCGATACATTCACTT
* *
586473 ATGTATCAATTCATTCACTT
1 ATGTATCGATACATTCACTT
586493 ATGTATCGATACATT
1 ATGTATCGATACATT
586508 ACCCTATTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTCACTT
Found at i:586865 original size:19 final size:19
Alignment explanation
Indices: 586841--586896 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
586831 TGTATCGTTA
*
586841 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGCT
* *
586860 CATTGTATCGTTACATACT
1 CATTGTATCGATACATGCT
586879 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
586897 AAAGTGGCAG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (19 bp):
CATTGTATCGATACATGCT
Found at i:587949 original size:45 final size:45
Alignment explanation
Indices: 587852--587950 Score: 119
Period size: 45 Copynumber: 2.2 Consensus size: 45
587842 TTGACTATAT
* * * * **
587852 CTAGTCAAACTCTTTTCATTTCGATTTGATGTGATGGTTTTTGCC
1 CTAGTCAAACCCTTTTCATTACGATTTGACGTGATGGTTCTCACC
587897 CTAGTCAAACCCTTTTCATTACTG-TTTGACGTGATGGTTCTCACC
1 CTAGTCAAACCCTTTTCATTAC-GATTTGACGTGATGGTTCTCACC
*
587942 CTGGTCAAA
1 CTAGTCAAA
587951 TATTTTTTCA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
45 45 0.98
46 1 0.02
ACGTcount: A:0.20, C:0.22, G:0.17, T:0.40
Consensus pattern (45 bp):
CTAGTCAAACCCTTTTCATTACGATTTGACGTGATGGTTCTCACC
Found at i:587983 original size:80 final size:80
Alignment explanation
Indices: 587897--588154 Score: 245
Period size: 78 Copynumber: 3.2 Consensus size: 80
587887 GGTTTTTGCC
* *
587897 CTAGTCAAACCCTTTTCATTACTGTTTGACGTGATGGTTCTCACCCTGGTCAAATATTTTTTCAT
1 CTAGTCAAACCCTTTTCATTACTGTTTGACGTGATGGTTCTCACCCTGGTCAAACATCTTTTCAT
587962 TATCGTTT-ATTGTAT
66 T-TCGTTTGATTGTAT
**** ** * * * * *
587977 CTAGTCAGGTTCTTTTCATTACCATTTGACTTGGTGGTCCTTACCTTGGTCAAACATCTTTTCAT
1 CTAGTCAAACCCTTTTCATTACTGTTTGACGTGATGGTTCTCACCCTGGTCAAACATCTTTTCAT
* *
588042 CTTCTTTTGACTGTAT
66 -TTCGTTTGATTGTAT
* * * * * *
588058 CTGGT--TA-CCTTTTCATTATTGTTTGATGTGATGGTTCTCACCCTAGTCAAACATGTTTTCAT
1 CTAGTCAAACCCTTTTCATTACTGTTTGACGTGATGGTTCTCACCCTGGTCAAACATCTTTTCAT
*
588120 TCTCGTTTGATAGTAT
66 T-TCGTTTGATTGTAT
**
588136 CTAGTCAAACTTTTTTCAT
1 CTAGTCAAACCCTTTTCAT
588155 CTTCCTTCGA
Statistics
Matches: 135, Mismatches: 37, Indels: 11
0.74 0.20 0.06
Matches are distributed among these distances:
77 1 0.01
78 58 0.43
80 58 0.43
81 18 0.13
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.46
Consensus pattern (80 bp):
CTAGTCAAACCCTTTTCATTACTGTTTGACGTGATGGTTCTCACCCTGGTCAAACATCTTTTCAT
TTCGTTTGATTGTAT
Found at i:592274 original size:32 final size:33
Alignment explanation
Indices: 592229--592319 Score: 107
Period size: 32 Copynumber: 2.8 Consensus size: 33
592219 TAATACTATC
592229 TTTC-AAGGCTAAGATAGAAACCTCCCTATC-T
1 TTTCAAAGGCTAAGATAGAAACCTCCCTATCTT
** *
592260 TTTCACGGGCTAAGATAGAACCTTTCTCCCTATCTT
1 TTTCAAAGGCTAAGATAGAAAC---CTCCCTATCTT
592296 TTTCAAAGGCTAAGATAG-AACCTC
1 TTTCAAAGGCTAAGATAGAAACCTC
592320 ACAATCACTT
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
31 4 0.08
32 17 0.35
35 11 0.22
36 17 0.35
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (33 bp):
TTTCAAAGGCTAAGATAGAAACCTCCCTATCTT
Done.