Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold79
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: 4189514
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 5041 characters in sequence are not A, C, G, or T
File 3 of 26
Found at i:286575 original size:96 final size:96
Alignment explanation
Indices: 286349--286584 Score: 312
Period size: 97 Copynumber: 2.4 Consensus size: 96
286339 TTATTTATCA
* * * *
286349 GGGATACTCCAACCCTATTCCTCCGACAGGATACTCCAACCTCGCTTTTAAACACATCAAAGTTT
1 GGGACACTCTAACCCCATTCCTCAGA-AGGATACTCCAACCTCGCTTTTAAACACATCAAAGTTT
286414 AAATCTTATTCTCACTTAAATTGTCACCATCG
65 AAATCTTATTCTCACTTAAATTGTCACCATCG
* * * **
286446 AGGACACTTTAACCCCATTCCTCAGAGGGGATACTCCAACCTCGCTTTTAAATGCATCAAAGTTT
1 GGGACACTCTAACCCCATTCCTCAGA-AGGATACTCCAACCTCGCTTTTAAACACATCAAAGTTT
* * *
286511 AAATTTTATT-TTACTTAAATTGTCATCATCG
65 AAATCTTATTCTCACTTAAATTGTCACCATCG
* *
286542 GGGACACTCTAACCCCATTCCTCTGAAGAGATACTCGAACCTC
1 GGGACACTCTAACCCCATTCCTCAGAAG-GATACTCCAACCTC
286585 ATTTTTCAAT
Statistics
Matches: 120, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
95 1 0.01
96 55 0.46
97 64 0.53
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (96 bp):
GGGACACTCTAACCCCATTCCTCAGAAGGATACTCCAACCTCGCTTTTAAACACATCAAAGTTTA
AATCTTATTCTCACTTAAATTGTCACCATCG
Found at i:291570 original size:21 final size:21
Alignment explanation
Indices: 291545--291592 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
291535 AACCTTGGCC
291545 TACATTATGGTCCTTGAAAAG
1 TACATTATGGTCCTTGAAAAG
291566 TACATTATGGTCCTTGAAAAG
1 TACATTATGGTCCTTGAAAAG
*
291587 TCCATT
1 TACATT
291593 TCGATCGAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (21 bp):
TACATTATGGTCCTTGAAAAG
Found at i:292825 original size:27 final size:27
Alignment explanation
Indices: 292787--293095 Score: 354
Period size: 27 Copynumber: 11.3 Consensus size: 27
292777 TAGTGGCATT
292787 CCCTTTTAAGTCCACAAC-TCTGTGGCA
1 CCCTTTTAAGTCCACAACTTC-GTGGCA
292814 CCCTTTTAAGTCCACAAC-TCTGTGGCA
1 CCCTTTTAAGTCCACAACTTC-GTGGCA
*
292841 ACCTTTTAAGTCCACAACTTCGTGGCA
1 CCCTTTTAAGTCCACAACTTCGTGGCA
* * *
292868 GCCTTATAAGCCCACAACTTCGTGGCA
1 CCCTTTTAAGTCCACAACTTCGTGGCA
* * * *
292895 GCCTTATAAGCCCACAACTTCGTGACA
1 CCCTTTTAAGTCCACAACTTCGTGGCA
* *
292922 ACCTTTTAAAGTCCACTAACTTTGTGGCA
1 CCCTTTT-AAGTCCAC-AACTTCGTGGCA
*
292951 CTCTTTTAAGTCCACAACTTCGTGGCA
1 CCCTTTTAAGTCCACAACTTCGTGGCA
292978 CCCTTTTAAAGTCCACAACTTCGTGGCA
1 CCCTTTT-AAGTCCACAACTTCGTGGCA
*
293006 -CCTTTTAAAGTCCACAACTTCGTGACA
1 CCCTTTT-AAGTCCACAACTTCGTGGCA
* *
293033 CCTTTTTAAAGTCCACAACTCCGTGGCA
1 CCCTTTT-AAGTCCACAACTTCGTGGCA
* ** *
293061 TCCTTTTAAAGTTTACAACTCCGTGGCA
1 CCCTTTT-AAGTCCACAACTTCGTGGCA
*
293089 ACCTTTT
1 CCCTTTT
293096 CAAAGCCCAC
Statistics
Matches: 254, Mismatches: 23, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
27 148 0.58
28 91 0.36
29 15 0.06
ACGTcount: A:0.25, C:0.30, G:0.14, T:0.30
Consensus pattern (27 bp):
CCCTTTTAAGTCCACAACTTCGTGGCA
Found at i:292975 original size:83 final size:81
Alignment explanation
Indices: 292788--293107 Score: 396
Period size: 83 Copynumber: 3.9 Consensus size: 81
292778 AGTGGCATTC
292788 CCTTTTAAGTCCACAAC-TCTGTGGCACCCTTTTAAGTCCACAAC-TCTGTGGCAACCTTTT-AA
1 CCTTTTAAGTCCACAACTTC-GTGGCACCCTTTTAAGTCCACAACTTC-GTGGCAACCTTTTAAA
292850 GTCCACAACTTCGTGGCA
64 GTCCACAACTTCGTGGCA
* * * * * *
292868 GCCTTATAAGCCCACAACTTCGTGGCAGCCTTATAAGCCCACAACTTCGTGACAACCTTTTAAAG
1 -CCTTTTAAGTCCACAACTTCGTGGCACCCTTTTAAGTCCACAACTTCGTGGCAACCTTTTAAAG
*
292933 TCCACTAACTTTGTGGCA
65 TCCAC-AACTTCGTGGCA
292951 CTCTTTTAAGTCCACAACTTCGTGGCACCCTTTTAAAGTCCACAACTTCGTGGC-ACCTTTTAAA
1 C-CTTTTAAGTCCACAACTTCGTGGCACCCTTTT-AAGTCCACAACTTCGTGGCAACCTTTTAAA
*
293015 GTCCACAACTTCGTGACA
64 GTCCACAACTTCGTGGCA
* * ** *
293033 CCTTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAAGTTTACAACTCCGTGGCAACCTTTTCA
1 CC-TTTT-AAGTCCACAACTTCGTGGCACCCTTTT-AAGTCCACAACTTCGTGGCAACCTTTT-A
*
293098 AAGCCCACAA
62 AAGTCCACAA
293108 GTCAGTGGCA
Statistics
Matches: 208, Mismatches: 21, Indels: 16
0.85 0.09 0.07
Matches are distributed among these distances:
81 49 0.24
82 28 0.13
83 97 0.47
84 24 0.12
85 10 0.05
ACGTcount: A:0.26, C:0.31, G:0.14, T:0.29
Consensus pattern (81 bp):
CCTTTTAAGTCCACAACTTCGTGGCACCCTTTTAAGTCCACAACTTCGTGGCAACCTTTTAAAGT
CCACAACTTCGTGGCA
Found at i:293070 original size:28 final size:28
Alignment explanation
Indices: 292764--293157 Score: 353
Period size: 27 Copynumber: 14.1 Consensus size: 28
292754 TAACCTCTTC
* * *
292764 AAAGTCCACGATTTAGTGGCATTCCCTTTT
1 AAAGTCCACAACTTCGTGGCA-T-CCTTTT
*
292794 -AAGTCCACAAC-TCTGTGGCACCCTTTT
1 AAAGTCCACAACTTC-GTGGCATCCTTTT
*
292821 -AAGTCCACAAC-TCTGTGGCAACCTTTT
1 AAAGTCCACAACTTC-GTGGCATCCTTTT
* *
292848 -AAGTCCACAACTTCGTGGCAGCCTTAT
1 AAAGTCCACAACTTCGTGGCATCCTTTT
* * *
292875 -AAGCCCACAACTTCGTGGCAGCCTTAT
1 AAAGTCCACAACTTCGTGGCATCCTTTT
* * *
292902 -AAGCCCACAACTTCGTGACAACCTTTT
1 AAAGTCCACAACTTCGTGGCATCCTTTT
*
292929 AAAGTCCACTAACTTTGTGGCA-CTCTTTT
1 AAAGTCCAC-AACTTCGTGGCATC-CTTTT
*
292958 -AAGTCCACAACTTCGTGGCACCCTTTT
1 AAAGTCCACAACTTCGTGGCATCCTTTT
292985 AAAGTCCACAACTTCGTGGCA-CCTTTT
1 AAAGTCCACAACTTCGTGGCATCCTTTT
*
293012 AAAGTCCACAACTTCGTGACA-CCTTTTT
1 AAAGTCCACAACTTCGTGGCATCC-TTTT
*
293040 AAAGTCCACAACTCCGTGGCATCCTTTT
1 AAAGTCCACAACTTCGTGGCATCCTTTT
** * *
293068 AAAGTTTACAACTCCGTGGCAACCTTTT
1 AAAGTCCACAACTTCGTGGCATCCTTTT
* * **
293096 CAAAGCCCACAA-GTCAGTGGCATCTCTTCA
1 -AAAGTCCACAACTTC-GTGGCATC-CTTTT
* * * *
293126 AAAGACCACAAGTTAGTGGCATCCTTTC
1 AAAGTCCACAACTTCGTGGCATCCTTTT
293154 AAAG
1 AAAG
293158 CTCACAAGTC
Statistics
Matches: 317, Mismatches: 34, Indels: 28
0.84 0.09 0.07
Matches are distributed among these distances:
27 148 0.47
28 100 0.32
29 65 0.21
30 4 0.01
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (28 bp):
AAAGTCCACAACTTCGTGGCATCCTTTT
Found at i:293115 original size:29 final size:29
Alignment explanation
Indices: 292972--293554 Score: 325
Period size: 29 Copynumber: 19.8 Consensus size: 29
292962 CCACAACTTC
* * *
292972 GTGGCACCCTTTT-AAAGTCCACAACTTC-
1 GTGGCAACCTTTTCAAAGCCCACAA-GTCA
* *
293000 GTGGC-ACCTTTT-AAAGTCCACAACTTC-
1 GTGGCAACCTTTTCAAAGCCCACAA-GTCA
* * * * *
293027 GTGAC-ACCTTTTTAAAGTCCACAACTCC
1 GTGGCAACCTTTTCAAAGCCCACAAGTCA
* *** * *
293055 GTGGCATCCTTTT-AAAGTTTACAACTCC
1 GTGGCAACCTTTTCAAAGCCCACAAGTCA
293083 GTGGCAACCTTTTCAAAGCCCACAAGTCA
1 GTGGCAACCTTTTCAAAGCCCACAAGTCA
* * * *
293112 GTGGC-ATCTCTTCAAAAGACCACAAGTTA
1 GTGGCAACCTTTTC-AAAGCCCACAAGTCA
* *
293141 GTGGCATCC-TTTCAAAGCTCACAAGTCA
1 GTGGCAACCTTTTCAAAGCCCACAAGTCA
* *
293169 GTGGCACCCCTTTT-TAAGCCCACAAGTCA
1 GTGGCA-ACCTTTTCAAAGCCCACAAGTCA
* * *
293198 GTGGC-ATCATTTCAAAGCCCACACAAGTCG
1 GTGGCAACCTTTTCAAAG-CC-CACAAGTCA
* * *
293228 GTGGTAACTCATTTGAAAGCCCACACAAGTC-
1 GTGGCAAC-CTTTTCAAAG-CC-CACAAGTCA
*
293259 GATGGCAACCCATTTCAAAGCCCACACAAGTC-
1 G-TGGCAA-CCTTTTCAAAG-CC-CACAAGTCA
** * *
293291 GATGGCTTCTCATTTGAAAGCCCACACAAGTCA
1 G-TGGCAAC-CTTTTCAAAG-CC-CACAAGTCA
* *
293324 ATGGTAACCCATTTT-AAAGCCCACACAAGTCA
1 GTGGCAA-CC-TTTTCAAAG-CC-CACAAGTCA
293356 GTGGCAACCTATTTCAAAGCCCACAAGTCA
1 GTGGCAACCT-TTTCAAAGCCCACAAGTCA
* * *
293386 GTGGCATCCTTCTCAAAGCCCATAAGTCA
1 GTGGCAACCTTTTCAAAGCCCACAAGTCA
* *
293415 GTGGCATCCTTCTCAAAGCCCACAAGTCA
1 GTGGCAACCTTTTCAAAGCCCACAAGTCA
* * * * *
293444 ATGGCATCCTTCTCAAAGCCCACACAAATTA
1 GTGGCAACCTTTTCAAAG-CC-CACAAGTCA
* * *
293475 GTGGC-ATCATTTCCAAGCCCACAAGTCA
1 GTGGCAACCTTTTCAAAGCCCACAAGTCA
* * * *
293503 GTGGCATCCTTCTCAAAGCCCATATAAATCA
1 GTGGCAACCTTTTCAAAGCCC--ACAAGTCA
*
293534 GTGGC-ATCTTTTCAAAGCCCA
1 GTGGCAACCTTTTCAAAGCCCA
293555 TACAAGTTAG
Statistics
Matches: 458, Mismatches: 71, Indels: 52
0.79 0.12 0.09
Matches are distributed among these distances:
27 38 0.08
28 85 0.19
29 138 0.30
30 56 0.12
31 32 0.07
32 104 0.23
33 5 0.01
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (29 bp):
GTGGCAACCTTTTCAAAGCCCACAAGTCA
Found at i:293190 original size:86 final size:86
Alignment explanation
Indices: 293055--293554 Score: 280
Period size: 96 Copynumber: 5.6 Consensus size: 86
293045 CCACAACTCC
* * * *
293055 GTGGCATCCTTTTAAAGTTTACAACTCCGTGGCAACCTTTTCAAAGCCCACAAGTCAGTGGCATC
1 GTGGCATCCTTTCAAAGCTCACAACTCAGTGGCAACCTTTTCAAAGCCCACAAGTCAGTGGCATC
293120 -TCTTCAAAAGACCACAAGTTA
66 AT-TTCAAAAGACCACAAGTTA
* * *
293141 GTGGCATCCTTTCAAAGCTCACAAGTCAGTGGCACCCCTTTT-TAAGCCCACAAGTCAGTGGCAT
1 GTGGCATCCTTTCAAAGCTCACAACTCAGTGGCA-ACCTTTTCAAAGCCCACAAGTCAGTGGCAT
* **
293205 CATTTC-AAAGCCCACACAAGTCG
65 CATTTCAAAAG-AC-CACAAGTTA
* * * * * *
293228 GTGGTAACTCATTTGAAAGCCCACACAAGTC-GATGGCAACCCATTTCAAAGCCCACACAAGTC-
1 GTGG-CA-TCCTTTCAAAG--CTCACAACTCAG-TGGCAA-CCTTTTCAAAG-CC-CACAAGTCA
* * * *
293291 GATGGCTTCTCATTT-GAAAGCCCACACAAGTCA
58 G-TGGC--ATCATTTCAAAAG-AC-CACAAGTTA
* * * * * *
293324 ATGGTAACCCATTTTAAAGCCCACACAAGTCAGTGGCAACCTATTTCAAAGCCCACAAGTCAGTG
1 GTGG-CATCC-TTTCAAAG--CTCACAACTCAGTGGCAACCT-TTTCAAAGCCCACAAGTCAGTG
* * * *
293389 GCATCCTTCTC-AAAGCCCATAAGTCA
61 GCATCATT-TCAAAAGACCACAAGTTA
* * * * * * *
293415 GTGGCATCCTTCTCAAAGCCCACAAGTCAATGGCATCCTTCTCAAAGCCCACACAAATTAGTGGC
1 GTGGCATCCTT-TCAAAGCTCACAACTCAGTGGCAACCTTTTCAAAG-CC-CACAAGTCAGTGGC
* * *
293480 ATCATTTC-CAAGCCCACAAGTCA
63 ATCATTTCAAAAGACCACAAGTTA
* * * *
293503 GTGGCATCCTTCTCAAAGCCCATATAAATCAGTGGC-ATCTTTTCAAAGCCCA
1 GTGGCATCCTT-TCAAAGCTC--ACAACTCAGTGGCAACCTTTTCAAAGCCCA
293555 TACAAGTTAG
Statistics
Matches: 340, Mismatches: 46, Indels: 55
0.77 0.10 0.12
Matches are distributed among these distances:
85 4 0.01
86 55 0.16
87 27 0.08
88 59 0.17
89 37 0.11
90 19 0.06
91 30 0.09
92 9 0.03
93 8 0.02
94 24 0.07
95 6 0.02
96 61 0.18
97 1 0.00
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.23
Consensus pattern (86 bp):
GTGGCATCCTTTCAAAGCTCACAACTCAGTGGCAACCTTTTCAAAGCCCACAAGTCAGTGGCATC
ATTTCAAAAGACCACAAGTTA
Found at i:293192 original size:57 final size:57
Alignment explanation
Indices: 293083--293524 Score: 219
Period size: 64 Copynumber: 7.4 Consensus size: 57
293073 TTACAACTCC
* * * *
293083 GTGGCAACCTTTTCAAAGCCCACAAGTCAGTGGCATCTCTTCAAAAGACCACAAGTTA
1 GTGGCATCC-TTTCAAAGCCCACAAGTCAGTGGCACCCCTTCAAAAGACCACAAGTCA
* *** *
293141 GTGGCATCCTTTCAAAGCTCACAAGTCAGTGGCACCCCTTTTTAAGCCCACAAGTCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCCTTCAAAAGACCACAAGTCA
* * * * * ** *
293198 GTGGCATCATTTCAAAGCCCACACAAGTCGGTGGTAACTCATTTGAAAGCCCACACAAGTC-
1 GTGGCATCCTTTCAAAG-CC-CACAAGTCAGTGG-CACCCCTTCAAAAG-AC-CACAAGTCA
* * * * ** *
293259 GATGGCAACCCATTTCAAAGCCCACACAAGTC-GATGGCTTCTCATTTGAAAGCCCACACAAGTC
1 G-TGGC-ATCC-TTTCAAAG-CC-CACAAGTCAG-TGGC-ACCCCTTCAAAAG-AC-CACAAGTC
293323 A
57 A
* * * * ** *
293324 ATGGTAACCCATTTTAAAGCCCACACAAGTCAGTGGCAACCTATTTC-AAAGCCCACAAGTCA
1 GTGG-CATCC-TTTCAAAG-CC-CACAAGTCAGTGGC-ACC-CCTTCAAAAGACCACAAGTCA
* * * *
293386 GTGGCATCCTTCTCAAAGCCCATAAGTCAGTGGCA-TCCTTCTCAAAGCCCACAAGTCA
1 GTGGCATCCTT-TCAAAGCCCACAAGTCAGTGGCACCCCTTC-AAAAGACCACAAGTCA
* * * * ** * *
293444 ATGGCATCCTTCTCAAAGCCCACACAAATTAGTGGCATCATTTC-CAAGCCCACAAGTCA
1 GTGGCATCCTT-TCAAAG-CC-CACAAGTCAGTGGCACCCCTTCAAAAGACCACAAGTCA
293503 GTGGCATCCTTCTCAAAGCCCA
1 GTGGCATCCTT-TCAAAGCCCA
293525 TATAAATCAG
Statistics
Matches: 317, Mismatches: 47, Indels: 41
0.78 0.12 0.10
Matches are distributed among these distances:
56 3 0.01
57 58 0.18
58 44 0.14
59 58 0.18
60 25 0.08
61 14 0.04
62 24 0.08
63 5 0.02
64 83 0.26
65 3 0.01
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.22
Consensus pattern (57 bp):
GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCCTTCAAAAGACCACAAGTCA
Found at i:293247 original size:32 final size:32
Alignment explanation
Indices: 293204--293380 Score: 216
Period size: 32 Copynumber: 5.5 Consensus size: 32
293194 GTCAGTGGCA
*
293204 TCATTTCAAAGCCCACACAAGTCGGTGGTAAC
1 TCATTTCAAAGCCCACACAAGTCGATGGTAAC
* *
293236 TCATTTGAAAGCCCACACAAGTCGATGGCAAC
1 TCATTTCAAAGCCCACACAAGTCGATGGTAAC
* *
293268 CCATTTCAAAGCCCACACAAGTCGATGGCT-TC
1 TCATTTCAAAGCCCACACAAGTCGATGG-TAAC
* *
293300 TCATTTGAAAGCCCACACAAGTCAATGGTAAC
1 TCATTTCAAAGCCCACACAAGTCGATGGTAAC
* * *
293332 CCATTTTAAAGCCCACACAAGTC-AGTGGCAAC
1 TCATTTCAAAGCCCACACAAGTCGA-TGGTAAC
293364 -CTATTTCAAAGCCCACA
1 TC-ATTTCAAAGCCCACA
293381 AGTCAGTGGC
Statistics
Matches: 126, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
31 3 0.02
32 123 0.98
ACGTcount: A:0.33, C:0.30, G:0.16, T:0.21
Consensus pattern (32 bp):
TCATTTCAAAGCCCACACAAGTCGATGGTAAC
Found at i:293281 original size:64 final size:64
Alignment explanation
Indices: 293189--293380 Score: 248
Period size: 64 Copynumber: 3.0 Consensus size: 64
293179 TTTTTAAGCC
* *
293189 CACAAGTCAGTGGC-A-TCATTTCAAAGCCCACACAAGTCGGTGGTAACTCATTTGAAAGCCCA
1 CACAAGTCAATGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGTAACTCATTTGAAAGCCCA
* * *
293251 CACAAGTCGATGGCAACCCATTTCAAAGCCCACACAAGTCGATGGCT-TCTCATTTGAAAGCCCA
1 CACAAGTCAATGGCAACCCATTTCAAAGCCCACACAAGTCGGTGG-TAACTCATTTGAAAGCCCA
* * * * *
293315 CACAAGTCAATGGTAACCCATTTTAAAGCCCACACAAGTCAGTGGCAAC-CTATTTCAAAGCCCA
1 CACAAGTCAATGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGTAACTC-ATTTGAAAGCCCA
293379 CA
1 CA
293381 AGTCAGTGGC
Statistics
Matches: 112, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
62 12 0.11
63 2 0.02
64 97 0.87
65 1 0.01
ACGTcount: A:0.33, C:0.30, G:0.17, T:0.20
Consensus pattern (64 bp):
CACAAGTCAATGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGTAACTCATTTGAAAGCCCA
Found at i:293313 original size:96 final size:96
Alignment explanation
Indices: 293160--293380 Score: 285
Period size: 96 Copynumber: 2.4 Consensus size: 96
293150 TTTCAAAGCT
* ** *
293160 CACAAGTCAGTGGC-ACCCCTTTTTAAG-CC-CACAAGTC-AGTGGC--ATCATTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCACACAAGTCGA-TGGCTTCTCATTTCAAAGCCCA
** *
293219 CACAAGTCGGTGGTAACTCATTTGAAAGCCCA
65 CACAAGTCAATGGTAACCCATTTGAAAGCCCA
*
293251 CACAAGTC-GATGGCAACCCATTTCAAAGCCCACACAAGTCGATGGCTTCTCATTTGAAAGCCCA
1 CACAAGTCAG-TGGCAACCCATTTCAAAGCCCACACAAGTCGATGGCTTCTCATTTCAAAGCCCA
*
293315 CACAAGTCAATGGTAACCCATTTTAAAGCCCA
65 CACAAGTCAATGGTAACCCATTTGAAAGCCCA
*
293347 CACAAGTCAGTGGCAACCTATTTCAAAGCCCACA
1 CACAAGTCAGTGGCAACCCATTTCAAAGCCCACA
293381 AGTCAGTGGC
Statistics
Matches: 112, Mismatches: 10, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
90 1 0.01
91 12 0.11
92 10 0.09
93 2 0.02
94 12 0.11
95 1 0.01
96 73 0.65
97 1 0.01
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.21
Consensus pattern (96 bp):
CACAAGTCAGTGGCAACCCATTTCAAAGCCCACACAAGTCGATGGCTTCTCATTTCAAAGCCCAC
ACAAGTCAATGGTAACCCATTTGAAAGCCCA
Found at i:293753 original size:46 final size:46
Alignment explanation
Indices: 293701--293933 Score: 313
Period size: 46 Copynumber: 5.0 Consensus size: 46
293691 TATTGGCACA
* * *
293701 TTTATTAGCTCAACGTCGTTGGCCTTGAATCAGCACATTATCCACC
1 TTTATTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACC
*
293747 TTTATTAGCTCAATATCGCTGGCCTTGAATCAGCACATTGTCCACC
1 TTTATTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACC
* * **
293793 TTTATTATCTTAATGTCGCTGGCCTTGAATCAGCACATTGTCCATT
1 TTTATTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACC
* * * *
293839 TTTCCCTTAGCTTAATGTCGCTGGCCTTGAATCAACACATTGTCCACT
1 TTT--ATTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACC
*
293887 TTTCCCTTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCAC
1 TTT--ATTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCAC
293934 TTTTCCCTCA
Statistics
Matches: 170, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
46 86 0.51
48 84 0.49
ACGTcount: A:0.22, C:0.28, G:0.15, T:0.35
Consensus pattern (46 bp):
TTTATTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACC
Found at i:293872 original size:48 final size:48
Alignment explanation
Indices: 293705--293941 Score: 329
Period size: 48 Copynumber: 5.0 Consensus size: 48
293695 GGCACATTTA
* * * * *
293705 TTAGCTCAACGTCGTTGGCCTTGAATCAGCACATTATCCACCTTT--A
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
* * *
293751 TTAGCTCAATATCGCTGGCCTTGAATCAGCACATTGTCCACCTTT--A
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
* * *
293797 TTATCTTAATGTCGCTGGCCTTGAATCAGCACATTGTCCATTTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
* *
293845 TTAGCTTAATGTCGCTGGCCTTGAATCAACACATTGTCCACTTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
293893 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
293941 T
1 T
293942 CATTTAGCTC
Statistics
Matches: 174, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
46 82 0.47
48 92 0.53
ACGTcount: A:0.21, C:0.29, G:0.15, T:0.35
Consensus pattern (48 bp):
TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
Found at i:294773 original size:20 final size:20
Alignment explanation
Indices: 294748--294823 Score: 107
Period size: 20 Copynumber: 3.8 Consensus size: 20
294738 TTTTTACCCA
294748 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
* * *
294768 AATGTATCGATACATGTATG
1 AATGTATCGATACATTTTTC
* *
294788 AATGTATCAATACATTCTTC
1 AATGTATCGATACATTTTTC
294808 AATGTATCGATACATT
1 AATGTATCGATACATT
294824 CTGTCTTTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACATTTTTC
Found at i:294824 original size:91 final size:91
Alignment explanation
Indices: 294667--294873 Score: 326
Period size: 91 Copynumber: 2.3 Consensus size: 91
294657 TTTGTCTTTT
* * * *
294667 TACATTTTTCAATGTATCGATACATGTATGAGTGTATCGATACGTTCTTCAACGTATCGACGCAT
1 TACATTTTTCAATGTATCGATACATGTATGAATGTATCAATACATTCTTCAACGTATCGACACAT
294732 TCTGT-TTTTTTACCCAAATGTATCGA
66 TCTGTCTTTTTT-CCCAAATGTATCGA
* *
294758 TACATTTTTCAATGTATCGATACATGTATGAATGTATCAATACATTCTTCAATGTATCGATACAT
1 TACATTTTTCAATGTATCGATACATGTATGAATGTATCAATACATTCTTCAACGTATCGACACAT
*
294823 TCTGTCTTTTTTCCCATATGTATCGA
66 TCTGTCTTTTTTCCCAAATGTATCGA
*
294849 TACATTTTTCAATGTATCGACACAT
1 TACATTTTTCAATGTATCGATACAT
294874 CTAGTTAAAA
Statistics
Matches: 107, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
91 101 0.94
92 6 0.06
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (91 bp):
TACATTTTTCAATGTATCGATACATGTATGAATGTATCAATACATTCTTCAACGTATCGACACAT
TCTGTCTTTTTTCCCAAATGTATCGA
Found at i:297189 original size:97 final size:97
Alignment explanation
Indices: 297031--297263 Score: 326
Period size: 97 Copynumber: 2.4 Consensus size: 97
297021 TATTTATCGG
* * *
297031 GGATACTCCAACCCTATTCCTCCGAGTGGATACTCCAACCCCGCTTTTAAACACATCAAAGTTTA
1 GGATACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCACGCTTTTAAACACATCAAAGTTTA
*
297096 AATCTTATTTTCACTTAAATTGTCA-CTATCCA
66 AATCTTATTCTCACTTAAATTGTCATC-ATCCA
* ** * *
297128 GGATACTTCAACCCCATTCCTCCGAGGGGATACTCCAACCACGCTTTTAAATGCATTAAAGTTTC
1 GGATACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCACGCTTTTAAACACATCAAAGTTTA
* **
297193 AATTTTATTCTCACTTAAATTGTCATCATCGG
66 AATCTTATTCTCACTTAAATTGTCATCATCCA
*
297225 GGACACTCCAA-CCCATTCCTCCGAGGGGATACTCCAACC
1 GGATACTCCAACCCCATTCCTCCGAGGGGATACTCCAACC
297264 CCGTTTTTCA
Statistics
Matches: 121, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
96 28 0.23
97 92 0.76
98 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.12, T:0.30
Consensus pattern (97 bp):
GGATACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCACGCTTTTAAACACATCAAAGTTTA
AATCTTATTCTCACTTAAATTGTCATCATCCA
Found at i:306120 original size:20 final size:21
Alignment explanation
Indices: 306074--306125 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
306064 ATGAAATTAT
* *
306074 TTAATTAAAAAATTTTAAATA
1 TTAAATAAATAATTTTAAATA
*
306095 TAAAATAAATAATTTT-AATA
1 TTAAATAAATAATTTTAAATA
306115 TTAAATAAATA
1 TTAAATAAATA
306126 TTAAATAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TTAAATAAATAATTTTAAATA
Found at i:310831 original size:21 final size:23
Alignment explanation
Indices: 310786--310834 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
310776 TGTAATTTTT
*
310786 TAAATTAAAAATATATTTTATTA
1 TAAATTAAAAATATATTCTATTA
*
310809 TAAATTTAAAATATA-TCTA-TA
1 TAAATTAAAAATATATTCTATTA
310830 TAAAT
1 TAAAT
310835 ATTTATGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 7 0.29
22 3 0.12
23 14 0.58
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
TAAATTAAAAATATATTCTATTA
Found at i:311168 original size:2 final size:2
Alignment explanation
Indices: 311161--311206 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
311151 TCAAGCACTG
** *
311161 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GG AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
311203 AT AT
1 AT AT
311207 TATTTATAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.48
Consensus pattern (2 bp):
AT
Found at i:319733 original size:85 final size:82
Alignment explanation
Indices: 319644--319872 Score: 284
Period size: 85 Copynumber: 2.7 Consensus size: 82
319634 CAAAGTAGAT
319644 AGGTCACCAAGAGTAAAAAGTTTACCAGAGACATAGTCGATAGGTAAACAAAGGGTAAGAAATG-
1 AGGTCACCAAGAG-AAAAAGTTTACCAGAGACATAGTCGATAGGTAAACAAAGGGTAAGAAA-GA
*
319708 CTGACTAGGGACAAAGCCGA
64 CTGACCAGGGACAAAGCC-A
* * * * *
319728 CAGGTCACCAAGAAGAAGAAG-TTAACTGAGGACATAGTCGACAAGTAAACAAAGGGTAAGAAAG
1 -AGGTCACCAAG-AGAAAAAGTTTACCAGA-GACATAGTCGATAGGTAAACAAAGGGTAAGAAAG
319792 ACTGACCAGGGACAAAGCCA
63 ACTGACCAGGGACAAAGCCA
* * * *
319812 A-GTCAACAAGGAGAAAAAGTTTACCAGGGACATAGCCGATAGGTAAACAAAAGGTAAGAAA
1 AGGTCACCAA-GAGAAAAAGTTTACCAGAGACATAGTCGATAGGTAAACAAAGGGTAAGAAA
319873 AGATGAAGAA
Statistics
Matches: 124, Mismatches: 15, Indels: 13
0.82 0.10 0.09
Matches are distributed among these distances:
82 43 0.35
83 7 0.06
84 8 0.06
85 64 0.52
86 2 0.02
ACGTcount: A:0.45, C:0.16, G:0.26, T:0.13
Consensus pattern (82 bp):
AGGTCACCAAGAGAAAAAGTTTACCAGAGACATAGTCGATAGGTAAACAAAGGGTAAGAAAGACT
GACCAGGGACAAAGCCA
Found at i:319939 original size:43 final size:42
Alignment explanation
Indices: 319892--319973 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 42
319882 AGTCTCCTGG
* * * **
319892 GTCTAAGCCGACGGGCAGATAATTGATAAAAGAAGTCTCTCAT
1 GTCTAAGCCGACGAGCAAACAAAAGATAAAA-AAGTCTCTCAT
319935 GTCTAAGCCGACGAGCAAACAAAAGATAAAAAAGTCTCT
1 GTCTAAGCCGACGAGCAAACAAAAGATAAAAAAGTCTCT
319974 AGGGTCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
42 8 0.24
43 26 0.76
ACGTcount: A:0.40, C:0.20, G:0.21, T:0.20
Consensus pattern (42 bp):
GTCTAAGCCGACGAGCAAACAAAAGATAAAAAAGTCTCTCAT
Found at i:320042 original size:43 final size:42
Alignment explanation
Indices: 319958--320252 Score: 161
Period size: 43 Copynumber: 7.0 Consensus size: 42
319948 AGCAAACAAA
** * * *
319958 AGATAAAAAAGTCTCTAGGGTCAAAACCGACAGTCAGACTTG
1 AGATAAAGCAGTCTCTAGGGTCAAAGCCGACAGACAAACTTG
* *
320000 AGATGAAGCAGTCTCTAGGGGTCAAAGCCGATAGACAAACTTG
1 AGATAAAGCAGTCTCTA-GGGTCAAAGCCGACAGACAAACTTG
* *
320043 TGATAAAGCAGTCTCTAGGGTCAAAGCCGACAGGA-AGAC-TG
1 AGATAAAGCAGTCTCTAGGGTCAAAGCCGACA-GACAAACTTG
* * * * * * *
320084 AAGGT-AAGAAAATCTCTAAGGTCAAAGCCGACAAACAGACTTAA
1 -AGATAAAG-CAGTCTCTAGGGTCAAAGCCGACAGACAAACTT-G
* * * * * * *
320128 AGATAAA-AAGTCTCCAAGATCAAAGCCAACA-AGCAGACTTA
1 AGATAAAGCAGTCTCTAGGGTCAAAGCCGACAGA-CAAACTTG
* * * * *
320169 AGAGTAATGAAGTCTCTAGGGTCAAAACCGACATG-CAGACTTA
1 AGA-TAAAGCAGTCTCTAGGGTCAAAGCCGACA-GACAAACTTG
* * * * * *
320212 AGGGTAAAGAAGTCTCCAAGGTCAAAGCCGATAGGCAAACT
1 A-GATAAAGCAGTCTCTAGGGTCAAAGCCGACAGACAAACT
320253 GAAGGTAAGA
Statistics
Matches: 202, Mismatches: 36, Indels: 29
0.76 0.13 0.11
Matches are distributed among these distances:
41 11 0.05
42 89 0.44
43 99 0.49
44 3 0.01
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.17
Consensus pattern (42 bp):
AGATAAAGCAGTCTCTAGGGTCAAAGCCGACAGACAAACTTG
Found at i:320133 original size:85 final size:84
Alignment explanation
Indices: 319959--320416 Score: 363
Period size: 85 Copynumber: 5.4 Consensus size: 84
319949 GCAAACAAAA
* * * * * * * *
319959 GATAAAAAAGTCTCTAGGGTCAAAACCGACAGTCAGACTTG-AGATGAAGCAGTCTCTAGGGGTC
1 GATAAAGAAGTCTCCAAGGTCAAAGCCGACAGGCAGAC-TGAAGGT-AAGAAGTCTCTA-AGGTC
* * *
320023 AAAGCCGATAGACAAACTT--G
63 AAAGCCGACAAACAGACTTAAG
* * * * *
320043 TGATAAAGCAGTCTCTAGGGTCAAAGCCGACAGGAAGACTGAAGGTAAGAAAATCTCTAAGGTCA
1 -GATAAAGAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGTAAG-AAGTCTCTAAGGTCA
*
320108 AAGCCGACAAACAGACTTAAA
64 AAGCCGACAAACAGACTTAAG
* * * * *
320129 GATAAA-AAGTCTCCAAGATCAAAGCCAACAAGCAGACTTAAGAGTAATGAAGTCTCTAGGGTCA
1 GATAAAGAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAG-GTAA-GAAGTCTCTAAGGTCA
* **
320193 AAACCGACATGCAGACTTAAG
64 AAGCCGACAAACAGACTTAAG
* * * * *
320214 GGTAAAGAAGTCTCCAAGGTCAAAGCCGATAGGCAAACTGAAGGTAAGAAAGTCT-TCAGAGTTA
1 GATAAAGAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGTAAG-AAGTCTCTAAG-GTCA
* *
320278 AAGCTGA-AAGATAGACTTAAG
64 AAGCCGACAA-ACAGACTTAAG
* * * *
320299 GATAAAGGAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTTG-AGGTGAGGTAGTCTCCAAAGTC
1 GATAAA-GAAGTCTCCAAGGTCAAAGCCGACAGGCAGAC-TGAAGGT-AAGAAGTCTCTAAGGTC
* **
320363 AAAGCTGACAAGTAGACTTAAG
63 AAAGCCGACAAACAGACTTAAG
* * *
320385 GATAAAGGAAGTCTTCAAAGTTAAAGCCGACA
1 GATAAA-GAAGTCTCCAAGGTCAAAGCCGACA
320417 AGTAGACTTA
Statistics
Matches: 303, Mismatches: 55, Indels: 29
0.78 0.14 0.07
Matches are distributed among these distances:
84 57 0.19
85 120 0.40
86 119 0.39
87 7 0.02
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (84 bp):
GATAAAGAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGTAAGAAGTCTCTAAGGTCAAA
GCCGACAAACAGACTTAAG
Found at i:320281 original size:128 final size:126
Alignment explanation
Indices: 320044--320429 Score: 368
Period size: 128 Copynumber: 3.0 Consensus size: 126
320034 ACAAACTTGT
* * * * *
320044 GATAAA-GCAGTCTCTAGGGTCAAAGCCGACAGGAAGACTGAAGGTAAGAAAATCTCTAAGGTCA
1 GATAAAGGAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTTAAGGTAAG-AAGTCTCCAAGGTCA
* * * * * *
320108 AAGCCGACAAACAGACTTAAAGATAA-AAAGTCTCCAAGATCAAAGCCAACAAGCAGACTTAA-
65 AAGCCGACAAGCAGAC-TAAAGGTAAGAAAGTCTTCAAG-TTAAAGCCGACAAGTAGACTTAAG
* * *
320170 GAGT-AATGAAGTCTCTAGGGTCAAAACCGACATGCAGACTTAAGGGTAAAGAAGTCTCCAAGGT
1 GA-TAAAGGAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTTAA-GGT-AAGAAGTCTCCAAGGT
* * * * *
320234 CAAAGCCGATAGGCAAACTGAAGGTAAGAAAGTCTTCAGAGTTAAAGCTGA-AAGATAGACTTAA
63 CAAAGCCGACAAGCAGACTAAAGGTAAGAAAGTCTTCA-AGTTAAAGCCGACAAG-TAGACTTAA
320298 G
126 G
* * * * * *
320299 GATAAAGGAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTTGAGGTGAGGTAGTCTCCAAAGTCA
1 GATAAAGGAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTTAAGGT-AAGAAGTCTCCAAGGTCA
* * * *
320364 AAGCTGACAAGTAGACTTAAGGATAAAGGAAGTCTTCAAAGTTAAAGCCGACAAGTAGACTTAAG
65 AAGCCGACAAGCAGACTAAAGG-T-AAGAAAGTCTTC-AAGTTAAAGCCGACAAGTAGACTTAAG
320429 G
1 G
320430 GTGAGGAAAG
Statistics
Matches: 211, Mismatches: 36, Indels: 22
0.78 0.13 0.08
Matches are distributed among these distances:
126 4 0.02
127 42 0.20
128 87 0.41
129 41 0.19
130 33 0.16
131 4 0.02
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.18
Consensus pattern (126 bp):
GATAAAGGAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTTAAGGTAAGAAGTCTCCAAGGTCAA
AGCCGACAAGCAGACTAAAGGTAAGAAAGTCTTCAAGTTAAAGCCGACAAGTAGACTTAAG
Found at i:320310 original size:86 final size:86
Alignment explanation
Indices: 320044--320416 Score: 323
Period size: 86 Copynumber: 4.4 Consensus size: 86
320034 ACAAACTTGT
* * * * * *
320044 GATAAA-GCAGTCTCTAGGGTCAAAGCCGACAGG-AAGAC-TGAAGGTAAGAAAATCTCTAAGGT
1 GATAAAGGAAGTCTCCAAGGTCAAAGCCGACAGGCAA-ACTTG-AGGTAAGAAAGTCTCCAAAGT
* ** *
320106 CAAAGCCGACAAACAGACTTAAA
64 CAAAGCTGACAAGTAGACTTAAG
* * * * * * **
320129 GATAAA--AAGTCTCCAAGATCAAAGCCAACAAGCAGACTTAAGAGTAATG-AAGTCTCTAGGGT
1 GATAAAGGAAGTCTCCAAGGTCAAAGCCGACAGGCAAACTTGAG-GTAA-GAAAGTCTCCAAAGT
* * * *
320191 CAAAACCGACATGCAGACTTAAG
64 CAAAGCTGACAAGTAGACTTAAG
* * * * *
320214 GGTAAA-GAAGTCTCCAAGGTCAAAGCCGATAGGCAAAC-TGAAGGTAAGAAAGTCTTCAGAGTT
1 GATAAAGGAAGTCTCCAAGGTCAAAGCCGACAGGCAAACTTG-AGGTAAGAAAGTCTCCAAAGTC
320277 AAAGCTGA-AAGATAGACTTAAG
65 AAAGCTGACAAG-TAGACTTAAG
* * **
320299 GATAAAGGAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTTGAGGTGAGGTAGTCTCCAAAGTCA
1 GATAAAGGAAGTCTCCAAGGTCAAAGCCGACAGGCAAACTTGAGGTAAGAAAGTCTCCAAAGTCA
320364 AAGCTGACAAGTAGACTTAAG
66 AAGCTGACAAGTAGACTTAAG
* * *
320385 GATAAAGGAAGTCTTCAAAGTTAAAGCCGACA
1 GATAAAGGAAGTCTCCAAGGTCAAAGCCGACA
320417 AGTAGACTTA
Statistics
Matches: 236, Mismatches: 41, Indels: 21
0.79 0.14 0.07
Matches are distributed among these distances:
84 27 0.11
85 82 0.35
86 122 0.52
87 5 0.02
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (86 bp):
GATAAAGGAAGTCTCCAAGGTCAAAGCCGACAGGCAAACTTGAGGTAAGAAAGTCTCCAAAGTCA
AAGCTGACAAGTAGACTTAAG
Found at i:320311 original size:44 final size:44
Alignment explanation
Indices: 320062--320429 Score: 258
Period size: 42 Copynumber: 8.6 Consensus size: 44
320052 AGTCTCTAGG
* * * * * * *
320062 GTCAAAGCCGACAGGAAGACTGAAGG-T-AAGAAAATCTCTAAG
1 GTCAAAGCCGACAAGTAGACTTAAGGATAAAGGAAGTCTCCAAA
** *
320104 GTCAAAGCCGACAAACAGACTTAAAGATAAA--AAGTCTCC-AA
1 GTCAAAGCCGACAAGTAGACTTAAGGATAAAGGAAGTCTCCAAA
* * * * **
320145 GATCAAAGCCAACAAGCAGACTTAA-GAGT-AATGAAGTCTCTAGG
1 G-TCAAAGCCGACAAGTAGACTTAAGGA-TAAAGGAAGTCTCCAAA
* * * * *
320189 GTCAAAACCGACATGCAGACTTAAGGGTAAA-GAAGTCTCCAAG
1 GTCAAAGCCGACAAGTAGACTTAAGGATAAAGGAAGTCTCCAAA
* * * * * * * *
320232 GTCAAAGCCGATAGGCAAACTGAAGG-T-AAGAAAGTCTTCAGA
1 GTCAAAGCCGACAAGTAGACTTAAGGATAAAGGAAGTCTCCAAA
* * *
320274 GTTAAAGCTGA-AAGATAGACTTAAGGATAAAGGAAGTCTCCAAG
1 GTCAAAGCCGACAAG-TAGACTTAAGGATAAAGGAAGTCTCCAAA
* * * * *
320318 GTCAAAGCCGACAGGCAGACTTGAGG-T-GAGGTAGTCTCCAAA
1 GTCAAAGCCGACAAGTAGACTTAAGGATAAAGGAAGTCTCCAAA
* *
320360 GTCAAAGCTGACAAGTAGACTTAAGGATAAAGGAAGTCTTCAAA
1 GTCAAAGCCGACAAGTAGACTTAAGGATAAAGGAAGTCTCCAAA
*
320404 GTTAAAGCCGACAAGTAGACTTAAGG
1 GTCAAAGCCGACAAGTAGACTTAAGG
320430 GTGAGGAAAG
Statistics
Matches: 255, Mismatches: 55, Indels: 30
0.75 0.16 0.09
Matches are distributed among these distances:
41 10 0.04
42 109 0.43
43 63 0.25
44 71 0.28
45 2 0.01
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.17
Consensus pattern (44 bp):
GTCAAAGCCGACAAGTAGACTTAAGGATAAAGGAAGTCTCCAAA
Found at i:320795 original size:10 final size:10
Alignment explanation
Indices: 320780--320871 Score: 81
Period size: 10 Copynumber: 9.7 Consensus size: 10
320770 TCCATAAATT
320780 TTTTTTTCTC
1 TTTTTTTCTC
320790 TTTTTTTCTC
1 TTTTTTTCTC
*
320800 -TATTTT-T-
1 TTTTTTTCTC
* *
320807 ATATTTTCATC
1 TTTTTTTC-TC
320818 -TTTTTTCT-
1 TTTTTTTCTC
320826 TTTTTTTCT-
1 TTTTTTTCTC
*
320835 TTCTTTTTTTC
1 TT-TTTTTCTC
320846 TTTTTTTCTC
1 TTTTTTTCTC
320856 TTTTTTT-TC
1 TTTTTTTCTC
320865 TTTTTTT
1 TTTTTTT
320872 TCAACAGCCA
Statistics
Matches: 71, Mismatches: 4, Indels: 15
0.79 0.04 0.17
Matches are distributed among these distances:
8 7 0.10
9 25 0.35
10 37 0.52
11 2 0.03
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTTTCTC
Found at i:320813 original size:20 final size:19
Alignment explanation
Indices: 320780--320871 Score: 91
Period size: 19 Copynumber: 4.8 Consensus size: 19
320770 TCCATAAATT
320780 TTTTTTTCTCTTTTTTTCTC
1 TTTTTTT-TCTTTTTTTCTC
* * *
320800 -TATTTTT-ATATTTTCATC
1 TTTTTTTTCTTTTTTTC-TC
* *
320818 TTTTTTCT-TTTTTTTCTT
1 TTTTTTTTCTTTTTTTCTC
320836 TCTTTTTTTCTTTTTTTCTC
1 T-TTTTTTTCTTTTTTTCTC
320856 TTTTTTTTCTTTTTTT
1 TTTTTTTTCTTTTTTT
320872 TCAACAGCCA
Statistics
Matches: 58, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
17 6 0.10
18 5 0.09
19 37 0.64
20 10 0.17
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTTTTCTTTTTTTCTC
Found at i:320871 original size:9 final size:9
Alignment explanation
Indices: 320779--320873 Score: 84
Period size: 9 Copynumber: 10.0 Consensus size: 9
320769 TTCCATAAAT
320779 TTTTTTTTC
1 TTTTTTTTC
320788 TCTTTTTTTC
1 T-TTTTTTTC
* *
320798 TCTATTTT-
1 TTTTTTTTC
* *
320806 TATATTTTC
1 TTTTTTTTC
*
320815 ATCTTTTTTC
1 -TTTTTTTTC
320825 TTTTTTTTC
1 TTTTTTTTC
320834 TTTCTTTTTTTC
1 --T-TTTTTTTC
320846 TTTTTTTCTC
1 TTTTTTT-TC
320856 TTTTTTTTC
1 TTTTTTTTC
320865 TTTTTTTTC
1 TTTTTTTTC
320874 AACAGCCAAA
Statistics
Matches: 73, Mismatches: 6, Indels: 14
0.78 0.06 0.15
Matches are distributed among these distances:
8 7 0.10
9 31 0.42
10 26 0.36
11 1 0.01
12 8 0.11
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:321803 original size:18 final size:20
Alignment explanation
Indices: 321782--321823 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
321772 TGCAAATCCC
*
321782 AATAT-CATGTAA-AATGCA
1 AATATGCATGAAACAATGCA
321800 AATATGCATGAAACAATGCA
1 AATATGCATGAAACAATGCA
321820 AATA
1 AATA
321824 CAAGCATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
19 6 0.29
20 10 0.48
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (20 bp):
AATATGCATGAAACAATGCA
Found at i:329428 original size:28 final size:28
Alignment explanation
Indices: 329390--329443 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
329380 ATTTTTCATT
* *
329390 TTTTTGATTTTATTATTTTTT-ATTTTGA
1 TTTTAGATTTTA-GATTTTTTGATTTTGA
329418 TTTTAGATTTTAGATTTTTTGATTTT
1 TTTTAGATTTTAGATTTTTTGATTTT
329444 TTTGATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.19, C:0.00, G:0.09, T:0.72
Consensus pattern (28 bp):
TTTTAGATTTTAGATTTTTTGATTTTGA
Found at i:329436 original size:21 final size:23
Alignment explanation
Indices: 329389--329453 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 23
329379 GATTTTTCAT
*
329389 TTTTTTGATTTTATTATTTT---
1 TTTTTTGATTTTATGATTTTAGA
329409 TTATTTTGATTTTA-GATTTTAGA
1 TT-TTTTGATTTTATGATTTTAGA
*
329432 TTTTTTGATTTTTTTGATTTTA
1 TTTTTTGA-TTTTATGATTTTA
329454 TATCGAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
20 7 0.19
21 11 0.30
22 6 0.16
23 6 0.16
24 7 0.19
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.72
Consensus pattern (23 bp):
TTTTTTGATTTTATGATTTTAGA
Found at i:329444 original size:16 final size:15
Alignment explanation
Indices: 329373--329443 Score: 67
Period size: 16 Copynumber: 4.8 Consensus size: 15
329363 TTTTTCATAT
**
329373 TTTTTTGATTTTTCA
1 TTTTTTGATTTTAGA
*
329388 TTTTTTTGATTTTATTA
1 -TTTTTTGATTTTA-GA
329405 TTTTTT-ATTTT-GA
1 TTTTTTGATTTTAGA
*
329418 -TTTTAGATTTTAGA
1 TTTTTTGATTTTAGA
329432 TTTTTTGATTTT
1 TTTTTTGATTTT
329444 TTTGATTTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
12 4 0.09
13 6 0.13
14 2 0.04
15 15 0.33
16 18 0.39
17 1 0.02
ACGTcount: A:0.17, C:0.01, G:0.08, T:0.73
Consensus pattern (15 bp):
TTTTTTGATTTTAGA
Found at i:329452 original size:7 final size:7
Alignment explanation
Indices: 329374--329444 Score: 54
Period size: 7 Copynumber: 9.7 Consensus size: 7
329364 TTTTCATATT
329374 TTTTTGA
1 TTTTTGA
*
329381 TTTTTCA
1 TTTTTGA
329388 TTTTTTTGA
1 --TTTTTGA
*
329397 TTTTATTA
1 TTTT-TGA
*
329405 TTTTTTA
1 TTTTTGA
329412 -TTTTGA
1 TTTTTGA
*
329418 TTTTAGA
1 TTTTTGA
*
329425 TTTTAGA
1 TTTTTGA
329432 TTTTTTGA
1 -TTTTTGA
329440 TTTTT
1 TTTTT
329445 TTGATTTTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
6 5 0.09
7 30 0.57
8 12 0.23
9 6 0.11
ACGTcount: A:0.17, C:0.01, G:0.08, T:0.73
Consensus pattern (7 bp):
TTTTTGA
Found at i:334754 original size:32 final size:30
Alignment explanation
Indices: 334701--334766 Score: 73
Period size: 32 Copynumber: 2.1 Consensus size: 30
334691 ATAATTAGTA
*
334701 TTATGTATATTTTGACATATTTATGTTATTTT
1 TTATGTATATTTTGACATATTT-T-TTATTCT
334733 TTATGTAGTATTTT-A-ATTATTTTTTATTCT
1 TTATGTA-TATTTTGACA-TATTTTTTATTCT
334763 TTAT
1 TTAT
334767 TTGTACCATG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
30 10 0.32
31 2 0.06
32 13 0.42
33 6 0.19
ACGTcount: A:0.24, C:0.03, G:0.08, T:0.65
Consensus pattern (30 bp):
TTATGTATATTTTGACATATTTTTTATTCT
Found at i:335042 original size:11 final size:11
Alignment explanation
Indices: 335022--335087 Score: 51
Period size: 11 Copynumber: 5.5 Consensus size: 11
335012 ATGTATTCAG
*
335022 ATTATGTTTAT
1 ATTATTTTTAT
335033 ATTATTTTTAT
1 ATTATTTTTAT
*
335044 ATCATATTATATTTT
1 AT--TATT-T-TTAT
335059 AATTATTTTTTAT
1 -ATTA-TTTTTAT
*
335072 ATTATATTTAT
1 ATTATTTTTAT
335083 ATTAT
1 ATTAT
335088 GCCTCATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
11 23 0.51
12 4 0.09
13 7 0.16
14 4 0.09
15 5 0.11
16 2 0.04
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (11 bp):
ATTATTTTTAT
Found at i:335156 original size:12 final size:12
Alignment explanation
Indices: 335127--335156 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
335117 TTATTATAAT
335127 AATTTAATTTTA
1 AATTTAATTTTA
*
335139 ATTTTAATTTTA
1 AATTTAATTTTA
335151 AATTTA
1 AATTTA
335157 TTCATATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
AATTTAATTTTA
Found at i:342976 original size:24 final size:25
Alignment explanation
Indices: 342929--342986 Score: 91
Period size: 24 Copynumber: 2.4 Consensus size: 25
342919 GAAAATCTAT
342929 TTGAAGCATAAAGCTTATGATTGAA
1 TTGAAGCATAAAGCTTATGATTGAA
*
342954 TTGAAGCATAAAGC-TATGATTGAG
1 TTGAAGCATAAAGCTTATGATTGAA
*
342978 TTAAAGCAT
1 TTGAAGCAT
342987 GAATTTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 17 0.55
25 14 0.45
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.31
Consensus pattern (25 bp):
TTGAAGCATAAAGCTTATGATTGAA
Found at i:344776 original size:22 final size:21
Alignment explanation
Indices: 344726--344781 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
344716 CTAACCTATG
344726 TATTTATTTTTTTATATTAATA
1 TATTTATTTTTTTATATT-ATA
* *
344748 AAATTATCATTTTTTATATT-TA
1 TATTTAT--TTTTTTATATTATA
344770 TATTTATTTTTT
1 TATTTATTTTTT
344782 ATTTTAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
20 5 0.18
22 12 0.43
24 11 0.39
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (21 bp):
TATTTATTTTTTTATATTATA
Found at i:346143 original size:16 final size:16
Alignment explanation
Indices: 346117--346152 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
346107 TAATATTTTG
346117 ATAATTTATTTT-AAA
1 ATAATTTATTTTCAAA
346132 ATAATATTATTTTCAAA
1 ATAAT-TTATTTTCAAA
346149 ATAA
1 ATAA
346153 ATTTTAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.26
16 7 0.37
17 7 0.37
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAATTTATTTTCAAA
Found at i:346865 original size:18 final size:18
Alignment explanation
Indices: 346842--346909 Score: 82
Period size: 18 Copynumber: 3.8 Consensus size: 18
346832 GATGGTGACG
* *
346842 AAAATAATATTAGTAACA
1 AAAATAATAATAGTAATA
*
346860 AAAATAATAATATTAATA
1 AAAATAATAATAGTAATA
* * *
346878 TAAATAATCATAATAATA
1 AAAATAATAATAGTAATA
346896 AAAATAATAATAGT
1 AAAATAATAATAGT
346910 GGAAATGAGA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (18 bp):
AAAATAATAATAGTAATA
Found at i:355084 original size:33 final size:33
Alignment explanation
Indices: 355009--355091 Score: 93
Period size: 33 Copynumber: 2.5 Consensus size: 33
354999 CGGGATTAAT
355009 TTTATTATTATAAATATATTAAAATATTAAAAAAA
1 TTTATTATT-TAAATA-ATTAAAATATTAAAAAAA
*
355044 -TTA-TATTTATATAATT-AAAT-TTAAATAAAAA
1 TTTATTATTTAAATAATTAAAATATT-AA-AAAAA
355075 TTTATTATTTAAATAAT
1 TTTATTATTTAAATAAT
355092 AATTATAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
29 2 0.05
30 6 0.14
31 8 0.19
32 8 0.19
33 15 0.36
34 3 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (33 bp):
TTTATTATTTAAATAATTAAAATATTAAAAAAA
Found at i:355094 original size:36 final size:34
Alignment explanation
Indices: 355009--355101 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 34
354999 CGGGATTAAT
355009 TTTATTATTATAAATAT-ATTAAAATATTAAAAAAA
1 TTTATTATT-TAAATATAATT-AAATATTAAAAAAA
355044 -TTA-TATTT--ATATAATTAAAT-TTAAATAAAAA
1 TTTATTATTTAAATATAATTAAATATT-AA-AAAAA
355075 TTTATTATTTAAATAATAATTATAATA
1 TTTATTATTTAAAT-ATAATTA-AATA
355102 CAATTAATTA
Statistics
Matches: 48, Mismatches: 0, Indels: 17
0.74 0.00 0.26
Matches are distributed among these distances:
29 2 0.04
30 10 0.21
31 8 0.17
32 4 0.08
33 9 0.19
34 3 0.06
35 2 0.04
36 7 0.15
37 3 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (34 bp):
TTTATTATTTAAATATAATTAAATATTAAAAAAA
Found at i:355753 original size:6 final size:5
Alignment explanation
Indices: 355735--355905 Score: 71
Period size: 5 Copynumber: 35.2 Consensus size: 5
355725 ACGATTATTA
* *
355735 AATAT AAT-T -ATAT GAATAT AATA- AATAT AAAAT AATTAA AATAT AATAT
1 AATAT AATAT AATAT -AATAT AATAT AATAT AATAT AA-TAT AATAT AATAT
* * * *
355784 AATAT AA-AT -ATAT ATTTT AA-ATT TATAT AATAT AA-AT TAT-T AATAT
1 AATAT AATAT AATAT AATAT AATA-T AATAT AATAT AATAT AATAT AATAT
* * * *
355830 ATTAA AAT-T AATAT AAATAT AAAAT -ATTT AAATAT AATTAT AAT-T
1 AATAT AATAT AATAT -AATAT AATAT AATAT -AATAT AA-TAT AATAT
* *
355875 -ATAT AAAAT -ATAT ACACAT AATAT AAATAT A
1 AATAT AATAT AATAT A-ATAT AATAT -AATAT A
355906 TGAATCCCAT
Statistics
Matches: 121, Mismatches: 24, Indels: 42
0.65 0.13 0.22
Matches are distributed among these distances:
3 5 0.04
4 26 0.21
5 60 0.50
6 30 0.25
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:355776 original size:16 final size:17
Alignment explanation
Indices: 355757--355905 Score: 60
Period size: 16 Copynumber: 8.4 Consensus size: 17
355747 TGAATATAAT
355757 AAATATAAAATAAT-TA
1 AAATATAAAATAATATA
*
355773 AAATATAATATAATATA
1 AAATATAAAATAATATA
*
355790 AATATATATTTTAAAT-TTATA
1 AA-ATATA----AAATAATATA
* *
355811 TAATAT-AAATTAT-TA
1 AAATATAAAATAATATA
*
355826 ATATATTAAAATTAATAT-
1 AAATA-TAAAA-TAATATA
*
355844 AAATATAAAAT-ATTTA
1 AAATATAAAATAATATA
* *
355860 AATATAATTATAATTATATA
1 AA-AT-A-TAAAATAATATA
355880 AAATATATACACATAATAT-
1 AAATATA-A-A-ATAATATA
355899 AAATATA
1 AAATATA
355906 TGAATCCCAT
Statistics
Matches: 100, Mismatches: 14, Indels: 35
0.67 0.09 0.23
Matches are distributed among these distances:
15 12 0.12
16 18 0.18
17 16 0.16
18 14 0.14
19 16 0.16
20 16 0.16
21 5 0.05
22 3 0.03
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATATAAAATAATATA
Found at i:355830 original size:33 final size:31
Alignment explanation
Indices: 355769--355857 Score: 103
Period size: 28 Copynumber: 2.9 Consensus size: 31
355759 ATATAAAATA
355769 ATTAAAATATAATATAATATAAA-TA-TATAT
1 ATTAAAAT-TAATATAATATAAATTATTATAT
* *
355799 -TTTAAATTTATATAATATAAATTATTAATAT
1 ATTAAAATTAATATAATATAAATTATT-ATAT
*
355830 ATTAAAATTAATATAAATATAAAATATT
1 ATTAAAATTAATAT-AATATAAATTATT
355858 TAAATATAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
28 13 0.27
29 8 0.16
30 1 0.02
31 4 0.08
32 11 0.22
33 12 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
ATTAAAATTAATATAATATAAATTATTATAT
Found at i:355895 original size:29 final size:28
Alignment explanation
Indices: 355810--355906 Score: 87
Period size: 29 Copynumber: 3.5 Consensus size: 28
355800 TTAAATTTAT
*
355810 ATAATATAAAT-TAT-TAATATATTAAA-
1 ATAATATAAATATATAAAATATA-TAAAC
* *
355836 ATTAATAT-AA-ATATAAAATATTTAAAT
1 A-TAATATAAATATATAAAATATATAAAC
* *
355863 ATAATTATAATTATATAAAATATATACAC
1 ATAA-TATAAATATATAAAATATATAAAC
355892 ATAATATAAATATAT
1 ATAATATAAATATAT
355907 GAATCCCATG
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
26 13 0.23
27 15 0.26
28 11 0.19
29 18 0.32
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (28 bp):
ATAATATAAATATATAAAATATATAAAC
Found at i:356101 original size:11 final size:11
Alignment explanation
Indices: 356047--356105 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
356037 TATTCGTAAT
*
356047 TTTTATATTTA
1 TTTTATATATA
*
356058 -TTTATATAAA
1 TTTTATATATA
356068 TTTTA-ATATA
1 TTTTATATATA
* *
356078 -TTAATAATTTA
1 TTTTAT-ATATA
356089 TTTTATATATA
1 TTTTATATATA
356100 TTTTAT
1 TTTTAT
356106 CATACTCATA
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
9 3 0.08
10 12 0.32
11 18 0.49
12 4 0.11
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TTTTATATATA
Found at i:356307 original size:17 final size:17
Alignment explanation
Indices: 356285--356325 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
356275 ATTTATCTTC
*
356285 AAATTATTTAAATTTAT
1 AAATTATTTAAATTCAT
*
356302 AAATTATTTGAATTCAT
1 AAATTATTTAAATTCAT
356319 AATATTA
1 AA-ATTA
356326 AAATCTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (17 bp):
AAATTATTTAAATTCAT
Found at i:359566 original size:31 final size:31
Alignment explanation
Indices: 359513--359572 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
359503 TGACAGTAAG
*
359513 TTTAAAATAATATAAACTCAAAATAATTTAA
1 TTTAAAATAATATAAACTCAAAACAATTTAA
359544 TTTAAAATAAT-TCAAA-TCCAAAACAATTT
1 TTTAAAATAATAT-AAACT-CAAAACAATTT
359573 GAACCTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (31 bp):
TTTAAAATAATATAAACTCAAAACAATTTAA
Found at i:360581 original size:27 final size:31
Alignment explanation
Indices: 360540--360618 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 31
360530 ATTATATATG
*
360540 ATATATT-ATATA-TT-TT-TATAAATTTTA
1 ATATATTAATATATTTATTATATAAAATTTA
360567 ATATATTAATA-ATTTACATTATATAAAATTTA
1 ATATATTAATATATTT--ATTATATAAAATTTA
360599 ATATATTAATATATATTATT
1 ATATATTAATATAT-TTATT
360619 CGTATTATAT
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
27 8 0.19
28 5 0.12
31 2 0.05
32 24 0.56
33 2 0.05
34 2 0.05
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (31 bp):
ATATATTAATATATTTATTATATAAAATTTA
Found at i:360603 original size:14 final size:14
Alignment explanation
Indices: 360556--360604 Score: 53
Period size: 16 Copynumber: 3.2 Consensus size: 14
360546 TATATATTTT
*
360556 TATAAATTTTAATA
1 TATAAAATTTAATA
360570 TATTAATAATTTACATTA
1 TA-TAA-AATTTA-A-TA
360588 TATAAAATTTAATA
1 TATAAAATTTAATA
360602 TAT
1 TAT
360605 TAATATATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
14 7 0.23
15 4 0.13
16 11 0.37
17 4 0.13
18 4 0.13
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (14 bp):
TATAAAATTTAATA
Found at i:363862 original size:50 final size:50
Alignment explanation
Indices: 363808--363952 Score: 247
Period size: 50 Copynumber: 2.9 Consensus size: 50
363798 TTGATTATCA
*
363808 TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTC
1 TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACAATTC
363858 TTCACCAACCTTTGACAATAGA-AGGAGGTGGCCATAATTGTTGACAATTC
1 TTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATAATTGTTGACAATTC
* *
363908 TTCACCAACCTTTGACAATAGAGGGAGGTAGCCATAATTGTTGAC
1 TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGAC
363953 TCTAAGTATA
Statistics
Matches: 90, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
49 1 0.01
50 89 0.99
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (50 bp):
TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACAATTC
Found at i:368421 original size:50 final size:50
Alignment explanation
Indices: 368346--368504 Score: 250
Period size: 50 Copynumber: 3.2 Consensus size: 50
368336 AGTTGTTGTC
*
368346 ATTGTTGACTA-TCATTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1 ATTGTTGACAATTC-TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
368396 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGA-AGGAGGTGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATA
* *
368446 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGTCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
368496 ATTGTTGAC
1 ATTGTTGAC
368505 TCTAAGTATA
Statistics
Matches: 102, Mismatches: 4, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
49 1 0.01
50 99 0.97
51 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (50 bp):
ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
Found at i:369366 original size:16 final size:16
Alignment explanation
Indices: 369345--369381 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
369335 AACATTAATT
*
369345 TTTTAAAAATAAAATA
1 TTTTAAAAATAAAAAA
*
369361 TTTTAAATATAAAAAA
1 TTTTAAAAATAAAAAA
369377 TTTTA
1 TTTTA
369382 TAATTAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TTTTAAAAATAAAAAA
Found at i:371728 original size:13 final size:13
Alignment explanation
Indices: 371710--371734 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
371700 TTAATTTATA
371710 TGATTTTTTAATG
1 TGATTTTTTAATG
371723 TGATTTTTTAAT
1 TGATTTTTTAAT
371735 ATAAATTACT
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:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (13 bp):
TGATTTTTTAATG
Found at i:372018 original size:27 final size:28
Alignment explanation
Indices: 371988--372086 Score: 101
Period size: 29 Copynumber: 3.2 Consensus size: 28
371978 ATAATTTATG
371988 TTTTAAATTATTAAATTTAATATTAATTT
1 TTTTAAATTATTAAATTTAATATTAA-TT
372017 TTTTAGAAGTTA-TAAATTTAAATTTTATTAAATT
1 TTTTA-AA-TTATTAAATTT-AA---TATT-AATT
*
372051 TTTTAAATTATTAAATTTAATATCAATT
1 TTTTAAATTATTAAATTTAATATTAATT
372079 TTTATAAA
1 TTT-TAAA
372087 AGTTATAAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 18
0.76 0.01 0.23
Matches are distributed among these distances:
28 7 0.12
29 12 0.20
30 9 0.15
31 5 0.08
32 5 0.08
33 9 0.15
34 11 0.18
35 2 0.03
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (28 bp):
TTTTAAATTATTAAATTTAATATTAATT
Found at i:372034 original size:30 final size:29
Alignment explanation
Indices: 371988--372098 Score: 109
Period size: 30 Copynumber: 3.6 Consensus size: 29
371978 ATAATTTATG
371988 TTTTAAA-TTATTAAATTTAATATTAATTT
1 TTTTAAAGTTA-TAAATTTAATATTAATTT
*
372017 TTTTAGAAGTTATAAATTTAAATTTTATTAAATT
1 TTTTA-AAGTTATAAATTT-AA---TATTAATTT
*
372051 TTTTAAA-TTATTAAATTTAATATCAATTT
1 TTTTAAAGTTA-TAAATTTAATATTAATTT
*
372080 TTATAAAAGTTATAAATTT
1 TT-TTAAAGTTATAAATTT
372099 TAATTTTATT
Statistics
Matches: 69, Mismatches: 4, Indels: 17
0.77 0.04 0.19
Matches are distributed among these distances:
29 14 0.20
30 20 0.29
31 8 0.12
32 5 0.07
33 9 0.13
34 13 0.19
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (29 bp):
TTTTAAAGTTATAAATTTAATATTAATTT
Found at i:372039 original size:36 final size:35
Alignment explanation
Indices: 371998--372104 Score: 104
Period size: 36 Copynumber: 3.2 Consensus size: 35
371988 TTTTAAATTA
371998 TTAAATTTAATATTAATTTTTTTAGAAGTTATAAAT
1 TTAAATTTAATATTAATTTTTTTA-AAGTTATAAAT
*
372034 TTAAATTT--TATTAAATTTTTTAAA--T-T--A-
1 TTAAATTTAATATTAATTTTTTTAAAGTTATAAAT
* *
372061 TTAAATTTAATATCAATTTTTATAAAAGTTATAAAT
1 TTAAATTTAATATTAATTTTT-TTAAAGTTATAAAT
*
372097 TTTAATTT
1 TTAAATTT
372105 TATTAAATTA
Statistics
Matches: 57, Mismatches: 5, Indels: 18
0.71 0.06 0.22
Matches are distributed among these distances:
27 8 0.14
28 1 0.02
29 9 0.16
30 5 0.09
31 1 0.02
32 1 0.02
33 3 0.05
34 13 0.23
35 1 0.02
36 15 0.26
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (35 bp):
TTAAATTTAATATTAATTTTTTTAAAGTTATAAAT
Found at i:372056 original size:63 final size:64
Alignment explanation
Indices: 371988--372124 Score: 222
Period size: 63 Copynumber: 2.1 Consensus size: 64
371978 ATAATTTATG
* * *
371988 TTTTAAATTATTAAATTTAATATTAATTTTTTTAGAAGTTATAAATTTAAATTTTATTAAATT-
1 TTTTAAATTATTAAATTTAATATCAATTTTTATAAAAGTTATAAATTTAAATTTTATTAAATTA
*
372051 TTTTAAATTATTAAATTTAATATCAATTTTTATAAAAGTTATAAATTTTAATTTTATTAAATTA
1 TTTTAAATTATTAAATTTAATATCAATTTTTATAAAAGTTATAAATTTAAATTTTATTAAATTA
372115 TTATTAAATT
1 TT-TTAAATT
372125 TTTTTATTAA
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
63 59 0.87
64 2 0.03
65 7 0.10
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (64 bp):
TTTTAAATTATTAAATTTAATATCAATTTTTATAAAAGTTATAAATTTAAATTTTATTAAATTA
Found at i:372755 original size:20 final size:20
Alignment explanation
Indices: 372730--372779 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
372720 TTTGATCGGT
372730 TTTTTAATTTT-TTCAAATTA
1 TTTTT-ATTTTGTTCAAATTA
*
372750 TTTTTATTTTGTTCAATTTA
1 TTTTTATTTTGTTCAAATTA
*
372770 TATTT-TTTTG
1 TTTTTATTTTG
372780 ATATTTTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 10 0.37
20 17 0.63
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.70
Consensus pattern (20 bp):
TTTTTATTTTGTTCAAATTA
Found at i:372806 original size:22 final size:22
Alignment explanation
Indices: 372781--372830 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
372771 ATTTTTTTGA
372781 TATTTTTGTTTTAATTGAG-TTT
1 TATTTTT-TTTTAATTGAGCTTT
*
372803 TATTATTTTTTAATTGAGCTTT
1 TATTTTTTTTTAATTGAGCTTT
372825 TATTTT
1 TATTTT
372831 AAGTTTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.20, C:0.02, G:0.10, T:0.68
Consensus pattern (22 bp):
TATTTTTTTTTAATTGAGCTTT
Found at i:372827 original size:19 final size:21
Alignment explanation
Indices: 372789--372830 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
372779 GATATTTTTG
*
372789 TTTTAATTGAGTTTTATTATT
1 TTTTAATTGAGTCTTATTATT
372810 TTTTAATTGAG-CTT-TTATT
1 TTTTAATTGAGTCTTATTATT
372829 TT
1 TT
372831 AAGTTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 2 0.10
21 11 0.55
ACGTcount: A:0.21, C:0.02, G:0.10, T:0.67
Consensus pattern (21 bp):
TTTTAATTGAGTCTTATTATT
Found at i:372927 original size:26 final size:27
Alignment explanation
Indices: 372867--372928 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 27
372857 TTTAAATGGG
*
372867 TTTAAGTTTAAATTTATATTTTATTAA
1 TTTAATTTTAAATTTATATTTTATTAA
*
372894 -ATATATTTTAAATATTA-A-TTTATTAA
1 TTTA-ATTTTAAAT-TTATATTTTATTAA
372920 TTTAATTTT
1 TTTAATTTT
372929 TTTATTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
26 15 0.52
27 11 0.38
28 3 0.10
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTAATTTTAAATTTATATTTTATTAA
Found at i:373009 original size:9 final size:9
Alignment explanation
Indices: 372978--373054 Score: 75
Period size: 9 Copynumber: 8.2 Consensus size: 9
372968 AATTAGCACT
372978 TTAAATTAA
1 TTAAATTAA
372987 TTAAAATTTAAA
1 TT-AAA-TT-AA
372999 TTAAATTAA
1 TTAAATTAA
373008 TTAAATTAA
1 TTAAATTAA
*
373017 TTAAATCAAA
1 TTAAAT-TAA
*
373027 TTTAATTAA
1 TTAAATTAA
**
373036 TT-TTTTAA
1 TTAAATTAA
373044 TTAAATTAA
1 TTAAATTAA
373053 TT
1 TT
373055 TTAAACGATT
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
8 6 0.11
9 29 0.52
10 12 0.21
11 5 0.09
12 4 0.07
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (9 bp):
TTAAATTAA
Found at i:373043 original size:23 final size:23
Alignment explanation
Indices: 372980--373054 Score: 77
Period size: 21 Copynumber: 3.4 Consensus size: 23
372970 TTAGCACTTT
*
372980 AAATTAATTAAA--ATTTAAATT
1 AAATTAATTAAATTATTTAAATC
*
373001 AAATTAATTAAATTAATTAAATC
1 AAATTAATTAAATTATTTAAATC
* *
373024 AAATTTAATT-AATT-TTTTAATT
1 AAA-TTAATTAAATTATTTAAATC
373046 AAATTAATT
1 AAATTAATT
373055 TTAAACGATT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
21 18 0.39
22 8 0.17
23 14 0.30
24 6 0.13
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (23 bp):
AAATTAATTAAATTATTTAAATC
Found at i:373052 original size:5 final size:5
Alignment explanation
Indices: 372978--373035 Score: 59
Period size: 5 Copynumber: 11.8 Consensus size: 5
372968 AATTAGCACT
*
372978 TTAAA TT-AA TTAAAA TTTAAA TTAAA TT-AA TTAAA TT-AA TTAAA TCAAA
1 TTAAA TTAAA TT-AAA -TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA
*
373027 TTTAA TTAA
1 TTAAA TTAA
373036 TTTTTTAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
4 12 0.27
5 25 0.57
6 5 0.11
7 2 0.05
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (5 bp):
TTAAA
Found at i:373913 original size:16 final size:16
Alignment explanation
Indices: 373894--373925 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
373884 TCATATGGTT
373894 TTTCTTGATAATTATA
1 TTTCTTGATAATTATA
*
373910 TTTCTTGATATTTATA
1 TTTCTTGATAATTATA
373926 GTATTTGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.59
Consensus pattern (16 bp):
TTTCTTGATAATTATA
Found at i:374081 original size:70 final size:69
Alignment explanation
Indices: 373987--374121 Score: 216
Period size: 70 Copynumber: 1.9 Consensus size: 69
373977 AGTGGGATGG
*
373987 TTAATTTTATGAGGAAACGTAACGAATGTTAGATACTTCAAAATGGAAGGATTTCTTGCAATCCT
1 TTAATTTTATGAGGAAACGTAACGAATGTTAGATACTTC-AAATCGAAGGATTTCTTGCAATCCT
374052 AAACA
65 AAACA
* * * *
374057 TTAATTTTATGGGGAGATGTAACGAATGTTAGATACTTCAAATCGAGGGATTTCTTGCAATCCTA
1 TTAATTTTATGAGGAAACGTAACGAATGTTAGATACTTCAAATCGAAGGATTTCTTGCAATCCTA
374122 TACTTTTCCT
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
69 24 0.40
70 36 0.60
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (69 bp):
TTAATTTTATGAGGAAACGTAACGAATGTTAGATACTTCAAATCGAAGGATTTCTTGCAATCCTA
AACA
Found at i:378268 original size:50 final size:50
Alignment explanation
Indices: 378209--378311 Score: 206
Period size: 50 Copynumber: 2.1 Consensus size: 50
378199 GAACTAAAAG
378209 TAAGAAAAATTATCAAGCACCAGCCCTTCCTCAACCCCCTCCCCAATAAA
1 TAAGAAAAATTATCAAGCACCAGCCCTTCCTCAACCCCCTCCCCAATAAA
378259 TAAGAAAAATTATCAAGCACCAGCCCTTCCTCAACCCCCTCCCCAATAAA
1 TAAGAAAAATTATCAAGCACCAGCCCTTCCTCAACCCCCTCCCCAATAAA
378309 TAA
1 TAA
378312 ATAAATAGGG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.39, C:0.37, G:0.06, T:0.18
Consensus pattern (50 bp):
TAAGAAAAATTATCAAGCACCAGCCCTTCCTCAACCCCCTCCCCAATAAA
Found at i:383567 original size:7 final size:7
Alignment explanation
Indices: 383549--383582 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
383539 TTGTTAAAAG
383549 ATTTTTA
1 ATTTTTA
* *
383556 TTTTTTC
1 ATTTTTA
383563 ATTTTTA
1 ATTTTTA
383570 ATTTTTA
1 ATTTTTA
383577 ATTTTT
1 ATTTTT
383583 TATCATTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (7 bp):
ATTTTTA
Found at i:384580 original size:16 final size:16
Alignment explanation
Indices: 384559--384610 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
384549 ACTTAAATTT
384559 GAAATGATCTGAACCC
1 GAAATGATCTGAACCC
*
384575 GAAATGAT-TCGAACTC
1 GAAATGATCT-GAACCC
*
384591 GAAATGATCCGAACCC
1 GAAATGATCTGAACCC
384607 GAAA
1 GAAA
384611 ATGACTTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 1 0.03
16 30 0.97
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.17
Consensus pattern (16 bp):
GAAATGATCTGAACCC
Found at i:384916 original size:19 final size:19
Alignment explanation
Indices: 384894--384937 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
384884 TAAATTATAT
384894 ATATAAAAATATTTAAAA-A
1 ATATAAAAA-ATTTAAAATA
*
384913 ATATTAATAAATTTAAAATA
1 ATA-TAAAAAATTTAAAATA
384933 ATATA
1 ATATA
384938 TTAAAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
ATATAAAAAATTTAAAATA
Found at i:384962 original size:16 final size:15
Alignment explanation
Indices: 384939--384977 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
384929 AATAATATAT
384939 TAAAATATATCAATA
1 TAAAATATATCAATA
*
384954 TAAATATATATTAATA
1 TAAA-ATATATCAATA
384970 TTAAAATA
1 -TAAAATA
384978 AAAATGATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 4 0.19
16 13 0.62
17 4 0.19
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAAATATATCAATA
Found at i:385491 original size:18 final size:19
Alignment explanation
Indices: 385461--385506 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
385451 TTATAATAAA
*
385461 AAATATAATTATTTTAATATAT
1 AAATAT-ATT-TTTAAATAT-T
385483 AAATATATTTTTAAATATT
1 AAATATATTTTTAAATATT
385502 AAATA
1 AAATA
385507 ATTATAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 6 0.26
20 8 0.35
21 3 0.13
22 6 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AAATATATTTTTAAATATT
Found at i:399536 original size:6 final size:6
Alignment explanation
Indices: 399525--399557 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
399515 TTGAGTCTTC
399525 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
399558 GTGCACGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:402989 original size:33 final size:33
Alignment explanation
Indices: 402942--403020 Score: 131
Period size: 33 Copynumber: 2.4 Consensus size: 33
402932 ATTGACATAG
*
402942 AGAACTGCATATGATTATTCCCTAAATTAAACT
1 AGAAATGCATATGATTATTCCCTAAATTAAACT
*
402975 AGAAATGCATATGATTATTCCCTATATTAAACT
1 AGAAATGCATATGATTATTCCCTAAATTAAACT
403008 AGAAATGACATAT
1 AGAAATG-CATAT
403021 CTGATAGGTC
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
33 38 0.88
34 5 0.12
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (33 bp):
AGAAATGCATATGATTATTCCCTAAATTAAACT
Found at i:406441 original size:2 final size:2
Alignment explanation
Indices: 406436--406466 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
406426 ACACGCACAA
406436 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
406467 GAAAATAATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:406736 original size:17 final size:17
Alignment explanation
Indices: 406718--406757 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
406708 ATTTAAAATA
406718 TTTATATATCTATATTAT
1 TTTATA-ATCTATATTAT
*
406736 TTTATAATTTATATTAT
1 TTTATAATCTATATTAT
406753 ATTTA
1 -TTTA
406758 ATTTTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTATAATCTATATTAT
Found at i:406774 original size:6 final size:6
Alignment explanation
Indices: 406715--406782 Score: 58
Period size: 6 Copynumber: 11.8 Consensus size: 6
406705 TTAATTTAAA
406715 ATATTT ATATATCT ATA-TT AT-TTT ATAATTT ATA-TT ATATTT A-ATTT
1 ATATTT ATAT-T-T ATATTT ATATTT AT-ATTT ATATTT ATATTT ATATTT
*
406762 -T-TTT ATATTT ATATTC ATATT
1 ATATTT ATATTT ATATTT ATATT
406783 GCGACTAATA
Statistics
Matches: 52, Mismatches: 1, Indels: 18
0.73 0.01 0.25
Matches are distributed among these distances:
4 3 0.06
5 17 0.33
6 22 0.42
7 6 0.12
8 4 0.08
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (6 bp):
ATATTT
Found at i:407574 original size:28 final size:33
Alignment explanation
Indices: 407528--407588 Score: 87
Period size: 30 Copynumber: 2.0 Consensus size: 33
407518 AAATTATTAA
407528 ATATTAATATAATATTT-AAT-TA-AATATTTT
1 ATATTAATATAATATTTAAATATATAATATTTT
407558 ATATTAAT-T-ATATTTAAATATATAATATTTT
1 ATATTAATATAATATTTAAATATATAATATTTT
407589 TAATATATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
28 6 0.21
29 4 0.14
30 10 0.36
31 8 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
ATATTAATATAATATTTAAATATATAATATTTT
Found at i:407585 original size:24 final size:24
Alignment explanation
Indices: 407523--407586 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
407513 AATATAAATT
*
407523 ATTAAATATTAATA-TAATATTTA
1 ATTAAATATTAATATTAATATATA
*
407546 ATTAAATATTTTATATTAAT-TATA
1 ATTAAATA-TTAATATTAATATATA
*
407570 TTTAAATATATAATATT
1 ATTAAATAT-TAATATT
407587 TTTAATATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
23 9 0.26
24 21 0.62
25 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
ATTAAATATTAATATTAATATATA
Found at i:407600 original size:14 final size:15
Alignment explanation
Indices: 407552--407612 Score: 58
Period size: 14 Copynumber: 4.1 Consensus size: 15
407542 TTTAATTAAA
*
407552 TATTTTATATTA-AT
1 TATTTTATAATATAT
407566 TATATTTA-AATATAT
1 TAT-TTTATAATATAT
407581 AATATTTT-TAATATAT
1 --TATTTTATAATATAT
407597 TATTTTATAAT-TAT
1 TATTTTATAATATAT
407611 TA
1 TA
407613 AAATATTATA
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
14 17 0.43
15 10 0.25
16 10 0.25
17 3 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TATTTTATAATATAT
Found at i:407618 original size:22 final size:22
Alignment explanation
Indices: 407582--407632 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
407572 TAAATATATA
* *
407582 ATATTTTTAATATATTAT-TTT
1 ATATTATTAAAATATTATATTT
407603 ATAATTATTAAAATATTATATTT
1 AT-ATTATTAAAATATTATATTT
407626 ATATTAT
1 ATATTAT
407633 ATTTTTATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 2 0.08
22 19 0.73
23 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
ATATTATTAAAATATTATATTT
Found at i:408429 original size:14 final size:15
Alignment explanation
Indices: 408377--408430 Score: 51
Period size: 14 Copynumber: 3.8 Consensus size: 15
408367 TTTTATATTT
* *
408377 TATATAATTTTATTA
1 TATATAATATTATAA
* *
408392 TATA-AAAAATA-AA
1 TATATAATATTATAA
408405 TATATAATATTATAA
1 TATATAATATTATAA
408420 TATA-AATATTA
1 TATATAATATTA
408431 AAAAAAATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
13 5 0.16
14 16 0.52
15 10 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TATATAATATTATAA
Found at i:408500 original size:12 final size:12
Alignment explanation
Indices: 408483--408507 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
408473 TTATTTAATT
408483 ATTAAAAATTAA
1 ATTAAAAATTAA
408495 ATTAAAAATTAA
1 ATTAAAAATTAA
408507 A
1 A
408508 AAAATAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATTAAAAATTAA
Found at i:410201 original size:2 final size:2
Alignment explanation
Indices: 410194--410221 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
410184 TTATAAATAA
410194 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
410222 GGGTCCAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:415913 original size:22 final size:22
Alignment explanation
Indices: 415883--415954 Score: 67
Period size: 22 Copynumber: 3.1 Consensus size: 22
415873 CGATTGTTAG
415883 ATTTATTTAAAAATTAAATTTTA
1 ATTT-TTTAAAAATTAAATTTTA
*
415906 ATTTTTTAAAATTTAAATTATT-
1 ATTTTTTAAAAATTAAATT-TTA
*
415928 ATTTTAATTATAAAATT-ATTTTTA
1 ATTTT--TTA-AAAATTAAATTTTA
415952 ATT
1 ATT
415955 AAATATAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
22 19 0.46
23 8 0.20
24 9 0.22
25 5 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTTTTAAAAATTAAATTTTA
Found at i:416040 original size:15 final size:16
Alignment explanation
Indices: 416020--416050 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
416010 AATAATCTAA
416020 AAATTTAA-TTAAATT
1 AAATTTAATTTAAATT
416035 AAATTTAATTTAAATT
1 AAATTTAATTTAAATT
416051 TAAAAAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AAATTTAATTTAAATT
Found at i:416716 original size:26 final size:25
Alignment explanation
Indices: 416662--416712 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
416652 AACCCAGTTC
416662 ATTTAATATTTTAATTTTTATTTCT
1 ATTTAATATTTTAATTTTTATTTCT
* *
416687 ATTTAGTATCTTTGATTTTT-TTTCT
1 ATTTAATAT-TTTAATTTTTATTTCT
416712 A
1 A
416713 ATTTTAAGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.24, C:0.06, G:0.04, T:0.67
Consensus pattern (25 bp):
ATTTAATATTTTAATTTTTATTTCT
Found at i:417245 original size:32 final size:31
Alignment explanation
Indices: 417200--417299 Score: 93
Period size: 27 Copynumber: 3.3 Consensus size: 31
417190 GTAATAGATC
* * *
417200 TTTAATTAAATATATCATAAGTATATAAATAT
1 TTTAAATATATATAT-ATAAATATATAAATAT
*
417232 TTTAAATATATATAATATAAAT-TATTAATAT
1 TTTAAATATATAT-ATATAAATATATAAATAT
*
417263 ATTAAA-AT-T-TATATAAATATA-AAATAT
1 TTTAAATATATATATATAAATATATAAATAT
*
417290 TTTAATTATA
1 TTTAAATATA
417300 ATTATTACAT
Statistics
Matches: 56, Mismatches: 8, Indels: 11
0.75 0.11 0.15
Matches are distributed among these distances:
27 17 0.30
28 5 0.09
29 1 0.02
30 2 0.04
31 13 0.23
32 16 0.29
33 2 0.04
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (31 bp):
TTTAAATATATATATATAAATATATAAATAT
Found at i:417274 original size:18 final size:17
Alignment explanation
Indices: 417238--417287 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
417228 ATATTTTAAA
417238 TATATATAATAT-AAA-T
1 TATATA-AATATAAAATT
417254 TAT-TAATATATTAAAATT
1 TATATAA-ATA-TAAAATT
417272 TATATAAATATAAAAT
1 TATATAAATATAAAAT
417288 ATTTTAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
14 1 0.03
15 5 0.17
16 4 0.14
17 9 0.31
18 7 0.24
19 3 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TATATAAATATAAAATT
Found at i:419679 original size:5 final size:5
Alignment explanation
Indices: 419669--419696 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
419659 CAAAGGGTGA
419669 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
419697 TGGATAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:427385 original size:156 final size:154
Alignment explanation
Indices: 427111--427407 Score: 387
Period size: 156 Copynumber: 1.9 Consensus size: 154
427101 TCGATGATAA
* * * *
427111 CCTAGGACTCAGTTTTAAGAAAATACGAAAATACCCTTAGGGGATACTTTAGACGTACAAGTACC
1 CCTAGGACTCAGTTCTAAGAAAATACGAAAATACCCCTAGGGGATACCTTAGACGTAAAAGTACC
*** * ** ** *
427176 CGGTACCCCTAAAGGACTTAAAAAGGTTTGAAATGCGATGAACCTATCTTAAATGCCCACCTTCG
66 CAACAACCCTAAAGGACTTAAAAAGACTAAAAATGCGATGAACCTATCCTAAATGCCCACCTTCG
*
427241 GTATAAAAGCGGATCCGGCGACAG
131 GCATAAAAGCGGATCCGGCGACAG
* * * * *
427265 CCTAGGACTCGGTTCTAGGAAAATATGAAAATACCCCTATGGGTATACCTTCGACGTAAAAGTAC
1 CCTAGGACTCAGTTCTAAGAAAATACGAAAATACCCCTA-GGGGATACCTTAGACGTAAAAGTAC
* *
427330 TCCAACAACCCTAAAGGACTTAAAAATACTAAAAATGCGATGAACCTATCCTAAATGCCTACCTT
65 -CCAACAACCCTAAAGGACTTAAAAAGACTAAAAATGCGATGAACCTATCCTAAATGCCCACCTT
427395 CGGCATAAAAGCG
129 CGGCATAAAAGCG
427408 TACCCGATGA
Statistics
Matches: 120, Mismatches: 21, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
154 34 0.28
155 21 0.17
156 65 0.54
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.23
Consensus pattern (154 bp):
CCTAGGACTCAGTTCTAAGAAAATACGAAAATACCCCTAGGGGATACCTTAGACGTAAAAGTACC
CAACAACCCTAAAGGACTTAAAAAGACTAAAAATGCGATGAACCTATCCTAAATGCCCACCTTCG
GCATAAAAGCGGATCCGGCGACAG
Found at i:427474 original size:156 final size:156
Alignment explanation
Indices: 427182--427484 Score: 338
Period size: 156 Copynumber: 1.9 Consensus size: 156
427172 TACCCGGTAC
** ** * *
427182 CCCTAAAGGACTTAAAAAGGTTTGAAATGCGATGAACCTATCTTAAATGCCCACCTTCGGTATAA
1 CCCTAAAGGACTTAAAAAGACTAAAAATGCGATGAACCTATCCTAAATGCCCACCTTCGGCATAA
* * * ** * ** *
427247 AAGCGGATCCGGCGACAGCCTAGGACTCGGTTCTAGGAAAATATGAAAATACCCCTATGGGTATA
66 AAGCGGACCCGACGACAACCTAAAACTCAGTTCTAGGAAAATACCAAAATACCCCTAAGGGTATA
*
427312 CCTTCGACGTAAAAGTACTCCAACAA
131 CCTTCGACGCAAAAGTACTCCAACAA
* *
427338 CCCTAAAGGACTTAAAAATACTAAAAATGCGATGAACCTATCCTAAATGCCTACCTTCGGCATAA
1 CCCTAAAGGACTTAAAAAGACTAAAAATGCGATGAACCTATCCTAAATGCCCACCTTCGGCATAA
* * * * * * *
427403 AAGCGTACCCGATGATAACCTAAAACTTAGTTTTAGGAAAATTACCAAAATGCCTCTAAGGG-AT
66 AAGCGGACCCGACGACAACCTAAAACTCAGTTCTAGGAAAA-TACCAAAATACCCCTAAGGGTAT
** *
427467 ATGTTCGATGCAAAAGTA
130 ACCTTCGACGCAAAAGTA
427485 TCTCATACCC
Statistics
Matches: 118, Mismatches: 28, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
156 103 0.87
157 15 0.13
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (156 bp):
CCCTAAAGGACTTAAAAAGACTAAAAATGCGATGAACCTATCCTAAATGCCCACCTTCGGCATAA
AAGCGGACCCGACGACAACCTAAAACTCAGTTCTAGGAAAATACCAAAATACCCCTAAGGGTATA
CCTTCGACGCAAAAGTACTCCAACAA
Found at i:428555 original size:163 final size:162
Alignment explanation
Indices: 428217--428668 Score: 595
Period size: 163 Copynumber: 2.8 Consensus size: 162
428207 TTGATATCTT
* * * *
428217 TTTATATTTGGAAAAAAATCATTTCGTACCTTAATGGACACCCGAAAAGATATGAAAAGTTTGTG
1 TTTAT-TTTTGAAAAAAATCATTTCGTACCTTAATGGATA-CCGAAAAGATACGAAAAGTTTTTG
* * * * * *
428282 AAATTTTTTATACCCCTACGGGTACCCATAATAATATAAAATA-TTAAAAACGATTAATGTTTAT
64 AAATCTTTTATACCCCTACGGATACCAATAAGAATATAAAAGATTTAAAAACGATTAATATTTAT
*
428346 TGTAATTTACGAGGAATATATTTAATATTATTTA
129 TGTAATTAACGAGGAATATATTTAATATTATTTA
* * * * *
428380 TTTCTTTTTGAAAAAAATTATTTCATACCTTAATGGATACTCGAAACGATACGAAAAGTTTTTTA
1 TTTATTTTTGAAAAAAATCATTTCGTACCTTAATGGATAC-CGAAAAGATACGAAAAGTTTTTGA
* ** * *
428445 AATCTTTTATACCCCTATGGATACTTATAGGAATATAAAAGATTTAAAAATGATTAATATTTATT
65 AATCTTTTATACCCCTACGGATACCAATAAGAATATAAAAGATTTAAAAACGATTAATATTTATT
* *
428510 GTAATTAATGA-GAAGTGA-ATTTAATTTTATTTA
130 GTAATTAACGAGGAA-T-ATATTTAATATTATTTA
*
428543 TTTATTTTTGAAAAAAATCATTTCGTAACTTAATGGATACCTGAAAAGATACGAAAAGTTTTTGA
1 TTTATTTTTGAAAAAAATCATTTCGTACCTTAATGGATACC-GAAAAGATACGAAAAGTTTTTGA
* *
428608 AATCTTTTATACCCCTACGGATACCAATAAGAATATAAAAGATTAAAAAACAATTAATATT
65 AATCTTTTATACCCCTACGGATACCAATAAGAATATAAAAGATTTAAAAACGATTAATATT
428669 AAAATATATA
Statistics
Matches: 249, Mismatches: 35, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
161 1 0.00
162 88 0.35
163 159 0.64
164 1 0.00
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.37
Consensus pattern (162 bp):
TTTATTTTTGAAAAAAATCATTTCGTACCTTAATGGATACCGAAAAGATACGAAAAGTTTTTGAA
ATCTTTTATACCCCTACGGATACCAATAAGAATATAAAAGATTTAAAAACGATTAATATTTATTG
TAATTAACGAGGAATATATTTAATATTATTTA
Found at i:429494 original size:17 final size:17
Alignment explanation
Indices: 429466--429508 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
429456 CTACCTATTT
429466 TCTCTATTTTTCTTTCTC
1 TCTCT-TTTTTCTTTCTC
* *
429484 TTTCTTTTTTCTTTTTC
1 TCTCTTTTTTCTTTCTC
429501 TCTCTTTT
1 TCTCTTTT
429509 CAGCCGATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.74
Consensus pattern (17 bp):
TCTCTTTTTTCTTTCTC
Found at i:430356 original size:167 final size:167
Alignment explanation
Indices: 430183--430484 Score: 358
Period size: 167 Copynumber: 1.8 Consensus size: 167
430173 AAAAAATTAA
* * *
430183 GAAAATGAAGGAATTTATGGA-AAACGATTTAATATGATAT-AAATAATGGTATTTTATGAATTT
1 GAAAATGAAGGAATTT-TGGATAAACGAATTAATATGA-ATCAAATAATGATATTTGATGAATTT
** * * *
430246 TAAAAATTTAAAACCAAGAAAAACCCTTTCAAAAAAATTTACGA-AGTAAAAAACACCGTATTTT
64 TAAAAATAAAAAACCAAGAAAAACCCATTCAAAAAAATTTAC-ATAGTAAAAAACACCATATTTC
430310 GAAAAAAATGGGTGTTTTAAGAAAAAAATAAAAAACCCAT
128 GAAAAAAATGGGTGTTTTAAGAAAAAAATAAAAAACCCAT
* * ** ** * *
430350 GAAAATGGATGAATTTTTTATAATTGAATTAATATGAATCAAATACTGATGTTTGATGAATTTTA
1 GAAAATGAAGGAATTTTGGATAAACGAATTAATATGAATCAAATAATGATATTTGATGAATTTTA
* * * * * *
430415 AAAATAAAAAACCGAGAAACATCCATTCGAAAAAATTTACATAGTAGAAAACACTATATTTCGAA
66 AAAATAAAAAACCAAGAAAAACCCATTCAAAAAAATTTACATAGTAAAAAACACCATATTTCGAA
430480 AAAAA
131 AAAAA
430485 GAGAATTTCA
Statistics
Matches: 110, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
166 5 0.05
167 105 0.95
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (167 bp):
GAAAATGAAGGAATTTTGGATAAACGAATTAATATGAATCAAATAATGATATTTGATGAATTTTA
AAAATAAAAAACCAAGAAAAACCCATTCAAAAAAATTTACATAGTAAAAAACACCATATTTCGAA
AAAAATGGGTGTTTTAAGAAAAAAATAAAAAACCCAT
Found at i:432152 original size:84 final size:83
Alignment explanation
Indices: 432050--432503 Score: 436
Period size: 84 Copynumber: 5.4 Consensus size: 83
432040 AATTTACCTG
* * * * *
432050 GGACTGAGCCGACAGGTAAATAATGAGATGAAGGTTAACCGGAGACTGAGTTGACAGGTTACCAT
1 GGACTAAGCCGACAGGTAAACAATG-GATGAAAGTTAACCGGAGACTGAGCTGACAGGTCACCAT
432115 -AGGGATAAAGGTTTATCGA
65 AAGGG-TAAAGGTTTATCGA
* ** * * * *
432134 GGACTTAGCCGATTGGTAAACAAAGGATGAAAGTTAAACGGAGACTAAGTTGACAGGTCACCATA
1 GGACTAAGCCGACAGGTAAACAATGGATGAAAGTTAACCGGAGACTGAGCTGACAGGTCACCATA
*
432199 AGGGTAATGAGTTTATCGA
66 AGGGTAAAG-GTTTATCGA
* * * * * *
432218 GGACTAAGTCGACAGGTAAACAGTGGATGAAAGTT-GCCTAGAGACTGAGCTGACCGATCACCAT
1 GGACTAAGCCGACAGGTAAACAATGGATGAAAGTTAACC-GGAGACTGAGCTGACAGGTCACCAT
* *
432282 AAGGGTAATGGGTTTACCGA
65 AAGGGTAA-AGGTTTATCGA
* *
432302 GGACTAAGCCAACCA-GTAAACAATGGAT-AAAGGCTAACCGGAGACTGAGCTGACAGGTCACCA
1 GGACTAAGCCGA-CAGGTAAACAATGGATGAAA-GTTAACCGGAGACTGAGCTGACAGGTCACCA
* *
432365 TAAGGGTAATGGGTTTA-CCA
64 TAAGGGTAA-AGGTTTATCGA
* * * * * *
432385 GGGACTATGCCAACAGGTAAAC-ATGGATG-AAGTTGACCAGAGTCTGAGCTGACAGGTCACCTT
1 -GGACTAAGCCGACAGGTAAACAATGGATGAAAGTTAACCGGAGACTGAGCTGACAGGTCACCAT
* * *
432448 AAAGGTAATGGATTTATCGG
65 AAGGGTAAAGG-TTTATCGA
* *
432468 GGACTAAGTCGACAGGTAAACAATGAAATGAAAGTT
1 GGACTAAGCCGACAGGTAAACAATG-GATGAAAGTT
432504 GTTTCCAAAG
Statistics
Matches: 307, Mismatches: 48, Indels: 29
0.80 0.12 0.08
Matches are distributed among these distances:
81 2 0.01
82 56 0.18
83 59 0.19
84 180 0.59
85 10 0.03
ACGTcount: A:0.35, C:0.16, G:0.28, T:0.21
Consensus pattern (83 bp):
GGACTAAGCCGACAGGTAAACAATGGATGAAAGTTAACCGGAGACTGAGCTGACAGGTCACCATA
AGGGTAAAGGTTTATCGA
Found at i:433176 original size:42 final size:42
Alignment explanation
Indices: 433097--433273 Score: 117
Period size: 42 Copynumber: 4.2 Consensus size: 42
433087 GATAAAGGAT
* * * * *
433097 AAAGAAGTAT-TTCGGGTCAAAGTCGACGAGCAAACAAAAGGC
1 AAAGAAGTCTCTT-GGGTCAAAGCCAACGGGCAGACAAAAGGC
* * *
433139 AAAGAAGGCTCTTGGGTCAAAGCCAACGGGCAGACAAAGGGT
1 AAAGAAGTCTCTTGGGTCAAAGCCAACGGGCAGACAAAAGGC
* * ** * * ** **
433181 GAAGGAGTCTCTCAGGTCAAAGTCGATTGGCAGACAAAAGAT
1 AAAGAAGTCTCTTGGGTCAAAGCCAACGGGCAGACAAAAGGC
* * * *
433223 AAAAAAGTCTCTCT-GGTTAAAGCCAAC-GGTAGACAAAGGGC
1 AAAGAAGTCTCT-TGGGTCAAAGCCAACGGGCAGACAAAAGGC
433264 AAAGAAGTCT
1 AAAGAAGTCT
433274 GTCAGGTCAA
Statistics
Matches: 101, Mismatches: 32, Indels: 5
0.73 0.23 0.04
Matches are distributed among these distances:
41 19 0.19
42 80 0.79
43 2 0.02
ACGTcount: A:0.39, C:0.18, G:0.28, T:0.16
Consensus pattern (42 bp):
AAAGAAGTCTCTTGGGTCAAAGCCAACGGGCAGACAAAAGGC
Found at i:433218 original size:84 final size:83
Alignment explanation
Indices: 433074--433284 Score: 201
Period size: 84 Copynumber: 2.5 Consensus size: 83
433064 TCCCAAGTCT
* * ** * * * *
433074 AAGCCAACAAGCAGATAAAGGATAAAGAAGTATTTCGGGTCAAAGTCGACGAGCAAACAAAAGGC
1 AAGCCAAC-GGCAGACAAAGGGCAAAGAAGTCTCTCAGGTCAAAGTCGACGAGCAAACAAAAGAC
*
433139 AAAGAAGGCTCT-TGGGTCA
65 AAAAAAGGCTCTCT-GGTCA
** * * *
433158 AAGCCAACGGGCAGACAAAGGGTGAAGGAGTCTCTCAGGTCAAAGTCGATTG-GCAGACAAAAGA
1 AAGCCAAC-GGCAGACAAAGGGCAAAGAAGTCTCTCAGGTCAAAGTCGA-CGAGCAAACAAAAGA
* * *
433222 TAAAAAAGTCTCTCTGGTTA
64 CAAAAAAGGCTCTCTGGTCA
* *
433242 AAGCCAACGGTAGACAAAGGGCAAAGAAGTCTGTCAGGTCAAA
1 AAGCCAACGGCAGACAAAGGGCAAAGAAGTCTCTCAGGTCAAA
433285 ACCGATGGGT
Statistics
Matches: 104, Mismatches: 21, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
83 30 0.29
84 72 0.69
85 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.27, T:0.15
Consensus pattern (83 bp):
AAGCCAACGGCAGACAAAGGGCAAAGAAGTCTCTCAGGTCAAAGTCGACGAGCAAACAAAAGACA
AAAAAGGCTCTCTGGTCA
Found at i:433301 original size:83 final size:84
Alignment explanation
Indices: 433126--433315 Score: 195
Period size: 83 Copynumber: 2.3 Consensus size: 84
433116 AAGTCGACGA
** * * * ** *
433126 GCAAACAAAAGGCAAAGAAGGCTCT-TGGGTCAAAGCCAACGGGCAGACAAAGGGTGAAGGAGTC
1 GCAAACAAAAGATAAAAAAGTCTCTCT-GGTTAAAGCCAACGGGCAGACAAAGGGCAAAGAAGTC
** *
433190 TCTCAGGTCAAAGTCGATTG
65 TCTCAGGTCAAAACCGATGG
* *
433210 GCAGACAAAAGATAAAAAAGTCTCTCTGGTTAAAGCCAAC-GGTAGACAAAGGGCAAAGAAGTCT
1 GCAAACAAAAGATAAAAAAGTCTCTCTGGTTAAAGCCAACGGGCAGACAAAGGGCAAAGAAGTCT
*
433274 GTCAGGTCAAAACCGATGG
66 CTCAGGTCAAAACCGATGG
* * * *
433293 GTAAACAAAGGGTAAAGAAGTCT
1 GCAAACAAAAGATAAAAAAGTCT
433316 GCTGGGTCAG
Statistics
Matches: 86, Mismatches: 19, Indels: 3
0.80 0.18 0.03
Matches are distributed among these distances:
83 53 0.62
84 32 0.37
85 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.28, T:0.15
Consensus pattern (84 bp):
GCAAACAAAAGATAAAAAAGTCTCTCTGGTTAAAGCCAACGGGCAGACAAAGGGCAAAGAAGTCT
CTCAGGTCAAAACCGATGG
Found at i:433386 original size:43 final size:43
Alignment explanation
Indices: 433339--433689 Score: 328
Period size: 43 Copynumber: 8.2 Consensus size: 43
433329 CGATGGGTAA
* * * * * *
433339 ACTTAAGGGTGAGGAAATCTCTATGGTAAAAGCCAACAAGCAG
1 ACTTAAGGGTGAAGAAGTCTCCAAGGTCAAAGCCGACAAGCAG
* * * *
433382 ACTTAAGGATGAAGAAGTCTCC-AGAGTCAAAGCTGATAAACAG
1 ACTTAAGGGTGAAGAAGTCTCCAAG-GTCAAAGCCGACAAGCAG
* * *
433425 ACTTAAGGGTGAGGAAGTCTCCAAGGTCAAAGCCGACAGGTAG
1 ACTTAAGGGTGAAGAAGTCTCCAAGGTCAAAGCCGACAAGCAG
* * * * *
433468 ATTTAAGGGTGAGGAAGTCTCCAAGGTCAAAGCTGACAGGCAA
1 ACTTAAGGGTGAAGAAGTCTCCAAGGTCAAAGCCGACAAGCAG
* *
433511 ACTTAAGGGTGAAGAAGTCTCC-AGAGTCAAAGCCGACATGAAG
1 ACTTAAGGGTGAAGAAGTCTCCAAG-GTCAAAGCCGACAAGCAG
* * * * *
433554 ACTTAAGGGTGAAGCAGTCTCTAGGGTCAAAGCCAACAGGCAG
1 ACTTAAGGGTGAAGAAGTCTCCAAGGTCAAAGCCGACAAGCAG
* * ** * * *
433597 ACTTAAGGGTGAGGAAGTATTAAAGGTTAGAGTCGACAAGCAG
1 ACTTAAGGGTGAAGAAGTCTCCAAGGTCAAAGCCGACAAGCAG
* ** * * *
433640 ACTTAATGGTGAAGAAGTCTTTAGGGTCAAAGGCAACAAGCAG
1 ACTTAAGGGTGAAGAAGTCTCCAAGGTCAAAGCCGACAAGCAG
433683 ACTTAAG
1 ACTTAAG
433690 ATTAAAGTAT
Statistics
Matches: 250, Mismatches: 54, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
42 3 0.01
43 244 0.98
44 3 0.01
ACGTcount: A:0.37, C:0.16, G:0.28, T:0.19
Consensus pattern (43 bp):
ACTTAAGGGTGAAGAAGTCTCCAAGGTCAAAGCCGACAAGCAG
Found at i:433613 original size:129 final size:129
Alignment explanation
Indices: 433339--433689 Score: 391
Period size: 129 Copynumber: 2.7 Consensus size: 129
433329 CGATGGGTAA
* * * ** *
433339 ACTTAAGGGTGAGGAAATCTCTATGGTAAAAGCCAACAAGCAGACTTAAGGATGAAGAAGTCTCC
1 ACTTAAGGGTGAGGAAGTCTCAAAGGTAAAAGCTGACAAGCAGACTTAAGGGTGAAGAAGTCTCC
* * * * *
433404 AGAGTCAAAGCTGATAAACAGACTTAAGGGTGAGGAAGTCTCCAAGGTCAAAGCCGACAGGTAG
66 AGAGTCAAAGCCGACAAACAGACTTAAGGGTGAAGAAGTCTCCAAGGTCAAAGCCAACAGGCAG
* * * * *
433468 ATTTAAGGGTGAGGAAGTCTCCAAGGTCAAAGCTGACAGGCAAACTTAAGGGTGAAGAAGTCTCC
1 ACTTAAGGGTGAGGAAGTCTCAAAGGTAAAAGCTGACAAGCAGACTTAAGGGTGAAGAAGTCTCC
* * * *
433533 AGAGTCAAAGCCGACATGA-AGACTTAAGGGTGAAGCAGTCTCTAGGGTCAAAGCCAACAGGCAG
66 AGAGTCAAAGCCGACA-AACAGACTTAAGGGTGAAGAAGTCTCCAAGGTCAAAGCCAACAGGCAG
* * * * * *
433597 ACTTAAGGGTGAGGAAGTATTAAAGGTTAGAG-TCGACAAGCAGACTTAATGGTGAAGAAGTCTT
1 ACTTAAGGGTGAGGAAGTCTCAAAGGTAAAAGCT-GACAAGCAGACTTAAGGGTGAAGAAGTCTC
* * * * *
433661 TAGGGTCAAAGGCAACAAGCAGACTTAAG
65 CAGAGTCAAAGCCGACAAACAGACTTAAG
433690 ATTAAAGTAT
Statistics
Matches: 184, Mismatches: 35, Indels: 6
0.82 0.16 0.03
Matches are distributed among these distances:
128 1 0.01
129 182 0.99
130 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.28, T:0.19
Consensus pattern (129 bp):
ACTTAAGGGTGAGGAAGTCTCAAAGGTAAAAGCTGACAAGCAGACTTAAGGGTGAAGAAGTCTCC
AGAGTCAAAGCCGACAAACAGACTTAAGGGTGAAGAAGTCTCCAAGGTCAAAGCCAACAGGCAG
Found at i:433964 original size:48 final size:48
Alignment explanation
Indices: 433897--434095 Score: 231
Period size: 48 Copynumber: 4.2 Consensus size: 48
433887 GAAAGAAACA
*
433897 AGTTTGACCAGGCCCTAACACCAATACAATCAAACGAGGGATGAAAAG
1 AGTTTGACCAAGCCCTAACACCAATACAATCAAACGAGGGATGAAAAG
* * * * * * *
433945 AGTTTGACGAGGCCCTAACACCAATGCAGTCAAAAGAGAGATGAAAAT
1 AGTTTGACCAAGCCCTAACACCAATACAATCAAACGAGGGATGAAAAG
* * * *
433993 AGTTTGACCAAGTCTTAA-AGCCAATACAATCAAACG-GGGGTGGAAAG
1 AGTTTGACCAAGCCCTAACA-CCAATACAATCAAACGAGGGATGAAAAG
* * * *
434040 AGATTGACCAAGCCCTAACACCAATACAGTCAAACAAGGGATGAAAAA
1 AGTTTGACCAAGCCCTAACACCAATACAATCAAACGAGGGATGAAAAG
434088 AGTTTGAC
1 AGTTTGAC
434096 TAGTTACAGT
Statistics
Matches: 122, Mismatches: 26, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
47 37 0.30
48 85 0.70
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.17
Consensus pattern (48 bp):
AGTTTGACCAAGCCCTAACACCAATACAATCAAACGAGGGATGAAAAG
Found at i:434070 original size:95 final size:96
Alignment explanation
Indices: 433891--434095 Score: 263
Period size: 95 Copynumber: 2.1 Consensus size: 96
433881 AGACAGGAAA
* * * * * *
433891 GAAACAAGTTTGACCAGGCCCTAACA-CCAATACAATCAAACGAGGGATGAAAAGAGTTTGACGA
1 GAAAAAAGTTTGACCAAGTCTTAA-AGCCAATACAATCAAACGAGGGATGAAAAGAGATTGACCA
* *
433955 GGCCCTAACACCAATGCAGTCAAA-AGAGAGAT
65 AGCCCTAACACCAATACAGTCAAACA-AGAGAT
* * *
433987 GAAAATAGTTTGACCAAGTCTTAAAGCCAATACAATCAAACG-GGGGTGGAAAGAGATTGACCAA
1 GAAAAAAGTTTGACCAAGTCTTAAAGCCAATACAATCAAACGAGGGATGAAAAGAGATTGACCAA
*
434051 GCCCTAACACCAATACAGTCAAACAAGGGAT
66 GCCCTAACACCAATACAGTCAAACAAGAGAT
434082 GAAAAAAGTTTGAC
1 GAAAAAAGTTTGAC
434096 TAGTTACAGT
Statistics
Matches: 94, Mismatches: 13, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
95 58 0.62
96 36 0.38
ACGTcount: A:0.42, C:0.20, G:0.21, T:0.16
Consensus pattern (96 bp):
GAAAAAAGTTTGACCAAGTCTTAAAGCCAATACAATCAAACGAGGGATGAAAAGAGATTGACCAA
GCCCTAACACCAATACAGTCAAACAAGAGAT
Found at i:435716 original size:18 final size:18
Alignment explanation
Indices: 435693--435727 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
435683 CATTCTTTCC
*
435693 TTTTTTCTTCTTTTTCAT
1 TTTTTTCTTCTCTTTCAT
435711 TTTTTTCTTCTCTTTCA
1 TTTTTTCTTCTCTTTCA
435728 CAACCCTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTTCTTCTCTTTCAT
Found at i:439638 original size:155 final size:156
Alignment explanation
Indices: 439398--439779 Score: 369
Period size: 156 Copynumber: 2.5 Consensus size: 156
439388 TTCGATGTAG
* * * * * * * **
439398 AAGTA-CTTGATACCCCTAAAAGACTGAAAAAAGACTATAGATACGACGAACCTATCATAAATAT
1 AAGTACCTTGACAACCCTAAAAGACT-TAAAAAGACTAGAAATACGATGAACCTATCCTAAATGC
* * * * * *
439462 CTACCTTC-GACGTAAAAGCAGACCCAGTGATAACCTAGGACTAGGTTTTA-AAAAATTACTAAA
65 CCACCTTCAG-CATAAAAGCAGACCCAGCGACAACCTAGGACTAGGTCTTATAAAAA-TACGAAA
* * ** * *
439525 GTGCCTCTAAGGG-ATACGTTCGACGTGA
128 ATGCCCCTAAGGGTATACCATCGACATAA
* * ** * * *
439553 AAGTATCC-TGATACCCCTAAAAGACTTAAAAAGGTTTGCAATATGATGAACCTATCCTAAATGC
1 AAGTA-CCTTGACAACCCTAAAAGACTTAAAAAGACTAGAAATACGATGAACCTATCCTAAATGC
* * *
439617 CCACCTTCAGCATAAAAGCAGACCCAGCGACAGCCTAGGACTTGGTCTTATGAAAATACGAAAAT
65 CCACCTTCAGCATAAAAGCAGACCCAGCGACAACCTAGGACTAGGTCTTATAAAAATACGAAAAT
*
439682 GCCCCTATGGGTATACCATCGACATAA
130 GCCCCTAAGGGTATACCATCGACATAA
* * * *
439709 AAGTACCTTGGCAACCCTAAAGGACTTAAAAAGACTAGAAATGCGATGACCCTATCCTAAATGCC
1 AAGTACCTTGACAACCCTAAAAGACTTAAAAAGACTAGAAATACGATGAACCTATCCTAAATGCC
439774 CACCTT
66 CACCTT
439780 TGGCAAGCAG
Statistics
Matches: 182, Mismatches: 39, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
155 90 0.49
156 91 0.50
157 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.23
Consensus pattern (156 bp):
AAGTACCTTGACAACCCTAAAAGACTTAAAAAGACTAGAAATACGATGAACCTATCCTAAATGCC
CACCTTCAGCATAAAAGCAGACCCAGCGACAACCTAGGACTAGGTCTTATAAAAATACGAAAATG
CCCCTAAGGGTATACCATCGACATAA
Found at i:440872 original size:163 final size:162
Alignment explanation
Indices: 440580--441034 Score: 671
Period size: 163 Copynumber: 2.8 Consensus size: 162
440570 AAATAATTGA
* * * *
440580 TATTTATTTATATTTAGAAAAAAATTATTTCGTACCTTAATGGACACTCGAAAAGATACGAAAAG
1 TATTTATTTAT-TTTTGAAAAAAATTATTTCGTACCTTAATAGATACTCGAAAAGATATGAAAAG
*
440645 TTTTTGAAATCCTTTATACCCCTACAGATACCCATAAGAATATAAAAGATTAAAAAACGATTAAT
65 TTTTTGAAATCTTTTATA-CCCTACAGATACCCATAAGAATATAAAAGATTAAAAAACGATTAAT
* *
440710 GTTTGTTGTAATTAACGAGAAGTGAATTTAATAT
129 ATTTGTTGTAATTAACGAGAACTGAATTTAATAT
440744 TATTTATTTATTTTTGAAAAAAATTATTTCGTACCTTAATAGATACTCGAAAAGATATGAAAAGT
1 TATTTATTTATTTTTGAAAAAAATTATTTCGTACCTTAATAGATACTCGAAAAGATATGAAAAGT
** * * * **
440809 TTTTGAAATCTTTTATACCCTTATGGATACTCATAGGAATATAAAAGATTTAAAAGTGATTAATA
66 TTTTGAAATCTTTTATACCC-TACAGATACCCATAAGAATATAAAAGATTAAAAAACGATTAATA
* * *
440874 TTTGTTGTAATTAATGTGGACTGAATTTAATAT
130 TTTGTTGTAATTAACGAGAACTGAATTTAATAT
* *
440907 TATTTATTTATTTTTGAAAAAAATCATTTCGTACCTTAATAGATACCCGAAAAG--ATGCAAAAC
1 TATTTATTTATTTTTGAAAAAAATTATTTCGTACCTTAATAGATACTCGAAAAGATATG-AAAA-
440970 GTTTTTGAAATCTTTTATACTCCTACAGATACCCATAAGAATATAAAAGATTAAAAAACGATTAA
64 GTTTTTGAAATCTTTTATAC-CCTACAGATACCCATAAGAATATAAAAGATTAAAAAACGATTAA
441035 CATTAAAATA
Statistics
Matches: 261, Mismatches: 26, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
161 3 0.01
162 7 0.03
163 238 0.91
164 13 0.05
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (162 bp):
TATTTATTTATTTTTGAAAAAAATTATTTCGTACCTTAATAGATACTCGAAAAGATATGAAAAGT
TTTTGAAATCTTTTATACCCTACAGATACCCATAAGAATATAAAAGATTAAAAAACGATTAATAT
TTGTTGTAATTAACGAGAACTGAATTTAATAT
Found at i:441608 original size:167 final size:163
Alignment explanation
Indices: 441377--441762 Score: 434
Period size: 167 Copynumber: 2.3 Consensus size: 163
441367 AAAAATTTAG
* * * * * * * *
441377 GAAAATGAAGGAATTTTTGGAAACGGATTTAATAT-GATATAAATAATGGTATTTGATGAATTTT
1 GAAAATAAATGAATTTTTGAAAACTGAATTAATATAAATA-AAATAATGATATTTGATAAATTTT
* * *
441441 AAAAATTTAAAACCAAGAAAAACCCCCCCGAAAAAATTCATGGAGTAGAAAATACCATATTTCGA
65 AAAAATTGAAAACCAAGAAAAACCCCCCCGAAAAAATTCACGGAGTAGAAAACACCATATTTCGA
**
441506 AAAAAGAGGAGTTTCAAGGAAATAAATTAAAAACTCAT
130 AAAAAGA-GAAATTCAA--AAA-AAATTAAAAACTCAT
** *
441544 GAAAATTGATGAATTTTTGAAAACTGAATTAATATAAATAAAATAATGATGTTTGATAAATTTTA
1 GAAAATAAATGAATTTTTGAAAACTGAATTAATATAAATAAAATAATGATATTTGATAAATTTTA
* * ** * * *
441609 AAAATTGAAAACCGAGAAAAATCCCTTCGAAAAAATTTACGGAGTAGAAAACACTATCTTTCGAA
66 AAAATTGAAAACCAAGAAAAACCCCCCCGAAAAAATTCACGGAGTAGAAAACACCATATTTCGAA
* *
441674 AAAATAGAAATTCCAAAAAAATTAAAAACTCAT
131 AAAAGAGAAATTCAAAAAAAATTAAAAACTCAT
* * * * *
441707 GAAAATAAATTAATTTTTTAAAAATGAATTAATATGAAAT-AAATGATAATATTTGA
1 GAAAATAAATGAATTTTTGAAAACTGAATTAATAT-AAATAAAATAATGATATTTGA
441763 GGAATTAAAA
Statistics
Matches: 185, Mismatches: 32, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
163 58 0.31
164 7 0.04
166 6 0.03
167 111 0.60
168 3 0.02
ACGTcount: A:0.50, C:0.09, G:0.13, T:0.29
Consensus pattern (163 bp):
GAAAATAAATGAATTTTTGAAAACTGAATTAATATAAATAAAATAATGATATTTGATAAATTTTA
AAAATTGAAAACCAAGAAAAACCCCCCCGAAAAAATTCACGGAGTAGAAAACACCATATTTCGAA
AAAAGAGAAATTCAAAAAAAATTAAAAACTCAT
Found at i:443041 original size:16 final size:16
Alignment explanation
Indices: 442966--443043 Score: 95
Period size: 16 Copynumber: 4.9 Consensus size: 16
442956 TCAATCCACT
* *
442966 TAATCTAAATTCAAAA
1 TAATTTAAATTTAAAA
* *
442982 TTAATTTAAAATCAAAA
1 -TAATTTAAATTTAAAA
*
442999 TTATTTAAATTTAAAA
1 TAATTTAAATTTAAAA
443015 TAATTT-AATTTAAAA
1 TAATTTAAATTTAAAA
443030 TAATTTAAATTTAA
1 TAATTTAAATTTAA
443044 TTAACTCGAA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
15 15 0.28
16 25 0.46
17 14 0.26
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (16 bp):
TAATTTAAATTTAAAA
Found at i:444936 original size:16 final size:15
Alignment explanation
Indices: 444911--444944 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
444901 GTGAATAAGA
444911 CAAAACAAAAAAAAAT
1 CAAAAC-AAAAAAAAT
*
444927 CAAAATAAAAAAAAT
1 CAAAACAAAAAAAAT
444942 CAA
1 CAA
444945 TGAAAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.79, C:0.12, G:0.00, T:0.09
Consensus pattern (15 bp):
CAAAACAAAAAAAAT
Found at i:445718 original size:35 final size:35
Alignment explanation
Indices: 445585--445713 Score: 115
Period size: 35 Copynumber: 3.6 Consensus size: 35
445575 TCTTTTAATT
*
445585 TTTAA-ATTT-ATTAATTT-TTTAAAATAAATATAA
1 TTTAATATTTAATT-ATTTATTTAATATAAATATAA
*
445618 TATTAATAATTTTTAATTA-TTATTTAACATAAATA-AA
1 T-TTAAT-A--TTTAATTATTTATTTAATATAAATATAA
* *
445655 TTTTAATATTTATTTCTTTATTTAATATAAATATAA
1 -TTTAATATTTAATTATTTATTTAATATAAATATAA
445691 TTTAATAGTTATAATTATTTATT
1 TTTAATA-TT-TAATTATTTATT
445714 ATATATATTT
Statistics
Matches: 78, Mismatches: 6, Indels: 20
0.75 0.06 0.19
Matches are distributed among these distances:
33 1 0.01
34 10 0.13
35 22 0.28
36 6 0.08
37 19 0.24
38 17 0.22
39 3 0.04
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (35 bp):
TTTAATATTTAATTATTTATTTAATATAAATATAA
Found at i:447618 original size:19 final size:20
Alignment explanation
Indices: 447589--447642 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
447579 ATAATTTTTT
*
447589 ATATGATTAATATTTTAATA
1 ATATAATTAATATTTTAATA
*
447609 A-ATTATTAATAATTTTAATA
1 ATATAATTAAT-ATTTTAATA
447629 ATATAATT-ATATTT
1 ATATAATTAATATTT
447643 ATTATACATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 12 0.40
20 13 0.43
21 5 0.17
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
ATATAATTAATATTTTAATA
Found at i:448146 original size:3 final size:3
Alignment explanation
Indices: 448138--448162 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
448128 TAACGTATCC
448138 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
448163 TCATTGATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:449004 original size:40 final size:40
Alignment explanation
Indices: 448949--449030 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
448939 ATGAAATCTG
448949 TAGTAGTTTGAACCATATATTGATTAGTCAATCACAGGTT
1 TAGTAGTTTGAACCATATATTGATTAGTCAATCACAGGTT
448989 TAGTAGTTTGAACCATATATTGATTAGTCAATCACAGGTT
1 TAGTAGTTTGAACCATATATTGATTAGTCAATCACAGGTT
449029 TA
1 TA
449031 TCTTTCCTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (40 bp):
TAGTAGTTTGAACCATATATTGATTAGTCAATCACAGGTT
Found at i:451012 original size:36 final size:34
Alignment explanation
Indices: 450972--451058 Score: 86
Period size: 36 Copynumber: 2.4 Consensus size: 34
450962 ATATGCATAC
**
450972 AATATTTTTAAAAAATCATTTATATCATATTTT-TTA
1 AATATTTTTAAAAAAT--TAAATATCAT-TTTTATTA
*
451008 AATATTAATTTAAAAAATTAAATATTATTTTTATTA
1 AATATT--TTTAAAAAATTAAATATCATTTTTATTA
451044 ATATATTTTTAAAAA
1 A-ATATTTTTAAAAA
451059 TATTGTTATT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
35 12 0.27
36 17 0.39
37 5 0.11
38 10 0.23
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (34 bp):
AATATTTTTAAAAAATTAAATATCATTTTTATTA
Found at i:453091 original size:2 final size:2
Alignment explanation
Indices: 453084--453113 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
453074 TTAAATTTAA
*
453084 AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
453114 GTAAAGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:454284 original size:16 final size:17
Alignment explanation
Indices: 454256--454292 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
454246 TATTCAAATC
454256 AAATTTAAAAATAATTT
1 AAATTTAAAAATAATTT
454273 AAATTT-AAAATAATTT
1 AAATTTAAAAATAATTT
454289 AAAT
1 AAAT
454293 CAATTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATTTAAAAATAATTT
Found at i:454289 original size:10 final size:10
Alignment explanation
Indices: 454274--454342 Score: 50
Period size: 11 Copynumber: 6.5 Consensus size: 10
454264 AAATAATTTA
454274 AATTTAAAAT
1 AATTTAAAAT
454284 AATTT-AAAT
1 AATTTAAAAT
*
454293 CAATTAAAAAATT
1 -AATT-TAAAA-T
454306 AATTTAAAAT
1 AATTTAAAAT
* *
454316 TATCTAAACAT
1 AATTTAAA-AT
*
454327 AAATTAAATAT
1 AATTTAAA-AT
454338 AATTT
1 AATTT
454343 TATTTTTAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 9
0.71 0.14 0.14
Matches are distributed among these distances:
9 4 0.09
10 16 0.36
11 17 0.38
12 7 0.16
13 1 0.02
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (10 bp):
AATTTAAAAT
Done.