Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold313
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1192932
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 126135 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:14676 original size:1 final size:1
Alignment explanation
Indices: 14670--14696 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
14660 ACTGGGAAGT
14670 GGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGG
14697 TCGATCATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:49380 original size:52 final size:52
Alignment explanation
Indices: 49286--49454 Score: 209
Period size: 52 Copynumber: 3.3 Consensus size: 52
49276 GTCCTCCGCT
* *
49286 CACGCATACCCTGACACACAAAACAC-AAGACTGTAT-TAAGAATTTATGTATC
1 CACGCATACCCTGACACAGAAAACACTAA-ACTGCATAT-AGAATTTATGTATC
* *
49338 CACGCATACCCTGACAAAGAAAACACTAAACTGCATATAGAATGTATGTATC
1 CACGCATACCCTGACACAGAAAACACTAAACTGCATATAGAATTTATGTATC
* * * * *
49390 CACGCGTACCCTGACACAG-AAATACTAGACTGCGTATAAAATTTATGTATC
1 CACGCATACCCTGACACAGAAAACACTAAACTGCATATAGAATTTATGTATC
*
49441 CATGCATACCCTGA
1 CACGCATACCCTGA
49455 TATAGACCAA
Statistics
Matches: 102, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
51 39 0.38
52 60 0.59
53 3 0.03
ACGTcount: A:0.38, C:0.25, G:0.14, T:0.23
Consensus pattern (52 bp):
CACGCATACCCTGACACAGAAAACACTAAACTGCATATAGAATTTATGTATC
Found at i:49749 original size:25 final size:25
Alignment explanation
Indices: 49701--49904 Score: 241
Period size: 25 Copynumber: 8.1 Consensus size: 25
49691 ATCTCGAGAT
*
49701 CCTACATACATATATATATCATACTGA
1 CCTACATAC--ATGTATATCATACTGA
49728 CCTACATACATGTATATCATACTGA
1 CCTACATACATGTATATCATACTGA
*
49753 CCTAAATACATGTATATCATACTGA
1 CCTACATACATGTATATCATACTGA
* *
49778 CCTACATGCATATATATCATACTGA
1 CCTACATACATGTATATCATACTGA
*
49803 CCTACATACATGTATATCATAGTGA
1 CCTACATACATGTATATCATACTGA
** * ** *
49828 GTTTCATACACATATATCATAGTGA
1 CCTACATACATGTATATCATACTGA
*
49853 CCTACCA-ACATGTATATCA-ATTTGA
1 CCTA-CATACATGTATATCATA-CTGA
*
49878 CCTACATACATGTATATCATATTGA
1 CCTACATACATGTATATCATACTGA
49903 CC
1 CC
49905 CTTTTTAAGT
Statistics
Matches: 154, Mismatches: 19, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
24 3 0.02
25 139 0.90
26 3 0.02
27 9 0.06
ACGTcount: A:0.37, C:0.22, G:0.08, T:0.33
Consensus pattern (25 bp):
CCTACATACATGTATATCATACTGA
Found at i:50108 original size:14 final size:14
Alignment explanation
Indices: 50089--50116 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
50079 GGTAAAGTTA
50089 GCTACTAGTAACTG
1 GCTACTAGTAACTG
50103 GCTACTAGTAACTG
1 GCTACTAGTAACTG
50117 AATACGAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (14 bp):
GCTACTAGTAACTG
Found at i:50181 original size:37 final size:37
Alignment explanation
Indices: 50100--50195 Score: 111
Period size: 37 Copynumber: 2.6 Consensus size: 37
50090 CTACTAGTAA
** *
50100 CTGGCTACTAGTAACTGAATACGAGAAGTAAGAAAAG
1 CTGGCTACTAGTAACTGGCTACGAGAAGAAAGAAAAG
* * **
50137 CTAGCTACTAGTAACTGGCTACGAGATGAAATCAAAG
1 CTGGCTACTAGTAACTGGCTACGAGAAGAAAGAAAAG
* *
50174 TTGGCTACTAGTAAATGGCTAC
1 CTGGCTACTAGTAACTGGCTAC
50196 TAGTAACTGG
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.23
Consensus pattern (37 bp):
CTGGCTACTAGTAACTGGCTACGAGAAGAAAGAAAAG
Found at i:50194 original size:14 final size:14
Alignment explanation
Indices: 50175--50207 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
50165 AAATCAAAGT
50175 TGGCTACTAGTAAA
1 TGGCTACTAGTAAA
*
50189 TGGCTACTAGTAAC
1 TGGCTACTAGTAAA
50203 TGGCT
1 TGGCT
50208 TCGAGAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.30
Consensus pattern (14 bp):
TGGCTACTAGTAAA
Found at i:50231 original size:88 final size:88
Alignment explanation
Indices: 50082--50254 Score: 274
Period size: 88 Copynumber: 2.0 Consensus size: 88
50072 TAAGATAGGT
* *
50082 AAAGTTAGCTACTAGTAACTGGCTACTAGTAACTGAATACGAGAAGTAAGAAAAGCTAGCTACTA
1 AAAGTTAGCTACTAGTAAATGGCTACTAGTAACTGAATACGAGAAGTAACAAAAGCTAGCTACTA
*
50147 GTAACTGGCTACGAGATGAAATC
66 ATAACTGGCTACGAGATGAAATC
* ** * *
50170 AAAGTTGGCTACTAGTAAATGGCTACTAGTAACTGGCTTCGAGAAGTTACAAAAGCTAGCTACTA
1 AAAGTTAGCTACTAGTAAATGGCTACTAGTAACTGAATACGAGAAGTAACAAAAGCTAGCTACTA
50235 ATAACTGGCTACGAGATGAA
66 ATAACTGGCTACGAGATGAA
50255 GGAAACTTGG
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 77 1.00
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (88 bp):
AAAGTTAGCTACTAGTAAATGGCTACTAGTAACTGAATACGAGAAGTAACAAAAGCTAGCTACTA
ATAACTGGCTACGAGATGAAATC
Found at i:50232 original size:51 final size:51
Alignment explanation
Indices: 50140--50246 Score: 126
Period size: 51 Copynumber: 2.1 Consensus size: 51
50130 AGAAAAGCTA
* * * *
50140 GCTACTAGTAACTGGCTACGAGATGAAATCAAAGTTGGCTACTAGTAAATG
1 GCTACTAGTAACTGGCTACGAGAAGAAATCAAAGCTAGCTACTAATAAATG
* ** *
50191 GCTACTAGTAACTGGCTTCGAGAAGTTA-CAAAAGCTAGCTACTAATAACTG
1 GCTACTAGTAACTGGCTACGAGAAGAAATC-AAAGCTAGCTACTAATAAATG
50242 GCTAC
1 GCTAC
50247 GAGATGAAGG
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
50 1 0.02
51 46 0.98
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (51 bp):
GCTACTAGTAACTGGCTACGAGAAGAAATCAAAGCTAGCTACTAATAAATG
Found at i:52346 original size:178 final size:176
Alignment explanation
Indices: 51875--52531 Score: 675
Period size: 177 Copynumber: 3.7 Consensus size: 176
51865 CATCTAATCG
* * * * * * * * *
51875 AATGTTCAAATTAGCAAGACTGGTACATAACATCAATCTATATATACAGTTACTTGAAATATGTG
1 AATGTTGAAATTAGCAAGACTGGCATATATCGTCAATCTATATATACAGCTACTTGAGATATATT
* * * * * *
51940 GACAAAACC-CTTAAAAAATAAAGATATTTGTAACTAAATGTACTAGTAGCTGACAAGATTTAA-
66 GACAAAACCGC--CAAAAATAAAGATATTTGTAACAAAATGCACTAGTAGCTGACTACA-TAAAG
* * * *
52003 AGAGATATCTGAGTAATTGTGTCATAAT-TTCATGTAGG-TGACCTT-ATAA
128 AGAGATATCTGAGTAATTGTGTCGTAGTATT-ATGT-GGAAGA-CTTGACAA
* * * * * * * * * * * *
52052 ATTGTTCAAATT-GACCATATTTGTAGATATCTTCAATTTATATATAGAGCTACTTGAGATATGT
1 AATGTTGAAATTAG-CAAGACTGGCATATATCGTCAATCTATATATACAGCTACTTGAGATATAT
* * *
52116 TGACAAAACTGTCAAAAAATAAAGATATTTGTAACAAAATGCAATAGTAGCTGACTACATAAAGA
65 TGACAAAACCG-CCAAAAATAAAGATATTTGTAACAAAATGCACTAGTAGCTGACTACATAAAGA
* *
52181 GAGCTATCTGAGTAATTGTGTCGT-GATATTATGT-TAATGACTTG-CAGA
129 GAGATATCTGAGTAATTGTGTCGTAG-TATTATGTGGAA-GACTTGACA-A
** * * * ** * **
52229 AATGTTGCTATTAGCATGTCTGGCATATATCTTTGATCTATATATATAGCGTTTTTGAGATATAT
1 AATGTTGAAATTAGCAAGACTGGCATATATCGTCAATCTATATATACAGC-TACTTGAGATATAT
* *
52294 TGACAAAACCGCCCAAAATTAAAGATATTTGTAACAAAATGCACTTGTAGCTGACTACATAAAGA
65 TGACAAAACCG-CCAAAAATAAAGATATTTGTAACAAAATGCACTAGTAGCTGACTACATAAAGA
52359 GAGATATCTGAGTAATTGTGTCGTAGTATTATGTGGAAGACTTGACAA
129 GAGATATCTGAGTAATTGTGTCGTAGTATTATGTGGAAGACTTGACAA
*
52407 AATGTTGAAATTAGCAAGACTGGCATATATCGTCAATTTATATATACAGCTACTTGAGATATATT
1 AATGTTGAAATTAGCAAGACTGGCATATATCGTCAATCTATATATACAGCTACTTGAGATATATT
* *
52472 GACAAAACCGCCAAAAATAAAGATATTTGTAGCAAAATGCACTAGTAGCTGACTTCATAA
66 GACAAAACCGCCAAAAATAAAGATATTTGTAACAAAATGCACTAGTAGCTGACTACATAA
52532 GAAGAAATAT
Statistics
Matches: 397, Mismatches: 68, Indels: 31
0.80 0.14 0.06
Matches are distributed among these distances:
176 54 0.14
177 185 0.47
178 152 0.38
179 6 0.02
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (176 bp):
AATGTTGAAATTAGCAAGACTGGCATATATCGTCAATCTATATATACAGCTACTTGAGATATATT
GACAAAACCGCCAAAAATAAAGATATTTGTAACAAAATGCACTAGTAGCTGACTACATAAAGAGA
GATATCTGAGTAATTGTGTCGTAGTATTATGTGGAAGACTTGACAA
Found at i:52637 original size:176 final size:177
Alignment explanation
Indices: 52076--52640 Score: 473
Period size: 178 Copynumber: 3.2 Consensus size: 177
52066 CCATATTTGT
* * * * * * *
52076 AGATATCTTCAATTTATATATAGAGCTACTTGAGATATGTTGACAAAACTGTCAAAAAATAAAGA
1 AGATATCGTCAACTTATATATACAGCTACTTGAGATATATTGACAAAACCGCCCAAAAATAAAGA
* ** * * *
52141 TATTTGTAACAAAATGCAATAGTAGCTGACTACATAAAGAGAGCTATCTGAGTAATTGTGTCGT-
66 TATTTGTAACAAAATGCACTAGTAGCTGACTACATAAAGAGAAATATCTCAGTAATTCTATCGTA
* * * ** *** *
52205 GATATTATGT-TAATGACTT-GCAGAAATGTTGCTATTAGCATGTCTGGC
131 G-TATTATATGGAA-GACTTAACA-AAATGTTGAAATTAGCAACACTGGA
* * ** * ** *
52253 ATATATCTTTGA-TCTATATATATAGCGTTTTTGAGATATATTGACAAAACCGCCCAAAATTAAA
1 AGATATCGTCAACT-TATATATACAGC-TACTTGAGATATATTGACAAAACCGCCCAAAAATAAA
* * * * *
52317 GATATTTGTAACAAAATGCACTTGTAGCTGACTACATAAAGAGAGATATCTGAGTAATTGTGTCG
64 GATATTTGTAACAAAATGCACTAGTAGCTGACTACATAAAGAGAAATATCTCAGTAATTCTATCG
* * * *
52382 TAGTATTATGTGGAAGACTTGACAAAATGTTGAAATTAGCAAGACTGGC
129 TAGTATTATATGGAAGACTTAACAAAATGTTGAAATTAGCAACACTGGA
* *
52431 ATATATCGTCAATTTATATATACAGCTACTTGAGATATATTGACAAAACCG-CCAAAAATAAAGA
1 AGATATCGTCAACTTATATATACAGCTACTTGAGATATATTGACAAAACCGCCCAAAAATAAAGA
* * * *
52495 TATTTGTAGCAAAATGCACTAGTAGCTGACTTCAT-AAGAAGAAATATCTCTGTACTTCTATCGT
66 TATTTGTAACAAAATGCACTAGTAGCTGACTACATAAAG-AGAAATATCTCAGTAATTCTATCGT
* * * * * * * *
52559 A-TCCTCT-TATGGATGACTTAATAGAATGTTGATATTAGTAACCCTTGA
130 AGT-AT-TATATGGAAGACTTAACAAAATGTTGAAATTAGCAACACTGGA
* * * *
52607 AGATGTCTTCAAACTT-TATGTACGGCTACTTGAG
1 AGATATCGTC-AACTTATATATACAGCTACTTGAG
52641 TTGCATGAAA
Statistics
Matches: 324, Mismatches: 54, Indels: 21
0.81 0.14 0.05
Matches are distributed among these distances:
175 4 0.01
176 119 0.37
177 48 0.15
178 147 0.45
179 6 0.02
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (177 bp):
AGATATCGTCAACTTATATATACAGCTACTTGAGATATATTGACAAAACCGCCCAAAAATAAAGA
TATTTGTAACAAAATGCACTAGTAGCTGACTACATAAAGAGAAATATCTCAGTAATTCTATCGTA
GTATTATATGGAAGACTTAACAAAATGTTGAAATTAGCAACACTGGA
Found at i:53076 original size:21 final size:21
Alignment explanation
Indices: 53047--53090 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
53037 TTTCTTACTT
53047 CTCGAAGCCAGTTACTAGTAG
1 CTCGAAGCCAGTTACTAGTAG
*
53068 CTCGTAGCCAGTTACTAGTAG
1 CTCGAAGCCAGTTACTAGTAG
53089 CT
1 CT
53091 AGCTTTTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (21 bp):
CTCGAAGCCAGTTACTAGTAG
Found at i:53127 original size:14 final size:14
Alignment explanation
Indices: 53108--53140 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
53098 CTTACTTCTC
53108 GTAGCCAGTTACTA
1 GTAGCCAGTTACTA
53122 GTAGCCAGTTACTA
1 GTAGCCAGTTACTA
53136 GTAGC
1 GTAGC
53141 TAACTTTACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.27
Consensus pattern (14 bp):
GTAGCCAGTTACTA
Found at i:62798 original size:2 final size:2
Alignment explanation
Indices: 62791--62830 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
62781 GCAAGCTCTC
62791 AG AG AG AG AG AG 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 AG AG AG AG AG AG
62831 NNNNNNNNNN
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:64850 original size:50 final size:49
Alignment explanation
Indices: 64787--64881 Score: 120
Period size: 49 Copynumber: 1.9 Consensus size: 49
64777 GTGTTTATTA
* * *
64787 ACATATGTGTAACATGTGATTGAGATCT-ACATATGTAAAACATATGGTTC
1 ACATATGTGTAACATATG--TAAAATCTAACATATGTAAAACATATGGTTC
* *
64837 ACATATGTTTAACATATGTAAAATCTAACATATGTTAAACATATG
1 ACATATGTGTAACATATGTAAAATCTAACATATGTAAAACATATG
64882 TGATGTTGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
48 6 0.15
49 17 0.44
50 16 0.41
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.35
Consensus pattern (49 bp):
ACATATGTGTAACATATGTAAAATCTAACATATGTAAAACATATGGTTC
Found at i:68239 original size:3 final size:3
Alignment explanation
Indices: 68233--68278 Score: 67
Period size: 3 Copynumber: 15.3 Consensus size: 3
68223 TGTTAATGTA
*
68233 TCT TCT TCT TCT TCT TCT T-T CTCT TTT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT -TCT TCT TCT TCT TCT TCT TCT TCT
68278 T
1 T
68279 AGCTACTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 1 0.03
3 37 0.95
4 1 0.03
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TCT
Found at i:72281 original size:13 final size:13
Alignment explanation
Indices: 72263--72292 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
72253 TAGTAGGAAA
72263 AAAAAAACAAAAC
1 AAAAAAACAAAAC
72276 AAAAAAACAAAAC
1 AAAAAAACAAAAC
72289 AAAA
1 AAAA
72293 CTAGATGCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAC
Found at i:72287 original size:18 final size:17
Alignment explanation
Indices: 72260--72293 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
72250 TCCTAGTAGG
72260 AAAAAAAAAACAAAACA
1 AAAAAAAAAACAAAACA
72277 AAAAAACAAAACAAAAC
1 AAAAAA-AAAACAAAAC
72294 TAGATGCTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAACAAAACA
Found at i:85215 original size:35 final size:35
Alignment explanation
Indices: 85176--85245 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
85166 CTTCCGACAT
85176 ACAGTTAAGATTTGAATAGTAATATATCTGTATCA
1 ACAGTTAAGATTTGAATAGTAATATATCTGTATCA
* *
85211 ACAGTTATGTTTTGAATAGTAATATATCTGTATCA
1 ACAGTTAAGATTTGAATAGTAATATATCTGTATCA
85246 GTCTTGTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (35 bp):
ACAGTTAAGATTTGAATAGTAATATATCTGTATCA
Found at i:88398 original size:12 final size:12
Alignment explanation
Indices: 88381--88409 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
88371 TGCTCAATAA
88381 GGTATACAAGTT
1 GGTATACAAGTT
88393 GGTATACAAGTT
1 GGTATACAAGTT
88405 GGTAT
1 GGTAT
88410 TTCTGTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.31, C:0.07, G:0.28, T:0.34
Consensus pattern (12 bp):
GGTATACAAGTT
Found at i:108893 original size:13 final size:13
Alignment explanation
Indices: 108870--108902 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
108860 CATAACCAGA
108870 TAATGATAATTATC
1 TAAT-ATAATTATC
108884 TAATATAATTATC
1 TAATATAATTATC
108897 TAATAT
1 TAATAT
108903 TTTTAGCCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (13 bp):
TAATATAATTATC
Found at i:114998 original size:2 final size:2
Alignment explanation
Indices: 114991--115058 Score: 113
Period size: 2 Copynumber: 35.0 Consensus size: 2
114981 AGACACAACA
*
114991 TC TC TC TC TC TC TC -C CC TC T- TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
115031 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
115059 AATAATGACT
Statistics
Matches: 63, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
1 2 0.03
2 61 0.97
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:126131 original size:122 final size:122
Alignment explanation
Indices: 125826--126131 Score: 422
Period size: 121 Copynumber: 2.5 Consensus size: 122
125816 AAAAAAAAAA
*
125826 AAAC-TTAGTTGCCTGACCCTGAGGACAAATGATCCTGATACTGTAGTATTAGATACTGCAGACT
1 AAACTTTAGTTGCCTTACCCTGAGGACAAATGATCCTGATACTGTAGTATTAGATACTGCAGACT
* * *
125890 CCAACTTATACCCTCGAGCCAAGTCTTGTAAACATTCTCCCATAACCCCCCCCTCCC
66 CCAACATATACCCTCGAGCCAAGCCTTGTAAACATTCTCCCATAACCCCCCCCTCAC
*
125947 AAACTTTAGTTGCCTTACCCTGA-GACAACTGATCCTGATACTGTAGTATTAGATACTGCAGACT
1 AAACTTTAGTTGCCTTACCCTGAGGACAAATGATCCTGATACTGTAGTATTAGATACTGCAGACT
* * * * * * *
126011 -GAA-ATATACTCTCGAGCTAAGCCTTTTTAACATTCTCCCATAAATCCTCCCCCTTAC
66 CCAACATATACCCTCGAGCCAAGCCTTGTAAACATTCTCCCAT-AA-CCCCCCCCTCAC
* * * *
126068 AAACTTTAGTTGCCTTACCCTGAGGATAAATGATCCTGATACTTTAGTAATATATACTGCAGAC
1 AAACTTTAGTTGCCTTACCCTGAGGACAAATGATCCTGATACTGTAGTATTAGATACTGCAGAC
126132 ATATACCAGT
Statistics
Matches: 164, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
119 32 0.20
120 4 0.02
121 76 0.46
122 52 0.32
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.29
Consensus pattern (122 bp):
AAACTTTAGTTGCCTTACCCTGAGGACAAATGATCCTGATACTGTAGTATTAGATACTGCAGACT
CCAACATATACCCTCGAGCCAAGCCTTGTAAACATTCTCCCATAACCCCCCCCTCAC
Found at i:132515 original size:2 final size:2
Alignment explanation
Indices: 132508--132554 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
132498 AAACCCACAT
132508 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
132550 TC TC T
1 TC TC T
132555 GAAATATGAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:138225 original size:12 final size:12
Alignment explanation
Indices: 138208--138235 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
138198 AAAGTTTACA
138208 GACGGACAGACG
1 GACGGACAGACG
138220 GACGGACAGACG
1 GACGGACAGACG
138232 GACG
1 GACG
138236 ACGGACAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.25, G:0.43, T:0.00
Consensus pattern (12 bp):
GACGGACAGACG
Found at i:141895 original size:17 final size:17
Alignment explanation
Indices: 141875--141907 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
141865 AACTCTCAGT
141875 TTAGCCGATAACTGGTC
1 TTAGCCGATAACTGGTC
141892 TTAGCCGATAACTGGT
1 TTAGCCGATAACTGGT
141908 ACAGTACCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (17 bp):
TTAGCCGATAACTGGTC
Found at i:143651 original size:90 final size:90
Alignment explanation
Indices: 143497--143675 Score: 277
Period size: 90 Copynumber: 2.0 Consensus size: 90
143487 GGAGTAGCTG
143497 GTGGCTGCATCCATTTTCCTGGTAGCAGTGTTCAGGATACCATCTTCCACCACCTCCTCAATGGA
1 GTGGCTGCATCCATTTTCCTGGTAGCAGTGTTCAGGATACCATCTTCCACCACCTCCTCAATGGA
*
143562 ACGATCCAGCCTCCTAGAATAACTT
66 ACGATCCAACCTCCTAGAATAACTT
* ** * * *
143587 GTGGCTGCATCCATTTTCCTTGTAGGGGTGTTCAGGATTCCATCTTCCAGCACCTCCTCTATGGA
1 GTGGCTGCATCCATTTTCCTGGTAGCAGTGTTCAGGATACCATCTTCCACCACCTCCTCAATGGA
**
143652 ACGATCCAACCTTTTAGAATAACT
66 ACGATCCAACCTCCTAGAATAACT
143676 GGTTGCAGCA
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.22, C:0.29, G:0.18, T:0.30
Consensus pattern (90 bp):
GTGGCTGCATCCATTTTCCTGGTAGCAGTGTTCAGGATACCATCTTCCACCACCTCCTCAATGGA
ACGATCCAACCTCCTAGAATAACTT
Found at i:144735 original size:57 final size:57
Alignment explanation
Indices: 144635--144742 Score: 171
Period size: 57 Copynumber: 1.9 Consensus size: 57
144625 CCCTATAACA
* * *
144635 AGCCCCCCCTTTACTTGTAACTCCCTGGTGGACTTCCTGTCTATCACCGACCCTACG
1 AGCCCCCCCTTTACCTGTAACTCCCCGGTGGACTTCCTCTCTATCACCGACCCTACG
* *
144692 AGCCTCCCCTTTACCTGTAACTCCCCGGTGGACTTTCTCTCTATCACCGAC
1 AGCCCCCCCTTTACCTGTAACTCCCCGGTGGACTTCCTCTCTATCACCGAC
144743 TCTGTGAATC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 46 1.00
ACGTcount: A:0.16, C:0.41, G:0.15, T:0.29
Consensus pattern (57 bp):
AGCCCCCCCTTTACCTGTAACTCCCCGGTGGACTTCCTCTCTATCACCGACCCTACG
Found at i:146994 original size:31 final size:31
Alignment explanation
Indices: 146958--147027 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
146948 TAAGAGTCTC
* *
146958 TACATCTTACCTTATCTCTCTGTGACACCTG
1 TACATCTTACCCTATCTCTCTGTGACACCAG
* *
146989 TACATCTTACCCTCTCTCTGTGTGACACCAG
1 TACATCTTACCCTATCTCTCTGTGACACCAG
147020 TACATCTT
1 TACATCTT
147028 TCTGTGATTG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.20, C:0.33, G:0.10, T:0.37
Consensus pattern (31 bp):
TACATCTTACCCTATCTCTCTGTGACACCAG
Found at i:147257 original size:13 final size:13
Alignment explanation
Indices: 147239--147269 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
147229 CATGCGGTTT
147239 TAATTTTTTTCAA
1 TAATTTTTTTCAA
147252 TAA-TTTTTTCAA
1 TAATTTTTTTCAA
147264 TAATTT
1 TAATTT
147270 CTACTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.61
Consensus pattern (13 bp):
TAATTTTTTTCAA
Found at i:158243 original size:16 final size:16
Alignment explanation
Indices: 158222--158258 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
158212 ACTATTCTCG
158222 GTGCCGAGTTCACCAA
1 GTGCCGAGTTCACCAA
* *
158238 GTGCCGAGTTTACCAT
1 GTGCCGAGTTCACCAA
158254 GTGCC
1 GTGCC
158259 AGGTTGACCA
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:0.19, C:0.30, G:0.27, T:0.24
Consensus pattern (16 bp):
GTGCCGAGTTCACCAA
Found at i:160429 original size:64 final size:63
Alignment explanation
Indices: 160351--160477 Score: 227
Period size: 64 Copynumber: 2.0 Consensus size: 63
160341 AGAAGGACCA
*
160351 ACTTTACCATCAGACGTGAATAAGCGTAAATTAAGTTTATATATAACTACTGCTTTGTTGGTC
1 ACTTTACCATCAGACGTGAATAAGCGTAAATCAAGTTTATATATAACTACTGCTTTGTTGGTC
*
160414 NACTTTACCATCAGACGTGAATAAGCGTAAATCAAGTTTATATATAATTACTGCTTTGTTGGTC
1 -ACTTTACCATCAGACGTGAATAAGCGTAAATCAAGTTTATATATAACTACTGCTTTGTTGGTC
160478 TTTTTGATAT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.36
Consensus pattern (63 bp):
ACTTTACCATCAGACGTGAATAAGCGTAAATCAAGTTTATATATAACTACTGCTTTGTTGGTC
Found at i:164545 original size:21 final size:21
Alignment explanation
Indices: 164515--164565 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
164505 TTCTTCTTCA
164515 TATTATTTAATAAAATGAAAG
1 TATTATTTAATAAAATGAAAG
* * *
164536 TATTAATTAATCAAATTAAAG
1 TATTATTTAATAAAATGAAAG
164557 -ATTATTTAA
1 TATTATTTAA
164566 ATTTTATGAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (21 bp):
TATTATTTAATAAAATGAAAG
Found at i:170090 original size:30 final size:30
Alignment explanation
Indices: 170055--170154 Score: 128
Period size: 30 Copynumber: 3.3 Consensus size: 30
170045 ATCTTAAGTA
* * *
170055 CAGTGAAAACATTGAATCTAGTATTGAACC
1 CAGTGAAAGCACTGAATCTAGTACTGAACC
* * *
170085 TAGTGAAAGCACCGAATCTGGTACTGAACC
1 CAGTGAAAGCACTGAATCTAGTACTGAACC
*
170115 CAGTGAAAGCACTGAATCTTGTACTGAACC
1 CAGTGAAAGCACTGAATCTAGTACTGAACC
*
170145 CAGGGAAAGC
1 CAGTGAAAGC
170155 TGTACACAGT
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (30 bp):
CAGTGAAAGCACTGAATCTAGTACTGAACC
Found at i:173851 original size:31 final size:32
Alignment explanation
Indices: 173795--173864 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
173785 GGTCTGCATC
*
173795 ACAGCTAAGTGGAAAAAAAAGTAACAGA-GGTT
1 ACAGCTAAGTGGAAAAAAAAGTAACA-ATGGCT
* * *
173827 ACAGCTATGT-GAAACAACAGTAACAATGGCT
1 ACAGCTAAGTGGAAAAAAAAGTAACAATGGCT
173858 ACAGCTA
1 ACAGCTA
173865 CAGGTAAGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 1 0.03
31 23 0.70
32 9 0.27
ACGTcount: A:0.46, C:0.16, G:0.21, T:0.17
Consensus pattern (32 bp):
ACAGCTAAGTGGAAAAAAAAGTAACAATGGCT
Found at i:177279 original size:178 final size:179
Alignment explanation
Indices: 176970--177330 Score: 609
Period size: 178 Copynumber: 2.0 Consensus size: 179
176960 TTAAATTTTT
* *
176970 GACATACGGTACTATAATTTTGTCCACTAACCAATATTTAGTAAAGGAAAAATCGAAATATTTTA
1 GACATACGGTACAATAATTTTGTCCACTAACCAATATTTAGTAAAGGAAAAATCCAAATATTTTA
* *
177035 GCTTTTTTAAATTTGAGCATTTTTAATACCAAACTCTTTGTCTTAGGAGGTAAATATAGTCTAGA
66 GC-TTTTAAAATTTGAGCATTTTCAATACCAAACTCTTTGTCTTAGGAGGTAAATATAGTCTAGA
*
177100 AATGGCCACGATGACCAAGCCCTCTTAACAAAA-ACATTGACATTCCATG
130 AATGGCCACGATGACCAAGCCCTCTTAACAAAACACATGGACATTCCATG
* * *
177149 NGACATACGGTACAATATTTTTGTCCATTAACTAATATTTAGTAAAGGAAAAATCCAAATATTTT
1 -GACATACGGTACAATAATTTTGTCCACTAACCAATATTTAGTAAAGGAAAAATCCAAATATTTT
177214 AGC-TTTAAAATTTGAGCATTTTCAATACCAAACTCTTTGTCTTAGGAGGTAAATATAGTCTAGA
65 AGCTTTTAAAATTTGAGCATTTTCAATACCAAACTCTTTGTCTTAGGAGGTAAATATAGTCTAGA
*
177278 AATGGCCACGATGATCAAGCCCTCTTAACAAAACACATGGACATTCCATG
130 AATGGCCACGATGACCAAGCCCTCTTAACAAAACACATGGACATTCCATG
177328 GAC
1 GAC
177331 TACTATAAAT
Statistics
Matches: 171, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
178 94 0.55
179 15 0.09
180 62 0.36
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (179 bp):
GACATACGGTACAATAATTTTGTCCACTAACCAATATTTAGTAAAGGAAAAATCCAAATATTTTA
GCTTTTAAAATTTGAGCATTTTCAATACCAAACTCTTTGTCTTAGGAGGTAAATATAGTCTAGAA
ATGGCCACGATGACCAAGCCCTCTTAACAAAACACATGGACATTCCATG
Found at i:188591 original size:31 final size:31
Alignment explanation
Indices: 188555--188619 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
188545 AGGAAAAAAG
* * *
188555 ATCATGTAATAGCCTAGGAGTTATTGAATTA
1 ATCATGCAATAGCCTAAGAGTTATTAAATTA
** *
188586 ATCATGCAATATTCTAAGTGTTATTAAATTA
1 ATCATGCAATAGCCTAAGAGTTATTAAATTA
188617 ATC
1 ATC
188620 TCCTTTTTCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (31 bp):
ATCATGCAATAGCCTAAGAGTTATTAAATTA
Found at i:207638 original size:327 final size:326
Alignment explanation
Indices: 207045--207679 Score: 1153
Period size: 327 Copynumber: 1.9 Consensus size: 326
207035 CCATAGGTGG
207045 GTATATGTATTATAATAATGCATTTGTCACTCTGTAAGGGTACTTAGTAGTATATATATATAAAA
1 GTATATGTATTATAATAATGCATTTGTCACTCTGTAAGGGTACTTAGTAGTATATATATATAAAA
*
207110 AATATTCCAGACGCAAAGCGTCCAGTTTGATCTGATGATCCGTGCTTGGCAACAAGATGTGATCC
66 AATATTCCAGACGCAAAGCGTCCAGTTTGATCTGATGATCCGTGCTTGGCAACAAGACGTGATCC
*
207175 AGCTCTTTGGATTAAGTTACAGTTATAATGATAAATTTATTATATACCCTTGTCTATTTAAAAGT
131 AGCTCTTTGGATTAAATTACAGTTATAATGATAAATTTATTATATACCCTTGTCTATTTAAAAGT
*
207240 TTTAATTACAAAACTTTGTTTTTGAAGTGAACTGTTTGACGTTTACTTATATAACAATGCTATTT
196 TTTAATTACAAAACTTTGTTTTTGAAGTCAACTGTTTGACGTTTACTTATATAACAATGCTATTT
* *
207305 TGAAATGAACTCTTTTAAAACGCACTAAAATAGAGACGTTATGGATGCATGTGTACTATGTCATC
261 TGAAATGAACTCTATTAAAACGCACTAAAATACAGACGTTATGGATGCATGTGTACTATGTCATC
207370 A
326 A
*
207371 GTATATGTATTATAATAATGCATTTGTCACTCTGTAAGGGTACTTAGTAGTATATATATGTAATA
1 GTATATGTATTATAATAATGCATTTGTCACTCTGTAAGGGTACTTAGTAGTATATATATATAA-A
* * **
207436 TATTATTCCAGACGTGAAGCGTCCAGTTTGATCTGATGATCCGTGCTTGGCAACAAGACGTGATC
65 AAATATTCCAGACGCAAAGCGTCCAGTTTGATCTGATGATCCGTGCTTGGCAACAAGACGTGATC
* *
207501 CGGCTCTTTGGATTAAATTACAGTTATAATGATAAATTTATTATATACCCTTGTCTATTTGAAAG
130 CAGCTCTTTGGATTAAATTACAGTTATAATGATAAATTTATTATATACCCTTGTCTATTTAAAAG
207566 TTTTAATTACAAAACTTTGTTTTTGAAGTCAACTGTTTGACGTTTACTTATATAACAATGCTATT
195 TTTTAATTACAAAACTTTGTTTTTGAAGTCAACTGTTTGACGTTTACTTATATAACAATGCTATT
207631 TTGAAATGAACTCTATTAAAACGCACTAAAATACAGACGTTATGGATGC
260 TTGAAATGAACTCTATTAAAACGCACTAAAATACAGACGTTATGGATGC
207680 GTACTACGTC
Statistics
Matches: 296, Mismatches: 12, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
326 62 0.21
327 234 0.79
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (326 bp):
GTATATGTATTATAATAATGCATTTGTCACTCTGTAAGGGTACTTAGTAGTATATATATATAAAA
AATATTCCAGACGCAAAGCGTCCAGTTTGATCTGATGATCCGTGCTTGGCAACAAGACGTGATCC
AGCTCTTTGGATTAAATTACAGTTATAATGATAAATTTATTATATACCCTTGTCTATTTAAAAGT
TTTAATTACAAAACTTTGTTTTTGAAGTCAACTGTTTGACGTTTACTTATATAACAATGCTATTT
TGAAATGAACTCTATTAAAACGCACTAAAATACAGACGTTATGGATGCATGTGTACTATGTCATC
A
Found at i:208455 original size:2 final size:2
Alignment explanation
Indices: 208448--208473 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
208438 AAGCATGAAT
208448 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
208474 AATTGCTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:210622 original size:9 final size:9
Alignment explanation
Indices: 210600--210647 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
210590 ATATCAATAT
210600 TATGTAATTA
1 TATGT-ATTA
210610 TATG-ATATA
1 TATGTAT-TA
210619 TATGTATTA
1 TATGTATTA
210628 TATGTATTA
1 TATGTATTA
*
210637 T-TGTATAA
1 TATGTATTA
210645 TAT
1 TAT
210648 AAGTAATTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
8 9 0.26
9 19 0.56
10 6 0.18
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (9 bp):
TATGTATTA
Found at i:210627 original size:18 final size:18
Alignment explanation
Indices: 210596--210637 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
210586 ACTAATATCA
210596 ATATTATGTAATTATATG
1 ATATTATGTAATTATATG
210614 ATATATATGT-ATTATATG
1 ATAT-TATGTAATTATATG
210632 -TATTAT
1 ATATTAT
210638 TGTATAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 3 0.13
17 3 0.13
18 12 0.52
19 5 0.22
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (18 bp):
ATATTATGTAATTATATG
Found at i:211869 original size:21 final size:22
Alignment explanation
Indices: 211843--211901 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 22
211833 CAGAATGCTG
211843 CTCCTCACTCTCCTCTTC-TTC-
1 CTCCTC-CTCTCCTCTTCGTTCT
*
211864 CTCCTCCTCCTCCTTTTCGTTCTT
1 CTCCTCCT-CTCCTCTTCGTTC-T
211888 CTCCTCTCTCTCCT
1 CTCCTC-CTCTCCT
211902 TCTCTTCTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
20 2 0.06
21 14 0.44
22 3 0.09
24 11 0.34
25 2 0.06
ACGTcount: A:0.02, C:0.51, G:0.02, T:0.46
Consensus pattern (22 bp):
CTCCTCCTCTCCTCTTCGTTCT
Found at i:215274 original size:21 final size:22
Alignment explanation
Indices: 215248--215306 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 22
215238 TAGAATGCTG
215248 CTCCTCACTCTCCTCTTC-TTC-
1 CTCCTC-CTCTCCTCTTCGTTCT
*
215269 CTCCTCCTCCTCCTTTTCGTTCTT
1 CTCCTCCT-CTCCTCTTCGTTC-T
215293 CTCCTCTCTCTCCT
1 CTCCTC-CTCTCCT
215307 TCTCTTCTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
20 2 0.06
21 14 0.44
22 3 0.09
24 11 0.34
25 2 0.06
ACGTcount: A:0.02, C:0.51, G:0.02, T:0.46
Consensus pattern (22 bp):
CTCCTCCTCTCCTCTTCGTTCT
Found at i:221788 original size:161 final size:161
Alignment explanation
Indices: 221607--221979 Score: 505
Period size: 161 Copynumber: 2.3 Consensus size: 161
221597 ACAGTTATGA
*
221607 CCCTTGGACATAGTAAAATTCCAGTTATTTGCAGTTTCCGCTCATTTTCTTCGCAAAGGACGAAC
1 CCCTTGGACATAGAAAAATTCCAGTTATTTGCAGTTTCCGCTCATTTTCTTCGCAAAGGACGAAC
* * *
221672 GTATTGAAATGAAATTTGGTATACAGGTTTATC-ATGATAATATCTAGGTCAAGTTCGATATTGG
66 ATATTGAAATGAAATTTCGTATACAGGTTTATCTA-AATAATATCTAGGTCAAGTTCGATATTGG
* **
221736 GTACCATCGAGCAATTTTCGACAGAGTAATGG
130 GTACCATAGAGCAATTTTCGACAGAGTAATAC
** * * * *
221768 GTCTTGGACATAGAAAAATTCCAGTTATTTGCAGTTTCCGCTCATTTTGTTCGCAGAGGATGCAC
1 CCCTTGGACATAGAAAAATTCCAGTTATTTGCAGTTTCCGCTCATTTTCTTCGCAAAGGACGAAC
* * * *
221833 ATATTGATATGAAATTTCGTATACAGGTTTATCTAAATAATGTCTAGGTCAAGTTTGATTTTGGG
66 ATATTGAAATGAAATTTCGTATACAGGTTTATCTAAATAATATCTAGGTCAAGTTCGATATTGGG
** * *
221898 TATGATAGAGCAATTTTCGGCAGAGTTATAC
131 TACCATAGAGCAATTTTCGACAGAGTAATAC
* * * *
221929 CCCTTGGACTTAAAAAAATTCCAGTTATTTGCAGTTTACGTTCATTTTCTT
1 CCCTTGGACATAGAAAAATTCCAGTTATTTGCAGTTTCCGCTCATTTTCTT
221980 TGTGGATGTT
Statistics
Matches: 183, Mismatches: 28, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
161 182 0.99
162 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.36
Consensus pattern (161 bp):
CCCTTGGACATAGAAAAATTCCAGTTATTTGCAGTTTCCGCTCATTTTCTTCGCAAAGGACGAAC
ATATTGAAATGAAATTTCGTATACAGGTTTATCTAAATAATATCTAGGTCAAGTTCGATATTGGG
TACCATAGAGCAATTTTCGACAGAGTAATAC
Found at i:223386 original size:162 final size:162
Alignment explanation
Indices: 223121--223673 Score: 572
Period size: 150 Copynumber: 3.5 Consensus size: 162
223111 TGGATAGTCA
*
223121 GATTGAGCAATTTTAGACAGAGTTATGGCCCTTGGACTT--AAAAAATTCCACTTATTTGCAGTT
1 GATTGAGCAATTTTAGACAGAGTTAT-GCCCTTGGACTTAGAAAAAATTCCAATTATTTGCAGTT
* * * *
223184 TCCATCCATTTTCTTCGCAGAGGTTGCACATACTGAAATGAGA-TTTTGTATA-ATGATTTATTA
65 TCCATTCATTTTCTTCGCAGAGGTTGCACATACTGAAATGAAACTTAT-TATACA-GATTTATCA
* * *
223247 TAATAATATCTA-GGTCAGGTTTGATTTTGGA-TAT
128 TAATAATATCTATGGTCAAGTTTGATTCT-GATTAC
223281 GATTGAGCAATTTTAGACAGAGTTATGCTCCTTGGACTTAGAAAAAATTCCAATTATTTGCAGTT
1 GATTGAGCAATTTTAGACAGAGTTATGC-CCTTGGACTTAGAAAAAATTCCAATTATTTGCAGTT
* * * *
223346 TCCGTTCATTTTCTTTGCGGAGGTTGCACATATTGAAATGAAACTTATTATACAGATTTATCATA
65 TCCATTCATTTTCTTCGCAGAGGTTGCACATACTGAAATGAAACTTATTATACAGATTTATCATA
* *
223411 ATAATGTTTATGGTCAAGTTTGATTCTGATTAC
130 ATAATATCTATGGTCAAGTTTGATTCTGATTAC
* * * * * *
223444 AATCGAGCAATTTTCGGCAGAGTTATGCCCCTTTGACTTAGAAAAAA-TCCAGTTATTTGCAGTT
1 GATTGAGCAATTTTAGACAGAGTTATG-CCCTTGGACTTAGAAAAAATTCCAATTATTTGCAGTT
** * * * *
223508 TCCATTCA--AGCTT-G-A-A-----CA-A-ATTGAAATGAAATTTAATATACAGATTTGTCATA
65 TCCATTCATTTTCTTCGCAGAGGTTGCACATACTGAAATGAAACTTATTATACAGATTTATCATA
* * *
223561 ATAATGTTTATGGTCAAGTTTGATTTTGATTAC
130 ATAATATCTATGGTCAAGTTTGATTCTGATTAC
* ** * * *
223594 AACCGAGCAATTTTCA-ACAGAGTTATGCCCCTTTGACGTAG-AAAAATTCCAAATATTTGCAGT
1 GATTGAGCAATTTT-AGACAGAGTTATG-CCCTTGGACTTAGAAAAAATTCCAATTATTTGCAGT
223657 TTCCATTCATTTTCTTC
64 TTCCATTCATTTTCTTC
223674 ATGGATGTTT
Statistics
Matches: 344, Mismatches: 36, Indels: 33
0.83 0.09 0.08
Matches are distributed among these distances:
149 5 0.01
150 122 0.35
151 1 0.00
152 5 0.01
157 1 0.00
159 3 0.01
160 39 0.11
162 107 0.31
163 60 0.17
164 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (162 bp):
GATTGAGCAATTTTAGACAGAGTTATGCCCTTGGACTTAGAAAAAATTCCAATTATTTGCAGTTT
CCATTCATTTTCTTCGCAGAGGTTGCACATACTGAAATGAAACTTATTATACAGATTTATCATAA
TAATATCTATGGTCAAGTTTGATTCTGATTAC
Found at i:227459 original size:15 final size:15
Alignment explanation
Indices: 227435--227469 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
227425 GGGTACCATG
*
227435 CCTGGTGGCAACATT
1 CCTGGAGGCAACATT
*
227450 CCTGGAGGCACCATT
1 CCTGGAGGCAACATT
227465 CCTGG
1 CCTGG
227470 CCCTGACATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.17, C:0.31, G:0.29, T:0.23
Consensus pattern (15 bp):
CCTGGAGGCAACATT
Found at i:230401 original size:3 final size:3
Alignment explanation
Indices: 230393--230439 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
230383 AAGTGTATAA
230393 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
230440 AGTAGAGAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:236608 original size:16 final size:16
Alignment explanation
Indices: 236587--236618 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
236577 ATTGTAGAAT
236587 TAATTCTTTTAATTTG
1 TAATTCTTTTAATTTG
*
236603 TAATTCTTTTTATTTG
1 TAATTCTTTTAATTTG
236619 ACCAAAAAAA
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:0.22, C:0.06, G:0.06, T:0.66
Consensus pattern (16 bp):
TAATTCTTTTAATTTG
Found at i:239928 original size:48 final size:48
Alignment explanation
Indices: 239857--240008 Score: 277
Period size: 48 Copynumber: 3.2 Consensus size: 48
239847 ATGTATGGAA
**
239857 CTGTAGCTTCGTGATCCTTCAATCTGAATGTCCTGTGGAGTTACAGTT
1 CTGTAGCTTCACGATCCTTCAATCTGAATGTCCTGTGGAGTTACAGTT
239905 CTGTAGCTTCACGATCCTTCAATCTGAATGTCCTGTGGAGTTACAGTT
1 CTGTAGCTTCACGATCCTTCAATCTGAATGTCCTGTGGAGTTACAGTT
239953 CTGTAGCTTCACGATCCTTCAATCTGAATGTCCTGTGGAGTTACAGTT
1 CTGTAGCTTCACGATCCTTCAATCTGAATGTCCTGTGGAGTTACAGTT
*
240001 CTGCAGCT
1 CTGTAGCT
240009 AGTTGTTTTG
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
48 101 1.00
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.36
Consensus pattern (48 bp):
CTGTAGCTTCACGATCCTTCAATCTGAATGTCCTGTGGAGTTACAGTT
Found at i:243487 original size:17 final size:17
Alignment explanation
Indices: 243444--243492 Score: 57
Period size: 15 Copynumber: 3.0 Consensus size: 17
243434 TTTGCAAAAT
*
243444 TTTACGGATATAACGGA
1 TTTACGGATATAACGAA
243461 -TT-CGGATATAACGAA
1 TTTACGGATATAACGAA
* *
243476 TTTACAGATATAGCGAA
1 TTTACGGATATAACGAA
243493 CTGATTTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 12 0.44
16 4 0.15
17 11 0.41
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (17 bp):
TTTACGGATATAACGAA
Found at i:244404 original size:13 final size:13
Alignment explanation
Indices: 244386--244410 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
244376 TATAAGTACA
244386 TGAATTCATGAAT
1 TGAATTCATGAAT
244399 TGAATTCATGAA
1 TGAATTCATGAA
244411 CATGAATTGA
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:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (13 bp):
TGAATTCATGAAT
Found at i:246923 original size:2 final size:2
Alignment explanation
Indices: 246916--246943 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
246906 ATAATTCATC
246916 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
246944 AAACAACGTT
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:247970 original size:15 final size:15
Alignment explanation
Indices: 247947--247977 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
247937 TGAAGTACCG
*
247947 GTATTTCTATTTAGA
1 GTATATCTATTTAGA
247962 GTATATCTATTTAGA
1 GTATATCTATTTAGA
247977 G
1 G
247978 ATGTACCTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.16, T:0.48
Consensus pattern (15 bp):
GTATATCTATTTAGA
Found at i:255418 original size:37 final size:37
Alignment explanation
Indices: 255376--255891 Score: 622
Period size: 37 Copynumber: 13.7 Consensus size: 37
255366 GCCGGATGTG
* * *
255376 GATTGATTCACTGACAGAAATCATCAGGAT-GAGTGAT
1 GATTGATTCATTGACAGCAATCAT-AAGATCGAGTGAT
* *
255413 AATTGATTCATAT-ACAGCAATCATGAGGATCATGTGATGAATGAT
1 GATTGATTCAT-TGACAGCAATCAT-AAGATC----GA-G--TGAT
* * * *
255458 GATTGATTTATTAACAGTAATCATAAGATCAAGTGAT
1 GATTGATTCATTGACAGCAATCATAAGATCGAGTGAT
*
255495 GATTGATTCATTGACAGCAATCATAAGGTCGAGTGAT
1 GATTGATTCATTGACAGCAATCATAAGATCGAGTGAT
*
255532 GATTGATTCATTGACAGCAATCATAAGGTCGAGTGAT
1 GATTGATTCATTGACAGCAATCATAAGATCGAGTGAT
* * * *
255569 GATTGATTTATTGACAGTACTCATAAGATCAAGTGAT
1 GATTGATTCATTGACAGCAATCATAAGATCGAGTGAT
*
255606 GATTGATTCATTGACAGCAATCATAAGATCAAGTGAT
1 GATTGATTCATTGACAGCAATCATAAGATCGAGTGAT
*
255643 GATTGATTCATTGACAGCAATCATAAGGTCGAGTGAT
1 GATTGATTCATTGACAGCAATCATAAGATCGAGTGAT
* * * *
255680 GATTGATTTATTGACAGTACTCATAAGATCAAGTGAT
1 GATTGATTCATTGACAGCAATCATAAGATCGAGTGAT
255717 GATTGATTCATTGACAGCAATCATAAGATCGAGTGAT
1 GATTGATTCATTGACAGCAATCATAAGATCGAGTGAT
* * * * *
255754 GATTGCTTTATTGACAGTACTCATAAGATCAAGTGAT
1 GATTGATTCATTGACAGCAATCATAAGATCGAGTGAT
*
255791 GATTGATTCATTGACAGCAATCATAAGGTCGAGTGAT
1 GATTGATTCATTGACAGCAATCATAAGATCGAGTGAT
* * * * * *
255828 AATTGCTTTATTGACAGGAATCATAAGATCAAGTAAT
1 GATTGATTCATTGACAGCAATCATAAGATCGAGTGAT
*
255865 GATTGATTCATTGATAGCAATCATAAG
1 GATTGATTCATTGACAGCAATCATAAG
255892 TTCAATTTAT
Statistics
Matches: 413, Mismatches: 56, Indels: 20
0.84 0.11 0.04
Matches are distributed among these distances:
37 378 0.92
38 1 0.00
39 1 0.00
40 1 0.00
42 2 0.00
43 1 0.00
44 6 0.01
45 23 0.06
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (37 bp):
GATTGATTCATTGACAGCAATCATAAGATCGAGTGAT
Found at i:255912 original size:74 final size:74
Alignment explanation
Indices: 255454--255891 Score: 687
Period size: 74 Copynumber: 5.9 Consensus size: 74
255444 ATGTGATGAA
*
255454 TGATGATTGATTTATTAACAGTAATCATAAGATCAAGTGATGATTGATTCATTGACAGCAATCAT
1 TGATGATTGATTTATTGACAGTAATCATAAGATCAAGTGATGATTGATTCATTGACAGCAATCAT
255519 AAGGTCGAG
66 AAGGTCGAG
* * * * * * *
255528 TGATGATTGATTCATTGACAGCAATCATAAGGTCGAGTGATGATTGATTTATTGACAGTACTCAT
1 TGATGATTGATTTATTGACAGTAATCATAAGATCAAGTGATGATTGATTCATTGACAGCAATCAT
* *
255593 AAGATCAAG
66 AAGGTCGAG
* *
255602 TGATGATTGATTCATTGACAGCAATCATAAGATCAAGTGATGATTGATTCATTGACAGCAATCAT
1 TGATGATTGATTTATTGACAGTAATCATAAGATCAAGTGATGATTGATTCATTGACAGCAATCAT
255667 AAGGTCGAG
66 AAGGTCGAG
*
255676 TGATGATTGATTTATTGACAGTACTCATAAGATCAAGTGATGATTGATTCATTGACAGCAATCAT
1 TGATGATTGATTTATTGACAGTAATCATAAGATCAAGTGATGATTGATTCATTGACAGCAATCAT
*
255741 AAGATCGAG
66 AAGGTCGAG
* *
255750 TGATGATTGCTTTATTGACAGTACTCATAAGATCAAGTGATGATTGATTCATTGACAGCAATCAT
1 TGATGATTGATTTATTGACAGTAATCATAAGATCAAGTGATGATTGATTCATTGACAGCAATCAT
255815 AAGGTCGAG
66 AAGGTCGAG
* * * * *
255824 TGATAATTGCTTTATTGACAGGAATCATAAGATCAAGTAATGATTGATTCATTGATAGCAATCAT
1 TGATGATTGATTTATTGACAGTAATCATAAGATCAAGTGATGATTGATTCATTGACAGCAATCAT
255889 AAG
66 AAG
255892 TTCAATTTAT
Statistics
Matches: 336, Mismatches: 28, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 336 1.00
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (74 bp):
TGATGATTGATTTATTGACAGTAATCATAAGATCAAGTGATGATTGATTCATTGACAGCAATCAT
AAGGTCGAG
Found at i:256001 original size:37 final size:37
Alignment explanation
Indices: 255959--256095 Score: 229
Period size: 37 Copynumber: 3.7 Consensus size: 37
255949 ACGAGGCCAA
*
255959 GTGATGATTGATTTACTGACAGCAATCATGAGGCCGC
1 GTGATGATTGATTCACTGACAGCAATCATGAGGCCGC
* *
255996 GTGATGATTGACTCACTGATAGCAATCATGAGGCCGC
1 GTGATGATTGATTCACTGACAGCAATCATGAGGCCGC
*
256033 GTGATGATTGATTCACTGATAGCAATCATGAGGCCGC
1 GTGATGATTGATTCACTGACAGCAATCATGAGGCCGC
*
256070 GTGATGATTGATTCACTGTCAGCAAT
1 GTGATGATTGATTCACTGACAGCAAT
256096 AATAAGACTG
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 94 1.00
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (37 bp):
GTGATGATTGATTCACTGACAGCAATCATGAGGCCGC
Found at i:256059 original size:74 final size:74
Alignment explanation
Indices: 255938--256095 Score: 237
Period size: 74 Copynumber: 2.1 Consensus size: 74
255928 GGCCTTATAT
* *
255938 TGATAGCATTCACGAGGCCAAGTGATGATTGATTTACTGACAGCAATCATGAGGCCGCGTGATGA
1 TGATAGCAATCACGAGGCCAAGTGATGATTGATTCACTGACAGCAATCATGAGGCCGCGTGATGA
256003 TTGACTCAC
66 TTGACTCAC
* ** *
256012 TGATAGCAATCATGAGGCCGCGTGATGATTGATTCACTGATAGCAATCATGAGGCCGCGTGATGA
1 TGATAGCAATCACGAGGCCAAGTGATGATTGATTCACTGACAGCAATCATGAGGCCGCGTGATGA
*
256077 TTGATTCAC
66 TTGACTCAC
256086 TG-TCAGCAAT
1 TGAT-AGCAAT
256096 AATAAGACTG
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
73 1 0.01
74 75 0.99
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.27
Consensus pattern (74 bp):
TGATAGCAATCACGAGGCCAAGTGATGATTGATTCACTGACAGCAATCATGAGGCCGCGTGATGA
TTGACTCAC
Found at i:256143 original size:129 final size:129
Alignment explanation
Indices: 255987--256268 Score: 483
Period size: 129 Copynumber: 2.2 Consensus size: 129
255977 ACAGCAATCA
* * * *
255987 TGAGGCCGCGTGATGATTGACTCACTGATAGCAATCATGAGGCCGCGTGATGATTGATTCACTGA
1 TGAGGCCGAGTGATGATTGATTTACTGACAGCAATCATGAGGCCGCGTGATGATTGATTCACTGA
*
256052 TAGCAATCATGAGGCCGCGTGATGATTGATTCACTGTCAGCAATAATAAGACTGACAACCATTT
66 TAGCAATCATGAGGCCGCGTGATGATTGATTCACTGACAGCAATAATAAGACTGACAACCATTT
256116 TGAGGCCGAGTGATGATTGATTTACTGACAGCAATCATGAGGCCGCGTGATGATTGATTCACTGA
1 TGAGGCCGAGTGATGATTGATTTACTGACAGCAATCATGAGGCCGCGTGATGATTGATTCACTGA
* * *
256181 TAGCAATCATGGGGCCGCGTGATGATTGATTCACTGACAGCATTAATACGACTGACAACCATTT
66 TAGCAATCATGAGGCCGCGTGATGATTGATTCACTGACAGCAATAATAAGACTGACAACCATTT
*
256245 TGAGGCCGAGTGATGATTGGTTTA
1 TGAGGCCGAGTGATGATTGATTTA
256269 TTAAGAACAA
Statistics
Matches: 144, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
129 144 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (129 bp):
TGAGGCCGAGTGATGATTGATTTACTGACAGCAATCATGAGGCCGCGTGATGATTGATTCACTGA
TAGCAATCATGAGGCCGCGTGATGATTGATTCACTGACAGCAATAATAAGACTGACAACCATTT
Found at i:256157 original size:37 final size:37
Alignment explanation
Indices: 256116--256222 Score: 178
Period size: 37 Copynumber: 2.9 Consensus size: 37
256106 ACAACCATTT
* *
256116 TGAGGCCGAGTGATGATTGATTTACTGACAGCAATCA
1 TGAGGCCGCGTGATGATTGATTCACTGACAGCAATCA
*
256153 TGAGGCCGCGTGATGATTGATTCACTGATAGCAATCA
1 TGAGGCCGCGTGATGATTGATTCACTGACAGCAATCA
*
256190 TGGGGCCGCGTGATGATTGATTCACTGACAGCA
1 TGAGGCCGCGTGATGATTGATTCACTGACAGCA
256223 TTAATACGAC
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 65 1.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (37 bp):
TGAGGCCGCGTGATGATTGATTCACTGACAGCAATCA
Found at i:256326 original size:129 final size:129
Alignment explanation
Indices: 256036--256303 Score: 392
Period size: 129 Copynumber: 2.1 Consensus size: 129
256026 AGGCCGCGTG
*
256036 ATGATTGATTCACTGATAGCAATCATGAGGCCGCGTGATGATTGATTCACTGTCAGCAATAATAA
1 ATGATTGATTCACTGATAGCAATCATGAGGCCGCGTGATGATTGATTCACTGACAGCAATAATAA
* * * * ****
256101 GACTGACAACCATTTTGAGGCCGAGTGATGATTGATTTACTGACAGCAATCATGAGGCCGCGTG
66 GACTGACAACCATTTTGAGGCCGAGTGATGATTGATTTACTAACAACAATCATGAAGCAGAACA
* * *
256165 ATGATTGATTCACTGATAGCAATCATGGGGCCGCGTGATGATTGATTCACTGACAGCATTAATAC
1 ATGATTGATTCACTGATAGCAATCATGAGGCCGCGTGATGATTGATTCACTGACAGCAATAATAA
* * * *
256230 GACTGACAACCATTTTGAGGCCGAGTGATGATTGGTTTATTAAGAACAATCATGAATCAGAACA
66 GACTGACAACCATTTTGAGGCCGAGTGATGATTGATTTACTAACAACAATCATGAAGCAGAACA
256294 ATGATTGATT
1 ATGATTGATT
256304 TATTGATGAC
Statistics
Matches: 123, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
129 123 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (129 bp):
ATGATTGATTCACTGATAGCAATCATGAGGCCGCGTGATGATTGATTCACTGACAGCAATAATAA
GACTGACAACCATTTTGAGGCCGAGTGATGATTGATTTACTAACAACAATCATGAAGCAGAACA
Found at i:256374 original size:37 final size:37
Alignment explanation
Indices: 256333--256414 Score: 112
Period size: 37 Copynumber: 2.2 Consensus size: 37
256323 GCCGATCGGA
256333 GATCGATTAAATGATAACAAT-TATGAGGTCAAGTTAT
1 GATCGATTAAATGATAACAATCT-TGAGGTCAAGTTAT
* * * *
256370 GATCGATTTATTGATAGCAGTCTTGAGGTCAAGTTAT
1 GATCGATTAAATGATAACAATCTTGAGGTCAAGTTAT
256407 GATCGATT
1 GATCGATT
256415 CATTGATAGC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
37 39 0.98
38 1 0.03
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.35
Consensus pattern (37 bp):
GATCGATTAAATGATAACAATCTTGAGGTCAAGTTAT
Found at i:256446 original size:37 final size:37
Alignment explanation
Indices: 256368--256460 Score: 105
Period size: 37 Copynumber: 2.5 Consensus size: 37
256358 AGGTCAAGTT
* * *** * **
256368 ATGATCGATTTATTGATAGCAGTCTTGAGGTCAAGTT
1 ATGATCGATTCATTGATAGCAATAAGGAGGCCAAGCG
256405 ATGATCGATTCATTGATAGCAATAAGGAGGCCAAGCG
1 ATGATCGATTCATTGATAGCAATAAGGAGGCCAAGCG
*
256442 ATGATTGATTCATTGATAG
1 ATGATCGATTCATTGATAG
256461 GGGGTATCCA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.32
Consensus pattern (37 bp):
ATGATCGATTCATTGATAGCAATAAGGAGGCCAAGCG
Found at i:256513 original size:2 final size:2
Alignment explanation
Indices: 256500--256539 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
256490 ACTCGTAGAA
*
256500 AG AG AA AG AG AG 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 AG AG AG AG AG AG
256540 CATATGTCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:265961 original size:37 final size:36
Alignment explanation
Indices: 265920--266040 Score: 109
Period size: 37 Copynumber: 3.3 Consensus size: 36
265910 ACAATGTGTA
265920 ATGATTGATTAACTAAAAGCAATCTTAAGGTCGAGTG
1 ATGATTGATTAA-TAAAAGCAATCTTAAGGTCGAGTG
* * * * * * *
265957 ATGATTGATTAATTGACAGTAATCATGAGG-CAAAGTT
1 ATGATTGATTAA-TAAAAGCAATCTTAAGGTC-GAGTG
* * *
265994 ATGATTGATTCATAGATAGCAATATTAAGGTCGAGTG
1 ATGATTGATTAATA-AAAGCAATCTTAAGGTCGAGTG
266031 ATGATTGATT
1 ATGATTGATT
266041 CATAGCCAGC
Statistics
Matches: 64, Mismatches: 17, Indels: 6
0.74 0.20 0.07
Matches are distributed among these distances:
36 2 0.03
37 61 0.95
38 1 0.02
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.33
Consensus pattern (36 bp):
ATGATTGATTAATAAAAGCAATCTTAAGGTCGAGTG
Found at i:266041 original size:37 final size:37
Alignment explanation
Indices: 265937--266857 Score: 628
Period size: 37 Copynumber: 24.9 Consensus size: 37
265927 ATTAACTAAA
* * * * *
265937 AGCAATCTTAAGGTCGAGTGATGATTGATTAATTGAC
1 AGCAATCATGAGGTCAAGTGATGATTGATTCATAGAC
* * *
265974 AGTAATCATGAGG-CAAAGTTATGATTGATTCATAGAT
1 AGCAATCATGAGGTC-AAGTGATGATTGATTCATAGAC
* * *
266011 AGCAAT-ATTAAGGTCGAGTGATGATTGATTCATAGCC
1 AGCAATCA-TGAGGTCAAGTGATGATTGATTCATAGAC
* *
266048 AGCAATCATGAGG-CAAAATGATGCTTGATTCATAGAC
1 AGCAATCATGAGGTC-AAGTGATGATTGATTCATAGAC
* *
266085 AGTAATCATGAGG-CAAAATGATGATTGATTCATAGAC
1 AGCAATCATGAGGTC-AAGTGATGATTGATTCATAGAC
* *
266122 GGCAATCGTGAGGTCAAGAT-ATGATTGATTC-TAGAC
1 AGCAATCATGAGGTCAAG-TGATGATTGATTCATAGAC
* *
266158 AGCAATCATGAGGTCGAGTGATGATTGATTCATTA-TC
1 AGCAATCATGAGGTCAAGTGATGATTGATTCA-TAGAC
* ** * * * *
266195 GGTTATCATGAGG-CAAAGTGATGATTAATTTAATTGAA
1 AGCAATCATGAGGTC-AAGTGATGATTGA-TTCATAGAC
* * *
266233 AGCAGTCATGAGG-CAAAATGATGATTGATTCATATAGAT
1 AGCAATCATGAGGTC-AAGTGATGATTGATTC--ATAGAC
* *
266272 AGCAATCATG-GGGCAAAGTGATGACTGATTCATAGAC
1 AGCAATCATGAGGTC-AAGTGATGATTGATTCATAGAC
* * * * *
266309 AGCAAT-ATTAAAGTCGAGTGATGATTGATTCAAAGCC
1 AGCAATCA-TGAGGTCAAGTGATGATTGATTCATAGAC
* * * *
266346 AGGAATCATGAGATCAAGTGATGATTAATTCATTGAC
1 AGCAATCATGAGGTCAAGTGATGATTGATTCATAGAC
* * * *
266383 AGTAATCATGAGGCCAAGTGAAT-TTTGATTCAGT-GAA
1 AGCAATCATGAGGTCAAGTG-ATGATTGATTCA-TAGAC
* * * * * * *
266420 AGAAATTA-AAGGTCGATTGATGACTGATTCATTGAC
1 AGCAATCATGAGGTCAAGTGATGATTGATTCATAGAC
* *
266456 AGTAATCATGATGTCAAGTGATGATTGATTCAT-GAAC
1 AGCAATCATGAGGTCAAGTGATGATTGATTCATAG-AC
* * * *
266493 AGTAATCGTG-GGTTCAAGTAATGATTGATTCATTGAC
1 AGCAATCATGAGG-TCAAGTGATGATTGATTCATAGAC
* * * *
266530 AGTAATCATGAGG-CAAAGTGATTACTGATTCATAGAT
1 AGCAATCATGAGGTC-AAGTGATGATTGATTCATAGAC
* * *
266567 AGCAATCATGAGGTCGAGTGATGATTTATTCATTGAC
1 AGCAATCATGAGGTCAAGTGATGATTGATTCATAGAC
** * * * * *
266604 AGTTATCATGAGG-CAAATTGATTATTAATTCATTGAT
1 AGCAATCATGAGGTC-AAGTGATGATTGATTCATAGAC
* * * * *
266641 AGTAATAATGAGGCCAAGTGTTGATTGATTCATTGAC
1 AGCAATCATGAGGTCAAGTGATGATTGATTCATAGAC
* * *
266678 AGTAATCATGAAG-CAAAGTGATGACTGATTCATAGAC
1 AGCAATCATGAGGTC-AAGTGATGATTGATTCATAGAC
* *
266715 AGCAATCATGAGATCGAA-TGATGATTTATTCA-ATGAC
1 AGCAATCATGAGGTC-AAGTGATGATTGATTCATA-GAC
* ** * * * *
266752 AGTACCCGTGAGGTCGACTGATGATTGATTCATAGAT
1 AGCAATCATGAGGTCAAGTGATGATTGATTCATAGAC
* * * *
266789 AGAAATCATGAGGTCGAGTGATGAGAT-ATTCATAGAT
1 AGCAATCATGAGGTCAAGTGATGA-TTGATTCATAGAC
*
266826 ACCAATCATGAGG-CAAAGTGATGATTGATTCA
1 AGCAATCATGAGGTC-AAGTGATGATTGATTCA
266858 GTGAAAGTAA
Statistics
Matches: 696, Mismatches: 148, Indels: 80
0.75 0.16 0.09
Matches are distributed among these distances:
35 4 0.01
36 67 0.10
37 547 0.79
38 49 0.07
39 29 0.04
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (37 bp):
AGCAATCATGAGGTCAAGTGATGATTGATTCATAGAC
Found at i:266070 original size:111 final size:111
Alignment explanation
Indices: 265953--266869 Score: 745
Period size: 111 Copynumber: 8.3 Consensus size: 111
265943 CTTAAGGTCG
* * *
265953 AGTGATGATTGATTAATTGACAGTAATCATGAGGCAAAGTTATGATTGATTCATAGATAGCAAT-
1 AGTGATGATTGATTCATTGACAGTAATCATGAGGCAAAGTGATGATTGATTCATAGACAGCAATC
* * *
266017 ATTAAGGTCGAGTGATGATTGATTCATAGCCAGCAATCATGAGGCAA
66 A-TGAGGTCAAGTGATGATTGATTCATAGACAGCAATCATGAGGCAA
* * * * *
266064 AATGATGCTTGATTCATAGACAGTAATCATGAGGCAAAATGATGATTGATTCATAGACGGCAATC
1 AGTGATGATTGATTCATTGACAGTAATCATGAGGCAAAGTGATGATTGATTCATAGACAGCAATC
* *
266129 GTGAGGTCAAGAT-ATGATTGATTC-TAGACAGCAATCATGAGGTC-G
66 ATGAGGTCAAG-TGATGATTGATTCATAGACAGCAATCATGAGG-CAA
* * * * * * *
266174 AGTGATGATTGATTCATT-ATCGGTTATCATGAGGCAAAGTGATGATTAATTTAATTGAAAGCAG
1 AGTGATGATTGATTCATTGA-CAGTAATCATGAGGCAAAGTGATGATTGA-TTCATAGACAGCAA
* * *
266238 TCATGAGG-CAAAATGATGATTGATTCATATAGATAGCAATCATGGGGCAA
64 TCATGAGGTC-AAGTGATGATTGATTC--ATAGACAGCAATCATGAGGCAA
* * * * * * * * *
266288 AGTGATGACTGATTCATAGACAGCAAT-ATTAAAGTC-GAGTGATGATTGATTCAAAGCCAGGAA
1 AGTGATGATTGATTCATTGACAGTAATCA-T-GAGGCAAAGTGATGATTGATTCATAGACAGCAA
* * * * *
266351 TCATGAGATCAAGTGATGATTAATTCATTGACAGTAATCATGAGGCCA
64 TCATGAGGTCAAGTGATGATTGATTCATAGACAGCAATCATGAGGCAA
* * * * * * * * * * *
266399 AGTGAAT-TTTGATTCAGTGAAAGAAATTA-AAGGTC-GATTGATGACTGATTCATTGACAGTAA
1 AGTG-ATGATTGATTCATTGACAGTAATCATGAGG-CAAAGTGATGATTGATTCATAGACAGCAA
* * *
266461 TCATGATGTCAAGTGATGATTGATTCAT-GAACAGTAATCGTG-GGTTC-A
64 TCATGAGGTCAAGTGATGATTGATTCATAG-ACAGCAATCATGAGG--CAA
* * * *
266509 AGTAATGATTGATTCATTGACAGTAATCATGAGGCAAAGTGATTACTGATTCATAGATAGCAATC
1 AGTGATGATTGATTCATTGACAGTAATCATGAGGCAAAGTGATGATTGATTCATAGACAGCAATC
* * * **
266574 ATGAGGTCGAGTGATGATTTATTCATTGACAGTTATCATGAGGCAA
66 ATGAGGTCAAGTGATGATTGATTCATAGACAGCAATCATGAGGCAA
* * * * * * * * *
266620 ATTGATTATTAATTCATTGATAGTAATAATGAGGCCAAGTGTTGATTGATTCATTGACAGTAATC
1 AGTGATGATTGATTCATTGACAGTAATCATGAGGCAAAGTGATGATTGATTCATAGACAGCAATC
* * * *
266685 ATGAAG-CAAAGTGATGACTGATTCATAGACAGCAATCATGAGATCGA
66 ATGAGGTC-AAGTGATGATTGATTCATAGACAGCAATCATGAG-GCAA
* * ** * * * * *
266732 A-TGATGATTTATTCAATGACAGTACCCGTGAGGTC-GACTGATGATTGATTCATAGATAGAAAT
1 AGTGATGATTGATTCATTGACAGTAATCATGAGG-CAAAGTGATGATTGATTCATAGACAGCAAT
* * * *
266795 CATGAGGTCGAGTGATGAGAT-ATTCATAGATACCAATCATGAGGCAA
65 CATGAGGTCAAGTGATGA-TTGATTCATAGACAGCAATCATGAGGCAA
* *
266842 AGTGATGATTGATTCAGTGAAAGTAATC
1 AGTGATGATTGATTCATTGACAGTAATC
266870 TAAGGTCGTT
Statistics
Matches: 636, Mismatches: 137, Indels: 66
0.76 0.16 0.08
Matches are distributed among these distances:
109 9 0.01
110 144 0.23
111 387 0.61
112 13 0.02
113 30 0.05
114 49 0.08
115 4 0.01
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (111 bp):
AGTGATGATTGATTCATTGACAGTAATCATGAGGCAAAGTGATGATTGATTCATAGACAGCAATC
ATGAGGTCAAGTGATGATTGATTCATAGACAGCAATCATGAGGCAA
Found at i:294587 original size:19 final size:19
Alignment explanation
Indices: 294516--294585 Score: 86
Period size: 19 Copynumber: 3.6 Consensus size: 19
294506 GCATGGCAGG
* *
294516 CCATCAGATTTTAGCGTAAA
1 CCATCAGACTTTAGCGT-GA
*
294536 CCATCAGACTTTAGCATGA
1 CCATCAGACTTTAGCGTGA
* *
294555 CCATCGGACTTTGGCGTGA
1 CCATCAGACTTTAGCGTGA
294574 CCATCAGACTTT
1 CCATCAGACTTT
294586 GGAGTCTACA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 28 0.65
20 15 0.35
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.29
Consensus pattern (19 bp):
CCATCAGACTTTAGCGTGA
Found at i:296795 original size:17 final size:17
Alignment explanation
Indices: 296754--296795 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
296744 ACCAATCAAA
296754 AAAATTGTATCTATTGT
1 AAAATTGTATCTATTGT
* *
296771 ACATTTGTA-CATATTGT
1 AAAATTGTATC-TATTGT
296788 AAAATTGT
1 AAAATTGT
296796 CCATTGTTCT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (17 bp):
AAAATTGTATCTATTGT
Found at i:298074 original size:2 final size:2
Alignment explanation
Indices: 298067--298113 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
298057 ATCCCAGATG
298067 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
298109 CT CT C
1 CT CT C
298114 CAATAGTTAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:299541 original size:2 final size:2
Alignment explanation
Indices: 299530--299574 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
299520 TCTAATCTCT
299530 GA GA -A GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
299571 GA GA
1 GA GA
299575 AGGGGTAATT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:303863 original size:2 final size:2
Alignment explanation
Indices: 303856--303906 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
303846 TGGGTCAATT
303856 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G- GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
303897 GA GA GA GA GA
1 GA GA GA GA GA
303907 TTTCCTCATT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:305202 original size:11 final size:11
Alignment explanation
Indices: 305186--305210 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
305176 CTGGCTTTTT
305186 TATTATACATG
1 TATTATACATG
305197 TATTATACATG
1 TATTATACATG
305208 TAT
1 TAT
305211 ATCTTTAGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (11 bp):
TATTATACATG
Found at i:307573 original size:25 final size:25
Alignment explanation
Indices: 307519--307765 Score: 173
Period size: 25 Copynumber: 9.7 Consensus size: 25
307509 TATAGTGAAT
* ***
307519 CTATTACATTTATTCTGTGGCACTG
1 CTATTACATTTATTCTGTAGTGGTG
*
307544 CTATTACATTTATTCTGTGGTGGTGG
1 CTATTACATTTATTCTGTAGTGGT-G
* *
307570 TATTATTACATTTAATCTGTAGTGGTG
1 --CTATTACATTTATTCTGTAGTGGTG
* *
307597 TTATTACGTGTACTTTTTTCTGTAGTGGTG
1 CTATTAC----A-TTTATTCTGTAGTGGTG
*
307627 CT-TT-CACTTTTTTCTGTAGTGGTG
1 CTATTACA-TTTATTCTGTAGTGGTG
* *
307651 CTATT-CCTTT-TT-TTTAAGTGGTG
1 CTATTACATTTATTCTGT-AGTGGTG
* *
307674 TTATTACATTTATTCTGTAATGGTG
1 CTATTACATTTATTCTGTAGTGGTG
* *
307699 CTGTTAC-TTTCTTCTGTAGTGGTG
1 CTATTACATTTATTCTGTAGTGGTG
* * *
307723 TTATTACATTTATTCTGTGGTGTTG
1 CTATTACATTTATTCTGTAGTGGTG
* *
307748 TTATTACATTTAATCTGT
1 CTATTACATTTATTCTGT
307766 GGTGATATTA
Statistics
Matches: 183, Mismatches: 25, Indels: 28
0.78 0.11 0.12
Matches are distributed among these distances:
22 2 0.01
23 13 0.07
24 48 0.26
25 75 0.41
26 3 0.02
27 1 0.01
28 22 0.12
29 3 0.02
30 16 0.09
ACGTcount: A:0.17, C:0.12, G:0.19, T:0.51
Consensus pattern (25 bp):
CTATTACATTTATTCTGTAGTGGTG
Found at i:307577 original size:28 final size:28
Alignment explanation
Indices: 307545--307602 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
307535 GTGGCACTGC
* *
307545 TATTACATTTATTCTGTGGTGGTGGTAT
1 TATTACATTTAATCTGTAGTGGTGGTAT
*
307573 TATTACATTTAATCTGTAGTGGTGTTAT
1 TATTACATTTAATCTGTAGTGGTGGTAT
307601 TA
1 TA
307603 CGTGTACTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.22, C:0.07, G:0.21, T:0.50
Consensus pattern (28 bp):
TATTACATTTAATCTGTAGTGGTGGTAT
Found at i:307670 original size:23 final size:25
Alignment explanation
Indices: 307608--307740 Score: 127
Period size: 24 Copynumber: 5.5 Consensus size: 25
307598 TATTACGTGT
307608 ACTTTTTTCTGTAGTGGTGCT-TTC
1 ACTTTTTTCTGTAGTGGTGCTATTC
307632 ACTTTTTTCTGTAGTGGTGCTATTC
1 ACTTTTTTCTGTAGTGGTGCTATTC
*
307657 -CTTTTTT-T-TAAGTGGTGTTATT-
1 ACTTTTTTCTGT-AGTGGTGCTATTC
* * *
307679 ACATTTATTCTGTAATGGTGCTGTT-
1 AC-TTTTTTCTGTAGTGGTGCTATTC
* *
307704 ACTTTCTTCTGTAGTGGTGTTATT-
1 ACTTTTTTCTGTAGTGGTGCTATTC
*
307728 ACATTTATTCTGT
1 AC-TTTTTTCTGT
307741 GGTGTTGTTA
Statistics
Matches: 92, Mismatches: 10, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
22 1 0.01
23 13 0.14
24 53 0.58
25 24 0.26
26 1 0.01
ACGTcount: A:0.14, C:0.13, G:0.19, T:0.54
Consensus pattern (25 bp):
ACTTTTTTCTGTAGTGGTGCTATTC
Found at i:307729 original size:49 final size:48
Alignment explanation
Indices: 307611--307740 Score: 158
Period size: 49 Copynumber: 2.7 Consensus size: 48
307601 TACGTGTACT
* * * *
307611 TTTTTCTGTAGTGGTGCT-TT-CACTTTTTTCTGTAGTGGTGCTATTCC
1 TTTTTCTGTAGTGGTGTTATTACA-TTTATTCTGTAATGGTGCTATTAC
* *
307658 TTTTT-TTTAAGTGGTGTTATTACATTTATTCTGTAATGGTGCTGTTAC
1 TTTTTCTGT-AGTGGTGTTATTACATTTATTCTGTAATGGTGCTATTAC
307706 TTTCTTCTGTAGTGGTGTTATTACATTTATTCTGT
1 TTT-TTCTGTAGTGGTGTTATTACATTTATTCTGT
307741 GGTGTTGTTA
Statistics
Matches: 71, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
46 2 0.03
47 13 0.18
48 25 0.35
49 29 0.41
50 2 0.03
ACGTcount: A:0.14, C:0.12, G:0.19, T:0.55
Consensus pattern (48 bp):
TTTTTCTGTAGTGGTGTTATTACATTTATTCTGTAATGGTGCTATTAC
Found at i:307766 original size:25 final size:25
Alignment explanation
Indices: 307711--307778 Score: 91
Period size: 25 Copynumber: 2.7 Consensus size: 25
307701 GTTACTTTCT
* * *
307711 TCTGTAGTGGTGTTATTACATTTAT
1 TCTGTGGTGATGTTATTACATTTAA
*
307736 TCTGTGGTGTTGTTATTACATTTAA
1 TCTGTGGTGATGTTATTACATTTAA
*
307761 TCTGTGGTGATATTATTA
1 TCTGTGGTGATGTTATTA
307779 AGGCCCCGCA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.21, C:0.07, G:0.21, T:0.51
Consensus pattern (25 bp):
TCTGTGGTGATGTTATTACATTTAA
Found at i:308066 original size:31 final size:31
Alignment explanation
Indices: 308031--308098 Score: 136
Period size: 31 Copynumber: 2.2 Consensus size: 31
308021 ACTATGCATA
308031 AGAATGAATGGGCAAAGAGAGATAACTGCTG
1 AGAATGAATGGGCAAAGAGAGATAACTGCTG
308062 AGAATGAATGGGCAAAGAGAGATAACTGCTG
1 AGAATGAATGGGCAAAGAGAGATAACTGCTG
308093 AGAATG
1 AGAATG
308099 TTACCATTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.43, C:0.09, G:0.32, T:0.16
Consensus pattern (31 bp):
AGAATGAATGGGCAAAGAGAGATAACTGCTG
Found at i:309451 original size:29 final size:29
Alignment explanation
Indices: 309419--309476 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
309409 GAACGATGTT
309419 GAATAATGGTTGAAGGAGGTTTTAACCAA
1 GAATAATGGTTGAAGGAGGTTTTAACCAA
309448 GAATAATGGTTGAAGGAGGTTTTAACCAA
1 GAATAATGGTTGAAGGAGGTTTTAACCAA
309477 TTGAATTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.07, G:0.28, T:0.28
Consensus pattern (29 bp):
GAATAATGGTTGAAGGAGGTTTTAACCAA
Found at i:321841 original size:25 final size:24
Alignment explanation
Indices: 321812--321859 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
321802 TAAAAAGTGG
321812 TTTTATAGAAATAGTAACTAAAACT
1 TTTTA-AGAAATAGTAACTAAAACT
* * *
321837 TTTTAATAAATAGTTAGTAAAAC
1 TTTTAAGAAATAGTAACTAAAAC
321860 CTATACACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.38
Consensus pattern (24 bp):
TTTTAAGAAATAGTAACTAAAACT
Found at i:326276 original size:245 final size:244
Alignment explanation
Indices: 325846--326334 Score: 951
Period size: 245 Copynumber: 2.0 Consensus size: 244
325836 TTAGCAGTGA
*
325846 CAGCGGCGGGTGTCAAAGTGACTGAACCCCCTTCATTAACTGACAATTCTATCCCTTTGATGATA
1 CAGCGGCGGGTGTCAAAGTGACTGAACCCCCTTCATTAACGGACAATTCTATCCCTTTGATGATA
325911 GCTGGTTTTGAGTTATCAACTGGAGTTATCGTGATGTTCAAATCATACACTGGAAGATCACCTGT
66 GCTGGTTTTGAGTTATCAACTGGAGTTATCGTGATGTTCAAATCATACACTGGAAGATCACCTGT
325976 CGCCATGAAGTTCTGATTGGATACAATAAAAGTTACAGTGTCTTTTATCATATTATTGCCCACCT
131 CGCCATGAAGTTCTGATTGGATACAATAAAAGTTACAGTGTCTTTTATCATATTATTGCCCACCT
326041 CTCCGCCTGTGTGGATGTACTTTACTTTGTTGCCATTAACGTCTTTCTG
196 CTCCGCCTGTGTGGATGTACTTTACTTTGTTGCCATTAACGTCTTTCTG
326090 NCAGCGGCGGGTGTCAAAGTGACTGAACCCCCTTCATTAACGGACAATTCTATCCCTTTGATGAT
1 -CAGCGGCGGGTGTCAAAGTGACTGAACCCCCTTCATTAACGGACAATTCTATCCCTTTGATGAT
*
326155 AGCTGGTTTTGAGTTATCAACTGGAGTTATCGTGATGTTCAAATCATATACTGGAAGATCACCTG
65 AGCTGGTTTTGAGTTATCAACTGGAGTTATCGTGATGTTCAAATCATACACTGGAAGATCACCTG
326220 TCGCCATGAAGTTCTGATTGGATACAATAAAAGTTACAGTGTCTTTTATCATATTATTGCCCACC
130 TCGCCATGAAGTTCTGATTGGATACAATAAAAGTTACAGTGTCTTTTATCATATTATTGCCCACC
326285 TCTCCGCCTGTGTGGATGTACTTTACTTTGTTGCCATTAACGTCTTTCTG
195 TCTCCGCCTGTGTGGATGTACTTTACTTTGTTGCCATTAACGTCTTTCTG
326335 TGTAAACTTG
Statistics
Matches: 242, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
245 242 1.00
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.34
Consensus pattern (244 bp):
CAGCGGCGGGTGTCAAAGTGACTGAACCCCCTTCATTAACGGACAATTCTATCCCTTTGATGATA
GCTGGTTTTGAGTTATCAACTGGAGTTATCGTGATGTTCAAATCATACACTGGAAGATCACCTGT
CGCCATGAAGTTCTGATTGGATACAATAAAAGTTACAGTGTCTTTTATCATATTATTGCCCACCT
CTCCGCCTGTGTGGATGTACTTTACTTTGTTGCCATTAACGTCTTTCTG
Found at i:357890 original size:21 final size:22
Alignment explanation
Indices: 357866--357915 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
357856 GCCATTAATA
357866 TATTTTTAGTT-ATTTATTTTT
1 TATTTTTAGTTCATTTATTTTT
* *
357887 TATTTTT-TTTCATTTTTTTTT
1 TATTTTTAGTTCATTTATTTTT
*
357908 TTTTTTTA
1 TATTTTTA
357916 CAAATTTTCG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.82
Consensus pattern (22 bp):
TATTTTTAGTTCATTTATTTTT
Found at i:357891 original size:11 final size:10
Alignment explanation
Indices: 357875--357914 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
357865 ATATTTTTAG
357875 TTATTTATTTT
1 TTATTT-TTTT
357886 TTATTTTTTT
1 TTATTTTTTT
*
357896 TCATTTTTTT
1 TTATTTTTTT
357906 TT-TTTTTTT
1 TTATTTTTTT
357915 ACAAATTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
9 7 0.26
10 14 0.52
11 6 0.22
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.88
Consensus pattern (10 bp):
TTATTTTTTT
Found at i:357913 original size:17 final size:17
Alignment explanation
Indices: 357881--357912 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
357871 TTAGTTATTT
357881 ATTTTTTATTTTTTTTC
1 ATTTTTTATTTTTTTTC
357898 ATTTTTT-TTTTTTTT
1 ATTTTTTATTTTTTTT
357913 TTACAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.09, C:0.03, G:0.00, T:0.88
Consensus pattern (17 bp):
ATTTTTTATTTTTTTTC
Found at i:357923 original size:19 final size:19
Alignment explanation
Indices: 357881--357923 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
357871 TTAGTTATTT
357881 ATTTTTTATTTTTTTTC-A
1 ATTTTTTATTTTTTTTCAA
* *
357899 TTTTTTTTTTTTTTTTACAA
1 ATTTTTTATTTTTTTT-CAA
357919 ATTTT
1 ATTTT
357924 CGATCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 14 0.70
19 1 0.05
20 5 0.25
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (19 bp):
ATTTTTTATTTTTTTTCAA
Found at i:360308 original size:200 final size:200
Alignment explanation
Indices: 359965--360362 Score: 780
Period size: 200 Copynumber: 2.0 Consensus size: 200
359955 TTAGTGAAAA
359965 GTTAGAATAATAAGATATTATTGTTCTCATTGCATAATACTTTGTGGTTTATGTACGTTACAACT
1 GTTAGAATAATAAGATATTATTGTTCTCATTGCATAATACTTTGTGGTTTATGTACGTTACAACT
360030 TCACCATTGCTCGATTTTTTCTTATCATTGAGTTGTATTACAATAAAACAATTGCTTGTAATCTT
66 TCACCATTGCTCGATTTTTTCTTATCATTGAGTTGTATTACAATAAAACAATTGCTTGTAATCTT
360095 GTGGTGCACTGTATGTTTTTGCAGTTGAACCTAACCGTCAGATGCACTGATTCATAAGTAAGGCT
131 GTGGTGCACTGTATGTTTTTGCAGTTGAACCTAACCGTCAGATGCACTGATTCATAAGTAAGGCT
360160 TTTGT
196 TTTGT
360165 GTTAGAATAATAAGATATTATTGTTCTCATTGCATAATACTTTGTGGTTTATGTACGTTACAACT
1 GTTAGAATAATAAGATATTATTGTTCTCATTGCATAATACTTTGTGGTTTATGTACGTTACAACT
360230 TCACCATTGCTCGATTTTTTCTTATCATTGAGTTGTATTACAATAAAACAATTTG-TTGTAATCT
66 TCACCATTGCTCGATTTTTTCTTATCATTGAGTTGTATTACAATAAAACAA-TTGCTTGTAATCT
360294 TGTGGTGCACTGTATGTTTTTGCAGTTGAACCTAACCGTCAGATGCACTGATTCATAAGTAAGGC
130 TGTGGTGCACTGTATGTTTTTGCAGTTGAACCTAACCGTCAGATGCACTGATTCATAAGTAAGGC
360359 TTTT
195 TTTT
360363 TTTTTTTTTT
Statistics
Matches: 197, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
200 194 0.98
201 3 0.02
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (200 bp):
GTTAGAATAATAAGATATTATTGTTCTCATTGCATAATACTTTGTGGTTTATGTACGTTACAACT
TCACCATTGCTCGATTTTTTCTTATCATTGAGTTGTATTACAATAAAACAATTGCTTGTAATCTT
GTGGTGCACTGTATGTTTTTGCAGTTGAACCTAACCGTCAGATGCACTGATTCATAAGTAAGGCT
TTTGT
Found at i:360365 original size:1 final size:1
Alignment explanation
Indices: 360359--360399 Score: 64
Period size: 1 Copynumber: 41.0 Consensus size: 1
360349 TAAGTAAGGC
* *
360359 TTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTCTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
360400 AATGGTAGAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.02, G:0.02, T:0.95
Consensus pattern (1 bp):
T
Found at i:362534 original size:3 final size:3
Alignment explanation
Indices: 362526--362564 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
362516 TTGTAAAGGA
* *
362526 AAC AAC AAC AAC AAA AAC AAC AAC GAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
362565 TCAGCCGACT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.67, C:0.31, G:0.03, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:377663 original size:1 final size:1
Alignment explanation
Indices: 377630--377654 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
377620 AAGTACATGA
377630 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
377655 ACATTTTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:383816 original size:40 final size:40
Alignment explanation
Indices: 383772--383996 Score: 227
Period size: 40 Copynumber: 5.6 Consensus size: 40
383762 CTGACGGGTC
* *
383772 CCAAGGGATTCAACAACATCGTAAGTACAGAAATCATGTT
1 CCAAGGGATTCAACAACATCATAAGTACAGAAATAATGTT
* *
383812 CCAAGGGATTCAACAAAATCATAAGTGCAGAAATAATGTT
1 CCAAGGGATTCAACAACATCATAAGTACAGAAATAATGTT
* * * *
383852 CCAATGGATTCAACAACATCATAAGTACAGACATACTGTC
1 CCAAGGGATTCAACAACATCATAAGTACAGAAATAATGTT
* * * * *
383892 CCTAGGGATTCAACAACATCGTTAGTACAGAAATACTATT
1 CCAAGGGATTCAACAACATCATAAGTACAGAAATAATGTT
* ** ** * **
383932 TCAAGATATTCTTCAACATCATAAGTACAGAGATAATGCC
1 CCAAGGGATTCAACAACATCATAAGTACAGAAATAATGTT
* *
383972 CCATA-AGATTCAACAACATCGTAAG
1 CCA-AGGGATTCAACAACATCATAAG
383997 CATACAGATA
Statistics
Matches: 149, Mismatches: 35, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
40 148 0.99
41 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (40 bp):
CCAAGGGATTCAACAACATCATAAGTACAGAAATAATGTT
Found at i:383982 original size:120 final size:120
Alignment explanation
Indices: 383769--383996 Score: 291
Period size: 120 Copynumber: 1.9 Consensus size: 120
383759 GCTCTGACGG
*
383769 GTCCCAAGGGATTCAACAACATCGTAAGTACAGAAATCATGTTCCAAGGGATTCAACAAAATCAT
1 GTCCCAAGGGATTCAACAACATCGTAAGTACAGAAATCATGTTCCAAGAGATTCAACAAAATCAT
* ** *
383834 AAGTGCAGAAATAATGTTCCAATGGATTCAACAACATCATAAGTACAGACATACT
66 AAGTACAGAAATAATGCCCCAATAGATTCAACAACATCATAAGTACAGACATACT
* * * ** *
383889 GTCCCTAGGGATTCAACAACATCGTTAGTACAGAAATACTAT-TT-CAAGATATTCTTCAACATC
1 GTCCCAAGGGATTCAACAACATCGTAAGTACAGAAAT-C-ATGTTCCAAGAGATTCAACAAAATC
* *
383952 ATAAGTACAGAGATAATGCCCC-ATAAGATTCAACAACATCGTAAG
64 ATAAGTACAGAAATAATGCCCCAAT-AGATTCAACAACATCATAAG
383997 CATACAGATA
Statistics
Matches: 92, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
119 2 0.02
120 85 0.92
121 3 0.03
122 2 0.02
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (120 bp):
GTCCCAAGGGATTCAACAACATCGTAAGTACAGAAATCATGTTCCAAGAGATTCAACAAAATCAT
AAGTACAGAAATAATGCCCCAATAGATTCAACAACATCATAAGTACAGACATACT
Found at i:390267 original size:19 final size:19
Alignment explanation
Indices: 390243--390281 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
390233 ATATCGCTGG
390243 AATACAATTAATTAGACGA
1 AATACAATTAATTAGACGA
390262 AATACAATTAATTAGACGA
1 AATACAATTAATTAGACGA
390281 A
1 A
390282 CACTGCTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.26
Consensus pattern (19 bp):
AATACAATTAATTAGACGA
Found at i:394418 original size:2 final size:2
Alignment explanation
Indices: 394411--394467 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
394401 TGGAGGTAAT
*
394411 GA GA GA GA GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
394453 GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA G
394468 TTCAATATAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:407830 original size:2 final size:2
Alignment explanation
Indices: 407823--407863 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
407813 TAAAAACTCN
407823 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
407864 GTATATCTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:408660 original size:3 final size:3
Alignment explanation
Indices: 408652--408696 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
408642 AGATTGTTTC
*
408652 GTT GTT GTT GTT GTT GTT GTT GTT GCT GTT GTT GTT GTT GTT GTT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
408697 TGGTTTTTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.00, C:0.02, G:0.33, T:0.64
Consensus pattern (3 bp):
GTT
Found at i:410049 original size:7 final size:6
Alignment explanation
Indices: 410022--410060 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
410012 TCTTTAATCG
410022 TTTG-T TTTGTT TTTGTT TTTGTT ATTTGTT ATTTGTT TT
1 TTTGTT TTTGTT TTTGTT TTTGTT -TTTGTT -TTTGTT TT
410061 GCCTTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 4 0.12
6 15 0.47
7 13 0.41
ACGTcount: A:0.05, C:0.00, G:0.15, T:0.79
Consensus pattern (6 bp):
TTTGTT
Found at i:416643 original size:14 final size:14
Alignment explanation
Indices: 416624--416657 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
416614 GATTTTTAGT
416624 CTTCAAATAGTTAA
1 CTTCAAATAGTTAA
416638 CTTCAAATAGTTAA
1 CTTCAAATAGTTAA
*
416652 CGTCAA
1 CTTCAA
416658 CTGCATTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (14 bp):
CTTCAAATAGTTAA
Found at i:419180 original size:11 final size:11
Alignment explanation
Indices: 419164--419200 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
419154 ATATTGTGTA
419164 TTTTCAATTAC
1 TTTTCAATTAC
419175 TTTTCAATTAC
1 TTTTCAATTAC
* *
419186 ATCTCAATTAC
1 TTTTCAATTAC
419197 TTTT
1 TTTT
419201 TTTCCAAGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.27, C:0.19, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTCAATTAC
Found at i:419793 original size:32 final size:33
Alignment explanation
Indices: 419742--419803 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
419732 AAATAAAACT
*
419742 AAAGTATTTGAAATGTAATTAATTACATTTATC
1 AAAGTAATTGAAATGTAATTAATTACATTTATC
*
419775 AAAGTAATTGAGA-GTAATTAATTACATTT
1 AAAGTAATTGAAATGTAATTAATTACATTT
419804 TAAAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 16 0.59
33 11 0.41
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (33 bp):
AAAGTAATTGAAATGTAATTAATTACATTTATC
Found at i:423776 original size:99 final size:96
Alignment explanation
Indices: 423639--424451 Score: 719
Period size: 99 Copynumber: 8.3 Consensus size: 96
423629 TTGTTTCTTA
** * * * * **
423639 TTGTCACAAAAATTAATATCTGCTCCTTTAG-CTAATAAAAGTTGAATAATGCTTCCATGTCAGC
1 TTGTCACATGAATTAATATCTGCTCCTTT-GTCTAATAAAAGTTGTACAGTGCTTTCATGTCCCC
* *
423703 ATTCATTGTCTTTATATAGAGGAATTTATTTGT
65 ATTCATTGGCTTTATGTAGAGG-ATTTATTTGT
*
423736 TTGTGCCACATGAATTAATATCTTCTCCTTTGTCTAATAAAAGTTGTACAGTGCTTTCATGTCCC
1 TTGT--CACATGAATTAATATCTGCTCCTTTGTCTAATAAAAGTTGTACAGTGCTTTCATGTCCC
* *
423801 CATTCACTGGCTTTATGTAGAGGAGTTACTTTG-
64 CATTCATTGGCTTTATGTAGAGGATTTA-TTTGT
* * * * *
423834 -TGTCACATGAATTAATATCTGCTCCTTTATTTAATAAAAGTTGTACAGTGTTTTTATGTCCCCT
1 TTGTCACATGAATTAATATCTGCTCCTTTGTCTAATAAAAGTTGTACAGTGCTTTCATGTCCCCA
* * *
423898 TTCACTAGCTTTATGTAGAGGAGTTTCTTTGTT
66 TTCATTGGCTTTATGTAGAGGA-TTTATTTG-T
* * * * *
423931 TGTGTTACACGAATTAATATCTTCTCCTTTGTCTAATAAAAGTTGTACAATGCTATCATGTCCCC
1 T-TGTCACATGAATTAATATCTGCTCCTTTGTCTAATAAAAGTTGTACAGTGCTTTCATGTCCCC
* *
423996 ATTCACTGGCTTTATGTAGAGGAGTTACTTTG-
65 ATTCATTGGCTTTATGTAGAGGATTTA-TTTGT
* *
424028 -TGTCACATGAATTAATATTTGCTCCTTTGTCTAATAAAAGTTGTACAGTGCTTTCATGT-CCCG
1 TTGTCACATGAATTAATATCTGCTCCTTTGTCTAATAAAAGTTGTACAGTGCTTTCATGTCCCCA
* * * *
424091 TTCTATTGGCTTTTTGTAAAGGGGTTTCTTTGT
66 TTC-ATTGGCTTTATGTAGA-GGATTTATTTGT
* * * **
424124 AGTTGTCATATGAATTAATATCTGCTCCTTTATCTAATAAAAGCTGTACAGTGCTTTCGCGTCCC
1 --TTGTCACATGAATTAATATCTGCTCCTTTGTCTAATAAAAGTTGTACAGTGCTTTCATGTCCC
* **
424189 CATTCACTGGCTTTATGTAGAGGAGTTTCGTTGTT
64 CATTCATTGGCTTTATGTAGAGGA-TTTATTTG-T
* * * * * * * * *
424224 TATATCACATAAATAAATATCTGCTCCTTTATTTAATATAAGTTGTAAAGTGCTTTCACTTTGCA
1 T-TGTCACATGAATTAATATCTGCTCCTTTGTCTAATAAAAGTTGTACAGTGCTTTCA-TGT-CC
** * * * *
424289 GTATAC-TT-GCTTTGTGGAGAGGAGTTTCTTTGT
63 CCATTCATTGGCTTTATGTAGAGGA-TTTATTTGT
* * * * * *
424322 TTAGGTCACATAAATTGATAGCTGCTCCTTTATTTAATAAAAGTTGTACAGTGCTTTTATGTCCT
1 TT--GTCACATGAATTAATATCTGCTCCTTTGTCTAATAAAAGTTGTACAGTGCTTTCATGTCC-
* * *
424387 CC-TTTACTT-GCTTTATGTAAAGGAGTTTCTTTGTT
63 CCATTCA-TTGGCTTTATGTAGAGGA-TTTATTTG-T
*
424422 TGTGTCACATGAATTGATATCTGCTCCTTT
1 T-TGTCACATGAATTAATATCTGCTCCTTT
424452 TTNTTGAAGA
Statistics
Matches: 590, Mismatches: 97, Indels: 56
0.79 0.13 0.08
Matches are distributed among these distances:
94 6 0.01
95 150 0.25
96 6 0.01
97 10 0.02
98 14 0.02
99 388 0.66
100 11 0.02
101 5 0.01
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.42
Consensus pattern (96 bp):
TTGTCACATGAATTAATATCTGCTCCTTTGTCTAATAAAAGTTGTACAGTGCTTTCATGTCCCCA
TTCATTGGCTTTATGTAGAGGATTTATTTGT
Found at i:423969 original size:194 final size:195
Alignment explanation
Indices: 423649--424451 Score: 886
Period size: 194 Copynumber: 4.1 Consensus size: 195
423639 TTGTCACAAA
* * * * * ** *
423649 AATTAATATCTGCTCCTTTAGCTAATAAAAGTTGAATAATGCTTCCATGTCAGCATTCA-TTGTC
1 AATTAATATCTGCTCCTTTATCTAATAAAAGTTGTACAGTGCTTTCATGTCCCCTTTCACTTG-C
* * * * * *
423713 TTTATATAGAGGAATTTATTTGTTTGTGCCACATGAATTAATATCTTCTCCTTTGTCTAATAAAA
65 TTTATGTAGAGGAGTTTCTTTGTTTGTGTCACATGAATTAATATCTGCTCCTTTATCTAATAAAA
423778 GTTGTACAGTGCTTTCATGTCCCCATTCACTGGCTTTATGTAGAGGAGTTAC-TTTGTGTCACAT
130 GTTGTACAGTGCTTTCATGTCCCCATTCACTGGCTTTATGTAGAGGAGTTACTTTTGTGTCACAT
423842 G
195 G
* * * *
423843 AATTAATATCTGCTCCTTTATTTAATAAAAGTTGTACAGTGTTTTTATGTCCCCTTTCACTAGCT
1 AATTAATATCTGCTCCTTTATCTAATAAAAGTTGTACAGTGCTTTCATGTCCCCTTTCACTTGCT
* * * *
423908 TTATGTAGAGGAGTTTCTTTGTTTGTGTTACACGAATTAATATCTTCTCCTTTGTCTAATAAAAG
66 TTATGTAGAGGAGTTTCTTTGTTTGTGTCACATGAATTAATATCTGCTCCTTTATCTAATAAAAG
* *
423973 TTGTACAATGCTATCATGTCCCCATTCACTGGCTTTATGTAGAGGAGTTAC-TTTGTGTCACATG
131 TTGTACAGTGCTTTCATGTCCCCATTCACTGGCTTTATGTAGAGGAGTTACTTTTGTGTCACATG
* * *
424037 AATTAATATTTGCTCCTTTGTCTAATAAAAGTTGTACAGTGCTTTCATGT-CCCGTTCTA-TTGG
1 AATTAATATCTGCTCCTTTATCTAATAAAAGTTGTACAGTGCTTTCATGTCCCCTTTC-ACTT-G
* * * * *
424100 CTTTTTGTAAAGGGGTTTCTTTG-TAGTTGTCATATGAATTAATATCTGCTCCTTTATCTAATAA
64 CTTTATGTAGAGGAGTTTCTTTGTTTG-TGTCACATGAATTAATATCTGCTCCTTTATCTAATAA
* ** * * *
424164 AAGCTGTACAGTGCTTTCGCGTCCCCATTCACTGGCTTTATGTAGAGGAGTTTCGTTGTTTATAT
128 AAGTTGTACAGTGCTTTCATGTCCCCATTCACTGGCTTTATGTAGAGGAGTTAC--T-TTTGTGT
*
424229 CACATA
190 CACATG
* * * * * * ** *
424235 AATAAATATCTGCTCCTTTATTTAATATAAGTTGTAAAGTGCTTTCACTTTGCAGTAT-ACTTGC
1 AATTAATATCTGCTCCTTTATCTAATAAAAGTTGTACAGTGCTTTCA-TGTCCCCTTTCACTTGC
* * * * * *
424299 TTTGTGGAGAGGAGTTTCTTTGTTTAG-GTCACATAAATTGATAGCTGCTCCTTTATTTAATAAA
65 TTTATGTAGAGGAGTTTCTTTGTTT-GTGTCACATGAATTAATATCTGCTCCTTTATCTAATAAA
* * * * *
424363 AGTTGTACAGTGCTTTTATGTCCTCC-TTTACTTGCTTTATGTAAAGGAGTTTCTTTGTTTGTGT
129 AGTTGTACAGTGCTTTCATGTCC-CCATTCACTGGCTTTATGTAGAGGAGTTAC--T-TTTGTGT
424427 CACATG
190 CACATG
*
424433 AATTGATATCTGCTCCTTT
1 AATTAATATCTGCTCCTTT
424452 TTNTTGAAGA
Statistics
Matches: 516, Mismatches: 79, Indels: 24
0.83 0.13 0.04
Matches are distributed among these distances:
193 9 0.02
194 318 0.62
195 2 0.00
198 177 0.34
199 7 0.01
200 3 0.01
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.42
Consensus pattern (195 bp):
AATTAATATCTGCTCCTTTATCTAATAAAAGTTGTACAGTGCTTTCATGTCCCCTTTCACTTGCT
TTATGTAGAGGAGTTTCTTTGTTTGTGTCACATGAATTAATATCTGCTCCTTTATCTAATAAAAG
TTGTACAGTGCTTTCATGTCCCCATTCACTGGCTTTATGTAGAGGAGTTACTTTTGTGTCACATG
Found at i:424156 original size:293 final size:291
Alignment explanation
Indices: 423616--424451 Score: 890
Period size: 293 Copynumber: 2.8 Consensus size: 291
423606 TAACCGGCGA
* * *
423616 TATGTAAAGGAGTTT-GTT-TCTTATTGTCACAAAAATTAATATCTGCTCCTTTAG-CTAATAAA
1 TATGTAGAGGAGTTTCGTTGT-TTA-TATCACACAAATTAATATCTGCTCCTTT-GTCTAATAAA
* * * * *
423678 AGTTGAATAATGCTTCCATGTCAGCATTCATTGTCTTTATATAGAGGAATTTA-TTTGTTTGTGC
63 AGTTGTA-AATGCTT-CATGTCAGCATTCACTGGCTTTATGTAGAGG-AGTTACTTTG-TTGT--
423742 CACATGAATTAATATCTT-CTCCTTTGTCTAATAAAAGTTGTACAGTGCTTTCATGTCCCCATTC
122 CACATGAATTAATAT-TTGCTCCTTTGTCTAATAAAAGTTGTACAGTGCTTTCATGT-CCCATTC
* * * *
423806 -ACTGGCTTTATGTAGAGGAGTTAC-TT-TG-TGTCACATGAATTAATATCTGCTCCTTTATTTA
185 TATTGGCTTTATGTAAAGGAGTTTCTTTGTGTTGTCACATGAATTAATATCTGCTCCTTTATCTA
* * * * *
423867 ATAAAAGTTGTACAGTGTTTTTATGTCCCCTTTCACTAGCTT
250 ATAAAAGCTGTACAGTGCTTTCACGTCCCCATTCACTAGCTT
* * * * * *
423909 TATGTAGAGGAGTTTCTTTGTTTGTGTTACACGAATTAATATCTTCTCCTTTGTCTAATAAAAGT
1 TATGTAGAGGAGTTTCGTTGTTTATATCACACAAATTAATATCTGCTCCTTTGTCTAATAAAAGT
**
423974 TGTACAATGCTATCATGTCCCCATTCACTGGCTTTATGTAGAGGAGTTACTTTG-TGTCACATGA
66 TGTA-AATGCT-TCATGTCAGCATTCACTGGCTTTATGTAGAGGAGTTACTTTGTTGTCACATGA
*
424038 ATTAATATTTGCTCCTTTGTCTAATAAAAGTTGTACAGTGCTTTCATGTCCCGTTCTATTGGCTT
129 ATTAATATTTGCTCCTTTGTCTAATAAAAGTTGTACAGTGCTTTCATGTCCCATTCTATTGGCTT
* * *
424103 TTTGTAAAGGGGTTTCTTTGTAGTTGTCATATGAATTAATATCTGCTCCTTTATCTAATAAAAGC
194 TATGTAAAGGAGTTTCTTTGT-GTTGTCACATGAATTAATATCTGCTCCTTTATCTAATAAAAGC
* *
424168 TGTACAGTGCTTTCGCGTCCCCATTCACTGGCTT
258 TGTACAGTGCTTTCACGTCCCCATTCACTAGCTT
* * * * *
424202 TATGTAGAGGAGTTTCGTTGTTTATATCACATAAATAAATATCTGCTCCTTTATTTAATATAAGT
1 TATGTAGAGGAGTTTCGTTGTTTATATCACACAAATTAATATCTGCTCCTTTGTCTAATAAAAGT
* * * * * *
424267 TGTAAAGTGCTTTCACTTTGCAGTA-T-ACTTGCTTTGTGGAGAGGAGTTTCTTTGTTTAGGTCA
66 TGTAAA-TGC-TTCA-TGT-CAGCATTCACTGGCTTTATGTAGAGGAGTTACTTTG-TT--GTCA
* * ** * * * *
424330 CATAAATTGATAGCTGCTCCTTTATTTAATAAAAGTTGTACAGTGCTTTTATGTCCTCCTT-TAC
124 CATGAATTAATATTTGCTCCTTTGTCTAATAAAAGTTGTACAGTGCTTTCATGTCC-CATTCTA-
* *
424394 TT-GCTTTATGTAAAGGAGTTTCTTTGTTTGTGTCACATGAATTGATATCTGCTCCTTT
187 TTGGCTTTATGTAAAGGAGTTTCTTTGTGT-TGTCACATGAATTAATATCTGCTCCTTT
424452 TTNTTGAAGA
Statistics
Matches: 459, Mismatches: 62, Indels: 40
0.82 0.11 0.07
Matches are distributed among these distances:
288 8 0.02
289 72 0.16
290 2 0.00
291 4 0.01
292 8 0.02
293 242 0.53
294 9 0.02
295 4 0.01
296 1 0.00
297 104 0.23
298 5 0.01
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.42
Consensus pattern (291 bp):
TATGTAGAGGAGTTTCGTTGTTTATATCACACAAATTAATATCTGCTCCTTTGTCTAATAAAAGT
TGTAAATGCTTCATGTCAGCATTCACTGGCTTTATGTAGAGGAGTTACTTTGTTGTCACATGAAT
TAATATTTGCTCCTTTGTCTAATAAAAGTTGTACAGTGCTTTCATGTCCCATTCTATTGGCTTTA
TGTAAAGGAGTTTCTTTGTGTTGTCACATGAATTAATATCTGCTCCTTTATCTAATAAAAGCTGT
ACAGTGCTTTCACGTCCCCATTCACTAGCTT
Found at i:428891 original size:2 final size:2
Alignment explanation
Indices: 428884--428935 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
428874 TGGTATGCCA
428884 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
428926 TC TC TC TC TC
1 TC TC TC TC TC
428936 ATATAAAATC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:431361 original size:24 final size:24
Alignment explanation
Indices: 431334--431383 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
431324 CCAGACACCT
*
431334 ACCATGGCACCATCAACAACA-ACC
1 ACCAAGGCACCA-CAACAACAGACC
*
431358 ACCAAGGGACCACAACAACAGACC
1 ACCAAGGCACCACAACAACAGACC
431382 AC
1 AC
431384 TCAACCCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.44, C:0.40, G:0.12, T:0.04
Consensus pattern (24 bp):
ACCAAGGCACCACAACAACAGACC
Found at i:431404 original size:69 final size:69
Alignment explanation
Indices: 431331--431620 Score: 424
Period size: 69 Copynumber: 4.2 Consensus size: 69
431321 CACCCAGACA
* * *
431331 CCTACCATGGCACCATCAACAACAACCACCAAGGGA-CCACAACAACAGACCACTCAACCCAATA
1 CCTACCATGGCACCATCTACCACAACCACCAAGGGACCCACAA-AACAGACCACTCACCCCAATA
431395 ACCCC
65 ACCCC
431400 CCTACCATGGCACCATCTACCACAACCACCAAGGGA-CCACAACAACAGACCACTCACCCCAATA
1 CCTACCATGGCACCATCTACCACAACCACCAAGGGACCCACAA-AACAGACCACTCACCCCAATA
*
431464 ACCCT
65 ACCCC
* * *
431469 CCTACCATGGCACCATCTACCACAACCACCCAGGGACCCCCAAAACAAACCACTCACCCCAATAA
1 CCTACCATGGCACCATCTACCACAACCACCAAGGGACCCACAAAACAGACCACTCACCCCAATAA
*
431534 CCCT
66 CCCC
* * * *
431538 CCTACCATGGCACCATCTACCACAACCACCCAGGGACCCCCAAAACCA-ACCACTCATCCCACTA
1 CCTACCATGGCACCATCTACCACAACCACCAAGGGACCCACAAAA-CAGACCACTCACCCCAATA
431602 ACCCC
65 ACCCC
431607 CCTACCATGGCACC
1 CCTACCATGGCACC
431621 TTCCACCGGT
Statistics
Matches: 209, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
69 202 0.97
70 7 0.03
ACGTcount: A:0.35, C:0.47, G:0.08, T:0.10
Consensus pattern (69 bp):
CCTACCATGGCACCATCTACCACAACCACCAAGGGACCCACAAAACAGACCACTCACCCCAATAA
CCCC
Found at i:432286 original size:21 final size:21
Alignment explanation
Indices: 432262--432377 Score: 169
Period size: 21 Copynumber: 5.2 Consensus size: 21
432252 AATCCCTATG
432262 ACAACAACAACCCAGCCAACT
1 ACAACAACAACCCAGCCAACT
432283 ACAACAACAACAACCCAGCCAACT
1 ---ACAACAACAACCCAGCCAACT
*
432307 ACAACAACAACCAAGCCAACT
1 ACAACAACAACCCAGCCAACT
432328 ACAACAACAACAACCCAGCCAACT
1 ---ACAACAACAACCCAGCCAACT
432352 ACAACAACAACCCAGCCAACT
1 ACAACAACAACCCAGCCAACT
432373 ACAAC
1 ACAAC
432378 TACTACTAAA
Statistics
Matches: 87, Mismatches: 2, Indels: 9
0.89 0.02 0.09
Matches are distributed among these distances:
21 46 0.53
24 41 0.47
ACGTcount: A:0.50, C:0.41, G:0.04, T:0.04
Consensus pattern (21 bp):
ACAACAACAACCCAGCCAACT
Found at i:432289 original size:24 final size:24
Alignment explanation
Indices: 432262--432377 Score: 181
Period size: 24 Copynumber: 5.1 Consensus size: 24
432252 AATCCCTATG
432262 ACAACAACAACCCAGCCAACTACA
1 ACAACAACAACCCAGCCAACTACA
432286 ACAACAACAACCCAGCCAACT---
1 ACAACAACAACCCAGCCAACTACA
*
432307 ACAACAACAACCAAGCCAACTACA
1 ACAACAACAACCCAGCCAACTACA
432331 ACAACAACAACCCAGCCAACT---
1 ACAACAACAACCCAGCCAACTACA
432352 ACAACAACAACCCAGCCAACTACA
1 ACAACAACAACCCAGCCAACTACA
432376 AC
1 AC
432378 TACTACTAAA
Statistics
Matches: 84, Mismatches: 2, Indels: 12
0.86 0.02 0.12
Matches are distributed among these distances:
21 41 0.49
24 43 0.51
ACGTcount: A:0.50, C:0.41, G:0.04, T:0.04
Consensus pattern (24 bp):
ACAACAACAACCCAGCCAACTACA
Found at i:432401 original size:45 final size:45
Alignment explanation
Indices: 432262--432377 Score: 223
Period size: 45 Copynumber: 2.6 Consensus size: 45
432252 AATCCCTATG
432262 ACAACAACAACCCAGCCAACTACAACAACAACAACCCAGCCAACT
1 ACAACAACAACCCAGCCAACTACAACAACAACAACCCAGCCAACT
*
432307 ACAACAACAACCAAGCCAACTACAACAACAACAACCCAGCCAACT
1 ACAACAACAACCCAGCCAACTACAACAACAACAACCCAGCCAACT
432352 ACAACAACAACCCAGCCAACTACAAC
1 ACAACAACAACCCAGCCAACTACAAC
432378 TACTACTAAA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 69 1.00
ACGTcount: A:0.50, C:0.41, G:0.04, T:0.04
Consensus pattern (45 bp):
ACAACAACAACCCAGCCAACTACAACAACAACAACCCAGCCAACT
Found at i:435927 original size:2 final size:2
Alignment explanation
Indices: 435920--436010 Score: 182
Period size: 2 Copynumber: 45.5 Consensus size: 2
435910 TTAAAACATA
435920 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
435962 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
436004 TC TC TC T
1 TC TC TC T
436011 GATTCGATTA
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 89 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:437176 original size:2 final size:2
Alignment explanation
Indices: 437169--437228 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
437159 AGATTCAGCT
437169 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
*
437211 GA GA GA GA TA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA
437229 TAATAACACT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.48, T:0.02
Consensus pattern (2 bp):
GA
Found at i:437325 original size:2 final size:2
Alignment explanation
Indices: 437318--437346 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
437308 AATAAGAAAA
437318 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
437347 TATTAAACCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:448853 original size:29 final size:28
Alignment explanation
Indices: 448815--448910 Score: 147
Period size: 29 Copynumber: 3.3 Consensus size: 28
448805 TCTTTCAAAT
*
448815 GAATTGCACATGAATATGTTTTTCAACAC
1 GAATTTCACATGAATATGTTTTTC-ACAC
448844 GAATTTCACATGAATATGTTTTATCACAC
1 GAATTTCACATGAATATGTTTT-TCACAC
448873 GAATTTCACATGAATATGTTTTTTCACAC
1 GAATTTCACATGAATATG-TTTTTCACAC
*
448902 GAAATTCAC
1 GAATTTCAC
448911 GTGGACAGAA
Statistics
Matches: 63, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
29 57 0.90
30 6 0.10
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.36
Consensus pattern (28 bp):
GAATTTCACATGAATATGTTTTTCACAC
Found at i:454920 original size:18 final size:18
Alignment explanation
Indices: 454897--454938 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
454887 CCAACTGATG
*
454897 TATTATTACTATCACTAT
1 TATTATTAATATCACTAT
*
454915 TATTATTAATATTACTAT
1 TATTATTAATATCACTAT
454933 TATTAT
1 TATTAT
454939 CATTATNNNN
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.55
Consensus pattern (18 bp):
TATTATTAATATCACTAT
Found at i:455742 original size:29 final size:30
Alignment explanation
Indices: 455710--455775 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 30
455700 CTCTCCCTCC
455710 AACCAAAAGAAAAAACAAA-AAA-AAACAAA
1 AACCAAAA-AAAAAACAAACAAACAAACAAA
455739 AACC--AAAAAAAACAAACAAACAAACAAA
1 AACCAAAAAAAAAACAAACAAACAAACAAA
*
455767 AAACAAAAA
1 AACCAAAAA
455776 CAACCTCTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
26 10 0.31
27 5 0.16
28 10 0.31
29 4 0.12
30 3 0.09
ACGTcount: A:0.82, C:0.17, G:0.02, T:0.00
Consensus pattern (30 bp):
AACCAAAAAAAAAACAAACAAACAAACAAA
Found at i:455776 original size:17 final size:16
Alignment explanation
Indices: 455720--455778 Score: 82
Period size: 16 Copynumber: 3.5 Consensus size: 16
455710 AACCAAAAGA
455720 AAAAACAAAAAAAAAC
1 AAAAACAAAAAAAAAC
*
455736 AAAAACCAAAAAAAAC
1 AAAAACAAAAAAAAAC
455752 AAACAAACAAACAAAAAAC
1 -AA-AAACAAA-AAAAAAC
455771 AAAAACAA
1 AAAAACAA
455779 CCTCTTCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
16 15 0.39
17 8 0.21
18 8 0.21
19 7 0.18
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAACAAAAAAAAAC
Found at i:458792 original size:2 final size:2
Alignment explanation
Indices: 458787--458838 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
458777 TATTTATATA
458787 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
458829 CT CT CT CT CT
1 CT CT CT CT CT
458839 GCAAAATACA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:473092 original size:28 final size:28
Alignment explanation
Indices: 473049--473425 Score: 459
Period size: 28 Copynumber: 13.4 Consensus size: 28
473039 TATATCACAA
* * * *
473049 TCTGCAAGGTCTTTTATTTGCCAGATTG
1 TCTGCAAGGTCATTTAGTGGTCAGATTG
*
473077 TCTGCAAGGTCATTTAGTGGTCATATTG
1 TCTGCAAGGTCATTTAGTGGTCAGATTG
*
473105 TCTGCAAAGGTCATTTAGTGGTCATATTG
1 TCTGC-AAGGTCATTTAGTGGTCAGATTG
* *
473134 TCTGCAAGGTCATTTACTGGTCATATTG
1 TCTGCAAGGTCATTTAGTGGTCAGATTG
*
473162 TCTGCAAGGTTATTTAGTGGTCAGATTG
1 TCTGCAAGGTCATTTAGTGGTCAGATTG
* * *
473190 TCTGCAAAGTCACTTAGTGGTCATATTG
1 TCTGCAAGGTCATTTAGTGGTCAGATTG
* * *
473218 TCTGCAAGGTCAATTACTGGTCAGATTT
1 TCTGCAAGGTCATTTAGTGGTCAGATTG
* * * *
473246 TCTACAAGGTCACTTAATGGCCAGATTG
1 TCTGCAAGGTCATTTAGTGGTCAGATTG
*
473274 TCTGCAAGGTCATTTAGTGGTCAGATTT
1 TCTGCAAGGTCATTTAGTGGTCAGATTG
* *
473302 TCTGCAAGGTCATTTATTGGTCAGATTT
1 TCTGCAAGGTCATTTAGTGGTCAGATTG
* * * * *
473330 TCTGCAAGGTCACTTAATGGCCGGATTT
1 TCTGCAAGGTCATTTAGTGGTCAGATTG
*
473358 TCTGCAAGGTCATTTAGTGGTCATATTG
1 TCTGCAAGGTCATTTAGTGGTCAGATTG
* *
473386 CCTGCAAGGTCATTTACTGGTCAGATAT-
1 TCTGCAAGGTCATTTAGTGGTCAGAT-TG
473414 TCTGCAAGGTCA
1 TCTGCAAGGTCA
473426 CTTAATGGCT
Statistics
Matches: 304, Mismatches: 43, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
28 275 0.90
29 29 0.10
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (28 bp):
TCTGCAAGGTCATTTAGTGGTCAGATTG
Found at i:473440 original size:84 final size:84
Alignment explanation
Indices: 473049--473434 Score: 529
Period size: 84 Copynumber: 4.6 Consensus size: 84
473039 TATATCACAA
* * * * * * * * *
473049 TCTGCAAGGTCTTTTATTTGCCAGATTGTCTGCAAGGTCATTTAGTGGTCATATTGTCTGCAAAG
1 TCTGCAAGGTCATTTACTGGTCAGATTTTCTGCAAGGTCACTTAATGGCCAGATTGTCTGC-AAG
473114 GTCATTTAGTGGTCATATTG
65 GTCATTTAGTGGTCATATTG
* * * * * * *
473134 TCTGCAAGGTCATTTACTGGTCATATTGTCTGCAAGGTTATTTAGTGGTCAGATTGTCTGCAAAG
1 TCTGCAAGGTCATTTACTGGTCAGATTTTCTGCAAGGTCACTTAATGGCCAGATTGTCTGCAAGG
*
473199 TCACTTAGTGGTCATATTG
66 TCATTTAGTGGTCATATTG
* *
473218 TCTGCAAGGTCAATTACTGGTCAGATTTTCTACAAGGTCACTTAATGGCCAGATTGTCTGCAAGG
1 TCTGCAAGGTCATTTACTGGTCAGATTTTCTGCAAGGTCACTTAATGGCCAGATTGTCTGCAAGG
* *
473283 TCATTTAGTGGTCAGATTT
66 TCATTTAGTGGTCATATTG
* * *
473302 TCTGCAAGGTCATTTATTGGTCAGATTTTCTGCAAGGTCACTTAATGGCCGGATTTTCTGCAAGG
1 TCTGCAAGGTCATTTACTGGTCAGATTTTCTGCAAGGTCACTTAATGGCCAGATTGTCTGCAAGG
473367 TCATTTAGTGGTCATATTG
66 TCATTTAGTGGTCATATTG
* *
473386 CCTGCAAGGTCATTTACTGGTCAGATATTCTGCAAGGTCACTTAATGGC
1 TCTGCAAGGTCATTTACTGGTCAGATTTTCTGCAAGGTCACTTAATGGC
473435 TGGATTGTTG
Statistics
Matches: 270, Mismatches: 31, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
84 216 0.80
85 54 0.20
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (84 bp):
TCTGCAAGGTCATTTACTGGTCAGATTTTCTGCAAGGTCACTTAATGGCCAGATTGTCTGCAAGG
TCATTTAGTGGTCATATTG
Found at i:474210 original size:1 final size:1
Alignment explanation
Indices: 474206--474236 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
474196 TTTTTTAAAA
*
474206 GGGGGGGGGGGGGGGGGGGGGGGGGAGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
474237 AGAGATGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.03, C:0.00, G:0.97, T:0.00
Consensus pattern (1 bp):
G
Found at i:476132 original size:47 final size:47
Alignment explanation
Indices: 476063--476638 Score: 640
Period size: 47 Copynumber: 12.0 Consensus size: 47
476053 CTGTGTTTAA
476063 TACTGGCCCATCTTACCTACAGGGAGGGGTCATAGAGTGCTGTAAAT
1 TACTGGCCCATCTTACCTACAGGGAGGGGTCATAGAGTGCTGTAAAT
* * *
476110 TACTGGCCCATCTTACCTACAGGGAGGGATCATATAATGCTGTAAAT
1 TACTGGCCCATCTTACCTACAGGGAGGGGTCATAGAGTGCTGTAAAT
* * * *
476157 TATTGGCCCATCTTACCTTCAGGGAGGGGTCATATAGTGCTGTAATT
1 TACTGGCCCATCTTACCTACAGGGAGGGGTCATAGAGTGCTGTAAAT
* * *
476204 TACTGGCCCATCTTACCTACAGGGAGGGATCATATAATGCTGTAAAT
1 TACTGGCCCATCTTACCTACAGGGAGGGGTCATAGAGTGCTGTAAAT
* * * * *
476251 TATTGGCCCATCTTACGTACAGGGAGGGATCATAGAGCGGTGTAAAT
1 TACTGGCCCATCTTACCTACAGGGAGGGGTCATAGAGTGCTGTAAAT
*
476298 TACTGGCCCATCTTACCTACAGTGAGGGGTCA-AGGAGTGCTGTAAAT
1 TACTGGCCCATCTTACCTACAGGGAGGGGTCATA-GAGTGCTGTAAAT
* * * *
476345 TACTGGTCCATCTTACGTATAGGGAGGGATCATAGAGTGCTGTAAAT
1 TACTGGCCCATCTTACCTACAGGGAGGGGTCATAGAGTGCTGTAAAT
*
476392 AACTGGGCAGACCCATCTTACCTACAGGGAGGGGTC-TAAGAGTGCTGTAAAT
1 TACT--G--G-CCCATCTTACCTACAGGGAGGGGTCAT-AGAGTGCTGTAAAT
* * * **
476444 CACTGGCCCATATTACCTACAGAGAGGATTCATAGAGTGCTGTAAAT
1 TACTGGCCCATCTTACCTACAGGGAGGGGTCATAGAGTGCTGTAAAT
* * * * *
476491 TACTAGCCCATCTTACCTACAGGTAGAGGTCATAGAGTG-TCATAATT
1 TACTGGCCCATCTTACCTACAGGGAGGGGTCATAGAGTGCT-GTAAAT
* * **
476538 TAATGGCCCAAT-GTACCTACAGAAAGGGGTC-TAAGAGTGCTGTAAAT
1 TACTGGCCC-ATCTTACCTACAGGGAGGGGTCAT-AGAGTGCTGTAAAT
* *
476585 CACTGGCCCATATTACCTACATGTACAGGGAGGGGTCATAGAGTGCTGTAAAT
1 TACTGGCCCATCTTA-C--C---TACAGGGAGGGGTCATAGAGTGCTGTAAAT
476638 T
1 T
476639 CCAACAAGGA
Statistics
Matches: 444, Mismatches: 64, Indels: 36
0.82 0.12 0.07
Matches are distributed among these distances:
46 5 0.01
47 362 0.82
48 7 0.02
49 1 0.00
50 2 0.00
51 2 0.00
52 38 0.09
53 26 0.06
54 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (47 bp):
TACTGGCCCATCTTACCTACAGGGAGGGGTCATAGAGTGCTGTAAAT
Found at i:480373 original size:15 final size:15
Alignment explanation
Indices: 480353--480381 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
480343 AAGAGCCTTA
480353 GTTGACCAAATACTT
1 GTTGACCAAATACTT
480368 GTTGACCAAATACT
1 GTTGACCAAATACT
480382 CATATCTGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (15 bp):
GTTGACCAAATACTT
Done.