Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold492
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 781693
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:298307 original size:32 final size:33
Alignment explanation
Indices: 298250--298313 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
298240 TACAAGCCAA
**
298250 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
298283 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
298314 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:298320 original size:19 final size:18
Alignment explanation
Indices: 298250--298320 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
298240 TACAAGCCAA
298250 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
298270 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
298283 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
298302 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
298321 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:305143 original size:19 final size:19
Alignment explanation
Indices: 305107--305186 Score: 81
Period size: 19 Copynumber: 3.9 Consensus size: 19
305097 TTCTTTTTCA
305107 AAAAAAAACACAAAAAAAAC
1 AAAAAAAA-ACAAAAAAAAC
305127 AACAAAAAAACACAAAAAAAAC
1 -A-AAAAAAA-ACAAAAAAAAC
305149 AAAAAAAAACAAAACAAAA-
1 AAAAAAAAACAAAA-AAAAC
* *
305168 GAAACAAAACAAAGAAAAA
1 AAAAAAAAACAAA-AAAAA
305187 GAGAGAAAAG
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
19 21 0.39
20 12 0.22
21 2 0.04
22 19 0.35
ACGTcount: A:0.84, C:0.14, G:0.03, T:0.00
Consensus pattern (19 bp):
AAAAAAAAACAAAAAAAAC
Found at i:305167 original size:10 final size:10
Alignment explanation
Indices: 305105--305186 Score: 94
Period size: 11 Copynumber: 7.9 Consensus size: 10
305095 CATTCTTTTT
305105 CAAAAAAAAA
1 CAAAAAAAAA
305115 CACAAAAAAAA
1 CA-AAAAAAAA
305126 CAACAAAAAAA
1 CAA-AAAAAAA
305137 CACAAAAAAAA
1 CA-AAAAAAAA
305148 CAAAAAAAAA
1 CAAAAAAAAA
*
305158 CAAAACAAAA
1 CAAAAAAAAA
* *
305168 -GAAACAAAA
1 CAAAAAAAAA
305177 CAAAGAAAAA
1 CAAA-AAAAA
305187 GAGAGAAAAG
Statistics
Matches: 63, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
9 8 0.13
10 22 0.35
11 32 0.51
12 1 0.02
ACGTcount: A:0.83, C:0.15, G:0.02, T:0.00
Consensus pattern (10 bp):
CAAAAAAAAA
Found at i:305179 original size:14 final size:14
Alignment explanation
Indices: 305144--305184 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
305134 AAACACAAAA
*
305144 AAAACAAAAAAAAAC
1 AAAAC-AAAAGAAAC
305159 AAAACAAAAGAAAC
1 AAAACAAAAGAAAC
305173 AAAAC-AAAGAAA
1 AAAACAAAAGAAA
305185 AAGAGAGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 7 0.28
14 13 0.52
15 5 0.20
ACGTcount: A:0.83, C:0.12, G:0.05, T:0.00
Consensus pattern (14 bp):
AAAACAAAAGAAAC
Found at i:305186 original size:24 final size:23
Alignment explanation
Indices: 305105--305186 Score: 87
Period size: 24 Copynumber: 3.4 Consensus size: 23
305095 CATTCTTTTT
305105 CAAAAAAAAACACAAAAAA-AACAA
1 CAAAAAAAAACA-AAAAAACAA-AA
*
305129 CAAAAAAACACAAAAAAAACAAAA
1 CAAAAAAAAAC-AAAAAAACAAAA
305153 -AAAAACAAAACAAAAGAAACAAAA
1 CAAAAA-AAAACAAAA-AAACAAAA
*
305177 CAAAGAAAAA
1 CAAAAAAAAA
305187 GAGAGAAAAG
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
23 9 0.18
24 34 0.68
25 7 0.14
ACGTcount: A:0.83, C:0.15, G:0.02, T:0.00
Consensus pattern (23 bp):
CAAAAAAAAACAAAAAAACAAAA
Found at i:306515 original size:55 final size:55
Alignment explanation
Indices: 306204--306764 Score: 551
Period size: 55 Copynumber: 9.9 Consensus size: 55
306194 TTTCCTTTTA
* ** * *
306204 AAAGCCCCCACAAGTTGGTGGCATTTTTCCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGAC-CC----CTTTC
* * * * *
306265 AAAGCCCACACAGGTTGGTGGCA-TTTTCCAATCCTCAAAGAGCAGGGCACCTTTTCTTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCA-GG-ACC---CCTTTC
* * *
306325 AAAGCCCACACAAGTTGGTGGCACC-CTCAGTCCTTAAAGAGCAGGACGCCTTTTCTTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGAC-CC----CTTTC
* * *
306384 AAAGCCTACACAAGTTGGTGGCACCTTT-AGTCCTCAAAGAGCATGACGCCTTTTCCTTC
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGAC-CC----CTTTC
* *
306443 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGTAGGACCCCTTTC
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACCCCTTTC
* *
306498 AAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACACCTCTT-
1 AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACCCCT-TTC
* *
306553 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTC
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACCCCTTTC
* * *
306608 AAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAAGACACCTCTT-
1 AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACCCCT-TTC
* * *
306663 AAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAACAGGACGCCTTTC
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACCCCTTTC
* * * *
306718 AAAGCCTACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGA
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGA
306765 TACACTTTAT
Statistics
Matches: 439, Mismatches: 40, Indels: 48
0.83 0.08 0.09
Matches are distributed among these distances:
54 10 0.02
55 225 0.51
56 10 0.02
57 2 0.00
58 3 0.01
59 99 0.23
60 64 0.15
61 24 0.05
62 2 0.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (55 bp):
AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACCCCTTTC
Found at i:306581 original size:110 final size:111
Alignment explanation
Indices: 306204--306764 Score: 657
Period size: 110 Copynumber: 4.9 Consensus size: 111
306194 TTTCCTTTTA
* ** * *
306204 AAAGCCCCCACAAGTTGGTGGCATTTTTCCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAG
1 AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGAC-CC----CTTTCAAAG
* * *
306269 CCCACACAGGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGGGCACCTTTTCTTTT
60 CCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACC--TTC--TT
* * *
306325 AAAGCCCACACAAGTTGGTGGCACC-CTCAGTCCTTAAAGAGCAGGACGCCTTTTCTTTTAAAGC
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGAC-CC----CTTTCAAAGC
* * * *
306389 CTACACAAGTTGGTGGCACCTTT--AGTCCTCAAAGAGCATGACGCCTTTTCCTT
61 CCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACACC--TT-CTT
* *
306442 CAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGTAGGACCCCTTTCAAAGCCCAC
1 -AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACCCCTTTCAAAGCCCAC
306507 ACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACC-TCTT
65 ACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTCTT
* *
306553 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACA
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACCCCTTTCAAAGCCCACA
*
306618 CAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAAGACACC-TCTT
66 CAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTCTT
* * * *
306663 AAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAACAGGACGCCTTTCAAAGCCTACA
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACCCCTTTCAAAGCCCACA
* *
306728 CGAGTTGGTGGCACTTTT-TAGTCCTCAAAGAGCAGGA
66 CAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGA
306765 TACACTTTAT
Statistics
Matches: 400, Mismatches: 33, Indels: 25
0.87 0.07 0.05
Matches are distributed among these distances:
110 196 0.49
111 7 0.02
112 1 0.00
113 3 0.01
114 26 0.06
115 20 0.05
117 2 0.00
118 49 0.12
119 70 0.17
120 4 0.01
121 22 0.05
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (111 bp):
AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACCCCTTTCAAAGCCCACA
CAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTCTT
Found at i:306649 original size:165 final size:164
Alignment explanation
Indices: 306166--306764 Score: 614
Period size: 165 Copynumber: 3.5 Consensus size: 164
306156 CTCCTTCCAC
* * **
306166 TTTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAAGCCCCCACAAGTTGGTGGCATTTT
1 TTTTCAGTCCTCAAAGAGCAGGACGCC---T-C--TT-AAAGCCCACACAAGTTGGTGGCACCTT
* * *
306231 TCCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAGGTTGGTGGCATTTTCCAA
59 T-CAGTCCTCAAAGAGCAGGACGCCTTTTC----AAAGCCCACACAAGTTGGTGGCATTTTCCAG
*
306296 TCCTCAAAGAGCAGGGCACCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA
119 TCCTCAAAGAGCA-GG-ACC----CCTTTAAAGCCCACACAAGTTGGTGGCA
*** * *
306348 CCCTCAGTCCTTAAAGAGCAGGACGCCTTTTCTTTTAAAGCCTACACAAGTTGGTGGCACCTTT-
1 TTTTCAGTCCTCAAAGAGCAGGACGCC---TC--TTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
306412 AGTCCTCAAAGAGCATGACGCCTTTTCCTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTC
61 AGTCCTCAAAGAGCAGGACGCC--TT--TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTC
* *
306476 CCCAAAGAGTAGGACCCCTTTCAAAGCCCACACAAGTTGGTGGCA
121 CTCAAAGAGCAGGACCCCTTT-AAAGCCCACACAAGTTGGTGGCA
*
306521 TTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTC
1 TTTT-CAGTCCTCAAAGAGCAGGACGCCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTC
* *
306586 CCCAAAGAGCAGGACACC-TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAG
65 CTCAAAGAGCAGGACGCCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAG
* *
306650 CAAGACACCTCTTAAAGCCCACACAAGTTGGTGGCA
130 CAGGACCCCT-TTAAAGCCCACACAAGTTGGTGGCA
* * * * *
306686 CCTTTT-AGTCCTCAAAGAACAGGACGCCT-TTCAAAGCCTACACGAGTTGGTGGCACTTTTTAG
1 --TTTTCAGTCCTCAAAGAGCAGGACGCCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAG
306749 TCCTCAAAGAGCAGGA
63 TCCTCAAAGAGCAGGA
306765 TACACTTTAT
Statistics
Matches: 366, Mismatches: 38, Indels: 43
0.82 0.09 0.10
Matches are distributed among these distances:
164 5 0.01
165 132 0.36
166 2 0.01
167 5 0.01
169 29 0.08
170 19 0.05
171 2 0.01
172 4 0.01
173 24 0.07
174 21 0.06
176 3 0.01
177 2 0.01
178 55 0.15
179 3 0.01
180 26 0.07
181 5 0.01
182 29 0.08
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (164 bp):
TTTTCAGTCCTCAAAGAGCAGGACGCCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
TCAAAGAGCAGGACGCCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGC
AGGACCCCTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:307416 original size:19 final size:18
Alignment explanation
Indices: 307392--307455 Score: 75
Period size: 19 Copynumber: 3.7 Consensus size: 18
307382 CAACAATTTA
307392 TATCGATACATAAGTGTTG
1 TATCGATACATAAGT-TTG
307411 TATCGATAC--AA---TG
1 TATCGATACATAAGTTTG
307424 TATCGATACATAAGTATTG
1 TATCGATACATAAGT-TTG
307443 TATCGATACATAA
1 TATCGATACATAA
307456 TTAGCTACTG
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
17 2 0.05
19 24 0.62
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (18 bp):
TATCGATACATAAGTTTG
Found at i:307427 original size:13 final size:13
Alignment explanation
Indices: 307409--307433 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
307399 ACATAAGTGT
307409 TGTATCGATACAA
1 TGTATCGATACAA
307422 TGTATCGATACA
1 TGTATCGATACA
307434 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:307428 original size:32 final size:32
Alignment explanation
Indices: 307392--307452 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
307382 CAACAATTTA
*
307392 TATCGATACATAAGTGTTGTATCGATACAATG
1 TATCGATACATAAGTATTGTATCGATACAATG
307424 TATCGATACATAAGTATTGTATCGATACA
1 TATCGATACATAAGTATTGTATCGATACA
307453 TAATTAGCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.34
Consensus pattern (32 bp):
TATCGATACATAAGTATTGTATCGATACAATG
Found at i:307514 original size:13 final size:13
Alignment explanation
Indices: 307496--307520 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
307486 ATTTTTCTGG
307496 GTATCGATACATT
1 GTATCGATACATT
307509 GTATCGATACAT
1 GTATCGATACAT
307521 GGATCTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:310002 original size:27 final size:28
Alignment explanation
Indices: 309972--310047 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 28
309962 TTTCTTCACA
309972 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
309999 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
***
310027 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
310048 ACTTTATTTC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 24 0.55
28 20 0.45
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:310098 original size:51 final size:51
Alignment explanation
Indices: 310030--310251 Score: 246
Period size: 52 Copynumber: 4.3 Consensus size: 51
310020 TTATTTCCGA
* * *** * *
310030 GGGGATACTCCAACCCCGACTTTATTTCCAAAATATTGACTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATC
* * * *
310081 GGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAA-TTTTTCACAATC
* * * **
310133 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTC-ACAATC
* *
310185 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCC-AAAACACCAATTTTTCACAATC
*
310237 GAGGATACTCCAACC
1 GGGGATACTCCAACC
310252 TCGTTATTTC
Statistics
Matches: 143, Mismatches: 25, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
51 37 0.26
52 92 0.64
53 14 0.10
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATC
Found at i:310146 original size:52 final size:50
Alignment explanation
Indices: 309863--310251 Score: 223
Period size: 52 Copynumber: 7.4 Consensus size: 50
309853 CTCAATTCTC
* * * * *
309863 CACAATCGGGGATATTCTAACTCCGATTTTATTTTCAAAACACTAA-TTTT
1 CACAATCGGGGATACTCCAACCCCGATTTTATTCT-AAAACACCAATTTTT
* * * *
309913 CTATAATCGAGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTT
1 C-ACAATCGGGGATACTCCAACCCCGATTTTA-TT-C-TAAAACACCAATTT-TT
* ** **
309968 CACAATCGGGGATACTCCAACCCCG-TTAATCATCGGGGATACTCCAAC-CCCGTTATTT
1 CACAATCGGGGATACTCCAACCCCGATT--T--T-----ATTCTAAAACACCAATT-TTT
* * * * *** *
310026 C-CGA--GGGGATACTCCAACCCCGACTTTATTTCCAAAATATTGACTTTT
1 CACAATCGGGGATACTCCAACCCCGATTTTA-TTCTAAAACACCAATTTTT
* * *
310074 CATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTT
1 CACAATCGGGGATACTCCAACCCCGATTTTATT-CTAAAACACCAA-TTTTT
* * *
310126 CACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTC
1 CACAATCGGGGATACTCCAACCCCGATTTTATTCT-AAAACACCAATTTTT
** * * *
310177 CTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
1 C-ACAATCGGGGATACTCCAACCCCGATTTTA-TT-CTAAAACACCAATTTTT
*
310230 CACAATCGAGGATACTCCAACC
1 CACAATCGGGGATACTCCAACC
310252 TCGTTATTTC
Statistics
Matches: 258, Mismatches: 53, Indels: 54
0.71 0.15 0.15
Matches are distributed among these distances:
47 1 0.00
48 8 0.03
49 2 0.01
50 3 0.01
51 62 0.24
52 91 0.35
53 27 0.10
54 24 0.09
55 22 0.09
56 1 0.00
57 3 0.01
58 7 0.03
59 4 0.02
60 1 0.00
61 1 0.00
62 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.31
Consensus pattern (50 bp):
CACAATCGGGGATACTCCAACCCCGATTTTATTCTAAAACACCAATTTTT
Found at i:310262 original size:31 final size:28
Alignment explanation
Indices: 310234--310310 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
310224 ATTTTTCACA
*
310234 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGAGGATACTCCAACCCCGTTATTTC
* **
310262 ATCGGGGATACTCCAACCCCGTTACCTC
1 ATCGAGGATACTCCAACCCCGTTATTTC
310290 --CGAGGGGATACTCCAACCCCG
1 ATCGA--GGATACTCCAACCCCG
310311 GCTTTATTCC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 2 0.05
28 40 0.95
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.22
Consensus pattern (28 bp):
ATCGAGGATACTCCAACCCCGTTATTTC
Found at i:310330 original size:263 final size:263
Alignment explanation
Indices: 309863--310361 Score: 797
Period size: 263 Copynumber: 1.9 Consensus size: 263
309853 CTCAATTCTC
* * * *
309863 CACAATCGGGGATATTCTAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGAGGATA
1 CACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGAGGATA
*
309928 CTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCCCG
66 CTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCCG
** *
309993 TTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTC
131 TTAATCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGACTTTATTCC
310058 CAAAATATTGACTTT-TCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATT
196 CAAAATATTGA-TTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATT
310122 TTTT
260 TTTT
* * *
310126 CACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGAT
1 CACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTT-CTATAATCGAGGAT
* *
310191 ACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAACCTC
65 ACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCC
* *
310254 GTTATTTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATT
130 GTTA-ATCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGACTTTATT
* *
310319 CCCAAAATATTGATTTCTCATAATTGGGGATACTTCAACCCCG
194 CCCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCG
310362 TTATTTCCGA
Statistics
Matches: 216, Mismatches: 17, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
262 31 0.14
263 150 0.69
264 35 0.16
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (263 bp):
CACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGAGGATA
CTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCCG
TTAATCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGACTTTATTCC
CAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTT
TTT
Found at i:310376 original size:107 final size:108
Alignment explanation
Indices: 310185--310389 Score: 250
Period size: 107 Copynumber: 1.9 Consensus size: 108
310175 TCCTTTAATC
* * *
310185 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
* **
310250 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACCTCCGA
66 CCCCGTTATTTCAGAGGGGATACTCCAACCCCGTTACCTCCGA
* * *** * * * *
310293 GGGGATACTCCAACCCCGGCTTTA-TTCCCAAAATATTGATTTCTCATAATTGGGGATACTTCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
* *
310357 CCCCGTTATTTCCGAGGGGATACTCCAATCCCG
66 CCCCGTTATTTCAGAGGGGATACTCCAACCCCG
310390 ATGCTTTTTT
Statistics
Matches: 80, Mismatches: 17, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
107 59 0.74
108 21 0.26
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (108 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
CCCCGTTATTTCAGAGGGGATACTCCAACCCCGTTACCTCCGA
Found at i:310413 original size:79 final size:79
Alignment explanation
Indices: 310264--310463 Score: 210
Period size: 79 Copynumber: 2.5 Consensus size: 79
310254 GTTATTTCAT
**
310264 CGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
* * *
310329 TGATTTCTCATAAT
66 CGATTTCTCACAAC
* * * * *
310343 TGGGGATACTTCAACCCCGTTATTTCCGAGGGGATACTCCAATCCCGATGCTTT-TT-TC-TAAT
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCG--GCTTTATTCCCAAAAT
310405 CATCGATTTCTCACAAC
64 -ATCGATTTCTCACAAC
* * * *
310422 CGGGGATACTCCAGCCCCGTCACTTT-CAAGGGGACACTCCAA
1 CGGGGATACTCCAACCCCGTTA-TTTCCGAGGGGATACTCCAA
310464 AATATTAAAT
Statistics
Matches: 101, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
78 3 0.03
79 88 0.87
80 5 0.05
81 5 0.05
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
CGATTTCTCACAAC
Found at i:311532 original size:27 final size:27
Alignment explanation
Indices: 311494--311546 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
311484 CATCAATTTT
*
311494 TCATTGGGGATACTCCAACCCCGTTAA
1 TCATGGGGGATACTCCAACCCCGTTAA
311521 TCATGGGGGATACTCCAACCCCGTTA
1 TCATGGGGGATACTCCAACCCCGTTA
311547 TTTCCGAGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.25
Consensus pattern (27 bp):
TCATGGGGGATACTCCAACCCCGTTAA
Found at i:311582 original size:31 final size:28
Alignment explanation
Indices: 311499--311571 Score: 96
Period size: 27 Copynumber: 2.6 Consensus size: 28
311489 ATTTTTCATT
* *
311499 GGGGATACTCCAACCCCGTTA-ATCATG-
1 GGGGATACTCCAACCCCGTTATTTC-CGA
311526 GGGGATACTCCAACCCCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTATTTCCGA
*
311554 GGGGATACTCCAATCCCG
1 GGGGATACTCCAACCCCG
311572 ATTTTATTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.23, C:0.32, G:0.23, T:0.22
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTCCGA
Found at i:314754 original size:21 final size:20
Alignment explanation
Indices: 314728--314766 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
314718 CGTTGGACCT
314728 TGTATCAATACATTCAAGAAA
1 TGTATCAATACATT-AAGAAA
*
314749 TGTATCGATACATTAAGA
1 TGTATCAATACATTAAGA
314767 CAAAAATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.31
Consensus pattern (20 bp):
TGTATCAATACATTAAGAAA
Found at i:319565 original size:10 final size:10
Alignment explanation
Indices: 319550--319575 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
319540 AGCTTTTTTA
319550 TTTTTAAAAT
1 TTTTTAAAAT
319560 TTTTTAAAAT
1 TTTTTAAAAT
319570 TTTTTA
1 TTTTTA
319576 CTTATTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTTTAAAAT
Found at i:320291 original size:30 final size:31
Alignment explanation
Indices: 320238--320301 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
320228 ATAAATTATG
*
320238 TAAATAGATAATAAAATAT-AAAAATTAAAT
1 TAAATAGATAATAAAATATAAAAAATAAAAT
* *
320268 TAAATA-ATTATAAATTATAAAAAAATAAAAT
1 TAAATAGATAATAAAATAT-AAAAAATAAAAT
320299 TAA
1 TAA
320302 TTTAATTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 10 0.34
30 6 0.21
31 13 0.45
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (31 bp):
TAAATAGATAATAAAATATAAAAAATAAAAT
Found at i:320801 original size:6 final size:6
Alignment explanation
Indices: 320790--320816 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
320780 TACTTCCTAA
320790 TATATT TATATT TATATT TATATT TAT
1 TATATT TATATT TATATT TATATT TAT
320817 GCTTTAGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATATT
Found at i:321173 original size:52 final size:52
Alignment explanation
Indices: 321111--321214 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
321101 TACATGCTTA
321111 TTCAGATAATTAAAATATGTGGACAATAAACGCTTGAAATAGTAGTTACCCT
1 TTCAGATAATTAAAATATGTGGACAATAAACGCTTGAAATAGTAGTTACCCT
321163 TTCAGATAATTAAAATATGTGGACAATAAACGCTTGAAATAGTAGTTACCCT
1 TTCAGATAATTAAAATATGTGGACAATAAACGCTTGAAATAGTAGTTACCCT
321215 GCCTTGAGCT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (52 bp):
TTCAGATAATTAAAATATGTGGACAATAAACGCTTGAAATAGTAGTTACCCT
Found at i:322084 original size:2 final size:2
Alignment explanation
Indices: 322079--322115 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
322069 TGTGTGTGTC
322079 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
322116 TACAGTTCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:322171 original size:2 final size:2
Alignment explanation
Indices: 322164--322199 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
322154 TTTTTATGAC
322164 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
322200 ATACACATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:326747 original size:2 final size:2
Alignment explanation
Indices: 326740--326790 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
326730 GGTTTTTGAT
326740 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
326782 TA TA AA TA T
1 TA TA TA TA T
326791 GCTGAAAAAC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:332837 original size:50 final size:50
Alignment explanation
Indices: 332778--332877 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
332768 CAACTTATTT
332778 TTTATTATAACCATATTTATCCTGTAAACTAGTAAAACTTGGGGGCACTA
1 TTTATTATAACCATATTTATCCTGTAAACTAGTAAAACTTGGGGGCACTA
332828 TTTATTATAACCATATTTATCCTGTAAACTAGTAAAACTTGGGGGCACTA
1 TTTATTATAACCATATTTATCCTGTAAACTAGTAAAACTTGGGGGCACTA
332878 AGCCTACAAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (50 bp):
TTTATTATAACCATATTTATCCTGTAAACTAGTAAAACTTGGGGGCACTA
Found at i:336605 original size:2 final size:2
Alignment explanation
Indices: 336600--336642 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
336590 AGTGAAAGAA
*
336600 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
336642 A
1 A
336643 CGTATTTGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:336807 original size:14 final size:14
Alignment explanation
Indices: 336790--336854 Score: 51
Period size: 14 Copynumber: 4.4 Consensus size: 14
336780 TTACATTTAA
*
336790 AATATTATAATATT
1 AATATTATAAAATT
*
336804 AATATTAAAAAATT
1 AATATTATAAAATT
**
336818 AATAATTATTTAATT
1 AAT-ATTATAAAATT
336833 AATAAGATTA-AAAATT
1 AAT---ATTATAAAATT
336849 AATATT
1 AATATT
336855 TTATTAAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
13 3 0.08
14 15 0.38
15 11 0.28
16 7 0.17
17 4 0.10
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (14 bp):
AATATTATAAAATT
Found at i:336959 original size:5 final size:5
Alignment explanation
Indices: 336944--336989 Score: 51
Period size: 5 Copynumber: 9.6 Consensus size: 5
336934 TATATATTAA
* * *
336944 TATTT TA-TT TATTT TATTT T-TTA TATTT TATTA TATTT TATGT TAT
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT TAT
336990 ATTGATAGTC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
4 7 0.21
5 27 0.79
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (5 bp):
TATTT
Found at i:336960 original size:24 final size:24
Alignment explanation
Indices: 336933--336984 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
336923 TTAAATTTGC
336933 TTATATATTAATATTTTATT-TATT
1 TTAT-TATTAATATTTTATTATATT
* *
336957 TTATTTTTTATATTTTATTATATT
1 TTATTATTAATATTTTATTATATT
336981 TTAT
1 TTAT
336985 GTTATATTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 13 0.52
24 12 0.48
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (24 bp):
TTATTATTAATATTTTATTATATT
Found at i:336992 original size:17 final size:16
Alignment explanation
Indices: 336936--336992 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
336926 AATTTGCTTA
336936 TATATTAATATTTTATT
1 TATATT-ATATTTTATT
* *
336953 TATTTTATTTTTTATAT
1 TATATTATATTTTAT-T
*
336970 TTTATTATATTTTATGT
1 TATATTATATTTTAT-T
336987 TATATT
1 TATATT
336993 GATAGTCTAT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
16 8 0.25
17 24 0.75
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (16 bp):
TATATTATATTTTATT
Found at i:337250 original size:6 final size:6
Alignment explanation
Indices: 337239--337279 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
337229 GTTTGATTGA
337239 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TT-TTT TT-TTT T
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT T
337280 AAATTTTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 9 0.26
6 26 0.74
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (6 bp):
TTCTTT
Found at i:338694 original size:4 final size:4
Alignment explanation
Indices: 338687--338719 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
338677 TTTTTCTGGT
338687 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
338720 GCATTGTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:339322 original size:18 final size:18
Alignment explanation
Indices: 339301--339336 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
339291 AATAATACGT
339301 AATATAAATT-AAATATAA
1 AATAT-AATTAAAATATAA
339319 AATATAATTAAAATATAA
1 AATATAATTAAAATATAA
339337 TAAAAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AATATAATTAAAATATAA
Found at i:339326 original size:23 final size:21
Alignment explanation
Indices: 339300--339348 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
339290 TAATAATACG
*
339300 TAATATAAATTAAATATAAAATA
1 TAATATAAAATAAA-ATAAAA-A
*
339323 TAAT-TAAAATATAATAAAAA
1 TAATATAAAATAAAATAAAAA
339343 TAATAT
1 TAATAT
339349 TAATATGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 5 0.22
21 7 0.30
22 7 0.30
23 4 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
TAATATAAAATAAAATAAAAA
Found at i:339347 original size:9 final size:10
Alignment explanation
Indices: 339315--339366 Score: 52
Period size: 11 Copynumber: 5.0 Consensus size: 10
339305 TAAATTAAAT
339315 ATAAAATATA
1 ATAAAATATA
339325 ATTAAAATATA
1 A-TAAAATATA
339336 ATAAAA-ATA
1 ATAAAATATA
* *
339345 ATATTAATATG
1 ATA-AAATATA
339356 ATATAAATATA
1 ATA-AAATATA
339367 TGATTATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
9 6 0.17
10 8 0.23
11 21 0.60
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (10 bp):
ATAAAATATA
Found at i:339412 original size:32 final size:33
Alignment explanation
Indices: 339351--339419 Score: 97
Period size: 32 Copynumber: 2.1 Consensus size: 33
339341 AATAATATTA
*
339351 ATATGATATAAATATATGATTATATTAAAATTT
1 ATATGATATAAATATATAATTATATTAAAATTT
*
339384 ATATTATATAAAT-TATTAATT-TATTAAAATTT
1 ATATGATATAAATATA-TAATTATATTAAAATTT
339416 ATAT
1 ATAT
339420 AAAATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
32 17 0.52
33 16 0.48
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (33 bp):
ATATGATATAAATATATAATTATATTAAAATTT
Found at i:339417 original size:27 final size:28
Alignment explanation
Indices: 339387--339439 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
339377 AAAATTTATA
*
339387 TTATATAAATTAT-TAAT-TTATTAAAAT
1 TTATATAAAATATATAATATT-TTAAAAT
339414 TTATATAAAATATATAATATTTTAAA
1 TTATATAAAATATATAATATTTTAAA
339440 TATAATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 12 0.52
28 9 0.39
29 2 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
TTATATAAAATATATAATATTTTAAAAT
Found at i:339913 original size:14 final size:14
Alignment explanation
Indices: 339885--339927 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
339875 TAATTATTTT
339885 ATAAAAAT-A-AAA
1 ATAAAAATAATAAA
339897 ATAAAAATAATAAA
1 ATAAAAATAATAAA
* *
339911 ATAAATATAATATA
1 ATAAAAATAATAAA
339925 ATA
1 ATA
339928 TATTTAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 8 0.30
13 1 0.04
14 18 0.67
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
ATAAAAATAATAAA
Found at i:339939 original size:15 final size:15
Alignment explanation
Indices: 339919--339977 Score: 68
Period size: 15 Copynumber: 3.9 Consensus size: 15
339909 AAATAAATAT
339919 AATATAATATATTTA
1 AATATAATATATTTA
339934 AATATAAT-TAATTT-
1 AATATAATAT-ATTTA
339948 AATATTAATTATATTTA
1 AATA-TAA-TATATTTA
*
339965 AATATATTATATT
1 AATATAATATATT
339978 ATATTTAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 5 0.13
15 21 0.55
16 7 0.18
17 5 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AATATAATATATTTA
Found at i:339970 original size:10 final size:10
Alignment explanation
Indices: 339924--339999 Score: 54
Period size: 10 Copynumber: 7.8 Consensus size: 10
339914 AATATAATAT
339924 AATATATTTA
1 AATATATTTA
*
339934 AATATAATT-
1 AATATATTTA
*
339943 AATTTAATATTA
1 AATAT-AT-TTA
*
339955 ATTATATTTA
1 AATATATTTA
339965 AATATA-TTA
1 AATATATTTA
*
339974 TATTATATTTA
1 -AATATATTTA
339985 AA-AT-TTT-
1 AATATATTTA
339992 AATATATT
1 AATATATT
340000 AATGCTTTAT
Statistics
Matches: 51, Mismatches: 8, Indels: 15
0.69 0.11 0.20
Matches are distributed among these distances:
7 2 0.04
8 5 0.10
9 11 0.22
10 23 0.45
11 7 0.14
12 3 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
AATATATTTA
Found at i:339980 original size:20 final size:19
Alignment explanation
Indices: 339949--339999 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
339939 AATTAATTTA
339949 ATATTAATTATATTTAAAT
1 ATATTAATTATATTTAAAT
339968 ATATTATATTATATTTAAA-
1 ATATTA-ATTATATTTAAAT
*
339987 ATTTTAA-TATATT
1 ATATTAATTATATT
340000 AATGCTTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 6 0.20
18 1 0.03
19 11 0.37
20 12 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATTAATTATATTTAAAT
Found at i:340604 original size:26 final size:24
Alignment explanation
Indices: 340574--340637 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 24
340564 ATGTCATCTG
340574 TAATTTAATAATTTTTAAAATGAATA
1 TAATTTAATAATTTTTAAAA-G-ATA
* *
340600 TAATTTCAA-AATTTTTTATAGATA
1 TAATTT-AATAATTTTTAAAAGATA
340624 TAATTTAATAATTT
1 TAATTTAATAATTT
340638 GATTATTATG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
23 2 0.06
24 14 0.41
25 1 0.03
26 15 0.44
27 2 0.06
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (24 bp):
TAATTTAATAATTTTTAAAAGATA
Found at i:341301 original size:22 final size:22
Alignment explanation
Indices: 341271--341317 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
341261 AGTATTTTAT
*
341271 TTTCGTACATAACTTTTAAAAG
1 TTTCATACATAACTTTTAAAAG
341293 TTTCATACATAACTTTTAAAAG
1 TTTCATACATAACTTTTAAAAG
341315 TTT
1 TTT
341318 GATTAGTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.45
Consensus pattern (22 bp):
TTTCATACATAACTTTTAAAAG
Found at i:341331 original size:11 final size:11
Alignment explanation
Indices: 341315--341339 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
341305 CTTTTAAAAG
341315 TTTGATTAGTA
1 TTTGATTAGTA
341326 TTTGATTAGTA
1 TTTGATTAGTA
341337 TTT
1 TTT
341340 TATTTTCATA
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:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (11 bp):
TTTGATTAGTA
Found at i:342148 original size:29 final size:29
Alignment explanation
Indices: 342102--342187 Score: 102
Period size: 31 Copynumber: 2.9 Consensus size: 29
342092 AATTATAAAT
*
342102 TTTTTAAAAGGTTATAGATGAAAAATATAA
1 TTTTTAAAA-GTAATAGATGAAAAATATAA
*
342132 TTTTTAAAAGTAATAGATGAATAAAATTTAA
1 TTTTTAAAAGTAATAGATG-A-AAAATATAA
* *
342163 CTTTTAAAAGTCATAGAT-AAAAATA
1 TTTTTAAAAGTAATAGATGAAAAATA
342188 AAATATGAGT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
28 5 0.10
29 10 0.20
30 10 0.20
31 24 0.49
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.36
Consensus pattern (29 bp):
TTTTTAAAAGTAATAGATGAAAAATATAA
Found at i:342464 original size:23 final size:23
Alignment explanation
Indices: 342421--342465 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
342411 GTTCCATAAT
* *
342421 TTTATATTTATTTTAATAATTTA
1 TTTAAATTTATTTTAAAAATTTA
342444 TTTAAATTT-TTTTATAAAATTT
1 TTTAAATTTATTTTA-AAAATTT
342466 TTAATTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTAAATTTATTTTAAAAATTTA
Found at i:344232 original size:20 final size:20
Alignment explanation
Indices: 344204--344243 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
344194 TGTTGAACCT
*
344204 AATAAATATAAAAATTTTAA
1 AATAAATATAAAAATATTAA
* *
344224 AATATATATTAAAATATTAA
1 AATAAATATAAAAATATTAA
344244 CAAATTTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAAATATAAAAATATTAA
Found at i:344438 original size:17 final size:17
Alignment explanation
Indices: 344405--344454 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
344395 TAAAAAAATA
*
344405 AAATTTAAAGGTATTAAT
1 AAATTTAAA-ATATTAAT
344423 -AATATTAAAATATTAAT
1 AAAT-TTAAAATATTAAT
344440 AAATTTAAAAT-TTAA
1 AAATTTAAAATATTAA
344455 ATTTACATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
16 4 0.14
17 17 0.59
18 8 0.28
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (17 bp):
AAATTTAAAATATTAAT
Found at i:346235 original size:14 final size:14
Alignment explanation
Indices: 346213--346262 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
346203 TATTACATAA
346213 AAAATTAATTAAAAT
1 AAAA-TAATTAAAAT
346228 AAAATAA-TAAATAT
1 AAAATAATTAAA-AT
*
346242 AATATAATTAAAAT
1 AAAATAATTAAAAT
*
346256 ATAATAA
1 AAAATAA
346263 AAAAAATCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 4 0.13
14 18 0.60
15 8 0.27
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
AAAATAATTAAAAT
Found at i:346806 original size:15 final size:15
Alignment explanation
Indices: 346778--346825 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
346768 ACTCAAAAAT
* *
346778 AAAATGAAAGGCCCA
1 AAAATCAAAAGCCCA
*
346793 AAAATCAAAAGCCCG
1 AAAATCAAAAGCCCA
*
346808 AAACTCAAATAGCCCA
1 AAAATCAAA-AGCCCA
346824 AA
1 AA
346826 GTCAACCTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 20 0.74
16 7 0.26
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.08
Consensus pattern (15 bp):
AAAATCAAAAGCCCA
Found at i:349719 original size:33 final size:33
Alignment explanation
Indices: 349666--349764 Score: 90
Period size: 33 Copynumber: 3.0 Consensus size: 33
349656 TTGGAGAGAG
349666 CGCGCATGAAGCTAAAGAGAAAGTTTCAGAAAC
1 CGCGCATGAAGCTAAAGAGAAAGTTTCAGAAAC
* * * * *
349699 CGCGCATGAGGTTAAGGAGAAGGTTTCAGAGAC
1 CGCGCATGAAGCTAAAGAGAAAGTTTCAGAAAC
* * * * * * *
349732 TGCACATGAAACCAAAGACAACGTTGCAGAAAC
1 CGCGCATGAAGCTAAAGAGAAAGTTTCAGAAAC
349765 AGCCCAGCAA
Statistics
Matches: 50, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.39, C:0.19, G:0.26, T:0.15
Consensus pattern (33 bp):
CGCGCATGAAGCTAAAGAGAAAGTTTCAGAAAC
Found at i:351623 original size:18 final size:17
Alignment explanation
Indices: 351577--351626 Score: 63
Period size: 15 Copynumber: 3.1 Consensus size: 17
351567 AAATATGTTA
351577 AAATTTATATAA-A-AT
1 AAATTTATATAATATAT
351592 AAA-TTAT-TAATATAT
1 AAATTTATATAATATAT
351607 AAATTTATATAATTATAT
1 AAATTTATATAA-TATAT
351625 AA
1 AA
351627 CACTTTAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 3 0.10
14 5 0.17
15 8 0.27
16 4 0.13
17 3 0.10
18 7 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATTTATATAATATAT
Found at i:354243 original size:25 final size:25
Alignment explanation
Indices: 354214--354273 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
354204 CTGAATTCAT
* *
354214 ATATTATTCACATTAAATTTATATA
1 ATATTATTCAAATTAAACTTATATA
* * **
354239 TTATTATTTAAATTTTACTTATATA
1 ATATTATTCAAATTAAACTTATATA
354264 ATATTATTCA
1 ATATTATTCA
354274 TCGGATATCT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (25 bp):
ATATTATTCAAATTAAACTTATATA
Found at i:354438 original size:43 final size:43
Alignment explanation
Indices: 354390--354477 Score: 108
Period size: 43 Copynumber: 2.0 Consensus size: 43
354380 AATATCCAAC
* *
354390 AAACAATTTTCAAATA-AAATATAACAAATTAGATA-ACAAAAAA
1 AAACAATTCTAAAATACAAA-A-AACAAATTAGATAGACAAAAAA
*
354433 AAACAATTCTAAAATACAAAAAACAAGTTAGATAGTACAAAAAA
1 AAACAATTCTAAAATACAAAAAACAAATTAGATAG-ACAAAAAA
354477 A
1 A
354478 GATAAATACG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
42 12 0.31
43 15 0.38
44 12 0.31
ACGTcount: A:0.65, C:0.10, G:0.05, T:0.20
Consensus pattern (43 bp):
AAACAATTCTAAAATACAAAAAACAAATTAGATAGACAAAAAA
Found at i:354973 original size:13 final size:13
Alignment explanation
Indices: 354955--355043 Score: 70
Period size: 13 Copynumber: 5.9 Consensus size: 13
354945 CATAAAGTGT
354955 TGTATCGATACAA
1 TGTATCGATACAA
354968 TGTATCGATACATAA
1 TGTATCGATAC--AA
354983 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
355000 TGTATCGATACATAA
1 TGTATCGATAC--AA
355015 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
355032 TGTATCGATACA
1 TGTATCGATACA
355044 TAAGTTTTGT
Statistics
Matches: 64, Mismatches: 0, Indels: 24
0.73 0.00 0.27
Matches are distributed among these distances:
13 34 0.53
15 4 0.06
17 4 0.06
19 22 0.34
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:354990 original size:32 final size:32
Alignment explanation
Indices: 354935--355067 Score: 248
Period size: 32 Copynumber: 4.1 Consensus size: 32
354925 TTCAACGATT
354935 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
354968 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
355000 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
355032 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
355064 TGTA
1 TGTA
355068 AGCTACTGCC
Statistics
Matches: 99, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
32 86 0.87
33 13 0.13
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:354992 original size:19 final size:18
Alignment explanation
Indices: 354933--355062 Score: 110
Period size: 19 Copynumber: 7.8 Consensus size: 18
354923 ATTTCAACGA
354933 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
354952 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
354968 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
354984 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
355000 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
355016 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
355032 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
355048 TTTTGTATCGATACA
1 -TTTGTATCGATACA
355063 ATGTAAGCTA
Statistics
Matches: 92, Mismatches: 0, Indels: 38
0.71 0.00 0.29
Matches are distributed among these distances:
13 33 0.36
15 6 0.07
17 6 0.07
19 35 0.38
20 12 0.13
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:355123 original size:13 final size:12
Alignment explanation
Indices: 355104--355193 Score: 61
Period size: 13 Copynumber: 7.8 Consensus size: 12
355094 CATTACTCAA
355104 ATGTATCGAGAC
1 ATGTATCGAGAC
*
355116 ATTGTATCGATAC
1 A-TGTATCGAGAC
355129 AT-TACTC-A-A-
1 ATGTA-TCGAGAC
355138 ATGTATCGAGAC
1 ATGTATCGAGAC
*
355150 ATTGTATCGATAC
1 A-TGTATCGAGAC
355163 AT-TACTC-A-A-
1 ATGTA-TCGAGAC
355172 ATGTATCGAGAC
1 ATGTATCGAGAC
355184 ATTGTATCGA
1 A-TGTATCGA
355194 TACACTGATC
Statistics
Matches: 63, Mismatches: 2, Indels: 25
0.70 0.02 0.28
Matches are distributed among these distances:
9 8 0.13
10 8 0.13
11 8 0.13
12 9 0.14
13 30 0.48
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (12 bp):
ATGTATCGAGAC
Found at i:355127 original size:34 final size:34
Alignment explanation
Indices: 355084--355197 Score: 228
Period size: 34 Copynumber: 3.4 Consensus size: 34
355074 TGCCAAAAAA
355084 TGTATCGATACATTACTCAAATGTATCGAGACAT
1 TGTATCGATACATTACTCAAATGTATCGAGACAT
355118 TGTATCGATACATTACTCAAATGTATCGAGACAT
1 TGTATCGATACATTACTCAAATGTATCGAGACAT
355152 TGTATCGATACATTACTCAAATGTATCGAGACAT
1 TGTATCGATACATTACTCAAATGTATCGAGACAT
355186 TGTATCGATACA
1 TGTATCGATACA
355198 CTGATCTTTG
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 80 1.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (34 bp):
TGTATCGATACATTACTCAAATGTATCGAGACAT
Found at i:355262 original size:52 final size:52
Alignment explanation
Indices: 355206--355334 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
355196 CACTGATCTT
*
355206 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
355258 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
355310 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
355335 TCATATTTTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:361097 original size:2 final size:2
Alignment explanation
Indices: 361090--361120 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
361080 TCAATAAATA
361090 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
361121 ACCTATAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:361409 original size:27 final size:26
Alignment explanation
Indices: 361370--361468 Score: 94
Period size: 27 Copynumber: 3.8 Consensus size: 26
361360 AAAGTTACCC
*
361370 TTTTATTTGTAAAAAATGGTGATTCCT
1 TTTTATTTATAAAAAATGGTGATT-CT
* * *
361397 TTTTATTTATAAAAGATGATGGTTCT
1 TTTTATTTATAAAAAATGGTGATTCT
* *
361423 TTTTGTTTATAAAAAATGGT-AGT-T
1 TTTTATTTATAAAAAATGGTGATTCT
* * *
361447 TATTATTTATCAAAATTGGTGA
1 TTTTATTTATAAAAAATGGTGA
361469 CTAATTTTTA
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
24 17 0.29
25 2 0.03
26 19 0.33
27 20 0.34
ACGTcount: A:0.32, C:0.04, G:0.15, T:0.48
Consensus pattern (26 bp):
TTTTATTTATAAAAAATGGTGATTCT
Found at i:366089 original size:27 final size:26
Alignment explanation
Indices: 366019--366081 Score: 90
Period size: 27 Copynumber: 2.4 Consensus size: 26
366009 AAAAACTACC
*
366019 CTTTTTGTTTGTTAAAAATGGTGATT
1 CTTTTTGTTTGTAAAAAATGGTGATT
* *
366045 CTTTTTTGTTTGTAAAAAATTGTGGTT
1 C-TTTTTGTTTGTAAAAAATGGTGATT
366072 CTTTTTGTTT
1 CTTTTTGTTT
366082 ATCAAAAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 10 0.30
27 23 0.70
ACGTcount: A:0.19, C:0.05, G:0.17, T:0.59
Consensus pattern (26 bp):
CTTTTTGTTTGTAAAAAATGGTGATT
Found at i:366564 original size:33 final size:31
Alignment explanation
Indices: 366527--366600 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
366517 TTTTGATTGG
* *
366527 TATAAT-TTACTTTAAATTATTATTTGAATAATA
1 TATAATATT-CTTTAAA-T-TTAATTAAATAATA
*
366560 TATAATATTTTTTAAATTTAATTAAATAATA
1 TATAATATTCTTTAAATTTAATTAAATAATA
366591 TATAAATATT
1 TAT-AATATT
366601 AATATAAAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
31 15 0.42
32 7 0.19
33 12 0.33
34 2 0.06
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (31 bp):
TATAATATTCTTTAAATTTAATTAAATAATA
Found at i:366615 original size:33 final size:31
Alignment explanation
Indices: 366553--366615 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
366543 TTATTATTTG
* * **
366553 AATAATATATAATATTTTTTAAATTTAATTA
1 AATAATATATAATATTATATAAAAGTAATTA
366584 AATAATATATAAATATTAATATAAAAGTAATT
1 AATAATATAT-AATATT-ATATAAAAGTAATT
366616 TTATATAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
31 10 0.38
32 6 0.23
33 10 0.38
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (31 bp):
AATAATATATAATATTATATAAAAGTAATTA
Found at i:368342 original size:26 final size:25
Alignment explanation
Indices: 368301--368351 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 25
368291 AAGTTATAAT
*
368301 TATTTTAAAATTTTATTTTATATTA
1 TATTTTAAAATATTATTTTATATTA
368326 TATTATTAAAATATTATTTTATATTA
1 TATT-TTAAAATATTATTTTATATTA
368352 ATAATTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
TATTTTAAAATATTATTTTATATTA
Found at i:368347 original size:21 final size:20
Alignment explanation
Indices: 368318--368372 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
368308 AAATTTTATT
* *
368318 TTATATTATATTATTAAAATA
1 TTATTTTATATTAAT-AAATA
*
368339 TTATTTTATATTAATAATTA
1 TTATTTTATATTAATAAATA
368359 -TATTTTATAATTAA
1 TTATTTTAT-ATTAA
368373 ATTTAAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.27
20 9 0.30
21 13 0.43
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTATTTTATATTAATAAATA
Found at i:368362 original size:19 final size:18
Alignment explanation
Indices: 368318--368373 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 18
368308 AAATTTTATT
*
368318 TTATATTATATTATTAAAA
1 TTATATTTTA-TATTAAAA
368337 -TATTATTTTATATTAATAA
1 TTA-TATTTTATATTAA-AA
368356 TTATATTTTATAATTAAA
1 TTATATTTTAT-ATTAAA
368374 TTTAAATAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
18 8 0.25
19 17 0.53
20 7 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTATATTTTATATTAAAA
Found at i:374922 original size:17 final size:17
Alignment explanation
Indices: 374896--374937 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
374886 TATTTTTATA
374896 TTAAAATAAATATAATT
1 TTAAAATAAATATAATT
* *
374913 TTAAATTAAATTTAATT
1 TTAAAATAAATATAATT
*
374930 ATAAAATA
1 TTAAAATA
374938 TATAATTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAAAATAAATATAATT
Found at i:376709 original size:23 final size:22
Alignment explanation
Indices: 376678--376733 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 22
376668 ATATTAAAAA
*
376678 TAAATATTAAATTATTCACTAT
1 TAAATATTAAAATATTCACTAT
*
376700 TAAAATATTAAAAATATTTACTAT
1 T-AAATATT-AAAATATTCACTAT
376724 TAAATATTAA
1 TAAATATTAA
376734 TATTCTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 3 0.10
23 14 0.47
24 13 0.43
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAATATTAAAATATTCACTAT
Found at i:377170 original size:21 final size:20
Alignment explanation
Indices: 377128--377185 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 20
377118 TTATTGAAAA
*
377128 TTAAAATATTAAAATAATTT
1 TTAAAATATAAAAATAATTT
377148 TTAAAAT-TAAAAATTATATTT
1 TTAAAATATAAAAA-TA-ATTT
* *
377169 TTATTAATATAATAATA
1 TTA-AAATATAAAAATA
377186 TTTGACTCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 5 0.16
20 9 0.29
21 7 0.23
22 5 0.16
23 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAAAATATAAAAATAATTT
Found at i:378946 original size:13 final size:13
Alignment explanation
Indices: 378928--378953 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
378918 CAATTTTTTG
378928 TGTATCGATACAT
1 TGTATCGATACAT
378941 TGTATCGATACAT
1 TGTATCGATACAT
378954 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:378968 original size:32 final size:33
Alignment explanation
Indices: 378908--378971 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
378898 TACAAGCCAA
** *
378908 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
378941 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
378972 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:380900 original size:13 final size:13
Alignment explanation
Indices: 380882--380906 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
380872 ACTGAAGCAA
380882 TGTATCGATACAT
1 TGTATCGATACAT
380895 TGTATCGATACA
1 TGTATCGATACA
380907 ATCTGGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:381521 original size:23 final size:24
Alignment explanation
Indices: 381476--381522 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
381466 CAAAGAATTG
*
381476 AACACAAATTCAATTAAGCACAAA
1 AACACAAATTCAATTAAGAACAAA
381500 AACACAAA-TCAATTGAA-AACAAA
1 AACACAAATTCAATT-AAGAACAAA
381523 TTTTCAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.62, C:0.19, G:0.04, T:0.15
Consensus pattern (24 bp):
AACACAAATTCAATTAAGAACAAA
Found at i:384631 original size:13 final size:13
Alignment explanation
Indices: 384613--384638 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
384603 CAATTTTTTG
384613 TGTATCGATACAT
1 TGTATCGATACAT
384626 TGTATCGATACAT
1 TGTATCGATACAT
384639 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:384653 original size:32 final size:33
Alignment explanation
Indices: 384593--384656 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
384583 TACAAGCCAA
** *
384593 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
384626 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
384657 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:385580 original size:16 final size:15
Alignment explanation
Indices: 385555--385588 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
385545 AAATCGAAAT
*
385555 TAATTCAAAAATAATA
1 TAATTAAAAAATAA-A
385571 TAATTAAAAAATAAA
1 TAATTAAAAAATAAA
385586 TAA
1 TAA
385589 ACAAAAATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (15 bp):
TAATTAAAAAATAAA
Found at i:385867 original size:90 final size:90
Alignment explanation
Indices: 385724--385904 Score: 290
Period size: 90 Copynumber: 2.0 Consensus size: 90
385714 ACCTTCACTC
* * *
385724 AAAAAAAATTTGTAATAAATTATTTTGTTTTCTTATTTTAAAAAATTATATATTAATTAACTCCA
1 AAAAAAAAATTATAATAAATTATTTTGTTTTCTTATTTTAAAAAATTACATATTAATTAACTCCA
*
385789 AAAACTAATCACATTTTAAAAACTA
66 AAAACAAATCACATTTTAAAAACTA
* *
385814 AAAAAAAAATTATCATAAATTATTTTGTTTTCTTATTTTAAAAAATTACATATTAATTAACTCTA
1 AAAAAAAAATTATAATAAATTATTTTGTTTTCTTATTTTAAAAAATTACATATTAATTAACTCCA
* *
385879 AAAGCAAATCACGTTTTAAAAACTA
66 AAAACAAATCACATTTTAAAAACTA
385904 A
1 A
385905 CCCATATTTC
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 83 1.00
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.40
Consensus pattern (90 bp):
AAAAAAAAATTATAATAAATTATTTTGTTTTCTTATTTTAAAAAATTACATATTAATTAACTCCA
AAAACAAATCACATTTTAAAAACTA
Found at i:403571 original size:30 final size:30
Alignment explanation
Indices: 403530--403596 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 30
403520 ATTAATTTAT
* *
403530 ATTAGAAATTT-ATTTAGGTATAAATTAAAA
1 ATTAAAAATTTAATTTA-ATATAAATTAAAA
403560 ATTAAAAATTTAATTTAATATAAATTAAAA
1 ATTAAAAATTTAATTTAATATAAATTAAAA
403590 ATTAAAA
1 ATTAAAA
403597 GCTTGTTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 29 0.85
31 5 0.15
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (30 bp):
ATTAAAAATTTAATTTAATATAAATTAAAA
Found at i:409536 original size:20 final size:20
Alignment explanation
Indices: 409497--409536 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
409487 TTATTTTTTT
*
409497 ATATTATAATTGTATTTAAA
1 ATATTATAATTGTATATAAA
409517 ATATTATATATT-TATATAAA
1 ATATTATA-ATTGTATATAAA
409537 TTTTGACATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
ATATTATAATTGTATATAAA
Found at i:411649 original size:29 final size:27
Alignment explanation
Indices: 411602--411657 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
411592 TATTTTAATA
* * *
411602 TTTAAATTTATTTTCAAAATATCATTTTT
1 TTTAAATATATTAT-AAAA-ATTATTTTT
411631 TTTAAATATATTATAAAAATTATTTTT
1 TTTAAATATATTATAAAAATTATTTTT
411658 ATCATACTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 8 0.33
28 4 0.17
29 12 0.50
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (27 bp):
TTTAAATATATTATAAAAATTATTTTT
Found at i:411852 original size:17 final size:17
Alignment explanation
Indices: 411830--411881 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 17
411820 TTACGTTACA
411830 AAAATAATAATATTTTG
1 AAAATAATAATATTTTG
411847 --AA-AAT-ATATTTT-
1 AAAATAATAATATTTTG
*
411859 AAAATAATAGTATTTTG
1 AAAATAATAATATTTTG
*
411876 ATAATA
1 AAAATA
411882 TATTTAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
13 7 0.25
14 5 0.18
15 5 0.18
16 6 0.21
17 5 0.18
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (17 bp):
AAAATAATAATATTTTG
Found at i:411863 original size:29 final size:29
Alignment explanation
Indices: 411830--411886 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
411820 TTACGTTACA
411830 AAAATAATAATATTTTGAAAATATATTTT
1 AAAATAATAATATTTTGAAAATATATTTT
* *
411859 AAAATAATAGTATTTTGATAATATATTT
1 AAAATAATAATATTTTGAAAATATATTT
411887 AAATATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (29 bp):
AAAATAATAATATTTTGAAAATATATTTT
Found at i:411864 original size:12 final size:13
Alignment explanation
Indices: 411839--411886 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
411829 AAAAATAATA
411839 ATATTTTGAAAAT
1 ATATTTTGAAAAT
*
411852 ATATTTTAAAATAAT
1 ATATTTT-GAA-AAT
*
411867 AGTATTTTGATAAT
1 A-TATTTTGAAAAT
411881 ATATTT
1 ATATTT
411887 AAATATTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
13 12 0.41
14 6 0.21
15 5 0.17
16 6 0.21
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (13 bp):
ATATTTTGAAAAT
Found at i:411932 original size:15 final size:14
Alignment explanation
Indices: 411885--411938 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 14
411875 GATAATATAT
411885 TTAAATATTAAAAGA
1 TTAAATATTAAAA-A
*
411900 -AAAATAGTTAAAAA
1 TTAAATA-TTAAAAA
*
411914 TTAAATATTAAAATT
1 TTAAATATTAAAA-A
411929 TTAAATATTA
1 TTAAATATTA
411939 TATAAGATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
14 12 0.36
15 21 0.64
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (14 bp):
TTAAATATTAAAAA
Found at i:412860 original size:2 final size:2
Alignment explanation
Indices: 412820--412849 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
412810 CTCTTGAAGC
412820 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
412850 AAAGTATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:413352 original size:18 final size:18
Alignment explanation
Indices: 413312--413353 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
413302 ATTAAAATAT
* *
413312 ATAAAATAATTATTTTTA
1 ATAAAATAATTATTATAA
413330 ATAAAATAA-TATTATAA
1 ATAAAATAATTATTATAA
*
413347 ATTAAAT
1 ATAAAAT
413354 TACGTTAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATAAAATAATTATTATAA
Found at i:417795 original size:13 final size:13
Alignment explanation
Indices: 417765--417800 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
417755 ATGGTACCCT
*
417765 TGTATCGATA-AG
1 TGTATCGATACAA
417777 TGTATCGATACAA
1 TGTATCGATACAA
417790 TGTATCGATAC
1 TGTATCGATAC
417801 TAAGAGCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:423283 original size:19 final size:19
Alignment explanation
Indices: 423255--423324 Score: 95
Period size: 19 Copynumber: 3.6 Consensus size: 19
423245 TATTTTAGTG
423255 TGTATCGATACAATGAACA
1 TGTATCGATACAATGAACA
* * *
423274 TGTATTGATACAAAGCAATA
1 TGTATCGATACAATG-AACA
*
423294 TGTATCGATACAATAAACA
1 TGTATCGATACAATGAACA
423313 TGTATCGATACA
1 TGTATCGATACA
423325 TCTGGGTGTG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
19 28 0.65
20 15 0.35
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (19 bp):
TGTATCGATACAATGAACA
Found at i:426562 original size:12 final size:12
Alignment explanation
Indices: 426532--426567 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 12
426522 TTATTAATTA
426532 ATTTTACTTTTTT
1 ATTTTA-TTTTTT
426545 AGTTTTATTTTTT
1 A-TTTTATTTTTT
426558 ATTTTATTTT
1 ATTTTATTTT
426568 ATTTTTGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 9 0.41
13 8 0.36
14 5 0.23
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.78
Consensus pattern (12 bp):
ATTTTATTTTTT
Found at i:427306 original size:24 final size:22
Alignment explanation
Indices: 427279--427332 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 22
427269 TTATTATACA
427279 ATAAAATTTAATTTAAAATTTTAT
1 ATAAAATTTAA-TTAAAA-TTTAT
*
427303 ATAAATAATTAATTAAAATTTAT
1 ATAAA-ATTTAATTAAAATTTAT
427326 A-AAAATT
1 ATAAAATT
427333 ACCAAAACCC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 2 0.07
22 3 0.11
23 6 0.22
24 11 0.41
25 5 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
ATAAAATTTAATTAAAATTTAT
Found at i:427324 original size:23 final size:25
Alignment explanation
Indices: 427286--427331 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
427276 ACAATAAAAT
*
427286 TTAATTTAAAATTTTATATAAATAA
1 TTAATTTAAAATTTTATAAAAATAA
427311 TTAA-TTAAAA-TTTATAAAAAT
1 TTAATTTAAAATTTTATAAAAAT
427332 TACCAAAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 6 0.30
25 4 0.20
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TTAATTTAAAATTTTATAAAAATAA
Found at i:427434 original size:17 final size:16
Alignment explanation
Indices: 427395--427438 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
427385 TAGTATTGCT
* *
427395 GTTAGAAAAAGTTTGG
1 GTTAAAAAAAGTTTAG
427411 GTTAAAAAAAGTTTAG
1 GTTAAAAAAAGTTTAG
*
427427 GTTGAAAAAAGT
1 GTTAAAAAAAGT
427439 ATATTTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.45, C:0.00, G:0.25, T:0.30
Consensus pattern (16 bp):
GTTAAAAAAAGTTTAG
Found at i:429105 original size:21 final size:20
Alignment explanation
Indices: 429016--429089 Score: 105
Period size: 20 Copynumber: 3.6 Consensus size: 20
429006 TTCAACAAAT
*
429016 TGTATCGATACA-ATAGGGTAA
1 TGTATCGATACATA-AGTG-AA
*
429037 TGTATTGATACATAAGTGAA
1 TGTATCGATACATAAGTGAA
429057 TGTATCGATACATAAGTGAA
1 TGTATCGATACATAAGTGAA
429077 TGTATCGATACAT
1 TGTATCGATACAT
429090 GTTTGAAATG
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
20 34 0.69
21 14 0.29
22 1 0.02
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.32
Consensus pattern (20 bp):
TGTATCGATACATAAGTGAA
Found at i:431901 original size:50 final size:50
Alignment explanation
Indices: 431814--431909 Score: 129
Period size: 50 Copynumber: 1.9 Consensus size: 50
431804 TAAATTTCTA
* * *
431814 GATTTTTCATCTCGGGGATACTCAAACCCTGACTTTATTTCTAAAATATT
1 GATTTTTCATCTCAGGGATACTCAAACCCCGACTTTATTTCCAAAATATT
** **
431864 GATTTTTCATCTCAGGGATACTTTAACCCCGGTTTTATTTCCAAAA
1 GATTTTTCATCTCAGGGATACTCAAACCCCGACTTTATTTCCAAAA
431910 AATCAATTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 39 1.00
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (50 bp):
GATTTTTCATCTCAGGGATACTCAAACCCCGACTTTATTTCCAAAATATT
Found at i:431919 original size:50 final size:50
Alignment explanation
Indices: 431815--431921 Score: 124
Period size: 50 Copynumber: 2.1 Consensus size: 50
431805 AAATTTCTAG
* * * * **
431815 ATTTTTCATCTCGGGGATACTCAAACCCTGACTTTATTTCTAAAATATTG
1 ATTTTTCATCTCAGGGATACTCAAACCCCGACTTTATTTCCAAAAAATCA
** **
431865 ATTTTTCATCTCAGGGATACTTTAACCCCGGTTTTATTTCCAAAAAATCA
1 ATTTTTCATCTCAGGGATACTCAAACCCCGACTTTATTTCCAAAAAATCA
431915 ATTTTTC
1 ATTTTTC
431922 CACAGTCGAG
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (50 bp):
ATTTTTCATCTCAGGGATACTCAAACCCCGACTTTATTTCCAAAAAATCA
Found at i:432032 original size:79 final size:79
Alignment explanation
Indices: 431878--432257 Score: 314
Period size: 79 Copynumber: 4.8 Consensus size: 79
431868 TTTCATCTCA
** ** * * * * * * * *
431878 GGGATACTTTAACCCCGGTTTTATTTCCAAAAAATCAATTTTTCCACAGTCGAGGATACTCCAAT
1 GGGATACTCCAACCCCGACTTTATTTCTAAAACATCGATTTCT-CACAATCGGGGATACTCTAAC
*
431943 CCTGTTATTTTTGAG
65 CCCGTTATTTTTGAG
* * * *
431958 GGGATACTCCAACCTCGGCTTTATTTCTAAAATATTGATTTCTCACAATCGGGGATACTCTAACC
1 GGGATACTCCAACCCCGACTTTATTTCTAAAACATCGATTTCTCACAATCGGGGATACTCTAACC
* *
432023 CCGTTATTTTGGCG
66 CCGTTATTTTTGAG
* * * * * * * *
432037 GGGATACTCCAACCCCGGCCTTATTTCTAAAGCGTCAATTTTTCACAATCGGGGATAGTCCAACC
1 GGGATACTCCAACCCCGACTTTATTTCTAAAACATCGATTTCTCACAATCGGGGATACTCTAACC
*
432102 CCGTTATTTTCGAG
66 CCGTTATTTTTGAG
* * ** * ** *
432116 GGGATACTCCAACCTCGATTTTATTT-TCAAAATGTCGATTTC-CTATAATTAGGGATGCTCTAA
1 GGGATACTCCAACCCCGACTTTATTTCT-AAAACATCGATTTCTC-ACAATCGGGGATACTCTAA
** *
432179 CCTTGTTATTTCTGAG
64 CCCCGTTATTTTTGAG
* * * * *
432195 GGGATACTCCAACCCCGATTTTATTTCTAGAACACCGATTTTTCATAATCAGGGGATACTCTA
1 GGGATACTCCAACCCCGACTTTATTTCTAAAACATCGATTTCTCACAATC-GGGGATACTCTA
432258 GCCTCGTTGT
Statistics
Matches: 240, Mismatches: 55, Indels: 10
0.79 0.18 0.03
Matches are distributed among these distances:
78 2 0.01
79 192 0.80
80 46 0.19
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (79 bp):
GGGATACTCCAACCCCGACTTTATTTCTAAAACATCGATTTCTCACAATCGGGGATACTCTAACC
CCGTTATTTTTGAG
Found at i:432236 original size:158 final size:157
Alignment explanation
Indices: 431878--432255 Score: 411
Period size: 158 Copynumber: 2.4 Consensus size: 157
431868 TTTCATCTCA
** * * * * *
431878 GGGATACTTTAACCCCGGTTTTATTTCCAAAAAATCAATTTTTCCACAGTCGAGGATACTCCAAT
1 GGGATACTCCAACCCCGGTTTTATTT-CTAAACATCAATTTTT-CACAATCGGGGATACTCCAAC
* * * *
431943 CCTGTTATTTTTGAGGGGATACTCCAACCTCGGCTTTATTTCTAAAATATTGATTTCTCACAATC
64 CCCGTTATTTTCGAGGGGATACTCCAACCTCGACTTTATTTCTAAAATATCGATTTCTCACAATC
* *
432008 GGGGATACTCTAACCCCGTTATTTTGGCG
129 AGGGATACTCTAACCCCGTTATTTTGGAG
** * *
432037 GGGATACTCCAACCCCGGCCTTATTTCTAAAGCGTCAATTTTTCACAATCGGGGATAGTCCAACC
1 GGGATACTCCAACCCCGGTTTTATTTCTAAA-CATCAATTTTTCACAATCGGGGATACTCCAACC
* * *
432102 CCGTTATTTTCGAGGGGATACTCCAACCTCGATTTTATTT-TCAAAATGTCGATTTC-CTATAAT
65 CCGTTATTTTCGAGGGGATACTCCAACCTCGACTTTATTTCT-AAAATATCGATTTCTC-ACAAT
* * **
432165 TAGGGATGCTCTAACCTTGTTATTTCT-GAG
128 CAGGGATACTCTAACCCCGTTATTT-TGGAG
* * * *
432195 GGGATACTCCAACCCCGATTTTATTTCTAGAACACCGATTTTTCATAATCAGGGGATACTC
1 GGGATACTCCAACCCCGGTTTTATTTCTA-AACATCAATTTTTCACAATC-GGGGATACTC
432256 TAGCCTCGTT
Statistics
Matches: 181, Mismatches: 32, Indels: 12
0.80 0.14 0.05
Matches are distributed among these distances:
157 2 0.01
158 136 0.75
159 43 0.24
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (157 bp):
GGGATACTCCAACCCCGGTTTTATTTCTAAACATCAATTTTTCACAATCGGGGATACTCCAACCC
CGTTATTTTCGAGGGGATACTCCAACCTCGACTTTATTTCTAAAATATCGATTTCTCACAATCAG
GGATACTCTAACCCCGTTATTTTGGAG
Found at i:433421 original size:18 final size:18
Alignment explanation
Indices: 433398--433439 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
433388 ATCACCTTCT
433398 TCTCAAATAAATGATTGA
1 TCTCAAATAAATGATTGA
433416 TCTCAAATAAATGATTGA
1 TCTCAAATAAATGATTGA
*
433434 TTTCAA
1 TCTCAA
433440 TATGCACTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.36
Consensus pattern (18 bp):
TCTCAAATAAATGATTGA
Found at i:444620 original size:13 final size:14
Alignment explanation
Indices: 444602--444653 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 14
444592 TCTTCTTTTT
444602 AAAAAAAACAACAAA
1 AAAAAAAACAAC-AA
444617 AAAACAAAACAACAA
1 AAAA-AAAACAACAA
*
444632 AAAAAAATAAAACAA
1 AAAAAAA-ACAACAA
*
444647 AGAAAAA
1 AAAAAAA
444654 TGAGAGAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
14 3 0.09
15 22 0.67
16 8 0.24
ACGTcount: A:0.85, C:0.12, G:0.02, T:0.02
Consensus pattern (14 bp):
AAAAAAAACAACAA
Found at i:444622 original size:8 final size:8
Alignment explanation
Indices: 444605--444652 Score: 53
Period size: 8 Copynumber: 5.9 Consensus size: 8
444595 TCTTTTTAAA
444605 AAAAACAAC
1 AAAAA-AAC
444614 AAAAAAAC
1 AAAAAAAC
*
444622 AAAACAAC
1 AAAAAAAC
444630 AAAAAAA-
1 AAAAAAAC
*
444637 AATAAAAC
1 AAAAAAAC
444645 AAAGAAAA
1 AAA-AAAA
444653 ATGAGAGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
7 6 0.18
8 18 0.55
9 9 0.27
ACGTcount: A:0.83, C:0.12, G:0.02, T:0.02
Consensus pattern (8 bp):
AAAAAAAC
Found at i:444627 original size:16 final size:15
Alignment explanation
Indices: 444602--444653 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 15
444592 TCTTCTTTTT
444602 AAAAAAAACAACAAA
1 AAAAAAAACAACAAA
444617 AAAACAAAACAACAAA
1 AAAA-AAAACAACAAA
444633 AAAAAATAA-AACAAA
1 AAAAAA-AACAACAAA
444648 GAAAAA
1 -AAAAA
444654 TGAGAGAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
15 12 0.35
16 22 0.65
ACGTcount: A:0.85, C:0.12, G:0.02, T:0.02
Consensus pattern (15 bp):
AAAAAAAACAACAAA
Found at i:444653 original size:18 final size:18
Alignment explanation
Indices: 444603--444646 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
444593 CTTCTTTTTA
*
444603 AAAAAAACAACAAAAAAAC
1 AAAACAACAA-AAAAAAAC
*
444622 AAAACAACAAAAAAAAAT
1 AAAACAACAAAAAAAAAC
444640 AAAACAA
1 AAAACAA
444647 AGAAAAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.84, C:0.14, G:0.00, T:0.02
Consensus pattern (18 bp):
AAAACAACAAAAAAAAAC
Found at i:445799 original size:94 final size:98
Alignment explanation
Indices: 445621--445806 Score: 247
Period size: 94 Copynumber: 1.9 Consensus size: 98
445611 ATCTAAACTT
** *
445621 TCTCCTTTCACTTTTTAGTCCTCAAAGAGCAAGACGCCTTCTCCTTTCAAAGCCCACACAAGTTG
1 TCTCCTTTCACCCTTTAGTCCTCAAAAAGCAAGACGCC-TCT-CTTTCAAAGCCCACACAAGTTG
445686 GTAGCACTTCCCAGTCCTCAAACAGCAGGACGCTC
64 GTAGCACTTCCCAGTCCTCAAACAGCAGGACGCTC
*
445721 TCTCCTTTCACCCTTTAGTCCTCAAAAAGCAGGACG-C-CT-TTT-AAAGCCCACACAAGTTGGT
1 TCTCCTTTCACCCTTTAGTCCTCAAAAAGCAAGACGCCTCTCTTTCAAAGCCCACACAAGTTGGT
* * *
445782 GGCACCTT-CTAGTCCTCAAAGAGCA
66 AGCA-CTTCCCAGTCCTCAAACAGCA
445807 AGACACCTTT
Statistics
Matches: 78, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
94 37 0.47
95 6 0.08
97 2 0.03
99 1 0.01
100 32 0.41
ACGTcount: A:0.26, C:0.33, G:0.16, T:0.26
Consensus pattern (98 bp):
TCTCCTTTCACCCTTTAGTCCTCAAAAAGCAAGACGCCTCTCTTTCAAAGCCCACACAAGTTGGT
AGCACTTCCCAGTCCTCAAACAGCAGGACGCTC
Found at i:445862 original size:61 final size:61
Alignment explanation
Indices: 445757--446436 Score: 793
Period size: 61 Copynumber: 11.1 Consensus size: 61
445747 AAGCAGGACG
*
445757 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAAGACACCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAAGACGCCTTTT
* * *
445818 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCTTCAAAGAGCAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAAGACGCCTTTT
* * * * * * *
445879 CCTTTTAAAGCCCACACAAGTTGGTGGCACCCTCCAATCCTCAAGGAGCAGGATGTCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAAGACGCCTTTT
* * * *
445940 CCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTTCAGTTCTCAAGGAGCAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCT-AGTCCTCAAAGAGCAAGACGCCTTTT
* * * *
446001 CCTTTTAAAGCCCACATAAGTTGGTGGCACTTTTCTAGTACTCAAAGAGCAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTCTAGTCCTCAAAGAGCAAGACGCCTTTT
* * *
446063 CCTTTTAAAGCCCACACAAGCTGGTGGCACCCTTC-AGTCCTCAAAGAGCAGGATGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTCTAGTCCTCAAAGAGCAAGACGCCTTTT
* * * *
446124 TCTTTTCAAGGCCCACACAAGCTGGTGGCACCCTT-TAGTCCTCAAAGAGCAAGATGCCTTTT
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCA-CCTTCTAGTCCTCAAAGAGCAAGACGCCTTTT
* *
446186 -CTTTTCAAAGCCCACACAAGTTGGTGGCACC-TCTTAGTTCTCAAAGAGCAAGACACCTTTT
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTC-TAGTCCTCAAAGAGCAAGACGCCTTTT
* **
446247 -CTTTTCAAAGCCCACACAAGTTGGTGGCACC-TCTTAGTCCTTAAAGAGCAAGATACCTTTT
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTC-TAGTCCTCAAAGAGCAAGACGCCTTTT
* * * * ** * *
446308 TCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCATCAAA-AATAAGGACACATTTT
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAA-GACGCCTTTT
* * * *
446370 -CTTTTCAAAGCCCACACAAGTTGATGGCACTTTTTAGTCCTCAAAGAGCATGACGCCTTTT
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAAGACGCCTTTT
*
446431 CTTTTT
1 CCTTTT
446437 CTCTTTTGCC
Statistics
Matches: 550, Mismatches: 56, Indels: 25
0.87 0.09 0.04
Matches are distributed among these distances:
59 1 0.00
60 4 0.01
61 381 0.69
62 159 0.29
63 5 0.01
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (61 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAAGACGCCTTTT
Found at i:446114 original size:184 final size:183
Alignment explanation
Indices: 445757--446436 Score: 881
Period size: 184 Copynumber: 3.7 Consensus size: 183
445747 AAGCAGGACG
*
445757 CCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAAGACACCTTTTCCT
1 CCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAGACACCTTTT-CT
* **
445821 TTT-AAAGCCCACACAAGTTGGTGGCACCTTCCAGTCTTCAAAGAGCAGGACGCCTTTTCCTTTT
65 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTTAGTC-TCAAAGAGCAGGACGCCTTTTCCTTTT
* * * *
445885 AAAGCCCACACAAGTTGGTGGCACCCTCCAATCCTCAAGGAGCAGGATGTCTTTT
129 AAAGCCCACACAAGTTGGTGGCACCCTTCAGTCCTCAAAGAGCAGGATGCCTTTT
* * * *
445940 CCTTTT-AAAGCCCACACAAGTTGGTGGCA-CTTTTCAGTTCTCAAGGAGCAGGACGCCTTTTCC
1 CCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTT-AGTCCTCAAAGAGCAAGACACCTTTT-C
*
446003 TTTT-AAAGCCCACATAAGTTGGTGGCACTTTTCTAGTACTCAAAGAGCAGGACGCCTTTTCCTT
64 TTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-TAGT-CTCAAAGAGCAGGACGCCTTTTCCTT
*
446067 TTAAAGCCCACACAAGCTGGTGGCACCCTTCAGTCCTCAAAGAGCAGGATGCCTTTT
127 TTAAAGCCCACACAAGTTGGTGGCACCCTTCAGTCCTCAAAGAGCAGGATGCCTTTT
* * * * **
446124 TCTTTTCAAGGCCCACACAAGCTGGTGGCACCCTTTAGTCCTCAAAGAGCAAGATGCCTTTTCTT
1 CCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAGACACCTTTTCTT
* * * *
446189 TTCAAAGCCCACACAAGTTGGTGGCACCTCTTAGTTCTCAAAGAGCAAGACACCTTTT-CTTTTC
66 TTCAAAGCCCACACAAGTTGGTGGCACTTTTTAG-TCTCAAAGAGCAGGACGCCTTTTCCTTTT-
* * *
446253 AAAGCCCACACAAGTTGGTGGCACCTCTT-AGTCCTTAAAGAGCAAGATACCTTTT
129 AAAGCCCACACAAGTTGGTGGCACC-CTTCAGTCCTCAAAGAGCAGGATGCCTTTT
* * * ** *
446308 TCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCATCAAA-AATAAGGACACATTTTCT
1 CCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAA-GACACCTTTTCT
* * *
446372 TTTCAAAGCCCACACAAGTTGATGGCACTTTTTAGTCCTCAAAGAGCATGACGCCTTTTCTTTTT
65 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTTAGT-CTCAAAGAGCAGGACGCCTTTTCCTTTT
446437 CTCTTTTGCC
Statistics
Matches: 438, Mismatches: 47, Indels: 22
0.86 0.09 0.04
Matches are distributed among these distances:
182 4 0.01
183 91 0.21
184 262 0.60
185 77 0.18
186 4 0.01
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (183 bp):
CCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAGACACCTTTTCTT
TTCAAAGCCCACACAAGTTGGTGGCACTTTTTAGTCTCAAAGAGCAGGACGCCTTTTCCTTTTAA
AGCCCACACAAGTTGGTGGCACCCTTCAGTCCTCAAAGAGCAGGATGCCTTTT
Found at i:446437 original size:123 final size:120
Alignment explanation
Indices: 445758--446436 Score: 813
Period size: 123 Copynumber: 5.5 Consensus size: 120
445748 AGCAGGACGC
* *
445758 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAAGACACCTTTTCCTTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAGACGCCTTTTCCTTT
** *
445823 TAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCTTCAAAGAGCAGGACGCCTTTT
66 TAAAGCCCACACAAGTTGGTGGCACCTTTTAGTC-TCAAAGAGCAGGACACCTTTT
* ** * * * * *
445879 CCTTTTAAAGCCCACACAAGTTGGTGGCACCCTCCAATCCTCAAGGAGCAGGATGTCTTTTCCTT
1 -CTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAGACGCCTTTTCCTT
* *
445944 TTAAAGCCCACACAAGTTGGTGGCA-CTTTTCAGTTCTCAAGGAGCAGGACGCCTTTT
65 TTAAAGCCCACACAAGTTGGTGGCACCTTTT-AG-TCTCAAAGAGCAGGACACCTTTT
* * * *
446001 CCTTTTAAAGCCCACATAAGTTGGTGGCACTTTTCTAGTACTCAAAGAGCAGGACGCCTTTTCCT
1 -CTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-TAGTCCTCAAAGAGCAAGACGCCTTTTCCT
* * * **
446066 TTTAAAGCCCACACAAGCTGGTGGCACCCTTCAGTCCTCAAAGAGCAGGATGCCTTTTT
64 TTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGT-CTCAAAGAGCAGGACACC-TTTT
* * * *
446125 CTTTTCAAGGCCCACACAAGCTGGTGGCACCCTTTAGTCCTCAAAGAGCAAGATGCCTTTT-CTT
1 CTTTT-AAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAGACGCCTTTTCCTT
* *
446189 TTCAAAGCCCACACAAGTTGGTGGCACCTCTTAGTTCTCAAAGAGCAAGACACCTTTT
65 TT-AAAGCCCACACAAGTTGGTGGCACCTTTTAG-TCTCAAAGAGCAGGACACCTTTT
* * ** *
446247 CTTTTCAAAGCCCACACAAGTTGGTGGCACCTCTTAGTCCTTAAAGAGCAAGATACCTTTTTCTT
1 CTTTT-AAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAGACGCCTTTTCCTT
* * ** *
446312 TTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCATCAAAAATAAGGACACATTTT
65 TT-AAAGCCCACACAAGTTGGTGGCACCTTTTAGTC-TCAAAGAGCAGGACACCTTTT
* * * *
446370 CTTTTCAAAGCCCACACAAGTTGATGGCACTTTTTAGTCCTCAAAGAGCATGACGCCTTTTCTTT
1 CTTTT-AAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAGACGCCTTTTCCTT
446435 TT
65 TT
446437 CTCTTTTGCC
Statistics
Matches: 483, Mismatches: 63, Indels: 21
0.85 0.11 0.04
Matches are distributed among these distances:
121 3 0.01
122 200 0.41
123 249 0.52
124 31 0.06
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (120 bp):
CTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAGACGCCTTTTCCTTT
TAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCTCAAAGAGCAGGACACCTTTT
Found at i:446584 original size:46 final size:45
Alignment explanation
Indices: 446450--446626 Score: 154
Period size: 46 Copynumber: 4.1 Consensus size: 45
446440 TTTTGCCCTT
* * * *
446450 AAAGAGCAGGACACATTTCATTTCCTTCTTTTCCCTTTTA-ACCTC
1 AAAGAGCAGGACGCACTTCATTTTCTTCTTTTCCC-TTTAGTCCTC
* * * ** *
446495 AAAGAGCAAGATG-ATTTTTTTTTATT-TTTT-CCTTT-GTCCTC
1 AAAGAGCAGGACGCACTTCATTTTCTTCTTTTCCCTTTAGTCCTC
*
446536 AAAGAGCAGGACGCACTTCATTTTCTTCTTTTCCCTTCTAGTTCTC
1 AAAGAGCAGGACGCACTTCATTTTCTTCTTTTCCCTT-TAGTCCTC
* * *
446582 AAAGAGCAGGACGCACTTTATTTTC--CTTTTTCTTTTA-TCCTC
1 AAAGAGCAGGACGCACTTCATTTTCTTCTTTTCCCTTTAGTCCTC
446624 AAA
1 AAA
446627 AAGTAGGATA
Statistics
Matches: 107, Mismatches: 19, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
41 18 0.17
42 18 0.17
43 10 0.09
44 21 0.20
45 11 0.10
46 29 0.27
ACGTcount: A:0.23, C:0.24, G:0.11, T:0.42
Consensus pattern (45 bp):
AAAGAGCAGGACGCACTTCATTTTCTTCTTTTCCCTTTAGTCCTC
Found at i:446649 original size:41 final size:41
Alignment explanation
Indices: 446520--446699 Score: 126
Period size: 41 Copynumber: 4.2 Consensus size: 41
446510 TTTTTTTTAT
* * ** * *
446520 TTTTTCCTTTGTCCTCAAAGAGCAGGACGCACTTCATTTTCTTC
1 TTTTTCCTTTATCCTCAAAAAGCAGGATACA-TTTAATTTC--C
* * * ** *
446564 TTTTCCCTTCTAGTTCTCAAAGAGCAGGACGCACTTTATTTTCC
1 TTTTTCCTT-TA-TCCTCAAAAAGCAGGATACA-TTTAATTTCC
* *
446608 TTTTTCTTTTATCCTCAAAAAGTAGGATACATTTAATTTCC
1 TTTTTCCTTTATCCTCAAAAAGCAGGATACATTTAATTTCC
* * * * *
446649 TCTTTCCTTTATCTTCAAAAGGCAGGATGCATTTTATTTCC
1 TTTTTCCTTTATCCTCAAAAAGCAGGATACATTTAATTTCC
446690 TTTTTTCCTT
1 -TTTTTCCTT
446700 AGTCCCCAAG
Statistics
Matches: 113, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
41 43 0.38
42 23 0.20
43 2 0.02
44 16 0.14
45 1 0.01
46 28 0.25
ACGTcount: A:0.21, C:0.23, G:0.11, T:0.44
Consensus pattern (41 bp):
TTTTTCCTTTATCCTCAAAAAGCAGGATACATTTAATTTCC
Found at i:447426 original size:20 final size:20
Alignment explanation
Indices: 447400--447454 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
447390 TTTTACCCAG
*
447400 ATGTATCGATACATTGTTCG
1 ATGTATCGATACATTGTTCA
* *
447420 TTGTATCGATACATTTTTCA
1 ATGTATCGATACATTGTTCA
447440 ATGTATCGATACATT
1 ATGTATCGATACATT
447455 CAAGCATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTGTTCA
Found at i:451911 original size:52 final size:52
Alignment explanation
Indices: 451833--451960 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
451823 CGAAATATGA
*
451833 AAATTTGCCTGCATGTATCGATACA-TTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGC
451885 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
451937 AAA-TTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
451961 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 21 0.28
52 48 0.65
53 5 0.07
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
Found at i:452071 original size:33 final size:33
Alignment explanation
Indices: 452034--452100 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
452024 AGTAGCTTAA
452034 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
452067 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
452100 A
1 A
452101 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:452074 original size:13 final size:13
Alignment explanation
Indices: 452056--452080 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
452046 CAAAAAAATA
452056 TGTATCGATACAT
1 TGTATCGATACAT
452069 TGTATCGATACA
1 TGTATCGATACA
452081 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Done.