Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold422
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: 278240
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.33
Warning! 7407 characters in sequence are not A, C, G, or T
Found at i:275 original size:74 final size:75
Alignment explanation
Indices: 191--330 Score: 212
Period size: 74 Copynumber: 1.9 Consensus size: 75
181 ATTTTTTTAA
* * *
191 AAACGCCACTAATAT-TAATCTACCTCAAGACCAAACGGTGCGTTTTCGTTAAGATA-TTTGCGG
1 AAACGCCACTAAT-TCTAATATACCTCAAAACCAAACGCTGCGTTTTCGTTAAGATATTTTGCGG
254 CGTTTTATCGT
65 CGTTTTATCGT
* *
265 AAACGCCACTAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGC
1 AAACGCCACTAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTCGTTAAGATATTTTGCGGC
330 G
66 G
331 CATAAAAATA
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
73 1 0.02
74 49 0.83
75 9 0.15
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (75 bp):
AAACGCCACTAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTCGTTAAGATATTTTGCGGC
GTTTTATCGT
Found at i:390 original size:114 final size:113
Alignment explanation
Indices: 265--642 Score: 463
Period size: 114 Copynumber: 3.3 Consensus size: 113
255 GTTTTATCGT
*
265 AAACGCCACTAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGC
1 AAACGCCACTAATACTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGC
* *
330 GCATAAAAATAAACGCCACTAATCATGTTCTTTTACGGCGTTTTTCTAA
66 GCTTACAAATAAACGCCACTAAT-ATGTTCTTTTACGGCGTTTTTCTAA
* * * * ** *
379 AAACGCCACTAATACTAATCTACCTCAAGACGAAACGGTGCGTTTTCATTAAGATA-TTTGCGGC
1 AAACGCCACTAATACTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGC
** * * * * * * *
443 GCTTTACCGA-AAACGCCGCTAATACTATTCTTTTGCAGCGTTTTACCAT
66 GC-TTACAAATAAACGCCACTAATA-TGTTCTTTTACGGCGTTTTTCTAA
* * * *
492 AAACGCCACTAATTCTAATATACATCAAAACCAAACACTGCGTTTTGGTTAAGGCATTTTGCGGC
1 AAACGCCACTAATACTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGC
*
557 GCTTCCAAATAAACGCCACTAATTATGTTCTTTTACGGCGTTTTTCTAA
66 GCTTACAAATAAACGCCACTAA-TATGTTCTTTTACGGCGTTTTTCTAA
* * *
606 AAACGCCACTAATACTAATCTACCTCAAGACGAAACG
1 AAACGCCACTAATACTAATATACCTCAAAACCAAACG
643 GTGCNNNNNN
Statistics
Matches: 213, Mismatches: 46, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
112 1 0.00
113 89 0.42
114 121 0.57
115 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.30
Consensus pattern (113 bp):
AAACGCCACTAATACTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGC
GCTTACAAATAAACGCCACTAATATGTTCTTTTACGGCGTTTTTCTAA
Found at i:400 original size:188 final size:188
Alignment explanation
Indices: 76--465 Score: 636
Period size: 188 Copynumber: 2.1 Consensus size: 188
66 CGTTTAACCA
76 TAAACGCCACTAATTCTAATATACATCAAAACCAAACACTGCGTTTTGGTTAAGGCATTTTGCGG
1 TAAACGCCACTAATTCTAATATACATCAAAACCAAACACTGCGTTTTGGTTAAGGCATTTTGCGG
* ** * * *
141 CGCTTCCAAATAAACGCCACTAATTATGTTCTTTTACGGCATTTTTTTAAAAACGCCACTAATAT
66 CGCATAAAAATAAACGCCACTAATCATGTTCTTTTACGGCATTTTTCTAAAAACGCCACTAATAC
* * *
206 TAATCTACCTCAAGACCAAACGGTGCGTTTTCGTTAAGATATTTGCGGCGTTTTATCG
131 TAATCTACCTCAAGACCAAACGGTGCGTTTTCATTAAGATATTTGCGGCGCTTTACCG
* * *
264 TAAACGCCACTAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGG
1 TAAACGCCACTAATTCTAATATACATCAAAACCAAACACTGCGTTTTGGTTAAGGCATTTTGCGG
*
329 CGCATAAAAATAAACGCCACTAATCATGTTCTTTTACGGCGTTTTTCTAAAAACGCCACTAATAC
66 CGCATAAAAATAAACGCCACTAATCATGTTCTTTTACGGCATTTTTCTAAAAACGCCACTAATAC
*
394 TAATCTACCTCAAGACGAAACGGTGCGTTTTCATTAAGATATTTGCGGCGCTTTACCG
131 TAATCTACCTCAAGACCAAACGGTGCGTTTTCATTAAGATATTTGCGGCGCTTTACCG
* *
452 AAAACGCCGCTAAT
1 TAAACGCCACTAAT
466 ACTATTCTTT
Statistics
Matches: 186, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
188 186 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (188 bp):
TAAACGCCACTAATTCTAATATACATCAAAACCAAACACTGCGTTTTGGTTAAGGCATTTTGCGG
CGCATAAAAATAAACGCCACTAATCATGTTCTTTTACGGCATTTTTCTAAAAACGCCACTAATAC
TAATCTACCTCAAGACCAAACGGTGCGTTTTCATTAAGATATTTGCGGCGCTTTACCG
Found at i:13264 original size:195 final size:196
Alignment explanation
Indices: 13044--13435 Score: 777
Period size: 195 Copynumber: 2.0 Consensus size: 196
13034 AATATTTTAT
13044 TTCTATTTGTTAACTCATTTTTAAAATTTTAAAAGAGAGAAATAAAAATTGCTAAATGGGGATGA
1 TTCTATTTGTTAACTCATTTTTAAAATTTTAAAAGAGAGAAATAAAAATTGCTAAATGGGGATGA
13109 AGACAAAGTGATAAAAAGTTTTAGAGGTTTATTATTATAATAATTTTTACAGAAATTATTATTAT
66 AGACAAAGTGATAAAAAGTTTTAGAGGTTTATTATTATAATAATTTTTACAGAAATTATTATTAT
13174 TAGAAATTCTATGTATATAGATGTGGAAATTATGAATTTAGAATATAAATATGTGTTTAAAAATA
131 TAGAAATTCTATGTATATAGATGTGGAAATTATGAATTTAGAATATAAATATGTGTTTAAAAATA
13239 A
196 A
13240 TTCTATTTG-TAACTCATTTTTAAAATTTTAAAAGAGAGAAATAAAAATTGCTAAATGGGGATGA
1 TTCTATTTGTTAACTCATTTTTAAAATTTTAAAAGAGAGAAATAAAAATTGCTAAATGGGGATGA
13304 AGACAAAGTGATAAAAAGTTTTAGAGGTTTATTATTATAATAATTTTTACAGAAATTATTATTAT
66 AGACAAAGTGATAAAAAGTTTTAGAGGTTTATTATTATAATAATTTTTACAGAAATTATTATTAT
13369 TAGAAATTCTATGTATATAGATGTGGAAATTATGAATTTAGAATATAAATATGTGTTTAAAAATA
131 TAGAAATTCTATGTATATAGATGTGGAAATTATGAATTTAGAATATAAATATGTGTTTAAAAATA
13434 A
196 A
13435 T
1 T
13436 ATATAATAAA
Statistics
Matches: 196, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
195 187 0.95
196 9 0.05
ACGTcount: A:0.43, C:0.04, G:0.14, T:0.39
Consensus pattern (196 bp):
TTCTATTTGTTAACTCATTTTTAAAATTTTAAAAGAGAGAAATAAAAATTGCTAAATGGGGATGA
AGACAAAGTGATAAAAAGTTTTAGAGGTTTATTATTATAATAATTTTTACAGAAATTATTATTAT
TAGAAATTCTATGTATATAGATGTGGAAATTATGAATTTAGAATATAAATATGTGTTTAAAAATA
A
Found at i:15070 original size:17 final size:17
Alignment explanation
Indices: 15048--15081 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
15038 TACATAAGAT
15048 TTATTT-TTTGTTCTTTC
1 TTATTTCTTT-TTCTTTC
15065 TTATTTCTTTTTCTTTC
1 TTATTTCTTTTTCTTTC
15082 CCGAGTCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.06, C:0.15, G:0.03, T:0.76
Consensus pattern (17 bp):
TTATTTCTTTTTCTTTC
Found at i:24972 original size:15 final size:15
Alignment explanation
Indices: 24938--24971 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
24928 TCATTGTACC
24938 CTTTTCTTTTCTTCT
1 CTTTTCTTTTCTTCT
24953 CTTTTCTTTTCTTC-
1 CTTTTCTTTTCTTCT
24967 CTTTT
1 CTTTT
24972 TTGCTGCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (15 bp):
CTTTTCTTTTCTTCT
Found at i:28430 original size:44 final size:44
Alignment explanation
Indices: 28355--28485 Score: 201
Period size: 44 Copynumber: 3.0 Consensus size: 44
28345 TGTCGACTCA
* * *
28355 TTGGCCAGGGGCGTTCACCCTACATACAATCTGTGAGTTCTAGT
1 TTGGCCAAGGGTGTTCACCCTACATACAATCTATGAGTTCTAGT
* * *
28399 TTGGTCAAGGGTGTTCAACCTACATACAATCTCTGAGTTCTAGT
1 TTGGCCAAGGGTGTTCACCCTACATACAATCTATGAGTTCTAGT
28443 TTGGCCAAGGGTGTTCACCCTACATACAA-CTATGAGTTCTAGT
1 TTGGCCAAGGGTGTTCACCCTACATACAATCTATGAGTTCTAGT
28486 CACAGGGATT
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
43 13 0.16
44 66 0.84
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (44 bp):
TTGGCCAAGGGTGTTCACCCTACATACAATCTATGAGTTCTAGT
Found at i:33434 original size:15 final size:15
Alignment explanation
Indices: 33414--33444 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
33404 ATGTTAATTG
33414 AGAATTTATATGGAC
1 AGAATTTATATGGAC
33429 AGAATTTATATGGAC
1 AGAATTTATATGGAC
33444 A
1 A
33445 TTCATTAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.32
Consensus pattern (15 bp):
AGAATTTATATGGAC
Found at i:41061 original size:175 final size:169
Alignment explanation
Indices: 40880--41261 Score: 398
Period size: 175 Copynumber: 2.2 Consensus size: 169
40870 TTTGAAAATA
*
40880 AAATGAAATAAATAGCAACTATTATAAGTATTCCAGAAAATATAAAAAAAAATTATAACAACACC
1 AAATGAAATAAATAGCAATTATTATAA-TATTCCAG-AAA-AT-AAAAAAAATTATAACAACACC
**
40945 AAACTCAAGCCTAAACGGGC-AATGAAATGAAATAAATAGAAATTATTATAATTATTCCAAAAAA
62 AAAC-CAAGCCTAAACGCCCAAATGAAATGAAATAAATAGAAATTATTATAATTATT-CAAAAAA
*
41009 ATAAAAAAAAATTTATTGCAACACCAACTC-ACACTCAATGCCT-T-A-G
125 AT--AAAAAAATTTATTGCAACA-C-ACTCAAC-CTAAATGCCTATAATG
* ** * *
41055 AAATGAAATGAAATA-AATATTATTATAATCATTTTAGAAAATAAAAAATATTATCACAACACCA
1 AAATGAAAT-AAATAGCA-ATTATTATAAT-ATTCCAGAAAATAAAAAAAATTATAACAACACCA
* * ** **
41119 GACCAAGCCTAAATGCCCAAAAATGAAATGAAATAAATATCAATTATTATAATTATTCTGAAAAA
63 AACCAAGCCTAAACGCCC--AAATGAAATGAAATAAATAGAAATTATTATAATTATTCAAAAAAA
*
41184 TAAAAAAATTTATTGCAATACACTCAAGCCTAAATGCCTCATAATG
126 TAAAAAAATTTATTGCAACACACTCAA-CCTAAATGCCT-ATAATG
*
41230 AAATGAAATAAATAGCTATTATTATAACTATT
1 AAATGAAATAAATAGCAATTATTATAA-TATT
41262 TTGGAAAGTA
Statistics
Matches: 175, Mismatches: 18, Indels: 29
0.79 0.08 0.13
Matches are distributed among these distances:
170 4 0.02
171 11 0.06
172 31 0.18
173 23 0.13
174 28 0.16
175 59 0.34
176 19 0.11
ACGTcount: A:0.52, C:0.14, G:0.08, T:0.27
Consensus pattern (169 bp):
AAATGAAATAAATAGCAATTATTATAATATTCCAGAAAATAAAAAAAATTATAACAACACCAAAC
CAAGCCTAAACGCCCAAATGAAATGAAATAAATAGAAATTATTATAATTATTCAAAAAAATAAAA
AAATTTATTGCAACACACTCAACCTAAATGCCTATAATG
Found at i:41098 original size:86 final size:86
Alignment explanation
Indices: 40899--41243 Score: 275
Period size: 86 Copynumber: 4.0 Consensus size: 86
40889 AAATAGCAAC
* * * ** * *
40899 TATTATAAGTATTCCAGAAAATATAAAAAAAAATTATAACAACACCAAACTCAAGCCTAAACGGG
1 TATTATAATTATTCTAGAAAATA-AAAAAAAATTTATTGCAACACC-AACTCAA-CCTAAA-TGC
*
40964 C-AATGAAATGAAAT-AAATAGAA-AT
62 CTCA-GAAATGAAATGAAATA-AATAT
* * *
40988 TATTATAATTATTCCAAAAAAATAAAAAAAAATTTATTGCAACACCAACTC-ACACTCAATGCCT
1 TATTATAATTATT-CTAGAAAATAAAAAAAAATTTATTGCAACACCAACTCAAC-CTAAATGCCT
*
41052 TAGAAATGAAATGAAATAAATAT
64 CAGAAATGAAATGAAATAAATAT
* * * **
41075 TATTATAATCATTTTAGAAAAT-AAAAAATA-TTATCACAACACCAGAC-CAAGCCTAAATGCC-
1 TATTATAATTATTCTAGAAAATAAAAAAAAATTTATTGCAACACCA-ACTCAA-CCTAAATGCCT
*
41136 CAAAAATGAAATGAAATAAATATCAAT
64 CAGAAATGAAATGAAAT-AA-AT--AT
* *
41163 TATTATAATTATTCT-GAAAA-ATAAAAAAATTTATTGCAATA-C-ACTCAAGCCTAAATGCCTC
1 TATTATAATTATTCTAGAAAATAAAAAAAAATTTATTGCAACACCAACTCAA-CCTAAATGCCTC
*
41224 A-TAATGAAATGAAATAAATA
65 AGAAATGAAATGAAATAAATA
41244 GCTATTATTA
Statistics
Matches: 212, Mismatches: 28, Indels: 39
0.76 0.10 0.14
Matches are distributed among these distances:
82 1 0.00
84 30 0.14
85 24 0.11
86 51 0.24
87 39 0.18
88 28 0.13
89 31 0.15
90 8 0.04
ACGTcount: A:0.52, C:0.14, G:0.08, T:0.26
Consensus pattern (86 bp):
TATTATAATTATTCTAGAAAATAAAAAAAAATTTATTGCAACACCAACTCAACCTAAATGCCTCA
GAAATGAAATGAAATAAATAT
Found at i:41251 original size:86 final size:88
Alignment explanation
Indices: 40880--41456 Score: 331
Period size: 89 Copynumber: 6.6 Consensus size: 88
40870 TTTGAAAATA
* * * * * **
40880 AAATGAAATAAATAGCAACTATTATAAGTATTCCAGAAAATATAAAAAAAAATTATAACAACACC
1 AAATGAAATAAATAGAAATTATTATAATTATT-CTGAAAA-AT-AAAAAAATTTATTGCAACACC
* **
40945 AAACTCAAGCCTAAACG-GGC--AATG
63 -AACTCAAGCCTAAATGCCTCATAATG
**
40969 AAATGAAATAAATAGAAATTATTATAATTATTCCAAAAAAATAAAAAAAAATTTATTGCAACACC
1 AAATGAAATAAATAGAAATTATTATAATTATT-CTGAAAAAT--AAAAAAATTTATTGCAACACC
*
41034 AACTC-A-CACTCAATGCCT--T-A-G
63 AACTCAAGC-CTAAATGCCTCATAATG
* * **
41055 AAATGAAATGAAATA-AATATTATTATAATCATT-TTAGAAAAT-AAAAAATATTATCACAACAC
1 AAATGAAAT-AAATAGAA-ATTATTATAATTATTCTGA-AAAATAAAAAAAT-TTATTGCAACAC
*
41117 CAGAC-CAAGCCTAAATGCC-CAAAAATG
62 CA-ACTCAAGCCTAAATGCCTC-ATAATG
** *
41144 AAATGAAATAAATATCAATTATTATAATTATTCTGAAAAATAAAAAAATTTATTGCAATA-C-AC
1 AAATGAAATAAATAGAAATTATTATAATTATTCTGAAAAATAAAAAAATTTATTGCAACACCAAC
41207 TCAAGCCTAAATGCCTCATAATG
66 TCAAGCCTAAATGCCTCATAATG
** * * * * * * *
41230 AAATGAAATAAATAGCTATTATTATAACTATTTTGGAAAGTAAAAATAAATTATTGTAGCACCAG
1 AAATGAAATAAATAGAAATTATTATAATTATTCTGAAAAATAAAAA-AATTTATTGCAACACCA-
* ** * *
41295 ACTCAAGTCT--CGGCTTTGGATAATG
64 ACTCAAGCCTAAATGC-CT-CATAATG
* * *
41320 AAATAAAATTAATA-ACAATTATTATAATTATTC-CAGAAAAT-AAAAAATATTATTGCAACACC
1 AAATGAAATAAATAGA-AATTATTATAATTATTCTGA-AAAATAAAAAAAT-TTATTGCAACACC
* * * **
41382 AGACTTAAGCCCAAGTGTCC-CGGGAATG
63 A-ACTCAAGCCTAAATG-CCTC-ATAATG
* * * *
41410 AAA-AAAATAATTAGCAATTATTATAATAATT-T-AGAAAATAAAAAAAT
1 AAATGAAATAAATAGAAATTATTATAATTATTCTGA-AAAATAAAAAAAT
41457 ATTTTAAAAG
Statistics
Matches: 386, Mismatches: 65, Indels: 74
0.74 0.12 0.14
Matches are distributed among these distances:
83 7 0.02
84 13 0.03
85 14 0.04
86 78 0.20
87 38 0.10
88 52 0.13
89 130 0.34
90 52 0.13
91 1 0.00
92 1 0.00
ACGTcount: A:0.50, C:0.13, G:0.09, T:0.27
Consensus pattern (88 bp):
AAATGAAATAAATAGAAATTATTATAATTATTCTGAAAAATAAAAAAATTTATTGCAACACCAAC
TCAAGCCTAAATGCCTCATAATG
Found at i:41295 original size:175 final size:175
Alignment explanation
Indices: 40924--41382 Score: 419
Period size: 175 Copynumber: 2.6 Consensus size: 175
40914 AGAAAATATA
* * * **
40924 AAAAAAAATTATAACAACACCAAACTCAAGCCTAAACGGGC---AATGAAATGAAATAAATAGAA
1 AAAAAAAATTATCACAACACCAGACTCAAGCCTAAATGCCCAAAAATGAAATGAAATAAATAGAA
*
40986 ATTATTATAATTATTCCAAAAAAATAAAAAAAAATTTATTGCAACACCAACTCACACTCAATGCC
66 ATTATTATAATTATTCCAAAAAAAT-AAAAAAAATTTATTGCAACACCAACTCACACTAAATGCC
41051 TTAGAAATGAAATGAAATAAATATTATTATAATCATTTTAGAAAAT
130 TTAGAAATGAAATGAAATAAATATTATTATAATCATTTTAGAAAAT
* **
41097 AAAAAATATTATCACAACACCAGAC-CAAGCCTAAATGCCCAAAAATGAAATGAAATAAATATCA
1 AAAAAAAATTATCACAACACCAGACTCAAGCCTAAATGCCCAAAAATGAAATGAAATAAATAGAA
** *
41161 ATTATTATAATTATT-CTGAAAAAT-AAAAAAATTTATTGCAATA-C-ACTCA-AGCCTAAATGC
66 ATTATTATAATTATTCCAAAAAAATAAAAAAAATTTATTGCAACACCAACTCACA--CTAAATGC
** * *
41221 CTCATAATGAAATGAAAT-AAATAGCTATTATTATAA-CTATTTTGGAAAGT
129 CT--T-A-GAAATGAAATGAAATAAATATTATTATAATC-ATTTTAGAAAAT
*** * * ** *** * * *
41271 AAAAATAAATTATTGTAGCACCAGACTCAAGTCT--CGGCTTTGGATAATGAAATAAAATTAATA
1 AAAAA-AAATTATCACAACACCAGACTCAAGCCTAAATGC--CCAAAAATGAAATGAAATAAATA
* *
41334 -ACAATTATTATAATTATTCC-AGAAAATAAAAAATA-TTATTGCAACACCA
63 GA-AATTATTATAATTATTCCAAAAAAATAAAAAAAATTTATTGCAACACCA
41383 GACTTAAGCC
Statistics
Matches: 232, Mismatches: 35, Indels: 33
0.77 0.12 0.11
Matches are distributed among these distances:
169 1 0.00
170 5 0.02
171 10 0.04
172 30 0.13
173 24 0.10
174 41 0.18
175 59 0.25
176 54 0.23
177 8 0.03
ACGTcount: A:0.50, C:0.14, G:0.08, T:0.27
Consensus pattern (175 bp):
AAAAAAAATTATCACAACACCAGACTCAAGCCTAAATGCCCAAAAATGAAATGAAATAAATAGAA
ATTATTATAATTATTCCAAAAAAATAAAAAAAATTTATTGCAACACCAACTCACACTAAATGCCT
TAGAAATGAAATGAAATAAATATTATTATAATCATTTTAGAAAAT
Found at i:41410 original size:90 final size:90
Alignment explanation
Indices: 41311--41530 Score: 234
Period size: 89 Copynumber: 2.4 Consensus size: 90
41301 GTCTCGGCTT
* *
41311 TGGATAATGAAATAAAATTAATAACAATTATTATAATTATTCCAGAAAAT-AAAAAATATTATTG
1 TGGA-AATGAAATAAAATTAATAGCAATTATTATAATTATT-CAGAAAATAAAAAAATATT-TTA
* * * * *
41375 CAA-CACCAGACTTAAGCCCAAGTGTCCC
63 AAAGCACCAGAATCAAACCCAAGT-ACCC
* * *
41403 -GGGAATGAAA-AAAA-TAATTAGCAATTATTATAATAATTTAGAAAATAAAAAAATATTTTAAA
1 TGGAAATGAAATAAAATTAA-TAGCAATTATTATAATTATTCAGAAAATAAAAAAATATTTTAAA
**
41465 AGCATTAGAATCAAACCCAAGTACCC
65 AGCACCAGAATCAAACCCAAGTACCC
* *
41491 TGGAAATGAAATAAAATAAATAGCAATTATTAAAATTATT
1 TGGAAATGAAATAAAATTAATAGCAATTATTATAATTATT
41531 GCAACACCGT
Statistics
Matches: 106, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
88 17 0.16
89 56 0.53
90 29 0.27
91 4 0.04
ACGTcount: A:0.51, C:0.11, G:0.10, T:0.28
Consensus pattern (90 bp):
TGGAAATGAAATAAAATTAATAGCAATTATTATAATTATTCAGAAAATAAAAAAATATTTTAAAA
GCACCAGAATCAAACCCAAGTACCC
Found at i:41658 original size:159 final size:157
Alignment explanation
Indices: 41368--41664 Score: 359
Period size: 159 Copynumber: 1.9 Consensus size: 157
41358 AATAAAAAAT
** * *
41368 ATTATTGCAACACCAGACTTAAGCCCAAGTGTCCCGGGAATGAAAAAAATAATTAGCAATTATTA
1 ATTATTGCAACACCAGACACAAGCCCAAGTGTCCCGGGAATGAAAAAAATAAATAGAAATTATTA
* * * **
41433 TAATAATTTAGAAAATAAAAAAATATTTTAAAAGCATTAGAATCAAACCCAAGTACCCTGGAAAT
66 TAATAATTCAGAAAATAAAAAAATATTTCAAAAGCACTAGAATCAAACCCAAGTACCCTAAAAAT
41498 GAAATAAAATAAATAGCAATTATTAAA
131 GAAATAAAATAAATAGCAATTATTAAA
* *
41525 ATTATTGCAACACC-GTACACAAGCCCAAGTG-CTCGAGGAATGAAATGAAATAAATAGAAATTA
1 ATTATTGCAACACCAG-ACACAAGCCCAAGTGTCCCG-GGAATGAAA-AAAATAAATAGAAATTA
* * * ** *
41588 TTATAATTATATCAGAAATTAAAAACATATTATCGCAA-CACTA-AACTCAAGCCCAAGTACCCT
63 TTATAATAAT-TCAGAAAATAAAAAAATATT-TCAAAAGCACTAGAA-TCAAACCCAAGTACCCT
41651 AAAAATGAAATAAA
125 AAAAATGAAATAAA
41665 TAATTATTAA
Statistics
Matches: 117, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
156 4 0.03
157 36 0.31
158 25 0.21
159 49 0.42
160 3 0.03
ACGTcount: A:0.49, C:0.15, G:0.11, T:0.24
Consensus pattern (157 bp):
ATTATTGCAACACCAGACACAAGCCCAAGTGTCCCGGGAATGAAAAAAATAAATAGAAATTATTA
TAATAATTCAGAAAATAAAAAAATATTTCAAAAGCACTAGAATCAAACCCAAGTACCCTAAAAAT
GAAATAAAATAAATAGCAATTATTAAA
Found at i:42025 original size:90 final size:90
Alignment explanation
Indices: 41544--44098 Score: 1198
Period size: 90 Copynumber: 28.6 Consensus size: 90
41534 ACACCGTACA
** * * *
41544 CAAGCCCAAGTG--CTCGAGGAATGAAATGAAATAAATAGAAATTATTATAATTATATCAGAAAT
1 CAAGCCCAAGTGTCCT-GA-GAATGAAATGAAATAAATATCAATTATTATAATTATTTCAAAAAA
* * * * *
41607 TAAAAACATATTATCGCAACACTAAACT
64 TAAAAAAATATTATTG-AGCACCAGACT
** * * ** **
41635 CAAGCCCAAGTACCCTAAAAATGAAAT-AAAT-AAT-T--ATTAACATAATTA-TTCTTGAAAAT
1 CAAGCCCAAGTGTCCTGAGAATGAAATGAAATAAATATCAATTATTATAATTATTTC-AAAAAAT
* * *
41694 -AAAAATTATTATTGCAGCGCCAAACT
65 AAAAAAATATTATTG-AGCACCAGACT
* * * * *
41720 CAAGCCCAAATATCTTGATAATGAAATAAAATAAATAGT-AATTATTATAATTATTTCAAAAAAA
1 CAAGCCCAAGTGTCCTGAGAATGAAATGAAATAAATA-TCAATTATTATAATTATTTC-AAAAAA
*
41784 TAAAAAAA-ATTATT-A-CAACACATGGCT
64 TAAAAAAATATTATTGAGC-AC-CA-GACT
* * * * * *
41811 AAAGCCCAAGTG-CCATGAAAATGAAATAAAATAAATACCAATTATTATAACTATTCCAAAAAAT
1 CAAGCCCAAGTGTCC-TGAGAATGAAATGAAATAAATATCAATTATTATAATTATTTCAAAAAAT
41875 ATCAAATAAA-ATTTATTGTAGCACCAGACT
65 A--AAA-AAATA-TTATTG-AGCACCAGACT
* * * *
41905 CAAGGCCAAATG-CCTCGGGAATGAAATGAAATAAATATCAGTTATTATAATTA-TT-AAAAAAT
1 CAAGCCCAAGTGTCCT-GAGAATGAAATGAAATAAATATCAATTATTATAATTATTTCAAAAAAT
* *
41967 AAAAAAAATATTATTAGTGCACTAGACT
65 -AAAAAAATATTATT-GAGCACCAGACT
* * * **
41995 CAAACCCAAGTGTCCTGAAAATGAAATGAAATAAATTTGCAATTATTATAATTA-TTCCTAAAAT
1 CAAGCCCAAGTGTCCTGAGAATGAAATGAAATAAATAT-CAATTATTATAATTATTTCAAAAAAT
* * * * *
42059 --AAAAATATTATTTCAACATCGGATT
65 AAAAAAATATTA-TTGAGCACCAGACT
* ** ** * * * * *
42084 CAAGCCTAAG-AACCCAAAAATAAAATAAAATAAAT-TGCAACTATTATAAATATTTC-AAAAAT
1 CAAGCCCAAGTGTCCTGAGAATGAAATGAAATAAATAT-CAATTATTATAATTATTTCAAAAAAT
* *
42146 AAAAAAATATTGTTGCAGCACTAGACT
65 AAAAAAATATTATTG-AGCACCAGACT
* * * * * *
42173 CAAGCCCAAGTGCCCCGAGAATAAAATGAAATAAATTTGCAATTATCATAATTATTTCGAAAAAT
1 CAAGCCCAAGTGTCCTGAGAATGAAATGAAATAAATAT-CAATTATTATAATTATTTCAAAAAAT
*
42238 -AAAAAA-ATTATTACAGCACCAGACT
65 AAAAAAATATTATT-GAGCACCAGACT
* *
42263 CAAGCCCAAGTGTCC----AATG-AATGAAA-AGGATAGCAATTATTATAATTATTTCAAAAAAT
1 CAAGCCCAAGTGTCCTGAGAATGAAATGAAATA-AATATCAATTATTATAATTATTTCAAAAAAT
* * * * *
42322 AAAAAAATATCATTATAGTACCAAAAT
65 AAAAAAATATTATT-GAGCACCAGACT
* * * * * ***
42349 CAAGCCCGAGTGCCCTGAGAATTAAAAGAAATAAATAGCAATTATTATAATTATTT-TGGAAATA
1 CAAGCCCAAGTGTCCTGAGAATGAAATGAAATAAATATCAATTATTATAATTATTTCAAAAAATA
*
42413 AAAAAATATTATTGCAACACCAGACT
66 AAAAAATATTATTG-AGCACCAGACT
* * * * * * ** **
42439 CTAGCCAAAGTGTCATGGGAATGAAAT-AAATTCAATAACAGGTATTATAATTATTTTGAAAAAT
1 CAAGCCCAAGTGTCCTGAGAATGAAATGAAA-TAAATATCAATTATTATAATTATTTCAAAAAAT
*
42503 AAAAAAA-ATTATTGCAGCACTAGACT
65 AAAAAAATATTATTG-AGCACCAGACT
* * * * * * * * *
42529 CAAACTCAAGTGTCCCGAAAATGAAATGAAATAAGCT-GCAATTATTATAATGATTTCGAAATAT
1 CAAGCCCAAGTGTCCTGAGAATGAAATGAAATAA-ATATCAATTATTATAATTATTTCAAAAAAT
*
42593 AAAAAAAGATTATTGCAGCACCAGACT
65 AAAAAAATATTATTG-AGCACCAGACT
* * * * * * ***
42620 CAATCCCAAATGTCCGGAGAATGAAATTAAATAAATAGCAATTATTATAACTATTTTGGAAAATA
1 CAAGCCCAAGTGTCCTGAGAATGAAATGAAATAAATATCAATTATTATAATTATTTCAAAAAATA
* * *
42685 AAAAAAAATGTAATTGCAATGCACTAAACT
66 AAAAAATAT-T-ATTG--A-GCACCAGACT
** * * * * *** *
42715 CAAGCCCAAGTACCGCGGA-AATGAAA-AAAATTAAATAGCAATTCTTATAATTA-TTCCTGAAG
1 CAAGCCCAAGTGTC-CTGAGAATGAAATGAAA-TAAATATCAATTATTATAATTATTTCAAAAAA
* * * *
42777 TTAAAAAAT-TTATTGCAACACCATATT
64 TAAAAAAATATTATTG-AGCACCAGACT
* * * * *
42804 CAAACCTAAGTGTCTTG-GAAATGAAATGAAATAAATA-CAAATTATTATAATTATTTTAGAAAA
1 CAAGCCCAAGTGTCCTGAG-AATGAAATGAAATAAATATC-AATTATTATAATTATTTCAAAAAA
* * * **
42867 T-AAGAAATATTAGTGTAGTAATAGACT
64 TAAAAAAATATTATTG-AGCACCAGACT
* * * ** * * *
42894 CCAGACCAAGTTTCCCAAGAATGAAA--AAATTAATAGT-AATTATTATAATTAATTCAAAAATT
1 CAAGCCCAAGTGTCCTGAGAATGAAATGAAATAAATA-TCAATTATTATAATTATTTCAAAAAAT
* * *
42956 AAATAACT-TTATTGTAGCACAAGACT
65 AAAAAAATATTATTG-AGCACCAGACT
* * * * *
42982 CAAGCTCAAGTGCCCCTG-GAATGAAATG-AATGAAT-TGC---------AATTATTCCAGAAAA
1 CAAGCCCAAGTG-TCCTGAGAATGAAATGAAATAAATAT-CAATTATTATAATTATTTCAAAAAA
*
43035 TAACAAAATATTATTGCAGCACCAGACT
64 TAAAAAAATATTATTG-AGCACCAGACT
* * * * * * * * ** * *
43063 CAAGCCCAAATG-CTTGAAAATTAAATGAAACATATAGCAAATATTATAATTA-TTCTGGACAGT
1 CAAGCCCAAGTGTCCTGAGAATGAAATGAAATAAATATCAATTATTATAATTATTTC-AAAAAAT
* *
43126 -AAAAAATTTTTTTGCAGCACCAGACT
65 AAAAAAATATTATTG-AGCACCAGACT
* * * * * * ** * *** *
43152 CAATCCCAAATGCCCAGGGAATTAAATGAAATGTATAGCAATTATTATAATTATTTTGGAAAGT-
1 CAAGCCCAAGTGTCCTGAGAATGAAATGAAATAAATATCAATTATTATAATTATTTCAAAAAATA
43216 AAAAAA-A-TATTGCAGCACCA-ACT
66 AAAAAATATTATTG-AGCACCAGACT
* * * **
43239 CAAGTCCAAGTGCTCCT-TGAATGAAATGAAATAAATTAT-AATTATTCTTAA--AAAT--AAAA
1 CAAGCCCAAGTG-TCCTGAGAATGAAATGAAATAAA-TATCAATTATT-ATAATTATTTCAAAAA
* * *
43298 ATAAAAATATATT-GTCA-CAACACAGACT
63 ATAAAAAAATATTATTGAGC-AC-CAGACT
* * * * * * * ** *
43326 TAAACTCAAATGCCCCGA-AATAAAATGAAATAAATAGAAATTATTATAATTATTTAAAAAAAAT
1 CAAGCCCAAGTGTCCTGAGAATGAAATGAAATAAATATCAATTATTATAATTATTT-CAAAAAAT
* *
43390 AGAAAAAA-ATTATTGTAGCATCAAACT
65 A-AAAAAATATTATTG-AGCACCAGACT
*
43417 CAAGCCCAAGTG-CACTGA-AATGAAATGAAATAAATAGCAATTATTATAATTATTTCAAAAAAT
1 CAAGCCCAAGTGTC-CTGAGAATGAAATGAAATAAATATCAATTATTATAATTATTTCAAAAAAT
** * **
43480 -AAAAAATATTATCACAACACC-TTCTT
65 AAAAAAATATTAT-TGAGCACCAGAC-T
** * * * * *
43506 CAAGCCCAAGTG-CCCCATGAATAAAATGAAATAAATAACAATTATTATAGTTA--TCCAAGAAT
1 CAAGCCCAAGTGTCCTGA-GAATGAAATGAAATAAATATCAATTATTATAATTATTTCAAAAAAT
* *
43568 TAAAAAATATTATTTTCAGCACCAGACT
65 AAAAAAATATTA--TTGAGCACCAGACT
* * * * * *
43596 CAAACTCAAGTG-CCTCAAAAATGAAATGAAATAAATAACAATTATTTTAATTATTTC-------
1 CAAGCCCAAGTGTCCT-GAGAATGAAATGAAATAAATATCAATTATTATAATTATTTCAAAAAAT
* ** *
43653 -AAAAAA-ATTACTGGAGCTTCAGGCT
65 AAAAAAATATTA-TTGAGCACCAGACT
* * * * *
43678 CAAGTCCAAGTG-CCT-ATGAATGAAGTGAAATAAATAGCAATTATTATAATTATTCCAGAAAAT
1 CAAGCCCAAGTGTCCTGA-GAATGAAATGAAATAAATATCAATTATTATAATTATTTCAAAAAAT
* *
43741 AAAAAAATATTATTGCAACACCAGCCT
65 AAAAAAATATTATTG-AGCACCAGACT
* * * * * * * * *
43768 CAAACCTAAGTCT-CTGAGGAATGAAATGAAACAAATAGCAATTATTGTAGTTATTTTAGAAAAT
1 CAAGCCCAAGTGTCCTGA-GAATGAAATGAAATAAATATCAATTATTATAATTATTTCAAAAAAT
* *
43832 AAAAAAA-A-TATTGCAGCACGAGTCT
65 AAAAAAATATTATTG-AGCACCAGACT
* * * * ** *
43857 CAAGCCCAAGTGCCCTGATAATGAAATGAAATAAATA--ATATATAGTATAAGTATTTTGAAAAT
1 CAAGCCCAAGTGTCCTGAGAATGAAATGAAATAAATATCA-AT-TATTATAATTATTTCAAAAAA
*
43920 TAAAAAAAAAATTATTGCAGCACCAGACT
64 T-AAAAAAATATTATTG-AGCACCAGACT
* *
43949 CAAGCCCAAGTGTCCCGACTCTCGGGAATGAAATGAAA-AAAAATGCAATTATTATAATTATTTC
1 CAAGCCCAAGTGT-----C-CT-GAGAATGAAATGAAATAAATAT-CAATTATTATAATTATTTC
* *
44013 ---GAA-AAAAAAATATTATTGTAGCACCAGGCT
58 AAAAAATAAAAAAATATTATTG-AGCACCAGACT
* * ** ** * * *
44043 CAATCTCAAGTACCCCAATAATGAAATGAAATAAATAGCAATCATTATAATTATTT
1 CAAGCCCAAGTGTCCTGAGAATGAAATGAAATAAATATCAATTATTATAATTATTT
44099 TGAAAAAAAT
Statistics
Matches: 1893, Mismatches: 417, Indels: 312
0.72 0.16 0.12
Matches are distributed among these distances:
79 3 0.00
80 26 0.01
81 65 0.03
82 21 0.01
83 4 0.00
84 36 0.02
85 72 0.04
86 80 0.04
87 100 0.05
88 128 0.07
89 251 0.13
90 477 0.25
91 365 0.19
92 61 0.03
93 15 0.01
94 98 0.05
95 47 0.02
96 8 0.00
97 2 0.00
98 6 0.00
99 25 0.01
100 2 0.00
101 1 0.00
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.28
Consensus pattern (90 bp):
CAAGCCCAAGTGTCCTGAGAATGAAATGAAATAAATATCAATTATTATAATTATTTCAAAAAATA
AAAAAATATTATTGAGCACCAGACT
Found at i:42169 original size:178 final size:175
Alignment explanation
Indices: 41567--43650 Score: 687
Period size: 176 Copynumber: 11.7 Consensus size: 175
41557 TCGAGGAATG
* * * * * * * * *
41567 AAATGAAATAAATAGAAATTATTATAATTATATCAGAAATTAAAAACATATTATCGCAACACTAA
1 AAATAAAATAAATAGCAACTATTATAATTATTTCA-AAAATAAAAAAATATTATTGCAGCACTAG
* * ** ** *
41632 ACTCAAGCCCAAGTACCCTAAAAATGAAAT-AAAT-AA-TT---ATTAACATAATTATTCTTGAA
65 ACTCAAACCCAAGTGCCCCGAAAATGAAATGAAATAAATTTGCAATTATTATAATTATTCCT-AA
* * * * * **
41691 A-ATAAAAATTATTATTGCAGCGCCAAACTCAAGCCCAAATATCTTGATAAT
129 ATATAAAAA-TATTATTACAACACCAGACTCAAG-CCAAAGA-C-CCA-AAT
* * * *
41742 GAAATAAAATAAATAGTAATTATTATAATTATTTCAAAAAAATAAAAAAA-ATTATTACAACAC-
1 -AAATAAAATAAATAGCAACTATTATAATTATTTC--AAAAATAAAAAAATATTATTGCAGCACT
* ** * ** *
41805 ATGGCT-AAAGCCCAAGTGCCATGAAAATGAAATAAAATAAA-TACCAATTATTATAACTATTCC
63 A-GACTCAAA-CCCAAGTGCCCCGAAAATGAAATGAAATAAATTTGCAATTATTATAATTATTCC
* * ** * *
41868 AAAAAATATCAAATAAAATTTATTGTAGCACCAGACTCAAGGCCAAATG-CCTCGGGAAT
126 --TAAATAT-AAA-AATA-TTATTACAACACCAGACTCAA-GCCAAA-GACC-C--AAAT
* * ** * *
41927 GAAATGAAATAAATATCAGTTATTATAATTA-TTAAAAAATAAAAAAAATATTATTAG-TGCACT
1 -AAATAAAATAAATAGCAACTATTATAATTATTTCAAAAAT-AAAAAAATATTATT-GCAGCACT
* *
41990 AGACTCAAACCCAAGTGTCCTGAAAATGAAATGAAATAAATTTGCAATTATTATAATTATTCCTA
63 AGACTCAAACCCAAGTGCCCCGAAAATGAAATGAAATAAATTTGCAATTATTATAATTATTCCTA
* * * * *
42055 AA-ATAAAAATATTATTTCAACATCGGATTCAAGCCTAAGAACCCAAAAAT
128 AATATAAAAATATTATTACAACACCAGACTCAAGCCAAAG-ACCC--AAAT
* * *
42105 AAAATAAAATAAATTGCAACTATTATAAATATTTCAAAAATAAAAAAATATTGTTGCAGCACTAG
1 -AAATAAAATAAATAGCAACTATTATAATTATTTCAAAAATAAAAAAATATTATTGCAGCACTAG
* * * * * *
42170 ACTCAAGCCCAAGTGCCCCGAGAATAAAATGAAATAAATTTGCAATTATCATAATTATTTCGAAA
65 ACTCAAACCCAAGTGCCCCGAAAATGAAATGAAATAAATTTGCAATTATTATAATTATTCCTAAA
* * * * **
42235 AATAAAAAAATTATTACAGCACCAGACTCAAGCCCAAGTGTCC-AAT
130 TATAAAAATATTATTACAACACCAGACTCAAGCCAAAG-ACCCAAAT
* ** * * ** * *
42281 GAATGAAAA-GGATAGCAATTATTATAATTATTTCAAAAAATAAAAAAATATCATTATAGTACCA
1 AAAT-AAAATAAATAGCAACTATTATAATTATTTC-AAAAATAAAAAAATATTATTGCAGCACTA
* * * * * * * * * *
42345 AAATCAAGCCCGAGTGCCCTGAGAATTAAAAGAAATAAA-TAGCAATTATTATAATTATT-TTGG
64 GACTCAAACCCAAGTGCCCCGAAAATGAAATGAAATAAATTTGCAATTATTATAATTATTCCT--
* * * ***
42408 AAATAAAAAAATATTATTGCAACACCAGACTCTAGCCAAAGTGTCATGGGAAT
127 AAATATAAAAATATTATTACAACACCAGACTCAAGCCAAAGACCCA----AAT
* * * ** *
42461 GAAATAAATTCAATAACAGGTATTATAATTATTTTGAAAAATAAAAAAA-ATTATTGCAGCACTA
1 -AAATAAAATAAATAGCAACTATTATAATTA-TTTCAAAAATAAAAAAATATTATTGCAGCACTA
* * ** * * *
42525 GACTCAAACTCAAGTGTCCCGAAAATGAAATGAAAT-AAGCTGCAATTATTATAATGATTTCGAA
64 GACTCAAACCCAAGTGCCCCGAAAATGAAATGAAATAAATTTGCAATTATTATAATTATTCCTAA
* * * * * *
42589 ATATAAAAAAAGATTATTGCAGCACCAGACTCAATCCCAAATGTCCGGAGAAT
129 ATAT--AAAAATATTATTACAACACCAGACTCAA-GCCAAA-GACC-CA-AAT
* * * ** *
42642 GAAATTAAATAAATAGCAATTATTATAACTATTTTGGAAAATAAAAAAAAATGTAATTGCAATGC
1 -AAATAAAATAAATAGCAACTATTATAATTA-TTTCAAAAATAAAAAAATAT-T-ATTGC-A-GC
* * * * * * * *
42707 ACTAAACTCAAGCCCAAGTACCGCGGAAATGAAA-AAAATTAAA-TAGCAATTCTTATAATTATT
60 ACTAGACTCAAACCCAAGTGCCCCGAAAATGAAATGAAA-TAAATTTGCAATTATTATAATTATT
* * * * * * * **
42770 CCTGAAGT-TAAAAA-ATTTATTGCAACACCATATTCAAACCTAAGTGTCTTGGAAAT
124 CCT-AAATATAAAAATA-TTATTACAACACCAGACTCAAGCC-AA-AGAC--CCAAAT
* * * * * * * *
42826 GAAATGAAATAAATA-CAAATTATTATAATTATTTTAGAAAAT-AAGAAATATTAGTGTAGTAAT
1 -AAATAAAATAAATAGC-AACTATTATAATTATTTCA-AAAATAAAAAAATATTATTGCAGCACT
* ** * * *
42889 AGACTCCAGA-CCAAGTTTCCC-AAGAATGAAA--AAATTAA-TAGTAATTATTATAATTAATTC
63 AGACT-CAAACCCAAGTGCCCCGAA-AATGAAATGAAATAAATTTGCAATTATTATAATT-ATTC
** ** * * * *
42949 AAAAAT-TAAATAACT-TTATTGTAGCACAAGACTCAAGCTC-AAGTGCCC--CT
125 CTAAATATAAA-AA-TATTATTACAACACCAGACTCAAGC-CAAAG-ACCCAAAT
* * * ** * * *
42999 GGAATGAAATGAAT-G--A--ATTGCAATTATTCCAGAAAATAACAAAATATTATTGCAGCACCA
1 -AAATAAAATAAATAGCAACTATTATAATTATTTCA-AAAATAAAAAAATATTATTGCAGCACTA
* * ** * * * * *
43059 GACTCAAGCCCAAATG-CTTGAAAATTAAATGAAACATA-TAGCAAATATTATAATTATT-CTGG
64 GACTCAAACCCAAGTGCCCCGAAAATGAAATGAAATAAATTTGCAATTATTATAATTATTCCT--
* * * * * *
43121 ACAGTA-AAAAATTTTTTTGCAGCACCAGACTCAATCCCAAATG-CCCAGGGAATT
127 A-AATATAAAAATATTATTACAACACCAGACTCAA-GCCAAA-GACCCA---AA-T
* ** * ** * *
43175 AAATGAAATGTATAGCAATTATTATAATTATTTTGGAAAGT-AAAAAA-A-TATTGCAGCACCA-
1 AAATAAAATAAATAGCAACTATTATAATTA-TTTCAAAAATAAAAAAATATTATTGCAGCACTAG
** * *** * * * **
43236 ACTCAAGTCCAAGTGCTCCTTGAATGAAATGAAATAAATTAT--AATTATTCTTAA-AAAT-AAA
65 ACTCAAACCCAAGTGCCCCGAAAATGAAATGAAATAAATT-TGCAATTATT-ATAATTATTCCTA
* * * * *
43297 AATA-AAAATATATTGTCACAACA-CAGACTTAAACTCAAATGCCCCGAAAT
128 AATATAAAA-ATATTATTACAACACCAGACTCAAGC-CAAA-GACCC-AAAT
* * * * *
43347 AAAATGAAATAAATAGAAATTATTATAATTATTTAAAAAAAATAGAAAAAA-ATTATTGTAGCA-
1 -AAATAAAATAAATAGCAACTATTATAATTATTT--CAAAAATA-AAAAAATATTATTGCAGCAC
* * * * * *
43410 TCAAACTCAAGCCCAAGTGCACTG-AAATGAAATGAAATAAA-TAGCAATTATTATAATTATTTC
62 T-AGACTCAAACCCAAGTGCCCCGAAAATGAAATGAAATAAATTTGCAATTATTATAATTATTCC
* * * ** * *
43473 AAAAAATAAAAAATATTATCACAACACC-TTCTTCAAGCCCAAGTGCCCCATGAAT
126 TAAATAT-AAAAATATTATTACAACACCAGAC-TCAAG-CCAA-AGACCCA--AAT
* * * * * * * * *
43528 AAAATGAAATAAATAACAATTATTATAGTTA-TCCAAGAATTAAAAAATATTATTTTCAGCACCA
1 -AAATAAAATAAATAGCAACTATTATAATTATTTCAAAAATAAAAAAATATTA-TTGCAGCACTA
* * * ** *
43592 GACTCAAACTCAAGTGCCTCAAAAATGAAATGAAATAAA-TAACAATTATTTTAATTATT
64 GACTCAAACCCAAGTGCCCCGAAAATGAAATGAAATAAATTTGCAATTATTATAATTATT
43651 TCAAAAAAAT
Statistics
Matches: 1452, Mismatches: 325, Indels: 258
0.71 0.16 0.13
Matches are distributed among these distances:
168 26 0.02
169 30 0.02
170 45 0.03
171 8 0.01
172 5 0.00
173 43 0.03
174 25 0.02
175 69 0.05
176 189 0.13
177 118 0.08
178 177 0.12
179 128 0.09
180 129 0.09
181 155 0.11
182 22 0.02
183 29 0.02
184 116 0.08
185 84 0.06
186 49 0.03
187 5 0.00
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.28
Consensus pattern (175 bp):
AAATAAAATAAATAGCAACTATTATAATTATTTCAAAAATAAAAAAATATTATTGCAGCACTAGA
CTCAAACCCAAGTGCCCCGAAAATGAAATGAAATAAATTTGCAATTATTATAATTATTCCTAAAT
ATAAAAATATTATTACAACACCAGACTCAAGCCAAAGACCCAAAT
Found at i:42668 original size:271 final size:268
Alignment explanation
Indices: 41562--44105 Score: 909
Period size: 275 Copynumber: 9.5 Consensus size: 268
41552 AGTGCTCGAG
* * * * * ** * * *
41562 GAATGAAATGAAATAAATAGAAATTATTATAATTATATCAGAAATTAAAAACATATTATCGCAAC
1 GAATAAAATAAAATAAATAGCAATTATTATAAATATTTTGGAAA-TAAAAAAATATTATTGCAGC
* * * * * **
41627 ACTAAACTCAAGCCCAAGTACCCT---AA--AAATGAAATAAATAATTA-TTAACATAATTATTC
65 ACCAGACTCAAGCCAAAGT-GCCTGGGAATGAAATGAAATAAATAA-CAGTTATTATAATTATT-
** * * * * * * ** * *
41686 TTG-AAAATAAAAATTATTATTGCAGCGCCAAACTCAAGCCCAAATATCTTGATAATGAAATAAA
127 TTGAAAAATAAAAAAAATTATTGCAGCACTAGACTCAAACCCAAGTGTCCCGAAAATGAAATGAA
* * ** *
41750 ATAA-ATAGTAATTATTATAATTATTTCAAAAAAATAAAAAAA-ATTATTACAACA-CATGGCTA
192 ATAAGAT-GCAATTATTATAATTATTTC--AAAAATAAAAAAATATTATTACAGCACCA-GAATC
* *
41812 AAGCCCAAGTG-CCATGA
253 AA-CCCAAATGACC-CGA
* * * * ****
41829 AAATGAAATAAAATAAATACCAATTATTATAACTATTCCAAAAAATATCAAATAAA-ATTTATTG
1 GAATAAAATAAAATAAATAGCAATTATTATAAATATT-TTGGAAATA--AAA-AAATA-TTATTG
* *
41893 TAGCACCAGACTCAAGGCCAAA-TGCCTCGGGAATGAAATGAAATAAATATCAGTTATTATAATT
61 CAGCACCAGACTCAA-GCCAAAGTGCCT-GGGAATGAAATGAAATAAATAACAGTTATTATAATT
* * *
41957 A--TTAAAAAATAAAAAAAATATTATTAG-TGCACTAGACTCAAACCCAAGTGTCCTGAAAATGA
124 ATTTTGAAAAAT-AAAAAAA-ATTATT-GCAGCACTAGACTCAAACCCAAGTGTCCCGAAAATGA
* * * * * *
42019 AATGAAATAA-ATTTGCAATTATTATAATTATTCCTAAAAT--AAAAATATTATTTCAACATCGG
186 AATGAAATAAGA--TGCAATTATTATAATTATTTCAAAAATAAAAAAATATTATTACAGCACCAG
* * * *
42081 ATTCAAGCCTAA-GAACCCAA
249 AATCAACCCAAATG-ACCCGA
* * * *** *
42101 AAATAAAATAAAATAAATTGCAACTATTATAAATATTTCAAAAATAAAAAAATATTGTTGCAGCA
1 GAATAAAATAAAATAAATAGCAATTATTATAAATATTTTGGAAATAAAAAAATATTATTGCAGCA
* * * * * ** * * *
42166 CTAGACTCAAGCCCAAGTGCCCCGAGAATAAAATGAAATAAATTTGCAATTATCATAATTATTTC
66 CCAGACTCAAGCCAAAGTG-CCTGGGAATGAAATGAAATAAA-TAACAGTTATTATAATTATTTT
* * *
42231 GAAAAAT-AAAAAAATTATTACAGCACCAGACTCAAGCCCAAGTGT-CC---AATG-AATGAAA-
129 GAAAAATAAAAAAAATTATTGCAGCACTAGACTCAAACCCAAGTGTCCCGAAAATGAAATGAAAT
* * * * *
42289 AGGATAGCAATTATTATAATTATTTCAAAAAATAAAAAAATATCATTATAGTACCAAAATCAAGC
194 AAGAT-GCAATTATTATAATTATTTC-AAAAATAAAAAAATATTATTACAGCACCAGAATCAA-C
* *
42354 CCGAGTG-CCCTGA
256 CCAAATGACCC-GA
* * *
42367 GAATTAAAA-GAAATAAATAGCAATTATTATAATTATTTTGGAAATAAAAAAATATTATTGCAAC
1 GAA-TAAAATAAAATAAATAGCAATTATTATAAATATTTTGGAAATAAAAAAATATTATTGCAGC
* * * *
42431 ACCAGACTCTAGCCAAAGTGTCATGGGAATGAAAT-AAATTCAATAACAGGTATTATAATTATTT
65 ACCAGACTCAAGCCAAAGTG-CCTGGGAATGAAATGAAA-TAAATAACAGTTATTATAATTATTT
*
42495 TGAAAAATAAAAAAAATTATTGCAGCACTAGACTCAAACTCAAGTGTCCCGAAAATGAAATGAAA
128 TGAAAAATAAAAAAAATTATTGCAGCACTAGACTCAAACCCAAGTGTCCCGAAAATGAAATGAAA
* * * * * *
42560 TAAGCTGCAATTATTATAATGATTTCGAAATATAAAAAAAGATTATTGCAGCACCAGACTCAATC
193 TAAGATGCAATTATTATAATTATTTC-AAAAATAAAAAAATATTATTACAGCACCAGAATCAA-C
* *
42625 CCAAATGTCCGGA
256 CCAAATGACCCGA
* * * *
42638 GAATGAAATTAAATAAATAGCAATTATTATAACTATTTTGGAAAATAAAAAAAAATGTAATTGCA
1 GAATAAAATAAAATAAATAGCAATTATTATAAATATTTTGG-AAATAAAAAAATAT-T-ATTGC-
* * * * * * * *
42703 ATGCACTAAACTCAAGCCCAAGTACC-GCGGAAATGAAA-AAAATTAAATAGCAATTCTTATAAT
62 A-GCACCAGACTCAAGCCAAAGTGCCTG-GG-AATGAAATGAAA-TAAATAACAGTTATTATAAT
* * * * * * * * * ** *
42766 TATTCCTG--AAGTTAAAAAATTTATTGCAACACCATATTCAAACCTAAGTGTCTTGGAAATGAA
123 TATT-TTGAAAAATAAAAAAAATTATTGCAGCACTAGACTCAAACCCAAGTGTCCCGAAAATGAA
* * * * ** * **
42829 ATGAAATAA-ATACAAATTATTATAATTATTTTAGAAAAT-AAGAAATATTAGTGTAGTAATAGA
187 ATGAAATAAGATGC-AATTATTATAATTATTTCA-AAAATAAAAAAATATTATTACAGCACCAGA
* * ** *
42892 CTCCAGA-CCAAGTTTCCCAA
250 AT-CA-ACCCAAATGACCCGA
* * * * * *** * * *
42912 GAAT-GAA-AAAATTAATAGTAATTATTATAATTAATTCAAAAATTAAATAACT-TTATTGTAGC
1 GAATAAAATAAAATAAATAGCAATTATTATAAATATTTTGGAAA-TAAAAAAATATTATTGCAGC
* * ** *
42974 ACAAGACTCAAGCTC-AAGTGCCCCT-GGAATGAAATG-AATGAATTGCA---ATTAT--TCCA-
65 ACCAGACTCAAGC-CAAAGTG--CCTGGGAATGAAATGAAATAAATAACAGTTATTATAAT-TAT
* * * * ** *
43030 ---G-AAAATAACAAAATATTATTGCAGCACCAGACTCAAGCCCAAATG-CTTGAAAATTAAATG
126 TTTGAAAAATAA-AAAAAATTATTGCAGCACTAGACTCAAACCCAAGTGTCCCGAAAATGAAATG
* * * ** * * * * * *
43090 AAA-CATATAGCAAATATTATAATTATTCTGGACAGT-AAAAAATTTTTTTGCAGCACCAGACTC
190 AAATAAGAT-GCAATTATTATAATTATT-TCAAAAATAAAAAAATATTATTACAGCACCAGAATC
*
43153 AATCCCAAATG-CCCAGG
253 AA-CCCAAATGACCC-GA
* * ** *
43170 GAATTAAATGAAATGTATAGCAATTATTATAATTATTTTGGAAAGT-AAAAAA-A-TATTGCAGC
1 GAATAAAATAAAATAAATAGCAATTATTATAAATATTTTGGAAA-TAAAAAAATATTATTGCAGC
* * * * *
43232 ACCA-ACTCAAGTCC-AAGTGCTCCT-TGAATGAAATGAAATAAATTATAATTATTCTTAA--A-
65 ACCAGACTCAAG-CCAAAGTG--CCTGGGAATGAAATGAAATAAATAACAGTTATT-ATAATTAT
** * * ** * * * * * *
43291 AAT-AAAAATAAAAATATATTGTCACAACAC-AGACTTAAACTCAAATGCCCCG-AAATAAAATG
126 TTTGAAAAATAAAAA-AAATTATTGCAGCACTAGACTCAAACCCAAGTGTCCCGAAAATGAAATG
* * ** *
43353 AAATAA-ATAGAAATTATTATAATTATTTAAAAAAAATAGAAAAAA-ATTATTGTAGCATCA-AA
190 AAATAAGAT-GCAATTATTATAATTATTT--CAAAAATA-AAAAAATATTATTACAGCACCAGAA
* *
43415 CTCAAGCCCAAGTG-CACTGA
251 -TCAA-CCCAAATGAC-CCGA
* * * ** * ** *
43435 -AATGAAATGAAATAAATAGCAATTATTATAATTA-TTTCAAAAAATAAAAAATATTATCACAAC
1 GAATAAAATAAAATAAATAGCAATTATTATAAATATTTTGGAAATA-AAAAAATATTATTGCAGC
** * *** * * *
43498 ACC-TTCTTCAAGCCCAAGTGCCCCATGAATAAAATGAAATAAATAACAATTATTATAGTTA--T
65 ACCAGAC-TCAAGCCAAAGTG-CCTGGGAATGAAATGAAATAAATAACAGTTATTATAATTATTT
** * * * * * *
43560 CCAAGAATTAAAAAATATTATTTTCAGCACCAGACTCAAACTCAAGTG-CCTCAAAAATGAAATG
128 TGAA-AAATAAAAAAAATTA-TTGCAGCACTAGACTCAAACCCAAGTGTCC-CGAAAATGAAATG
* * * ** ** **
43624 AAATAA-ATAACAATTATTTTAATTATTTC-------AAAAAA-ATTACTGGAGCTTCAGGCTCA
190 AAATAAGAT-GCAATTATTATAATTATTTCAAAAATAAAAAAATATTATTACAGCACCAGAATCA
* * *
43680 AGTCCAAGTG--CCTA
254 A-CCCAAATGACCCGA
* * * * ** * *
43694 TGAATGAAGTGAAATAAATAGCAATTATTATAATTATTCCAGAAAATAAAAAAATATTATTGCAA
1 -GAATAAAATAAAATAAATAGCAATTATTATAAATATT-TTGGAAATAAAAAAATATTATTGCAG
* * * * * * * *
43759 CACCAGCCTCAAACCTAAGT-CTCTGAGGAATGAAATGAAACAAATAGCAATTATTGTAGTTATT
64 CACCAGACTCAAGCCAAAGTGC-CTG-GGAATGAAATGAAATAAATAACAGTTATTATAATTATT
* * * *
43823 TT-AGAAAATAAAAAAAA-TATTGCAGCACGAGTCTCAAGCCCAAGTG-CCCTGATAATGAAATG
127 TTGA-AAAATAAAAAAAATTATTGCAGCACTAGACTCAAACCCAAGTGTCCC-GAAAATGAAATG
* * * * *
43885 AAATAA-AT--AATATATAGTATAAGTATTTTGAAAATTAAAAAAAAAATTATTGCAGCACCAGA
190 AAATAAGATGCAAT-TAT--TATAATTA-TTTCAAAAAT-AAAAAAATATTATTACAGCACCAGA
* * *
43947 CTCAAGCCCAAGTGTCCCGACTCTCGG
250 ATCAA-CCCAA--AT---GAC-C-CGA
* * * * *
43974 GAATGAAATGAAAAAAAAT-GCAATTATTATAATTA-TTTCG-AA-AAAAAAATATTATTGTAGC
1 GAATAAAAT-AAAATAAATAGCAATTATTATAAATATTTTGGAAATAAAAAAATATTATTGCAGC
* * * **** * * *
44035 ACCAGGCTCAATCTC-AAGTACCCCAATAATGAAATGAAATAAATAGCAATCATTATAATTATTT
65 ACCAGACTCAAGC-CAAAGT-GCCTGGGAATGAAATGAAATAAATAACAGTTATTATAATTATTT
44099 TGAAAAA
128 TGAAAAA
44106 AATATTATTA
Statistics
Matches: 1747, Mismatches: 374, Indels: 304
0.72 0.15 0.13
Matches are distributed among these distances:
256 1 0.00
257 34 0.02
258 90 0.05
259 41 0.02
260 30 0.02
261 118 0.07
262 89 0.05
263 88 0.05
264 68 0.04
265 73 0.04
266 146 0.08
267 109 0.06
268 83 0.05
269 55 0.03
270 50 0.03
271 175 0.10
272 91 0.05
273 29 0.02
274 53 0.03
275 214 0.12
276 72 0.04
277 4 0.00
278 1 0.00
279 25 0.01
280 8 0.00
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.28
Consensus pattern (268 bp):
GAATAAAATAAAATAAATAGCAATTATTATAAATATTTTGGAAATAAAAAAATATTATTGCAGCA
CCAGACTCAAGCCAAAGTGCCTGGGAATGAAATGAAATAAATAACAGTTATTATAATTATTTTGA
AAAATAAAAAAAATTATTGCAGCACTAGACTCAAACCCAAGTGTCCCGAAAATGAAATGAAATAA
GATGCAATTATTATAATTATTTCAAAAATAAAAAAATATTATTACAGCACCAGAATCAACCCAAA
TGACCCGA
Found at i:43658 original size:85 final size:85
Alignment explanation
Indices: 43435--44197 Score: 254
Period size: 90 Copynumber: 8.6 Consensus size: 85
43425 AGTGCACTGA
* * * * *
43435 AATGAAATGAAATAAATAGCAATTATTATAATTATTTCAAAAAATAAAAAATATTATCACAACAC
1 AATGAAATGAAATAAATAACAATTATTATAATTATTTC--AAAA-AAATATTATT-T-GCAGCAC
** * * * *
43500 C-TTCTTCAAGCCCAAGTGCCCCATG
61 CAGAC-TCAAACTCAAGTGCCTCAAG
* * * *
43525 AATAAAATGAAATAAATAACAATTATTATAGTTA-TCCAAGAATTAAAAAATATTATTTTCAGCA
1 AATGAAATGAAATAAATAACAATTATTATAATTATTTC----A--AAAAAATATTATTTGCAGCA
*
43589 CCAGACTCAAACTCAAGTGCCTCAAA
60 CCAGACTCAAACTCAAGTGCCTCAAG
* * * ** *
43615 AATGAAATGAAATAAATAACAATTATTTTAATTATTTC-AAAAAA-ATTA-CTGGAGCTTCAGGC
1 AATGAAATGAAATAAATAACAATTATTATAATTATTTCAAAAAAATATTATTTGCAGCACCAGAC
* *
43677 TC-AAGTCCAAGTGCCT-ATG
66 TCAAACT-CAAGTGCCTCAAG
* * * *
43696 AATGAAGTGAAATAAATAGCAATTATTATAATTATTCCAGAAAATAAAAAAATATTA-TTGCAAC
1 AATGAAATGAAATAAATAACAATTATTATAATTATTTC-------AAAAAAATATTATTTGCAGC
* * *
43760 ACCAGCCTCAAAC-CTAAGT-CTCTGAGG
59 ACCAGACTCAAACTC-AAGTGC-CTCAAG
* * * * * * ** *
43787 AATGAAATGAAACAAATAGCAATTATTGTAGTTATTTTAGAAAATAAAAAAAATATTGCAGCACG
1 AATGAAATGAAATAAATAACAATTATTATAATTA-TTT-CAAAA-AAATATTAT-TTGCAGCACC
* * * * *
43852 AGTCTCAAGCCCAAGTGCC-CTGAT
62 AGACTCAAACTCAAGTGCCTC-AAG
* * * * * *
43876 AATGAAATGAAATAAATAATATATAGTATAAGTATTTTGAAAATTAAAAAAAAAATTA-TTGCAG
1 AATGAAATGAAATAAATAACA-AT--TATTA-TA-ATT---ATTTCAAAAAAATATTATTTGCAG
* * **
43940 CACCAGACTCAAGCCCAAGTGTCCCGACTCTCGGG
58 CACCAGACTCAAACTCAA--GT---G-C-CTCAAG
*
43975 AATGAAATGAAA-AAA-AATGCAATTATTATAATTATTTCGAAAAAAAAATATTA-TTGTAGCAC
1 AATGAAATGAAATAAATAA--CAATTATTATAATTATTTC---AAAAAAATATTATTTGCAGCAC
* * * * *
44037 CAGGCTCAATCTCAAGTACCCCAAT
61 CAGACTCAAACTCAAGTGCCTCAAG
* * * * *
44062 AATGAAATGAAATAAATAGCAATCATTATAATTATTTTGAAAAAAATATTA-TTACAACACCAGA
1 AATGAAATGAAATAAATAACAATTATTATAATTA-TTTCAAAAAAATATTATTTGCAGCACCAGA
* * *
44126 CTC-AAGTCCAAATATCC-CGAA-
65 CTCAAACT-CAAGT-GCCTC-AAG
* *
44147 AATGAAAT-AAATTAAATAGA-AATTATTTTAATTATTCTAAAAAAAATATTA
1 AATGAAATGAAA-TAAATA-ACAATTATTATAATTATT-TCAAAAAAATATTA
44198 CGACTCAAGC
Statistics
Matches: 513, Mismatches: 102, Indels: 121
0.70 0.14 0.16
Matches are distributed among these distances:
81 38 0.07
82 19 0.04
83 4 0.01
84 13 0.03
85 68 0.13
86 8 0.02
87 33 0.06
88 7 0.01
89 50 0.10
90 107 0.21
91 43 0.08
92 37 0.07
93 5 0.01
94 43 0.08
95 6 0.01
96 6 0.01
97 4 0.01
98 6 0.01
99 15 0.03
100 1 0.00
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.28
Consensus pattern (85 bp):
AATGAAATGAAATAAATAACAATTATTATAATTATTTCAAAAAAATATTATTTGCAGCACCAGAC
TCAAACTCAAGTGCCTCAAG
Found at i:43812 original size:172 final size:172
Alignment explanation
Indices: 43505--43823 Score: 412
Period size: 172 Copynumber: 1.9 Consensus size: 172
43495 AACACCTTCT
* * *
43505 TCAAGCCCAAGTGCCCCATGAATAAAATGAAATAAATAACAATTATTATAGTTATCCAAGAATTA
1 TCAAGCCCAAGTGCCCCATGAATAAAATGAAATAAATAACAATTATTATAATTATCCAAAAATAA
* * *
43570 AAAAATATTATTTTCAGCACCAGACTCAAACTCAAGTGCCTCAAAAATGAAATGAAATAAATAAC
66 AAAAATATTATTTGCAACACCAGACTCAAACTCAAGTGCCTCAAAAATGAAATGAAACAAATAAC
*
43635 AATTATTTTAATTATTTCAAAAAAATTACTGGAGCTTCAGGC
131 AATTATTGTAATTATTTCAAAAAAATTACTGGAGCTTCAGGC
* * * * *
43677 TCAAGTCCAAGTG-CCTATGAATGAAGTGAAATAAATAGCAATTATTATAATTATTCCAGAAAAT
1 TCAAGCCCAAGTGCCCCATGAATAAAATGAAATAAATAACAATTATTATAATTA-TCCA-AAAAT
* * **
43741 AAAAAAATATTA-TTGCAACACCAGCCTCAAAC-CTAAGT-CTCTGAGGAATGAAATGAAACAAA
64 AAAAAAATATTATTTGCAACACCAGACTCAAACTC-AAGTGC-CTCAAAAATGAAATGAAACAAA
* *
43803 TAGCAATTATTGTAGTTATTT
127 TAACAATTATTGTAATTATTT
43824 TAGAAAATAA
Statistics
Matches: 125, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
171 37 0.30
172 73 0.58
173 15 0.12
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (172 bp):
TCAAGCCCAAGTGCCCCATGAATAAAATGAAATAAATAACAATTATTATAATTATCCAAAAATAA
AAAAATATTATTTGCAACACCAGACTCAAACTCAAGTGCCTCAAAAATGAAATGAAACAAATAAC
AATTATTGTAATTATTTCAAAAAAATTACTGGAGCTTCAGGC
Found at i:43869 original size:261 final size:261
Alignment explanation
Indices: 43392--43894 Score: 595
Period size: 261 Copynumber: 1.9 Consensus size: 261
43382 AAAAAAATAG
* *
43392 AAAAAAATTATTGTAGCATCAAACTCAAGCCCAAGTGCACTGAAATGAAATGAAATAAATAGCAA
1 AAAAAAATTACTGGAGCATCAAACTCAAGCCCAAGTGCACTGAAATGAAATGAAATAAATAGCAA
* ** * *
43457 TTATTATAATTATTTCAAAAAATAAAAAATATTATCACAACACCTTCTTCAAGCCCAAGTGCCCC
66 TTATTATAATTATTCCAAAAAATAAAAAATATTATCACAACACCAGCCTCAAACCCAAGTGCCCC
* * * * *
43522 ATGAATAAAATGAAATAAATAACAATTATTATAGTTATCCAAGAATTAAAAAATATTATTTTCAG
131 AGGAATAAAATGAAACAAATAACAATTATTATAGTTATCCAAGAAATAAAAAATAATATTTGCAG
*
43587 CACCAGACTCAAACTCAAGTG-CCTCAAAAATGAAATGAAATAAATAACAATTATTTTAATTATT
196 CACCAGACTCAAACCCAAGTGCCCT-AAAAATGAAATGAAATAAATAACAATTATTTTAATTATT
43651 TC
260 TC
* ** * *
43653 AAAAAAATTACTGGAGCTTCAGGCTCAAGTCCAAGTGC-CT-ATGAATGAAGTGAAATAAATAGC
1 AAAAAAATTACTGGAGCATCAAACTCAAGCCCAAGTGCACTGA--AATGAAATGAAATAAATAGC
* ** *
43716 AATTATTATAATTATTCCAGAAAATAAAAAAATATTATTGCAACACCAGCCTCAAACCTAAGT-C
64 AATTATTATAATTATTCCAAAAAAT-AAAAAATATTATCACAACACCAGCCTCAAACCCAAGTGC
** * * * ***
43780 TCTGAGGAATGAAATGAAACAAATAGCAATTATTGTAGTTATTTTAGAAAATAAAAAA-AATA-T
128 -CCCAGGAATAAAATGAAACAAATAACAATTATTATAGTTATCCAAG-AAATAAAAAATAATATT
* * * * *
43843 TGCAGCACGAGTCTCAAGCCCAAGTGCCCTGATAATGAAATGAAATAAATAA
191 TGCAGCACCAGACTCAAACCCAAGTGCCCTAAAAATGAAATGAAATAAATAA
43895 TATATAGTAT
Statistics
Matches: 201, Mismatches: 35, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
259 1 0.00
260 2 0.01
261 117 0.58
262 72 0.36
263 9 0.04
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (261 bp):
AAAAAAATTACTGGAGCATCAAACTCAAGCCCAAGTGCACTGAAATGAAATGAAATAAATAGCAA
TTATTATAATTATTCCAAAAAATAAAAAATATTATCACAACACCAGCCTCAAACCCAAGTGCCCC
AGGAATAAAATGAAACAAATAACAATTATTATAGTTATCCAAGAAATAAAAAATAATATTTGCAG
CACCAGACTCAAACCCAAGTGCCCTAAAAATGAAATGAAATAAATAACAATTATTTTAATTATTT
C
Found at i:44104 original size:186 final size:178
Alignment explanation
Indices: 41563--44104 Score: 714
Period size: 181 Copynumber: 14.2 Consensus size: 178
41553 GTGCTCGAGG
* ** * * * *
41563 AATGAAATGAAATAAATAGAAATTATTATAATTATATCAGAAATTAAAAACATATTATCGCAACA
1 AATGAAATGAAATAAATAGCAA-TATTATAATTAT-TTTGAAAATAAAAAAAAATTATTGCAACA
* * * * * *** **
41628 CTAAACTCAAGCCCAAGTACCCT----AA--AAATGAAATAAATAATTATTAACATAATTATTCT
64 CCAGACTCAAACCCAAGT-CTCTGAGGAATGAAATGAAAAAAATAGCAATTATTATAATTATT-T
* * * ** * * ***
41687 T-GAAAATAAAAATTATTATTGCAGCGCCAAACTCAAGCCCAAATATCTTGAT
127 TAGAAAATAAAAA-AAATATTGCAGCACCAGGCTCAAGCCCAAGTACCCCAAT
* * ** * *
41739 AATGAAATAAAATAAATAGTAATTATTATAATTATTTCAAAAAAATAAAAAAAATTATTACAACA
1 AATGAAATGAAATAAATAGCAA-TATTATAATTATTTTGAAAATA-AAAAAAAATTATTGCAACA
* * * *
41804 -CATGGCT-AAAGCCCAAGTGC-CATGA-AAATGAAAT-AAAATAAATACCAATTATTATAACTA
64 CCA-GACTCAAA-CCCAAGT-CTC-TGAGGAATGAAATGAAAA-AAATAGCAATTATTATAATTA
** * * * * * * * ***
41864 TTCCAAAAAATATCAAATAAAATTTATTGTAGCACCAGACTCAAGGCCAAATGCCTCGGG
124 TTTTAGAAAATA--AAA-AAAA--TATTGCAGCACCAGGCTCAAGCCCAAGTACCCCAAT
* * ** **
41924 AATGAAATGAAATAAATATCAGTTATTATAATTA-TTAAAAAATAAAAAAAATATTATTAG-TGC
1 AATGAAATGAAATAAATAGCA-ATATTATAATTATTTTGAAAATAAAAAAAA-ATTATT-GCAAC
* * * * *
41987 ACTAGACTCAAACCCAAGTGTCCTGA-AAATGAAATGAAATAAATTTGCAATTATTATAATTATT
63 ACCAGACTCAAACCCAAGTCT-CTGAGGAATGAAATGAAA-AAAATAGCAATTATTATAATTATT
* * * * * * * * * *
42051 CCT--AAAATAAAAATATTATTTCAACATC-GGATTCAAGCCTAAG-AACCCAAA
126 -TTAGAAAATAAAAAAAATATTGCAGCACCAGG-CTCAAGCCCAAGTACCCCAAT
* * * * ** * * *
42102 AATAAAATAAAATAAATTGCAACTATTATAAATATTTCAAAAATAAAAAAATATTGTTGCAGCAC
1 AATGAAATGAAATAAATAGCAA-TATTATAATTATTTTGAAAATAAAAAAAAATTATTGCAACAC
* * * * * * * *
42167 TAGACTCAAGCCCAAGTGCCCCGA-GAATAAAATGAAATAAATTTGCAATTATCATAATTA-TTT
65 CAGACTCAAACCCAAGT-CTCTGAGGAATGAAATGAAA-AAAATAGCAATTATTATAATTATTTT
* * * * **
42230 CGAAAAATAAAAAAATTATTACAGCACCAGACTCAAGCCCAAGT-GTCC---
128 AG-AAAATAAAAAAAATATTGCAGCACCAGGCTCAAGCCCAAGTACCCCAAT
* ** * * ** **
42278 AATG-AATGAAA-AGGATAGCAATTATTATAATTATTTCAAAAAATAAAAAAATATCATTATAGT
1 AATGAAATGAAATA-AATAGCAA-TATTATAATTATTT-TGAAAATAAAAAAAAATTATTGCAAC
* * * * * * * *
42341 ACCAAAATCAAGCCCGAGTGCCCTGA-GAATTAAAAGAAATAAATAGCAATTATTATAATTATTT
63 ACCAGACTCAAACCCAAGT-CTCTGAGGAATGAAATGAAAAAAATAGCAATTATTATAATTATTT
* * * * * ** *****
42405 T-GGAAATAAAAAAATATTATTGCAACACCAGACTCTAGCCAAAGTGTCATGGG
127 TAGAAAATAAAAAAA-A-TATTGCAGCACCAGGCTCAAGCCCAAGTACCCCAAT
* * * *
42458 AATGAAAT-AAATTCAATAACAGGTATTATAATTATTTTGAAAA-ATAAAAAAAATTATTGCAGC
1 AATGAAATGAAA-TAAATAGCA-ATATTATAATTATTTTGAAAATA-AAAAAAAATTATTGCAAC
* * * * * ** *
42521 ACTAGACTCAAACTCAAGTGTCCCGA-AAATGAAATGAAATAAGCT-GCAATTATTATAATGA-T
63 ACCAGACTCAAACCCAAGTCT-CTGAGGAATGAAATGAAA-AAAATAGCAATTATTATAATTATT
* * * * ** ** *
42583 TTCGAAATATAAAAAAAGATTATTGCAGCACCAGACTCAATCCCAAATGTCCGGAG
126 TTAGAAA-ATAAAAAAA-A-TATTGCAGCACCAGGCTCAAGCCCAAGTACCCCAAT
* *
42639 AATGAAATTAAATAAATAGCAATTATTATAACTATTTTGGAAAATAAAAAAAAATGTAATTGCAA
1 AATGAAATGAAATAAATAGCAA-TATTATAATTATTTT-GAAAATAAAAAAAAAT-T-ATTGCAA
* * * * *
42704 TGCACTAAACTCAAGCCCAAGTAC-C-GCGGAAATGAAA--AAAATTAAATAGCAATTCTTATAA
62 --CACCAGACTCAAACCCAAGT-CTCTGAGG-AATGAAATGAAAA--AAATAGCAATTATTATAA
* ** ** * *** * * * ****
42765 TTATTCCT-GAAGTTAAAAAATTTATTGCAACACCATATTCAAACCTAAGTGTCTTGGA-
121 TTATT-TTAGAAAATAAAAAAAATATTGCAGCACCAGGCTCAAGCCCAAGT-ACCCCAAT
* * * * **
42823 AATGAAATGAAATAAATA-CAAATTATTATAATTATTTTAGAAAAT-AAGAAATATTAGTGTAGT
1 AATGAAATGAAATAAATAGC-AA-TATTATAATTATTTT-GAAAATAAAAAAAAATTATTGCAAC
** * * ** * ** * *
42886 AATAGACTCCAGA-CCAAGTTTCCCAAGAATGAAA--AAATTAATAGTAATTATTATAATTAATT
63 ACCAGACT-CAAACCCAAGTCTCTGAGGAATGAAATGAAAAAAATAGCAATTATTATAATTATTT
* *** * * * * *
42948 CA-AAAATTAAATAACTTTATTGTAGCACAAGACTCAAGCTCAAGTGCCCC---
127 TAGAAAA-TAAA-AAAAATATTGCAGCACCAGGCTCAAGCCCAAGTACCCCAAT
* * ** ** * * *
42998 --TGGAATGAAATGAAT-G--A-ATTGCAATTATTCCAGAAAATAACAAAATATTATTGCAGCAC
1 AATGAAATGAAATAAATAGCAATATTATAATTATT-TTGAAAATAAAAAAAAATTATTGCAACAC
* * * * * * * * *
43057 CAGACTCAAGCCCAAATGCT-TGA-AAATTAAATGAAACATATAGCAAATATTATAATTATTCTG
65 CAGACTCAAACCCAAGT-CTCTGAGGAATGAAATGAAAAAAATAGCAATTATTATAATTATTTTA
* * ** * * * * * **
43120 GACAGTAAAAAATTTTTTTGCAGCACCAGACTCAATCCCAAAT-GCCCAGGG
129 GAAAATAAAAAA-AATATTGCAGCACCAGGCTCAAGCCCAAGTACCCCA-AT
* ** * *
43171 AATTAAATGAAATGTATAGCAATTATTATAATTATTTTGGAAAGT--AAAAAAA-TATTGCAGCA
1 AATGAAATGAAATAAATAGCAA-TATTATAATTATTTT-GAAAATAAAAAAAAATTATTGCAACA
** * * * *
43233 CCA-ACTCAAGTCCAAGTGCTCCT--TGAATGAAATGAAATAAATTA-TAATTATTCTTAA--A-
64 CCAGACTCAAACCCAAGT-CT-CTGAGGAATGAAATGAAA-AAAATAGCAATTATT-ATAATTAT
** * * * * * * * *
43291 AATA-AAAAT-AAAAATATATTGTCA-CAACACAGACTTAAACTCAAATGCCCCGA-
125 TTTAGAAAATAAAAAAAATATTG-CAGC-AC-CAGGCTCAAGCCCAAGTACCCCAAT
* * ** * * *
43344 AATAAAATGAAATAAATAGAAATTATTATAATTATTTAAAAAAAATAGAAAAAAATTATTGTAGC
1 AATGAAATGAAATAAATAGCAA-TATTATAATTATTT--TGAAAATAAAAAAAAATTATTGCAAC
* * * * *
43409 ATCAAACTCAAGCCCAAGTGCACTGA--AATGAAATGAAATAAATAGCAATTATTATAATTATTT
63 ACCAGACTCAAACCCAAGT-CTCTGAGGAATGAAATGAAAAAAATAGCAATTATTATAATTATTT
* * * ** * ** *
43472 CAAAAAATAAAAAATATTATCACAACACC-TTCTTCAAGCCCAAGTGCCCC-AT
127 TAGAAAATAAAAAA-AATATTGCAGCACCAGGC-TCAAGCCCAAGTACCCCAAT
* * * ** * * * *
43524 GAATAAAATGAAATAAATAACAATTATTATAGTTA--TCCAAGAATTAAAAAATATTATTTTCAG
1 -AATGAAATGAAATAAATAGCAA-TATTATAATTATTTTGAA-AATAAAAAAAAATTA-TTGCAA
* * ** * * *
43587 CACCAGACTCAAACTCAAGTGC-CTCAAAAATGAAATGAAATAAATAACAATTATTTTAATTA-T
62 CACCAGACTCAAACCCAAGT-CTCTGAGGAATGAAATGAAAAAAATAGCAATTATTATAATTATT
* * * * ** * * *
43650 TT------CAAAAAAATTACTGGAGCTTCAGGCTCAAGTCCAAGT--GCCTAT
126 TTAGAAAATAAAAAAAATATTGCAGCACCAGGCTCAAGCCCAAGTACCCCAAT
* ** *
43695 GAATGAAGTGAAATAAATAGCAATTATTATAATTATTCCAGAAAATAAAAAAATATTATTGCAAC
1 -AATGAAATGAAATAAATAGCAA-TATTATAATTATT-TTGAAAATAAAAAAAAATTATTGCAAC
* * * * *
43760 ACCAGCCTCAAACCTAAGTCTCTGAGGAATGAAATGAAACAAATAGCAATTATTGTAGTTATTTT
63 ACCAGACTCAAACCCAAGTCTCTGAGGAATGAAATGAAAAAAATAGCAATTATTATAATTATTTT
* * * **
43825 AGAAAATAAAAAAAATATTGCAGCACGAGTCTCAAGCCCAAGTGCCCTGAT
128 AGAAAATAAAAAAAATATTGCAGCACCAGGCTCAAGCCCAAGTACCCCAAT
** * * *
43876 AATGAAATGAAATAAATAATATATAGTATAAGTATTTTGAAAATTAAAAAAAAAATTATTGCAGC
1 AATGAAATGAAATAAATAGCA-ATATTATAATTATTTTGAAAA-T-AAAAAAAAATTATTGCAAC
*
43941 ACCAGACTCAAGCCCAAGTGTCCCGACTCTCG-GGAATGAAATGAAAAAAA-ATGCAATTATTAT
63 ACCAGACTCAAACCCAA--GT-----CTCT-GAGGAATGAAATGAAAAAAATA-GCAATTATTAT
* * * * * *
44004 AATTA-TTTCGAAAA-AAAAATATTATTGTAGCACCAGGCTCAATCTCAAGTACCCCAAT
119 AATTATTTTAGAAAATAAAAAAAATATTGCAGCACCAGGCTCAAGCCCAAGTACCCCAAT
44062 AATGAAATGAAATAAATAGCAATCATTATAATTATTTTGAAAA
1 AATGAAATGAAATAAATAGCAAT-ATTATAATTATTTTGAAAA
44105 AAATATTATT
Statistics
Matches: 1777, Mismatches: 430, Indels: 308
0.71 0.17 0.12
Matches are distributed among these distances:
168 24 0.01
169 30 0.02
170 53 0.03
171 36 0.02
172 78 0.04
173 79 0.04
174 35 0.02
175 69 0.04
176 175 0.10
177 90 0.05
178 159 0.09
179 154 0.09
180 171 0.10
181 200 0.11
182 25 0.01
183 24 0.01
184 117 0.07
185 91 0.05
186 117 0.07
187 13 0.01
188 36 0.02
189 1 0.00
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.28
Consensus pattern (178 bp):
AATGAAATGAAATAAATAGCAATATTATAATTATTTTGAAAATAAAAAAAAATTATTGCAACACC
AGACTCAAACCCAAGTCTCTGAGGAATGAAATGAAAAAAATAGCAATTATTATAATTATTTTAGA
AAATAAAAAAAATATTGCAGCACCAGGCTCAAGCCCAAGTACCCCAAT
Found at i:44192 original size:87 final size:85
Alignment explanation
Indices: 43975--44197 Score: 231
Period size: 85 Copynumber: 2.6 Consensus size: 85
43965 GACTCTCGGG
* * ** *
43975 AATGAAATGAAA-AAAAATGCAATTATTATAATTATTTCGAAAAAAAAATATTATTGTAGCACCA
1 AATGAAATGAAATAAATA-GAAATTATTATAATTATTT--AAAAAAAAATATTATTACAACACCA
* *
44039 GGCTCAATCTCAAGTACCCCAAT
63 GACTCAATCTCAAATACCCCAAT
* * **
44062 AATGAAATGAAATAAATAGCAATCATTATAATTATTTTGAAAAAAATATTATTACAACACCAGAC
1 AATGAAATGAAATAAATAGAAATTATTATAATTATTTAAAAAAAAATATTATTACAACACCAGAC
*
44127 TCAAGTC-CAAATATCCCGAA-
66 TCAA-TCTCAAATA-CCCCAAT
*
44147 AATGAAAT-AAATTAAATAGAAATTATTTTAATTATTCT-AAAAAAAATATTA
1 AATGAAATGAAA-TAAATAGAAATTATTATAATTATT-TAAAAAAAAATATTA
44198 CGACTCAAGC
Statistics
Matches: 117, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
84 3 0.03
85 72 0.62
86 8 0.07
87 30 0.26
88 4 0.03
ACGTcount: A:0.50, C:0.12, G:0.08, T:0.30
Consensus pattern (85 bp):
AATGAAATGAAATAAATAGAAATTATTATAATTATTTAAAAAAAAATATTATTACAACACCAGAC
TCAATCTCAAATACCCCAAT
Found at i:48249 original size:30 final size:30
Alignment explanation
Indices: 48204--48294 Score: 128
Period size: 30 Copynumber: 3.0 Consensus size: 30
48194 TTTGTTTCTC
*
48204 ATTTCTTTCATCACAAGTAATATTATCAGA
1 ATTTCTTTCATCACAAGCAATATTATCAGA
* * *
48234 ATTTCGTTCACCACAAGCAATATTATCAAA
1 ATTTCTTTCATCACAAGCAATATTATCAGA
* *
48264 ATTTCTTTCATCACAAGCAGTATTATTAGA
1 ATTTCTTTCATCACAAGCAATATTATCAGA
48294 A
1 A
48295 ACAAACTTAT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.36
Consensus pattern (30 bp):
ATTTCTTTCATCACAAGCAATATTATCAGA
Found at i:54252 original size:115 final size:115
Alignment explanation
Indices: 54050--54283 Score: 459
Period size: 115 Copynumber: 2.0 Consensus size: 115
54040 GTCACAACAA
54050 CTATCTAATTTGTAAGAATGTTCTAGTTTGATGAAAATTTCTGAGTACCCTTATCAATGTCATAT
1 CTATCTAATTTGTAAGAATGTTCTAGTTTGATGAAAATTTCTGAGTACCCTTATCAATGTCATAT
*
54115 TGCATTCTTTTGATGTTAAGCATGGTGCTATGCAGATGTGCTTAATTATG
66 TGCATTCTTTTGATGTTAAGCATGGTGCTATGCAGATATGCTTAATTATG
54165 CTATCTAATTTGTAAGAATGTTCTAGTTTGATGAAAATTTCTGAGTACCCTTATCAATGTCATAT
1 CTATCTAATTTGTAAGAATGTTCTAGTTTGATGAAAATTTCTGAGTACCCTTATCAATGTCATAT
54230 TGCATTCTTTTGATGTTAAGCATGGTGCTATGCAGATATGCTTAATTATG
66 TGCATTCTTTTGATGTTAAGCATGGTGCTATGCAGATATGCTTAATTATG
54280 CTAT
1 CTAT
54284 GCATTCTTCT
Statistics
Matches: 118, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
115 118 1.00
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (115 bp):
CTATCTAATTTGTAAGAATGTTCTAGTTTGATGAAAATTTCTGAGTACCCTTATCAATGTCATAT
TGCATTCTTTTGATGTTAAGCATGGTGCTATGCAGATATGCTTAATTATG
Found at i:63448 original size:17 final size:17
Alignment explanation
Indices: 63396--63449 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
63386 CCAACGTTAG
63396 AATTTATATATAATAT-A
1 AATTTATATA-AATATAA
63413 AA-TTAT-TAAAATATCAA
1 AATTTATAT-AAATAT-AA
63430 AATTTATATAAATATAA
1 AATTTATATAAATATAA
63447 AAT
1 AAT
63450 ATCTTAAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
15 6 0.19
16 5 0.16
17 10 0.31
18 10 0.31
19 1 0.03
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
AATTTATATAAATATAA
Found at i:68044 original size:78 final size:78
Alignment explanation
Indices: 67915--68087 Score: 328
Period size: 78 Copynumber: 2.2 Consensus size: 78
67905 TTTTTCTTTC
*
67915 AAATTTTCCATCTTTCCTACCAAGCACACCTATGGAAAGAAAAATTATATTTTCCATCTTTCTTT
1 AAATTTTCCATCTTTCCTACCAAGCACACCTATGGAAAGAAAAATTATATTTTCCATCTTTCTAT
67980 TTTTCTACCCCTT
66 TTTTCTACCCCTT
67993 AAATTTTCCATCTTTCCTACCAAGCACACCTATGGAAAGAAAAATTATATTTTCCATCTTTCTAT
1 AAATTTTCCATCTTTCCTACCAAGCACACCTATGGAAAGAAAAATTATATTTTCCATCTTTCTAT
68058 TTTTCTACCCCTT
66 TTTTCTACCCCTT
*
68071 CAATTTTCCATCTTTCC
1 AAATTTTCCATCTTTCC
68088 AATTTTCTTT
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
78 93 1.00
ACGTcount: A:0.28, C:0.27, G:0.05, T:0.41
Consensus pattern (78 bp):
AAATTTTCCATCTTTCCTACCAAGCACACCTATGGAAAGAAAAATTATATTTTCCATCTTTCTAT
TTTTCTACCCCTT
Found at i:68726 original size:15 final size:15
Alignment explanation
Indices: 68706--68740 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
68696 ATTTGAAGTA
68706 TCCTTAACTTTCCGC
1 TCCTTAACTTTCCGC
68721 TCCTTAACTTTCCGC
1 TCCTTAACTTTCCGC
68736 TCCTT
1 TCCTT
68741 TTTCTCACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.11, C:0.40, G:0.06, T:0.43
Consensus pattern (15 bp):
TCCTTAACTTTCCGC
Found at i:70329 original size:42 final size:42
Alignment explanation
Indices: 70280--70448 Score: 338
Period size: 42 Copynumber: 4.0 Consensus size: 42
70270 AAAGTATACT
70280 TCTCCCTTCTTATCATTCAAATTTGAAAGGATTAATTTTTTA
1 TCTCCCTTCTTATCATTCAAATTTGAAAGGATTAATTTTTTA
70322 TCTCCCTTCTTATCATTCAAATTTGAAAGGATTAATTTTTTA
1 TCTCCCTTCTTATCATTCAAATTTGAAAGGATTAATTTTTTA
70364 TCTCCCTTCTTATCATTCAAATTTGAAAGGATTAATTTTTTA
1 TCTCCCTTCTTATCATTCAAATTTGAAAGGATTAATTTTTTA
70406 TCTCCCTTCTTATCATTCAAATTTGAAAGGATTAATTTTTTA
1 TCTCCCTTCTTATCATTCAAATTTGAAAGGATTAATTTTTTA
70448 T
1 T
70449 ACATTAAGAT
Statistics
Matches: 127, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 127 1.00
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (42 bp):
TCTCCCTTCTTATCATTCAAATTTGAAAGGATTAATTTTTTA
Found at i:73102 original size:38 final size:37
Alignment explanation
Indices: 73060--73141 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 37
73050 AATCATACCT
*
73060 TTATACTGAATGGATGCTTAACCAAACAAATCCTACTA
1 TTATACTGAAT-GATGCTTAACCAAACAAATCCTAATA
* * * * * *
73098 TTATACTGACTGATGTTTTATCAAACAAATTCTAATG
1 TTATACTGAATGATGCTTAACCAAACAAATCCTAATA
73135 TTATACT
1 TTATACT
73142 AAGTAAAGCT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
37 27 0.73
38 10 0.27
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (37 bp):
TTATACTGAATGATGCTTAACCAAACAAATCCTAATA
Found at i:76408 original size:31 final size:31
Alignment explanation
Indices: 76365--76459 Score: 145
Period size: 31 Copynumber: 3.0 Consensus size: 31
76355 GATTGTTATT
76365 CTTTTTTTAATGAATTTAATCTAATGGATTG
1 CTTTTTTTAATGAATTTAATCTAATGGATTG
* *
76396 CTTTTTTCAATGAATTTAATCTAATGGATTA
1 CTTTTTTTAATGAATTTAATCTAATGGATTG
*
76427 TTATTATTTTAATGAATTTAATCTAATGGATTG
1 CT-TT-TTTTAATGAATTTAATCTAATGGATTG
76460 TTATTCTTTC
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
31 30 0.53
32 2 0.04
33 25 0.44
ACGTcount: A:0.32, C:0.06, G:0.12, T:0.51
Consensus pattern (31 bp):
CTTTTTTTAATGAATTTAATCTAATGGATTG
Found at i:76446 original size:33 final size:32
Alignment explanation
Indices: 76329--76464 Score: 148
Period size: 33 Copynumber: 4.1 Consensus size: 32
76319 TTTCATTGCG
* *
76329 ATTTTTTAACGAATTTAATCTTTATGGATTGTTATT
1 ATTTTTTAATGAATTTAATC-TAATGGA---TTATT
* **
76365 CTTTTTTTAATGAATTTAATCTAATGGATTGCT
1 -ATTTTTTAATGAATTTAATCTAATGGATTATT
*
76398 -TTTTTCAATGAATTTAATCTAATGGATTATT
1 ATTTTTTAATGAATTTAATCTAATGGATTATT
*
76429 ATTATTTTAATGAATTTAATCTAATGGATTGTT
1 ATT-TTTTAATGAATTTAATCTAATGGATTATT
76462 ATT
1 ATT
76465 CTTTCTTTCT
Statistics
Matches: 87, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
31 28 0.32
32 2 0.02
33 33 0.38
36 6 0.07
37 18 0.21
ACGTcount: A:0.30, C:0.06, G:0.11, T:0.53
Consensus pattern (32 bp):
ATTTTTTAATGAATTTAATCTAATGGATTATT
Found at i:97251 original size:8 final size:8
Alignment explanation
Indices: 97240--97265 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
97230 ATAGATATAT
97240 ATGTATGC
1 ATGTATGC
97248 ATGTATGC
1 ATGTATGC
97256 ATGTATGC
1 ATGTATGC
97264 AT
1 AT
97266 TGCTGAGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (8 bp):
ATGTATGC
Found at i:102048 original size:23 final size:22
Alignment explanation
Indices: 102007--102066 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 22
101997 ATTAAGACAA
*
102007 AAAAAATTAAATATTAAATTAG
1 AAAAAATTAAATATCAAATTAG
*
102029 AAAAAATATAAGTATCAAATT--
1 AAAAAAT-TAAATATCAAATTAG
*
102050 -AAACATTAAATATCAAA
1 AAAAAATTAAATATCAAA
102067 ATAATATACT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
19 10 0.30
20 5 0.15
22 7 0.21
23 11 0.33
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.28
Consensus pattern (22 bp):
AAAAAATTAAATATCAAATTAG
Found at i:103346 original size:212 final size:210
Alignment explanation
Indices: 102981--103409 Score: 781
Period size: 212 Copynumber: 2.0 Consensus size: 210
102971 ACTGAAACAG
102981 AGACATTAGAGAGGACCATTAGTAGAATTTATCGCTCTGGACTGATTTTCTTTCGGATGTGGATA
1 AGACATTAGAGAGGACCATTAGTAGAATTTATCGCTCTGGACTGATTTTCTTTCGGATGTGGATA
*
103046 GCGAGATTCACGAGGCTAAAACAAGCATGCTCAGCTTTCTTCCTAAGACTATAGCCCAAAACAGA
66 GCGAGACTCACGAGGCTAAAACAAGCATGCTCAGCTTTCTTCCTAAGACTATAGCCCAAAACAGA
*
103111 AAACCCTTTCTTATTCTAAGAAATCAAAAGGGAACACCAATTCCACTTGTTTGAAATGCAGCACA
131 AAACCCTTTCTTATTCTAAGAAATCAAAAGGGAACACCAATTCCACTTGTTTGAAATGAAGCACA
103176 TGTATCTAGCTTAAA
196 TGTATCTAGCTTAAA
103191 AGACATTAGAGAGGACCATTAGTAGAATTTATCGATCTCTGGACTGATTTTCTTTCGGATGTGGA
1 AGACATTAGAGAGGACCATTAGTAGAATTTATCG--CTCTGGACTGATTTTCTTTCGGATGTGGA
103256 TA-CTGAGACTCACGAGGCTAAAACAAGCATGCTCAGCTTTCTTCCTAAGACTATAGCCCAAAAT
64 TAGC-GAGACTCACGAGGCTAAAACAAGCATGCTCAGCTTTCTTCCTAAGACTATAGCCCAAAA-
*
103320 CA-AAAACCCTTTCTTATTCTAAGAAATCAGAAGGGAACACCAATTCCACTTGTTTGAAATGAAG
127 CAGAAAACCCTTTCTTATTCTAAGAAATCAAAAGGGAACACCAATTCCACTTGTTTGAAATGAAG
103384 CACATGTATCTAGCTTAAA
192 CACATGTATCTAGCTTAAA
103403 AGACATT
1 AGACATT
103410 TGGTTAAAGG
Statistics
Matches: 212, Mismatches: 3, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
210 34 0.16
211 1 0.00
212 175 0.83
213 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (210 bp):
AGACATTAGAGAGGACCATTAGTAGAATTTATCGCTCTGGACTGATTTTCTTTCGGATGTGGATA
GCGAGACTCACGAGGCTAAAACAAGCATGCTCAGCTTTCTTCCTAAGACTATAGCCCAAAACAGA
AAACCCTTTCTTATTCTAAGAAATCAAAAGGGAACACCAATTCCACTTGTTTGAAATGAAGCACA
TGTATCTAGCTTAAA
Found at i:107654 original size:6 final size:6
Alignment explanation
Indices: 107643--107684 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
107633 AAAATTTAAA
107643 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
107685 TAGTTTATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:107691 original size:18 final size:18
Alignment explanation
Indices: 107643--107694 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
107633 AAAATTTAAA
*
107643 ATTTTTATTTTTATTTTT
1 ATTTTTATGTTTATTTTT
*
107661 ATTTTTATTTTTATTTTT
1 ATTTTTATGTTTATTTTT
107679 ATTTTT-TAGTTTATTT
1 ATTTTTAT-GTTTATTT
107695 ATTTTTCAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 1 0.03
18 31 0.97
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.81
Consensus pattern (18 bp):
ATTTTTATGTTTATTTTT
Found at i:108547 original size:19 final size:18
Alignment explanation
Indices: 108516--108554 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
108506 TTTTTTATTG
*
108516 TTAATTTATATTTTGTAA
1 TTAATTTAAATTTTGTAA
*
108534 TTAATGTTAAATTTTTTAA
1 TTAAT-TTAAATTTTGTAA
108553 TT
1 TT
108555 TGAGCTAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
TTAATTTAAATTTTGTAA
Found at i:109457 original size:28 final size:28
Alignment explanation
Indices: 109417--109475 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
109407 AAGAAAAAGA
109417 AGATAGTTCAATGAGGTACTACTAATAT
1 AGATAGTTCAATGAGGTACTACTAATAT
109445 AGATAGTTCAATGAGGTACTACTAATAT
1 AGATAGTTCAATGAGGTACTACTAATAT
109473 AGA
1 AGA
109476 ACTTAAAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.31
Consensus pattern (28 bp):
AGATAGTTCAATGAGGTACTACTAATAT
Found at i:111687 original size:13 final size:13
Alignment explanation
Indices: 111671--111721 Score: 68
Period size: 13 Copynumber: 3.9 Consensus size: 13
111661 TAAACCAAAT
111671 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
*
111684 TTTTTC-ACAGCAC
1 -TTTTCAAAAGCAC
111697 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
*
111710 TTCTCAAAAGCA
1 TTTTCAAAAGCA
111722 TTGCCAAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
12 5 0.15
13 23 0.70
14 5 0.15
ACGTcount: A:0.35, C:0.25, G:0.08, T:0.31
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:111932 original size:26 final size:27
Alignment explanation
Indices: 111903--111953 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
111893 TATTATTTTC
111903 ATTTTTCAATT-TT-ATAAATTTATACG
1 ATTTTTCAATTATTGA-AAATTTATACG
*
111929 ATTTTTCATTTATTGAAAATTTATA
1 ATTTTTCAATTATTGAAAATTTATA
111954 TATAGCCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 10 0.45
27 11 0.50
28 1 0.05
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (27 bp):
ATTTTTCAATTATTGAAAATTTATACG
Found at i:115275 original size:279 final size:280
Alignment explanation
Indices: 114938--115498 Score: 1115
Period size: 279 Copynumber: 2.0 Consensus size: 280
114928 AATTAATACA
114938 ATGATAAAAATTATATTTTATTAATAAAAAGTTCATAATTCAAATTTCACCCTAAATTTTTTTTT
1 ATGATAAAAATTATATTTTATTAATAAAAAGTTCATAATTCAAATTTCACCCTAAATTTTTTTTT
115003 CTTCATCCATGTATTTATATAGTAATCACTTAATATTTGCTTATGTTACCCAACGCGCCTTATTT
66 CTTCATCCATGTATTTATATAGTAATCACTTAATATTTGCTTATGTTACCCAACGCGCCTTATTT
115068 TATGATTAATTATTTTTAAATTTGATATTACAAAATATTACAAAAAGAATATAATTTATTAATGA
131 TATGATTAATTATTTTTAAATTTGATATTACAAAATATTACAAAAAGAATATAATTTATTAATGA
115133 ATATAATTTCAATATACGGGTTATTTTAGTTATATGTATAGCATACAATACATATTTGTAAAGCA
196 ATATAATTTCAATATACGGGTTATTTTAGTTATATGTATAGCATACAATACATATTTGTAAAGCA
115198 TTTCTAATAGATTCGTGTGT
261 TTTCTAATAGATTCGTGTGT
115218 ATGATAAAAA-TATATTTTATTAATAAAAAGTTCATAATTCAAATTTCACCCTAAATTTTTTTTT
1 ATGATAAAAATTATATTTTATTAATAAAAAGTTCATAATTCAAATTTCACCCTAAATTTTTTTTT
115282 CTTCATCCATGTATTTATATAGTAATCACTTAATATTTGCTTATGTTACCCAACGCGCCTTATTT
66 CTTCATCCATGTATTTATATAGTAATCACTTAATATTTGCTTATGTTACCCAACGCGCCTTATTT
115347 TATGATTAATTATTTTTAAATTTGATATTACAAAATATTACAAAAAGAATATAATTTATTAATGA
131 TATGATTAATTATTTTTAAATTTGATATTACAAAATATTACAAAAAGAATATAATTTATTAATGA
115412 ATATAATTTCAATATACGGGTTATTTTAGTTATATGTATAGCATACAATACATATTTGTAAAGCA
196 ATATAATTTCAATATACGGGTTATTTTAGTTATATGTATAGCATACAATACATATTTGTAAAGCA
115477 TTTCTAATAGATTCGTGTGT
261 TTTCTAATAGATTCGTGTGT
115497 AT
1 AT
115499 ATGATTTTAT
Statistics
Matches: 281, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
279 271 0.96
280 10 0.04
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (280 bp):
ATGATAAAAATTATATTTTATTAATAAAAAGTTCATAATTCAAATTTCACCCTAAATTTTTTTTT
CTTCATCCATGTATTTATATAGTAATCACTTAATATTTGCTTATGTTACCCAACGCGCCTTATTT
TATGATTAATTATTTTTAAATTTGATATTACAAAATATTACAAAAAGAATATAATTTATTAATGA
ATATAATTTCAATATACGGGTTATTTTAGTTATATGTATAGCATACAATACATATTTGTAAAGCA
TTTCTAATAGATTCGTGTGT
Found at i:116493 original size:99 final size:99
Alignment explanation
Indices: 116309--116524 Score: 396
Period size: 99 Copynumber: 2.2 Consensus size: 99
116299 TAAAAAATAA
*
116309 TATAAAATTTTATTTAAATTCAGATCGGATAAAAATGTTAAAATTTTAACCCAACCCAGTTTAGT
1 TATATAATTTTA-TTAAATTCAGATCGGATAAAAATGTTAAAATTTTAACCCAACCCAGTTTAGT
*
116374 TTGCCCGTATTAAATTTTTTTAATATTATTATTTT
65 TTGCCCGTATTAAATTTTTTTAATATTAATATTTT
116409 TATATAATTTTATTAAATTCAGATCGGATAAAAATGTTAAAATTTTAACCCAACCCAGTTTAGTT
1 TATATAATTTTATTAAATTCAGATCGGATAAAAATGTTAAAATTTTAACCCAACCCAGTTTAGTT
116474 TGCCCGTATTAAATTTTTTTAATATTAATATTTT
66 TGCCCGTATTAAATTTTTTTAATATTAATATTTT
*
116508 TATATAATTTTTTTAAA
1 TATATAATTTTATTAAA
116525 AAATATAATA
Statistics
Matches: 113, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
99 102 0.90
100 11 0.10
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (99 bp):
TATATAATTTTATTAAATTCAGATCGGATAAAAATGTTAAAATTTTAACCCAACCCAGTTTAGTT
TGCCCGTATTAAATTTTTTTAATATTAATATTTT
Found at i:116501 original size:16 final size:15
Alignment explanation
Indices: 116480--116523 Score: 56
Period size: 13 Copynumber: 3.0 Consensus size: 15
116470 AGTTTGCCCG
116480 TATTAAATTTTTTTAA
1 TATT-AATTTTTTTAA
*
116496 TATTAATATTTTT-A
1 TATTAATTTTTTTAA
116510 TA-TAATTTTTTTAA
1 TATTAATTTTTTTAA
116524 AAAATATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 9 0.36
14 4 0.16
15 8 0.32
16 4 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TATTAATTTTTTTAA
Found at i:118573 original size:21 final size:23
Alignment explanation
Indices: 118549--118596 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
118539 AGACCCACCC
118549 ATATTAT-TT-TTTAAAATATTT
1 ATATTATATTATTTAAAATATTT
* *
118570 ATATTATATTATTTTAAATTTTT
1 ATATTATATTATTTAAAATATTT
118593 ATAT
1 ATAT
118597 AGTTATCTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 7 0.30
22 2 0.09
23 14 0.61
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
ATATTATATTATTTAAAATATTT
Found at i:120920 original size:12 final size:11
Alignment explanation
Indices: 120886--120926 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
120876 AAATCTCCCG
120886 AGAAAAAAAAA
1 AGAAAAAAAAA
**
120897 AGAAATTAAAA
1 AGAAAAAAAAA
120908 AGAAAAAATAAA
1 AGAAAAAA-AAA
120920 AGAAAAA
1 AGAAAAA
120927 GAGAGAGAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (11 bp):
AGAAAAAAAAA
Found at i:124272 original size:29 final size:29
Alignment explanation
Indices: 124239--124301 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
124229 TATTTTATCC
* *
124239 ATGGGTTGGGTCGAAGGTCTGTCTGAAAA
1 ATGGGTTGGGTCGAAGGCCTGCCTGAAAA
124268 ATGGGTTGGGTCGAAGGCCTGCCTGAAAA
1 ATGGGTTGGGTCGAAGGCCTGCCTGAAAA
*
124297 GTGGG
1 ATGGG
124302 AAGTGGGAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.22, C:0.13, G:0.41, T:0.24
Consensus pattern (29 bp):
ATGGGTTGGGTCGAAGGCCTGCCTGAAAA
Found at i:125651 original size:19 final size:20
Alignment explanation
Indices: 125608--125665 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
125598 TCTCATAACA
125608 AAAAATTTAAAATAATTTTC
1 AAAAATTTAAAATAATTTTC
* *
125628 AAAAATTTAAAATATTTTTT
1 AAAAATTTAAAATAATTTTC
*
125648 AAAATTTTCAAAAATAAT
1 AAAAATTT--AAAATAAT
125666 AATTTTGGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 25 0.78
22 7 0.22
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAAATTTAAAATAATTTTC
Found at i:130078 original size:91 final size:91
Alignment explanation
Indices: 129946--130124 Score: 268
Period size: 91 Copynumber: 2.0 Consensus size: 91
129936 TTTTGCTCCT
* * *
129946 TTAATTCCTCAATTTCTATTCAAGGTATCTACTTACTTACCATCTTTGCTACTGCTTTTTCTTCC
1 TTAATTCCTAAATTTCTATTCAAGGTATATACTTACTTACCATCTTTGCTACCGCTTTTTCTTCC
*
130011 ATAAATTGGAATCAAGAGTCCAACCC
66 ATAAATTGAAATCAAGAGTCCAACCC
* * * *
130037 TTAATTTCTAAATTTCTATTCAAGGTATATATTTACTTACCATCTTTGCTGCCGCTTTTTCTTTC
1 TTAATTCCTAAATTTCTATTCAAGGTATATACTTACTTACCATCTTTGCTACCGCTTTTTCTTCC
* *
130102 ATAAATTGAAATCGAGATTCCAA
66 ATAAATTGAAATCAAGAGTCCAA
130125 AACTAGAGTG
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
91 78 1.00
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.42
Consensus pattern (91 bp):
TTAATTCCTAAATTTCTATTCAAGGTATATACTTACTTACCATCTTTGCTACCGCTTTTTCTTCC
ATAAATTGAAATCAAGAGTCCAACCC
Found at i:130842 original size:14 final size:14
Alignment explanation
Indices: 130823--130849 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
130813 AAGGAGTTGA
130823 AAGCTTCTATTTCC
1 AAGCTTCTATTTCC
130837 AAGCTTCTATTTC
1 AAGCTTCTATTTC
130850 TCGAGGCTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.26, G:0.07, T:0.44
Consensus pattern (14 bp):
AAGCTTCTATTTCC
Found at i:133706 original size:34 final size:34
Alignment explanation
Indices: 133663--133733 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
133653 GAAATTACTC
*
133663 ATTGGCCGATTTCTATCTAATCTGCACTGCTAAA
1 ATTGGCCGATTTCTATCTAATCTGCACCGCTAAA
133697 ATTGGCCGATTTCTATCTAATCTGCACCGCTAAA
1 ATTGGCCGATTTCTATCTAATCTGCACCGCTAAA
133731 ATT
1 ATT
133734 AACCTATCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (34 bp):
ATTGGCCGATTTCTATCTAATCTGCACCGCTAAA
Found at i:134924 original size:2 final size:2
Alignment explanation
Indices: 134917--134943 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
134907 TAAAATCTGC
134917 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 A
134944 AGTATTTGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:137422 original size:19 final size:19
Alignment explanation
Indices: 137398--137436 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
137388 TAGATGGTTC
137398 CATTTTATAGTGGCCTCAG
1 CATTTTATAGTGGCCTCAG
137417 CATTTTATAGTGGCCTCAG
1 CATTTTATAGTGGCCTCAG
137436 C
1 C
137437 CTTTCACTGA
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:0.21, C:0.23, G:0.21, T:0.36
Consensus pattern (19 bp):
CATTTTATAGTGGCCTCAG
Found at i:149360 original size:40 final size:40
Alignment explanation
Indices: 149305--149382 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
149295 GGCCTTAGAA
* *
149305 GATCCGCTCGTCCAAACTCACCTAAGTCAATATTTACTGT
1 GATCCGCTCATCCAAACTCACCTAAGTCAACATTTACTGT
*
149345 GATCCGCTCATCCAAACTCACCTAAGTCAGCATTTACT
1 GATCCGCTCATCCAAACTCACCTAAGTCAACATTTACT
149383 CAAGTGAGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.28, C:0.32, G:0.12, T:0.28
Consensus pattern (40 bp):
GATCCGCTCATCCAAACTCACCTAAGTCAACATTTACTGT
Found at i:151531 original size:32 final size:32
Alignment explanation
Indices: 151493--151566 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
151483 GTTAGATTGA
*
151493 ATTCTAAAAAGCCAAAAATCTCGCGATAAAGT
1 ATTCTAAAAAACCAAAAATCTCGCGATAAAGT
* * * *
151525 TTTCTAAAAAACCAAAAATTTTGGGATAAAGT
1 ATTCTAAAAAACCAAAAATCTCGCGATAAAGT
*
151557 ATTCTGAAAA
1 ATTCTAAAAA
151567 CCGGATAATC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.27
Consensus pattern (32 bp):
ATTCTAAAAAACCAAAAATCTCGCGATAAAGT
Found at i:153658 original size:451 final size:452
Alignment explanation
Indices: 152811--153718 Score: 1800
Period size: 451 Copynumber: 2.0 Consensus size: 452
152801 TTAATTTGCA
152811 CAAAGCCTCAATATCTTCTTCATCAGGATTCTCATATTCACCAAGTAATTTCTTGATGCATTCAT
1 CAAAGCCTCAATATCTTCTTCATCAGGATTCTCATATTCACCAAGTAATTTCTTGATGCATTCAT
152876 GCATGATTCTCTCAGTTAACATTTTCTTCTTGTACAACTCTCCAATAAATCTAATGTTACCCAAC
66 GCATGATTCTCTCAGTTAACATTTTCTTCTTGTACAACTCTCCAATAAATCTAATGTTACCCAAC
152941 ATTCGTCTCCGTGCCTTGATTCTCTTCTCCTCTCTTTCCTCCTCAGACCGTTTAGACTCACCCAC
131 ATTCGTCTCCGTGCCTTGATTCTCTTCTCCTCTCTTTCCTCCTCAGACCGTTTAGACTCACCCAC
153006 TTCCTCAACTTTATTTGCTTCTTCTTGCTCTCTCCCCCCTCTTTCAAATTCCTCCTGGCACTTGT
196 TTCCTCAACTTTATTTGCTTCTTCTTGCTCTCTCCCCCCTCTTTCAAATTCCTCCTGGCACTTGT
153071 TCAGCAGCAATCTCTTGAAAGTAATCTTTTCATTGCCTTCACTAAATTCAGGCAACTCTCCTGCC
261 TCAGCAGCAATCTCTTGAAAGTAATCTTTTCATTGCCTTCACTAAATTCAGGCAACTCTCCTGCC
153136 AGATGATAACAGAAGTTCGCATACATTTTAGGCTCCATCAAAGCTTTGTCAAAGATTTGTAAGAT
326 AGATGATAACAGAAGTTCGCATACATTTTAGGCTCCATCAAAGCTTTGTCAAAGATTTGTAAGAT
153201 GACACCAGTGAGTGTAACTGCATTGTCAATGTTCACTGCTTTTACTTGCTCAAAGAGTTTCT
391 GACACCAGTGAGTGTAACTGCATTGTCAATGTTCACTGCTTTTACTTGCTCAAAGAGTTTCT
153263 CAAA-CCTCAATATCTTCTTCATCAGGATTCTCATATTCACCAAGTAATTTCTTGATGCATTCAT
1 CAAAGCCTCAATATCTTCTTCATCAGGATTCTCATATTCACCAAGTAATTTCTTGATGCATTCAT
153327 GCATGATTCTCTCAGTTAACATTTTCTTCTTGTACAACTCTCCAATAAATCTAATGTTACCCAAC
66 GCATGATTCTCTCAGTTAACATTTTCTTCTTGTACAACTCTCCAATAAATCTAATGTTACCCAAC
153392 ATTCGTCTCCGTGCCTTGATTCTCTTCTCCTCTCTTTCCTCCTCAGACCGTTTAGACTCACCCAC
131 ATTCGTCTCCGTGCCTTGATTCTCTTCTCCTCTCTTTCCTCCTCAGACCGTTTAGACTCACCCAC
*
153457 TTCCTCAACTTTATTTGCTTCTTCTTGCTCTCTCTCCCCTCTTTCAAATTCCTCCTGGCACTTGT
196 TTCCTCAACTTTATTTGCTTCTTCTTGCTCTCTCCCCCCTCTTTCAAATTCCTCCTGGCACTTGT
153522 TCAGCAGCAATCTCTTGAAAGTAATCTTTTCATTGCCTTCACTAAATTCAGGCAACTCTCCTGCC
261 TCAGCAGCAATCTCTTGAAAGTAATCTTTTCATTGCCTTCACTAAATTCAGGCAACTCTCCTGCC
153587 AGATGATAACAGAAGTTCGCATACATTTTAGGCTCCATCAAAGCTTTGTCAAAGATTTGTAAGAT
326 AGATGATAACAGAAGTTCGCATACATTTTAGGCTCCATCAAAGCTTTGTCAAAGATTTGTAAGAT
153652 GACACCAGTGAGTGTAACTGCATTGTCAATGTTCACTGCTTTTACTTGCTCAAAGAGTTTCT
391 GACACCAGTGAGTGTAACTGCATTGTCAATGTTCACTGCTTTTACTTGCTCAAAGAGTTTCT
153714 CAAAG
1 CAAAG
153719 TTTTGGGGAG
Statistics
Matches: 454, Mismatches: 1, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
451 450 0.99
452 4 0.01
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.36
Consensus pattern (452 bp):
CAAAGCCTCAATATCTTCTTCATCAGGATTCTCATATTCACCAAGTAATTTCTTGATGCATTCAT
GCATGATTCTCTCAGTTAACATTTTCTTCTTGTACAACTCTCCAATAAATCTAATGTTACCCAAC
ATTCGTCTCCGTGCCTTGATTCTCTTCTCCTCTCTTTCCTCCTCAGACCGTTTAGACTCACCCAC
TTCCTCAACTTTATTTGCTTCTTCTTGCTCTCTCCCCCCTCTTTCAAATTCCTCCTGGCACTTGT
TCAGCAGCAATCTCTTGAAAGTAATCTTTTCATTGCCTTCACTAAATTCAGGCAACTCTCCTGCC
AGATGATAACAGAAGTTCGCATACATTTTAGGCTCCATCAAAGCTTTGTCAAAGATTTGTAAGAT
GACACCAGTGAGTGTAACTGCATTGTCAATGTTCACTGCTTTTACTTGCTCAAAGAGTTTCT
Found at i:163428 original size:8 final size:8
Alignment explanation
Indices: 163415--163443 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
163405 CACTAGAGAC
163415 CAGTGTTA
1 CAGTGTTA
163423 CAGTGTTA
1 CAGTGTTA
163431 CAGTGTTA
1 CAGTGTTA
163439 CAGTG
1 CAGTG
163444 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:163564 original size:23 final size:23
Alignment explanation
Indices: 163530--163627 Score: 171
Period size: 23 Copynumber: 4.3 Consensus size: 23
163520 AGTGTTATTG
163530 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
163553 CTCAGTGTTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
163576 -TCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
163598 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
163621 ATCAGTG
1 ATCAGTG
163628 TGGCACTTAT
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
22 21 0.30
23 50 0.70
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:163595 original size:45 final size:46
Alignment explanation
Indices: 163530--163627 Score: 171
Period size: 45 Copynumber: 2.2 Consensus size: 46
163520 AGTGTTATTG
* *
163530 ATCAGTGGTAGCTTCGGCTACATCTCAGTGTTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
163576 -TCAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
163621 ATCAGTG
1 ATCAGTG
163628 TGGCACTTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
45 43 0.88
46 6 0.12
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.32
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
Found at i:171932 original size:23 final size:23
Alignment explanation
Indices: 171898--171950 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
171888 AGTGTTATTG
171898 ATCAGTGATAGCTTCGGCTACAT
1 ATCAGTGATAGCTTCGGCTACAT
*
171921 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGATAGCTTCGGCTACAT
171944 ATCAGTG
1 ATCAGTG
171951 TGGCACTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (23 bp):
ATCAGTGATAGCTTCGGCTACAT
Found at i:173284 original size:27 final size:27
Alignment explanation
Indices: 173246--173301 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
173236 GAAGATAAGT
*
173246 TAGAATTTCTAAACCTTCCTCATAGAA
1 TAGAATTTCTAAAACTTCCTCATAGAA
173273 TAGAATTTCTAAAACTTCCTCATAGAA
1 TAGAATTTCTAAAACTTCCTCATAGAA
173300 TA
1 TA
173302 TCAAACCATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (27 bp):
TAGAATTTCTAAAACTTCCTCATAGAA
Found at i:174643 original size:20 final size:20
Alignment explanation
Indices: 174606--174642 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 20
174596 ATAAGCTCTA
174606 TTTTCCCTTTTATTTTTTAT
1 TTTTCCCTTTTATTTTTTAT
174626 TTTTCCC-TTTATTTTTT
1 TTTTCCCTTTTATTTTTT
174643 TCTTCCTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTCCCTTTTATTTTTTAT
Found at i:174783 original size:12 final size:12
Alignment explanation
Indices: 174766--174790 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
174756 TTCGGCCACC
174766 GTGTCGACGGCG
1 GTGTCGACGGCG
174778 GTGTCGACGGCG
1 GTGTCGACGGCG
174790 G
1 G
174791 CTCTCCTCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.24, G:0.52, T:0.16
Consensus pattern (12 bp):
GTGTCGACGGCG
Found at i:175718 original size:22 final size:22
Alignment explanation
Indices: 175666--175719 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
175656 ACTTTATGAT
* * *
175666 TTTTATCTATTTTCCTTTATTG
1 TTTTATTTATGTTCATTTATTG
*
175688 TTTTTTTTATGTTCATTTATT-
1 TTTTATTTATGTTCATTTATTG
175709 TGTTTATTTAT
1 T-TTTATTTAT
175720 TTATATGTCC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 1 0.04
22 25 0.96
ACGTcount: A:0.15, C:0.07, G:0.06, T:0.72
Consensus pattern (22 bp):
TTTTATTTATGTTCATTTATTG
Found at i:175750 original size:31 final size:29
Alignment explanation
Indices: 175687--175754 Score: 77
Period size: 28 Copynumber: 2.3 Consensus size: 29
175677 TTCCTTTATT
* *
175687 GTTT-TTTTTATGTTCATTTATTTGTTTA
1 GTTTATTTATATGTCCATTTATTTGTTTA
*
175715 -TTTATTTATATGTCCATTTTTTATGTTTTA
1 GTTTATTTATATGTCCATTTATT-TG-TTTA
175745 GTTTATTTAT
1 GTTTATTTAT
175755 TTATTTATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
27 3 0.09
28 15 0.45
29 2 0.06
30 4 0.12
31 9 0.27
ACGTcount: A:0.18, C:0.04, G:0.09, T:0.69
Consensus pattern (29 bp):
GTTTATTTATATGTCCATTTATTTGTTTA
Found at i:176348 original size:110 final size:110
Alignment explanation
Indices: 176016--176464 Score: 731
Period size: 110 Copynumber: 4.1 Consensus size: 110
176006 NNNNNNNNNN
176016 TGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAAT-TTCAAAATAAGGCAAT
1 TGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATGTT-AAAATAAGGCAAT
*
176080 GTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGG
65 GTTTTGCGTTTGCGAAATTCGAGAAAACATGCCCTAAGGTGCTGGG
* *
176126 TGTCGTTTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAAATTTTAAAATAAGGCAAT
1 TGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTT-AAAAATGTTAAAATAAGGCAAT
*
176191 GTTTTGCGTTTGCGAAATTCGCGAAAACATGCCCTAAGGTGCTGGG
65 GTTTTGCGTTTGCGAAATTCGAGAAAACATGCCCTAAGGTGCTGGG
* *
176237 TGTCTATTTTTCTCGTTCAACCAAATGGCTTAAAATCCTTTTAAAAATGTTAAAATAAGGCAATG
1 TGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATGTTAAAATAAGGCAATG
176302 TTTTGCGTTTGCGAAATTCGAGAAAACATGCCCTAAGGTGCTGGG
66 TTTTGCGTTTGCGAAATTCGAGAAAACATGCCCTAAGGTGCTGGG
* *
176347 TGTCGATTTTTCTCGTTCAACCAAGTGGCTTAATATCCTTTTAAAAATGTTAAAATAAGGCAATA
1 TGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATGTTAAAATAAGGCAATG
* * ** * *
176412 TTTTACGTTTG-GAAATTCAAGAAAATGTGCCCTAATGTGCTGGA
66 TTTTGCGTTTGCGAAATTCGAGAAAACATGCCCTAAGGTGCTGGG
*
176456 TTTCGATTT
1 TGTCGATTT
176465 CTCGTTTGAC
Statistics
Matches: 318, Mismatches: 19, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
109 36 0.11
110 178 0.56
111 102 0.32
112 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (110 bp):
TGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATGTTAAAATAAGGCAATG
TTTTGCGTTTGCGAAATTCGAGAAAACATGCCCTAAGGTGCTGGG
Found at i:180619 original size:43 final size:43
Alignment explanation
Indices: 180558--180696 Score: 185
Period size: 43 Copynumber: 3.2 Consensus size: 43
180548 AAAAGGGCGG
180558 CTCAAATTTTTAATCATAATGGGACATTAGGTGATCAGAGCGA
1 CTCAAATTTTTAATCATAATGGGACATTAGGTGATCAGAGCGA
* *
180601 CTCAAATTTTTTATCATAATGGGACATTAGGTGATCAGAGTGA
1 CTCAAATTTTTAATCATAATGGGACATTAGGTGATCAGAGCGA
* * *
180644 CTCAAA-TTTTAGATCA-AATTGGGGCATGAGGCGATCAGAGC-A
1 CTCAAATTTTTA-ATCATAA-TGGGACATTAGGTGATCAGAGCGA
180686 GCTCAAATTTT
1 -CTCAAATTTT
180697 GATCAGATCG
Statistics
Matches: 85, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
42 7 0.08
43 75 0.88
44 3 0.04
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (43 bp):
CTCAAATTTTTAATCATAATGGGACATTAGGTGATCAGAGCGA
Found at i:181947 original size:100 final size:100
Alignment explanation
Indices: 181781--183488 Score: 2451
Period size: 100 Copynumber: 17.1 Consensus size: 100
181771 TGTAATTCAG
* * *
181781 AAGATTGAAGTCACAACCGCGAATCTTACTTCACAGGCGATGCAGCGGAACAGATTGAAGCTACG
1 AAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACG
* *
181846 ACGGTGAATCTCACTTCCCCGACATTACAATTCAA
66 ACGGTGAATCTCACTTCCCCGACATTGCAATTTAA
* * *
181881 AATATTGAAGCCACAACGGCGAATCTTACTTCTCAGGCGATGCAGCGGAATAGATTGAAGCTACG
1 AAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACG
* *
181946 ACGGTGAATCTCACTTCCCCGACATTGCAATTCAG
66 ACGGTGAATCTCACTTCCCCGACATTGCAATTTAA
* *
181981 AAGATTGAAGCCACAACGACGAATCTTACTTCCCAGGCGATGCAGCGGAATAGATTGAAGCTACG
1 AAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACG
* *
182046 ACGGTAAATCTCACTTCCCCGACATTGCAATTCAA
66 ACGGTGAATCTCACTTCCCCGACATTGCAATTTAA
* * * * * *
182081 AATATTGAAGCCACAACAGTGAATCTTACTTTCCAGGCGATGCAGCGAAACAGATTGAAGCTACA
1 AAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACG
** *
182146 ACGGTGAATCTTGCTTCCCTGACATTGC-A-TT-A
66 ACGGTGAATCTCACTTCCCCGACATTGCAATTTAA
* * * * ** *
182178 AAGGTTGAAGTCGCAACGGCGAATCTTACTTCCCAGGTGATATAGCAGAACAGATTGAAGCTACG
1 AAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACG
182243 ACGGTGAATCTCACTTCCCCGACATTGCAATTTAA
66 ACGGTGAATCTCACTTCCCCGACATTGCAATTTAA
* * * * *
182278 AAGATTGAAGCCATAACGGTGAATCTTACTTCCCAGGCGATACAGCGAAATAGATTGAAGCTACG
1 AAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACG
*
182343 ACAGTGAATCTCACTTCCCCGACATTGCAATTTAA
66 ACGGTGAATCTCACTTCCCCGACATTGCAATTTAA
* *
182378 AAGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGCGATGCAACGGAACAGATTGAAGCTACG
1 AAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACG
* ** *
182443 ACAGTGAATCTTGCTTCTCCGACATTGCAATTTAA
66 ACGGTGAATCTCACTTCCCCGACATTGCAATTTAA
* *
182478 AAGATTGAAGCCACAACGGTGAATCTCACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACG
1 AAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACG
* ** *
182543 ACAGTGAATCTTGCTTCTCCGACATTGCAATTTAA
66 ACGGTGAATCTCACTTCCCCGACATTGCAATTTAA
*
182578 AAGATTGAAGCCACAACGGCAAATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACG
1 AAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACG
182643 ACGGTGAATCTCACTTCCCCGACATTGCAA-TTAA
66 ACGGTGAATCTCACTTCCCCGACATTGCAATTTAA
* * * *
182677 CAAGATTGAAGCCACAACGGTGAATCTTACTTCCTAGGCGATGCATCGGAATAGATTGAAGCTAC
1 -AAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTAC
* ** *
182742 GACAGCAAATCTCACTTCCCCGACATTG-AAATTAA
65 GACGGTGAATCTCACTTCCCCGACATTGCAATTTAA
* * *
182777 TAAGATTGAAGCCACAACGACGAATCTTACTTCCCAGGTGATGCAGCGGTACAGATTGAAGCTAC
1 -AAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTAC
*
182842 GACGGCGAATCTCACTTCCCCGACATTGCAA-TTAA
65 GACGGTGAATCTCACTTCCCCGACATTGCAATTTAA
* * * *
182877 CAAGATTGAAGCCACAACGGTGAATCTTACTTCCTAGGCGATGCATCGGAATAGATTGAAGCTAC
1 -AAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTAC
* ** *
182942 GACAGCAAATCTCACTTCCCCGACATTG-AAATTAA
65 GACGGTGAATCTCACTTCCCCGACATTGCAATTTAA
* * *
182977 TAAGATTGAAGCCACAACGACGAATCTTACTTCCCAGGTGATGCAGCGGTACAGATTGAAGCTAC
1 -AAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTAC
*
183042 GACGGCGAATCTCACTTCCCCGACATTGCAATTTAA
65 GACGGTGAATCTCACTTCCCCGACATTGCAATTTAA
* *
183078 AGGATTGAAGCCACAACGGCGAATTTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACG
1 AAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACG
* *
183143 ATGGCGAATCTCACTTCCCCGACATTGCAATTTAA
66 ACGGTGAATCTCACTTCCCCGACATTGCAATTTAA
* * * *
183178 AAGATTGAAGCTACAACGGTGAATCTTACTTCCCAGGCGATGCAGCCGAACAGATTGAAGCTACA
1 AAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACG
* * * * *
183243 ACAGCGAAACTCACTTCCCCGATATTGTAATTTAA
66 ACGGTGAATCTCACTTCCCCGACATTGCAATTTAA
* *
183278 AAGATTGAAGCCACAACGACGAATCTTACTTCCCAGGCGATGCAGCAGAACAGATTGAAGCTACG
1 AAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACG
* ** *
183343 ATGGCAAATCTCACTTCCCCGACATTGTAA-TTAA
66 ACGGTGAATCTCACTTCCCCGACATTGCAATTTAA
* * *
183377 AAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGAAATAGATTGAAGGTACG
1 AAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACG
* *
183442 ACGGCGAATCTCACTTCCCCGACATTGTAATTTAA
66 ACGGTGAATCTCACTTCCCCGACATTGCAATTTAA
183477 AAGATTGAAGCC
1 AAGATTGAAGCC
183489 GCAATGGTGA
Statistics
Matches: 1457, Mismatches: 142, Indels: 18
0.90 0.09 0.01
Matches are distributed among these distances:
97 78 0.05
98 2 0.00
99 103 0.07
100 1266 0.87
101 8 0.01
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (100 bp):
AAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACG
ACGGTGAATCTCACTTCCCCGACATTGCAATTTAA
Found at i:184009 original size:15 final size:16
Alignment explanation
Indices: 183983--184012 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
183973 CCTAAAATCA
183983 GACCTAAACCCATTTT
1 GACCTAAACCCATTTT
183999 GACCT-AACCCATTT
1 GACCTAAACCCATTT
184013 CAGCCCAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.30, C:0.33, G:0.07, T:0.30
Consensus pattern (16 bp):
GACCTAAACCCATTTT
Found at i:185539 original size:24 final size:22
Alignment explanation
Indices: 185497--185546 Score: 64
Period size: 24 Copynumber: 2.2 Consensus size: 22
185487 TTTATTGTTA
*
185497 TTATTTTTTTATGTTCATTTAT
1 TTATTTTTTTATGTCCATTTAT
*
185519 TTATTTATTTATATGTCCATTTTT
1 TTATTT-TTT-TATGTCCATTTAT
185543 TTAT
1 TTAT
185547 GTTGTAGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 6 0.25
23 3 0.12
24 15 0.62
ACGTcount: A:0.20, C:0.06, G:0.04, T:0.70
Consensus pattern (22 bp):
TTATTTTTTTATGTCCATTTAT
Found at i:185910 original size:110 final size:110
Alignment explanation
Indices: 185716--186216 Score: 792
Period size: 110 Copynumber: 4.6 Consensus size: 110
185706 TTTCTAATTG
* * * *
185716 AGGCAATGTTTTGCGTTT-GGAAATTCGAGAAAACATGTCCTAAGGTGTTAGGTGTCGTTTTTTC
1 AGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTC
185780 TCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTCAAAATA
66 TCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTCAAAATA
185825 AGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTC
1 AGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTC
* *
185890 TCGTTTAACCAAATGACTTAATATCCTTTTAAAAATTTCAAAATA
66 TCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTCAAAATA
*
185935 AGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCATAAGGTGCTGGGTGTCGATTTTTC
1 AGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTC
186000 TCGTTCAACCAAATGGCTTAATATCCTTTTAAAAAATTTCAAAATA
66 TCGTTCAACCAAATGGCTTAATATCCTTTT-AAAAATTTCAAAATA
* * *
186046 AAGCAATGTTTTGTGTTTGGGAAATTCGAGAAAACATGCCATAAGGTGCTGGGTGTCGATTTTTC
1 AGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTC
*
186111 TCGTTCAACCAAATGGCTTAATATCCTTTAAAAAATGTT-AAAATA
66 TCGTTCAACCAAATGGCTTAATATCCTTTTAAAAAT-TTCAAAATA
* * * ** * * *
186156 AGGCAATATTTTACGTTT-GAAAATTCGAGAAAATGTGCCCTAATGTGCTGGATTTCGATTT
1 AGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTT
186217 CTCGTTTGAC
Statistics
Matches: 366, Mismatches: 23, Indels: 6
0.93 0.06 0.02
Matches are distributed among these distances:
109 54 0.15
110 203 0.55
111 109 0.30
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.35
Consensus pattern (110 bp):
AGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTC
TCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTCAAAATA
Found at i:186123 original size:221 final size:218
Alignment explanation
Indices: 185716--186216 Score: 788
Period size: 221 Copynumber: 2.3 Consensus size: 218
185706 TTTCTAATTG
* * *
185716 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGTCCTAAGGTGTTAGGTGTCGTTTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATG-CCTAAGGTGCTGGGTGTCGATTTTTCT
*
185781 CGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGG
65 CGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTCAAAATAAAGCAATGTTTTGCGTTTGGG
* *
185846 AAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTTAACCAAATGACTTAA
130 AAATTCGAGAAAACATGCCATAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATGACTTAA
*
185911 TATCCTTTTAAAAAT-TTCAAAATA
195 TATCCTTTAAAAAATGTT-AAAATA
185935 AGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCATAAGGTGCTGGGTGTCGATTTTTC
1 AGGCAATGTTTTGCGTTT-GGAAATTCGAGAAAACATGCC-TAAGGTGCTGGGTGTCGATTTTTC
*
186000 TCGTTCAACCAAATGGCTTAATATCCTTTTAAAAAATTTCAAAATAAAGCAATGTTTTGTGTTTG
64 TCGTTCAACCAAATGGCTTAATATCCTTTT-AAAAATTTCAAAATAAAGCAATGTTTTGCGTTTG
*
186065 GGAAATTCGAGAAAACATGCCATAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATGGCTT
128 GGAAATTCGAGAAAACATGCCATAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATGACTT
186130 AATATCCTTTAAAAAATGTTAAAATA
193 AATATCCTTTAAAAAATGTTAAAATA
* * * ** * * *
186156 AGGCAATATTTTACGTTTGAAAATTCGAGAAAATGTGCCCTAATGTGCTGGATTTCGATTT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATG-CCTAAGGTGCTGGGTGTCGATTT
186217 CTCGTTTGAC
Statistics
Matches: 260, Mismatches: 17, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
219 20 0.08
220 104 0.40
221 134 0.52
222 2 0.01
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.35
Consensus pattern (218 bp):
AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCTAAGGTGCTGGGTGTCGATTTTTCTC
GTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTCAAAATAAAGCAATGTTTTGCGTTTGGGA
AATTCGAGAAAACATGCCATAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATGACTTAAT
ATCCTTTAAAAAATGTTAAAATA
Found at i:192533 original size:10 final size:10
Alignment explanation
Indices: 192510--192555 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
192500 TACTTCATGC
*
192510 TATTTTTCTTT
1 TATTTTT-TAT
192521 TATTTTTTAT
1 TATTTTTTAT
192531 TA-TTTTT-T
1 TATTTTTTAT
192539 TATTTTTTAT
1 TATTTTTTAT
*
192549 AATTTTT
1 TATTTTT
192556 ATTTTTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
8 3 0.10
9 10 0.32
10 11 0.35
11 7 0.23
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.80
Consensus pattern (10 bp):
TATTTTTTAT
Found at i:192544 original size:16 final size:16
Alignment explanation
Indices: 192525--192578 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 16
192515 TTCTTTTATT
192525 TTTTATTATTTTTTTA
1 TTTTATTATTTTTTTA
*
192541 TTTT-TTATAATTTTTA
1 TTTTATTAT-TTTTTTA
192557 TTTTTATT-TTTTTTTAA
1 -TTTTATTATTTTTTT-A
192574 TTTTA
1 TTTTA
192579 AAATTTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
15 4 0.12
16 20 0.62
17 6 0.19
18 2 0.06
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTATTATTTTTTTA
Found at i:192560 original size:23 final size:23
Alignment explanation
Indices: 192535--192577 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
192525 TTTTATTATT
192535 TTTTTA-TTTTTTATAATTTTTA
1 TTTTTATTTTTTTATAATTTTTA
*
192557 TTTTTATTTTTTTTTAATTTT
1 TTTTTATTTTTTTATAATTTT
192578 AAAATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (23 bp):
TTTTTATTTTTTTATAATTTTTA
Found at i:192570 original size:15 final size:15
Alignment explanation
Indices: 192510--192570 Score: 54
Period size: 15 Copynumber: 4.1 Consensus size: 15
192500 TACTTCATGC
*
192510 TATTTTTCTTTTATTT
1 TATTTTTATTTT-TTT
*
192526 T-TTATTA-TTTTTT
1 TATTTTTATTTTTTT
**
192539 TATTTTTTATAATTTT
1 TA-TTTTTATTTTTTT
192555 TATTTTTATTTTTTT
1 TATTTTTATTTTTTT
192570 T
1 T
192571 TAATTTTAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
13 4 0.11
14 3 0.09
15 21 0.60
16 7 0.20
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.82
Consensus pattern (15 bp):
TATTTTTATTTTTTT
Found at i:192596 original size:33 final size:33
Alignment explanation
Indices: 192518--192597 Score: 92
Period size: 33 Copynumber: 2.4 Consensus size: 33
192508 GCTATTTTTC
* * *
192518 TTTTATTTTTTATTATTTTTTTATTTTTTATAA
1 TTTTAATTTTTATTATTTTTTTATATTTTAAAA
*
192551 TTTTTATTTTTATT-TTTTTTTA-ATTTTAAAA
1 TTTTAATTTTTATTATTTTTTTATATTTTAAAA
192582 TTTTAAATTATTTATT
1 TTTT-AATT-TTTATT
192598 GATGTTGTCC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 11 0.28
32 11 0.28
33 18 0.45
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (33 bp):
TTTTAATTTTTATTATTTTTTTATATTTTAAAA
Found at i:201564 original size:60 final size:58
Alignment explanation
Indices: 201466--201627 Score: 166
Period size: 60 Copynumber: 2.7 Consensus size: 58
201456 AAATTTCAAG
* * *
201466 ATAGTTGGGTGACCAAAAAAGAATTTACTAATAGTTAGGTTA-TCACTTTGTAACATTTT-
1 ATAGTT-GGTGACCAAAAAAAAATTTACTAATAATTAGGTGACT-ACTTTGTAAC-TTTTC
*
201525 ATAGTTAGGTGACCAAAAAACAAATTTACTAATAATTAGGTGACTATTTTGTAACTTTTC
1 ATAGTT-GGTGACCAAAAAA-AAATTTACTAATAATTAGGTGACTACTTTGTAACTTTTC
* * * * *
201585 ATAGTTGTATGACTAAAAGAGAAATTTACTAATAGTTGGGTGA
1 ATAGTTG-GTGACCAAAA-AAAAATTTACTAATAATTAGGTGA
201628 TTAGGAGTGT
Statistics
Matches: 88, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
59 24 0.27
60 62 0.70
61 2 0.02
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (58 bp):
ATAGTTGGTGACCAAAAAAAAATTTACTAATAATTAGGTGACTACTTTGTAACTTTTC
Found at i:202649 original size:16 final size:16
Alignment explanation
Indices: 202628--202673 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
202618 CTCTTTTATT
202628 TTTATATATTATATAA
1 TTTATATATTATATAA
*
202644 TTTATA-ATTCATAAAA
1 TTTATATATT-ATATAA
*
202660 TTTAAAT-TTATATA
1 TTTATATATTATATA
202674 TGTAAACATT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 7 0.28
16 18 0.72
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTATATATTATATAA
Found at i:205053 original size:2 final size:2
Alignment explanation
Indices: 205048--205092 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
205038 TCTCTCTCTC
205048 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
205089 TA TA
1 TA TA
205093 ATTTTCATGT
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:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:210973 original size:27 final size:28
Alignment explanation
Indices: 210935--210990 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 28
210925 TGAATTTGAA
210935 TATTTATCTAAAATAATTA-GTTTATTT
1 TATTTATCTAAAATAATTATGTTTATTT
*
210962 TATTT-TCATAAAATAATTATTTTTATTT
1 TATTTATC-TAAAATAATTATGTTTATTT
210990 T
1 T
210991 TATAACGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 2 0.08
27 16 0.62
28 8 0.31
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.59
Consensus pattern (28 bp):
TATTTATCTAAAATAATTATGTTTATTT
Found at i:216299 original size:2 final size:2
Alignment explanation
Indices: 216292--216332 Score: 73
Period size: 2 Copynumber: 20.0 Consensus size: 2
216282 CAAGTAAACA
216292 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG CAG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -AG AG
216333 GAGTACGAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:218895 original size:22 final size:22
Alignment explanation
Indices: 218870--218911 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
218860 TTATCGAGGG
*
218870 TGTCGCGACACCGAAGCCTGGA
1 TGTCACGACACCGAAGCCTGGA
* *
218892 TGTCACGACACTGATGCCTG
1 TGTCACGACACCGAAGCCTG
218912 ACTAAGTGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.21, C:0.31, G:0.29, T:0.19
Consensus pattern (22 bp):
TGTCACGACACCGAAGCCTGGA
Found at i:221486 original size:24 final size:22
Alignment explanation
Indices: 221444--221488 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
221434 TTTAAAAATT
*
221444 AGAAAATACTAAAAGAATTTAA
1 AGAAAATACTAAAACAATTTAA
221466 AGAAAATTACTGAAAACAATTTA
1 AGAAAA-TACT-AAAACAATTTA
221489 GACTCTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 4 0.20
24 10 0.50
ACGTcount: A:0.60, C:0.07, G:0.09, T:0.24
Consensus pattern (22 bp):
AGAAAATACTAAAACAATTTAA
Found at i:222355 original size:7 final size:7
Alignment explanation
Indices: 222343--222369 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
222333 ATATGTGGTC
222343 TAGGGTT
1 TAGGGTT
222350 TAGGGTT
1 TAGGGTT
222357 TAGGGTT
1 TAGGGTT
222364 TAGGGT
1 TAGGGT
222370 CTACAGCATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.44, T:0.41
Consensus pattern (7 bp):
TAGGGTT
Found at i:224437 original size:21 final size:19
Alignment explanation
Indices: 224403--224441 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
224393 AAACCTCCTG
*
224403 CAATATCTCAAACACAATTT
1 CAATATCCCAAACA-AATTT
224423 CAATATTCCCAAACAAATT
1 CAATA-TCCCAAACAAATT
224442 CAGTTGTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (19 bp):
CAATATCCCAAACAAATTT
Found at i:230200 original size:3 final size:3
Alignment explanation
Indices: 230192--230229 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
230182 TCTTCCAATA
230192 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
230230 GTTTTGATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:239218 original size:504 final size:505
Alignment explanation
Indices: 238262--239270 Score: 2011
Period size: 504 Copynumber: 2.0 Consensus size: 505
238252 GTATGATTGC
238262 TGAACACTAAAAGATTTATTTTTTAAAAATAAAAATAAAAAAACAATACCGAAGTAAAACCACAA
1 TGAACACTAAAAGATTTATTTTTTAAAAATAAAAATAAAAAAACAATACCGAAGTAAAACCACAA
238327 CTCCAATTTTTCTTTCATAATATGGTACCTGAGAATCGTCAAATCCATTAGCTTTAGCTCCAAAT
66 CTCCAATTTTTCTTTCATAATATGGTACCTGAGAATCGTCAAATCCATTAGCTTTAGCTCCAAAT
238392 TCATCGACATTGATTACCTTGAGAGTGACCCTATCAATCCTCGACCAAACTTCATTATTGTTGAT
131 TCATCGACATTGATTACCTTGAGAGTGACCCTATCAATCCTCGACCAAACTTCATTATTGTTGAT
238457 GGGATTAACGTTGTCTTGTTGGTTGTAGGTTGTTGGGCGGCTATAAACATGAGTTTGTCGAACAT
196 GGGATTAACGTTGTCTTGTTGGTTGTAGGTTGTTGGGCGGCTATAAACATGAGTTTGTCGAACAT
238522 CACTGTGAAATGGGTCCTCTCTGTAACTCCCAAAACAAGATGTGGACAAACAGATGAATGTAATG
261 CACTGTGAAATGGGTCCTCTCTGTAACTCCCAAAACAAGATGTGGACAAACAGATGAATGTAATG
238587 AAAAGTGGGACACAAAGGGTTTTTAACCACATTATCAGACAAATGTCGAAAGGAGCTATCACTTG
326 AAAAGTGGGACACAAAGGGTTTTTAACCACATTATCAGACAAATGTCGAAAGGAGCTATCACTTG
238652 AACATGTTTAGTCATGTAAGTCACTATATTTATATATAAATAATAGAGGCGAAAGTGGAGGTTTA
391 AACATGTTTAGTCATGTAAGTCACTATATTTATATATAAATAATAGAGGCGAAAGTGGAGGTTTA
238717 GGGTGCTTAATTTCTTCAACTAATGAAGAAAAGAGATGGAAAGTGGGGGA
456 GGGTGCTTAATTTCTTCAACTAATGAAGAAAAGAGATGGAAAGTGGGGGA
238767 TGAACACT-AAAGATTTATTTTTTAAAAATAAAAATAAAAAAACAATACCGAAGTAAAACCACAA
1 TGAACACTAAAAGATTTATTTTTTAAAAATAAAAATAAAAAAACAATACCGAAGTAAAACCACAA
238831 CTCCAATTTTTCTTTCATAATATGGTACCTGAGAATCGTCAAATCCATTAGCTTTAGCTCCAAAT
66 CTCCAATTTTTCTTTCATAATATGGTACCTGAGAATCGTCAAATCCATTAGCTTTAGCTCCAAAT
238896 TCATCGACATTGATTACCTTGAGAGTGACCCTATCAATCCTCGACCAAACTTCATTATTGTTGAT
131 TCATCGACATTGATTACCTTGAGAGTGACCCTATCAATCCTCGACCAAACTTCATTATTGTTGAT
238961 GGGATTAACGTTGTCTTGTTGGTTGTAGGTTGTTGGGCGGCTATAAACATGAGTTTGTCGAACAT
196 GGGATTAACGTTGTCTTGTTGGTTGTAGGTTGTTGGGCGGCTATAAACATGAGTTTGTCGAACAT
239026 CACTGTGAAATGGGTCCTCTCTGTAACTCCCAAAACAAGATGTGGACAAACAGATGAATGTAATG
261 CACTGTGAAATGGGTCCTCTCTGTAACTCCCAAAACAAGATGTGGACAAACAGATGAATGTAATG
239091 AAAAGTGGGACACAAAGGGTTTTTAACCACATTATCAGACAAATGTCGAAAGGAGCTATCACTTG
326 AAAAGTGGGACACAAAGGGTTTTTAACCACATTATCAGACAAATGTCGAAAGGAGCTATCACTTG
239156 AACATGTTTAGTCATGTAAGTCACTATATTTATATATAAATAATAGAGGCGAAAGTGGAGGTTTA
391 AACATGTTTAGTCATGTAAGTCACTATATTTATATATAAATAATAGAGGCGAAAGTGGAGGTTTA
239221 GGGTGCTTAATTTCTTCAACTAATGAAGAAAAGAGATGGAAAGTGGGGGA
456 GGGTGCTTAATTTCTTCAACTAATGAAGAAAAGAGATGGAAAGTGGGGGA
239271 AGTTAAGTTA
Statistics
Matches: 504, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
504 496 0.98
505 8 0.02
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (505 bp):
TGAACACTAAAAGATTTATTTTTTAAAAATAAAAATAAAAAAACAATACCGAAGTAAAACCACAA
CTCCAATTTTTCTTTCATAATATGGTACCTGAGAATCGTCAAATCCATTAGCTTTAGCTCCAAAT
TCATCGACATTGATTACCTTGAGAGTGACCCTATCAATCCTCGACCAAACTTCATTATTGTTGAT
GGGATTAACGTTGTCTTGTTGGTTGTAGGTTGTTGGGCGGCTATAAACATGAGTTTGTCGAACAT
CACTGTGAAATGGGTCCTCTCTGTAACTCCCAAAACAAGATGTGGACAAACAGATGAATGTAATG
AAAAGTGGGACACAAAGGGTTTTTAACCACATTATCAGACAAATGTCGAAAGGAGCTATCACTTG
AACATGTTTAGTCATGTAAGTCACTATATTTATATATAAATAATAGAGGCGAAAGTGGAGGTTTA
GGGTGCTTAATTTCTTCAACTAATGAAGAAAAGAGATGGAAAGTGGGGGA
Found at i:240375 original size:17 final size:18
Alignment explanation
Indices: 240355--240401 Score: 71
Period size: 17 Copynumber: 2.7 Consensus size: 18
240345 CTTTTTTGAA
*
240355 TTTTGAATTATTT-TAAT
1 TTTTAAATTATTTATAAT
240372 TTTTAAATT-TTTATAAT
1 TTTTAAATTATTTATAAT
240389 TTTTAAATTATTT
1 TTTTAAATTATTT
240402 GTTGACGTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 3 0.11
17 21 0.78
18 3 0.11
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (18 bp):
TTTTAAATTATTTATAAT
Found at i:240382 original size:8 final size:8
Alignment explanation
Indices: 240355--240397 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
240345 CTTTTTTGAA
*
240355 TTTTGAAT
1 TTTTAAAT
*
240363 TATTTTAAT
1 T-TTTAAAT
240372 TTTTAAAT
1 TTTTAAAT
240380 TTTTATAAT
1 TTTTA-AAT
240389 TTTTAAAT
1 TTTTAAAT
240397 T
1 T
240398 ATTTGTTGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
8 16 0.52
9 15 0.48
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (8 bp):
TTTTAAAT
Found at i:240614 original size:22 final size:20
Alignment explanation
Indices: 240573--240615 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
240563 TTAGTTCAAA
* *
240573 ATAAAATAAAAGTCAAATTG
1 ATAAAAAAAAAGTAAAATTG
240593 ATAAAAAAAAATGTAAACATTG
1 ATAAAAAAAAA-GTAAA-ATTG
240615 A
1 A
240616 GAATTGAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 10 0.53
21 4 0.21
22 5 0.26
ACGTcount: A:0.63, C:0.05, G:0.09, T:0.23
Consensus pattern (20 bp):
ATAAAAAAAAAGTAAAATTG
Found at i:246263 original size:1 final size:1
Alignment explanation
Indices: 246257--246287 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
246247 TTCAACTTGT
*
246257 AAAAAAAAGAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
246288 GGCTTTCAAA
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:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:246293 original size:299 final size:299
Alignment explanation
Indices: 245959--246556 Score: 1169
Period size: 299 Copynumber: 2.0 Consensus size: 299
245949 CTCTCTCTCC
* **
245959 AAAAAAAGCAAAGCAAAAAAAAAAAAAAAAGGCTTTCAAATAGTTCTTTTTTTCTTGGTAGCATC
1 AAAAAAAGAAAAAAAAAAAAAAAAAAAAAAGGCTTTCAAATAGTTCTTTTTTTCTTGGTAGCATC
246024 AATGGGGATGATATATTTATACAAATAAAATTATTTTTGTTGTTCAATAAAATCTCCTTCTTCTT
66 AATGGGGATGATATATTTATACAAATAAAATTATTTTTGTTGTTCAATAAAATCTCCTTCTTCTT
246089 TTATTGTATCTATAGCCTTTGATAATTGATCTCTTTAGATCCTTAAAATCATATCTCGAATGCTT
131 TTATTGTATCTATAGCCTTTGATAATTGATCTCTTTAGATCCTTAAAATCATATCTCGAATGCTT
246154 TCCACAACTTAAGCTATATATATAAATATACCCTTTTTTTCCCCTTAGATCTGTTTCAAGCTTTC
196 TCCACAACTTAAGCTATATATATAAATATACCCTTTTTTTCCCCTTAGATCTGTTTCAAGCTTTC
246219 CCTTTGCTTTGCTTACGAGAGTTTGAGCTTCAACTTGTA
261 CCTTTGCTTTGCTTACGAGAGTTTGAGCTTCAACTTGTA
246258 AAAAAAAGAAAAAAAAAAAAAAAAAAAAAAGGCTTTCAAATAGTTCTTTTTTTCTTGGTAGCATC
1 AAAAAAAGAAAAAAAAAAAAAAAAAAAAAAGGCTTTCAAATAGTTCTTTTTTTCTTGGTAGCATC
246323 AATGGGGATGATATATTTATACAAATAAAATTATTTTTGTTGTTCAATAAAATCTCCTTCTTCTT
66 AATGGGGATGATATATTTATACAAATAAAATTATTTTTGTTGTTCAATAAAATCTCCTTCTTCTT
246388 TTATTGTATCTATAGCCTTTGATAATTGATCTCTTTAGATCCTTAAAATCATATCTCGAATGCTT
131 TTATTGTATCTATAGCCTTTGATAATTGATCTCTTTAGATCCTTAAAATCATATCTCGAATGCTT
246453 TCCACAACTTAAGCTATATATATAAATATACCCTTTTTTTCCCCTTAGATCTGTTTCAAGCTTTC
196 TCCACAACTTAAGCTATATATATAAATATACCCTTTTTTTCCCCTTAGATCTGTTTCAAGCTTTC
246518 CCTTTGCTTTGCTTACGAGAGTTTGAGCTTCAACTTGTA
261 CCTTTGCTTTGCTTACGAGAGTTTGAGCTTCAACTTGTA
246557 TTTTTCTTAT
Statistics
Matches: 296, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
299 296 1.00
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.39
Consensus pattern (299 bp):
AAAAAAAGAAAAAAAAAAAAAAAAAAAAAAGGCTTTCAAATAGTTCTTTTTTTCTTGGTAGCATC
AATGGGGATGATATATTTATACAAATAAAATTATTTTTGTTGTTCAATAAAATCTCCTTCTTCTT
TTATTGTATCTATAGCCTTTGATAATTGATCTCTTTAGATCCTTAAAATCATATCTCGAATGCTT
TCCACAACTTAAGCTATATATATAAATATACCCTTTTTTTCCCCTTAGATCTGTTTCAAGCTTTC
CCTTTGCTTTGCTTACGAGAGTTTGAGCTTCAACTTGTA
Found at i:255578 original size:4 final size:4
Alignment explanation
Indices: 255569--255623 Score: 110
Period size: 4 Copynumber: 13.8 Consensus size: 4
255559 CAACATGACT
255569 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
255617 CATA CAT
1 CATA CAT
255624 GTATGTATAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:255963 original size:16 final size:18
Alignment explanation
Indices: 255942--255981 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 18
255932 AGGACCACTC
255942 ATTTTTTA-ATAATA-TT
1 ATTTTTTATATAATATTT
*
255958 A-TTTTTATTTAATATTT
1 ATTTTTTATATAATATTT
255975 ATTTTTT
1 ATTTTTT
255982 TACATTCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
15 6 0.30
16 6 0.30
17 3 0.15
18 5 0.25
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
ATTTTTTATATAATATTT
Found at i:256284 original size:14 final size:16
Alignment explanation
Indices: 256260--256291 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
256250 ATAAAGTTAT
256260 AATATAATA-TTAAAA
1 AATATAATATTTAAAA
256275 AATA-AATATTTAAAA
1 AATATAATATTTAAAA
256290 AA
1 AA
256292 AAGGGACACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AATATAATATTTAAAA
Found at i:261576 original size:19 final size:20
Alignment explanation
Indices: 261552--261590 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
261542 AATATAATAA
*
261552 AAAATATTTTTTTA-ATTTT
1 AAAATACTTTTTTAGATTTT
261571 AAAATACTTTTTTAGATTTT
1 AAAATACTTTTTTAGATTTT
261591 TTTATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (20 bp):
AAAATACTTTTTTAGATTTT
Found at i:261611 original size:29 final size:29
Alignment explanation
Indices: 261557--261612 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
261547 AATAAAAAAT
**
261557 ATTTTTTTAATTTTAAAATACTTTTTTAG
1 ATTTTTTTAATTTTAAAATAAATTTTTAG
*
261586 ATTTTTTTATTTTTAAAATAAATTTTT
1 ATTTTTTTAATTTTAAAATAAATTTTT
261613 GGTGTTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (29 bp):
ATTTTTTTAATTTTAAAATAAATTTTTAG
Found at i:262649 original size:14 final size:14
Alignment explanation
Indices: 262632--262665 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
262622 TATAATATCC
262632 AAATAATAACAATA
1 AAATAATAACAATA
*
262646 AAATAGTAACAATA
1 AAATAATAACAATA
*
262660 TAATAA
1 AAATAA
262666 CGAAATAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.24
Consensus pattern (14 bp):
AAATAATAACAATA
Found at i:269668 original size:16 final size:18
Alignment explanation
Indices: 269629--269662 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
269619 TAAATTTTTA
269629 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
269646 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
269663 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:274710 original size:10 final size:10
Alignment explanation
Indices: 274697--274732 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
274687 TCTTTTTGGA
274697 TTTTTTTATT
1 TTTTTTTATT
274707 TTTTTTTATT
1 TTTTTTTATT
**
274717 TTTTTTGCTT
1 TTTTTTTATT
274727 TTTTTT
1 TTTTTT
274733 CTTCACTCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.06, C:0.03, G:0.03, T:0.89
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:278133 original size:42 final size:43
Alignment explanation
Indices: 278074--278181 Score: 164
Period size: 43 Copynumber: 2.5 Consensus size: 43
278064 TATTGTCAAT
*
278074 GCCGCTATAGATCAGGACCTTTAGCGACGC-TTTTCCAAAAAC
1 GCCGCTATAGATCAGGACCTTTAGCGACGCTTTTTACAAAAAC
* *
278116 GCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTTATAAAAAC
1 GCCGCTATAGATCAGGACCTTTAGCGACGCTTTTTACAAAAAC
* *
278159 GCAGCTATAGGTCAGGACCTTTA
1 GCCGCTATAGATCAGGACCTTTA
278182 CGCTTTGATT
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
42 29 0.48
43 31 0.52
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (43 bp):
GCCGCTATAGATCAGGACCTTTAGCGACGCTTTTTACAAAAAC
Done.