Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007863.1 Hibiscus syriacus cultivar Beakdansim tig00110234_pilon, whole genome shotgun sequence
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: 1653362
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 8
Found at i:250313 original size:25 final size:25
Alignment explanation
Indices: 250268--250319 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
250258 AGTTAAGGAC
**
250268 AAAATCCTAAAAATATTCAAATAAT
1 AAAATCCTAAAAATAAACAAATAAT
* *
250293 AAAATCCTAAAGATAAACAAATGAT
1 AAAATCCTAAAAATAAACAAATAAT
250318 AA
1 AA
250320 TTTCGAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.62, C:0.12, G:0.04, T:0.23
Consensus pattern (25 bp):
AAAATCCTAAAAATAAACAAATAAT
Found at i:251290 original size:18 final size:18
Alignment explanation
Indices: 251269--251303 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
251259 CAGTCACACA
251269 CTAAGTCACAGACTTAGG
1 CTAAGTCACAGACTTAGG
251287 CTAAGTCACAGACTTAG
1 CTAAGTCACAGACTTAG
251304 TGAGGCGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (18 bp):
CTAAGTCACAGACTTAGG
Found at i:251574 original size:24 final size:24
Alignment explanation
Indices: 251547--251603 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
251537 CACCACAACT
*
251547 CGTATAAATTGCACTGAAGTGCCA
1 CGTATAAATTGCACCGAAGTGCCA
* *
251571 CGTAGAAATTGCACCGAAGTGTCA
1 CGTATAAATTGCACCGAAGTGCCA
*
251595 CATATAAAT
1 CGTATAAAT
251604 GTCCCGAAGG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
CGTATAAATTGCACCGAAGTGCCA
Found at i:251621 original size:23 final size:23
Alignment explanation
Indices: 251595--251664 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
251585 CGAAGTGTCA
251595 CATATAAATGTCCCGAAGGACCG
1 CATATAAATGTCCCGAAGGACCG
* **
251618 CATAGT-ATTGTCCCGAAGGA-TA
1 CATA-TAAATGTCCCGAAGGACCG
* *
251640 AAGTAGAAATGTCCCGAAGGACCG
1 CA-TATAAATGTCCCGAAGGACCG
251664 C
1 C
251665 GCATAACCCC
Statistics
Matches: 34, Mismatches: 9, Indels: 7
0.68 0.18 0.14
Matches are distributed among these distances:
22 1 0.03
23 32 0.94
24 1 0.03
ACGTcount: A:0.34, C:0.23, G:0.24, T:0.19
Consensus pattern (23 bp):
CATATAAATGTCCCGAAGGACCG
Found at i:258393 original size:20 final size:20
Alignment explanation
Indices: 258356--258398 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
258346 GAAAAGTTAA
* *
258356 GACCATTTGATAATAGACTT
1 GACCATTTGATAAGAGACGT
258376 GACC-TTTGATGAAGAGACGT
1 GACCATTTGAT-AAGAGACGT
258396 GAC
1 GAC
258399 TTATTATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (20 bp):
GACCATTTGATAAGAGACGT
Found at i:267808 original size:43 final size:42
Alignment explanation
Indices: 267761--268092 Score: 312
Period size: 43 Copynumber: 7.8 Consensus size: 42
267751 CAATAGGCCA
* *
267761 ATATCTATTA-CGGCGTTTTTTGAACAAACGCCGCAAAATGTC
1 ATATCTA-TAGCGGCGTTTTTGGAACAAACGCCGCAAAAAGTC
* *
267803 GATATCTATAGCGGCGTTTTTGGAATAAACGCCGCAAAAAGTT
1 -ATATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAAGTC
* * * *
267846 ATGATATATAGCGGCGTTTCTAGAAAAAACGCCGCAAAAAGTC
1 AT-ATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAAGTC
* *
267889 ATAACTATAGCGGCGTTTTTGGATACAAACGCCGC-AAAAGATA
1 ATATCTATAGCGGCGTTTTTGGA-ACAAACGCCGCAAAAAG-TC
* * * * *
267932 AGA-CATATA-CTGGCGTTTTTAGAACAAACACCGTAAAAGGTC
1 ATATC-TATAGC-GGCGTTTTTGGAACAAACGCCGCAAAAAGTC
* * * *
267974 AGACCTATAGTGGCGTTTTTGGACACAAACGCCGCAAAATGTC
1 ATATCTATAGCGGCGTTTTTGGA-ACAAACGCCGCAAAAAGTC
* * * *
268017 AGACCTATAACGGCGTTTTTGAACACAAACGCCGCAAAAAGTC
1 ATATCTATAGCGGCGTTTTTGGA-ACAAACGCCGCAAAAAGTC
* * *
268060 AAACCTATAGCGGTGTTTTTGGATACAAACGCC
1 ATATCTATAGCGGCGTTTTTGGA-ACAAACGCC
268093 ACTAATTACC
Statistics
Matches: 244, Mismatches: 35, Indels: 20
0.82 0.12 0.07
Matches are distributed among these distances:
42 56 0.23
43 188 0.77
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (42 bp):
ATATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAAGTC
Found at i:267906 original size:128 final size:126
Alignment explanation
Indices: 267765--268092 Score: 324
Period size: 128 Copynumber: 2.5 Consensus size: 126
267755 AGGCCAATAT
* * *
267765 CTATTACGGCGTTTTTTGA-ACAAACGCCGCAAAATGTCGATATCTATAGCGGCGTTTTTGGAAT
1 CTATAACGGCGTTTTTTGACACAAACGCCGCAAAA-GTC-A-AACTATAGCGGCGTTTTTGGAAC
* * *
267829 AAACGCCGCAAAAAGTTATGATATATAGCGGCGTTTCTAGA-AAAAACGCCGCAAAAAGTCATAA
63 AAACGCCGCAAAAAGTCA-GACATATAGCGGCGTTTCTAGACAAAAACGCCGCAAAAAGTCAGAA
* * * *
267893 CTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGAT-AAGACATATA-CTGGCGTTTTTAGAA
1 CTATAACGGCGTTTTTTGACACAAACGCCGCAAAAG-TCAA-AC-TATAGC-GGCGTTTTTGGAA
* * * * * * * * * *
267956 CAAACACCGTAAAAGGTCAGACCTATAGTGGCGTTTTTGGACACAAACGCCGCAAAATGTCAGAC
62 CAAACGCCGCAAAAAGTCAGACATATAGCGGCGTTTCTAGACAAAAACGCCGCAAAAAGTCAGAA
*
268021 CTATAACGGCG-TTTTTGAACACAAACGCCGCAAAAAGTCAAACCTATAGCGGTGTTTTTGGATA
1 CTATAACGGCGTTTTTTG-ACACAAACGCCGC-AAAAGTCAAA-CTATAGCGGCGTTTTTGGA-A
268085 CAAACGCC
62 CAAACGCC
268093 ACTAATTACC
Statistics
Matches: 163, Mismatches: 25, Indels: 23
0.77 0.12 0.11
Matches are distributed among these distances:
126 1 0.01
127 25 0.15
128 104 0.64
129 33 0.20
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (126 bp):
CTATAACGGCGTTTTTTGACACAAACGCCGCAAAAGTCAAACTATAGCGGCGTTTTTGGAACAAA
CGCCGCAAAAAGTCAGACATATAGCGGCGTTTCTAGACAAAAACGCCGCAAAAAGTCAGAA
Found at i:267947 original size:85 final size:83
Alignment explanation
Indices: 267769--268092 Score: 357
Period size: 85 Copynumber: 3.8 Consensus size: 83
267759 CAATATCTAT
* * * * *
267769 TACGGCGTTTTTTGAACAAACGCCGCAAAATGTCGATATCTATAGCGGCGTTTTTGGA-ATAAAC
1 TACGGCGTTTTTAGAAAAAACGCCGCAAAAAGTC-ATAACTATAGCGGCGTTTTTGGATACAAAC
* *
267833 GCCGCAAAAAGTTATGATATA
65 GCCGC-AAAAG-TAAGACATA
*
267854 TAGCGGCGTTTCTAGAAAAAACGCCGCAAAAAGTCATAACTATAGCGGCGTTTTTGGATACAAAC
1 TA-CGGCGTTTTTAGAAAAAACGCCGCAAAAAGTCATAACTATAGCGGCGTTTTTGGATACAAAC
267919 GCCGCAAAAGATAAGACATA
65 GCCGCAAAAG-TAAGACATA
* * * * * * * *
267939 TACTGGCGTTTTTAGAACAAACACCGTAAAAGGTCAGACCTATAGTGGCGTTTTTGGACACAAAC
1 TAC-GGCGTTTTTAGAAAAAACGCCGCAAAAAGTCATAACTATAGCGGCGTTTTTGGATACAAAC
* *
268004 GCCGCAAAATGTCAGACCTA
65 GCCGCAAAA-GTAAGACATA
*
268024 TAACGGCGTTTTT-GAACACAAACGCCGCAAAAAGTCA-AACCTATAGCGGTGTTTTTGGATACA
1 T-ACGGCGTTTTTAGAA-A-AAACGCCGCAAAAAGTCATAA-CTATAGCGGCGTTTTTGGATACA
268087 AACGCC
62 AACGCC
268093 ACTAATTACC
Statistics
Matches: 203, Mismatches: 28, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
84 4 0.02
85 117 0.58
86 82 0.40
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.24
Consensus pattern (83 bp):
TACGGCGTTTTTAGAAAAAACGCCGCAAAAAGTCATAACTATAGCGGCGTTTTTGGATACAAACG
CCGCAAAAGTAAGACATA
Found at i:270004 original size:9 final size:10
Alignment explanation
Indices: 269979--270005 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
269969 TTTACTAAAC
269979 CCAAAAAGAG
1 CCAAAAAGAG
269989 CCAAAAAGAG
1 CCAAAAAGAG
269999 CCAAAAA
1 CCAAAAA
270006 ACCTTCAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.63, C:0.22, G:0.15, T:0.00
Consensus pattern (10 bp):
CCAAAAAGAG
Found at i:272466 original size:125 final size:123
Alignment explanation
Indices: 272296--272748 Score: 361
Period size: 125 Copynumber: 3.7 Consensus size: 123
272286 GCATTTGAAT
* * * * * *
272296 AAAAACGCCACTAAAGTACGAGTCTGTAGCGGCGTTTGTATAAAAATGTCAATAAAGTACGAGTC
1 AAAAACGCCACTAAAGTACAAGTCTATAACGACGTTTGAATAAAAATGCCAATAAAGTACGAGTC
* * *
272361 TTTAGCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTAGCGACGTTTATAA
66 TTTAGCGGAGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGACGTTTATAA
* * * *
272419 ACACAAACGCCACTATAGTACAAGTGTATAACGACGTTTGAATAAAAATGCCACTAAAGTACGCG
1 A-A-AAACGCCACTAAAGTACAAGTCTATAACGACGTTTGAATAAAAATGCCAATAAAGTACGAG
* * * *
272484 TCTTTAGCGGAGTTTGTATAAAAACGCCACTAAAGTATGAGTCTTTAGCGGCGTTTGTAT
64 TCTTTAGCGGAGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGACGTTTATAA
* ** * * ** ** * * * *
272544 AAAAACGCCACTAAATTATGAGTCTTTAGCGGTGTTTGTGTTTACAAACGCCACTATAGTAC-AT
1 AAAAACGCCACTAAAGTACAAGTCTATAACGACG-TT-TGAATAAAAATGCCAATAAAGTACGA-
* * * * * * * * * *
272608 GTGTATAAC-GACGTTTGTATAAAAATGCCACTAAAGTACAATTCTATAGCGGCGTTTGTAT
63 GTCTTTAGCGGA-GTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGACGTTTATAA
* * * * * * * * * * *
272669 AAAAATGCCACTAAATTACGAGTATTTAGCGGCGTTTGTATAAAAATGCCACTAAAGTACTACTC
1 AAAAACGCCACTAAAGTACAAGTCTATAACGACGTTTGAATAAAAATGCCAATAAAGTACGAGTC
* *
272734 TTTTGCGGCGTTTGT
66 TTTAGCGGAGTTTGT
272749 TGAAAAAATG
Statistics
Matches: 268, Mismatches: 54, Indels: 16
0.79 0.16 0.05
Matches are distributed among these distances:
123 54 0.20
124 10 0.04
125 204 0.76
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (123 bp):
AAAAACGCCACTAAAGTACAAGTCTATAACGACGTTTGAATAAAAATGCCAATAAAGTACGAGTC
TTTAGCGGAGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGACGTTTATAA
Found at i:272520 original size:166 final size:166
Alignment explanation
Indices: 272240--272748 Score: 730
Period size: 166 Copynumber: 3.1 Consensus size: 166
272230 TTGTAAACTT
* * * *
272240 GCGACGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAGCGGCATTTGAATAAAAACGCC
1 GCGACGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGACGTTTGAATAAAAATGCC
* * *
272305 ACTAAAGTACGAGTCTGTAGCGGCGTTTGTATAAAAATGTCAATAAAGTACGAGTCTTTAGCGGC
66 ACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGGC
272370 GTTTGTATAAAAATGCCACTAAATTACGAGTCTTTA
131 GTTTGTATAAAAATGCCACTAAATTACGAGTCTTTA
*
272406 GCGACGTTTATAAACACAAACGCCACTATAGTACAAGTGTATAACGACGTTTGAATAAAAATGCC
1 GCGACGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGACGTTTGAATAAAAATGCC
* * * * *
272471 ACTAAAGTACGCGTCTTTAGCGGAGTTTGTATAAAAACGCCACTAAAGTATGAGTCTTTAGCGGC
66 ACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGGC
* *
272536 GTTTGTATAAAAACGCCACTAAATTATGAGTCTTTA
131 GTTTGTATAAAAATGCCACTAAATTACGAGTCTTTA
** **** * *
272572 GCGGTGTTTGTGTTTACAAACGCCACTATAGTACATGTGTATAACGACGTTTGTATAAAAATGCC
1 GCGACGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGACGTTTGAATAAAAATGCC
* * * *
272637 ACTAAAGTACAATTCTATAGCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTATTTAGCGGC
66 ACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGGC
* * * *
272702 GTTTGTATAAAAATGCCACTAAAGTACTACTCTTTT
131 GTTTGTATAAAAATGCCACTAAATTACGAGTCTTTA
*
272738 GCGGCGTTTGT
1 GCGACGTTTGT
272749 TGAAAAAATG
Statistics
Matches: 304, Mismatches: 39, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
166 304 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (166 bp):
GCGACGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGACGTTTGAATAAAAATGCC
ACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGGC
GTTTGTATAAAAATGCCACTAAATTACGAGTCTTTA
Found at i:272755 original size:41 final size:41
Alignment explanation
Indices: 272261--272761 Score: 511
Period size: 41 Copynumber: 12.1 Consensus size: 41
272251 AAACACAAAC
* * * * * * *
272261 GCCACTATAGTACAAGTGTATAGCGGCATTTGAATAAAAAC
1 GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAAT
*
272302 GCCACTAAAGTACGAGTCTGTAGCGGCGTTTGTATAAAAAT
1 GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAAT
* *
272343 GTCAATAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAAT
1 GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAAT
* * * * *
272384 GCCACTAAATTACGAGTCTTTAGCGACGTTTATAAACACAAAC
1 GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATA-A-AAAT
* * * * * * *
272427 GCCACTATAGTACAAGTGTATAACGACGTTTGAATAAAAAT
1 GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAAT
* * *
272468 GCCACTAAAGTACGCGTCTTTAGCGGAGTTTGTATAAAAAC
1 GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAAT
* *
272509 GCCACTAAAGTATGAGTCTTTAGCGGCGTTTGTATAAAAAC
1 GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAAT
* * * * * *
272550 GCCACTAAATTATGAGTCTTTAGCGGTGTTTGTGTTTACAAAC
1 GCCACTAAAGTACGAGTCTTTAGCGGCG-TT-TGTATAAAAAT
* * * * *
272593 GCCACTATAGTAC-ATGTGTATAACGACGTTTGTATAAAAAT
1 GCCACTAAAGTACGA-GTCTTTAGCGGCGTTTGTATAAAAAT
* * *
272634 GCCACTAAAGTACAATTCTATAGCGGCGTTTGTATAAAAAT
1 GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAAT
* *
272675 GCCACTAAATTACGAGTATTTAGCGGCGTTTGTATAAAAAT
1 GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAAT
* * *
272716 GCCACTAAAGTACTACTCTTTTGCGGCGTTTGT-TGAAAAAAT
1 GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTAT--AAAAAT
272758 GCCA
1 GCCA
272762 TTATCGATGA
Statistics
Matches: 382, Mismatches: 70, Indels: 15
0.82 0.15 0.03
Matches are distributed among these distances:
40 1 0.00
41 306 0.80
42 18 0.05
43 57 0.15
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (41 bp):
GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAAT
Found at i:273531 original size:18 final size:19
Alignment explanation
Indices: 273494--273531 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
273484 CAACCTGACC
*
273494 TAAAATAATATATATTTAT
1 TAAAAAAATATATATTTAT
*
273513 TAAAAAAAT-TATTTTTAT
1 TAAAAAAATATATATTTAT
273531 T
1 T
273532 CAATACAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TAAAAAAATATATATTTAT
Found at i:273802 original size:2 final size:2
Alignment explanation
Indices: 273797--273838 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
273787 ACGCCAAAAG
273797 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
273839 ATTTAATAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:275239 original size:21 final size:21
Alignment explanation
Indices: 275213--275267 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
275203 ATTATCTAAT
*
275213 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
275234 AAACTTGAAATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
*
275255 AAAATTGAAATCC
1 AAACTTGAAATCC
275268 GTAATAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.51, C:0.24, G:0.05, T:0.20
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:293251 original size:41 final size:38
Alignment explanation
Indices: 293200--293311 Score: 93
Period size: 41 Copynumber: 2.8 Consensus size: 38
293190 CGTTTGTAAG
* * *
293200 AAAAATGCCACTAAAGTACTAGATTTTAGCGGAGTTTGTCT
1 AAAAACGCCACTAAAGTACTAGATTTTAGC-GA-TTTAT-A
**
293241 AAAAACGCCACTATATATGTACTCTATTGTT-GC-ATTTATA
1 AAAAACGCCACTA-A-A-GTACTAGATT-TTAGCGATTTATA
*
293281 AAAAACGCCACTAAAGTACTAGGTTTTAGCG
1 AAAAACGCCACTAAAGTACTAGATTTTAGCG
293312 TCGTTTGCCT
Statistics
Matches: 57, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
36 2 0.04
37 9 0.16
38 1 0.02
39 1 0.02
40 13 0.23
41 16 0.28
42 2 0.04
43 1 0.02
44 10 0.18
45 2 0.04
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (38 bp):
AAAAACGCCACTAAAGTACTAGATTTTAGCGATTTATA
Found at i:295819 original size:16 final size:15
Alignment explanation
Indices: 295796--295825 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
295786 AACTTTCTAA
295796 TAAAAATAAATTTAT
1 TAAAAATAAATTTAT
295811 TAAAGAATAAATTTA
1 TAAA-AATAAATTTA
295826 AATCACTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (15 bp):
TAAAAATAAATTTAT
Found at i:298066 original size:20 final size:21
Alignment explanation
Indices: 298041--298092 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
298031 TTTTCCCAAT
298041 TCGCAATGCGAATAAGT-AAA
1 TCGCAATGCGAATAAGTAAAA
* **
298061 TCGCAACGCGAATTGGTAAAA
1 TCGCAATGCGAATAAGTAAAA
*
298082 TTGCAATGCGA
1 TCGCAATGCGA
298093 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATAAGTAAAA
Found at i:298109 original size:20 final size:20
Alignment explanation
Indices: 298084--298194 Score: 100
Period size: 20 Copynumber: 5.5 Consensus size: 20
298074 TGGTAAAATT
*
298084 GCAATGCGATACTGACTATC
1 GCAACGCGATACTGACTATC
* *
298104 GCAATGCGATACTTACTATC
1 GCAACGCGATACTGACTATC
* * *
298124 GCAATGCGATAAT-ACAAAATC
1 GCAACGCGATACTGAC--TATC
* *
298145 GCAACGAGATACTGACTTTC
1 GCAACGCGATACTGACTATC
*
298165 GCAACGCGATTA-TGACTTTC
1 GCAACGCGA-TACTGACTATC
298185 GCAACGCGAT
1 GCAACGCGAT
298195 TTACATAGCG
Statistics
Matches: 78, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
19 3 0.04
20 58 0.74
21 15 0.19
22 2 0.03
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.24
Consensus pattern (20 bp):
GCAACGCGATACTGACTATC
Found at i:298798 original size:19 final size:19
Alignment explanation
Indices: 298751--298792 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
298741 ACGAGAGAAT
*
298751 CGCAACGCGAAATAAAAAA
1 CGCAACGCGAAACAAAAAA
*
298770 CGCAACGCGAAACAAAAAT
1 CGCAACGCGAAACAAAAAA
298789 CGCA
1 CGCA
298793 TTGCGATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.52, C:0.26, G:0.17, T:0.05
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAA
Found at i:298810 original size:19 final size:19
Alignment explanation
Indices: 298788--298952 Score: 134
Period size: 19 Copynumber: 9.1 Consensus size: 19
298778 GAAACAAAAA
*
298788 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
298807 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
298826 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
298845 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
298859 TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
298878 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
298892 TCTCGTTGTGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
298911 TCCACGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
298931 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
298951 TC
1 TC
298953 AACCAAAAGA
Statistics
Matches: 118, Mismatches: 16, Indels: 24
0.75 0.10 0.15
Matches are distributed among these distances:
14 18 0.15
16 4 0.03
17 5 0.04
19 60 0.51
20 30 0.25
21 1 0.01
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:298844 original size:38 final size:33
Alignment explanation
Indices: 298793--298927 Score: 144
Period size: 33 Copynumber: 3.9 Consensus size: 33
298783 AAAAATCGCA
*
298793 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGA--TTC---TCTCG
298831 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* **
298864 TCGCGATAGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* ** *
298897 TTGTGATAGTCATTTCCACGTTGCGATTCTC
1 TTGCGATTTTCATTT-CGCGTTGCGATTCTC
298928 ATTATCTCGT
Statistics
Matches: 89, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
33 47 0.53
34 14 0.16
36 3 0.03
38 25 0.28
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:298929 original size:20 final size:20
Alignment explanation
Indices: 298906--298952 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
298896 GTTGTGATAG
298906 TCATTTCCACGTTGCGATTC
1 TCATTTCCACGTTGCGATTC
* *
298926 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCACGTTGCGATTC
298946 TCATTTC
1 TCATTTC
298953 AACCAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.15, C:0.26, G:0.13, T:0.47
Consensus pattern (20 bp):
TCATTTCCACGTTGCGATTC
Found at i:301122 original size:21 final size:21
Alignment explanation
Indices: 301098--301164 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
301088 TCATTCCTCG
301098 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
301119 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
301140 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
301161 AGAG
1 AGAG
301165 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:301122 original size:42 final size:42
Alignment explanation
Indices: 301046--301164 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
301036 GACTCGCCTG
* * * * * * *
301046 TCATCCCTCAAGAGTCCGCTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
301088 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
301130 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
301165 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:302543 original size:14 final size:14
Alignment explanation
Indices: 302524--302559 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
302514 ATTATTTAAT
302524 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
302538 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
302552 TGATTTGT
1 TGATTTGT
302560 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:302690 original size:19 final size:17
Alignment explanation
Indices: 302675--302727 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 17
302665 TATCGCAATG
302675 CGAAATGAAAATCGCAA
1 CGAAATGAAAATCGCAA
*
302692 CG--A-GAGAATCGCAACA
1 CGAAATGAAAATCGC-A-A
302708 CGAAATGAAAATCGCAA
1 CGAAATGAAAATCGCAA
302725 CGA
1 CGA
302728 GAGAATCGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 8 0.28
15 2 0.07
16 3 0.10
17 6 0.21
18 2 0.07
19 8 0.28
ACGTcount: A:0.49, C:0.21, G:0.21, T:0.09
Consensus pattern (17 bp):
CGAAATGAAAATCGCAA
Found at i:302703 original size:14 final size:14
Alignment explanation
Indices: 302684--302740 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
302674 GCGAAATGAA
302684 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
302698 AATCGCAACACGAAATGAA
1 AATCGC-A-ACG--A-GAG
302717 AATCGCAACGAGAG
1 AATCGCAACGAGAG
302731 AATCGCAACG
1 AATCGCAACG
302741 CGAAATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
15 2 0.06
16 3 0.08
17 3 0.08
18 2 0.06
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:302712 original size:33 final size:33
Alignment explanation
Indices: 302666--302755 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
302656 AAAAAGTACT
*
302666 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
302699 ATCGCAACACGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
302732 ATCGCAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
302756 GTTGCGATTT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.13
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:302773 original size:19 final size:19
Alignment explanation
Indices: 302751--302867 Score: 119
Period size: 19 Copynumber: 6.7 Consensus size: 19
302741 CGAAATTAAA
*
302751 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
302770 TTCGCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
302789 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
* *
302803 TTAGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
302822 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
302838 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
302855 TTCGCATTGCGAT
1 TTCGCATTGCGAT
302868 AGTAATTTCC
Statistics
Matches: 79, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
14 17 0.22
16 7 0.09
17 7 0.09
19 48 0.61
ACGTcount: A:0.15, C:0.21, G:0.20, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:302818 original size:33 final size:34
Alignment explanation
Indices: 302776--302866 Score: 141
Period size: 33 Copynumber: 2.7 Consensus size: 34
302766 TCATTTCGCA
302776 TTGCGATTTTCATTTCGCATTGCGAAAT-TAGCG
1 TTGCGATTTTCATTTCGCATTGCGAAATCTAGCG
* **
302809 TTGCGATTTTCATTTCGCATTGCG-ATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGAAATCTAGCG
302842 TTGCGATTTTCATTTCGCATTGCGA
1 TTGCGATTTTCATTTCGCATTGCGA
302867 TAGTAATTTC
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 2 0.04
33 51 0.96
ACGTcount: A:0.16, C:0.21, G:0.20, T:0.43
Consensus pattern (34 bp):
TTGCGATTTTCATTTCGCATTGCGAAATCTAGCG
Found at i:305177 original size:12 final size:12
Alignment explanation
Indices: 305160--305184 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
305150 TCTTCGGGGA
305160 CTTTTTCTTCTT
1 CTTTTTCTTCTT
305172 CTTTTTCTTCTT
1 CTTTTTCTTCTT
305184 C
1 C
305185 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:305393 original size:24 final size:24
Alignment explanation
Indices: 305359--305412 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
305349 CTGAAACATC
*
305359 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
305383 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
305407 ATCAAA
1 ATCAAA
305413 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:306182 original size:20 final size:20
Alignment explanation
Indices: 306157--306207 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
306147 TGTATTATCT
306157 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
306177 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
306197 CGTTGCGAAAG
1 CGTTGCGAAAG
306208 GTAATCATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.20, G:0.31, T:0.20
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:306516 original size:20 final size:20
Alignment explanation
Indices: 306420--306510 Score: 146
Period size: 20 Copynumber: 4.5 Consensus size: 20
306410 ATTCATTTGA
* *
306420 CTATCACAACACGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
306440 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGCGAAAATGG
306460 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
306480 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
306500 CTATCGTAACG
1 CTATCGCAACG
306511 ACAAAACCGC
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 66 1.00
ACGTcount: A:0.36, C:0.24, G:0.22, T:0.18
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:306579 original size:19 final size:19
Alignment explanation
Indices: 306536--306600 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
306526 GAAATGAAAA
306536 TCGCATTGCGA-TTT--TT
1 TCGCATTGCGATTTTCATT
306552 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
306569 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
306588 TCGCATTGTGATT
1 TCGCATTGCGATT
306601 CTCTCGTTGC
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
14 6 0.14
15 3 0.07
16 3 0.07
17 5 0.12
19 26 0.60
ACGTcount: A:0.14, C:0.18, G:0.18, T:0.49
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:306631 original size:20 final size:20
Alignment explanation
Indices: 306606--306644 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
306596 TGATTCTCTC
306606 GTTGCGATAGTCAGTTTTGT
1 GTTGCGATAGTCAGTTTTGT
*
306626 GTTGCGATAGTCTGTTTTG
1 GTTGCGATAGTCAGTTTTG
306645 CCTTCAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.10, G:0.31, T:0.46
Consensus pattern (20 bp):
GTTGCGATAGTCAGTTTTGT
Found at i:306746 original size:14 final size:14
Alignment explanation
Indices: 306727--306763 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
306717 CATCAATTAA
306727 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
306741 ACAAATCATCTTTT
1 ACAAATCAACATTT
306755 ACAAATCAA
1 ACAAATCAA
306764 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:308656 original size:20 final size:20
Alignment explanation
Indices: 308633--308686 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
308623 GAAACTTAAA
308633 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
* *
308653 ATCGCAACGC-AGAAATGGCT
1 ATCGCAATGCGA-AAATGACT
*
308673 ATCGTAATGCGAAA
1 ATCGCAATGCGAAA
308687 TGAAAATCGC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.19
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:308708 original size:14 final size:14
Alignment explanation
Indices: 308689--308746 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
308679 ATGCGAAATG
308689 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
308703 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
308719 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
308735 AAAATCGCAACG
1 AAAATCGCAACG
308747 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:308731 original size:32 final size:33
Alignment explanation
Indices: 308681--308751 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 33
308671 CTATCGTAAT
308681 GCGAAATGAAAATCGCAACGACAAAATCGCAAC
1 GCGAAATGAAAATCGCAACGACAAAATCGCAAC
308714 GCGAAATG-AAATCGCAACGACAAAATCGCAAC
1 GCGAAATGAAAATCGCAACGACAAAATCGCAAC
308746 GCGAAA
1 GCGAAA
308752 CACAAATCGC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 30 0.79
33 8 0.21
ACGTcount: A:0.48, C:0.24, G:0.20, T:0.08
Consensus pattern (33 bp):
GCGAAATGAAAATCGCAACGACAAAATCGCAAC
Found at i:308802 original size:14 final size:14
Alignment explanation
Indices: 308780--308837 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
308770 TTTCATTTCG
*
308780 CGTTACGATTTTGT
1 CGTTGCGATTTTGT
*
308794 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
308810 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
308826 CGTTGCGATTTT
1 CGTTGCGATTTT
308838 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:308844 original size:33 final size:33
Alignment explanation
Indices: 308763--308853 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
308753 ACAAATCGCA
* *
308763 TTGCGATTTTCATTTCGCGTTACGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
308796 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
308828 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
308854 AACCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:308880 original size:20 final size:19
Alignment explanation
Indices: 308826--308892 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
308816 GCGATTTTGT
**
308826 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAATCATTTCG
* *
308845 CATTGCGATAACCATTTCCG
1 CGTTGCGATAATCATTT-CG
*
308865 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAATCA-TTTCG
*
308885 TGTTGCGA
1 CGTTGCGA
308893 AAGTAAACTA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
19 13 0.34
20 22 0.58
21 3 0.08
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.39
Consensus pattern (19 bp):
CGTTGCGATAATCATTTCG
Found at i:309401 original size:18 final size:18
Alignment explanation
Indices: 309375--309419 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
309365 GTCGATCAGA
*
309375 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
309393 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
309411 TGATGGCTC
1 TGATGGCTC
309420 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:310787 original size:20 final size:20
Alignment explanation
Indices: 310739--310797 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
310729 AATAGTTTCT
** *
310739 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
310759 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
310779 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
310798 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:311076 original size:20 final size:21
Alignment explanation
Indices: 311051--311099 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
311041 TCTGAGAGAT
311051 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATTTCGCC
* *
311071 GGAGATGGGGACGGATTTCGTC
1 GGAGAT-GAGACGGATTTCGCC
*
311093 AGAGATG
1 GGAGATG
311100 GGTGAGAGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 6 0.25
21 1 0.04
22 17 0.71
ACGTcount: A:0.24, C:0.14, G:0.41, T:0.20
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGCC
Found at i:311085 original size:22 final size:22
Alignment explanation
Indices: 311058--311101 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
311048 GATGGAGATA
*
311058 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
*
311080 GACGGATTTCGTCAGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
311102 TGAGAGATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCAGAGATGGG
Found at i:311369 original size:20 final size:20
Alignment explanation
Indices: 311261--311395 Score: 94
Period size: 20 Copynumber: 6.7 Consensus size: 20
311251 CGCTTTGAAA
*
311261 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTAAGT
* * * *
311282 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTAAGT
* * *
311302 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* * * *
311322 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTAAGT
311343 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* *
311363 GTCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTAAGT
311383 ATCGCATTGCGAT
1 ATCGCATTGCGAT
311396 TTTCCCAATT
Statistics
Matches: 94, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
19 5 0.05
20 64 0.68
21 23 0.24
22 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:311373 original size:61 final size:61
Alignment explanation
Indices: 311261--311398 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 61
311251 CGCTTTGAAA
* * * *
311261 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * ** *
311322 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTGTCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
311383 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
311399 CCCAATTCGC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:311414 original size:61 final size:61
Alignment explanation
Indices: 311261--311416 Score: 152
Period size: 61 Copynumber: 2.6 Consensus size: 61
311251 CGCTTTGAAA
* ** * * * *
311261 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
* * ** * * ** *
311322 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTGTCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
311383 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
311417 TTACTTATTC
Statistics
Matches: 78, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
61 76 0.97
62 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:313336 original size:265 final size:266
Alignment explanation
Indices: 312846--313382 Score: 1031
Period size: 265 Copynumber: 2.0 Consensus size: 266
312836 CACTATTATA
*
312846 AAATATAATGTTAAAAAGTATCACCTAAACAATTTTAGTAATTAAATGAATGATTATCATAACTA
1 AAATATAATGTTAAAAAGTATCACCTAAACAATTTTAATAATTAAATGAATGATTATCATAACTA
312911 AAATATAATTAAACATGAAATCAATCTAATATTTAATCATATTAAATAATCAAGAATAATAAATA
66 AAATATAATTAAACATGAAATCAATCTAATATTTAATCATATTAAATAATCAAGAATAATAAATA
312976 TTAGATTTACGAAAATGTACCTAAATTCATTGTTGAAGATTACTTAGAAGGTCGAGATCTTAAAG
131 TTAGATTTACGAAAATGTACCTAAATTCATTGTTGAAGATTACTTAGAAGGTCGAGATCTTAAAG
313041 ATTATCTTATGGTTGTGATATTCCAAGAATATAAAATTCTATTGAGTATAATCTCTTTGGCAAGA
196 ATTATCTTATGGTTGTGATATTCCAAGAATATAAAATTCTATTGAGTATAATCTCTTTGGCAAGA
313106 TAAGAG
261 TAAGAG
*
313112 AAATATAATGTT-AAAGGTATCACCTAAACAATTTTAATAATTAAATGAATGATTATCATAACTA
1 AAATATAATGTTAAAAAGTATCACCTAAACAATTTTAATAATTAAATGAATGATTATCATAACTA
313176 AAATATAATTAAACATGAAATCAATCTAATATTTAATCATATTAAATAATCAAGAATAATAAATA
66 AAATATAATTAAACATGAAATCAATCTAATATTTAATCATATTAAATAATCAAGAATAATAAATA
* *
313241 TTAGATTTGCGAAAATGTACCTGAATTCATTGTTGAAGATTACTTAGAAGGTCGAGATCTTAAAG
131 TTAGATTTACGAAAATGTACCTAAATTCATTGTTGAAGATTACTTAGAAGGTCGAGATCTTAAAG
313306 ATTATCTTATGGTTGTGATATTCCAAGAATATAAAATTCTATTGAGTATAATCTCTTTGGCAAGA
196 ATTATCTTATGGTTGTGATATTCCAAGAATATAAAATTCTATTGAGTATAATCTCTTTGGCAAGA
313371 TAAGAG
261 TAAGAG
313377 AAATAT
1 AAATAT
313383 GAAATGATCT
Statistics
Matches: 267, Mismatches: 4, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
265 255 0.96
266 12 0.04
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (266 bp):
AAATATAATGTTAAAAAGTATCACCTAAACAATTTTAATAATTAAATGAATGATTATCATAACTA
AAATATAATTAAACATGAAATCAATCTAATATTTAATCATATTAAATAATCAAGAATAATAAATA
TTAGATTTACGAAAATGTACCTAAATTCATTGTTGAAGATTACTTAGAAGGTCGAGATCTTAAAG
ATTATCTTATGGTTGTGATATTCCAAGAATATAAAATTCTATTGAGTATAATCTCTTTGGCAAGA
TAAGAG
Found at i:317928 original size:16 final size:16
Alignment explanation
Indices: 317907--317939 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
317897 TTTAACAAGA
317907 AAGCTCGACAATCCCT
1 AAGCTCGACAATCCCT
*
317923 AAGCTCGGCAATCCCT
1 AAGCTCGACAATCCCT
317939 A
1 A
317940 TTAAGAATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.36, G:0.15, T:0.18
Consensus pattern (16 bp):
AAGCTCGACAATCCCT
Found at i:320872 original size:22 final size:19
Alignment explanation
Indices: 320819--320872 Score: 56
Period size: 22 Copynumber: 2.7 Consensus size: 19
320809 TGCAAAAAAT
320819 GTATCGATACCATAATAGA
1 GTATCGATACCATAATAGA
*
320838 GTATC-AGTGCCATAATATAGTA
1 GTATCGA-TACCAT-A-ATAG-A
320860 GTATCGATACCAT
1 GTATCGATACCAT
320873 GGTAGGGGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
18 1 0.04
19 10 0.36
20 1 0.04
21 4 0.14
22 11 0.39
23 1 0.04
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.30
Consensus pattern (19 bp):
GTATCGATACCATAATAGA
Found at i:321297 original size:54 final size:54
Alignment explanation
Indices: 321214--321574 Score: 508
Period size: 54 Copynumber: 6.7 Consensus size: 54
321204 TTACCAAATA
*
321214 GGCACTAAGTGTGCAATTCATGGAATTCATCATAGGTTGATGAACAATCGTTTC
1 GGCACTAAGTGTGCAATTCATGGAATTCATCATATGTTGATGAACAATCGTTTC
* * *
321268 AGCACTAAGTGTGGAATTCATGGAATTCATCATAGGTTGATGAACAATCGTTTC
1 GGCACTAAGTGTGCAATTCATGGAATTCATCATATGTTGATGAACAATCGTTTC
* * * *
321322 AGCACTAAGTGTGCAATTCATGGAATTCATCATATGTTGATGAACACTCATTTT
1 GGCACTAAGTGTGCAATTCATGGAATTCATCATATGTTGATGAACAATCGTTTC
* * ** * *
321376 GGCACAAAGTGTACAATTCACAGAATTCATCATATGTTGATGAACAA-CTATTTT
1 GGCACTAAGTGTGCAATTCATGGAATTCATCATATGTTGATGAACAATC-GTTTC
* *
321430 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAACAACCGTTTC
1 GGCACTAAGTGTGCAATTCATGGAATTCATCATATGTTGATGAACAATCGTTTC
* * * *
321484 GGCACTAAGTGTGCAATTCACGAAATTCATTATATGTTGATGAACAACCGTTTC
1 GGCACTAAGTGTGCAATTCATGGAATTCATCATATGTTGATGAACAATCGTTTC
* *
321538 GGCACTAAGTGTGCAATTCATGAAATTCATCAAATGT
1 GGCACTAAGTGTGCAATTCATGGAATTCATCATATGT
321575 ATTTAGTTGG
Statistics
Matches: 282, Mismatches: 23, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
53 1 0.00
54 280 0.99
55 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (54 bp):
GGCACTAAGTGTGCAATTCATGGAATTCATCATATGTTGATGAACAATCGTTTC
Found at i:321322 original size:26 final size:26
Alignment explanation
Indices: 321239--321322 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
321229 ATTCATGGAA
321239 TTCATCATAGGTTGATGAACAATCGT
1 TTCATCATAGGTTGATGAACAATCGT
* * * *
321265 TTCAGCACTAAG-TG-TGGAATTC-ATGGAA
1 TTCATCA-TAGGTTGAT-GAA--CAATCG-T
321293 TTCATCATAGGTTGATGAACAATCGT
1 TTCATCATAGGTTGATGAACAATCGT
321319 TTCA
1 TTCA
321323 GCACTAAGTG
Statistics
Matches: 42, Mismatches: 8, Indels: 16
0.64 0.12 0.24
Matches are distributed among these distances:
25 1 0.02
26 16 0.38
27 12 0.29
28 12 0.29
29 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.33
Consensus pattern (26 bp):
TTCATCATAGGTTGATGAACAATCGT
Found at i:322721 original size:24 final size:22
Alignment explanation
Indices: 322677--322725 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 22
322667 TTCAAACCCA
322677 AAATCATATAAAAACTATTTAGT
1 AAATCATATAAAAACTATTTA-T
322700 AAATCAGTATAAAAA-TATTTTAT
1 AAATCA-TATAAAAACTA-TTTAT
322723 AAA
1 AAA
322726 ATAATTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.35
Consensus pattern (22 bp):
AAATCATATAAAAACTATTTAT
Found at i:322727 original size:24 final size:24
Alignment explanation
Indices: 322676--322727 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
322666 ATTCAAACCC
322676 AAAATCATATAAAAACTATTTAGT
1 AAAATCATATAAAAACTATTTAGT
322700 -AAATCAGTATAAAAA-TATTTTA-T
1 AAAATCA-TATAAAAACTA-TTTAGT
322723 AAAAT
1 AAAAT
322728 AATTCAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.35
Consensus pattern (24 bp):
AAAATCATATAAAAACTATTTAGT
Found at i:325869 original size:316 final size:305
Alignment explanation
Indices: 325282--325902 Score: 1102
Period size: 316 Copynumber: 2.0 Consensus size: 305
325272 TGAACTTTAG
325282 ATAGAATACTAATTTGACTCTTCAAATTTAAATAAATTATCATTTTAACCCTAACTTTAATAATA
1 ATAGAATACTAATTTGACTCTTCAAATTTAAATAAATTATCATTTTAACCCTAACTTTAATAATA
325347 TTAATTTGACCTTACATTTTAGATATAAAAATCAACTTTAATATCAATTTGATCCCAAAATTAGA
66 TTAATTTGACCTTACATTTTAGATATAAAAATCAACTTTAATATCAATTTGATCCCAAAATTAGA
325412 TAGAATACTAATTTGGCCCTTGAACTTTAGATAAAATATCATTTTAACCTAAACTTAACAAATCA
131 TAGAATACTAATTTGGCCCTTGAACTTTAGATAAAATATCATTTTAACCTAAACTTAACAAATCA
325477 TGTAGTCTCCCACCTCTAACCATCACTCACTATCGTCATCGTTGGTCACCGTCATTGTCGATGAC
196 TGTAGTCTCCCACCTCTAACCATCACTCACTATCGTCATCGTTGGTCACCGTCATTGTCGATGAC
325542 TGCTTGACATAAAAAAATTTCTAGTTCACTCA-TTTGTCTTCTAAA
261 TGCTTGACAT-AAAAAATTTCTAGTTCACTCATTTTGTCTTCTAAA
325587 ATAGAATACTAATTTGACTCTTCAAATTTAAATAAATTATCATTTTAACCCTAAACTTTATATAA
1 ATAGAATACTAATTTGACTCTTCAAATTTAAATAAATTATCATTTTAACCCT-AACTTTA-AT-A
*
325652 ATATTAATTTGACCTTACATTTTAGATAT-AATATCAAACTTTAAATATCAATTTGATCCCAAAA
63 ATATTAATTTGACCTTACATTTTAGATATAAAAATC-AACTTT-AATATCAATTTGATCCCAAAA
325716 TTAGATAGAATACTAATTTGGCCCTTGAACTTTAGATAAAATATCATTTTAACCCTAAACTTAAG
126 TTAGATAGAATACTAATTTGGCCCTTGAACTTTAGATAAAATATCATTTTAA-CCTAAACTT-A-
325781 ACAAAATATCATGTTAGTCTCCCACCTCTAACCATCACTCACTATCGTCATCGTTGGTCACCGTC
188 AC--AA-ATCATG-TAGTCTCCCACCTCTAACCATCACTCACTATCGTCATCGTTGGTCACCGTC
325846 ATTGTCGATGACTGCTTGACATAAAAAATTTCTAGTTCACTCATTTTGTCTTCTAAA
249 ATTGTCGATGACTGCTTGACATAAAAAATTTCTAGTTCACTCATTTTGTCTTCTAAA
325903 TGTGAATATG
Statistics
Matches: 302, Mismatches: 1, Indels: 15
0.95 0.00 0.05
Matches are distributed among these distances:
305 52 0.17
306 7 0.02
307 7 0.02
308 36 0.12
309 73 0.24
310 9 0.03
311 1 0.00
312 2 0.01
314 2 0.01
315 27 0.09
316 86 0.28
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.37
Consensus pattern (305 bp):
ATAGAATACTAATTTGACTCTTCAAATTTAAATAAATTATCATTTTAACCCTAACTTTAATAATA
TTAATTTGACCTTACATTTTAGATATAAAAATCAACTTTAATATCAATTTGATCCCAAAATTAGA
TAGAATACTAATTTGGCCCTTGAACTTTAGATAAAATATCATTTTAACCTAAACTTAACAAATCA
TGTAGTCTCCCACCTCTAACCATCACTCACTATCGTCATCGTTGGTCACCGTCATTGTCGATGAC
TGCTTGACATAAAAAATTTCTAGTTCACTCATTTTGTCTTCTAAA
Found at i:326807 original size:16 final size:16
Alignment explanation
Indices: 326786--326818 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
326776 ATGAAGGTAA
326786 TAATATTCTACTTCCG
1 TAATATTCTACTTCCG
326802 TAATATTCTACTTCCG
1 TAATATTCTACTTCCG
326818 T
1 T
326819 CCCATAGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.45
Consensus pattern (16 bp):
TAATATTCTACTTCCG
Found at i:330864 original size:18 final size:18
Alignment explanation
Indices: 330841--330877 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
330831 TGATTAAGTG
*
330841 GCATTGACACTTTGTCTC
1 GCATTGACACATTGTCTC
330859 GCATTGACACATTGTCTC
1 GCATTGACACATTGTCTC
330877 G
1 G
330878 AATCTTGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.19, C:0.27, G:0.19, T:0.35
Consensus pattern (18 bp):
GCATTGACACATTGTCTC
Found at i:336634 original size:30 final size:30
Alignment explanation
Indices: 336584--336654 Score: 106
Period size: 30 Copynumber: 2.4 Consensus size: 30
336574 TTGTACTGGA
* *
336584 ACTGATGGTGGACTAAGAGCTGCTGTTGGG
1 ACTGGTGGTGTACTAAGAGCTGCTGTTGGG
*
336614 ACTGGTGGTGTACTAGGAGCTGCTGTTGGG
1 ACTGGTGGTGTACTAAGAGCTGCTGTTGGG
*
336644 GCTGGTGGTGT
1 ACTGGTGGTGT
336655 TGATCGAACT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.14, C:0.13, G:0.44, T:0.30
Consensus pattern (30 bp):
ACTGGTGGTGTACTAAGAGCTGCTGTTGGG
Found at i:343676 original size:21 final size:19
Alignment explanation
Indices: 343638--343683 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
343628 ATTTAATCCT
343638 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
343658 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
343679 A-TAAT
1 ACTAAT
343684 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:344139 original size:11 final size:11
Alignment explanation
Indices: 344123--344148 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
344113 GTATCTCTCG
344123 ATGCTCTTACA
1 ATGCTCTTACA
344134 ATGCTCTTACA
1 ATGCTCTTACA
344145 ATGC
1 ATGC
344149 CGATACATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (11 bp):
ATGCTCTTACA
Found at i:346164 original size:42 final size:42
Alignment explanation
Indices: 346118--346202 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
346108 ACTATAACTA
* * * *
346118 ATGGTAAAGGCTCAAACCTTTAACCAGTCCATGCTTAAAGTT
1 ATGGTAAAGGCTCAAACCTCTAACCACTCCATACTGAAAGTT
*
346160 ATGGTAAAGGCTCCAACCTCTAACCACTCCATACTGAAAGTT
1 ATGGTAAAGGCTCAAACCTCTAACCACTCCATACTGAAAGTT
346202 A
1 A
346203 GGTTCATCTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (42 bp):
ATGGTAAAGGCTCAAACCTCTAACCACTCCATACTGAAAGTT
Found at i:349089 original size:26 final size:25
Alignment explanation
Indices: 349060--349115 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 25
349050 ACCGTAGTGC
349060 TACACATAAGGTCGTGCCCACCATAA
1 TACACATAAGGTCGTGCCCACCAT-A
349086 TACACATAAGGTCGTGCCCACCATA
1 TACACATAAGGTCGTGCCCACCATA
349111 TACAC
1 TACAC
349116 TTAGTGTCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 6 0.20
26 24 0.80
ACGTcount: A:0.34, C:0.32, G:0.14, T:0.20
Consensus pattern (25 bp):
TACACATAAGGTCGTGCCCACCATA
Found at i:350749 original size:30 final size:31
Alignment explanation
Indices: 350709--350770 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
350699 AATTACCATT
*
350709 AAACCGAGACACCT-AACCTTATCATCTTCC
1 AAACCAAGACACCTAAACCTTATCATCTTCC
350739 AAACCAAGACACCTAAACCTTATCATCTTCC
1 AAACCAAGACACCTAAACCTTATCATCTTCC
350770 A
1 A
350771 TAAGTCAAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 13 0.43
31 17 0.57
ACGTcount: A:0.37, C:0.35, G:0.05, T:0.23
Consensus pattern (31 bp):
AAACCAAGACACCTAAACCTTATCATCTTCC
Found at i:353031 original size:41 final size:41
Alignment explanation
Indices: 352827--353131 Score: 184
Period size: 41 Copynumber: 7.4 Consensus size: 41
352817 ATTAACAGCA
* * * *
352827 TTTTTCGACAAACGCCG-TAGAAAAT-CGTACTTTAGTGGCC
1 TTTTTAGACAAACGCCGCTA-AAACTAAGTACTTTAGTGGCG
* * *
352867 TTTATTCGACAAACGCCACTAAAGA-TAAGTATTTTAGTGGCG
1 TTT-TTAGACAAACGCCGCTAAA-ACTAAGTACTTTAGTGGCG
* * * * * *
352909 TTTGTAAACAAACGCCGCCATAGAA-TCA-TTCTTTAGTGGCA
1 TTTTTAGACAAACGCCG-C-TAAAACTAAGTACTTTAGTGGCG
* * ** *
352950 TTTTAAAACAAACATCGC-AAAA--AAGGTACATATATCGTGGCG
1 TTTTTAGACAAACGCCGCTAAAACTAA-GTAC-T-T-TAGTGGCG
*
352992 TTTTTAGATAAACGCCGCTAAAACCT-AGTACTTTAGTGGCG
1 TTTTTAGACAAACGCCGCTAAAA-CTAAGTACTTTAGTGGCG
* * *
353033 TTTTAAG-CAAAACGCCGCTAAAACTCA-TACTTTAGAGGCG
1 TTTTTAGAC-AAACGCCGCTAAAACTAAGTACTTTAGTGGCG
* *
353073 TTTATTGGACAAACACCGCTAAAGA-TAAGTACTTTAGTGGCG
1 TTT-TTAGACAAACGCCGCTAAA-ACTAAGTACTTTAGTGGCG
*
353115 TTTTTAAACAAACGCCG
1 TTTTTAGACAAACGCCG
353132 TAATAGGTAC
Statistics
Matches: 205, Mismatches: 39, Indels: 41
0.72 0.14 0.14
Matches are distributed among these distances:
37 1 0.00
38 3 0.01
39 2 0.01
40 22 0.11
41 105 0.51
42 59 0.29
43 8 0.04
44 4 0.02
45 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (41 bp):
TTTTTAGACAAACGCCGCTAAAACTAAGTACTTTAGTGGCG
Found at i:355194 original size:21 final size:21
Alignment explanation
Indices: 355168--355208 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
355158 CTTTGATTTA
355168 TTGTTATGGATTTCAAGTTTC
1 TTGTTATGGATTTCAAGTTTC
355189 TTGTTATGGATTTCAAGTTT
1 TTGTTATGGATTTCAAGTTT
355209 GTGTCTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.07, G:0.20, T:0.54
Consensus pattern (21 bp):
TTGTTATGGATTTCAAGTTTC
Found at i:355558 original size:128 final size:128
Alignment explanation
Indices: 355330--355755 Score: 541
Period size: 128 Copynumber: 3.3 Consensus size: 128
355320 TGAAAGGTAA
* * ** * * **
355330 TTAGCGGCGTTTGTATCCAAAAAACACCACTATAGGTCT-GACCTTTTGCGGCGTTTATTTAAAA
1 TTAGCGGCGTTTGT-TCC-AAAAACGCCGCTATAAATCTCGACCATTAGCGGCGTTTATTCCAAA
* * *** * *
355394 AACGCTGCTATAGATCTAACGTTTAGCTATGTTTGTTCCAAAAACGCCGCTATTGATCTCGACCA
64 AACGCCGCTATAGATCTGACGTTTAGCCGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCT
** *
355459 TTAGCGGCGTTTGTTCCAAAAGTGCCGCTACT-GATCTCGACCATTAGCGGCGTTTATTCCAAAA
1 TTAGCGGCGTTTGTTCCAAAAACGCCGCTA-TAAATCTCGACCATTAGCGGCGTTTATTCCAAAA
*
355523 ACGCCGCTATAGATCTGACGTTTAGCCGCGTTTGTTCCAAAAACGTCGCTATAGATCTCGACCT
65 ACGCCGCTATAGATCTGACGTTTAGCCGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCT
* * * *
355587 TTAGCGGTGTTTGTTCCAAAAACGCCGCTATAAATCTCGACCATTAGCGACTTTTGTTCCAAAAA
1 TTAGCGGCGTTTGTTCCAAAAACGCCGCTATAAATCTCGACCATTAGCGGCGTTTATTCCAAAAA
* * * * *
355652 CGCCGCTATAGATCTCGACCTTTAGCGGCGTTTGTTTCAAAAACACCGTTATAGATCTCGACCT
66 CGCCGCTATAGATCT-GACGTTTAGCCGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCT
*
355716 TTAGAGGCGTTTGTTCCAAAAACGCCGCTATAAATCTCGA
1 TTAGCGGCGTTTGTTCCAAAAACGCCGCTATAAATCTCGA
355756 TTTTTTGCAA
Statistics
Matches: 261, Mismatches: 32, Indels: 8
0.87 0.11 0.03
Matches are distributed among these distances:
127 14 0.05
128 153 0.59
129 94 0.36
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (128 bp):
TTAGCGGCGTTTGTTCCAAAAACGCCGCTATAAATCTCGACCATTAGCGGCGTTTATTCCAAAAA
CGCCGCTATAGATCTGACGTTTAGCCGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCT
Found at i:355770 original size:43 final size:43
Alignment explanation
Indices: 355330--355755 Score: 509
Period size: 43 Copynumber: 9.9 Consensus size: 43
355320 TGAAAGGTAA
* * *
355330 TTAGCGGCGTTTGTATCCAAAAAACACCACTATAGGTCT-GACCT
1 TTAGCGGCGTTTGT-TCC-AAAAACGCCGCTATAGATCTCGACCT
* * ** * * *
355374 TTTGCGGCGTTTATTTAAAAAACGCTGCTATAGATCT-AACGT
1 TTAGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCT
*** * *
355416 TTAGCTATGTTTGTTCCAAAAACGCCGCTATTGATCTCGACCA
1 TTAGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCT
** *
355459 TTAGCGGCGTTTGTTCCAAAAGTGCCGCTACT-GATCTCGACCA
1 TTAGCGGCGTTTGTTCCAAAAACGCCGCTA-TAGATCTCGACCT
* *
355502 TTAGCGGCGTTTATTCCAAAAACGCCGCTATAGATCT-GACGT
1 TTAGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCT
* *
355544 TTAGCCGCGTTTGTTCCAAAAACGTCGCTATAGATCTCGACCT
1 TTAGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCT
* * *
355587 TTAGCGGTGTTTGTTCCAAAAACGCCGCTATAAATCTCGACCA
1 TTAGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCT
* *
355630 TTAGCGACTTTTGTTCCAAAAACGCCGCTATAGATCTCGACCT
1 TTAGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCT
* * *
355673 TTAGCGGCGTTTGTTTCAAAAACACCGTTATAGATCTCGACCT
1 TTAGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCT
* *
355716 TTAGAGGCGTTTGTTCCAAAAACGCCGCTATAAATCTCGA
1 TTAGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGA
355756 TTTTTTGCAA
Statistics
Matches: 322, Mismatches: 56, Indels: 9
0.83 0.14 0.02
Matches are distributed among these distances:
42 85 0.26
43 224 0.70
44 13 0.04
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (43 bp):
TTAGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCT
Found at i:367555 original size:25 final size:25
Alignment explanation
Indices: 367522--367572 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
367512 CCCTTAGTTG
367522 TAAGATGATTACAAAGTAATATATC
1 TAAGATGATTACAAAGTAATATATC
* *
367547 TAAGGTGATTATAAAGTAATATATC
1 TAAGATGATTACAAAGTAATATATC
367572 T
1 T
367573 TCTAAATACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (25 bp):
TAAGATGATTACAAAGTAATATATC
Found at i:368362 original size:23 final size:23
Alignment explanation
Indices: 368292--368384 Score: 87
Period size: 23 Copynumber: 4.0 Consensus size: 23
368282 ACCATTTTTA
* * *
368292 CCTCTACTTCAACTGTTCTGCCG
1 CCTCTACTCCAACTGCTCCGCCG
* **
368315 CCACTACTCCAACTGCTTTGCCG
1 CCTCTACTCCAACTGCTCCGCCG
*
368338 CCTCTACTCCAACTGCTCCGTCG
1 CCTCTACTCCAACTGCTCCGCCG
* * *
368361 CCATGTTCCCCAACTGCTCCGCCG
1 CC-TCTACTCCAACTGCTCCGCCG
368385 TCATGTTCCC
Statistics
Matches: 57, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
23 40 0.70
24 17 0.30
ACGTcount: A:0.14, C:0.45, G:0.14, T:0.27
Consensus pattern (23 bp):
CCTCTACTCCAACTGCTCCGCCG
Found at i:368377 original size:24 final size:24
Alignment explanation
Indices: 368346--368399 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
368336 CGCCTCTACT
*
368346 CCAACTGCTCCGTCGCCATGTTCC
1 CCAACTGCTCCGCCGCCATGTTCC
*
368370 CCAACTGCTCCGCCGTCATGTTCC
1 CCAACTGCTCCGCCGCCATGTTCC
368394 CCAACT
1 CCAACT
368400 AGTTGCTGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.15, C:0.46, G:0.15, T:0.24
Consensus pattern (24 bp):
CCAACTGCTCCGCCGCCATGTTCC
Found at i:375406 original size:5 final size:5
Alignment explanation
Indices: 375391--375469 Score: 74
Period size: 5 Copynumber: 15.8 Consensus size: 5
375381 CATCCATCAG
* *
375391 GAAAA -AAAA GAAAA GAAAGA GAAAAA AAAAA GAAAA CAAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAA-A G-AAAA GAAAA GAAAA -GAAAA GAAAA
* *
375438 GAGAA -AAGA GAAAA GAAAA GAAAA -AAAA GAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAA
375470 TTGAATCAAG
Statistics
Matches: 60, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
4 10 0.17
5 40 0.67
6 7 0.12
7 3 0.05
ACGTcount: A:0.81, C:0.01, G:0.18, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:375417 original size:19 final size:18
Alignment explanation
Indices: 375393--375460 Score: 61
Period size: 17 Copynumber: 3.8 Consensus size: 18
375383 TCCATCAGGA
375393 AAAAAAAGAAAAGAAAGAG
1 AAAAAAA-AAAAGAAAGAG
*
375412 -AAAAAAAAAAGAAA-AC
1 AAAAAAAAAAAGAAAGAG
*
375428 AAAAAGAAAAGAGAAA-AG
1 AAAAA-AAAAAAGAAAGAG
* *
375446 AGAAAAGAAAAGAAA
1 AAAAAAAAAAAGAAA
375461 AAAAAGAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
16 1 0.02
17 20 0.49
18 20 0.49
ACGTcount: A:0.81, C:0.01, G:0.18, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAGAAAGAG
Found at i:375431 original size:12 final size:11
Alignment explanation
Indices: 375392--375465 Score: 85
Period size: 11 Copynumber: 6.5 Consensus size: 11
375382 ATCCATCAGG
375392 AAAAAAAAGAA
1 AAAAAAAAGAA
* *
375403 AAGAAAGAGAA
1 AAAAAAAAGAA
375414 AAAAAAAAGAA
1 AAAAAAAAGAA
*
375425 AACAAAAAGAA
1 AAAAAAAAGAA
*
375436 AAGAGAAAAGAGA
1 AA-AAAAAAGA-A
*
375449 AAAGAAAAGAA
1 AAAAAAAAGAA
375460 AAAAAA
1 AAAAAA
375466 GAAATTGAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
11 36 0.68
12 14 0.26
13 3 0.06
ACGTcount: A:0.82, C:0.01, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:375432 original size:33 final size:33
Alignment explanation
Indices: 375391--375469 Score: 108
Period size: 33 Copynumber: 2.4 Consensus size: 33
375381 CATCCATCAG
*
375391 GAAAAAAAAGAAAAGA-AAGAGA-AAAAAAAAA
1 GAAAAAAAAGAAAAGAGAAAAGAGAAAAAAAAA
*
375422 GAAAACAAAAAGAAAAGAGAAAAGAGAAAAGAAAA
1 G-AAA-AAAAAGAAAAGAGAAAAGAGAAAAAAAAA
375457 GAAAAAAAAGAAA
1 GAAAAAAAAGAAA
375470 TTGAATCAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
31 1 0.02
32 3 0.07
33 21 0.50
34 8 0.19
35 9 0.21
ACGTcount: A:0.81, C:0.01, G:0.18, T:0.00
Consensus pattern (33 bp):
GAAAAAAAAGAAAAGAGAAAAGAGAAAAAAAAA
Found at i:377003 original size:51 final size:50
Alignment explanation
Indices: 376872--377116 Score: 330
Period size: 51 Copynumber: 4.8 Consensus size: 50
376862 GGTCCATATT
* *
376872 ATCCATGTGGGTATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTT
1 ATCCATGTGGGCATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTA
* * * *
376922 ATCCATATGGGTATCTTGAAGGCTCACATCAGGATGAAATGATAGAAGTA
1 ATCCATGTGGGCATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTA
* * *
376972 ATCTATGTGGGACATCTTAAAGGCTCACATCAGCATGAAAAGATATAAGTA
1 ATCCATGTGGG-CATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTA
* *
377023 ATCCATATGGGGCATCTTGAAGGCTCACATCAACATGAAAAAGATAGAAGTA
1 ATCCATGT-GGGCATCTTGAAGGCTCACATCAGCATG-AAAAGATAGAAGTA
*
377075 ATCCATGTGGGACATCTTGAAGGCTTACA-CTAGCATGAAAAG
1 ATCCATGTGGG-CATCTTGAAGGCTCACATC-AGCATGAAAAG
377117 GTTAGGATAT
Statistics
Matches: 171, Mismatches: 19, Indels: 9
0.86 0.10 0.05
Matches are distributed among these distances:
50 55 0.32
51 72 0.42
52 44 0.26
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.24
Consensus pattern (50 bp):
ATCCATGTGGGCATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTA
Found at i:377110 original size:103 final size:101
Alignment explanation
Indices: 376872--377116 Score: 359
Period size: 103 Copynumber: 2.4 Consensus size: 101
376862 GGTCCATATT
* * *
376872 ATCCATGTGGG-TATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTTATCCATATGGGTAT
1 ATCCATGTGGGACATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTAATCCATATGGGCAT
** *
376936 CTTGAAGGCTCACATCAGGATGAAATGATAGAAGTA
66 CTTGAAGGCTCACATCAACATGAAAAGATAGAAGTA
* * *
376972 ATCTATGTGGGACATCTTAAAGGCTCACATCAGCATGAAAAGATATAAGTAATCCATATGGGGCA
1 ATCCATGTGGGACATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTAATCCATAT-GGGCA
377037 TCTTGAAGGCTCACATCAACATGAAAAAGATAGAAGTA
65 TCTTGAAGGCTCACATCAACATG-AAAAGATAGAAGTA
*
377075 ATCCATGTGGGACATCTTGAAGGCTTACA-CTAGCATGAAAAG
1 ATCCATGTGGGACATCTTGAAGGCTCACATC-AGCATGAAAAG
377117 GTTAGGATAT
Statistics
Matches: 129, Mismatches: 12, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
100 10 0.08
101 43 0.33
102 26 0.20
103 50 0.39
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.24
Consensus pattern (101 bp):
ATCCATGTGGGACATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTAATCCATATGGGCAT
CTTGAAGGCTCACATCAACATGAAAAGATAGAAGTA
Found at i:377648 original size:14 final size:14
Alignment explanation
Indices: 377631--377658 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
377621 AACCAATGAT
377631 TATGGTGTTGAACC
1 TATGGTGTTGAACC
377645 TATGGTGTTGAACC
1 TATGGTGTTGAACC
377659 AATGTTGCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.29, T:0.36
Consensus pattern (14 bp):
TATGGTGTTGAACC
Found at i:379017 original size:173 final size:176
Alignment explanation
Indices: 378667--379026 Score: 521
Period size: 173 Copynumber: 2.1 Consensus size: 176
378657 CTATATCCCA
* * *
378667 GATTTGTAAGTCCTACTGGTCATCCATAAGACCGTCAGTACATGATGTTTTCAAATGAGATTTTA
1 GATTTGTAAGTCCTACGGGCCATCCATAAGACCGTCAGTACATGATGTTTTCAAATAAGATTTTA
* * * *
378732 GAAACCAAGCCTTCGGGGGTTTTCTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAAC
66 AAAACCAAGCCTTCGGGGG-TTTCTAACTATCTCAAAAGAGCTGTTAAAGGAAGCCAAGCCTAAC
* * *
378797 AAAAGGGTTCCTTGACAACTAAAAAACTAAGCCTTCAGCGTTTTCTT
130 AAAAGGGTTCATTGACAACTAAAAAACTAAGCCTTCAGAGGTTTCTT
* *
378844 GATTTGTAAGTCCTACGGGCCATCCATAAGACCTTCAGTGC-TGGATGTTTTCAAATAAGATTTT
1 GATTTGTAAGTCCTACGGGCCATCCATAAGACCGTCAGTACAT-GATGTTTTCAAATAAGATTTT
* *
378908 AAAAATCAAGCCTTCGGGGG-TT-T-ACTATCTCAAAAGAGCTGTTAAAGGAAGCCGAGCCTAAC
65 AAAAACCAAGCCTTCGGGGGTTTCTAACTATCTCAAAAGAGCTGTTAAAGGAAGCCAAGCCTAAC
* * *
378970 AAAGGGGTTCATTGACAACTAAGAAACTAAGCCTTCGGAGGTTTCTT
130 AAAAGGGTTCATTGACAACTAAAAAACTAAGCCTTCAGAGGTTTCTT
379017 GATTTGTAAG
1 GATTTGTAAG
379027 CCCCATCTAT
Statistics
Matches: 165, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
173 86 0.52
174 1 0.01
175 2 0.01
176 1 0.01
177 75 0.45
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (176 bp):
GATTTGTAAGTCCTACGGGCCATCCATAAGACCGTCAGTACATGATGTTTTCAAATAAGATTTTA
AAAACCAAGCCTTCGGGGGTTTCTAACTATCTCAAAAGAGCTGTTAAAGGAAGCCAAGCCTAACA
AAAGGGTTCATTGACAACTAAAAAACTAAGCCTTCAGAGGTTTCTT
Found at i:380273 original size:50 final size:52
Alignment explanation
Indices: 380218--380326 Score: 152
Period size: 50 Copynumber: 2.2 Consensus size: 52
380208 CTTATTCATC
*
380218 AATATATCCGTAACAATTATTTTGAACAGAATCA-AGAACATTC-TTTTGGT
1 AATATATCCGTAACAATTATTGTGAACAGAATCATAGAACATTCTTTTTGGT
* ***
380268 AATATATCTGTAATGTTTATTGTGAACAGAATCATAGAACATTCTTTTTGGT
1 AATATATCCGTAACAATTATTGTGAACAGAATCATAGAACATTCTTTTTGGT
380320 AAT-TATC
1 AATATATC
380327 ACTATTGATG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
50 29 0.56
51 13 0.25
52 10 0.19
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (52 bp):
AATATATCCGTAACAATTATTGTGAACAGAATCATAGAACATTCTTTTTGGT
Found at i:382640 original size:2 final size:2
Alignment explanation
Indices: 382633--382663 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
382623 TCTAATGATT
382633 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
382664 TCACTAATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:387537 original size:15 final size:15
Alignment explanation
Indices: 387519--387562 Score: 61
Period size: 17 Copynumber: 2.8 Consensus size: 15
387509 ACCGGCTTCG
387519 GTTTTAAAAAAACCA
1 GTTTTAAAAAAACCA
387534 GTTTTTTAAAAAAACCA
1 G--TTTTAAAAAAACCA
*
387551 GTTATAAAAAAA
1 GTTTTAAAAAAA
387563 TCGATTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 11 0.42
17 15 0.58
ACGTcount: A:0.55, C:0.09, G:0.07, T:0.30
Consensus pattern (15 bp):
GTTTTAAAAAAACCA
Found at i:387542 original size:17 final size:17
Alignment explanation
Indices: 387520--387553 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
387510 CCGGCTTCGG
387520 TTTTAAAAAAACCAGTT
1 TTTTAAAAAAACCAGTT
387537 TTTTAAAAAAACCAGTT
1 TTTTAAAAAAACCAGTT
387554 ATAAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCAGTT
Found at i:388743 original size:33 final size:32
Alignment explanation
Indices: 388678--388775 Score: 160
Period size: 32 Copynumber: 3.0 Consensus size: 32
388668 AACTCAACAT
* * *
388678 AATTGAAATACTTAAATACTTCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCAAGTTCGATA
388710 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
388743 AATTCAAATACTTAAAAACTTCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCAAGTTCGATA
388775 A
1 A
388776 TTGAAACAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
32 31 0.50
33 31 0.50
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.33
Consensus pattern (32 bp):
AATTCAAATACTTAAAAACTTCAAGTTCGATA
Found at i:388794 original size:21 final size:21
Alignment explanation
Indices: 388770--388810 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
388760 ACTTCAAGTT
388770 CGATAATTGAAACAAAGTTTG
1 CGATAATTGAAACAAAGTTTG
*
388791 CGATAATTGAAATAAAGTTT
1 CGATAATTGAAACAAAGTTT
388811 AAAAATAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.07, G:0.17, T:0.32
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTG
Found at i:400630 original size:3 final size:3
Alignment explanation
Indices: 400622--400674 Score: 97
Period size: 3 Copynumber: 17.3 Consensus size: 3
400612 AATATTTATT
400622 TAA TAA TAA TAA TAA TAA TAA TAA TAA TATA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
400668 TAA TAA T
1 TAA TAA T
400675 TTTAAAATAA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:401114 original size:45 final size:45
Alignment explanation
Indices: 401041--401154 Score: 147
Period size: 45 Copynumber: 2.5 Consensus size: 45
401031 TCAAAAAGCT
* * * **
401041 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGA
1 CCCGAAGGC--TTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
401088 CCCGGAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
401133 CCCGAAGGTTTTGAAAACATCA
1 CCCGAAGGCTTTGAAAACATCA
401155 AAAAGCTCCC
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
45 51 0.86
47 8 0.14
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.25
Consensus pattern (45 bp):
CCCGAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
Found at i:401155 original size:121 final size:121
Alignment explanation
Indices: 400934--401472 Score: 827
Period size: 121 Copynumber: 4.5 Consensus size: 121
400924 TAAAATCTCA
* * * * * * *
400934 TTTGAAAACATCCTGCACTGGAGGTCTTATGGATGGCCCTG-AGGTCTT---ATCATCTTGCACT
1 TTTGAAAACATCCTGCACTGTAGGGCTTACGGATGACCC-GAAGGTTTTGAAAACATCATGCACT
* * * * *
400995 GTAGGTCTTACAGATGACCCGGAGGCTTTGAAAATATCAAAAAGCTCCCGAAGGCTT
65 GAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
* * * *
401052 TTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGGAGGCTTTGAAAACATCATGCACTG
1 TTTGAAAACATCCTGCACTGTAGGGCTTACGGATGACCCGAAGGTTTTGAAAACATCATGCACTG
401117 AAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
66 AAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
401173 TTTGAAAACATCCTGCACTGTAGGGCTTACGGATGACCCGAAGGTTTTGAAAACATCATGCACTG
1 TTTGAAAACATCCTGCACTGTAGGGCTTACGGATGACCCGAAGGTTTTGAAAACATCATGCACTG
* *
401238 AAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAGAAAGCTCCCGATGGCTT
66 AAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
* * *
401294 TTTAAAAACATCATGCACTGTAGGGCTTACGGATGACCCGAAGGTTTTGAAAACATCATGTACTG
1 TTTGAAAACATCCTGCACTGTAGGGCTTACGGATGACCCGAAGGTTTTGAAAACATCATGCACTG
401359 AAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
66 AAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
*
401415 TTTGAAAACATCTTGCACTGTAGGGCTTACAGG-TGACCCGAAGGTTTTGAAAACATCA
1 TTTGAAAACATCCTGCACTGTAGGGCTTAC-GGATGACCCGAAGGTTTTGAAAACATCA
401473 AAAAGCTCCC
Statistics
Matches: 392, Mismatches: 24, Indels: 7
0.93 0.06 0.02
Matches are distributed among these distances:
117 1 0.00
118 42 0.11
121 347 0.89
122 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (121 bp):
TTTGAAAACATCCTGCACTGTAGGGCTTACGGATGACCCGAAGGTTTTGAAAACATCATGCACTG
AAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
Found at i:401228 original size:45 final size:45
Alignment explanation
Indices: 401162--401275 Score: 183
Period size: 45 Copynumber: 2.5 Consensus size: 45
401152 TCAAAAAGCT
* * *
401162 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGGCTTACGGATGA
1 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
401209 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
401254 CCCGAAGGTTTTGAAAACATCA
1 CCCGAAGGTTTTGAAAACATCA
401276 GAAAGCTCCC
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
45 56 0.88
47 8 0.12
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.24
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
Found at i:401349 original size:45 final size:45
Alignment explanation
Indices: 401293--401396 Score: 172
Period size: 45 Copynumber: 2.3 Consensus size: 45
401283 CCCGATGGCT
* * *
401293 TTTTAAAAACATCATGCACTGTAGGGCTTACGGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
*
401338 TTTTGAAAACATCATGTACTGAAGGGCTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
401383 TTTTGAAAACATCA
1 TTTTGAAAACATCA
401397 AAAAGCTCCC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (45 bp):
TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
Found at i:401418 original size:76 final size:75
Alignment explanation
Indices: 401330--401519 Score: 292
Period size: 76 Copynumber: 2.5 Consensus size: 75
401320 TTACGGATGA
*
401330 CCCGAAGG-TTTTGAAAACATCATGTACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACA
1 CCCGAAGGCTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACA
401394 TCAAAAAGCT
66 TCAAAAAGCT
* * *
401404 CCCGAAGGCTTTTTGAAAACATCTTGCACTGTAGGGCTTACAGGTGACCCGAAGGTTTTGAAAAC
1 CCCGAAGGC-TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAAC
401469 ATCAAAAAGCT
65 ATCAAAAAGCT
* * *
401480 CCCGAAGGCCTTTTGAAAACATCCTGCACTGTAGGTCTTA
1 CCCGAAGG-CTTTTGAAAACATCATGCACTGAAGGGCTTA
401520 TGGATGTGGG
Statistics
Matches: 107, Mismatches: 6, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
74 8 0.07
76 98 0.92
77 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.25
Consensus pattern (75 bp):
CCCGAAGGCTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACA
TCAAAAAGCT
Found at i:402651 original size:54 final size:54
Alignment explanation
Indices: 402578--402714 Score: 143
Period size: 54 Copynumber: 2.6 Consensus size: 54
402568 ACCATAACTG
* * * * * * *
402578 GTTCGTAAA-CACTTGACAACATATTCATCCTTTCTTTTGATTTCT-GCATGGAT
1 GTTCGTAAAGCATTTGACAACACATTCATCCTTTCATGTGACTTATGGC-TAGAT
* * * * *
402631 TTTCGTAAAGCATTTAACAACACATTTATCGTTTCATGTGGCTTATGGCTAGAT
1 GTTCGTAAAGCATTTGACAACACATTCATCCTTTCATGTGACTTATGGCTAGAT
402685 GTTCGTAAAGCATTTGACAACACATTCATC
1 GTTCGTAAAGCATTTGACAACACATTCATC
402715 ATTTTCTGTG
Statistics
Matches: 67, Mismatches: 15, Indels: 3
0.79 0.18 0.04
Matches are distributed among these distances:
53 8 0.12
54 57 0.85
55 2 0.03
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.38
Consensus pattern (54 bp):
GTTCGTAAAGCATTTGACAACACATTCATCCTTTCATGTGACTTATGGCTAGAT
Found at i:407240 original size:1 final size:1
Alignment explanation
Indices: 407236--407269 Score: 59
Period size: 1 Copynumber: 34.0 Consensus size: 1
407226 TCCTTTTTCC
*
407236 TTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
407270 ATTAAACGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:409940 original size:43 final size:44
Alignment explanation
Indices: 409859--409941 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 44
409849 ACGTGCATCA
* * *
409859 AACAAAACTTTTACATGCAGGGGACAGCTTTCAGTCCTAATTTC
1 AACAAAACTTTTACATACAGGGGACAACTTTCACTCCTAATTTC
* * *
409903 AACAAAAC-TTTACATATAGGGGATAACTTTCCCTCCTAA
1 AACAAAACTTTTACATACAGGGGACAACTTTCACTCCTAA
409942 CTTCTCTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
43 25 0.76
44 8 0.24
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (44 bp):
AACAAAACTTTTACATACAGGGGACAACTTTCACTCCTAATTTC
Found at i:412759 original size:24 final size:26
Alignment explanation
Indices: 412732--412790 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
412722 ATAATTTAAA
412732 TAAAATA-AAATAAA-A-TATATATAT
1 TAAAATATAAATAAATATTAT-TATAT
* *
412756 TAAAAAATAAATAAATATTATTATTT
1 TAAAATATAAATAAATATTATTATAT
412782 TAAAATATA
1 TAAAATATA
412791 TATATATGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 6 0.21
25 7 0.24
26 13 0.45
27 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
TAAAATATAAATAAATATTATTATAT
Found at i:412767 original size:20 final size:22
Alignment explanation
Indices: 412738--412778 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
412728 TAAATAAAAT
*
412738 AAAATAAAATATATA-TATTAA
1 AAAATAAAATAAATATTATTAA
412759 AAAAT-AAATAAATATTATTA
1 AAAATAAAATAAATATTATTA
412779 TTTTAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAATAAAATAAATATTATTAA
Found at i:412793 original size:2 final size:2
Alignment explanation
Indices: 412786--412827 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
412776 TTATTTTAAA
* * *
412786 AT AT AT AT AT AT GT AT AT AT AT AT AT AT TT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
412828 TTTTATATGA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (2 bp):
AT
Found at i:412826 original size:14 final size:14
Alignment explanation
Indices: 412786--412835 Score: 64
Period size: 14 Copynumber: 3.4 Consensus size: 14
412776 TTATTTTAAA
412786 ATATATATATATGTAT
1 ATATATATATAT-T-T
412802 ATATATATATATTT
1 ATATATATATATTT
*
412816 ATATTTATATATTT
1 ATATATATATATTT
*
412830 TTATAT
1 ATATAT
412836 GACTAAGATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
14 18 0.58
15 1 0.03
16 12 0.39
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (14 bp):
ATATATATATATTT
Found at i:412828 original size:8 final size:8
Alignment explanation
Indices: 412786--412835 Score: 50
Period size: 8 Copynumber: 6.5 Consensus size: 8
412776 TTATTTTAAA
*
412786 ATATATAT
1 ATATTTAT
*
412794 ATATGTAT
1 ATATTTAT
*
412802 ATATATAT
1 ATATTTAT
412810 ATA-TT-T
1 ATATTTAT
412816 ATATTTAT
1 ATATTTAT
*
412824 ATATTTTT
1 ATATTTAT
412832 ATAT
1 ATAT
412836 GACTAAGATA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
6 4 0.11
7 3 0.08
8 29 0.81
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (8 bp):
ATATTTAT
Found at i:412832 original size:16 final size:16
Alignment explanation
Indices: 412786--412835 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
412776 TTATTTTAAA
*
412786 ATATATATATATGTAT
1 ATATATATATATTTAT
412802 ATATATATATATTTAT
1 ATATATATATATTTAT
* *
412818 ATTTATATATTTTTAT
1 ATATATATATATTTAT
412834 AT
1 AT
412836 GACTAAGATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (16 bp):
ATATATATATATTTAT
Found at i:414198 original size:3 final size:3
Alignment explanation
Indices: 414190--414248 Score: 91
Period size: 3 Copynumber: 19.3 Consensus size: 3
414180 AATATTTATT
**
414190 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TATA TGT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
414236 TAA TAA TAA TAA T
1 TAA TAA TAA TAA T
414249 TTTAAAATTA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
3 49 0.96
4 2 0.04
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:415504 original size:15 final size:16
Alignment explanation
Indices: 415466--415509 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
415456 CATGTCACAT
415466 TTTTTTAAAATAAAATA
1 TTTTTT-AAATAAAATA
* *
415483 TTATTTAAA-AATATA
1 TTTTTTAAATAAAATA
415498 TTTTTTAAATAA
1 TTTTTTAAATAA
415510 TTTGAACCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 13 0.57
16 5 0.22
17 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTTTTAAATAAAATA
Found at i:418032 original size:3 final size:3
Alignment explanation
Indices: 418024--418104 Score: 117
Period size: 3 Copynumber: 27.0 Consensus size: 3
418014 TTAATATATT
* * *
418024 TAA TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
418072 TAA TAA TAA TAA TTA TAG TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
418105 ATAAATCAAA
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:418537 original size:124 final size:123
Alignment explanation
Indices: 418344--418781 Score: 452
Period size: 124 Copynumber: 3.6 Consensus size: 123
418334 GAGTCATTCC
* * *
418344 AAAGGTTGAATAAGCTCTTCTTATTTTGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC-TTCTTCTTCAGATGAGTTCTTCTCATT
* * * * * *
418409 ATGAACTTTCTCTGGAAAGGTTGATGCTAATCTATCTGCTTTTTTGATAAAAAT-TATGCA
65 ATGAACTTTCTCTGGAAAAGTTGATGCCAATCTATCTCCTTCTGTGAT-AAAATCGA-GCA
* * *
418469 AAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTA
1 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
* * ***
418534 TGAACTTTCTCTGGAAAAGTTGGTGCCGATCTATCTCCTTCTGTGATAGCGTCGAGCA
66 TGAACTTTCTCTGGAAAAGTTGATGCCAATCTATCTCCTTCTGTGATAAAATCGAGCA
* * *
418592 AAAGATTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTC-TTCTTCAGATGAGTTCTTCTCATT
** * * * * *
418657 ATGAACACT-TCTGGCAAATGTTGAT-CC-ATC-A--------AGAGATGAATTCGAGCA
65 ATGAACTTTCTCTGG-AAAAGTTGATGCCAATCTATCTCCTTCTGTGATAAAATCGAGCA
* * *
418705 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATT
418770 ATGAACTCTTCT
65 ATGAACT-TTCT
418782 AGCAATGCTG
Statistics
Matches: 269, Mismatches: 38, Indels: 22
0.82 0.12 0.07
Matches are distributed among these distances:
113 76 0.28
114 2 0.01
115 1 0.00
121 1 0.00
122 3 0.01
123 48 0.18
124 104 0.39
125 34 0.13
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (123 bp):
AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTTTCTCTGGAAAAGTTGATGCCAATCTATCTCCTTCTGTGATAAAATCGAGCA
Found at i:418724 original size:113 final size:112
Alignment explanation
Indices: 418585--418797 Score: 347
Period size: 113 Copynumber: 1.9 Consensus size: 112
418575 TGTGATAGCG
418585 TCGAGCAAAAGATTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCT
1 TCGAGCAAAAGATTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCT
* *
418650 TCTCATTATGAACACTTCTGGCAAATGTTGATCCATCAAGAGATGAAT
66 TCTCATTATGAACACTTCTAGC-AATGCTGATCCATCAAGAGATGAAT
* * *
418698 TCGAGCAAAA-AGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTC
1 TCGAGCAAAAGA-TTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTC
*
418762 TTCTCATTATGAACTCTTCTAGCAATGCTGATCCAT
65 TTCTCATTATGAACACTTCTAGCAATGCTGATCCAT
418798 TGAATGATGG
Statistics
Matches: 93, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
112 13 0.14
113 80 0.86
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (112 bp):
TCGAGCAAAAGATTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCT
TCTCATTATGAACACTTCTAGCAATGCTGATCCATCAAGAGATGAAT
Found at i:418756 original size:24 final size:23
Alignment explanation
Indices: 418721--418765 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
418711 TGAACAAGTT
418721 CTTCTCATTATGAACTTCTTCTTC
1 CTTCTCATTATG-ACTTCTTCTTC
*
418745 CTTCTTCA-TATGAGTTCTTCT
1 CTTC-TCATTATGACTTCTTCT
418766 CATTATGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 8 0.42
25 3 0.16
ACGTcount: A:0.16, C:0.27, G:0.07, T:0.51
Consensus pattern (23 bp):
CTTCTCATTATGACTTCTTCTTC
Found at i:419275 original size:95 final size:95
Alignment explanation
Indices: 419108--419307 Score: 373
Period size: 95 Copynumber: 2.1 Consensus size: 95
419098 TGCAACATGT
*
419108 TGATTATGATAACAACTCATCTGATTATGAAGTGACCTTTCAAGATGATTTCACAGATATCGATA
1 TGATTCTGATAACAACTCATCTGATTATGAAGTGACCTTTCAAGATGATTTCACAGATATCGATA
* *
419173 GTTCTTTTAATACCGAGAAATCTTGATTTC
66 GTACTTTTAATACCGAGAAATCTTGAATTC
419203 TGATTCTGATAACAACTCATCTGATTATGAAGTGACCTTTCAAGATGATTTCACAGATATCGATA
1 TGATTCTGATAACAACTCATCTGATTATGAAGTGACCTTTCAAGATGATTTCACAGATATCGATA
419268 GTACTTTTAATACCGAGAAATCTTGAATTC
66 GTACTTTTAATACCGAGAAATCTTGAATTC
419298 TGATTCTGAT
1 TGATTCTGAT
419308 GAGGAGAATA
Statistics
Matches: 102, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
95 102 1.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (95 bp):
TGATTCTGATAACAACTCATCTGATTATGAAGTGACCTTTCAAGATGATTTCACAGATATCGATA
GTACTTTTAATACCGAGAAATCTTGAATTC
Found at i:419730 original size:92 final size:89
Alignment explanation
Indices: 419634--419943 Score: 380
Period size: 82 Copynumber: 3.6 Consensus size: 89
419624 GGTTTTATAT
* * * *
419634 CAAACCAAATCAGAGAACTCAAAAAACACTTCCAGAAGATGCTATTAGCACATTCATCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAAAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAA
419699 TTCAATAAATGGTTCTGTGGTTCATAC
66 TTCAAT-AAT-GTTCTGTGGTTC-TAC
*
419726 CAAACCAGATCAGATAACT-AAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTTTTCCAA
1 CAAACCAGATCAGATAACTCAAAA-AACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAA
*
419790 ATTC---AATGAT-TGAT--TT-TAC
65 ATTCAATAATGTTCTG-TGGTTCTAC
*
419809 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTT-CAAA
1 CAAACCAGATCAGATAACTCAAAAAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAA
* *
419873 ---ATTAATG-AC--TGGTTCTAC
66 TTCAATAATGTTCTGTGGTTCTAC
*
419891 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACAT
1 CAAACCAGATCAGATAACTCAAAAAACACTTCCAGAAGATGCTATGAGCACAT
419944 GGCATTTGTT
Statistics
Matches: 199, Mismatches: 9, Indels: 30
0.84 0.04 0.13
Matches are distributed among these distances:
79 1 0.01
81 2 0.01
82 64 0.32
83 57 0.29
84 3 0.02
85 2 0.01
86 2 0.01
87 3 0.02
88 3 0.02
91 4 0.02
92 58 0.29
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.25
Consensus pattern (89 bp):
CAAACCAGATCAGATAACTCAAAAAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAA
TTCAATAATGTTCTGTGGTTCTAC
Found at i:419862 original size:83 final size:82
Alignment explanation
Indices: 419634--419943 Score: 406
Period size: 83 Copynumber: 3.6 Consensus size: 82
419624 GGTTTTATAT
* * * * *
419634 CAAACCAAATCAGAGAACTCAAAAAACACTTCCAGAAGATGCTATTAGCACATTCATCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAA
*
419699 TTCAATAAATGGTTCTGTGGTTCATAC
66 TTC----AAT-GAT-TGT--TT--TAC
* *
419726 CAAACCAGATCAGATAACTAAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTTTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAA
419791 TTCAATGATTGATTTTAC
66 TTCAATGATTG-TTTTAC
*
419809 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCAAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAA
* *
419874 TT-AATGACTGGTTCTAC
66 TTCAATGA-TTGTTTTAC
419891 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACAT
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACAT
419944 GGCATTTGTT
Statistics
Matches: 203, Mismatches: 13, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
82 63 0.31
83 69 0.34
85 2 0.01
86 2 0.01
87 3 0.01
88 3 0.01
92 61 0.30
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.25
Consensus pattern (82 bp):
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAA
TTCAATGATTGTTTTAC
Found at i:420988 original size:16 final size:17
Alignment explanation
Indices: 420935--420989 Score: 69
Period size: 16 Copynumber: 3.2 Consensus size: 17
420925 TTCATAGAAG
*
420935 AATAAATTGAATTTTCGAA
1 AATAAATTGAATCTT--AA
420954 AATAAATTGAATCTT-A
1 AATAAATTGAATCTTAA
420970 AATAAATTGAA-CTTAA
1 AATAAATTGAATCTTAA
420986 AATA
1 AATA
420990 GATAGAATTG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
15 3 0.09
16 17 0.50
19 14 0.41
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (17 bp):
AATAAATTGAATCTTAA
Found at i:421323 original size:7 final size:7
Alignment explanation
Indices: 421307--421356 Score: 61
Period size: 7 Copynumber: 7.4 Consensus size: 7
421297 ATCTTGACCC
421307 TTTT-TT
1 TTTTCTT
421313 TTTTCTT
1 TTTTCTT
421320 TTTT-TT
1 TTTTCTT
*
421326 TTCT-TT
1 TTTTCTT
421332 TTTTCTTT
1 TTTTC-TT
421340 TTTTCTT
1 TTTTCTT
421347 TTTTCTT
1 TTTTCTT
421354 TTT
1 TTT
421357 CTTCTTTTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
6 14 0.36
7 18 0.46
8 7 0.18
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (7 bp):
TTTTCTT
Found at i:421323 original size:9 final size:9
Alignment explanation
Indices: 421309--421370 Score: 67
Period size: 9 Copynumber: 7.1 Consensus size: 9
421299 CTTGACCCTT
421309 TTTTTTTTC
1 TTTTTTTTC
*
421318 TTTTTTTTT
1 TTTTTTTTC
421327 TCTTTTTTTC
1 T-TTTTTTTC
421337 -TTTTTTTC
1 TTTTTTTTC
421345 --TTTTTTC
1 TTTTTTTTC
*
421352 TTTTTCTTC
1 TTTTTTTTC
*
421361 TTTTTCTTC
1 TTTTTTTTC
421370 T
1 T
421371 CTTCAAGCAT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
7 7 0.15
8 8 0.17
9 25 0.53
10 7 0.15
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:421326 original size:16 final size:16
Alignment explanation
Indices: 421307--421365 Score: 75
Period size: 16 Copynumber: 3.8 Consensus size: 16
421297 ATCTTGACCC
*
421307 TTTTTT-TTTTCTTTT
1 TTTTTTCTTTTTTTTT
*
421322 TTTTTTCTTTTTTTCT
1 TTTTTTCTTTTTTTTT
*
421338 TTTTTTCTTTTTTCTT
1 TTTTTTCTTTTTTTTT
*
421354 TTTCTTCTTTTT
1 TTTTTTCTTTTT
421366 CTTCTCTTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
15 6 0.16
16 32 0.84
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTTTTCTTTTTTTTT
Found at i:421365 original size:1 final size:1
Alignment explanation
Indices: 421307--421356 Score: 55
Period size: 1 Copynumber: 50.0 Consensus size: 1
421297 ATCTTGACCC
* * * * *
421307 TTTTTTTTTTCTTTTTTTTTTCTTTTTTTCTTTTTTTCTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
421357 CTTCTTTTTC
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (1 bp):
T
Found at i:421366 original size:15 final size:15
Alignment explanation
Indices: 421309--421368 Score: 81
Period size: 15 Copynumber: 4.1 Consensus size: 15
421299 CTTGACCCTT
*
421309 TTTTTTTTCTTTTT-
1 TTTTTCTTCTTTTTC
421323 TTTTTCTT-TTTTTC
1 TTTTTCTTCTTTTTC
421337 TTTTT-TTCTTTTTTC
1 TTTTTCTTC-TTTTTC
421352 TTTTTCTTCTTTTTC
1 TTTTTCTTCTTTTTC
421367 TT
1 TT
421369 CTCTTCAAGC
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
13 7 0.17
14 12 0.29
15 19 0.46
16 3 0.07
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (15 bp):
TTTTTCTTCTTTTTC
Found at i:428619 original size:15 final size:15
Alignment explanation
Indices: 428596--428627 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
428586 TGAAATGAAT
428596 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
428611 AATGCATGTATGCAA
1 AATGAATGTATGCAA
428626 AA
1 AA
428628 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:433935 original size:3 final size:3
Alignment explanation
Indices: 433927--434003 Score: 102
Period size: 3 Copynumber: 26.0 Consensus size: 3
433917 TTAATATATT
* * *
433927 TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
433975 TAA TAA T-A TTA TAG TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
434004 ATAAATCAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
2 2 0.03
3 62 0.97
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (3 bp):
TAA
Done.