Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold173
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: 2040036
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 4 of 16
Found at i:488143 original size:48 final size:48
Alignment explanation
Indices: 488032--488214 Score: 234
Period size: 48 Copynumber: 3.9 Consensus size: 48
488022 CCCGAAATGA
* *
488032 TGCCAATGTGCTGAGTCAAGGCCAGTTATATTGGACTT-AA--T--GG
1 TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGGTGAGG
488075 TG-CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGGTGAGG
1 TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGGTGAGG
*
488122 TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGG
1 TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGG
* * * * *
488171 TGCCAATATGCTGATTCAGGGCCAGCTATATTGGGCTTAGAAGG
1 TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTA-AAGG
488215 GTTGCCACCG
Statistics
Matches: 123, Mismatches: 9, Indels: 9
0.87 0.06 0.06
Matches are distributed among these distances:
42 33 0.27
43 4 0.03
45 1 0.01
47 4 0.03
48 41 0.33
49 37 0.30
50 3 0.02
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.26
Consensus pattern (48 bp):
TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGGTGAGG
Found at i:488289 original size:32 final size:31
Alignment explanation
Indices: 488202--488304 Score: 154
Period size: 33 Copynumber: 3.3 Consensus size: 31
488192 CCAGCTATAT
488202 TGGGC-TTAGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAAGGGTTGCCACCGACTTGTG
*
488232 TAGGCTTTAGAGAGTGGTTGCCACCGACTTGTG
1 TGGGCTTTAGA-AG-GGTTGCCACCGACTTGTG
*
488265 TGGGCTTTAGGAAGAGTTGCCACCGACTTGTG
1 TGGGCTTTA-GAAGGGTTGCCACCGACTTGTG
488297 TGGGCTTT
1 TGGGCTTT
488305 GGGAAGGGAG
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
30 4 0.06
31 5 0.08
32 27 0.41
33 28 0.42
34 2 0.03
ACGTcount: A:0.17, C:0.18, G:0.35, T:0.30
Consensus pattern (31 bp):
TGGGCTTTAGAAGGGTTGCCACCGACTTGTG
Found at i:488310 original size:32 final size:31
Alignment explanation
Indices: 488202--488312 Score: 143
Period size: 32 Copynumber: 3.5 Consensus size: 31
488192 CCAGCTATAT
*
488202 TGGGC-TTAGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTGGAAGGGTTGCCACCGACTTGTG
* *
488232 TAGGCTTTAGAGAGTGGTTGCCACCGACTTGTG
1 TGGGCTTTGGA-AG-GGTTGCCACCGACTTGTG
*
488265 TGGGCTTTAGGAAGAGTTGCCACCGACTTGTG
1 TGGGCTTT-GGAAGGGTTGCCACCGACTTGTG
488297 TGGGCTTTGGGAAGGG
1 TGGGCTTT-GGAAGGG
488313 AGAAAGATGC
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.06
31 5 0.07
32 33 0.46
33 27 0.38
34 2 0.03
ACGTcount: A:0.17, C:0.17, G:0.38, T:0.28
Consensus pattern (31 bp):
TGGGCTTTGGAAGGGTTGCCACCGACTTGTG
Found at i:488365 original size:35 final size:32
Alignment explanation
Indices: 488315--488828 Score: 360
Period size: 34 Copynumber: 15.7 Consensus size: 32
488305 GGGAAGGGAG
* *
488315 AAAGATGCCACGGAGTTGTGGACTTAAAAGGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAA--GAA
488349 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAA
1 AAAG-GTGCCACGGAGTTGTGGGC-TTAAAAGAA
488383 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
1 AAAGGTGCCACGGAGTTGTGGGC-TT-AAAA--GAA
* * *
488419 AAAGAATGCCACGGAGTTGTGGGCTT---TGAG
1 AAAG-GTGCCACGGAGTTGTGGGCTTAAAAGAA
* * **
488449 AAAGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTG
1 AAAGG-TGCCACGGA-GT-TGTGGGC-TTA-A-AA--GAA
* * *
488489 AAAGATGCCACGAAGTTGTGGACTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGCTT-AAAAGAA
* *
488522 CAAGGTGCCACGGAGTTGTGGACTTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGC-TT-AAAAGAA
**
488556 AAAGGGTGCCACGGAGTTGTGGGCTTTGAA-AA
1 AAA-GGTGCCACGGAGTTGTGGGCTTAAAAGAA
* * *
488588 GAAGGTGCCATGGAGTTGTGGACTTAAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGCTT--AAAAGAA
488622 AAAGGTGCCACGGAGTTGTGGGCTTAAAAG--
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAGAA
*
488652 ---GGTGCCACGGAGTTGTGGACTTAAAGATGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAA-A-GAA
*
488683 AAAAGTGCCACGGAGTTGTGGGCTTAAAAG--
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAGAA
**
488713 ---GGTGCCACGGAGTTGTGGGCTTTGAA-AA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAGAA
* * *
488741 GAAGGTGCCACGGAGTCGTGGACTTTAAAAGGGAA
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAA--GAA
* * *
488776 AAAGAGTGCCATGGAGTTATGGGCTTTGAAAG--
1 AAAG-GTGCCACGGAGTTGTGGGC-TTAAAAGAA
* *
488808 GAAGGTGCCACGGAGTCGTGG
1 AAAGGTGCCACGGAGTTGTGG
488829 ACTTTGAGCA
Statistics
Matches: 388, Mismatches: 52, Indels: 83
0.74 0.10 0.16
Matches are distributed among these distances:
27 47 0.12
28 1 0.00
29 1 0.00
30 14 0.04
31 53 0.14
32 24 0.06
33 50 0.13
34 77 0.20
35 43 0.11
36 39 0.10
37 25 0.06
38 1 0.00
39 7 0.02
40 6 0.02
ACGTcount: A:0.31, C:0.13, G:0.35, T:0.21
Consensus pattern (32 bp):
AAAGGTGCCACGGAGTTGTGGGCTTAAAAGAA
Found at i:488555 original size:173 final size:174
Alignment explanation
Indices: 488263--488588 Score: 534
Period size: 174 Copynumber: 1.9 Consensus size: 174
488253 CACCGACTTG
* * *
488263 TGTGGGCTTTAGGAAGAGTTGCCACCGACTTGTGTGGGCTTTGGGAAGGGAGAAAGATGCCACGG
1 TGTGGGCTTTAGAAAGAGTTGCCACCGACTTGTGTGGGCTTTGAGAAGGGAGAAAGATGCCACGA
* *
488328 AGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAA-GGTGCC
66 AGTTGTGGACTTAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGACTTTAAAAGAAAAAGGGTGCC
488392 ACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAATGCCACGGAGT
131 ACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAATGCCACGGAGT
*
488436 TGTGGGCTTTGAGAAAG-GTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTGAAAGATGCCAC
1 TGTGGGCTTT-AGAAAGAGTTGCCACCGACTTGTGTGGGCTTT-GAGAAGGGAGAAAGATGCCAC
*
488500 GAAGTTGTGGACTTAAAA-AGAACAAG-GTGCCACGGAGTTGTGGACTTTAAAAAGAAAAAGGGT
64 GAAGTTGTGGACTTAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGACTTT-AAAAGAAAAAGGGT
488563 GCCACGGAGTTGTGGGCTTTGAAAAG
128 GCCACGGAGTTGTGGGCTTTGAAAAG
488589 AAGGTGCCAT
Statistics
Matches: 142, Mismatches: 7, Indels: 7
0.91 0.04 0.04
Matches are distributed among these distances:
172 21 0.15
173 51 0.36
174 70 0.49
ACGTcount: A:0.30, C:0.13, G:0.35, T:0.22
Consensus pattern (174 bp):
TGTGGGCTTTAGAAAGAGTTGCCACCGACTTGTGTGGGCTTTGAGAAGGGAGAAAGATGCCACGA
AGTTGTGGACTTAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGACTTTAAAAGAAAAAGGGTGCC
ACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAATGCCACGGAGT
Found at i:488593 original size:139 final size:129
Alignment explanation
Indices: 488315--488929 Score: 429
Period size: 139 Copynumber: 4.7 Consensus size: 129
488305 GGGAAGGGAG
* * **
488315 AAAGATGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
1 AAAGGTGCCACCGAGTTGTGGACTTAAAAAAGAAAAAGA-TGCCACGGAGTTGTGGGC-TTAAAA
* * *
488380 GAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAATGCCACGGAGTTGTGGGCTT
64 G-AAAAGGTGCCACGGAGTTGTGGACTTT-AAAA-AGAAAAAGAGTGCCACGGAGTTGTGGGCTT
*
488445 TGAG
126 TGAA
* * ** ** * *
488449 AAAGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTGAAAGATGCCACGAAGTTGTGGACTT
1 AAAGG-TGCCACCGA-GT-TGTGGAC-TTA-A-AAAAGAAAAAGATGCCACGGAGTTGTGGGCTT
*
488514 AAAAAGAACAAGGTGCCACGGAGTTGTGGACTTTAAAAAGAAAAAGGGTGCCACGGAGTTGTGGG
60 -AAAAGAA-AAGGTGCCACGGAGTTGTGGACTTTAAAAAGAAAAAGAGTGCCACGGAGTTGTGGG
488579 CTTTGAAA
123 CTTTG-AA
** *
488587 AGAAGGTGCCATGGAGTTGTGGACTTAAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTAAAAG
1 A-AAGGTGCCACCGAGTTGTGGACTTAAAAAAGAAAAAGATGCCACGGAGTTGTGGGCTTAAAAG
*
488652 ----GGTGCCACGGAGTTGTGGAC-TTAAAGATGAAAAA-AGTGCCACGGAGTTGTGGGC-TT-A
65 AAAAGGTGCCACGGAGTTGTGGACTTTAAA-AAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGA
488709 A
129 A
* * * ** * * *
488710 AAGGGTGCCACGGAGTTGTGGGCTTTGAAAAG---AAGGTGCCACGGAGTCGTGGACTTTAAAAG
1 AAAGGTGCCACCGAGTTGTGGACTTAAAAAAGAAAAAGATGCCACGGAGTTGTGGGC-TTAAAA-
* * * * * * *
488772 GGAAAAAGAGTGCCATGGAGTTATGGGCTTT-GAAAG--GAAG-GTGCCACGGAGTCGTGGACTT
64 -G-AAAAG-GTGCCACGGAGTTGTGGACTTTAAAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTT
*
488833 TGAGC
126 TGA-A
* * * * ** * * * * **
488838 AGAGATTGCCACTGAGTCGTGGACTT--TGAAGAAAAGGATGCCACTGAGTCGTGGACTT-TGAG
1 AAAG-GTGCCACCGAGTTGTGGACTTAAAAAAGAAAAAGATGCCACGGAGTTGTGGGCTTAAAAG
* *
488900 AAGAAGGTGCCACAGAGTCGTGGACTTTAA
65 AA-AAGGTGCCACGGAGTTGTGGACTTTAA
488930 GAAGGCATTT
Statistics
Matches: 389, Mismatches: 61, Indels: 70
0.75 0.12 0.13
Matches are distributed among these distances:
119 20 0.05
120 6 0.02
122 27 0.07
123 3 0.01
125 40 0.10
126 30 0.08
127 34 0.09
128 20 0.05
129 21 0.05
130 19 0.05
132 5 0.01
133 25 0.06
134 5 0.01
135 11 0.03
136 7 0.02
137 36 0.09
138 20 0.05
139 50 0.13
140 10 0.03
ACGTcount: A:0.31, C:0.13, G:0.34, T:0.21
Consensus pattern (129 bp):
AAAGGTGCCACCGAGTTGTGGACTTAAAAAAGAAAAAGATGCCACGGAGTTGTGGGCTTAAAAGA
AAAGGTGCCACGGAGTTGTGGACTTTAAAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAA
Found at i:488595 original size:31 final size:31
Alignment explanation
Indices: 488494--488927 Score: 320
Period size: 31 Copynumber: 13.7 Consensus size: 31
488484 GGGTGAAAGA
* *
488494 TGCCACGAAGTTGTGGAC-TTAAAAAGAACAAGG
1 TGCCACGGAGTTGTGGACTTTGAAAAG---AAGG
*
488527 TGCCACGGAGTTGTGGACTTTAAAAAGAAAAAGGG
1 TGCCACGGAGTTGTGGACTTTGAAAAG---AA-GG
*
488562 TGCCACGGAGTTGTGGGCTTTGAAAAGAAGG
1 TGCCACGGAGTTGTGGACTTTGAAAAGAAGG
* **
488593 TGCCATGGAGTTGTGGACTTAAAAAAGAAAAAGG
1 TGCCACGGAGTTGTGGACTTTGAAAAG---AAGG
*
488627 TGCCACGGAGTTGTGGGC-TT-AAAAG--GG
1 TGCCACGGAGTTGTGGACTTTGAAAAGAAGG
488654 TGCCACGGAGTTGTGGACTTAAAGATGAAAA-AA-G
1 TGCCACGGAGTTGTGGACTT-----TGAAAAGAAGG
*
488688 TGCCACGGAGTTGTGGGC-TT-AAAAG--GG
1 TGCCACGGAGTTGTGGACTTTGAAAAGAAGG
*
488715 TGCCACGGAGTTGTGGGCTTTGAAAAGAAGG
1 TGCCACGGAGTTGTGGACTTTGAAAAGAAGG
*
488746 TGCCACGGAGTCGTGGACTTT-AAAAGGGAAAAAGAG
1 TGCCACGGAGTTGTGGACTTTGAAAA--G---AAG-G
* * * *
488782 TGCCATGGAGTTATGGGCTTTGAAAGGAAGG
1 TGCCACGGAGTTGTGGACTTTGAAAAGAAGG
* ** *
488813 TGCCACGGAGTCGTGGACTTTGAGCAG-AGAT
1 TGCCACGGAGTTGTGGACTTTGAAAAGAAG-G
* *
488844 TGCCACTGAGTCGTGGACTTTGAAGAA-AAGG
1 TGCCACGGAGTTGTGGACTTTGAA-AAGAAGG
* * *
488875 ATGCCACTGAGTCGTGGACTTTGAGAAGAAGG
1 -TGCCACGGAGTTGTGGACTTTGAAAAGAAGG
* *
488907 TGCCACAGAGTCGTGGACTTT
1 TGCCACGGAGTTGTGGACTTT
488928 AAGAAGGCAT
Statistics
Matches: 335, Mismatches: 34, Indels: 66
0.77 0.08 0.15
Matches are distributed among these distances:
27 42 0.13
28 4 0.01
29 5 0.01
30 6 0.02
31 111 0.33
32 41 0.12
33 20 0.06
34 54 0.16
35 31 0.09
36 18 0.05
37 3 0.01
ACGTcount: A:0.30, C:0.14, G:0.34, T:0.22
Consensus pattern (31 bp):
TGCCACGGAGTTGTGGACTTTGAAAAGAAGG
Found at i:488658 original size:27 final size:27
Alignment explanation
Indices: 488620--488773 Score: 155
Period size: 27 Copynumber: 5.3 Consensus size: 27
488610 CTTAAAAAAG
*
488620 AAAAAGGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTT
*
488647 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTT
*
488674 AAAGATGAAAAAAGTGCCACGGAGTTGTGGGCTT
1 AAA-A-G-----GGTGCCACGGAGTTGTGGGCTT
488708 AAAAGGGTGCCACGGAGTTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGGC-TT
* *
488736 GAAAAGAAGGTGCCACGGAGTCGTGGACTTT
1 -AAAAG--GGTGCCACGGAGTTGTGGGC-TT
488767 AAAAGGG
1 AAAAGGG
488774 AAAAAGAGTG
Statistics
Matches: 109, Mismatches: 7, Indels: 21
0.80 0.05 0.15
Matches are distributed among these distances:
27 47 0.43
28 5 0.05
29 6 0.06
30 5 0.05
31 21 0.19
32 1 0.01
33 1 0.01
34 23 0.21
ACGTcount: A:0.29, C:0.14, G:0.36, T:0.21
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTTGTGGGCTT
Found at i:488684 original size:61 final size:61
Alignment explanation
Indices: 488320--488773 Score: 394
Period size: 61 Copynumber: 7.0 Consensus size: 61
488310 GGGAGAAAGA
488320 TGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
1 TGCCACGGAGTTGTGGACTTAAAA-GGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAG----
488385 AGG
60 -GG
* *
488388 TGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAATGCCACGGAGTTGTGGGCTTTGAGAAAG
1 TGCCACGGAGTTGTGGAC-TT-AAAA-GGAAAAAG-GTGCCACGGAGTTGTGGGCTTT-A-AAAG
*
488453 GT
60 GG
* * * ** * * * *
488455 TGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTGAAAGATGCCACGAAGTTGTGGACTTAAAAAG
1 TGCCACGGA-GT-TGTGGAC-TTA-A-AA-GGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAG
488520 AACAAGG
60 -----GG
*
488527 TGCCACGGAGTTGTGGACTTTAAAAAGAAAAAGGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGAAAAA-GGTGCCACGGAGTTGTGGGCTTT-AAAAG--G
488592 G
61 G
* *
488593 TGCCATGGAGTTGTGGACTTAAAAAAGAAAAAGGTGCCACGGAGTTGTGGGC-TTAAAAGGG
1 TGCCACGGAGTTGTGGACTT-AAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGG
* *
488654 TGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAGTTGTGGGC-TTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAA-AGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGG
* ** * * *
488715 TGCCACGGAGTTGTGGGCTTTGAA--AAGAAGGTGCCACGGAGTCGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGG
488774 AAAAAGAGTG
Statistics
Matches: 336, Mismatches: 32, Indels: 45
0.81 0.08 0.11
Matches are distributed among these distances:
58 21 0.06
59 9 0.03
60 4 0.01
61 76 0.23
63 5 0.01
64 2 0.01
65 22 0.07
66 32 0.10
67 17 0.05
68 41 0.12
69 38 0.11
70 54 0.16
71 2 0.01
72 13 0.04
ACGTcount: A:0.31, C:0.13, G:0.35, T:0.21
Consensus pattern (61 bp):
TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGG
Found at i:488816 original size:67 final size:67
Alignment explanation
Indices: 488708--488833 Score: 216
Period size: 67 Copynumber: 1.9 Consensus size: 67
488698 TTGTGGGCTT
* *
488708 AAAAGGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTTAAAAGG
1 AAAAGAGTGCCACGGAGTTATGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTTAAAAGG
488773 GA
66 GA
* *
488775 AAAAGAGTGCCATGGAGTTATGGGCTTTGAAAGGAAGGTGCCACGGAGTCGTGGACTTT
1 AAAAGAGTGCCACGGAGTTATGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTT
488834 GAGCAGAGAT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 55 1.00
ACGTcount: A:0.29, C:0.13, G:0.37, T:0.21
Consensus pattern (67 bp):
AAAAGAGTGCCACGGAGTTATGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTTAAAAGG
GA
Found at i:488921 original size:94 final size:97
Alignment explanation
Indices: 488654--488927 Score: 239
Period size: 94 Copynumber: 2.9 Consensus size: 97
488644 CTTAAAAGGG
* * * ** * *
488654 TGCCACGGAGTTGTGGAC-TTAAAGATGAAAAA-AGTGCCACGGAGTTGTGGGC-TT-AAA--AG
1 TGCCACGGAGTCGTGGACTTTAAA-AGGAAAAAGAGTGCCATGGAGTCATGGACTTTGAAAGGAA
* * * ** *
488713 GGTGCCACGGAGTTGTGGGCTTTGAAAAGA-AGG
65 GGTGCCACAGAGTCGTGGACTTTGAGCAGAGA-T
* *
488746 TGCCACGGAGTCGTGGACTTTAAAAGGGAAAAAGAGTGCCATGGAGTTATGGGCTTTGAAAGGAA
1 TGCCACGGAGTCGTGGACTTTAAAA-GGAAAAAGAGTGCCATGGAGTCATGGACTTTGAAAGGAA
*
488811 GGTGCCACGGAGTCGTGGACTTTGAGCAGAGAT
65 GGTGCCACAGAGTCGTGGACTTTGAGCAGAGAT
* * * *
488844 TGCCACTGAGTCGTGGACTTT-GAA-GAAAAGGA-TGCCACT-GAGTCGTGGACTTTGAGAA-GA
1 TGCCACGGAGTCGTGGACTTTAAAAGGAAAAAGAGTGCCA-TGGAGTCATGGACTTTGA-AAGGA
488904 AGGTGCCACAGAGTCGTGGACTTT
64 AGGTGCCACAGAGTCGTGGACTTT
488928 AAGAAGGCAT
Statistics
Matches: 155, Mismatches: 17, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
92 18 0.12
93 11 0.07
94 61 0.39
95 12 0.08
96 3 0.02
97 2 0.01
98 47 0.30
99 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.35, T:0.22
Consensus pattern (97 bp):
TGCCACGGAGTCGTGGACTTTAAAAGGAAAAAGAGTGCCATGGAGTCATGGACTTTGAAAGGAAG
GTGCCACAGAGTCGTGGACTTTGAGCAGAGAT
Found at i:488921 original size:161 final size:157
Alignment explanation
Indices: 488489--488934 Score: 474
Period size: 161 Copynumber: 2.8 Consensus size: 157
488479 GAGAAGGGTG
* * * * * * *
488489 AAAGATGCCACGAAGTTGTGGACTTAAAAAGAACAAGGTGCCACGGAGTTGTGGACTTTAAAAAG
1 AAAGGTGCCACGGAGTCGTGGACTTAAGATGAAAAAAGTGCCACGGAGTTGTGGACTTT---AAG
* * *
488554 AAAAAGGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCATGGAGTTGTGGAC-TTAAAAA
63 -AAAAGGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTTAAAAG
* *
488618 AGAAAAAGGTGCCACGGAGTTGTGGGCTTAA
127 GGAAAAAGGTGCCACGGAGTTATGGGCTTAA
* * *
488649 AAGGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAGTTGTGGGC-TT---AA
1 AAAGGTGCCACGGAGTCGTGGACTT-AAGATGAAAAAAGTGCCACGGAGTTGTGGACTTTAAGAA
488710 AAGGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTTAAAAGGGA
65 AAGGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTTAAAAGGGA
*
488775 AAAAGAGTGCCATGGAGTTATGGGCTTTGAA
130 AAAAG-GTGCCACGGAGTTATGGGC-TT-AA
* * * * * * *
488806 AGGAAGGTGCCACGGAGTCGTGGACTT-TGA-GCAGAGATTGCCACTGAGTCGTGGACTTTGAAG
1 A--AAGGTGCCACGGAGTCGTGGACTTAAGATGAAAAAAGTGCCACGGAGTTGTGGACTTT-AAG
* * * * * *
488869 AAAAGGATGCCACTGAGTCGTGGACTTTGAGAAGAAGGTGCCACAGAGTCGTGGACTTTAAGAAG
63 AAAAGGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTTAA-AAG
488934 G
127 G
488935 CATTTGAAGA
Statistics
Matches: 243, Mismatches: 30, Indels: 24
0.82 0.10 0.08
Matches are distributed among these distances:
153 54 0.22
154 13 0.05
155 17 0.07
156 21 0.09
157 7 0.03
159 22 0.09
160 24 0.10
161 81 0.33
162 4 0.02
ACGTcount: A:0.31, C:0.14, G:0.34, T:0.21
Consensus pattern (157 bp):
AAAGGTGCCACGGAGTCGTGGACTTAAGATGAAAAAAGTGCCACGGAGTTGTGGACTTTAAGAAA
AGGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTTAAAAGGGAA
AAAGGTGCCACGGAGTTATGGGCTTAA
Found at i:489857 original size:1 final size:1
Alignment explanation
Indices: 489853--489924 Score: 54
Period size: 1 Copynumber: 72.0 Consensus size: 1
489843 GGGTTTTTCG
** * * * * * * * *
489853 TTTTTTTTTCCTTTTTTTTGTTTTTTTTTTGTTTCTTCTTTTTTTTTCTTTTTTGTTTTGTTTCT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
489918 TTTTTTT
1 TTTTTTT
489925 GGAAAAGAAC
Statistics
Matches: 53, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.00, C:0.08, G:0.06, T:0.86
Consensus pattern (1 bp):
T
Found at i:489862 original size:11 final size:10
Alignment explanation
Indices: 489846--489906 Score: 63
Period size: 10 Copynumber: 6.2 Consensus size: 10
489836 TGAAAAAGGG
489846 TTTTTCGTTTT
1 TTTTTC-TTTT
*
489857 TTTTTCCTTT
1 TTTTTCTTTT
*
489867 TTTTT-GTTT
1 TTTTTCTTTT
*
489876 TTTTT-TTGT
1 TTTTTCTTTT
*
489885 TTCTTCTTTT
1 TTTTTCTTTT
489895 TTTTTCTTTT
1 TTTTTCTTTT
489905 TT
1 TT
489907 GTTTTGTTTC
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
9 14 0.33
10 22 0.52
11 6 0.14
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:489867 original size:10 final size:9
Alignment explanation
Indices: 489854--489924 Score: 65
Period size: 9 Copynumber: 7.9 Consensus size: 9
489844 GGTTTTTCGT
489854 TTTTTTTTCC
1 TTTTTTTT-C
*
489864 TTTTTTTTG
1 TTTTTTTTC
489873 TTTTTTTT-
1 TTTTTTTTC
*
489881 TTGTTTCTTC
1 TT-TTTTTTC
489891 TTTTTTTT-
1 TTTTTTTTC
* *
489899 TCTTTTTTG
1 TTTTTTTTC
*
489908 TTTTGTTTC
1 TTTTTTTTC
489917 TTTTTTTT
1 TTTTTTTT
489925 GGAAAAGAAC
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
8 9 0.18
9 31 0.62
10 10 0.20
ACGTcount: A:0.00, C:0.08, G:0.06, T:0.86
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:489878 original size:29 final size:28
Alignment explanation
Indices: 489846--489925 Score: 87
Period size: 27 Copynumber: 2.9 Consensus size: 28
489836 TGAAAAAGGG
*
489846 TTTTTCGTTTTTTTTTCCTTTTTTTTGT-
1 TTTTTTGTTTTTTTTT-CTTTTTTTTGTC
*
489874 TTTTTT-TTTGTTTCTTCTTTTTTTT-TC
1 TTTTTTGTTT-TTTTTTCTTTTTTTTGTC
*
489901 TTTTTTG-TTTTGTTTCTTTTTTTTG
1 TTTTTTGTTTTTTTTTCTTTTTTTTG
489926 GAAAAGAACA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
26 14 0.32
27 20 0.45
28 10 0.23
ACGTcount: A:0.00, C:0.09, G:0.07, T:0.84
Consensus pattern (28 bp):
TTTTTTGTTTTTTTTTCTTTTTTTTGTC
Found at i:489894 original size:16 final size:15
Alignment explanation
Indices: 489846--489924 Score: 74
Period size: 16 Copynumber: 5.3 Consensus size: 15
489836 TGAAAAAGGG
*
489846 TTTTTCGTTT-TTTT
1 TTTTTTGTTTCTTTT
* *
489860 TTCCTTTTTTTTGTTTT
1 TT--TTTTGTTTCTTTT
*
489877 TTTTTTGTTTC-TTC
1 TTTTTTGTTTCTTTT
489891 TTTTTT-TTTCTTTT
1 TTTTTTGTTTCTTTT
489905 TTGTTTTGTTTCTTTT
1 TT-TTTTGTTTCTTTT
489921 TTTT
1 TTTT
489925 GGAAAAGAAC
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
13 4 0.08
14 14 0.26
15 13 0.25
16 16 0.30
17 6 0.11
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.85
Consensus pattern (15 bp):
TTTTTTGTTTCTTTT
Found at i:489894 original size:24 final size:23
Alignment explanation
Indices: 489853--489924 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 23
489843 GGGTTTTTCG
* *
489853 TTTTTTT-TTCCTTTTTTTTGTTT
1 TTTTTTTGTTTCTTCTTTTT-TTT
489876 TTTTTTTGTTTCTTCTTTTTTTT
1 TTTTTTTGTTTCTTCTTTTTTTT
*
489899 TCTTTTTTGTTTTGTTTCTTTTTTTT
1 T-TTTTTTG-TTT-CTTCTTTTTTTT
489925 GGAAAAGAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
23 11 0.26
24 17 0.40
25 3 0.07
26 11 0.26
ACGTcount: A:0.00, C:0.08, G:0.06, T:0.86
Consensus pattern (23 bp):
TTTTTTTGTTTCTTCTTTTTTTT
Found at i:497108 original size:52 final size:52
Alignment explanation
Indices: 497030--497158 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
497020 CGAAATATGA
*
497030 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
* *
497082 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
*
497134 AAATTTTCCTGCATGTATCGATACA
1 AAATTTACCTGCATGTATCGATACA
497159 AAGATCAATG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (52 bp):
AAATTTACCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
Found at i:497169 original size:52 final size:51
Alignment explanation
Indices: 497030--497178 Score: 210
Period size: 52 Copynumber: 2.9 Consensus size: 51
497020 CGAAATATGA
*
497030 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACA-TTAATAATGTATCGATACATCTGGGC
* *
497082 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACA-TTAATAATGTATCGATACATCTGGGC
* *
497134 AAATTTTCCTGCATGTATCGATACA-AAGATCAATGTATCGATACA
1 AAATTTACCTGCATGTATCGATACATTA-AT-AATGTATCGATACA
497179 ATGTATCGAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 87 0.98
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Consensus pattern (51 bp):
AAATTTACCTGCATGTATCGATACATTAATAATGTATCGATACATCTGGGC
Found at i:497182 original size:13 final size:13
Alignment explanation
Indices: 497164--497191 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
497154 ATACAAAGAT
497164 CAATGTATCGATA
1 CAATGTATCGATA
497177 CAATGTATCGATA
1 CAATGTATCGATA
497190 CA
1 CA
497192 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:497269 original size:33 final size:33
Alignment explanation
Indices: 497232--497298 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
497222 AGTAGCTTAA
497232 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
497265 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
497298 A
1 A
497299 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:497272 original size:13 final size:13
Alignment explanation
Indices: 497254--497278 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
497244 CAAAAAAATA
497254 TGTATCGATACAT
1 TGTATCGATACAT
497267 TGTATCGATACA
1 TGTATCGATACA
497279 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:501595 original size:17 final size:16
Alignment explanation
Indices: 501574--501631 Score: 82
Period size: 16 Copynumber: 3.6 Consensus size: 16
501564 GTTCTTTTCC
501574 AAAAAAAGAAACAAAA
1 AAAAAAAGAAACAAAA
*
501590 CAAAAAAGAAA-AAAA
1 AAAAAAAGAAACAAAA
*
501605 AAAAGAAGAAACAAAA
1 AAAAAAAGAAACAAAA
501621 AAAAAGAAGAA
1 AAAAA-AAGAA
501632 GAAGGGAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
15 13 0.36
16 18 0.50
17 5 0.14
ACGTcount: A:0.84, C:0.05, G:0.10, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAAACAAAA
Found at i:501596 original size:16 final size:16
Alignment explanation
Indices: 501574--501631 Score: 77
Period size: 17 Copynumber: 3.7 Consensus size: 16
501564 GTTCTTTTCC
501574 AAAAA-AAGAAACAAA
1 AAAAAGAAGAAACAAA
501589 ACAAAA-AAGAAA-AAA
1 A-AAAAGAAGAAACAAA
501604 AAAAAGAAGAAACAAAA
1 AAAAAGAAGAAAC-AAA
501621 AAAAAGAAGAA
1 AAAAAGAAGAA
501632 GAAGGGAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.10
15 11 0.28
16 10 0.26
17 14 0.36
ACGTcount: A:0.84, C:0.05, G:0.10, T:0.00
Consensus pattern (16 bp):
AAAAAGAAGAAACAAA
Found at i:501601 original size:12 final size:13
Alignment explanation
Indices: 501586--501622 Score: 58
Period size: 12 Copynumber: 2.8 Consensus size: 13
501576 AAAAAGAAAC
501586 AAAACAAAAAAGA
1 AAAACAAAAAAGA
501599 AAAA-AAAAAAGA
1 AAAACAAAAAAGA
501611 AGAAACAAAAAA
1 A-AAACAAAAAA
501623 AAAGAAGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 9 0.41
13 7 0.32
14 6 0.27
ACGTcount: A:0.86, C:0.05, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAACAAAAAAGA
Found at i:501608 original size:19 final size:19
Alignment explanation
Indices: 501586--501625 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
501576 AAAAAGAAAC
*
501586 AAAACAAAAAAGAAAAAAA
1 AAAACAAAAAACAAAAAAA
* *
501605 AAAAGAAGAAACAAAAAAA
1 AAAACAAAAAACAAAAAAA
501624 AA
1 AA
501626 GAAGAAGAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.88, C:0.05, G:0.07, T:0.00
Consensus pattern (19 bp):
AAAACAAAAAACAAAAAAA
Found at i:501642 original size:20 final size:20
Alignment explanation
Indices: 501597--501634 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
501587 AAACAAAAAA
501597 GAAAAAAAAAAAGAAGAAAC
1 GAAAAAAAAAAAGAAGAAAC
501617 -AAAAAAAAAGAAGAAGAA
1 GAAAAAAAAA-AAGAAGAA
501635 GGGAAAAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.82, C:0.03, G:0.16, T:0.00
Consensus pattern (20 bp):
GAAAAAAAAAAAGAAGAAAC
Found at i:502714 original size:34 final size:34
Alignment explanation
Indices: 502676--503223 Score: 505
Period size: 34 Copynumber: 16.9 Consensus size: 34
502666 GCACCATTTT
*
502676 AAGCCCACAACTCTGTGGCACTCTTTTTCCTTCA
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCA
* *
502710 AAGCCCATAACTCCGTGGCAC-C--CTT--TT--
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCA
*
502737 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCA
* * *
502771 AAGTCCACAACTTCGTGGCAC-C--CTT--TT--
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCA
*
502798 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCA
* * *
502832 AAGTCCACAACTCCGTGGCAC-CTTTTTCTTTTTA
1 AAGCCCACAACTCCGTGGCACTCTTTTTC-CTTCA
502866 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCA
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCA
502900 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCA
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCA
*
502934 AAGCCCACAACTCCGTGGCAC-C--CTT--TT--
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCA
* *
502961 AAGCCCACAACTCCGTGGCATTCTTTTTCCTTCT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCA
* * * *
502995 ACGTCCACAACTCCGTGGCAC-CTTTTTCTTTTTA
1 AAGCCCACAACTCCGTGGCACTCTTTTTC-CTTCA
* * **
503029 AAGCCCACAAC-CCTGTGGCA-TCCTGTTCCTTTT
1 AAGCCCACAACTCC-GTGGCACTCTTTTTCCTTCA
* * *
503062 AAGTCCGCAACTCCGTGGCACTCTTTTTCCCTTTTA
1 AAGCCCACAACTCCGTGGCACTCTTTTT-CC-TTCA
*
503098 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCA
* *
503132 AAGTCCACAACTCCGTGGCAC-C--CTT--TT--
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCA
* * *
503159 AAGCCCACAACTCCGTGACATTCTTTTTCCTTCT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCA
* * * *
503193 ACGTCCATAACTCCGTGGCA-TCTTTCTCCTT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTT
503224 TTTCTAAAGC
Statistics
Matches: 424, Mismatches: 53, Indels: 75
0.77 0.10 0.14
Matches are distributed among these distances:
27 77 0.18
28 4 0.01
29 8 0.02
30 8 0.02
31 8 0.02
32 8 0.02
33 48 0.11
34 223 0.53
35 11 0.03
36 29 0.07
ACGTcount: A:0.19, C:0.36, G:0.13, T:0.32
Consensus pattern (34 bp):
AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCA
Found at i:502730 original size:61 final size:61
Alignment explanation
Indices: 502616--503124 Score: 435
Period size: 61 Copynumber: 8.0 Consensus size: 61
502606 CTTTTCTGCA
* * * * *
502616 AAGCCCACAACTACGTGGCACT-ATTTTCCTTTTAAGTCCACAACTCTGTGGCACCATTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCTTTT
* * * *
502676 AAGCCCACAACTCTGTGGCACTCTTTTTCCTTCAAAGCCCATAACTCCGTGGCACCCTTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCTTTT
*
502737 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTTCGTGGCACCCTTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCTTTT
502798 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCTTTTTCTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACC-----C-TT
502863 TT
60 TT
* * *
502865 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCC
1 -AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCAC-C--CTT--
502930 TT
60 TT
* *
502932 CAAAGCCCACAACTCCGTGGCA--C-----CCTTTTAAGCCCACAACTCCGTGGCATTCTTTTTC
1 --AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCA--C-----C
*
502990 CTTCT
57 CTTTT
* * * * *
502995 ACGTCCACAACTCCGTGGCAC-CTTTTTCTTTTTAAAGCCCACAAC-CCTGTGGCATCCTGTTCC
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT-AAGTCCACAACTCC-GTGGCA--C----CC
503058 TTTT
58 TTTT
* * * * *
503062 AAGTCCGCAACTCCGTGGCACTCTTTTTCCCTTTTAAAGCCCACAACTCCGTGGCACTCTTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTT-CCTTCT-AAGTCCACAACTCCGTGGCACCCTTTT
503125 TCCTTCTAAG
Statistics
Matches: 388, Mismatches: 32, Indels: 55
0.82 0.07 0.12
Matches are distributed among these distances:
60 20 0.05
61 184 0.47
62 1 0.00
63 7 0.02
65 4 0.01
66 4 0.01
67 43 0.11
68 99 0.26
69 24 0.06
70 2 0.01
ACGTcount: A:0.20, C:0.35, G:0.13, T:0.32
Consensus pattern (61 bp):
AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCTTTT
Found at i:502844 original size:122 final size:125
Alignment explanation
Indices: 502615--503158 Score: 459
Period size: 129 Copynumber: 4.2 Consensus size: 125
502605 CCTTTTCTGC
* * * *
502615 AAAGCCCACAACTACGTGGCACT-ATTTTCCTTTTAAGTCCACAAC-TCTGTGGCACCATTTTAA
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTTC-GTGGCACCCTTTTAA
* *
502678 GCCCACAACTCTGTGGCACTCTTTTTCCTTCAAAGCCCATAACTCCGTGGCACC-C-TTTT
65 GCCCACAACTCCGTGGCACTCTTTTTCCTTCAAAGCCCACAACTCCGTGGCACCTCTTTTT
502737 -AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTTCGTGGCACCCTTTTAAG
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTTCGTGGCACCCTTTTAAG
* *
502801 CCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
66 CCCACAACTCCGTGGCACTCTTTTTCCTTCAAAGCCCACAACTCCGTGGCACC----TCTTTTT
* * * *
502865 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCC
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTTCGTGGCAC-C--CTT--
* * *
502930 TTCAAAGCCCACAACTCCGTGGCAC-C--CTT--TT--AAGCCCACAACTCCGTGGCATTCTTTT
61 TT--AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCAAAGCCCACAACTCCGTGGCA-CCTCTT
502988 TCCTT
123 T--TT
* * * * * * *
502993 CTACGTCCACAACTCCGTGGCAC-CTTTTTCTTTTTAAAGCCCACAAC-CCTGTGGCATCCTGTT
1 -AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT-AAGTCCACAACTTC-GTGGCA--C----
* * *
503056 CCTTTTAAGTCCGCAACTCCGTGGCACTCTTTTTCCCTTTTAAAGCCCACAACTCCGTGGCACTC
57 CCTTTTAAGCCCACAACTCCGTGGCACTCTTTTT-CC-TTCAAAGCCCACAACTCCGTGGCAC-C
*
503121 TTTTTCCTT
119 TCTTT--TT
* * *
503130 CTAAGTCCACAACTCCGTGGCACCCTTTT
1 -AAAGCCCACAACTCCGTGGCACTCTTTT
503159 AAGCCCACAA
Statistics
Matches: 356, Mismatches: 28, Indels: 60
0.80 0.06 0.14
Matches are distributed among these distances:
121 21 0.06
122 84 0.24
123 2 0.01
126 4 0.01
127 1 0.00
128 36 0.10
129 108 0.30
130 4 0.01
131 5 0.01
132 4 0.01
133 2 0.01
134 4 0.01
135 3 0.01
136 21 0.06
137 52 0.15
138 5 0.01
ACGTcount: A:0.20, C:0.35, G:0.13, T:0.32
Consensus pattern (125 bp):
AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTTCGTGGCACCCTTTTAAG
CCCACAACTCCGTGGCACTCTTTTTCCTTCAAAGCCCACAACTCCGTGGCACCTCTTTTT
Found at i:502953 original size:163 final size:160
Alignment explanation
Indices: 502675--503124 Score: 617
Period size: 163 Copynumber: 2.8 Consensus size: 160
502665 GGCACCATTT
* * * * *
502675 TAAGCCCACAACTCTGTGGCACTCTTTTTC-CTTCAAAGCCCATAACTCCGTGGCAC-C-CTT--
1 TAAGTCCACAACTCCGTGGCAC-CTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTCTTCC
* * *
502735 TTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTTCGTGGCACCCTTTTAA
65 TTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCAAAGCCCACAACTCCGTGGCACCCTTTTAA
502800 GCCCACAACTCCGTGGCACTCTTTTTCCTTC
130 GCCCACAACTCCGTGGCACTCTTTTTCCTTC
*
502831 TAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
1 TAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTC-TCTTCC
502896 TTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCAAAGCCCACAACTCCGTGGCACCCTTTT
65 TT--AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCAAAGCCCACAACTCCGTGGCACCCTTTT
*
502961 AAGCCCACAACTCCGTGGCATTCTTTTTCCTTC
128 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTC
* *
502994 TACGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAAC-CCTGTGGCA-TCCTGTTC
1 TAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCC-GTGGCACT-CTCTTC
* * * *
503057 CTTTTAAGTCCGCAACTCCGTGGCACTCTTTTTCCCTTTTAAAGCCCACAACTCCGTGGCACTCT
64 C--TTAAGCCCACAACTCCGTGGCACTCTTTTT-CC-TTCAAAGCCCACAACTCCGTGGCACCCT
503122 TTT
125 TTT
503125 TCCTTCTAAG
Statistics
Matches: 264, Mismatches: 16, Indels: 20
0.88 0.05 0.07
Matches are distributed among these distances:
155 7 0.03
156 43 0.16
157 1 0.00
159 2 0.01
161 2 0.01
162 34 0.13
163 144 0.55
164 31 0.12
ACGTcount: A:0.20, C:0.36, G:0.13, T:0.32
Consensus pattern (160 bp):
TAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTCTTCCT
TAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCAAAGCCCACAACTCCGTGGCACCCTTTTAAG
CCCACAACTCCGTGGCACTCTTTTTCCTTC
Found at i:503146 original size:198 final size:197
Alignment explanation
Indices: 502672--503238 Score: 650
Period size: 198 Copynumber: 2.9 Consensus size: 197
502662 TGTGGCACCA
* * *
502672 TTTT-AAGCCCACAACTCTGTGGCACTCTTTTTCCTTCAAAGCCCATAACTCCGTGGCAC-C--C
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCAAAGCCCACAACTCCGTGGCACTCTTT
* * * *
502733 TT--TT--AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTTCGTGGCA--C
66 TTCCTTCAAAGCCCACAACTCCGTGGCA--C-----CCTTTTAAGCCCACAACTCCGTGACATTC
* * * * * *
502792 -----CCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT-AAGTCCACAACTCCGTGGC
124 TTTTTCCTTCTACGTCCACAACTCCGTGGCAC-CTTTTTCTTTTTAAAGCCCACAACTCCGTGGC
* *
502851 ACCTTTTTCT
188 ACCTTGTTCC
502861 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCAAAGCCCACAACTCCGTGGCACTCTTT
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCAAAGCCCACAACTCCGTGGCACTCTTT
*
502926 TTCCTTCAAAGCCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCATTCTTTTTCC
66 TTCCTTCAAAGCCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGACATTCTTTTTCC
502991 TTCTACGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAAC-CCTGTGGCATCC-TG
131 TTCTACGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCC-GTGGCA-CCTTG
503054 TTCC
194 TTCC
* * *
503058 TTTT-AAGTCCGCAACTCCGTGGCACTCTTTTTCCCTTTTAAAGCCCACAACTCCGTGGCACTCT
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTT-CC-TTCAAAGCCCACAACTCCGTGGCACTCT
* *
503122 TTTTCCTTCTAAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGACATTCTTTTT
64 TTTTCCTTCAAAGCCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGACATTCTTTTT
* * *
503187 CCTTCTACGTCCATAACTCCGTGGCATCTTTCTCCTTTTTCTAAAGCCCACA
129 CCTTCTACGTCCACAACTCCGTGGCACCTTT-TTC-TTTT-TAAAGCCCACA
503239 CAAGTTGGTG
Statistics
Matches: 332, Mismatches: 23, Indels: 34
0.85 0.06 0.09
Matches are distributed among these distances:
189 4 0.01
190 76 0.23
191 1 0.00
192 1 0.00
193 2 0.01
195 3 0.01
196 38 0.11
197 70 0.21
198 120 0.36
199 2 0.01
200 4 0.01
201 11 0.03
ACGTcount: A:0.20, C:0.36, G:0.12, T:0.32
Consensus pattern (197 bp):
TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCAAAGCCCACAACTCCGTGGCACTCTTT
TTCCTTCAAAGCCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGACATTCTTTTTCC
TTCTACGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTGTT
CC
Found at i:503167 original size:61 final size:62
Alignment explanation
Indices: 502836--503212 Score: 377
Period size: 61 Copynumber: 5.8 Consensus size: 62
502826 CCTTCTAAGT
* * * *
502836 CCACAACTCCGTGGCAC-CTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCA
1 CCACAACTCCGTGGCACTCTTTTTCCTTCT-AAGTCCACAACTCCGTGGCAC-C--CTT--TT-A
502900 AAGC
59 AAGC
* *
502904 CCACAACTCCGTGGCACTCTTTTTCCTTCAAAGCCCACAACTCCGTGGCACCCTTTT-AAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCTTTTAAAGC
* *
502965 CCACAACTCCGTGGCATTCTTTTTCCTTCTACGTCCACAACTCCGTGGCACCTTTTTCTTTTTAA
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACC-----C-TTTTAA
503030 AGC
60 AGC
* * * *
503033 CCACAAC-CCTGTGGCA-TCCTGTTCCTTTTAAGTCCGCAACTCCGTGGCACTCTTTTTCCCTTT
1 CCACAACTCC-GTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCA--------CCCTTT
503096 TAAAGC
57 TAAAGC
503102 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCTTTT-AAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCTTTTAAAGC
* * * *
503163 CCACAACTCCGTGACATTCTTTTTCCTTCTACGTCCATAACTCCGTGGCA
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCA
503213 TCTTTCTCCT
Statistics
Matches: 269, Mismatches: 21, Indels: 45
0.80 0.06 0.13
Matches are distributed among these distances:
61 102 0.38
62 7 0.03
63 2 0.01
65 2 0.01
66 1 0.00
67 35 0.13
68 55 0.20
69 31 0.12
70 32 0.12
75 2 0.01
ACGTcount: A:0.19, C:0.36, G:0.13, T:0.32
Consensus pattern (62 bp):
CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCTTTTAAAGC
Found at i:503185 original size:27 final size:27
Alignment explanation
Indices: 503126--503178 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
503116 CACTCTTTTT
* * *
503126 CCTTCTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGCCCACAACTCCGTGACAC
503153 CCTTTTAAGCCCACAACTCCGTGACA
1 CCTTTTAAGCCCACAACTCCGTGACA
503179 TTCTTTTTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.13, T:0.23
Consensus pattern (27 bp):
CCTTTTAAGCCCACAACTCCGTGACAC
Found at i:503227 original size:137 final size:132
Alignment explanation
Indices: 502792--503226 Score: 416
Period size: 129 Copynumber: 3.3 Consensus size: 132
502782 TTCGTGGCAC
* * * *
502792 CCTTTTAAGCCCACAACTCCGTGGCACTCTTTTT-CCTTCTAAGTCCACAACTCCGTGGCAC-CT
1 CCTTCTAAGTCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAGCCCACAACTCCGTGGCACTCT
* * * * *
502855 TTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCAAAGCCCACAACTCC-GTGGC
66 TTTTCCTTCT-AAGTCCACAACTCCGTGGCAC-CTCTTT--TT-AAAGCCCACAAC-CCTGTGAC
* *
502919 ACTCTTTTT
125 A-TCCTGTT
* * *
502928 CCTTCAAAGCCCACAACTCCGTGGCA--------CCCTTTTAAGCCCACAACTCCGTGGCATTCT
1 CCTTCTAAGTCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAGCCCACAACTCCGTGGCACTCT
* *
502985 TTTTCCTTCTACGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACCCTGTGGCAT
66 TTTTCCTTCTAAGTCCACAACTCCGTGGCACC----TCTTTTTAAAGCCCACAACCCTGTGACAT
503050 CCTGTT
127 CCTGTT
* *
503056 CCTTTTAAGTCCGCAACTCCGTGGCACTCTTTTTCCCTTTTAAAGCCCACAACTCCGTGGCACTC
1 CCTTCTAAGTCCACAACTCCGTGGCACTCTTTTTCCCTTTT-AAGCCCACAACTCCGTGGCACTC
503121 TTTTTCCTTCTAAGTCCACAACTCCGTGGCACC-C-TTTT-AAGCCCACAACTCC-GTGACATTC
65 TTTTTCCTTCTAAGTCCACAACTCCGTGGCACCTCTTTTTAAAGCCCACAAC-CCTGTGACA-TC
* *
503182 TTTTT
128 CTGTT
* * * *
503187 CCTTCTACGTCCATAACTCCGTGGCA-TCTTTCTCCTTTTT
1 CCTTCTAAGTCCACAACTCCGTGGCACTCTTTTTCCCTTTT
503227 CTAAAGCCCA
Statistics
Matches: 254, Mismatches: 27, Indels: 42
0.79 0.08 0.13
Matches are distributed among these distances:
128 30 0.12
129 61 0.24
130 40 0.16
131 33 0.13
132 5 0.02
136 31 0.12
137 54 0.21
ACGTcount: A:0.19, C:0.36, G:0.12, T:0.34
Consensus pattern (132 bp):
CCTTCTAAGTCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAGCCCACAACTCCGTGGCACTCT
TTTTCCTTCTAAGTCCACAACTCCGTGGCACCTCTTTTTAAAGCCCACAACCCTGTGACATCCTG
TT
Found at i:503303 original size:33 final size:33
Alignment explanation
Indices: 503226--503454 Score: 349
Period size: 33 Copynumber: 7.0 Consensus size: 33
503216 TTCTCCTTTT
*
503226 TCTAAAGCCCACACAAGTTGGTGGCAACCCTTC
1 TCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
*
503259 -CAAAAGCCCACACAAGTCGGTGGCAACCCTTC
1 TCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
* *
503291 TCTAAAGCCCACACAAGTCGGTGGCAACCTTTT
1 TCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
* *
503324 TC-AAAGCTCAAACAAGTCGGTGGCAA-CCTTC
1 TCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
503355 TTCTAAAGCCCACACAAGTCGGTGGCAACCC-TC
1 -TCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
* *
503388 TCTAAAGCCCACACAAGTTGGTGGCAACCATTC
1 TCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
503421 TCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
1 TCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
503454 T
1 T
503455 AAGCCCAATA
Statistics
Matches: 176, Mismatches: 15, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
31 3 0.02
32 82 0.47
33 89 0.51
34 2 0.01
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.20
Consensus pattern (33 bp):
TCTAAAGCCCACACAAGTCGGTGGCAACCCTTC
Found at i:503307 original size:65 final size:64
Alignment explanation
Indices: 503226--503461 Score: 341
Period size: 65 Copynumber: 3.7 Consensus size: 64
503216 TTCTCCTTTT
*
503226 TCTAAAGCCCACACAAGTTGGTGGCAACCCTTCCAAAAGCCCACACAAGTCGGTGGCAACCCTTC
1 TCTAAAGCCCACACAAGTCGGTGGCAACCCTTCC-AAAGCCCACACAAGTCGGTGGCAACCCTTC
* * * *
503291 TCTAAAGCCCACACAAGTCGGTGGCAACCTTTTTCAAAGCTCAAACAAGTCGGTGGCAA-CCTTC
1 TCTAAAGCCCACACAAGTCGGTGGCAACC-CTTCCAAAGCCCACACAAGTCGGTGGCAACCCTTC
* * *
503355 TTCTAAAGCCCACACAAGTCGGTGGCAACCCTCTCTAAAGCCCACACAAGTTGGTGGCAACCATT
1 -TCTAAAGCCCACACAAGTCGGTGGCAACCCT-TCCAAAGCCCACACAAGTCGGTGGCAACCCTT
503420 C
64 C
*
503421 TCTAAAGCCCACACAAGTCGGTGGCAACCCTT-CTAAGCCCA
1 TCTAAAGCCCACACAAGTCGGTGGCAACCCTTCCAAAGCCCA
503462 ATATAGCTGG
Statistics
Matches: 153, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
63 7 0.05
64 7 0.05
65 132 0.86
66 7 0.05
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.19
Consensus pattern (64 bp):
TCTAAAGCCCACACAAGTCGGTGGCAACCCTTCCAAAGCCCACACAAGTCGGTGGCAACCCTTC
Found at i:503563 original size:43 final size:43
Alignment explanation
Indices: 503500--503773 Score: 323
Period size: 43 Copynumber: 6.1 Consensus size: 43
503490 GCACCTTCTT
* *
503500 CTTTAAGTCCAATGTAGCTGGGCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* * *
503543 CTTTAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C
* *
503590 ATCTTTAAGTCCAATGTAGCTAGCCTTGAATCAGCACATTGGCAC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* * *
503635 CTTTAAGTCGAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C
* *
503682 TTCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTAGCAC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
*
503727 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
503770 CTTT
1 CTTT
503774 TCCATCTTTA
Statistics
Matches: 196, Mismatches: 23, Indels: 24
0.81 0.09 0.10
Matches are distributed among these distances:
43 118 0.60
45 2 0.01
47 2 0.01
49 74 0.38
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:503618 original size:92 final size:92
Alignment explanation
Indices: 503449--503826 Score: 603
Period size: 92 Copynumber: 4.1 Consensus size: 92
503439 CGGTGGCAAC
* *
503449 CCTTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATG
1 CCTT-TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
*
503514 TAGCTGGGCTTGAATCAGCACATTGGCA
65 TAGCTGGCCTTGAATCAGCACATTGGCA
* *
503542 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
*
503607 AGCTAGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* * *
503634 CCTTTAAGTCGAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
*
503699 AGCTGGCCTTGAATCAGCACATTAGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
*
503726 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAA
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTTTAAGTCCAA
*
503791 TGTAGCTGGCCTTGAATCAGCACATTGACA
63 TGTAGCTGGCCTTGAATCAGCACATTGGCA
503821 TCCTTT
1 -CCTTT
503827 TTTCTCATTT
Statistics
Matches: 264, Mismatches: 17, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
92 212 0.80
93 4 0.02
94 2 0.01
95 41 0.16
96 5 0.02
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.32
Consensus pattern (92 bp):
CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
AGCTGGCCTTGAATCAGCACATTGGCA
Found at i:503751 original size:22 final size:21
Alignment explanation
Indices: 503684--503751 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 21
503674 GCACCTTCTT
503684 CTTTAAGTCCAATGTAGCTGGC
1 CTTTAAGTCCAAT-TAGCTGGC
* *
503706 CTTGAA-TCAGCACATTAGC--AC
1 CTTTAAGTC--CA-ATTAGCTGGC
503727 CTTTAAGTCCAATATAGCTGGC
1 CTTTAAGTCCAAT-TAGCTGGC
503749 CTT
1 CTT
503752 GAATCAGCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 14
0.66 0.08 0.26
Matches are distributed among these distances:
19 2 0.06
20 6 0.17
21 8 0.23
22 11 0.31
23 6 0.17
24 2 0.06
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (21 bp):
CTTTAAGTCCAATTAGCTGGC
Found at i:503805 original size:52 final size:53
Alignment explanation
Indices: 503727--503881 Score: 177
Period size: 52 Copynumber: 2.9 Consensus size: 53
503717 ACATTAGCAC
503727 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
* * * *
503779 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC--TTTTCTCAT
* * * * * * *
503835 TTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTT
503882 ATCACTTTTC
Statistics
Matches: 84, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
52 38 0.45
53 5 0.06
55 6 0.07
56 35 0.42
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
Found at i:504502 original size:8 final size:9
Alignment explanation
Indices: 504481--504514 Score: 68
Period size: 9 Copynumber: 3.8 Consensus size: 9
504471 GACGAATATG
504481 TTTTTTAGA
1 TTTTTTAGA
504490 TTTTTTAGA
1 TTTTTTAGA
504499 TTTTTTAGA
1 TTTTTTAGA
504508 TTTTTTA
1 TTTTTTA
504515 AAAAACGGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.71
Consensus pattern (9 bp):
TTTTTTAGA
Found at i:504752 original size:13 final size:13
Alignment explanation
Indices: 504734--504758 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
504724 CATAAAGTGT
504734 TGTATCGATACAA
1 TGTATCGATACAA
504747 TGTATCGATACA
1 TGTATCGATACA
504759 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:504777 original size:32 final size:33
Alignment explanation
Indices: 504714--504779 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 33
504704 TTCAATGATT
*
504714 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCAATACAA
*
504747 TGTATCGATACAT-AAGTTTTGTATCAATACAA
1 TGTATCGATACATAAAGTGTTGTATCAATACAA
504779 T
1 T
504780 TTAAGCTACT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.58
33 13 0.42
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCAATACAA
Found at i:504838 original size:13 final size:13
Alignment explanation
Indices: 504820--504844 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
504810 ATTACTCAAC
504820 TGTATCGATACAT
1 TGTATCGATACAT
504833 TGTATCGATACA
1 TGTATCGATACA
504845 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:504897 original size:52 final size:52
Alignment explanation
Indices: 504853--504981 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
504843 CACTGATCTT
*
504853 TGTATCGATACATGTAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
504905 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
504957 TGTATCGATACATGCAAGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
504982 TCATATTTCG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:508933 original size:97 final size:97
Alignment explanation
Indices: 508818--509061 Score: 337
Period size: 97 Copynumber: 2.5 Consensus size: 97
508808 TTTTTGATTG
508818 AAAAAC-GAGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGAAGTGTCCCCAATGATGACAATTT
1 AAAAACAG-GGTTGGAGTATCCCCTCGGAGGAATGGGGTTGAAGTGTCCCCAATGATGACAATTT
**
508882 AAGTGTGAATAAAATTTAAACTTTGATGCGTTT
65 AAGTAAGAATAAAATTTAAACTTTGATGCGTTT
** * * * *
508915 AAAAATGGGGTTGGAGTATCCCCTCGGAGGAATGGGATTAAAGTGTCCCCGATGGTGACAATTTA
1 AAAAACAGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGAAGTGTCCCCAATGATGACAATTTA
* *
508980 AGTAAGAATAAGATTTAAACTTTGATGTGTTT
66 AGTAAGAATAAAATTTAAACTTTGATGCGTTT
* * * * *
509012 AAAAGCAGGGTTAGAGTATCCCCTCGGAGAAATAGGGTTGAAGTATCCCC
1 AAAAACAGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGAAGTGTCCCC
509062 GATAAATAAA
Statistics
Matches: 128, Mismatches: 18, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
97 127 0.99
98 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (97 bp):
AAAAACAGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGAAGTGTCCCCAATGATGACAATTTA
AGTAAGAATAAAATTTAAACTTTGATGCGTTT
Found at i:511331 original size:20 final size:20
Alignment explanation
Indices: 511294--511332 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
511284 GGCCACTCAT
** *
511294 TTTCCTTTTTTTTGTTTTTG
1 TTTCCTTTTTGATATTTTTG
511314 TTTCCTTTTTGATATTTTT
1 TTTCCTTTTTGATATTTTT
511333 TTGTTAATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.05, C:0.10, G:0.08, T:0.77
Consensus pattern (20 bp):
TTTCCTTTTTGATATTTTTG
Found at i:516000 original size:20 final size:20
Alignment explanation
Indices: 515975--516013 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
515965 ATAATAATTT
**
515975 CAACAAAATTTAGCATCATG
1 CAACAAAATCAAGCATCATG
515995 CAACAAAATCAAGCATCAT
1 CAACAAAATCAAGCATCAT
516014 ACCTCCATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.23, G:0.08, T:0.21
Consensus pattern (20 bp):
CAACAAAATCAAGCATCATG
Found at i:516224 original size:21 final size:20
Alignment explanation
Indices: 516181--516225 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
516171 TTTTGCTTGT
* *
516181 TGTTGCTTGTTTGCTGCTGG
1 TGTTGCTTGGTTGCTGCTAG
*
516201 TGTTGCTTAGGTTGTTGCTAG
1 TGTTGCTT-GGTTGCTGCTAG
516222 TGTT
1 TGTT
516226 ACTACTAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.04, C:0.11, G:0.33, T:0.51
Consensus pattern (20 bp):
TGTTGCTTGGTTGCTGCTAG
Found at i:516300 original size:10 final size:11
Alignment explanation
Indices: 516274--516305 Score: 57
Period size: 10 Copynumber: 3.0 Consensus size: 11
516264 ATAGCTGCTA
516274 TTTTGTTTCTG
1 TTTTGTTTCTG
516285 TTTTGTTTCT-
1 TTTTGTTTCTG
516295 TTTTGTTTCTG
1 TTTTGTTTCTG
516306 GTATTTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.00, C:0.09, G:0.16, T:0.75
Consensus pattern (11 bp):
TTTTGTTTCTG
Found at i:516881 original size:35 final size:35
Alignment explanation
Indices: 516824--516910 Score: 120
Period size: 35 Copynumber: 2.5 Consensus size: 35
516814 CATTACATCT
* * *
516824 CAACAACTTTATTTCTTCTTCATTGCTGCCGTTTG
1 CAACAGCTTTATTTCTTATTCATTGCTGCCATTTG
* *
516859 CAGCAGCTTTATTTCTTATTCATTGTTGCCATTTG
1 CAACAGCTTTATTTCTTATTCATTGCTGCCATTTG
*
516894 CAACGGCTTTATTTCTT
1 CAACAGCTTTATTTCTT
516911 CTATATTAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.17, C:0.23, G:0.13, T:0.47
Consensus pattern (35 bp):
CAACAGCTTTATTTCTTATTCATTGCTGCCATTTG
Found at i:517083 original size:13 final size:13
Alignment explanation
Indices: 517065--517101 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
517055 TCATTTCTCC
517065 AATCTCATGCATG
1 AATCTCATGCATG
517078 AATCTCATGCATG
1 AATCTCATGCATG
517091 AAT-TCATGCAT
1 AATCTCATGCAT
517102 TGCCACCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (13 bp):
AATCTCATGCATG
Found at i:517274 original size:17 final size:16
Alignment explanation
Indices: 517254--517296 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
517244 TATTTTTATT
517254 TTTTTTATATTTTCTTA
1 TTTTTTATATTTTC-TA
* *
517271 TTTTATGTATTTTCTA
1 TTTTTTATATTTTCTA
*
517287 TTTTTAATAT
1 TTTTTTATAT
517297 CAAATAAACC
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.72
Consensus pattern (16 bp):
TTTTTTATATTTTCTA
Found at i:521597 original size:15 final size:15
Alignment explanation
Indices: 521577--521697 Score: 68
Period size: 15 Copynumber: 7.5 Consensus size: 15
521567 TTTCATATTT
*
521577 TTTTTCTTTTTTTCC
1 TTTTTCTTTCTTTCC
521592 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTCTTTC--C
521609 TTCATCTTCTTTCTTT-C
1 TT--T-TTCTTTCTTTCC
** *
521626 TTTCTTACCTAACTTT-T
1 TTT-TT--CTTTCTTTCC
*
521643 TTTTTCTTTTTTTCC
1 TTTTTCTTTCTTTCC
521658 TTTTTCTTTCTTT-C
1 TTTTTCTTTCTTTCC
*
521672 TTTTTCATCTTCTTTCT
1 TTTTTC-T-TTCTTTCC
521689 TTCTTTCTT
1 TT-TTTCTT
521698 ACTTAACTTT
Statistics
Matches: 84, Mismatches: 10, Indels: 23
0.72 0.09 0.20
Matches are distributed among these distances:
14 12 0.14
15 30 0.36
16 9 0.11
17 18 0.21
18 4 0.05
19 1 0.01
20 10 0.12
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTTCTTTCTTTCC
Found at i:521601 original size:11 final size:10
Alignment explanation
Indices: 521574--521690 Score: 71
Period size: 10 Copynumber: 11.3 Consensus size: 10
521564 CCATTTCATA
521574 TTTTT-TTTC
1 TTTTTCTTTC
*
521583 TTTTT-TTCC
1 TTTTTCTTTC
521592 TTTTTCTTTC
1 TTTTTCTTTC
521602 TTTCTTCTTCATC
1 TTT-TTCTT--TC
521615 TTCTTTCTTTC
1 TT-TTTCTTTC
**
521626 TTTCTTACCTAAC
1 TTT-TT--CTTTC
*
521639 TTTTTTTTTC
1 TTTTTCTTTC
*
521649 TTTTT-TTCC
1 TTTTTCTTTC
521658 TTTTTCTTTC
1 TTTTTCTTTC
521668 TTTCTT-TTTC
1 TTT-TTCTTTC
* *
521678 ATCTTCTTTC
1 TTTTTCTTTC
521688 TTT
1 TTT
521691 CTTTCTTACT
Statistics
Matches: 84, Mismatches: 13, Indels: 21
0.71 0.11 0.18
Matches are distributed among these distances:
9 23 0.27
10 30 0.36
11 13 0.15
12 2 0.02
13 15 0.18
14 1 0.01
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:521603 original size:4 final size:4
Alignment explanation
Indices: 521579--521697 Score: 74
Period size: 4 Copynumber: 30.5 Consensus size: 4
521569 TCATATTTTT
* *
521579 TTTC TTTT TTTC CTT- TTTC TTTC TTTC -TTC -TTC ATCTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC -T-TTC TTTC TTTC
* ** * *
521626 TTTC TTACC TAAC TTT- TTT- TTTC TTTT TTTC CTT- TTTC TTTC TTTC
1 TTTC TT-TC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
521672 -TT- TTTC ATCTTC TTTC TTTC TTTC TT
1 TTTC TTTC -T-TTC TTTC TTTC TTTC TT
521698 ACTTAACTTT
Statistics
Matches: 91, Mismatches: 13, Indels: 22
0.72 0.10 0.17
Matches are distributed among these distances:
3 20 0.22
4 60 0.66
5 5 0.05
6 6 0.07
ACGTcount: A:0.04, C:0.24, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTC
Found at i:521626 original size:24 final size:23
Alignment explanation
Indices: 521568--521697 Score: 118
Period size: 24 Copynumber: 6.0 Consensus size: 23
521558 GCCACTCCAT
*
521568 TTCATATTTTT-TTTCTTT-TT-
1 TTCATCTTTTTCTTTCTTTCTTC
521588 TTC--CTTTTTCTTTCTTTCTTC
1 TTCATCTTTTTCTTTCTTTCTTC
521609 TTCATCTTCTTTCTTTCTTTCTTAC
1 TTCATCTT-TTTCTTTCTTTCTT-C
* * *
521634 CT-AACTTTTTTTTTCTTT-TT-
1 TTCATCTTTTTCTTTCTTTCTTC
*
521654 TTC--CTTTTTCTTTCTTTCTTT
1 TTCATCTTTTTCTTTCTTTCTTC
521675 TTCATCTTCTTTCTTTCTTTCTT
1 TTCATCTT-TTTCTTTCTTTCTT
521698 ACTTAACTTT
Statistics
Matches: 91, Mismatches: 6, Indels: 22
0.76 0.05 0.18
Matches are distributed among these distances:
18 5 0.05
19 20 0.22
20 8 0.09
21 6 0.07
22 2 0.02
23 16 0.18
24 32 0.35
25 2 0.02
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.72
Consensus pattern (23 bp):
TTCATCTTTTTCTTTCTTTCTTC
Found at i:521651 original size:66 final size:66
Alignment explanation
Indices: 521574--521712 Score: 260
Period size: 66 Copynumber: 2.1 Consensus size: 66
521564 CCATTTCATA
521574 TTTTTTTTCTTTTTTTCCTTTTTCTTTCTTTCTTCTTCATCTTCTTTCTTTCTTTCTTACCTAAC
1 TTTTTTTTCTTTTTTTCCTTTTTCTTTCTTTCTTCTTCATCTTCTTTCTTTCTTTCTTACCTAAC
521639 T
66 T
* *
521640 TTTTTTTTCTTTTTTTCCTTTTTCTTTCTTTCTTTTTCATCTTCTTTCTTTCTTTCTTACTTAAC
1 TTTTTTTTCTTTTTTTCCTTTTTCTTTCTTTCTTCTTCATCTTCTTTCTTTCTTTCTTACCTAAC
521705 T
66 T
521706 TTTTTTT
1 TTTTTTT
521713 AGCCCATAAC
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 71 1.00
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.73
Consensus pattern (66 bp):
TTTTTTTTCTTTTTTTCCTTTTTCTTTCTTTCTTCTTCATCTTCTTTCTTTCTTTCTTACCTAAC
T
Found at i:521694 original size:20 final size:21
Alignment explanation
Indices: 521585--521694 Score: 91
Period size: 20 Copynumber: 5.1 Consensus size: 21
521575 TTTTTTTCTT
* *
521585 TTTTTCCTTTTTCTTTCTTTC
1 TTTTTCCATCTTCTTTCTTTC
*
521606 TTCTT-CATCTTCTTTCTTTC
1 TTTTTCCATCTTCTTTCTTTC
* *
521626 TTTCTTACCTAACTT-TTTTTTTC
1 TTT-TT-CC-ATCTTCTTTCTTTC
* *
521649 TTTTTTTCCTTTTTCTTTCTTTC
1 --TTTTTCCATCTTCTTTCTTTC
521672 TTTTT-CATCTTCTTTCTTTC
1 TTTTTCCATCTTCTTTCTTTC
521692 TTT
1 TTT
521695 CTTACTTAAC
Statistics
Matches: 70, Mismatches: 12, Indels: 15
0.72 0.12 0.15
Matches are distributed among these distances:
20 31 0.44
21 11 0.16
22 2 0.03
23 17 0.24
24 6 0.09
25 3 0.04
ACGTcount: A:0.05, C:0.24, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTTCCATCTTCTTTCTTTC
Found at i:522396 original size:18 final size:16
Alignment explanation
Indices: 522371--522410 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
522361 GACTTTTCTC
*
522371 TTTTTTTTTGCTTTTT
1 TTTTTTTTTGATTTTT
522387 GTTTTCTTTTTGATTTTT
1 -TTTT-TTTTTGATTTTT
522405 TTTTTT
1 TTTTTT
522411 GGTTAGTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 2 0.10
17 8 0.38
18 11 0.52
ACGTcount: A:0.03, C:0.05, G:0.07, T:0.85
Consensus pattern (16 bp):
TTTTTTTTTGATTTTT
Found at i:522653 original size:2 final size:2
Alignment explanation
Indices: 522646--522677 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
522636 ACATTTGTAA
522646 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
522678 CAAAGAAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:523876 original size:16 final size:16
Alignment explanation
Indices: 523857--523887 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
523847 ATAAAGATAA
*
523857 TTTTGAGTTAAAAATG
1 TTTTGAGTAAAAAATG
523873 TTTTGAGTAAAAAAT
1 TTTTGAGTAAAAAAT
523888 AGAAAGAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (16 bp):
TTTTGAGTAAAAAATG
Found at i:525782 original size:22 final size:22
Alignment explanation
Indices: 525749--525819 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
525739 ACTTACATAT
525749 TATAA-AATAAATAATTAAATTA
1 TATAATAA-AAATAATTAAATTA
* *
525771 TATAATAAAAATATATAAAAATA
1 TATAATAAAAATA-ATTAAATTA
* * *
525794 -AGAATATAAATATTTAAAATTA
1 TATAATAAAAATAATT-AAATTA
525816 TATA
1 TATA
525820 TTATATTATT
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
21 1 0.03
22 25 0.68
23 11 0.30
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (22 bp):
TATAATAAAAATAATTAAATTA
Found at i:525845 original size:17 final size:17
Alignment explanation
Indices: 525825--525857 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
525815 ATATATTATA
525825 TTAT-TAAATATTAAAAT
1 TTATATAAA-ATTAAAAT
525842 TTATATAAAATTAAAA
1 TTATATAAAATTAAAA
525858 ATATTATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TTATATAAAATTAAAAT
Found at i:525864 original size:19 final size:19
Alignment explanation
Indices: 525822--525872 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
525812 ATTATATATT
525822 ATATTAT-TAAATATTAAA
1 ATATTATATAAATATTAAA
525840 AT-TTATATAAA-ATTAAAA
1 ATATTATATAAATATT-AAA
*
525858 ATATTATATTAATAT
1 ATATTATATAAATAT
525873 ATAATATAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
17 7 0.25
18 11 0.39
19 8 0.29
20 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATATTATATAAATATTAAA
Found at i:526102 original size:17 final size:16
Alignment explanation
Indices: 526071--526138 Score: 50
Period size: 15 Copynumber: 4.2 Consensus size: 16
526061 TAATAAGAAT
*
526071 TATTAACATATTAAAATT
1 TATTAA-ATA-TAAAATA
*
526089 TATATAATTATAAAATA
1 TAT-TAAATATAAAATA
*
526106 TATTAAATAT-AATTA
1 TATTAAATATAAAATA
* *
526121 TAAT-ATTATAAAATA
1 TATTAAATATAAAATA
526136 TAT
1 TAT
526139 GATATGGATA
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
14 4 0.10
15 13 0.32
16 6 0.15
17 9 0.22
18 5 0.12
19 3 0.08
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (16 bp):
TATTAAATATAAAATA
Found at i:526115 original size:22 final size:21
Alignment explanation
Indices: 526090--526137 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 21
526080 ATTAAAATTT
*
526090 ATATAATTATAAAATATATTAA
1 ATATAATTATAAAAT-TATAAA
*
526112 ATATAATTATAATATTATAAA
1 ATATAATTATAAAATTATAAA
526133 ATATA
1 ATATA
526138 TGATATGGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATATAATTATAAAATTATAAA
Found at i:526786 original size:11 final size:11
Alignment explanation
Indices: 526767--526797 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
526757 ATATTATAAA
526767 AAATAAAAATT
1 AAATAAAAATT
*
526778 AATTAAAAATT
1 AAATAAAAATT
526789 AAATAAAAA
1 AAATAAAAA
526798 ATAGAATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AAATAAAAATT
Found at i:528098 original size:3 final size:3
Alignment explanation
Indices: 528090--528133 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
528080 TTTTTTACAT
528090 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
528134 CTACATTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:528327 original size:2 final size:2
Alignment explanation
Indices: 528322--528351 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
528312 ATATTGACTA
528322 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
528352 TTTTTATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:529526 original size:20 final size:19
Alignment explanation
Indices: 529505--529571 Score: 56
Period size: 20 Copynumber: 3.7 Consensus size: 19
529495 TTTTATTTTA
529505 TTATAATTATATATAAAAT
1 TTATAATTATATATAAAAT
*
529524 ATTTTATATT-TATAT-AAAT
1 -TTATA-ATTATATATAAAAT
529543 TT-TAA-TATAT-TAATAAT
1 TTATAATTATATATAA-AAT
529560 TTAT-ATTATATA
1 TTATAATTATATA
529572 AATTTTAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 15
0.71 0.02 0.27
Matches are distributed among these distances:
15 2 0.05
16 5 0.13
17 8 0.21
18 8 0.21
19 4 0.10
20 9 0.23
21 3 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTATAATTATATATAAAAT
Found at i:529551 original size:32 final size:33
Alignment explanation
Indices: 529483--529603 Score: 108
Period size: 32 Copynumber: 3.7 Consensus size: 33
529473 ATATATGTAT
* * *
529483 TATATTAATATTTTTTATTT-TATTATAATTAT-A
1 TATATAAATATTTTATATTTATA-TA-AATTTTAA
529516 TATA-AAATATTTTATATTTATATAAATTTTAA
1 TATATAAATATTTTATATTTATATAAATTTTAA
* *
529548 TATATTAATAATTTATA-TTATATAAATTTTAA
1 TATATAAATATTTTATATTTATATAAATTTTAA
* **
529580 AATATTTATATATTTATA-TTATAT
1 TATATAAATAT-TTTATATTTATAT
529604 TATAATTATT
Statistics
Matches: 76, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
31 5 0.07
32 43 0.57
33 28 0.37
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (33 bp):
TATATAAATATTTTATATTTATATAAATTTTAA
Found at i:529591 original size:40 final size:42
Alignment explanation
Indices: 529539--529651 Score: 110
Period size: 40 Copynumber: 2.7 Consensus size: 42
529529 ATATTTATAT
529539 AAAT-TTTAATATATTAATAATTTATATTAT-A-TAAATTTTA
1 AAATATTTAATATATTAAT-ATTTATATTATAATTAAATTTTA
* **
529579 AAATATTT-ATATATTTATA-TTATATTATAATTATTTTTTA
1 AAATATTTAATATATTAATATTTATATTATAATTAAATTTTA
*
529619 AAATTATATTCATATAATTAATATTTAATATTA
1 AAA-TAT-TTAATAT-ATTAATATTT-ATATTA
529652 GTTAAAAACT
Statistics
Matches: 60, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
38 9 0.15
39 2 0.03
40 23 0.38
41 6 0.10
42 2 0.03
43 4 0.07
44 6 0.10
45 2 0.03
46 6 0.10
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (42 bp):
AAATATTTAATATATTAATATTTATATTATAATTAAATTTTA
Found at i:529594 original size:18 final size:18
Alignment explanation
Indices: 529518--529594 Score: 52
Period size: 18 Copynumber: 4.0 Consensus size: 18
529508 TAATTATATA
529518 TAAAATATTT-TATATTT
1 TAAAATATTTATATATTT
*
529535 ATATAAAT-TTTA-ATATAT
1 -TA-AAATATTTATATATTT
529553 TAATAATTTATATTATATAAATTT
1 TAA-AA--TAT-TTATAT--ATTT
529577 TAAAATATTTATATATTT
1 TAAAATATTTATATATTT
529595 ATATTATATT
Statistics
Matches: 47, Mismatches: 2, Indels: 20
0.68 0.03 0.29
Matches are distributed among these distances:
16 1 0.02
17 4 0.09
18 14 0.30
19 5 0.11
20 7 0.15
21 6 0.13
22 2 0.04
23 2 0.04
24 6 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TAAAATATTTATATATTT
Found at i:529595 original size:33 final size:33
Alignment explanation
Indices: 529521--529603 Score: 125
Period size: 32 Copynumber: 2.5 Consensus size: 33
529511 TTATATATAA
*
529521 AATAT-TTTATATTTATATAAATTTTAATATATT
1 AATATATTTATA-TTATATAAATTTTAAAATATT
529554 AATA-ATTTATATTATATAAATTTTAAAATATT
1 AATATATTTATATTATATAAATTTTAAAATATT
*
529586 TATATATTTATATTATAT
1 AATATATTTATATTATAT
529604 TATAATTATT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
32 23 0.50
33 23 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (33 bp):
AATATATTTATATTATATAAATTTTAAAATATT
Found at i:529606 original size:18 final size:18
Alignment explanation
Indices: 529480--529607 Score: 73
Period size: 16 Copynumber: 7.7 Consensus size: 18
529470 TACATATATG
529480 TATTATATTA-ATATTT-
1 TATTATATTATATATTTA
* *
529496 T-TTATTTTATTATAATTA
1 TATTATATTA-TATATTTA
**
529514 TA-TATAAAATAT-TTTA
1 TATTATATTATATATTTA
*
529530 TATT-TA-TATAAATTT-
1 TATTATATTATATATTTA
*
529545 TAATATATTA-ATAATTTA
1 TATTATATTATAT-ATTTA
*
529563 TATTATA-TAAAT-TTTA
1 TATTATATTATATATTTA
* *
529579 AAATAT-TTATATATTTA
1 TATTATATTATATATTTA
529596 TATTATATTATA
1 TATTATATTATA
529608 ATTATTTTTT
Statistics
Matches: 82, Mismatches: 16, Indels: 26
0.66 0.13 0.21
Matches are distributed among these distances:
15 13 0.16
16 26 0.32
17 25 0.30
18 18 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTATATTATATATTTA
Found at i:530026 original size:11 final size:11
Alignment explanation
Indices: 530010--530048 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
530000 AAAATATTTA
530010 TATATTTATAT
1 TATATTTATAT
530021 TATATTT-TAAT
1 TATATTTAT-AT
530032 TAT-TTTATAT
1 TATATTTATAT
530042 TATATTT
1 TATATTT
530049 GTATAATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TATATTTATAT
Found at i:530053 original size:29 final size:29
Alignment explanation
Indices: 529983--530047 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 29
529973 GTCAATAATT
*
529983 TATA-TTATA-TAAATTTTAAAATATTTA
1 TATATTTATATTATATTTTAAAATATTTA
*
530010 TATATTTATATTATATTTT-AATTATTT-
1 TATATTTATATTATATTTTAAAATATTTA
530037 TATA-TTATATT
1 TATATTTATATT
530048 TGTATAATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 7 0.21
27 8 0.24
28 12 0.35
29 7 0.21
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (29 bp):
TATATTTATATTATATTTTAAAATATTTA
Found at i:532191 original size:15 final size:16
Alignment explanation
Indices: 532171--532208 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
532161 TATAGTTAAA
*
532171 AAATTATAATT-ATTT
1 AAATTATAATTAAATT
532186 AAATTA-AATTAAATT
1 AAATTATAATTAAATT
532201 AAATTATA
1 AAATTATA
532209 TTTTTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 4 0.20
15 15 0.75
16 1 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATTATAATTAAATT
Found at i:533153 original size:30 final size:30
Alignment explanation
Indices: 533106--533169 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
533096 ATAATTTAAC
*
533106 ATAT-TTTTTAATATTTATACT-ATAATATT
1 ATATATTTTTAATATTTATA-TGATAAAATT
* *
533135 ATATATTTTTATTTTTTATATGATAAAATT
1 ATATATTTTTAATATTTATATGATAAAATT
533165 ATATA
1 ATATA
533170 ATGTAAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 5 0.17
30 25 0.83
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (30 bp):
ATATATTTTTAATATTTATATGATAAAATT
Found at i:533974 original size:14 final size:15
Alignment explanation
Indices: 533940--533969 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
533930 ATTATTTTTT
*
533940 AATAATTTTTAATAA
1 AATAATTTTAAATAA
533955 AATAATTTTAAATAA
1 AATAATTTTAAATAA
533970 TTAATAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATAATTTTAAATAA
Found at i:534700 original size:21 final size:21
Alignment explanation
Indices: 534641--534700 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 21
534631 AATTATTATT
*
534641 TTTAATAAAATAAAAATAATA
1 TTTAATAAATTAAAAATAATA
*
534662 TTTAATTAAGTTTTAAAAA-AATA
1 TTTAA-TAA--ATTAAAAATAATA
534685 TATTAATAAATTAAAA
1 T-TTAATAAATTAAAA
534701 TATTAATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
21 11 0.34
22 3 0.09
23 8 0.25
24 10 0.31
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
TTTAATAAATTAAAAATAATA
Found at i:534929 original size:16 final size:17
Alignment explanation
Indices: 534904--534936 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
534894 GAAGAGAGCT
534904 TTTAAAATTT-TAAAAA
1 TTTAAAATTTGTAAAAA
*
534920 TTTAATATTTGTAAAAA
1 TTTAAAATTTGTAAAAA
534937 ATTTTATCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
TTTAAAATTTGTAAAAA
Found at i:535129 original size:24 final size:23
Alignment explanation
Indices: 535085--535141 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 23
535075 TTTAAGTATT
535085 ATTTATTTTTATTTATAAAATTA
1 ATTTATTTTTATTTATAAAATTA
*
535108 ATTTA-TTTTATTT-T--TATTAA
1 ATTTATTTTTATTTATAAAATT-A
535128 ATTTATTTTTATTT
1 ATTTATTTTTATTT
535142 GATTATGTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
19 3 0.10
20 6 0.19
21 9 0.29
22 8 0.26
23 5 0.16
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (23 bp):
ATTTATTTTTATTTATAAAATTA
Found at i:535146 original size:20 final size:20
Alignment explanation
Indices: 535107--535146 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
535097 TTATAAAATT
*
535107 AATTTATTTTATTTTTATTA
1 AATTTATTTTATTTTGATTA
535127 AATTTATTTT-TATTTGATTA
1 AATTTATTTTAT-TTTGATTA
535147 TGTGAGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (20 bp):
AATTTATTTTATTTTGATTA
Found at i:535712 original size:74 final size:73
Alignment explanation
Indices: 535576--535714 Score: 163
Period size: 74 Copynumber: 1.9 Consensus size: 73
535566 TTATTTGATT
* * * **
535576 ATATGGGTTTAAATTTTTAGGGTATAATTTATTTTAATTTCTAAAAATTTAATTATGTTTTTTAT
1 ATATGAGTTTAAATTTTTAGGATATAATTTATTTTAATTTATAAAAATTTAAGAATGTTTTTTAT
535641 TAGGTATG
66 TAGGTATG
* * * *
535649 ATATGAGTTTAAATTTTTAATGATGTAATTTAATTTT-ATTTATACAAATTTAAGAATTATTTTT
1 ATATGAGTTTAAATTTTT-AGGATATAATTT-ATTTTAATTTATAAAAATTTAAGAA-TGTTTTT
535713 TA
63 TA
535715 ATTTGATTAT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
73 17 0.31
74 24 0.44
75 13 0.24
ACGTcount: A:0.35, C:0.01, G:0.11, T:0.53
Consensus pattern (73 bp):
ATATGAGTTTAAATTTTTAGGATATAATTTATTTTAATTTATAAAAATTTAAGAATGTTTTTTAT
TAGGTATG
Found at i:536922 original size:14 final size:14
Alignment explanation
Indices: 536903--536930 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
536893 AGACTTGAGA
536903 CACACACATTTCAT
1 CACACACATTTCAT
536917 CACACACATTTCAT
1 CACACACATTTCAT
536931 TTCCTATGCA
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:0.36, C:0.36, G:0.00, T:0.29
Consensus pattern (14 bp):
CACACACATTTCAT
Found at i:538280 original size:52 final size:52
Alignment explanation
Indices: 538224--538322 Score: 119
Period size: 52 Copynumber: 1.9 Consensus size: 52
538214 AATATATATA
* *
538224 TTTTTAAAATTAATTAAT-TTTTTTTATTTTATTAAAAATTATAATAAAAACC
1 TTTTT-AAATTAATTAATAATTTTTTATTTTATTAAAAAATATAATAAAAACC
*** * *
538276 TTTTTTTTTTAATTTATAATTTTTTATTTTTTTAAAAAATATAATAA
1 TTTTTAAATTAATTAATAATTTTTTATTTTATTAAAAAATATAATAA
538323 TTAATATTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
51 8 0.21
52 31 0.79
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (52 bp):
TTTTTAAATTAATTAATAATTTTTTATTTTATTAAAAAATATAATAAAAACC
Found at i:538343 original size:55 final size:51
Alignment explanation
Indices: 538243--538353 Score: 123
Period size: 52 Copynumber: 2.1 Consensus size: 51
538233 TTAATTAATT
* * * *
538243 TTTTTTATTTTATTAAAAATTATAATAAAAACCTTTTTTTTTTAATTTATAA
1 TTTTTTATTTTATTAAAAAATATAATAAAAACATTTTTTTGTTAATCTA-AA
* * *
538295 TTTTTTATTTTTTTAAAAAATATAATAATTAATATTTTAATTTGTTAATCTAAA
1 TTTTTTATTTTATTAAAAAATATAATAA-AAACATTTT--TTTGTTAATCTAAA
538349 TTTTT
1 TTTTT
538354 GAAATTTAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
52 26 0.53
53 6 0.12
54 7 0.14
55 10 0.20
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.59
Consensus pattern (51 bp):
TTTTTTATTTTATTAAAAAATATAATAAAAACATTTTTTTGTTAATCTAAA
Found at i:538388 original size:129 final size:127
Alignment explanation
Indices: 538141--539015 Score: 1020
Period size: 129 Copynumber: 6.9 Consensus size: 127
538131 AAAATTTATT
* *
538141 ATTATAATAAAAAACCCTTTTTATTTTTTAATTTAAAATATTTTA-TTTTAAAAAACATAATAAT
1 ATTATAAT-AAAAA-CC-TTTTATTTTTTAATTT-AAATTTTTTATTTTTAAAAAATATAATAAT
* * * *
538205 TAATATATTAA-----T-ATATATA-TTTTTAAAATTAATT-AAT-TT-TTTTTATTTTATTAAA
62 TAATATTTTAATTTGTTAATGTAAATTTTTTAAACTTAATTAAATATTATTTTTATTTTATTAAA
538260 A
127 A
538261 ATTATAATAAAAACCTTTT-TTTTTTAATTTATAATTTTTTATTTTTTTAAAAAATATAATAATT
1 ATTATAATAAAAACCTTTTATTTTTTAATTTA-AATTTTTTA--TTTTTAAAAAATATAATAATT
* * *
538325 AATATTTTAATTTGTTAATCTAAATTTTTGAAATTTAATTAAATATTATTTTTATTTTATTAAAA
63 AATATTTTAATTTGTTAATGTAAATTTTTTAAACTTAATTAAATATTATTTTTATTTTATTAAAA
*
538390 ATTATAATAAAAATCTTGTTTATTTTATTAATTTAAATTTTTTA--TTT-AAAAATATAATAATT
1 ATTATAATAAAAA-CCT-TTTATTTT-TTAATTTAAATTTTTTATTTTTAAAAAATATAATAATT
* *
538452 AATATTTTAATTTGTTAATATTAATTTTTTTGAAACTTAATTAAAT-TATATTTTTATTTTATTA
63 AATATTTTAATTTGTTAAT-GTAAATTTTTT-AAACTTAATTAAATAT-TATTTTTATTTTATTA
538516 AAA
125 AAA
* *
538519 ATTATAATAAAACCCTTTTTATTTTTTAATTTATAATTTTTTATTTTTAAAAAACATAATAATTA
1 ATTATAATAAAAACC-TTTTATTTTTTAATTTA-AATTTTTTATTTTTAAAAAATATAATAATTA
*
538584 ATTTTTTAATTTGTTAATGTAAATTTTTTTAAACTTAATTAAATATTATTTTTTATTTTATTAAA
64 ATATTTTAATTTGTTAATGTAAA-TTTTTTAAACTTAATTAAATATTA-TTTTTATTTTATTAAA
538649 A
127 A
**
538650 ATTATAATAAAAACC---CCTTTTTTAATTTAAAATTTTTTA-TTTTAAAAAATATAATAATTAA
1 ATTATAATAAAAACCTTTTATTTTTTAATTT-AAATTTTTTATTTTTAAAAAATATAATAATTAA
* *
538711 TATTTTAATTTGTTAATGTAATTTTTTTAAACTTAATT-AATATTATTTTTATTTTAATAAAA
65 TATTTTAATTTGTTAATGTAAATTTTTTAAACTTAATTAAATATTATTTTTATTTTATTAAAA
* *
538773 ATTATAATAGAAAAGCCTTTTTTATTTTTTAATTTAAATTTTTTATTTTAAAAAAATATGATAAT
1 ATTATAATA-AAAA-CC--TTTTATTTTTTAATTTAAATTTTTTATTTTTAAAAAATATAATAAT
* *
538838 TAATATTTTAA-TTGTTACTGTAATTTTTTTAAAAC-TAATTAAATATTA---TT-TTTTATTAA
62 TAATATTTTAATTTGTTAATGTAAATTTTTT-AAACTTAATTAAATATTATTTTTATTTTATTAA
538897 ATA
126 A-A
* * * * *
538900 ATGATAAT--AACCCTTTTA-TTTTT-ATTTAAAGGTTTTTATTTTTAAAAAATATAGTGATTAA
1 ATTATAATAAAAACCTTTTATTTTTTAATTTAAA-TTTTTTATTTTTAAAAAATATAATAATTAA
* * *
538961 TATTTTAATTTGTTAATATAAAATTTTTTAAACTTAATTATATATTATCTTTATT
65 TATTTTAATTTGTTAATGT-AAATTTTTTAAACTTAATTAAATATTATTTTTATT
539016 AAAAATAATA
Statistics
Matches: 664, Mismatches: 42, Indels: 92
0.83 0.05 0.12
Matches are distributed among these distances:
115 1 0.00
116 19 0.03
117 4 0.01
118 2 0.00
119 40 0.06
120 46 0.07
121 17 0.03
122 20 0.03
123 27 0.04
124 14 0.02
125 25 0.04
126 65 0.10
127 75 0.11
128 33 0.05
129 108 0.16
130 74 0.11
131 73 0.11
132 13 0.02
133 8 0.01
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (127 bp):
ATTATAATAAAAACCTTTTATTTTTTAATTTAAATTTTTTATTTTTAAAAAATATAATAATTAAT
ATTTTAATTTGTTAATGTAAATTTTTTAAACTTAATTAAATATTATTTTTATTTTATTAAAA
Found at i:538687 original size:15 final size:15
Alignment explanation
Indices: 538667--538696 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
538657 TAAAAACCCC
538667 TTTTTTAATTTAAAA
1 TTTTTTAATTTAAAA
*
538682 TTTTTTATTTTAAAA
1 TTTTTTAATTTAAAA
538697 AATATAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTTTAATTTAAAA
Found at i:538715 original size:384 final size:379
Alignment explanation
Indices: 538141--539008 Score: 1134
Period size: 376 Copynumber: 2.3 Consensus size: 379
538131 AAAATTTATT
*
538141 ATTATAATAAAAAACCCTTTTTATTTTTTAATTTAAAATATTTTA-TTTTAAAAAACATAATAAT
1 ATTATAAT--AAAACCCTTTTTATTTTTTAATTT-AAATTTTTTATTTTTAAAAAACATAATAAT
* * * *
538205 TAA----T-A--TATTAATATATATATTTTTAAAATTAATT-A-ATT-TTTTTTATTTTATTAAA
63 TAATTTTTAATTTGTTAATATAAATTTTTTTAAACTTAATTAATATTATTTTTTATTTTATTAAA
** *
538260 AATTATAATAAAAACCTTTTTTTTTTAATTTATAATTTTTTATTTTTTTAAAAAATATAATAATT
128 AATTATAATAAAAACC-TCCTTTTTTAATTTAAAATTTTTTA--TTTTTAAAAAATATAATAATT
* *
538325 AATATTTTAATTTGTTAATCTAAATTTTTGAAATTTAATTAAATATTATTTTTATTTTATTAAAA
190 AATATTTTAATTTGTTAATCTAAATTTTTGAAACTTAATT-AATATTATTTTTATTTTAATAAAA
*
538390 ATTATAATA-AAAA-TCTTGTTTATTTTATTAATTTAAATTTTTTA-TTT-AAAAATATAATAAT
254 ATTATAATAGAAAAGCCTTGTTTATTTT-TTAATTTAAATTTTTTATTTTAAAAAATATAATAAT
* * *
538451 TAATATTTTAATTTGTTAATATTAATTTTTTTGAAACTTAATTAAATTATATTTTTATTTTATTA
318 TAATATTTTAA-TTGTTAAT-GTAATTTTTTTAAAAC-TAATT-AA--ATATTATT-TTTTATTA
538516 AA-A
376 AATA
538519 ATTATAATAAAACCCTTTTTATTTTTTAATTTATAATTTTTTATTTTTAAAAAACATAATAATTA
1 ATTATAATAAAACCCTTTTTATTTTTTAATTTA-AATTTTTTATTTTTAAAAAACATAATAATTA
*
538584 ATTTTTTAATTTGTTAATGTAAATTTTTTTAAACTTAATTAAATATTATTTTTTATTTTATTAAA
65 A-TTTTTAATTTGTTAATATAAATTTTTTTAAACTTAATT-AATATTATTTTTTATTTTATTAAA
538649 AATTATAATAAAAACC-CCTTTTTTAATTTAAAATTTTTTA-TTTTAAAAAATATAATAATTAAT
128 AATTATAATAAAAACCTCCTTTTTTAATTTAAAATTTTTTATTTTTAAAAAATATAATAATTAAT
* * *
538712 ATTTTAATTTGTTAATGTAATTTTTTTAAACTTAATTAATATTATTTTTATTTTAATAAAAATTA
193 ATTTTAATTTGTTAATCTAAATTTTTGAAACTTAATTAATATTATTTTTATTTTAATAAAAATTA
* *
538777 TAATAGAAAAGCCTTTTTTATTTTTTAATTTAAATTTTTTATTTTAAAAAAATATGATAATTAAT
258 TAATAGAAAAGCCTTGTTTATTTTTTAATTTAAATTTTTTATTTT-AAAAAATATAATAATTAAT
*
538842 ATTTTAATTGTTACTGTAATTTTTTTAAAACTAATTAAATATTATTTTTTATTAAATA
322 ATTTTAATTGTTAATGTAATTTTTTTAAAACTAATTAAATATTATTTTTTATTAAATA
* * * * *
538900 ATGATAAT--AACCC-TTTTA-TTTTT-ATTTAAAGGTTTTTATTTTTAAAAAATATAGTGATTA
1 ATTATAATAAAACCCTTTTTATTTTTTAATTTAAA-TTTTTTATTTTTAAAAAACATAATAATTA
*
538960 ATATTTTAATTTGTTAATATAAAATTTTTTAAACTTAATTATATATTAT
65 AT-TTTTAATTTGTTAATATAAATTTTTTTAAACTTAATTA-ATATTAT
539009 CTTTATTAAA
Statistics
Matches: 439, Mismatches: 28, Indels: 48
0.85 0.05 0.09
Matches are distributed among these distances:
375 5 0.01
376 105 0.24
377 27 0.06
378 13 0.03
379 5 0.01
380 10 0.02
381 15 0.03
382 1 0.00
383 35 0.08
384 82 0.19
385 52 0.12
386 7 0.02
387 46 0.10
388 3 0.01
389 33 0.08
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (379 bp):
ATTATAATAAAACCCTTTTTATTTTTTAATTTAAATTTTTTATTTTTAAAAAACATAATAATTAA
TTTTTAATTTGTTAATATAAATTTTTTTAAACTTAATTAATATTATTTTTTATTTTATTAAAAAT
TATAATAAAAACCTCCTTTTTTAATTTAAAATTTTTTATTTTTAAAAAATATAATAATTAATATT
TTAATTTGTTAATCTAAATTTTTGAAACTTAATTAATATTATTTTTATTTTAATAAAAATTATAA
TAGAAAAGCCTTGTTTATTTTTTAATTTAAATTTTTTATTTTAAAAAATATAATAATTAATATTT
TAATTGTTAATGTAATTTTTTTAAAACTAATTAAATATTATTTTTTATTAAATA
Found at i:540600 original size:18 final size:17
Alignment explanation
Indices: 540558--540600 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
540548 AATATAAAAA
* *
540558 TAATATTTAAATTTTAT
1 TAATTTTTAAATTTAAT
540575 TAATTTTTAAATATTAAT
1 TAATTTTTAAAT-TTAAT
*
540593 TTATTTTT
1 TAATTTTT
540601 TTAACAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TAATTTTTAAATTTAAT
Found at i:541785 original size:13 final size:13
Alignment explanation
Indices: 541767--541792 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
541757 CAATTTTTTG
541767 TGTATCGATACAT
1 TGTATCGATACAT
541780 TGTATCGATACAT
1 TGTATCGATACAT
541793 ACTTAATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:541877 original size:20 final size:20
Alignment explanation
Indices: 541852--541924 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
541842 CAACTTTTTT
541852 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
541872 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
541893 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
541913 ATGTATCGATAC
1 ATGTATCGATAC
541925 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:541890 original size:41 final size:41
Alignment explanation
Indices: 541831--541924 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
541821 CTGCCAAGAA
*
541831 ATGTATCGATACAACTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
*
541872 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
541913 ATGTATCGATAC
1 ATGTATCGATAC
541925 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
Found at i:541906 original size:21 final size:21
Alignment explanation
Indices: 541831--541906 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
541821 CTGCCAAGAA
* *
541831 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
541852 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
541872 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
541893 ATGTATCGATACAT
1 ATGTATCGATACAT
541907 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:544382 original size:13 final size:13
Alignment explanation
Indices: 544364--544402 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
544354 ATAATCACCC
*
544364 TGTATCGATACAG
1 TGTATCGATACAA
544377 TGTATCGATACAA
1 TGTATCGATACAA
544390 TGTATCGATACAA
1 TGTATCGATACAA
544403 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:544413 original size:20 final size:20
Alignment explanation
Indices: 544388--544466 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
544378 GTATCGATAC
544388 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
544408 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
544433 GATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
544453 CATGTATCGATACA
1 AATGTATCGATACA
544467 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
20 32 0.65
25 16 0.33
26 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:550592 original size:13 final size:13
Alignment explanation
Indices: 550574--550599 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
550564 CAATTTTTTG
550574 TGTATCGATACAT
1 TGTATCGATACAT
550587 TGTATCGATACAT
1 TGTATCGATACAT
550600 ACTTAATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:550684 original size:20 final size:20
Alignment explanation
Indices: 550659--550731 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
550649 CAACTTTTTT
550659 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
550679 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
550700 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
550720 ATGTATCGATAC
1 ATGTATCGATAC
550732 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:550697 original size:41 final size:41
Alignment explanation
Indices: 550638--550731 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
550628 CTGCCAAGAA
*
550638 ATGTATCGATACAACTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
*
550679 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
550720 ATGTATCGATAC
1 ATGTATCGATAC
550732 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
Found at i:550713 original size:21 final size:21
Alignment explanation
Indices: 550638--550713 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
550628 CTGCCAAGAA
* *
550638 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
550659 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
550679 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
550700 ATGTATCGATACAT
1 ATGTATCGATACAT
550714 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:552498 original size:42 final size:42
Alignment explanation
Indices: 552439--552548 Score: 175
Period size: 42 Copynumber: 2.6 Consensus size: 42
552429 AAAAGAAAGA
* *
552439 AGAGAGAGGAGGGATGATAGGAGGAGAGACATGAGAGATAGT
1 AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
*
552481 AGAGATAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
1 AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
* *
552523 AGAGAGAGGAGGGATGACAAGAGGAG
1 AGAGAGAGGAGGGATGATAGGAGGAG
552549 GAGAGAAGAA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.42, C:0.03, G:0.45, T:0.10
Consensus pattern (42 bp):
AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
Found at i:552509 original size:24 final size:24
Alignment explanation
Indices: 552439--552524 Score: 76
Period size: 24 Copynumber: 3.8 Consensus size: 24
552429 AAAAGAAAGA
*
552439 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
552463 AGAGACATGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
552481 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
552505 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
552525 AGAGAGGAGG
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
18 10 0.21
20 2 0.04
21 6 0.13
22 2 0.04
24 27 0.57
ACGTcount: A:0.42, C:0.02, G:0.44, T:0.12
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:552532 original size:18 final size:19
Alignment explanation
Indices: 552505--552554 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
552495 TGATAGGAGG
*
552505 AGAGACAGGAGAGAT-A-A
1 AGAGAGAGGAGAGATGACA
*
552522 TAGAGAGAGGAGGGATGACA
1 -AGAGAGAGGAGAGATGACA
552542 AGAG-GAGGAGAGA
1 AGAGAGAGGAGAGA
552555 AGAAGATGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 21 0.78
19 5 0.19
20 1 0.04
ACGTcount: A:0.46, C:0.04, G:0.44, T:0.06
Consensus pattern (19 bp):
AGAGAGAGGAGAGATGACA
Found at i:553486 original size:20 final size:20
Alignment explanation
Indices: 553458--553532 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
553448 TTTTACCTTG
553458 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
553478 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * * *
553498 GTGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
553518 ATGTATCGATACATT
1 ATGTATCGATACATT
553533 ATGTCTTTTT
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:553504 original size:40 final size:39
Alignment explanation
Indices: 553459--553535 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 39
553449 TTTACCTTGA
* *
553459 TGTATCGATACATTTTTCAATATATCGATACATGTATGAG
1 TGTATCGATACATTCTACAATATATCGATACAT-TATGAG
* *
553499 TGTATCGATATATTCTACAATGTATCGATACATTATG
1 TGTATCGATACATTCTACAATATATCGATACATTATG
553536 TCTTTTTACC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.40
Consensus pattern (39 bp):
TGTATCGATACATTCTACAATATATCGATACATTATGAG
Found at i:560624 original size:23 final size:24
Alignment explanation
Indices: 560566--560625 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 24
560556 AAGTTCCCTT
560566 AAAAA-TGACAAAAAAAGTCAAAAG
1 AAAAAGTG-CAAAAAAAGTCAAAAG
* ** *
560590 CAAAAGCACAAAAAAA-TGAAAAG
1 AAAAAGTGCAAAAAAAGTCAAAAG
560613 AAAAAGTGCAAAA
1 AAAAAGTGCAAAA
560626 GCAAAATAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
23 16 0.57
24 12 0.43
ACGTcount: A:0.70, C:0.10, G:0.13, T:0.07
Consensus pattern (24 bp):
AAAAAGTGCAAAAAAAGTCAAAAG
Found at i:560935 original size:12 final size:12
Alignment explanation
Indices: 560904--560936 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
560894 CTAAAAAAAG
560904 AAAAAAAA-CAA
1 AAAAAAAACCAA
560915 AAAAAAAACCAA
1 AAAAAAAACCAA
560927 AAAAAAAACC
1 AAAAAAAACC
560937 TTTTCACCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.38
12 13 0.62
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAACCAA
Found at i:561988 original size:27 final size:27
Alignment explanation
Indices: 561950--563246 Score: 1910
Period size: 27 Copynumber: 48.3 Consensus size: 27
561940 ACTGTGACCT
*
561950 CTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
561977 CTTTTAAGTCCACAATTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
562005 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
562032 CTTTTAAGTCCATAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
562060 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
562087 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
562114 CTTTTAAAGTCCACAACTCTGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
562142 CTTTTTAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
562169 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
**
562196 CTTTTAAGTCCACAACTCCGTGGCATT
1 CTTTTAAGTCCACAACTCCGTGGCACC
562223 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
562250 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
562277 CTTTTAAGTCCACAACTTCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
562305 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
562332 ATTTTAAGTCCACAACTTCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
562359 CTTTTAAGTCCACAACTCCGTGGCA--
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
562384 ----TAAGTCCACAACTTCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
**
562407 CTTTTAAAGTCCACAACTCCGTGGCATT
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* **
562435 CTTTTAAATCCACAACTCCGTGGCATT
1 CTTTTAAGTCCACAACTCCGTGGCACC
562462 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
562489 CTTTTAAGTCCATAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
562516 CTTTTAAGTCCACAACTCCGTGGCAAC
1 CTTTTAAGTCCACAACTCCGTGGCACC
562543 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
562571 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
562598 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
562626 CTTTTAAGTCCACAACTCCGTGGCA--
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
562651 ----TAAGTCCACAACTTCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
**
562674 CTTTTAAAGTCCACAACTCCGTGGCATT
1 CTTTT-AAGTCCACAACTCCGTGGCACC
**
562702 CTTTTAAGTCCACAACTCCGTGGCATT
1 CTTTTAAGTCCACAACTCCGTGGCACC
562729 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
562756 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
562783 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* * **
562811 CTTTTAAGACCATAACTCCGTGGCATAT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
562839 CTTTTAAGTCCACAACTCTGTGGCACT
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
562866 CTTTTAAGTCCACAACTCTGTGGCACT
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
562893 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
562920 CTTTTAAGTCCACAACTCCGTGGCACT
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
562947 CTTTTAAGTCCACAACTCTGTGGTACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
562974 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
563001 CTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
563028 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
563055 CTTTTAAGTCCACAACTCCGTGGCAGC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
563082 CTTTTAAGTCTACAATTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
563109 CTTTTAAGTCCACAACTCCATGGCA--
1 CTTTTAAGTCCACAACTCCGTGGCACC
563134 ----TAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
563158 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
563185 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * *
563212 CTTTTAAAATCCACAACTCTGTGGCACT
1 CTTTT-AAGTCCACAACTCCGTGGCACC
563240 CTTTTAA
1 CTTTTAA
563247 AATCCACACA
Statistics
Matches: 1173, Mismatches: 68, Indels: 58
0.90 0.05 0.04
Matches are distributed among these distances:
21 60 0.05
27 814 0.69
28 299 0.25
ACGTcount: A:0.23, C:0.33, G:0.15, T:0.29
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:562389 original size:21 final size:21
Alignment explanation
Indices: 562363--562405 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
562353 GGCACCCTTT
562363 TAAGTCCACAACTCCGTGGCA
1 TAAGTCCACAACTCCGTGGCA
*
562384 TAAGTCCACAACTTCGTGGCA
1 TAAGTCCACAACTCCGTGGCA
562405 T
1 T
562406 CCTTTTAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (21 bp):
TAAGTCCACAACTCCGTGGCA
Found at i:562656 original size:21 final size:21
Alignment explanation
Indices: 562630--562672 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
562620 GCATCCCTTT
562630 TAAGTCCACAACTCCGTGGCA
1 TAAGTCCACAACTCCGTGGCA
*
562651 TAAGTCCACAACTTCGTGGCA
1 TAAGTCCACAACTCCGTGGCA
562672 T
1 T
562673 CCTTTTAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (21 bp):
TAAGTCCACAACTCCGTGGCA
Found at i:563139 original size:21 final size:21
Alignment explanation
Indices: 563113--563155 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
563103 GGCACCCTTT
563113 TAAGTCCACAACTCCATGGCA
1 TAAGTCCACAACTCCATGGCA
*
563134 TAAGTCCACAACTCCGTGGCA
1 TAAGTCCACAACTCCATGGCA
563155 T
1 T
563156 CCCTTTTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.33, G:0.16, T:0.21
Consensus pattern (21 bp):
TAAGTCCACAACTCCATGGCA
Found at i:563247 original size:28 final size:28
Alignment explanation
Indices: 563138--563254 Score: 166
Period size: 28 Copynumber: 4.2 Consensus size: 28
563128 ATGGCATAAG
*
563138 TCCACAACTCCGTGGCATCCCTTTTAAGA
1 TCCACAACTCCGTGGCA-CCCTTTTAAAA
*
563167 -CCACAACTCCGTGGCACCCTTTT-AAG
1 TCCACAACTCCGTGGCACCCTTTTAAAA
*
563193 TCCACAACTCTGTGGCACCCTTTTAAAA
1 TCCACAACTCCGTGGCACCCTTTTAAAA
* *
563221 TCCACAACTCTGTGGCACTCTTTTAAAA
1 TCCACAACTCCGTGGCACCCTTTTAAAA
563249 TCCACA
1 TCCACA
563255 CAAGTCGGTG
Statistics
Matches: 81, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
26 1 0.01
27 29 0.36
28 51 0.63
ACGTcount: A:0.26, C:0.34, G:0.12, T:0.27
Consensus pattern (28 bp):
TCCACAACTCCGTGGCACCCTTTTAAAA
Found at i:563287 original size:32 final size:32
Alignment explanation
Indices: 563250--563790 Score: 827
Period size: 32 Copynumber: 16.9 Consensus size: 32
563240 CTTTTAAAAT
563250 CCACACAAGTCGGTGGCAACCCATTTCAAAGC
1 CCACACAAGTCGGTGGCAACCCATTTCAAAGC
*
563282 CCACACAAGTCGGTGGCAACCCTTTTCAAAGC
1 CCACACAAGTCGGTGGCAACCCATTTCAAAGC
563314 CCACACAAGTCGGTGGCAACCCATTTCAAAGC
1 CCACACAAGTCGGTGGCAACCCATTTCAAAGC
*
563346 CCACAAAAGTCGGTGGCAACCCATTTCAAAGC
1 CCACACAAGTCGGTGGCAACCCATTTCAAAGC
*
563378 CCACACAAGTCGGTGGCAA-CAATTTTCAAAGC
1 CCACACAAGTCGGTGGCAACCCA-TTTCAAAGC
563410 CCACACAAGTCGGTGGCAA-CCATTTTCAAAGC
1 CCACACAAGTCGGTGGCAACCCA-TTTCAAAGC
* *
563442 CCACACAAGTCGGTGGCAACCCATTCCGAAGC
1 CCACACAAGTCGGTGGCAACCCATTTCAAAGC
*
563474 CCACACAAGTCAGTGGCAACCCATTTCAAAGC
1 CCACACAAGTCGGTGGCAACCCATTTCAAAGC
* *
563506 CCACACAAGT-GGTGGAAACCCTTTTCAAAGC
1 CCACACAAGTCGGTGGCAACCCATTTCAAAGC
** * *
563537 CCACACAAGTTAGTGGAAACCCTTTTCAAAGC
1 CCACACAAGTCGGTGGCAACCCATTTCAAAGC
*
563569 CCACACAAGTCAGTGGCAACCCATTTCAAAGC
1 CCACACAAGTCGGTGGCAACCCATTTCAAAGC
563601 CCACACAAGTCGGTGGCAACCCATTTCAAAGC
1 CCACACAAGTCGGTGGCAACCCATTTCAAAGC
* *
563633 CCACACAAGTCGGTGGCTACCCATTCCAAAGC
1 CCACACAAGTCGGTGGCAACCCATTTCAAAGC
* *
563665 CCACATAAGTCGGTGGTAACCCATTTCAAAGC
1 CCACACAAGTCGGTGGCAACCCATTTCAAAGC
* * *
563697 CCACACAAGTTGGTGGAAACCCTTTTCAAAGC
1 CCACACAAGTCGGTGGCAACCCATTTCAAAGC
*
563729 CCACACAAGTCGGTGGCAACCCATTTAAAAGC
1 CCACACAAGTCGGTGGCAACCCATTTCAAAGC
* * *
563761 CCACGCAAGTCAGTGGCAACCCTTTTCAAA
1 CCACACAAGTCGGTGGCAACCCATTTCAAA
563791 TCACCATTTT
Statistics
Matches: 469, Mismatches: 37, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
31 30 0.06
32 436 0.93
33 3 0.01
ACGTcount: A:0.32, C:0.32, G:0.18, T:0.18
Consensus pattern (32 bp):
CCACACAAGTCGGTGGCAACCCATTTCAAAGC
Found at i:563876 original size:45 final size:46
Alignment explanation
Indices: 563821--563943 Score: 131
Period size: 49 Copynumber: 2.6 Consensus size: 46
563811 AAGTCCGATA
* *
563821 TCGCTAGCCTTGAATCAGCATATTGGCACCTTT-CTAAGCCCAATG
1 TCGCTGGCCTTGAATCAGCACATTGGCACCTTTCCTAAGCCCAATG
* * *
563866 TCGCTGGCCTTGAGTCAGCACATTGGTCCACTTTTCCCTTAGCCCAATG
1 TCGCTGGCCTTGAATCAGCACATTGG--CACCTTT-CCTAAGCCCAATG
* * **
563915 TCGTTGGCTTTGAATTGGCACATTGGCAC
1 TCGCTGGCCTTGAATCAGCACATTGGCAC
563944 TCCTCTCATC
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
45 23 0.36
47 9 0.14
49 32 0.50
ACGTcount: A:0.20, C:0.28, G:0.21, T:0.31
Consensus pattern (46 bp):
TCGCTGGCCTTGAATCAGCACATTGGCACCTTTCCTAAGCCCAATG
Found at i:564363 original size:40 final size:39
Alignment explanation
Indices: 564318--564394 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 39
564308 TTTACCTTGA
* *
564318 TGTATCGATACATTTTTCAATATATCAATACATGTATGAG
1 TGTATCGATACATTCTACAATATATCAATACAT-TATGAG
* * *
564358 TGTATCGATATATTCTACAATGTATCGATACATTATG
1 TGTATCGATACATTCTACAATATATCAATACATTATG
564395 TCTTTTTACC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 28 0.88
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
TGTATCGATACATTCTACAATATATCAATACATTATGAG
Done.