Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003421.1 Hibiscus syriacus cultivar Beakdansim tig00007204_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 882701
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 1 of 5
Found at i:5778 original size:29 final size:29
Alignment explanation
Indices: 5739--5819 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
5729 TATGTGATAT
5739 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
5769 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
*
5798 GATAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
5820 AAATATAAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 7 0.14
29 38 0.76
30 5 0.10
ACGTcount: A:0.44, C:0.16, G:0.21, T:0.19
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:18289 original size:23 final size:21
Alignment explanation
Indices: 18236--18298 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 21
18226 TTTTGGTGCA
*
18236 GAGGGAATCGATTCCCCCCCT
1 GAGGGAACCGATTCCCCCCCT
**
18257 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCCT
18278 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
18299 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
21 19 0.53
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.37, G:0.25, T:0.17
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCCT
Found at i:18306 original size:21 final size:21
Alignment explanation
Indices: 18238--18318 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
18228 TTGGTGCAGA
* *
18238 GGGAATCGATTCCCCCC-CTG
1 GGGAACCGATTCCCCCCACAG
*
18258 AGGGAACCGATTCCCCCTTTGA-AG
1 -GGGAACCGATTCCCCC---CACAG
18282 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCCACAG
* *
18303 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
18319 TGGGGTTCTG
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 1 0.02
21 31 0.63
23 16 0.33
24 1 0.02
ACGTcount: A:0.22, C:0.37, G:0.25, T:0.16
Consensus pattern (21 bp):
GGGAACCGATTCCCCCCACAG
Found at i:21086 original size:21 final size:21
Alignment explanation
Indices: 21060--21117 Score: 116
Period size: 21 Copynumber: 2.8 Consensus size: 21
21050 ATTTTACACT
21060 TAGGGAACCGATTCCCTATGA
1 TAGGGAACCGATTCCCTATGA
21081 TAGGGAACCGATTCCCTATGA
1 TAGGGAACCGATTCCCTATGA
21102 TAGGGAACCGATTCCC
1 TAGGGAACCGATTCCC
21118 CCCACTGTCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (21 bp):
TAGGGAACCGATTCCCTATGA
Found at i:22248 original size:29 final size:29
Alignment explanation
Indices: 22209--22289 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
22199 TATGTGATAT
22209 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
22239 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
*
22268 GATAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
22290 ACATATAAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 7 0.14
29 38 0.76
30 5 0.10
ACGTcount: A:0.44, C:0.16, G:0.21, T:0.19
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:23298 original size:28 final size:28
Alignment explanation
Indices: 23244--23300 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
23234 CCGCCGTTGT
* * *
23244 TTTCAAGCACTTGCTCGCCAGCATAATG
1 TTTCAAGCACTAGCTCGACAACATAATG
* *
23272 TTTCAAGCGCTAGCTCGACAACTTAATG
1 TTTCAAGCACTAGCTCGACAACATAATG
23300 T
1 T
23301 AAAAGTTATG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (28 bp):
TTTCAAGCACTAGCTCGACAACATAATG
Found at i:23977 original size:90 final size:89
Alignment explanation
Indices: 23825--23997 Score: 283
Period size: 90 Copynumber: 1.9 Consensus size: 89
23815 ACACACCCTT
* *
23825 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
1 TTATAGCCAAGTTACCCAAATCATATTAGGATTTTATTATTTCAAATTAATTAAATCTATATTTA
* *
23890 ATTAATTGGAATTTAATAATCCTC
66 ATTAATTGAAATTAAATAATCCTC
* *
23914 TTATATCCAAGTTACCCAAATCATATTAGGAATTTTATTATTTGAAATTAATTAAATCTATATTT
1 TTATAGCCAAGTTACCCAAATCATATTAGG-ATTTTATTATTTCAAATTAATTAAATCTATATTT
23979 AATTAATTGAAATTAAATA
65 AATTAATTGAAATTAAATA
23998 TTCAGGATTA
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 28 0.36
90 49 0.64
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.43
Consensus pattern (89 bp):
TTATAGCCAAGTTACCCAAATCATATTAGGATTTTATTATTTCAAATTAATTAAATCTATATTTA
ATTAATTGAAATTAAATAATCCTC
Found at i:29307 original size:18 final size:18
Alignment explanation
Indices: 29245--29308 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
29235 TTTATTGAAA
* *
29245 AACCGATAAATCGAACCG
1 AACCGAAAAACCGAACCG
29263 AACCGAAAAACCCGAACCG
1 AACCGAAAAA-CCGAACCG
29282 TTAA---AAAAACCGAACCG
1 --AACCGAAAAACCGAACCG
29299 AACCGAAAAA
1 AACCGAAAAA
29309 ACCGGTTTCG
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
15 2 0.05
17 8 0.21
18 19 0.50
19 7 0.18
21 2 0.05
ACGTcount: A:0.52, C:0.28, G:0.14, T:0.06
Consensus pattern (18 bp):
AACCGAAAAACCGAACCG
Found at i:31380 original size:10 final size:10
Alignment explanation
Indices: 31365--31398 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
31355 TCGGGTATGT
31365 AAAATTTTAA
1 AAAATTTTAA
31375 AAAATTTTAAA
1 AAAATTTT-AA
31386 TAAAATTTTAA
1 -AAAATTTTAA
31397 AA
1 AA
31399 TTTAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 10 0.45
11 4 0.18
12 8 0.36
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
AAAATTTTAA
Found at i:31392 original size:12 final size:12
Alignment explanation
Indices: 31364--31397 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
31354 GTCGGGTATG
31364 TAAAATTTT-AA
1 TAAAATTTTAAA
31375 -AAAATTTTAAA
1 TAAAATTTTAAA
31386 TAAAATTTTAAA
1 TAAAATTTTAAA
31398 ATTTAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.38
11 2 0.10
12 11 0.52
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAAATTTTAAA
Found at i:34291 original size:24 final size:23
Alignment explanation
Indices: 34242--34293 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
34232 AACTGTCACA
**
34242 TAGAATTACACCGAAGTGCCGTG
1 TAGAATTACACCGAAGTGCCACG
* *
34265 TAGAATATGCACCGAAGTGCTACG
1 TAGAAT-TACACCGAAGTGCCACG
34289 TAGAA
1 TAGAA
34294 ATGTCCCGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (23 bp):
TAGAATTACACCGAAGTGCCACG
Found at i:34313 original size:23 final size:23
Alignment explanation
Indices: 34287--34339 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
34277 CGAAGTGCTA
34287 CGTAGAAATGTCCCGAAGGACCG
1 CGTAGAAATGTCCCGAAGGACCG
**
34310 CGTAGAAATGTTTCGAAGGACCG
1 CGTAGAAATGTCCCGAAGGACCG
*
34333 CATAGAA
1 CGTAGAA
34340 CTCTCGACTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.34, C:0.21, G:0.28, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGTCCCGAAGGACCG
Found at i:42737 original size:40 final size:40
Alignment explanation
Indices: 42662--42739 Score: 106
Period size: 40 Copynumber: 1.9 Consensus size: 40
42652 TTGTTGTTGT
* *
42662 GTGCTTTCAATTTTTCTTTCTTTTTGTTTTCTTCTTTTGA
1 GTGCTTTCAATTTTTCTTTCTATTTGTTTTATTCTTTTGA
42702 GTGCTTTCAA-TTTTCTTTGCTGATTT-TTTTATTCTTTT
1 GTGCTTTCAATTTTTCTTT-CT-ATTTGTTTTATTCTTTT
42740 ACTTGCAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 8 0.24
40 23 0.68
41 3 0.09
ACGTcount: A:0.09, C:0.14, G:0.10, T:0.67
Consensus pattern (40 bp):
GTGCTTTCAATTTTTCTTTCTATTTGTTTTATTCTTTTGA
Found at i:42890 original size:24 final size:24
Alignment explanation
Indices: 42862--42920 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
42852 ATTATGGAAT
42862 CGAAGTGCCACGTAGAATATGCAC
1 CGAAGTGCCACGTAGAATATGCAC
* *
42886 TGAAGTGTCACGTAGAATATGCAC
1 CGAAGTGCCACGTAGAATATGCAC
*
42910 CGATGTGCCAC
1 CGAAGTGCCAC
42921 ATATAAATGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (24 bp):
CGAAGTGCCACGTAGAATATGCAC
Found at i:48973 original size:30 final size:31
Alignment explanation
Indices: 48906--48993 Score: 108
Period size: 31 Copynumber: 2.9 Consensus size: 31
48896 AGATAGTTGT
* * *
48906 TTACCTATGTCTTTCGAGACATATGGATAGA
1 TTACCTATGTCCTTCAAGACATATGGACAGA
*
48937 TTACCTATGTCCTTCAAGTCATATGGACAG-
1 TTACCTATGTCCTTCAAGACATATGGACAGA
*
48967 TTACCTATGTTCTTCGAA-ACATATGGA
1 TTACCTATGTCCTTC-AAGACATATGGA
48994 TATGTTCTTC
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
30 22 0.44
31 28 0.56
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.35
Consensus pattern (31 bp):
TTACCTATGTCCTTCAAGACATATGGACAGA
Found at i:54528 original size:30 final size:30
Alignment explanation
Indices: 54443--54529 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 30
54433 ATGGATAGTT
54443 GTTTACCTATG-TCTTTCGAGACATATAGACA
1 GTTTACCTATGTTC-TTCGA-ACATATAGACA
* * * *
54474 GATTATCTATGTCCTTCGGGACATATAGACA
1 GTTTACCTATGTTCTTC-GAACATATAGACA
54505 -TTTACCTATGTTCTTCAGAACATAT
1 GTTTACCTATGTTCTTC-GAACATAT
54530 GGATAGGTCC
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
30 20 0.44
31 23 0.51
32 2 0.04
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (30 bp):
GTTTACCTATGTTCTTCGAACATATAGACA
Found at i:59280 original size:56 final size:57
Alignment explanation
Indices: 59184--59635 Score: 625
Period size: 56 Copynumber: 8.0 Consensus size: 57
59174 TGGGGGTGTT
*
59184 ACAAAGTGCCCATACAGAAATTCATAAACTTATTATGAATTTCTTAAC-TTTTGCAC
1 ACAAAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCAC
* * * * *
59240 ACAAAGTACCCATACGGAAATTCATATACTCATTACGAATTTCTTACCTTTTTTGCAC
1 ACAAAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAAC-TTTTTGCAC
* * *
59298 ACAAAGTGCACATACAGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCGC
1 ACAAAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCAC
*
59355 ACAAAGTGCCCATACGAAAATTCATAAACTTATTATGAATTTCTTAACTTTTT--AC
1 ACAAAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCAC
* * * **
59410 ACATAAGTGCCCATAAGGTAATTCAAAAACGCATTATG-ATTTCTTAACTTTTTGCAC
1 ACA-AAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCAC
* *
59467 ACAAAGTGCTCATACGGAAGTTCAT-AACTTATTATGAATTTCTTAACTTTTTGCAC
1 ACAAAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCAC
* * *
59523 ACAAAGTACCCATACGGAAATTTATAAACTTATTATGAATTTCTTAATTTTTTGCAC
1 ACAAAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCAC
*
59580 ACAAAGTGCCTATAC--ATAATTCAT-AACTTATTATGAATTTCTTAAC-TTTTGCAC
1 ACAAAGTGCCCATACGGA-AATTCATAAACTTATTATGAATTTCTTAACTTTTTGCAC
59634 AC
1 AC
59636 TCAGTGCCAT
Statistics
Matches: 348, Mismatches: 40, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
54 10 0.03
55 50 0.14
56 133 0.38
57 106 0.30
58 49 0.14
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.36
Consensus pattern (57 bp):
ACAAAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAACTTTTTGCAC
Found at i:66000 original size:20 final size:20
Alignment explanation
Indices: 65991--66117 Score: 179
Period size: 19 Copynumber: 6.5 Consensus size: 20
65981 ATTTCCTAAT
65991 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
66011 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
66032 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
66052 TCGCAATGCGAATACGT-AA
1 TCGCAATGCGAATACGTAAA
66071 TCGCAATGCGAATACGT-AA
1 TCGCAATGCGAATACGTAAA
66090 TCGCAATGCGAATACGT-AA
1 TCGCAATGCGAATACGTAAA
66109 TCGCAATGC
1 TCGCAATGC
66118 AAATCTGACT
Statistics
Matches: 96, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
19 49 0.51
20 32 0.33
21 15 0.16
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:66333 original size:22 final size:22
Alignment explanation
Indices: 66308--66373 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
66298 GGCAACATCC
66308 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
66330 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
66352 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
66374 TTCACGGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.24, C:0.39, G:0.15, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:66715 original size:19 final size:19
Alignment explanation
Indices: 66690--66758 Score: 93
Period size: 19 Copynumber: 3.6 Consensus size: 19
66680 AATGCGATTC
66690 TGTTGCGATTTTCATTTCG
1 TGTTGCGATTTTCATTTCG
* ***
66709 CGTTGCGATAGCCATTTTCG
1 TGTTGCGATTTTCA-TTTCG
66729 TGTTGCGATTTTCATTTCG
1 TGTTGCGATTTTCATTTCG
66748 TGTTGCGATTT
1 TGTTGCGATTT
66759 AAAGTTTCAG
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 26 0.63
20 15 0.37
ACGTcount: A:0.12, C:0.17, G:0.23, T:0.48
Consensus pattern (19 bp):
TGTTGCGATTTTCATTTCG
Found at i:68668 original size:19 final size:19
Alignment explanation
Indices: 68644--68781 Score: 78
Period size: 19 Copynumber: 7.7 Consensus size: 19
68634 GCAACGAGAG
68644 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
68663 AATCGCAA--C--AA-CAA
1 AATCGCAATGCGAAATGAA
* *
68677 AATCGCAACGCGGAAATGAC
1 AATCGCAATGC-GAAATGAA
* * *
68697 TATCGCAATGCGAAAGGAC
1 AATCGCAATGCGAAATGAA
* * * *
68716 TATTGCAATGCGAATTGAC
1 AATCGCAATGCGAAATGAA
* * *
68735 TATTGCAA-ACGAAA-G--
1 AATCGCAATGCGAAATGAA
68750 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
68769 AATCGCATTGCGA
1 AATCGCAATGCGA
68782 TTATCTCGTT
Statistics
Matches: 94, Mismatches: 15, Indels: 20
0.73 0.12 0.16
Matches are distributed among these distances:
14 10 0.11
15 8 0.09
16 6 0.06
17 3 0.03
18 4 0.04
19 53 0.56
20 10 0.11
ACGTcount: A:0.42, C:0.20, G:0.21, T:0.17
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:68703 original size:20 final size:19
Alignment explanation
Indices: 68678--68781 Score: 90
Period size: 19 Copynumber: 5.6 Consensus size: 19
68668 CAACAACAAA
*
68678 ATCGCAACGCGGAAATGACT
1 ATCGCAATGC-GAAATGACT
*
68698 ATCGCAATGCGAAAGGACT
1 ATCGCAATGCGAAATGACT
* *
68717 ATTGCAATGCGAATTGACT
1 ATCGCAATGCGAAATGACT
* *
68736 ATTGCAA-ACGAAA-GA--
1 ATCGCAATGCGAAATGACT
**
68751 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGACT
*
68770 ATCGCATTGCGA
1 ATCGCAATGCGA
68782 TTATCTCGTT
Statistics
Matches: 70, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
15 6 0.09
16 5 0.07
17 4 0.06
18 4 0.06
19 42 0.60
20 9 0.13
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.19
Consensus pattern (19 bp):
ATCGCAATGCGAAATGACT
Found at i:68815 original size:20 final size:20
Alignment explanation
Indices: 68790--68876 Score: 120
Period size: 20 Copynumber: 4.3 Consensus size: 20
68780 GATTATCTCG
68790 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
68810 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
68830 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
** *
68850 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
68870 TTGCGAT
1 TTGCGAT
68877 TTAAGTTCAG
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:69438 original size:21 final size:21
Alignment explanation
Indices: 69349--69453 Score: 104
Period size: 21 Copynumber: 5.0 Consensus size: 21
69339 GACTCACTTG
*
69349 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
69371 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
69391 TCATCCATCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * *
69412 CCATCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
69433 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
69454 CCAACATTCT
Statistics
Matches: 65, Mismatches: 17, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 3 0.05
21 61 0.94
22 1 0.02
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:69446 original size:42 final size:42
Alignment explanation
Indices: 69347--69456 Score: 125
Period size: 42 Copynumber: 2.6 Consensus size: 42
69337 CCGACTCACT
* * *
69347 TGTCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCCCC
1 TGTCATCGTTCAAGAGTCC-CCTCCCATCGTTCAAGAGGCCAC
* **
69389 TATCATCCATCAAGAGTCCCCTCCCATCGTTCAAGAGGCCAC
1 TGTCATCGTTCAAGAGTCCCCTCCCATCGTTCAAGAGGCCAC
*
69431 TGTCATCGTTGAAGAGGT-CCCTCCCA
1 TGTCATCGTTCAAGA-GTCCCCTCCCA
69457 ACATTCTAGA
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
41 2 0.04
42 52 0.93
43 2 0.04
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.24
Consensus pattern (42 bp):
TGTCATCGTTCAAGAGTCCCCTCCCATCGTTCAAGAGGCCAC
Found at i:70844 original size:14 final size:14
Alignment explanation
Indices: 70825--70860 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
70815 ATTGTTTAAT
70825 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
70839 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
70853 TGATTTGT
1 TGATTTGT
70861 TTAATTGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:70985 original size:14 final size:14
Alignment explanation
Indices: 70966--71019 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
70956 AAAACAGACT
70966 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
70980 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
70999 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
71013 ATCGCAA
1 ATCGCAA
71020 TGCGAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:71003 original size:33 final size:34
Alignment explanation
Indices: 70966--71041 Score: 145
Period size: 33 Copynumber: 2.3 Consensus size: 34
70956 AAAACAGACT
70966 ATCGCAACGAGAGAATCGCAATGCG-AAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
70999 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
71033 ATCGCAACG
1 ATCGCAACG
71042 CGAAACTAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 25 0.60
34 17 0.40
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.12
Consensus pattern (34 bp):
ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
Found at i:71037 original size:20 final size:19
Alignment explanation
Indices: 70979--71046 Score: 74
Period size: 20 Copynumber: 3.8 Consensus size: 19
70969 GCAACGAGAG
70979 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
70998 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
71012 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
71032 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
71047 CTAAATTCGC
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 10 0.25
15 1 0.03
16 2 0.05
17 2 0.05
19 12 0.30
20 13 0.32
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:71081 original size:20 final size:19
Alignment explanation
Indices: 71052--71152 Score: 87
Period size: 20 Copynumber: 5.7 Consensus size: 19
71042 CGAAACTAAA
*
71052 TTCGCGTTGCGATTTTCATT
1 TTCGCATTGCGATTTTCA-T
71072 TTCGCATTGCGA--TTCA-
1 TTCGCATTGCGATTTTCAT
*
71088 CTCG--TTGCGATTTTCATT
1 TTCGCATTGCGATTTTCA-T
71106 TTCGCATTGCGA--TTCA-
1 TTCGCATTGCGATTTTCAT
*
71122 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
71139 TTCGCATTGCGATT
1 TTCGCATTGCGATT
71153 CTCTCGTTGC
Statistics
Matches: 65, Mismatches: 5, Indels: 23
0.70 0.05 0.25
Matches are distributed among these distances:
14 12 0.18
16 14 0.22
17 3 0.05
18 11 0.17
19 8 0.12
20 17 0.26
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.45
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:71097 original size:14 final size:14
Alignment explanation
Indices: 71078--71165 Score: 50
Period size: 14 Copynumber: 5.5 Consensus size: 14
71068 CATTTTCGCA
71078 TTGCGATTCACTCG
1 TTGCGATTCACTCG
*
71092 TTGCGATTTTCATTTTCG
1 TTGCGA--TTCA--CTCG
71110 CATTGCGATTCACTCG
1 --TTGCGATTCACTCG
*
71126 TTGCGATTTTCATTTCG
1 TTGCGA--TTCA-CTCG
*
71143 CATTGCGATTCTCTCG
1 --TTGCGATTCACTCG
71159 TTGCGAT
1 TTGCGAT
71166 AGTCATTTCC
Statistics
Matches: 58, Mismatches: 5, Indels: 22
0.68 0.06 0.26
Matches are distributed among these distances:
14 19 0.33
16 14 0.24
17 6 0.10
18 7 0.12
19 6 0.10
20 6 0.10
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (14 bp):
TTGCGATTCACTCG
Found at i:71174 original size:33 final size:34
Alignment explanation
Indices: 71056--71165 Score: 204
Period size: 34 Copynumber: 3.3 Consensus size: 34
71046 ACTAAATTCG
71056 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
71090 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
*
71124 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
71157 CGTTGCGAT
1 CGTTGCGAT
71166 AGTCATTTCC
Statistics
Matches: 75, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
33 27 0.36
34 48 0.64
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.44
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:71186 original size:20 final size:20
Alignment explanation
Indices: 71157--71231 Score: 114
Period size: 20 Copynumber: 3.8 Consensus size: 20
71147 GCGATTCTCT
71157 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
71177 CGTTGTGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
71197 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
71217 TGTTGCGATAATCAT
1 CGTTGCGATAGTCAT
71232 ATTCGCATTG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:73687 original size:24 final size:24
Alignment explanation
Indices: 73653--73706 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
73643 CTGAAAAATC
73653 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
73677 ATCAAAGTCCGGGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
73701 ATCAAA
1 ATCAAA
73707 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:74589 original size:20 final size:20
Alignment explanation
Indices: 74548--74590 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
74538 AAATTCATTA
* *
74548 TTGCGATAGTCAGAATCTCG
1 TTGCAATAGTCAGAATCGCG
*
74568 TTGCAATAGTCAGATTCGCG
1 TTGCAATAGTCAGAATCGCG
74588 TTG
1 TTG
74591 TGATTTACGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.33
Consensus pattern (20 bp):
TTGCAATAGTCAGAATCGCG
Found at i:74652 original size:20 final size:20
Alignment explanation
Indices: 74581--74654 Score: 94
Period size: 20 Copynumber: 3.7 Consensus size: 20
74571 CAATAGTCAG
* *
74581 ATTCGCGTTGTGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
74601 ATTTGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
74621 ATTCACATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
74641 AATCGCAATGCGAT
1 ATTCGCATTGCGAT
74655 AGTCATAATC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:81997 original size:60 final size:58
Alignment explanation
Indices: 81824--82006 Score: 152
Period size: 60 Copynumber: 3.1 Consensus size: 58
81814 CATATGTCCT
* * * * * * * * *
81824 TAAACTATAACTCTAATTTTAAATTGGTTCTTAAATTTTTAAATATTTTAATTTCATCCC
1 TAAAATATATCTCTCATTCTAAATTAGTCCTCAAACTTTTGAATA-TTTAATTTCAT-CC
* * * * * **
81884 CAAATTATATCTCTCATTCTAAATTAGTCCTTAAACATTGGAGCATTATAATTTCATCC
1 TAAAATATATCTCTCATTCTAAATTAGTCCTCAAACTTTTGAATATT-TAATTTCATCC
*
81943 ATAAAATATGA-CTCTCTTTCTAAATTAGTCCTCAAACTTTTGAATATTTCAATTTCATCC
1 -TAAAATAT-ATCTCTCATTCTAAATTAGTCCTCAAACTTTTGAATATTT-AATTTCATCC
82003 TAAA
1 TAAA
82007 TGCATTCAAA
Statistics
Matches: 98, Mismatches: 21, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
59 9 0.09
60 88 0.90
61 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.05, T:0.43
Consensus pattern (58 bp):
TAAAATATATCTCTCATTCTAAATTAGTCCTCAAACTTTTGAATATTTAATTTCATCC
Found at i:84574 original size:28 final size:28
Alignment explanation
Indices: 84541--84597 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
84531 GTCAGAGGCA
84541 TACCGCTTTGGGTAATAAAAGAGGCGGT
1 TACCGCTTTGGGTAATAAAAGAGGCGGT
84569 TACCGCTTTGGGTAATAAAAGAGGCGGT
1 TACCGCTTTGGGTAATAAAAGAGGCGGT
84597 T
1 T
84598 CATCCTGGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.28, C:0.14, G:0.32, T:0.26
Consensus pattern (28 bp):
TACCGCTTTGGGTAATAAAAGAGGCGGT
Found at i:87063 original size:16 final size:17
Alignment explanation
Indices: 87030--87065 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
87020 CGAATAACTA
*
87030 TTTTAGGTATCCGAAAT
1 TTTTAAGTATCCGAAAT
87047 TTTTAAGTATCCG-AAT
1 TTTTAAGTATCCGAAAT
87063 TTT
1 TTT
87066 CAAATCGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (17 bp):
TTTTAAGTATCCGAAAT
Found at i:93913 original size:17 final size:18
Alignment explanation
Indices: 93891--93936 Score: 62
Period size: 16 Copynumber: 2.7 Consensus size: 18
93881 TGTGCATTTG
93891 ACTAATATTAATAAAA-A
1 ACTAATATTAATAAAATA
93908 ACTAATA-TAATAAAATA
1 ACTAATATTAATAAAATA
*
93925 A-TAATATCAATA
1 ACTAATATTAATA
93937 TCAATCGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 13 0.50
17 13 0.50
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (18 bp):
ACTAATATTAATAAAATA
Found at i:110671 original size:66 final size:66
Alignment explanation
Indices: 110601--110733 Score: 257
Period size: 66 Copynumber: 2.0 Consensus size: 66
110591 ACTTTACGAG
110601 ATAGTTTGTTTTCAAAGAATTAACCTGTCCAATATTGTAAGAAATCATTCTCAACAGAGACAGGG
1 ATAGTTTGTTTTCAAAGAATTAACCTGTCCAATATTGTAAGAAATCATTCTCAACAGAGACAGGG
110666 A
66 A
*
110667 ATAGTTTTTTTTCAAAGAATTAACCTGTCCAATATTGTAAGAAATCATTCTCAACAGAGACAGGG
1 ATAGTTTGTTTTCAAAGAATTAACCTGTCCAATATTGTAAGAAATCATTCTCAACAGAGACAGGG
110732 A
66 A
110733 A
1 A
110734 ATATCTTCAG
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (66 bp):
ATAGTTTGTTTTCAAAGAATTAACCTGTCCAATATTGTAAGAAATCATTCTCAACAGAGACAGGG
A
Found at i:118251 original size:35 final size:35
Alignment explanation
Indices: 118205--118276 Score: 108
Period size: 35 Copynumber: 2.1 Consensus size: 35
118195 AATAGTCCTT
* *
118205 AATTTCATTCTAAACCCTAAATTCCAAAATAATTC
1 AATTACATTCTAAACCCCAAATTCCAAAATAATTC
* *
118240 AATTACATTCTAAACCCCAAATTCTAAAATACTTC
1 AATTACATTCTAAACCCCAAATTCCAAAATAATTC
118275 AA
1 AA
118277 AATAATATTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (35 bp):
AATTACATTCTAAACCCCAAATTCCAAAATAATTC
Found at i:123913 original size:90 final size:89
Alignment explanation
Indices: 123760--123936 Score: 291
Period size: 90 Copynumber: 2.0 Consensus size: 89
123750 CCTAACACAC
* *
123760 TCTTTTATAGACAAGTTACCCTAATCATATTAGGGTTTTATTATTTTAAATTAATTAAATCTATA
1 TCTTTTATAGACAAGTTACCCTAATCATATCAGGGTTTTATTATTTCAAATTAATTAAATCTATA
* *
123825 TTTAATTAATTGGAATTTAATAAT
66 TTTAATTAATTGAAATTAAATAAT
**
123849 TCTTTTATATCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 TCTTTTATAGACAAGTTACCCTAATCATATCAGGG-TTTTATTATTTCAAATTAATTAAATCTAT
123914 ATTTAATTAATTGAAATTAAATA
65 ATTTAATTAATTGAAATTAAATA
123937 TTCAGGATTA
Statistics
Matches: 81, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 32 0.40
90 49 0.60
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.46
Consensus pattern (89 bp):
TCTTTTATAGACAAGTTACCCTAATCATATCAGGGTTTTATTATTTCAAATTAATTAAATCTATA
TTTAATTAATTGAAATTAAATAAT
Found at i:134760 original size:37 final size:36
Alignment explanation
Indices: 134719--134914 Score: 122
Period size: 37 Copynumber: 5.3 Consensus size: 36
134709 AAGCAAATAT
*
134719 TTTATCTCACTTTAGACAGTTTCACTCGAAACAGAAA
1 TTTATCTCACTTGAGACAGTTTCACTCGAAACA-AAA
* * ** ** *
134756 TTTATCTCACTCGAGATAGTTTTTCTTAAAACAAAT
1 TTTATCTCACTTGAGACAGTTTCACTCGAAACAAAA
* *
134792 TTTCTCTCGCTTGAGACAATTGTTTCACTCGAAACAAAA
1 TTTATCTCACTTGAGAC-A--GTTTCACTCGAAACAAAA
* * ** ** *
134831 TTTTATCTCACTCGAGATAGTTTTTCTTAAAACAAAC
1 -TTTATCTCACTTGAGACAGTTTCACTCGAAACAAAA
** * * * * *
134868 TTCGTCTCACTTGAGACAATTTTCCCTCAAAATAAAT
1 TTTATCTCACTTGAGAC-AGTTTCACTCGAAACAAAA
134905 TTTATCTCAC
1 TTTATCTCAC
134915 ATGATATAGT
Statistics
Matches: 116, Mismatches: 38, Indels: 10
0.71 0.23 0.06
Matches are distributed among these distances:
36 28 0.24
37 61 0.53
39 14 0.12
40 13 0.11
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.37
Consensus pattern (36 bp):
TTTATCTCACTTGAGACAGTTTCACTCGAAACAAAA
Found at i:134827 original size:76 final size:76
Alignment explanation
Indices: 134723--134942 Score: 269
Period size: 76 Copynumber: 3.0 Consensus size: 76
134713 AAATATTTTA
*
134723 TCTCACTTTAGAC-A-GTTTCACTCGAAACAGAAA-TTTATCTCACTCGAGATAGTTTTTCTTAA
1 TCTCACTTGAGACAATGTTTCACTCGAAACA-AAATTTTATCTCACTCGAGATAGTTTTTCTTAA
134785 AACAAATTTTC-
65 AACAAATTTTCG
*
134796 TCTCGCTTGAGACAATTGTTTCACTCGAAACAAAATTTTATCTCACTCGAGATAGTTTTTCTTAA
1 TCTCACTTGAGACAA-TGTTTCACTCGAAACAAAATTTTATCTCACTCGAGATAGTTTTTCTTAA
*
134861 AACAAA-CTTCG
65 AACAAATTTTCG
* * ** *
134872 TCTCACTTGAGACAAT-TTTCCCTC-AAA-ATAAATTTTATCTCACAT-GATATAGTTCCTCTTC
1 TCTCACTTGAGACAATGTTTCACTCGAAACA-AAATTTTATCTCAC-TCGAGATAGTTTTTCTTA
134933 AAACAAATTT
64 AAACAAATTT
134943 CTTTTCATTC
Statistics
Matches: 129, Mismatches: 10, Indels: 15
0.84 0.06 0.10
Matches are distributed among these distances:
72 1 0.01
73 47 0.36
74 10 0.08
75 7 0.05
76 64 0.50
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.37
Consensus pattern (76 bp):
TCTCACTTGAGACAATGTTTCACTCGAAACAAAATTTTATCTCACTCGAGATAGTTTTTCTTAAA
ACAAATTTTCG
Found at i:135654 original size:119 final size:118
Alignment explanation
Indices: 135505--135734 Score: 345
Period size: 119 Copynumber: 1.9 Consensus size: 118
135495 CTCACTCGAG
* **
135505 GGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAA-AAGGGAGAAGAAGTT
1 GGATCAACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGAAGAA-AAAGAAGAAGTT
* * *
135569 CATAATGAGAAGAACTTGTTCAACATTTTTCTAGATTCCATCACAGAAGGAGAT
65 CATAATAAAAAGAACTTGTTCAACATTTTGCTAGATTCCATCACAGAAGGAGAT
*
135623 GGATCAACATTTTCAATGAAAGAGTTCATAATGAGAAGAACTCATCCGAAGAAAAAGAAGAAGTT
1 GGATCAACATTTCCAATG-AAGAGTTCATAATGAGAAGAACTCATCCGAAGAAAAAGAAGAAGTT
* * *
135688 CATAATAAAAAGAACTTGTTCAACCTTTTGCTTGATTCTATCACAGA
65 CATAATAAAAAGAACTTGTTCAACATTTTGCTAGATTCCATCACAGA
135735 GAAAGAGAGA
Statistics
Matches: 100, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
118 17 0.17
119 81 0.81
120 2 0.02
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (118 bp):
GGATCAACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGAAGAAAAAGAAGAAGTTC
ATAATAAAAAGAACTTGTTCAACATTTTGCTAGATTCCATCACAGAAGGAGAT
Found at i:136475 original size:22 final size:22
Alignment explanation
Indices: 136432--136473 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
136422 TCTTTTTCGA
*
136432 AATAAAAAACAGTTAGTTAAAT
1 AATAAAAAACAGTTAGTAAAAT
*
136454 AATAAAAAATAG-TAGTAAAA
1 AATAAAAAACAGTTAGTAAAA
136474 ATGATTTTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.64, C:0.02, G:0.10, T:0.24
Consensus pattern (22 bp):
AATAAAAAACAGTTAGTAAAAT
Found at i:136800 original size:2 final size:2
Alignment explanation
Indices: 136795--136855 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
136785 ATTGGGGGGA
136795 AT AT AT AT AT AT 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 AT AT AT AT AT AT
136837 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
136856 ACTTAGGTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:140344 original size:20 final size:20
Alignment explanation
Indices: 140319--140618 Score: 232
Period size: 20 Copynumber: 14.5 Consensus size: 20
140309 GATTTTCCAT
* *
140319 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGTA
* **
140339 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAATACGTA
*
140359 AATCGCAACGCG-ATTC-TGA
1 AATCGCAACGCGAATACGT-A
* * * * *
140378 CTATCGCAATGAGTATCCGTAA
1 -AATCGCAACGCGAATACGT-A
* *
140400 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
140420 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACGT-A
* *
140441 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
*
140461 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
140481 AATCGCAACGCGGAA-ATCGCAATGCAGA
1 AATCGCAACGC-GAATA-CG---T----A
* *
140509 AATCACAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
*
140529 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATACGTA
*
140549 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATACGTA
*
140569 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATACGTA
*
140589 AATCGCAATGCGAAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
140609 AATCGCAACG
1 AATCGCAACG
140619 AGATTCTGAC
Statistics
Matches: 234, Mismatches: 28, Indels: 36
0.79 0.09 0.12
Matches are distributed among these distances:
18 1 0.00
19 3 0.01
20 169 0.72
21 41 0.18
22 2 0.01
24 2 0.01
27 5 0.02
28 11 0.05
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGAATACGTA
Found at i:140422 original size:61 final size:60
Alignment explanation
Indices: 140338--140618 Score: 190
Period size: 61 Copynumber: 4.5 Consensus size: 60
140328 GCGAATATGA
* * ** * ** *
140338 AAATCGCAACGCGAACATATAAATCGCAACGCGATTC-TGACTATCGCAATGAGTATCCGT
1 AAATCGCAACGAGAATACGTAAATCGCAACGCGATACGT-AAAATCGCAACGAGTATCCGT
* * * * *
140398 AAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGAGAATACGTAAATCGCAACG-CGATACGTAAAATCGCAACGAGTATCCGT
* * * *
140460 AAATCGCAACGAGAATACGTAAATCGCAACGCGGAAATCGCAATGCAGAAATCACAACGAGAATA
1 AAATCGCAACGAGAATACGTAAATCGCAACGC-GATA-CG---T--A-AAATCGCAACGAGTATC
140525 CGT
58 CGT
* * * * * * *
140528 AAATCGCAATGCGAATACGTAAATCGCAATGCGAATACGT-AAATCGCAATGCGAATACGT
1 AAATCGCAACGAGAATACGTAAATCGCAACGCG-ATACGTAAAATCGCAACGAGTATCCGT
* *
140588 AAATCGCAATGCGAAT-CTGTAAATCGCAACG
1 AAATCGCAACGAGAATAC-GTAAATCGCAACG
140619 AGATTCTGAC
Statistics
Matches: 180, Mismatches: 28, Indels: 25
0.77 0.12 0.11
Matches are distributed among these distances:
59 1 0.01
60 46 0.26
61 56 0.31
62 23 0.13
63 1 0.01
64 1 0.01
65 1 0.01
67 4 0.02
68 47 0.26
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.18
Consensus pattern (60 bp):
AAATCGCAACGAGAATACGTAAATCGCAACGCGATACGTAAAATCGCAACGAGTATCCGT
Found at i:140499 original size:14 final size:14
Alignment explanation
Indices: 140480--140522 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
140470 GAGAATACGT
*
140480 AAATCGCAACGCGG
1 AAATCGCAACGCAG
*
140494 AAATCGCAATGCAG
1 AAATCGCAACGCAG
*
140508 AAATCACAACG-AG
1 AAATCGCAACGCAG
140521 AA
1 AA
140523 TACGTAAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
13 4 0.16
14 21 0.84
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (14 bp):
AAATCGCAACGCAG
Found at i:141531 original size:24 final size:24
Alignment explanation
Indices: 141473--141519 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
141463 AGTCAGTATT
*
141473 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATCTTGGTCAATACC
141497 CGAACTTTGATCTTGGTCAATAC
1 CGAACTTTGATCTTGGTCAATAC
141520 TCGGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATCTTGGTCAATACC
Found at i:144109 original size:33 final size:34
Alignment explanation
Indices: 144072--144141 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 34
144062 ATTACTATCA
* *
144072 CAACGAGAGAATCGCAATGC-GAAATGAAAATCG
1 CAACGAGAAAATCGCAATACGGAAATGAAAATCG
* **
144105 CAACGTGAAAATCGCAATACGGAAATGACTATCG
1 CAACGAGAAAATCGCAATACGGAAATGAAAATCG
144139 CAA
1 CAA
144142 TGCGAAATGA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
33 17 0.55
34 14 0.45
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.14
Consensus pattern (34 bp):
CAACGAGAAAATCGCAATACGGAAATGAAAATCG
Found at i:144139 original size:53 final size:52
Alignment explanation
Indices: 144081--144193 Score: 154
Period size: 53 Copynumber: 2.2 Consensus size: 52
144071 ACAACGAGAG
* * *
144081 AATCGCAATGCGAAATGAAAATCGCAACGTGAAAATCGCAATACGGAAATGAC
1 AATCGCAATGCGAAATGAAAATCACAACGAGAAAATCGCAATAC-GAAATGAA
* * * *
144134 TATCGCAATGCGAAATGAAAATCATAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCACAACGAGAAAATCGCAATACGAAATGAA
144186 AATCGCAA
1 AATCGCAA
144194 CGAGGGAATC
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
52 14 0.27
53 38 0.73
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.16
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCACAACGAGAAAATCGCAATACGAAATGAA
Found at i:144174 original size:33 final size:33
Alignment explanation
Indices: 144135--144227 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
144125 GGAAATGACT
*
144135 ATCGCAATGCGAAATGAAAATCATAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
* *
144168 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
* *
144201 ATCACAATGCGAAATGAAAATCGCAAC
1 ATCGCAATGCGAAATGAAAATCACAAC
144228 ACAAATTTAG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCACAACGAGAGA
Found at i:144257 original size:19 final size:19
Alignment explanation
Indices: 144233--144273 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
144223 GCAACACAAA
**
144233 TTTAGTTTTGCGTTGCGAT
1 TTTAGTTTCACGTTGCGAT
144252 TTTAGTTTCACGTTGCGAT
1 TTTAGTTTCACGTTGCGAT
144271 TTT
1 TTT
144274 GTCATTGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.12, C:0.12, G:0.22, T:0.54
Consensus pattern (19 bp):
TTTAGTTTCACGTTGCGAT
Found at i:144319 original size:33 final size:33
Alignment explanation
Indices: 144243--144336 Score: 116
Period size: 33 Copynumber: 2.8 Consensus size: 33
144233 TTTAGTTTTG
* * * * *
144243 CGTTGCGATTTTAGTTTCACGTTGCGATTTTGT
1 CGTTGCGATTTTAATTTCGCATTGCGATTCTCT
* *
144276 CATTGTGATTTTAATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTAATTTCGCATTGCGATTCTCT
*
144309 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTAATTTCGCATTGCGAT
144337 AGTCATTTTT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.15, C:0.18, G:0.20, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTAATTTCGCATTGCGATTCTCT
Found at i:144462 original size:14 final size:14
Alignment explanation
Indices: 144443--144479 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
144433 CATCAATTAA
144443 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
144457 ACAAATCATCTTTT
1 ACAAATCAACTTTT
144471 ACAAATCAA
1 ACAAATCAA
144480 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:145897 original size:21 final size:21
Alignment explanation
Indices: 145831--145897 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
145821 GTGAATCGGG
145831 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAATGGTGGGAGGGGA
* * * ** * *
145851 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAATGGTGGGAGGGGA
145873 CTCTTGAATGGTGGGAGGGGA
1 CTCTTGAATGGTGGGAGGGGA
145894 CTCT
1 CTCT
145898 CGAGGAATGA
Statistics
Matches: 31, Mismatches: 14, Indels: 2
0.66 0.30 0.04
Matches are distributed among these distances:
21 29 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.19, G:0.36, T:0.25
Consensus pattern (21 bp):
CTCTTGAATGGTGGGAGGGGA
Found at i:145939 original size:42 final size:42
Alignment explanation
Indices: 145870--145949 Score: 97
Period size: 42 Copynumber: 1.9 Consensus size: 42
145860 CGATGACAGT
* * * *
145870 GGCCTCTTGAATGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAATGATAGGAGGGAACTCTCGAGGAATGATAGG
* * *
145912 GGCCTCTTCAATGATAGGAGTGAACTCTTGAGGGATGA
1 GGCCTCTTCAATGATAGGAGGGAACTCTCGAGGAATGA
145950 CAGGCGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 31 1.00
ACGTcount: A:0.24, C:0.15, G:0.38, T:0.24
Consensus pattern (42 bp):
GGCCTCTTCAATGATAGGAGGGAACTCTCGAGGAATGATAGG
Found at i:146605 original size:21 final size:21
Alignment explanation
Indices: 146581--146655 Score: 52
Period size: 21 Copynumber: 3.7 Consensus size: 21
146571 GTGACGGGAT
146581 AGGTGATGGCTCTCGTTGTAG
1 AGGTGATGGCTCTCGTTGTAG
* ** *
146602 AGGTGTATAG-TCGGGTTG-ATC
1 AGGTG-ATGGCTCTCGTTGTA-G
*
146623 AGGTGATGGCTCT-G-GGT-G
1 AGGTGATGGCTCTCGTTGTAG
146641 AGGTGATGGCTCTCG
1 AGGTGATGGCTCTCG
146656 AAGTGGAGGA
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
18 13 0.32
19 2 0.05
20 5 0.12
21 18 0.44
22 3 0.07
ACGTcount: A:0.15, C:0.13, G:0.41, T:0.31
Consensus pattern (21 bp):
AGGTGATGGCTCTCGTTGTAG
Found at i:147940 original size:20 final size:20
Alignment explanation
Indices: 147915--147977 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
147905 TTTTGGTTGA
147915 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
147935 AATGAAAATCGCAACGCAGA-
1 AATGAAAATCGCAACG-AGAG
**
147955 AATGACTATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
147975 AAT
1 AAT
147978 CGCAACGCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.08
20 33 0.85
21 3 0.08
ACGTcount: A:0.48, C:0.17, G:0.22, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:148051 original size:21 final size:20
Alignment explanation
Indices: 148033--148104 Score: 92
Period size: 20 Copynumber: 3.5 Consensus size: 20
148023 CGTTTCTCTC
148033 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCAT
** *
148053 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCAT
148074 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
148094 GTTGCGATTTT
1 GTTGCGATTTT
148105 AAGTTTAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
20 30 0.67
21 15 0.33
ACGTcount: A:0.12, C:0.17, G:0.19, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:148609 original size:20 final size:20
Alignment explanation
Indices: 148584--148797 Score: 168
Period size: 20 Copynumber: 10.6 Consensus size: 20
148574 CTTTAAAAAT
148584 CGCGTTGCGATTTACGAATA
1 CGCGTTGCGATTTACGAATA
*
148604 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGAATA
* *
148624 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGAATA
* * * *
148645 CGCATTACGATTTACGTATT
1 CGCGTTGCGATTTACGAATA
*
148665 CTCGTTGCGATTTAC-AGATA
1 CGCGTTGCGATTTACGA-ATA
* *
148685 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGAATA
* * *
148705 CTCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGAATA
*
148725 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGAATA
* *
148746 CTCGTTGCGATAGT-CAGAAT-
1 CGCGTTGCGAT-TTAC-GAATA
* *
148766 CGCGTTGCGATTTTC-ATATT
1 CGCGTTGCGATTTACGA-ATA
148786 CGCGTTGCGATT
1 CGCGTTGCGATT
148798 ATGGAAAATC
Statistics
Matches: 156, Mismatches: 27, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
18 1 0.01
19 3 0.02
20 112 0.72
21 40 0.26
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGAATA
Found at i:148670 original size:40 final size:41
Alignment explanation
Indices: 148586--148797 Score: 263
Period size: 40 Copynumber: 5.2 Consensus size: 41
148576 TTAAAAATCG
* *
148586 CGTTGCGATTTACGAATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
148627 CGTTGCGATTTACGGATACGCATTACGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
148667 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
148707 CATTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * * *
148748 CGTTGCGATAGT-CAGA-ATCGCGTTGCGATTTT-CATATTCG
1 CGTTGCGAT-TTACGGATA-CGCGTTGCGATTTTACGTATTCT
148788 CGTTGCGATT
1 CGTTGCGATT
148798 ATGGAAAATC
Statistics
Matches: 149, Mismatches: 19, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
40 88 0.59
41 60 0.40
42 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:148740 original size:81 final size:80
Alignment explanation
Indices: 148586--148797 Score: 268
Period size: 81 Copynumber: 2.6 Consensus size: 80
148576 TTAAAAATCG
*
148586 CGTTGCGATTTAC-GAATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCAT
1 CGTTGCGATTTACAG-ATACGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACGCAT
* *
148650 TACGATTTACGTATTCT
64 TACGATTTACGGATACT
* * *
148667 CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCTCATTGCGATTTACGGATACGCGTTG
1 CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCATTA
148732 CGATTTTACGGATACT
66 CGA-TTTACGGATACT
* * * *
148748 CGTTGCGATAGT-CAGA-ATCGCGTTGCGATTTTCATATTCGCGTTGCGATT
1 CGTTGCGAT-TTACAGATA-CGCGTTGCGATTTACGTATTCTCGTTGCGATT
148798 ATGGAAAATC
Statistics
Matches: 116, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
80 37 0.32
81 77 0.66
82 2 0.02
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (80 bp):
CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCATTA
CGATTTACGGATACT
Found at i:148858 original size:42 final size:42
Alignment explanation
Indices: 148750--148858 Score: 100
Period size: 42 Copynumber: 2.6 Consensus size: 42
148740 CGGATACTCG
* * *
148750 TTGCGA-TAGTCAGAATCGCGTTGCG-ATTTTCATATTCGCG
1 TTGCGATTATTCAAAATCGCGTTGCGAATTTTCATATTCGCA
** **
148790 TTGCGATTATGGAAAATCGCAATGCGAATTTGT-ACTA-TCGCA
1 TTGCGATTATTCAAAATCGCGTTGCGAATTT-TCA-TATTCGCA
*
148832 TTGCGATTATTCATAATCGCGTTGCGA
1 TTGCGATTATTCAAAATCGCGTTGCGA
148859 TTCTGGGAAC
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
40 6 0.11
41 13 0.25
42 31 0.58
43 3 0.06
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (42 bp):
TTGCGATTATTCAAAATCGCGTTGCGAATTTTCATATTCGCA
Found at i:149803 original size:14 final size:13
Alignment explanation
Indices: 149749--149804 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 13
149739 AATATCCAAA
149749 ATATTTAAATTTT
1 ATATTTAAATTTT
* *
149762 ATAATTGAAATGTT
1 AT-ATTTAAATTTT
149776 AGCTATTT-AATTTT
1 A--TATTTAAATTTT
149790 ATATTTCAAATTTT
1 ATATTT-AAATTTT
149804 A
1 A
149805 AATATTTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
12 5 0.15
13 2 0.06
14 23 0.68
15 3 0.09
16 1 0.03
ACGTcount: A:0.38, C:0.04, G:0.05, T:0.54
Consensus pattern (13 bp):
ATATTTAAATTTT
Found at i:149810 original size:28 final size:28
Alignment explanation
Indices: 149747--149812 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
149737 ATAATATCCA
*
149747 AAATATTTAAATTTTATAATTGAAATGTT
1 AAATATTT-AATTTTATAATTCAAATGTT
** * *
149776 AGCTATTTAATTTTATATTTCAAATTTT
1 AAATATTTAATTTTATAATTCAAATGTT
149804 AAATATTTA
1 AAATATTTA
149813 TTGCATATTT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
28 24 0.80
29 6 0.20
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.52
Consensus pattern (28 bp):
AAATATTTAATTTTATAATTCAAATGTT
Found at i:156471 original size:56 final size:56
Alignment explanation
Indices: 156390--156882 Score: 688
Period size: 56 Copynumber: 8.9 Consensus size: 56
156380 ATTACCAAAT
* * *
156390 GGCACCGTGTGTGC-AAAACTAAGAAATTCATAATAAGTTAATGAATTTTCGTATG
1 GGCACTGTGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* * *
156445 GGCACCGTGTTTGCAAAAACTAAGAAATTCATAATAA-TTTATGAATTTCCGTATA
1 GGCACTGTGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* * *
156500 GACACTGTGTGTGCAAAAACTAAAAAATTCATAATGAGTTTATGAATTTCCGTATG
1 GGCACTGTGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* * * * * *
156556 TGCACTGTGTGTGCAAAAACTAAAAAATTCCTAATGAGTTTATGAATTTTCGTATA
1 GGCACTGTGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* *
156612 GGCACTATGTGTGCAAAAACTAAGAAATTTATAATAAGTTTATGAATTTCCGTATG
1 GGCACTGTGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* *
156668 AGCACTGTGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCTTATG
1 GGCACTGTGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* * *
156724 GACATTTTGTGTG-AAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
1 GGCACTGTGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* * *
156779 GGCACTTTGCGAGCAAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
1 GGCACTGTGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* * * * *
156835 GGCACTTTGTGTGC-AAAGCTAAGAAAGTCATACTAAGTATATGAATTT
1 GGCACTGTGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATGAATTT
156883 TTGTATTGAT
Statistics
Matches: 393, Mismatches: 42, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
55 140 0.36
56 253 0.64
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.33
Consensus pattern (56 bp):
GGCACTGTGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
Found at i:156795 original size:111 final size:111
Alignment explanation
Indices: 156397--156882 Score: 679
Period size: 111 Copynumber: 4.4 Consensus size: 111
156387 AATGGCACCG
* * * * *
156397 TGTGTGCAAAACTAAGAAATTCATAATAAGTTAATGAATTTTCGTATGGGCACCGTGTTTGCAAA
1 TGTGTGAAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGCAAA
* *
156462 AACTAAGAAATTCATAATAA-TTTATGAATTTCCGTATAGACACTG
66 AACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGACACTT
* * *
156507 TGTGTGCAAAAACTAAAAAATTCATAATGAGTTTATGAATTTCCGTATGTGCACTGTGTGTGCAA
1 TGTGTG-AAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGCAA
* * * * *
156572 AAACTAAAAAATTCCTAATGAGTTTATGAATTTTCGTATAGG-CACTA
65 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT-GGACACTT
* *
156619 TGTGTGCAAAAACTAAGAAATTTATAATAAGTTTATGAATTTCCGTATGAGCACTGTGTGTGCAA
1 TGTGTG-AAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGCAA
* *
156684 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCTTATGGACATTT
65 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGACACTT
* * *
156731 TGTGTGAAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGCGAGCAAA
1 TGTGTGAAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGCAAA
*
156796 AACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTT
66 AACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGACACTT
* * * * *
156842 TGTGTGCAAAGCTAAGAAAGTCATACTAAGTATATGAATTT
1 TGTGTGAAAAACTAAGAAATTCATAATAAGTTTATGAATTT
156883 TTGTATTGAT
Statistics
Matches: 334, Mismatches: 38, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
110 6 0.02
111 203 0.61
112 124 0.37
113 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (111 bp):
TGTGTGAAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGCAAA
AACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGACACTT
Found at i:156797 original size:223 final size:222
Alignment explanation
Indices: 156397--156882 Score: 713
Period size: 223 Copynumber: 2.2 Consensus size: 222
156387 AATGGCACCG
* * * *
156397 TGTGTGCAAAACTAAGAAATTCATAATAAGTTAATGAATTTTCGTATGGGCACCGTGTTTGCAAA
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGAGCACCGTGTGTGCAAA
156462 AACTAAGAAATTCATAATAATTTATGAATTTCCGTATAGACACTGTGTGTGCAAAAACTAAAAAA
66 AACTAAGAAATTCATAATAATTTATGAATTTCCGTATAGACACTGTGTGTGCAAAAACTAAAAAA
* * * * * *
156527 TTCATAATGAGTTTATGAATTTCCGTATGTGCACTGTGTGTGCAAAAACTAAAAAATTCCTAATG
131 TTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGCGAGCAAAAACTAAAAAATTCATAATA
*
156592 AGTTTATGAATTTTCGTATAGGCACTA
196 AGTTTATGAATTTCCGTATAGGCACTA
* *
156619 TGTGTGCAAAAACTAAGAAATTTATAATAAGTTTATGAATTTCCGTATGAGCACTGTGTGTGCAA
1 TGTGTGC-AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGAGCACCGTGTGTGCAA
* * * * *
156684 AAACTAAGAAATTCATAATAAGTTTATGAATTTCCTTATGGACATTTTGTGTG-AAAAACTAAGA
65 AAACTAAGAAATTCATAATAA-TTTATGAATTTCCGTATAGACACTGTGTGTGCAAAAACTAAAA
* *
156748 AATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGCGAGCAAAAACTAAGAAATTCATAA
129 AATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGCGAGCAAAAACTAAAAAATTCATAA
* *
156813 TAAGTTTATGAATTTCCGTATGGGCACTT
194 TAAGTTTATGAATTTCCGTATAGGCACTA
* * * *
156842 TGTGTGCAAAGCTAAGAAAGTCATACTAAGTATATGAATTT
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTT
156883 TTGTATTGAT
Statistics
Matches: 235, Mismatches: 27, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
222 36 0.15
223 172 0.73
224 27 0.11
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (222 bp):
TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGAGCACCGTGTGTGCAAA
AACTAAGAAATTCATAATAATTTATGAATTTCCGTATAGACACTGTGTGTGCAAAAACTAAAAAA
TTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGCGAGCAAAAACTAAAAAATTCATAATA
AGTTTATGAATTTCCGTATAGGCACTA
Found at i:159937 original size:54 final size:54
Alignment explanation
Indices: 159873--160531 Score: 743
Period size: 54 Copynumber: 12.2 Consensus size: 54
159863 CTATGTGTAC
* ** *
159873 TACATGCACTATGTGTGTAACCCACGGAATTCATCATAAGTTGATGAATAACCG
1 TACATGCACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAATAACCG
* *
159927 TACATGCACTATGTGTGTAATTCAC-GAATTCATCATAAGTTGATGAATAACCG
1 TACATGCACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAATAACCG
* * * * * *
159980 TACATGTACTATATGTACAATTCATGGAATTCATCATAAGTTGATGAATAATCG
1 TACATGCACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAATAACCG
* * * * * * **
160034 TATAGGCACTATGTATGCAATTCATGAAATTCATCATGAGTTGATCAATAATTG
1 TACATGCACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAATAACCG
* * * *
160088 TACAGGCACTATGTGTGTAATTCACGGAATTTATCATGGGTTGATGAATAACCG
1 TACATGCACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAATAACCG
* * * * *
160142 TACATGCACTATGTGTGCAATCCACAGAATTCATCATAAGTTGATAAATAATCG
1 TACATGCACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAATAACCG
* * *
160196 TACAAGCACTATGTGTGCAATTCATGAAATTCATCATGAGTTGATGAATAACCG
1 TACATGCACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAATAACCG
* *
160250 TACA-GACACTATGTGTGCAACTCACAGAATTCATCATGAGTTGATGAATAACCG
1 TACATG-CACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAATAACCG
* * ** ** * *
160304 TGCAAT-CACTATGTGTACAACCCACAAAATTCATCATGAGTTGATAAATAACTG
1 TAC-ATGCACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAATAACCG
*
160358 TACATGCACTATGTGTGCAAATTCAGGGAATTCATCATGAGTTGATGAATAACCG
1 TACATGCACTATGTGTGC-AATTCACGGAATTCATCATGAGTTGATGAATAACCG
* * *
160413 TACA-GACGCTGTATGTGCAATTCACGGAATTCATCATGAGTTGATGAATAACCG
1 TACATG-CACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAATAACCG
* * ** * **
160467 TACAGGTACTATGTGTGCAACCCGCAAAATTCATCATGAGTTGATGAACT-ACCG
1 TACATGCACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAA-TAACCG
* *
160521 TATAGGCACTA
1 TACATGCACTA
160532 CGTGAGCATC
Statistics
Matches: 517, Mismatches: 79, Indels: 18
0.84 0.13 0.03
Matches are distributed among these distances:
53 51 0.10
54 421 0.81
55 45 0.09
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (54 bp):
TACATGCACTATGTGTGCAATTCACGGAATTCATCATGAGTTGATGAATAACCG
Found at i:165075 original size:20 final size:20
Alignment explanation
Indices: 165050--165096 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
165040 GATGCAATTA
165050 GTATCGAGACT-GAGAGGAGG
1 GTATCGAGACTAGAGA-GAGG
* *
165070 GTATCGATACTATAGAGAGG
1 GTATCGAGACTAGAGAGAGG
165090 GTATCGA
1 GTATCGA
165097 TACCATTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 21 0.88
21 3 0.12
ACGTcount: A:0.32, C:0.11, G:0.36, T:0.21
Consensus pattern (20 bp):
GTATCGAGACTAGAGAGAGG
Found at i:165569 original size:45 final size:44
Alignment explanation
Indices: 165506--165594 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 44
165496 CTAAATGGAA
*
165506 CCGTGTGTACAAAACTAAGAAATTCATAATAAGTTTATGAATTT
1 CCGTGTGTAAAAAACTAAGAAATTCATAATAAGTTTATGAATTT
165550 CCGTGTGTATAAAAACTAAGAAATTCATAATAAGTTTATGAATTT
1 CCGTGTGTA-AAAAACTAAGAAATTCATAATAAGTTTATGAATTT
165595 TCGTATGGAC
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 9 0.21
45 34 0.79
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (44 bp):
CCGTGTGTAAAAAACTAAGAAATTCATAATAAGTTTATGAATTT
Found at i:166118 original size:55 final size:55
Alignment explanation
Indices: 165561--166094 Score: 726
Period size: 56 Copynumber: 9.6 Consensus size: 55
165551 CGTGTGTATA
* * **
165561 AAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGACACTGCGTGTGC
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGC
** * * * * * *
165616 AGAAACTAAGAAATTCATAACGAGTATATGATTTTTCATATGGGCACTGTGTGTGAA
1 A-AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTG-C
* * *
165673 AAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTGTGTGTGAA
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTG-C
* *
165729 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTACGGGCACTTTGTGTGC
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGC
* * * *
165784 AAAACTAAGAAATTCATAATAAATTTATGAATTTTCGTACGGGCACTTTGTGTTC
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGC
* * **
165839 AATACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGAGCACAGTGTGTGC
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGC
*
165894 AAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCTTATGGGCACTTTGTGTGC
1 -AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGC
*
165950 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGAGTGC
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGC
* * *
166005 AAAAACTAAGAAATTTATATTAAGTTTATGAATTTCTGTATGGGCACTTTGTGTGC
1 -AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGC
* * *
166061 AAAGCTAAGAAAGTCATAATAAGTATATGAATTT
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTT
166095 TTGTATTGAT
Statistics
Matches: 429, Mismatches: 46, Indels: 8
0.89 0.10 0.02
Matches are distributed among these distances:
55 181 0.42
56 247 0.58
57 1 0.00
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (55 bp):
AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGC
Found at i:166118 original size:111 final size:111
Alignment explanation
Indices: 165560--166100 Score: 746
Period size: 111 Copynumber: 4.9 Consensus size: 111
165550 CCGTGTGTAT
* **
165560 AAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGACACTGCGTGTGCAGAAACTAA
1 AAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTTTGTGTGCA-AAACTAA
** * * * *
165625 GAAATTCATAACGAGTATATG-ATTTTTCATATGGGCACTGTGTGTGA
65 GAAATTCATAATAAGTTTATGAATTTCT-GTATGGGCACTGTGTGTGC
* *
165672 AAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTGTGTGTGAAAAAACTAA
1 AAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTTTGTGTG-CAAAACTAA
* *
165737 GAAATTCATAATAAGTTTATGAATTTCTGTACGGGCACTTTGTGTGC
65 GAAATTCATAATAAGTTTATGAATTTCTGTATGGGCACTGTGTGTGC
* * * *
165784 -AAAACTAAGAAATTCATAATAAATTTATGAATTTTCGTACGGGCACTTTGTGTTCAATACTAAG
1 AAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTTTGTGTGCAAAACTAAG
* * *
165848 AAATTCATAATAAGTTTATGAATTTCCGTATGAGCACAGTGTGTGC
66 AAATTCATAATAAGTTTATGAATTTCTGTATGGGCACTGTGTGTGC
* *
165894 AAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCTTATGGGCACTTTGTGTGCAAAACTAAG
1 AAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTTTGTGTGCAAAACTAAG
* * *
165959 AAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGAGTGC
66 AAATTCATAATAAGTTTATGAATTTCTGTATGGGCACTGTGTGTGC
* * *
166005 AAAAACTAAGAAATTTATATTAAGTTTATGAA-TTTCTGTATGGGCACTTTGTGTGCAAAGCTAA
1 AAAAACTAAGAAATTCATAATAAGTTTATGAATTTTC-GTATGGGCACTTTGTGTGCAAAACTAA
* * *
166069 GAAAGTCATAATAAGTATATGAATTTTTGTAT
65 GAAATTCATAATAAGTTTATGAATTTCTGTAT
166101 TGATAGTGGG
Statistics
Matches: 384, Mismatches: 41, Indels: 9
0.88 0.09 0.02
Matches are distributed among these distances:
110 52 0.14
111 233 0.61
112 93 0.24
113 6 0.02
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (111 bp):
AAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTTTGTGTGCAAAACTAAG
AAATTCATAATAAGTTTATGAATTTCTGTATGGGCACTGTGTGTGC
Found at i:173836 original size:22 final size:20
Alignment explanation
Indices: 173811--173857 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
173801 GAGGTATCAG
173811 TACCATGGTATAGTAGTATCGA
1 TACCATGGTA-AG-AGTATCGA
* *
173833 TACCATGTTAAGGGTATCGA
1 TACCATGGTAAGAGTATCGA
173853 TACCA
1 TACCA
173858 GGAAACATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 12 0.52
21 2 0.09
22 9 0.39
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (20 bp):
TACCATGGTAAGAGTATCGA
Found at i:174346 original size:11 final size:12
Alignment explanation
Indices: 174325--174357 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
174315 GTAATTGTGA
174325 ATGAGTATAAATG
1 ATGA-TATAAATG
174338 AT-ATATAAATG
1 ATGATATAAATG
174349 ATGATATAA
1 ATGATATAA
174358 GAATATGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 10 0.53
12 7 0.37
13 2 0.11
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (12 bp):
ATGATATAAATG
Found at i:180305 original size:24 final size:24
Alignment explanation
Indices: 180278--180361 Score: 99
Period size: 23 Copynumber: 3.7 Consensus size: 24
180268 GGGAAAAATA
180278 TGGCACTTCGGTGCAAAACTTATG
1 TGGCACTTCGGTGCAAAACTTATG
*
180302 TGGCACTTCGGTGC-AAACCTATG
1 TGGCACTTCGGTGCAAAACTTATG
*
180325 TGGTC-CTTCGG-G-ACAA-TTATG
1 TGG-CACTTCGGTGCAAAACTTATG
180346 TGGCACTTC-GTGCAAA
1 TGGCACTTCGGTGCAAA
180362 TTACGAGATG
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
20 2 0.04
21 12 0.24
22 5 0.10
23 17 0.33
24 15 0.29
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.29
Consensus pattern (24 bp):
TGGCACTTCGGTGCAAAACTTATG
Found at i:190766 original size:23 final size:23
Alignment explanation
Indices: 190707--190767 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
190697 CTCGTATAAA
*
190707 TGCACCGAAGTGCAACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
190730 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
190753 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
190768 TATAAGATTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:197488 original size:23 final size:23
Alignment explanation
Indices: 197456--197516 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
197446 CTCATATAAA
197456 TACACCGAAGTGCCACGTAGAAT
1 TACACCGAAGTGCCACGTAGAAT
* ***
197479 TCCACCGAAGTGCTGTGTAGAAT
1 TACACCGAAGTGCCACGTAGAAT
*
197502 TACACCGTAGTGCCA
1 TACACCGAAGTGCCA
197517 TATAAGATTG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (23 bp):
TACACCGAAGTGCCACGTAGAAT
Found at i:198231 original size:64 final size:65
Alignment explanation
Indices: 198157--198319 Score: 199
Period size: 64 Copynumber: 2.6 Consensus size: 65
198147 ATCCCTTGAC
* *
198157 GGGTGCATCGATGCACTATC-TATGCATCGATACA-TAAATCCCATTCGATGTTTGTATTTTAAG
1 GGGTGCATCGATGCACTATCATGTGCATCGATACACT-AATCCCATTCGATGTTTGTATTTTAAA
198220 G
65 G
* * ** * *
198221 GGGTGCATCGATGCACTA-CTTGTGCATCGATACACTGATGGCATTCGATGTTTTTATTTTAAAT
1 GGGTGCATCGATGCACTATCATGTGCATCGATACACTAATCCCATTCGATGTTTGTATTTTAAAG
* *
198285 GAGTGCATCGATACACT-TCATGTGCATCGATACAC
1 GGGTGCATCGATGCACTATCATGTGCATCGATACAC
198320 CTTGAACAAT
Statistics
Matches: 86, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
63 1 0.01
64 84 0.98
65 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.34
Consensus pattern (65 bp):
GGGTGCATCGATGCACTATCATGTGCATCGATACACTAATCCCATTCGATGTTTGTATTTTAAAG
Found at i:198524 original size:47 final size:47
Alignment explanation
Indices: 198473--198566 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
198463 ATACAATTAC
198473 TTAAACTAATTATTATCCATTCAATACCTTTAAAACTTAGAAATACA
1 TTAAACTAATTATTATCCATTCAATACCTTTAAAACTTAGAAATACA
198520 TTAAACTAATTATTATCCATTCAATACCTTTAAAACTTAGAAATACA
1 TTAAACTAATTATTATCCATTCAATACCTTTAAAACTTAGAAATACA
198567 ATCCTCTATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.45, C:0.17, G:0.02, T:0.36
Consensus pattern (47 bp):
TTAAACTAATTATTATCCATTCAATACCTTTAAAACTTAGAAATACA
Found at i:199973 original size:18 final size:18
Alignment explanation
Indices: 199950--200000 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
199940 ATTCTGAATG
* *
199950 TTTACAGATATTATATGT
1 TTTACAGATATCAGATGT
*
199968 TTTACAGTTATCAGATGT
1 TTTACAGATATCAGATGT
*
199986 TTTACAGTTATCAGA
1 TTTACAGATATCAGA
200001 CACAGATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45
Consensus pattern (18 bp):
TTTACAGATATCAGATGT
Found at i:200253 original size:26 final size:26
Alignment explanation
Indices: 200224--200273 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
200214 GTTTTGTGCC
200224 TAGTATGCACCTTAAACTCATGTATT
1 TAGTATGCACCTTAAACTCATGTATT
*
200250 TAGTGTGCACCTTAAACTCATGTA
1 TAGTATGCACCTTAAACTCATGTA
200274 CCTTATATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (26 bp):
TAGTATGCACCTTAAACTCATGTATT
Found at i:205319 original size:29 final size:31
Alignment explanation
Indices: 205252--205321 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 31
205242 AAAATTACCT
*
205252 CTTTGGTC-CTTAAACTTTTCTAAAGTTTATA
1 CTTTGGTCAC-TAAACTTTTCTAAAATTTATA
205283 CTTT--TCACTAAAC-TTTC-AAAATTTATA
1 CTTTGGTCACTAAACTTTTCTAAAATTTATA
*
205310 TTTTGGTCACTA
1 CTTTGGTCACTA
205322 TCTAAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
27 12 0.35
28 4 0.12
29 13 0.38
30 1 0.03
31 4 0.12
ACGTcount: A:0.29, C:0.17, G:0.07, T:0.47
Consensus pattern (31 bp):
CTTTGGTCACTAAACTTTTCTAAAATTTATA
Found at i:205759 original size:850 final size:851
Alignment explanation
Indices: 203945--206502 Score: 4094
Period size: 850 Copynumber: 3.0 Consensus size: 851
203935 ACAAATTGGC
*
203945 ATGAATTTTAGACTAATTTCATGCTAATTTATCTTTAATTTAAACTTTAGTGAATATTAAATTTA
1 ATGAATTTTAGACTAATTTCATGCTAATTTATCTTTAATTTAAACTTTAATGAATATTAAATTTA
* * *
204010 TTTAATAGGG-AAAGGCCAATTTACCCTTAATGAAACTGCATATTTACCATCAAACCAAGACACC
66 TTTAATTGGGAAAAGACCAATTTACCCTTAATGAAACTTCATATTTACCATCAAACCAAGACACC
* * *
204074 TCAACCATATAATCTTCCTAAAGTCAAACATGAACAAACAAAATCTTACTTTATCGATTTGCCCT
131 TCAACCTTATCATCTTCCTAAAGTCAAATATGAACAAACAAAATCTTACTTTATCGATTTGCCCT
*
204139 TGCCTTTATCCAAAAATTACAATCTTGCCACTTTAATCCAACAGTCCAAATTAAGTATGGAATTA
196 TGCCTTTATCCAAAAATTACAATCTTGCCACTTTAATCCAACAGTCCAAATTAATTATGGAATTA
*
204204 AATCCTCAAATCCAAAGATTTATATAA-TTTTCAAACATTTT-ATATGTGGAAATAATATTTTTA
261 AATCCTCAAATCCAAAGATTTATATAATTTTTC-AACATTTTAAAATGTGGAAATAATATTTTTA
* *
204267 ATTCTAATTTATCATCCTTCAGATTTTACTGAATTTTCTATTCGATCCGATTTACTGAATCTTTC
325 ATTCAAATTTATCATCCTTCAGATTTTCCTGAATTTTCTATTCGATCCGATTTACTGAATCTTTC
* *
204332 CTCAAACTTCAACACTTTATAACTATTTATTTACGAGGGAAAATGTAACTTTTTAAAATTACCTC
390 CTCAAACTTCAACGCTTTATAACTATTTATTTACGAGGAAAAATGTAACTTTTTAAAATTACCTC
* * * *
204397 TTTGGTCCCTAAACTTTTCCAAAGTTTATACTTTGGCCAGTAAACTTTCAAAATTTGTATTTTGG
455 TTTGGTCCCTAAACTTTTCTAAAGTTTATACTTT-GTCACTAAACTTTCAAAATTTATATTTTGG
* * *
204462 TCACTATCTAAAATTTAGAGTATTACAACTCTCCCCCGTTAAATAAAATTCATCATCAAATTTTA
519 TCACTATCTAAAATTTAGGGTATTACAACTCTCCCCAGTTAAATAAAATTCGTCATCAAATTTTA
*
204527 AGACATACCTGTAGTGAAGAGGTGTGGATATTGCTTTCTCATGTCCTACTCTCTTTCTTAAGTAG
584 AGACATACCTGTAGTGAAGAGGTGTGGATATTGC--T-TCATGTCCTACTCTCTTTCCTAAGTAG
* * * **
204592 CGTCCTCGATTTTATGATTTTGTCAAAGGACTTTGACTAATGTAATCGTCTTGCTACATGGTTAT
646 CGTCCTCGACTTTATGATTTTGCCAAAGCACTTTGACTAATGTAATCGTCTTGCTACACAGTTAT
*
204657 TTGATTTCTCAAGCCAATATCCGTATTGGTTCTTCTTCATAAGTCAAATCTGGGATCTCAATTTC
711 TTGATTTCTCGAGCCAATATCCGTATTGGTTCTTCTTCATAAGTCAAATCTGGGATCTCAATTTC
* * *
204722 CTCTAATGTAATGACATGTGAAAGATCCGATCGATACTTTCTAAGCATCGACACATGAAAAACAT
776 CTCTGATGCAATGACATGTGAAAGATTCGATCGATACTTTCTAAGCATCGACACATGAAAAACAT
204787 TATGAACTTTG
841 TATGAACTTTG
*
204798 ATGAATTTTAGACTAATTTAATGCTAATTTATCTTTAATTTAAACTTTAATGAATATTAAATTTA
1 ATGAATTTTAGACTAATTTCATGCTAATTTATCTTTAATTTAAACTTTAATGAATATTAAATTTA
* *
204863 TTTAATTAGGAAAAGACCAATTTACCCTTAATGAAACTTTATATTTACCATCAAACCAAGACACC
66 TTTAATTGGGAAAAGACCAATTTACCCTTAATGAAACTTCATATTTACCATCAAACCAAGACACC
* * *
204928 TCAACCTTATCGTCTTCCTAAAGTCAAATATAAACAAACAAAATCTTACTTTATCGATTTTCCCT
131 TCAACCTTATCATCTTCCTAAAGTCAAATATGAACAAACAAAATCTTACTTTATCGATTTGCCCT
* * * *
204993 TGACTTTAT-AAAAAATGTACAATCTTGCCACTTTAATCCAATAGTCCAAATTAATTATCGAATT
196 TGCCTTTATCCAAAAAT-TACAATCTTGCCACTTTAATCCAACAGTCCAAATTAATTATGGAATT
205057 AAATCCTCAAATCCAAAGATTTATATAATTTTTCAACATTTTAAAATGTGGAAA-AATATTTTTA
260 AAATCCTCAAATCCAAAGATTTATATAATTTTTCAACATTTTAAAATGTGGAAATAATATTTTTA
* * *
205121 TTTCAAATTTATCATCCTTCAAATTTTCCTGAATTTTTTATTCGATCCGATTTACTGAATCTTTC
325 ATTCAAATTTATCATCCTTCAGATTTTCCTGAATTTTCTATTCGATCCGATTTACTGAATCTTTC
* * * *
205186 CTCAAACTTTATCGCTTGATAACTATTTATTTCCGATGGCAAAAATGTAACTTTTTAAAATTACC
390 CTCAAACTTCAACGCTTTATAACTATTTATTTACGA-GG-AAAAATGTAACTTTTTAAAATTACC
*
205251 TCTTTGGTCCTTAAACTTTTCTAAAGTTTATACTTT-TCACTAAACTTTCAAAATTTATATTTTG
453 TCTTTGGTCCCTAAACTTTTCTAAAGTTTATACTTTGTCACTAAACTTTCAAAATTTATATTTTG
*
205315 GTCACTATCTAAAATTTAGGGTATT-CAACTCTCCCCAGTTAAATAAAATTTGTCATCAAATTTT
518 GTCACTATCTAAAATTTAGGGTATTACAACTCTCCCCAGTTAAATAAAATTCGTCATCAAATTTT
*
205379 AAGACATACCTGTAGTGAAGAGGTGTGGATATTGCTTCATGTCCTACTCTCTTTCCTAAGTAACG
583 AAGACATACCTGTAGTGAAGAGGTGTGGATATTGCTTCATGTCCTACTCTCTTTCCTAAGTAGCG
* *
205444 TCCTCGACTTTATGATTTTGCCAAAGCACTTTGACTAGTGTAATCGTCTTGCTAAACAGTTATTT
648 TCCTCGACTTTATGATTTTGCCAAAGCACTTTGACTAATGTAATCGTCTTGCTACACAGTTATTT
* *
205509 GATTTCTCGAGCCAATATCCGTATTGGTTCTTCTTAATAAGTCAAATATGGGATCTCAATTTCCT
713 GATTTCTCGAGCCAATATCCGTATTGGTTCTTCTTCATAAGTCAAATCTGGGATCTCAATTTCCT
*
205574 CTGATGCAATGACATGTGAATGATTCGATCGATACTTTCTAAGCATCGACACATGAAAAACATTA
778 CTGATGCAATGACATGTGAAAGATTCGATCGATACTTTCTAAGCATCGACACATGAAAAACATTA
205639 TGAACTTTG
843 TGAACTTTG
*
205648 ATGAATTTTAGACTAATTTCATGCTAATTTATCTTTAATTTAAACTTTAATGAATATTAAATTCA
1 ATGAATTTTAGACTAATTTCATGCTAATTTATCTTTAATTTAAACTTTAATGAATATTAAATTTA
* * * *
205713 TTTAATTGGGAAAATACCAATTTACGCTTAATGAAACTTCATATTTACCATCAAACCAAGGCAAC
66 TTTAATTGGGAAAAGACCAATTTACCCTTAATGAAACTTCATATTTACCATCAAACCAAGACACC
* * *
205778 TCAACCTTATCATCTACTTAAAGTCAAATATGATCAAACAAAATCTTACTTTATCGATTTGCCCT
131 TCAACCTTATCATCTTCCTAAAGTCAAATATGAACAAACAAAATCTTACTTTATCGATTTGCCCT
* * *
205843 TGCCTTTATCCAAAAACTACAATCTTCCCACTTTAATCCAACAGTCCAAATTAATCATGGAATTA
196 TGCCTTTATCCAAAAATTACAATCTTGCCACTTTAATCCAACAGTCCAAATTAATTATGGAATTA
* * *
205908 AATCCTCAAATCCAAAGATTTATATAATTTTCCAACATTTTAAAATATGGAAATAATAGTTTTAA
261 AATCCTCAAATCCAAAGATTTATATAATTTTTCAACATTTTAAAATGTGGAAATAATATTTTTAA
* * *
205973 TT-ATAATTTATCATCCTTCAGATTTTCCTAAATTTTCTATTTGATCCGATTTACTAAATCTTTC
326 TTCA-AATTTATCATCCTTCAGATTTTCCTGAATTTTCTATTCGATCCGATTTACTGAATCTTTC
206037 CTCAAACTTCAACGCTTTATAACTATTTATTTACGAGGGTAAAAATGTAACTTTTTAAAATTACC
390 CTCAAACTTCAACGCTTTATAACTATTTATTTACGA-GG-AAAAATGTAACTTTTTAAAATTACC
* * * * *
206102 ACTTTAGTCCCTAAACTTTTCTAAAGTTTATACTTTGGTTACTAAACTTTTAAATTTTATATTTT
453 TCTTTGGTCCCTAAACTTTTCTAAAGTTTATACTTT-GTCACTAAACTTTCAAAATTTATATTTT
* *
206167 GGTCACTATCAAAAATTTAGGGTATTACAACTCTCCCCTGTTAAATAAAATTCGTCATCAAATTT
517 GGTCACTATCTAAAATTTAGGGTATTACAACTCTCCCCAGTTAAATAAAATTCGTCATCAAATTT
* * * * *
206232 TAAGACTTACCTGTAGTGAAGAGATGTGAATATTGTTTCCTCATGTCCTACTCTC-TTCCTATGT
582 TAAGACATACCTGTAGTGAAGAGGTGTGGATATTG---CTTCATGTCCTACTCTCTTTCCTAAGT
*
206296 AGCGTCCTCGACTTTATGATTTTGCCAAAGCACTTTGACTACTGTAATCGTCTTGCTACACAGTT
644 AGCGTCCTCGACTTTATGATTTTGCCAAAGCACTTTGACTAATGTAATCGTCTTGCTACACAGTT
* *
206361 ATTTGATTTCTCGATCCAATATCCGTATTGGTTCTTCTTCATAAGTCAAATCTGGGATATCAATT
709 ATTTGATTTCTCGAGCCAATATCCGTATTGGTTCTTCTTCATAAGTCAAATCTGGGATCTCAATT
* *
206426 TCCTCTGATGCAATGACATTTGAAGGA-TCTGATCGATACTTTCTAAGCATCGACACATG-AAAA
774 TCCTCTGATGCAATGACATGTGAAAGATTC-GATCGATACTTTCTAAGCATCGACACATGAAAAA
206489 CATTATGAACTTTG
838 CATTATGAACTTTG
206503 TCTAACTCCG
Statistics
Matches: 1575, Mismatches: 114, Indels: 30
0.92 0.07 0.02
Matches are distributed among these distances:
850 502 0.32
851 164 0.10
853 197 0.13
854 416 0.26
855 37 0.02
856 243 0.15
857 16 0.01
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (851 bp):
ATGAATTTTAGACTAATTTCATGCTAATTTATCTTTAATTTAAACTTTAATGAATATTAAATTTA
TTTAATTGGGAAAAGACCAATTTACCCTTAATGAAACTTCATATTTACCATCAAACCAAGACACC
TCAACCTTATCATCTTCCTAAAGTCAAATATGAACAAACAAAATCTTACTTTATCGATTTGCCCT
TGCCTTTATCCAAAAATTACAATCTTGCCACTTTAATCCAACAGTCCAAATTAATTATGGAATTA
AATCCTCAAATCCAAAGATTTATATAATTTTTCAACATTTTAAAATGTGGAAATAATATTTTTAA
TTCAAATTTATCATCCTTCAGATTTTCCTGAATTTTCTATTCGATCCGATTTACTGAATCTTTCC
TCAAACTTCAACGCTTTATAACTATTTATTTACGAGGAAAAATGTAACTTTTTAAAATTACCTCT
TTGGTCCCTAAACTTTTCTAAAGTTTATACTTTGTCACTAAACTTTCAAAATTTATATTTTGGTC
ACTATCTAAAATTTAGGGTATTACAACTCTCCCCAGTTAAATAAAATTCGTCATCAAATTTTAAG
ACATACCTGTAGTGAAGAGGTGTGGATATTGCTTCATGTCCTACTCTCTTTCCTAAGTAGCGTCC
TCGACTTTATGATTTTGCCAAAGCACTTTGACTAATGTAATCGTCTTGCTACACAGTTATTTGAT
TTCTCGAGCCAATATCCGTATTGGTTCTTCTTCATAAGTCAAATCTGGGATCTCAATTTCCTCTG
ATGCAATGACATGTGAAAGATTCGATCGATACTTTCTAAGCATCGACACATGAAAAACATTATGA
ACTTTG
Found at i:206167 original size:29 final size:31
Alignment explanation
Indices: 206102--206174 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 31
206092 TAAAATTACC
* *
206102 ACTTTAGTCCCTAAACTTTTCTAAAGTTTAT
1 ACTTTGGTCACTAAACTTTTCTAAAGTTTAT
* *
206133 ACTTTGGTTACTAAAC-TTT-TAAATTTTAT
1 ACTTTGGTCACTAAACTTTTCTAAAGTTTAT
*
206162 ATTTTGGTCACTA
1 ACTTTGGTCACTA
206175 TCAAAAATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
29 20 0.56
30 3 0.08
31 13 0.36
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.48
Consensus pattern (31 bp):
ACTTTGGTCACTAAACTTTTCTAAAGTTTAT
Found at i:217862 original size:15 final size:15
Alignment explanation
Indices: 217785--217864 Score: 69
Period size: 14 Copynumber: 5.6 Consensus size: 15
217775 AAGTTAACAG
*
217785 GTTGACTCGAAC-GA
1 GTTGACTCGGACTGA
*
217799 GTTGACTC-AACTG-
1 GTTGACTCGGACTGA
* *
217812 GTCGACTCAGACTGA
1 GTTGACTCGGACTGA
* *
217827 GTTGACTTGGA-TGG
1 GTTGACTCGGACTGA
217841 GTTGACTCGGACTGA
1 GTTGACTCGGACTGA
*
217856 ATTGACTCG
1 GTTGACTCG
217865 ATGACTAGAC
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
13 10 0.19
14 25 0.47
15 18 0.34
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.28
Consensus pattern (15 bp):
GTTGACTCGGACTGA
Found at i:227058 original size:14 final size:14
Alignment explanation
Indices: 227041--227079 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
227031 AGTTCACGGG
*
227041 TCAAAGTCAACATA
1 TCAAAGTCAACAAA
*
227055 TCAAAGGCAACAAA
1 TCAAAGTCAACAAA
227069 TCAAAGTCAAC
1 TCAAAGTCAAC
227080 GGGTTGACTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.51, C:0.23, G:0.10, T:0.15
Consensus pattern (14 bp):
TCAAAGTCAACAAA
Found at i:227095 original size:14 final size:14
Alignment explanation
Indices: 227078--227232 Score: 130
Period size: 14 Copynumber: 10.9 Consensus size: 14
227068 ATCAAAGTCA
227078 ACGGGTTGACTCAG
1 ACGGGTTGACTCAG
*
227092 ACGGGTTGACTCGG
1 ACGGGTTGACTCAG
* *
227106 ACGGGTTAACTCGG
1 ACGGGTTGACTCAG
*
227120 ACGGGTTGACTCGG
1 ACGGGTTGACTCAG
* **
227134 ACGAGTTGACTTGG
1 ACGGGTTGACTCAG
* **
227148 ACGAGTTGACTTGG
1 ACGGGTTGACTCAG
227162 ACGGGTTGACTCAG
1 ACGGGTTGACTCAG
* *
227176 ACTGAGTTTACTCAG
1 AC-GGGTTGACTCAG
** *
227191 ACTAAGTTGACTCAT
1 AC-GGGTTGACTCAG
*
227206 ACAGGTTGACTCAG
1 ACGGGTTGACTCAG
*
227220 ACTGAGTTGACTC
1 AC-GGGTTGACTC
227233 GGTGAGTGGA
Statistics
Matches: 122, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
14 90 0.74
15 32 0.26
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.26
Consensus pattern (14 bp):
ACGGGTTGACTCAG
Found at i:227124 original size:42 final size:42
Alignment explanation
Indices: 227078--227234 Score: 170
Period size: 42 Copynumber: 3.7 Consensus size: 42
227068 ATCAAAGTCA
* *
227078 ACGGGTTGACTCAGACGGGTTGACTCGGACGGGTTAACTCGG
1 ACGGGTTGACTCAGACGAGTTGACTCGGACGAGTTAACTCGG
* * * *
227120 ACGGGTTGACTCGGACGAGTTGACTTGGACGAGTTGACTTGG
1 ACGGGTTGACTCAGACGAGTTGACTCGGACGAGTTAACTCGG
* * * * **
227162 ACGGGTTGACTCAGACTGAGTTTACTCAGACTAAGTTGACTCAT
1 ACGGGTTGACTCAGAC-GAGTTGACTCGGAC-GAGTTAACTCGG
*
227206 ACAGGTTGACTCAGACTGAGTTGACTCGG
1 ACGGGTTGACTCAGAC-GAGTTGACTCGG
227235 TGAGTGGACT
Statistics
Matches: 96, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
42 51 0.53
43 11 0.11
44 34 0.35
ACGTcount: A:0.22, C:0.20, G:0.32, T:0.25
Consensus pattern (42 bp):
ACGGGTTGACTCAGACGAGTTGACTCGGACGAGTTAACTCGG
Found at i:227222 original size:29 final size:30
Alignment explanation
Indices: 227166--227232 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 30
227156 ACTTGGACGG
* *
227166 GTTGACTCAGACTGAGTTTACTCAGACTAA
1 GTTGACTCAGACAGAGTTGACTCAGACTAA
* *
227196 GTTGACTCATACAG-GTTGACTCAGACTGA
1 GTTGACTCAGACAGAGTTGACTCAGACTAA
227225 GTTGACTC
1 GTTGACTC
227233 GGTGAGTGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
29 21 0.64
30 12 0.36
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (30 bp):
GTTGACTCAGACAGAGTTGACTCAGACTAA
Found at i:242936 original size:2 final size:2
Alignment explanation
Indices: 242929--242991 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
242919 CGTAATGCAA
242929 AT AT AT AT AT AT 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 AT AT AT AT AT AT
242971 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
242992 AATAAAAACA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:244197 original size:19 final size:18
Alignment explanation
Indices: 244175--244210 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
244165 TTTGAACTTT
244175 TATTATTATAAAACAAAAG
1 TATTATTATAAAA-AAAAG
*
244194 TATTATTTTAAAAAAAA
1 TATTATTATAAAAAAAA
244211 TCTTTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (18 bp):
TATTATTATAAAAAAAAG
Found at i:248652 original size:21 final size:21
Alignment explanation
Indices: 248620--248729 Score: 134
Period size: 21 Copynumber: 5.3 Consensus size: 21
248610 TAACAAGGAT
*
248620 GAGAAGAGCATTCATAAAGAC
1 GAGAAGACCATTCATAAAGAC
* * *
248641 GAGAATATCATTCATCAAGAC
1 GAGAAGACCATTCATAAAGAC
*
248662 GAGAATG-CCATTCATCAAGAC
1 GAGAA-GACCATTCATAAAGAC
*
248683 GAGAAGACCCTTCATAAAGAC
1 GAGAAGACCATTCATAAAGAC
*
248704 GAGAAGACC-TTCGTAAAGAC
1 GAGAAGACCATTCATAAAGAC
248724 GAGAAG
1 GAGAAG
248730 TCCACATCGC
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
20 17 0.22
21 62 0.78
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (21 bp):
GAGAAGACCATTCATAAAGAC
Found at i:253152 original size:12 final size:12
Alignment explanation
Indices: 253113--253200 Score: 51
Period size: 12 Copynumber: 7.2 Consensus size: 12
253103 TCATAAAGAG
253113 AAAG-AAGAGAA
1 AAAGAAAGAGAA
253124 ATATAGAAAGAGAA
1 A-A-AGAAAGAGAA
253138 AAAGAAA-AGATA
1 AAAGAAAGAGA-A
253150 AAA-AAATGATG-A
1 AAAGAAA-GA-GAA
* *
253162 AATGAAAAAGAA
1 AAAGAAAGAGAA
* *
253174 AATA-AAAAAGGA
1 AA-AGAAAGAGAA
253186 AAAGAAAGAGAA
1 AAAGAAAGAGAA
253198 AAA
1 AAA
253201 TTGAAAATGA
Statistics
Matches: 60, Mismatches: 6, Indels: 21
0.69 0.07 0.24
Matches are distributed among these distances:
11 9 0.15
12 35 0.58
13 7 0.12
14 9 0.15
ACGTcount: A:0.73, C:0.00, G:0.19, T:0.08
Consensus pattern (12 bp):
AAAGAAAGAGAA
Found at i:253200 original size:25 final size:25
Alignment explanation
Indices: 253113--253201 Score: 69
Period size: 24 Copynumber: 3.6 Consensus size: 25
253103 TCATAAAGAG
* *
253113 AAAG-AAGAGAAATATAGAAAGAGAA
1 AAAGAAAGAGAAAAATA-AAAGAGGA
* *
253138 AAAGAAA-AGATAAAA-AAATGATGA
1 AAAGAAAGAGA-AAAATAAAAGAGGA
* * *
253162 AATGAAAAAG-AAAATAAAAAAGGA
1 AAAGAAAGAGAAAAATAAAAGAGGA
253186 AAAGAAAGAGAAAAAT
1 AAAGAAAGAGAAAAAT
253202 TGAAAATGAG
Statistics
Matches: 49, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
23 4 0.08
24 25 0.51
25 15 0.31
26 5 0.10
ACGTcount: A:0.72, C:0.00, G:0.19, T:0.09
Consensus pattern (25 bp):
AAAGAAAGAGAAAAATAAAAGAGGA
Found at i:253223 original size:16 final size:16
Alignment explanation
Indices: 253193--253222 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
253183 GGAAAAGAAA
253193 GAGAAAAATTGAAAAT
1 GAGAAAAATTGAAAAT
253209 GAGAAAAA-TGAAAA
1 GAGAAAAATTGAAAA
253223 AAAAGAATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.67, C:0.00, G:0.20, T:0.13
Consensus pattern (16 bp):
GAGAAAAATTGAAAAT
Found at i:255966 original size:36 final size:37
Alignment explanation
Indices: 255925--256159 Score: 218
Period size: 36 Copynumber: 6.5 Consensus size: 37
255915 AAGTCAATCT
255925 TAAGCCTTCACCGAAGAGA-AGTGAAGCAAACCATCC
1 TAAGCCTTCACCGAAGAGATAGTGAAGCAAACCATCC
*
255961 TAAGCCTTCACCGGAGA-ATAGTGAAGCAAACCAT-C
1 TAAGCCTTCACCGAAGAGATAGTGAAGCAAACCATCC
* * * *
255996 TGAAGCCTTCACCGGAGA-ATAGTGAAACAATCAAT-C
1 T-AAGCCTTCACCGAAGAGATAGTGAAGCAAACCATCC
* *
256032 TGAAGCCTTCACCGGAGA-ATAGTGAAGCAAACCATCA
1 T-AAGCCTTCACCGAAGAGATAGTGAAGCAAACCATCC
* *
256069 TAAGTCTTCACC--AGAGAGTAGTGAAGCAAACCATCT
1 TAAGCCTTCACCGAAGAGA-TAGTGAAGCAAACCATCC
* * * * **
256105 TAAGTCTTCACCAAAAAG-TAGTGAAGCAGATCCATTT
1 TAAGCCTTCACCGAAGAGATAGTGAAGCA-AACCATCC
* *
256142 TAAGCCTTCTCAGAAGAG
1 TAAGCCTTCACCGAAGAG
256160 TGTTGGAACA
Statistics
Matches: 173, Mismatches: 18, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
34 3 0.02
35 4 0.02
36 143 0.83
37 20 0.12
38 3 0.02
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (37 bp):
TAAGCCTTCACCGAAGAGATAGTGAAGCAAACCATCC
Found at i:256045 original size:108 final size:108
Alignment explanation
Indices: 255918--256116 Score: 310
Period size: 108 Copynumber: 1.8 Consensus size: 108
255908 TGGAGCAAAG
* * *
255918 TCAATCTTAAGCCTTCACCGAAGAGA-AGTGAAGCAAACCATCCTAAGCCTTCACCGGAGAATAG
1 TCAATCTGAAGCCTTCACCGAAGA-ATAGTGAAGCAAACCATCATAAGCCTTCACCAGAGAATAG
255982 TGAAGCAAACCATCTGAAGCCTTCACCGGAGAATAGTGAAACAA
65 TGAAGCAAACCATCTGAAGCCTTCACCGGAGAATAGTGAAACAA
* * *
256026 TCAATCTGAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCATAAGTCTTCACCAGAGAGTAGT
1 TCAATCTGAAGCCTTCACCGAAGAATAGTGAAGCAAACCATCATAAGCCTTCACCAGAGAATAGT
* *
256091 GAAGCAAACCATCTTAAGTCTTCACC
66 GAAGCAAACCATCTGAAGCCTTCACC
256117 AAAAAGTAGT
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
107 1 0.01
108 81 0.99
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.20
Consensus pattern (108 bp):
TCAATCTGAAGCCTTCACCGAAGAATAGTGAAGCAAACCATCATAAGCCTTCACCAGAGAATAGT
GAAGCAAACCATCTGAAGCCTTCACCGGAGAATAGTGAAACAA
Found at i:256132 original size:72 final size:70
Alignment explanation
Indices: 255925--256116 Score: 258
Period size: 72 Copynumber: 2.7 Consensus size: 70
255915 AAGTCAATCT
* *
255925 TAAGCCTTCACCGAAGAGAAGTGAAGCAAACCATCCTAAGCCTTCACCGGAGAATAGTGAAGCAA
1 TAAGCCTTCACCG-AGAGTAGTGAAGCAAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGCAA
255990 ACCATC
65 ACCATC
* * * * *
255996 TGAAGCCTTCACCGGAGAATAGTGAAACAATCAATCTGAAGCCTTCACCGGAGAATAGTGAAGCA
1 T-AAGCCTTCACC-GAGAGTAGTGAAGCAAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGCA
256061 AACCATC
64 AACCATC
* *
256068 ATAAGTCTTCACCAGAGAGTAGTGAAGCAAACCATCTTAAGTCTTCACC
1 -TAAGCCTTCACC-GAGAGTAGTGAAGCAAACCATCTTAAGCCTTCACC
256117 AAAAAGTAGT
Statistics
Matches: 103, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
71 1 0.01
72 100 0.97
73 2 0.02
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (70 bp):
TAAGCCTTCACCGAGAGTAGTGAAGCAAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAA
CCATC
Found at i:256607 original size:51 final size:51
Alignment explanation
Indices: 256530--257268 Score: 855
Period size: 51 Copynumber: 14.3 Consensus size: 51
256520 TGAAAATATG
* *
256530 CGAGTTTTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
1 CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
* * *
256581 GGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGA-GATGT
1 CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATG-T-T
* * * * * * *
256633 CTAAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATC
1 C-GAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
* * * *
256685 CGAGTTCCATACTCCTTAATGAAAGAAGGAGCAAACCCGTTTGAAGATGTT
1 CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
** * ** *
256736 CGAGTTCTATACTCTTTAAAGAGAGAAGGAGCGAACCCGTAAGAAGAAGATTTT
1 CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGT---TTGAAGATGTT
* * *
256790 TGAGTTCTATACTCCCTGAAGAAA-AAGGGAGCAAACCCAG-TTGAAGATGTT
1 CGAGTTCTATACTCCCTAAAGAAAGAA-GGAGCGAACCC-GTTTGAAGATGTT
* * *
256841 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG--TGAAGAGATGTT
1 CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTG-A-AGATGTT
* *
256892 CGAGTTCTATACTCCCTAAAGAAAGAGGGAGTGAACCCGTTTGAAGATGTT
1 CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
*
256943 CGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
1 CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
* *
256994 CGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCG--TGAAGAGATGTT
1 CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTG-A-AGATGTT
**
257045 CGAGTTCTATACTCCCTAAAGAAAGGGGGAGCGAACCCGTTTGAAGATGTT
1 CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
* *
257096 CGAGTTCTATACTCCTTAAAGAAAGAAGGAGCAAACCCGTTTGAAGATGTT
1 CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
* * *
257147 CGAGTTCTATACTCCTTAAATAAAGAAGGAGCGAACCCATTTGAAGAGATGTT
1 CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTG-A-AGATGTT
* * * *
257200 CGAGTTCTATACTCCCTAGAGAAATAGGGAGCAAACCCGTTTGTTGAAGATTGTT
1 CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCG--T-TTGAAGA-TGTT
257255 CGAG-TCTTATACTC
1 CGAGTTC-TATACTC
257269 TCTGAATAAA
Statistics
Matches: 595, Mismatches: 68, Indels: 46
0.84 0.10 0.06
Matches are distributed among these distances:
49 4 0.01
50 4 0.01
51 431 0.72
52 6 0.01
53 87 0.15
54 42 0.07
55 18 0.03
56 3 0.01
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (51 bp):
CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
Found at i:257385 original size:53 final size:55
Alignment explanation
Indices: 257242--257545 Score: 454
Period size: 55 Copynumber: 5.6 Consensus size: 55
257232 AAACCCGTTT
*
257242 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAATAAATAGGGGGCAGACGCAATC
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
* * * *
257297 GTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAAACGCGATT
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
* * *
257352 GATGAAGATTG-T-GGGTCTTATACTCTCTGAAGAATTAGGGGGCAGACGCAATC
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
* * *
257405 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATT
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
* * *
257460 GATGAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATC
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
257513 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAA
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAA
257546 AAGAATAAAG
Statistics
Matches: 221, Mismatches: 24, Indels: 8
0.87 0.09 0.03
Matches are distributed among these distances:
53 93 0.42
54 4 0.02
55 124 0.56
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.29
Consensus pattern (55 bp):
GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
Found at i:257408 original size:108 final size:108
Alignment explanation
Indices: 257187--257545 Score: 551
Period size: 108 Copynumber: 3.3 Consensus size: 108
257177 GCGAACCCAT
* * * * * *
257187 TTGAAGAGATGTTCGAGT-TCTATACTCCCT-AGAGAAATAGGGAGCAAACCCGTTTGTTGAAGA
1 TTGAAGA-TTGTTCGAGTCT-TATACTCTCTGA-AGAAATAGGGGGCAAACGCGATTGATGAAGA
* *
257250 TTGTTCGAGTCTTATACTCTCTGAATAAATAGGGGGCAGACGCAATCG
63 TTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCG
*
257298 TTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAAACGCGATTGATGAAGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAAACGCGATTGATGAAGATTG
*
257363 TGGGTCTTATACTCTCTGAAGAATTAGGGGGCAGACGCAATCG
66 TGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCG
*
257406 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATTGATGAAGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAAACGCGATTGATGAAGATTG
*
257471 TGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATCG
66 TGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCG
257514 TTGAAGATTGTTCGAGTCTTATACTCTCTGAA
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAA
257546 AAGAATAAAG
Statistics
Matches: 232, Mismatches: 14, Indels: 7
0.92 0.06 0.03
Matches are distributed among these distances:
108 175 0.75
109 1 0.00
110 47 0.20
111 9 0.04
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29
Consensus pattern (108 bp):
TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAAACGCGATTGATGAAGATTG
TGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCG
Found at i:262152 original size:21 final size:20
Alignment explanation
Indices: 262066--262223 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
262056 AAATGACCAA
**
262066 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
262085 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
262105 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
262125 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
262146 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
262167 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
262187 CAAGAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
262208 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
262224 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 42 0.40
21 46 0.44
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:262252 original size:20 final size:20
Alignment explanation
Indices: 262191--262419 Score: 230
Period size: 20 Copynumber: 11.4 Consensus size: 20
262181 GATTTTCAAG
* ** *
262191 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
262211 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
262231 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
262251 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
262271 AATAGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
262291 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
262311 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
262331 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
262351 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
262371 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
262391 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
262411 AATCACAAC
1 AATCGCAAC
262420 ACTGAAATTT
Statistics
Matches: 175, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 171 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:263151 original size:24 final size:24
Alignment explanation
Indices: 263112--263158 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
263102 AAATTTGGTC
263112 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
263136 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
263159 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:265748 original size:72 final size:71
Alignment explanation
Indices: 265655--265888 Score: 284
Period size: 72 Copynumber: 3.3 Consensus size: 71
265645 GCAACGAGAG
265655 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAAT-CG
265720 AAATGAA
65 AAATGAA
* * *
265727 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATACG
1 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAAT-CG
265792 AAATGAA
65 AAATGAA
* * * * * *
265799 AATCGCAACGAGAGAATCG-CAATGCGAA-ATGAAAATCGCAATGC-GAAATGAAAATCGCAA-C
1 AATCGCAATGCGA-AAT-GAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATC
*
265860 G--A-GAG
64 GAAATGAA
265865 AATCGCAATGCGGAAATGAAAATC
1 AATCGCAATGC-GAAATGAAAATC
265889 ATAATGCGAA
Statistics
Matches: 140, Mismatches: 18, Indels: 14
0.81 0.10 0.08
Matches are distributed among these distances:
65 1 0.01
66 17 0.12
67 3 0.02
69 2 0.01
71 16 0.11
72 92 0.66
73 8 0.06
74 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATCGA
AATGAA
Found at i:265776 original size:53 final size:52
Alignment explanation
Indices: 265641--265910 Score: 388
Period size: 53 Copynumber: 5.1 Consensus size: 52
265631 CGGAAATTAC
*
265641 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C--AA-GAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
265688 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
265746 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATACGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
265799 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
**
265851 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCATAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
265904 AATCGCA
1 AATCGCA
265911 TTGCGATTCT
Statistics
Matches: 203, Mismatches: 7, Indels: 20
0.88 0.03 0.09
Matches are distributed among these distances:
47 8 0.04
49 1 0.00
50 1 0.00
52 65 0.32
53 112 0.55
55 2 0.01
56 1 0.00
57 2 0.01
58 11 0.05
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:265910 original size:72 final size:70
Alignment explanation
Indices: 265622--265888 Score: 270
Period size: 72 Copynumber: 3.8 Consensus size: 70
265612 GCATTTGACT
** * * * *
265622 ATCGCAACACGGAAATTACAATCGCAACG-A-GAGAATCGCAATGCGAAATGAAAATCCCAAC-A
1 ATCGCAATGCGGAAATGAAAATCGCAACGAATGAAAATCGCAATGCGAAATGAAAATCGCAACGA
265684 AGAAA
66 AGAAA
265689 ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 ATCGCAATGCGGAAATGAAAATCGCAA--CG-AATGAAAATCGCAATGCGAAATGAAAATCGCAA
*
265754 CG-AGAGA
63 CGAAGAAA
*
265761 ATCGCAATGCGGAAATGAAAATCGCAATACGAAATGAAAATCGCAA--CG--A-GAGAATCGCAA
1 ATCGCAATGCGGAAATGAAAATCGC-A-ACG-AATGAAAATCGCAATGCGAAATGAAAATCGCAA
265821 TGCGAAATGAAA
63 --CG-AA-GAAA
*
265833 ATCGCAATGC-GAAATGAAAATCGCAACG-A-GAGAATCGCAATGCGGAAATGAAAATC
1 ATCGCAATGCGGAAATGAAAATCGCAACGAATGAAAATCGCAATGC-GAAATGAAAATC
265889 ATAATGCGAA
Statistics
Matches: 170, Mismatches: 11, Indels: 33
0.79 0.05 0.15
Matches are distributed among these distances:
66 10 0.06
67 34 0.20
68 2 0.01
69 8 0.05
70 3 0.02
71 17 0.10
72 94 0.55
73 1 0.01
74 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (70 bp):
ATCGCAATGCGGAAATGAAAATCGCAACGAATGAAAATCGCAATGCGAAATGAAAATCGCAACGA
AGAAA
Found at i:265930 original size:105 final size:105
Alignment explanation
Indices: 265641--265910 Score: 399
Period size: 105 Copynumber: 2.6 Consensus size: 105
265631 CGGAAATTAC
*
265641 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATC-CCA-AC--AA-GAAAATCGCAATGCG
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCACAATACGAAATGAAAATCGCAA--C-
*
265700 GAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
63 G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
265746 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATACGAAATGAAAATCGCAACGAG
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCACAATACGAAATGAAAATCGCAACGAG
265811 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
66 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
* *
265851 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCATAATGCGAAATGAAAATCGCA
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCACAATACGAAATGAAAATCGCA
265911 TTGCGATTCT
Statistics
Matches: 154, Mismatches: 5, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
105 122 0.79
106 13 0.08
107 2 0.01
108 3 0.02
109 1 0.01
110 2 0.01
111 11 0.07
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (105 bp):
AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCACAATACGAAATGAAAATCGCAACGAG
AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:265950 original size:53 final size:52
Alignment explanation
Indices: 265893--266002 Score: 157
Period size: 53 Copynumber: 2.1 Consensus size: 52
265883 AAAATCATAA
265893 TGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCAT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCAT
** ** **
265946 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
265998 TGCGA
1 TGCGA
266003 TTTTCATTTC
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
52 10 0.20
53 41 0.80
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.40
Consensus pattern (52 bp):
TGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
Found at i:265965 original size:19 final size:19
Alignment explanation
Indices: 265925--266012 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
265915 GATTCTCTCG
265925 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
265945 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
265964 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
265978 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
265997 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
266013 AACATAATGC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.10
16 7 0.11
17 7 0.11
19 26 0.43
20 15 0.25
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:266122 original size:14 final size:14
Alignment explanation
Indices: 266103--266139 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
266093 CATCAATTAC
266103 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
266117 ACAAATCATCTTTT
1 ACAAATCAACTTTT
266131 ACAAATCAA
1 ACAAATCAA
266140 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:268184 original size:33 final size:33
Alignment explanation
Indices: 268138--268230 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
268128 GCGAAACCAA
268138 AATCGCAACGCGAAATGAAAATCGCAACAACAG
1 AATCGCAACGCGAAATGAAAATCGCAACAACAG
* * * *
268171 AATCGCAATGCGAAATGAAAATCGCACCGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACAACAG
268204 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
268231 TGCGATTTTG
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACAACAG
Found at i:268195 original size:19 final size:19
Alignment explanation
Indices: 268063--268235 Score: 143
Period size: 19 Copynumber: 9.6 Consensus size: 19
268053 TAGTTTACTT
* *
268063 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
* *
268083 TCGCAACGTGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
268102 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
268121 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
268140 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
268159 TCGCAA--C-AACA-G--AA
1 TCGCAACGCGAA-ATGAAAA
*
268173 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
268192 TCGC-AC-CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
268206 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
268225 TCGCAATGCGA
1 TCGCAACGCGA
268236 TTTTGGTTTC
Statistics
Matches: 126, Mismatches: 15, Indels: 25
0.76 0.09 0.15
Matches are distributed among these distances:
14 16 0.13
15 3 0.02
16 7 0.06
17 7 0.06
18 2 0.02
19 80 0.63
20 11 0.09
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:268266 original size:14 final size:14
Alignment explanation
Indices: 268247--268305 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
268237 TTTGGTTTCG
268247 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
268261 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
268278 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
268294 CGTTGCGATTTT
1 CGTTGCGATTTT
268306 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:268273 original size:33 final size:33
Alignment explanation
Indices: 268231--268354 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
268221 AAAATCGCAA
*
268231 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
268264 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
268297 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
268330 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
268355 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Done.