Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009068.1 Hibiscus syriacus cultivar Beakdansim tig00112495_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: 670922
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:303 original size:3 final size:3
Alignment explanation
Indices: 295--328 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
285 ATATTAATTA
295 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
329 TTATAATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1085 original size:21 final size:21
Alignment explanation
Indices: 1061--1100 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1051 ATTAATTTGA
1061 AATCTGAAA-TAACTCGAATCG
1 AATCT-AAATTAACTCGAATCG
*
1082 AATCTAAATTGACTCGAAT
1 AATCTAAATTAACTCGAAT
1101 TTAGTTGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.28
Consensus pattern (21 bp):
AATCTAAATTAACTCGAATCG
Found at i:6284 original size:18 final size:17
Alignment explanation
Indices: 6261--6300 Score: 71
Period size: 18 Copynumber: 2.3 Consensus size: 17
6251 AACAGACCCA
6261 TCACCGGATACATCATC
1 TCACCGGATACATCATC
6278 TTCACCGGATACATCATC
1 -TCACCGGATACATCATC
6296 TCACC
1 TCACC
6301 AGAAATAGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.28, C:0.38, G:0.10, T:0.25
Consensus pattern (17 bp):
TCACCGGATACATCATC
Found at i:8966 original size:21 final size:19
Alignment explanation
Indices: 8933--9152 Score: 98
Period size: 21 Copynumber: 10.7 Consensus size: 19
8923 CGTTACGATT
* *
8933 TTGGACTATCGCAACGAAT
1 TTGGAATATCGCAACGAAC
8952 TTGGAATGAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAA--CGAAC
* *
8975 TTCGACTATCGCAACGAAC
1 TTGGAATATCGCAACGAAC
* * *
8994 TTAGACTATCGCAACGAAT
1 TTGGAATATCGCAACGAAC
*
9013 TTGTAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAA--CGAAC
* * *
9036 TTGGACTATCGCAACAAAT
1 TTGGAATATCGCAACGAAC
* ***
9055 TTAGAATAAATTATAACGCGAAC
1 TTGGAAT--ATCGCAA--CGAAC
* *
9078 TTGGACTATCGCAACGAAT
1 TTGGAATATCGCAACGAAC
* *
9097 TTGAAAAATCGCAACGCGAAC
1 TTGGAATATCGCAA--CGAAC
* *
9118 TTCGACTATCGCAACGCGAAC
1 TTGGAATATCGCAA--CGAAC
*
9139 TTGGACTATCGCAA
1 TTGGAATATCGCAA
9153 TGCGAATATG
Statistics
Matches: 151, Mismatches: 36, Indels: 26
0.71 0.17 0.12
Matches are distributed among these distances:
19 55 0.36
21 70 0.46
23 26 0.17
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.23
Consensus pattern (19 bp):
TTGGAATATCGCAACGAAC
Found at i:9031 original size:61 final size:61
Alignment explanation
Indices: 8936--9059 Score: 203
Period size: 61 Copynumber: 2.0 Consensus size: 61
8926 TACGATTTTG
* *
8936 GACTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGACTATCGCAACGAACTTA
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACAAACTTA
* * *
8997 GACTATCGCAACGAATTTGTAATAAATCGCAACGCGAACTTGGACTATCGCAACAAATTTA
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACAAACTTA
9058 GA
1 GA
9060 ATAAATTATA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.23
Consensus pattern (61 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACAAACTTA
Found at i:9048 original size:42 final size:41
Alignment explanation
Indices: 8982--9133 Score: 211
Period size: 42 Copynumber: 3.7 Consensus size: 41
8972 AACTTCGACT
*
8982 ATCGCAA--CGAACTTAGACTATCGCAACGAATTTGTAATAA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTG-AATAA
*
9022 ATCGCAACGCGAACTTGGACTATCGCAACAAATTTAGAATAA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTT-GAATAA
***
9064 ATTATAACGCGAACTTGGACTATCGCAACGAATTTGAA-AA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGAATAA
*
9104 ATCGCAACGCGAACTTCGACTATCGCAACG
1 ATCGCAACGCGAACTTGGACTATCGCAACG
9134 CGAACTTGGA
Statistics
Matches: 99, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
40 35 0.35
41 3 0.03
42 60 0.61
43 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.22
Consensus pattern (41 bp):
ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGAATAA
Found at i:9112 original size:103 final size:102
Alignment explanation
Indices: 8933--9152 Score: 266
Period size: 103 Copynumber: 2.1 Consensus size: 102
8923 CGTTACGATT
* * * *
8933 TTGGACTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGACTATCGCAACGAACTTAG
1 TTGGACTATCGCAACAAATTTAGAATAAATCACAACGCGAACTTCGACTATCGCAACGAACTTAG
** *
8998 ACTATCGCAA-CGAA-TTTGTAATAAATCGCAACGCGAAC
66 AAAATCGCAACCGAACTTCG-AAT--ATCGCAACGCGAAC
* * * *
9036 TTGGACTATCGCAACAAATTTAGAATAAATTATAACGCGAACTTGGACTATCGCAACGAA-TTTG
1 TTGGACTATCGCAACAAATTTAGAATAAATCACAACGCGAACTTCGACTATCGCAACGAACTTAG
*
9100 AAAAATCGCAACGCGAACTTCGACTATCGCAACGCGAAC
66 -AAAATCGCAAC-CGAACTTCGAATATCGCAACGCGAAC
9139 TTGGACTATCGCAA
1 TTGGACTATCGCAA
9153 TGCGAATATG
Statistics
Matches: 101, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
102 3 0.03
103 89 0.88
105 6 0.06
106 3 0.03
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.23
Consensus pattern (102 bp):
TTGGACTATCGCAACAAATTTAGAATAAATCACAACGCGAACTTCGACTATCGCAACGAACTTAG
AAAATCGCAACCGAACTTCGAATATCGCAACGCGAAC
Found at i:18438 original size:30 final size:30
Alignment explanation
Indices: 18404--18463 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
18394 AAGTATGCAG
18404 AATTA-AGTATAATATAAAGATA-AATAAATA
1 AATTATAGTAT-ATA-AAAGATATAATAAATA
* *
18434 AATTATTGTATATAGAAGATATAATAAATA
1 AATTATAGTATATAAAAGATATAATAAATA
18464 TTATATCTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
29 6 0.23
30 16 0.62
31 4 0.15
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (30 bp):
AATTATAGTATATAAAAGATATAATAAATA
Found at i:18689 original size:15 final size:16
Alignment explanation
Indices: 18663--18698 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
18653 TATTATCAAA
18663 AAATAGAATTTTATAT
1 AAATAGAATTTTATAT
*
18679 AAATA-AATTTTATTT
1 AAATAGAATTTTATAT
18694 AAATA
1 AAATA
18699 TTTAGAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
AAATAGAATTTTATAT
Found at i:18867 original size:16 final size:19
Alignment explanation
Indices: 18846--18887 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
18836 AACATTCCCA
18846 GTAATC-CTATT-CC-CTG
1 GTAATCTCTATTCCCACTG
*
18862 GTAATCTTTATTCCCACTG
1 GTAATCTCTATTCCCACTG
18881 GTAATCT
1 GTAATCT
18888 TACATTCCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 6 0.27
17 4 0.18
18 2 0.09
19 10 0.45
ACGTcount: A:0.21, C:0.26, G:0.12, T:0.40
Consensus pattern (19 bp):
GTAATCTCTATTCCCACTG
Found at i:26046 original size:14 final size:12
Alignment explanation
Indices: 26015--26039 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
26005 ATTGAGCCAA
26015 TGAAAAAGGAAG
1 TGAAAAAGGAAG
26027 TGAAAAAGGAAG
1 TGAAAAAGGAAG
26039 T
1 T
26040 CTGAAAACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.32, T:0.12
Consensus pattern (12 bp):
TGAAAAAGGAAG
Found at i:27224 original size:32 final size:33
Alignment explanation
Indices: 27183--27248 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 33
27173 AAGTTAGAGA
27183 CATAATCACAT-AAAGAA-AAAGAAAAACTATGT
1 CATAATCACATAAAAGAAGAAA-AAAAACTATGT
*
27215 CATAGTCACATAAAAAGAAGAAAAAAAACTATGT
1 CATAATCACAT-AAAAGAAGAAAAAAAACTATGT
27249 TAACTTAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 10 0.33
34 17 0.57
35 3 0.10
ACGTcount: A:0.59, C:0.12, G:0.11, T:0.18
Consensus pattern (33 bp):
CATAATCACATAAAAGAAGAAAAAAAACTATGT
Found at i:29447 original size:33 final size:33
Alignment explanation
Indices: 29405--29477 Score: 137
Period size: 33 Copynumber: 2.2 Consensus size: 33
29395 AAACGGCGTG
29405 TCCATTAATGTCAATGGCCAAAGAATTACCGTT
1 TCCATTAATGTCAATGGCCAAAGAATTACCGTT
29438 TCCATTAATGTCAATGGCCAAAGAATTACCGTT
1 TCCATTAATGTCAATGGCCAAAGAATTACCGTT
*
29471 TCAATTA
1 TCCATTA
29478 TCTGTACAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.32
Consensus pattern (33 bp):
TCCATTAATGTCAATGGCCAAAGAATTACCGTT
Found at i:34645 original size:30 final size:30
Alignment explanation
Indices: 34609--34672 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
34599 GAAGGACCTG
* *
34609 TCCAGAGGTTACAAAGAACCCCGGTAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
* * *
34639 TCCAGAGGTCATAAAGATCCTCGGCAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
34669 TCCA
1 TCCA
34673 TATGTTCCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGAACCCCGGCAACTA
Found at i:35390 original size:64 final size:65
Alignment explanation
Indices: 35303--35428 Score: 184
Period size: 64 Copynumber: 2.0 Consensus size: 65
35293 GCACTACTTG
* * *
35303 TGCATCGGTGCATAAAATGCATTCGATGTTTTTATTTTAAAAGG-ATGCATCGATGCA-TTATCT
1 TGCATCGATGCATAAAAGGCATTCGATGTTCTTATTTT-AAAGGAATGCATCGATGCACTTATCT
35366 A
65 A
* *
35367 TGCATCGATGCATCAAAGGCATTCGATGTTCTTCTTTTAAAGGAATGCATCGATGCACTTAT
1 TGCATCGATGCATAAAAGGCATTCGATGTTCTTATTTTAAAGGAATGCATCGATGCACTTAT
35429 GAATGTGCAT
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
63 5 0.09
64 46 0.84
65 4 0.07
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (65 bp):
TGCATCGATGCATAAAAGGCATTCGATGTTCTTATTTTAAAGGAATGCATCGATGCACTTATCTA
Found at i:39443 original size:18 final size:17
Alignment explanation
Indices: 39420--39473 Score: 81
Period size: 18 Copynumber: 3.1 Consensus size: 17
39410 CACTGAATGT
39420 TTGTCCCGAAGGACCAC
1 TTGTCCCGAAGGACCAC
39437 ATTGTCCCGAAGGACCAC
1 -TTGTCCCGAAGGACCAC
*
39455 TATGTCCCGAATGACCAC
1 T-TGTCCCGAAGGACCAC
39473 T
1 T
39474 GTAAATCCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
17 1 0.03
18 33 0.97
ACGTcount: A:0.26, C:0.33, G:0.20, T:0.20
Consensus pattern (17 bp):
TTGTCCCGAAGGACCAC
Found at i:44563 original size:18 final size:18
Alignment explanation
Indices: 44537--44609 Score: 94
Period size: 18 Copynumber: 4.1 Consensus size: 18
44527 GCACTGAATG
*
44537 TTTGTCCCGAATGACCAC
1 TTTGTCCCGAAGGACCAC
*
44555 TTTGCCCCGAAGGACCA-
1 TTTGTCCCGAAGGACCAC
44572 TTATGTCCCGAAGGACCAC
1 TT-TGTCCCGAAGGACCAC
* *
44591 TATGTCTCGAAGGACCAC
1 TTTGTCCCGAAGGACCAC
44609 T
1 T
44610 GTAAATCCCT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
17 2 0.04
18 45 0.94
19 1 0.02
ACGTcount: A:0.25, C:0.32, G:0.21, T:0.23
Consensus pattern (18 bp):
TTTGTCCCGAAGGACCAC
Found at i:53898 original size:16 final size:15
Alignment explanation
Indices: 53868--53901 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
53858 CCTCGACTCA
*
53868 AAACATCAAACCAAT
1 AAACATCAAAACAAT
53883 AAACATGCAAAACAAT
1 AAACAT-CAAAACAAT
53899 AAA
1 AAA
53902 ATTTCGAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.65, C:0.21, G:0.03, T:0.12
Consensus pattern (15 bp):
AAACATCAAAACAAT
Found at i:55592 original size:23 final size:24
Alignment explanation
Indices: 55553--55600 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
55543 AAAAACCAAG
* *
55553 ACCGGTTTTTTTACCGGATAAAAA
1 ACCGGTTTTTATACCGGAAAAAAA
55577 ACCGGTTTTTAT-CCGGAAAAAAA
1 ACCGGTTTTTATACCGGAAAAAAA
55600 A
1 A
55601 AACCGGTCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.29
Consensus pattern (24 bp):
ACCGGTTTTTATACCGGAAAAAAA
Found at i:55601 original size:24 final size:25
Alignment explanation
Indices: 55553--55607 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
55543 AAAAACCAAG
* *
55553 ACCGGTTTTTTTACCGG-ATAAAAA
1 ACCGGTTTTTATACCGGAAAAAAAA
55577 ACCGGTTTTTAT-CCGGAAAAAAAAA
1 ACCGGTTTTTATACCGG-AAAAAAAA
55602 ACCGGT
1 ACCGGT
55608 CTGGGTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 4 0.15
24 11 0.41
25 12 0.44
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (25 bp):
ACCGGTTTTTATACCGGAAAAAAAA
Found at i:57904 original size:21 final size:21
Alignment explanation
Indices: 57880--57919 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
57870 TTTATTTTAT
57880 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
57901 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
57920 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:57967 original size:33 final size:33
Alignment explanation
Indices: 57914--58050 Score: 173
Period size: 33 Copynumber: 4.4 Consensus size: 33
57904 TTTGTTTCAA
57914 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
57946 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
57979 TTATCAAACTTGGAAGTATTTAAGTATTTCAA-
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
*
58011 TTAT-G---TT-G-AGTTAATTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTT-TTTAAGTATTTGAAT
58039 TTATCGAACTTG
1 TTATCGAACTTG
58051 AGGTTTGATG
Statistics
Matches: 90, Mismatches: 7, Indels: 15
0.80 0.06 0.13
Matches are distributed among these distances:
26 3 0.03
27 13 0.14
28 6 0.07
29 1 0.01
32 17 0.19
33 50 0.56
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:58480 original size:21 final size:18
Alignment explanation
Indices: 58435--58468 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
58425 GGTTTTTTAT
58435 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
58452 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
58469 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:61745 original size:20 final size:20
Alignment explanation
Indices: 61720--61760 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
61710 TCCCAAATTC
61720 TACGTAAATCGCAACGCGAA
1 TACGTAAATCGCAACGCGAA
*
61740 TACGTAAATCGCAATGCGAA
1 TACGTAAATCGCAACGCGAA
61760 T
1 T
61761 CTGACTATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.20
Consensus pattern (20 bp):
TACGTAAATCGCAACGCGAA
Found at i:62371 original size:20 final size:20
Alignment explanation
Indices: 62346--62397 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
62336 CAACGAGTGA
62346 ATCGCAAAGAGAAAATGACT
1 ATCGCAAAGAGAAAATGACT
* * **
62366 ATCGCAATGCGAATTTGACT
1 ATCGCAAAGAGAAAATGACT
*
62386 ATCGCAACGAGA
1 ATCGCAAAGAGA
62398 GAATCGCAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (20 bp):
ATCGCAAAGAGAAAATGACT
Found at i:62492 original size:20 final size:20
Alignment explanation
Indices: 62407--62493 Score: 86
Period size: 20 Copynumber: 4.4 Consensus size: 20
62397 AGAATCGCAA
62407 TGCGATTTTCATTTT-GCGT
1 TGCGATTTTCATTTTCGCGT
** **
62426 TGCGATAGTCAAATTCGCGT
1 TGCGATTTTCATTTTCGCGT
** *
62446 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
* *
62466 TGTGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
62486 TGCGATTT
1 TGCGATTT
62494 AAAGTTTCAG
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
19 11 0.20
20 45 0.80
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.47
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGCGT
Found at i:62501 original size:20 final size:20
Alignment explanation
Indices: 62458--62501 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
62448 CGATAGTCAT
* ** *
62458 TTTCGTGTTGTGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
62478 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
62498 TTTC
1 TTTC
62502 AGGAACTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.11, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:64364 original size:20 final size:20
Alignment explanation
Indices: 64339--64422 Score: 90
Period size: 20 Copynumber: 4.5 Consensus size: 20
64329 AGAATAGTTT
*
64339 ACTATCGCAATACGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
64359 ACTATCGTAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
64379 ACTATCGCAAT--G-AGA-G
1 ACTATCGCAATGCGAAAATG
64395 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
64413 ACTATCGCAA
1 ACTATCGCAA
64423 CGAAAGAATC
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
14 8 0.16
16 3 0.06
17 4 0.08
18 3 0.06
20 33 0.65
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.19
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:64408 original size:34 final size:34
Alignment explanation
Indices: 64370--64443 Score: 130
Period size: 34 Copynumber: 2.2 Consensus size: 34
64360 CTATCGTAAC
* *
64370 GCGAAAATGACTATCGCAATGAGAGAATCGCAAT
1 GCGAAAATGACTATCGCAACGAAAGAATCGCAAT
64404 GCGAAAATGACTATCGCAACGAAAGAATCGCAAT
1 GCGAAAATGACTATCGCAACGAAAGAATCGCAAT
64438 GCGAAA
1 GCGAAA
64444 TGAAAATCGC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15
Consensus pattern (34 bp):
GCGAAAATGACTATCGCAACGAAAGAATCGCAAT
Found at i:64453 original size:19 final size:18
Alignment explanation
Indices: 64395--64460 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 18
64385 GCAATGAGAG
64395 AATCGCAATGCGAAAATGA
1 AATCGCAATGCG-AAATGA
*
64414 CTATCGCAA--CGAAA-G-
1 -AATCGCAATGCGAAATGA
64429 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATG-A
*
64448 AATCGCATTGCGA
1 AATCGCAATGCGA
64461 TTCTCTCGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
14 7 0.18
16 6 0.16
17 4 0.11
18 2 0.05
19 12 0.32
20 7 0.18
ACGTcount: A:0.42, C:0.20, G:0.21, T:0.17
Consensus pattern (18 bp):
AATCGCAATGCGAAATGA
Found at i:64494 original size:20 final size:20
Alignment explanation
Indices: 64469--64607 Score: 123
Period size: 20 Copynumber: 7.3 Consensus size: 20
64459 GATTCTCTCG
*
64469 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATATTCGCA
* * *
64489 TTGCGATAGTCATTTTTGCG
1 TTGCGATAGTCATATTCGCA
**
64509 TTGCGATTTTCAT-TT-GCA
1 TTGCGATAGTCATATTCGCA
*
64527 TTGCGAT--TC----TCTCA
1 TTGCGATAGTCATATTCGCA
*
64541 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATATTCGCA
*
64561 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATATTCGCA
* *
64581 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATATTCGCA
64601 TTGCGAT
1 TTGCGAT
64608 TTTAAGTTTC
Statistics
Matches: 100, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
13 1 0.01
14 9 0.09
16 4 0.04
18 9 0.09
19 2 0.02
20 75 0.75
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATATTCGCA
Found at i:64533 original size:72 final size:72
Alignment explanation
Indices: 64452--64587 Score: 245
Period size: 72 Copynumber: 1.9 Consensus size: 72
64442 AATGAAAATC
* * *
64452 GCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTTGCGTTGCGATT
1 GCATTGCGATTCTCTCATTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGATT
64517 TTCATTT
66 TTCATTT
64524 GCATTGCGATTCTCTCATTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGAT
1 GCATTGCGATTCTCTCATTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGAT
64588 AGTCATTTTC
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 61 1.00
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.39
Consensus pattern (72 bp):
GCATTGCGATTCTCTCATTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGATT
TTCATTT
Found at i:64565 original size:52 final size:54
Alignment explanation
Indices: 64487--64587 Score: 134
Period size: 52 Copynumber: 1.9 Consensus size: 54
64477 GTCAAATTCG
** * * **
64487 CATTGCGATAGTCATTTTTGCGTTGCGATTTTCA-TTT-GCATTGCGATTCTCT
1 CATTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGATTCTCT
64539 CATTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGAT
1 CATTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGAT
64588 AGTCATTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
52 28 0.68
53 3 0.07
54 10 0.24
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (54 bp):
CATTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGATTCTCT
Found at i:65180 original size:21 final size:21
Alignment explanation
Indices: 65089--65193 Score: 86
Period size: 21 Copynumber: 5.0 Consensus size: 21
65079 GATTCACCTG
*
65089 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
65111 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** **
65131 TCATCCCTCAAGAATCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
65152 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
65173 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
65194 CCAACATTCT
Statistics
Matches: 61, Mismatches: 21, Indels: 3
0.72 0.25 0.04
Matches are distributed among these distances:
20 3 0.05
21 57 0.93
22 1 0.02
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:65193 original size:42 final size:42
Alignment explanation
Indices: 65086--65196 Score: 111
Period size: 42 Copynumber: 2.6 Consensus size: 42
65076 CCCGATTCAC
* *
65086 CTGTCATCGTTCAAGAGG--CCTCCCCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGGTCCCT-CCC-ACCGTTCAAGAGGCCA
* ** *
65128 CTATCATCCCTCAAGA-ATCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGGT-CCCTCCCACCGTTCAAGAGGCCA
*
65170 CTGTCATCGTTGAAGAGGTCCCTCCCA
1 CTGTCATCGTTCAAGAGGTCCCTCCCA
65197 ACATTCTAGA
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
42 47 0.87
43 4 0.07
44 3 0.06
ACGTcount: A:0.22, C:0.38, G:0.18, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGGTCCCTCCCACCGTTCAAGAGGCCA
Found at i:66569 original size:14 final size:14
Alignment explanation
Indices: 66550--66585 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
66540 ATTGTTTAAT
66550 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
66564 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
66578 TGATTTGT
1 TGATTTGT
66586 TTAATTGATG
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:66764 original size:33 final size:33
Alignment explanation
Indices: 66722--66789 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
66712 AACGAGAGAA
**
66722 TCGCATTGCGATTCACTCGTTGCGATTTTCATT
1 TCGCATTGCGATTCACTCGTTGCGATAGTCATT
*
66755 TCGCATTGCGATTCTCTCGTTGCGATAGTCATT
1 TCGCATTGCGATTCACTCGTTGCGATAGTCATT
66788 TC
1 TC
66790 CGTGTTGCGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.15, C:0.25, G:0.19, T:0.41
Consensus pattern (33 bp):
TCGCATTGCGATTCACTCGTTGCGATAGTCATT
Found at i:66798 original size:20 final size:20
Alignment explanation
Indices: 66772--66860 Score: 108
Period size: 20 Copynumber: 4.5 Consensus size: 20
66762 GCGATTCTCT
66772 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* * *
66792 TGTTGCGATAGTCAATTCTG
1 CGTTGCGATAGTCATTTCCG
*
66812 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
66832 TGTTGCGATAGCCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
66852 CGTTGCGAT
1 CGTTGCGAT
66861 TTCCACGTTG
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 55 0.96
21 2 0.04
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:66821 original size:40 final size:40
Alignment explanation
Indices: 66774--66860 Score: 140
Period size: 40 Copynumber: 2.2 Consensus size: 40
66764 GATTCTCTCG
*
66774 TTGCGATAGTCATTTCCGTGTTGCGATAGTCA-ATTCTGCA
1 TTGCGATAGTCATTTCCGTGTTGCGATAGCCATATTC-GCA
*
66814 TTGCGATAGTCATTTCCGTGTTGCGATAGCCATATTCGCG
1 TTGCGATAGTCATTTCCGTGTTGCGATAGCCATATTCGCA
66854 TTGCGAT
1 TTGCGAT
66861 TTCCACGTTG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
40 40 0.91
41 4 0.09
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (40 bp):
TTGCGATAGTCATTTCCGTGTTGCGATAGCCATATTCGCA
Found at i:70238 original size:20 final size:20
Alignment explanation
Indices: 70215--70316 Score: 152
Period size: 20 Copynumber: 5.1 Consensus size: 20
70205 ATCTCGTTGT
70215 GATTTACAG-ATTCGCATTGC
1 GATTTAC-GTATTCGCATTGC
70235 GATTTACGTATTCGCATTGC
1 GATTTACGTATTCGCATTGC
* *
70255 GATTTACGTAATCGCATTCC
1 GATTTACGTATTCGCATTGC
* *
70275 GATTTACGTAATCGCGTTGC
1 GATTTACGTATTCGCATTGC
70295 GATTTACGTATTCGCATTGC
1 GATTTACGTATTCGCATTGC
70315 GA
1 GA
70317 ATTAGGAAAA
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
19 1 0.01
20 74 0.99
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.36
Consensus pattern (20 bp):
GATTTACGTATTCGCATTGC
Found at i:70337 original size:21 final size:21
Alignment explanation
Indices: 70313--70353 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
70303 TATTCGCATT
70313 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
70334 GCGAATTTGGGAAATCGCAA
1 GCGAATTAGGAAAATCGCAA
70354 TGCGGTAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.27, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:85560 original size:28 final size:29
Alignment explanation
Indices: 85528--85603 Score: 127
Period size: 30 Copynumber: 2.6 Consensus size: 29
85518 ATAAGCCAGT
*
85528 TACATAAGACTTAAAA-AGTCTTGCAAAC
1 TACATAAAACTTAAAACAGTCTTGCAAAC
85556 TACATAAAACTTAAAAACAGTCTTGCAAAC
1 TACATAAAACTT-AAAACAGTCTTGCAAAC
85586 TACATAAAACTTAAAACA
1 TACATAAAACTTAAAACA
85604 CTTACATCTA
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
28 11 0.24
29 10 0.22
30 24 0.53
ACGTcount: A:0.51, C:0.18, G:0.07, T:0.24
Consensus pattern (29 bp):
TACATAAAACTTAAAACAGTCTTGCAAAC
Found at i:104466 original size:24 final size:26
Alignment explanation
Indices: 104418--104467 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
104408 AAAATTAAAT
*
104418 ATAAAAAATATAATAGTCGGTTATAAC
1 ATAAAAAATATAATA-TCGGATATAAC
104445 ATAAAAAAT-TAAT-TCGGATATAA
1 ATAAAAAATATAATATCGGATATAA
104468 TATTAAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 9 0.41
26 4 0.18
27 9 0.41
ACGTcount: A:0.54, C:0.06, G:0.10, T:0.30
Consensus pattern (26 bp):
ATAAAAAATATAATATCGGATATAAC
Found at i:105202 original size:2 final size:2
Alignment explanation
Indices: 105197--105237 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
105187 TCTCTCTCTC
105197 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
105238 TCATATGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:106426 original size:57 final size:57
Alignment explanation
Indices: 106359--106473 Score: 187
Period size: 57 Copynumber: 2.0 Consensus size: 57
106349 GAAGATGGAA
*
106359 TGTATATGTCTCCGGTCTCCACCTCT-TGATTAGTGCATAAACGAAGGTGGGTTGAAG
1 TGTATATGTCTCCGGTCTCCACCTCTCT-ATTAGTGCAGAAACGAAGGTGGGTTGAAG
* *
106416 TGTATGTGTCTCCGGTCTCCACCTCTCTATTAGTGCAGAAACGAGGGTGGGTTGAAG
1 TGTATATGTCTCCGGTCTCCACCTCTCTATTAGTGCAGAAACGAAGGTGGGTTGAAG
106473 T
1 T
106474 TTACAACCTC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
57 53 0.98
58 1 0.02
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (57 bp):
TGTATATGTCTCCGGTCTCCACCTCTCTATTAGTGCAGAAACGAAGGTGGGTTGAAG
Found at i:107557 original size:22 final size:24
Alignment explanation
Indices: 107514--107560 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
107504 TATACTTAAT
107514 ATATTTTTTATAATAAATAAAATTA
1 ATATTTTTTAT-ATAAATAAAATTA
107539 ATATTTTTTAT-T-AATAAAATTA
1 ATATTTTTTATATAAATAAAATTA
107561 TCATACATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 10 0.45
23 1 0.05
25 11 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
ATATTTTTTATATAAATAAAATTA
Found at i:122825 original size:16 final size:16
Alignment explanation
Indices: 122789--122825 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
122779 AGTTTTAACT
122789 ATAC-AAATATAAAAA
1 ATACTAAATATAAAAA
122804 A-A-TAAATATAAAAA
1 ATACTAAATATAAAAA
122818 ATACTAAA
1 ATACTAAA
122826 AAATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
14 13 0.68
15 2 0.11
16 4 0.21
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (16 bp):
ATACTAAATATAAAAA
Found at i:123319 original size:22 final size:23
Alignment explanation
Indices: 123286--123333 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
123276 TTTATACATA
123286 AATTTTAATTTAT-A-ACTTTAT
1 AATTTTAATTTATAAGACTTTAT
*
123307 AATTTTATTTTTATAAGACTTTAT
1 AATTTTA-ATTTATAAGACTTTAT
123331 AAT
1 AAT
123334 ATGTATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 7 0.30
22 5 0.22
23 1 0.04
24 10 0.43
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (23 bp):
AATTTTAATTTATAAGACTTTAT
Found at i:133464 original size:16 final size:17
Alignment explanation
Indices: 133445--133481 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
133435 TAAAATATTA
133445 TTTTA-AATAATTAC-AT
1 TTTTACAATAA-TACTAT
133461 TTTTACAATAATACTAT
1 TTTTACAATAATACTAT
133478 TTTT
1 TTTT
133482 TTCATCCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTTACAATAATACTAT
Found at i:134831 original size:2 final size:2
Alignment explanation
Indices: 134819--134854 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
134809 TACATAATTT
*
134819 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
134855 ACTCAAACTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:135217 original size:5 final size:5
Alignment explanation
Indices: 135207--135263 Score: 114
Period size: 5 Copynumber: 11.4 Consensus size: 5
135197 GTATACAAAT
135207 GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC
135257 GACCC GA
1 GACCC GA
135264 GACGAGACGG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 52 1.00
ACGTcount: A:0.21, C:0.58, G:0.21, T:0.00
Consensus pattern (5 bp):
GACCC
Found at i:135851 original size:19 final size:19
Alignment explanation
Indices: 135827--135892 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
135817 TCTTTTTTTT
135827 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
* * ** *
135846 CAACGACAACTGTAGACTACCG
1 CAACG--AA-TTTGGAAAATCG
135868 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
135887 CAACGA
1 CAACGA
135893 CAACTGCAGT
Statistics
Matches: 34, Mismatches: 10, Indels: 6
0.68 0.20 0.12
Matches are distributed among these distances:
19 18 0.53
20 2 0.06
21 2 0.06
22 12 0.35
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.17
Consensus pattern (19 bp):
CAACGAATTTGGAAAATCG
Found at i:135927 original size:20 final size:20
Alignment explanation
Indices: 135902--135964 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
135892 ACAACTGCAG
*
135902 TGGAAAATTGCAACGCGAAA
1 TGGAAAATCGCAACGCGAAA
*
135922 TGGAAAATCGCAACGCGAAT
1 TGGAAAATCGCAACGCGAAA
** *
135942 TTCAACTATCGCAACGCGAAA
1 TGGAA-AATCGCAACGCGAAA
135963 TG
1 TG
135965 CAACGCGAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
20 21 0.60
21 14 0.40
ACGTcount: A:0.40, C:0.21, G:0.22, T:0.17
Consensus pattern (20 bp):
TGGAAAATCGCAACGCGAAA
Found at i:135968 original size:21 final size:21
Alignment explanation
Indices: 135911--135968 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
135901 GTGGAAAATT
*
135911 GCAACGCGAAATGGAA-AATC
1 GCAACGCGAAATGCAACAATC
* * *
135931 GCAACGCGAATTTCAACTATC
1 GCAACGCGAAATGCAACAATC
135952 GCAACGCGAAATGCAAC
1 GCAACGCGAAATGCAAC
135969 GCGAATTTGC
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
20 13 0.42
21 18 0.58
ACGTcount: A:0.40, C:0.26, G:0.21, T:0.14
Consensus pattern (21 bp):
GCAACGCGAAATGCAACAATC
Found at i:136029 original size:101 final size:101
Alignment explanation
Indices: 135911--136092 Score: 294
Period size: 101 Copynumber: 1.8 Consensus size: 101
135901 GTGGAAAATT
*
135911 GCAACGCGAAATGGAAAATCGCAACGCGAATTTCAACTATCGC-AACGCGAAATGCAACGCGAAT
1 GCAACGCGAAATGGAAAAACGCAACGCGAATTTCAACTATC-CTAACGCGAAATGCAACGCGAAT
135975 TTGCGATAGTGGAGATCACGTTGCGATTTCAACTATC
65 TTGCGATAGTGGAGATCACGTTGCGATTTCAACTATC
* ** * *
136012 GCAACGCGAAATGGAAAAACGCAACGCGATTTTCAACTATCCTAGTGCGAAATGCACCGTGAATT
1 GCAACGCGAAATGGAAAAACGCAACGCGAATTTCAACTATCCTAACGCGAAATGCAACGCGAATT
136077 TGCGATAGTGGAGATC
66 TGCGATAGTGGAGATC
136093 GTATTGCGAT
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
100 1 0.01
101 73 0.99
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.21
Consensus pattern (101 bp):
GCAACGCGAAATGGAAAAACGCAACGCGAATTTCAACTATCCTAACGCGAAATGCAACGCGAATT
TGCGATAGTGGAGATCACGTTGCGATTTCAACTATC
Found at i:136974 original size:2 final size:2
Alignment explanation
Indices: 136969--136993 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
136959 AAAAAAATGA
136969 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
136994 GCGTCGATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:137547 original size:29 final size:30
Alignment explanation
Indices: 137514--137571 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
137504 ATTTAAAAAT
*
137514 AATGTTTA-AAATAA-ACAAAAATAATTTTG
1 AATGTTAATAAATAATA-AAAAATAATTTTG
*
137543 AATGTTAATAAATAATAAAAAATTATTTT
1 AATGTTAATAAATAATAAAAAATAATTTT
137572 TCTGACATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.28
30 17 0.68
31 1 0.04
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (30 bp):
AATGTTAATAAATAATAAAAAATAATTTTG
Found at i:158978 original size:33 final size:33
Alignment explanation
Indices: 158941--159006 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
158931 AACTTTCATT
158941 GTTTTCAAAATTATTCCTAATGCTTACTTTGTA
1 GTTTTCAAAATTATTCCTAATGCTTACTTTGTA
* *
158974 GTTTTCATAATTATTCCTAATGTTTACTTTGTA
1 GTTTTCAAAATTATTCCTAATGCTTACTTTGTA
159007 TTTCATTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.26, C:0.14, G:0.09, T:0.52
Consensus pattern (33 bp):
GTTTTCAAAATTATTCCTAATGCTTACTTTGTA
Found at i:160245 original size:23 final size:23
Alignment explanation
Indices: 160204--160247 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
160194 TTTCATATAT
* *
160204 TTTAAAATATAATTAATATAAGA
1 TTTAAAATAAAAATAATATAAGA
*
160227 TTTAAAATAAAAATGATATAA
1 TTTAAAATAAAAATAATATAA
160248 ACAATTATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (23 bp):
TTTAAAATAAAAATAATATAAGA
Found at i:169095 original size:25 final size:26
Alignment explanation
Indices: 169067--169115 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
169057 AATCACATTT
169067 AATATTT-TTATT-TATCAAATTAAAA
1 AATATTTCTT-TTATATCAAATTAAAA
*
169092 AATATTTCTTTTATATTAAATTAA
1 AATATTTCTTTTATATCAAATTAA
169116 TGTTTAAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (26 bp):
AATATTTCTTTTATATCAAATTAAAA
Found at i:169429 original size:20 final size:20
Alignment explanation
Indices: 169404--169459 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
169394 AATATTTTTT
169404 AAAGTTTGATTTGAGATTTA
1 AAAGTTTGATTTGAGATTTA
* *
169424 AAAGTTTAATATTGATA-TTA
1 AAAGTTTGAT-TTGAGATTTA
*
169444 AAA-TGTGATTTGAGAT
1 AAAGTTTGATTTGAGAT
169460 GATAAATGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 5 0.17
19 4 0.14
20 15 0.52
21 5 0.17
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.43
Consensus pattern (20 bp):
AAAGTTTGATTTGAGATTTA
Found at i:177150 original size:33 final size:33
Alignment explanation
Indices: 177100--177163 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
177090 ATTTCAAAAT
177100 TATAATTATGAAAAAAATATATATTAATTTATA
1 TATAATTATGAAAAAAATATATATTAATTTATA
* * *
177133 TATATTTAT-AAATAAAATATTTATTTATTTA
1 TATAATTATGAAA-AAAATATATATTAATTTA
177164 GAAATATCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 3 0.11
33 24 0.89
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (33 bp):
TATAATTATGAAAAAAATATATATTAATTTATA
Found at i:177255 original size:20 final size:19
Alignment explanation
Indices: 177216--177257 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
177206 TTTCCTCGAT
177216 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
177235 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
177255 ATT
1 ATT
177258 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:177368 original size:120 final size:120
Alignment explanation
Indices: 177129--177361 Score: 285
Period size: 120 Copynumber: 2.0 Consensus size: 120
177119 TATATTAATT
* * * *
177129 TATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAGGTGCCT
1 TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAAGACATCCAGGTGCCT
* *
177194 TAAGACAGCTCTTTTCCTCGATATTAAAAAATAAATAAATAATTAAAACAATTAA
66 TAAGACAGCTCCTTTCCTCAATATTAAAAAATAAATAAATAATTAAAACAATTAA
** * *
177249 TATATA-ATTTATAAAATAGGATATTTATTTATTTAAAAATATCAGAAAATAGACATCCAGTTGT
1 TATATATATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAA-AGACATCCAGGTGC
* ** * *
177313 TTTAAGATTGC-CCTTT-CTTAATATTGAAAAATAAATAAAT-ATTAAAACA
64 CTTAAGACAGCTCCTTTCCTCAATATTAAAAAATAAATAAATAATTAAAACA
177362 TGATTAAAAT
Statistics
Matches: 96, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
118 9 0.09
119 27 0.28
120 43 0.45
121 17 0.18
ACGTcount: A:0.46, C:0.09, G:0.08, T:0.37
Consensus pattern (120 bp):
TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAAGACATCCAGGTGCCT
TAAGACAGCTCCTTTCCTCAATATTAAAAAATAAATAAATAATTAAAACAATTAA
Found at i:178823 original size:3 final size:3
Alignment explanation
Indices: 178815--178867 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
178805 TGTAATTATT
* *
178815 TAA TAA TAA TATA TAA TAA TAAA TAA -AA TTA TAA TAA T-A TAT TAA
1 TAA TAA TAA TA-A TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
178860 TAA TAA TA
1 TAA TAA TA
178868 CTAAAAACAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
2 4 0.10
3 32 0.76
4 6 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:178830 original size:10 final size:10
Alignment explanation
Indices: 178817--178864 Score: 64
Period size: 10 Copynumber: 4.9 Consensus size: 10
178807 TAATTATTTA
178817 ATAATAATAT
1 ATAATAATAT
*
178827 ATAATAATAA
1 ATAATAATAT
178837 ATAA-AAT-T
1 ATAATAATAT
178845 ATAATAATAT
1 ATAATAATAT
178855 ATTAATAATA
1 A-TAATAATA
178865 ATACTAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
8 4 0.12
9 6 0.18
10 15 0.45
11 8 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
ATAATAATAT
Found at i:182597 original size:20 final size:20
Alignment explanation
Indices: 182572--182650 Score: 79
Period size: 20 Copynumber: 3.9 Consensus size: 20
182562 CTTTTGGTGT
182572 TTTAATAAAAAATTGGTAGG
1 TTTAATAAAAAATTGGTAGG
* ** * *
182592 TTTAATAATATTTTAGT-GT
1 TTTAATAAAAAATTGGTAGG
182611 TTTAATAAAAAAATTGGTAGG
1 TTTAAT-AAAAAATTGGTAGG
*
182632 TTTAAAAAAATAATTGGTA
1 TTTAATAAAA-AATTGGTA
182651 TATTTAGACT
Statistics
Matches: 45, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
19 7 0.16
20 24 0.53
21 14 0.31
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (20 bp):
TTTAATAAAAAATTGGTAGG
Found at i:182614 original size:39 final size:40
Alignment explanation
Indices: 182558--182636 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
182548 ATCATTACAT
* *
182558 TAATCTTTTGGTGTTTTAAT-AAAAAATTGGTAGGTTTAA
1 TAATATTTTAGTGTTTTAATAAAAAAATTGGTAGGTTTAA
182597 TAATATTTTAGTGTTTTAATAAAAAAATTGGTAGGTTTAA
1 TAATATTTTAGTGTTTTAATAAAAAAATTGGTAGGTTTAA
182637 AAAAATAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
39 18 0.49
40 19 0.51
ACGTcount: A:0.37, C:0.01, G:0.16, T:0.46
Consensus pattern (40 bp):
TAATATTTTAGTGTTTTAATAAAAAAATTGGTAGGTTTAA
Found at i:182641 original size:21 final size:21
Alignment explanation
Indices: 182611--182650 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
182601 ATTTTAGTGT
*
182611 TTTAATAAAAAAATTGGTAGG
1 TTTAAAAAAAAAATTGGTAGG
*
182632 TTTAAAAAAATAATTGGTA
1 TTTAAAAAAAAAATTGGTA
182651 TATTTAGACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (21 bp):
TTTAAAAAAAAAATTGGTAGG
Found at i:184397 original size:14 final size:16
Alignment explanation
Indices: 184370--184401 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
184360 CTTTAAAGAT
184370 TAAATTATTATTATTA
1 TAAATTATTATTATTA
184386 TAAA-TATT-TTATTA
1 TAAATTATTATTATTA
184400 TA
1 TA
184402 TTTTCTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 4 0.25
16 4 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TAAATTATTATTATTA
Found at i:187710 original size:13 final size:13
Alignment explanation
Indices: 187688--187717 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
187678 AATATTTTGT
*
187688 TTTCACAAATTTA
1 TTTCAAAAATTTA
187701 TTTCAAAAATTTA
1 TTTCAAAAATTTA
187714 TTTC
1 TTTC
187718 CACAAATTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTCAAAAATTTA
Found at i:201363 original size:4 final size:4
Alignment explanation
Indices: 201354--201380 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
201344 GCAGCTGTTC
201354 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
201381 TATTAAAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:203175 original size:20 final size:20
Alignment explanation
Indices: 203146--203184 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
203136 ATCTGAAAAT
*
203146 TATATACTTTTATATTTTTC
1 TATATACTTTTAGATTTTTC
*
203166 TATATTCTTTTAGATTTTT
1 TATATACTTTTAGATTTTT
203185 ATCTTTTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.08, G:0.03, T:0.67
Consensus pattern (20 bp):
TATATACTTTTAGATTTTTC
Found at i:203373 original size:23 final size:22
Alignment explanation
Indices: 203330--203373 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
203320 AAATTATATA
* *
203330 AAAATAAAATAAGAATTAAATT
1 AAAATAAAAGAAGAATGAAATT
*
203352 AAAATATAAAGAATAATGAAAT
1 AAAATA-AAAGAAGAATGAAAT
203374 ATTAAATCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (22 bp):
AAAATAAAAGAAGAATGAAATT
Found at i:205770 original size:6 final size:6
Alignment explanation
Indices: 205759--205791 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
205749 ATCTCCCCTT
205759 CTACAA CTACAA CTACAA CTACAA CTACAA CTA
1 CTACAA CTACAA CTACAA CTACAA CTACAA CTA
205792 GGTTCTAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.18
Consensus pattern (6 bp):
CTACAA
Found at i:214175 original size:182 final size:180
Alignment explanation
Indices: 213817--214434 Score: 722
Period size: 182 Copynumber: 3.4 Consensus size: 180
213807 GATACAAATG
* * * * * * *
213817 AAAAATGTATCGCTCCATAGCAATATAACATGTAAAAATATGATAAAACCAGTTTC-ATTATGAT
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGA-AATGAT
** * * *
213881 AAAACCGGTAAACCGCTACTGGATATATCGAAAGTATCAATTAGAATTAA-ATAAGTATCGACAC
65 AAAACCGGTAAAAAGCTAC-GGATATATTGAAAGTGTCGA-TAG--TTAATATAAGTATCGACAC
* * **
213945 TTTTGGAATTTAAAAGAGAAGAAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
126 TTTTTGAATTTAAAAGAGAAGAAGTTATAGATCCTATAAAGTGTCGATACTTTAT
* * * * * *
214000 AAAAACGTATCGATCCATAACAATATAACATGTATAAGTATGACAAAACCGGTCACGAAATCATA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGATA
* * *
214065 AAACCGGTAAAGAGCTATCGGATATATTGAAAGTGTCGATACGTTAATATAAATATCAACACTTT
66 AAACCGGTAAAAAGCTA-CGGATATATTGAAAGTGTCGATA-GTTAATATAAGTATCGACACTTT
214130 TTGAATTTAAAAGAGAAGAAGTTATAGATCCTATAAAGTGTCGATACTTTAT
129 TTGAATTTAAAAGAGAAGAAGTTATAGATCCTATAAAGTGTCGATACTTTAT
* * * * *
214182 ACAAATGTATCAATCCATAGCAATATAACAGGTAAGAATATGACAAAACAGGTCTCGAAATGATA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGATA
* *
214247 AAACCGGTAAAAAGCTACCAGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACAC-TT
66 AAACCGGTAAAAAGCTA-CGGATATATTGAAAGTGTCGAT-AGTTAATATAAGTATCGACACTTT
* *
214311 TTGTAATTTAAAAGAGAAGAAGTTATAGCGT-CTAAAAAGTGTCGATACTTTAT
129 TTG-AATTTAAAAGAGAAGAAGTTATAG-ATCCTATAAAGTGTCGATACTTTAT
* * * * * * * * *
214364 GATAATGTATTGATCCATAATAATATAATAGGTAAAAATATGACAAAACCGATATCAAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGATA
214429 AAACCG
66 AAACCG
214435 ATATCGAAAT
Statistics
Matches: 373, Mismatches: 55, Indels: 15
0.84 0.12 0.03
Matches are distributed among these distances:
181 9 0.02
182 275 0.74
183 87 0.23
184 2 0.01
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.27
Consensus pattern (180 bp):
AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGATA
AAACCGGTAAAAAGCTACGGATATATTGAAAGTGTCGATAGTTAATATAAGTATCGACACTTTTT
GAATTTAAAAGAGAAGAAGTTATAGATCCTATAAAGTGTCGATACTTTAT
Found at i:214428 original size:20 final size:20
Alignment explanation
Indices: 214403--214454 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
214393 AGGTAAAAAT
214403 ATGACAAAACCGATATCAAA
1 ATGACAAAACCGATATCAAA
*
214423 ATGACAAAACCGATATCGAA
1 ATGACAAAACCGATATCAAA
214443 ATGACAAAACCG
1 ATGACAAAACCG
214455 GTAAAGCACT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.52, C:0.21, G:0.13, T:0.13
Consensus pattern (20 bp):
ATGACAAAACCGATATCAAA
Found at i:215874 original size:22 final size:22
Alignment explanation
Indices: 215823--215878 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 22
215813 ATGCTTTTGT
*
215823 TTTTTTTATATAAAATGATGGTA
1 TTTTATTATATAAAATGAT-GTA
*
215846 TAGTTATTATATAAAATGAT-TAA
1 T-TTTATTATATAAAATGATGT-A
215869 TTTTATTATA
1 TTTTATTATA
215879 AATTCAGGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 9 0.32
23 3 0.11
24 16 0.57
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (22 bp):
TTTTATTATATAAAATGATGTA
Found at i:216576 original size:18 final size:18
Alignment explanation
Indices: 216553--216587 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
216543 AGAAAATTTG
*
216553 AAGAAGAAAATATGGAGA
1 AAGAAGAAAAGATGGAGA
216571 AAGAAGAAAAGATGGAG
1 AAGAAGAAAAGATGGAG
216588 GAAATGATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.31, T:0.09
Consensus pattern (18 bp):
AAGAAGAAAAGATGGAGA
Found at i:216914 original size:17 final size:17
Alignment explanation
Indices: 216892--216927 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
216882 TTTAAATATT
216892 TCATGAAAAGATATTAA
1 TCATGAAAAGATATTAA
216909 TCATGAAAAGATATTAA
1 TCATGAAAAGATATTAA
216926 TC
1 TC
216928 CTAATGATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.31
Consensus pattern (17 bp):
TCATGAAAAGATATTAA
Found at i:218074 original size:19 final size:19
Alignment explanation
Indices: 218050--218099 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
218040 AAATGTAGGG
218050 TTAATTTTGTATAAGATTT
1 TTAATTTTGTATAAGATTT
*
218069 TTAATTTTGTATACGATTT
1 TTAATTTTGTATAAGATTT
* *
218088 ATAATGTTGTAT
1 TTAATTTTGTAT
218100 GTTAATGTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.30, C:0.02, G:0.12, T:0.56
Consensus pattern (19 bp):
TTAATTTTGTATAAGATTT
Found at i:218840 original size:196 final size:196
Alignment explanation
Indices: 218434--218892 Score: 599
Period size: 196 Copynumber: 2.3 Consensus size: 196
218424 GTAAACATAT
*
218434 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATTGAGACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACA-TGAGATCCATAATTATAATGTAATA
*
218499 GGTAAATTATGAATCTAACCGGTCTAAATACACCAGTTTATGAGAAAATAGGTGTACATAAAGTA
65 -GTAAATTATGAATCTAACCGGTCTAAATACACCAGTTTATGAGAAAACAGGTGTACATAAAGTA
* ** * ** * **
218564 TCGACACTTATTGAATTTGTGTCGATACTTTGTGTCCAGAATGATTTCCTTACCAAGTGCATGAA
129 TCGACACTTATTGAATTTGTGTCAATACTTTGTGTCCAGAATGATAACCTCAAAAAATGCACAAA
*
218629 AAT
194 AAA
*
218632 GTGTCGATACATTTATAACAAGTATCGATCCCAAAAACATCGAGATCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACAT-GAGATCCATAATTATAATGTAATA
* *
218697 GTAAATTATGAATCT-ACCGGTCTAAATACTCCGGTTTATGAGAAAACAGGTGTACATAAAGTAT
65 GTAAATTATGAATCTAACCGGTCTAAATACACCAGTTTATGAGAAAACAGGTGTACATAAAGTAT
* *
218761 CGACACTCT-TTG-ATTTGTGTTAATACGTTT-TGTCCAGAATG-TAAACGGTCAAAAAATGCAC
130 CGACACT-TATTGAATTTGTGTCAATAC-TTTGTGTCCAGAATGAT-AAC-CTCAAAAAATGCAC
218822 AAAAAA
191 AAAAAA
* * * *
218828 GTTTCGATACATTTATAAAAAGTATCGAT-CCTAAAACAATGAAATTCATAATT-TGAATGTAAT
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAAC-ATGAGATCCATAATTAT-AATGTAAT
218891 AG
64 AG
218893 GTCATTTTGC
Statistics
Matches: 232, Mismatches: 22, Indels: 17
0.86 0.08 0.06
Matches are distributed among these distances:
194 2 0.01
195 52 0.22
196 100 0.43
197 17 0.07
198 61 0.26
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (196 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATGAGATCCATAATTATAATGTAATAG
TAAATTATGAATCTAACCGGTCTAAATACACCAGTTTATGAGAAAACAGGTGTACATAAAGTATC
GACACTTATTGAATTTGTGTCAATACTTTGTGTCCAGAATGATAACCTCAAAAAATGCACAAAAA
A
Found at i:219619 original size:2 final size:2
Alignment explanation
Indices: 219612--219637 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
219602 ATGGGGAAGG
219612 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
219638 CTCCGGAGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:222616 original size:201 final size:200
Alignment explanation
Indices: 222102--222926 Score: 902
Period size: 201 Copynumber: 4.1 Consensus size: 200
222092 AATGAATTTG
* *
222102 CTTTATTCATTCGTGTCGATACATGTA-GTCCAGAATGTA-TTTCCAAATCAAGTGCACGAACAA
1 CTTTATTCATTTGTGTCGATAC-TGTATGTCCAGAATGTATTTTCCAAA-CAAGTGCACGAAAAA
* *
222165 AGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAAT
64 AGTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAAT
* * * * * *
222230 AGGTAAAATAACAATGTAACCGATCTAAATATATCGATTTATGAGAAAAGAGGTATACATAAAGT
129 AGGTAACATAACAATGTAACCGGTCTAAATATATGGTTTTATGAGAAAATAGGTATACATAATGT
*
222295 ATCAACA
194 ATCGACA
* * * * *
222302 CTTTATACATTTGTGTCGATACTTTGTGTCCATAATGTATTTTCCAACCAAAACAAGTTCAC-AA
1 CTTTATTCATTTGTGTCGATACTGTATGTCCAGAATGTATTTT----CC-AAACAAGTGCACGAA
* ** *
222366 ATAAGTGTCGATACATTTATATCAAGTGTCGATCCCAAAAACATCGAAACCCATAACTATAATGT
61 AAAAGTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGT
* * * * * * *
222431 AATAGGTCACTTTATAATGTAACCGGTTTAAATTTACTGGTTTTATGAGAAAATAGGTCTACA-A
126 AATAGGTAACATAACAATGTAACCGGTCTAAATATA-TGGTTTTATGAGAAAATAGGTATACATA
222495 TATGTATCGACA
190 -ATGTATCGACA
222507 CTTTATTCATTTGTGTCGATACATGT-TGTCCAGAATGTA-TTTCCAAACCAAGTGCACGAAAAA
1 CTTTATTCATTTGTGTCGATAC-TGTATGTCCAGAATGTATTTTCCAAA-CAAGTGCACGAAAAA
* *
222570 AGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTAAT
64 AGTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAAT
* * * *
222635 AGGTAACATAATAATGTAACCAGTCTAAATATATCAGTTATTA--A-AAAA-AAGTATACATAAT
129 AGGTAACATAACAATGTAACCGGTCTAAATATAT-GGTT-TTATGAGAAAATAGGTATACATAAT
*
222696 GTATCGATA
192 GTATCGACA
* * * * ** * *
222705 CTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCGAAACAAGTTCACG--AAAAG
1 CTTTATTCATTTGTGTCGATACTGTATGTCCAGAATGTATTTTCCAAACAAGTGCACGAAAAAAG
* * * * *
222768 TGTCGATACATTTAGAAAAAATGTCGATCCTAAAAACATCGAAACCCGTAATTATAATGTAATAT
66 TGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAG
* * * * * * * *
222833 GTCACTTTACAATGTAACCGGTTTAAATTTACGGGTTTTTTGAGAAAATAGGTCTACATAATGTA
131 GTAACATAACAATGTAACCGGTCTAAATATA-TGGTTTTATGAGAAAATAGGTATACATAATGTA
*
222898 TCGATA
195 TCGACA
* *
222904 CTTT-TTAAATTAGTGTCGATACT
1 CTTTATT-CATTTGTGTCGATACT
222927 TTTTAAAATT
Statistics
Matches: 526, Mismatches: 76, Indels: 47
0.81 0.12 0.07
Matches are distributed among these distances:
195 2 0.00
196 90 0.17
197 3 0.01
198 61 0.12
199 54 0.10
200 43 0.08
201 99 0.19
202 3 0.01
204 92 0.17
205 74 0.14
206 5 0.01
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (200 bp):
CTTTATTCATTTGTGTCGATACTGTATGTCCAGAATGTATTTTCCAAACAAGTGCACGAAAAAAG
TGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAG
GTAACATAACAATGTAACCGGTCTAAATATATGGTTTTATGAGAAAATAGGTATACATAATGTAT
CGACA
Found at i:222714 original size:22 final size:21
Alignment explanation
Indices: 222686--222731 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
222676 TAAAAAAAAG
*
222686 TATACATAATGTATCGATACTT
1 TATACAT-ATGTATCGACACTT
* *
222708 TATACATTTGTGTCGACACTT
1 TATACATATGTATCGACACTT
222729 TAT
1 TAT
222732 GTCCATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.43
Consensus pattern (21 bp):
TATACATATGTATCGACACTT
Found at i:226545 original size:87 final size:87
Alignment explanation
Indices: 226441--226603 Score: 263
Period size: 87 Copynumber: 1.9 Consensus size: 87
226431 AAATAGGTCA
* *
226441 ATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATTTGTTATTGTACTTAATAATATTT
1 ATATAAGCACTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTAATAATATTT
226506 CTGGTTAAATGCCTATTTTATT
66 CTGGTTAAATGCCTATTTTATT
* * * *
226528 ATATAAGCACTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATTTTT
1 ATATAAGCACTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTAATAATATTT
*
226593 TTGGTTAAATG
66 CTGGTTAAATG
226604 ATATAACATA
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 69 1.00
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (87 bp):
ATATAAGCACTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTAATAATATTT
CTGGTTAAATGCCTATTTTATT
Found at i:226575 original size:23 final size:23
Alignment explanation
Indices: 226525--226569 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
226515 TGCCTATTTT
*
226525 ATTATATAAGCACTACCTATTAC
1 ATTATATAAGCACTACCTAATAC
*
226548 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCACTACCTAATA
226570 TGTTATTGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCACTACCTAATAC
Found at i:240635 original size:12 final size:12
Alignment explanation
Indices: 240620--240645 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
240610 TTGAGGAATA
240620 GGAGGAGGATTT
1 GGAGGAGGATTT
240632 GGAGGAGGATTT
1 GGAGGAGGATTT
240644 GG
1 GG
240646 TTGACGACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.54, T:0.23
Consensus pattern (12 bp):
GGAGGAGGATTT
Found at i:270403 original size:32 final size:35
Alignment explanation
Indices: 270328--270406 Score: 94
Period size: 35 Copynumber: 2.3 Consensus size: 35
270318 AAAAAATAGA
* *
270328 TTAATATATATAATTCATAAAAATAAGATATTTAT
1 TTAATATATATAATTCAAAAAAATAAGATATTTAC
270363 TTATATATATATAA-T-AAAATAAATAA-ATA-TTAC
1 TTA-ATATATATAATTCAAAA-AAATAAGATATTTAC
270396 TTAATATATAT
1 TTAATATATAT
270407 TTATATGATT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
32 8 0.20
33 6 0.15
34 6 0.15
35 10 0.25
36 10 0.25
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (35 bp):
TTAATATATATAATTCAAAAAAATAAGATATTTAC
Found at i:271920 original size:3 final size:3
Alignment explanation
Indices: 271816--271904 Score: 87
Period size: 3 Copynumber: 29.7 Consensus size: 3
271806 TTTGGGTCTG
*
271816 TAA TAA TAA CTTAA TTAA TAA TTA TAA TAAA TAA TAA TAA TAA TAA T-A
1 TAA TAA TAA --TAA -TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
* *
271864 TAA TAG TAA -AA TAA -AA TAA TAT TAA TAA TAA T-A TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
271905 TTATTATTTA
Statistics
Matches: 73, Mismatches: 6, Indels: 14
0.78 0.06 0.15
Matches are distributed among these distances:
2 8 0.11
3 55 0.75
4 7 0.10
5 3 0.04
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:272342 original size:136 final size:124
Alignment explanation
Indices: 272216--272785 Score: 369
Period size: 113 Copynumber: 4.9 Consensus size: 124
272206 TACCTCCTTC
* * * *
272216 ATCTATATCTTTCTGTGGTAGAATCAAT-CAAAAGGCTGAACAAGCTCTTCTCATTATGAACTTA
1 ATCTATCTCCTTCTATGATAGAATC-ATGCAAAAGGCTGAACAAGCTCTTCTCATTATGAACTTA
*
272280 TTCTTC-CTCTTCATATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTG
65 TTCTTCTCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTG
* * *
272339 ATCTATCTCCTTCTATGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
1 ATCTATCTCCTTCTATGATAGAATCATGCAAAAGGCTGAACAAGCTCTTCTCATTATGAACTTAT
* *
272404 TCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-TCTGG-AAA----A-GTTG
66 TCTTCTCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTG
* ** ** * ** *
272456 ATCCA--T-C--GAATGAT-GAATTCAAACAAAAGGTTTGAACAAATTCTTCTCATTATGAATTT
1 ATCTATCTCCTTCTATGATAGAA-TCATGCAAAAGG-CTGAACAAGCTCTTCTCATTATGAACTT
** *
272515 CCTCTTC-CTTCTTCAGATAAGTTCTTCTCATTATGAAC--TCTCTGG--AA----ATGCTG
64 ATTCTTCTC-TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTG
* *** * ** * * * * *
272568 ATCCATC-AAGT-GATGA-A-TTTGA-GCAAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCT
1 ATCTATCTCCTTCTATGATAGAATCATGCAAAAGGCTGAACAAGCTCTTCTCATTATGAACTTAT
*
272628 TCTTC-CTTCTTCAGATAAATTCTTCTCATTATGAACTTTCTCTGG-AAA--TGA---TG
66 TCTTCTC-TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTG
* *** * ** * * * *
272681 ATCCATC-AAGT-GATGA-A-TTTGA-GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCT
1 ATCTATCTCCTTCTATGATAGAATCATGCAAAAGGCTGAACAAGCTCTTCTCATTATGAACTTAT
*
272741 TCTTC-CTTCTTCAGATAAATTCTTCTCATTATGAACTTTCTCTGG
66 TCTTCTC-TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGG
272786 CAATGGTAAT
Statistics
Matches: 396, Mismatches: 33, Indels: 46
0.83 0.07 0.10
Matches are distributed among these distances:
111 69 0.17
112 35 0.09
113 174 0.44
114 3 0.01
115 5 0.01
116 1 0.00
117 8 0.02
118 1 0.00
122 5 0.01
123 65 0.16
124 30 0.08
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (124 bp):
ATCTATCTCCTTCTATGATAGAATCATGCAAAAGGCTGAACAAGCTCTTCTCATTATGAACTTAT
TCTTCTCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTG
Found at i:272756 original size:224 final size:224
Alignment explanation
Indices: 272366--272777 Score: 666
Period size: 224 Copynumber: 1.8 Consensus size: 224
272356 ATAGAGTCAT
* * *
272366 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAATTCTTCTC
*
272431 ATTATGAACTTTTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAACAAAAGGTTTGAACAAA
66 ATTATGAACTTTTCTGGAAAAGATGATCCATCGAATGATGAATTCAAACAAAAGGTTTGAACAAA
* *
272496 TTCTTCTCATTATGAATTTCCTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTCTCTGGA
131 TTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATAAATTCTTCTCATTATGAACTCTCTGGA
272561 AATGCTGATCCATCAAGTGATGAATTTGA
196 AATGCTGATCCATCAAGTGATGAATTTGA
* *
272590 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATAAATTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAATTCTTCTC
* ** *
272655 ATTATGAACTTTCTCTGGAAATGATGATCCATC-AAGTGATGAATTTGAGCAAAAGG-TTGAACA
66 ATTATGAACTTT-TCTGGAAAAGATGATCCATCGAA-TGATGAATTCAAACAAAAGGTTTGAACA
* *
272718 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAATTCTTCTCATTATGAACT
129 AATTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATAAATTCTTCTCATTATGAACT
272778 TTCTCTGGCA
Statistics
Matches: 172, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
224 137 0.80
225 35 0.20
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (224 bp):
GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAATTCTTCTC
ATTATGAACTTTTCTGGAAAAGATGATCCATCGAATGATGAATTCAAACAAAAGGTTTGAACAAA
TTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATAAATTCTTCTCATTATGAACTCTCTGGA
AATGCTGATCCATCAAGTGATGAATTTGA
Found at i:272808 original size:113 final size:113
Alignment explanation
Indices: 272366--272799 Score: 660
Period size: 113 Copynumber: 3.9 Consensus size: 113
272356 ATAGAGTCAT
* * * *
272366 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAATTCTTCTC
* * **
272431 ATTATGAACTTT-TCTGGAAAAGTTGATCCATCGAA-TGATGAATTCAA
66 ATTATGAACTTTCTCTGGAAATGATGATCCATC-AAGTGATGAATTTGA
* * * * *
272478 ACAAAAGGTTTGAACAAATTCTTCTCATTATGAATTTCCTCTTCCTTCTTCAGATAAGTTCTTCT
1 GCAAAAGG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAATTCTTCT
*
272543 CATTATGAAC--TCTCTGGAAATGCTGATCCATCAAGTGATGAATTTGA
65 CATTATGAACTTTCTCTGGAAATGATGATCCATCAAGTGATGAATTTGA
*
272590 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATAAATTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAATTCTTCTC
272655 ATTATGAACTTTCTCTGGAAATGATGATCCATCAAGTGATGAATTTGA
66 ATTATGAACTTTCTCTGGAAATGATGATCCATCAAGTGATGAATTTGA
272703 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAATTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAATTCTTCTC
* * *
272768 ATTATGAACTTTCTCTGGCAATGGTAATCCAT
66 ATTATGAACTTTCTCTGGAAATGATGATCCAT
272800 TGGGTGATGG
Statistics
Matches: 297, Mismatches: 20, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
111 66 0.22
112 42 0.14
113 189 0.64
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAATTCTTCTC
ATTATGAACTTTCTCTGGAAATGATGATCCATCAAGTGATGAATTTGA
Found at i:272831 original size:12 final size:12
Alignment explanation
Indices: 272814--272847 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
272804 TGATGGATTC
*
272814 AAATCTTTGCTA
1 AAATCTTTGATA
272826 AAATCTTTGATA
1 AAATCTTTGATA
272838 AAATCTTTGA
1 AAATCTTTGA
272848 AGTTCCTGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (12 bp):
AAATCTTTGATA
Found at i:273235 original size:22 final size:22
Alignment explanation
Indices: 273184--273241 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
273174 GATAAAGCTT
* *
273184 TCATCTTCGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
273206 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
273228 TCATCTTTGAAGAG
1 TCATCTTTGAAGAG
273242 TATAGATGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:274274 original size:75 final size:75
Alignment explanation
Indices: 274142--274305 Score: 256
Period size: 75 Copynumber: 2.2 Consensus size: 75
274132 GATACAGACC
* * *
274142 TTCAGCATGCCCCAACATTGGCTAATACAAGCATTCAACATGCGTCAACATTCTTCATTCTGATT
1 TTCAGCATGCCCCAACATTGGCTAATACAAGCATTCAAAATGCGTCAAAATTATTCATTCTGATT
274207 GAAAGAGGCT
66 GAAAGAGGCT
* *
274217 TTCAGCATGCCCCAACATTGGCTAATACAAGCGTTCAAAATGCGTGAAAATTATTCATTCTGATT
1 TTCAGCATGCCCCAACATTGGCTAATACAAGCATTCAAAATGCGTCAAAATTATTCATTCTGATT
*
274282 GAAAGGGGCT
66 GAAAGAGGCT
* *
274292 TTCATCATACCCCA
1 TTCAGCATGCCCCA
274306 GTGTTTGCTT
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 81 1.00
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.28
Consensus pattern (75 bp):
TTCAGCATGCCCCAACATTGGCTAATACAAGCATTCAAAATGCGTCAAAATTATTCATTCTGATT
GAAAGAGGCT
Found at i:276748 original size:32 final size:32
Alignment explanation
Indices: 276707--276769 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
276697 TGAAGAAATG
*
276707 ATTGTTATGCTCATCTTGTAGAGATACTTCTC
1 ATTGTTATGCTCATCTCGTAGAGATACTTCTC
276739 ATTGTTATGCTCATCTCGTAGAGATACTTCT
1 ATTGTTATGCTCATCTCGTAGAGATACTTCT
276770 TGTGTCTGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.43
Consensus pattern (32 bp):
ATTGTTATGCTCATCTCGTAGAGATACTTCTC
Found at i:277284 original size:7 final size:8
Alignment explanation
Indices: 277265--277294 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
277255 CTTGGTTCAA
277265 TTTTTTCC
1 TTTTTTCC
277273 TTTTTTCC
1 TTTTTTCC
277281 TTTTTTCC
1 TTTTTTCC
277289 TTTTTT
1 TTTTTT
277295 TTTCAAGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTTCC
Found at i:279956 original size:8 final size:8
Alignment explanation
Indices: 279945--279997 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 8
279935 GCAAATATGC
279945 AAATGAAA
1 AAATGAAA
279953 AAATGAAA
1 AAATGAAA
279961 AAATGAAA
1 AAATGAAA
* *
279969 ATATAAATA
1 AAATGAA-A
* *
279978 TAAACGTAA
1 -AAATGAAA
279987 AAATGAAA
1 AAATGAAA
279995 AAA
1 AAA
279998 AAAATGCAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
8 30 0.86
9 2 0.06
10 3 0.09
ACGTcount: A:0.72, C:0.02, G:0.09, T:0.17
Consensus pattern (8 bp):
AAATGAAA
Found at i:280021 original size:12 final size:13
Alignment explanation
Indices: 279999--280027 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
279989 ATGAAAAAAA
279999 AAATGCAAAATGT
1 AAATGCAAAATGT
280012 AAATGC-AAATGT
1 AAATGCAAAATGT
280024 AAAT
1 AAAT
280028 ATGTGAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.24
Consensus pattern (13 bp):
AAATGCAAAATGT
Found at i:283786 original size:22 final size:18
Alignment explanation
Indices: 283757--283845 Score: 96
Period size: 17 Copynumber: 4.9 Consensus size: 18
283747 TTTGGGTCTG
283757 TAATAATAACTTAATTAATAA
1 TAATAATAA--TAA-TAATAA
283778 TAAATAATAATAATAATAA
1 T-AATAATAATAATAATAA
*
283797 TAATAAT-ATAATAGTAA
1 TAATAATAATAATAATAA
*
283814 -AATAA-AATAATATTAA
1 TAATAATAATAATAATAA
283830 TAAT-ATAATAATAATA
1 TAATAATAATAATAATA
283846 TTATTATTTA
Statistics
Matches: 61, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
16 15 0.25
17 21 0.34
18 6 0.10
19 7 0.11
20 3 0.05
21 1 0.02
22 8 0.13
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (18 bp):
TAATAATAATAATAATAA
Found at i:283789 original size:25 final size:23
Alignment explanation
Indices: 283757--283845 Score: 105
Period size: 22 Copynumber: 3.9 Consensus size: 23
283747 TTTGGGTCTG
283757 TAATAATAACTTAATTAATAATAA-A
1 TAATAATAA--TAA-TAATAATAATA
283782 TAATAATAATAATAATAATAATA
1 TAATAATAATAATAATAATAATA
*
283805 TAATAGTAA-AATAA-AATAATA
1 TAATAATAATAATAATAATAATA
283826 TTAATAAT-ATAATAATAATA
1 -TAATAATAATAATAATAATA
283846 TTATTATTTA
Statistics
Matches: 58, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
21 8 0.14
22 25 0.43
23 16 0.28
25 9 0.16
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (23 bp):
TAATAATAATAATAATAATAATA
Found at i:283861 original size:3 final size:3
Alignment explanation
Indices: 283757--283845 Score: 96
Period size: 3 Copynumber: 29.7 Consensus size: 3
283747 TTTGGGTCTG
283757 TAA TAA TAA CTTAA TTAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA T-A
1 TAA TAA TAA --TAA -TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
* *
283805 TAA TAG TAA -AA TAA -AA TAA TAT TAA TAA T-A TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
283846 TTATTATTTA
Statistics
Matches: 75, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
2 8 0.11
3 57 0.76
4 7 0.09
5 3 0.04
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:284536 original size:20 final size:20
Alignment explanation
Indices: 284513--284564 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
284503 AACGCGATCC
284513 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
284533 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
284553 CCAAAATCGCAA
1 CCAGAATCGCAA
284565 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:284581 original size:21 final size:20
Alignment explanation
Indices: 284554--284652 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
284544 AATCAGTTTC
284554 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
284575 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
284596 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
284616 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
284637 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
284653 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
20 16 0.26
21 45 0.74
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:284681 original size:20 final size:20
Alignment explanation
Indices: 284619--284888 Score: 251
Period size: 20 Copynumber: 13.5 Consensus size: 20
284609 CGATTTTCCA
* ** *
284619 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
284639 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
284659 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
284679 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
284699 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
284719 AAATCGCAATGTGTATCTGT
1 AAATCGCAACGCGTATCCGT
*
284739 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
284759 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
284779 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
284799 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
284819 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
284839 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
284859 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
284879 AAATCACAAC
1 AAATCGCAAC
284889 ACTGAAATTT
Statistics
Matches: 206, Mismatches: 36, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 202 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:284705 original size:40 final size:40
Alignment explanation
Indices: 284658--284888 Score: 286
Period size: 40 Copynumber: 5.8 Consensus size: 40
284648 CGCGAACACA
* * *
284658 TAAATCGCAACGCGTATCCGTAAATCGCAACG-TGTATCCG
1 TAAATCGCAACGAGAATCCGTAAATCGCAACGAT-AATCCG
* * * * * *
284698 TATATCGCAACGCGTATCCGTAAATCGCAATG-TGTATCTG
1 TAAATCGCAACGAGAATCCGTAAATCGCAACGAT-AATCCG
* * *
284738 TATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCG
1 TAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCG
*
284778 TAAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCG
1 TAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCG
*
284818 TAAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCG
1 TAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCG
* *
284858 TAAATCGCAACGAGAATCTGTAAATCACAAC
1 TAAATCGCAACGAGAATCCGTAAATCGCAAC
284889 ACTGAAATTT
Statistics
Matches: 179, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
40 178 0.99
41 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (40 bp):
TAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCG
Found at i:285610 original size:24 final size:24
Alignment explanation
Indices: 285571--285617 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
285561 AAATTTGGTC
285571 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
285595 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
285618 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:288100 original size:33 final size:34
Alignment explanation
Indices: 288049--288213 Score: 183
Period size: 33 Copynumber: 4.7 Consensus size: 34
288039 CGGAAATTAC
* *
288049 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
*
288082 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGC-GAAATGAA
288116 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C--AATGAAAATCGCAATGCGAAATGAA
* *
288154 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
288187 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAA--C--AATGAAAATCGCAA
288214 CGAGAGAATC
Statistics
Matches: 113, Mismatches: 7, Indels: 19
0.81 0.05 0.14
Matches are distributed among these distances:
32 1 0.01
33 50 0.44
34 16 0.14
35 1 0.01
36 2 0.02
37 1 0.01
38 26 0.23
39 16 0.14
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAACAATGAAAATCGCAATGCGAAATGAA
Found at i:288132 original size:19 final size:19
Alignment explanation
Indices: 288063--288251 Score: 210
Period size: 19 Copynumber: 10.7 Consensus size: 19
288053 GCAACGAGAG
288063 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
288082 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
288096 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
288116 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
288135 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
288154 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
288168 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
288187 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
288206 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
* *
288220 AATCACAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
288239 AATCGCATTGCGA
1 AATCGCAATGCGA
288252 TTCTCCCGTT
Statistics
Matches: 144, Mismatches: 10, Indels: 32
0.77 0.05 0.17
Matches are distributed among these distances:
14 31 0.22
15 2 0.01
16 5 0.03
17 5 0.03
18 2 0.01
19 83 0.58
20 16 0.11
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:288190 original size:52 final size:52
Alignment explanation
Indices: 288049--288251 Score: 272
Period size: 52 Copynumber: 3.9 Consensus size: 52
288039 CGGAAATTAC
*
288049 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C---ATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
288096 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
288154 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
* * *
288206 AATCGCAACGAGAGAATCACAATGCGAAATTAAAATCGCATTGCGA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
288252 TTCTCCCGTT
Statistics
Matches: 139, Mismatches: 6, Indels: 17
0.86 0.04 0.10
Matches are distributed among these distances:
47 8 0.06
49 1 0.01
50 1 0.01
52 84 0.60
53 29 0.21
55 2 0.01
56 1 0.01
58 13 0.09
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:288300 original size:19 final size:19
Alignment explanation
Indices: 288260--288357 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
288250 GATTCTCCCG
288260 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
288280 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
288299 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
288313 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
288332 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
288351 TTGCGAT
1 TTGCGAT
288358 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:288354 original size:52 final size:53
Alignment explanation
Indices: 288241--288357 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
288231 GAAATTAAAA
288241 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
*
288294 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
288346 TCGCATTGCGAT
1 TCGCATTGCGAT
288358 AGTCAATTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.48
53 33 0.52
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:288483 original size:14 final size:14
Alignment explanation
Indices: 288464--288500 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
288454 CATCAATTAC
288464 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
288478 ACAAATCATCTTTT
1 ACAAATCAACTTTT
288492 ACAAATCAA
1 ACAAATCAA
288501 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:290496 original size:14 final size:14
Alignment explanation
Indices: 290477--290533 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
290467 GCGAAATGAA
*
290477 AATCGCAACGACAG
1 AATCGCAACGAAAG
290491 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
290508 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
290524 AATCGCAACG
1 AATCGCAACG
290534 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:290504 original size:33 final size:33
Alignment explanation
Indices: 290458--290550 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
290448 GCGAAACCAA
*
290458 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
290491 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
290524 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
290551 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:290515 original size:19 final size:19
Alignment explanation
Indices: 290421--290555 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
290411 TAGTTTACTT
* *
290421 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
290441 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
290460 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
290479 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
290493 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
290512 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
290526 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
290545 TCGCAATGCGA
1 TCGCAACGCGA
290556 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:290573 original size:19 final size:19
Alignment explanation
Indices: 290551--290679 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
290541 AAAATCGCAA
290551 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
290570 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
290584 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
290603 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
290617 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
290636 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
290655 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
290675 TGCGA
1 TGCGA
290680 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:290593 original size:33 final size:33
Alignment explanation
Indices: 290551--290642 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
290541 AAAATCGCAA
290551 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
290584 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
290617 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
290643 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:290843 original size:93 final size:93
Alignment explanation
Indices: 290727--291288 Score: 1108
Period size: 93 Copynumber: 6.1 Consensus size: 93
290717 ATGGATTGCA
290727 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
290791 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
290819 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
290884 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
290912 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
290977 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
291005 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
291070 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
291098 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
291163 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
291191 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
291256 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
291284 TTACT
1 TTACT
291289 AAGCAATCTA
Statistics
Matches: 468, Mismatches: 1, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
92 4 0.01
93 464 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Done.