Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold495
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: 586005
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 2 of 5
Found at i:154755 original size:52 final size:51
Alignment explanation
Indices: 154614--154762 Score: 201
Period size: 52 Copynumber: 2.9 Consensus size: 51
154604 CGAAATATGA
*
154614 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
* * *
154666 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATAGATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
* *
154718 AAATTTGCTTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
154763 ATGTATCGAT
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.98
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
Found at i:154769 original size:13 final size:13
Alignment explanation
Indices: 154751--154775 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
154741 CAAAGATCAG
154751 TGTATCGATACAA
1 TGTATCGATACAA
154764 TGTATCGATACA
1 TGTATCGATACA
154776 TTTTTTGGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:154829 original size:33 final size:33
Alignment explanation
Indices: 154751--154859 Score: 111
Period size: 33 Copynumber: 3.3 Consensus size: 33
154741 CAAAGATCAG
154751 TGTATCGATACAA-TGTATCGATACAT-TTTTTGGCA
1 TGTATCGATA-AATTGTATCGATACATATTTTT---A
* *
154786 -GTAGC-TTAAATTGTATCGATACATATTTTTA
1 TGTATCGATAAATTGTATCGATACATATTTTTA
*
154817 TGTATCGATAAATTGTATCGATACA-ACATTTTA
1 TGTATCGATAAATTGTATCGATACATA-TTTTTA
154850 TGTATCGATA
1 TGTATCGATA
154860 TAAATCATTG
Statistics
Matches: 64, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
31 1 0.02
32 7 0.11
33 47 0.73
34 9 0.14
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (33 bp):
TGTATCGATAAATTGTATCGATACATATTTTTA
Found at i:155636 original size:52 final size:53
Alignment explanation
Indices: 155536--155703 Score: 144
Period size: 53 Copynumber: 3.2 Consensus size: 53
155526 TATTGGGTTC
* * * * *
155536 AAAGATGAGAAAAAGGATGTCAATGTGCTGATTCACGGTCAGCGACATT-AGAATT
1 AAAGATGAG-AAAA--ATGCCAATGTGCTGATTCAAGGCCAACAACATTGAGAATT
* * **
155591 GAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAACAACATTGGGTTTT
1 AAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAACAACATTGAGAATT
** * * * *
155644 AAAGATGATG-AAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTG-GACTT
1 AAAGATGA-GAAAAATGCCAATGTGCTGATTCAAGGCCAACAACATTGAGAATT
155696 AAAGATGA
1 AAAGATGA
155704 AGGTGAGAAA
Statistics
Matches: 94, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
52 39 0.41
53 42 0.45
54 5 0.05
55 8 0.09
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.24
Consensus pattern (53 bp):
AAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAACAACATTGAGAATT
Found at i:155811 original size:55 final size:52
Alignment explanation
Indices: 155752--155955 Score: 225
Period size: 43 Copynumber: 4.1 Consensus size: 52
155742 ACGACCAACG
* * *
155752 ATATTGGGCTTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCAAGGCCAGCT
1 ATATTGGACTTAAAGATG-G-AAAAGG-TGCCAATATGCTGATTCAAGGCCAGCT
*
155807 ATATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCT
1 ATATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCT
* *
155859 ATATTGGAC-T-----T---AAAGGTGCCAATGTGCTGATTCAAGGCTAGCT
1 ATATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCT
* *
155902 ACATTGGACTTAAAGAT---AAAGGTGCCAATATGCTGATTCAAGGCCAGCG
1 ATATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCT
155951 ATATT
1 ATATT
155956 AGGTTTAGAA
Statistics
Matches: 131, Mismatches: 12, Indels: 18
0.81 0.07 0.11
Matches are distributed among these distances:
43 38 0.29
44 1 0.01
46 1 0.01
49 34 0.26
51 1 0.01
52 33 0.25
53 6 0.05
54 1 0.01
55 16 0.12
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (52 bp):
ATATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCT
Found at i:155974 original size:95 final size:93
Alignment explanation
Indices: 155774--155955 Score: 285
Period size: 95 Copynumber: 1.9 Consensus size: 93
155764 AAGATGAGAA
* *
155774 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTATATTGAACTTAAAGATGGAAAAGGTGCCAAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGAT-G-AAAGGTGCCAAT
*
155839 ATGCTGATTCAAGGCCAGCTATATTGGACTT
63 ATGCTGATTCAAGGCCAGCGATATTGGACTT
* *
155870 AAAGGTGCCAATGTGCTGATTCAAGGCTAGCTACATTGGACTTAAAGAT-AAAGGTGCCAATATG
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAAGGTGCCAATATG
155934 CTGATTCAAGGCCAGCGATATT
66 CTGATTCAAGGCCAGCGATATT
155956 AGGTTTAGAA
Statistics
Matches: 81, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
92 36 0.44
95 40 0.49
96 5 0.06
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.26
Consensus pattern (93 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAAGGTGCCAATATG
CTGATTCAAGGCCAGCGATATTGGACTT
Found at i:156063 original size:61 final size:64
Alignment explanation
Indices: 155962--156127 Score: 241
Period size: 65 Copynumber: 2.6 Consensus size: 64
155952 TATTAGGTTT
*
155962 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT-GAGAAGGGTTGCCA-CG-TTGTGTGGGCTTT-A
1 AGAA-GGTTGCCACCGACTTGTGTGGGCTTTAGAG-GGGGTTGCCACCGATTGTGTGGGCTTTGA
*
156023 G
64 A
*
156024 AGAAGGTTGCCACCAACTTGTGTGGGCTTTAGAGGGGGTTGCCACCGACTTGTGTGGGCTTTGAA
1 AGAAGGTTGCCACCGACTTGTGTGGGCTTTAGAGGGGGTTGCCACCGA-TTGTGTGGGCTTTGAA
*
156089 AGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGGGGGT
1 AGAAGGTTGCCACCGACTTGTGTGGGCTTTAGAGGGGGT
156128 GAAAGATGCC
Statistics
Matches: 94, Mismatches: 5, Indels: 7
0.89 0.05 0.07
Matches are distributed among these distances:
61 34 0.36
62 9 0.10
64 13 0.14
65 38 0.40
ACGTcount: A:0.17, C:0.17, G:0.39, T:0.28
Consensus pattern (64 bp):
AGAAGGTTGCCACCGACTTGTGTGGGCTTTAGAGGGGGTTGCCACCGATTGTGTGGGCTTTGAA
Found at i:156101 original size:33 final size:32
Alignment explanation
Indices: 155959--156127 Score: 240
Period size: 32 Copynumber: 5.4 Consensus size: 32
155949 CGATATTAGG
155959 TTTAGA-AGGGTTGCCACCGACTTGTGTGGGC
1 TTTAGAGAGGGTTGCCACCGACTTGTGTGGGC
155990 TTT-GAGAAGGGTTGCCA-CG--TTGTGTGGGC
1 TTTAGAG-AGGGTTGCCACCGACTTGTGTGGGC
* *
156019 TTTAGAGAAGGTTGCCACCAACTTGTGTGGGC
1 TTTAGAGAGGGTTGCCACCGACTTGTGTGGGC
*
156051 TTTAGAGGGGGTTGCCACCGACTTGTGTGGGC
1 TTTAGAGAGGGTTGCCACCGACTTGTGTGGGC
*
156083 TTTGAAAGAGGGTTGCCACCGACTTGTGTGGGC
1 TTT-AGAGAGGGTTGCCACCGACTTGTGTGGGC
*
156116 TTTAGAGGGGGT
1 TTTAGAGAGGGT
156128 GAAAGATGCC
Statistics
Matches: 122, Mismatches: 9, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
29 22 0.18
30 6 0.05
31 5 0.04
32 59 0.48
33 30 0.25
ACGTcount: A:0.17, C:0.17, G:0.38, T:0.29
Consensus pattern (32 bp):
TTTAGAGAGGGTTGCCACCGACTTGTGTGGGC
Found at i:156195 original size:34 final size:33
Alignment explanation
Indices: 156129--156459 Score: 292
Period size: 34 Copynumber: 10.0 Consensus size: 33
156119 AGAGGGGGTG
* *
156129 AAAGATGCCACGGAGTTGTGGAC-TTAAAAGGA
1 AAAGGTGCCACGAAGTTGTGGACTTTAAAAGGA
156161 ACAAGGTGCCACGAAGTTGTGGACTTTAAAAGGAA
1 A-AAGGTGCCACGAAGTTGTGGACTTTAAAAGG-A
*
156196 AAAGGTGCCACGAAGTTGTGGAC-TTAGAAGGAA
1 AAAGGTGCCACGAAGTTGTGGACTTTAAAAGG-A
* *
156229 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGGGA
1 AAAG-GTGCCACGAAGTTGTGGACTTTAAAA--GGA
*
156265 AAAGAGTGCCACAGAA-TTGTGGGCTTTAAAA-G-
1 AAAG-GTGCCAC-GAAGTTGTGGACTTTAAAAGGA
*
156297 ---GGTGCCAC-AGAGTTGTGGAC-TTAGAAGGA
1 AAAGGTGCCACGA-AGTTGTGGACTTTAAAAGGA
* * *
156326 AAAGGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAA-G-GTGCCACGAAGTTGTGGACTTT-AAAAGGA
156362 AAAGGTGCCACGAAGTTGTGGA-TTTAAAAGGA
1 AAAGGTGCCACGAAGTTGTGGACTTTAAAAGGA
* * **
156394 AAAGAGTGCCACGTAGTTGTGGGCTTT-GCA-GA
1 AAAG-GTGCCACGAAGTTGTGGACTTTAAAAGGA
* *
156426 AAAGGATGCCACTAAGTCGTGGACTTTAAGAAGG
1 AAAGG-TGCCACGAAGTTGTGGACTTTAA-AAGG
156460 TATTTGAAGA
Statistics
Matches: 247, Mismatches: 26, Indels: 49
0.77 0.08 0.15
Matches are distributed among these distances:
26 1 0.00
27 6 0.02
28 15 0.06
29 1 0.00
31 1 0.00
32 34 0.14
33 55 0.22
34 83 0.34
35 11 0.04
36 36 0.15
37 4 0.02
ACGTcount: A:0.34, C:0.13, G:0.33, T:0.21
Consensus pattern (33 bp):
AAAGGTGCCACGAAGTTGTGGACTTTAAAAGGA
Found at i:156321 original size:98 final size:95
Alignment explanation
Indices: 156129--156392 Score: 331
Period size: 98 Copynumber: 2.7 Consensus size: 95
156119 AGAGGGGGTG
* *
156129 AAAGA-TGCCACGGAGTTGTGGAC-TTAAAAGGAACAAGGTGCCACGAAGTTGTGGACTTTAAAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAA-AAGGTGCCACGAAGTTGTGGGCTTTAAAA
156192 GGAAAAAGGTGCCACGAAGTTGTGGACTTAGAAGGAA
65 -G-----GGTGCCACGAAGTTGTGGACTTAGAAGGAA
156229 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGGGAAAAGAGTGCCACAGAA-TTGTGGGCTTTA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAA--GGAAAAG-GTGCCAC-GAAGTTGTGGGCTTTA
156293 AAAGGGTGCCAC-AGAGTTGTGGACTTAGAAGGAA
62 AAAGGGTGCCACGA-AGTTGTGGACTTAGAAGGAA
* * *
156327 AAGGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGAAGTTGT-GGATTTAAAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAGGAAAAGGTGCCACGAAGTTGTGGGCTTTAAAA
156391 GG
65 GG
156393 AAAAGAGTGC
Statistics
Matches: 150, Mismatches: 5, Indels: 23
0.84 0.03 0.13
Matches are distributed among these distances:
95 14 0.09
96 11 0.07
97 7 0.05
98 54 0.36
99 4 0.03
100 5 0.03
101 17 0.11
102 6 0.04
103 4 0.03
104 25 0.17
105 3 0.02
ACGTcount: A:0.35, C:0.12, G:0.33, T:0.20
Consensus pattern (95 bp):
AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAGGTGCCACGAAGTTGTGGGCTTTAAAAG
GGTGCCACGAAGTTGTGGACTTAGAAGGAA
Found at i:156580 original size:8 final size:8
Alignment explanation
Indices: 156567--156602 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
156557 AGGATGTTAT
*
156567 TGATGTTA
1 TGATGTCA
156575 TGATGTCA
1 TGATGTCA
*
156583 TAATGTCA
1 TGATGTCA
156591 TGATGTCA
1 TGATGTCA
156599 TGAT
1 TGAT
156603 TACAGCACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.42
Consensus pattern (8 bp):
TGATGTCA
Found at i:157445 original size:30 final size:30
Alignment explanation
Indices: 157411--157471 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 30
157401 TGAAAAGGGG
* *
157411 TTTTTCCCTTTTTTTTTTTGTTTC-TTCTT
1 TTTTTTCCTTTTTTGTTTTGTTTCTTTCTT
157440 TTTTTTCCTTTTTTGTTTTGTTTCTTTCTT
1 TTTTTTCCTTTTTTGTTTTGTTTCTTTCTT
157470 TT
1 TT
157472 GGAAAAGAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (30 bp):
TTTTTTCCTTTTTTGTTTTGTTTCTTTCTT
Found at i:157466 original size:16 final size:15
Alignment explanation
Indices: 157420--157471 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 15
157410 GTTTTTCCCT
157420 TTTTTTTTTTGTTTC
1 TTTTTTTTTTGTTTC
* *
157435 -TTCTTTTTT-TTCC
1 TTTTTTTTTTGTTTC
157448 TTTTTTGTTTTGTTTC
1 TTTTTT-TTTTGTTTC
157464 TTTCTTTT
1 TTT-TTTT
157472 GGAAAAGAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
13 3 0.10
14 12 0.41
15 4 0.14
16 7 0.24
17 3 0.10
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.83
Consensus pattern (15 bp):
TTTTTTTTTTGTTTC
Found at i:157727 original size:12 final size:11
Alignment explanation
Indices: 157710--157761 Score: 68
Period size: 12 Copynumber: 4.5 Consensus size: 11
157700 CCTTTGCACC
*
157710 TTTTTTCTGTGT
1 TTTTTTTTGT-T
157722 TTTTTTTTGTT
1 TTTTTTTTGTT
157733 TTTGTTTTTGTT
1 TTT-TTTTTGTT
157745 TTTGTTTTTGTT
1 TTT-TTTTTGTT
157757 TTTTT
1 TTTTT
157762 CATCACTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
11 6 0.16
12 32 0.84
ACGTcount: A:0.00, C:0.02, G:0.13, T:0.85
Consensus pattern (11 bp):
TTTTTTTTGTT
Found at i:157736 original size:6 final size:6
Alignment explanation
Indices: 157721--157759 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
157711 TTTTTCTGTG
157721 TTTT-T TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTT
157760 TTCATCACTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.12
6 29 0.88
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (6 bp):
TTTTGT
Found at i:164701 original size:52 final size:52
Alignment explanation
Indices: 164623--164751 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
164613 CGAAATATGA
*
164623 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
* *
164675 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
164727 AAATTTACCTGCATGTATCGATACA
1 AAATTTACCTGCATGTATCGATACA
164752 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (52 bp):
AAATTTACCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
Found at i:164764 original size:52 final size:51
Alignment explanation
Indices: 164623--164771 Score: 219
Period size: 52 Copynumber: 2.9 Consensus size: 51
164613 CGAAATATGA
164623 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
* * *
164675 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
*
164727 AAATTTACCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTACCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
164772 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 86 0.98
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (51 bp):
AAATTTACCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
Found at i:164778 original size:13 final size:13
Alignment explanation
Indices: 164760--164797 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
164750 CAAAGATCAG
164760 TGTATCGATACAA
1 TGTATCGATACAA
164773 TGTATCGATACAA
1 TGTATCGATACAA
164786 TGTATCGATACA
1 TGTATCGATACA
164798 TTTGAGTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:165983 original size:49 final size:49
Alignment explanation
Indices: 165759--166256 Score: 507
Period size: 49 Copynumber: 10.3 Consensus size: 49
165749 TGAGACAAGT
* * * * * * *
165759 GATAAAGATGCCAATATGTTGATTCACGACCAACGATATTGGGCTTAAA
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
* * * *
165808 GATGAGAAAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
1 GAT-----AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
165863 GATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T---
1 GAT---AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
* *
165911 --TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
* *
165958 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGACTT---
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
* *
166004 G---AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
*
166050 GA-AGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAG
1 GATA-AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
*
166099 GA-AGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAG
1 GATA-AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
*
166148 GA-AGAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T---
1 GATA-AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
* * *
166193 --TAAAGGTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAA
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
166240 GATGAAAAAGGTGCCAA
1 GAT---AAAGGTGCCAA
166257 GCGGCGCCCG
Statistics
Matches: 387, Mismatches: 34, Indels: 53
0.82 0.07 0.11
Matches are distributed among these distances:
43 113 0.29
44 3 0.01
46 3 0.01
48 1 0.00
49 178 0.46
51 1 0.00
52 43 0.11
53 7 0.02
54 4 0.01
55 34 0.09
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (49 bp):
GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
Found at i:166003 original size:92 final size:92
Alignment explanation
Indices: 165816--166256 Score: 643
Period size: 92 Copynumber: 4.7 Consensus size: 92
165806 AAGATGAGAA
* *
165816 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT---AAAGGTGCCAAT
165881 ATGCTGATTCAAGGCCAGCTATATTGGACTT
62 ATGCTGATTCAAGGCCAGCTATATTGGACTT
165912 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
* *
165977 TGATTCAAGGCCAGCGATATTAGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
*
166004 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-AGAAGGTGCCAATATG
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATA-AAGGTGCCAATATG
166068 CTGATTCAAGGCCAGCTATATTGGACTT
65 CTGATTCAAGGCCAGCTATATTGGACTT
* * * *
166096 AAGGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAGGA-AGAAAGTGCC
1 -----A-AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATA-AAGGTGCC
166160 AATATGCTGATTCAAGGCCAGCTATATTGGACTT
59 AATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
166194 AAAGGTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAAGATGAAAAAGGTGCCAA
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT---AAAGGTGCCAA
166257 GCGGCGCCCG
Statistics
Matches: 317, Mismatches: 17, Indels: 23
0.89 0.05 0.06
Matches are distributed among these distances:
91 1 0.00
92 171 0.54
93 1 0.00
95 51 0.16
96 6 0.02
98 87 0.27
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
TGATTCAAGGCCAGCTATATTGGACTT
Found at i:166161 original size:190 final size:185
Alignment explanation
Indices: 165816--166256 Score: 661
Period size: 190 Copynumber: 2.3 Consensus size: 185
165806 AAGATGAGAA
* *
165816 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA--GAAAAGGTGCCAAT
*
165881 ATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTAC
63 ATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATATGCTGATTCAAGGCCAGCTAC
*
165946 ATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGACTT
128 ATTGGACTTAAAGATAAAAGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGACTT
* *
166004 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-AGAAGGTGCCAATATG
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAGAAAAGGTGCCAATATG
166068 CTGATTCAAGGCCAGCTATATTGGACTTAAGGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGC
66 CTGATTCAAGGCCAGCTATATTGGACTT-----A-AAGGTGCCAATATGCTGATTCAAGGCCAGC
* * * *
166133 TATATTGGACTTAAGGA-AGAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
125 TACATTGGACTTAAAGATA-AAAGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGACTT
*
166194 AAAGGTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAAGATGAAAAAGGTGCCAA
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-G-AAAAGGTGCCAA
166257 GCGGCGCCCG
Statistics
Matches: 230, Mismatches: 13, Indels: 15
0.89 0.05 0.06
Matches are distributed among these distances:
184 43 0.19
187 41 0.18
188 4 0.02
189 2 0.01
190 129 0.56
193 11 0.05
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (185 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAGAAAAGGTGCCAATATG
CTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATT
GGACTTAAAGATAAAAGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGACTT
Found at i:171366 original size:25 final size:27
Alignment explanation
Indices: 171338--171391 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 27
171328 ATATAAAAAT
*
171338 ATTAATATAAT-ATATTT-TAAATGAA
1 ATTAATATAATAAAATTTATAAATGAA
*
171363 ATTAATTTAATAAAATTTATAAATGAA
1 ATTAATATAATAAAATTTATAAATGAA
171390 AT
1 AT
171392 AAAAATATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 10 0.40
26 5 0.20
27 10 0.40
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (27 bp):
ATTAATATAATAAAATTTATAAATGAA
Found at i:172483 original size:11 final size:11
Alignment explanation
Indices: 172464--172493 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
172454 TGATTTAATG
*
172464 ATTATATAAAA
1 ATTAAATAAAA
172475 ATTAAATAAAA
1 ATTAAATAAAA
172486 ATTAAATA
1 ATTAAATA
172494 GTTAAATATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
ATTAAATAAAA
Found at i:174158 original size:27 final size:27
Alignment explanation
Indices: 174127--174180 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
174117 TAAAATTATC
* *
174127 AACATCAATAAATCTCAAAATACTAAT
1 AACATCAACAAATCTCAAAATAATAAT
174154 AACATCAACAAATCTCAAAATAATAAT
1 AACATCAACAAATCTCAAAATAATAAT
174181 CATTTGTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.57, C:0.19, G:0.00, T:0.24
Consensus pattern (27 bp):
AACATCAACAAATCTCAAAATAATAAT
Found at i:175777 original size:2 final size:2
Alignment explanation
Indices: 175770--175795 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
175760 AAGAGATGCT
175770 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
175796 GGTGACGACA
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):
TA
Found at i:175779 original size:259 final size:260
Alignment explanation
Indices: 175308--175777 Score: 732
Period size: 259 Copynumber: 1.8 Consensus size: 260
175298 ATTCAAGGAT
* * *
175308 TATGTAACATCTTGTATCATTAAATATTTTTAACTGATTTTTTTTGTTTAAATCTTCGATTTTAA
1 TATGTAACACCTTGTATCATTAAATATTTTTAACTGATTTTTTTTATTTAAATCTTCGATCTTAA
* * * *
175373 GATGCAAATCAAGATTAGCTATTAGACTTAAAATTTAAGACACAATTAAACCTAATTGTTAGTTC
66 GATGCAAATCAAGATTAACTATTAGACTTAAAATTTAACACACAAATAAACCTAATTGTCAGTTC
** * *
175438 ATACTCATGTTACCGCACCTAGTCTAATCACATAGAAAATGTCAATAGCTATGAAAAATGTAGAA
131 ATACTCATGCGACCGCACCTAATCTAATCACATAGAAAAGGTCAATAGCTATGAAAAATGTAGAA
175503 GAGAGATACTGATATATAGGTGATGACATCGCTTTAGAAAAATAATAAATTGGTTAATTTAAGAA
196 GAGAGATACTGATATATAGGTGATGACATCGCTTTAGAAAAATAATAAATTGGTTAATTTAAGAA
*
175568 TATGTAACACCTTGTATCATTAAATATTTTTAATTGA-TTTTTTTATTTAAATCTTC-ATCCTTA
1 TATGTAACACCTTGTATCATTAAATATTTTTAACTGATTTTTTTTATTTAAATCTTCGAT-CTTA
* * **
175631 ATATGCAAATCAAGATTAATTATTAGACTTAAAATTTAACACACAAATAAATTTAATTGTCAGTT
65 AGATGCAAATCAAGATTAACTATTAGACTTAAAATTTAACACACAAATAAACCTAATTGTCAGTT
*
175696 CATACTCATGCGACCGCACCTAATCTAATCACATAGAAAAGGTCAATAGCTGTGAAAAATGTA-A
130 CATACTCATGCGACCGCACCTAATCTAATCACATAGAAAAGGTCAATAGCTATGAAAAATGTAGA
* *
175760 A-AGAGATGCTTATATATA
195 AGAGAGATACTGATATATA
175778 TATATATATA
Statistics
Matches: 190, Mismatches: 19, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
257 15 0.08
258 4 0.02
259 136 0.72
260 35 0.18
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (260 bp):
TATGTAACACCTTGTATCATTAAATATTTTTAACTGATTTTTTTTATTTAAATCTTCGATCTTAA
GATGCAAATCAAGATTAACTATTAGACTTAAAATTTAACACACAAATAAACCTAATTGTCAGTTC
ATACTCATGCGACCGCACCTAATCTAATCACATAGAAAAGGTCAATAGCTATGAAAAATGTAGAA
GAGAGATACTGATATATAGGTGATGACATCGCTTTAGAAAAATAATAAATTGGTTAATTTAAGAA
Found at i:176936 original size:19 final size:20
Alignment explanation
Indices: 176890--176937 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
176880 ATTACATATA
176890 AAAATTAAAAATATTTATTTT
1 AAAATT-AAAATATTTATTTT
*
176911 AATAATTAATATATTT-TTTT
1 AA-AATTAAAATATTTATTTT
176931 AAAATTA
1 AAAATTA
176938 TGAAACATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 5 0.20
20 6 0.24
21 10 0.40
22 4 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AAAATTAAAATATTTATTTT
Found at i:187405 original size:21 final size:22
Alignment explanation
Indices: 187366--187410 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
187356 AGTATAATAT
* *
187366 TATATATTTATTTTTTATATGA
1 TATATATTTATTCTTTATAAGA
187388 TATATATTTA-TCTTTATAAGA
1 TATATATTTATTCTTTATAAGA
187409 TA
1 TA
187411 AAAATTACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (22 bp):
TATATATTTATTCTTTATAAGA
Found at i:187897 original size:30 final size:30
Alignment explanation
Indices: 187862--187920 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
187852 CATGAAATAT
187862 TGAAAATATTTTATTCATTTTGAATGAAAC
1 TGAAAATATTTTATTCATTTTGAATGAAAC
187892 TGAAAATATTTTATTCATTTTGAATGAAA
1 TGAAAATATTTTATTCATTTTGAATGAAA
187921 TTATTTGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (30 bp):
TGAAAATATTTTATTCATTTTGAATGAAAC
Found at i:188332 original size:33 final size:34
Alignment explanation
Indices: 188287--188358 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 34
188277 AGAATAGTAC
*
188287 ATAAA-TATTT-AAATATTTCAAAATTTATAT-TAT
1 ATAAATTATTTAAAATATTT--AAATTTATATAAAT
188320 ATAAATTA-TTAAAATATTTAAATTTATATAAAT
1 ATAAATTATTTAAAATATTTAAATTTATATAAAT
188353 ATAAAT
1 ATAAAT
188359 ATATAATAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
32 10 0.29
33 15 0.43
34 10 0.29
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (34 bp):
ATAAATTATTTAAAATATTTAAATTTATATAAAT
Found at i:188373 original size:32 final size:33
Alignment explanation
Indices: 188307--188389 Score: 84
Period size: 32 Copynumber: 2.5 Consensus size: 33
188297 AAATATTTCA
* *
188307 AAATTTATAT-TATATAAATTATTAAAATATTT
1 AAATTTATATAAATATAAATTATTAAAATACTT
*
188339 AAATTTATATAAATATAAA-TA-TATAATAACTT
1 AAATTTATATAAATATAAATTATTAAAAT-ACTT
188371 AAATATTAT-TATAATATAA
1 AAAT-TTATATA-AATATAA
188390 TAAAATACAT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
31 5 0.11
32 21 0.48
33 18 0.41
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (33 bp):
AAATTTATATAAATATAAATTATTAAAATACTT
Found at i:190052 original size:14 final size:14
Alignment explanation
Indices: 190002--190054 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
189992 ATTCATACTT
*
190002 TAATTATAATAAATAT
1 TAATTAT-A-AAATAA
*
190018 TAATTAAAAAATAA
1 TAATTATAAAATAA
*
190032 AAATTATAAAATAA
1 TAATTATAAAATAA
190046 TAATTATAA
1 TAATTATAA
190055 TATTATATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 25 0.78
15 1 0.03
16 6 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TAATTATAAAATAA
Found at i:191027 original size:25 final size:24
Alignment explanation
Indices: 190999--191048 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
190989 ATATTTTCAG
*
190999 ATTTAATAATTTTAAATATGACATA
1 ATTTAATAA-TATAAATATGACATA
*
191024 ATTTCATAATATAAATATGACATA
1 ATTTAATAATATAAATATGACATA
191048 A
1 A
191049 AAAATTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (24 bp):
ATTTAATAATATAAATATGACATA
Found at i:191210 original size:6 final size:6
Alignment explanation
Indices: 191199--191230 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
191189 GATATTTGTC
*
191199 ATATAA ATATAA ATATAA TTATAA ATATAA AT
1 ATATAA ATATAA ATATAA ATATAA ATATAA AT
191231 GTATGTAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
ATATAA
Found at i:191769 original size:21 final size:18
Alignment explanation
Indices: 191745--191788 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 18
191735 TATTTTTATT
191745 TAAACTTTTTTAAATATTAAA
1 TAAA-TTTTTT-AAT-TTAAA
191766 TAAATTTTTTAATTTAAA
1 TAAATTTTTTAATTTAAA
191784 TAAAT
1 TAAAT
191789 AATTTAACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.43
19 3 0.13
20 6 0.26
21 4 0.17
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
TAAATTTTTTAATTTAAA
Found at i:191794 original size:18 final size:18
Alignment explanation
Indices: 191761--191795 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
191751 TTTTTAAATA
**
191761 TTAAATAAATTTTTTAAT
1 TTAAATAAATAATTTAAT
191779 TTAAATAAATAATTTAA
1 TTAAATAAATAATTTAA
191796 CTCATAAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTAAATAAATAATTTAAT
Found at i:194001 original size:62 final size:61
Alignment explanation
Indices: 193928--194050 Score: 194
Period size: 62 Copynumber: 2.0 Consensus size: 61
193918 ATATTGGTAC
*
193928 GTATTAATTAGTATCGATTG-ATATAAAATTTCGATTTTAATTTTTAAATTTTTACTTGTTTG
1 GTATTAATTAGTATCGA-TGAATATAAAATTTCGATTTTAATTTTTAAA-ATTTACTTGTTTG
* *
193990 GTATTAGTTAGTATCGATGAATATAAAATTTTGATTTTAATTTTTAAAATTTACTTGTTTG
1 GTATTAATTAGTATCGATGAATATAAAATTTCGATTTTAATTTTTAAAATTTACTTGTTTG
194051 ATTTTTTTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
61 14 0.25
62 43 0.75
ACGTcount: A:0.32, C:0.04, G:0.12, T:0.52
Consensus pattern (61 bp):
GTATTAATTAGTATCGATGAATATAAAATTTCGATTTTAATTTTTAAAATTTACTTGTTTG
Found at i:197260 original size:25 final size:25
Alignment explanation
Indices: 197171--197261 Score: 73
Period size: 25 Copynumber: 3.6 Consensus size: 25
197161 TTCAATTAAG
* *
197171 ATTTTTTTATTATTTT-ATTATAAA-
1 ATTTTATT-TTATTTTAATTTTAAAT
*
197195 ATTTTATTTATGATTATTAACTTT-AAT
1 ATTTTATTT-T-ATT-TTAATTTTAAAT
* *
197222 -TTTAATTTTCTTTTAATTTTAAAT
1 ATTTTATTTTATTTTAATTTTAAAT
197246 ATTTTATTTTATTTTA
1 ATTTTATTTTATTTTA
197262 TCTTATTTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
23 8 0.15
24 13 0.25
25 17 0.33
26 11 0.21
27 3 0.06
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (25 bp):
ATTTTATTTTATTTTAATTTTAAAT
Found at i:198352 original size:31 final size:31
Alignment explanation
Indices: 198308--198367 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
198298 TCCTAGGCTG
* *
198308 ATTTTGGAATATTTTCATGTATTTTAGATGC
1 ATTTTGGAATATTTTCAAGCATTTTAGATGC
**
198339 ATTTTGGTGTATTTTCAAGCATTTTAGAT
1 ATTTTGGAATATTTTCAAGCATTTTAGAT
198368 TGTTTAGGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.25, C:0.07, G:0.17, T:0.52
Consensus pattern (31 bp):
ATTTTGGAATATTTTCAAGCATTTTAGATGC
Found at i:203512 original size:15 final size:15
Alignment explanation
Indices: 203443--203513 Score: 54
Period size: 15 Copynumber: 4.5 Consensus size: 15
203433 TTATGAGAGG
203443 TTATTTTAGGTTTAAA
1 TTATTTTA-GTTTAAA
* **
203459 -TATTTTGAATTTTGA
1 TTATTTT-AGTTTAAA
*
203474 TAATTTTAGATTTAATA
1 TTATTTTAG-TTTAA-A
*
203491 TTTTTTTAGTTTAAA
1 TTATTTTAGTTTAAA
203506 TTATTTTA
1 TTATTTTA
203514 AATTCGAATT
Statistics
Matches: 41, Mismatches: 10, Indels: 9
0.68 0.17 0.15
Matches are distributed among these distances:
15 19 0.46
16 14 0.34
17 8 0.20
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (15 bp):
TTATTTTAGTTTAAA
Found at i:203773 original size:18 final size:18
Alignment explanation
Indices: 203750--203784 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
203740 CATAAAAAAA
*
203750 TATATAAAATTAATTTGT
1 TATATAAAATAAATTTGT
203768 TATATAAAATAAATTTG
1 TATATAAAATAAATTTG
203785 CTAAATAATT
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:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (18 bp):
TATATAAAATAAATTTGT
Found at i:203792 original size:18 final size:18
Alignment explanation
Indices: 203753--203792 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
203743 AAAAAAATAT
* * *
203753 ATAAAATTAATTTGTTAT
1 ATAAAATAAATTTGCTAA
203771 ATAAAATAAATTTGCTAA
1 ATAAAATAAATTTGCTAA
203789 ATAA
1 ATAA
203793 TTGATTACAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.40
Consensus pattern (18 bp):
ATAAAATAAATTTGCTAA
Found at i:204484 original size:12 final size:12
Alignment explanation
Indices: 204467--204493 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
204457 GACACATCAC
204467 ATATATAAATAA
1 ATATATAAATAA
204479 ATATATAAATAA
1 ATATATAAATAA
204491 ATA
1 ATA
204494 AAATATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
ATATATAAATAA
Found at i:205394 original size:16 final size:16
Alignment explanation
Indices: 205360--205402 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
205350 TTTTGAAATG
* *
205360 TTTCAAAGTTAAATTA
1 TTTCAAATTTAAATCA
*
205376 TTTCAAATTTTAATCA
1 TTTCAAATTTAAATCA
*
205392 TTTTAAATTTA
1 TTTCAAATTTA
205403 TATTTTTATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (16 bp):
TTTCAAATTTAAATCA
Found at i:206100 original size:17 final size:18
Alignment explanation
Indices: 206078--206114 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
206068 TATTTTAAAA
*
206078 TTATTATT-ATAAATATT
1 TTATTATTAATAAAAATT
206095 TTATTATTAATAAAAATT
1 TTATTATTAATAAAAATT
206113 TT
1 TT
206115 GATTTTATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTATTATTAATAAAAATT
Found at i:206825 original size:25 final size:26
Alignment explanation
Indices: 206796--206852 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 26
206786 TTTATGTGAA
206796 AATTATATTAAATTATT-AT-AAAAATT
1 AATTAT-TTAAA-TATTAATGAAAAATT
*
206822 -ATTATTTTAATATTAATGAAAAATT
1 AATTATTTAAATATTAATGAAAAATT
206847 AATTAT
1 AATTAT
206853 GAAGATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 4 0.15
24 6 0.22
25 12 0.44
26 5 0.19
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (26 bp):
AATTATTTAAATATTAATGAAAAATT
Found at i:208964 original size:2 final size:2
Alignment explanation
Indices: 208957--208991 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
208947 AATTCTTCTT
208957 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 T
208992 TGTTATGGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:209202 original size:2 final size:2
Alignment explanation
Indices: 209197--209229 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
209187 TTTTTTTAAT
209197 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
209230 CATACCTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:210522 original size:19 final size:18
Alignment explanation
Indices: 210488--210526 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
210478 TTTCATTTAA
210488 TAATTTTAATAAAAAAAC
1 TAATTTTAATAAAAAAAC
210506 TAATTTTAATAAAAAAAC
1 TAATTTTAATAAAAAAAC
210524 TAA
1 TAA
210527 CTTAATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (18 bp):
TAATTTTAATAAAAAAAC
Found at i:210531 original size:17 final size:18
Alignment explanation
Indices: 210488--210533 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
210478 TTTCATTTAA
*
210488 TAATTTTAATAAAAAAAC
1 TAATCTTAATAAAAAAAC
*
210506 TAATTTTAATAAAAAAAC
1 TAATCTTAATAAAAAAAC
210524 TAA-CTTAATA
1 TAATCTTAATA
210534 TATATACATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 6 0.22
18 21 0.78
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (18 bp):
TAATCTTAATAAAAAAAC
Found at i:210685 original size:22 final size:21
Alignment explanation
Indices: 210643--210698 Score: 51
Period size: 22 Copynumber: 2.5 Consensus size: 21
210633 TCGGTTAGTT
*
210643 TAAAAAATTTAATTTATTAATAA
1 TAAAAAA-TTAATATATTAAT-A
*
210666 TAAAAAATTAATGATA-TAATT
1 TAAAAAATTAAT-ATATTAATA
210687 TAAAAAAATTAA
1 T-AAAAAATTAA
210699 AATTTATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 1 0.03
22 19 0.66
23 9 0.31
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
TAAAAAATTAATATATTAATA
Found at i:213474 original size:28 final size:28
Alignment explanation
Indices: 213461--213531 Score: 70
Period size: 32 Copynumber: 2.4 Consensus size: 28
213451 ATAAAAAATT
213461 AATATTAATTATAAATTTAATAAATATTA
1 AATA-TAATTATAAATTTAATAAATATTA
* *
213490 AATATAATTACTCATAACTTTGATGAATATTA
1 AATATAATTA-T-A-AA-TTTAATAAATATTA
*
213522 AACATAATTA
1 AATATAATTA
213532 CTCTTAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 6 0.17
29 5 0.14
30 1 0.03
31 2 0.06
32 21 0.60
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.41
Consensus pattern (28 bp):
AATATAATTATAAATTTAATAAATATTA
Found at i:214902 original size:49 final size:49
Alignment explanation
Indices: 214839--214937 Score: 153
Period size: 49 Copynumber: 2.0 Consensus size: 49
214829 GTCACGCAGG
* * * *
214839 AATGGGGACGAGGTTGATCAACATTTAAATTTGCAAGATAAAGAAGGTT
1 AATGGAGACAAGGTTCATCAACATTTAAATTTGCAAGATAAAAAAGGTT
*
214888 AATGGAGACAAGGTTCATCAACCTTTAAATTTGCAAGATAAAAAAGGTT
1 AATGGAGACAAGGTTCATCAACATTTAAATTTGCAAGATAAAAAAGGTT
214937 A
1 A
214938 TGTTTTTTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.26
Consensus pattern (49 bp):
AATGGAGACAAGGTTCATCAACATTTAAATTTGCAAGATAAAAAAGGTT
Found at i:217979 original size:29 final size:28
Alignment explanation
Indices: 217921--217975 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
217911 ATTATTATTT
*
217921 TAATATTATTTTAAATATATTAAAAATA
1 TAATATTATTTAAAATATATTAAAAATA
217949 TAATGATTATTTAAAATA-ATTAAAAAT
1 TAAT-ATTATTTAAAATATATTAAAAAT
217976 TATATAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (28 bp):
TAATATTATTTAAAATATATTAAAAATA
Found at i:221211 original size:19 final size:19
Alignment explanation
Indices: 221189--221236 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
221179 AAAGTTAATT
*
221189 TTATATATTTATTTAAATA
1 TTATATATTTATATAAATA
*
221208 TTATATATTTATATAAATT
1 TTATATATTTATATAAATA
221227 TTAATATATT
1 TT-ATATATT
221237 AATAATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTATATATTTATATAAATA
Found at i:221355 original size:16 final size:16
Alignment explanation
Indices: 221336--221367 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
221326 TTTAAACTTG
221336 AAATTGACTCAACTCA
1 AAATTGACTCAACTCA
221352 AAATTGACTCAACTCA
1 AAATTGACTCAACTCA
221368 TTTGATTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.25, G:0.06, T:0.25
Consensus pattern (16 bp):
AAATTGACTCAACTCA
Found at i:221580 original size:18 final size:17
Alignment explanation
Indices: 221557--221609 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 17
221547 AATTTTATTT
221557 TAAAAAGTATTAATTTAA
1 TAAAAA-TATTAATTTAA
*
221575 TAAAAATAATAATTATAA
1 TAAAAATATTAATT-TAA
*
221593 TATAAATTATTAATTTA
1 TA-AAAATATTAATTTA
221610 TTTTAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 7 0.23
18 13 0.43
19 10 0.33
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
TAAAAATATTAATTTAA
Found at i:223972 original size:13 final size:13
Alignment explanation
Indices: 223954--224000 Score: 58
Period size: 13 Copynumber: 3.4 Consensus size: 13
223944 TTTAATTTTT
223954 AAATAAATTATTA
1 AAATAAATTATTA
223967 AAATAATATTAATTTA
1 AAATAA-ATT-A-TTA
*
223983 AAATAAATTATCA
1 AAATAAATTATTA
223996 AAATA
1 AAATA
224001 TTATTATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 13 0.43
14 4 0.13
15 4 0.13
16 9 0.30
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATAAATTATTA
Found at i:223989 original size:29 final size:29
Alignment explanation
Indices: 223945--224012 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
223935 CAATGTATCT
* *
223945 TTAATTTTTAAATAAATTATTAAAATAATA
1 TTAA-TTTAAAATAAATTATCAAAATAATA
*
223975 TTAATTTAAAATAAATTATCAAAATATTA
1 TTAATTTAAAATAAATTATCAAAATAATA
*
224004 TTATTTTAA
1 TTAATTTAA
224013 CTTGTAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 30 0.88
30 4 0.12
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (29 bp):
TTAATTTAAAATAAATTATCAAAATAATA
Found at i:224620 original size:38 final size:37
Alignment explanation
Indices: 224578--224662 Score: 116
Period size: 38 Copynumber: 2.3 Consensus size: 37
224568 ACGATTACAG
*
224578 TTTAAATTTTAAAATAATTAGACGATTACAACTCTTAA
1 TTTAAATTTTAAAATAATTAGACGATTACAA-TCTAAA
* * *
224616 TTTAAATTTAAAAATAATTAGATGATTATAATCTAAA
1 TTTAAATTTTAAAATAATTAGACGATTACAATCTAAA
*
224653 TTAAAATTTT
1 TTTAAATTTT
224663 TAATTAAACA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
37 13 0.32
38 28 0.68
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (37 bp):
TTTAAATTTTAAAATAATTAGACGATTACAATCTAAA
Found at i:224794 original size:26 final size:26
Alignment explanation
Indices: 224758--224820 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 26
224748 AAAATAATTT
224758 TTTA-AATAATA-AAACTATTATTATA
1 TTTATAATAATATAAACTATTATTA-A
* * *
224783 TTTATAATAATATTATCTTTTATTAA
1 TTTATAATAATATAAACTATTATTAA
*
224809 TTTATAAAAATA
1 TTTATAATAATA
224821 CCAACGTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
25 4 0.12
26 19 0.59
27 9 0.28
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (26 bp):
TTTATAATAATATAAACTATTATTAA
Found at i:224892 original size:38 final size:39
Alignment explanation
Indices: 224827--224900 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 39
224817 AATACCAACG
224827 TAATAATATAACTAAAAAATATGAACATAATAATAACCC
1 TAATAATATAACTAAAAAATATGAACATAATAATAACCC
* * * *
224866 TAATAATATTA-TTAAAAATATTAACATTATAATAA
1 TAATAATATAACTAAAAAATATGAACATAATAATAA
224901 TAACAGTTGG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 21 0.68
39 10 0.32
ACGTcount: A:0.58, C:0.08, G:0.01, T:0.32
Consensus pattern (39 bp):
TAATAATATAACTAAAAAATATGAACATAATAATAACCC
Found at i:225136 original size:16 final size:15
Alignment explanation
Indices: 225111--225159 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 15
225101 TAATATTTAA
225111 TAATTTATTTTAAAT
1 TAATTTATTTTAAAT
225126 TAATATTATTTT-AA-
1 TAAT-TTATTTTAAAT
*
225140 TAATTTATTTAAAAAT
1 TAATTTATTT-TAAAT
225156 TAAT
1 TAAT
225160 AGCATTTTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
13 6 0.21
14 4 0.14
15 8 0.28
16 11 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAATTTATTTTAAAT
Found at i:225147 original size:13 final size:13
Alignment explanation
Indices: 225106--225149 Score: 61
Period size: 13 Copynumber: 3.2 Consensus size: 13
225096 AACATTAATA
225106 TTTAATAATTTAT
1 TTTAATAATTTAT
225119 TTTAAATTAATATTAT
1 TTT-AA-TAAT-TTAT
225135 TTTAATAATTTAT
1 TTTAATAATTTAT
225148 TT
1 TT
225150 AAAAATTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 9 0.32
14 6 0.21
15 6 0.21
16 7 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTTAATAATTTAT
Found at i:225167 original size:30 final size:29
Alignment explanation
Indices: 225106--225167 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
225096 AACATTAATA
* **
225106 TTTAATAATTTATTTTAAATTAATATTAT
1 TTTAATAATTTATTTAAAATTAATAGCAT
225135 TTTAATAATTTATTTAAAAATTAATAGCAT
1 TTTAATAATTTATTT-AAAATTAATAGCAT
225165 TTT
1 TTT
225168 GATCAATGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 15 0.52
30 14 0.48
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (29 bp):
TTTAATAATTTATTTAAAATTAATAGCAT
Found at i:226078 original size:62 final size:62
Alignment explanation
Indices: 225952--226134 Score: 240
Period size: 62 Copynumber: 2.9 Consensus size: 62
225942 ATCTACATTC
* ** * * * *
225952 CCAATTATAATGAGAGATAGGTTTAGAAAAAAAGGTAACAGGTTAGTGTTAGGGCTATCGACCAT
1 CCAATTATAATGATAGATAGG--TAG-GGAAAAGGTGATAGGTTAGTGTTAGGGTTATCAACCAT
226017 CCAATTATAATGATAGATAGGTAGGGAAAAGGTGATAGGTTAGTGTTAGGGTTATCAACCAT
1 CCAATTATAATGATAGATAGGTAGGGAAAAGGTGATAGGTTAGTGTTAGGGTTATCAACCAT
* * * *
226079 CCAATTATGATGATAGATAGGCAGGGAAAAGGTGCTAGGTTAGTGTTAAGGTTATC
1 CCAATTATAATGATAGATAGGTAGGGAAAAGGTGATAGGTTAGTGTTAGGGTTATC
226135 TGTTCTTCAA
Statistics
Matches: 107, Mismatches: 11, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
62 84 0.79
63 3 0.03
65 20 0.19
ACGTcount: A:0.36, C:0.09, G:0.27, T:0.28
Consensus pattern (62 bp):
CCAATTATAATGATAGATAGGTAGGGAAAAGGTGATAGGTTAGTGTTAGGGTTATCAACCAT
Found at i:226342 original size:24 final size:24
Alignment explanation
Indices: 226299--226345 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
226289 GTAGGTATGT
* *
226299 TAAATATATTGTGTTAATTATATA
1 TAAATATATTATATTAATTATATA
*
226323 TAAATATATTATATTTATTATAT
1 TAAATATATTATATTAATTATAT
226346 TATTTTTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (24 bp):
TAAATATATTATATTAATTATATA
Found at i:226354 original size:11 final size:13
Alignment explanation
Indices: 226327--226363 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
226317 TATATATAAA
226327 TATATTATATTTAT
1 TATATT-TATTTAT
226341 TATA-TTATTT-T
1 TATATTTATTTAT
226352 TATATTTATTTA
1 TATATTTATTTA
226364 ATGTATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 5 0.24
12 11 0.52
13 1 0.05
14 4 0.19
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TATATTTATTTAT
Found at i:226370 original size:24 final size:26
Alignment explanation
Indices: 226327--226380 Score: 67
Period size: 24 Copynumber: 2.1 Consensus size: 26
226317 TATATATAAA
*
226327 TATATTATATTTATTATATT-ATTTT
1 TATATTATATTTAATATATTAATTTT
*
226352 TATATT-TATTTAATGTATTAAATTTT
1 TATATTATATTTAATATATT-AATTTT
226378 TAT
1 TAT
226381 TATGTTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 11 0.44
25 6 0.24
26 8 0.32
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (26 bp):
TATATTATATTTAATATATTAATTTT
Found at i:227028 original size:13 final size:13
Alignment explanation
Indices: 227012--227036 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
227002 TTATAATTTT
227012 AAATATAATATAA
1 AAATATAATATAA
227025 AAATATAATATA
1 AAATATAATATA
227037 TTTTATATCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATATAATATAA
Found at i:228012 original size:18 final size:18
Alignment explanation
Indices: 227989--228023 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
227979 AATTGATCTT
227989 ATATAGATTGAAATTTGA
1 ATATAGATTGAAATTTGA
*
228007 ATATAGATTGAAGTTTG
1 ATATAGATTGAAATTTG
228024 GATGAACTTA
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:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (18 bp):
ATATAGATTGAAATTTGA
Found at i:231944 original size:27 final size:27
Alignment explanation
Indices: 231914--231991 Score: 65
Period size: 27 Copynumber: 2.9 Consensus size: 27
231904 ATTATATTAG
231914 TATAAATTAATTA-AT-ATTACATAATTT
1 TATAAATTAATTATATAATTA-AT-ATTT
* *
231941 TATAATTTTA-TATATAATTAATATTT
1 TATAAATTAATTATATAATTAATATTT
*
231967 TAATAAATTAATAAT-TAATTTAATA
1 T-ATAAATTAATTATATAA-TTAATA
231992 ATATAATTAC
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
26 7 0.17
27 22 0.54
28 12 0.29
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (27 bp):
TATAAATTAATTATATAATTAATATTT
Found at i:231975 original size:16 final size:18
Alignment explanation
Indices: 231945--231979 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
231935 TAATTTTATA
231945 ATTTTATATATAATTAAT
1 ATTTTATATATAATTAAT
231963 ATTTTA-ATA-AATTAAT
1 ATTTTATATATAATTAAT
231979 A
1 A
231980 ATTAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTTATATATAATTAAT
Found at i:231998 original size:20 final size:19
Alignment explanation
Indices: 231942--231998 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
231932 ACATAATTTT
*
231942 ATAATTTTAT-ATATAATTA
1 ATAATTTAATAATATAA-TA
*
231961 ATATTTTAATAA-ATTAATA
1 ATAATTTAATAATA-TAATA
231980 ATTAATTTAATAATATAAT
1 A-TAATTTAATAATATAAT
231999 TACAATCCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 12 0.39
20 18 0.58
21 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATAATTTAATAATATAATA
Found at i:233375 original size:29 final size:29
Alignment explanation
Indices: 233315--233375 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
233305 TGCCTATATT
* *
233315 ATATTTTTTAATTAATTTTTAAAAATTTA
1 ATATTTTTTAATTAAATTTTAAAAATTAA
233344 ATATTTTTTAATTAAATTTT-AAAATATAA
1 ATATTTTTTAATTAAATTTTAAAAAT-TAA
233373 ATA
1 ATA
233376 GCTTAATATG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 5 0.17
29 24 0.83
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
ATATTTTTTAATTAAATTTTAAAAATTAA
Found at i:233463 original size:23 final size:26
Alignment explanation
Indices: 233434--233480 Score: 73
Period size: 23 Copynumber: 1.9 Consensus size: 26
233424 TTTTTATATG
233434 ATAAAATT-ATA-ATA-TATATAAAT
1 ATAAAATTAATATATATTATATAAAT
233457 ATAAAATTAATATATATTATATAA
1 ATAAAATTAATATATATTATATAA
233481 TTAAAAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 8 0.38
24 3 0.14
25 3 0.14
26 7 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
ATAAAATTAATATATATTATATAAAT
Found at i:233488 original size:26 final size:23
Alignment explanation
Indices: 233436--233488 Score: 61
Period size: 26 Copynumber: 2.2 Consensus size: 23
233426 TTTATATGAT
*
233436 AAAATTATAATATATATAAATAT
1 AAAATTATAATATATATAAATAA
*
233459 AAAATTAATATATATTATATAATTAA
1 AAAATT-ATA-ATA-TATATAAATAA
233485 AAAA
1 AAAA
233489 CATGTCAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.24
24 3 0.12
25 3 0.12
26 13 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AAAATTATAATATATATAAATAA
Found at i:246991 original size:2 final size:2
Alignment explanation
Indices: 246984--247012 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
246974 GAAGGGCTTA
246984 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
247013 AAATATTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:248173 original size:26 final size:26
Alignment explanation
Indices: 248144--248196 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
248134 ATGTGTCAAT
248144 ATTA-AAAAGATTTAAACTTAAAAATA
1 ATTATAAAA-ATTTAAACTTAAAAATA
** *
248170 ATTATTTAAATTTAAACTTAAATATA
1 ATTATAAAAATTTAAACTTAAAAATA
248196 A
1 A
248197 AATAATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 21 0.91
27 2 0.09
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (26 bp):
ATTATAAAAATTTAAACTTAAAAATA
Found at i:248220 original size:15 final size:14
Alignment explanation
Indices: 248173--248230 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
248163 AAAAATAATT
248173 ATTTAAATTT--AA
1 ATTTAAATTTAAAA
* *
248185 ACTTAAATATAAAATA
1 ATTTAAAT-TTAAA-A
248201 ATTTAAAATTTAAAA
1 ATTT-AAATTTAAAA
248216 ATTTAAATTTAAAA
1 ATTTAAATTTAAAA
248230 A
1 A
248231 AAATATAAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
12 7 0.19
13 1 0.03
14 11 0.30
15 6 0.16
16 8 0.22
17 4 0.11
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (14 bp):
ATTTAAATTTAAAA
Found at i:248231 original size:15 final size:15
Alignment explanation
Indices: 248187--248231 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
248177 AAATTTAAAC
*
248187 TTAAATATAAAATAAT
1 TTAAATTTAAAA-AAT
248203 TTAAAATTT-AAAAAT
1 TT-AAATTTAAAAAAT
248218 TTAAATTTAAAAAA
1 TTAAATTTAAAAAA
248232 AATATAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.23
15 10 0.38
16 5 0.19
17 5 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TTAAATTTAAAAAAT
Found at i:248683 original size:19 final size:19
Alignment explanation
Indices: 248638--248685 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
248628 TTAATATAAA
*
248638 ATTAATTAA-TTTATATATT
1 ATTAA-TAATTTTATATATG
* *
248657 TTTTATAATTTTATATATG
1 ATTAATAATTTTATATATG
248676 ATTAATAATT
1 ATTAATAATT
248686 AAATAAGTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 3 0.13
19 20 0.87
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
ATTAATAATTTTATATATG
Found at i:249974 original size:22 final size:23
Alignment explanation
Indices: 249930--249974 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
249920 AAATCGAATC
* *
249930 TTAAAATATAATTTTTTTTAAAT
1 TTAAAATATAATTTATTTAAAAT
249953 TTAAAAT-TAATTTATTTAAAAT
1 TTAAAATATAATTTATTTAAAAT
249975 AATACGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TTAAAATATAATTTATTTAAAAT
Found at i:250941 original size:2 final size:2
Alignment explanation
Indices: 250934--250966 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
250924 AAAAATATTA
250934 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
250967 CGTTGTTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:255034 original size:50 final size:51
Alignment explanation
Indices: 254980--255084 Score: 151
Period size: 53 Copynumber: 2.0 Consensus size: 51
254970 CTAGCCGTGA
*
254980 CTCCCACCATCCCCA-AG-CCATCTCTATCATCTACTCAACCACCATTTTCT
1 CTCCCACCAT-CCAAGAGACCATCTCTATCATCTACTCAACCACCATTTTCT
*
255030 CTCCCACCATCCAAGAGAACCCATCTCTATCATCTACTCAGCCACCATTTTCT
1 CTCCCACCATCCAAGAG-A-CCATCTCTATCATCTACTCAACCACCATTTTCT
255083 CT
1 CT
255085 TACTTCCCCT
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
49 3 0.06
50 12 0.24
53 34 0.69
ACGTcount: A:0.25, C:0.44, G:0.04, T:0.28
Consensus pattern (51 bp):
CTCCCACCATCCAAGAGACCATCTCTATCATCTACTCAACCACCATTTTCT
Found at i:255898 original size:21 final size:22
Alignment explanation
Indices: 255869--255915 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
255859 CTAACATTCT
255869 CACCAAATA-CATT-ACCTAACA
1 CACCAAATAGC-TTCACCTAACA
*
255890 CACCTAATATGCTTCACCTAACA
1 CACCAAATA-GCTTCACCTAACA
255913 CAC
1 CAC
255916 TTAACAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 8 0.36
22 2 0.09
23 12 0.55
ACGTcount: A:0.40, C:0.36, G:0.02, T:0.21
Consensus pattern (22 bp):
CACCAAATAGCTTCACCTAACA
Found at i:264091 original size:55 final size:55
Alignment explanation
Indices: 264024--264127 Score: 163
Period size: 55 Copynumber: 1.9 Consensus size: 55
264014 ACCATATATG
* *
264024 TTTGCAACAATTTTATATATACTTTTGTTCCAAAAACTAGTTAAGAGAATTTATA
1 TTTGCAACAATTTTATATATACTTTTATTCCAAAAACTAGTTAAAAGAATTTATA
* * *
264079 TTTGCAATAATTTTATGTATACTTTTATTGCAAAAACTAGTTAAAAGAA
1 TTTGCAACAATTTTATATATACTTTTATTCCAAAAACTAGTTAAAAGAA
264128 CCTATTACAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 44 1.00
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (55 bp):
TTTGCAACAATTTTATATATACTTTTATTCCAAAAACTAGTTAAAAGAATTTATA
Found at i:264672 original size:17 final size:18
Alignment explanation
Indices: 264650--264683 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
264640 TATTAAAATA
264650 TTCATGCTA-GTTTTGTG
1 TTCATGCTATGTTTTGTG
*
264667 TTCATGTTATGTTTTGT
1 TTCATGCTATGTTTTGT
264684 TTAGTCATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.12, C:0.09, G:0.21, T:0.59
Consensus pattern (18 bp):
TTCATGCTATGTTTTGTG
Found at i:264901 original size:5 final size:5
Alignment explanation
Indices: 264891--264926 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
264881 TTCAGATTTA
264891 AAATT AAATT AAATT AAATT AAATTT AAA-T AAATT A
1 AAATT AAATT AAATT AAATT AAA-TT AAATT AAATT A
264927 TTTGATCGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.14
5 20 0.69
6 5 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
AAATT
Found at i:265253 original size:26 final size:24
Alignment explanation
Indices: 265198--265262 Score: 64
Period size: 26 Copynumber: 2.7 Consensus size: 24
265188 GTAATGAAAT
265198 ATAATAATA-AAT-ATTTATTTAAA
1 ATAA-AATATAATAATTTATTTAAA
265221 ATAAAATATAATAATTTAATTATAAA
1 ATAAAATATAATAATTT-ATT-TAAA
*
265247 ATTAAAT-TAGATAATT
1 ATAAAATATA-ATAATT
265263 ATGCATATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
22 4 0.11
23 7 0.19
24 4 0.11
25 5 0.14
26 16 0.44
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (24 bp):
ATAAAATATAATAATTTATTTAAA
Found at i:268992 original size:23 final size:23
Alignment explanation
Indices: 268928--268997 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 23
268918 GTTTATCTAT
*
268928 ATTTTT-AAATAAATAA-TTTAA
1 ATTTTTAAAATATATAATTTTAA
268949 ATTTATTTATATTAATATATAATTTTAA
1 A-TT-TTTA-A--AATATATAATTTTAA
*
268977 ATTTTTAAAATATATATTTTT
1 ATTTTTAAAATATATAATTTT
268998 TGTTTAATTC
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
21 1 0.03
22 2 0.05
23 15 0.38
25 2 0.05
26 4 0.10
27 10 0.25
28 6 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTTTTAAAATATATAATTTTAA
Found at i:269124 original size:16 final size:16
Alignment explanation
Indices: 269111--269168 Score: 57
Period size: 16 Copynumber: 3.8 Consensus size: 16
269101 TCTATATATG
269111 ATATAAATTATATAAT
1 ATATAAATTATATAAT
* *
269127 ATATAAA-TAAAAAAT
1 ATATAAATTATATAAT
* *
269142 A-ATATATTATATATT
1 ATATAAATTATATAAT
*
269157 ATATAAACTATA
1 ATATAAATTATA
269169 AAATGGTCCG
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
14 4 0.12
15 13 0.41
16 15 0.47
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATAAATTATATAAT
Found at i:269722 original size:43 final size:42
Alignment explanation
Indices: 269661--269752 Score: 148
Period size: 43 Copynumber: 2.2 Consensus size: 42
269651 GTATCTCTCA
* *
269661 GAAGCTTGTTGGAGTGTATGGTTTGTATTTTTAAATATTTGT
1 GAAGCTTGTTGGAGTGTATGGTTTGTACTGTTAAATATTTGT
*
269703 GGAAGCTTGTTGGAGTGTATGGTTTGTACTGTTGAATATTTGT
1 -GAAGCTTGTTGGAGTGTATGGTTTGTACTGTTAAATATTTGT
269746 GAAGCTT
1 GAAGCTT
269753 TGTGCCGAAC
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
42 7 0.15
43 39 0.85
ACGTcount: A:0.21, C:0.04, G:0.29, T:0.46
Consensus pattern (42 bp):
GAAGCTTGTTGGAGTGTATGGTTTGTACTGTTAAATATTTGT
Found at i:271902 original size:24 final size:23
Alignment explanation
Indices: 271869--271919 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
271859 ATTATTCAAA
*
271869 TAAAAAAAATTAAAAATATATTT
1 TAAAAAAAATTAAAAATATAATT
*
271892 TAAAAATAAATTAAAAATTTAATT
1 TAAAAA-AAATTAAAAATATAATT
271916 TAAA
1 TAAA
271920 CATTTAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
TAAAAAAAATTAAAAATATAATT
Found at i:272256 original size:27 final size:27
Alignment explanation
Indices: 272226--272279 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
272216 ATATATTATT
*
272226 AATTATGTAATTATTGTTAAATGAATA
1 AATTATGTAATTATTGATAAATGAATA
* * * *
272253 AATTCTTTATTTATTGATAAATTAATA
1 AATTATGTAATTATTGATAAATGAATA
272280 TATAAATATT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (27 bp):
AATTATGTAATTATTGATAAATGAATA
Found at i:274241 original size:34 final size:35
Alignment explanation
Indices: 274141--274243 Score: 131
Period size: 35 Copynumber: 3.0 Consensus size: 35
274131 AAAAGCTTTC
* * *
274141 TCTTTTTATGAATAGAAAGTTGGAAGCGGATTTTT
1 TCTTTTCATGAATTGAAAGTTGGAAGCGGAATTTT
*
274176 TCTTTCCA--ATATTAGAAAGTTGGAAGCGGAATTTT
1 TCTTTTCATGA-ATT-GAAAGTTGGAAGCGGAATTTT
274211 TCTTTTCATGAATTGAAAGTT-GAAGCGGAATTT
1 TCTTTTCATGAATTGAAAGTTGGAAGCGGAATTT
274244 GTGGTTGCAG
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
33 1 0.02
34 14 0.24
35 40 0.68
36 3 0.05
37 1 0.02
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (35 bp):
TCTTTTCATGAATTGAAAGTTGGAAGCGGAATTTT
Found at i:274814 original size:2 final size:2
Alignment explanation
Indices: 274809--274843 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
274799 GTTTTTTAAA
274809 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
274844 AGCCTTGTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:276974 original size:15 final size:14
Alignment explanation
Indices: 276949--276983 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
276939 TATAAATATG
276949 AATAAATTTAAATA
1 AATAAATTTAAATA
*
276963 GATAACATTTAAATA
1 AATAA-ATTTAAATA
276978 AATAAA
1 AATAAA
276984 AAAAGAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (14 bp):
AATAAATTTAAATA
Found at i:277408 original size:9 final size:10
Alignment explanation
Indices: 277388--277420 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
277378 AATTCACTGC
*
277388 AAAATTATAA
1 AAAATAATAA
277398 AAAATAA-AA
1 AAAATAATAA
277407 AAAATAATAA
1 AAAATAATAA
277417 AAAA
1 AAAA
277421 ATTTCTCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (10 bp):
AAAATAATAA
Found at i:278241 original size:17 final size:17
Alignment explanation
Indices: 278206--278241 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
278196 TTTATATATA
*
278206 AAATTAATTTGTTATAT
1 AAATTAATTTGTTAAAT
*
278223 AAATTAATTTTTTAAAT
1 AAATTAATTTGTTAAAT
278240 AA
1 AA
278242 TTTATTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
AAATTAATTTGTTAAAT
Found at i:278415 original size:23 final size:24
Alignment explanation
Indices: 278383--278430 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
278373 AATTAATATT
278383 TAAAAAATTT-AAAATATATTTAA
1 TAAAAAATTTAAAAATATATTTAA
* *
278406 TAAAATATTTAAAAATCTATTTAA
1 TAAAAAATTTAAAAATATATTTAA
278430 T
1 T
278431 CTTAACTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
TAAAAAATTTAAAAATATATTTAA
Found at i:278499 original size:6 final size:7
Alignment explanation
Indices: 278484--278508 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
278474 AAACTCAATT
278484 AAAATAA
1 AAAATAA
278491 AAAATAA
1 AAAATAA
278498 AAAATAA
1 AAAATAA
278505 AAAA
1 AAAA
278509 AACGTAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAATAA
Found at i:279437 original size:16 final size:16
Alignment explanation
Indices: 279427--279477 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
279417 GTTCGAGCTT
* *
279427 TTTCGGGTTCGGGTTG
1 TTTCGGGTTCGGATTA
279443 TTTCGGGTTCGGATTA
1 TTTCGGGTTCGGATTA
* *
279459 TTTCGGGTTTGGATAA
1 TTTCGGGTTCGGATTA
279475 TTT
1 TTT
279478 GAGATTTGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.10, C:0.10, G:0.33, T:0.47
Consensus pattern (16 bp):
TTTCGGGTTCGGATTA
Found at i:279909 original size:13 final size:13
Alignment explanation
Indices: 279891--279916 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
279881 TTCAATAAAA
279891 TTATTATATTAAT
1 TTATTATATTAAT
279904 TTATTATATTAAT
1 TTATTATATTAAT
279917 AATAAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTATTATATTAAT
Found at i:282757 original size:27 final size:26
Alignment explanation
Indices: 282691--282757 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 26
282681 ATTTATATTA
*
282691 ATATATAT-TTTTAATTTTTTAAAAT
1 ATATATTTCTTTTAATTTTTTAAAAT
*
282716 ATATATTTTTGTTTAA-TTTTTAATAAT
1 ATATATTTCT-TTTAATTTTTTAA-AAT
*
282743 TTAATATTTCTTTTA
1 AT-ATATTTCTTTTA
282758 TTAAATTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
25 7 0.20
26 8 0.23
27 13 0.37
28 7 0.20
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (26 bp):
ATATATTTCTTTTAATTTTTTAAAAT
Found at i:282989 original size:15 final size:15
Alignment explanation
Indices: 282969--283004 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
282959 ATTAATTTTA
282969 TTTTTTTATCTAATT
1 TTTTTTTATCTAATT
*
282984 TTTTTTTGTCTAATT
1 TTTTTTTATCTAATT
282999 TTTTTT
1 TTTTTT
283005 AAGCTCAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.06, G:0.03, T:0.78
Consensus pattern (15 bp):
TTTTTTTATCTAATT
Found at i:285471 original size:13 final size:13
Alignment explanation
Indices: 285453--285477 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
285443 AAATTAAAAA
285453 ATTTTAAAAATAT
1 ATTTTAAAAATAT
285466 ATTTTAAAAATA
1 ATTTTAAAAATA
285478 AATGAAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTTTAAAAATAT
Found at i:285831 original size:27 final size:27
Alignment explanation
Indices: 285801--285854 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
285791 ATATATTATT
*
285801 AATTATGTAATTATTGTTAAATGAATA
1 AATTATGTAATTATTGATAAATGAATA
* * * *
285828 AATTCTTTATTTATTGATAAATTAATA
1 AATTATGTAATTATTGATAAATGAATA
285855 TATAAATATT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (27 bp):
AATTATGTAATTATTGATAAATGAATA
Found at i:287817 original size:34 final size:35
Alignment explanation
Indices: 287717--287819 Score: 131
Period size: 35 Copynumber: 3.0 Consensus size: 35
287707 AAAAGCTTTC
* * *
287717 TCTTTTTATGAATAGAAAGTTGGAAGCGGATTTTT
1 TCTTTTCATGAATTGAAAGTTGGAAGCGGAATTTT
*
287752 TCTTTCCA--ATATTAGAAAGTTGGAAGCGGAATTTT
1 TCTTTTCATGA-ATT-GAAAGTTGGAAGCGGAATTTT
287787 TCTTTTCATGAATTGAAAGTT-GAAGCGGAATTT
1 TCTTTTCATGAATTGAAAGTTGGAAGCGGAATTT
287820 GTGGTTGCAG
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
33 1 0.02
34 14 0.24
35 40 0.68
36 3 0.05
37 1 0.02
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (35 bp):
TCTTTTCATGAATTGAAAGTTGGAAGCGGAATTTT
Found at i:290541 original size:15 final size:14
Alignment explanation
Indices: 290516--290550 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
290506 TATAAATATG
290516 AATAAATTTAAATA
1 AATAAATTTAAATA
*
290530 GATAACATTTAAATA
1 AATAA-ATTTAAATA
290545 AATAAA
1 AATAAA
290551 AAAAGAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (14 bp):
AATAAATTTAAATA
Found at i:290972 original size:9 final size:10
Alignment explanation
Indices: 290952--290984 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
290942 AATTCACTGC
*
290952 AAAATTATAA
1 AAAATAATAA
290962 AAAATAA-AA
1 AAAATAATAA
290971 AAAATAATAA
1 AAAATAATAA
290981 AAAA
1 AAAA
290985 ATTTCTCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (10 bp):
AAAATAATAA
Found at i:291806 original size:18 final size:18
Alignment explanation
Indices: 291767--291806 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
291757 ATATTTATAT
*
291767 ATAAAATTAATTTGTTAT
1 ATAAAATTAATTTGTTAA
*
291785 ATAAAATTAATTTTTTAA
1 ATAAAATTAATTTGTTAA
291803 ATAA
1 ATAA
291807 TTTATTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
ATAAAATTAATTTGTTAA
Found at i:291980 original size:23 final size:24
Alignment explanation
Indices: 291948--291995 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
291938 AATTAATATT
291948 TAAAAAATTT-AAAATATATTTAA
1 TAAAAAATTTAAAAATATATTTAA
* *
291971 TAAAATATTTAAAAATCTATTTAA
1 TAAAAAATTTAAAAATATATTTAA
291995 T
1 T
291996 CTTAACTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
TAAAAAATTTAAAAATATATTTAA
Found at i:293002 original size:16 final size:16
Alignment explanation
Indices: 292992--293042 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
292982 GTTCGAGCTT
* *
292992 TTTCGGGTTCGGGTTG
1 TTTCGGGTTCGGATTA
293008 TTTCGGGTTCGGATTA
1 TTTCGGGTTCGGATTA
* *
293024 TTTCGGGTTTGGATAA
1 TTTCGGGTTCGGATTA
293040 TTT
1 TTT
293043 GAGATTTGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.10, C:0.10, G:0.33, T:0.47
Consensus pattern (16 bp):
TTTCGGGTTCGGATTA
Found at i:293474 original size:13 final size:13
Alignment explanation
Indices: 293456--293481 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
293446 TTCAATAAAA
293456 TTATTATATTAAT
1 TTATTATATTAAT
293469 TTATTATATTAAT
1 TTATTATATTAAT
293482 AATAAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTATTATATTAAT
Found at i:296322 original size:27 final size:26
Alignment explanation
Indices: 296256--296322 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 26
296246 ATTTATATTA
*
296256 ATATATAT-TTTTAATTTTTTAAAAT
1 ATATATTTCTTTTAATTTTTTAAAAT
*
296281 ATATATTTTTGTTTAA-TTTTTAATAAT
1 ATATATTTCT-TTTAATTTTTTAA-AAT
*
296308 TTAATATTTCTTTTA
1 AT-ATATTTCTTTTA
296323 TTAAATTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
25 7 0.20
26 8 0.23
27 13 0.37
28 7 0.20
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (26 bp):
ATATATTTCTTTTAATTTTTTAAAAT
Found at i:296551 original size:14 final size:14
Alignment explanation
Indices: 296534--296569 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
296524 ATTAATTTTA
296534 TTTTTTTATCTAAT
1 TTTTTTTATCTAAT
*
296548 TTTTTTTGTCTAAT
1 TTTTTTTATCTAAT
296562 TTTTTTTA
1 TTTTTTTA
296570 AGCTCAATAT
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:0.17, C:0.06, G:0.03, T:0.75
Consensus pattern (14 bp):
TTTTTTTATCTAAT
Found at i:299036 original size:13 final size:13
Alignment explanation
Indices: 299018--299042 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
299008 AAATTAAAAA
299018 ATTTTAAAAATAT
1 ATTTTAAAAATAT
299031 ATTTTAAAAATA
1 ATTTTAAAAATA
299043 AATGAAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTTTAAAAATAT
Found at i:299397 original size:27 final size:27
Alignment explanation
Indices: 299367--299420 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
299357 ATATATTATT
*
299367 AATTATGTAATTATTGTTAAATGAATA
1 AATTATGTAATTATTGATAAATGAATA
* * * *
299394 AATTCTTTATTTATTGATAAATTAATA
1 AATTATGTAATTATTGATAAATGAATA
299421 TATAAATATT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (27 bp):
AATTATGTAATTATTGATAAATGAATA
Found at i:301383 original size:34 final size:35
Alignment explanation
Indices: 301283--301385 Score: 131
Period size: 35 Copynumber: 3.0 Consensus size: 35
301273 AAAAGCTTTC
* * *
301283 TCTTTTTATGAATAGAAAGTTGGAAGCGGATTTTT
1 TCTTTTCATGAATTGAAAGTTGGAAGCGGAATTTT
*
301318 TCTTTCCA--ATATTAGAAAGTTGGAAGCGGAATTTT
1 TCTTTTCATGA-ATT-GAAAGTTGGAAGCGGAATTTT
301353 TCTTTTCATGAATTGAAAGTT-GAAGCGGAATTT
1 TCTTTTCATGAATTGAAAGTTGGAAGCGGAATTT
301386 GTGGTTGCAG
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
33 1 0.02
34 14 0.24
35 40 0.68
36 3 0.05
37 1 0.02
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (35 bp):
TCTTTTCATGAATTGAAAGTTGGAAGCGGAATTTT
Done.