Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold414
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: 2018024
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 13
Found at i:953109 original size:27 final size:27
Alignment explanation
Indices: 953074--953162 Score: 90
Period size: 27 Copynumber: 3.2 Consensus size: 27
953064 GCTTTAGAAG
*
953074 AAGG-TGCCACGGACTTGTGGACTTAA
1 AAGGATGCCACGGAGTTGTGGACTTAA
*
953100 AAGGATGCCACGGAGTTGTGGGCTTTGAA
1 AAGGATGCCACGGAGTTGTGGAC-TT-AA
* * *
953129 AAGAAGGTGCCACGGAGTCGTGGACTTAG
1 AAG--GATGCCACGGAGTTGTGGACTTAA
953158 AAGGA
1 AAGGA
953163 AAACGAGTGC
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
26 4 0.08
27 17 0.33
28 2 0.04
29 9 0.18
30 2 0.04
31 17 0.33
ACGTcount: A:0.28, C:0.16, G:0.36, T:0.20
Consensus pattern (27 bp):
AAGGATGCCACGGAGTTGTGGACTTAA
Found at i:953139 original size:58 final size:60
Alignment explanation
Indices: 953059--953220 Score: 204
Period size: 65 Copynumber: 2.7 Consensus size: 60
953049 CACCGACTTG
* * * * *
953059 TGTGGGCTTT-AGAAGAAGGTGCCACGGACTTGTGGACTT-AAAAGGA-TGCCACGGAGT
1 TGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTAAAAACGAGTGCCACGAAGT
953116 TGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTAGAAGGAAAACGAGTGCCACGAAGT
1 TGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTT---A--AAAACGAGTGCCACGAAGT
*
953181 TGTGGGCTTTGAAAGGAAGGTGCCACGGAGTCGTGGACTT
1 TGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTT
953221 TGAGCAGAGA
Statistics
Matches: 91, Mismatches: 6, Indels: 8
0.87 0.06 0.08
Matches are distributed among these distances:
57 10 0.11
58 26 0.29
64 6 0.07
65 49 0.54
ACGTcount: A:0.27, C:0.15, G:0.36, T:0.22
Consensus pattern (60 bp):
TGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTAAAAACGAGTGCCACGAAGT
Found at i:953321 original size:31 final size:31
Alignment explanation
Indices: 953060--953321 Score: 193
Period size: 31 Copynumber: 8.5 Consensus size: 31
953050 ACCGACTTGT
* * *
953060 GTGGGCTTT-AGAAGAAGGTGCCACGGACTT
1 GTGGACTTTAAGAAGAAGGTGCCACGGAGTC
* *
953090 GTGGAC-TTAA-AAG--GATGCCACGGAGTT
1 GTGGACTTTAAGAAGAAGGTGCCACGGAGTC
*
953117 GTGGGCTTTGAA-AAGAAGGTGCCACGGAGTC
1 GTGGACTTT-AAGAAGAAGGTGCCACGGAGTC
* * *
953148 GTGGACTTAGAAGGAA-AACGAGTGCCACGAAGTT
1 GTGGACTT-TAA-GAAGAA-G-GTGCCACGGAGTC
* *
953182 GTGGGCTTTGAA-AGGAAGGTGCCACGGAGTC
1 GTGGACTTT-AAGAAGAAGGTGCCACGGAGTC
* * * * * *
953213 GTGGACTTTGAGCAG-AGATTGTCACTGAGCC
1 GTGGACTTTAAGAAGAAG-GTGCCACGGAGTC
*
953244 GTGGACTTTGAAGAA-AAGGATGCCACTGAGTC
1 GTGGACTTT-AAGAAGAAGG-TGCCACGGAGTC
*
953276 GTGGACTTTGAGAAGAAGGTGCCACGGAGTC
1 GTGGACTTTAAGAAGAAGGTGCCACGGAGTC
*
953307 ATGGACTTTAAGAAG
1 GTGGACTTTAAGAAG
953322 GTATTTGAAG
Statistics
Matches: 182, Mismatches: 32, Indels: 35
0.73 0.13 0.14
Matches are distributed among these distances:
27 17 0.09
28 2 0.01
29 10 0.05
30 9 0.05
31 87 0.48
32 32 0.18
33 5 0.03
34 20 0.11
ACGTcount: A:0.28, C:0.16, G:0.35, T:0.21
Consensus pattern (31 bp):
GTGGACTTTAAGAAGAAGGTGCCACGGAGTC
Found at i:963642 original size:13 final size:13
Alignment explanation
Indices: 963624--963651 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
963614 ATACAAAGAT
963624 CAATGTATCGATA
1 CAATGTATCGATA
963637 CAATGTATCGATA
1 CAATGTATCGATA
963650 CA
1 CA
963652 TTTAAGTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:963729 original size:33 final size:33
Alignment explanation
Indices: 963692--963758 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
963682 AGTAGCTTAA
963692 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
963725 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
963758 A
1 A
963759 AATCGTTGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:963732 original size:13 final size:13
Alignment explanation
Indices: 963714--963738 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
963704 CAAAAAAATA
963714 TGTATCGATACAT
1 TGTATCGATACAT
963727 TGTATCGATACA
1 TGTATCGATACA
963739 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:964826 original size:49 final size:49
Alignment explanation
Indices: 964619--965126 Score: 644
Period size: 49 Copynumber: 10.7 Consensus size: 49
964609 AAAAGGATGT
* *
964619 CAATGTGCTGATTCAAGGCAAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* *
964671 C-ATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTG-
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
964712 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
964760 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
964809 CAATGTGCTGAGTCAAGGCTAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
964858 TAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
964907 CAATATGCTGATTCAAAGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
964950 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
964999 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
965042 CAATGTGCTGATTCAAGGCCAGCTACACTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
965091 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
965127 GAAGGGTTGC
Statistics
Matches: 400, Mismatches: 35, Indels: 45
0.83 0.07 0.09
Matches are distributed among these distances:
41 1 0.00
42 37 0.09
43 76 0.19
45 2 0.00
47 8 0.02
48 41 0.10
49 205 0.51
51 29 0.07
52 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:964984 original size:141 final size:142
Alignment explanation
Indices: 964619--965126 Score: 580
Period size: 141 Copynumber: 3.6 Consensus size: 142
964609 AAAAGGATGT
* *
964619 CAATGTGCTGATTCAAGGCAAGCTACATTGAACTTAAAGATGGAAAAGGTGCC-ATATGCTGATT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTT--A-A--G--AAGGTGCCAATATGCTGATT
* * *
964683 CAAGGCCAGCTATATTGGAC-T-----TAAAGGTGCAATGTGCTGATTCAAGGCCAGCTACATTG
59 CAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCAATATGCTGATTCAAGGCCAGCTATATTG
*
964742 GACTTAAAGGTG-AGGTGC
124 GACTTAAAGATGAAGGTGC
* *
964760 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTT--A-A-GAAGGTGCCAATATGCTGATTCAA
*
964825 GGCTAGCTACATTGGACTTAAAGATAAAGGTGCTAATATGCTGATTCAAGGCCAGCTATATTGGA
62 GGCCAGCTACATTGGACTTAAAGATAAAGGTGC-AATATGCTGATTCAAGGCCAGCTATATTGGA
964890 CTTAAAGATGAAGGTGC
126 CTTAAAGATGAAGGTGC
* * * * *
964907 CAATATGCTGATTCAAAGCCAGCGATATTGGACTT-A-AAGGTGCCAATGTGCTGATTCAAGGCC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAGAAGGTGCCAATATGCTGATTCAAGGCC
* *
964970 AGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-
66 AGCTACATTGGACTTAAAGATAAAGGTG-CAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
965034 ---A--AAGGTGC
130 AAGATGAAGGTGC
*
965042 CAATGTGCTGATTCAAGGCCAGCTACACTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTT--A-A-GAAGGTGCCAATATGCTGATTCAA
* *
965107 GGCCAGCTATATTGGGCTTA
62 GGCCAGCTACATTGGACTTA
965127 GAAGGGTTGC
Statistics
Matches: 325, Mismatches: 26, Indels: 32
0.85 0.07 0.08
Matches are distributed among these distances:
135 37 0.11
137 1 0.00
138 8 0.02
139 28 0.09
140 2 0.01
141 163 0.50
142 1 0.00
143 1 0.00
145 9 0.03
146 38 0.12
147 37 0.11
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (142 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAGAAGGTGCCAATATGCTGATTCAAGGCC
AGCTACATTGGACTTAAAGATAAAGGTGCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAA
AGATGAAGGTGC
Found at i:964992 original size:92 final size:92
Alignment explanation
Indices: 964663--965131 Score: 630
Period size: 92 Copynumber: 5.1 Consensus size: 92
964653 TAAAGATGGA
* * *
964663 AAAGGTGCC-ATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTG-CAATGTGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
964720 TGATTCAAGGCCAGCTACATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
964747 AAAGGTGAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAA
1 -AA----AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAA
* * * *
964812 TGTGCTGAGTCAAGGCTAGCTACATTGGACTTAAAGAT
61 TATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T
* * *
964850 AAAGGTGCTAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
* *
964915 TGATTCAAAGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
964942 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
965007 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
*
965034 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACACTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
965099 TGATTCAAGGCCAGCTATATTGGGCTT
66 TGATTCAAGGCCAGCTATATTGGACTT
965126 AGAAGG
1 A-AAGG
965132 GTTGCCACCG
Statistics
Matches: 345, Mismatches: 20, Indels: 30
0.87 0.05 0.08
Matches are distributed among these distances:
85 2 0.01
89 7 0.02
90 31 0.09
92 179 0.52
93 4 0.01
94 1 0.00
96 6 0.02
97 32 0.09
98 80 0.23
102 2 0.01
103 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
TGATTCAAGGCCAGCTATATTGGACTT
Found at i:965170 original size:33 final size:33
Alignment explanation
Indices: 965126--965245 Score: 183
Period size: 32 Copynumber: 3.7 Consensus size: 33
965116 TATTGGGCTT
965126 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
965159 AGAATGGTTGCCACCGACTTGTGTGGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
965191 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
965224 AAGAA-GG-TGCCACGGACTTGTG
1 -AGAAGGGTTGCCACCGACTTGTG
965246 GACTTAAAAG
Statistics
Matches: 80, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
32 44 0.55
33 33 0.41
34 3 0.04
ACGTcount: A:0.20, C:0.18, G:0.35, T:0.27
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:965292 original size:58 final size:60
Alignment explanation
Indices: 965212--965373 Score: 195
Period size: 65 Copynumber: 2.7 Consensus size: 60
965202 CACCGACTTG
* * * * *
965212 TGTGGGCTTT-AGAAGAAGGTGCCACGGACTTGTGGACTT-AAAAGGA-TGCCACGGAGT
1 TGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTAAAAACGAGTGCCACGAAGT
*
965269 TGTGGGCTTTGAAAAGAAGGTGCCACGAAGTCGTGGACTTAGAAGGAAAACGAGTGCCACGAAGT
1 TGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTT---A--AAAACGAGTGCCACGAAGT
*
965334 TGTGGGCTTTGAAAGGAAGGTGCCACGGAGTCGTGGACTT
1 TGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTT
965374 TGAGCAGAGA
Statistics
Matches: 89, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
57 10 0.11
58 25 0.28
64 6 0.07
65 48 0.54
ACGTcount: A:0.27, C:0.15, G:0.36, T:0.22
Consensus pattern (60 bp):
TGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTAAAAACGAGTGCCACGAAGT
Found at i:965294 original size:31 final size:31
Alignment explanation
Indices: 965224--965467 Score: 187
Period size: 31 Copynumber: 7.9 Consensus size: 31
965214 TGGGCTTTAG
*
965224 AAGAAGGTGCCACGGACTTGTGGAC-TT-AA
1 AAGAAGGTGCCACGGAGTTGTGGACTTTGAA
* *
965253 AAG--GATGCCACGGAGTTGTGGGCTTTGAA
1 AAGAAGGTGCCACGGAGTTGTGGACTTTGAA
* * *
965282 AAGAAGGTGCCACGAAGTCGTGGACTTAGAA
1 AAGAAGGTGCCACGGAGTTGTGGACTTTGAA
* *
965313 GGAA-AACGAGTGCCACGAAGTTGTGGGCTTTGAA
1 --AAGAA-G-GTGCCACGGAGTTGTGGACTTTGAA
* * *
965347 AGGAAGGTGCCACGGAGTCGTGGACTTTGAG
1 AAGAAGGTGCCACGGAGTTGTGGACTTTGAA
* * * **
965378 CAG-AGATTGCCACTGAGCCGTGGACTTTGAA
1 AAGAAG-GTGCCACGGAGTTGTGGACTTTGAA
* * * *
965409 GA-AAGGATGCCACTGAGTCGTGGACTTTGAG
1 AAGAAGG-TGCCACGGAGTTGTGGACTTTGAA
**
965440 AAGAAGGTGCCACGGAGTCATGGACTTT
1 AAGAAGGTGCCACGGAGTTGTGGACTTT
965468 AAGAAGGTAT
Statistics
Matches: 173, Mismatches: 29, Indels: 24
0.77 0.13 0.11
Matches are distributed among these distances:
27 17 0.10
28 2 0.01
29 8 0.05
30 2 0.01
31 109 0.63
32 8 0.05
33 5 0.03
34 22 0.13
ACGTcount: A:0.28, C:0.17, G:0.34, T:0.21
Consensus pattern (31 bp):
AAGAAGGTGCCACGGAGTTGTGGACTTTGAA
Found at i:966490 original size:17 final size:17
Alignment explanation
Indices: 966468--966505 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
966458 CTCACCGAGA
*
966468 TTTTCTGTTTTGTTTTT
1 TTTTCTGTTTTCTTTTT
*
966485 TTTTCTTTTTTCTTTTT
1 TTTTCTGTTTTCTTTTT
966502 TTTT
1 TTTT
966506 TTGTGTTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.00, C:0.08, G:0.05, T:0.87
Consensus pattern (17 bp):
TTTTCTGTTTTCTTTTT
Found at i:975798 original size:13 final size:13
Alignment explanation
Indices: 975780--975807 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
975770 ATACAAAGAT
975780 CAATGTATCGATA
1 CAATGTATCGATA
975793 CAATGTATCGATA
1 CAATGTATCGATA
975806 CA
1 CA
975808 TTTAAGTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:975885 original size:33 final size:33
Alignment explanation
Indices: 975848--975914 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
975838 AGTAGCTTAA
975848 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
975881 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
975914 A
1 A
975915 AATCGTTGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:975888 original size:13 final size:13
Alignment explanation
Indices: 975870--975894 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
975860 CAAAAAAATA
975870 TGTATCGATACAT
1 TGTATCGATACAT
975883 TGTATCGATACA
1 TGTATCGATACA
975895 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:976983 original size:49 final size:49
Alignment explanation
Indices: 976775--977283 Score: 653
Period size: 49 Copynumber: 10.7 Consensus size: 49
976765 AAAAGGATGT
* *
976775 CAATGTGCTGATTCAAGGCAAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* *
976827 C-ATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
976869 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
976917 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
976966 CAATGTGCTGAGTCAAGGCTAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
977015 TAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
977064 CAATATGCTGATTCAAAGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
977107 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
977156 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
977199 CAATGTGCTGATTCAAGGCCAGCTACACTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
977248 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
977284 GAAGGGTTGC
Statistics
Matches: 402, Mismatches: 35, Indels: 43
0.84 0.07 0.09
Matches are distributed among these distances:
42 8 0.02
43 107 0.27
45 2 0.00
47 3 0.01
48 47 0.12
49 205 0.51
51 29 0.07
52 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:977149 original size:92 final size:92
Alignment explanation
Indices: 976819--977288 Score: 639
Period size: 92 Copynumber: 5.1 Consensus size: 92
976809 TAAAGATGGA
* * *
976819 AAAGGTGCC-ATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCAATGTGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
976877 TGATTCAAGGCCAGCTACATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
976904 AAAGGTGAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAA
1 -AA----AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAA
* * * *
976969 TGTGCTGAGTCAAGGCTAGCTACATTGGACTTAAAGAT
61 TATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T
* * *
977007 AAAGGTGCTAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
* *
977072 TGATTCAAAGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
977099 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
977164 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
*
977191 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACACTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
977256 TGATTCAAGGCCAGCTATATTGGGCTT
66 TGATTCAAGGCCAGCTATATTGGACTT
977283 AGAAGG
1 A-AAGG
977289 GTTGCCACCG
Statistics
Matches: 346, Mismatches: 20, Indels: 29
0.88 0.05 0.07
Matches are distributed among these distances:
86 2 0.01
90 7 0.02
91 31 0.09
92 179 0.52
93 4 0.01
95 1 0.00
97 39 0.11
98 80 0.23
102 2 0.01
103 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
TGATTCAAGGCCAGCTATATTGGACTT
Found at i:977327 original size:33 final size:33
Alignment explanation
Indices: 977283--977402 Score: 183
Period size: 32 Copynumber: 3.7 Consensus size: 33
977273 TATTGGGCTT
977283 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
977316 AGAATGGTTGCCACCGACTTGTGTGGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
977348 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
977381 AAGAA-GG-TGCCACGGACTTGTG
1 -AGAAGGGTTGCCACCGACTTGTG
977403 GACTTAAAAG
Statistics
Matches: 80, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
32 44 0.55
33 33 0.41
34 3 0.04
ACGTcount: A:0.20, C:0.18, G:0.35, T:0.27
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:977449 original size:58 final size:60
Alignment explanation
Indices: 977369--977530 Score: 195
Period size: 65 Copynumber: 2.7 Consensus size: 60
977359 CACCGACTTG
* * * * *
977369 TGTGGGCTTT-AGAAGAAGGTGCCACGGACTTGTGGACTT-AAAAGGA-TGCCACGGAGT
1 TGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTAAAAACGAGTGCCACGAAGT
*
977426 TGTGGGCTTTGAAAAGAAGGTGCCACGAAGTCGTGGACTTAGAAGGAAAACGAGTGCCACGAAGT
1 TGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTT---A--AAAACGAGTGCCACGAAGT
*
977491 TGTGGGCTTTGAAAGGAAGGTGCCACGGAGTCGTGGACTT
1 TGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTT
977531 TGAGCAGAGA
Statistics
Matches: 89, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
57 10 0.11
58 25 0.28
64 6 0.07
65 48 0.54
ACGTcount: A:0.27, C:0.15, G:0.36, T:0.22
Consensus pattern (60 bp):
TGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTAAAAACGAGTGCCACGAAGT
Found at i:977609 original size:63 final size:61
Alignment explanation
Indices: 977507--977630 Score: 160
Period size: 63 Copynumber: 2.0 Consensus size: 61
977497 CTTTGAAAGG
* * * *
977507 AAGGTGCCACGGAGTCGTGGACTTTGAGCAGAGATTGCCACTGAGCCGTGGACTTTGAAGAA
1 AAGGTGCCACGGAGTCGTGGACTTTGAGAAGAGAGTGCCACGGAGCCATGGACTTT-AAGAA
* *
977569 AAGGATGCCACTGAGTCGTGGACTTTGAGAAGA-AGGTGCCACGGAGTCATGGACTTTAAGAA
1 AAGG-TGCCACGGAGTCGTGGACTTTGAGAAGAGA-GTGCCACGGAGCCATGGACTTTAAGAA
977631 GGTATTTGAA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
62 10 0.19
63 44 0.81
ACGTcount: A:0.28, C:0.18, G:0.33, T:0.21
Consensus pattern (61 bp):
AAGGTGCCACGGAGTCGTGGACTTTGAGAAGAGAGTGCCACGGAGCCATGGACTTTAAGAA
Found at i:977631 original size:31 final size:31
Alignment explanation
Indices: 977370--977631 Score: 193
Period size: 31 Copynumber: 8.5 Consensus size: 31
977360 ACCGACTTGT
* * *
977370 GTGGGCTTT-AGAAGAAGGTGCCACGGACTT
1 GTGGACTTTAAGAAGAAGGTGCCACGGAGTC
* *
977400 GTGGAC-TTAA-AAG--GATGCCACGGAGTT
1 GTGGACTTTAAGAAGAAGGTGCCACGGAGTC
* *
977427 GTGGGCTTTGAA-AAGAAGGTGCCACGAAGTC
1 GTGGACTTT-AAGAAGAAGGTGCCACGGAGTC
* * *
977458 GTGGACTTAGAAGGAA-AACGAGTGCCACGAAGTT
1 GTGGACTT-TAA-GAAGAA-G-GTGCCACGGAGTC
* *
977492 GTGGGCTTTGAA-AGGAAGGTGCCACGGAGTC
1 GTGGACTTT-AAGAAGAAGGTGCCACGGAGTC
* * * * *
977523 GTGGACTTTGAGCAG-AGATTGCCACTGAGCC
1 GTGGACTTTAAGAAGAAG-GTGCCACGGAGTC
*
977554 GTGGACTTTGAAGAA-AAGGATGCCACTGAGTC
1 GTGGACTTT-AAGAAGAAGG-TGCCACGGAGTC
*
977586 GTGGACTTTGAGAAGAAGGTGCCACGGAGTC
1 GTGGACTTTAAGAAGAAGGTGCCACGGAGTC
*
977617 ATGGACTTTAAGAAG
1 GTGGACTTTAAGAAG
977632 GTATTTGAAG
Statistics
Matches: 184, Mismatches: 30, Indels: 35
0.74 0.12 0.14
Matches are distributed among these distances:
27 17 0.09
28 2 0.01
29 10 0.05
30 9 0.05
31 87 0.47
32 33 0.18
33 5 0.03
34 21 0.11
ACGTcount: A:0.28, C:0.16, G:0.35, T:0.21
Consensus pattern (31 bp):
GTGGACTTTAAGAAGAAGGTGCCACGGAGTC
Found at i:987990 original size:52 final size:52
Alignment explanation
Indices: 987912--988060 Score: 237
Period size: 52 Copynumber: 2.9 Consensus size: 52
987902 CGAAATATGA
*
987912 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGAATAATGTATCGATACATCTGGGC
**
987964 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGAATAATGTATCGATACATCTGGGC
**
988016 AAATTTGCCTGCATGTATCGATACAAAG-ATCAATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAAT-AATGTATCGATACA
988061 ATGTATCGAT
Statistics
Matches: 90, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
51 2 0.02
52 88 0.98
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTGAATAATGTATCGATACATCTGGGC
Found at i:988064 original size:13 final size:13
Alignment explanation
Indices: 988046--988073 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
988036 ATACAAAGAT
988046 CAATGTATCGATA
1 CAATGTATCGATA
988059 CAATGTATCGATA
1 CAATGTATCGATA
988072 CA
1 CA
988074 TTTAAGTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:988151 original size:33 final size:33
Alignment explanation
Indices: 988114--988180 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
988104 AGTAGCTTAA
988114 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
988147 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
988180 A
1 A
988181 AATCGTTGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:988154 original size:13 final size:13
Alignment explanation
Indices: 988136--988160 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
988126 CAAAAAAATA
988136 TGTATCGATACAT
1 TGTATCGATACAT
988149 TGTATCGATACA
1 TGTATCGATACA
988161 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:989249 original size:49 final size:49
Alignment explanation
Indices: 989041--989549 Score: 653
Period size: 49 Copynumber: 10.7 Consensus size: 49
989031 AAAAGGATGT
* *
989041 CAATGTGCTGATTCAAGGCAAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* *
989093 C-ATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
989135 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
989183 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
989232 CAATGTGCTGAGTCAAGGCTAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
989281 TAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
989330 CAATATGCTGATTCAAAGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
989373 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
989422 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
989465 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAAATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
989514 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
989550 GAAGGGTTGC
Statistics
Matches: 404, Mismatches: 33, Indels: 43
0.84 0.07 0.09
Matches are distributed among these distances:
42 8 0.02
43 108 0.27
45 2 0.00
47 3 0.01
48 47 0.12
49 206 0.51
51 29 0.07
52 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:989415 original size:92 final size:92
Alignment explanation
Indices: 989085--989554 Score: 639
Period size: 92 Copynumber: 5.1 Consensus size: 92
989075 TAAAGATGGA
* * *
989085 AAAGGTGCC-ATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCAATGTGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
989143 TGATTCAAGGCCAGCTACATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
989170 AAAGGTGAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAA
1 -AA----AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAA
* * * *
989235 TGTGCTGAGTCAAGGCTAGCTACATTGGACTTAAAGAT
61 TATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T
* * *
989273 AAAGGTGCTAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
* *
989338 TGATTCAAAGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
989365 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
989430 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
*
989457 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAAATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
989522 TGATTCAAGGCCAGCTATATTGGGCTT
66 TGATTCAAGGCCAGCTATATTGGACTT
989549 AGAAGG
1 A-AAGG
989555 GTTGCCACCG
Statistics
Matches: 346, Mismatches: 20, Indels: 29
0.88 0.05 0.07
Matches are distributed among these distances:
86 2 0.01
90 7 0.02
91 31 0.09
92 179 0.52
93 4 0.01
95 1 0.00
97 39 0.11
98 80 0.23
102 2 0.01
103 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
TGATTCAAGGCCAGCTATATTGGACTT
Found at i:989593 original size:33 final size:33
Alignment explanation
Indices: 989549--989668 Score: 183
Period size: 32 Copynumber: 3.7 Consensus size: 33
989539 TATTGGGCTT
989549 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
989582 AGAATGGTTGCCACCGACTTGTGTGGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
989614 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
989647 AAGAA-GG-TGCCACGGACTTGTG
1 -AGAAGGGTTGCCACCGACTTGTG
989669 GACTTAAAAG
Statistics
Matches: 80, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
32 44 0.55
33 33 0.41
34 3 0.04
ACGTcount: A:0.20, C:0.18, G:0.35, T:0.27
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:989685 original size:27 final size:27
Alignment explanation
Indices: 989650--989738 Score: 90
Period size: 27 Copynumber: 3.2 Consensus size: 27
989640 GCTTTAGAAG
*
989650 AAGG-TGCCACGGACTTGTGGACTTAA
1 AAGGATGCCACGGAGTTGTGGACTTAA
*
989676 AAGGATGCCACGGAGTTGTGGGCTTTGAA
1 AAGGATGCCACGGAGTTGTGGAC-TT-AA
* * *
989705 AAGAAGGTGCCACGGAGTCGTGGACTTAG
1 AAG--GATGCCACGGAGTTGTGGACTTAA
989734 AAGGA
1 AAGGA
989739 AAACGAGTGC
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
26 4 0.08
27 17 0.33
28 2 0.04
29 9 0.18
30 2 0.04
31 17 0.33
ACGTcount: A:0.28, C:0.16, G:0.36, T:0.20
Consensus pattern (27 bp):
AAGGATGCCACGGAGTTGTGGACTTAA
Found at i:989715 original size:58 final size:60
Alignment explanation
Indices: 989635--989796 Score: 204
Period size: 65 Copynumber: 2.7 Consensus size: 60
989625 CACCGACTTG
* * * * *
989635 TGTGGGCTTT-AGAAGAAGGTGCCACGGACTTGTGGACTT-AAAAGGA-TGCCACGGAGT
1 TGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTAAAAACGAGTGCCACGAAGT
989692 TGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTAGAAGGAAAACGAGTGCCACGAAGT
1 TGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTT---A--AAAACGAGTGCCACGAAGT
*
989757 TGTGGGCTTTGAAAGGAAGGTGCCACGGAGTCGTGGACTT
1 TGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTT
989797 TGAGCAGAGA
Statistics
Matches: 91, Mismatches: 6, Indels: 8
0.87 0.06 0.08
Matches are distributed among these distances:
57 10 0.11
58 26 0.29
64 6 0.07
65 49 0.54
ACGTcount: A:0.27, C:0.15, G:0.36, T:0.22
Consensus pattern (60 bp):
TGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTAAAAACGAGTGCCACGAAGT
Found at i:989875 original size:63 final size:61
Alignment explanation
Indices: 989641--989896 Score: 168
Period size: 65 Copynumber: 4.1 Consensus size: 61
989631 CTTGTGTGGG
* * * *** *
989641 CTTT-AGAAGAAGGTGCCACGGACTTGTGGAC-TT-AAAAG-GA-TGCCACGGAGTTGTGGG
1 CTTTAAGAA-AAGGTGCCACGGAGTCGTGGACTTTGAGAAGAGAGTGCCACGGAGCCATGGA
* * * ***
989698 CTTTGAA-AAGAAGGTGCCACGGAGTCGTGGACTTAGAAGGAAAACGAGTGCCACGAAGTTGTGG
1 CTTT-AAGAA-AAGGTGCCACGGAGTCGTGGACTTTG-A-GAAGA-GAGTGCCACGGAGCCATGG
*
989762 G
61 A
* * * * *
989763 CTTTGAA-AGGAAGGTGCCACGGAGTCGTGGACTTTGAGCAGAGATTGCCACTGAGCCGTGGA
1 CTTT-AAGA-AAAGGTGCCACGGAGTCGTGGACTTTGAGAAGAGAGTGCCACGGAGCCATGGA
* *
989825 CTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTTGAGAAGA-AGGTGCCACGGAGTCATGGA
1 CTTT-AAGAAAAGG-TGCCACGGAGTCGTGGACTTTGAGAAGAGA-GTGCCACGGAGCCATGGA
989888 CTTTAAGAA
1 CTTTAAGAA
989897 GGTATTTGAA
Statistics
Matches: 163, Mismatches: 23, Indels: 21
0.79 0.11 0.10
Matches are distributed among these distances:
57 4 0.02
58 23 0.14
59 2 0.01
61 1 0.01
62 33 0.20
63 48 0.29
64 3 0.02
65 49 0.30
ACGTcount: A:0.29, C:0.16, G:0.34, T:0.21
Consensus pattern (61 bp):
CTTTAAGAAAAGGTGCCACGGAGTCGTGGACTTTGAGAAGAGAGTGCCACGGAGCCATGGA
Found at i:989888 original size:94 final size:96
Alignment explanation
Indices: 989712--989891 Score: 251
Period size: 94 Copynumber: 1.9 Consensus size: 96
989702 GAAAAGAAGG
* * *
989712 TGCCACGGAGTCGTGGACTTAGAAGGAAAACGAGTGCCACGAAGTTGTGGGCTTTGAAAGGAAGG
1 TGCCACGGAGCCGTGGACTTAGAAGGAAAACGAGTGCCACGAAGTCGTGGACTTTGAAAGGAAGG
*
989777 TGCCACGGAGTCGTGGACTTTGAGCAGAGAT
66 TGCCACGGAGTCATGGACTTTGAGCAGAGAT
* * *
989808 TGCCACTGAGCCGTGGACTTTGAA-GAAAAGGA-TGCCACTG-AGTCGTGGACTTTGAGAA-GAA
1 TGCCACGGAGCCGTGGACTTAGAAGGAAAACGAGTGCCAC-GAAGTCGTGGACTTTGA-AAGGAA
989869 GGTGCCACGGAGTCATGGACTTT
64 GGTGCCACGGAGTCATGGACTTT
989892 AAGAAGGTAT
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
94 44 0.59
95 10 0.13
96 21 0.28
ACGTcount: A:0.27, C:0.18, G:0.34, T:0.21
Consensus pattern (96 bp):
TGCCACGGAGCCGTGGACTTAGAAGGAAAACGAGTGCCACGAAGTCGTGGACTTTGAAAGGAAGG
TGCCACGGAGTCATGGACTTTGAGCAGAGAT
Found at i:989897 original size:31 final size:31
Alignment explanation
Indices: 989636--989897 Score: 202
Period size: 31 Copynumber: 8.5 Consensus size: 31
989626 ACCGACTTGT
* * *
989636 GTGGGCTTT-AGAAGAAGGTGCCACGGACTT
1 GTGGACTTTAAGAAGAAGGTGCCACGGAGTC
* *
989666 GTGGAC-TTAA-AAG--GATGCCACGGAGTT
1 GTGGACTTTAAGAAGAAGGTGCCACGGAGTC
*
989693 GTGGGCTTTGAA-AAGAAGGTGCCACGGAGTC
1 GTGGACTTT-AAGAAGAAGGTGCCACGGAGTC
* * *
989724 GTGGACTTAGAAGGAA-AACGAGTGCCACGAAGTT
1 GTGGACTT-TAA-GAAGAA-G-GTGCCACGGAGTC
* *
989758 GTGGGCTTTGAA-AGGAAGGTGCCACGGAGTC
1 GTGGACTTT-AAGAAGAAGGTGCCACGGAGTC
* * * * *
989789 GTGGACTTTGAGCAG-AGATTGCCACTGAGCC
1 GTGGACTTTAAGAAGAAG-GTGCCACGGAGTC
*
989820 GTGGACTTTGAAGAA-AAGGATGCCACTGAGTC
1 GTGGACTTT-AAGAAGAAGG-TGCCACGGAGTC
*
989852 GTGGACTTTGAGAAGAAGGTGCCACGGAGTC
1 GTGGACTTTAAGAAGAAGGTGCCACGGAGTC
*
989883 ATGGACTTTAAGAAG
1 GTGGACTTTAAGAAG
989898 GTATTTGAAG
Statistics
Matches: 184, Mismatches: 30, Indels: 35
0.74 0.12 0.14
Matches are distributed among these distances:
27 17 0.09
28 2 0.01
29 10 0.05
30 9 0.05
31 88 0.48
32 33 0.18
33 5 0.03
34 20 0.11
ACGTcount: A:0.28, C:0.16, G:0.35, T:0.21
Consensus pattern (31 bp):
GTGGACTTTAAGAAGAAGGTGCCACGGAGTC
Found at i:1000282 original size:52 final size:52
Alignment explanation
Indices: 1000204--1000352 Score: 219
Period size: 52 Copynumber: 2.9 Consensus size: 52
1000194 CGAAATATGA
* *
1000204 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGG
1 AAATTTGCCTGCATGTATCGATACATTGAATAATGTATCGATACATCTGGGC
* **
1000256 AAATTTGCTTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGAATAATGTATCGATACATCTGGGC
**
1000308 AAATTTGCCTGCATGTATCGATACAAAG-ATCAATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAAT-AATGTATCGATACA
1000353 ATGTATCGAT
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
51 2 0.02
52 85 0.98
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTGAATAATGTATCGATACATCTGGGC
Found at i:1000356 original size:13 final size:13
Alignment explanation
Indices: 1000338--1000365 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1000328 ATACAAAGAT
1000338 CAATGTATCGATA
1 CAATGTATCGATA
1000351 CAATGTATCGATA
1 CAATGTATCGATA
1000364 CA
1 CA
1000366 TTTAAGTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1000443 original size:33 final size:33
Alignment explanation
Indices: 1000406--1000472 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1000396 AGTAGCTTAA
1000406 ATTGTATAGATACAAAAAAATATGTATCGATAC
1 ATTGTATAGATACAAAAAAATATGTATCGATAC
* * ***
1000439 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATAGATACAAAAAAATATGTATCGATAC
1000472 A
1 A
1000473 AATCGTTGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATAGATACAAAAAAATATGTATCGATAC
Found at i:1000446 original size:13 final size:13
Alignment explanation
Indices: 1000428--1000452 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1000418 CAAAAAAATA
1000428 TGTATCGATACAT
1 TGTATCGATACAT
1000441 TGTATCGATACA
1 TGTATCGATACA
1000453 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1001476 original size:22 final size:22
Alignment explanation
Indices: 1001448--1001489 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1001438 GATTAAATAG
1001448 TGATTTGATAGTTTGCCATTGT
1 TGATTTGATAGTTTGCCATTGT
* *
1001470 TGATTTGGTGGTTTGCCATT
1 TGATTTGATAGTTTGCCATT
1001490 ATTAACTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.14, C:0.10, G:0.26, T:0.50
Consensus pattern (22 bp):
TGATTTGATAGTTTGCCATTGT
Found at i:1001518 original size:34 final size:34
Alignment explanation
Indices: 1001471--1001619 Score: 190
Period size: 34 Copynumber: 4.4 Consensus size: 34
1001461 TGCCATTGTT
* *
1001471 GATTTGGTGGTTTGCCATTATTAACTAAATGAGA
1 GATTTGGTGGTTTGCCATTGTTGACTAAATGAGA
* * * *
1001505 GATTTGGTAGTTTGCCATTGTTGATTAAATGGGT
1 GATTTGGTGGTTTGCCATTGTTGACTAAATGAGA
*
1001539 GATTTGGTGGTTTTCCATTGTTGACTAAATGAGA
1 GATTTGGTGGTTTGCCATTGTTGACTAAATGAGA
* * * * *
1001573 GATTTGGTAGTTTACCATTGTTGATTAAATGGGT
1 GATTTGGTGGTTTGCCATTGTTGACTAAATGAGA
1001607 GATTTGGTGGTTT
1 GATTTGGTGGTTT
1001620 TTACTAAACC
Statistics
Matches: 98, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 98 1.00
ACGTcount: A:0.23, C:0.07, G:0.28, T:0.43
Consensus pattern (34 bp):
GATTTGGTGGTTTGCCATTGTTGACTAAATGAGA
Found at i:1001620 original size:68 final size:68
Alignment explanation
Indices: 1001470--1001620 Score: 266
Period size: 68 Copynumber: 2.2 Consensus size: 68
1001460 TTGCCATTGT
* *
1001470 TGATTTGGTGGTTTGCCATTATTAACTAAATGAGAGATTTGGTAGTTTGCCATTGTTGATTAAAT
1 TGATTTGGTGGTTTTCCATTATTAACTAAATGAGAGATTTGGTAGTTTACCATTGTTGATTAAAT
1001535 GGG
66 GGG
* *
1001538 TGATTTGGTGGTTTTCCATTGTTGACTAAATGAGAGATTTGGTAGTTTACCATTGTTGATTAAAT
1 TGATTTGGTGGTTTTCCATTATTAACTAAATGAGAGATTTGGTAGTTTACCATTGTTGATTAAAT
1001603 GGG
66 GGG
1001606 TGATTTGGTGGTTTT
1 TGATTTGGTGGTTTT
1001621 TACTAAACCT
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 79 1.00
ACGTcount: A:0.23, C:0.07, G:0.27, T:0.44
Consensus pattern (68 bp):
TGATTTGGTGGTTTTCCATTATTAACTAAATGAGAGATTTGGTAGTTTACCATTGTTGATTAAAT
GGG
Found at i:1005289 original size:19 final size:18
Alignment explanation
Indices: 1005267--1005308 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 18
1005257 TTTATTTCAT
1005267 TTAAAC-AAATAAACTCTAA
1 TTAAACTAAATAAA-TCT-A
1005286 TTAAACTTAAATAAATCTA
1 TTAAAC-TAAATAAATCTA
1005305 TTAA
1 TTAA
1005309 TAAATGAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 11 0.52
20 3 0.14
21 7 0.33
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (18 bp):
TTAAACTAAATAAATCTA
Found at i:1008007 original size:29 final size:29
Alignment explanation
Indices: 1007967--1008043 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
1007957 AATATTTCAT
* * *
1007967 TATAAAATTTTATTTTAATATTTGTTAAAA
1 TATAAAAATTTATTTTAATA-TTATAAAAA
*
1007997 -ATAAAAATTTATTTAAATATTATAAAAA
1 TATAAAAATTTATTTTAATATTATAAAAA
*
1008025 TATAAAAATATATGTTTAA
1 TATAAAAATTTAT-TTTAA
1008044 AAAATACAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
28 7 0.18
29 28 0.72
30 4 0.10
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (29 bp):
TATAAAAATTTATTTTAATATTATAAAAA
Found at i:1009474 original size:25 final size:25
Alignment explanation
Indices: 1009432--1009480 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1009422 TCATTTTTTA
*
1009432 ATAAATTTATTTAAAATAAAAAATT
1 ATAAATTTATATAAAATAAAAAATT
*
1009457 ATAAATTTA-ATAATAATACAAAAT
1 ATAAATTTATATAA-AATAAAAAAT
1009481 ATATCTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 3 0.14
25 18 0.86
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (25 bp):
ATAAATTTATATAAAATAAAAAATT
Found at i:1010564 original size:73 final size:72
Alignment explanation
Indices: 1010334--1010663 Score: 346
Period size: 73 Copynumber: 4.6 Consensus size: 72
1010324 TTTAGATATG
* * * * * ** * *
1010334 TTATACGAGTTTAAA-TTTTTAAGTTATAATTTATTTTTATTTGCAGAAATTTTTATTTGTATTT
1 TTATAGGAGTTTAAATTTTTTAAGGTATGATTTA-TTTTATTTGTAGAAGTTTAAATTTATTTTT
*
1010398 TGGTTTGA
65 TGATTTGA
* * *
1010406 TTATAGGAGTTTAAA-TTTTTAAGGTATTATTTA--TT-TTTATAGAATTTTAAATTTATTTTTT
1 TTATAGGAGTTTAAATTTTTTAAGGTATGATTTATTTTATTTGTAGAAGTTTAAATTTATTTTTT
* *
1010467 AGGTATGA
66 -GATTTGA
* *
1010475 TTATAGGAGCTTAATTTTTTTAAGGTATGATTTATTTTATTTGTAGAAGTTTAAATTTATTTTTT
1 TTATAGGAGTTTAAATTTTTTAAGGTATGATTTATTTTATTTGTAGAAGTTTAAATTTATTTTTT
*
1010540 GATTTTA
66 GATTTGA
* * * * * *
1010547 TTATACGAGTTTAAATTTTTTAAGATATGATTTATTTTTATTTGTAAAAGATTAAGTTTGTTTTT
1 TTATAGGAGTTTAAATTTTTTAAGGTATGATTTA-TTTTATTTGTAGAAGTTTAAATTTATTTTT
*
1010612 TGAGTTGA
65 TGATTTGA
*
1010620 TTATAGGAGTTAAAATTTTTTTAAGGTATGATTTAATTTTATTT
1 TTATAGGAGTTTAAA-TTTTTTAAGGTATGATTT-ATTTTATTT
1010664 TTAAGATTAG
Statistics
Matches: 218, Mismatches: 32, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
68 19 0.09
69 21 0.10
70 17 0.08
72 66 0.30
73 69 0.32
74 25 0.11
75 1 0.00
ACGTcount: A:0.30, C:0.01, G:0.14, T:0.55
Consensus pattern (72 bp):
TTATAGGAGTTTAAATTTTTTAAGGTATGATTTATTTTATTTGTAGAAGTTTAAATTTATTTTTT
GATTTGA
Found at i:1010611 original size:72 final size:72
Alignment explanation
Indices: 1010320--1010663 Score: 319
Period size: 72 Copynumber: 4.8 Consensus size: 72
1010310 TTTGTAAAAG
* * * * *
1010320 TGTTTTTAGATATG-TTATACGAGTTTAAA-TTTTTAAGTTATAATTTATTTTTATTTGCAGAAA
1 TGTTTTT-GATTTGATTATAGGAGTTTAAATTTTTTAAGGTATGATTTATTTTTATTTGTA-AAA
**
1010383 -TTTTTATT
64 GTTTAAATT
* * * *
1010391 TGTATTTTGGTTTGATTATAGGAGTTTAAA-TTTTTAAGGTATTATTTATTTTTA----TAGAAT
1 TGT-TTTTGATTTGATTATAGGAGTTTAAATTTTTTAAGGTATGATTTATTTTTATTTGTAAAAG
1010451 TTTAAATT
65 TTTAAATT
* * * * * *
1010459 TATTTTTTAGGTATGATTATAGGAGCTTAATTTTTTTAAGGTATGATTTA-TTTTATTTGTAGAA
1 T-GTTTTT-GATTTGATTATAGGAGTTTAAATTTTTTAAGGTATGATTTATTTTTATTTGTAAAA
1010523 GTTTAAATT
64 GTTTAAATT
* * * *
1010532 TATTTTTTGATTTTATTATACGAGTTTAAATTTTTTAAGATATGATTTATTTTTATTTGTAAAAG
1 T-GTTTTTGATTTGATTATAGGAGTTTAAATTTTTTAAGGTATGATTTATTTTTATTTGTAAAAG
* *
1010597 ATTAAGTT
65 TTTAAATT
* * *
1010605 TGTTTTTTGAGTTGATTATAGGAGTTAAAATTTTTTTAAGGTATGATTTAATTTTATTT
1 TG-TTTTTGATTTGATTATAGGAGTTTAAA-TTTTTTAAGGTATGATTTATTTTTATTT
1010664 TTAAGATTAG
Statistics
Matches: 228, Mismatches: 32, Indels: 23
0.81 0.11 0.08
Matches are distributed among these distances:
67 2 0.01
68 12 0.05
69 25 0.11
70 17 0.07
71 7 0.03
72 74 0.32
73 65 0.29
74 26 0.11
ACGTcount: A:0.29, C:0.01, G:0.14, T:0.56
Consensus pattern (72 bp):
TGTTTTTGATTTGATTATAGGAGTTTAAATTTTTTAAGGTATGATTTATTTTTATTTGTAAAAGT
TTAAATT
Found at i:1011913 original size:39 final size:38
Alignment explanation
Indices: 1011865--1011952 Score: 122
Period size: 39 Copynumber: 2.3 Consensus size: 38
1011855 TTAATCCTGT
* *
1011865 TTTTCAGATTTTAATAAATAATTTATACATTATTAACATC
1 TTTT-AGATTTTAATAAAAAATTTATACATTAATAACA-C
*
1011905 TTTTAGATTTTAATAAAAAATTTATGCATTAATAACAC
1 TTTTAGATTTTAATAAAAAATTTATACATTAATAACAC
*
1011943 TTTTAAATTT
1 TTTTAGATTT
1011953 CAATTAACCC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
38 10 0.23
39 30 0.68
40 4 0.09
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.48
Consensus pattern (38 bp):
TTTTAGATTTTAATAAAAAATTTATACATTAATAACAC
Found at i:1013528 original size:16 final size:16
Alignment explanation
Indices: 1013385--1013521 Score: 148
Period size: 16 Copynumber: 8.6 Consensus size: 16
1013375 TTTGAATTAT
* *
1013385 TTTCAGGTTCGGATCA
1 TTTCGGGTTCGGGTCA
1013401 TTTCGGGTTCGGGTCA
1 TTTCGGGTTCGGGTCA
* *
1013417 TTTCGGATTCAGGTCA
1 TTTCGGGTTCGGGTCA
*
1013433 TTTCAGGTTCGGGTCA
1 TTTCGGGTTCGGGTCA
* *
1013449 TTTCGGATTCGAGTCA
1 TTTCGGGTTCGGGTCA
* *
1013465 TTTCAGGTTTGGGTCA
1 TTTCGGGTTCGGGTCA
* *
1013481 TTTCGGGTTTGGGTTA
1 TTTCGGGTTCGGGTCA
* * *
1013497 ATTCAGGTTCAGGTCA
1 TTTCGGGTTCGGGTCA
1013513 TTTCGGGTT
1 TTTCGGGTT
1013522 TAGGTCAATC
Statistics
Matches: 98, Mismatches: 23, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 98 1.00
ACGTcount: A:0.14, C:0.16, G:0.30, T:0.40
Consensus pattern (16 bp):
TTTCGGGTTCGGGTCA
Found at i:1014340 original size:14 final size:15
Alignment explanation
Indices: 1014300--1014353 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 15
1014290 ACATTTTTTA
* *
1014300 ATTTTTTAATAATTT
1 ATTTTTAAATAAATT
*
1014315 ATATTATAAATAAATT
1 AT-TTTTAAATAAATT
*
1014331 -TTTTTAAATATATT
1 ATTTTTAAATAAATT
1014345 ATTTTTAAA
1 ATTTTTAAA
1014354 ATATAACTAC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
14 11 0.34
15 11 0.34
16 10 0.31
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTTTAAATAAATT
Found at i:1019225 original size:16 final size:16
Alignment explanation
Indices: 1019204--1019323 Score: 127
Period size: 16 Copynumber: 7.5 Consensus size: 16
1019194 TAATTATTCA
1019204 GGTCATTTCGGGTTCG
1 GGTCATTTCGGGTTCG
*
1019220 GGTCA-TTCTAGGTTCG
1 GGTCATTTC-GGGTTCG
1019236 GGTCATTTCGGGTTCG
1 GGTCATTTCGGGTTCG
* * *
1019252 AGTCA-TTCTGGATTCA
1 GGTCATTTC-GGGTTCG
*
1019268 GGTTATTTCGGGTTCG
1 GGTCATTTCGGGTTCG
*
1019284 GATCATTTCGGGTTCG
1 GGTCATTTCGGGTTCG
**
1019300 GGTCATTTCGAATTCG
1 GGTCATTTCGGGTTCG
*
1019316 AGTCATTT
1 GGTCATTT
1019324 TTGGGTTCAG
Statistics
Matches: 85, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
15 6 0.07
16 73 0.86
17 6 0.07
ACGTcount: A:0.13, C:0.17, G:0.30, T:0.39
Consensus pattern (16 bp):
GGTCATTTCGGGTTCG
Found at i:1019300 original size:64 final size:64
Alignment explanation
Indices: 1019199--1019322 Score: 187
Period size: 64 Copynumber: 1.9 Consensus size: 64
1019189 CGGGTTAATT
* **
1019199 ATTCAGGTCATTTCGGGTTCGGGTCATTCTAGGTTCGGGTCATTTCGGGTTCGAGTCATTCTGG
1 ATTCAGGTCATTTCGGGTTCGGATCATTCTAGGTTCGGGTCATTTCGAATTCGAGTCATTCTGG
* *
1019263 ATTCAGGTTATTTCGGGTTCGGATCATT-TCGGGTTCGGGTCATTTCGAATTCGAGTCATT
1 ATTCAGGTCATTTCGGGTTCGGATCATTCT-AGGTTCGGGTCATTTCGAATTCGAGTCATT
1019323 TTTGGGTTCA
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
63 1 0.02
64 53 0.98
ACGTcount: A:0.15, C:0.18, G:0.29, T:0.39
Consensus pattern (64 bp):
ATTCAGGTCATTTCGGGTTCGGATCATTCTAGGTTCGGGTCATTTCGAATTCGAGTCATTCTGG
Found at i:1019322 original size:32 final size:32
Alignment explanation
Indices: 1019204--1019331 Score: 143
Period size: 32 Copynumber: 4.0 Consensus size: 32
1019194 TAATTATTCA
* *
1019204 GGTCATTTCGGGTTCGGGTCATTCTAGGTTCG
1 GGTCATTTCGGGTTCGAGTCATTCTGGGTTCG
* *
1019236 GGTCATTTCGGGTTCGAGTCATTCTGGATTCA
1 GGTCATTTCGGGTTCGAGTCATTCTGGGTTCG
*
1019268 GGTTATTTCGGGTTCG-GATCATT-TCGGGTTCG
1 GGTCATTTCGGGTTCGAG-TCATTCT-GGGTTCG
** *
1019300 GGTCATTTCGAATTCGAGTCATTTTTGGGTTC
1 GGTCATTTCGGGTTCGAGTCA-TTCTGGGTTC
1019332 AGATTAATCG
Statistics
Matches: 81, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
31 2 0.02
32 69 0.85
33 9 0.11
34 1 0.01
ACGTcount: A:0.12, C:0.17, G:0.30, T:0.40
Consensus pattern (32 bp):
GGTCATTTCGGGTTCGAGTCATTCTGGGTTCG
Found at i:1021803 original size:18 final size:17
Alignment explanation
Indices: 1021782--1021823 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
1021772 ATTTTACATA
*
1021782 TATATTTTTGTACATTTT
1 TATATTTTTGT-CATATT
*
1021800 TATATTTGTGTCATATT
1 TATATTTTTGTCATATT
1021817 TAT-TTTT
1 TATATTTT
1021824 GTTTTGTGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 3 0.14
17 8 0.38
18 10 0.48
ACGTcount: A:0.21, C:0.05, G:0.07, T:0.67
Consensus pattern (17 bp):
TATATTTTTGTCATATT
Found at i:1021824 original size:17 final size:16
Alignment explanation
Indices: 1021776--1021825 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
1021766 TATAATATTT
*
1021776 TACATATATATTTTTG
1 TACATATTTATTTTTG
*
1021792 TACATTTTTATATTTGTG
1 TACATATTTAT-TTT-TG
1021810 T-CATATTTATTTTTG
1 TACATATTTATTTTTG
1021825 T
1 T
1021826 TTTGTGTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 3 0.10
16 12 0.41
17 11 0.38
18 3 0.10
ACGTcount: A:0.24, C:0.06, G:0.08, T:0.62
Consensus pattern (16 bp):
TACATATTTATTTTTG
Found at i:1022738 original size:20 final size:19
Alignment explanation
Indices: 1022681--1022744 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 19
1022671 ATTTAATTAC
1022681 ATAAAATT-TTAAAATATA
1 ATAAAATTATTAAAATATA
*
1022699 A-AAAATTATTTAAATA-A
1 ATAAAATTATTAAAATATA
*
1022716 ATAATAATTATTAAAAAATA
1 ATAA-AATTATTAAAATATA
1022736 ATAATAATT
1 ATAA-AATT
1022745 TAATTAAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
17 8 0.21
18 10 0.26
19 11 0.28
20 10 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
ATAAAATTATTAAAATATA
Found at i:1022747 original size:36 final size:35
Alignment explanation
Indices: 1022670--1022753 Score: 98
Period size: 36 Copynumber: 2.4 Consensus size: 35
1022660 TTTAACTCTA
* *
1022670 AATTTAATTACATAAAATTTTAAAATATAAAAAAT
1 AATTTAATTAAATAAAATTTTAAAAAATAAAAAAT
* * *
1022705 TATTTAAATAAATAATAATTATTAAAAAAT-AATAAT
1 AATTTAATTAAATAA-AATT-TTAAAAAATAAAAAAT
1022741 AATTTAATTAAAT
1 AATTTAATTAAAT
1022754 TTAATTTAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
35 12 0.30
36 20 0.50
37 8 0.20
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (35 bp):
AATTTAATTAAATAAAATTTTAAAAAATAAAAAAT
Found at i:1023881 original size:20 final size:19
Alignment explanation
Indices: 1023856--1023893 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1023846 TTATTTTTAA
*
1023856 TATATTTATTTATTAAAATC
1 TATATTTATATA-TAAAATC
1023876 TATATTTATATATAAAAT
1 TATATTTATATATAAAAT
1023894 TAATTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
TATATTTATATATAAAATC
Found at i:1024313 original size:62 final size:62
Alignment explanation
Indices: 1024196--1024313 Score: 139
Period size: 62 Copynumber: 1.9 Consensus size: 62
1024186 CTTAAAACTC
* ** * *
1024196 AAAACCTAATTTTTTCCTTTGGTAGTTTGCAATTCTTATTTTTTTAGCATCAGTAAGAACCT
1 AAAACCTAATTTTTTCCCTTGGTAGTGCGCAACTCTTATTTTCTTAGCATCAGTAAGAACCT
* * * *
1024258 AAAACTTAATTTTTTCCCTTGGTAG-GCGTAACTCTTATTTTCCTTAGTATTAGTAA
1 AAAACCTAATTTTTTCCCTTGGTAGTGCGCAACTCTTATTTT-CTTAGCATCAGTAA
1024314 AAATCCAAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
61 12 0.26
62 34 0.74
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.45
Consensus pattern (62 bp):
AAAACCTAATTTTTTCCCTTGGTAGTGCGCAACTCTTATTTTCTTAGCATCAGTAAGAACCT
Found at i:1024843 original size:18 final size:17
Alignment explanation
Indices: 1024810--1024843 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1024800 ATAATTTTTT
1024810 TAAACAATTTAAATATA
1 TAAACAATTTAAATATA
*
1024827 TAAATAATTTAAA-ATA
1 TAAACAATTTAAATATA
1024843 T
1 T
1024844 GATTTTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAACAATTTAAATATA
Found at i:1025142 original size:2 final size:2
Alignment explanation
Indices: 1025137--1025218 Score: 59
Period size: 2 Copynumber: 44.0 Consensus size: 2
1025127 TATGTGTGTG
* * * * *
1025137 TA TA TA TA TA TA TA TG TA T- TT TA TA TA TA TA TA TA TG TG TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1025178 TA TA TA TA TA TA T- TA TA -A TA AA TA T- TA TA -A TA AA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1025215 TA TA
1 TA TA
1025219 AAGTCATTGC
Statistics
Matches: 65, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
1 6 0.09
2 59 0.91
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1025202 original size:12 final size:12
Alignment explanation
Indices: 1025187--1025219 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
1025177 GTATATATAT
1025187 ATATTATAATAA
1 ATATTATAATAA
1025199 ATATTATAATAA
1 ATATTATAATAA
1025211 ATATTATAA
1 ATATTATAA
1025220 AGTCATTGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
ATATTATAATAA
Found at i:1028248 original size:16 final size:15
Alignment explanation
Indices: 1028229--1028259 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1028219 GATTTTTTAA
1028229 AGTTTAGGTTCTTTCG
1 AGTTTAGGTT-TTTCG
1028245 AGTTTAGGTTTTTCG
1 AGTTTAGGTTTTTCG
1028260 GGTCCAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.13, C:0.10, G:0.26, T:0.52
Consensus pattern (15 bp):
AGTTTAGGTTTTTCG
Found at i:1030046 original size:27 final size:27
Alignment explanation
Indices: 1030008--1030060 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
1029998 TGCAGCCTTC
* *
1030008 ACTATTTCAAATTGAATTTCATAATTT
1 ACTATTTCAAATTGAATGTCAAAATTT
1030035 ACTATTTCAAATTGAATGTCAAAATT
1 ACTATTTCAAATTGAATGTCAAAATT
1030061 GGCGGCACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (27 bp):
ACTATTTCAAATTGAATGTCAAAATTT
Found at i:1030074 original size:12 final size:12
Alignment explanation
Indices: 1030059--1030090 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1030049 AATGTCAAAA
*
1030059 TTGGCGGCACAG
1 TTGGCAGCACAG
1030071 TTGGCAGCACAG
1 TTGGCAGCACAG
1030083 TTGGCAGC
1 TTGGCAGC
1030091 CTTTGTTGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.25, G:0.38, T:0.19
Consensus pattern (12 bp):
TTGGCAGCACAG
Found at i:1034833 original size:27 final size:27
Alignment explanation
Indices: 1034795--1034847 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
1034785 TGCAGCCTTC
* *
1034795 ACTATTTCAAATTGAATTTCATAATTT
1 ACTATTTCAAATTGAATGTCAAAATTT
1034822 ACTATTTCAAATTGAATGTCAAAATT
1 ACTATTTCAAATTGAATGTCAAAATT
1034848 GGCGGCACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (27 bp):
ACTATTTCAAATTGAATGTCAAAATTT
Found at i:1034861 original size:12 final size:12
Alignment explanation
Indices: 1034846--1034877 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1034836 AATGTCAAAA
*
1034846 TTGGCGGCACAG
1 TTGGCAGCACAG
1034858 TTGGCAGCACAG
1 TTGGCAGCACAG
1034870 TTGGCAGC
1 TTGGCAGC
1034878 CTTTGTTGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.25, G:0.38, T:0.19
Consensus pattern (12 bp):
TTGGCAGCACAG
Found at i:1039984 original size:64 final size:64
Alignment explanation
Indices: 1039827--1040003 Score: 243
Period size: 64 Copynumber: 2.8 Consensus size: 64
1039817 ATGCTTCCAA
* * * **
1039827 CGATAATTCACATG-AATGGCACTTGGAATATTCTTAAGACCTGGAGTTTCCCTAATGCTAGCT
1 CGATAATCCACATGAAATGGCGCTTGGAATCTTCTTAAGATTTGGAGTTTCCCTAATGCTAGCT
* *
1039890 -TAGTAATCCACATGAAATGGTGCTTGGAATCTTCTTAAGATTTGGAGTTTCCCTAATGCTAGCT
1 CGA-TAATCCACATGAAATGGCGCTTGGAATCTTCTTAAGATTTGGAGTTTCCCTAATGCTAGCT
*
1039954 CGATAATCCACATGAAATGGCGCTTGGAATCTT-TTCAAAATTTGGAGTTT
1 CGATAATCCACATGAAATGGCGCTTGGAATCTTCTT-AAGATTTGGAGTTT
1040004 TTTAGTGCTA
Statistics
Matches: 100, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
62 1 0.01
63 12 0.12
64 86 0.86
65 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (64 bp):
CGATAATCCACATGAAATGGCGCTTGGAATCTTCTTAAGATTTGGAGTTTCCCTAATGCTAGCT
Found at i:1043906 original size:21 final size:20
Alignment explanation
Indices: 1043880--1043918 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1043870 ATTGAGACCT
*
1043880 TGTATCGATATATTCTAGAAA
1 TGTATCGATACATT-TAGAAA
1043901 TGTATCGATACATTTAGA
1 TGTATCGATACATTTAGA
1043919 CAAAAATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATTTAGAAA
Found at i:1046953 original size:2 final size:2
Alignment explanation
Indices: 1046946--1046990 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1046936 TTGTCTTTAC
1046946 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1046988 AT A
1 AT A
1046991 AAGGAAGATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1047934 original size:20 final size:23
Alignment explanation
Indices: 1047909--1047950 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 23
1047899 TTCCTAAGTA
1047909 ATAAACAA-C-ATAAAA-AATAG
1 ATAAACAATCAATAAAATAATAG
1047929 ATAAACAATCAATAAAATAATA
1 ATAAACAATCAATAAAATAATA
1047951 AAATTCTCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
21 1 0.05
22 6 0.32
23 4 0.21
ACGTcount: A:0.69, C:0.10, G:0.02, T:0.19
Consensus pattern (23 bp):
ATAAACAATCAATAAAATAATAG
Found at i:1048434 original size:25 final size:25
Alignment explanation
Indices: 1048406--1048456 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
1048396 CAGGGCTTAA
*
1048406 ACCCTAAATTTTATAGATTTCATAG
1 ACCCTAAATATTATAGATTTCATAG
1048431 ACCCTAAATATTATAGATTTCATAG
1 ACCCTAAATATTATAGATTTCATAG
1048456 A
1 A
1048457 TCGGAACTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (25 bp):
ACCCTAAATATTATAGATTTCATAG
Found at i:1049359 original size:16 final size:17
Alignment explanation
Indices: 1049328--1049362 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1049318 TAAGGAAAAA
*
1049328 ATAATCATCATTACTAT
1 ATAATCATCATAACTAT
1049345 ATAAT-ATCATAACTAT
1 ATAATCATCATAACTAT
1049361 AT
1 AT
1049363 TATAATCGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (17 bp):
ATAATCATCATAACTAT
Found at i:1050582 original size:3 final size:3
Alignment explanation
Indices: 1050576--1050604 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1050566 CTACTACTAC
1050576 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1050605 TATTGTAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1059648 original size:6 final size:6
Alignment explanation
Indices: 1059625--1059667 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
1059615 AGATATGAGA
* *
1059625 ATGTGC ATGTGA ATGTGC ATGTGC CTGTGC ATGTGC ATGTGC A
1 ATGTGC ATGTGC ATGTGC ATGTGC ATGTGC ATGTGC ATGTGC A
1059668 ATAATCACTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.19, C:0.16, G:0.33, T:0.33
Consensus pattern (6 bp):
ATGTGC
Found at i:1059770 original size:24 final size:25
Alignment explanation
Indices: 1059743--1059798 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 25
1059733 TTAATAATTT
1059743 TATATTAGATATAATTAT-ATATAA
1 TATATTAGATATAATTATGATATAA
*
1059767 TATA--A-AAATAATTATGATATAA
1 TATATTAGATATAATTATGATATAA
*
1059789 AATATT-GATA
1 TATATTAGATA
1059799 AGATATTCAG
Statistics
Matches: 25, Mismatches: 3, Indels: 8
0.69 0.08 0.22
Matches are distributed among these distances:
21 9 0.36
22 10 0.40
24 6 0.24
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (25 bp):
TATATTAGATATAATTATGATATAA
Found at i:1062374 original size:27 final size:27
Alignment explanation
Indices: 1062344--1062414 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
1062334 GAACAGTACT
* * *
1062344 GTTGAAGATAATATTGAAGCAGCCAGC
1 GTTGAAGAAAATAGTGAACCAGCCAGC
*
1062371 GTTGAAGAAAATGGTGAACCAGCCAGC
1 GTTGAAGAAAATAGTGAACCAGCCAGC
*
1062398 GTTGAAGAAAATGGTGA
1 GTTGAAGAAAATAGTGA
1062415 GCAAAATTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.38, C:0.13, G:0.30, T:0.20
Consensus pattern (27 bp):
GTTGAAGAAAATAGTGAACCAGCCAGC
Found at i:1064387 original size:13 final size:13
Alignment explanation
Indices: 1064369--1064393 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1064359 TATTCTTTAC
1064369 AAATATAATATAA
1 AAATATAATATAA
1064382 AAATATAATATA
1 AAATATAATATA
1064394 TAAGTCATAA
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:1064659 original size:15 final size:14
Alignment explanation
Indices: 1064639--1064668 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1064629 TTAGATATAA
1064639 AAAGAAAAATAAAAG
1 AAAGAAAAA-AAAAG
1064654 AAAGAAAAAAAAAG
1 AAAGAAAAAAAAAG
1064668 A
1 A
1064669 GGCGGAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.03
Consensus pattern (14 bp):
AAAGAAAAAAAAAG
Found at i:1065005 original size:20 final size:21
Alignment explanation
Indices: 1064982--1065036 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
1064972 TTATTTTATT
1064982 TTATTTTATATTTTTTAAA-A
1 TTATTTTATATTTTTTAAATA
*
1065002 TTATTATTTTATTTTTTAAATA
1 TTATT-TTATATTTTTTAAATA
*
1065024 TT-TTTTAAATTTT
1 TTATTTTATATTTT
1065037 AATATATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 12 0.40
21 15 0.50
22 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
TTATTTTATATTTTTTAAATA
Found at i:1065015 original size:5 final size:5
Alignment explanation
Indices: 1064966--1064990 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1064956 TTGATAAATA
1064966 TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT
1064991 ATTTTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:1065078 original size:26 final size:26
Alignment explanation
Indices: 1065034--1065096 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
1065024 TTTTTTAAAT
1065034 TTTAATATATATTAGATATATATTAA
1 TTTAATATATATTAGATATATATTAA
* *
1065060 TTTACATATATA-TATATATATATTTA
1 TTTA-ATATATATTAGATATATATTAA
*
1065086 TAT-ATATATAT
1 TTTAATATATAT
1065097 GAATATTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
24 7 0.22
26 18 0.56
27 7 0.22
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (26 bp):
TTTAATATATATTAGATATATATTAA
Found at i:1065113 original size:2 final size:2
Alignment explanation
Indices: 1065038--1065096 Score: 61
Period size: 2 Copynumber: 31.0 Consensus size: 2
1065028 TTAAATTTTA
* * *
1065038 AT AT AT AT -T AG AT AT AT AT -T A- AT TT AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1065077 AT AT AT TT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
1065097 GAATATTTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
1 3 0.07
2 43 0.93
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1066112 original size:50 final size:51
Alignment explanation
Indices: 1066043--1066179 Score: 163
Period size: 51 Copynumber: 2.7 Consensus size: 51
1066033 TATAAAAAGA
*
1066043 AAATGTATTGATACA-TTTTTATTGTATCGATACATTTTGAG-TTTTGATCT
1 AAATGTATTGATACATTTTTTATTGTATCGATACATTCTG-GTTTTTGATCT
* * *
1066093 AAATATATTGATA-ATTTTTTTATTGTATTGATATATTCTGGTTTTTGATCT
1 AAATGTATTGATACA-TTTTTTATTGTATCGATACATTCTGGTTTTTGATCT
* * * *
1066144 AAATGTGTTGATACATTCTTCAATGTATCGATACAT
1 AAATGTATTGATACATTTTTTATTGTATCGATACAT
1066180 CCAATTAAAT
Statistics
Matches: 72, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
49 1 0.01
50 13 0.18
51 57 0.79
52 1 0.01
ACGTcount: A:0.29, C:0.08, G:0.13, T:0.50
Consensus pattern (51 bp):
AAATGTATTGATACATTTTTTATTGTATCGATACATTCTGGTTTTTGATCT
Found at i:1071025 original size:20 final size:21
Alignment explanation
Indices: 1070966--1071027 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 21
1070956 TCTCTAAAGC
1070966 AAAAGATTGATCCCTTACA-AT
1 AAAAGATTGATCCCTTA-AGAT
** *
1070987 AAAAGACCGAT-CCTCTAAGGT
1 AAAAGATTGATCCCT-TAAGAT
1071008 -AAAGATTGATCCCTTAAGAT
1 AAAAGATTGATCCCTTAAGAT
1071028 CCAATAGTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
20 17 0.53
21 15 0.47
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (21 bp):
AAAAGATTGATCCCTTAAGAT
Found at i:1072616 original size:16 final size:16
Alignment explanation
Indices: 1072597--1072652 Score: 85
Period size: 16 Copynumber: 3.4 Consensus size: 16
1072587 AATTAGAGAA
1072597 AATTTAAATTTAAAAT
1 AATTTAAATTTAAAAT
*
1072613 AATTAAAATTTAAAAT
1 AATTTAAATTTAAAAT
*
1072629 AATTTAAATATAAAATT
1 AATTTAAATTTAAAA-T
1072646 AATTTAA
1 AATTTAA
1072653 TTATAAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
16 28 0.78
17 8 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTTAAATTTAAAAT
Found at i:1072648 original size:17 final size:16
Alignment explanation
Indices: 1072597--1072659 Score: 81
Period size: 16 Copynumber: 3.9 Consensus size: 16
1072587 AATTAGAGAA
*
1072597 AATTTAAATTTAAAAT
1 AATTTAAATATAAAAT
* *
1072613 AATTAAAATTTAAAAT
1 AATTTAAATATAAAAT
1072629 AATTTAAATATAAAATT
1 AATTTAAATATAAAA-T
*
1072646 AATTTAATTATAAA
1 AATTTAAATATAAA
1072660 TTTGCAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
16 28 0.67
17 14 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTTAAATATAAAAT
Found at i:1072756 original size:34 final size:38
Alignment explanation
Indices: 1072682--1072756 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 38
1072672 AATTTAATAT
1072682 TAAAATAAGAATAATTTAATTATATACTATTAATTTTTA
1 TAAAATAAGAAT-ATTTAATTATATACTATTAATTTTTA
* *
1072721 TAAAATAA-AAT-TTTAATTATTTA-T-TTTATTTTTA
1 TAAAATAAGAATATTTAATTATATACTATTAATTTTTA
1072755 TA
1 TA
1072757 TATTTTTTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
34 11 0.32
35 1 0.03
36 11 0.32
38 3 0.09
39 8 0.24
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (38 bp):
TAAAATAAGAATATTTAATTATATACTATTAATTTTTA
Found at i:1076166 original size:2 final size:2
Alignment explanation
Indices: 1076159--1076194 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1076149 TAACGTTACA
1076159 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1076195 GTGTGTGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1076199 original size:2 final size:2
Alignment explanation
Indices: 1076194--1076232 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1076184 TATATATATA
*
1076194 TG TG TG TG TG TG TG TG TG TG TG CG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1076233 ATATATATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.03, G:0.49, T:0.49
Consensus pattern (2 bp):
TG
Found at i:1076928 original size:2 final size:2
Alignment explanation
Indices: 1076921--1076952 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1076911 TCGCAGATTA
*
1076921 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1076953 TATGTATTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1080183 original size:104 final size:102
Alignment explanation
Indices: 1080054--1080307 Score: 292
Period size: 104 Copynumber: 2.4 Consensus size: 102
1080044 TTTATTAAAT
* * * * **
1080054 TTTTTAAATTTAAATTAATAAATATTTAGAAATGGAGTCCACATTATATTAATCTATTTTAAAAT
1 TTTTAAAATTTAAATTAATAAATATTTAAAAATAGAGTCCACATTATATTAATCCACATTAAAAT
*
1080119 AAATAAAAACTTTCTTATTTAAATATATAATTTTATTA
66 AAAT-AAAACTTTCATATTTAAATATATAATTTTATTA
*
1080157 TTTTAAAATTTAAATCTAATAAATATTTAAAAATAGAGTTCACATTATATTAATCCACATTAAAA
1 TTTTAAAATTTAAAT-TAATAAATATTTAAAAATAGAGTCCACATTATATTAATCCACATTAAAA
* * * *
1080222 TTAATGAAATTTTCATATTTTAATATATAATTTTATTAA
65 TAAATAAAACTTTCATATTTAAATATATAATTTTATT-A
*
1080261 TTTATTTAAATTTAAATTTAAATTAATAAATATTTAAGAATAGAGTC
1 --T-TTT--A---AAATTTAAATTAATAAATATTTAAAAATAGAGTC
1080308 AATATGATAT
Statistics
Matches: 127, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
103 42 0.33
104 48 0.38
106 1 0.01
107 3 0.02
109 1 0.01
111 22 0.17
112 10 0.08
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.45
Consensus pattern (102 bp):
TTTTAAAATTTAAATTAATAAATATTTAAAAATAGAGTCCACATTATATTAATCCACATTAAAAT
AAATAAAACTTTCATATTTAAATATATAATTTTATTA
Found at i:1080305 original size:111 final size:109
Alignment explanation
Indices: 1080162--1080385 Score: 287
Period size: 111 Copynumber: 2.0 Consensus size: 109
1080152 TATTATTTTA
1080162 AAATTTAAATCTAATAAATATTTAAAAATAGAGTTCACAT-T-ATATT-AATCCACATTAAAATT
1 AAATTTAAATCTAATAAATATTTAAAAATAGAG-TCA-ATATGATATTAAAT-CACATTAAAATT
* *
1080224 AATGAAATTTTCATATTTTAATATATAA-TTTTATTAATTTATTTAAATTT
63 AAT-AAACTTT--T-TTTTAATATATAATTTTTATTAAGTTATTTAAATTT
* * *
1080274 AAATTTAAAT-TAATAAATATTTAAGAATAGAGTCAATATGATATTAAATGACTTTAAAATTAAT
1 AAATTTAAATCTAATAAATATTTAAAAATAGAGTCAATATGATATTAAATCACATTAAAATTAAT
* *
1080338 AAACTTTTTTTTAATATGTAATTTTTATTAAGTTATTTGAATTT
66 AAACTTTTTTTTAATATATAATTTTTATTAAGTTATTTAAATTT
1080382 AAAT
1 AAAT
1080386 GAGCTAAATA
Statistics
Matches: 101, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
107 12 0.12
108 25 0.25
109 2 0.02
110 10 0.10
111 39 0.39
112 13 0.13
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (109 bp):
AAATTTAAATCTAATAAATATTTAAAAATAGAGTCAATATGATATTAAATCACATTAAAATTAAT
AAACTTTTTTTTAATATATAATTTTTATTAAGTTATTTAAATTT
Found at i:1080967 original size:20 final size:23
Alignment explanation
Indices: 1080926--1080972 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
1080916 CGATGCACAG
1080926 TTAATATTTTAATATATATAAAA
1 TTAATATTTTAATATATATAAAA
* *
1080949 TTAAT-TTTTAATTTATAAAAAA
1 TTAATATTTTAATATATATAAAA
1080971 TT
1 TT
1080973 TTATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TTAATATTTTAATATATATAAAA
Found at i:1083050 original size:43 final size:43
Alignment explanation
Indices: 1083003--1083084 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 43
1082993 AAAGCAATGA
***
1083003 ATGAAATTAATATATTATAATAATTTCAACGAATGAGATTAAG
1 ATGAAATTAATATATTATAATAAAAACAACGAATGAGATTAAG
*
1083046 ATGAAATTAATATATTATATTAAAAACAACGAATGAGAT
1 ATGAAATTAATATATTATAATAAAAACAACGAATGAGAT
1083085 AAAATTTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.51, C:0.05, G:0.11, T:0.33
Consensus pattern (43 bp):
ATGAAATTAATATATTATAATAAAAACAACGAATGAGATTAAG
Found at i:1083547 original size:43 final size:45
Alignment explanation
Indices: 1083499--1083596 Score: 139
Period size: 43 Copynumber: 2.2 Consensus size: 45
1083489 GCAATTAATG
1083499 AAATTAATATATTATATTAAAT-TCAATGAATGAAG-T-TGAGATA
1 AAATTAATATATTATATTAAATAT-AATGAATGAAGATATGAGATA
*
1083542 AAATTAATATATTATATTACATATAATGAATGAAGATGAATGAGATA
1 AAATTAATATATTATATTAAATATAATGAATGAAGAT--ATGAGATA
1083589 AAATTAAT
1 AAATTAAT
1083597 TGGTCAAATT
Statistics
Matches: 49, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
43 32 0.65
44 2 0.04
47 15 0.31
ACGTcount: A:0.51, C:0.02, G:0.11, T:0.36
Consensus pattern (45 bp):
AAATTAATATATTATATTAAATATAATGAATGAAGATATGAGATA
Found at i:1083721 original size:15 final size:16
Alignment explanation
Indices: 1083701--1083732 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1083691 ATAAAAAAAC
1083701 TATATTATATA-TATA
1 TATATTATATAGTATA
1083716 TATATTATATAGTATA
1 TATATTATATAGTATA
1083732 T
1 T
1083733 TACACACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TATATTATATAGTATA
Found at i:1083849 original size:174 final size:174
Alignment explanation
Indices: 1083548--1083894 Score: 561
Period size: 174 Copynumber: 2.0 Consensus size: 174
1083538 GATAAAATTA
* * * *
1083548 ATATATTATATTACATATAATGAATGAAGATGAATGAGATAAAATTAATTGGTCAAATTAATATT
1 ATATAGTATATTACACACAATGAATGAAGATGAATGAGATAAAATTAATTGATCAAATTAATATT
* *
1083613 ATACATTGAATTCAATGAATTAATTTTATAATAAATGAAAAAATTTTGAAAAACCCCATAATAAA
66 ATACATTGAATTCAATGAATTAATTTTATAATAAATGAAAAAATTTTAAAAAAACCCATAATAAA
1083678 TATTAGCATTTATATAAAAAAACTATATTATATATATA-TATATT
131 TATTAGCATTTATA-AAAAAAACTATATTATATATATATTATATT
*
1083722 ATATAGTATATTACACACAATGAATGAAGATGGATGAGATAAAATTAATTGATCAAATTAATATT
1 ATATAGTATATTACACACAATGAATGAAGATGAATGAGATAAAATTAATTGATCAAATTAATATT
* * **
1083787 ATACATTGAATTCAATGAATTATTTTTATAATATATGAAAAAATTTTAAAAAAATGCATAATAAA
66 ATACATTGAATTCAATGAATTAATTTTATAATAAATGAAAAAATTTTAAAAAAACCCATAATAAA
* *
1083852 TATTAGCATTTATACAAAAAACTATATTTTATATATATTATAT
131 TATTAGCATTTATAAAAAAAACTATATTATATATATATTATAT
1083895 AGATAAGTAT
Statistics
Matches: 159, Mismatches: 13, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
173 21 0.13
174 138 0.87
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (174 bp):
ATATAGTATATTACACACAATGAATGAAGATGAATGAGATAAAATTAATTGATCAAATTAATATT
ATACATTGAATTCAATGAATTAATTTTATAATAAATGAAAAAATTTTAAAAAAACCCATAATAAA
TATTAGCATTTATAAAAAAAACTATATTATATATATATTATATT
Found at i:1083970 original size:22 final size:22
Alignment explanation
Indices: 1083919--1083982 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
1083909 AAAAAAATTA
*
1083919 AATAATTAGTAAATGATGAATAT
1 AATAA-TAGTAAATGATTAATAT
*
1083942 AAGAATAGTAAATGATTAATA-
1 AATAATAGTAAATGATTAATAT
**
1083963 ACATAATAACAAATGATTAA
1 A-ATAATAGTAAATGATTAA
1083983 CAGCATGTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 1 0.03
22 30 0.86
23 4 0.11
ACGTcount: A:0.56, C:0.03, G:0.11, T:0.30
Consensus pattern (22 bp):
AATAATAGTAAATGATTAATAT
Found at i:1085646 original size:12 final size:12
Alignment explanation
Indices: 1085629--1085654 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1085619 AAAGATTACC
1085629 AAAAAAAGGTAA
1 AAAAAAAGGTAA
1085641 AAAAAAAGGTAA
1 AAAAAAAGGTAA
1085653 AA
1 AA
1085655 CATTTTAAAG
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:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (12 bp):
AAAAAAAGGTAA
Found at i:1087418 original size:21 final size:21
Alignment explanation
Indices: 1087364--1087418 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
1087354 CATCCACTCA
*
1087364 TTGGCAGCACTGGGGGCCACC
1 TTGGCAGCATTGGGGGCCACC
* *
1087385 TTGGCAGCATTGGGGGTCACT
1 TTGGCAGCATTGGGGGCCACC
*
1087406 TTGGCAGCTTTGG
1 TTGGCAGCATTGG
1087419 CGGTAACATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.13, C:0.24, G:0.38, T:0.25
Consensus pattern (21 bp):
TTGGCAGCATTGGGGGCCACC
Found at i:1087430 original size:21 final size:21
Alignment explanation
Indices: 1087362--1087431 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
1087352 ACCATCCACT
* * **
1087362 CATTGGCAGCACTGGGGGCCA
1 CATTGGCAGCATTGGCGGTAA
* * *
1087383 CCTTGGCAGCATTGGGGGTCA
1 CATTGGCAGCATTGGCGGTAA
* *
1087404 CTTTGGCAGCTTTGGCGGTAA
1 CATTGGCAGCATTGGCGGTAA
1087425 CATTGGC
1 CATTGGC
1087432 GGCACAACTG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (21 bp):
CATTGGCAGCATTGGCGGTAA
Found at i:1087912 original size:2 final size:2
Alignment explanation
Indices: 1087896--1087933 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
1087886 ATTGCATGCT
*
1087896 TA TA GA TA T- 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 T
1087934 TAACTGGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1089552 original size:18 final size:17
Alignment explanation
Indices: 1089523--1089576 Score: 83
Period size: 18 Copynumber: 3.2 Consensus size: 17
1089513 GAAATTTATA
1089523 ATTCTTAAAAATCTGTG
1 ATTCTTAAAAATCTGTG
*
1089540 ATTCTTAAAAAATCTATG
1 ATTCTT-AAAAATCTGTG
1089558 ATTCTT-AAAATCTGTG
1 ATTCTTAAAAATCTGTG
1089574 ATT
1 ATT
1089577 GATACTAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
16 12 0.35
17 6 0.18
18 16 0.47
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (17 bp):
ATTCTTAAAAATCTGTG
Found at i:1094530 original size:17 final size:17
Alignment explanation
Indices: 1094505--1094552 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
1094495 CTATTACGAC
*
1094505 TTTTACCTCTGGTTTGA
1 TTTTGCCTCTGGTTTGA
*
1094522 TTTTGCCTCTAGTTTGA
1 TTTTGCCTCTGGTTTGA
* *
1094539 TTCTGCTTCTGGTT
1 TTTTGCCTCTGGTT
1094553 GCTGTTACTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.08, C:0.19, G:0.19, T:0.54
Consensus pattern (17 bp):
TTTTGCCTCTGGTTTGA
Found at i:1094685 original size:30 final size:30
Alignment explanation
Indices: 1094581--1094720 Score: 112
Period size: 30 Copynumber: 4.9 Consensus size: 30
1094571 GCCTATCTAT
* * *
1094581 TTCTGGTTGCTGTTGCTATTGTTGATCTAC
1 TTCTGGTTGTTGTTGCTATTGTCGATCTGC
* * *
1094611 TTCTGGTTGTTGTTGCTATTATCAATCAGC
1 TTCTGGTTGTTGTTGCTATTGTCGATCTGC
* * *
1094641 TTCTAGTTGCTGTTGCTATTGCCGATCTGC
1 TTCTGGTTGTTGTTGCTATTGTCGATCTGC
* * *
1094671 TT-T--TGGTTATTG---TTGTCGATCTAC
1 TTCTGGTTGTTGTTGCTATTGTCGATCTGC
* *
1094695 TTCTAGTTATTGTTGCTATTGTCGAT
1 TTCTGGTTGTTGTTGCTATTGTCGAT
1094721 TGTTCTTATT
Statistics
Matches: 84, Mismatches: 20, Indels: 12
0.72 0.17 0.10
Matches are distributed among these distances:
24 12 0.14
25 1 0.01
27 12 0.14
29 1 0.01
30 58 0.69
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.49
Consensus pattern (30 bp):
TTCTGGTTGTTGTTGCTATTGTCGATCTGC
Found at i:1094767 original size:22 final size:22
Alignment explanation
Indices: 1094736--1094786 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
1094726 TTATTGTTAT
*
1094736 TGTTAAGTTTAGTTGCTACTAG
1 TGTTAAGTTTAATTGCTACTAG
*
1094758 TGTTAGGTTTAATTGCTACTAG
1 TGTTAAGTTTAATTGCTACTAG
1094780 TGTTAAG
1 TGTTAAG
1094787 GCATGCCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.45
Consensus pattern (22 bp):
TGTTAAGTTTAATTGCTACTAG
Found at i:1094867 original size:11 final size:11
Alignment explanation
Indices: 1094853--1094877 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1094843 TTTGTTATTT
1094853 TTTTAATTGGG
1 TTTTAATTGGG
1094864 TTTTAATTGGG
1 TTTTAATTGGG
1094875 TTT
1 TTT
1094878 GGGTTTAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.24, T:0.60
Consensus pattern (11 bp):
TTTTAATTGGG
Found at i:1099542 original size:18 final size:18
Alignment explanation
Indices: 1099519--1099575 Score: 87
Period size: 18 Copynumber: 3.2 Consensus size: 18
1099509 TATAATTTTT
1099519 AAAAATCAGTGATTCTTA
1 AAAAATCAGTGATTCTTA
*
1099537 AAAAATCAGTGATTCCTA
1 AAAAATCAGTGATTCTTA
* *
1099555 AAAAATCTGTAATTCTTA
1 AAAAATCAGTGATTCTTA
1099573 AAA
1 AAA
1099576 TCTGTGATTG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.32
Consensus pattern (18 bp):
AAAAATCAGTGATTCTTA
Found at i:1103038 original size:33 final size:33
Alignment explanation
Indices: 1102996--1103062 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1102986 TTCAACGATT
1102996 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
* *** *
1103029 TGTATCGATATATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
1103062 T
1 T
1103063 TTAAGCTACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:1103121 original size:13 final size:13
Alignment explanation
Indices: 1103103--1103127 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1103093 ATCACTTAAA
1103103 TGTATCGATACAT
1 TGTATCGATACAT
1103116 TGTATCGATACA
1 TGTATCGATACA
1103128 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1103192 original size:52 final size:52
Alignment explanation
Indices: 1103136--1103316 Score: 317
Period size: 52 Copynumber: 3.5 Consensus size: 52
1103126 CACTGATCTT
* * * **
1103136 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATAAATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATATACTATTCAA
1103188 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATATACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATATACTATTCAA
1103240 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATATACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATATACTATTCAA
1103292 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1103317 TCATATTTCG
Statistics
Matches: 124, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 124 1.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATATACTATTCAA
Found at i:1110885 original size:40 final size:37
Alignment explanation
Indices: 1110796--1110885 Score: 119
Period size: 38 Copynumber: 2.4 Consensus size: 37
1110786 GCTAGCTTTC
*
1110796 ATCTTAT-AAAATTAAGGTGCTTAGTTATAGCAGTTT
1 ATCTTATAAAAATTAAGCTGCTTAGTTATAGCAGTTT
*
1110832 ATATCTATAAAAATTAAGCTGCTTAGTTATAGCAATGTTT
1 ATCT-TATAAAAATTAAGCTGCTTAGTTATAGC-A-GTTT
1110872 ATCTTATAGAAAAT
1 ATCTTATA-AAAAT
1110886 GAGGTGATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
36 3 0.07
37 3 0.07
38 23 0.50
39 5 0.11
40 12 0.26
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (37 bp):
ATCTTATAAAAATTAAGCTGCTTAGTTATAGCAGTTT
Found at i:1111975 original size:27 final size:26
Alignment explanation
Indices: 1111917--1111986 Score: 77
Period size: 27 Copynumber: 2.7 Consensus size: 26
1111907 ATTAAAAAAT
* * *
1111917 GGGGTTGGAGTATCTCTTCGAGGAAT
1 GGGGTTGGAGTATCCCCTCGAGGAAA
*
1111943 GAGGTTGGAGTATCCCCTCGGAGGAAA
1 GGGGTTGGAGTATCCCCTC-GAGGAAA
* *
1111970 GGGGTTAGAGTGTCCCC
1 GGGGTTGGAGTATCCCC
1111987 GATGATGGCA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
26 16 0.44
27 20 0.56
ACGTcount: A:0.20, C:0.17, G:0.39, T:0.24
Consensus pattern (26 bp):
GGGGTTGGAGTATCCCCTCGAGGAAA
Found at i:1114443 original size:20 final size:20
Alignment explanation
Indices: 1114379--1114432 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1114369 AAAAACAGAA
1114379 TGTATTGATACATTGAAAAC
1 TGTATTGATACATTGAAAAC
*
1114399 TGTATTGAAACATTGAAAAC
1 TGTATTGATACATTGAAAAC
1114419 TGTATTGATACATT
1 TGTATTGATACATT
1114433 CACACATGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (20 bp):
TGTATTGATACATTGAAAAC
Found at i:1116853 original size:2 final size:2
Alignment explanation
Indices: 1116846--1116878 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1116836 TTCCACTTCT
1116846 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 T
1116879 GCATTATAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1117248 original size:42 final size:41
Alignment explanation
Indices: 1117202--1117328 Score: 115
Period size: 42 Copynumber: 3.2 Consensus size: 41
1117192 ATATGCATAT
* *
1117202 ATAATAAATAATTAAATTTTG-TTAAAATCATATTTATATTAA
1 ATAATAAAT-ATAAAATTTAGATT-AAATCATATTTATATTAA
* * *
1117244 ATAATCAAATATAAAATTTAGATTAATTTATGTTTATATTAA
1 ATAAT-AAATATAAAATTTAGATTAAATCATATTTATATTAA
*
1117286 ATAATAAA-ATATAAA-TTA-A--AACT-ATATTTATATTAA
1 ATAATAAATATA-AAATTTAGATTAAATCATATTTATATTAA
1117322 ATAATAA
1 ATAATAA
1117329 TTTTTAATTT
Statistics
Matches: 75, Mismatches: 7, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
36 19 0.25
37 3 0.04
39 1 0.01
40 6 0.08
41 6 0.08
42 34 0.45
43 6 0.08
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (41 bp):
ATAATAAATATAAAATTTAGATTAAATCATATTTATATTAA
Found at i:1117331 original size:17 final size:17
Alignment explanation
Indices: 1117276--1117331 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
1117266 TTAATTTATG
1117276 TTTATATTAAATAATAAAA
1 TTTATATTAAATAAT--AA
* * *
1117295 TATAAATTAAA-ACTATA
1 TTTATATTAAATAATA-A
1117312 TTTATATTAAATAATAA
1 TTTATATTAAATAATAA
1117329 TTT
1 TTT
1117332 TTAATTTTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
16 1 0.03
17 14 0.48
18 5 0.17
19 9 0.31
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTATATTAAATAATAA
Found at i:1117334 original size:19 final size:19
Alignment explanation
Indices: 1117276--1117334 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
1117266 TTAATTTATG
*
1117276 TTTATATTAAATAATAAAA
1 TTTATATTAAATAATAATA
* * *
1117295 TATAAATTAAA-ACT-ATA
1 TTTATATTAAATAATAATA
*
1117312 TTTATATTAAATAATAATT
1 TTTATATTAAATAATAATA
1117331 TTTA
1 TTTA
1117335 ATTTTTAAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
17 11 0.37
18 4 0.13
19 15 0.50
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTATATTAAATAATAATA
Found at i:1117352 original size:38 final size:36
Alignment explanation
Indices: 1117250--1117360 Score: 100
Period size: 36 Copynumber: 3.1 Consensus size: 36
1117240 TTAAATAATC
* * * *
1117250 AAAT-ATAAAATTTAGATT-AATTTATGTTTATATT
1 AAATAATAAAATATAAATTAAAATTATATTTATATT
*
1117284 AAATAATAAAATATAAATTAAAACTATATTTATATT
1 AAATAATAAAATATAAATTAAAATTATATTTATATT
** * * *
1117320 AAATAATAATTTTTAATTTTTAAAATTATATTTAAATT
1 AAATAATAAAATATAA--ATTAAAATTATATTTATATT
1117358 AAA
1 AAA
1117361 AATTATTAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
34 4 0.06
35 12 0.19
36 26 0.42
38 20 0.32
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (36 bp):
AAATAATAAAATATAAATTAAAATTATATTTATATT
Found at i:1117710 original size:25 final size:25
Alignment explanation
Indices: 1117659--1117711 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
1117649 ATTAAATATT
* * *
1117659 TTTTATATTTTTAATTATTATTTAA
1 TTTTATATTTTTAATAATTAATAAA
1117684 TTTTAT-TTTTTAATAATTTAATAAA
1 TTTTATATTTTTAATAA-TTAATAAA
1117709 TTT
1 TTT
1117712 AAATATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (25 bp):
TTTTATATTTTTAATAATTAATAAA
Done.