Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 115 of 210
Found at i:33972550 original size:21 final size:21
Alignment explanation
Indices: 33972524--33972567 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
33972514 ATACTATGCA
33972524 TATTGCAGTAACTCACCCGAC
1 TATTGCAGTAACTCACCCGAC
33972545 TATTGCAGTAACTCACCCGAC
1 TATTGCAGTAACTCACCCGAC
33972566 TA
1 TA
33972568 ATACTTCACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.32, G:0.14, T:0.25
Consensus pattern (21 bp):
TATTGCAGTAACTCACCCGAC
Found at i:33972837 original size:43 final size:43
Alignment explanation
Indices: 33972756--33973055 Score: 170
Period size: 43 Copynumber: 7.3 Consensus size: 43
33972746 TGACATATCA
* * *
33972756 AAACAACT-TACTGGCATACACAGTGCATCATCAGATATACCG
1 AAACAACTATACTAGCACACACAGTGCATCATCAAATATACCG
** *
33972798 AAGTAACTATACTAGCACACGCAGTGCATCATCAAATATACCG
1 AAACAACTATACTAGCACACACAGTGCATCATCAAATATACCG
* * * *
33972841 AAACAACTATACTAGCACACACAGCGCACCATCGAATATATC-
1 AAACAACTATACTAGCACACACAGTGCATCATCAAATATACCG
* *
33972883 AAAGGC-AC-ATAGT-GTATCA-ACA--G-AT-AT---AT-T---G
1 AAA--CAACTATACTAGCA-CACACAGTGCATCATCAAATATACCG
** * * * * *
33972914 AAGTAACTGTACTGGCACACATAGTGCATCATTAGATATACCG
1 AAACAACTATACTAGCACACACAGTGCATCATCAAATATACCG
* ** * *
33972957 CAGTAACTATACTAGCACACACAGTGCATCATCAGATATA-CT
1 AAACAACTATACTAGCACACACAGTGCATCATCAAATATACCG
* * *
33972999 AAAGTAACTATACTAGCACATACAGTGCATCATCGAATATACC-
1 AAA-CAACTATACTAGCACACACAGTGCATCATCAAATATACCG
*
33973042 AAAGTAACTATACT
1 AAA-CAACTATACT
33973056 TGAACATACA
Statistics
Matches: 203, Mismatches: 33, Indels: 43
0.73 0.12 0.15
Matches are distributed among these distances:
30 2 0.01
31 7 0.03
32 4 0.02
33 1 0.00
34 3 0.01
35 2 0.01
36 2 0.01
37 2 0.01
38 1 0.00
39 3 0.01
40 1 0.00
41 5 0.02
42 17 0.08
43 151 0.74
44 2 0.01
ACGTcount: A:0.40, C:0.24, G:0.14, T:0.23
Consensus pattern (43 bp):
AAACAACTATACTAGCACACACAGTGCATCATCAAATATACCG
Found at i:33972996 original size:116 final size:116
Alignment explanation
Indices: 33972777--33972989 Score: 291
Period size: 116 Copynumber: 1.8 Consensus size: 116
33972767 TGGCATACAC
* *
33972777 AGTGCATCATCAGATATACCGAAGTAACTATACTAGCACACGCAGTGCATCATCAAATATACCGA
1 AGTGCATCAACAGATATACCGAAGTAACTATACTAGCACACACAGTGCATCATCAAATATACCGA
33972842 AACAACTATACTAGCACACACAGCGCACCATCGAATATATCAAAGGCACAT
66 AACAACTATACTAGCACACACAGCGCACCATCGAATATATCAAAGGCACAT
* ** * * * * * *
33972893 AGTGTATCAACAGATATATTGAAGTAACTGTACTGGCACACATAGTGCATCATTAGATATACCGC
1 AGTGCATCAACAGATATACCGAAGTAACTATACTAGCACACACAGTGCATCATCAAATATACCGA
** * *
33972958 AGTAACTATACTAGCACACACAGTGCATCATC
66 AACAACTATACTAGCACACACAGCGCACCATC
33972990 AGATATACTA
Statistics
Matches: 82, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
116 82 1.00
ACGTcount: A:0.38, C:0.24, G:0.15, T:0.22
Consensus pattern (116 bp):
AGTGCATCAACAGATATACCGAAGTAACTATACTAGCACACACAGTGCATCATCAAATATACCGA
AACAACTATACTAGCACACACAGCGCACCATCGAATATATCAAAGGCACAT
Found at i:33973030 original size:86 final size:86
Alignment explanation
Indices: 33972888--33973096 Score: 240
Period size: 86 Copynumber: 2.4 Consensus size: 86
33972878 ATATCAAAGG
* * * * * *
33972888 CACATAGTGTATCAACAGATATATTGAAGTAACTGTACTGGCACACATAGTGCATCATTAG-ATA
1 CACACAGTGTATCATCAGATATACTGAAGTAACTATACTAGCACACACAGTGCATCA-TAGAATA
** *
33972952 TACCGCAGTAACTATACTAGCA
65 TACCAAAGTAACTATACTAGAA
* * * *
33972974 CACACAGTGCATCATCAGATATACTAAAGTAACTATACTAGCACATACAGTGCATCATCGAATAT
1 CACACAGTGTATCATCAGATATACTGAAGTAACTATACTAGCACACACAGTGCATCATAGAATAT
*
33973039 ACCAAAGTAACTATACTTGAA
66 ACCAAAGTAACTATACTAGAA
* * * *
33973060 CATACAATGTATTATCAGATATACGGAAGTAACTATA
1 CACACAGTGTATCATCAGATATACTGAAGTAACTATA
33973097 TTGCCACTTG
Statistics
Matches: 102, Mismatches: 20, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
85 2 0.02
86 100 0.98
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (86 bp):
CACACAGTGTATCATCAGATATACTGAAGTAACTATACTAGCACACACAGTGCATCATAGAATAT
ACCAAAGTAACTATACTAGAA
Found at i:33973063 original size:43 final size:43
Alignment explanation
Indices: 33972914--33973096 Score: 206
Period size: 43 Copynumber: 4.3 Consensus size: 43
33972904 AGATATATTG
* * * * * *
33972914 AAGTAACTGTACTGGCACACATAGTGCATCATTAGATATACCG
1 AAGTAACTATACTAGCACATACAGTGCATCATCAGATATACCA
* * *
33972957 CAGTAACTATACTAGCACACACAGTGCATCATCAGATATACTA
1 AAGTAACTATACTAGCACATACAGTGCATCATCAGATATACCA
33973000 AAGTAACTATACTAGCACATACAGTGCATCATC-GAATATACCA
1 AAGTAACTATACTAGCACATACAGTGCATCATCAG-ATATACCA
* * * * * **
33973043 AAGTAACTATACTTGAACATACAATGTATTATCAGATATACGG
1 AAGTAACTATACTAGCACATACAGTGCATCATCAGATATACCA
33973086 AAGTAACTATA
1 AAGTAACTATA
33973097 TTGCCACTTG
Statistics
Matches: 121, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
42 1 0.01
43 119 0.98
44 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (43 bp):
AAGTAACTATACTAGCACATACAGTGCATCATCAGATATACCA
Found at i:33973111 original size:86 final size:86
Alignment explanation
Indices: 33972914--33973126 Score: 223
Period size: 86 Copynumber: 2.5 Consensus size: 86
33972904 AGATATATTG
* * * * * ** *
33972914 AAGTAACTGTACTGGCACACATAGTGCATCAT-TAGATATACCGCAGTAACTATACTAGCACACA
1 AAGTAACTATACTAGCACATACAGTGCATCATCGA-ATATACCAAAGTAACTATACTAGAACACA
* *
33972978 CAGTGCATCATCAGATATACTA
65 CAATGCATCATCAGATATACGA
* *
33973000 AAGTAACTATACTAGCACATACAGTGCATCATCGAATATACCAAAGTAACTATACTTGAACATAC
1 AAGTAACTATACTAGCACATACAGTGCATCATCGAATATACCAAAGTAACTATACTAGAACACAC
* * *
33973065 AATGTATTATCAGATATACGG
66 AATGCATCATCAGATATACGA
* * * *
33973086 AAGTAACTATA-TTGCCACTTGCAGTGCATTATCGAATATAC
1 AAGTAACTATACTAG-CACATACAGTGCATCATCGAATATAC
33973127 TGTAACAGCC
Statistics
Matches: 106, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
85 2 0.02
86 103 0.97
87 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (86 bp):
AAGTAACTATACTAGCACATACAGTGCATCATCGAATATACCAAAGTAACTATACTAGAACACAC
AATGCATCATCAGATATACGA
Found at i:33973117 original size:43 final size:43
Alignment explanation
Indices: 33972914--33973126 Score: 182
Period size: 43 Copynumber: 5.0 Consensus size: 43
33972904 AGATATATTG
* * * * * *
33972914 AAGTAACTGTACTGGCACACATAGTGCATCAT-TAGATATACCG
1 AAGTAACTATACTTGCACATACAGTGCATCATCGA-ATATACCA
* * * *
33972957 CAGTAACTATACTAGCACACACAGTGCATCATC-AGATATACTA
1 AAGTAACTATACTTGCACATACAGTGCATCATCGA-ATATACCA
*
33973000 AAGTAACTATACTAGCACATACAGTGCATCATCGAATATACCA
1 AAGTAACTATACTTGCACATACAGTGCATCATCGAATATACCA
* * * * **
33973043 AAGTAACTATACTTGAACATACAATGTATTATC-AGATATACGG
1 AAGTAACTATACTTGCACATACAGTGCATCATCGA-ATATACCA
* * *
33973086 AAGTAACTATA-TTGCCACTTGCAGTGCATTATCGAATATAC
1 AAGTAACTATACTTG-CACATACAGTGCATCATCGAATATAC
33973127 TGTAACAGCC
Statistics
Matches: 144, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
42 4 0.03
43 138 0.96
44 2 0.01
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (43 bp):
AAGTAACTATACTTGCACATACAGTGCATCATCGAATATACCA
Found at i:33975698 original size:43 final size:43
Alignment explanation
Indices: 33975631--33975893 Score: 217
Period size: 43 Copynumber: 6.1 Consensus size: 43
33975621 ACATATACTA
* * * *
33975631 AAGTAACTATACTTGAACATACAATGCATCATCAGATACACCG
1 AAGTAACTATACTAGCACACACAATGCATCATCAGATATACCG
* **
33975674 AAGTAACTATACTGGCACACACAATGCATCATTGGATATACCG
1 AAGTAACTATACTAGCACACACAATGCATCATCAGATATACCG
* * * *
33975717 AAGTAACTATACTAGAACATACAATGCATCATCGGATATACCA
1 AAGTAACTATACTAGCACACACAATGCATCATCAGATATACCG
* * * * **
33975760 AAGTAACTATACCACCACACATAGTGCATCATCAGATATATTG
1 AAGTAACTATACTAGCACACACAATGCATCATCAGATATACCG
* * * * * * **
33975803 AAGTAACTGTACTGGCACAAATAGTTCATCATCAGATATATTG
1 AAGTAACTATACTAGCACACACAATGCATCATCAGATATACCG
* * * *
33975846 ATA-TAACTATA-TTGATACATACAGTGCATCATC-GTATATACCG
1 A-AGTAACTATACTAG-CACACACAATGCATCATCAG-ATATACCG
33975889 AAGTA
1 AAGTA
33975894 TAACCTGGAT
Statistics
Matches: 181, Mismatches: 35, Indels: 8
0.81 0.16 0.04
Matches are distributed among these distances:
42 4 0.02
43 176 0.97
44 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (43 bp):
AAGTAACTATACTAGCACACACAATGCATCATCAGATATACCG
Found at i:33975779 original size:86 final size:86
Alignment explanation
Indices: 33975631--33975815 Score: 244
Period size: 86 Copynumber: 2.2 Consensus size: 86
33975621 ACATATACTA
* * ***
33975631 AAGTAACTATACTTGAACATACAATGCATCATCAGATACACCGAAGTAACTATACTGGCACACAC
1 AAGTAACTATACTAGAACATACAATGCATCATCAGATACACCAAAGTAACTATACCACCACACAC
**
33975696 AATGCATCATTGGATATACCG
66 AATGCATCATCAGATATACCG
* * *
33975717 AAGTAACTATACTAGAACATACAATGCATCATCGGATATACCAAAGTAACTATACCACCACACAT
1 AAGTAACTATACTAGAACATACAATGCATCATCAGATACACCAAAGTAACTATACCACCACACAC
* **
33975782 AGTGCATCATCAGATATATTG
66 AATGCATCATCAGATATACCG
*
33975803 AAGTAACTGTACT
1 AAGTAACTATACT
33975816 GGCACAAATA
Statistics
Matches: 85, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
86 85 1.00
ACGTcount: A:0.41, C:0.22, G:0.13, T:0.24
Consensus pattern (86 bp):
AAGTAACTATACTAGAACATACAATGCATCATCAGATACACCAAAGTAACTATACCACCACACAC
AATGCATCATCAGATATACCG
Found at i:33975833 original size:129 final size:129
Alignment explanation
Indices: 33975655--33975893 Score: 302
Period size: 129 Copynumber: 1.9 Consensus size: 129
33975645 GAACATACAA
* **
33975655 TGCATCATCAGATACACCGAAGTAACTATACTGGCACACACAATGCATCATTGGATATACCGA-A
1 TGCATCATCAGATACACCGAAGTAACTATACTGGCACAAACAATGCATCATCAGATATACCGATA
33975719 GTAACTATACTAGA-ACATACAATGCATCATCGGATATACCAAAGTAACTATACCACCACACATA
66 -TAACTATA-TAGATACATACAATGCATCATCGGATATACCAAAGTAACTATACCACCACACATA
33975783 G
129 G
* ** * * * * **
33975784 TGCATCATCAGATATATTGAAGTAACTGTACTGGCACAAATAGTTCATCATCAGATATATTGATA
1 TGCATCATCAGATACACCGAAGTAACTATACTGGCACAAACAATGCATCATCAGATATACCGATA
* * * *
33975849 TAACTATATTGATACATACAGTGCATCATCGTATATACCGAAGTA
66 TAACTATATAGATACATACAATGCATCATCGGATATACCAAAGTA
33975894 TAACCTGGAT
Statistics
Matches: 92, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
128 3 0.03
129 88 0.96
130 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.26
Consensus pattern (129 bp):
TGCATCATCAGATACACCGAAGTAACTATACTGGCACAAACAATGCATCATCAGATATACCGATA
TAACTATATAGATACATACAATGCATCATCGGATATACCAAAGTAACTATACCACCACACATAG
Found at i:33988429 original size:95 final size:92
Alignment explanation
Indices: 33988317--33988489 Score: 238
Period size: 95 Copynumber: 1.8 Consensus size: 92
33988307 GTGCATGGTC
* * ** * * *
33988317 CTTCATTAACTAGCTTTAATGTATCAGCTGGATGCATGAATTTCTAGCTGAAAAAAAATAGTTCC
1 CTTCATTAAATAGCTTTAATGTATAAGCTAAATACATGAATTTCCAGC--AAAAAAAA-AGCTCC
33988382 CTTTGTTCATGCACATTCGGGTACATTGCT
63 CTTTGTTCATGCACATTCGGGTACATTGCT
* *
33988412 CTTCATTAAATAGCTTTAATGTATAAGCTAAATACATGAATTTCCAGCCACAAAAAAGCTCCCTT
1 CTTCATTAAATAGCTTTAATGTATAAGCTAAATACATGAATTTCCAGCAAAAAAAAAGCTCCCTT
33988477 TGTTCATGCACAT
66 TGTTCATGCACAT
33988490 GTGGGTGCAT
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
92 21 0.30
93 6 0.09
95 42 0.61
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (92 bp):
CTTCATTAAATAGCTTTAATGTATAAGCTAAATACATGAATTTCCAGCAAAAAAAAAGCTCCCTT
TGTTCATGCACATTCGGGTACATTGCT
Found at i:33994909 original size:21 final size:24
Alignment explanation
Indices: 33994885--33994933 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
33994875 GAAAGGTCGA
33994885 GGCCATGTGG-G-TGGA-TCACAT
1 GGCCATGTGGTGTTGGAGTCACAT
*
33994906 GGCCGTGTGGTGTTGGAGTCACAT
1 GGCCATGTGGTGTTGGAGTCACAT
33994930 GGCC
1 GGCC
33994934 GTGCGAACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 9 0.38
22 1 0.04
23 4 0.17
24 10 0.42
ACGTcount: A:0.14, C:0.20, G:0.41, T:0.24
Consensus pattern (24 bp):
GGCCATGTGGTGTTGGAGTCACAT
Found at i:34019047 original size:15 final size:16
Alignment explanation
Indices: 34019015--34019088 Score: 66
Period size: 15 Copynumber: 4.9 Consensus size: 16
34019005 CACTATAGTA
*
34019015 TCAGTATCTATAGTTT
1 TCAGAATCTATAGTTT
*
34019031 TCAGAATCTAAAG-TT
1 TCAGAATCTATAGTTT
* *
34019046 TCA-CA-GTATAGTTT
1 TCAGAATCTATAGTTT
*
34019060 TCAGAATCTAGAG-TT
1 TCAGAATCTATAGTTT
*
34019075 TCATAATCTATAGT
1 TCAGAATCTATAGT
34019089 ATTCTATACT
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
13 4 0.09
14 6 0.14
15 19 0.43
16 15 0.34
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (16 bp):
TCAGAATCTATAGTTT
Found at i:34019755 original size:7 final size:7
Alignment explanation
Indices: 34019741--34019776 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
34019731 TGCAAAAACC
34019741 ATCCAAA
1 ATCCAAA
*
34019748 AACCAAA
1 ATCCAAA
34019755 ATCCAAA
1 ATCCAAA
34019762 ATCCAAA
1 ATCCAAA
*
34019769 GTCCAAA
1 ATCCAAA
34019776 A
1 A
34019777 GAAAGTTCCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.58, C:0.28, G:0.03, T:0.11
Consensus pattern (7 bp):
ATCCAAA
Found at i:34033136 original size:51 final size:50
Alignment explanation
Indices: 34032953--34033296 Score: 295
Period size: 51 Copynumber: 6.8 Consensus size: 50
34032943 ATTTTTATCA
* * *
34032953 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATC--AGTT
1 TTCGGTACACATAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTT
* * * *
34033001 TTACAGTTCACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAGTT
1 TT-CGGTACACATAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTT
* *
34033051 TTACGGCT-CACGTAGTAGCCTTCACATAGTACTACATACGTGACCAAAGCTT
1 TT-CGG-TACACATAGTAGCCTTCACATAGTACTACACACGTGACCAAAG-TT
* * * * * *
34033103 TTCGGTACCCATTGTAGCCTTCACTTAGTACTACACATGTAACCATAGTT
1 TTCGGTACACATAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTT
* * * * **
34033153 TACCGATACACGTAGTAGCATTCACGCAGTACTACACACGTG-CTCAAAGCTT
1 T-TCGGTACACATAGTAGCCTTCACATAGTACTACACACGTGAC-CAAAG-TT
** * *
34033205 TTCGGTACACATAGTAGCCTTCATTTAGTACTACACATGTGACCATTA-TT
1 TTCGGTACACATAGTAGCCTTCACATAGTACTACACACGTGACCA-AAGTT
* * * * *
34033255 TATCGATACACGTAGTAGCCTCCACACAGTACTACGCACGTG
1 T-TCGGTACACATAGTAGCCTTCACATAGTACTACACACGTG
34033297 TTCGTCGACA
Statistics
Matches: 242, Mismatches: 42, Indels: 21
0.79 0.14 0.07
Matches are distributed among these distances:
48 2 0.01
49 39 0.16
50 52 0.21
51 140 0.58
52 9 0.04
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (50 bp):
TTCGGTACACATAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTT
Found at i:34033194 original size:102 final size:102
Alignment explanation
Indices: 34032955--34033296 Score: 410
Period size: 102 Copynumber: 3.4 Consensus size: 102
34032945 TTTTATCATT
* * * * *
34032955 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATC--AG-TTTTACAGTTCACGTAGT
1 CGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTT-CGGTACACATAGT
* * *
34033017 AGCCTTCACATAGTACTACACACGTGATCA-AGTTTTAC
65 AGCCTTCACTTAGTACTACACATGTGACCATAG-TTTAC
* * * * * *
34033055 GGCT-CACGTAGTAGCCTTCACATAGTACTACATACGTGACCAAAGCTTTTCGGTACCCATTGTA
1 CGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGTA
*
34033119 GCCTTCACTTAGTACTACACATGTAACCATAGTTTAC
66 GCCTTCACTTAGTACTACACATGTGACCATAGTTTAC
* *
34033156 CGATACACGTAGTAGCATTCACGCAGTACTACACACGTG-CTCAAAGCTTTTCGGTACACATAGT
1 CGATACACGTAGTAGCCTTCACACAGTACTACACACGTGAC-CAAAGCTTTTCGGTACACATAGT
* *
34033220 AGCCTTCATTTAGTACTACACATGTGACCATTA-TTTAT
65 AGCCTTCACTTAGTACTACACATGTGACCA-TAGTTTAC
* *
34033258 CGATACACGTAGTAGCCTCCACACAGTACTACGCACGTG
1 CGATACACGTAGTAGCCTTCACACAGTACTACACACGTG
34033297 TTCGTCGACA
Statistics
Matches: 207, Mismatches: 28, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
99 35 0.17
100 2 0.01
101 44 0.21
102 124 0.60
103 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.28
Consensus pattern (102 bp):
CGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACATAGTA
GCCTTCACTTAGTACTACACATGTGACCATAGTTTAC
Found at i:34033275 original size:153 final size:149
Alignment explanation
Indices: 34032953--34033295 Score: 370
Period size: 153 Copynumber: 2.3 Consensus size: 149
34032943 ATTTTTATCA
* * *
34032953 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAGTTTTACAGTTCACGTAGTA
1 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTAACCAGTTTTACAGTACACGTAGTA
* * *
34033018 GCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGCTCACGTAGTAGCCTTCACATAGTAC
66 GCATTCACACAGTACTACACACGTGATCAAGTTTTACGGCTCACATAGTAGCCTTCACATAGTAC
*
34033083 TACATACGTGACCAAAGCTT
131 TACACACGTGACCAAA-CTT
* * * * * * *
34033103 TTCGGTACCCATTGTAGCCTTCACTTAGTACTACACATGTAACCA-TAGTTTACCGATACACGTA
1 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTAACCAGT--TTTACAG-TACACGTA
* * **
34033167 GTAGCATTCACGCAGTACTACACACGTGCTCAAAGCTTTT-CGG-TACACATAGTAGCCTTCATT
63 GTAGCATTCACACAGTACTACACACGTGATC-AAG-TTTTACGGCT-CACATAGTAGCCTTCACA
* *
34033230 TAGTACTACACATGTGACCATTA-TT
125 TAGTACTACACACGTGACCA-AACTT
* * *
34033255 TATCGATACACGTAGTAGCCTCCACACAGTACTACGCACGT
1 T-TCGATACACGTAGTAGCCTTCACATAGTACTACACACGT
34033296 GTTCGTCGAC
Statistics
Matches: 156, Mismatches: 29, Indels: 13
0.79 0.15 0.07
Matches are distributed among these distances:
149 1 0.01
150 37 0.24
151 6 0.04
152 38 0.24
153 69 0.44
154 5 0.03
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (149 bp):
TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTAACCAGTTTTACAGTACACGTAGTA
GCATTCACACAGTACTACACACGTGATCAAGTTTTACGGCTCACATAGTAGCCTTCACATAGTAC
TACACACGTGACCAAACTT
Found at i:34033410 original size:15 final size:17
Alignment explanation
Indices: 34033390--34033422 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
34033380 GTTACGAAAC
34033390 ATAACAA-A-AATAATT
1 ATAACAATATAATAATT
34033405 ATAACAATATAATAATT
1 ATAACAATATAATAATT
34033422 A
1 A
34033423 CATACAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 1 0.06
17 8 0.50
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (17 bp):
ATAACAATATAATAATT
Found at i:34040245 original size:25 final size:25
Alignment explanation
Indices: 34040213--34040262 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
34040203 ATAAAGTTTA
34040213 AATATCCCCAAATATACAACTCATT
1 AATATCCCCAAATATACAACTCATT
34040238 AATATCCCCAAATATACAACTCATT
1 AATATCCCCAAATATACAACTCATT
34040263 TGCTTACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.28, G:0.00, T:0.28
Consensus pattern (25 bp):
AATATCCCCAAATATACAACTCATT
Found at i:34040654 original size:49 final size:50
Alignment explanation
Indices: 34040589--34040861 Score: 232
Period size: 51 Copynumber: 5.4 Consensus size: 50
34040579 TATCATTCGA
*
34040589 TACACGTAGTAACCTTCACATAGTACTACACACGTGATC-AGTTTTACAG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACAG
* *
34040638 TTCACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACAG
* * * * *
34040688 CT-CACGTAGTAGCCTTCACATAGTATTACATATGTGACCAAAGCTTTT-CTG
1 -TACACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAG-TTTTACAG
* * * * * * * * *
34040739 TACCCATTGTAGCCTTCACTTAGTACTACACATGTAACCGTAG-TTTACCG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAGTTTTACAG
* * * * **
34040789 ATACACGTAGTAGCATTCACACAGTACTACACACGTGCTTAAAGCTTTT-TGG
1 -TACACGTAGTAGCCTTCACATAGTACTACACACGTG-ATCAAG-TTTTACAG
*
34040841 TACACATAGTAGCCTTCACAT
1 TACACGTAGTAGCCTTCACAT
34040862 GTGACCATTA
Statistics
Matches: 179, Mismatches: 35, Indels: 18
0.77 0.15 0.08
Matches are distributed among these distances:
49 40 0.22
50 45 0.25
51 86 0.48
52 5 0.03
53 3 0.02
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.30
Consensus pattern (50 bp):
TACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACAG
Found at i:34040834 original size:102 final size:101
Alignment explanation
Indices: 34040586--34040861 Score: 283
Period size: 102 Copynumber: 2.7 Consensus size: 101
34040576 TTTTATCATT
* * * * * *
34040586 CGATACACGTAGTAACCTTCACATAGTACTACACACGTGAT-CAG-TTTTACAGTTCACGTAGTA
1 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGCTAAAGCTTTT-CTGTACACATAGTA
* *
34040649 GCCTTCACATAGTACTACACACGTGATCAAGTTTTAC
65 GCCTTCACATAGTACTACACACGTAACCAAGTTTTAC
* * * * * * * *
34040686 GGCT-CACGTAGTAGCCTTCACATAGTATTACATATGTGACCAAAGCTTTTCTGTACCCATTGTA
1 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTG-CTAAAGCTTTTCTGTACACATAGTA
* * *
34040750 GCCTTCACTTAGTACTACACATGTAACCGTAG-TTTAC
65 GCCTTCACATAGTACTACACACGTAACC-AAGTTTTAC
* *
34040787 CGATACACGTAGTAGCATTCACACAGTACTACACACGTGCTTAAAGCTTTT-TGGTACACATAGT
1 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGC-TAAAGCTTTTCT-GTACACATAGT
34040851 AGCCTTCACAT
64 AGCCTTCACAT
34040862 GTGACCATTA
Statistics
Matches: 139, Mismatches: 30, Indels: 12
0.77 0.17 0.07
Matches are distributed among these distances:
99 30 0.22
100 2 0.01
101 44 0.32
102 63 0.45
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (101 bp):
CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGCTAAAGCTTTTCTGTACACATAGTAG
CCTTCACATAGTACTACACACGTAACCAAGTTTTAC
Found at i:34041030 original size:15 final size:17
Alignment explanation
Indices: 34041012--34041045 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
34041002 TGTTACGAAA
34041012 TATAACAA-A-AATAAT
1 TATAACAATATAATAAT
34041027 TATAACAATATAATAAT
1 TATAACAATATAATAAT
34041044 TA
1 TA
34041046 CATACAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 1 0.06
17 8 0.47
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (17 bp):
TATAACAATATAATAAT
Found at i:34042158 original size:22 final size:22
Alignment explanation
Indices: 34042133--34042192 Score: 111
Period size: 22 Copynumber: 2.7 Consensus size: 22
34042123 AAGATCAATC
*
34042133 AAAATTAATCAAAATTTATTAT
1 AAAATTAATTAAAATTTATTAT
34042155 AAAATTAATTAAAATTTATTAT
1 AAAATTAATTAAAATTTATTAT
34042177 AAAATTAATTAAAATT
1 AAAATTAATTAAAATT
34042193 CAACATGTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
AAAATTAATTAAAATTTATTAT
Found at i:34042160 original size:12 final size:12
Alignment explanation
Indices: 34042143--34042187 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
34042133 AAAATTAATC
34042143 AAAATTTATTAT
1 AAAATTTATTAT
*
34042155 AAAA-TTAAT-T
1 AAAATTTATTAT
34042165 AAAATTTATTAT
1 AAAATTTATTAT
*
34042177 AAAATTAATTA
1 AAAATTTATTA
34042188 AAATTCAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 5 0.18
11 8 0.29
12 15 0.54
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AAAATTTATTAT
Found at i:34044866 original size:12 final size:12
Alignment explanation
Indices: 34044849--34044874 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
34044839 ACCTCAAAGA
34044849 TTTTATAAATAT
1 TTTTATAAATAT
34044861 TTTTATAAATAT
1 TTTTATAAATAT
34044873 TT
1 TT
34044875 ATGGAGTGTT
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTTATAAATAT
Found at i:34046652 original size:51 final size:51
Alignment explanation
Indices: 34046576--34046737 Score: 263
Period size: 51 Copynumber: 3.2 Consensus size: 51
34046566 GATCAGTAAT
*
34046576 AAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATTAGTGACAAGTGAC
1 AAGTGATAAGTAGTAGCTTTAGCTACACTTATCTGATTAGTGACAAGTGAC
* *
34046627 AAGTGATAATTAGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGAC
1 AAGTGATAAGTAGTAGCTTTAGCTACACTTATCTGATTAGTGACAAGTGAC
* *
34046678 AAGTGATAAGTGGTAGCTTTAGCTACACTTATTTG-TTCAGTGACAAGTGAC
1 AAGTGATAAGTAGTAGCTTTAGCTACACTTATCTGATT-AGTGACAAGTGAC
34046729 AAGTGATAA
1 AAGTGATAA
34046738 ATGTGATGTA
Statistics
Matches: 103, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
50 1 0.01
51 102 0.99
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (51 bp):
AAGTGATAAGTAGTAGCTTTAGCTACACTTATCTGATTAGTGACAAGTGAC
Found at i:34048766 original size:16 final size:15
Alignment explanation
Indices: 34048741--34048774 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
34048731 AAAGTTGATA
*
34048741 ATAATTAATATATATT
1 ATAATAAATATA-ATT
34048757 ATAATAAATATAATT
1 ATAATAAATATAATT
34048772 ATA
1 ATA
34048775 TACTAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:34052689 original size:50 final size:52
Alignment explanation
Indices: 34052563--34052689 Score: 118
Period size: 50 Copynumber: 2.5 Consensus size: 52
34052553 ATGAACAAAT
* * * *
34052563 GAGTTACTTAACGCA-AGACTTAATTTAATGATGCAGGCTTAAACTAACATGC
1 GAGTTACATAATGCATA-ACTTTATTTAATGATGCAGACTTAAACTAACATGC
** * * *
34052615 GAGTTACATAATGCATGTCATTATTT-ATGATGCATACTT-AACTAGCATG-
1 GAGTTACATAATGCATAACTTTATTTAATGATGCAGACTTAAACTAACATGC
*
34052664 GAAGTTACATAATGCCTAACTTTATT
1 G-AGTTACATAATGCATAACTTTATT
34052690 AAATCCAGAA
Statistics
Matches: 60, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
49 1 0.02
50 29 0.48
51 11 0.18
52 19 0.32
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Consensus pattern (52 bp):
GAGTTACATAATGCATAACTTTATTTAATGATGCAGACTTAAACTAACATGC
Found at i:34056940 original size:20 final size:18
Alignment explanation
Indices: 34056915--34056953 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
34056905 ACCTAACACG
34056915 AATTAAATTTAAGACATATT
1 AATTAAA-TTAA-ACATATT
34056935 AATTAAATTAAACATATT
1 AATTAAATTAAACATATT
34056953 A
1 A
34056954 GCATCACAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.42
19 4 0.21
20 7 0.37
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (18 bp):
AATTAAATTAAACATATT
Found at i:34058640 original size:33 final size:33
Alignment explanation
Indices: 34058603--34058669 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
34058593 AACATGGAAC
*
34058603 AGAGATAGCCTGTTGGAACAGTAAACACAAAAT
1 AGAGATAGCCTGCTGGAACAGTAAACACAAAAT
** * *
34058636 AGAGATAGTTTGCTGGGACAGTAAACACAGAAT
1 AGAGATAGCCTGCTGGAACAGTAAACACAAAAT
34058669 A
1 A
34058670 AAGTAAGTCC
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:0.43, C:0.13, G:0.24, T:0.19
Consensus pattern (33 bp):
AGAGATAGCCTGCTGGAACAGTAAACACAAAAT
Found at i:34058708 original size:99 final size:97
Alignment explanation
Indices: 34058538--34058728 Score: 215
Period size: 99 Copynumber: 1.9 Consensus size: 97
34058528 TGGCATCCAC
* * *
34058538 AGAGATAATCTGCTAGGATAGTAAACACAGAACAAGTAAGTCTTCCAAGACAGTAAACATGGAAC
1 AGAGATAATCTGCTAGGACAGTAAACACAGAAAAAGTAAGTCATCCAAGACAGTAAACAT-GAAC
**
34058603 AGAGATAGCCTGTTGGAACAGTAAACACAAAAT
65 AGAGATAGCCTGGCGGAACAGTAAACACAAAAT
* * * *
34058636 AGAGATAGTTTGCTGGGACAGTAAACACAGAATAAAGTAAGTCCAT-CAAGATAGTATACACAT-
1 AGAGATAATCTGCTAGGACAGTAAACACAGAA-AAAGTAAGT-CATCCAAGACAGTA-A-ACATG
* * *
34058699 AATAGAGATAGTCTGGCGGGACAGTAAACA
62 AACAGAGATAGCCTGGCGGAACAGTAAACA
34058729 AGGAGTAAGT
Statistics
Matches: 77, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
98 28 0.36
99 42 0.55
100 3 0.04
101 4 0.05
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.19
Consensus pattern (97 bp):
AGAGATAATCTGCTAGGACAGTAAACACAGAAAAAGTAAGTCATCCAAGACAGTAAACATGAACA
GAGATAGCCTGGCGGAACAGTAAACACAAAAT
Found at i:34060928 original size:16 final size:17
Alignment explanation
Indices: 34060903--34060937 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
34060893 ACTTTTTCAA
34060903 TCATCCCTCATCC-CTC
1 TCATCCCTCATCCTCTC
*
34060919 TCATCTCTCATCCTCTC
1 TCATCCCTCATCCTCTC
34060936 TC
1 TC
34060938 TCAAATCTCT
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:0.11, C:0.51, G:0.00, T:0.37
Consensus pattern (17 bp):
TCATCCCTCATCCTCTC
Found at i:34066329 original size:17 final size:17
Alignment explanation
Indices: 34066307--34066341 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
34066297 TCGTTCTGTT
34066307 TAAATTTTAAATTTGTA
1 TAAATTTTAAATTTGTA
34066324 TAAATTTTAAATTTGTA
1 TAAATTTTAAATTTGTA
34066341 T
1 T
34066342 GTTAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (17 bp):
TAAATTTTAAATTTGTA
Found at i:34067799 original size:16 final size:17
Alignment explanation
Indices: 34067772--34067807 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
34067762 AGAGAGTTGA
34067772 GAGAGAGGATGAGAGAT
1 GAGAGAGGATGAGAGAT
*
34067789 GAGAG-GGATGAGGGAT
1 GAGAGAGGATGAGAGAT
34067805 GAG
1 GAG
34067808 GGATGATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.36, C:0.00, G:0.53, T:0.11
Consensus pattern (17 bp):
GAGAGAGGATGAGAGAT
Found at i:34069785 original size:45 final size:45
Alignment explanation
Indices: 34069730--34069816 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
34069720 CAGATACTCG
* *
34069730 GTGGATTCAGCACATAGCAACCACCTTATTAATCAATAATGTCCT
1 GTGGAATCAGCACATAGCAACCACCTTACTAATCAATAATGTCCT
* *
34069775 GTGGAATCAGCACATAGCAACCACCTTACTAATTAATGATGT
1 GTGGAATCAGCACATAGCAACCACCTTACTAATCAATAATGT
34069817 TCGGTTCACA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (45 bp):
GTGGAATCAGCACATAGCAACCACCTTACTAATCAATAATGTCCT
Found at i:34069885 original size:51 final size:50
Alignment explanation
Indices: 34069827--34070009 Score: 208
Period size: 51 Copynumber: 3.6 Consensus size: 50
34069817 TCGGTTCACA
* *
34069827 TAGTAGCCTGCACATAGTACTATACATGTGACCATTACCATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATCCGATACACG
* * * * * *
34069878 TAGTAGCCTACACATAGTACTACACACGTGATCGAAACTATCC-AGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATACCATCCGA-TACACG
* * * *
34069929 TAGTAGCCTGCACATAGTACTACACATGTGACC-TATCATTCCGGTATACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATACCA-TCCGATACACG
34069979 TAGTAGCCTGCACATAGTACTACACACGTGA
1 TAGTAGCCTGCACATAGTACTACACACGTGA
34070010 TCATCACTTT
Statistics
Matches: 109, Mismatches: 19, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
49 2 0.02
50 38 0.35
51 67 0.61
52 2 0.02
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATACCATCCGATACACG
Found at i:34070010 original size:101 final size:101
Alignment explanation
Indices: 34069825--34070011 Score: 304
Period size: 101 Copynumber: 1.8 Consensus size: 101
34069815 GTTCGGTTCA
*
34069825 CATAGTAGCCTGCACATAGTACTATACATGTGACCATTACCATCCGATACACGTAGTAGCCTACA
1 CATAGTAGCCTGCACATAGTACTACACATGTGACCA-TACCATCCGATACACGTAGTAGCCTACA
34069890 CATAGTACTACACACGTGATCGAAACTATCCAGTACG
65 CATAGTACTACACACGTGATCGAAACTATCCAGTACG
* * * *
34069927 CATAGTAGCCTGCACATAGTACTACACATGTGACC-TATCATTCCGGTATACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGTGACCATACCA-TCCGATACACGTAGTAGCCTACA
34069991 CATAGTACTACACACGTGATC
65 CATAGTACTACACACGTGATC
34070012 ATCACTTTCA
Statistics
Matches: 79, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
100 4 0.05
101 41 0.52
102 34 0.43
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.25
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGTGACCATACCATCCGATACACGTAGTAGCCTACAC
ATAGTACTACACACGTGATCGAAACTATCCAGTACG
Found at i:34077064 original size:50 final size:50
Alignment explanation
Indices: 34077010--34077378 Score: 468
Period size: 50 Copynumber: 7.3 Consensus size: 50
34077000 TATCCCAGAT
** * * * *
34077010 ATGGTCTTACATGAGAGTTCTCATATAGGTGCCCATGCCATGTCCCAAAC
1 ATGGTCTTACATGAGACCTCTCATCTCGGTGCCAACGCCATGTCCCAAAC
** * *
34077060 ATGGTCTTACGGGGGACCTCTCATCTTGGTGCCAACGCCATGTCCCAAAC
1 ATGGTCTTACATGAGACCTCTCATCTCGGTGCCAACGCCATGTCCCAAAC
* * *
34077110 TTGGTCTTCCATGAGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
1 ATGGTCTTACATGAGACCTCTCATCTCGGTGCCAACGCCATGTCCCAAAC
* *
34077160 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTCCCAAAC
1 ATGGTCTTACATGAGACCTCTCATCTCGGTGCCAACGCCATGTCCCAAAC
* * *
34077210 ATGGTCTTACATGGGACCTCTCATCTCAGTGCCAACGCCATGTCCCAGAC
1 ATGGTCTTACATGAGACCTCTCATCTCGGTGCCAACGCCATGTCCCAAAC
*
34077260 ATGGTCTTACATGAGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
1 ATGGTCTTACATGAGACCTCTCATCTCGGTGCCAACGCCATGTCCCAAAC
* ** *
34077310 ATGGTCTTACATGGGACCTCTCATAATCTCAATAATGCCAATGCCATGTCCCAAAC
1 ATGGTCTTACATGAGACCTCTC---ATCTC---GGTGCCAACGCCATGTCCCAAAC
*
34077366 TTGGTCTTACATG
1 ATGGTCTTACATG
34077379 GGATCTCTTT
Statistics
Matches: 281, Mismatches: 32, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
50 245 0.87
53 5 0.02
56 31 0.11
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (50 bp):
ATGGTCTTACATGAGACCTCTCATCTCGGTGCCAACGCCATGTCCCAAAC
Found at i:34077210 original size:150 final size:150
Alignment explanation
Indices: 34077002--34077386 Score: 545
Period size: 150 Copynumber: 2.5 Consensus size: 150
34076992 CAATGTCATA
* * ** * * *
34077002 TCCCAGATATGGTCTTACATGAGAGTTCTCATATAGGTGCCCATGCCATGTCCCAAACATGGTCT
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTCCCAAACATGGTCT
* ** * *
34077067 TACGGGGGACCTCTCATCTTGGTGCCAACGCCATGTCCCAAACTTGGTCTTCCATGAGACCTCTC
66 TACAGGGGACCTCTCATCTCAGTGCCAACGCCATGTCCCAAACATGGTCTTACATGAGACCTCTC
34077132 ATCTCGGTGCCAACGCCATG
131 ATCTCGGTGCCAACGCCATG
34077152 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTCCCAAACATGGTCT
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTCCCAAACATGGTCT
* *
34077217 TACATGGGACCTCTCATCTCAGTGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTC
66 TACAGGGGACCTCTCATCTCAGTGCCAACGCCATGTCCCAAACATGGTCTTACATGAGACCTCTC
34077282 ATCTCGGTGCCAACGCCATG
131 ATCTCGGTGCCAACGCCATG
** *
34077302 TCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATAATGCCAATGCCATGTCCCAAACT
1 TCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC---GGTGCCAATGCCATGTCCCAAACA
* *
34077367 TGGTCTTACATGGGATCTCT
60 TGGTCTTACAGGGGACCTCT
34077387 TTACCCAAAT
Statistics
Matches: 211, Mismatches: 18, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
150 166 0.79
153 5 0.02
156 40 0.19
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (150 bp):
TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGCCATGTCCCAAACATGGTCT
TACAGGGGACCTCTCATCTCAGTGCCAACGCCATGTCCCAAACATGGTCTTACATGAGACCTCTC
ATCTCGGTGCCAACGCCATG
Found at i:34080432 original size:16 final size:17
Alignment explanation
Indices: 34080407--34080441 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
34080397 ACTTTTTCAA
34080407 TCATCCCTCATCC-CTC
1 TCATCCCTCATCCTCTC
*
34080423 TCATCTCTCATCCTCTC
1 TCATCCCTCATCCTCTC
34080440 TC
1 TC
34080442 TCAACTCTAT
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:0.11, C:0.51, G:0.00, T:0.37
Consensus pattern (17 bp):
TCATCCCTCATCCTCTC
Found at i:34082930 original size:131 final size:131
Alignment explanation
Indices: 34082690--34082952 Score: 420
Period size: 131 Copynumber: 2.0 Consensus size: 131
34082680 AATGGTCAAG
* * *
34082690 AGAAAAACTTGGGTATTAGGAGTTGTAGGGAAAAATGCACTCTAGTATTTTATTTAAGTGAAGAA
1 AGAAAAACTTGGGTAATAGGAGTTGTAGGGAAAAATACACTCCAGTATTTTATTTAAGTGAAGAA
* * * *
34082755 AAGAAATATAGGAGAAGAGGTGGAATGATAATTTGGAGATGGATCAAGTAGAGGACTTGAAGAAG
66 AAGAAATATAGGAGAAGAGGTGGAAGGATAATTTGGAAAGGGATCAAGTAGAGGACTTGAAAAAG
34082820 T
131 T
* *
34082821 AGAAAAACATT-GGTAATAGGAGTTGTAGGGGAAACTACACTCCAGTATTTTATTTAAGTGAAGA
1 AGAAAAAC-TTGGGTAATAGGAGTTGTAGGGAAAAATACACTCCAGTATTTTATTTAAGTGAAGA
*
34082885 AAAGAAATATAGGAGAAGAGGTGGAAGGATAATTTGGAAAGGGATCAAGTAGAGTACTTGAAAAA
65 AAAGAAATATAGGAGAAGAGGTGGAAGGATAATTTGGAAAGGGATCAAGTAGAGGACTTGAAAAA
34082950 GT
130 GT
34082952 A
1 A
34082953 TGGACTTCCT
Statistics
Matches: 121, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
131 119 0.98
132 2 0.02
ACGTcount: A:0.42, C:0.05, G:0.28, T:0.25
Consensus pattern (131 bp):
AGAAAAACTTGGGTAATAGGAGTTGTAGGGAAAAATACACTCCAGTATTTTATTTAAGTGAAGAA
AAGAAATATAGGAGAAGAGGTGGAAGGATAATTTGGAAAGGGATCAAGTAGAGGACTTGAAAAAG
T
Found at i:34106441 original size:27 final size:27
Alignment explanation
Indices: 34106408--34106484 Score: 145
Period size: 27 Copynumber: 2.9 Consensus size: 27
34106398 TTTACTTTGG
34106408 TAAAATTTTGACGATTTTACCCTTCGA
1 TAAAATTTTGACGATTTTACCCTTCGA
34106435 TAAAATTTTGACGATTTTACCCTTCGA
1 TAAAATTTTGACGATTTTACCCTTCGA
*
34106462 TAAAATTTTGACAATTTTACCCT
1 TAAAATTTTGACGATTTTACCCT
34106485 AAGTAAAATT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.42
Consensus pattern (27 bp):
TAAAATTTTGACGATTTTACCCTTCGA
Found at i:34110669 original size:43 final size:43
Alignment explanation
Indices: 34110603--34110859 Score: 309
Period size: 43 Copynumber: 6.0 Consensus size: 43
34110593 AAGGAGGAAG
* * * * *
34110603 TTACTGACAGTTTATCTGCAATTATTGGCGGTTTATCCACAAA
1 TTACTGGCAGTTTATCTGCAATTACTGGTGGTTTATCCATAAC
* ** * * *
34110646 TTACTGGCAATTTATCTATAATTACTAGTGATTTATTCATAAC
1 TTACTGGCAGTTTATCTGCAATTACTGGTGGTTTATCCATAAC
* *
34110689 TTACTGGCAGTTTTTTTGCAATTACTGGTGGTTTATCCATAAC
1 TTACTGGCAGTTTATCTGCAATTACTGGTGGTTTATCCATAAC
** *
34110732 TTACTGGCAGTTTATCTAAAATTACTGGTGGTTTATCCACAAC
1 TTACTGGCAGTTTATCTGCAATTACTGGTGGTTTATCCATAAC
* *
34110775 TTACTGACAGTTTATTTGCAATT-CTTGGTGGTTTATCCATAAC
1 TTACTGGCAGTTTATCTGCAATTAC-TGGTGGTTTATCCATAAC
* * *
34110818 TTACTAGCAGTTTATTTGTAATTACTGGTGGTTTATCCATAA
1 TTACTGGCAGTTTATCTGCAATTACTGGTGGTTTATCCATAA
34110860 TGCAATGTAT
Statistics
Matches: 180, Mismatches: 32, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
42 1 0.01
43 178 0.99
44 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (43 bp):
TTACTGGCAGTTTATCTGCAATTACTGGTGGTTTATCCATAAC
Found at i:34110670 original size:21 final size:21
Alignment explanation
Indices: 34110603--34110860 Score: 110
Period size: 21 Copynumber: 12.0 Consensus size: 21
34110593 AAGGAGGAAG
* **
34110603 TTACTGACAGTTTATCTGCAA
1 TTACTGGCAGTTTATCTATAA
* * * *
34110624 TTATTGGCGGTTTATCCACAAA
1 TTACTGGCAGTTTATCTA-TAA
*
34110646 TTACTGGCAATTTATCTATAA
1 TTACTGGCAGTTTATCTATAA
34110667 TTACTAGTG-A-TTTAT-TCATAA
1 TTACT-G-GCAGTTTATCT-ATAA
* * **
34110688 CTTACTGGCAGTTTTTTTGCAA
1 -TTACTGGCAGTTTATCTATAA
** *
34110710 TTACTGGTGGTTTATCCATAA
1 TTACTGGCAGTTTATCTATAA
*
34110731 CTTACTGGCAGTTTATCTAAAA
1 -TTACTGGCAGTTTATCTATAA
** * *
34110753 TTACTGGTGGTTTATCCACAA
1 TTACTGGCAGTTTATCTATAA
* * **
34110774 CTTACTGACAGTTTATTTGCAA
1 -TTACTGGCAGTTTATCTATAA
** *
34110796 TT-CTTGGTGGTTTATCCATAA
1 TTAC-TGGCAGTTTATCTATAA
* * *
34110817 CTTACTAGCAGTTTATTTGTAA
1 -TTACTGGCAGTTTATCTATAA
** *
34110839 TTACTGGTGGTTTATCCATAA
1 TTACTGGCAGTTTATCTATAA
34110860 T
1 T
34110861 GCAATGTATA
Statistics
Matches: 170, Mismatches: 54, Indels: 26
0.68 0.22 0.10
Matches are distributed among these distances:
20 3 0.02
21 90 0.53
22 74 0.44
23 3 0.02
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (21 bp):
TTACTGGCAGTTTATCTATAA
Found at i:34110748 original size:86 final size:86
Alignment explanation
Indices: 34110603--34110859 Score: 354
Period size: 86 Copynumber: 3.0 Consensus size: 86
34110593 AAGGAGGAAG
* * * * * *
34110603 TTACTGACAGTTTATCTGCAATTATTGGCGGTTTATCCACAAATTACTGGCAATTTATCTATAAT
1 TTACTGACAGTTTATTTGCAATTACTGGTGGTTTATCCATAACTTACTGGCAGTTTATCTATAAT
* * *
34110668 TACTAGTGATTTATTCATAAC
66 TACTGGTGGTTTATCCATAAC
* * *
34110689 TTACTGGCAGTTTTTTTGCAATTACTGGTGGTTTATCCATAACTTACTGGCAGTTTATCTAAAAT
1 TTACTGACAGTTTATTTGCAATTACTGGTGGTTTATCCATAACTTACTGGCAGTTTATCTATAAT
*
34110754 TACTGGTGGTTTATCCACAAC
66 TACTGGTGGTTTATCCATAAC
* * *
34110775 TTACTGACAGTTTATTTGCAATT-CTTGGTGGTTTATCCATAACTTACTAGCAGTTTATTTGTAA
1 TTACTGACAGTTTATTTGCAATTAC-TGGTGGTTTATCCATAACTTACTGGCAGTTTATCTATAA
34110839 TTACTGGTGGTTTATCCATAA
65 TTACTGGTGGTTTATCCATAA
34110860 TGCAATGTAT
Statistics
Matches: 150, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
85 1 0.01
86 149 0.99
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (86 bp):
TTACTGACAGTTTATTTGCAATTACTGGTGGTTTATCCATAACTTACTGGCAGTTTATCTATAAT
TACTGGTGGTTTATCCATAAC
Found at i:34110841 original size:129 final size:129
Alignment explanation
Indices: 34110603--34110859 Score: 345
Period size: 129 Copynumber: 2.0 Consensus size: 129
34110593 AAGGAGGAAG
** * * *
34110603 TTACTGACAGTTTATCTGCAATTATTGGCGGTTTATCCACAAATTACTGGCAATTTATCTATAAT
1 TTACTGACAGTTTATCTAAAATTACTGGCGGTTTATCCACAAATTACTGACAATTTATCTACAAT
* * *
34110668 TACTAGTGATTTATTCATAACTTACTGGCAGTTTTTTTGCAATTACTGGTGGTTTATCCATAAC
66 TACTAGTGATTTATCCATAACTTACTAGCAGTTTATTTGCAATTACTGGTGGTTTATCCATAAC
* * * * * *
34110732 TTACTGGCAGTTTATCTAAAATTACTGGTGGTTTATCCACAACTTACTGACAGTTTATTTGCAAT
1 TTACTGACAGTTTATCTAAAATTACTGGCGGTTTATCCACAAATTACTGACAATTTATCTACAAT
* * *
34110797 T-CTTGGTGGTTTATCCATAACTTACTAGCAGTTTATTTGTAATTACTGGTGGTTTATCCATAA
66 TAC-TAGTGATTTATCCATAACTTACTAGCAGTTTATTTGCAATTACTGGTGGTTTATCCATAA
34110860 TGCAATGTAT
Statistics
Matches: 110, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
128 1 0.01
129 109 0.99
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (129 bp):
TTACTGACAGTTTATCTAAAATTACTGGCGGTTTATCCACAAATTACTGACAATTTATCTACAAT
TACTAGTGATTTATCCATAACTTACTAGCAGTTTATTTGCAATTACTGGTGGTTTATCCATAAC
Found at i:34111848 original size:186 final size:186
Alignment explanation
Indices: 34111534--34111907 Score: 739
Period size: 186 Copynumber: 2.0 Consensus size: 186
34111524 ATAAACACGC
*
34111534 TAAGTTTTTCTTCAAAGATAAGTAGATGACCTAAAAAGGCAGTTTTGAAAATCTAATTATTTTAC
1 TAAGTTTTTCTTCAAAGATAAGCAGATGACCTAAAAAGGCAGTTTTGAAAATCTAATTATTTTAC
34111599 TAGGTCATTTCAGTGGCCAATGTAGCCTTCAGAATCCAACTGTAACATCTAGGTCGGGTTAAGGA
66 TAGGTCATTTCAGTGGCCAATGTAGCCTTCAGAATCCAACTGTAACATCTAGGTCGGGTTAAGGA
34111664 GGTTACATAATATTATTCCCTTTCACCCCCAATTTTATCTACTAGGTTCACCGTCT
131 GGTTACATAATATTATTCCCTTTCACCCCCAATTTTATCTACTAGGTTCACCGTCT
34111720 TAAGTTTTTCTTCAAAGATAAGCAGATGACCTAAAAAGGCAGTTTTGAAAATCTAATTATTTTAC
1 TAAGTTTTTCTTCAAAGATAAGCAGATGACCTAAAAAGGCAGTTTTGAAAATCTAATTATTTTAC
34111785 TAGGTCATTTCAGTGGCCAATGTAGCCTTCAGAATCCAACTGTAACATCTAGGTCGGGTTAAGGA
66 TAGGTCATTTCAGTGGCCAATGTAGCCTTCAGAATCCAACTGTAACATCTAGGTCGGGTTAAGGA
34111850 GGTTACATAATATTATTCCCTTTCACCCCCAATTTTATCTACTAGGTTCACCGTCT
131 GGTTACATAATATTATTCCCTTTCACCCCCAATTTTATCTACTAGGTTCACCGTCT
34111906 TA
1 TA
34111908 TTTCTCTTTC
Statistics
Matches: 187, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
186 187 1.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (186 bp):
TAAGTTTTTCTTCAAAGATAAGCAGATGACCTAAAAAGGCAGTTTTGAAAATCTAATTATTTTAC
TAGGTCATTTCAGTGGCCAATGTAGCCTTCAGAATCCAACTGTAACATCTAGGTCGGGTTAAGGA
GGTTACATAATATTATTCCCTTTCACCCCCAATTTTATCTACTAGGTTCACCGTCT
Found at i:34113379 original size:20 final size:20
Alignment explanation
Indices: 34113354--34113392 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
34113344 CGTAAAATGA
*
34113354 TTTCTGGAAAATGTTTTACG
1 TTTCTGGAAAATGATTTACG
*
34113374 TTTCTGTAAAATGATTTAC
1 TTTCTGGAAAATGATTTAC
34113393 TGGAAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.46
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACG
Found at i:34113388 original size:34 final size:35
Alignment explanation
Indices: 34113340--34113405 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 35
34113330 AGTAAAATAT
*
34113340 TTTCCGTAAAATGATTT-CTGGAAAATGTTTTACG
1 TTTCCGTAAAATGATTTACTGGAAAATATTTTACG
*
34113374 TTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTCCGTAAAATGATTTACTGGAAAATATTTT
34113406 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.44
Consensus pattern (35 bp):
TTTCCGTAAAATGATTTACTGGAAAATATTTTACG
Found at i:34118154 original size:3 final size:3
Alignment explanation
Indices: 34118146--34118196 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
34118136 ATGTTTGGAT
34118146 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
34118194 TAA
1 TAA
34118197 AAAATACTGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:34124716 original size:2 final size:2
Alignment explanation
Indices: 34124709--34124779 Score: 106
Period size: 2 Copynumber: 35.5 Consensus size: 2
34124699 TAGCGTAGAT
* * * *
34124709 AC AC AC AC AC AC AC GC GC GC GC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
34124751 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
34124780 TATATTATCA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.45, C:0.49, G:0.06, T:0.00
Consensus pattern (2 bp):
AC
Found at i:34128659 original size:1 final size:1
Alignment explanation
Indices: 34128655--34128681 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
34128645 AGATGTAATG
34128655 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
34128682 GGGGCACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:34129920 original size:20 final size:20
Alignment explanation
Indices: 34129890--34129938 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
34129880 GAACAAAAAT
*
34129890 CAAAGGTATTGATACCTTTTA
1 CAAA-GTATTGATACCTTCTA
* *
34129911 TAAAGTATTGGTACCTTCTA
1 CAAAGTATTGATACCTTCTA
34129931 CAAAGTAT
1 CAAAGTAT
34129939 CAATACTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 21 0.88
21 3 0.12
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (20 bp):
CAAAGTATTGATACCTTCTA
Found at i:34132186 original size:17 final size:16
Alignment explanation
Indices: 34132157--34132198 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
34132147 TTACTTTTAT
34132157 AATTTATAATTTAATAC
1 AATTT-TAATTTAATAC
34132174 AATTTTAATTTTAATAC
1 AATTTTAA-TTTAATAC
*
34132191 TATTTTAA
1 AATTTTAA
34132199 CAATTTAGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 3 0.13
17 20 0.87
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTTTAATTTAATAC
Found at i:34135601 original size:35 final size:35
Alignment explanation
Indices: 34135555--34135626 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
34135545 ACTGAATTGT
34135555 GAAAATTTCAAAATTAAAGGGTAGAATTGAAAATA
1 GAAAATTTCAAAATTAAAGGGTAGAATTGAAAATA
*
34135590 GAAAATTTCAAAATTAAGGGGTAGAATTGAAAATA
1 GAAAATTTCAAAATTAAAGGGTAGAATTGAAAATA
34135625 GA
1 GA
34135627 GAGCTAAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.53, C:0.03, G:0.19, T:0.25
Consensus pattern (35 bp):
GAAAATTTCAAAATTAAAGGGTAGAATTGAAAATA
Found at i:34137520 original size:54 final size:54
Alignment explanation
Indices: 34137398--34137525 Score: 141
Period size: 54 Copynumber: 2.4 Consensus size: 54
34137388 CACGGCCTAC
* * * * * * *
34137398 GACACGGCCGTGTGACCCAAGTCAGTGAGTTACACGGGTAGAGACATGGGCTGA
1 GACACAGCCGTGTGTCCCAAGTAAGTAAGTTACACGGGCAGAGACATGAGATGA
* * *
34137452 GACA-TGACCGTGTGTCCCAAGTAAGTAAGTTACATGGGCAGAGACATGAGATGG
1 GACACAG-CCGTGTGTCCCAAGTAAGTAAGTTACACGGGCAGAGACATGAGATGA
*
34137506 GACACAGCCATGTGTCCCAA
1 GACACAGCCGTGTGTCCCAA
34137526 CTTCAAAAGT
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
53 1 0.02
54 59 0.97
55 1 0.02
ACGTcount: A:0.29, C:0.22, G:0.31, T:0.18
Consensus pattern (54 bp):
GACACAGCCGTGTGTCCCAAGTAAGTAAGTTACACGGGCAGAGACATGAGATGA
Found at i:34139092 original size:27 final size:28
Alignment explanation
Indices: 34139062--34139184 Score: 144
Period size: 27 Copynumber: 4.5 Consensus size: 28
34139052 TGTTCACCAT
* *
34139062 TTTGGCTTGCACTTGGACTATCCTCC-C
1 TTTGGCTTGCACTTGGACTGTCCGCCAC
*
34139089 TTTGGCTTGTACTTGGACTGTCCGCCAC
1 TTTGGCTTGCACTTGGACTGTCCGCCAC
* * * *
34139117 -TTGGCTTGTACTTGGATTGTTCACCAC
1 TTTGGCTTGCACTTGGACTGTCCGCCAC
* *
34139144 -TTGGCTTGCACTTGGACTGTCCGCTAT
1 TTTGGCTTGCACTTGGACTGTCCGCCAC
34139171 TTTGGCTTGCACTT
1 TTTGGCTTGCACTT
34139185 TTGTCTTGTA
Statistics
Matches: 82, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
27 68 0.83
28 14 0.17
ACGTcount: A:0.11, C:0.27, G:0.23, T:0.39
Consensus pattern (28 bp):
TTTGGCTTGCACTTGGACTGTCCGCCAC
Found at i:34141602 original size:28 final size:28
Alignment explanation
Indices: 34141518--34141629 Score: 100
Period size: 28 Copynumber: 4.0 Consensus size: 28
34141508 TAGCTCGTTG
* *
34141518 TTAGACTGTCCGCTATTTTGGGTTGCAC
1 TTAGACTGTCCGCCATTTTGGCTTGCAC
* ** * * * *
34141546 TTGGGTTGTTCGCCA-CTTAGCTTGTAC
1 TTAGACTGTCCGCCATTTTGGCTTGCAC
34141573 TTAGACTGTCCGCCATTTTGGCTTGCAC
1 TTAGACTGTCCGCCATTTTGGCTTGCAC
* * * *
34141601 TTGGACTATCTGCCACTTTGGCTTGCAC
1 TTAGACTGTCCGCCATTTTGGCTTGCAC
34141629 T
1 T
34141630 GTCCACCATT
Statistics
Matches: 63, Mismatches: 20, Indels: 2
0.74 0.24 0.02
Matches are distributed among these distances:
27 19 0.30
28 44 0.70
ACGTcount: A:0.13, C:0.25, G:0.23, T:0.38
Consensus pattern (28 bp):
TTAGACTGTCCGCCATTTTGGCTTGCAC
Found at i:34141672 original size:16 final size:17
Alignment explanation
Indices: 34141638--34141672 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
34141628 CTGTCCACCA
*
34141638 TTTTGACTTGCACCTTT
1 TTTTGACTAGCACCTTT
34141655 TTTTGACTAGCACCTTT
1 TTTTGACTAGCACCTTT
34141672 T
1 T
34141673 GCATATCGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.23, G:0.11, T:0.51
Consensus pattern (17 bp):
TTTTGACTAGCACCTTT
Found at i:34146440 original size:25 final size:26
Alignment explanation
Indices: 34146412--34146462 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
34146402 AAAATTTAAC
*
34146412 AAGTACCAAAT-CGAAAAAAAATATT
1 AAGTACCAAATAAGAAAAAAAATATT
34146437 AAGTACCAAATAAAGAAAAAAAATAT
1 AAGTACCAAAT-AAGAAAAAAAATAT
34146463 CAAATTTAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 11 0.48
27 12 0.52
ACGTcount: A:0.65, C:0.10, G:0.08, T:0.18
Consensus pattern (26 bp):
AAGTACCAAATAAGAAAAAAAATATT
Found at i:34148298 original size:66 final size:66
Alignment explanation
Indices: 34148228--34148397 Score: 165
Period size: 66 Copynumber: 2.6 Consensus size: 66
34148218 TTTCCCAATT
* *
34148228 TATATGTATACATACTTATACATATATTCTTTATATTCTGTAATCTATATACAT-TTTTTATTTT
1 TATATATATACATACTTATACATATATTCTTTATATT-T-TAATCTATATACATCTTTCTATTTT
34148292 CA-
64 CAC
* * * **
34148294 TATATATATATATA-TATATACATACGTACTC-ATATATTTTTGTCTATATACATCTTTCTATTT
1 TATATATATACATACT-TATACATA--TATTCTTTATATTTTAATCTATATACATCTTTCTATTT
34148357 TCAC
63 TCAC
* *
34148361 GA-ATATATACATACTTAT--ATATATTTTTTATATTTTA
1 TATATATATACATACTTATACATATATTCTTTATATTTTA
34148398 TAATTTTTAT
Statistics
Matches: 84, Mismatches: 13, Indels: 17
0.74 0.11 0.15
Matches are distributed among these distances:
62 3 0.04
63 8 0.10
64 3 0.04
65 13 0.15
66 45 0.54
67 8 0.10
68 4 0.05
ACGTcount: A:0.34, C:0.12, G:0.03, T:0.52
Consensus pattern (66 bp):
TATATATATACATACTTATACATATATTCTTTATATTTTAATCTATATACATCTTTCTATTTTCA
C
Found at i:34150656 original size:56 final size:56
Alignment explanation
Indices: 34150589--34150697 Score: 200
Period size: 56 Copynumber: 1.9 Consensus size: 56
34150579 TGAAGGTACG
* *
34150589 TTTCTGTTTATTACCACTTTTGAACCCAATACTCATCTTTCGTTGTCTTTAATACA
1 TTTCTGTTTATTACCACTTTTGAACCCAATACTCATCCTTCGTTGTCTCTAATACA
34150645 TTTCTGTTTATTACCACTTTTGAACCCAATACTCATCCTTCGTTGTCTCTAAT
1 TTTCTGTTTATTACCACTTTTGAACCCAATACTCATCCTTCGTTGTCTCTAAT
34150698 CACTATTCCA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.22, C:0.25, G:0.07, T:0.46
Consensus pattern (56 bp):
TTTCTGTTTATTACCACTTTTGAACCCAATACTCATCCTTCGTTGTCTCTAATACA
Found at i:34163550 original size:34 final size:35
Alignment explanation
Indices: 34163512--34163578 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
34163502 CAGTAAAATA
*
34163512 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTGC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTGC
* *
34163546 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
34163579 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.30, C:0.09, G:0.16, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTGC
Found at i:34164200 original size:39 final size:39
Alignment explanation
Indices: 34164157--34164290 Score: 125
Period size: 39 Copynumber: 3.5 Consensus size: 39
34164147 GTTATATTTA
* *
34164157 AAGTGGATCTTATATTTAAATTAAGTTTTAAATATAATC
1 AAGTGAATCTCATATTTAAATTAAGTTTTAAATATAATC
* * *
34164196 AAGTGAATCTCATTTTTAATATATATAG--TT--ATAT-TTA
1 AAGTGAATCTCATATTTAA-AT-TA-AGTTTTAAATATAATC
** *
34164233 AAGTGGGTCTTATATTTAAATTAAGTTTTAAATATAATC
1 AAGTGAATCTCATATTTAAATTAAGTTTTAAATATAATC
*
34164272 AAGTGAATCTCATTTTTAA
1 AAGTGAATCTCATATTTAA
34164291 TATATATATA
Statistics
Matches: 72, Mismatches: 15, Indels: 16
0.70 0.15 0.16
Matches are distributed among these distances:
34 2 0.03
35 2 0.03
36 4 0.06
37 16 0.22
38 8 0.11
39 32 0.44
40 4 0.06
41 2 0.03
42 2 0.03
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (39 bp):
AAGTGAATCTCATATTTAAATTAAGTTTTAAATATAATC
Found at i:34164228 original size:76 final size:76
Alignment explanation
Indices: 34164102--34164298 Score: 331
Period size: 76 Copynumber: 2.6 Consensus size: 76
34164092 AAACAGACCC
* * * * * *
34164102 TAAGTTTTAAATATGATTAAGTCAGTCCCATTTTTAATACATATAGTTATATTTAAAGTGGATCT
1 TAAGTTTTAAATATAATCAAGTGAATCTCATTTTTAATATATATAGTTATATTTAAAGTGGATCT
34164167 TATATTTAAAT
66 TATATTTAAAT
*
34164178 TAAGTTTTAAATATAATCAAGTGAATCTCATTTTTAATATATATAGTTATATTTAAAGTGGGTCT
1 TAAGTTTTAAATATAATCAAGTGAATCTCATTTTTAATATATATAGTTATATTTAAAGTGGATCT
34164243 TATATTTAAAT
66 TATATTTAAAT
34164254 TAAGTTTTAAATATAATCAAGTGAATCTCATTTTTAATATATATA
1 TAAGTTTTAAATATAATCAAGTGAATCTCATTTTTAATATATATA
34164299 TACACAAAAA
Statistics
Matches: 114, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 114 1.00
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.45
Consensus pattern (76 bp):
TAAGTTTTAAATATAATCAAGTGAATCTCATTTTTAATATATATAGTTATATTTAAAGTGGATCT
TATATTTAAAT
Found at i:34167428 original size:22 final size:21
Alignment explanation
Indices: 34167401--34167448 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
34167391 AAATAATTTA
* *
34167401 TCAATATATAATTA-AAAAAT
1 TCAAAATATAAATATAAAAAT
34167421 TCAAAATATAAATATAAAAAT
1 TCAAAATATAAATATAAAAAT
34167442 TCAAAAT
1 TCAAAAT
34167449 TTATTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (21 bp):
TCAAAATATAAATATAAAAAT
Found at i:34167429 original size:20 final size:20
Alignment explanation
Indices: 34167401--34167457 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
34167391 AAATAATTTA
*
34167401 TCAATATATAATTAAAAAAT
1 TCAAAATATAATTAAAAAAT
*
34167421 TCAAAATATAAATATAAAAAT
1 TCAAAATATAATTA-AAAAAT
*
34167442 TCAAAAT-TTATTAAAA
1 TCAAAATATAATTAAAA
34167458 TTTATAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 3 0.09
20 16 0.50
21 13 0.41
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
TCAAAATATAATTAAAAAAT
Found at i:34167521 original size:19 final size:18
Alignment explanation
Indices: 34167481--34167528 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
34167471 ACAAAAATAT
*
34167481 TATAAAATATTCAAAAAT
1 TATAAAATATTCAAAAAG
34167499 TATAAAATTACTTC-AAAAG
1 TATAAAA-TA-TTCAAAAAG
*
34167518 TATATAATATT
1 TATAAAATATT
34167529 ATTGATACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 2 0.08
18 9 0.35
19 12 0.46
20 3 0.12
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (18 bp):
TATAAAATATTCAAAAAG
Found at i:34167529 original size:21 final size:20
Alignment explanation
Indices: 34167474--34167516 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
34167464 AAAAAATACA
34167474 AAAATATTATAAAA-TA-TTC
1 AAAA-ATTATAAAATTACTTC
34167493 AAAAATTATAAAATTACTTC
1 AAAAATTATAAAATTACTTC
34167513 AAAA
1 AAAA
34167517 GTATATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.41
19 6 0.27
20 7 0.32
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAATTATAAAATTACTTC
Found at i:34170887 original size:36 final size:36
Alignment explanation
Indices: 34170823--34170902 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 36
34170813 CGATCTTAAA
* * *
34170823 TCAACGAGCCTTAGTAAAATCAGTTGTGAATGTAGG
1 TCAACGAGCCTTAATAAAATCAGCTGTGAACGTAGG
* * *
34170859 TCAATGAGCCTTAATAACATTAGCTGTGAACGTAGG
1 TCAACGAGCCTTAATAAAATCAGCTGTGAACGTAGG
*
34170895 TCAGCGAG
1 TCAACGAG
34170903 TTGTTAGGAG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (36 bp):
TCAACGAGCCTTAATAAAATCAGCTGTGAACGTAGG
Found at i:34171012 original size:104 final size:104
Alignment explanation
Indices: 34170863--34171084 Score: 336
Period size: 104 Copynumber: 2.1 Consensus size: 104
34170853 TGTAGGTCAA
* * * *
34170863 TGAGCCTTAATAACATTAGCTGTGAACGTAGGTCAGCGAGTTGTTAGGAGTTGCGATCTTAAATC
1 TGAGCCTTAATAATATTAGCTGTGAACGTACGTCAGCGAGCTGTTAGGAGTTGCGATATTAAATC
* * *
34170928 AGCTAACTTAAATAATCGGAGGTTGCGATCTTAAATTAG
66 AGCTAACTCAAATAATCGAAGGTTGCGATCTTAAATCAG
* * * *
34170967 TGAGCCTTAGTAATATTCGTTGTGAACGTACGTCAGCGAGCTGTTAGGAGTTGGGATATTAAATC
1 TGAGCCTTAATAATATTAGCTGTGAACGTACGTCAGCGAGCTGTTAGGAGTTGCGATATTAAATC
*
34171032 AGCTAACTCAAATAATCGAAGGTTGCTATCTTAAATCAG
66 AGCTAACTCAAATAATCGAAGGTTGCGATCTTAAATCAG
34171071 TGAGCCTTAATAAT
1 TGAGCCTTAATAAT
34171085 GGAAACTAAC
Statistics
Matches: 105, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
104 105 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (104 bp):
TGAGCCTTAATAATATTAGCTGTGAACGTACGTCAGCGAGCTGTTAGGAGTTGCGATATTAAATC
AGCTAACTCAAATAATCGAAGGTTGCGATCTTAAATCAG
Found at i:34186222 original size:12 final size:12
Alignment explanation
Indices: 34186205--34186229 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34186195 CATGAAGTGC
34186205 AAAAAAAATTCA
1 AAAAAAAATTCA
34186217 AAAAAAAATTCA
1 AAAAAAAATTCA
34186229 A
1 A
34186230 GTTGTATTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:34189033 original size:50 final size:52
Alignment explanation
Indices: 34188979--34189096 Score: 143
Period size: 50 Copynumber: 2.3 Consensus size: 52
34188969 TAATAAAGTT
*
34188979 ATGCATTATGTAACTTCCATGCTAG-TTAAGTATGCATCA-TAAA-TAATGAC
1 ATGCATTATGTAACTTCCATGCTAGTTTAAGTATACATCATTAAATTAA-GAC
* * * *
34189029 ATGCATTATGTAACTCCCATGTTAGTTTAAGTCTACATCATTAAATTAAGTC
1 ATGCATTATGTAACTTCCATGCTAGTTTAAGTATACATCATTAAATTAAGAC
* *
34189081 TTGCATTAAGTAACTT
1 ATGCATTATGTAACTT
34189097 TTGTTCATTT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
50 23 0.40
51 12 0.21
52 19 0.33
53 3 0.05
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (52 bp):
ATGCATTATGTAACTTCCATGCTAGTTTAAGTATACATCATTAAATTAAGAC
Found at i:34189236 original size:27 final size:27
Alignment explanation
Indices: 34189185--34189236 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
34189175 CTCATCTTAG
* *
34189185 TTTAATTAATAAGTGTTTTTGTTAAAC
1 TTTAATTAATAAGTGTTTCTCTTAAAC
*
34189212 TTTATTTAATAAGTGTTTCTCTTAA
1 TTTAATTAATAAGTGTTTCTCTTAA
34189237 TTAATCTAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.31, C:0.06, G:0.10, T:0.54
Consensus pattern (27 bp):
TTTAATTAATAAGTGTTTCTCTTAAAC
Found at i:34191388 original size:13 final size:13
Alignment explanation
Indices: 34191370--34191409 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
34191360 TCTGATACTC
34191370 TGTTTTCAAGATA
1 TGTTTTCAAGATA
*
34191383 TGTTTTCAAGTTA
1 TGTTTTCAAGATA
34191396 TGTTTT-AA-ATA
1 TGTTTTCAAGATA
34191407 TGT
1 TGT
34191410 GTTTTACGCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 5 0.20
12 2 0.08
13 18 0.72
ACGTcount: A:0.28, C:0.05, G:0.15, T:0.53
Consensus pattern (13 bp):
TGTTTTCAAGATA
Found at i:34200963 original size:27 final size:27
Alignment explanation
Indices: 34200900--34200965 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
34200890 CCCCAAAGTA
* *
34200900 ACCCCATGATTATTATCCCAATGAATT
1 ACCCCATGTTTATTATCCCAATGAACT
* *
34200927 ACCCCATGTTTATTTTCCCAATGGACT
1 ACCCCATGTTTATTATCCCAATGAACT
*
34200954 ACCCCGTGTTTA
1 ACCCCATGTTTA
34200966 CTGTCCCGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.35
Consensus pattern (27 bp):
ACCCCATGTTTATTATCCCAATGAACT
Found at i:34215360 original size:22 final size:20
Alignment explanation
Indices: 34215332--34215376 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 20
34215322 GATTTGATGG
34215332 TGAAGAATTACCCAAATGAAGA
1 TGAAGAATTA-CCAAATG-AGA
*
34215354 TGAAGAATTATCAAATGAGA
1 TGAAGAATTACCAAATGAGA
34215374 TGA
1 TGA
34215377 GTTTTGATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.27
21 6 0.27
22 10 0.45
ACGTcount: A:0.49, C:0.09, G:0.20, T:0.22
Consensus pattern (20 bp):
TGAAGAATTACCAAATGAGA
Found at i:34215687 original size:19 final size:18
Alignment explanation
Indices: 34215658--34215694 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
34215648 TGAATCAGGA
34215658 TTTTTAAAATTTTTTAAT
1 TTTTTAAAATTTTTTAAT
34215676 TTTTTAATAATTTTTTAAT
1 TTTTTAA-AATTTTTTAAT
34215695 CTGACCGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTTAAAATTTTTTAAT
Found at i:34220198 original size:14 final size:14
Alignment explanation
Indices: 34220179--34220205 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
34220169 GCTCGTCGAA
34220179 GATCAGTAGTTTTT
1 GATCAGTAGTTTTT
34220193 GATCAGTAGTTTT
1 GATCAGTAGTTTT
34220206 AGATGTTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.07, G:0.22, T:0.48
Consensus pattern (14 bp):
GATCAGTAGTTTTT
Found at i:34223526 original size:17 final size:19
Alignment explanation
Indices: 34223493--34223527 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
34223483 GATATTATCA
34223493 GATGTGAGTGAAAGATTGT
1 GATGTGAGTGAAAGATTGT
34223512 GATGTGA-TG-AAGATTG
1 GATGTGAGTGAAAGATTG
34223528 CATTCAGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 2 0.12
19 7 0.44
ACGTcount: A:0.31, C:0.00, G:0.37, T:0.31
Consensus pattern (19 bp):
GATGTGAGTGAAAGATTGT
Found at i:34232250 original size:95 final size:93
Alignment explanation
Indices: 34232084--34232273 Score: 238
Period size: 95 Copynumber: 2.0 Consensus size: 93
34232074 TCTTCTCTTA
* * ** * * * *
34232084 TTGGATGTTTAATTGGACGTTGGAAACCTTTATGATCTTTTGAACTACACTAATAACATTTCATG
1 TTGGATATTTAATTGGACATCAGAAACCCTCATGATCTTTTGAACTACACCAATAACATTTCATC
* * *
34232149 AAAGGTGATAGCTCAATCTTATCTCTCTCT
66 AAAGGTGAAAGATCAATCGTA-CTC-CTCT
*
34232179 TTGGATATTTAATTGGACATCAGAAACCCTCATGATCTTTTGAACTACACCGATAACATTTCA-C
1 TTGGATATTTAATTGGACATCAGAAACCCTCATGATCTTTTGAACTACACCAATAACATTTCATC
34232243 AACAGGTGAAAGATCAATCGTACTCCTCT
66 AA-AGGTGAAAGATCAATCGTACTCCTCT
34232272 TT
1 TT
34232274 TCGTTTGACC
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
93 6 0.07
94 5 0.06
95 71 0.87
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (93 bp):
TTGGATATTTAATTGGACATCAGAAACCCTCATGATCTTTTGAACTACACCAATAACATTTCATC
AAAGGTGAAAGATCAATCGTACTCCTCT
Found at i:34237765 original size:190 final size:190
Alignment explanation
Indices: 34237442--34237812 Score: 564
Period size: 190 Copynumber: 2.0 Consensus size: 190
34237432 TTTAGATGAA
* *
34237442 TATGAATGGTAAGTTAATTTTCAATATACGAACTTACTAAGCATTAAATGCTTACTCAATTTTTC
1 TATGAATGGTAAGTTAATTTTCAATATACAAACTCACTAAGCATTAAATGCTTACTCAATTTTTC
* *
34237507 TTTCCTTTATTTTATAGTACTCAGAAGCTCGTAAAGGTTAAAAGCGGGTTGGAGCAAGATCACAC
66 TTTCCTCTATTTTATAGTACTCAGAAGCTCGTAAAGGTTAAAAGCGGGTCGGAGCAAGATCACAC
* *
34237572 TATCCTTCAGCTCACCTTGGTATAATTAGTAAAATTACTTTTGGTATAATGCTTACTCGG
131 TATCCTTCAGCTCACCTTGGTATAATTAGTAAAATAACTTTTGATATAATGCTTACTCGG
* ** * * **
34237632 TATGAATGGTAAGTTGA-TTTCTGTTATACAAACTCATTAAGCATTAAATGTTTACTCGTTTTTT
1 TATGAATGGTAAGTTAATTTTC-AATATACAAACTCACTAAGCATTAAATGCTTACTCAATTTTT
* * **
34237696 CTTTCCTCTGTTTTATAGTACTCGGAAGCTCGTAAAGGTTGGAAGCGGGTCGGAGCAAGATCACA
65 CTTTCCTCTATTTTATAGTACTCAGAAGCTCGTAAAGGTTAAAAGCGGGTCGGAGCAAGATCACA
*
34237761 CTATCCTTTAGCTCACCTTGGTATAATTAGTAAAATAACTTTTGATATAATG
130 CTATCCTTCAGCTCACCTTGGTATAATTAGTAAAATAACTTTTGATATAATG
34237813 GCAAGTATAG
Statistics
Matches: 162, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
189 4 0.02
190 158 0.98
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (190 bp):
TATGAATGGTAAGTTAATTTTCAATATACAAACTCACTAAGCATTAAATGCTTACTCAATTTTTC
TTTCCTCTATTTTATAGTACTCAGAAGCTCGTAAAGGTTAAAAGCGGGTCGGAGCAAGATCACAC
TATCCTTCAGCTCACCTTGGTATAATTAGTAAAATAACTTTTGATATAATGCTTACTCGG
Found at i:34239053 original size:6 final size:6
Alignment explanation
Indices: 34239042--34239069 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
34239032 AACAAGAGCG
34239042 AAAAAC AAAAAC AAAAAC AAAAAC AAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAA
34239070 TGGAATTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:34246668 original size:13 final size:13
Alignment explanation
Indices: 34246625--34246677 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
34246615 TTATTCACGT
*
34246625 TTCTTTTTTTTTC
1 TTCTTTATTTTTC
* * *
34246638 GTTCTTTCTCTTTA
1 -TTCTTTATTTTTC
34246652 TTCTTTATTTTTC
1 TTCTTTATTTTTC
*
34246665 TTCTCTATTTTTC
1 TTCTTTATTTTTC
34246678 CGCTGCCATT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 22 0.69
14 10 0.31
ACGTcount: A:0.06, C:0.19, G:0.02, T:0.74
Consensus pattern (13 bp):
TTCTTTATTTTTC
Found at i:34250695 original size:104 final size:103
Alignment explanation
Indices: 34250508--34250698 Score: 301
Period size: 104 Copynumber: 1.8 Consensus size: 103
34250498 AACTTTACAA
* * *
34250508 AAACATTCTTCTCAAAATCACCTATCAAAAGCAATGCTAACTAACCTTAATCTAAGTCATCCATC
1 AAACATTCTTCTCAAAATCACCTATCAAAAGAAATACTAACTAACCTTAATCTAAGTCATACATC
34250573 CACTAAATTATAAAGTGGTGTAAGCACTAACTTTTAAG
66 CACTAAATTATAAAGTGGTGTAAGCACTAACTTTTAAG
* * * *
34250611 AAACATTCTTCTCAAAATCACTTATCAAAAGAAATACTAAGTAGCCCTTAATCTAAGTCCTACAT
1 AAACATTCTTCTCAAAATCACCTATCAAAAGAAATACTAACTA-ACCTTAATCTAAGTCATACAT
*
34250676 CCCCTAAATTATAAAGTGGTGTA
65 CCACTAAATTATAAAGTGGTGTA
34250699 GGCATTGCAT
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
103 39 0.49
104 40 0.51
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.29
Consensus pattern (103 bp):
AAACATTCTTCTCAAAATCACCTATCAAAAGAAATACTAACTAACCTTAATCTAAGTCATACATC
CACTAAATTATAAAGTGGTGTAAGCACTAACTTTTAAG
Found at i:34267856 original size:15 final size:15
Alignment explanation
Indices: 34267838--34267868 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
34267828 TTAGTTCTAG
34267838 TTTGAGTTAAATTCT
1 TTTGAGTTAAATTCT
*
34267853 TTTGAGTTTAATTCT
1 TTTGAGTTAAATTCT
34267868 T
1 T
34267869 CATTAAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.06, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTGAGTTAAATTCT
Found at i:34271644 original size:9 final size:9
Alignment explanation
Indices: 34271626--34271710 Score: 91
Period size: 9 Copynumber: 9.4 Consensus size: 9
34271616 TTTGGTTAAA
34271626 AATTAACCG
1 AATTAACCG
*
34271635 AATTACCCG
1 AATTAACCG
34271644 AATTAACCG
1 AATTAACCG
*
34271653 AATTAATCG
1 AATTAACCG
* *
34271662 GATTACCCG
1 AATTAACCG
*
34271671 AATTAACTG
1 AATTAACCG
34271680 AATT-ACCAG
1 AATTAACC-G
*
34271689 AATTAACAG
1 AATTAACCG
*
34271698 AATTAACCA
1 AATTAACCG
34271707 AATT
1 AATT
34271711 GAATCACTAC
Statistics
Matches: 61, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
8 2 0.03
9 57 0.93
10 2 0.03
ACGTcount: A:0.44, C:0.20, G:0.11, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:34276178 original size:10 final size:10
Alignment explanation
Indices: 34276165--34276210 Score: 74
Period size: 10 Copynumber: 4.5 Consensus size: 10
34276155 CTGTGACTAA
34276165 ATGTGATTAT
1 ATGTGATTAT
*
34276175 ATGTAATTAT
1 ATGTGATTAT
34276185 ATGTGATTAT
1 ATGTGATTAT
34276195 ATGTGATTGAT
1 ATGTGATT-AT
34276206 ATGTG
1 ATGTG
34276211 TCGGAATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
10 26 0.79
11 7 0.21
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (10 bp):
ATGTGATTAT
Found at i:34280449 original size:6 final size:6
Alignment explanation
Indices: 34280440--34280485 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
34280430 TAAAATGAAA
* *
34280440 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAC AAAAAC AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
34280486 GCTCGAAAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.85, C:0.04, G:0.00, T:0.11
Consensus pattern (6 bp):
AAAAAT
Found at i:34292409 original size:40 final size:41
Alignment explanation
Indices: 34292328--34292435 Score: 105
Period size: 40 Copynumber: 2.7 Consensus size: 41
34292318 CCAGATTATT
* *
34292328 CCTGAATTGCACATACGTGCCCCTATTTGTACTTTGTTACC
1 CCTGAATTGCACATAAGTGCCCCTATTTGTACTTAGTTACC
* * *
34292369 CCTGAATTGC-GATAAGTGCCTCTGTTTGTACTTCAG-TACC
1 CCTGAATTGCACATAAGTGCCCCTATTTGTACTT-AGTTACC
* * * *
34292409 CTTGCATTGCACACATGTGCCCC-ATTT
1 CCTGAATTGCACATAAGTGCCCCTATTT
34292436 TGTAATTCGA
Statistics
Matches: 53, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
40 34 0.64
41 19 0.36
ACGTcount: A:0.19, C:0.29, G:0.17, T:0.35
Consensus pattern (41 bp):
CCTGAATTGCACATAAGTGCCCCTATTTGTACTTAGTTACC
Found at i:34298816 original size:41 final size:43
Alignment explanation
Indices: 34298770--34298872 Score: 122
Period size: 41 Copynumber: 2.4 Consensus size: 43
34298760 CTCTGAGGTG
* *
34298770 TGATTTCATGTAAGACCATGTCTGGGACA-TTGCATC-ATATA
1 TGATTTCATGTAAGACCATGTCTGGGACAGTGGCATCGAAATA
*
34298811 TGATTT-AGTGTAAGACCCTGTCTGGGACAGTGGCATCGAAATA
1 TGATTTCA-TGTAAGACCATGTCTGGGACAGTGGCATCGAAATA
* **
34298854 TTATAACATGTAAGACCAT
1 TGATTTCATGTAAGACCAT
34298873 ATCTAGGATA
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
40 1 0.02
41 26 0.51
42 6 0.12
43 17 0.33
44 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (43 bp):
TGATTTCATGTAAGACCATGTCTGGGACAGTGGCATCGAAATA
Found at i:34299169 original size:24 final size:24
Alignment explanation
Indices: 34299124--34299169 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
34299114 GAGTTGGTTA
**
34299124 TATTTACTTCATGTGTTATAAGTT
1 TATTTACTTCATGACTTATAAGTT
34299148 TATTTACTT-ATGACTTACTAAG
1 TATTTACTTCATGACTTA-TAAG
34299170 ATTCCAAAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.50
Consensus pattern (24 bp):
TATTTACTTCATGACTTATAAGTT
Found at i:34306611 original size:61 final size:61
Alignment explanation
Indices: 34306502--34306638 Score: 148
Period size: 61 Copynumber: 2.2 Consensus size: 61
34306492 AACATAGGCT
* * * * * **
34306502 GCCACAAAGGCTATCTTGTCTAGAGTTTTTCCACAAAGGTTGGCCTTTACATTTAGTACTC
1 GCCACAAAGGCTATCTTGTCCAGAGTTGTGCCACAAAGGCTAGCCTTTACATCCAGTACTC
* * ** * *
34306563 GCCACAAAGGCTTTCTTGTCCAGAGTTGTGCCATAAAGGCTATTCTTTATATCCAGTACTG
1 GCCACAAAGGCTATCTTGTCCAGAGTTGTGCCACAAAGGCTAGCCTTTACATCCAGTACTC
*
34306624 GCCACAAAGACTATC
1 GCCACAAAGGCTATC
34306639 ATTTATATCC
Statistics
Matches: 61, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.31
Consensus pattern (61 bp):
GCCACAAAGGCTATCTTGTCCAGAGTTGTGCCACAAAGGCTAGCCTTTACATCCAGTACTC
Found at i:34306715 original size:93 final size:93
Alignment explanation
Indices: 34306556--34306725 Score: 234
Period size: 93 Copynumber: 1.8 Consensus size: 93
34306546 CTTTACATTT
* * * *
34306556 AGTACTCGCCACAAAGGCTTTCTTGTCCAGAGTTGTGCCATAAAGGCTATTCTTTATATCCAGTA
1 AGTACTCGCCACAAAGGCTTTCCTATCCAGAGTTGTGCCACAAAGGCTATCCTTTATATCCAGTA
**
34306621 CTGGCCACAAAGACTATCATTTATATCC
66 CTCACCACAAAGACTATCATTTATATCC
* * * *
34306649 AGTACTTGCCACAAAGGCTTTCCTATCTAGAGTTGTTCCACAAAGGCTATCCTTTATAT-TAGGT
1 AGTACTCGCCACAAAGGCTTTCCTATCCAGAGTTGTGCCACAAAGGCTATCCTTTATATCCA-GT
34306713 ACTCACCACAAAG
65 ACTCACCACAAAG
34306726 GTTTTCCTTC
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
92 1 0.02
93 65 0.98
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.31
Consensus pattern (93 bp):
AGTACTCGCCACAAAGGCTTTCCTATCCAGAGTTGTGCCACAAAGGCTATCCTTTATATCCAGTA
CTCACCACAAAGACTATCATTTATATCC
Found at i:34307671 original size:22 final size:22
Alignment explanation
Indices: 34307643--34307686 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
34307633 AACATTCTTC
*
34307643 TTAACTCAACCGAAGTGTCCAT
1 TTAACTCAACCGAAGTCTCCAT
*
34307665 TTAACTCAACCTAAGTCTCCAT
1 TTAACTCAACCGAAGTCTCCAT
34307687 GGGAACTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.32, C:0.30, G:0.09, T:0.30
Consensus pattern (22 bp):
TTAACTCAACCGAAGTCTCCAT
Found at i:34313013 original size:2 final size:2
Alignment explanation
Indices: 34313006--34313046 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
34312996 GAAGTAGAAG
34313006 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34313047 TGGTGAAATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:34319224 original size:22 final size:22
Alignment explanation
Indices: 34319199--34319240 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
34319189 TCTTTAAAAA
34319199 ATTAATAATGT-TAATAAATTGG
1 ATTAAT-ATGTGTAATAAATTGG
34319221 ATTAATATGTGTAATAAATT
1 ATTAATATGTGTAATAAATT
34319241 TTAAATTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.43
Consensus pattern (22 bp):
ATTAATATGTGTAATAAATTGG
Found at i:34321504 original size:17 final size:17
Alignment explanation
Indices: 34321458--34321504 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
34321448 TAACATTTTA
* *
34321458 ATTATTTATATTATTAAT
1 ATTATTT-TAATATAAAT
34321476 -TTATTATTAATATAAAT
1 ATTATT-TTAATATAAAT
34321493 ATTATTTTAATA
1 ATTATTTTAATA
34321505 ACTTTTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 19 0.76
18 6 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTATTTTAATATAAAT
Found at i:34321585 original size:18 final size:15
Alignment explanation
Indices: 34321546--34321577 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
34321536 TTTAAAAATA
34321546 TTATTTTACTAATCT
1 TTATTTTACTAATCT
34321561 TTATTTTACTAATCT
1 TTATTTTACTAATCT
34321576 TT
1 TT
34321578 CTTATTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.12, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATTTTACTAATCT
Found at i:34321667 original size:13 final size:11
Alignment explanation
Indices: 34321631--34321660 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
34321621 ATTACTCAAT
34321631 ATATATTTTTA
1 ATATATTTTTA
34321642 ATATATTTTTA
1 ATATATTTTTA
34321653 ATATATTT
1 ATATATTT
34321661 GATTAATCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
ATATATTTTTA
Found at i:34325904 original size:36 final size:37
Alignment explanation
Indices: 34325863--34325945 Score: 98
Period size: 36 Copynumber: 2.3 Consensus size: 37
34325853 ATGATGATTG
* * *
34325863 ATGTGAAAGTGA-ATATGAGGGTGTGTTGTTCATCCC
1 ATGTGAAAGTGATATATGAGGGTATATTATTCATCCC
* * *
34325899 ATGTGACAGT-ATATATGTGGGTATATTATTCATGCC
1 ATGTGAAAGTGATATATGAGGGTATATTATTCATCCC
34325935 ATGTGAAAGTG
1 ATGTGAAAGTG
34325946 TTTATAATGT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
35 1 0.03
36 37 0.97
ACGTcount: A:0.28, C:0.10, G:0.28, T:0.35
Consensus pattern (37 bp):
ATGTGAAAGTGATATATGAGGGTATATTATTCATCCC
Found at i:34334377 original size:15 final size:15
Alignment explanation
Indices: 34334353--34334383 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
34334343 CTAATTCCAC
*
34334353 TAGTTTTATTTAATT
1 TAGTTGTATTTAATT
34334368 TAGTTGTATTTAATT
1 TAGTTGTATTTAATT
34334383 T
1 T
34334384 CTATAGGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.65
Consensus pattern (15 bp):
TAGTTGTATTTAATT
Found at i:34337069 original size:54 final size:54
Alignment explanation
Indices: 34336952--34337076 Score: 144
Period size: 54 Copynumber: 2.3 Consensus size: 54
34336942 TTATTTCAAG
* * * * * *
34336952 TCAGTGAGTTACATGGTCTAGCACACGGCCTGCGACATGGTTGTGTGTCGCAAG
1 TCAGTGAGTTACACGGTCTAGCACACGGCCTGCGACACGATCGTGTGACGCAAA
** **
34337006 TCAAAGAGTTACACGGTCTAGCACACGGTTTGCGACACGATCGTGTGAC-CTAAA
1 TCAGTGAGTTACACGGTCTAGCACACGGCCTGCGACACGATCGTGTGACGC-AAA
34337060 TCAGTGAGTTACACGGT
1 TCAGTGAGTTACACGGT
34337077 TTAAGACACG
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
53 1 0.02
54 57 0.98
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (54 bp):
TCAGTGAGTTACACGGTCTAGCACACGGCCTGCGACACGATCGTGTGACGCAAA
Found at i:34338528 original size:3 final size:3
Alignment explanation
Indices: 34338515--34338549 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
34338505 GACATCGACT
*
34338515 TCA TTA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
34338550 TATTGAAGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.37
Consensus pattern (3 bp):
TCA
Found at i:34345420 original size:26 final size:26
Alignment explanation
Indices: 34345382--34345431 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
34345372 TCATGCTATA
* *
34345382 TGGACTTTAATTTTGGGACTTTGGTT
1 TGGACTTTAATTTAGGAACTTTGGTT
* *
34345408 TGGATTTTGATTTAGGAACTTTGG
1 TGGACTTTAATTTAGGAACTTTGG
34345432 ATAATATTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.18, C:0.06, G:0.28, T:0.48
Consensus pattern (26 bp):
TGGACTTTAATTTAGGAACTTTGGTT
Found at i:34347580 original size:13 final size:13
Alignment explanation
Indices: 34347562--34347599 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
34347552 AAATTATCCA
*
34347562 ACCCAACTCAATT
1 ACCCAACCCAATT
34347575 ACCCAACCCAATT
1 ACCCAACCCAATT
34347588 ACCCAACCCAAT
1 ACCCAACCCAAT
34347600 AAAACTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.39, C:0.45, G:0.00, T:0.16
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:34347680 original size:38 final size:39
Alignment explanation
Indices: 34347580--34347696 Score: 218
Period size: 39 Copynumber: 3.0 Consensus size: 39
34347570 CAATTACCCA
34347580 ACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
1 ACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
34347619 ACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
1 ACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
*
34347658 ACCCAATTA-CCAACCCAATAAAAATAAAACTAAAGTCT
1 ACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
34347696 A
1 A
34347697 ACTCTTAGTA
Statistics
Matches: 77, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
38 29 0.38
39 48 0.62
ACGTcount: A:0.50, C:0.29, G:0.03, T:0.18
Consensus pattern (39 bp):
ACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
Found at i:34347850 original size:17 final size:17
Alignment explanation
Indices: 34347830--34347893 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
34347820 TTAATTTCAA
34347830 TAATTATGTAATGTTTT
1 TAATTATGTAATGTTTT
* **
34347847 TAATTATGTAGTGATTCA
1 TAATTATGTAATG-TTTT
* *
34347865 AAGACTTATGTAATATTTT
1 TA-A-TTATGTAATGTTTT
34347884 TAATTATGTA
1 TAATTATGTA
34347894 GTGATTCAAT
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
17 19 0.54
18 4 0.11
19 4 0.11
20 8 0.23
ACGTcount: A:0.34, C:0.03, G:0.12, T:0.50
Consensus pattern (17 bp):
TAATTATGTAATGTTTT
Found at i:34347915 original size:9 final size:9
Alignment explanation
Indices: 34347901--34347949 Score: 71
Period size: 9 Copynumber: 5.4 Consensus size: 9
34347891 GTAGTGATTC
*
34347901 AATTCGGGT
1 AATTCGGTT
*
34347910 AATTCGGGT
1 AATTCGGTT
*
34347919 AATTCGATT
1 AATTCGGTT
34347928 AATTCGGTT
1 AATTCGGTT
34347937 AATTCGGTT
1 AATTCGGTT
34347946 AATT
1 AATT
34347950 TTTAACCAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (9 bp):
AATTCGGTT
Found at i:34347932 original size:27 final size:28
Alignment explanation
Indices: 34347896--34347949 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
34347886 ATTATGTAGT
34347896 GATTCAATTCGGGTAATTCGGGTAATTC
1 GATTCAATTCGGGTAATTCGGGTAATTC
* *
34347924 GATT-AATTCGGTTAATTCGGTTAATT
1 GATTCAATTCGGGTAATTCGGGTAATT
34347950 TTTAACCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.26, C:0.11, G:0.22, T:0.41
Consensus pattern (28 bp):
GATTCAATTCGGGTAATTCGGGTAATTC
Found at i:34357219 original size:9 final size:9
Alignment explanation
Indices: 34357205--34357278 Score: 67
Period size: 9 Copynumber: 8.2 Consensus size: 9
34357195 TTCAAAGAAG
*
34357205 ATAATAAGA
1 ATAATAATA
*
34357214 ATAATAAGA
1 ATAATAATA
* *
34357223 ATAAGATTA
1 ATAATAATA
* *
34357232 AGAATAAGA
1 ATAATAATA
*
34357241 ATAAGAATA
1 ATAATAATA
*
34357250 ATTATAATA
1 ATAATAATA
34357259 ATAATAATA
1 ATAATAATA
*
34357268 ATAATGATA
1 ATAATAATA
34357277 AT
1 AT
34357279 GGCTGTAGAG
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
9 51 1.00
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.28
Consensus pattern (9 bp):
ATAATAATA
Found at i:34357256 original size:18 final size:18
Alignment explanation
Indices: 34357213--34357272 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
34357203 AGATAATAAG
*
34357213 AATAATAAGAATAAGATT
1 AATAATAAGAATAAGAAT
*
34357231 AAGAATAAGAATAAGAAT
1 AATAATAAGAATAAGAAT
* * *
34357249 AATTATAATAATAATAAT
1 AATAATAAGAATAAGAAT
34357267 AATAAT
1 AATAAT
34357273 GATAATGGCT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.28
Consensus pattern (18 bp):
AATAATAAGAATAAGAAT
Found at i:34357279 original size:6 final size:6
Alignment explanation
Indices: 34357205--34357278 Score: 67
Period size: 6 Copynumber: 12.3 Consensus size: 6
34357195 TTCAAAGAAG
* * * * * * * *
34357205 ATAATA AGAATA ATAAGA ATAAGA TTAAGA ATAAGA ATAAGA ATAATT
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
*
34357253 ATAATA ATAATA ATAATA ATGATA AT
1 ATAATA ATAATA ATAATA ATAATA AT
34357279 GGCTGTAGAG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.28
Consensus pattern (6 bp):
ATAATA
Found at i:34359683 original size:3 final size:3
Alignment explanation
Indices: 34359675--34359746 Score: 135
Period size: 3 Copynumber: 24.0 Consensus size: 3
34359665 ATTCAAAGAA
*
34359675 AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
34359723 AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT
34359747 GGCTGTAAAG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:34362701 original size:2 final size:2
Alignment explanation
Indices: 34362694--34362725 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
34362684 TGAAATGAGG
34362694 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
34362726 TTCTAGCGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:34369291 original size:13 final size:13
Alignment explanation
Indices: 34369275--34369309 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
34369265 ATCGAGCCCA
34369275 TAAATATTTTTAT
1 TAAATATTTTTAT
34369288 TAAATATTTTTAT
1 TAAATATTTTTAT
34369301 TAAATATTT
1 TAAATATTT
34369310 ATAGAGTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATATTTTTAT
Found at i:34376036 original size:42 final size:42
Alignment explanation
Indices: 34375956--34376129 Score: 224
Period size: 42 Copynumber: 4.2 Consensus size: 42
34375946 ATCGACAGTT
* * * * *
34375956 AGCCTGCTAGACATATAGTCT-AAAATGTTTCACTGGCATTA
1 AGCCTGCTAGACGTAAAGTCTGATATTGTTTCACCGGCATTA
** *
34375997 AGCCAACTAGATGTAAAGTCTGATATTGTTTCACCGGCATTA
1 AGCCTGCTAGACGTAAAGTCTGATATTGTTTCACCGGCATTA
* * *
34376039 AGCCTGCTAGACGTAAAGTCTGAAATTATTTCACCGACATTA
1 AGCCTGCTAGACGTAAAGTCTGATATTGTTTCACCGGCATTA
* *
34376081 AGCCTGCTAGACGTAAAGTCTGATATTGTTTCACTGGCACTA
1 AGCCTGCTAGACGTAAAGTCTGATATTGTTTCACCGGCATTA
34376123 AGCCTGC
1 AGCCTGC
34376130 CAGGCACTAA
Statistics
Matches: 113, Mismatches: 19, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
41 16 0.14
42 97 0.86
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (42 bp):
AGCCTGCTAGACGTAAAGTCTGATATTGTTTCACCGGCATTA
Found at i:34376146 original size:84 final size:84
Alignment explanation
Indices: 34375983--34376148 Score: 219
Period size: 84 Copynumber: 2.0 Consensus size: 84
34375973 GTCTAAAATG
* * * * *
34375983 TTTCACTGGCATTAAGCCAACTAGATGTAAAGTCTGATATTGTTTCACCGGCATTAAGCCTGCTA
1 TTTCACCGACATTAAGCCAACTAGACGTAAAGTCTGATATTGTTTCACCGGCACTAAGCCTGCCA
*
34376048 GACGTAAAGTCTGAAATTA
66 GACGTAAAGCCTGAAATTA
** *
34376067 TTTCACCGACATTAAGCCTGCTAGACGTAAAGTCTGATATTGTTTCACTGGCACTAAGCCTGCCA
1 TTTCACCGACATTAAGCCAACTAGACGTAAAGTCTGATATTGTTTCACCGGCACTAAGCCTGCCA
34376132 GGCAC-T-AAGCCTGAAAT
66 -G-ACGTAAAGCCTGAAAT
34376149 CTCAATTTCA
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
84 67 0.94
85 2 0.03
86 2 0.03
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (84 bp):
TTTCACCGACATTAAGCCAACTAGACGTAAAGTCTGATATTGTTTCACCGGCACTAAGCCTGCCA
GACGTAAAGCCTGAAATTA
Found at i:34376879 original size:10 final size:10
Alignment explanation
Indices: 34376864--34376892 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
34376854 TCAAGAACAT
34376864 ATACATATAG
1 ATACATATAG
34376874 ATACATATAG
1 ATACATATAG
34376884 ATACATATA
1 ATACATATA
34376893 TAATTATTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.31
Consensus pattern (10 bp):
ATACATATAG
Found at i:34377072 original size:4 final size:4
Alignment explanation
Indices: 34377063--34377151 Score: 178
Period size: 4 Copynumber: 22.2 Consensus size: 4
34377053 AAAATAAAAT
34377063 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
34377111 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
34377152 GATTTAATAA
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 85 1.00
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Done.