Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
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: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 120 of 199
Found at i:39782684 original size:21 final size:22
Alignment explanation
Indices: 39782658--39782704 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
39782648 CTCTGCTCAA
*
39782658 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
39782679 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
39782701 ACTC
1 ACTC
39782705 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:39785623 original size:18 final size:18
Alignment explanation
Indices: 39785584--39785623 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
39785574 GATTATTATG
*
39785584 TTATAATTTTTATATCTC
1 TTATAATTTTTATATCTA
39785602 TTATAATTTTTATGAT-TA
1 TTATAATTTTTAT-ATCTA
39785620 TTAT
1 TTAT
39785624 GTTTATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (18 bp):
TTATAATTTTTATATCTA
Found at i:39785704 original size:19 final size:19
Alignment explanation
Indices: 39785680--39785721 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
39785670 ATATTTCTAT
*
39785680 ATTTTTTAA-TTTTTATAA
1 ATTTTTAAATTTTTTATAA
39785698 CATTTTTAAATTTTTTATAA
1 -ATTTTTAAATTTTTTATAA
39785718 ATTT
1 ATTT
39785722 AAAATATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTTTAAATTTTTTATAA
Found at i:39785730 original size:20 final size:20
Alignment explanation
Indices: 39785689--39785733 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
39785679 TATTTTTTAA
**
39785689 TTTTTATAACATTTTTAAAT
1 TTTTTATAACATTTAAAAAT
39785709 TTTTTATAA-ATTTAAAATAT
1 TTTTTATAACATTTAAAA-AT
39785729 TTTTT
1 TTTTT
39785734 TTCTATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTTATAACATTTAAAAAT
Found at i:39785802 original size:18 final size:17
Alignment explanation
Indices: 39785767--39785815 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
39785757 TAAATTTTCT
39785767 TTTATAA-A-TTTTATA
1 TTTATAATATTTTTATA
39785782 TTTCAT-ATATTTTTATAA
1 TTT-ATAATATTTTTAT-A
*
39785800 TTTTTAATATTTTTAT
1 TTTATAATATTTTTAT
39785816 TGATTAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 4 0.14
16 3 0.11
17 7 0.25
18 14 0.50
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTATAATATTTTTATA
Found at i:39787080 original size:20 final size:19
Alignment explanation
Indices: 39787031--39787088 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
39787021 AAATTTTAGA
*
39787031 AATTTTATAAA-TATTTTG
1 AATTTTAGAAATTATTTTG
*
39787049 AGTTTTAGAAATTATTTTG
1 AATTTTAGAAATTATTTTG
*
39787068 AATTTTTGAAAATTATTTTG
1 AATTTTAG-AAATTATTTTG
39787088 A
1 A
39787089 TTCTTTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.26
19 13 0.38
20 12 0.35
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.53
Consensus pattern (19 bp):
AATTTTAGAAATTATTTTG
Found at i:39788197 original size:11 final size:11
Alignment explanation
Indices: 39788175--39788225 Score: 68
Period size: 11 Copynumber: 4.6 Consensus size: 11
39788165 AACTAATCCT
39788175 CTCTCAAATTTC
1 CTCTC-AATTTC
39788187 CTCTCAATTTC
1 CTCTCAATTTC
*
39788198 CTCTTAATTTC
1 CTCTCAATTTC
*
39788209 CTCTCAAGTTC
1 CTCTCAATTTC
39788220 CT-TCAA
1 CTCTCAA
39788226 AAATTCTCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
10 4 0.11
11 27 0.75
12 5 0.14
ACGTcount: A:0.22, C:0.33, G:0.02, T:0.43
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:39788248 original size:11 final size:11
Alignment explanation
Indices: 39788229--39788272 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
39788219 CCTTCAAAAA
39788229 TTCTCTTAACT
1 TTCTCTTAACT
* *
39788240 TTTTCTTAAGT
1 TTCTCTTAACT
* *
39788251 TCCTCTTAAGT
1 TTCTCTTAACT
39788262 TTCTCTTAACT
1 TTCTCTTAACT
39788273 CTATTTTTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.18, C:0.23, G:0.05, T:0.55
Consensus pattern (11 bp):
TTCTCTTAACT
Found at i:39788311 original size:12 final size:12
Alignment explanation
Indices: 39788289--39788319 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
39788279 TTTTAAATAA
39788289 TTTTAAAAATTT
1 TTTTAAAAATTT
39788301 TTTTAAAAATTT
1 TTTTAAAAATTT
39788313 TTTTAAA
1 TTTTAAA
39788320 CCGTAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TTTTAAAAATTT
Found at i:39789434 original size:7 final size:7
Alignment explanation
Indices: 39789422--39789446 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
39789412 AGTCGATTGA
39789422 TATTTAG
1 TATTTAG
39789429 TATTTAG
1 TATTTAG
39789436 TATTTAG
1 TATTTAG
39789443 TATT
1 TATT
39789447 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:39790120 original size:18 final size:18
Alignment explanation
Indices: 39790097--39790131 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
39790087 AGGTGCGTTT
39790097 CCTAACCCTTATATGTAC
1 CCTAACCCTTATATGTAC
*
39790115 CCTAACTCTTATATGTA
1 CCTAACCCTTATATGTA
39790132 TCATTTTCCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.37
Consensus pattern (18 bp):
CCTAACCCTTATATGTAC
Found at i:39790420 original size:21 final size:21
Alignment explanation
Indices: 39790391--39790441 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
39790381 AATGTCGAAT
*
39790391 CGAAAGAACCAGAATCCCCAG
1 CGAAGGAACCAGAATCCCCAG
* *
39790412 CGGAGGAACCAGAATCCCTAG
1 CGAAGGAACCAGAATCCCCAG
39790433 CGAAGGAAC
1 CGAAGGAAC
39790442 AACAACCGCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.39, C:0.29, G:0.25, T:0.06
Consensus pattern (21 bp):
CGAAGGAACCAGAATCCCCAG
Found at i:39790584 original size:44 final size:44
Alignment explanation
Indices: 39790521--39790607 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 44
39790511 TTATTTGTAC
*
39790521 AATTATTTTGAGTATTTTGATATTATTTTATGTAA-AAGAATAGA
1 AATTATTTTGAGTATTTTGATATTATTTGATGTAATAA-AATAGA
39790565 AATT-TTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAG
1 AATTATTTTGAG-TATTTTGATATTATTTGATGTAATAAAATAG
39790608 GAGTCTATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
43 7 0.17
44 31 0.77
45 2 0.05
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (44 bp):
AATTATTTTGAGTATTTTGATATTATTTGATGTAATAAAATAGA
Found at i:39790622 original size:25 final size:25
Alignment explanation
Indices: 39790588--39790654 Score: 125
Period size: 25 Copynumber: 2.7 Consensus size: 25
39790578 ATTTTGATAT
*
39790588 TATTTGATGTAATAAAATAGGAGTC
1 TATTTGATGTAATAAAATAGAAGTC
39790613 TATTTGATGTAATAAAATAGAAGTC
1 TATTTGATGTAATAAAATAGAAGTC
39790638 TATTTGATGTAATAAAA
1 TATTTGATGTAATAAAA
39790655 ACCCTAACTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.43, C:0.03, G:0.16, T:0.37
Consensus pattern (25 bp):
TATTTGATGTAATAAAATAGAAGTC
Found at i:39790710 original size:29 final size:29
Alignment explanation
Indices: 39790670--39791000 Score: 261
Period size: 29 Copynumber: 12.3 Consensus size: 29
39790660 AACTTAATTT
39790670 AACCCTAAACCCTAACCTAATTTAATTAAA
1 AACCCT-AACCCTAACCTAATTTAATTAAA
* * ** *
39790700 AATCTTAACCCTAACCTTAACCTAATTTAA
1 AACCCTAACCCTAACC-TAATTTAATTAAA
* ** * **
39790730 TA-CAAAACCCTACCCTAATTGGATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
39790758 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
*
39790787 AACCCTAACCCTAACATAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
39790816 AACCCT-A----AACC----TTAACTTAAA
1 AACCCTAACCCTAACCTAATTTAA-TTAAA
* *
39790837 AACCCTAAACCT----TAACTT-A--AAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
39790859 AACCCTAA------CCTAATTTAA-TACAA
1 AACCCTAACCCTAACCTAATTTAATTA-AA
*
39790882 AACCCTTA-CCTAA--T--TTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
*
39790906 AACCCTAACCCTACCCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
*
39790935 AACCCTAACCCTATCCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
*
39790964 AATCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
39790993 AACCCTAA
1 AACCCTAA
39791001 ACCTTAAATT
Statistics
Matches: 243, Mismatches: 30, Indels: 57
0.74 0.09 0.17
Matches are distributed among these distances:
20 9 0.04
21 12 0.05
22 13 0.05
23 9 0.04
24 17 0.07
25 7 0.03
26 3 0.01
27 1 0.00
28 10 0.04
29 147 0.60
30 15 0.06
ACGTcount: A:0.45, C:0.27, G:0.01, T:0.28
Consensus pattern (29 bp):
AACCCTAACCCTAACCTAATTTAATTAAA
Found at i:39790793 original size:23 final size:23
Alignment explanation
Indices: 39790764--39791089 Score: 176
Period size: 29 Copynumber: 13.3 Consensus size: 23
39790754 TAAAAACCCT
39790764 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
39790787 AACCCTAACCCTAACATAATTTAATTAAA
1 AACCCTAA--C---C-TAATTTAATTAAA
39790816 AACCCTAAACC----TTAACTTAAA
1 AACCCT-AACCTAATTTAA-TTAAA
*
39790837 AACCCTAAACCTTAACTT-A--AAA
1 AACCCT-AACC-TAATTTAATTAAA
39790859 AACCCTAACCTAATTTAA-TACAA
1 AACCCTAACCTAATTTAATTA-AA
*
39790882 AACCCTTACCTAATTTTAATTAAA
1 AACCCTAACCTAA-TTTAATTAAA
39790906 AACCCTAACCCTACCCTAATTTAATTAAA
1 AACCCT-A----A-CCTAATTTAATTAAA
39790935 AACCCTAACCCTATCCTAATTTAATTAAAAA
1 AACCCT-A----A-CCTAATTTAATT--AAA
39790966 TCCTAACCCTAACCTAATTTAATTAAA
1 ----AACCCTAACCTAATTTAATTAAA
* *
39790993 AACCCTAAACC---TTAAATTAGA
1 AACCCT-AACCTAATTTAATTAAA
*
39791014 AACCCTAAACCTTAA-CT--TTAAA
1 AACCCT-AACC-TAATTTAATTAAA
****
39791036 AACCCTAACCTAATTTAACCCTA
1 AACCCTAACCTAATTTAATTAAA
39791059 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
39791082 AACCCTAA
1 AACCCTAA
39791090 ACAAAGTTAA
Statistics
Matches: 247, Mismatches: 18, Indels: 76
0.72 0.05 0.22
Matches are distributed among these distances:
20 12 0.05
21 45 0.18
22 20 0.08
23 56 0.23
24 17 0.07
25 5 0.02
26 2 0.01
27 3 0.01
28 2 0.01
29 67 0.27
30 8 0.03
31 3 0.01
34 1 0.00
35 6 0.02
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.28
Consensus pattern (23 bp):
AACCCTAACCTAATTTAATTAAA
Found at i:39790869 original size:21 final size:21
Alignment explanation
Indices: 39790807--39790866 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
39790797 CTAACATAAT
39790807 TTAA-TTAAAAACCCTAAACC
1 TTAACTTAAAAACCCTAAACC
39790827 TTAACTTAAAAACCCTAAACC
1 TTAACTTAAAAACCCTAAACC
39790848 TTAACTTAAAAAACCCTAA
1 TTAACTT-AAAAACCCTAA
39790867 CCTAATTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.11
21 23 0.61
22 11 0.29
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (21 bp):
TTAACTTAAAAACCCTAAACC
Found at i:39790955 original size:177 final size:176
Alignment explanation
Indices: 39790735--39791089 Score: 593
Period size: 177 Copynumber: 2.0 Consensus size: 176
39790725 TTTAATACAA
*
39790735 AACCCTACCCTAATTGGATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTA
1 AACCCTACCCTAATTGAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTA
*
39790800 ACATAATTTAATTAAAAACCCTAAACCTTAACTTAAAAACCCTAAACCTTAACTTAAAAAACCCT
66 ACATAATTTAATTAAAAACCCTAAACCTTAAATTAAAAACCCTAAACCTTAACTTAAAAAACCCT
* *
39790865 AACCTAATTTAATACAAAACCCTTACCTAATTTTAATTAAAAACCCT
131 AACCTAATTTAACACAAAACCCTAACCTAA-TTTAATTAAAAACCCT
* * *
39790912 AACCCTACCCTAATTTAATTAAAAACCCTAACCCTATCCTAATTTAATTAAAAATCCTAACCCTA
1 AACCCTACCCTAATTGAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTA
* * *
39790977 ACCTAATTTAATTAAAAACCCTAAACCTTAAATTAGAAACCCTAAACCTTAACTTTAAAAACCCT
66 ACATAATTTAATTAAAAACCCTAAACCTTAAATTAAAAACCCTAAACCTTAACTTAAAAAACCCT
* *
39791042 AACCTAATTTAACCCTAAACCCTAACCTAATTTAATTAAAAACCCT
131 AACCTAATTTAACACAAAACCCTAACCTAATTTAATTAAAAACCCT
39791088 AA
1 AA
39791090 ACAAAGTTAA
Statistics
Matches: 166, Mismatches: 12, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
176 18 0.11
177 148 0.89
ACGTcount: A:0.45, C:0.27, G:0.01, T:0.28
Consensus pattern (176 bp):
AACCCTACCCTAATTGAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTA
ACATAATTTAATTAAAAACCCTAAACCTTAAATTAAAAACCCTAAACCTTAACTTAAAAAACCCT
AACCTAATTTAACACAAAACCCTAACCTAATTTAATTAAAAACCCT
Found at i:39791045 original size:21 final size:21
Alignment explanation
Indices: 39790984--39791053 Score: 92
Period size: 21 Copynumber: 3.4 Consensus size: 21
39790974 CTAACCTAAT
39790984 TTAA-TTAAAAACCCTAAACC
1 TTAATTTAAAAACCCTAAACC
* *
39791004 TTAAATTAGAAACCCTAAACC
1 TTAATTTAAAAACCCTAAACC
39791025 TTAACTTTAAAAACCCT-AACC
1 TTAA-TTTAAAAACCCTAAACC
39791046 -TAATTTAA
1 TTAATTTAA
39791054 CCCTAAACCC
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
19 5 0.11
20 7 0.16
21 23 0.51
22 10 0.22
ACGTcount: A:0.47, C:0.23, G:0.01, T:0.29
Consensus pattern (21 bp):
TTAATTTAAAAACCCTAAACC
Found at i:39791050 original size:148 final size:142
Alignment explanation
Indices: 39790752--39791089 Score: 384
Period size: 148 Copynumber: 2.3 Consensus size: 142
39790742 CCCTAATTGG
39790752 ATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACATAATTTAATTAAAA
1 ATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACATAATTTAATTAAAA
* *
39790817 ACCCTAAACCTTAACTTAAAAACCCTAAACCTTAACTTAAAAAACCCTAACCTAATTTAATACAA
66 ACCCTAAACCTTAACTTAAAAACCCTAAACCTTAAATTAAAAAACCCTAACCTAACTT-ATACAA
*
39790882 AACCCTTACCTAATTTTA
130 AACCCTAACC-----TTA
* * *
39790900 ATTAAAAACCCTAACCCTACCCTAATTTAATTAAAAACCCTAACCCTATCCTAATTTAATTAAAA
1 ATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACATAATTTAATTAAAA
* *
39790965 ATCCTAACCCTAACCTAATTTAA-TTAAAAACCCTAAACCTTAAATT-AGAAACCCTAAACCTTA
66 ACCCT-A----AACC----TTAACTTAAAAACCCTAAACCTTAAATTAAAAAACCCT-AACC-TA
39791028 ACTT-TA-AAAACCCTAACC-TA
120 ACTTATACAAAACCCTAACCTTA
*
39791048 ATT--TAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAA
1 ATTAAAAACCCT-AACCCTAACCTAATTTAATTAAAAACCCTAA
39791090 ACAAAGTTAA
Statistics
Matches: 168, Mismatches: 10, Indels: 25
0.83 0.05 0.12
Matches are distributed among these distances:
146 6 0.04
147 30 0.18
148 71 0.42
149 1 0.01
153 4 0.02
154 11 0.07
155 10 0.06
156 26 0.15
157 9 0.05
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (142 bp):
ATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACATAATTTAATTAAAA
ACCCTAAACCTTAACTTAAAAACCCTAAACCTTAAATTAAAAAACCCTAACCTAACTTATACAAA
ACCCTAACCTTA
Found at i:39794414 original size:125 final size:125
Alignment explanation
Indices: 39794248--39794600 Score: 535
Period size: 126 Copynumber: 2.8 Consensus size: 125
39794238 CCCAAACATG
*
39794248 CTACTATAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
**
39794313 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAATAATTATTTCTTTTGTGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAATAATTATTTCTTCCGTGAC
* * * * *
39794373 TTACTGTAGCAAAAGCGCGTCCTCGATGGCGCGATTTCACAATTTCTTCTCACATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* *
39794438 TAGAAGCGATTTTATACTATTTGCTCAAAAACGTAAAAAAAATAATTATTTCTTCCGTGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGT-CAAAAAATAATTATTTCTTCCGTGAC
* * * * *
39794499 CTACTGTAGCAAAAGCGTGTCCACGAGGGCGTGATTTCACAAATTCTTCCCAAATAACATCCTGT
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* * *
39794564 TAGAAGTGATTTTATACTATTTGATTAGAAACGTCAA
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA
39794601 CTCGAAATTA
Statistics
Matches: 202, Mismatches: 25, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
125 94 0.47
126 108 0.53
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAATAATTATTTCTTCCGTGAC
Found at i:39795637 original size:22 final size:21
Alignment explanation
Indices: 39795599--39795641 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
39795589 TTTTATAAGA
*
39795599 AATTTATCTTTTAAATAGAAAT
1 AATTTATCTATTAAATA-AAAT
39795621 AATTTATACTATT-AATAAAAT
1 AATTTAT-CTATTAAATAAAAT
39795642 CTCTAATCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 4 0.21
22 11 0.58
23 4 0.21
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (21 bp):
AATTTATCTATTAAATAAAAT
Found at i:39796257 original size:18 final size:18
Alignment explanation
Indices: 39796234--39796269 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
39796224 AGCAAAACTT
*
39796234 TATTTTGATTTTCTTATG
1 TATTTTAATTTTCTTATG
*
39796252 TATTTTAATTTTTTTATG
1 TATTTTAATTTTCTTATG
39796270 CACACTATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.03, G:0.08, T:0.69
Consensus pattern (18 bp):
TATTTTAATTTTCTTATG
Found at i:39798751 original size:3 final size:3
Alignment explanation
Indices: 39798745--39798777 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
39798735 AAAGAGTCTA
39798745 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
39798778 TTGTAATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:39800759 original size:25 final size:25
Alignment explanation
Indices: 39800731--39800778 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
39800721 AAGAAAAGTA
39800731 AAATACTAGAAAAGAAAAAAAAAAG
1 AAATACTAGAAAAGAAAAAAAAAAG
** * *
39800756 AAATTGTGGAAAAGAAGAAAAAA
1 AAATACTAGAAAAGAAAAAAAAA
39800779 CGTGAAAGGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.71, C:0.02, G:0.17, T:0.10
Consensus pattern (25 bp):
AAATACTAGAAAAGAAAAAAAAAAG
Found at i:39803811 original size:600 final size:600
Alignment explanation
Indices: 39802664--39803869 Score: 2313
Period size: 600 Copynumber: 2.0 Consensus size: 600
39802654 CTCGCAACCA
39802664 AAACTCGCATTTATTCAACTTAGCGTAAAGTTGTTTTTTATGGAGTATCTGCAGAACTATTTTAA
1 AAACTCGCATTTATTCAACTTAGCGTAAAGTTGTTTTTTATGGAGTATCTGCAGAACTATTTTAA
39802729 GGTGTTCATCATGCTCATCCTTAGTTTTAGAATAAATCAAAATATCCTCGATAAAAACCGCGATA
66 GGTGTTCATCATGCTCATCCTTAGTTTTAGAATAAATCAAAATATCCTCGATAAAAACCGCGATA
* * *
39802794 AACTGATTCAAATACGGCTAAAACACCAGATTCATTAGATCCATAAATGCACCCGGAGAGTTCGT
131 AACTGATCCAAATACGACTAAAACACCAGATTCATCAGATCCATAAATGCACCCGGAGAGTTCGT
39802859 CAAAATGAATGGCATGACTAGGAACTCGTAATGGCCATAACGAGTCCTAAAAACAATCTTATACA
196 CAAAATGAATGGCATGACTAGGAACTCGTAATGGCCATAACGAGTCCTAAAAACAATCTTATACA
39802924 TATCAGTCTCTTTAACCTTGTGGTCATGGTACCTAGAATGAAGGTCGATTTTAGAAAATACGGAT
261 TATCAGTCTCTTTAACCTTGTGGTCATGGTACCTAGAATGAAGGTCGATTTTAGAAAATACGGAT
*
39802989 GCTCCACGAAATTGATCAAATAGGTCGTCAATTCTCGGAAGTGGATACTTATTCTTTACCGTCAA
326 GCTCCACGAAATTGATCAAATAGGTCATCAATTCTCGGAAGTGGATACTTATTCTTTACCGTCAA
*
39803054 CTTATTCAGCTGATGATAATCTACACGCATTCTCATCGTGCCCTCCTTCTTTACAAACAGAACTA
391 CTTATTCAGCTGATGATAATCTACACGCATTCTCATCGTGCCATCCTTCTTTACAAACAGAACTA
*
39803119 GTGCTTCCCATGGGGACACACTTGGCCTGATGAACCCTCGATCAAGAAGTTCTTAAAGTTAAGCC
456 GTGCTTCCCATAGGGACACACTTGGCCTGATGAACCCTCGATCAAGAAGTTCTTAAAGTTAAGCC
39803184 TTTAATTCTATAAGCTCTTTTGGTGCCATGCAATAAGGGGCAATGAACACAGGAGCTGTACTTGG
521 TTTAATTCTATAAGCTCTTTTGGTGCCATGCAATAAGGGGCAATGAACACAGGAGCTGTACTTGG
39803249 CAGGAGTTCAATACC
586 CAGGAGTTCAATACC
*
39803264 AAACTCTCATTTATTCAACTTAGCGTAAAGTTGTTTTTTATGGAGTATCTGCAGAACTATTTTAA
1 AAACTCGCATTTATTCAACTTAGCGTAAAGTTGTTTTTTATGGAGTATCTGCAGAACTATTTTAA
* * *
39803329 GGTGTTCATCATGCTCATCCTTATTTTTAGAATAAATCAAAATATCCTCGATAAAAACCGTGATG
66 GGTGTTCATCATGCTCATCCTTAGTTTTAGAATAAATCAAAATATCCTCGATAAAAACCGCGATA
39803394 AACTGATCCAAATACGACTAAAACACCAGATTCATCAGATCCATAAATGCACCCGGAGAGTTCGT
131 AACTGATCCAAATACGACTAAAACACCAGATTCATCAGATCCATAAATGCACCCGGAGAGTTCGT
39803459 CAAAATGAATGGCATGACTAGGAACTCGTAATGGCCATAACGAGTCCTAAAAACAATCTTATACA
196 CAAAATGAATGGCATGACTAGGAACTCGTAATGGCCATAACGAGTCCTAAAAACAATCTTATACA
39803524 TATCAGTCTCTTTAACCTTGTGGTCATGGTACCTAGAATGAAGGTCGATTTTAGAAAATACGGAT
261 TATCAGTCTCTTTAACCTTGTGGTCATGGTACCTAGAATGAAGGTCGATTTTAGAAAATACGGAT
39803589 GCTCCACGAAATTGATCAAATAGGTCATCAATTCTCGGAAGTGGATACTTATTCTTTACCGTCAA
326 GCTCCACGAAATTGATCAAATAGGTCATCAATTCTCGGAAGTGGATACTTATTCTTTACCGTCAA
39803654 CTTATTCAGCTGATGATAATCTACACGCATTCTCATCGTGCCATCCTTCTTTACAAACAGAACTA
391 CTTATTCAGCTGATGATAATCTACACGCATTCTCATCGTGCCATCCTTCTTTACAAACAGAACTA
*
39803719 GTGCTTCCTATAGGGACACACTTGGCCTGATGAACCCTCGATCAAGAAGTTCTTAAAGTTAAGCC
456 GTGCTTCCCATAGGGACACACTTGGCCTGATGAACCCTCGATCAAGAAGTTCTTAAAGTTAAGCC
39803784 TTTAATTCTATAAGCTCTTTTGGTGCCATGCAATAAGGGGCAATGAACACAGGAGCTGTACTTGG
521 TTTAATTCTATAAGCTCTTTTGGTGCCATGCAATAAGGGGCAATGAACACAGGAGCTGTACTTGG
39803849 CAGGAGTTCAATACC
586 CAGGAGTTCAATACC
39803864 AAACTC
1 AAACTC
39803870 AACCTCCTTG
Statistics
Matches: 595, Mismatches: 11, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
600 595 1.00
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.30
Consensus pattern (600 bp):
AAACTCGCATTTATTCAACTTAGCGTAAAGTTGTTTTTTATGGAGTATCTGCAGAACTATTTTAA
GGTGTTCATCATGCTCATCCTTAGTTTTAGAATAAATCAAAATATCCTCGATAAAAACCGCGATA
AACTGATCCAAATACGACTAAAACACCAGATTCATCAGATCCATAAATGCACCCGGAGAGTTCGT
CAAAATGAATGGCATGACTAGGAACTCGTAATGGCCATAACGAGTCCTAAAAACAATCTTATACA
TATCAGTCTCTTTAACCTTGTGGTCATGGTACCTAGAATGAAGGTCGATTTTAGAAAATACGGAT
GCTCCACGAAATTGATCAAATAGGTCATCAATTCTCGGAAGTGGATACTTATTCTTTACCGTCAA
CTTATTCAGCTGATGATAATCTACACGCATTCTCATCGTGCCATCCTTCTTTACAAACAGAACTA
GTGCTTCCCATAGGGACACACTTGGCCTGATGAACCCTCGATCAAGAAGTTCTTAAAGTTAAGCC
TTTAATTCTATAAGCTCTTTTGGTGCCATGCAATAAGGGGCAATGAACACAGGAGCTGTACTTGG
CAGGAGTTCAATACC
Found at i:39820647 original size:29 final size:29
Alignment explanation
Indices: 39820605--39820932 Score: 347
Period size: 29 Copynumber: 11.3 Consensus size: 29
39820595 TGTGCTAAAC
* * *
39820605 GATGGTCATAACCATCCCTTTTCATATTT
1 GATGGTCGTCACCATCCCTTTTCATAGTT
*
39820634 GATGGTTGTCACCATCCCTTTTCATA-TT
1 GATGGTCGTCACCATCCCTTTTCATAGTT
** * *
39820662 CGATGGTCGGAACCATCCCTTTTCATTAATC
1 -GATGGTCGTCACCATCCCTTTTCA-TAGTT
*
39820693 GATAGTCGTCACCATCCCTTTTCATAGTT
1 GATGGTCGTCACCATCCCTTTTCATAGTT
* *
39820722 GATGGTCATCACCATCCCTTTTCATAGTC
1 GATGGTCGTCACCATCCCTTTTCATAGTT
* *** *
39820751 GATAGTCAAAACTATCCCTTTTCATA-TT
1 GATGGTCGTCACCATCCCTTTTCATAGTT
* * * *
39820779 CAATTGTCGTCACTATCCATTTTCATAGTT
1 -GATGGTCGTCACCATCCCTTTTCATAGTT
*
39820809 GATGGTTGTCACCATCCCTTTTCATAGTT
1 GATGGTCGTCACCATCCCTTTTCATAGTT
* ** * *
39820838 GATAGTCGAAACTATCCCTTTTCATATTT
1 GATGGTCGTCACCATCCCTTTTCATAGTT
*
39820867 GATGGTTGTCACCATCCCTTTTCATAGTT
1 GATGGTCGTCACCATCCCTTTTCATAGTT
39820896 GATGGTCGTTC-CCATCCCTTTTCATAGTT
1 GATGGTCG-TCACCATCCCTTTTCATAGTT
*
39820925 GATAGTCG
1 GATGGTCG
39820933 AATTTATCCC
Statistics
Matches: 248, Mismatches: 45, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
28 3 0.01
29 217 0.88
30 27 0.11
31 1 0.00
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.39
Consensus pattern (29 bp):
GATGGTCGTCACCATCCCTTTTCATAGTT
Found at i:39820826 original size:87 final size:87
Alignment explanation
Indices: 39820615--39820956 Score: 470
Period size: 87 Copynumber: 3.9 Consensus size: 87
39820605 GATGGTCATA
* * * * * *
39820615 ACCATCCCTTTTCATATTTGATGGTTGTCACCATCCCTTTTCATATTCGATGGTCGGAACCATCC
1 ACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGTCGATAGTCGAAACTATCC
*
39820680 CTTTTCATTAATCGATAGTCGTC
66 CTTTTCA-TATTCGATAGTCGTC
* *
39820703 ACCATCCCTTTTCATAGTTGATGGTCATCACCATCCCTTTTCATAGTCGATAGTCAAAACTATCC
1 ACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGTCGATAGTCGAAACTATCC
* *
39820768 CTTTTCATATTCAATTGTCGTC
66 CTTTTCATATTCGATAGTCGTC
* * * *
39820790 ACTATCCATTTTCATAGTTGATGGTTGTCACCATCCCTTTTCATAGTTGATAGTCGAAACTATCC
1 ACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGTCGATAGTCGAAACTATCC
* * *
39820855 CTTTTCATATTTGATGGTTGTC
66 CTTTTCATATTCGATAGTCGTC
* **
39820877 ACCATCCCTTTTCATAGTTGATGGTCGTTC-CCATCCCTTTTCATAGTTGATAGTCGAATTTATC
1 ACCATCCCTTTTCATAGTTGATGGTCG-TCACCATCCCTTTTCATAGTCGATAGTCGAAACTATC
39820941 CCTTTTCATATTCGAT
65 CCTTTTCATATTCGAT
39820957 GCTTATCAAT
Statistics
Matches: 226, Mismatches: 27, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
87 160 0.71
88 66 0.29
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.40
Consensus pattern (87 bp):
ACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGTCGATAGTCGAAACTATCC
CTTTTCATATTCGATAGTCGTC
Found at i:39829020 original size:38 final size:39
Alignment explanation
Indices: 39828978--39829055 Score: 122
Period size: 38 Copynumber: 2.0 Consensus size: 39
39828968 CTTATCACAT
*
39828978 ATTAAAGATGTTCAAATTATGACATAGTTAAA-ACTCAA
1 ATTAAAGATGTTCAAATTATGACATAATTAAATACTCAA
* *
39829016 ATTAATGATGTTCAAATTATGGCATAATTAAATACTCAA
1 ATTAAAGATGTTCAAATTATGACATAATTAAATACTCAA
39829055 A
1 A
39829056 CTTTAATAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
38 29 0.81
39 7 0.19
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.33
Consensus pattern (39 bp):
ATTAAAGATGTTCAAATTATGACATAATTAAATACTCAA
Found at i:39840324 original size:18 final size:18
Alignment explanation
Indices: 39840303--39840342 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
39840293 ATATTTAAAT
39840303 TTTTAATAATTTTTTAGA
1 TTTTAATAATTTTTTAGA
* *
39840321 TTTTCATGATTTTTTAGA
1 TTTTAATAATTTTTTAGA
39840339 TTTT
1 TTTT
39840343 TATACTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.25, C:0.03, G:0.07, T:0.65
Consensus pattern (18 bp):
TTTTAATAATTTTTTAGA
Found at i:39840382 original size:20 final size:21
Alignment explanation
Indices: 39840350--39840397 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
39840340 TTTTATACTT
39840350 TAAAAAGTCTATATA-TATTTAA
1 TAAAAA-T-TATATATTATTTAA
*
39840372 TAAAAATTATATATTTTTTAA
1 TAAAAATTATATATTATTTAA
39840393 TAAAA
1 TAAAA
39840398 TAAAGACATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 6 0.25
21 12 0.50
22 6 0.25
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
TAAAAATTATATATTATTTAA
Found at i:39843591 original size:27 final size:28
Alignment explanation
Indices: 39843559--39843614 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 28
39843549 AAGGCCCATT
39843559 TTTAAC-ATTATTTATAGAAATGGGCCA
1 TTTAACAATTATTTATAGAAATGGGCCA
*
39843586 TTTAACAAATTATTTATCGAAATGGGCCA
1 TTTAAC-AATTATTTATAGAAATGGGCCA
39843615 AAAAATCTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 6 0.23
29 20 0.77
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (28 bp):
TTTAACAATTATTTATAGAAATGGGCCA
Found at i:39851955 original size:17 final size:17
Alignment explanation
Indices: 39851904--39851948 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
39851894 GCAATAATTG
39851904 ACGTTTTGAAAATGAATA
1 ACGTTTTGAAAA-GAATA
*
39851922 ACGTTTTGCAAGAGAATA
1 ACGTTTTG-AAAAGAATA
39851940 AC-TTTTGAA
1 ACGTTTTGAA
39851949 TACGAATCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 2 0.08
17 5 0.20
18 15 0.60
19 3 0.12
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.33
Consensus pattern (17 bp):
ACGTTTTGAAAAGAATA
Found at i:39860078 original size:20 final size:20
Alignment explanation
Indices: 39860050--39860088 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
39860040 AATTTTTCTC
39860050 CTAAATTTT-AATTTGATTAT
1 CTAAATTTTCAATTT-ATTAT
*
39860070 CTAATTTTTCAATTTATTA
1 CTAAATTTTCAATTTATTA
39860089 AAATATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (20 bp):
CTAAATTTTCAATTTATTAT
Found at i:39874391 original size:5 final size:5
Alignment explanation
Indices: 39874381--39874406 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
39874371 TTACTTCGAC
39874381 TCTTT TCTTT TCTTT TCTTT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT T
39874407 TTAAGTATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TCTTT
Found at i:39882868 original size:16 final size:15
Alignment explanation
Indices: 39882845--39882886 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
39882835 ATAAAATGAG
39882845 TGACTAAAATGAAAT
1 TGACTAAAATGAAAT
* *
39882860 CTTACTAAAGT-AAAT
1 -TGACTAAAATGAAAT
39882875 TGACTAAAATGA
1 TGACTAAAATGA
39882887 GTCTACAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
14 8 0.38
15 5 0.24
16 8 0.38
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.29
Consensus pattern (15 bp):
TGACTAAAATGAAAT
Found at i:39891724 original size:24 final size:24
Alignment explanation
Indices: 39891709--39891760 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
39891699 AATCAAAGTC
39891709 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
* * *
39891733 AAATATATTATACTCATAAATACT
1 AAATATATTATGCTAATAAATGCT
39891757 AAAT
1 AAAT
39891761 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:39896082 original size:24 final size:24
Alignment explanation
Indices: 39896055--39896104 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
39896045 TCAAAGTCAC
* *
39896055 ATATATTATGCTAATAAATGCTAA
1 ATATATTATACTAATAAATACTAA
*
39896079 ATATATTATACTCATAAATACTAA
1 ATATATTATACTAATAAATACTAA
39896103 AT
1 AT
39896105 CTTCTAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.38
Consensus pattern (24 bp):
ATATATTATACTAATAAATACTAA
Found at i:39898866 original size:45 final size:45
Alignment explanation
Indices: 39898839--39899094 Score: 467
Period size: 45 Copynumber: 5.7 Consensus size: 45
39898829 TTGTTCTATA
* * *
39898839 AATTATGCATGATGTTGGCCAAATGCTTCCTTAAATTCTTCCATG
1 AATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTCCCATG
*
39898884 AATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTTCCATG
1 AATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTCCCATG
*
39898929 AATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTCCTATG
1 AATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTCCCATG
39898974 AATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTCCCATG
1 AATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTCCCATG
39899019 AATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTCCCATG
1 AATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTCCCATG
39899064 AATTATGCATGATGTTGGTCAAATGCTTCCT
1 AATTATGCATGATGTTGGTCAAATGCTTCCT
39899095 TAATTTCATG
Statistics
Matches: 206, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 206 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (45 bp):
AATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTCCCATG
Found at i:39905305 original size:45 final size:45
Alignment explanation
Indices: 39905254--39905486 Score: 396
Period size: 45 Copynumber: 5.2 Consensus size: 45
39905244 TCGACCATGG
* * * *
39905254 TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
39905299 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
39905344 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
39905389 TGCTTCCTCAAATTC-TCCTATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCC-ATGAATTATGCATGATGTTGGTCAAA
*
39905434 TGCTTCCTCAAATTCTCCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
39905479 TGCTTCCT
1 TGCTTCCT
39905487 TAATTTCATG
Statistics
Matches: 179, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
44 3 0.02
45 174 0.97
46 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:39907826 original size:196 final size:196
Alignment explanation
Indices: 39907492--39907887 Score: 765
Period size: 196 Copynumber: 2.0 Consensus size: 196
39907482 TAAAGGCTTG
*
39907492 TCTAATGATCTTGTCATTACTGTGTTACCTTTATAGGATATCCTCAATCTCTTTGGGTTATATTT
1 TCTAATGATCTTGTCATTACTGTGTTACCCTTATAGGATATCCTCAATCTCTTTGGGTTATATTT
*
39907557 GTTCACCCAATATGATTATATTTTATCTTATAGTAACCATTACATCTTTCTTCATGAAAAGTCAA
66 GTTCACCCAATATGATCATATTTTATCTTATAGTAACCATTACATCTTTCTTCATGAAAAGTCAA
39907622 TTACTAGCAAATAGTAATTAAATCATTTTTCCTAGAGAAATGACCCGTAGTCATGTTACTTTTCC
131 TTACTAGCAAATAGTAATTAAATCATTTTTCCTAGAGAAATGACCCGTAGTCATGTTACTTTTCC
39907687 A
196 A
39907688 TCTAATGATCTTGTCATTACTGTGTTACCCTTATAGGATATCCTCAATCTCTTTGGGTTATATTT
1 TCTAATGATCTTGTCATTACTGTGTTACCCTTATAGGATATCCTCAATCTCTTTGGGTTATATTT
39907753 GTTCACCCAATATGATCATATTTTATCTTATAGTAACCATTACATCTTTCTTCATGAAAAGTCAA
66 GTTCACCCAATATGATCATATTTTATCTTATAGTAACCATTACATCTTTCTTCATGAAAAGTCAA
*
39907818 TTACTAGCAAATAGTAATTAAATCATTTTTCCTAGAGAAATGACTCGTAGTCATGTTACTTTTCC
131 TTACTAGCAAATAGTAATTAAATCATTTTTCCTAGAGAAATGACCCGTAGTCATGTTACTTTTCC
39907883 A
196 A
39907884 TCTA
1 TCTA
39907888 TCATGTAATT
Statistics
Matches: 197, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
196 197 1.00
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.41
Consensus pattern (196 bp):
TCTAATGATCTTGTCATTACTGTGTTACCCTTATAGGATATCCTCAATCTCTTTGGGTTATATTT
GTTCACCCAATATGATCATATTTTATCTTATAGTAACCATTACATCTTTCTTCATGAAAAGTCAA
TTACTAGCAAATAGTAATTAAATCATTTTTCCTAGAGAAATGACCCGTAGTCATGTTACTTTTCC
A
Found at i:39909579 original size:43 final size:43
Alignment explanation
Indices: 39909521--39909641 Score: 147
Period size: 43 Copynumber: 2.8 Consensus size: 43
39909511 AACGCTGCTA
* *
39909521 AAAG-TCATGATCTTTAACGGCGCTT-TTCTCACAAATGCCGCT
1 AAAGATCATGACCTTTAACGGCGCTTCTAC-CACAAATGCCGCT
* * *
39909563 AAAGATCATGACCTTTAGCGGTGCTTCTACCACAAATGCTGCT
1 AAAGATCATGACCTTTAACGGCGCTTCTACCACAAATGCCGCT
* * *
39909606 AAAGAACATGACCTTTAACGACGCTTATACCACAAA
1 AAAGATCATGACCTTTAACGGCGCTTCTACCACAAA
39909642 CGCCACTATA
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
42 4 0.06
43 61 0.91
44 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (43 bp):
AAAGATCATGACCTTTAACGGCGCTTCTACCACAAATGCCGCT
Found at i:39911036 original size:27 final size:26
Alignment explanation
Indices: 39911000--39911050 Score: 93
Period size: 27 Copynumber: 1.9 Consensus size: 26
39910990 AAATATAAAG
39911000 GGGGTTGCTAAGTGCTGATTTCCCCAA
1 GGGGTTGCTAAGTGCTGA-TTCCCCAA
39911027 GGGGTTGCTAAGTGCTGATTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
39911051 GATTCATTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.16, C:0.24, G:0.31, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCAA
Found at i:39911104 original size:103 final size:103
Alignment explanation
Indices: 39910922--39911122 Score: 357
Period size: 103 Copynumber: 2.0 Consensus size: 103
39910912 ATTGAATATG
* *
39910922 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCGACTGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
39910987 TTTAAATATAAAGGGGGTTGCTAAGTGCTGATTTCCCC
66 TTTAAATATAAAGGGGGTTGCTAAGTGCTGATTTCCCC
*
39911025 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
* *
39911090 TTTAAATGTGAAGGGGGTTGCTAAGTGCTGATT
66 TTTAAATATAAAGGGGGTTGCTAAGTGCTGATT
39911123 CCCTGATTCA
Statistics
Matches: 93, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 93 1.00
ACGTcount: A:0.21, C:0.17, G:0.28, T:0.33
Consensus pattern (103 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTTAAATATAAAGGGGGTTGCTAAGTGCTGATTTCCCC
Found at i:39911118 original size:76 final size:76
Alignment explanation
Indices: 39911025--39911237 Score: 354
Period size: 76 Copynumber: 2.8 Consensus size: 76
39911015 TGATTTCCCC
39911025 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
39911090 TTTAAATGTGA
66 TTTAAATGTGA
* * *
39911101 AGGGGGTTGCTAAGTGCTGATTCCCTGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCATATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
*
39911166 TTTGAATGTGA
66 TTTAAATGTGA
* * * *
39911177 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTAGTGGTTGCTAAGTGCTGAATCCACCG
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCG
39911238 ATAACGGTTA
Statistics
Matches: 126, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 126 1.00
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.32
Consensus pattern (76 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTTAAATGTGA
Found at i:39911123 original size:43 final size:42
Alignment explanation
Indices: 39911062--39911200 Score: 152
Period size: 43 Copynumber: 3.5 Consensus size: 42
39911052 ATTCATTGGT
39911062 GGTTGCTAAGTGCTGATTCCACCGTATCTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTT-AATGTGAAGGG
* * *
39911105 GGTTGCTAAGTGCTGATTCC-CTG-A---TTCAT-T---GGT
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTTAATGTGAAGGG
* *
39911138 GGTTGCTAAGTGCTGATTCCACCATATCTTTGAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTT-AATGTGAAGGG
39911181 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
39911201 CCGAATCACT
Statistics
Matches: 78, Mismatches: 8, Indels: 20
0.74 0.08 0.19
Matches are distributed among these distances:
33 22 0.28
34 1 0.01
35 1 0.01
36 1 0.01
37 2 0.03
38 4 0.05
39 2 0.03
40 1 0.01
41 1 0.01
42 2 0.03
43 41 0.53
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.35
Consensus pattern (42 bp):
GGTTGCTAAGTGCTGATTCCACCGTATCTTTAATGTGAAGGG
Found at i:39915129 original size:22 final size:23
Alignment explanation
Indices: 39915074--39915131 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
39915064 TATGTTTGTG
*
39915074 AAGTTGGGGGTTTCAAGGGGGGA
1 AAGTTGGGGATTTCAAGGGGGGA
* * *
39915097 AA-TTAGAGATTT-TAGGGGGGA
1 AAGTTGGGGATTTCAAGGGGGGA
39915118 AAGTTGGGGATTTC
1 AAGTTGGGGATTTC
39915132 GGGGGAGGTG
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
21 10 0.37
22 15 0.56
23 2 0.07
ACGTcount: A:0.26, C:0.03, G:0.43, T:0.28
Consensus pattern (23 bp):
AAGTTGGGGATTTCAAGGGGGGA
Found at i:39915136 original size:22 final size:22
Alignment explanation
Indices: 39915074--39915136 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 22
39915064 TATGTTTGTG
*
39915074 AAGTTGGGGGTTTCAAGGGGGGA
1 AAGTTGGGGATTTC-AGGGGGGA
* * *
39915097 AA-TTAGAGATTTTAGGGGGGA
1 AAGTTGGGGATTTCAGGGGGGA
39915118 AAGTTGGGGATTTC-GGGGG
1 AAGTTGGGGATTTCAGGGGG
39915137 AGGTGATTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
21 15 0.47
22 15 0.47
23 2 0.06
ACGTcount: A:0.24, C:0.03, G:0.48, T:0.25
Consensus pattern (22 bp):
AAGTTGGGGATTTCAGGGGGGA
Found at i:39915336 original size:123 final size:124
Alignment explanation
Indices: 39915182--39915418 Score: 359
Period size: 123 Copynumber: 1.9 Consensus size: 124
39915172 TAAAATTATT
* * * ** * *
39915182 TTTTGTGGCATTTTTCATTAAAATGTGACAAAAAATTATTTAATTTGGAATAAAACTACATTGTT
1 TTTTGCGGCATTTTTCATAAAAACGCCACAAAAAATTATTTAATTTGGAATAAAACGACACTGTT
**
39915247 TTGCTATATAAAATGGTGCTA-TTTTTTAAAAGTAAAATTATTTTTTGTATTGCTTACC
66 TTGCTATATAAAATGGCACTATTTTTTTAAAAGTAAAATTATTTTTTGTATTGCTTACC
* *
39915305 TTTTGCGGCGTTTTTCATAAAAACGCCACAAAAAATTATTTCATTTGGAATAAAACGACACTGTT
1 TTTTGCGGCATTTTTCATAAAAACGCCACAAAAAATTATTTAATTTGGAATAAAACGACACTGTT
*
39915370 TTGCTATATAAAATGGCACTATTTTTTTTAAAGTAAAATTATTTTTTGT
66 TTGCTATATAAAATGGCACTATTTTTTTAAAAGTAAAATTATTTTTTGT
39915419 GGCGTTTTTT
Statistics
Matches: 101, Mismatches: 12, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
123 75 0.74
124 26 0.26
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.43
Consensus pattern (124 bp):
TTTTGCGGCATTTTTCATAAAAACGCCACAAAAAATTATTTAATTTGGAATAAAACGACACTGTT
TTGCTATATAAAATGGCACTATTTTTTTAAAAGTAAAATTATTTTTTGTATTGCTTACC
Found at i:39916577 original size:97 final size:97
Alignment explanation
Indices: 39916367--39916577 Score: 266
Period size: 96 Copynumber: 2.2 Consensus size: 97
39916357 ACTAACTCCT
* * *
39916367 AACCCCAAACCCTTAACCCCTAAACCTTATTTAATATATAAATTAAAAAAACACTAATTAATCTA
1 AACCCTAAACCC-TAACCCCTAAACATTATTTAATATATAAATTAAAAAAACACTAACTAATCTA
* * *
39916432 AACCCCAAACCCTAACCTGACCTCGAATCCCTA
65 AACCCCAAACCCCAACCTGACCTCAAATCCATA
* *
39916465 ACCCCT-AACCTCTAACCCCTAAACATTATTTAATATATAAATT-AAAATACACTAACTAATCTA
1 AACCCTAAACC-CTAACCCCTAAACATTATTTAATATATAAATTAAAAAAACACTAACTAATCTA
** *
39916528 AACCTTAAACCCCAACTTGACAC-CAAATCCATA
65 AACCCCAAACCCCAACCTGAC-CTCAAATCCATA
39916561 AACCCTAAATCCCTAAC
1 AACCCTAAA-CCCTAAC
39916578 TCTTAACCTC
Statistics
Matches: 97, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
96 48 0.49
97 42 0.43
98 7 0.07
ACGTcount: A:0.43, C:0.31, G:0.01, T:0.24
Consensus pattern (97 bp):
AACCCTAAACCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAAACACTAACTAATCTAA
ACCCCAAACCCCAACCTGACCTCAAATCCATA
Found at i:39916659 original size:14 final size:15
Alignment explanation
Indices: 39916637--39916669 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
39916627 CTTAAATTAG
*
39916637 AATCTCTAA-TCCAT
1 AATCCCTAATTCCAT
39916651 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
39916666 AATC
1 AATC
39916670 TATAAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.33
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:39925532 original size:41 final size:41
Alignment explanation
Indices: 39925472--39925670 Score: 229
Period size: 41 Copynumber: 4.9 Consensus size: 41
39925462 AAATGTTTTT
* *
39925472 GCGGCGCTTCTTGAAAAACGCCGCTAAAGCCTCGAACATTA
1 GCGGCGCTTCTTGAAAAACGCCGCTAAAGCCCCGAGCATTA
* * * *
39925513 GCGGCGCTTATTGATAAACGCCGTTAAAGCCCCTAGCATTA
1 GCGGCGCTTCTTGAAAAACGCCGCTAAAGCCCCGAGCATTA
*
39925554 GCGGCGCTTCTTGAAAAATGCCGCTAAAGCCCCGAGCATTA
1 GCGGCGCTTCTTGAAAAACGCCGCTAAAGCCCCGAGCATTA
* * *** * *
39925595 GCTGCGCTT-TATCAAAAACGCCGCTAAAAATCTGAGCACTA
1 GCGGCGCTTCT-TGAAAAACGCCGCTAAAGCCCCGAGCATTA
* * *
39925636 GCGGCGCTTTTTTAAAAACACCGCTAAAGCCCCGA
1 GCGGCGCTTCTTGAAAAACGCCGCTAAAGCCCCGA
39925671 ATGGTAGACA
Statistics
Matches: 130, Mismatches: 26, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
40 1 0.01
41 128 0.98
42 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (41 bp):
GCGGCGCTTCTTGAAAAACGCCGCTAAAGCCCCGAGCATTA
Found at i:39934934 original size:804 final size:802
Alignment explanation
Indices: 39933381--39934991 Score: 2576
Period size: 804 Copynumber: 2.0 Consensus size: 802
39933371 AGCCAACCAG
* * * *
39933381 TCCATAGTCCAAAAGATACATCAACAACCCCAAATAAGTAATAAATTTTAGGCATTAATGGAAAA
1 TCCATAGTCCAAAAGATACATCAAAAACCCCAAATAAGTAATAAATTCTAGGCATTAACGAAAAA
39933446 TAGTCTAAAATTTACGTGTGGCCACCATCGAGTCCTCCAATGCACCGACCCGTCAAGTATGGGGA
66 TAGTCTAAAATTTACGTGTGGCCACCATCGAGTCCTCCAATGCACCGACCCGTCAAGTATGGGGA
* * *
39933511 TTACCTGTACAGATAAAACAGAGGAAGGGTGAGTTTTCGCAAACTCAGTGTGTAATCCTCACAGA
131 TTACCTGTACAGATAAAACAGAGAAAGGGTGAGTTTTCGCAAACTCAATGTGTAATCCCCACAGA
* * * ** ** *
39933576 AAACATGCATACAGATAATCAACAGAATTCAGTTAAATACAGTCTGGGGCCCGTGCCCATCATAG
196 AAACATGCATACAGATAATCAAAAAAATTCAGTTAAATACAGACTGAAGCCCAAGCCCATCACAG
* *
39933641 AATTGTTTGGGCCTTAGCCATTCAGATAAAGTCTCATAAATACATTAGGGCCTTGGCCCATATCA
261 AATTGTTTGGGACTTAGCCATTCAGATAAAGTCTCAAAAATACATTAGGGCCTTGGCCCATATCA
* **
39933706 GATACAGAATGCAGATACAGTAAATCAGAATCCTACCCACCAGCCTCTACACACCATCTTGGTCC
326 GATACAGAATGCAGATACAATAAATCAGAATCCTACCCACCAGCCTCTACACACCATCTCCGTCC
*
39933771 AACCCTACACACCATGTGGGGATTAAATCAACTCACCCATCCCTACACACCACGTTGTACCAAAA
391 AACCCTACACACCATGTGGGGATTAAATCAACTCACCCATCCCTACACACCACGCTGTACCAAAA
* * * * *
39933836 TGTGGCACATAATTAGAAGGTTGCAGCTGGGCTGCCAGATAATAGGCTTAATAGCCTTTCAGGCA
456 TGTGGCACATAATCAGAAGGTTGCAGCTGAGATGCCAGATAACAGGCTTAATAGCCTTTCAGACA
*
39933901 CTTCCTCCAAATATCATCAACCCACCCCGATGCAATGCAACATACAAAATATGTCATGCCATTAT
521 CTTCCTCCAAATATCATCAACCCACCCCGAAGCAATGCAACATACAAAATATGTCATGCCATTAT
* *
39933966 GAAATTAATAGTACATACATTCAGATATCATAAGTCATGCTCGGTATAGAAATCCGACAGACAGA
586 GAAATTAATAGTACATACATTCAGATATCATAAGTCATGCTCAGTATAGAAATCAGACAGACAGA
* *
39934031 TCACACATATAGGAGTCTAAGTAAAACTTATCGGCCCTACAGTAGGTCCACAGTCGACTTGGGCG
651 TCACACATATAGGAGTCTAAGTAAAACTTACCGACCCTACAGTAGGTCCACAGTCGACTTGGGCG
* *
39934096 ACCTGTGCAACCTTACAGAACTTTTCAAAAAAATGGGCTCACACGCCCATATTGCCCACTCGGCC
716 ACCTGTGCAACCTTACAGAACTTTTCAAAAAAATGGGCCCACACGCCCATATGGCCCACTCGGCC
* *
39934161 CAAATTGACCTTGGCCACGTGA
781 CAAATTGACCGTGGCCACATGA
* *
39934183 TCCATAGTCTAGAAGATACATCAAAAACCCCAAATAAGTAATAAATTCTAGGCATTAACGAAAAA
1 TCCATAGTCCAAAAGATACATCAAAAACCCCAAATAAGTAATAAATTCTAGGCATTAACGAAAAA
* * * * *
39934248 TAGTCTAAAATTTACGTGTGGCCACCATCGAGTCCTTCACTGCATCGACCCGTCAAGTCTGGGGT
66 TAGTCTAAAATTTACGTGTGGCCACCATCGAGTCCTCCAATGCACCGACCCGTCAAGTATGGGGA
* *
39934313 TTACCTGTACAGATTAAGCAGAGAAAGGGTGAGTTTTCGCAAACTCAATGTGTAATCCCCACAGA
131 TTACCTGTACAGATAAAACAGAGAAAGGGTGAGTTTTCGCAAACTCAATGTGTAATCCCCACAGA
* *
39934378 AAACATGCATACAGATAATCAAAAAAATTTAGTTAGATACAGACTGAAGCCCAAGCCCATCACA-
196 AAACATGCATACAGATAATCAAAAAAATTCAGTTAAATACAGACTGAAGCCCAAGCCCATCACAG
* * *
39934442 AATTTAGTTTGGGATTTAGCCTATTCAGATACAGTCTTAAAAATACATTAGGGCCTTGGCCCATA
261 AA-TT-GTTTGGGACTTAGCC-ATTCAGATAAAGTCTCAAAAATACATTAGGGCCTTGGCCCATA
* *
39934507 TTAGATACAGAATGCAGATACAATAAATCAGAATCCTACCTACCAGCCTCTACACACCATCTCCG
323 TCAGATACAGAATGCAGATACAATAAATCAGAATCCTACCCACCAGCCTCTACACACCATCTCCG
* * * *
39934572 TCTAATCCTACACACCATGTGGGTATTAAATCAACTCACCCATCCCTACACACCATGCTGTACCA
388 TCCAACCCTACACACCATGTGGGGATTAAATCAACTCACCCATCCCTACACACCACGCTGTACCA
*
39934637 AAATGTGGCACATAATCAGAAGGTTGCAGTTGAGATGCCAGATAACAGGCTTAATAGCCTTTCAG
453 AAATGTGGCACATAATCAGAAGGTTGCAGCTGAGATGCCAGATAACAGGCTTAATAGCCTTTCAG
39934702 ACACTTCCTCCAAATATCATCAACCCACCCCGAAGCAATGCAACATACAAAATATGTCATGCCAT
518 ACACTTCCTCCAAATATCATCAACCCACCCCGAAGCAATGCAACATACAAAATATGTCATGCCAT
* * * *
39934767 TATGCAATTAATATTACATACATTCAGATATCATAAGTCATGCTTAGTATAGAAATCAGATAGAC
583 TATGAAATTAATAGTACATACATTCAGATATCATAAGTCATGCTCAGTATAGAAATCAGACAGAC
* * *
39934832 AGATCACACATATAGGGGTCTAAGTAAAGCTTACCGACCCTACAGTAGGTTCACAGTCGACTTGG
648 AGATCACACATATAGGAGTCTAAGTAAAACTTACCGACCCTACAGTAGGTCCACAGTCGACTTGG
* * *
39934897 GTGACCTGTGCAACCTTACAGAACTTTTCAGAAAAATGGGCCCACACGCCCATGTGGCCCACTCG
713 GCGACCTGTGCAACCTTACAGAACTTTTCAAAAAAATGGGCCCACACGCCCATATGGCCCACTCG
* *
39934962 TCCCAAATTGGCCGTGGCCACATGA
778 GCCCAAATTGACCGTGGCCACATGA
39934987 TCCAT
1 TCCAT
39934992 TTTTAATGTA
Statistics
Matches: 738, Mismatches: 68, Indels: 4
0.91 0.08 0.00
Matches are distributed among these distances:
801 2 0.00
802 235 0.32
803 13 0.02
804 488 0.66
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (802 bp):
TCCATAGTCCAAAAGATACATCAAAAACCCCAAATAAGTAATAAATTCTAGGCATTAACGAAAAA
TAGTCTAAAATTTACGTGTGGCCACCATCGAGTCCTCCAATGCACCGACCCGTCAAGTATGGGGA
TTACCTGTACAGATAAAACAGAGAAAGGGTGAGTTTTCGCAAACTCAATGTGTAATCCCCACAGA
AAACATGCATACAGATAATCAAAAAAATTCAGTTAAATACAGACTGAAGCCCAAGCCCATCACAG
AATTGTTTGGGACTTAGCCATTCAGATAAAGTCTCAAAAATACATTAGGGCCTTGGCCCATATCA
GATACAGAATGCAGATACAATAAATCAGAATCCTACCCACCAGCCTCTACACACCATCTCCGTCC
AACCCTACACACCATGTGGGGATTAAATCAACTCACCCATCCCTACACACCACGCTGTACCAAAA
TGTGGCACATAATCAGAAGGTTGCAGCTGAGATGCCAGATAACAGGCTTAATAGCCTTTCAGACA
CTTCCTCCAAATATCATCAACCCACCCCGAAGCAATGCAACATACAAAATATGTCATGCCATTAT
GAAATTAATAGTACATACATTCAGATATCATAAGTCATGCTCAGTATAGAAATCAGACAGACAGA
TCACACATATAGGAGTCTAAGTAAAACTTACCGACCCTACAGTAGGTCCACAGTCGACTTGGGCG
ACCTGTGCAACCTTACAGAACTTTTCAAAAAAATGGGCCCACACGCCCATATGGCCCACTCGGCC
CAAATTGACCGTGGCCACATGA
Found at i:39939083 original size:27 final size:27
Alignment explanation
Indices: 39939045--39939099 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
39939035 ATTTAAAATG
39939045 TCAGTGTCACACGGGTAATACACTCAA
1 TCAGTGTCACACGGGTAATACACTCAA
*
39939072 TCAGTGTCACACGGGTATTACACTCAA
1 TCAGTGTCACACGGGTAATACACTCAA
39939099 T
1 T
39939100 GTGTACAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (27 bp):
TCAGTGTCACACGGGTAATACACTCAA
Found at i:39939466 original size:26 final size:26
Alignment explanation
Indices: 39939431--39939487 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
39939421 TAAAAGCCAA
* * *
39939431 AATCAGGAAGTTCACAAAGAACTTTT
1 AATCAAGAAGCTCACAAAGAACCTTT
* *
39939457 AATCAAGAAGCTCACGAAGAGCCTTT
1 AATCAAGAAGCTCACAAAGAACCTTT
39939483 AATCA
1 AATCA
39939488 GGAGCTCCGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (26 bp):
AATCAAGAAGCTCACAAAGAACCTTT
Found at i:39945676 original size:24 final size:25
Alignment explanation
Indices: 39945623--39945673 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
39945613 ATTGTAAATC
*
39945623 AATAAATATATGTACAAAAATTTAA
1 AATAAATATATATACAAAAATTTAA
39945648 AATAAATA-ATATACAAGAAATTTAA
1 AATAAATATATATACAA-AAATTTAA
39945673 A
1 A
39945674 TAAGCAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (25 bp):
AATAAATATATATACAAAAATTTAA
Found at i:39949920 original size:10 final size:10
Alignment explanation
Indices: 39949907--39949990 Score: 55
Period size: 10 Copynumber: 8.2 Consensus size: 10
39949897 TTTTACATAC
39949907 TTTTTTAATT
1 TTTTTTAATT
*
39949917 TTTTTTAA-A
1 TTTTTTAATT
*
39949926 TTTTTAAATAT
1 TTTTTTAAT-T
**
39949937 TTTTAAAATACT
1 TTTTTTAAT--T
39949949 TTTTTTAATT
1 TTTTTTAATT
***
39949959 TTAAAATAA-T
1 TT-TTTTAATT
39949969 TTTTTTAATT
1 TTTTTTAATT
39949979 TTTTTTAATT
1 TTTTTTAATT
39949989 TT
1 TT
39949991 AAAATATTTT
Statistics
Matches: 56, Mismatches: 13, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
9 10 0.18
10 27 0.48
11 11 0.20
12 8 0.14
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTTTAATT
Found at i:39949924 original size:40 final size:42
Alignment explanation
Indices: 39949876--39949960 Score: 138
Period size: 40 Copynumber: 2.1 Consensus size: 42
39949866 AATATATTTA
*
39949876 TTTTTTTAAATTTTAAAATATTTTT-ACATAC-TTTTTTAAT
1 TTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTAAT
*
39949916 TTTTTTTAAATTTTTAAATATTTTTAAAATACTTTTTTTAAT
1 TTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTAAT
39949958 TTT
1 TTT
39949961 AAAATAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
40 24 0.59
41 5 0.12
42 12 0.29
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.65
Consensus pattern (42 bp):
TTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTAAT
Found at i:39949929 original size:30 final size:28
Alignment explanation
Indices: 39949895--39950001 Score: 115
Period size: 30 Copynumber: 3.6 Consensus size: 28
39949885 ATTTTAAAAT
*
39949895 ATTTTTACATACTTTTTTAATTTTTTTTAA
1 ATTTTTAAATA-TTTTTTAATTTTTTTT-A
*
39949925 ATTTTTAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTAAATATTTTT-TAAT--TTTTTTTA
*
39949956 ATTTTAAAATAATTTTTTTAATTTTTTTTA
1 ATTTTTAAAT-A-TTTTTTAATTTTTTTTA
*
39949986 ATTTTAAAATATTTTT
1 ATTTTTAAATATTTTT
39950002 AAAATATTTT
Statistics
Matches: 68, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
28 5 0.07
29 6 0.09
30 31 0.46
31 10 0.15
32 11 0.16
33 5 0.07
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (28 bp):
ATTTTTAAATATTTTTTAATTTTTTTTA
Found at i:39949940 original size:11 final size:11
Alignment explanation
Indices: 39949874--39950027 Score: 66
Period size: 11 Copynumber: 14.9 Consensus size: 11
39949864 TAAATATATT
*
39949874 TATTTTTTTAA
1 TATTTTTTAAA
*
39949885 -A-TTTTAAAA
1 TATTTTTTAAA
*
39949894 TA-TTTTTACA
1 TATTTTTTAAA
39949904 TACTTTTTT-AA
1 TA-TTTTTTAAA
*
39949915 T-TTTTTTTAA
1 TATTTTTTAAA
39949925 -A-TTTTTAAA
1 TATTTTTTAAA
*
39949934 TATTTTTAAAA
1 TATTTTTTAAA
39949945 TACTTTTTT---
1 TA-TTTTTTAAA
* *
39949954 TAATTTTAAAA
1 TATTTTTTAAA
*
39949965 TAATTTTTTTAA
1 T-ATTTTTTAAA
39949977 T-TTTTTT---
1 TATTTTTTAAA
* *
39949984 TAATTTTAAAA
1 TATTTTTTAAA
*
39949995 TATTTTTAAAA
1 TATTTTTTAAA
*
39950006 TATTTTTAAAA
1 TATTTTTTAAA
39950017 TACTTTTTTAA
1 TA-TTTTTTAA
39950028 TTTTTAAAAA
Statistics
Matches: 109, Mismatches: 17, Indels: 33
0.69 0.11 0.21
Matches are distributed among these distances:
7 1 0.01
8 8 0.07
9 21 0.19
10 19 0.17
11 35 0.32
12 25 0.23
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (11 bp):
TATTTTTTAAA
Found at i:39949952 original size:72 final size:70
Alignment explanation
Indices: 39949876--39950042 Score: 198
Period size: 72 Copynumber: 2.3 Consensus size: 70
39949866 AATATATTTA
**
39949876 TTTTTTTAAATTTTAAAATATTTTTACATACTTTTTTAATTTTTTTTAA-ATTTTT-AAATATTT
1 TTTTTTTAAATTTTAAAATATTTTTA-AT-CTTTTTTAA--TTTTAAAATATTTTTAAAATATTT
39949939 TTAAAATAC
62 TTAAAATAC
*
39949948 TTTTTTT-AATTTTAAAATAATTTTTTTAATTTTTTTTAATTTTAAAATATTTTTAAAATATTTT
1 TTTTTTTAAATTTTAAAAT-A--TTTTTAATCTTTTTTAATTTTAAAATATTTTTAAAATATTTT
39950012 TAAAATAC
63 TAAAATAC
* *
39950020 -TTTTTTAATTTTTAAAAAATTTT
1 TTTTTTTAAATTTTAAAATATTTT
39950043 AAAATAAAAA
Statistics
Matches: 84, Mismatches: 5, Indels: 15
0.81 0.05 0.14
Matches are distributed among these distances:
69 4 0.05
70 6 0.07
71 24 0.29
72 42 0.50
73 2 0.02
74 6 0.07
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (70 bp):
TTTTTTTAAATTTTAAAATATTTTTAATCTTTTTTAATTTTAAAATATTTTTAAAATATTTTTAA
AATAC
Found at i:39950001 original size:20 final size:20
Alignment explanation
Indices: 39949937--39949980 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
39949927 TTTTAAATAT
*
39949937 TTTTAAAATACTTTTTTTAA
1 TTTTAAAATAATTTTTTTAA
39949957 TTTTAAAATAATTTTTTTAA
1 TTTTAAAATAATTTTTTTAA
39949977 TTTT
1 TTTT
39949981 TTTTAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTAAAATAATTTTTTTAA
Found at i:39950002 original size:41 final size:42
Alignment explanation
Indices: 39949955--39950049 Score: 124
Period size: 41 Copynumber: 2.3 Consensus size: 42
39949945 TACTTTTTTT
** *
39949955 AATTTTAAAATAATTTTTTTAAT-TTTTTTTAA-TTTTAAAA
1 AATTTTAAAATAATTTTTAAAATACTTTTTTAATTTTTAAAA
*
39949995 TATTTTTAAAAT-ATTTTTAAAATACTTTTTTAATTTTTAAAA
1 -AATTTTAAAATAATTTTTAAAATACTTTTTTAATTTTTAAAA
39950037 AATTTTAAAATAA
1 AATTTTAAAATAA
39950050 AAATGGGCCG
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
40 9 0.20
41 28 0.61
42 9 0.20
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (42 bp):
AATTTTAAAATAATTTTTAAAATACTTTTTTAATTTTTAAAA
Found at i:39950012 original size:30 final size:30
Alignment explanation
Indices: 39949916--39950012 Score: 133
Period size: 30 Copynumber: 3.2 Consensus size: 30
39949906 CTTTTTTAAT
*
39949916 TTTTTTTAAATTTTTAAATATTTTTAAAATA
1 TTTTTTT-AATTTTAAAATATTTTTAAAATA
**
39949947 CTTTTTTTAATTTTAAAATAATTTTTTTAAT-
1 -TTTTTTTAATTTTAAAAT-ATTTTTAAAATA
39949978 TTTTTTTAATTTTAAAATATTTTTAAAATA
1 TTTTTTTAATTTTAAAATATTTTTAAAATA
39950008 TTTTT
1 TTTTT
39950013 AAAATACTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
29 9 0.16
30 23 0.40
31 10 0.17
32 16 0.28
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (30 bp):
TTTTTTTAATTTTAAAATATTTTTAAAATA
Found at i:39950319 original size:20 final size:19
Alignment explanation
Indices: 39950296--39950356 Score: 56
Period size: 20 Copynumber: 3.3 Consensus size: 19
39950286 TTTCTAGAAG
39950296 TTTAACTATTTTTTTATAAT
1 TTTAACTA-TTTTTTATAAT
*
39950316 TTTAA--ATTTTTTAGAA-
1 TTTAACTATTTTTTATAAT
* *
39950332 TTTAACTAATCTTTTATATT
1 TTTAACT-ATTTTTTATAAT
39950352 TTTAA
1 TTTAA
39950357 TTTTTCTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
16 5 0.15
17 9 0.27
18 1 0.03
19 8 0.24
20 10 0.30
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTAACTATTTTTTATAAT
Found at i:39950327 original size:17 final size:17
Alignment explanation
Indices: 39950305--39950371 Score: 55
Period size: 17 Copynumber: 3.8 Consensus size: 17
39950295 GTTTAACTAT
39950305 TTTTTTATAATTTTAAA
1 TTTTTTATAATTTTAAA
* *
39950322 TTTTTTAGAATTTAACTAA
1 TTTTTTATAATTTTA--AA
* *
39950341 TCTTTTAT-ATTTTTAA
1 TTTTTTATAATTTTAAA
*
39950357 TTTTTCTATACTTTT
1 TTTTT-TATAATTTT
39950372 TTGGATATTT
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
16 6 0.16
17 16 0.42
18 8 0.21
19 8 0.21
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.64
Consensus pattern (17 bp):
TTTTTTATAATTTTAAA
Found at i:39950336 original size:36 final size:37
Alignment explanation
Indices: 39950284--39950364 Score: 112
Period size: 36 Copynumber: 2.2 Consensus size: 37
39950274 CCCTAAATGC
* *
39950284 TTTTTCTAGAAGTTTAACTATTTTTTTATAATTTTAAA
1 TTTTTCTAGAAGTTTAACTAATCTTTTAT-ATTTTAAA
*
39950322 TTTTT-TAGAA-TTTAACTAATCTTTTATATTTTTAA
1 TTTTTCTAGAAGTTTAACTAATCTTTTATATTTTAAA
39950357 TTTTTCTA
1 TTTTTCTA
39950365 TACTTTTTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
35 12 0.31
36 17 0.44
37 5 0.13
38 5 0.13
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.60
Consensus pattern (37 bp):
TTTTTCTAGAAGTTTAACTAATCTTTTATATTTTAAA
Found at i:39950501 original size:27 final size:27
Alignment explanation
Indices: 39950455--39950509 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
39950445 TAAATATTTT
*
39950455 TATTTTTATAAATTTTGAATTTTTATA
1 TATTTTTATAAATTTTGAATTTATATA
*
39950482 TATTTTTA-GAATTTTAGAATTTATATA
1 TATTTTTATAAATTTT-GAATTTATATA
39950509 T
1 T
39950510 CTCTACTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 6 0.24
27 19 0.76
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (27 bp):
TATTTTTATAAATTTTGAATTTATATA
Found at i:39954113 original size:16 final size:16
Alignment explanation
Indices: 39954071--39954116 Score: 60
Period size: 14 Copynumber: 3.0 Consensus size: 16
39954061 AATTAAAAAA
39954071 ATTTAAATTTTGAGTT
1 ATTTAAATTTTGAGTT
* *
39954087 AATTGAA--TTGAGTT
1 ATTTAAATTTTGAGTT
39954101 ATTTAAATTTTGAGTT
1 ATTTAAATTTTGAGTT
39954117 TTGTAATTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
14 12 0.50
16 12 0.50
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (16 bp):
ATTTAAATTTTGAGTT
Found at i:39954192 original size:9 final size:9
Alignment explanation
Indices: 39954163--39954192 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
39954153 TGGATTTCAC
39954163 AATTCGAAT
1 AATTCGAAT
*
39954172 AACTCGAAT
1 AATTCGAAT
39954181 AATTCGAAT
1 AATTCGAAT
39954190 AAT
1 AAT
39954193 AGATTGGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:39954353 original size:24 final size:25
Alignment explanation
Indices: 39954324--39954376 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
39954314 AAAATTCAAA
* *
39954324 ATATTTATAAAAATTTC-AAAATTT
1 ATATTTATAAAAAATTCTAAAAATT
*
39954348 ATATTTTTAAAAAATTCTAAAAATT
1 ATATTTATAAAAAATTCTAAAAATT
39954373 ATAT
1 ATAT
39954377 AAAAAATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 15 0.60
25 10 0.40
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATTTATAAAAAATTCTAAAAATT
Found at i:39954370 original size:26 final size:27
Alignment explanation
Indices: 39954327--39954377 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
39954317 ATTCAAAATA
*
39954327 TTTATAAAAATTTCAAAATT-TATATT
1 TTTATAAAAATTTAAAAATTATATATT
39954353 TTTA-AAAAATTCTAAAAATTATATA
1 TTTATAAAAATT-TAAAAATTATATA
39954378 AAAAATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 11 0.50
27 4 0.18
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (27 bp):
TTTATAAAAATTTAAAAATTATATATT
Found at i:39954400 original size:45 final size:44
Alignment explanation
Indices: 39954307--39954399 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 44
39954297 ATTTTTTAAT
*
39954307 AATTTTT--AAAATTCAAAATATTTATAAAAATTTCAAAATTTA
1 AATTTTTAAAAAATTCAAAATATTTATAAAAAATTCAAAATTTA
*
39954349 TATTTTTAAAAAATTCTAAAA-ATTATATAAAAAATT-AAAATTTA
1 AATTTTTAAAAAATTC-AAAATATT-TATAAAAAATTCAAAATTTA
39954393 AATTTTT
1 AATTTTT
39954400 TTCTAAAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
42 6 0.14
44 24 0.55
45 14 0.32
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (44 bp):
AATTTTTAAAAAATTCAAAATATTTATAAAAAATTCAAAATTTA
Found at i:39955603 original size:43 final size:43
Alignment explanation
Indices: 39955550--39955645 Score: 113
Period size: 43 Copynumber: 2.2 Consensus size: 43
39955540 ACCACCACTA
* * * *
39955550 ATTTACAGATATAAACTGTCACTAGGTTGTGA-ATGTACAACAT
1 ATTTGCAGATAAAAACTGCCACTAGGTTG-GAGATGCACAACAT
* *
39955593 ATTTGCAGATAAAAACTGCCACTGGGTTGGAGATGCGCAACAT
1 ATTTGCAGATAAAAACTGCCACTAGGTTGGAGATGCACAACAT
*
39955636 ATTTGTAGAT
1 ATTTGCAGAT
39955646 GAACTGCCAC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 2 0.04
43 43 0.96
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (43 bp):
ATTTGCAGATAAAAACTGCCACTAGGTTGGAGATGCACAACAT
Found at i:39957556 original size:42 final size:42
Alignment explanation
Indices: 39957505--39957603 Score: 162
Period size: 42 Copynumber: 2.4 Consensus size: 42
39957495 CTCTTGGTAC
* *
39957505 CGCACACTTAGTGCCCGTTATTCAGCATCATCATTTTAATTT
1 CGCACACTTAGTGCCCATTATTCAACATCATCATTTTAATTT
* *
39957547 CGCACACTTAGTGCCCATTATTCAACATCGTCATTTTAGTTT
1 CGCACACTTAGTGCCCATTATTCAACATCATCATTTTAATTT
39957589 CGCACACTTAGTGCC
1 CGCACACTTAGTGCC
39957604 GTTCATATAG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.35
Consensus pattern (42 bp):
CGCACACTTAGTGCCCATTATTCAACATCATCATTTTAATTT
Found at i:39961740 original size:132 final size:132
Alignment explanation
Indices: 39961503--39962459 Score: 1581
Period size: 132 Copynumber: 7.2 Consensus size: 132
39961493 ACATTAGTTT
* * * *
39961503 TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCCTTGATCTACTCCACTACTG
1 TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTA
* *
39961568 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTACTGCCCACGGAGATAGAATTACTG
66 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTG
39961633 GC
131 GC
* * * ** * * * *
39961635 TTCAATATGCTCCACTATAACCTCAGGGAGGTAAAATCTGCCATCCTTGGTCAGCTCCACTACTG
1 TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTA
* * *
39961700 CTTAGGGAGATAAGATCTGGAATCTTTAATCTATTCCACTACTGCCCAGGGAGATAGAATTACTG
66 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTG
39961765 GC
131 GC
*
39961767 TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCTTTGATCTACTCCACTACTA
1 TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTA
*
39961832 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCTAGGGAGATAGAATTACTG
66 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTG
39961897 GC
131 GC
*
39961899 TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTA
1 TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTA
39961964 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTG
66 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTG
39962029 GC
131 GC
39962031 TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTA
1 TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTA
* * *
39962096 CTTAGGGAGATAAGATCTGTAATCTTAAATCTATTCCACTGTTGCCCAGGGGGATAGAATTACTG
66 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTG
39962161 GC
131 GC
* * *
39962163 TTCAACGTATTCCACTGTAACCTCAGGGAGGTATAATCCACCATCTTTGATCTGCTCCACTACTA
1 TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTA
*
39962228 CTTAGGGAGATAAGATCTGTAATCTTTAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTG
66 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTG
39962293 GC
131 GC
* *
39962295 TTCAATGTACTCCACTATAACCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCTACTACTA
1 TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTA
** * * * *
39962360 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTATTTCCTAGGGGGATAGAATTATTG
66 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTG
39962425 GC
131 GC
*
39962427 CTCAATGTACTCCACTGTAACCTCAGGGAGGTA
1 TTCAATGTACTCCACTGTAACCTCAGGGAGGTA
39962460 GAACTGCCAT
Statistics
Matches: 774, Mismatches: 51, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 774 1.00
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.29
Consensus pattern (132 bp):
TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTA
CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTG
GC
Found at i:39962253 original size:44 final size:44
Alignment explanation
Indices: 39962205--39962400 Score: 121
Period size: 44 Copynumber: 4.5 Consensus size: 44
39962195 ATAATCCACC
* * *
39962205 ATCTTTGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTA
1 ATCTTTAATCTACTCCACTACTACTCAGGGAGATAAGATCTGTA
* * * * *
39962249 ATCTTTAATCTATTCCACTGCTGCCCAGGGAGAT-AGA-AT-TA
1 ATCTTTAATCTACTCCACTACTACTCAGGGAGATAAGATCTGTA
* * * * * ****
39962290 CTGGCTTCAATGTACTCCACTA-TAACCTCAGGGAGGTAAAATCCACC
1 AT--CTTTAATCTACTCCACTACT-A-CTCAGGGAGATAAGATCTGTA
* * * *
39962337 ATCTTTGATCTGCTCTACTACTACTTAGGGAGATAAGATCTGTA
1 ATCTTTAATCTACTCCACTACTACTCAGGGAGATAAGATCTGTA
* *
39962381 ATCTTCAATCTATTCCACTA
1 ATCTTTAATCTACTCCACTA
39962401 TTTCCTAGGG
Statistics
Matches: 105, Mismatches: 39, Indels: 16
0.66 0.24 0.10
Matches are distributed among these distances:
41 3 0.03
42 2 0.02
43 17 0.16
44 65 0.62
45 16 0.15
46 1 0.01
47 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (44 bp):
ATCTTTAATCTACTCCACTACTACTCAGGGAGATAAGATCTGTA
Found at i:39963286 original size:13 final size:13
Alignment explanation
Indices: 39963268--39963292 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39963258 AAATTGTCGA
39963268 GGATAACAAAGAT
1 GGATAACAAAGAT
39963281 GGATAACAAAGA
1 GGATAACAAAGA
39963293 AATTGATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.24, T:0.12
Consensus pattern (13 bp):
GGATAACAAAGAT
Found at i:39965676 original size:40 final size:40
Alignment explanation
Indices: 39965621--39965842 Score: 365
Period size: 40 Copynumber: 5.6 Consensus size: 40
39965611 ATTTGAATAC
39965621 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
*
39965661 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
*
39965701 ATACGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
*
39965741 ATCCGGGCTAAGA-CCGAAGGCAATTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
* * *
39965780 ATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
* *
39965820 ACCCGGGTTAAGACCCGAAGGCA
1 ATCCGGGCTAAGACCCGAAGGCA
39965843 ATTGAGCTTG
Statistics
Matches: 170, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
39 38 0.22
40 132 0.78
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
Found at i:39965861 original size:119 final size:120
Alignment explanation
Indices: 39965621--39965869 Score: 376
Period size: 119 Copynumber: 2.1 Consensus size: 120
39965611 ATTTGAATAC
*
39965621 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
* * * * *
39965686 TGTGCGAGTTGATATATACGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
66 CGTGCGAGTTGATATACACGGGCTAAGACCCGAAGGCAATTGAGCAAGTGGATAT
39965741 ATCCGGGCTAAGA-CCGAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
* * * ** *
39965805 CGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGAGCTTGTGGTTAT
66 CGTGCGAGTTGATATACACGGGCTAAGACCCGAAGGCAATTGAGCAAGTGGATAT
39965860 ATCC-GGCTAA
1 ATCCGGGCTAA
39965870 ATTCCAAAGA
Statistics
Matches: 117, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
118 6 0.05
119 98 0.84
120 13 0.11
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (120 bp):
ATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
CGTGCGAGTTGATATACACGGGCTAAGACCCGAAGGCAATTGAGCAAGTGGATAT
Found at i:39968274 original size:20 final size:20
Alignment explanation
Indices: 39968249--39968290 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
39968239 AATTTGGTAG
39968249 AAAAAAATC-TGAAAGAATGA
1 AAAAAAATCGT-AAAGAATGA
39968269 AAAAAAATCGTAAAGAATGA
1 AAAAAAATCGTAAAGAATGA
39968289 AA
1 AA
39968291 GAACATTTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.67, C:0.05, G:0.14, T:0.14
Consensus pattern (20 bp):
AAAAAAATCGTAAAGAATGA
Found at i:39970774 original size:118 final size:119
Alignment explanation
Indices: 39970593--39970807 Score: 294
Period size: 118 Copynumber: 1.8 Consensus size: 119
39970583 TCCTCGTTCA
*
39970593 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* *
39970658 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCGGATTTAGTAACTCGCACC
* * **
39970712 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* *
39970774 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTA
39970808 GCCCGGACAT
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
117 4 0.05
118 60 0.71
119 20 0.24
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (119 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCGGATTTAGTAACTCGCACC
Found at i:39970814 original size:40 final size:40
Alignment explanation
Indices: 39970591--39970814 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
39970581 GCTCCTCGTT
* *
39970591 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
39970631 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
39970671 CAAATGCCTTCGGGACTTA-ACCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
39970710 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
39970749 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
39970790 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
39970815 CATCATTCAA
Statistics
Matches: 161, Mismatches: 16, Indels: 14
0.84 0.08 0.07
Matches are distributed among these distances:
38 6 0.04
39 58 0.36
40 85 0.53
41 12 0.07
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:39979272 original size:76 final size:80
Alignment explanation
Indices: 39979113--39979281 Score: 256
Period size: 76 Copynumber: 2.2 Consensus size: 80
39979103 GCTCCTCGTT
* *
39979113 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAACCCGATTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
*
39979178 ATTTAGTAACTCGCA
66 AATTAGTAACTCGCA
* *
39979193 CAAATGCCTTCGGGACTTAACCCGATT-TAGTAACTCGCAC-AATGCCTTCGGG-CTTAGCCC-G
1 CAAATGCCTTCGGGACATAACCCGATTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
*
39979254 AATTAGTATCTCGCA
66 AATTAGTAACTCGCA
39979269 CAAATGCCTTCGG
1 CAAATGCCTTCGG
39979282 ATCTTAGTCC
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
76 27 0.33
77 7 0.08
78 12 0.14
79 13 0.16
80 24 0.29
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACATAACCCGATTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
AATTAGTAACTCGCA
Found at i:39979294 original size:116 final size:118
Alignment explanation
Indices: 39979115--39979332 Score: 291
Period size: 116 Copynumber: 1.9 Consensus size: 118
39979105 TCCTCGTTCA
**
39979115 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* *
39979180 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGATTTAGTAACTCGCAC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGATTTAGTAACTCGCAC
* * **
39979233 AATGCCTTCGGG-CTTAGCCCGAAT-TAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGA
1 AATGCCTTCGGGACATAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGA
* * *
39979295 TATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
65 TATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCG
39979333 GACATCATTC
Statistics
Matches: 87, Mismatches: 11, Indels: 6
0.84 0.11 0.06
Matches are distributed among these distances:
115 3 0.03
116 55 0.63
117 17 0.20
118 12 0.14
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (118 bp):
AATGCCTTCGGGACATAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGATTTAGTAACTCGCAC
Found at i:39979334 original size:40 final size:40
Alignment explanation
Indices: 39979113--39979334 Score: 276
Period size: 40 Copynumber: 5.7 Consensus size: 40
39979103 GCTCCTCGTT
* *
39979113 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
39979153 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
39979193 CAAATGCCTTCGGGACTTAACCC-GATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
39979232 C-AATGCCTTCGGG-CTTAGCCCGAAT-TAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * * *
39979269 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
39979310 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
39979335 CATCATTCAA
Statistics
Matches: 161, Mismatches: 14, Indels: 14
0.85 0.07 0.07
Matches are distributed among these distances:
37 21 0.13
38 23 0.14
39 27 0.17
40 79 0.49
41 11 0.07
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:39985664 original size:18 final size:18
Alignment explanation
Indices: 39985633--39985667 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39985623 AATAATTTCT
* *
39985633 AAAAACATGTATATGTAA
1 AAAAAAATGCATATGTAA
39985651 AAAAAAATGCATATGTA
1 AAAAAAATGCATATGTA
39985668 TTATAAAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.06, G:0.11, T:0.26
Consensus pattern (18 bp):
AAAAAAATGCATATGTAA
Found at i:39988911 original size:30 final size:30
Alignment explanation
Indices: 39988877--39988975 Score: 119
Period size: 30 Copynumber: 3.3 Consensus size: 30
39988867 ATGTGTGTAT
** *
39988877 GGAGCTGAATTAAAGCATGCATGTGTTTAG
1 GGAGCTGAATTGGAGCATGCATGTATTTAG
* * *
39988907 GGAGCTAAATGGGGGCATGCATGTATTTAG
1 GGAGCTGAATTGGAGCATGCATGTATTTAG
* *
39988937 GAAGCTGAA-TGGAGCATGCATGAATTTAG
1 GGAGCTGAATTGGAGCATGCATGTATTTAG
39988966 GGAGCTGAAT
1 GGAGCTGAAT
39988976 GGGGATGCTA
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
29 25 0.45
30 31 0.55
ACGTcount: A:0.30, C:0.10, G:0.33, T:0.26
Consensus pattern (30 bp):
GGAGCTGAATTGGAGCATGCATGTATTTAG
Found at i:39988963 original size:29 final size:29
Alignment explanation
Indices: 39988890--39988977 Score: 122
Period size: 29 Copynumber: 3.0 Consensus size: 29
39988880 GCTGAATTAA
* *
39988890 AGCATGCATGTGTTTAGGGAGCTAAATGGG
1 AGCATGCATGTATTTAGGGAGCTGAAT-GG
* *
39988920 GGCATGCATGTATTTAGGAAGCTGAATGG
1 AGCATGCATGTATTTAGGGAGCTGAATGG
*
39988949 AGCATGCATGAATTTAGGGAGCTGAATGG
1 AGCATGCATGTATTTAGGGAGCTGAATGG
39988978 GGATGCTAGA
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 28 0.55
30 23 0.45
ACGTcount: A:0.28, C:0.10, G:0.35, T:0.26
Consensus pattern (29 bp):
AGCATGCATGTATTTAGGGAGCTGAATGG
Found at i:39991052 original size:2 final size:2
Alignment explanation
Indices: 39991045--39991072 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39991035 ATATGGTAAA
39991045 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
39991073 CTAAAAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:40002667 original size:7 final size:7
Alignment explanation
Indices: 40002655--40002683 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
40002645 AAAGTGAATA
40002655 ATATGTG
1 ATATGTG
40002662 ATATGTG
1 ATATGTG
40002669 ATATGTG
1 ATATGTG
40002676 ATATGTG
1 ATATGTG
40002683 A
1 A
40002684 GCATGTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.28, T:0.41
Consensus pattern (7 bp):
ATATGTG
Found at i:40002921 original size:48 final size:48
Alignment explanation
Indices: 40002846--40002941 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 48
40002836 GCAATTTATT
40002846 TGTGATTATGTGGCCATTATCGACATTTATGTGGTGGCTTGTCCACAA
1 TGTGATTATGTGGCCATTATCGACATTTATGTGGTGGCTTGTCCACAA
* *
40002894 TGTG-TTATGTGGTCGTTCATCGACATTTATGTGGTGGCTTGTCCACAA
1 TGTGATTATGTGGCCATT-ATCGACATTTATGTGGTGGCTTGTCCACAA
40002942 ATGGTGTGTT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
47 11 0.24
48 34 0.76
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.39
Consensus pattern (48 bp):
TGTGATTATGTGGCCATTATCGACATTTATGTGGTGGCTTGTCCACAA
Found at i:40005443 original size:16 final size:15
Alignment explanation
Indices: 40005418--40005447 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
40005408 GTAAGCACTA
40005418 ATTTGATAGGTGAAC
1 ATTTGATAGGTGAAC
40005433 ATTTAGATAGGTGAA
1 ATTT-GATAGGTGAA
40005448 ACTGAGAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.33
Consensus pattern (15 bp):
ATTTGATAGGTGAAC
Found at i:40011471 original size:17 final size:18
Alignment explanation
Indices: 40011451--40011485 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
40011441 CGAATTACCT
40011451 GAATTAAAGTATT-AATC
1 GAATTAAAGTATTGAATC
40011468 GAATTAAAGTATTGAATC
1 GAATTAAAGTATTGAATC
40011486 ACTACATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.34
Consensus pattern (18 bp):
GAATTAAAGTATTGAATC
Found at i:40013161 original size:238 final size:239
Alignment explanation
Indices: 40012708--40013179 Score: 802
Period size: 238 Copynumber: 2.0 Consensus size: 239
40012698 AAATACAAAC
*
40012708 ATTAAGACACAACATCTTCTTGCACTCTCTCTTTTCCACCACAACACACTCCTTAAACTTTTTTA
1 ATTAAGACACAACATCTTCTTACACTCTCTCTTTTCCACCACAACACACTCCTTAAACTTTTTTA
* * *
40012773 ATCTAACTGGAGATTGTCTCACATATCTAATAGTCCCCTAATACGTTCAACAGATTTATTCATTT
66 ATCTAACTGAAGATTGTCTCACATATCTAATAGTCCCCCAACACGTTCAACAGATTTATTCATTT
* * *
40012838 CCTTTAAGTCTTCAACAACAATTAAATTCACAATGTGTGTCATGCATCTCATATGAAGATATTTA
131 CCTTTAAGTCTTCAACAACAATCAAATCCACAATGCGTGTCATGCATCTCATATGAAGATATTTA
40012903 CCATTTTGAACAAAACCCCCTCGAGGGTTAAATTTTTTTCTCAT
196 CCATTTTGAACAAAACCCCCTCGAGGGTTAAATTTTTTTCTCAT
*
40012947 ATTAAGAGACAACATCTTCTTACACTCTCTCTTTTCCACCACAACACACTCCTTAAACTTTTTTA
1 ATTAAGACACAACATCTTCTTACACTCTCTCTTTTCCACCACAACACACTCCTTAAACTTTTTTA
* *
40013012 ATCTAACTGAAGATTGTCTCACATATGTAATAG-CCCCCAACACTTTCAACAGATTTATTCATTT
66 ATCTAACTGAAGATTGTCTCACATATCTAATAGTCCCCCAACACGTTCAACAGATTTATTCATTT
* *
40013076 CCTTTAAGTCTTTAACAACAATCAAATCCACAATGCGTGTCATTCATCTCATATGAAGATATTTA
131 CCTTTAAGTCTTCAACAACAATCAAATCCACAATGCGTGTCATGCATCTCATATGAAGATATTTA
* * *
40013141 CCATTTTGAACTAGACCCCCTCGAGGGTTAATTTTTTTT
196 CCATTTTGAACAAAACCCCCTCGAGGGTTAAATTTTTTT
40013180 AAATAACCAA
Statistics
Matches: 218, Mismatches: 15, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
238 124 0.57
239 94 0.43
ACGTcount: A:0.31, C:0.25, G:0.09, T:0.36
Consensus pattern (239 bp):
ATTAAGACACAACATCTTCTTACACTCTCTCTTTTCCACCACAACACACTCCTTAAACTTTTTTA
ATCTAACTGAAGATTGTCTCACATATCTAATAGTCCCCCAACACGTTCAACAGATTTATTCATTT
CCTTTAAGTCTTCAACAACAATCAAATCCACAATGCGTGTCATGCATCTCATATGAAGATATTTA
CCATTTTGAACAAAACCCCCTCGAGGGTTAAATTTTTTTCTCAT
Found at i:40015688 original size:25 final size:25
Alignment explanation
Indices: 40015652--40015738 Score: 81
Period size: 25 Copynumber: 3.5 Consensus size: 25
40015642 ATTCAGGAAT
*
40015652 GCTCATATGAGCATGTAAACGAGAA
1 GCTCATGTGAGCATGTAAACGAGAA
* *
40015677 GCTC-TTTCGAGCCATAT-AACGAGAA
1 GCTCATGT-GAG-CATGTAAACGAGAA
*
40015702 GCTCATGTGAG-TTGTATAACGAGAA
1 GCTCATGTGAGCATGTA-AACGAGAA
*
40015727 GCTCATGCGAGC
1 GCTCATGTGAGC
40015739 CAAATATCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
23 2 0.04
24 2 0.04
25 40 0.80
26 6 0.12
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (25 bp):
GCTCATGTGAGCATGTAAACGAGAA
Found at i:40015811 original size:24 final size:24
Alignment explanation
Indices: 40015724--40015814 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
40015714 TGTATAACGA
**
40015724 GAAGCTCATGCGAGCCAAATATCAA
1 GAAGCTCATGCGAGCCAAAT-TCGG
* *
40015749 TAAGCTCATGCGAGCCATAA-ACGG
1 GAAGCTCATGCGAGCCA-AATTCGG
***
40015773 GAAGCTCAAAAGAGCCAAATTCGG
1 GAAGCTCATGCGAGCCAAATTCGG
*
40015797 GAGGCTCATGCGAGCCAA
1 GAAGCTCATGCGAGCCAA
40015815 TATCAGGAAG
Statistics
Matches: 51, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
23 2 0.04
24 31 0.61
25 16 0.31
26 2 0.04
ACGTcount: A:0.36, C:0.24, G:0.25, T:0.14
Consensus pattern (24 bp):
GAAGCTCATGCGAGCCAAATTCGG
Found at i:40015908 original size:25 final size:25
Alignment explanation
Indices: 40015839--40015908 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
40015829 GGAGAGCCAT
*
40015839 ATATC-GGATGCTCATAAGAGTTAA
1 ATATCGGGATGCTCATAAGAGTCAA
* * * * *
40015863 ATAACGGAAAGCTCGTGAGAGTCAA
1 ATATCGGGATGCTCATAAGAGTCAA
*
40015888 GTATCGGGATGCTCATAAGAG
1 ATATCGGGATGCTCATAAGAG
40015909 CTGTTGTGTG
Statistics
Matches: 33, Mismatches: 12, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
24 4 0.12
25 29 0.88
ACGTcount: A:0.36, C:0.14, G:0.27, T:0.23
Consensus pattern (25 bp):
ATATCGGGATGCTCATAAGAGTCAA
Found at i:40026129 original size:42 final size:42
Alignment explanation
Indices: 40026082--40026165 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
40026072 CCTATTTCGT
*
40026082 ACACACGGGCAGAG-ACATGGGCGTGT-GTCTTGGCCGTGTGTC
1 ACACACGGCCA-AGCACATGGGCGTGTGGT-TTGGCCGTGTGTC
*
40026124 ACACACGGCCAAGCACATGGGCGTGTGGTTTGGTCGTGTGTC
1 ACACACGGCCAAGCACATGGGCGTGTGGTTTGGCCGTGTGTC
40026166 CCCTGCATCT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
41 2 0.05
42 34 0.89
43 2 0.05
ACGTcount: A:0.17, C:0.24, G:0.37, T:0.23
Consensus pattern (42 bp):
ACACACGGCCAAGCACATGGGCGTGTGGTTTGGCCGTGTGTC
Found at i:40030279 original size:25 final size:25
Alignment explanation
Indices: 40030225--40030271 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
40030215 AAATCTACTC
40030225 TAAAAAGAAAAGAGAAAGCCTAAAT
1 TAAAAAGAAAAGAGAAAGCCTAAAT
40030250 TAAAAATGAAAAGA-AAA-CCTAA
1 TAAAAA-GAAAAGAGAAAGCCTAA
40030272 CCTTAAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.24
25 9 0.43
26 7 0.33
ACGTcount: A:0.66, C:0.09, G:0.13, T:0.13
Consensus pattern (25 bp):
TAAAAAGAAAAGAGAAAGCCTAAAT
Found at i:40031671 original size:26 final size:26
Alignment explanation
Indices: 40031642--40031720 Score: 115
Period size: 26 Copynumber: 3.1 Consensus size: 26
40031632 GCCAACACAC
*
40031642 CAATATCGCAGCAAAGCTGCCAGTAT
1 CAATATCGCAGCAAAGCTGCCAGTAA
*
40031668 CAATAACGCAGCAAAGCTGCCAGTAA
1 CAATATCGCAGCAAAGCTGCCAGTAA
* *
40031694 CAGTATCGCAGCAGAGCTGCCAG-AA
1 CAATATCGCAGCAAAGCTGCCAGTAA
40031719 CA
1 CA
40031721 GTACACTTCC
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
25 4 0.08
26 44 0.92
ACGTcount: A:0.37, C:0.28, G:0.22, T:0.14
Consensus pattern (26 bp):
CAATATCGCAGCAAAGCTGCCAGTAA
Found at i:40031921 original size:27 final size:27
Alignment explanation
Indices: 40031891--40032247 Score: 295
Period size: 27 Copynumber: 13.2 Consensus size: 27
40031881 GATATAGTGG
* *
40031891 TAATTTTACCATTCGGGGGCATTTTGA
1 TAATTTTACCATTCGAGGGTATTTTGA
* *
40031918 TAATTTTACCCA-TCGAGGGTATTTCGG
1 TAATTTTA-CCATTCGAGGGTATTTTGA
* *
40031945 TAATTTTATCC-TTC-AGGGGCATTTCGA
1 TAATTTTA-CCATTCGA-GGGTATTTTGA
* * *
40031972 TAATTTTACCTTTTGGGGGTATTTTGA
1 TAATTTTACCATTCGAGGGTATTTTGA
*
40031999 TAATTTTACCCTTCGAGGGTATTTT-A
1 TAATTTTACCATTCGAGGGTATTTTGA
*
40032025 GTAATTTTACCCA-TCGAGGGTATTTTAA
1 -TAATTTTA-CCATTCGAGGGTATTTTGA
* * *
40032053 TAATTTTACTCTTTAG-GGGTA-TTTCA
1 TAATTTTAC-CATTCGAGGGTATTTTGA
* * *
40032079 GTAATTTTACCCATT-GGGGGTATTTCGG
1 -TAATTTTA-CCATTCGAGGGTATTTTGA
* *
40032107 TAATTTTACCCTTCGAGGGTA-TTTCA
1 TAATTTTACCATTCGAGGGTATTTTGA
* * *
40032133 GTAATTTTACCCTTCGAGAGTATTTCGA
1 -TAATTTTACCATTCGAGGGTATTTTGA
*
40032161 TAATTTTACTCA-TCGAGGGTATTTTGG
1 TAATTTTAC-CATTCGAGGGTATTTTGA
*
40032188 TAATTTTACCCA-TCGAAGGTATTTTGA
1 TAATTTTA-CCATTCGAGGGTATTTTGA
* **
40032215 TAATTTTACCCTTCGAGGGTATTTCAA
1 TAATTTTACCATTCGAGGGTATTTTGA
40032242 TAATTT
1 TAATTT
40032248 ACCCACGAAT
Statistics
Matches: 270, Mismatches: 40, Indels: 40
0.77 0.11 0.11
Matches are distributed among these distances:
26 18 0.07
27 236 0.87
28 16 0.06
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.43
Consensus pattern (27 bp):
TAATTTTACCATTCGAGGGTATTTTGA
Found at i:40031952 original size:54 final size:54
Alignment explanation
Indices: 40031891--40032252 Score: 367
Period size: 54 Copynumber: 6.7 Consensus size: 54
40031881 GATATAGTGG
* * * *
40031891 TAATTTTACCATTCGGGGGCATTTTGATAATTTTACCCATCGAGGGTATTTCGG
1 TAATTTTACCCTTCGAGGGTATTTTGATAATTTTACCCATCGAGGGTATTTCGA
* * * ** * * *
40031945 TAATTTTATCCTTC-AGGGGCATTTCGATAATTTTACCTTTTGGGGGTATTTTGA
1 TAATTTTACCCTTCGA-GGGTATTTTGATAATTTTACCCATCGAGGGTATTTCGA
**
40031999 TAATTTTACCCTTCGAGGGTATTTT-AGTAATTTTACCCATCGAGGGTATTTTAA
1 TAATTTTACCCTTCGAGGGTATTTTGA-TAATTTTACCCATCGAGGGTATTTCGA
* * * * * *
40032053 TAATTTTACTCTT-TAGGGGTA-TTTCAGTAATTTTACCCATTGGGGGTATTTCGG
1 TAATTTTACCCTTCGA-GGGTATTTTGA-TAATTTTACCCATCGAGGGTATTTCGA
* * *
40032107 TAATTTTACCCTTCGAGGGTA-TTTCAGTAATTTTACCCTTCGAGAGTATTTCGA
1 TAATTTTACCCTTCGAGGGTATTTTGA-TAATTTTACCCATCGAGGGTATTTCGA
* * * * *
40032161 TAATTTTACTCATCGAGGGTATTTTGGTAATTTTACCCATCGAAGGTATTTTGA
1 TAATTTTACCCTTCGAGGGTATTTTGATAATTTTACCCATCGAGGGTATTTCGA
**
40032215 TAATTTTACCCTTCGAGGGTATTTCAATAA-TTTACCCA
1 TAATTTTACCCTTCGAGGGTATTTTGATAATTTTACCCA
40032253 CGAATCGAAA
Statistics
Matches: 256, Mismatches: 45, Indels: 15
0.81 0.14 0.05
Matches are distributed among these distances:
53 13 0.05
54 238 0.93
55 5 0.02
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (54 bp):
TAATTTTACCCTTCGAGGGTATTTTGATAATTTTACCCATCGAGGGTATTTCGA
Found at i:40032001 original size:81 final size:81
Alignment explanation
Indices: 40031891--40032252 Score: 408
Period size: 81 Copynumber: 4.5 Consensus size: 81
40031881 GATATAGTGG
* * *
40031891 TAATTTTACCATTCGGGGGCATTTTGATAATTTTACCCATCGAGGGTATTTCGGTAATTTTATCC
1 TAATTTTACCCTTCGGGGGTATTTTGATAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCC
* *
40031956 TTC-AGGGGCATTTCGA
66 ATCGA-GGGTATTTCGA
* * * **
40031972 TAATTTTACCTTTTGGGGGTATTTTGATAATTTTACCCTTCGAGGGTATTTTAGTAATTTTACCC
1 TAATTTTACCCTTCGGGGGTATTTTGATAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCC
**
40032037 ATCGAGGGTATTTTAA
66 ATCGAGGGTATTTCGA
* ** * * *
40032053 TAATTTTACTCTTTAGGGGTA-TTTCAGTAATTTTACCCATTGGGGGTATTTCGGTAATTTTACC
1 TAATTTTACCCTTCGGGGGTATTTTGA-TAATTTTACCCATCGAGGGTATTTCGGTAATTTTACC
*
40032117 CTTCGAGGGTATTTC-A
65 CATCGAGGGTATTTCGA
* * * * *
40032133 GTAATTTTACCCTTCGAGAGTATTTCGATAATTTTACTCATCGAGGGTATTTTGGTAATTTTACC
1 -TAATTTTACCCTTCGGGGGTATTTTGATAATTTTACCCATCGAGGGTATTTCGGTAATTTTACC
* *
40032198 CATCGAAGGTATTTTGA
65 CATCGAGGGTATTTCGA
* **
40032215 TAATTTTACCCTTCGAGGGTATTTCAATAA-TTTACCCA
1 TAATTTTACCCTTCGGGGGTATTTTGATAATTTTACCCA
40032253 CGAATCGAAA
Statistics
Matches: 237, Mismatches: 39, Indels: 11
0.83 0.14 0.04
Matches are distributed among these distances:
80 12 0.05
81 220 0.93
82 5 0.02
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (81 bp):
TAATTTTACCCTTCGGGGGTATTTTGATAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCC
ATCGAGGGTATTTCGA
Found at i:40034931 original size:90 final size:90
Alignment explanation
Indices: 40034769--40035015 Score: 216
Period size: 90 Copynumber: 2.7 Consensus size: 90
40034759 CTCAGTTTAA
* * * * * * * *
40034769 AAATTCGGTGAATGT-ATCAAGTCTACCTTACTAGGACCACCCAAAGC-CTGAGATATGAATTCA
1 AAATTTGGTGAAT-TCATCAAGTCTATCTCAATAAGACCACCCAAA-CTCTGGGCTATGAACTCA
* * ***
40034832 TTAAGAACATTTAGTGGCTCATCCTAT
64 TTAAAAACATCTAAAAGCTCATCCTAT
* * * *
40034859 AAATTTGGT-AAGTTCATCAAGTTTGTCTCAATAGGAACC-CCCGAAA-TCTGGGTTATGAACTC
1 AAATTTGGTGAA-TTCATCAAGTCTATCTCAATAAG-ACCACCC-AAACTCTGGGCTATGAACTC
*
40034921 ATTAAAAACATCTAAAAGTTCATCCTAT
63 ATTAAAAACATCTAAAAGCTCATCCTAT
* * * *
40034949 GAATTTGGTGAATTTATCAAGTCTATCTTAATAAGACCATCCAAACTCTGGGCTATGAACTCATT
1 AAATTTGGTGAATTCATCAAGTCTATCTCAATAAGACCACCCAAACTCTGGGCTATGAACTCATT
40035014 AA
66 AA
40035016 GAGCACAGAG
Statistics
Matches: 126, Mismatches: 23, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
89 9 0.07
90 109 0.87
91 8 0.06
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.31
Consensus pattern (90 bp):
AAATTTGGTGAATTCATCAAGTCTATCTCAATAAGACCACCCAAACTCTGGGCTATGAACTCATT
AAAAACATCTAAAAGCTCATCCTAT
Found at i:40038713 original size:18 final size:18
Alignment explanation
Indices: 40038671--40038714 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
40038661 TATGAGTTAT
40038671 AAATTAC-ATAATATATA
1 AAATTACAATAATATATA
*
40038688 AAAATACAATAATATA-A
1 AAATTACAATAATATATA
40038705 AACATTACAA
1 AA-ATTACAA
40038715 ACTAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (18 bp):
AAATTACAATAATATATA
Found at i:40039301 original size:58 final size:58
Alignment explanation
Indices: 40039234--40039347 Score: 158
Period size: 58 Copynumber: 2.0 Consensus size: 58
40039224 TTTTCTTTTT
*
40039234 CTTTACAACCAGTC-ACACTCTTTCTTTGATTTTTCTCTCTGTCACTCTTTTGATTGGC
1 CTTTACAACCAGTCGAC-CTCTTTCTTTGATTTTTCTCTCTGTCACTCTTTCGATTGGC
* * ** *
40039292 CTTTTCAACCAGTCGACCTTTTTCTTTTCTTTTTCTCTCTGTTACTCTTTCGATTG
1 CTTTACAACCAGTCGACCTCTTTCTTTGATTTTTCTCTCTGTCACTCTTTCGATTG
40039348 CTCTCAATTG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
58 47 0.96
59 2 0.04
ACGTcount: A:0.13, C:0.27, G:0.10, T:0.50
Consensus pattern (58 bp):
CTTTACAACCAGTCGACCTCTTTCTTTGATTTTTCTCTCTGTCACTCTTTCGATTGGC
Found at i:40040223 original size:13 final size:13
Alignment explanation
Indices: 40040205--40040229 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40040195 AAATTGCCCA
40040205 AAATTGAAATATC
1 AAATTGAAATATC
40040218 AAATTGAAATAT
1 AAATTGAAATAT
40040230 GCCCAAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.32
Consensus pattern (13 bp):
AAATTGAAATATC
Found at i:40041584 original size:23 final size:24
Alignment explanation
Indices: 40041556--40041618 Score: 96
Period size: 23 Copynumber: 2.7 Consensus size: 24
40041546 TTGTTTTGAT
40041556 ATTGTTCTTGATTTGTT-CTGGAA
1 ATTGTTCTTGATTTGTTGCTGGAA
40041579 ATTGTT-TTGA-TTGTCTGCTGGAA
1 ATTGTTCTTGATTTGT-TGCTGGAA
40041602 ATTGTTCTTGATTTGTT
1 ATTGTTCTTGATTTGTT
40041619 AGTCAGTAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
21 4 0.11
22 5 0.14
23 18 0.50
24 5 0.14
25 4 0.11
ACGTcount: A:0.16, C:0.08, G:0.22, T:0.54
Consensus pattern (24 bp):
ATTGTTCTTGATTTGTTGCTGGAA
Found at i:40044426 original size:11 final size:11
Alignment explanation
Indices: 40044410--40044436 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
40044400 TAGAAATTAG
40044410 TTTGTGAAACT
1 TTTGTGAAACT
40044421 TTTGTGAAACT
1 TTTGTGAAACT
40044432 TTTGT
1 TTTGT
40044437 ATTGATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (11 bp):
TTTGTGAAACT
Found at i:40044541 original size:21 final size:20
Alignment explanation
Indices: 40044491--40044548 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 20
40044481 TTCTTGTCAT
***
40044491 TTTAAATTTTAAATTTTTTG
1 TTTAAATTTTAAATTTTAAA
40044511 TGTTATAATTTTAAATTTTAAAA
1 T-TTA-AATTTTAAATTTT-AAA
40044534 TTTAAATTTTAAATT
1 TTTAAATTTTAAATT
40044549 ATAGTTTGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
20 1 0.03
21 14 0.44
22 16 0.50
23 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TTTAAATTTTAAATTTTAAA
Found at i:40044542 original size:6 final size:7
Alignment explanation
Indices: 40044489--40044548 Score: 66
Period size: 7 Copynumber: 8.4 Consensus size: 7
40044479 ATTTCTTGTC
40044489 ATTTTAA
1 ATTTTAA
40044496 ATTTTAA
1 ATTTTAA
**
40044503 ATTTTTT
1 ATTTTAA
* *
40044510 GTGTTATA
1 ATTTTA-A
40044518 ATTTTAA
1 ATTTTAA
40044525 ATTTTAA
1 ATTTTAA
*
40044532 AATTTAA
1 ATTTTAA
40044539 ATTTTAA
1 ATTTTAA
40044546 ATT
1 ATT
40044549 ATAGTTTGTG
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
7 38 0.90
8 4 0.10
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (7 bp):
ATTTTAA
Found at i:40044560 original size:46 final size:43
Alignment explanation
Indices: 40044491--40044575 Score: 143
Period size: 46 Copynumber: 1.9 Consensus size: 43
40044481 TTCTTGTCAT
40044491 TTTAAATTTTAAATTTTTTGTGTTATAATTTTAAATTTTAAAA
1 TTTAAATTTTAAATTTTTTGTGTTATAATTTTAAATTTTAAAA
40044534 TTTAAATTTTAAATTATAGTTTGTGTTATAATTTTAAATTTT
1 TTTAAATTTTAAATT-T--TTTGTGTTATAATTTTAAATTTT
40044576 TTGTGGTATG
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
43 15 0.38
44 1 0.03
46 23 0.59
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (43 bp):
TTTAAATTTTAAATTTTTTGTGTTATAATTTTAAATTTTAAAA
Found at i:40046160 original size:120 final size:120
Alignment explanation
Indices: 40046033--40046690 Score: 1156
Period size: 120 Copynumber: 5.5 Consensus size: 120
40046023 AATTATTTTA
*
40046033 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATCTTT
40046097 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
40046153 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
40046218 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
40046273 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
*
40046338 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAT
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* * * * *
40046393 AATTTTATTAAATTATGTATTTTAATTATAATATATTTAATAATAATTATATTAAATTATATTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
40046458 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* * *
40046513 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
* *
40046578 ATAGTATCATATATTATGATTTCAGTAAATTCATATAAGAATATTAATTATAAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* * *
40046633 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATATTTATGTTTAAAT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATG-TTAAAT
40046691 ATAATTAAAT
Statistics
Matches: 523, Mismatches: 13, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
120 515 0.98
121 8 0.02
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:40046433 original size:15 final size:16
Alignment explanation
Indices: 40046413--40046453 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
40046403 AATTATGTAT
40046413 TTTAATTATAA-TATA
1 TTTAATTATAATTATA
*
40046428 TTTAATAATAATTATA
1 TTTAATTATAATTATA
*
40046444 TTAAATTATA
1 TTTAATTATA
40046454 TTTTATAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTTAATTATAATTATA
Found at i:40046548 original size:16 final size:16
Alignment explanation
Indices: 40046527--40046573 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
40046517 TTATTAAATT
40046527 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
40046543 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
40046558 AT-TATGTTAAATTATA
1 ATATAT-TTTAATTATA
40046574 TTTTATAGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.42
16 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:40046667 original size:18 final size:18
Alignment explanation
Indices: 40046621--40046668 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
40046611 TATAAGAATA
*
40046621 TTAATTATAA-AGA-ATT
1 TTAATTATAATATATATT
40046637 TT-ATTA-AATTATATATT
1 TTAATTATAA-TATATATT
40046654 TTAATTATAATATAT
1 TTAATTATAATATAT
40046669 TTAATAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
14 2 0.08
15 4 0.15
16 4 0.15
17 5 0.19
18 9 0.35
19 2 0.08
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TTAATTATAATATATATT
Found at i:40046856 original size:39 final size:42
Alignment explanation
Indices: 40046813--40046922 Score: 127
Period size: 39 Copynumber: 2.6 Consensus size: 42
40046803 TTTTTCCATT
*
40046813 ATACTATTACACCTCTATTCCATT-CAATCAA-ACACAA-GA
1 ATACTATTACACCTCTATTCCATTACAATCAACAAACAATGA
* * *
40046852 ATACTATTACGCCTCTATTCCATTACATTCAACCAAACAATTA
1 ATACTATTACACCTCTATTCCATTACAATCAA-CAAACAATGA
*
40046895 ATTTGCTATTACACCTCTATTCCATTAC
1 A--TACTATTACACCTCTATTCCATTAC
40046923 GCCTCTATTC
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
39 23 0.39
40 6 0.10
42 5 0.08
43 2 0.03
45 23 0.39
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (42 bp):
ATACTATTACACCTCTATTCCATTACAATCAACAAACAATGA
Found at i:40046927 original size:16 final size:16
Alignment explanation
Indices: 40046902--40046939 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
40046892 TTAATTTGCT
40046902 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
40046918 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
40046934 AATACA
1 ATTACA
40046940 GCGAACCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.29, C:0.34, G:0.03, T:0.34
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:40052733 original size:161 final size:161
Alignment explanation
Indices: 40052468--40052771 Score: 608
Period size: 161 Copynumber: 1.9 Consensus size: 161
40052458 GACTAAACTA
40052468 AATAAGTCTAAAATAGATTAATAAGAGAATTTGAATGACTAAAATAAATAAACAAGGAAAATAAA
1 AATAAGTCTAAAATAGATTAATAAGAGAATTTGAATGACTAAAATAAATAAACAAGGAAAATAAA
40052533 CAAATGACTAAACAAATAAAATCAATAGAAATATTAACTTGTTTTAGGGTTTGTAATTAACTTCG
66 CAAATGACTAAACAAATAAAATCAATAGAAATATTAACTTGTTTTAGGGTTTGTAATTAACTTCG
40052598 GATTAAGGTTTTAATTAATATATATAATAGT
131 GATTAAGGTTTTAATTAATATATATAATAGT
40052629 AATAAGTCTAAAATAGATTAATAAGAGAATTTGAATGACTAAAATAAATAAACAAGGAAAATAAA
1 AATAAGTCTAAAATAGATTAATAAGAGAATTTGAATGACTAAAATAAATAAACAAGGAAAATAAA
40052694 CAAATGACTAAACAAATAAAATCAATAGAAATATTAACTTGTTTTAGGGTTTGTAATTAACTTCG
66 CAAATGACTAAACAAATAAAATCAATAGAAATATTAACTTGTTTTAGGGTTTGTAATTAACTTCG
40052759 GATTAAGGTTTTA
131 GATTAAGGTTTTA
40052772 GGGTAGATTA
Statistics
Matches: 143, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
161 143 1.00
ACGTcount: A:0.50, C:0.07, G:0.13, T:0.31
Consensus pattern (161 bp):
AATAAGTCTAAAATAGATTAATAAGAGAATTTGAATGACTAAAATAAATAAACAAGGAAAATAAA
CAAATGACTAAACAAATAAAATCAATAGAAATATTAACTTGTTTTAGGGTTTGTAATTAACTTCG
GATTAAGGTTTTAATTAATATATATAATAGT
Done.