Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr6
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: 26303135
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 1968672 characters in sequence are not A, C, G, or T
File 1 of 66
Found at i:12 original size:7 final size:7
Alignment explanation
Indices: 2--119 Score: 110
Period size: 7 Copynumber: 15.7 Consensus size: 7
1 T
*
2 AAACCCT
1 AAACCCC
*
9 AAACCCT
1 AAACCCC
*
16 AAACCCT
1 AAACCCC
23 AAACCCC
1 AAACCCC
30 AAACCCC
1 AAACCCC
37 AAACCCC
1 AAACCCC
*
44 CAACCCC
1 AAACCCC
51 AAACCCCC
1 AAA-CCCC
59 AAACCCCCC
1 AAA--CCCC
68 AAACCCCC
1 AAA-CCCC
76 AAACCCCCC
1 AAA--CCCC
85 AAACCCCC
1 AAA-CCCC
93 AAACCCCC
1 AAA-CCCC
101 AAACCCC
1 AAACCCC
* *
108 CAACCCT
1 AAACCCC
115 AAACC
1 AAACC
120 TAAACCTAAA
Statistics
Matches: 102, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
7 55 0.54
8 31 0.30
9 16 0.16
ACGTcount: A:0.39, C:0.58, G:0.00, T:0.03
Consensus pattern (7 bp):
AAACCCC
Found at i:46 original size:8 final size:8
Alignment explanation
Indices: 26--110 Score: 131
Period size: 8 Copynumber: 10.8 Consensus size: 8
16 AAACCCTAAA
26 CCCCAAA-
1 CCCCAAAC
33 CCCCAAAC
1 CCCCAAAC
41 CCCC-AA-
1 CCCCAAAC
47 CCCCAAAC
1 CCCCAAAC
55 CCCCAAACC
1 CCCCAAA-C
64 CCCCAAAC
1 CCCCAAAC
72 CCCCAAACC
1 CCCCAAA-C
81 CCCCAAAC
1 CCCCAAAC
89 CCCCAAAC
1 CCCCAAAC
97 CCCCAAAC
1 CCCCAAAC
105 CCCCAA
1 CCCCAA
111 CCCTAAACCT
Statistics
Matches: 73, Mismatches: 0, Indels: 9
0.89 0.00 0.11
Matches are distributed among these distances:
6 4 0.05
7 11 0.15
8 42 0.58
9 16 0.22
ACGTcount: A:0.36, C:0.64, G:0.00, T:0.00
Consensus pattern (8 bp):
CCCCAAAC
Found at i:69 original size:17 final size:16
Alignment explanation
Indices: 26--110 Score: 131
Period size: 17 Copynumber: 5.4 Consensus size: 16
16 AAACCCTAAA
26 CCCCAAA-CCCCAAAC
1 CCCCAAACCCCCAAAC
41 CCCC-AA-CCCCAAAC
1 CCCCAAACCCCCAAAC
55 CCCCAAACCCCCCAAAC
1 CCCCAAA-CCCCCAAAC
72 CCCCAAACCCCCCAAAC
1 CCCCAAA-CCCCCAAAC
89 CCCCAAACCCCCAAAC
1 CCCCAAACCCCCAAAC
105 CCCCAA
1 CCCCAA
111 CCCTAAACCT
Statistics
Matches: 67, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
14 14 0.21
15 6 0.09
16 15 0.22
17 32 0.48
ACGTcount: A:0.36, C:0.64, G:0.00, T:0.00
Consensus pattern (16 bp):
CCCCAAACCCCCAAAC
Found at i:123 original size:6 final size:6
Alignment explanation
Indices: 112--170 Score: 97
Period size: 6 Copynumber: 10.3 Consensus size: 6
102 AACCCCCAAC
112 CCTAAA CCTAAA CCTAAA -CTAAA -CTAAA -CTAAA CCTAAA CCTAAA
1 CCTAAA CCTAAA CCTAAA CCTAAA CCTAAA CCTAAA CCTAAA CCTAAA
157 CCTAAA CCTAAA CC
1 CCTAAA CCTAAA CC
171 GCCAAACTAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
5 15 0.29
6 37 0.71
ACGTcount: A:0.51, C:0.32, G:0.00, T:0.17
Consensus pattern (6 bp):
CCTAAA
Found at i:7405 original size:1 final size:1
Alignment explanation
Indices: 7399--7423 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
7389 TTTCCAGTAT
7399 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
7424 CCTAAACCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:7440 original size:7 final size:7
Alignment explanation
Indices: 7424--7813 Score: 393
Period size: 7 Copynumber: 59.1 Consensus size: 7
7414 AAAAAAAAAA
7424 CCTAAA-
1 CCTAAAC
7430 CCTAAAC
1 CCTAAAC
7437 CCTAAAC
1 CCTAAAC
7444 CCT-AAC
1 CCTAAAC
7450 CCTAAAC
1 CCTAAAC
7457 CCTAAAC
1 CCTAAAC
7464 CTCTAAAC
1 C-CTAAAC
7472 CCTAAAC
1 CCTAAAC
7479 CCTAAAC
1 CCTAAAC
*
7486 CCAAAAC
1 CCTAAAC
7493 CC-AAAC
1 CCTAAAC
*
7499 CCCAAAC
1 CCTAAAC
*
7506 CCCAAAC
1 CCTAAAC
*
7513 CC-AACC
1 CCTAAAC
* *
7519 CCCAACC
1 CCTAAAC
*
7526 CCAAAAC
1 CCTAAAC
*
7533 CCTAACC
1 CCTAAAC
*
7540 CCCAAAC
1 CCTAAAC
* *
7547 CCCAACC
1 CCTAAAC
7554 CCTAAAC
1 CCTAAAC
7561 CCTAAA-
1 CCTAAAC
7567 CCTAAAC
1 CCTAAAC
7574 CCTAAAC
1 CCTAAAC
7581 CCT-AAC
1 CCTAAAC
*
7587 CCTTAAC
1 CCTAAAC
*
7594 CCCAAAC
1 CCTAAAC
*
7601 CCCAAACC
1 CCTAAA-C
*
7609 CCT-ACC
1 CCTAAAC
*
7615 CCTAACC
1 CCTAAAC
7622 CCTAAAC
1 CCTAAAC
7629 CCT-AAC
1 CCTAAAC
7635 CCTAAA-
1 CCTAAAC
7641 CCTAAA-
1 CCTAAAC
7647 CCTAAA-
1 CCTAAAC
7653 CCTAAAC
1 CCTAAAC
7660 CCTAAAC
1 CCTAAAC
7667 CCT-AAC
1 CCTAAAC
7673 CCTAAAC
1 CCTAAAC
7680 CCT-AAC
1 CCTAAAC
7686 CCTAAAAC
1 CCT-AAAC
7694 CC-AAAC
1 CCTAAAC
7700 CCTAAAC
1 CCTAAAC
*
7707 CCTAACC
1 CCTAAAC
7714 CCT-AA-
1 CCTAAAC
7719 CCT-AAC
1 CCTAAAC
7725 CCT-AAC
1 CCTAAAC
*
7731 CCTAACC
1 CCTAAAC
7738 CCT-AAC
1 CCTAAAC
*
7744 CCTAACC
1 CCTAAAC
7751 CCTAAAC
1 CCTAAAC
7758 CCTAAAC
1 CCTAAAC
7765 CCT-AA-
1 CCTAAAC
7770 CCTAAA-
1 CCTAAAC
7776 CCTAAA-
1 CCTAAAC
7782 CCTAAA-
1 CCTAAAC
7788 CCTAAA-
1 CCTAAAC
7794 CCTAAA-
1 CCTAAAC
7800 CCTAAA-
1 CCTAAAC
7806 CCTAAAC
1 CCTAAAC
7813 C
1 C
7814 AAACCAAAAA
Statistics
Matches: 342, Mismatches: 22, Indels: 39
0.85 0.05 0.10
Matches are distributed among these distances:
5 8 0.02
6 136 0.40
7 183 0.54
8 15 0.04
ACGTcount: A:0.41, C:0.47, G:0.00, T:0.13
Consensus pattern (7 bp):
CCTAAAC
Found at i:7440 original size:13 final size:13
Alignment explanation
Indices: 7421--7813 Score: 299
Period size: 13 Copynumber: 29.8 Consensus size: 13
7411 AAAAAAAAAA
7421 AAACCTAAA-CCT
1 AAACCTAAACCCT
7433 AAACCCTAAACCCT
1 AAA-CCTAAACCCT
*
7447 AACCCTAAACCCT
1 AAACCTAAACCCT
7460 AAACCTCTAAACCCT
1 AAA-C-CTAAACCCT
*
7475 AAACCCTAAACCCA
1 AAA-CCTAAACCCT
* *
7489 AAACCCAAACCCC
1 AAACCTAAACCCT
*
7502 AAACCCCAAACCC-
1 AAA-CCTAAACCCT
* * * *
7515 AACCCCCAACCCCA
1 AA-ACCTAAACCCT
* *
7529 AAACCCTAACCCCC
1 AAA-CCTAAACCCT
* *
7543 AAACCCCAACCCCT
1 AAA-CCTAAACCCT
7557 AAACCCTAAA-CCT
1 AAA-CCTAAACCCT
7570 AAACCCTAAACCCT
1 AAA-CCTAAACCCT
* * *
7584 AACCCTTAACCCC
1 AAACCTAAACCCT
*
7597 AAACCCCAAACCCCT
1 AAA-CCTAAA-CCCT
** *
7612 ACCCCTAACCCCT
1 AAACCTAAACCCT
7625 AAACCCT-AACCCT
1 AAA-CCTAAACCCT
7638 AAACCTAAA-CCT
1 AAACCTAAACCCT
7650 AAACCTAAACCCT
1 AAACCTAAACCCT
7663 AAACCCT-AACCCT
1 AAA-CCTAAACCCT
7676 AAACCCT-AACCCT
1 AAA-CCTAAACCCT
*
7689 AAAACCCAAACCCT
1 -AAACCTAAACCCT
*
7703 AAACCCTAACCCCT
1 AAA-CCTAAACCCT
7717 -AACCT-AACCCT
1 AAACCTAAACCCT
* *
7728 AACCCTAACCCCT
1 AAACCTAAACCCT
* *
7741 AACCCTAACCCCT
1 AAACCTAAACCCT
7754 AAACCCTAAACCCT
1 AAA-CCTAAACCCT
7768 -AACCTAAA-CCT
1 AAACCTAAACCCT
7779 AAACCTAAA-CCT
1 AAACCTAAACCCT
7791 AAACCTAAA-CCT
1 AAACCTAAACCCT
7803 AAACCTAAACC
1 AAACCTAAACC
7814 AAACCAAAAA
Statistics
Matches: 322, Mismatches: 36, Indels: 45
0.80 0.09 0.11
Matches are distributed among these distances:
11 8 0.02
12 63 0.20
13 132 0.41
14 101 0.31
15 18 0.06
ACGTcount: A:0.41, C:0.46, G:0.00, T:0.12
Consensus pattern (13 bp):
AAACCTAAACCCT
Found at i:7824 original size:12 final size:12
Alignment explanation
Indices: 7809--7833 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7799 ACCTAAACCT
7809 AAACCAAACCAA
1 AAACCAAACCAA
7821 AAACCAAACCAA
1 AAACCAAACCAA
7833 A
1 A
7834 CCAAAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (12 bp):
AAACCAAACCAA
Found at i:7829 original size:17 final size:18
Alignment explanation
Indices: 7768--7840 Score: 89
Period size: 18 Copynumber: 4.1 Consensus size: 18
7758 CCTAAACCCT
*
7768 AACCTAAACCTAAACC-TA
1 AACCTAAACC-AAACCAAA
*
7786 AACCTAAACCTAAACC-TA
1 AACCTAAACC-AAACCAAA
7804 AACCTAAACCAAACCAAA
1 AACCTAAACCAAACCAAA
7822 AACC-AAACCAAACCAAA
1 AACCTAAACCAAACCAAA
7839 AA
1 AA
7841 AAAAAAAAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
17 20 0.38
18 33 0.62
ACGTcount: A:0.58, C:0.33, G:0.00, T:0.10
Consensus pattern (18 bp):
AACCTAAACCAAACCAAA
Found at i:7951 original size:62 final size:61
Alignment explanation
Indices: 7853--7978 Score: 182
Period size: 62 Copynumber: 2.0 Consensus size: 61
7843 AAAAAAAAAA
* *
7853 TGGAAAACGCTCTCAACTCCCATGCCTTTCCCCCTCTCCCTAGCACTCATGGTTTGACGGC
1 TGGAAAACGCTATCAACTCCCATGCCTTTCCCCCTCTCCCAAGCACTCATGGTTTGACGGC
* * *
7914 NTGGAAAACGCTATCAACTCCCGTCGCC-TTCCTCCTCTCCCAAGCACTCATGGTTTGGCGGC
1 -TGGAAAACGCTATCAACTCCCAT-GCCTTTCCCCCTCTCCCAAGCACTCATGGTTTGACGGC
7976 TGG
1 TGG
7979 TCGACCTCCG
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
61 3 0.05
62 52 0.90
63 3 0.05
ACGTcount: A:0.17, C:0.37, G:0.19, T:0.25
Consensus pattern (61 bp):
TGGAAAACGCTATCAACTCCCATGCCTTTCCCCCTCTCCCAAGCACTCATGGTTTGACGGC
Found at i:14814 original size:7 final size:7
Alignment explanation
Indices: 14804--15258 Score: 399
Period size: 7 Copynumber: 65.7 Consensus size: 7
14794 AAAAAAAAAA
14804 AAACCCT
1 AAACCCT
14811 AAACCCT
1 AAACCCT
14818 -AACCCT
1 AAACCCT
14824 -AACCCT
1 AAACCCT
14830 AAACCCT
1 AAACCCT
14837 AAACCCT
1 AAACCCT
14844 AAACCCT
1 AAACCCT
14851 AAACCCT
1 AAACCCT
14858 AAACCCT
1 AAACCCT
14865 -AACCCT
1 AAACCCT
14871 AAACCCT
1 AAACCCT
14878 AAACCCT
1 AAACCCT
14885 AAACCCT
1 AAACCCT
*
14892 -AACCCA
1 AAACCCT
14898 AAACCCT
1 AAACCCT
14905 AAACCCT
1 AAACCCT
14912 AAACCCT
1 AAACCCT
*
14919 AACCCCT
1 AAACCCT
*
14926 AACCCCT
1 AAACCCT
14933 AAACCCT
1 AAACCCT
14940 AAACCCT
1 AAACCCT
* *
14947 GACCCCT
1 AAACCCT
* *
14954 GACCCCT
1 AAACCCT
* *
14961 GACCCCT
1 AAACCCT
* *
14968 GACCCCT
1 AAACCCT
*
14975 GAACCCT
1 AAACCCT
*
14982 GAACCCT
1 AAACCCT
*
14989 GAACCCT
1 AAACCCT
*
14996 GAACCCT
1 AAACCCT
* *
15003 GACCCCT
1 AAACCCT
*
15010 -GACCCTT
1 AAACCC-T
* * *
15017 GACCCCNC
1 AAACCC-T
* ****
15025 CAGGTTT
1 AAACCCT
****
15032 AAAAAAA
1 AAACCCT
****
15039 AAAAAAA
1 AAACCCT
****
15046 AAAAAAA
1 AAACCCT
15053 AAACCCT
1 AAACCCT
15060 -AACCCT
1 AAACCCT
15066 AAACCCT
1 AAACCCT
15073 AAACCCT
1 AAACCCT
*
15080 AACCCCT
1 AAACCCT
15087 -AACCCT
1 AAACCCT
15093 -AACCCT
1 AAACCCT
*
15099 AACCCCT
1 AAACCCT
15106 -AACCCT
1 AAACCCT
*
15112 AACCCCT
1 AAACCCT
15119 AAACCCT
1 AAACCCT
15126 AAA-CCT
1 AAACCCT
*
15132 AACCCCT
1 AAACCCT
15139 AAACCCT
1 AAACCCT
15146 AAACCCT
1 AAACCCT
15153 AAACCCT
1 AAACCCT
15160 AAACCCT
1 AAACCCT
15167 AAAACCCT
1 -AAACCCT
*
15175 AACCCCT
1 AAACCCT
15182 AAACCCCT
1 AAA-CCCT
*
15190 AACCCCT
1 AAACCCT
15197 AAACCCT
1 AAACCCT
15204 AAACCCT
1 AAACCCT
15211 AAACCCT
1 AAACCCT
15218 AAAACCCT
1 -AAACCCT
15226 AAACCCT
1 AAACCCT
15233 AAACCCT
1 AAACCCT
15240 AAACCCT
1 AAACCCT
15247 AAACCCT
1 AAACCCT
15254 AAACC
1 AAACC
15259 TAACTTAGTC
Statistics
Matches: 394, Mismatches: 42, Indels: 24
0.86 0.09 0.05
Matches are distributed among these distances:
6 53 0.13
7 317 0.80
8 24 0.06
ACGTcount: A:0.39, C:0.44, G:0.03, T:0.14
Consensus pattern (7 bp):
AAACCCT
Found at i:19953 original size:15 final size:15
Alignment explanation
Indices: 19933--19964 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
19923 TATTTACAGC
19933 TTCAGTAATTTAATT
1 TTCAGTAATTTAATT
19948 TTCAGTAATTTAATT
1 TTCAGTAATTTAATT
19963 TT
1 TT
19965 ATTCTGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.56
Consensus pattern (15 bp):
TTCAGTAATTTAATT
Found at i:20213 original size:7 final size:7
Alignment explanation
Indices: 20203--20659 Score: 478
Period size: 7 Copynumber: 65.3 Consensus size: 7
20193 AAAAAAAAAA
20203 AAACCCT
1 AAACCCT
*
20210 AAACCAT
1 AAACCCT
20217 AAACCCT
1 AAACCCT
20224 AAACCCT
1 AAACCCT
20231 AAACCCT
1 AAACCCT
*
20238 AACCCCT
1 AAACCCT
*
20245 AACCCCT
1 AAACCCT
*
20252 AAACCCA
1 AAACCCT
20259 AAACCCT
1 AAACCCT
*
20266 AACCCCT
1 AAACCCT
20273 -AACCC-
1 AAACCCT
* *
20278 CAACCCC
1 AAACCCT
*
20285 AAACCCC
1 AAACCCT
*
20292 AAACCCCA
1 AAA-CCCT
20300 AAACCC-
1 AAACCCT
*
20306 AAACCCC
1 AAACCCT
*
20313 AAACCCC
1 AAACCCT
20320 AAACCCCT
1 AAA-CCCT
20328 -AACCCT
1 AAACCCT
*
20334 AAACCCC
1 AAACCCT
*
20341 AAACCCC
1 AAACCCT
*
20348 AACCCCT
1 AAACCCT
*
20355 AACCCCT
1 AAACCCT
*
20362 AAACCCC
1 AAACCCT
*
20369 AAACCCC
1 AAACCCT
*
20376 AAACCCCA
1 AAA-CCCT
20384 AAACCC-
1 AAACCCT
*
20390 AAACCCC
1 AAACCCT
*
20397 AAACCCCA
1 AAA-CCCT
20405 AAACCC-
1 AAACCCT
*
20411 AAACCCC
1 AAACCCT
*
20418 AAACCCC
1 AAACCCT
*
20425 AAACCCC
1 AAACCCT
* *
20432 CAACCCC
1 AAACCCT
* *
20439 CAACCCC
1 AAACCCT
*
20446 AAACCCC
1 AAACCCT
* *
20453 CAACCCC
1 AAACCCT
* *
20460 CAACCCC
1 AAACCCT
*
20467 AAACCCCA
1 AAA-CCCT
20475 AAACCCT
1 AAACCCT
20482 -AACCCT
1 AAACCCT
*
20488 AAACCCC
1 AAACCCT
20495 AAACCCT
1 AAACCCT
*
20502 AACCCCT
1 AAACCCT
20509 AAACCCT
1 AAACCCT
20516 AAACCCT
1 AAACCCT
20523 AAACCCT
1 AAACCCT
20530 AAACCCT
1 AAACCCT
20537 AAACCCT
1 AAACCCT
20544 AAACCCT
1 AAACCCT
20551 AAACCCT
1 AAACCCT
20558 AAACCCT
1 AAACCCT
20565 AAACCCT
1 AAACCCT
20572 AAACCCT
1 AAACCCT
20579 AAACCCT
1 AAACCCT
20586 AAACCCT
1 AAACCCT
20593 AAACCCT
1 AAACCCT
20600 AAACCCT
1 AAACCCT
20607 AAACCCT
1 AAACCCT
20614 AAACCCT
1 AAACCCT
20621 ANAAACCCT
1 --AAACCCT
20630 AAACCCT
1 AAACCCT
*
20637 AAACCCC
1 AAACCCT
20644 AAACCCT
1 AAACCCT
20651 AAACCCT
1 AAACCCT
20658 AA
1 AA
20660 CCCAAAAAAA
Statistics
Matches: 406, Mismatches: 30, Indels: 28
0.88 0.06 0.06
Matches are distributed among these distances:
6 37 0.09
7 335 0.83
8 27 0.07
9 7 0.02
ACGTcount: A:0.42, C:0.50, G:0.00, T:0.08
Consensus pattern (7 bp):
AAACCCT
Found at i:36978 original size:7 final size:7
Alignment explanation
Indices: 36966--37021 Score: 78
Period size: 7 Copynumber: 8.1 Consensus size: 7
36956 NNNNNNNNNN
36966 CCCTAAC
1 CCCTAAC
36973 CCCTAAC
1 CCCTAAC
36980 CCCTAA-
1 CCCTAAC
36986 CCCTAAC
1 CCCTAAC
*
36993 CCCTAAA
1 CCCTAAC
*
37000 CCCTAAA
1 CCCTAAC
37007 CCCTAAC
1 CCCTAAC
*
37014 CCTTAAC
1 CCCTAAC
37021 C
1 C
37022 TTAACCTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
6 6 0.13
7 39 0.87
ACGTcount: A:0.32, C:0.52, G:0.00, T:0.16
Consensus pattern (7 bp):
CCCTAAC
Found at i:36991 original size:13 final size:13
Alignment explanation
Indices: 36966--37039 Score: 78
Period size: 13 Copynumber: 5.5 Consensus size: 13
36956 NNNNNNNNNN
36966 CCCTAACCCCTAAC
1 CCCTAA-CCCTAAC
36980 CCCTAACCCTAAC
1 CCCTAACCCTAAC
*
36993 CCCTAAACCCTAAA
1 CCCT-AACCCTAAC
37007 CCCTAACCCTTAA-
1 CCCTAACCC-TAAC
* *
37020 CCTTAACCTTAAC
1 CCCTAACCCTAAC
*
37033 CCTTAAC
1 CCCTAAC
37040 TTAACCTTAA
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
12 3 0.06
13 30 0.56
14 21 0.39
ACGTcount: A:0.32, C:0.47, G:0.00, T:0.20
Consensus pattern (13 bp):
CCCTAACCCTAAC
Found at i:37036 original size:7 final size:6
Alignment explanation
Indices: 37014--37101 Score: 142
Period size: 6 Copynumber: 14.3 Consensus size: 6
37004 AAACCCTAAC
37014 CCTTAA CCTTAA CCTTAA CCCTTAA -CTTAA CCTTAA CCTTAA CCTTAA
1 CCTTAA CCTTAA CCTTAA -CCTTAA CCTTAA CCTTAA CCTTAA CCTTAA
37062 CCTTAA CCTTAA CCTTAAA CCTTAA CCCTTAA CCTTAA CC
1 CCTTAA CCTTAA CCTT-AA CCTTAA -CCTTAA CCTTAA CC
37102 ACCAAAAAAC
Statistics
Matches: 78, Mismatches: 0, Indels: 8
0.91 0.00 0.09
Matches are distributed among these distances:
5 5 0.06
6 55 0.71
7 18 0.23
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.32
Consensus pattern (6 bp):
CCTTAA
Found at i:44432 original size:7 final size:7
Alignment explanation
Indices: 44422--44825 Score: 399
Period size: 7 Copynumber: 58.3 Consensus size: 7
44412 AAAAAAAAAA
44422 AAACCCT
1 AAACCCT
44429 AAACCCT
1 AAACCCT
*
44436 TAACCCT
1 AAACCCT
44443 AAACCCT
1 AAACCCT
44450 AAACCCT
1 AAACCCT
44457 AAAAAACCCT
1 ---AAACCCT
*
44467 AAA---A
1 AAACCCT
44471 AAACCCT
1 AAACCCT
44478 AAACCCT
1 AAACCCT
44485 AAACCCCT
1 AAA-CCCT
44493 AAACCCT
1 AAACCCT
*
44500 CAACCCT
1 AAACCCT
*
44507 AACCCCT
1 AAACCCT
*
44514 AACCCCT
1 AAACCCT
44521 AAACCC-
1 AAACCCT
44527 AAACCCCT
1 AAA-CCCT
44535 AAACCCCCT
1 AAA--CCCT
*
44544 TAACCCT
1 AAACCCT
*
44551 AACCCCT
1 AAACCCT
*
44558 -AACCCC
1 AAACCCT
44564 AAACCCCT
1 AAA-CCCT
44572 -AACCCT
1 AAACCCT
*
44578 AACCCCT
1 AAACCCT
44585 AAACCCCT
1 AAA-CCCT
44593 AAAACCCT
1 -AAACCCT
*
44601 AACCCCT
1 AAACCCT
44608 AAACCCT
1 AAACCCT
44615 AAACCCT
1 AAACCCT
44622 AAACCCT
1 AAACCCT
*
44629 AAAACCT
1 AAACCCT
44636 AAACCCT
1 AAACCCT
44643 AAACCCT
1 AAACCCT
44650 -AACCCT
1 AAACCCT
*
44656 AACCCCT
1 AAACCCT
*
44663 AACCCCT
1 AAACCCT
* *
44670 AACCCCA
1 AAACCCT
*
44677 AAACCCA
1 AAACCCT
44684 AAACCCT
1 AAACCCT
*
44691 AACCCCT
1 AAACCCT
*
44698 AACCCCT
1 AAACCCT
44705 AAA-CCT
1 AAACCCT
44711 AAACCCT
1 AAACCCT
44718 AAACCCT
1 AAACCCT
44725 -AACCCT
1 AAACCCT
44731 AAA-CCT
1 AAACCCT
44737 -AACCCT
1 AAACCCT
*
44743 AACCCCT
1 AAACCCT
44750 -AACCCT
1 AAACCCT
44756 -AACCCT
1 AAACCCT
44762 AAACCCT
1 AAACCCT
44769 AAACCCT
1 AAACCCT
*
44776 AACCCCT
1 AAACCCT
44783 -AACCCT
1 AAACCCT
44789 AAACCCCT
1 AAA-CCCT
44797 -AA-CCT
1 AAACCCT
*
44802 AACCCCT
1 AAACCCT
44809 AAAACCCT
1 -AAACCCT
44817 AAACCCT
1 AAACCCT
44824 AA
1 AA
44826 NNNNNNNNNN
Statistics
Matches: 339, Mismatches: 32, Indels: 52
0.80 0.08 0.12
Matches are distributed among these distances:
4 3 0.01
5 5 0.01
6 52 0.15
7 231 0.68
8 31 0.09
9 10 0.03
10 7 0.02
ACGTcount: A:0.40, C:0.47, G:0.00, T:0.14
Consensus pattern (7 bp):
AAACCCT
Found at i:44465 original size:10 final size:10
Alignment explanation
Indices: 44450--44480 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
44440 CCTAAACCCT
44450 AAACCCTAAA
1 AAACCCTAAA
44460 AAACCCTAAAA
1 AAACCCT-AAA
44471 AAACCCTAAA
1 AAACCCTAAA
44481 CCCTAAACCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.61, C:0.29, G:0.00, T:0.10
Consensus pattern (10 bp):
AAACCCTAAA
Found at i:44473 original size:11 final size:11
Alignment explanation
Indices: 44450--44480 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
44440 CCTAAACCCT
44450 AAACCCT-AAA
1 AAACCCTAAAA
44460 AAACCCTAAAA
1 AAACCCTAAAA
44471 AAACCCTAAA
1 AAACCCTAAA
44481 CCCTAAACCC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.35
11 13 0.65
ACGTcount: A:0.61, C:0.29, G:0.00, T:0.10
Consensus pattern (11 bp):
AAACCCTAAAA
Found at i:45178 original size:7 final size:7
Alignment explanation
Indices: 45073--45205 Score: 166
Period size: 7 Copynumber: 19.4 Consensus size: 7
45063 NNNNNNNNNN
*
45073 CCCTAAC
1 CCCTAAA
*
45080 CCCTAAC
1 CCCTAAA
45087 CCCTAAA
1 CCCTAAA
45094 CCCTAAA
1 CCCTAAA
*
45101 CCCTAAC
1 CCCTAAA
*
45108 CCCTAAC
1 CCCTAAA
*
45115 CCCTAAC
1 CCCTAAA
45122 CCCTAAA
1 CCCTAAA
45129 CCCCTAAA
1 -CCCTAAA
*
45137 CCCCAAA
1 CCCTAAA
*
45144 CCCCAAA
1 CCCTAAA
45151 CCCTAAA
1 CCCTAAA
45158 CCCTAAA
1 CCCTAAA
45165 CCCTAAA
1 CCCTAAA
45172 CCCTAAA
1 CCCTAAA
45179 CCC-AAA
1 CCCTAAA
45185 --C-AAA
1 CCCTAAA
45189 CCCTAAA
1 CCCTAAA
45196 CCCTAAA
1 CCCTAAA
45203 CCC
1 CCC
45206 AAAAAAAAAA
Statistics
Matches: 117, Mismatches: 5, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
4 4 0.03
6 4 0.03
7 102 0.87
8 7 0.06
ACGTcount: A:0.39, C:0.50, G:0.00, T:0.11
Consensus pattern (7 bp):
CCCTAAA
Found at i:45212 original size:1 final size:1
Alignment explanation
Indices: 45206--45232 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
45196 CCCTAAACCC
45206 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
45233 CGGAAAACTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:56786 original size:7 final size:7
Alignment explanation
Indices: 56776--57294 Score: 513
Period size: 7 Copynumber: 75.1 Consensus size: 7
56766 AAAAAAAAAA
56776 AAACCCT
1 AAACCCT
56783 AAACCCT
1 AAACCCT
*
56790 TAACCCT
1 AAACCCT
56797 AAACCCT
1 AAACCCT
56804 AAACCCT
1 AAACCCT
56811 AAAAAACCCT
1 ---AAACCCT
*
56821 AAA---A
1 AAACCCT
56825 AAACCCT
1 AAACCCT
56832 AAACCCT
1 AAACCCT
56839 AAACCCCT
1 AAA-CCCT
56847 AAACCCT
1 AAACCCT
*
56854 CAACCCT
1 AAACCCT
*
56861 AACCCCT
1 AAACCCT
*
56868 AACCCCT
1 AAACCCT
56875 AAACCC-
1 AAACCCT
56881 AAACCCCT
1 AAA-CCCT
56889 AAACCCCCT
1 AAA--CCCT
*
56898 TAACCCT
1 AAACCCT
*
56905 AACCCCT
1 AAACCCT
*
56912 -AACCCC
1 AAACCCT
56918 AAACCCCT
1 AAA-CCCT
56926 -AACCCT
1 AAACCCT
*
56932 AACCCCT
1 AAACCCT
56939 AAACCCCT
1 AAA-CCCT
56947 AAAACCCT
1 -AAACCCT
*
56955 AACCCCT
1 AAACCCT
56962 AAACCCT
1 AAACCCT
56969 AAACCCT
1 AAACCCT
56976 AAACCCT
1 AAACCCT
*
56983 AAAACCT
1 AAACCCT
56990 AAACCCT
1 AAACCCT
56997 AAACCCT
1 AAACCCT
57004 -AACCCT
1 AAACCCT
*
57010 AACCCCT
1 AAACCCT
*
57017 AACCCCT
1 AAACCCT
* *
57024 AACCCCA
1 AAACCCT
*
57031 AAACCCA
1 AAACCCT
57038 AAACCCT
1 AAACCCT
*
57045 AACCCCT
1 AAACCCT
*
57052 AACCCCT
1 AAACCCT
57059 AAA-CCT
1 AAACCCT
57065 AAACCCT
1 AAACCCT
57072 AAACCCT
1 AAACCCT
57079 -AACCCT
1 AAACCCT
57085 AAA-CCT
1 AAACCCT
57091 -AACCCT
1 AAACCCT
*
57097 AACCCCT
1 AAACCCT
57104 -AACCCT
1 AAACCCT
57110 -AACCCT
1 AAACCCT
57116 AAACCCT
1 AAACCCT
57123 AAACCCT
1 AAACCCT
*
57130 AACCCCT
1 AAACCCT
57137 -AACCCT
1 AAACCCT
57143 AAACCCCT
1 AAA-CCCT
57151 -AA-CCT
1 AAACCCT
*
57156 AACCCCT
1 AAACCCT
57163 AAAACCCT
1 -AAACCCT
57171 AAACCCT
1 AAACCCT
*
57178 -AA--NT
1 AAACCCT
57182 AAACCC-
1 AAACCCT
*
57188 AAACCCCC
1 AAA-CCCT
*
57196 AAACCCC
1 AAACCCT
*
57203 AAACCCC
1 AAACCCT
*
57210 AAACCCCA
1 AAA-CCCT
57218 AAACCCT
1 AAACCCT
57225 AAACCCT
1 AAACCCT
57232 AAACCCT
1 AAACCCT
57239 AAACCCT
1 AAACCCT
57246 AAACCCT
1 AAACCCT
57253 -AACCCT
1 AAACCCT
57259 AAACCCT
1 AAACCCT
57266 AAACCCT
1 AAACCCT
57273 AAACCCT
1 AAACCCT
*
57280 AAACCTT
1 AAACCCT
*
57287 AAGCCCT
1 AAACCCT
57294 A
1 A
57295 CATTATTGAA
Statistics
Matches: 440, Mismatches: 39, Indels: 66
0.81 0.07 0.12
Matches are distributed among these distances:
4 4 0.01
5 7 0.02
6 63 0.14
7 309 0.70
8 40 0.09
9 10 0.02
10 7 0.02
ACGTcount: A:0.40, C:0.46, G:0.00, T:0.13
Consensus pattern (7 bp):
AAACCCT
Found at i:56819 original size:10 final size:10
Alignment explanation
Indices: 56804--56834 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
56794 CCTAAACCCT
56804 AAACCCTAAA
1 AAACCCTAAA
56814 AAACCCTAAAA
1 AAACCCT-AAA
56825 AAACCCTAAA
1 AAACCCTAAA
56835 CCCTAAACCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.61, C:0.29, G:0.00, T:0.10
Consensus pattern (10 bp):
AAACCCTAAA
Found at i:56827 original size:11 final size:11
Alignment explanation
Indices: 56804--56834 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
56794 CCTAAACCCT
56804 AAACCCT-AAA
1 AAACCCTAAAA
56814 AAACCCTAAAA
1 AAACCCTAAAA
56825 AAACCCTAAA
1 AAACCCTAAA
56835 CCCTAAACCC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.35
11 13 0.65
ACGTcount: A:0.61, C:0.29, G:0.00, T:0.10
Consensus pattern (11 bp):
AAACCCTAAAA
Found at i:73331 original size:35 final size:34
Alignment explanation
Indices: 73268--73400 Score: 90
Period size: 35 Copynumber: 3.9 Consensus size: 34
73258 TTCCACCAAG
* *
73268 CTTTTACAATGGCTTTTCATAGGCTCAACCACAA
1 CTTTTACAATGGCTTTTCACAGGATCAACCACAA
* * *
73302 CTTTTAACAATGGTTTTTCACGGGATCAACCAAAA
1 CTTTT-ACAATGGCTTTTCACAGGATCAACCACAA
** * * * **
73337 C--CCAAAATGGCTTTTCACAGGCTTAGTCACAA
1 CTTTTACAATGGCTTTTCACAGGATCAACCACAA
* * * *
73369 CATTTAATAATGGTTTTTCTCAGGATCAACCA
1 C-TTTTACAATGGCTTTTCACAGGATCAACCA
73401 AAACCCAAAA
Statistics
Matches: 71, Mismatches: 24, Indels: 7
0.70 0.24 0.07
Matches are distributed among these distances:
32 22 0.31
34 5 0.07
35 44 0.62
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.32
Consensus pattern (34 bp):
CTTTTACAATGGCTTTTCACAGGATCAACCACAA
Found at i:73359 original size:67 final size:67
Alignment explanation
Indices: 73275--73410 Score: 200
Period size: 67 Copynumber: 2.0 Consensus size: 67
73265 AAGCTTTTAC
* * *
73275 AATGGCTTTTCATAGGCTCAACCACAACTTTTAACAATGGTTTTTCACGGGATCAACCAAAACCC
1 AATGGCTTTTCACAGGCTCAACCACAACATTTAACAATGGTTTTTCACAGGATCAACCAAAACCC
73340 AA
66 AA
* ** * *
73342 AATGGCTTTTCACAGGCTTAGTCACAACATTTAATAATGGTTTTTCTCAGGATCAACCAAAACCC
1 AATGGCTTTTCACAGGCTCAACCACAACATTTAACAATGGTTTTTCACAGGATCAACCAAAACCC
73407 AA
66 AA
73409 AA
1 AA
73411 CTAACTTTTC
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
67 61 1.00
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.28
Consensus pattern (67 bp):
AATGGCTTTTCACAGGCTCAACCACAACATTTAACAATGGTTTTTCACAGGATCAACCAAAACCC
AA
Found at i:73892 original size:73 final size:73
Alignment explanation
Indices: 73802--74008 Score: 288
Period size: 73 Copynumber: 2.8 Consensus size: 73
73792 TTCTAAGATA
*
73802 GTGAGCTTTTAGTTGGCTAATCATTCTTCTTAGTCGATTAAGTCTTTTTTGTCTCGCAATCAAAT
1 GTGAGCTTTTAGCTGGCTAATCATTCTTCTTAGTCGATTAAGTCTTTTTTGTCTCGCAATCAAAT
*
73867 TTTTTATT
66 TTTTTATC
* * * **
73875 GTGAGCTTTTAACTGGCTAACCATTCTTCTTAGTTGATTAAGTCTTTTTTGTCTTACAATCAAAT
1 GTGAGCTTTTAGCTGGCTAATCATTCTTCTTAGTCGATTAAGTCTTTTTTGTCTCGCAATCAAAT
73940 TTTTTATC
66 TTTTTATC
** * * * * *
73948 GTGATTTTTTAGCTAGCTAATCATACTTTTTAGTCAATTAAGTCTTATTTGTCTCGCAATC
1 GTGAGCTTTTAGCTGGCTAATCATTCTTCTTAGTCGATTAAGTCTTTTTTGTCTCGCAATC
74009 TGCTTTACTC
Statistics
Matches: 115, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
73 115 1.00
ACGTcount: A:0.23, C:0.16, G:0.14, T:0.48
Consensus pattern (73 bp):
GTGAGCTTTTAGCTGGCTAATCATTCTTCTTAGTCGATTAAGTCTTTTTTGTCTCGCAATCAAAT
TTTTTATC
Found at i:78103 original size:2 final size:2
Alignment explanation
Indices: 78096--78184 Score: 128
Period size: 2 Copynumber: 44.0 Consensus size: 2
78086 GTCATTCAAT
*
78096 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA NT- TG TCA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA T-A
78139 T- TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
78181 TA TA
1 TA TA
78185 GACACACACA
Statistics
Matches: 81, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
1 2 0.02
2 76 0.94
3 3 0.04
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:81060 original size:59 final size:59
Alignment explanation
Indices: 80976--81088 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 59
80966 AGGGTGATTT
* * * *
80976 TTATTAAATATTTAGGAAGCTTTTATTATGTAAGATGAATATTTGTAGAATGATTTTAA
1 TTATTAAATATGTAGGAAGCCTTTATTATCTAAGATAAATATTTGTAGAATGATTTTAA
* * * *
81035 TTATTATATATGTAGGATGCCTTTATTATCTAGGATAAATATTTGTATAATGAT
1 TTATTAAATATGTAGGAAGCCTTTATTATCTAAGATAAATATTTGTAGAATGAT
81089 AATTTTTGTG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
59 46 1.00
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.46
Consensus pattern (59 bp):
TTATTAAATATGTAGGAAGCCTTTATTATCTAAGATAAATATTTGTAGAATGATTTTAA
Found at i:92785 original size:17 final size:19
Alignment explanation
Indices: 92763--92799 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
92753 TTTAAAACAC
92763 ATACAC-GT-ATACGTTTA
1 ATACACAGTAATACGTTTA
92780 ATACACATGTAATACGTTTA
1 ATACACA-GTAATACGTTTA
92800 TTAAATGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.35
19 2 0.12
20 9 0.53
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (19 bp):
ATACACAGTAATACGTTTA
Found at i:92848 original size:9 final size:9
Alignment explanation
Indices: 92834--92890 Score: 60
Period size: 9 Copynumber: 6.3 Consensus size: 9
92824 ACAGGATTAA
*
92834 TAACATGTT
1 TAACACGTT
* *
92843 TAACATGAT
1 TAACACGTT
*
92852 TAATACGTT
1 TAACACGTT
*
92861 TAACACGAT
1 TAACACGTT
92870 TAACACGTT
1 TAACACGTT
*
92879 TAACACGAT
1 TAACACGTT
92888 TAA
1 TAA
92891 ATAAAAATAT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 40 1.00
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (9 bp):
TAACACGTT
Found at i:92863 original size:18 final size:18
Alignment explanation
Indices: 92834--92890 Score: 87
Period size: 18 Copynumber: 3.2 Consensus size: 18
92824 ACAGGATTAA
* *
92834 TAACATGTTTAACATGAT
1 TAACACGTTTAACACGAT
*
92852 TAATACGTTTAACACGAT
1 TAACACGTTTAACACGAT
92870 TAACACGTTTAACACGAT
1 TAACACGTTTAACACGAT
92888 TAA
1 TAA
92891 ATAAAAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (18 bp):
TAACACGTTTAACACGAT
Found at i:97225 original size:30 final size:28
Alignment explanation
Indices: 97193--97249 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
97183 AATGTCATGG
*
97193 TGGT-GTAAAATTACAATTTTGCCACTA
1 TGGTGGTAAAATTACAATTTTACCACTA
* *
97220 TGGTGGTAAAATTACCATTTTACCCCTA
1 TGGTGGTAAAATTACAATTTTACCACTA
97248 TG
1 TG
97250 CTTTGAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 4 0.15
28 22 0.85
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.37
Consensus pattern (28 bp):
TGGTGGTAAAATTACAATTTTACCACTA
Found at i:102165 original size:28 final size:29
Alignment explanation
Indices: 102124--102183 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
102114 GTCTATGGGC
*
102124 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
102152 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
102182 AA
1 AA
102184 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:109796 original size:11 final size:11
Alignment explanation
Indices: 109780--109804 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
109770 GAGCCTTTGA
109780 AGATGGACTGG
1 AGATGGACTGG
109791 AGATGGACTGG
1 AGATGGACTGG
109802 AGA
1 AGA
109805 AGAGAAAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.08, G:0.44, T:0.16
Consensus pattern (11 bp):
AGATGGACTGG
Found at i:110821 original size:20 final size:20
Alignment explanation
Indices: 110793--110831 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
110783 CCAACTTGAT
* *
110793 AAATGGATATTTAAAAAGAA
1 AAATAGATACTTAAAAAGAA
110813 AAATAGATACTTAAAAAGA
1 AAATAGATACTTAAAAAGA
110832 GAACACTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.03, G:0.13, T:0.23
Consensus pattern (20 bp):
AAATAGATACTTAAAAAGAA
Found at i:119981 original size:10 final size:10
Alignment explanation
Indices: 119966--119994 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
119956 TTTGTAATTT
119966 AAAAATTAAA
1 AAAAATTAAA
119976 AAAAATT-AA
1 AAAAATTAAA
119985 AAAAATTAAA
1 AAAAATTAAA
119995 GAAACCCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
AAAAATTAAA
Found at i:133432 original size:35 final size:35
Alignment explanation
Indices: 133393--133481 Score: 110
Period size: 35 Copynumber: 2.5 Consensus size: 35
133383 GAATAATAAG
** *
133393 AACAATTATTACAAGTGAAGCTT-TACTTTA-AGCAA
1 AACAATTAGAACAAGTGAAG-TTATACTTCACA-CAA
133428 AACAATTAGAACAAGTGAAGTTATACTTCACACAA
1 AACAATTAGAACAAGTGAAGTTATACTTCACACAA
*
133463 AACAATTAGAATAAGTGAA
1 AACAATTAGAACAAGTGAA
133482 ACACTACTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
34 2 0.04
35 45 0.94
36 1 0.02
ACGTcount: A:0.48, C:0.13, G:0.12, T:0.26
Consensus pattern (35 bp):
AACAATTAGAACAAGTGAAGTTATACTTCACACAA
Found at i:133490 original size:35 final size:35
Alignment explanation
Indices: 133425--133493 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
133415 TTACTTTAAG
**
133425 CAAAACAATTAGAACAAGTGAAGTTATACTTCACA
1 CAAAACAATTAGAACAAGTGAAGACATACTTCACA
*
133460 CAAAACAATTAGAATAAGTGAA-ACACTACTTCAC
1 CAAAACAATTAGAACAAGTGAAGACA-TACTTCAC
133494 GCGAAATAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 1 0.03
35 29 0.97
ACGTcount: A:0.49, C:0.19, G:0.10, T:0.22
Consensus pattern (35 bp):
CAAAACAATTAGAACAAGTGAAGACATACTTCACA
Found at i:144801 original size:24 final size:24
Alignment explanation
Indices: 144768--144827 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
144758 AATAAGCAAA
144768 CTATCCAAAAGTGTAGATACCAACT
1 CTAT-CAAAAGTGTAGATACCAACT
144793 CTATCAAAAGTGTAGATACCAACT
1 CTATCAAAAGTGTAGATACCAACT
144817 CTATCAAAAGT
1 CTATCAAAAGT
144828 TGGGACAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 31 0.89
25 4 0.11
ACGTcount: A:0.42, C:0.22, G:0.12, T:0.25
Consensus pattern (24 bp):
CTATCAAAAGTGTAGATACCAACT
Found at i:156317 original size:9 final size:9
Alignment explanation
Indices: 156300--156334 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
156290 CATATATAAG
*
156300 TTCCTCATA
1 TTCCCCATA
156309 TTCCCCATA
1 TTCCCCATA
*
156318 TTCCCCATG
1 TTCCCCATA
156327 TTCCCCAT
1 TTCCCCAT
156335 TACTAGCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.17, C:0.43, G:0.03, T:0.37
Consensus pattern (9 bp):
TTCCCCATA
Found at i:159904 original size:2 final size:2
Alignment explanation
Indices: 159899--159928 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
159889 ACACACACAC
159899 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
159929 NNNNNNNNNN
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:160031 original size:2 final size:2
Alignment explanation
Indices: 160024--160076 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
160014 NNNNNNNNNN
160024 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
160066 TA TA TA TA TA T
1 TA TA TA TA TA T
160077 TCCATAGCTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:173858 original size:49 final size:49
Alignment explanation
Indices: 173755--173869 Score: 131
Period size: 49 Copynumber: 2.3 Consensus size: 49
173745 TCGTTTAAAG
* * * * * *
173755 AGTCTTATGACTTAATCTTGAATGAACGATTTAGAGATTTTACTACAAG
1 AGTCTTATGACTTGATATCGAATGAACGATTTAGAGACTTCACTACAAA
* * * *
173804 GGTCTTATGACTTGATATCGAATGAATGATTTAGAGACTTCGCTCCAAA
1 AGTCTTATGACTTGATATCGAATGAACGATTTAGAGACTTCACTACAAA
173853 AGTCTTTATGACTTGAT
1 AGTC-TTATGACTTGAT
173870 CTTGAACAAA
Statistics
Matches: 54, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
49 42 0.78
50 12 0.22
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (49 bp):
AGTCTTATGACTTGATATCGAATGAACGATTTAGAGACTTCACTACAAA
Found at i:173974 original size:48 final size:47
Alignment explanation
Indices: 173922--174132 Score: 155
Period size: 48 Copynumber: 4.4 Consensus size: 47
173912 TTTGGAACAA
*
173922 CTTTGATTCTTCAGATCTTTTTCTTGGATTTGTGGAAATTTGGAAAGG
1 CTTTGATTCTTCAGATCTTTTTCTTGGATTTGTGGAACTTT-GAAAGG
* * **
173970 CTTTG-GTCTTTAGAT-TTTCCTTCTTGGATTTGTAGG-ACTCTAAAAAGG
1 CTTTGATTCTTCAGATCTTT--TTCTTGGATTTGT-GGAACT-TTGAAAGG
* *
174018 CTTTGGTTCTTCAAATCTTTTTTCTT-GACTTTGTGGAACTTTGAAGAGG
1 CTTTGATTCTTCAGATC-TTTTTCTTGGA-TTTGTGGAACTTTGAA-AGG
* * * * *
174067 CTTT-AGTTTTTCATATC-CTTTCTTGGATTTGTGGAACTCTAGAAGGG
1 CTTTGA-TTCTTCAGATCTTTTTCTTGGATTTGTGGAACT-TTGAAAGG
* * *
174114 CTTTGGTTTTTCAAATCTT
1 CTTTGATTCTTCAGATCTT
174133 CCTTCTAGAG
Statistics
Matches: 129, Mismatches: 19, Indels: 30
0.72 0.11 0.17
Matches are distributed among these distances:
46 3 0.02
47 41 0.32
48 43 0.33
49 39 0.30
51 3 0.02
ACGTcount: A:0.19, C:0.14, G:0.20, T:0.46
Consensus pattern (47 bp):
CTTTGATTCTTCAGATCTTTTTCTTGGATTTGTGGAACTTTGAAAGG
Found at i:174090 original size:96 final size:97
Alignment explanation
Indices: 173922--174132 Score: 254
Period size: 96 Copynumber: 2.2 Consensus size: 97
173912 TTTGGAACAA
* * * *
173922 CTTTGATTCTTCAGATC-TTTTTCTTGGATTTGTGGAAATTTGGAAAGGCTTTGGTCTTTAGATT
1 CTTTGGTTCTTCAAATCTTTTTTCTTGGATTTGTGGAAATTTGGAAAGGCTTTAGTCTTTACATT
*
173986 TTCCTTCTTGGATTTGTAGG-ACTCTAAAAAGG
66 ATCCTTCTTGGATTTGT-GGAACTCTAAAAAGG
* *
174018 CTTTGGTTCTTCAAATCTTTTTTCTT-GACTTTGTGGAACTTT-GAAGAGGCTTTAGT-TTTTCA
1 CTTTGGTTCTTCAAATCTTTTTTCTTGGA-TTTGTGGAAATTTGGAA-AGGCTTTAGTCTTTACA
* *
174080 -TATCCTTTCTTGGATTTGTGGAACTCTAGAAGGG
64 TTATCC-TTCTTGGATTTGTGGAACTCTAAAAAGG
*
174114 CTTTGGTTTTTCAAATCTT
1 CTTTGGTTCTTCAAATCTT
174133 CCTTCTAGAG
Statistics
Matches: 100, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
95 6 0.06
96 65 0.65
97 29 0.29
ACGTcount: A:0.19, C:0.14, G:0.20, T:0.46
Consensus pattern (97 bp):
CTTTGGTTCTTCAAATCTTTTTTCTTGGATTTGTGGAAATTTGGAAAGGCTTTAGTCTTTACATT
ATCCTTCTTGGATTTGTGGAACTCTAAAAAGG
Found at i:176019 original size:58 final size:58
Alignment explanation
Indices: 175952--176064 Score: 163
Period size: 58 Copynumber: 1.9 Consensus size: 58
175942 GCATATGGTG
**
175952 ATACATACCTTAATATGTCTTGTCATACCAATGAAAATTACATGCCTTGCATGTCTCA
1 ATACATACCTTAATATGTCTCATCATACCAATGAAAATTACATGCCTTGCATGTCTCA
* * * **
176010 ATACATACCTTAGTATGTCTCATTATACCATTGTGAATTACATGCCTTGCATGTC
1 ATACATACCTTAATATGTCTCATCATACCAATGAAAATTACATGCCTTGCATGTC
176065 CTGATATATA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
58 48 1.00
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (58 bp):
ATACATACCTTAATATGTCTCATCATACCAATGAAAATTACATGCCTTGCATGTCTCA
Found at i:176020 original size:21 final size:22
Alignment explanation
Indices: 175990--176031 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
175980 CAATGAAAAT
*
175990 TACATGCCTT-GCATGTCTCAA
1 TACATACCTTAGCATGTCTCAA
*
176011 TACATACCTTAGTATGTCTCA
1 TACATACCTTAGCATGTCTCA
176032 TTATACCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.36
Consensus pattern (22 bp):
TACATACCTTAGCATGTCTCAA
Found at i:176534 original size:29 final size:29
Alignment explanation
Indices: 176471--176532 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
176461 ACTAAATGGA
* * *
176471 GTTTCCTTGATTCCATTCTTTTGAGTAAG
1 GTTTTCTTGATTCCATTCTTTTAAATAAG
*
176500 GTTTTCTTGTTTCCATTCTTTTAAAT-AG
1 GTTTTCTTGATTCCATTCTTTTAAATAAG
176528 GTTTT
1 GTTTT
176533 TCCTAATTCC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 7 0.24
29 22 0.76
ACGTcount: A:0.16, C:0.15, G:0.15, T:0.55
Consensus pattern (29 bp):
GTTTTCTTGATTCCATTCTTTTAAATAAG
Found at i:181330 original size:21 final size:21
Alignment explanation
Indices: 181304--181347 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
181294 CGGCTCTGTC
181304 ACCTTTAGTTAAATAATTGAG
1 ACCTTTAGTTAAATAATTGAG
181325 ACCTTTAGTTAAATAATTGAG
1 ACCTTTAGTTAAATAATTGAG
181346 AC
1 AC
181348 ACATAAGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (21 bp):
ACCTTTAGTTAAATAATTGAG
Found at i:199089 original size:37 final size:37
Alignment explanation
Indices: 199009--199107 Score: 119
Period size: 37 Copynumber: 2.7 Consensus size: 37
198999 ACTTTTGACA
*
199009 CATGCCACTAGGATTAATTGTGGTTCTAATTCTGACT
1 CATGCCACTAGGATTAATTGTGGTTCTAATTCTAACT
* * * *
199046 CGTGCCACTGGGGTTAATTGTGGTTCTGATTCTAAGCT
1 CATGCCACTAGGATTAATTGTGGTTCTAATTCTAA-CT
* *
199084 -ATGCCACAAGGATTAAATGTGGTT
1 CATGCCACTAGGATTAATTGTGGTT
199108 GTAGCATGTT
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
37 49 0.96
38 2 0.04
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (37 bp):
CATGCCACTAGGATTAATTGTGGTTCTAATTCTAACT
Found at i:212862 original size:66 final size:66
Alignment explanation
Indices: 212779--212906 Score: 213
Period size: 66 Copynumber: 1.9 Consensus size: 66
212769 AATTATATTA
*
212779 TCCATGAAAATCAGTCCTTAAAAAGAAAATATTTCTACTT-TTTGGAGAAAACAATTGTAAATAT
1 TCCATGAAAATCAGTCCTTAAAAAGAAAATATTTCTA-TTGTTTGGAGAAAACAATGGTAAATAT
212843 AT
65 AT
* *
212845 TCCATGAAAGTCAGTCCTTAAAAAGAAAATATTTCTATTGTTTGGAGAAATCAATGGTAAAT
1 TCCATGAAAATCAGTCCTTAAAAAGAAAATATTTCTATTGTTTGGAGAAAACAATGGTAAAT
212907 TTTTCCTTTG
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
65 2 0.03
66 56 0.97
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (66 bp):
TCCATGAAAATCAGTCCTTAAAAAGAAAATATTTCTATTGTTTGGAGAAAACAATGGTAAATATA
T
Found at i:219821 original size:2 final size:2
Alignment explanation
Indices: 219814--219838 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
219804 TAAAAGACTA
219814 GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT G
219839 AGAGAGAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:219843 original size:2 final size:2
Alignment explanation
Indices: 219838--219865 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
219828 GTGTGTGTGT
219838 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
219866 AGAAGTAGTT
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):
GA
Found at i:219896 original size:2 final size:2
Alignment explanation
Indices: 219889--219913 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
219879 AAAGTAAGTA
219889 GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT G
219914 AGAGAGAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:219918 original size:2 final size:2
Alignment explanation
Indices: 219913--219942 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
219903 GTGTGTGTGT
219913 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
219943 AAGAATTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:245742 original size:25 final size:24
Alignment explanation
Indices: 245708--245763 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 24
245698 TAATCTGTTG
*
245708 TTTTGAATGTTATCGAGAATTCAA
1 TTTTCAATGTTATCGAGAATTCAA
* * *
245732 TTGTTCAATGTTATTGAGCATTCGA
1 TT-TTCAATGTTATCGAGAATTCAA
245757 TTTTCAA
1 TTTTCAA
245764 ACCCTCAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 7 0.26
25 20 0.74
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.45
Consensus pattern (24 bp):
TTTTCAATGTTATCGAGAATTCAA
Found at i:248164 original size:3 final size:3
Alignment explanation
Indices: 248158--248186 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
248148 ATCTATTATT
248158 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
248187 TATTTTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:248821 original size:21 final size:20
Alignment explanation
Indices: 248774--248852 Score: 65
Period size: 21 Copynumber: 4.0 Consensus size: 20
248764 GAAGGCTATG
* *
248774 GAGGAGGAGATGAGGAGGGAA
1 GAGGAGAAGA-GAGGAGAGAA
**
248795 TTGGAGAAGAGGAGGAGAGAA
1 GAGGAGAAGA-GAGGAGAGAA
*
248816 GAGGAGGAGAG-GGAGAG-A
1 GAGGAGAAGAGAGGAGAGAA
248834 GAGAGAGAAGAGAGG-GAGA
1 GAG-GAGAAGAGAGGAGAGA
248853 GGGAGAGGGA
Statistics
Matches: 46, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
18 4 0.09
19 16 0.35
20 3 0.07
21 23 0.50
ACGTcount: A:0.42, C:0.00, G:0.54, T:0.04
Consensus pattern (20 bp):
GAGGAGAAGAGAGGAGAGAA
Found at i:248832 original size:6 final size:6
Alignment explanation
Indices: 248821--248874 Score: 54
Period size: 6 Copynumber: 8.5 Consensus size: 6
248811 GAGAAGAGGA
* * *
248821 GGAGAG GGAGAG AGAGAGAG AAGAGAG GGAGAG GGAGAG GGAAAG GGAAAG
1 GGAGAG GGAGAG -G-GAGAG -GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG
248872 GGA
1 GGA
248875 AGGAGATTAC
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
6 31 0.72
7 6 0.14
8 6 0.14
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (6 bp):
GGAGAG
Found at i:248847 original size:13 final size:13
Alignment explanation
Indices: 248798--248845 Score: 62
Period size: 13 Copynumber: 3.6 Consensus size: 13
248788 GAGGGAATTG
248798 GAGAAGAGGAGGA
1 GAGAAGAGGAGGA
248811 GAGAAGAGGAGGA
1 GAGAAGAGGAGGA
*
248824 GAG-GGAGAGAGAGA
1 GAGAAGAG-GAG-GA
248838 GAGAAGAG
1 GAGAAGAG
248846 AGGGAGAGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 3 0.10
13 19 0.63
14 5 0.17
15 3 0.10
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (13 bp):
GAGAAGAGGAGGA
Found at i:248853 original size:21 final size:21
Alignment explanation
Indices: 248798--248859 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
248788 GAGGGAATTG
248798 GAGAAGAG-GAGGAGAGA-AGA
1 GAGAAGAGAG-GGAGAGAGAGA
*
248818 G-GAGGAGAGGGAGAGAGAGA
1 GAGAAGAGAGGGAGAGAGAGA
*
248838 GAGAAGAGAGGGAGAGGGAGA
1 GAGAAGAGAGGGAGAGAGAGA
248859 G
1 G
248860 GGAAAGGGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 12 0.33
20 6 0.17
21 18 0.50
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (21 bp):
GAGAAGAGAGGGAGAGAGAGA
Found at i:250576 original size:3 final size:3
Alignment explanation
Indices: 250568--250594 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
250558 GTAGCCATAG
250568 CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT
250595 TTTTTTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:254106 original size:6 final size:6
Alignment explanation
Indices: 254097--254144 Score: 78
Period size: 6 Copynumber: 7.7 Consensus size: 6
254087 AATCTCGCTC
254097 CTCCCT CTCCCT CTCCCT CTCCCT CTCCCT CTCCCTT CTCCCAT CTCC
1 CTCCCT CTCCCT CTCCCT CTCCCT CTCCCT CTCCC-T CTCCC-T CTCC
254145 TTCACAAAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
6 29 0.73
7 11 0.28
ACGTcount: A:0.02, C:0.65, G:0.00, T:0.33
Consensus pattern (6 bp):
CTCCCT
Found at i:258463 original size:2 final size:2
Alignment explanation
Indices: 258456--258493 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
258446 TTCCTATCTT
258456 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
258494 CACACACTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:265675 original size:87 final size:86
Alignment explanation
Indices: 265529--265706 Score: 306
Period size: 87 Copynumber: 2.1 Consensus size: 86
265519 GTATTAAGAT
*
265529 AGTTTCGGTCGGGTAAAATGAAGAATAAAATGACACTCAAGTTTAATTTACCTCTAATAAGATTT
1 AGTTTCGGTCGGGTAAAATGAAGAATAAAATGACACTCAAGCTTAATTTACCTCTAATAAGA-TT
*
265594 AAGACACACTGAATAAGATTGC
65 AAGACACACTGAATAAGAATGC
265616 AGTTTCAGG-CGGGTAAAATGAAGAATAAAATGACACTCAAGCTTAATTTACCTCTAATAAGATT
1 AGTTTC-GGTCGGGTAAAATGAAGAATAAAATGACACTCAAGCTTAATTTACCTCTAATAAGATT
265680 AAGACACACTGAATAAGAATGC
65 AAGACACACTGAATAAGAATGC
265702 A-TTTC
1 AGTTTC
265707 CACAAGAAAC
Statistics
Matches: 88, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
85 4 0.05
86 24 0.27
87 58 0.66
88 2 0.02
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.28
Consensus pattern (86 bp):
AGTTTCGGTCGGGTAAAATGAAGAATAAAATGACACTCAAGCTTAATTTACCTCTAATAAGATTA
AGACACACTGAATAAGAATGC
Found at i:273192 original size:21 final size:20
Alignment explanation
Indices: 273154--273193 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
273144 CTTCATTTAG
*
273154 CTTTTCCCTTTGCTTGCTTT
1 CTTTTCCCTTTGCCTGCTTT
*
273174 CTTTTCCTCTTTTCCTGCTT
1 CTTTTCC-CTTTGCCTGCTT
273194 AAATCATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.00, C:0.33, G:0.07, T:0.60
Consensus pattern (20 bp):
CTTTTCCCTTTGCCTGCTTT
Found at i:286393 original size:37 final size:37
Alignment explanation
Indices: 286338--286435 Score: 97
Period size: 37 Copynumber: 2.6 Consensus size: 37
286328 GGTGTAGATT
** * * *
286338 TAATTTTAAGGGTGTTTTCGTAATCTAATAAGTCATG
1 TAATTTTAAAAGTATTTTCATAATCGAATAAGTCATG
* **
286375 TAATTTTAAAAGTATTTTCATCATCGAATGTGTCATG
1 TAATTTTAAAAGTATTTTCATAATCGAATAAGTCATG
* * *
286412 TAAGTTTAAAAATATTTTAATAAT
1 TAATTTTAAAAGTATTTTCATAAT
286436 TTGATATGTG
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (37 bp):
TAATTTTAAAAGTATTTTCATAATCGAATAAGTCATG
Found at i:288417 original size:10 final size:10
Alignment explanation
Indices: 288404--288429 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
288394 CAAATACTAA
288404 CAAATTTCCT
1 CAAATTTCCT
288414 CAAATTTCCT
1 CAAATTTCCT
288424 CAAATT
1 CAAATT
288430 CCAAGGATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.35, C:0.27, G:0.00, T:0.38
Consensus pattern (10 bp):
CAAATTTCCT
Found at i:303244 original size:2 final size:2
Alignment explanation
Indices: 303232--303269 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
303222 ATTAATATCG
* *
303232 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
303270 ATTATGAGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:304540 original size:15 final size:16
Alignment explanation
Indices: 304514--304547 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
304504 ATCTATGTCA
304514 ATTTTTAGTTATAATT
1 ATTTTTAGTTATAATT
*
304530 ATTTTTA-TTATTATT
1 ATTTTTAGTTATAATT
304545 ATT
1 ATT
304548 ATTCTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
ATTTTTAGTTATAATT
Found at i:305267 original size:250 final size:248
Alignment explanation
Indices: 304984--306373 Score: 1254
Period size: 250 Copynumber: 5.5 Consensus size: 248
304974 TAAACTCGTT
* *
304984 AATATAAATTTAAATGTTTGTTTTTTATTAAAATTAGA-TTTTTTTACTTAATTGACATGTTACG
1 AATATAAATTTAAATG-TTATTTTCT-TTAAAATTAGATTTTTTTTACTTAATTGACATGTTACG
* * * *
305048 TTTACTCTTACACATTTACGTTAGGATTTTAAATTTGCTTGTTCTACCTTTATGAGTTTTTACGC
64 TTAACTCTCACACATTTACGTTAAGATTTTAAATTTGCTTGTTCTACCTTTATGAGTTTTTACGA
* * *
305113 T-AATTCTTATAGCTTTACGTCAAAGGCTTTTCAACAGAACCTTTTAACTATAATAATTTTTATC
129 TCAATTCTTACAGCTTTACGTC-AAGGCTTTTCAA-GGAA-CTTTTAACTATAATTATTTTTATC
* * * * * * * *
305177 TTTATAATTATTTATTTTAAAATTAAAAATTGCAAATCATTATATACTTTTCGCCCGAG
191 TTTATTATTCTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTTTTC-CTCGAG
* * * ** *
305236 AATATAAATTTAAATGTTATTTTCTTTAAAATTAGAATTTTGTGACTTAATTGAGTTGTTATGTT
1 AATATAAATTTAAATGTTATTTTCTTTAAAATTAGATTTTTTTTACTTAATTGACATGTTACGTT
* * * * * *
305301 AA-TGCAT-AAACATTTATGTTAAGATTTTAAATATGTTTGTTCTGCCATTATGAGTTTTTAC-A
66 AACT-C-TCACACATTTACGTTAAGATTTTAAATTTGCTTGTTCTACCTTTATGAGTTTTTACGA
* * * * * * *
305363 TCAATTCTTAGAACTTTACGTCAACGCTTTTCAATGACAACTTTTAACCAAAATTATTTTTATTT
129 TCAATTCTTACAGCTTTACGTCAAGGCTTTTCAA-G-GAACTTTTAACTATAATTATTTTTATCT
* * * *
305428 TTATTATTCTTTATTTTAAAATTAAAATTTGCATATCATTAAATACTTTTACCTTGAC
192 TTATTATTCTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTTTT-CCTCGAG
* * * *
305486 AATATGAATTTAAATGTT-TGTTT-TTAACAAAAATAAGATTTTTTTTTACTTAATTAACATGTT
1 AATATAAATTTAAATGTTAT-TTTCTT---TAAAATTAGA-TTTTTTTTACTTAATTGACATGTT
* * *
305549 ACGTTAACTTTCACACATTTACGTTAGGATTTTAAATTCGCTTGTT-T-CACTTCTATGAGTTTT
61 ACGTTAACTCTCACACATTTACGTTAAGATTTTAAATTTGCTTGTTCTAC-CTT-TATGAGTTTT
* * * * * *
305612 TACG-TTAATTCTTACAGTTTTACATCAAGGCATTTCAATGGCACCTTTTAACTATAATTATATT
124 TACGATCAATTCTTACAGCTTTACGTCAAGGCTTTTCAA-GG-AACTTTTAACTATAATTATTTT
* * * **
305676 TATCCTTATTATTTTTTATTTTAAAATTAAAATTTGTATATCGTTAAAT-TTTTTAATCGAG
187 TATCTTTATTATTCTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTTTTCCTCGAG
* * * * * * **
305737 AATATAAATTTAAATATTTATTTTTCCTTAAAATTAGATTTTTTTTACATAATTAACTTATTATA
1 AATATAAATTTAAAT-GTTA-TTTTCTTTAAAATTAGATTTTTTTTACTTAATTGACATGTTACG
* * * * * *
305802 TTAACTCTCACACATTTACATTAAGATTTTAAATTTGCTTATTCCACTTTTATAAGTTTTCACG-
64 TTAACTCTCACACATTTACGTTAAGATTTTAAATTTGCTTGTTCTACCTTTATGAGTTTTTACGA
* * * * *
305866 TCAATTCTTACAACTTTACATTAAGGCTTTTCGAAGGTAACTTTTAACTATAATTATTCTTATCC
129 TCAATTCTTACAGCTTTACGTCAAGGCTTTTC-AAGG-AACTTTTAACTATAATTATTTTTATCT
* * * *
305931 TTCTTATTCTTTATTGTAAAATTAAAATTTGTATATCGTTAAATATTTTTACCTTGAG
192 TTATTATTCTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTTTT-CCTCGAG
* * * * * * *
305989 AATGTAAATTTAAATGTTTGTTTTTCATTGAAATTATATTTTTTTTACTTACTTGACATGTTACT
1 AATATAAATTTAAATG-TT-ATTTTCTTTAAAATTAGATTTTTTTTACTTAATTGACATGTTACG
* * * * * *
306054 TTAAGTCTCACATATTTACGTCT-AGATTTCAAATTTGCTTGGTCTACCATTAT-ATGTTTTCAC
64 TTAACTCTCACACATTTACGT-TAAGATTTTAAATTTGCTTGTTCTACCTTTATGA-GTTTTTAC
* * * *
306117 -ATCAATTCTTACAGCTATATGTTAAAGGGTTTTCAATGGTAACTTTTAACTATAATTATTTTTA
127 GATCAATTCTTACAGCTTTACG-TCAAGGCTTTTCAA-GG-AACTTTTAACTATAATTATTTTTA
* * * ** *
306181 TTTTTATTATTCTTTA-TTTAAAATT-AAATTTATATATCGTTAAACACTTTTAGTCCGAA
189 TCTTTATTATTCTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTTTTCCT-CGAG
* ** * * *
306240 AATATAAATTTAAATATTTACTTTTCAATAAAATTAGATTTTTTTT-CTTAATTG-CTTTATTAT
1 AATATAAATTTAAAT-GTTA-TTTTCTTTAAAATTAGATTTTTTTTACTTAATTGAC-ATGTTAC
* * * ** * * *
306303 GTTAACTCTCACACATTTATGTTAAAATTTTAAACTTAATTATTTTACCTTTATGAGTTTTTA-T
63 GTTAACTCTCACACATTTACGTTAAGATTTTAAATTTGCTTGTTCTACCTTTATGAGTTTTTACG
306367 ATCAATT
128 ATCAATT
306374 TTATTACTTT
Statistics
Matches: 926, Mismatches: 172, Indels: 82
0.78 0.15 0.07
Matches are distributed among these distances:
249 5 0.01
250 343 0.37
251 200 0.22
252 166 0.18
253 209 0.23
254 3 0.00
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (248 bp):
AATATAAATTTAAATGTTATTTTCTTTAAAATTAGATTTTTTTTACTTAATTGACATGTTACGTT
AACTCTCACACATTTACGTTAAGATTTTAAATTTGCTTGTTCTACCTTTATGAGTTTTTACGATC
AATTCTTACAGCTTTACGTCAAGGCTTTTCAAGGAACTTTTAACTATAATTATTTTTATCTTTAT
TATTCTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTTTTCCTCGAG
Found at i:305433 original size:15 final size:16
Alignment explanation
Indices: 305415--305444 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
305405 TTTAACCAAA
305415 ATTATT-TTTATTTTT
1 ATTATTCTTTATTTTT
305430 ATTATTCTTTATTTT
1 ATTATTCTTTATTTT
305445 AAAATTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (16 bp):
ATTATTCTTTATTTTT
Found at i:305897 original size:503 final size:500
Alignment explanation
Indices: 304984--306336 Score: 1519
Period size: 503 Copynumber: 2.7 Consensus size: 500
304974 TAAACTCGTT
*
304984 AATATAAATTTAAATGTTTGTTTTTTATTAAAATTAGA-TTTTTTTACTTAATTGACATGTTACG
1 AATATAAATTTAAATGTTTGTTTTTAATTAAAATTAGATTTTTTTTACTTAATTGACATGTTACG
*
305048 TTTACTCTT-ACACATTTACGTTAGGATTTTAAATTTGCTTGTTCTACCTTTATGAGTTTTTACG
66 TTAACT-TTCACACATTTACGTTAGGATTTTAAATTTGCTTGTTCTACCTTTATGAGTTTTTACG
* * * ** *
305112 CTAATTCTTATAGCTTTACGTCAAAGGCTTTTCAACAGAACCTTTTAACTATAATAATTTTTATC
130 TTAATTCTTACAGCTTTACATC-AAGGCTTTTCAATGGAACCTTTTAACTATAATTATTTTTATC
* * * * * * ****
305177 TTTATAATTATTTATTTTAAAATTAAAAATTGCAAATCATTATATACTTTTCGCCCGAGAATATA
194 TTTATTATTATTTATTTTAAAATTAAAATTTGTATATCGTTA-A-AATTTTTAATCGAGAATATA
* * * * * * *
305242 AATTTAAAT-GTTATTTTCTTTAAAATTAGAATTTTGTGACTTAATTGAGTTGTTATGTTAA-TG
257 AATTTAAATATTTATTTTCATTAAAATTAGATTTTTTTTACTTAATT-ACTTATTATGTTAACT-
* * * ** * *
305305 CAT-AAACATTTATGTTAAGATTTTAAATATGTTTGTTCTGCCATTATGAGTTTTTACATCAATT
320 C-TCACACATTTATGTTAAGATTTTAAATATGCTTATTCCACCATTATAAGTTTTCACATCAATT
* * * **
305369 CTTAGAACTTTACGTCAACGCTTTTC-AATGACAACTTTTAACCAAAATTATTTTTATTTTTATT
384 CTTACAACTTTACATCAACGCTTTTCGAA-GACAACTTTTAACCAAAATTATTCTTATCCTTATT
*
305433 ATTCTTTATTTTAAAATTAAAATTTGCATATCATTAAATACTTTTACCTTGAC
448 ATTCTTTATTGTAAAATTAAAATTTGCATATCATTAAATACTTTTACCTTGAC
* ** * *
305486 AATATGAATTTAAATGTTTGTTTTTAACAAAAATAAGATTTTTTTTTACTTAATTAACATGTTAC
1 AATATAAATTTAAATGTTTGTTTTTAATTAAAATTAGA-TTTTTTTTACTTAATTGACATGTTAC
*
305551 GTTAACTTTCACACATTTACGTTAGGATTTTAAATTCGCTTGTT-T-CACTTCTATGAGTTTTTA
65 GTTAACTTTCACACATTTACGTTAGGATTTTAAATTTGCTTGTTCTAC-CTT-TATGAGTTTTTA
* * * *
305614 CGTTAATTCTTACAGTTTTACATCAAGGCATTTCAATGGCACCTTTTAACTATAATTATATTTAT
128 CGTTAATTCTTACAGCTTTACATCAAGGCTTTTCAATGGAACCTTTTAACTATAATTATTTTTAT
* * *
305679 CCTTATTATTTTTTATTTTAAAATTAAAATTTGTATATCGTTAAATTTTTTAATCGAGAATATAA
193 CTTTATTATTATTTATTTTAAAATTAAAATTTGTATATCGTTAAAATTTTTAATCGAGAATATAA
* * *
305744 ATTTAAATATTTATTTTTCCTTAAAATTAGATTTTTTTTACATAATTAACTTATTATATTAACTC
258 ATTTAAATATTTA-TTTTCATTAAAATTAGATTTTTTTTACTTAATT-ACTTATTATGTTAACTC
** * ** *
305809 TCACACATTTACATTAAGATTTTAAATTTGCTTATTCCACTTTTATAAGTTTTCACGTCAATTCT
321 TCACACATTTATGTTAAGATTTTAAATATGCTTATTCCACCATTATAAGTTTTCACATCAATTCT
* * ** * * *
305874 TACAACTTTACATTAAGGCTTTTCGAAGGTAACTTTTAACTATAATTATTCTTATCCTTCTTATT
386 TACAACTTTACATCAACGCTTTTCGAAGACAACTTTTAACCAAAATTATTCTTATCCTTATTATT
* * * *
305939 CTTTATTGTAAAATTAAAATTTGTATATCGTTAAATATTTTTACCTTGAG
451 CTTTATTGTAAAATTAAAATTTGCATATCATTAAATACTTTTACCTTGAC
* * * * * *
305989 AATGTAAATTTAAATGTTTGTTTTTCATTGAAATTATATTTTTTTTACTTACTTGACATGTTACT
1 AATATAAATTTAAATGTTTGTTTTTAATTAAAATTAGATTTTTTTTACTTAATTGACATGTTACG
* * * * * * *
306054 TTAAGTCTCACATATTTACGTCTA-GATTTCAAATTTGCTTGGTCTACCATTAT-ATGTTTTCAC
66 TTAACTTTCACACATTTACGT-TAGGATTTTAAATTTGCTTGTTCTACCTTTATGA-GTTTTTAC
* * * ** * *
306117 ATCAATTCTTACAGCTATATGTTAAAGGGTTTTCAATGGTAA-CTTTTAACTATAATTATTTTTA
129 GTTAATTCTTACAGCTTTA-CATCAAGGCTTTTCAATGG-AACCTTTTAACTATAATTATTTTTA
* * * * * *
306181 TTTTTATTATTCTTTA-TTTAAAATT-AAATTTATATATCGTTAAACACTTTTAGTCCGAAAATA
192 TCTTTATTATTATTTATTTTAAAATTAAAATTTGTATATCGTTAAA-ATTTTTAAT-CGAGAATA
* *
306244 TAAATTTAAATATTTACTTTTCAATAAAATTAGATTTTTTTT-CTTAATTGCTTTATTATGTTAA
255 TAAATTTAAATATTTA-TTTTCATTAAAATTAGATTTTTTTTACTTAATTAC-TTATTATGTTAA
*
306308 CTCTCACACATTTATGTTAAAATTTTAAA
318 CTCTCACACATTTATGTTAAGATTTTAAA
306337 CTTAATTATT
Statistics
Matches: 715, Mismatches: 117, Indels: 38
0.82 0.13 0.04
Matches are distributed among these distances:
501 44 0.06
502 180 0.25
503 391 0.55
504 100 0.14
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (500 bp):
AATATAAATTTAAATGTTTGTTTTTAATTAAAATTAGATTTTTTTTACTTAATTGACATGTTACG
TTAACTTTCACACATTTACGTTAGGATTTTAAATTTGCTTGTTCTACCTTTATGAGTTTTTACGT
TAATTCTTACAGCTTTACATCAAGGCTTTTCAATGGAACCTTTTAACTATAATTATTTTTATCTT
TATTATTATTTATTTTAAAATTAAAATTTGTATATCGTTAAAATTTTTAATCGAGAATATAAATT
TAAATATTTATTTTCATTAAAATTAGATTTTTTTTACTTAATTACTTATTATGTTAACTCTCACA
CATTTATGTTAAGATTTTAAATATGCTTATTCCACCATTATAAGTTTTCACATCAATTCTTACAA
CTTTACATCAACGCTTTTCGAAGACAACTTTTAACCAAAATTATTCTTATCCTTATTATTCTTTA
TTGTAAAATTAAAATTTGCATATCATTAAATACTTTTACCTTGAC
Found at i:322470 original size:13 final size:12
Alignment explanation
Indices: 322440--322472 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
322430 AATAATCATC
322440 AATAATTAATGT
1 AATAATTAATGT
322452 -ATAATTATATGT
1 AATAATTA-ATGT
322464 AATAATTAA
1 AATAATTAA
322473 ATATATAGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 7 0.37
12 5 0.26
13 7 0.37
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (12 bp):
AATAATTAATGT
Found at i:323165 original size:23 final size:23
Alignment explanation
Indices: 323122--323167 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
323112 TATGCTCTCG
*
323122 ATTTCTCTCTCCAGCGTTTTCAA
1 ATTTCTCTCTCCAGCGCTTTCAA
*
323145 ATTTCTCAT-TCCTGCGCTTTCAA
1 ATTTCTC-TCTCCAGCGCTTTCAA
323168 GACACAAAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.17, C:0.30, G:0.09, T:0.43
Consensus pattern (23 bp):
ATTTCTCTCTCCAGCGCTTTCAA
Found at i:323608 original size:30 final size:29
Alignment explanation
Indices: 323533--323628 Score: 108
Period size: 29 Copynumber: 3.3 Consensus size: 29
323523 AAGTGTTAAA
* * *
323533 GTGTAATAA-AATA-TTTTTGAATATGAC
1 GTGTAACAACAATATTTTTTTAACATGAC
323560 GTGTAACAACAATATTTTTTTAACATGGA-
1 GTGTAACAACAATATTTTTTTAACAT-GAC
* *
323589 GTGTAACAATAATATTTTTTTTAATATGAC
1 GTGTAACAACAATA-TTTTTTTAACATGAC
323619 GTGTAACAAC
1 GTGTAACAAC
323629 CTAATCATGG
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
27 8 0.14
28 4 0.07
29 24 0.41
30 22 0.38
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.40
Consensus pattern (29 bp):
GTGTAACAACAATATTTTTTTAACATGAC
Found at i:323846 original size:24 final size:24
Alignment explanation
Indices: 323814--323871 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
323804 ACAACCTAAC
*
323814 CATGACGTGTCACATGTTTTTGTA
1 CATGACGTGTCACATGTTTTTATA
* *
323838 CATGGCGTGTGACATGTTTTTATA
1 CATGACGTGTCACATGTTTTTATA
*
323862 CACGACGTGT
1 CATGACGTGT
323872 AATTTCATTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (24 bp):
CATGACGTGTCACATGTTTTTATA
Found at i:323846 original size:45 final size:45
Alignment explanation
Indices: 323618--323847 Score: 325
Period size: 45 Copynumber: 5.1 Consensus size: 45
323608 TTTAATATGA
* * * *
323618 CGTGTAACAACCTAATCATGGCGTGTCACATGTTTTTGTACTTGA
1 CGTGTAACAACCTAACCATGACGTGTCACATGTTTTTGTACATGG
* * *
323663 CGTGTAACAACCTAACCATGACGTGTTACATATTTTTGTACATAG
1 CGTGTAACAACCTAACCATGACGTGTCACATGTTTTTGTACATGG
* * * *
323708 CATGTAACAACCTAACCATGACATATCACATGTTTTTGTACATGA
1 CGTGTAACAACCTAACCATGACGTGTCACATGTTTTTGTACATGG
* * * *
323753 CATGTAACAACATAACCATGACGTGTCACATGTTTTTGTATATAG
1 CGTGTAACAACCTAACCATGACGTGTCACATGTTTTTGTACATGG
323798 CGTGTAACAACCTAACCATGACGTGTCACATGTTTTTGTACATGG
1 CGTGTAACAACCTAACCATGACGTGTCACATGTTTTTGTACATGG
323843 CGTGT
1 CGTGT
323848 GACATGTTTT
Statistics
Matches: 161, Mismatches: 24, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 161 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (45 bp):
CGTGTAACAACCTAACCATGACGTGTCACATGTTTTTGTACATGG
Found at i:323914 original size:158 final size:157
Alignment explanation
Indices: 323735--324050 Score: 560
Period size: 158 Copynumber: 2.0 Consensus size: 157
323725 ATGACATATC
*
323735 ACATGTTTTTGTACATGACATGTAACAACATAACCATGACGTGTCACATGTTTTTGTATATAGCG
1 ACATGTTTTTGTACATGACATGTAACAACATAACCATGACGTGTCACATGTTTTTATATATAGCG
* *
323800 TGTAACAACCTAACCATGACGTGTCACATGTTTTTGTACATGGCGTGTGACATGTTTTTATACAC
66 TGTAACAACCCAACCACGACGTGTCACATGTTTTTGTACATGGCGTGTGACATG-TTTTATACAC
323865 GACGTGTAATTTCATTGAGAGTAATTTT
130 GACGTGTAATTTCATTGAGAGTAATTTT
* *
323893 ACATGTTTTTGTACATGACATGTAACTACCTAACCATGACGTGTCACATGTTTTTATATATAGCG
1 ACATGTTTTTGTACATGACATGTAACAACATAACCATGACGTGTCACATGTTTTTATATATAGCG
* *
323958 TGTAACAACCCAACCACGACGTGTCACATGTTTTTGTACATGGTGTGTGACATGTTTTATACATG
66 TGTAACAACCCAACCACGACGTGTCACATGTTTTTGTACATGGCGTGTGACATGTTTTATACACG
324023 ACGTGTAATTTCATTGAGAGTAATTTT
131 ACGTGTAATTTCATTGAGAGTAATTTT
324050 A
1 A
324051 TCCAATTTGA
Statistics
Matches: 151, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
157 38 0.25
158 113 0.75
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (157 bp):
ACATGTTTTTGTACATGACATGTAACAACATAACCATGACGTGTCACATGTTTTTATATATAGCG
TGTAACAACCCAACCACGACGTGTCACATGTTTTTGTACATGGCGTGTGACATGTTTTATACACG
ACGTGTAATTTCATTGAGAGTAATTTT
Found at i:323946 original size:45 final size:46
Alignment explanation
Indices: 323893--323999 Score: 146
Period size: 45 Copynumber: 2.4 Consensus size: 46
323883 GAGTAATTTT
* * *
323893 ACATGTTTTTGTACATGA-CATGTAACTACCTAACCATGACGTGTC
1 ACATGTTTTTGTACATGAGCATGTAACAACCCAACCACGACGTGTC
* * *
323938 ACATGTTTTTATATAT-AGCGTGTAACAACCCAACCACGACGTGTC
1 ACATGTTTTTGTACATGAGCATGTAACAACCCAACCACGACGTGTC
323983 ACATGTTTTTGTACATG
1 ACATGTTTTTGTACATG
324000 GTGTGTGACA
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
44 1 0.02
45 51 0.98
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (46 bp):
ACATGTTTTTGTACATGAGCATGTAACAACCCAACCACGACGTGTC
Found at i:324028 original size:23 final size:24
Alignment explanation
Indices: 323975--324028 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
323965 ACCCAACCAC
*
323975 GACGTGTCACATGTTTTTGTACAT
1 GACGTGTCACATGTTTTTATACAT
** *
323999 GGTGTGTGACATG-TTTTATACAT
1 GACGTGTCACATGTTTTTATACAT
324022 GACGTGT
1 GACGTGT
324029 AATTTCATTG
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.20, C:0.13, G:0.26, T:0.41
Consensus pattern (24 bp):
GACGTGTCACATGTTTTTATACAT
Found at i:327357 original size:40 final size:41
Alignment explanation
Indices: 327272--327412 Score: 144
Period size: 40 Copynumber: 3.5 Consensus size: 41
327262 GATAATATTT
* * * *
327272 TAGTTATTTAAGTTTATGTTGTTTGTTTGGATCTTTGTGTT
1 TAGTTATTTAAGTTTATGTTGTTTATTTGGATATTTATGTA
*
327313 TAGTTATTTAAGTTTTTGTTG-TTATTTGGATATTTATGTA
1 TAGTTATTTAAGTTTATGTTGTTTATTTGGATATTTATGTA
* ** * * *
327353 TAGTTATTTAAGTTTATATCATTGTA--TGGATATTTGTTTT
1 TAGTTATTTAAGTTTATGTTGTT-TATTTGGATATTTATGTA
*
327393 TAGTTATTTAAATTTATGTT
1 TAGTTATTTAAGTTTATGTT
327413 TAAAATCTTT
Statistics
Matches: 83, Mismatches: 15, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
40 60 0.72
41 21 0.25
42 2 0.02
ACGTcount: A:0.22, C:0.01, G:0.17, T:0.60
Consensus pattern (41 bp):
TAGTTATTTAAGTTTATGTTGTTTATTTGGATATTTATGTA
Found at i:327466 original size:15 final size:15
Alignment explanation
Indices: 327446--327491 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
327436 TAAATTTAAA
*
327446 TTTTATTATTTTTAT
1 TTTTATTAATTTTAT
327461 TTTTATTAATTTTAT
1 TTTTATTAATTTTAT
**
327476 TAGTAGTTAATTTTAT
1 TTTTA-TTAATTTTAT
327492 GAAATACGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 17 0.63
16 10 0.37
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (15 bp):
TTTTATTAATTTTAT
Found at i:330144 original size:20 final size:21
Alignment explanation
Indices: 330106--330145 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
330096 GGGGGAAAAC
330106 AAAATAGAAAAGAAAGGCTAT
1 AAAATAGAAAAGAAAGGCTAT
*
330127 AAAATGGAAAAG-AAGGCTA
1 AAAATAGAAAAGAAAGGCTA
330146 CAGCCCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.60, C:0.05, G:0.23, T:0.12
Consensus pattern (21 bp):
AAAATAGAAAAGAAAGGCTAT
Found at i:334602 original size:145 final size:147
Alignment explanation
Indices: 334452--334722 Score: 372
Period size: 151 Copynumber: 1.8 Consensus size: 147
334442 ATCTTATAAA
* *
334452 TATTAAAAGTTAGAAATTATTGTTTTCAAATATTTTTTACT-A-AAATAAA-T-AAAAGAAAAAA
1 TATTAAAAGTTAGAAATTATTATTTTCAAATATTTTTTACTAATAAATAAAGTAAAAAAAAAAAA
* *
334513 AAACCCTTCAAATGTCCAAAGCAA-TGTAGTTTTGACATAAGGTGTAAAAAAAATTAATTTAATT
66 AAAACCTTCAAATGT-CAAAACAACT-TAGTTTTGACATAAGGTGTAAAAAAAATTAATTTAATT
334577 AAGAATGACAAATGTCAAT
129 AAGAATGACAAATGTCAAT
* * * *
334596 TNATTAAAAGTTATAAATTATTATTTTTAAGTATTTTTTATTAAAATAAATAAAGTAAAAAAAAA
1 T-ATTAAAAGTTAGAAATTATTATTTTCAAATATTTTTTACT--AATAAATAAAGT-AAAAAAAA
*
334661 AAAAAAAACCTTCAAATGTCAAAACAACTTATTTTTGACATAAGGTGTAAAAAAAATTAATT
62 AAAAAAAACCTTCAAATGTCAAAACAACTTAGTTTTGACATAAGGTGTAAAAAAAATTAATT
334723 CAATAGAAAA
Statistics
Matches: 109, Mismatches: 9, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
144 1 0.01
145 35 0.32
148 1 0.01
149 7 0.06
150 1 0.01
151 39 0.36
152 25 0.23
ACGTcount: A:0.50, C:0.07, G:0.08, T:0.34
Consensus pattern (147 bp):
TATTAAAAGTTAGAAATTATTATTTTCAAATATTTTTTACTAATAAATAAAGTAAAAAAAAAAAA
AAAACCTTCAAATGTCAAAACAACTTAGTTTTGACATAAGGTGTAAAAAAAATTAATTTAATTAA
GAATGACAAATGTCAAT
Found at i:334857 original size:65 final size:66
Alignment explanation
Indices: 334785--334916 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
334775 CTTGTCATTC
334785 AATTGAAGACTCAATTG-AAAAAAATTAAAAGAAATTGAAACATCCTACTTTTATATATATTATA
1 AATTGAAGACTCAATTGAAAAAAAATTAAAAGAAATTGAAACATCCTACTTTTATATATATTATA
334849 G
66 G
* * *
334850 AATTGAAGACTCAATTGAAAAAAAATTGAAAGAAATTGAAATATCCTATTTTTATATATATTATA
1 AATTGAAGACTCAATTGAAAAAAAATTAAAAGAAATTGAAACATCCTACTTTTATATATATTATA
334915 G
66 G
334916 A
1 A
334917 TATGTTAGAT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
65 17 0.27
66 46 0.73
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.33
Consensus pattern (66 bp):
AATTGAAGACTCAATTGAAAAAAAATTAAAAGAAATTGAAACATCCTACTTTTATATATATTATA
G
Found at i:347623 original size:2 final size:2
Alignment explanation
Indices: 347616--347661 Score: 83
Period size: 2 Copynumber: 22.5 Consensus size: 2
347606 ATCATACCTC
347616 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
347659 AT A
1 AT A
347662 AACCTTATGA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:348879 original size:17 final size:17
Alignment explanation
Indices: 348848--348894 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 17
348838 TAAAATATAA
348848 TATTAAAAT--TATATT
1 TATTAAAATAATATATT
348863 TATTAAAATAATATATT
1 TATTAAAATAATATATT
*
348880 TGATTGAAAAAAATA
1 T-ATT-AAAATAATA
348895 ATTATTTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 9 0.33
17 7 0.26
18 3 0.11
19 8 0.30
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (17 bp):
TATTAAAATAATATATT
Found at i:348894 original size:19 final size:17
Alignment explanation
Indices: 348852--348894 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
348842 ATATAATATT
*
348852 AAAATTATATTTATTAA
1 AAAAATATATTTATTAA
*
348869 AATAATATATTTGATTGAA
1 AAAAATATATTT-ATT-AA
348888 AAAAATA
1 AAAAATA
348895 ATTATTTCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 10 0.48
18 3 0.14
19 8 0.38
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (17 bp):
AAAAATATATTTATTAA
Found at i:352611 original size:97 final size:97
Alignment explanation
Indices: 352439--352631 Score: 341
Period size: 97 Copynumber: 2.0 Consensus size: 97
352429 CATCACCTTC
* * *
352439 TTTGCGTGTTGTATGTGTAAGCTCATAAGATCTCATATAAACAACAAAACCACAATGAAGCACTG
1 TTTGCATGTTGTACGTGTAAGCTAATAAGATCTCATATAAACAACAAAACCACAATGAAGCACTG
* *
352504 CTGTAGTTCAAATTTTAGTTATCTTATGAATT
66 CTGGAATTCAAATTTTAGTTATCTTATGAATT
352536 TTTGCATGTTGTACGTGTAAGCTAATAAGATCTCATATAAACAACAAAACCACAATGAAGCACTG
1 TTTGCATGTTGTACGTGTAAGCTAATAAGATCTCATATAAACAACAAAACCACAATGAAGCACTG
352601 CTGGAATTCAAATTTTAGTTATCTTATGAAT
66 CTGGAATTCAAATTTTAGTTATCTTATGAAT
352632 CTGTGCCTTT
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
97 91 1.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Consensus pattern (97 bp):
TTTGCATGTTGTACGTGTAAGCTAATAAGATCTCATATAAACAACAAAACCACAATGAAGCACTG
CTGGAATTCAAATTTTAGTTATCTTATGAATT
Found at i:374678 original size:2 final size:2
Alignment explanation
Indices: 374671--374716 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
374661 TAATTCAAGG
374671 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
374712 TA TA T
1 TA TA T
374717 GTATTATGTA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:375294 original size:3 final size:3
Alignment explanation
Indices: 375281--375318 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
375271 GGAGAACCAA
*
375281 AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
375319 AAGAGCTAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:379076 original size:2 final size:2
Alignment explanation
Indices: 379069--379098 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
379059 TAGGGTTGGT
379069 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
379099 AAGCTATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:394867 original size:21 final size:21
Alignment explanation
Indices: 394805--394867 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
394795 CTTGCTTCGT
* *
394805 TGCATTTGCATCTGCTCAGAA
1 TGCATTTGCATCTGGTCAGAG
* *
394826 TGGATTTGAATCTGGTCAGAG
1 TGCATTTGCATCTGGTCAGAG
394847 TGCATTTGCATCTGGTCAGAG
1 TGCATTTGCATCTGGTCAGAG
394868 AAATAGTGCT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.33
Consensus pattern (21 bp):
TGCATTTGCATCTGGTCAGAG
Found at i:402605 original size:2 final size:2
Alignment explanation
Indices: 402598--402660 Score: 85
Period size: 2 Copynumber: 32.5 Consensus size: 2
402588 AATGGATGAG
* *
402598 TA TA TA TA CA TA TA TA TA TA T- TA TA TA TA T- TA TA TA TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
402638 TA TA TA TT TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
402661 TAATATTGGT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
1 2 0.04
2 51 0.96
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:403012 original size:23 final size:23
Alignment explanation
Indices: 402986--403031 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
402976 TAGAATAACA
* *
402986 ATTCATAATTCTATTAGGATAAG
1 ATTCATAATTATATTAAGATAAG
*
403009 ATTCCTAATTATATTAAGATAAG
1 ATTCATAATTATATTAAGATAAG
403032 GTTATTGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (23 bp):
ATTCATAATTATATTAAGATAAG
Found at i:406515 original size:23 final size:23
Alignment explanation
Indices: 406489--406534 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
406479 TAGAATAACA
* *
406489 ATTCCTAATTCTATTAGGATAAG
1 ATTCCTAATTATATTAAGATAAG
406512 ATTCCTAATTATATTAAGATAAG
1 ATTCCTAATTATATTAAGATAAG
406535 GTTATTGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (23 bp):
ATTCCTAATTATATTAAGATAAG
Found at i:432938 original size:16 final size:16
Alignment explanation
Indices: 432917--432951 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
432907 TAATTTTTTT
432917 TATTTTAATAAAAAAA
1 TATTTTAATAAAAAAA
* *
432933 TATTTTGATAAATAAA
1 TATTTTAATAAAAAAA
432949 TAT
1 TAT
432952 AACATAAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
TATTTTAATAAAAAAA
Found at i:434969 original size:31 final size:31
Alignment explanation
Indices: 434931--434991 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
434921 AAACTGTGAA
*
434931 TGTTGTTTCCATCTCCTCCGAAGGTGAATGT
1 TGTTGTTTCCATCTCCTCCGAAGGTCAATGT
*
434962 TGTTGTTTCCATCTCCTCTGAAGGTCAATG
1 TGTTGTTTCCATCTCCTCCGAAGGTCAATG
434992 CTGCTTGTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.16, C:0.23, G:0.21, T:0.39
Consensus pattern (31 bp):
TGTTGTTTCCATCTCCTCCGAAGGTCAATGT
Found at i:442715 original size:15 final size:15
Alignment explanation
Indices: 442695--442723 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
442685 TTGTTAATAT
442695 ATAAGTAAGAACCAC
1 ATAAGTAAGAACCAC
442710 ATAAGTAAGAACCA
1 ATAAGTAAGAACCA
442724 AGCATTCCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.17, G:0.14, T:0.14
Consensus pattern (15 bp):
ATAAGTAAGAACCAC
Found at i:449966 original size:141 final size:140
Alignment explanation
Indices: 449588--449958 Score: 396
Period size: 141 Copynumber: 2.6 Consensus size: 140
449578 GAAATTTTTT
* * * *
449588 TTTCAAAAATTGAATTGAAGTTTAATTT-TTAGAGTTCAATGTATAAAATAATAATCCATCTATA
1 TTTCAAAAATTGAATTAAAGTTTCATTTATGA-AGTTCAATGTATAAAATAATAATCCATTTATA
* ** * *
449652 GTTCCTATTCGTAAAATTTC-AAGTCATAATTTTTATTTAATCACTTGGGATCAGATCATTTCAG
65 ATTAATATTCGTAAAATTTCAAAGTCATAATTTTTATTTAATCACTTGAGATCAGATCATTTCAA
449716 GTCAAGAAAAGA
130 GT-AAGAAAAGA
* * **
449728 TTTCAAAAATTGAATTAAAGTTTTGATTTTTGAAACTCAATGTATAAAATAATAATCCATTTATA
1 TTTCAAAAATTGAATTAAAG-TTTCATTTATGAAGTTCAATGTATAAAATAATAATCCATTTATA
* * * *
449793 ATTAATGTTCGTAAATTTTTAAA-TCATAATTTTTGTTTAATCACTTGAGATCAGATCATTTCAA
65 ATTAATATTCGTAAAATTTCAAAGTCATAATTTTTATTTAATCACTTGAGATCAGATCATTTCAA
* **
449857 GT-TGAAAATTT
130 GTAAGAAAA-GA
* * * * *
449868 TTTCGAAAATT-AGATTAGAG-TTCATTTAATGAAGTTCAATGTATAGAATAATAGTTCATTTAT
1 TTTCAAAAATTGA-ATTAAAGTTTCATTT-ATGAAGTTCAATGTATAAAATAATAATCCATTTAT
*
449931 AATTAATACTT-GCAAAATTTCAAAGTCA
64 AATTAATA-TTCGTAAAATTTCAAAGTCA
449959 CATATTTTCT
Statistics
Matches: 192, Mismatches: 31, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
138 6 0.03
139 52 0.27
140 40 0.21
141 90 0.47
142 4 0.02
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.40
Consensus pattern (140 bp):
TTTCAAAAATTGAATTAAAGTTTCATTTATGAAGTTCAATGTATAAAATAATAATCCATTTATAA
TTAATATTCGTAAAATTTCAAAGTCATAATTTTTATTTAATCACTTGAGATCAGATCATTTCAAG
TAAGAAAAGA
Found at i:453988 original size:26 final size:25
Alignment explanation
Indices: 453956--454008 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
453946 AAAATTCAAA
*
453956 TAATTTTTA-ATTTTTATATTTAATT
1 TAATTTTTATATTTTTAT-TTTAAAT
453981 TAATTTTTATATTTTTATTTTAAAT
1 TAATTTTTATATTTTTATTTTAAAT
454006 TAA
1 TAA
454009 ATAATTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 18 0.69
26 8 0.31
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (25 bp):
TAATTTTTATATTTTTATTTTAAAT
Found at i:454015 original size:15 final size:15
Alignment explanation
Indices: 453997--454031 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
453987 TTATATTTTT
453997 ATTTTAAATTAAATA
1 ATTTTAAATTAAATA
**
454012 ATTTTTTATTAAATA
1 ATTTTAAATTAAATA
454027 ATTTT
1 ATTTT
454032 TTGTCATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTTAAATTAAATA
Found at i:454032 original size:15 final size:15
Alignment explanation
Indices: 454004--454033 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
453994 TTTATTTTAA
454004 ATTAAATAATTTTTT
1 ATTAAATAATTTTTT
454019 ATTAAATAATTTTTT
1 ATTAAATAATTTTTT
454034 GTCATTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTAAATAATTTTTT
Found at i:454096 original size:21 final size:21
Alignment explanation
Indices: 454072--454111 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
454062 TATGAAAATG
454072 AATAATATCACATGATTATAC
1 AATAATATCACATGATTATAC
* *
454093 AATAATGTCACATTATTAT
1 AATAATATCACATGATTAT
454112 TTATTATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (21 bp):
AATAATATCACATGATTATAC
Found at i:481051 original size:2 final size:2
Alignment explanation
Indices: 481044--481073 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
481034 AAAATTTCAA
*
481044 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
481074 TATTTTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:488051 original size:2 final size:2
Alignment explanation
Indices: 488044--488080 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
488034 TAGGGTATAT
488044 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
488081 GACATAAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:489595 original size:2 final size:2
Alignment explanation
Indices: 489590--489626 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
489580 AAGAAGGCAA
489590 AG AG AG AG AG AG AG AG AG AG -G ACG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG A-G AG AG AG AG AG AG A
489627 AGGGAGCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.91
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:502246 original size:15 final size:15
Alignment explanation
Indices: 502226--502256 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
502216 ATAGTTTATC
*
502226 TAAAGAATGCCGGAG
1 TAAAGAATGCAGGAG
502241 TAAAGAATGCAGGAG
1 TAAAGAATGCAGGAG
502256 T
1 T
502257 TTTTGAAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.10, G:0.32, T:0.16
Consensus pattern (15 bp):
TAAAGAATGCAGGAG
Found at i:504889 original size:37 final size:38
Alignment explanation
Indices: 504838--504911 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 38
504828 TTAGGTTACC
504838 TTTTAGTGAGTTATTTTAATT-TTATGT-TATTTTTTTTA
1 TTTTAGTGAGTTA-TTT-ATTATTATGTATATTTTTTTTA
* *
504876 TTTTAGTTA-TTATTTATTATTATTTATATTTTTTTT
1 TTTTAGTGAGTTATTTATTATTATGTATATTTTTTTT
504912 GTAAGATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
35 3 0.09
36 8 0.25
37 13 0.41
38 8 0.25
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.72
Consensus pattern (38 bp):
TTTTAGTGAGTTATTTATTATTATGTATATTTTTTTTA
Found at i:504895 original size:19 final size:18
Alignment explanation
Indices: 504838--504896 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 18
504828 TTAGGTTACC
* *
504838 TTTTAGTGAGTTATTTTAA
1 TTTTAGTTA-TTATTTTTA
*
504857 TTTTATGTTATTTTTTTTA
1 TTTTA-GTTATTATTTTTA
504876 TTTTAGTTATTATTTATTA
1 TTTTAGTTATTATTT-TTA
504895 TT
1 TT
504897 ATTTATATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
18 9 0.26
19 22 0.65
20 3 0.09
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.69
Consensus pattern (18 bp):
TTTTAGTTATTATTTTTA
Found at i:505998 original size:14 final size:14
Alignment explanation
Indices: 505979--506005 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
505969 TTGGTTTTAA
505979 TTTTAGTTAATTAG
1 TTTTAGTTAATTAG
505993 TTTTAGTTAATTA
1 TTTTAGTTAATTA
506006 ATAAATTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (14 bp):
TTTTAGTTAATTAG
Found at i:510550 original size:251 final size:251
Alignment explanation
Indices: 509941--512001 Score: 2421
Period size: 251 Copynumber: 8.2 Consensus size: 251
509931 GTAAGGATAA
* * * * * *
509941 AATAACTAAATTTAAAATCTTAACGTAAATATGTGAGAGTTAACGTAATAAGTCAATTGAG-GAA
1 AATAACTAAATTTTAAATCTTAACGTAAATGTGTGAGAGTTAACATAACAAGTCAATTAAGTAAA
* * * *
510005 AAAATTTAATTTTAATGAAAAATAAATATTTAAATTTATATTTTCAGACTAAAAGTGTTTAACGA
66 AAAATCTAATTTTAGTGAAAAACAAATATTTAAATTTATATTCTCAGACTAAAAGTGTTTAACGA
*
510070 TATAAAAATTTTAA-TTTT---T--A-AAT-A-AA--A-AAAAATAATTATAGTTCAAAATTGAC
131 TATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAATAATTATAGTTCAAAATTGAC
* * *
510123 ATA-AATAAG-CTTTGATGTAAAACTGTAACAATTGACATAAAAGCTTATAAAAGTGG
196 ATAGAA-AAGTC-TTGATGTAAAACTGTAACAATTGACGTAAAAACTTATAAAGGTGG
* *
510179 AATAACTAAATTTTAAATCTTAATGTAAATGTGTGAGAGTTAACATAACCAG-CTAATTAAGTAA
1 AATAACTAAATTTTAAATCTTAACGTAAATGTGTGAGAGTTAACATAACAAGTC-AATTAAGTAA
* * * * * *
510243 AAAAATCTAATTTTAGTGAAAAATAAACATTTAAATTTATATTATCAAATTAAAAGTGTTTAACA
65 AAAAATCTAATTTTAGTGAAAAACAAATATTTAAATTTATATTCTCAGACTAAAAGTGTTTAACG
*
510308 ATATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATGAAAATAATTATAGTTCAAAATTGA
130 ATATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAATAATTATAGTTCAAAATTGA
* * * * * * *
510373 CATAGAAAAATATTGATGTAAAATTGTAGCAATTGATGTAAAAACTTATCAAGATGG
195 CATAGAAAAGTCTTGATGTAAAACTGTAACAATTGACGTAAAAACTTATAAAGGTGG
* *
510430 AATATCTAAATTTTAAATCTTAACGTAAATGAGTGAGAGTTAA-AGTAACAAGTCAATTAAGTAA
1 AATAACTAAATTTTAAATCTTAACGTAAATGTGTGAGAGTTAACA-TAACAAGTCAATTAAGTAA
* * *
510494 AAAAATCTAAGTTTAGTGAAAAACAAATATTTAAATTCATATTCTCGGACTAAAAGTGTTTAACG
65 AAAAATCTAATTTTAGTGAAAAACAAATATTTAAATTTATATTCTCAGACTAAAAGTGTTTAACG
* *
510559 ATATAAAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAATAATTATAGTTTAAAATTGA
130 ATATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAATAATTATAGTTCAAAATTGA
* * * * **
510624 CAAAGATAAGTCTTAATGTAAAACAGTAACAATTGACGTAAAAACTTATAAAGGTAA
195 CATAGAAAAGTCTTGATGTAAAACTGTAACAATTGACGTAAAAACTTATAAAGGTGG
* * * * *
510681 AATAACTAAATTTTTAATCATAACATAAATATGTGAGAGTTAATATAACAAGTCAATTAAGTAAA
1 AATAACTAAATTTTAAATCTTAACGTAAATGTGTGAGAGTTAACATAACAAGTCAATTAAGT-AA
* * ** * *
510746 AAAAATCTAATTTTAGTGAACAACAAACATTTAAATTTATATTCTTGGACTAAACGTGTTTAACA
65 AAAAATCTAATTTTAGTGAAAAACAAATATTTAAATTTATATTCTCAGACTAAAAGTGTTTAACG
* *
510811 ATATACAAATTTTAATTTTTAAGA-AAAGAATAATAAGGATAAAAATAATTATAGCTCAAATTTG
130 ATATACAAATTTTAATTTTTAA-ATAAAGAATAATAAGGATAAAAATAATTATAGTTCAAAATTG
* ** * * * * * *
510875 ACATAAAAAAACCTTAATGTAAAATTGTAAGAATTGACTTAAAAACTTATTAAGGTGA
194 ACATAGAAAAGTCTTGATGTAAAACTGTAACAATTGACGTAAAAACTTATAAAGGTGG
*
510933 AATAACTAAATTTTAAATCTTAACGTAAATGTGTGAGAGTTAATATAACAAGTCAATTAAGTAAA
1 AATAACTAAATTTTAAATCTTAACGTAAATGTGTGAGAGTTAACATAACAAGTCAATTAAGT-AA
* * * * *
510998 AAAAATCTAATTCTAGTGAAAAACAAATATTTAAATTTATATTCTCAAAATAAACGTATTTAACG
65 AAAAATCTAATTTTAGTGAAAAACAAATATTTAAATTTATATTCTCAGACTAAAAGTGTTTAACG
* * * * *
511063 ATACACCAATTTTAATTTTTAAATAAAAAATAATAAGGTTAAAAATAATTATACTTCAAAATTGA
130 ATATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAATAATTATAGTTCAAAATTGA
* * * * *
511128 TATAGAAAAGTTTTGACGTAAAACTGTAAGAATTGACGTAAAAACTTATAAAGGTAG
195 CATAGAAAAGTCTTGATGTAAAACTGTAACAATTGACGTAAAAACTTATAAAGGTGG
*
511185 AATAACTAAATTTTAAATCTTAACGTAAATGTGTGAGAATTAACATAACAAGTCAATTAAGTAAA
1 AATAACTAAATTTTAAATCTTAACGTAAATGTGTGAGAGTTAACATAACAAGTCAATTAAGT---
*
511250 AAAAAAATCTAATTTTAGTGAAAAACAAATATTTAAATTTATATTCTCAGACTAAAAGTGTTCAA
63 AAAAAAATCTAATTTTAGTGAAAAACAAATATTTAAATTTATATTCTCAGACTAAAAGTGTTTAA
*
511315 CGATATACAAATTTTAATTTTTAAATAAAGAATAATAAGAATAAAAATAATTATAGTTCAAAATT
128 CGATATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAATAATTATAGTTCAAAATT
* * ** * * *
511380 GATATA-AATAAGCCTTGACATAAATCTGTAATAATTGACGTAAAAACTTATAAAGGTGA
193 GACATAGAA-AAGTCTTGATGTAAAACTGTAACAATTGACGTAAAAACTTATAAAGGTGG
* *
511439 AATTACTAAATTTTAAATCTTAACGTAAATGTGTGAGAGTTAACGTAACAAGTCAATTAAGTAAA
1 AATAACTAAATTTTAAATCTTAACGTAAATGTGTGAGAGTTAACATAACAAGTCAATTAAGTAAA
* * *
511504 AAAATCTAATTTTAGTAAAAAATAAATATTTAAATTTATATTCTC-GAGCT-AAAGTGTTTAGCG
66 AAAATCTAATTTTAGTGAAAAACAAATATTTAAATTTATATTCTCAGA-CTAAAAGTGTTTAACG
**
511567 ATATACAAATTTTAATTTTTAAATAAAGAATAATAATAATAATAATAATTATTATTATTATTGTT
130 ATATACAAATTTTAATTTTTAAATAAAGAATAATAAGGAT-A-AA-AA-TA--ATTA-TA--GTT
* * ** * * *
511632 TAAAATTGACATAGATAAG-CTTTGACATAAAACTGTAACAATTGACATAAAATCTTATAAATGT
186 CAAAATTGACATAGAAAAGTC-TTGATGTAAAACTGTAACAATTGACGTAAAAACTTATAAAGGT
*
511696 TG
250 GG
* * * * ** *
511698 AATAGCTAAATTTTAAATATGAACGTAAATGTGTGAGAGTTAAACGTAATTAGTTAATTAAGTAA
1 AATAACTAAATTTTAAATCTTAACGTAAATGTGTGAGAGTT-AACATAACAAGTCAATTAAGTAA
* * * * * * * * * * *
511763 CAAAATCTAATTTTAATGGAAAATAAATATTTATATTTATATTATCTGGCTAAAAGTATGTAACA
65 AAAAATCTAATTTTAGTGAAAAACAAATATTTAAATTTATATTCTCAGACTAAAAGTGTTTAACG
* * * *
511828 ATATTCAAATTTTTA-TTTTAAATAAAGAATAATAAAGATAAAGATAATTATAGTT-AAAAGTT-
130 ATATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAATAATTATAGTTCAAAA-TTG
* * ** * * * * *
511890 ACTATTGAAAAGGCTTGACT-TAAAGTTGTAAAAATTAACGTCAAATCTTATAAAAGTGG
194 AC-ATAGAAAAGTCTTGA-TGTAAAACTGTAACAATTGACGTAAAAACTTATAAAGGTGG
* * * *
511949 AATAAAC-AAATTTAAAATCTTAACCTAAATGTGTGAAAGTTAACGTAACAAGT
1 AAT-AACTAAATTTTAAATCTTAACGTAAATGTGTGAGAGTTAACATAACAAGT
512002 GATAATAGTA
Statistics
Matches: 1581, Mismatches: 197, Indels: 78
0.85 0.11 0.04
Matches are distributed among these distances:
237 1 0.00
238 52 0.03
239 73 0.05
240 4 0.00
243 1 0.00
245 1 0.00
246 3 0.00
247 1 0.00
248 2 0.00
250 70 0.04
251 468 0.30
252 452 0.29
253 7 0.00
254 233 0.15
256 6 0.00
257 3 0.00
258 3 0.00
259 93 0.06
260 85 0.05
261 23 0.01
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.34
Consensus pattern (251 bp):
AATAACTAAATTTTAAATCTTAACGTAAATGTGTGAGAGTTAACATAACAAGTCAATTAAGTAAA
AAAATCTAATTTTAGTGAAAAACAAATATTTAAATTTATATTCTCAGACTAAAAGTGTTTAACGA
TATACAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAATAATTATAGTTCAAAATTGAC
ATAGAAAAGTCTTGATGTAAAACTGTAACAATTGACGTAAAAACTTATAAAGGTGG
Found at i:514531 original size:28 final size:29
Alignment explanation
Indices: 514483--514548 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 29
514473 GTAAATTTTT
**
514483 AAAAATTACACTTTTACCCCCGTAAAGTG
1 AAAAATTACACTTTTACCCCCAAAAAGTG
** *
514512 AAAAATTACA-TTTTTGCCCCAAAAATTG
1 AAAAATTACACTTTTACCCCCAAAAAGTG
514540 AAAAATTAC
1 AAAAATTAC
514549 CCATAGACAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 22 0.69
29 10 0.31
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.29
Consensus pattern (29 bp):
AAAAATTACACTTTTACCCCCAAAAAGTG
Found at i:527347 original size:96 final size:96
Alignment explanation
Indices: 527183--527668 Score: 679
Period size: 96 Copynumber: 5.1 Consensus size: 96
527173 AGTGAAATTA
* * * * * *
527183 AGAGTTTAAAGTATGAAATTGAAAAGTTGAAGGGATTGTTGAAGTGTGATGAAAATAATCAAAAG
1 AGAGTTTGAAGTGTGAAATTGAAAAGTTGAAGGGATTATTGGAGTATGATAAAAATAATCAAAAG
* *
527248 TTGAAAGAAAGAGAGAAGCAACTGGAGTATG
66 TTGAAAGAAAAAGAGAAGCAACAGGAGTATG
* * *
527279 AGAGTTTGAAGTGTGAAATTAAAAAGTTGAAGGGATTATTGGAGTATAATAAAAATAGTCAAAAG
1 AGAGTTTGAAGTGTGAAATTGAAAAGTTGAAGGGATTATTGGAGTATGATAAAAATAATCAAAAG
* *
527344 TTGAAAGAAAAAGAGGAGCAACAAGAGTA-G
66 TTGAAAGAAAAAGAGAAGCAACAGGAGTATG
* * * *
527374 TAGAGTTTGAAGTGTGAAATTGAAAAGTTGAAGGGATTATTAGAATATGATGAAAATAGTCAAAA
1 -AGAGTTTGAAGTGTGAAATTGAAAAGTTGAAGGGATTATTGGAGTATGATAAAAATAATCAAAA
* * * * * *
527439 GCTAAAAGAAAAAGAGAAACAACGGGTGAATG
65 GTTGAAAGAAAAAGAGAAGCAACAGGAGTATG
*
527471 AGAGTTTGAAGTGTGAAATTGAAAAGTTGAAGGGATTGTTGGAGTATGATAAAAATAATCAAAAG
1 AGAGTTTGAAGTGTGAAATTGAAAAGTTGAAGGGATTATTGGAGTATGATAAAAATAATCAAAAG
* *
527536 TTGAAAGAAAAAGAGAAGTAACAAGAGTATG
66 TTGAAAGAAAAAGAGAAGCAACAGGAGTATG
* *
527567 AGAGTTTGAAGAGTGAAATTGAAAAGTTGAAGGAATTATTGGAGTATGATAAAAATAATCAAAAG
1 AGAGTTTGAAGTGTGAAATTGAAAAGTTGAAGGGATTATTGGAGTATGATAAAAATAATCAAAAG
**
527632 TTGAAAGAAAAAGAGAAGCAATGGGAGTATG
66 TTGAAAGAAAAAGAGAAGCAACAGGAGTATG
527663 AG-GTTT
1 AGAGTTT
527669 TTGTTAGCTT
Statistics
Matches: 342, Mismatches: 46, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
95 5 0.01
96 336 0.98
97 1 0.00
ACGTcount: A:0.47, C:0.03, G:0.27, T:0.23
Consensus pattern (96 bp):
AGAGTTTGAAGTGTGAAATTGAAAAGTTGAAGGGATTATTGGAGTATGATAAAAATAATCAAAAG
TTGAAAGAAAAAGAGAAGCAACAGGAGTATG
Found at i:533707 original size:68 final size:66
Alignment explanation
Indices: 533627--533812 Score: 173
Period size: 68 Copynumber: 2.8 Consensus size: 66
533617 TGTTGATTAA
* * *
533627 CTGGACAGCGCTGCAGCGCTGGGAGTGTGGCGCTGCAGCGCTAATGCTACTGCCTTGTTGATATG
1 CTGGACAGCGCTGCAGCGCTGGGAGTGTGGCGCTGCAGCGCTAATGCTACTGCCTTGGT-AAAAG
533692 GTG
65 G-G
* * * * * * * * *
533695 CTGGACAACGCTGTAGCGCTGTGAGTATGGCACTGCAACGCTAGA-GGTTCTG-TTTGGTAAAAG
1 CTGGACAGCGCTGCAGCGCTGGGAGTGTGGCGCTGCAGCGCTA-ATGCTACTGCCTTGGTAAAAG
533758 GG
65 GG
** * *
533760 --GGACAGCGCTGCAGCTTTGGGAGTGTGGCGTTGCAGCGCTGATGCTACTGCCT
1 CTGGACAGCGCTGCAGCGCTGGGAGTGTGGCGCTGCAGCGCTAATGCTACTGCCT
533813 CGTAGAAATG
Statistics
Matches: 90, Mismatches: 25, Indels: 10
0.72 0.20 0.08
Matches are distributed among these distances:
62 1 0.01
63 36 0.40
64 1 0.01
65 1 0.01
66 4 0.04
67 4 0.04
68 42 0.47
69 1 0.01
ACGTcount: A:0.17, C:0.22, G:0.36, T:0.25
Consensus pattern (66 bp):
CTGGACAGCGCTGCAGCGCTGGGAGTGTGGCGCTGCAGCGCTAATGCTACTGCCTTGGTAAAAGG
G
Found at i:539996 original size:249 final size:249
Alignment explanation
Indices: 539398--541966 Score: 2868
Period size: 252 Copynumber: 10.3 Consensus size: 249
539388 CGTAAAGTAA
* * * * * * *
539398 TAAGAATTTACATAAAAACTCATAAAAGAGAAATAACTAAATTTTAAATCTTAACATAAATATGT
1 TAAGAATTGACGTAAAAACTTATAAAAGTGGAATAACTAAATTTTAAATCTTAACGTAAATGTGT
* * *
539463 GAAAGTTAACATAACAAGTCAATTAAGTTAAAAAAATCTAAATTTAATGAAAAATAAATATTTAA
66 GAGAGTTAACGTAACAAGTCAATTAAGTAAAAAAAATCTAAATTTAAT-AAAAATAAATATTTAA
* *
539528 ATTTATATTCT-AGGGCTAAAAGTGTTTAATGATATA-AAGATTTTAATTTTTAAATAAAGAATA
130 ATTTATATTCTCA-GGCTGAAAGTGTTTAACGATATACAA-ATTTTAATTTTTAAATAAAGAATA
* * *
539591 ATAAGGATAAAAATAATTATAGTTCAAAATTGACGTAGAAAAGCCTT-ATCGTAAAACTG
193 ATAAGGATAAAAATAATTATAGTTCAAAATTGACATTG--AAGCTTTGA-CGTAAAACTG
* * *
539650 TAAAGAATTGACGTAAAAACTTATAAAAGTTGAATAACTAAATTTTAAATCTTAACATAAATGTA
1 T-AAGAATTGACGTAAAAACTTATAAAAGTGGAATAACTAAATTTTAAATCTTAACGTAAATGTG
*
539715 TGAGAGTTAACGTAACAAGTCAATTAAGTAAAAAAAATCTAAATCTAATAAAAGA-AAATATTTA
65 TGAGAGTTAACGTAACAAGTCAATTAAGTAAAAAAAATCTAAATTTAATAAAA-ATAAATATTTA
* * * * * *
539779 AATTTATACTCTCGGGGCTGAAAGTGTTTAACGATAAAAAAATTTTAATTTTTCAATTAAGAATA
129 AATTTATATTCTC-AGGCTGAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATA
* * *
539844 AGAAGGATAAAAATAATTATAGTTCAAAGTTGACATTG-AGCTTTGACGTAAAATTG
193 ATAAGGATAAAAATAATTATAGTTCAAAATTGACATTGAAGCTTTGACGTAAAACTG
* * * * * *
539900 TAAGAATTGACGTTAAAACTTGTAAAGGTAGAATAACTAAATTTTAAATCTTAACGTAAGTTTGT
1 TAAGAATTGACGTAAAAACTTATAAAAGTGGAATAACTAAATTTTAAATCTTAACGTAAATGTGT
* * * *
539965 GAGAGTTAACGTAATAAGTCAACTAAGTAAAAATAATCTAAATTTAATAAAAACAAATATTT-AA
66 GAGAGTTAACGTAACAAGTCAATTAAGTAAAAAAAATCTAAATTTAATAAAAATAAATATTTAAA
540029 TTTATATTCTCAGGCTGAAAGTGTTTAACG----AC--A---TAA----TAAATAAAGAATAATA
131 TTTATATTCTCAGGCTGAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAATA
* ** * * *
540081 AGAATAAAAATAATTATAGTTCAAAATTGATGTAGAAAAGTTTTAACGTAAAACTG
196 AGGATAAAAATAATTATAGTTCAAAATTGACATTG--AAGCTTTGACGTAAAACTG
* * *
540137 TAAGAATTGACGTAAAAACTTATAAAAGTGGAATAACTAAATTATAAATCTTAATGTAAACGTGT
1 TAAGAATTGACGTAAAAACTTATAAAAGTGGAATAACTAAATTTTAAATCTTAACGTAAATGTGT
* *
540202 GAGAGTTAACGTAATAAGTCAATTAAGTAAAAACAA-CATAAATTTAATGAAAAATAAATATTTA
66 GAGAGTTAACGTAACAAGTCAATTAAGTAAAAAAAATC-TAAATTTAAT-AAAAATAAATATTTA
* ** ** * * *
540266 AATTTATATTTTTTGATTGAAAGTGTTTAATGATAAAGAAATTTTAATTTTTAAATAAAGAATAA
129 AATTTATATTCTCAGGCTGAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAA
* * * * * *
540331 TAAGGATAAAAATTATGATAGTTCAAAGTTGATA-TGAAAAAGCCTTGACATAAAACTG
194 TAAGGATAAAAATAATTATAGTTCAAAATTGACATTG---AAGCTTTGACGTAAAACTG
* * * *
540389 TAAGAATTGACGTAAAAACTTGTAAAAGTGAAATTACTAAATTTTAAATCTTAACGTAAATGTAT
1 TAAGAATTGACGTAAAAACTTATAAAAGTGGAATAACTAAATTTTAAATCTTAACGTAAATGTGT
* * * * **
540454 GAGACTTTACGTAACAAGTCAATCAAGTAAAAAAAATTTAAATTTAATAAAAGCAAATATTTAAA
66 GAGAGTTAACGTAACAAGTCAATTAAGTAAAAAAAATCTAAATTTAATAAAAATAAATATTTAAA
* * * *
540519 TTTATATTCTCTA-GCTAAAAATGTTTAACGATATACGAATTTTAATTTTTAAATTAAGAATAAT
131 TTTATATTCTC-AGGCTGAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAAT
* * * *
540583 AAAGATAAAAAAAATTATAGTTCAAAGTTGACA-TGAAAAAGCCTTGACGTAAAACTG
195 AAGGATAAAAATAATTATAGTTCAAAATTGACATTG---AAGCTTTGACGTAAAACTG
* * ** *
540640 TAAGAATTGACGTAAAAACTTGT-AAAGTTGAAATAACTAAATTTTAAATCTTAGTGTAAATGTA
1 TAAGAATTGACGTAAAAACTTATAAAAG-TGGAATAACTAAATTTTAAATCTTAACGTAAATGTG
* **
540704 TGAGAGTTAACATAACAAGTCAACCAAGTAAAAAAAATCTAAATTTAAT-AAAA-AAATATTTAA
65 TGAGAGTTAACGTAACAAGTCAATTAAGTAAAAAAAATCTAAATTTAATAAAAATAAATATTTAA
* * *
540767 ATTTATATTCTC-GAGCTGAAAGTGTTTAACGATATACAAATTTTAAGTTTTGAATTAAGAATAA
130 ATTTATATTCTCAG-GCTGAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAA
* * *
540831 TAAAGATAAAAATAATTATAGTTCAAAATTGATA-TGAAAAAG-TCTTAACGTAAAACTG
194 TAAGGATAAAAATAATTATAGTTCAAAATTGACATTG---AAGCT-TTGACGTAAAACTG
* * * * *
540889 TAAGAATTGAAGTAAAAACTTGTAAATGTGGAATAATTAAATTTTAAGTCTTAAC--------GT
1 TAAGAATTGACGTAAAAACTTATAAAAGTGGAATAACTAAATTTTAAATCTTAACGTAAATGTGT
* * *
540946 GAGAGTTAACATAACAAGTCAATTAAGTAAAAATAATCTAAATTTAATAAAAAGAAAATATTTAA
66 GAGAGTTAACGTAACAAGTCAATTAAGTAAAAAAAATCTAAATTTAATAAAAA-TAAATATTTAA
* * * * * *
541011 ATTTATATTCTCAGGCTGAAAATGTTTACCCATATAAAAAATTTAATTTTTAAATTAAGAATAAT
130 ATTTATATTCTCAGGCTGAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAAT
* * ** *
541076 AAGGATAAAAATAATTATAGTTCAAAGTTGACATGGAAAATCTTGATGTAAAACTG
195 AAGGATAAAAATAATTATAGTTCAAAATTGACATTGAAGCT-TTGACGTAAAACTG
* * *
541132 TAAAAATTGACGTAAAAACTTATAAATGTGGAATAACTAAATTTTAAATCTTAACGTAAGTGTGT
1 TAAGAATTGACGTAAAAACTTATAAAAGTGGAATAACTAAATTTTAAATCTTAACGTAAATGTGT
*
541197 GAGAGTTAACGTAACAAGTCAATTAAGTAAAAACAATCTAAATTTAATAAAAATAAATATTTAAA
66 GAGAGTTAACGTAACAAGTCAATTAAGTAAAAAAAATCTAAATTTAATAAAAATAAATATTTAAA
* * * * * *
541262 TTTATGTTTTCAGACTAAAAGTGTTTAACAATATACAAATTTTAATTTTTAAACAAAG-ATAATA
131 TTTATATTCTCAGGCTGAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAATA
* *
541326 AGGATAAAAATAATTATAGTTCAAAATT-AGCATAGAAAAGCATTGACGTAAAACTG
196 AGGATAAAAATAATTATAGTTCAAAATTGA-CATTG--AAGCTTTGACGTAAAACTG
* * ** * *
541382 CAAGAATTGACGTAAAAACTTATAAGAGTAAAATAACTAAATTTTAAATCTTAACATAAGTGTGT
1 TAAGAATTGACGTAAAAACTTATAAAAGTGGAATAACTAAATTTTAAATCTTAACGTAAATGTGT
* * *
541447 GGGAGTTAACGT-ATAAGTCAATTAAGTAAAAAAAATCTATATTTAATAAAAAATAAATATTTAA
66 GAGAGTTAACGTAACAAGTCAATTAAGTAAAAAAAATCTAAATTTAAT-AAAAATAAATATTTAA
* * * * *
541511 ATTTCTATTTTCTCAAGC-AATAAGTGTTTAACGATATGCAAATTTTAATTTTTAAATAAAAAAT
130 A-TT-TATATTCTCAGGCTGA-AAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAAT
* * * *
541575 AATAATGATAAAAATAATTATAGTTCAAAATTGACGTAGGAAAG-TCCTGACGTAAAACTG
192 AATAAGGATAAAAATAATTATAGTTCAAAATTGACAT-TG-AAGCT-TTGACGTAAAACTG
* **
541635 TAAGAATTGACGTAAAAACTTGTAAAAGTGGAATAACTAAATTTTAAATCTTAACGTAAGCGTGT
1 TAAGAATTGACGTAAAAACTTATAAAAGTGGAATAACTAAATTTTAAATCTTAACGTAAATGTGT
* * * *
541700 GAGAGTTAACATAACAAGCCAATTAAGTAAAAACAATCTAATTTTAATGAAAAATAAATATTTAA
66 GAGAGTTAACGTAACAAGTCAATTAAGTAAAAAAAATCTAAATTTAAT-AAAAATAAATATTTAA
* * * * * * *
541765 ATTTATACTCTCGGGTTCAAAATATTTAACGATATACAAATTTTAATTTTTAAATAAAAAATAAT
130 ATTTATATTCTCAGGCTGAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAAT
* * * * * **
541830 AAGGATAAGAATAATTATAGTTTAAAGTT-ACTATTAGAAGGGTTTGACGTTAAGTTG
195 AAGGATAAAAATAATTATAGTTCAAAATTGAC-ATT-GAA-GCTTTGACGTAAAACTG
* * ** * * * *
541887 TAAGAATTGACGTAAAATCTTATAAAGGTATAATAAAC-ATATTTAAAATCTTAACGTTAATCTG
1 TAAGAATTGACGTAAAAACTTATAAAAGTGGAAT-AACTAAATTTTAAATCTTAACGTAAATGTG
* *
541951 TAAGAGTTAATGTAAC
65 TGAGAGTTAACGTAAC
541967 TAGTAATAAG
Statistics
Matches: 1997, Mismatches: 254, Indels: 132
0.84 0.11 0.06
Matches are distributed among these distances:
234 43 0.02
236 1 0.00
237 115 0.06
238 16 0.01
239 26 0.01
241 47 0.02
242 6 0.00
243 66 0.03
244 96 0.05
245 3 0.00
247 18 0.01
248 17 0.01
249 344 0.17
250 182 0.09
251 282 0.14
252 380 0.19
253 304 0.15
254 51 0.03
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (249 bp):
TAAGAATTGACGTAAAAACTTATAAAAGTGGAATAACTAAATTTTAAATCTTAACGTAAATGTGT
GAGAGTTAACGTAACAAGTCAATTAAGTAAAAAAAATCTAAATTTAATAAAAATAAATATTTAAA
TTTATATTCTCAGGCTGAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATAAAGAATAATA
AGGATAAAAATAATTATAGTTCAAAATTGACATTGAAGCTTTGACGTAAAACTG
Found at i:540757 original size:20 final size:21
Alignment explanation
Indices: 540732--540771 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
540722 GTCAACCAAG
540732 TAAAAAAA-ATCTAAATTTAA
1 TAAAAAAATATCTAAATTTAA
*
540752 TAAAAAAATATTTAAATTTA
1 TAAAAAAATATCTAAATTTA
540772 TATTCTCGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAAAAAATATCTAAATTTAA
Found at i:541587 original size:995 final size:979
Alignment explanation
Indices: 539399--541941 Score: 3272
Period size: 995 Copynumber: 2.6 Consensus size: 979
539389 GTAAAGTAAT
* * * *
539399 AAGAATTTACATAAAAACTCATAAAAG-AGAAATAACTAAATTTTAAATCTTAACATAAATATGT
1 AAGAATTGACGTAAAAACTTATAAAAGTA-AAATAACTAAATTTTAAATCTTAACATAAATGTGT
* * *
539463 GAAAGTTAACATAACAAGTCAATTAAGTTAAAAAAATCTAAATTTAATGAAAAATAAATATTTAA
65 GAGAGTTAACGTAACAAGTCAATTAAGTAAAAAAAATCTAAATTTAAT-AAAAATAAATATTTAA
* * *
539528 ATTTATATTCT-AGGGCTAAAAGTGTTTAATGATATAAAGATTTTAATTTTTAAATAAAGAATAA
129 ATTTATATTCTCA-AGCTAAAAGTGTTTAACGATATCAA-ATTTTAATTTTTAAATAAAGAATAA
*
539592 TAAGGATAAAAATAATTATAGTTCAAAATTGACGTAGAAAAGCCTT-ATCGTAAAACTGTAAAGA
192 TAAAGATAAAAATAATTATAGTTCAAAATTGACGTAGAAAAGCCTTGA-CGTAAAACTGT-AAGA
* *
539656 ATTGACGTAAAAACTTATAAAAGTTGAATAACTAAATTTTAAATCTTAACATAAATGTATGAGAG
255 ATTGACGTAAAAACTTGTAAAAGTTGAATAACTAAATTTTAAATCTTAACGTAAATGTATGAGAG
* *
539721 TTAACGTAACAAGTCAATTAAGTAAAAAAAATCTAAATCTAATAAAAGAAAATATTTAAATTTAT
320 TTAACATAACAAGTCAATTAAGTAAAAAAAATCTAAATTTAATAAAA-AAAATATTTAAATTTAT
* * * *
539786 ACTCTCGGGGCTGAAAGTGTTTAACGATAAAAAAATTTTAATTTTTCAATTAAGAATAAGAAGGA
384 ACTCTC-GGGCTGAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATTAAGAATAATAAGGA
* * * * *
539851 TAAAAATAATTATAGTTCAAAGTTGACATTGAGCTTTGACGTAAAATTGTAAGAATTGACGTTAA
448 TAAAAATAATTATAGTTCAAAATTGACATTGAGCTTTAACGTAAAACTGTAAGAATTGAAGTAAA
* *
539916 AACTTGTAAAGGTAGAATAACTAAATTTTAAATCTTAACGTAAGTTTGTGAGAGTTAACGTAATA
513 AACTTGTAAAGGTAGAATAACTAAATTTTAAATCTTAAC-------TGTGAGAGTTAACATAACA
*
539981 AGTCAACTAAGTAAAAATAATCTAAATTTAATAAAAACAAATATTTAATTTATATTCTCAGGCTG
571 AGTCAACTAAGTAAAAATAATCTAAATTTAATAAAAAAAAATATTTAATTTATATTCTCAGGCTG
* ** *
540046 AAAGTGTTTAACGACATAATAAATAAAGAATAATAAGAATAAAAATAATTATAGTTCAAAATTGA
636 AAAATGTTTAAAAAAATAATAAATAAAGAATAATAAGAATAAAAATAATTATAGTTCAAAATTGA
** * *
540111 TGTAGAAAAGTTTTAACGTAAAACTGTAAGAATTGACGTAAAAACTTATAAAAGTGGAATAACTA
701 CATAGAAAAGTCTTAACGTAAAACTGTAAAAATTGACGTAAAAACTTATAAAAGTGGAATAACTA
* *
540176 AATTATAAATCTTAATGTAAACGTGTGAGAGTTAACGTAATAAGTCAATTAAGTAAAAACAACAT
766 AATTATAAATCTTAACGTAAACGTGTGAGAGTTAACGTAACAAGTCAATTAAGTAAAAACAACAT
** * * ** *
540241 AAATTTAATGAAAAATAAATATTTAAATTTATATTTTTTGATTGAAAGTGTTTAATGATAAAGAA
831 AAATTTAATGAAAAATAAATATTTAAATTTATATTTTCAGACTAAAAGTGTTTAACAATAAACAA
* * *
540306 ATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAATTATGATAGTTCAAAGTTGATATGAAAA
896 ATTTTAATTTTTAAACAAAGAATAATAAGGATAAAAATAATGATAGTTCAAAATTGATATGAAAA
* *
540371 AGCCTTGACATAAAACTGT
961 AGCATTGACATAAAACTGC
* * * * *
540390 AAGAATTGACGTAAAAACTTGTAAAAGTGAAATTACTAAATTTTAAATCTTAACGTAAATGTATG
1 AAGAATTGACGTAAAAACTTATAAAAGTAAAATAACTAAATTTTAAATCTTAACATAAATGTGTG
* * * * **
540455 AGACTTTACGTAACAAGTCAATCAAGTAAAAAAAATTTAAATTTAATAAAAGCAAATATTTAAAT
66 AGAGTTAACGTAACAAGTCAATTAAGTAAAAAAAATCTAAATTTAATAAAAATAAATATTTAAAT
* * * *
540520 TTATATTCTCTAGCTAAAAATGTTTAACGATATACGAATTTTAATTTTTAAATTAAGAATAATAA
131 TTATATTCTCAAGCTAAAAGTGTTTAACGATAT-CAAATTTTAATTTTTAAATAAAGAATAATAA
* * *
540585 AGATAAAAAAAATTATAGTTCAAAGTTGACAT-GAAAAAGCCTTGACGTAAAACTGTAAGAATTG
195 AGATAAAAATAATTATAGTTCAAAATTGACGTAG-AAAAGCCTTGACGTAAAACTGTAAGAATTG
**
540649 ACGTAAAAACTTGT-AAAGTTGAAATAACTAAATTTTAAATCTTAGTGTAAATGTATGAGAGTTA
259 ACGTAAAAACTTGTAAAAGTTG-AATAACTAAATTTTAAATCTTAACGTAAATGTATGAGAGTTA
** *
540713 ACATAACAAGTCAACCAAGTAAAAAAAATCTAAATTTAAT-AAAAAAATATTTAAATTTATATTC
323 ACATAACAAGTCAATTAAGTAAAAAAAATCTAAATTTAATAAAAAAAATATTTAAATTTATACTC
* * * *
540777 TCGAGCTGAAAGTGTTTAACGATATACAAATTTTAAGTTTTGAATTAAGAATAATAAAGATAAAA
388 TCGGGCTGAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATTAAGAATAATAAGGATAAAA
*
540842 ATAATTATAGTTCAAAATTGATA-TGAAAAAG-TCTTAACGTAAAACTGTAAGAATTGAAGTAAA
453 ATAATTATAGTTCAAAATTGACATTG----AGCT-TTAACGTAAAACTGTAAGAATTGAAGTAAA
* * * * *
540905 AACTTGTAAATGTGGAATAATTAAATTTTAAGTCTTAAC-GTGAGAGTTAACATAACAAGTCAAT
513 AACTTGTAAAGGTAGAATAACTAAATTTTAAATCTTAACTGTGAGAGTTAACATAACAAGTCAAC
540969 TAAGTAAAAATAATCTAAATTTAATAAAAAGAAAATATTTAAATTTATATTCTCAGGCTGAAAAT
578 TAAGTAAAAATAATCTAAATTTAATAAAAA-AAAATATTT-AATTTATATTCTCAGGCTGAAAAT
* *
541034 GTTTACCCATATAAAAAATTTAATTTTTAAATTAAGAATAATAAGGATAAAAATAATTATAGTTC
641 G-TT-----TA-AAAAAA--TAA----TAAATAAAGAATAATAAGAATAAAAATAATTATAGTTC
* * * * *
541099 AAAGTTGACATGGAAAA-TCTTGATGTAAAACTGTAAAAATTGACGTAAAAACTTATAAATGTGG
693 AAAATTGACATAGAAAAGTCTTAACGTAAAACTGTAAAAATTGACGTAAAAACTTATAAAAGTGG
* **
541163 AATAACTAAATTTTAAATCTTAACGTAAGTGTGTGAGAGTTAACGTAACAAGTCAATTAAGTAAA
758 AATAACTAAATTATAAATCTTAACGTAAACGTGTGAGAGTTAACGTAACAAGTCAATTAAGTAAA
*
541228 AACAATC-TAAATTTAAT-AAAAATAAATATTTAAATTTATGTTTTCAGACTAAAAGTGTTTAAC
823 AACAA-CATAAATTTAATGAAAAATAAATATTTAAATTTATATTTTCAGACTAAAAGTGTTTAAC
* *
541291 AATATACAAATTTTAATTTTTAAACAAAG-ATAATAAGGATAAAAATAATTATAGTTCAAAATTA
887 AATAAACAAATTTTAATTTTTAAACAAAGAATAATAAGGATAAAAATAATGATAGTTCAAAATT-
*
541355 GCATA-G-AAAAGCATTGACGTAAAACTGC
951 G-ATATGAAAAAGCATTGACATAAAACTGC
* *
541383 AAGAATTGACGTAAAAACTTATAAGAGTAAAATAACTAAATTTTAAATCTTAACATAAGTGTGTG
1 AAGAATTGACGTAAAAACTTATAAAAGTAAAATAACTAAATTTTAAATCTTAACATAAATGTGTG
* * *
541448 GGAGTTAACGT-ATAAGTCAATTAAGTAAAAAAAATCTATATTTAATAAAAAATAAATATTTAAA
66 AGAGTTAACGTAACAAGTCAATTAAGTAAAAAAAATCTAAATTTAAT-AAAAATAAATATTTAAA
* *
541512 TTTCTATTTTCTCAAGC-AATAAGTGTTTAACGATATGCAAATTTTAATTTTTAAATAAAAAATA
130 -TT-TATATTCTCAAGCTAA-AAGTGTTTAACGATAT-CAAATTTTAATTTTTAAATAAAGAATA
* *
541576 ATAATGATAAAAATAATTATAGTTCAAAATTGACGTAGGAAAGTCC-TGACGTAAAACTGTAAGA
191 ATAAAGATAAAAATAATTATAGTTCAAAATTGACGTAGAAAAG-CCTTGACGTAAAACTGTAAGA
* ** *
541640 ATTGACGTAAAAACTTGTAAAAGTGGAATAACTAAATTTTAAATCTTAACGTAAGCGTGTGAGAG
255 ATTGACGTAAAAACTTGTAAAAGTTGAATAACTAAATTTTAAATCTTAACGTAAATGTATGAGAG
* * *
541705 TTAACATAACAAGCCAATTAAGTAAAAACAATCTAATTTTAATGAAAAATAAATATTTAAATTTA
320 TTAACATAACAAGTCAATTAAGTAAAAAAAATCTAAATTTAAT-AAAAA-AAATATTTAAATTTA
* * * * * *
541770 TACTCTCGGGTTCAAAATATTTAACGATATACAAATTTTAATTTTTAAATAAAAAATAATAAGGA
383 TACTCTCGGGCTGAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATTAAGAATAATAAGGA
* * * * * * ** *
541835 TAAGAATAATTATAGTTTAAAGTT-ACTATTAGAAGGGTTTGACGTTAAGTTGTAAGAATTGACG
448 TAAAAATAATTATAGTTCAAAATTGAC-ATT-G-A-GCTTTAACGTAAAACTGTAAGAATTGAAG
* * * * *
541899 TAAAATCTTATAAAGGTATAATAAAC-ATATTTAAAATCTTAAC
509 TAAAAACTTGTAAAGGTAGAAT-AACTAAATTTTAAATCTTAAC
541942 GTTAATCTGT
Statistics
Matches: 1344, Mismatches: 163, Indels: 83
0.85 0.10 0.05
Matches are distributed among these distances:
981 52 0.04
982 8 0.01
983 24 0.02
984 2 0.00
985 2 0.00
986 77 0.06
987 22 0.02
988 11 0.01
989 162 0.12
990 122 0.09
991 97 0.07
992 34 0.03
993 131 0.10
994 71 0.05
995 314 0.23
996 59 0.04
997 7 0.01
998 144 0.11
999 4 0.00
1000 1 0.00
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (979 bp):
AAGAATTGACGTAAAAACTTATAAAAGTAAAATAACTAAATTTTAAATCTTAACATAAATGTGTG
AGAGTTAACGTAACAAGTCAATTAAGTAAAAAAAATCTAAATTTAATAAAAATAAATATTTAAAT
TTATATTCTCAAGCTAAAAGTGTTTAACGATATCAAATTTTAATTTTTAAATAAAGAATAATAAA
GATAAAAATAATTATAGTTCAAAATTGACGTAGAAAAGCCTTGACGTAAAACTGTAAGAATTGAC
GTAAAAACTTGTAAAAGTTGAATAACTAAATTTTAAATCTTAACGTAAATGTATGAGAGTTAACA
TAACAAGTCAATTAAGTAAAAAAAATCTAAATTTAATAAAAAAAATATTTAAATTTATACTCTCG
GGCTGAAAGTGTTTAACGATATACAAATTTTAATTTTTAAATTAAGAATAATAAGGATAAAAATA
ATTATAGTTCAAAATTGACATTGAGCTTTAACGTAAAACTGTAAGAATTGAAGTAAAAACTTGTA
AAGGTAGAATAACTAAATTTTAAATCTTAACTGTGAGAGTTAACATAACAAGTCAACTAAGTAAA
AATAATCTAAATTTAATAAAAAAAAATATTTAATTTATATTCTCAGGCTGAAAATGTTTAAAAAA
ATAATAAATAAAGAATAATAAGAATAAAAATAATTATAGTTCAAAATTGACATAGAAAAGTCTTA
ACGTAAAACTGTAAAAATTGACGTAAAAACTTATAAAAGTGGAATAACTAAATTATAAATCTTAA
CGTAAACGTGTGAGAGTTAACGTAACAAGTCAATTAAGTAAAAACAACATAAATTTAATGAAAAA
TAAATATTTAAATTTATATTTTCAGACTAAAAGTGTTTAACAATAAACAAATTTTAATTTTTAAA
CAAAGAATAATAAGGATAAAAATAATGATAGTTCAAAATTGATATGAAAAAGCATTGACATAAAA
CTGC
Done.