Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 1 of 93
Found at i:6449 original size:7 final size:7
Alignment explanation
Indices: 6433--6583 Score: 234
Period size: 7 Copynumber: 21.9 Consensus size: 7
6423 TTTAAAAAAA
6433 AAACCCT
1 AAACCCT
*
6440 AAACCTT
1 AAACCCT
6447 AAACCCT
1 AAACCCT
6454 AAACCCT
1 AAACCCT
6461 AAACCCT
1 AAACCCT
*
6468 AACCCCT
1 AAACCCT
*
6475 AACCCCT
1 AAACCCT
6482 AAACCCT
1 AAACCCT
6489 AAACCCT
1 AAACCCT
6496 AAACCCT
1 AAACCCT
6503 AAACCCT
1 AAACCCT
*
6510 AACCCCT
1 AAACCCT
*
6517 AACCCCT
1 AAACCCT
6524 AAACCCT
1 AAACCCT
6531 AAACCC-
1 AAACCCT
6537 AAACCCT
1 AAACCCT
6544 AAACCCT
1 AAACCCT
6551 AAACCCT
1 AAACCCT
6558 AAACCCT
1 AAACCCT
6565 -AACCCT
1 AAACCCT
*
6571 AAACTCT
1 AAACCCT
6578 AAACCC
1 AAACCC
6584 CGAACCCCGA
Statistics
Matches: 134, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
6 12 0.09
7 122 0.91
ACGTcount: A:0.40, C:0.45, G:0.00, T:0.15
Consensus pattern (7 bp):
AAACCCT
Found at i:10630 original size:51 final size:51
Alignment explanation
Indices: 10549--10649 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 51
10539 GTTCAGCATG
* *
10549 TTCAGACAGCCCAATGATCAGCCCAACAAATGCCAACAATCAAGAGATATA
1 TTCAGACAGCCCAATGAGCAGCCCAACAAATGCCAACAACCAAGAGATATA
* * * * *
10600 TTCATACAGCCTAATGGGCAGCCCAACAAATTCCAACAACCAGGAGATAT
1 TTCAGACAGCCCAATGAGCAGCCCAACAAATGCCAACAACCAAGAGATAT
10650 GATTAAAGGA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.41, C:0.28, G:0.15, T:0.17
Consensus pattern (51 bp):
TTCAGACAGCCCAATGAGCAGCCCAACAAATGCCAACAACCAAGAGATATA
Found at i:11289 original size:7 final size:7
Alignment explanation
Indices: 11279--11303 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
11269 AAAAAAAAAA
11279 AACCTTG
1 AACCTTG
11286 AACCTTG
1 AACCTTG
11293 AACCTTG
1 AACCTTG
11300 AACC
1 AACC
11304 CTAAACTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.12, T:0.24
Consensus pattern (7 bp):
AACCTTG
Found at i:11661 original size:7 final size:7
Alignment explanation
Indices: 11644--11932 Score: 120
Period size: 7 Copynumber: 42.4 Consensus size: 7
11634 CTGAATCCTG
*
11644 AACCCTG
1 AACCCTA
*
11651 AACCCAA
1 AACCCTA
*
11658 AACCCAA
1 AACCCTA
11665 AACCCTA
1 AACCCTA
*
11672 AACCTTA
1 AACCCTA
*
11679 AACCCCA
1 AACCCTA
*
11686 AACCTTA
1 AACCCTA
*
11693 AATCCGT-
1 AA-CCCTA
*
11700 AACCCAA
1 AACCCTA
*
11707 AACCCAA
1 AACCCTA
11714 AACCC-A
1 AACCCTA
*
11720 AACCC-G
1 AACCCTA
*
11726 AATCCTA
1 AACCCTA
*
11733 AACCCCA
1 AACCCTA
11740 AACCCTA
1 AACCCTA
11747 AACCC-A
1 AACCCTA
*
11753 AACCC-G
1 AACCCTA
*
11759 AATCCTA
1 AACCCTA
*
11766 AACCCCA
1 AACCCTA
11773 AACCCTA
1 AACCCTA
11780 AACCC-A
1 AACCCTA
*
11786 AACCCCA
1 AACCCTA
* *
11793 AACTC-G
1 AACCCTA
*
11799 AA-CCTCG
1 AACCCT-A
*
11806 AACCCTG
1 AACCCTA
*
11813 AACCCTG
1 AACCCTA
* *
11820 AATCCTG
1 AACCCTA
11827 AA-CCTGA
1 AACCCT-A
* *
11834 AACTCGA
1 AACCCTA
*
11841 ACCCCTA
1 AACCCTA
*
11848 ACCCCT-
1 AACCCTA
*
11854 AA-CCTCG
1 AACCCT-A
*
11861 AACCCTG
1 AACCCTA
**
11868 AACCCCG
1 AACCCTA
11875 AACCC-A
1 AACCCTA
11881 AACTCCTA
1 AAC-CCTA
11889 AACCC-A
1 AACCCTA
*
11895 AA-CCTCG
1 AACCCT-A
*
11902 AACCCAA
1 AACCCTA
11909 AACCCTA
1 AACCCTA
*
11916 AACCCTC
1 AACCCTA
11923 AACCCTA
1 AACCCTA
11930 AAC
1 AAC
11933 TTTAAAAAAA
Statistics
Matches: 222, Mismatches: 42, Indels: 36
0.74 0.14 0.12
Matches are distributed among these distances:
5 6 0.03
6 40 0.18
7 160 0.72
8 16 0.07
ACGTcount: A:0.40, C:0.44, G:0.05, T:0.11
Consensus pattern (7 bp):
AACCCTA
Found at i:11737 original size:33 final size:33
Alignment explanation
Indices: 11664--11790 Score: 166
Period size: 33 Copynumber: 3.8 Consensus size: 33
11654 CCAAAACCCA
* * **
11664 AAACCCTAAACCTTAAACCCCAAACCTTAAATCCGT
1 AAACCCCAAACCCTAAA-CCCAAACC-CGAATCC-T
* *
11700 -AACCCAAAACCCAAAACCCAAACCCGAATCCT
1 AAACCCCAAACCCTAAACCCAAACCCGAATCCT
11732 AAACCCCAAACCCTAAACCCAAACCCGAATCCT
1 AAACCCCAAACCCTAAACCCAAACCCGAATCCT
11765 AAACCCCAAACCCTAAACCCAAACCC
1 AAACCCCAAACCCTAAACCCAAACCC
11791 CAAACTCGAA
Statistics
Matches: 83, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
32 1 0.01
33 61 0.73
34 8 0.10
35 13 0.16
ACGTcount: A:0.44, C:0.43, G:0.02, T:0.10
Consensus pattern (33 bp):
AAACCCCAAACCCTAAACCCAAACCCGAATCCT
Found at i:11862 original size:21 final size:21
Alignment explanation
Indices: 11742--11906 Score: 78
Period size: 20 Copynumber: 8.1 Consensus size: 21
11732 AAACCCCAAA
*
11742 CCCTAAACCCAAACC-CGAA-
1 CCCTAACCCCAAACCTCGAAC
* * *
11761 TCCTAAACCCCAAACC-CTAAA
1 CCCT-AACCCCAAACCTCGAAC
*
11782 CCCAAACCCCAAA-CTCGAAC
1 CCCTAACCCCAAACCTCGAAC
* * **
11802 CTCGAACCCTGAACC-CTGAA-
1 CCCTAACCCCAAACCTC-GAAC
* **
11822 TCCTGAACCTGAAA-CTCGAAC
1 CCCT-AACCCCAAACCTCGAAC
*
11843 CCCTAACCCCTAACCTCGAA-
1 CCCTAACCCCAAACCTCGAAC
* *
11863 CCCTGAACCCCGAACC-CAAAC
1 CCCT-AACCCCAAACCTCGAAC
* *
11884 TCCTAAACCCAAACCTCGAAC
1 CCCTAACCCCAAACCTCGAAC
11905 CC
1 CC
11907 AAAACCCTAA
Statistics
Matches: 106, Mismatches: 28, Indels: 22
0.68 0.18 0.14
Matches are distributed among these distances:
19 4 0.04
20 62 0.58
21 40 0.38
ACGTcount: A:0.36, C:0.45, G:0.07, T:0.12
Consensus pattern (21 bp):
CCCTAACCCCAAACCTCGAAC
Found at i:11905 original size:27 final size:27
Alignment explanation
Indices: 11868--11920 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
11858 TCGAACCCTG
11868 AACCCCGAACCC-AAACTCCTAAACCCA
1 AACCCCGAACCCAAAAC-CCTAAACCCA
*
11895 AACCTCGAACCCAAAACCCTAAACCC
1 AACCCCGAACCCAAAACCCTAAACCC
11921 TCAACCCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.42, C:0.47, G:0.04, T:0.08
Consensus pattern (27 bp):
AACCCCGAACCCAAAACCCTAAACCCA
Found at i:11926 original size:21 final size:20
Alignment explanation
Indices: 11658--11932 Score: 66
Period size: 20 Copynumber: 13.5 Consensus size: 20
11648 CTGAACCCAA
**
11658 AACCCAAAACCCTAAACCTTA
1 AACCCAAAACCC-AAACCTCG
* * *
11679 AACCCCAAACCTTAAATC-CG
1 AACCCAAAACC-CAAACCTCG
*
11699 TAACCCAAAACCCAAAACC-CA
1 -AACCCAAAACCC-AAACCTCG
* * * * *
11720 AACCCGAATCCTAAACCCCA
1 AACCCAAAACCCAAACCTCG
*
11740 AACCCTAAACCCAAACC-CG
1 AACCCAAAACCCAAACCTCG
* * *
11759 AATCCTAAACCCCAAACC-CTA
1 AA-CCCAAAACCCAAACCTC-G
*
11780 AACCCAAACCCCAAA-CTCG
1 AACCCAAAACCCAAACCTCG
* *
11799 AACCTC-GAACCCTGAACC-CTG
1 AACC-CAAAACCC-AAACCTC-G
* ** *
11820 AATCCTGAACCTGAAA-CTCG
1 AACCCAAAACC-CAAACCTCG
* * *
11840 AACCCCTAACCCCTAACCTCG
1 AA-CCCAAAACCCAAACCTCG
* * * *
11861 AACCCTGAACCCCGAACC-CA
1 AACCC-AAAACCCAAACCTCG
*
11881 AACTCCTAAACCCAAACCTCG
1 AAC-CCAAAACCCAAACCTCG
11902 AACCCAAAACCCTAAACCCTC-
1 AACCCAAAACCC-AAA-CCTCG
*
11923 AACCCTAAAC
1 AACCCAAAAC
11933 TTTAAAAAAA
Statistics
Matches: 191, Mismatches: 42, Indels: 42
0.69 0.15 0.15
Matches are distributed among these distances:
19 17 0.09
20 86 0.45
21 84 0.44
22 4 0.02
ACGTcount: A:0.40, C:0.44, G:0.05, T:0.11
Consensus pattern (20 bp):
AACCCAAAACCCAAACCTCG
Found at i:11930 original size:41 final size:40
Alignment explanation
Indices: 11658--11932 Score: 112
Period size: 41 Copynumber: 6.8 Consensus size: 40
11648 CTGAACCCAA
* * * * *
11658 AACCCAAAACCCTAAACCTTAAACCCCAAACCTTAAATC-CG
1 AACCCAAAACCCCAAACC-CAAACCCTAAACC-CAAACCTCG
* * * * * *
11699 TAACCCAAAACCCAAAACCCAAACCCGAATCCTAAACCCCA
1 -AACCCAAAACCCCAAACCCAAACCCTAAACCCAAACCTCG
* * * *
11740 AACCCTAAA-CCCAAACCCGAATCCTAAACCCCAAACC-CTA
1 AACCCAAAACCCCAAACCCAAACCCTAAA-CCCAAACCTC-G
* * * *
11780 AACCC-AAACCCCAAACTCGAA-CCTCGAACCCTGAACC-CTG
1 AACCCAAAACCCCAAACCCAAACCCT-AAACCC-AAACCTC-G
* ** ** * * * *
11820 AATCCTGAACCTGAAACTCGAACCCCTAACCCCTAACCTCG
1 AACCCAAAACCCCAAAC-CCAAACCCTAAACCCAAACCTCG
** *
11861 AACCCTGAACCCCGAACCCAAACTCCTAAACCCAAACCTCG
1 AACCCAAAACCCCAAACCCAAAC-CCTAAACCCAAACCTCG
* *
11902 AACCCAAAACCCTAAACCCTCAACCCTAAAC
1 AACCCAAAACCCCAAACCC-AAACCCTAAAC
11933 TTTAAAAAAA
Statistics
Matches: 180, Mismatches: 41, Indels: 25
0.73 0.17 0.10
Matches are distributed among these distances:
39 24 0.13
40 53 0.29
41 74 0.41
42 26 0.14
43 3 0.02
ACGTcount: A:0.40, C:0.44, G:0.05, T:0.11
Consensus pattern (40 bp):
AACCCAAAACCCCAAACCCAAACCCTAAACCCAAACCTCG
Found at i:31510 original size:34 final size:34
Alignment explanation
Indices: 31472--31580 Score: 84
Period size: 34 Copynumber: 3.2 Consensus size: 34
31462 TGCTTCTCGA
31472 AGAATTTATACTGCTTACACAATTTTTTTGCTAT
1 AGAATTTATACTGCTTACACAATTTTTTTGCTAT
* * ** * *
31506 AGAATTT-T-CT--AT-GATGATTTTCCTTGCTTCT
1 AGAATTTATACTGCTTACACAATTTT-TTTGC-TAT
31537 CGAAGAATTTATACTGCTTACACAATTTTTTTGCTAT
1 ---AGAATTTATACTGCTTACACAATTTTTTTGCTAT
31574 AGAATTT
1 AGAATTT
31581 TCTATGATGA
Statistics
Matches: 53, Mismatches: 12, Indels: 20
0.62 0.14 0.24
Matches are distributed among these distances:
29 6 0.11
30 5 0.09
31 2 0.04
32 2 0.04
33 1 0.02
34 21 0.40
35 1 0.02
36 2 0.04
37 2 0.04
38 5 0.09
39 6 0.11
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.47
Consensus pattern (34 bp):
AGAATTTATACTGCTTACACAATTTTTTTGCTAT
Found at i:31541 original size:68 final size:68
Alignment explanation
Indices: 31461--31596 Score: 272
Period size: 68 Copynumber: 2.0 Consensus size: 68
31451 TTCACCGGTA
31461 TTGCTTCTCGAAGAATTTATACTGCTTACACAATTTTTTTGCTATAGAATTTTCTATGATGATTT
1 TTGCTTCTCGAAGAATTTATACTGCTTACACAATTTTTTTGCTATAGAATTTTCTATGATGATTT
31526 TCC
66 TCC
31529 TTGCTTCTCGAAGAATTTATACTGCTTACACAATTTTTTTGCTATAGAATTTTCTATGATGATTT
1 TTGCTTCTCGAAGAATTTATACTGCTTACACAATTTTTTTGCTATAGAATTTTCTATGATGATTT
31594 TCC
66 TCC
31597 CTGGCTTAGT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.47
Consensus pattern (68 bp):
TTGCTTCTCGAAGAATTTATACTGCTTACACAATTTTTTTGCTATAGAATTTTCTATGATGATTT
TCC
Found at i:38251 original size:115 final size:116
Alignment explanation
Indices: 38049--38279 Score: 356
Period size: 115 Copynumber: 2.0 Consensus size: 116
38039 TTGATGGCTG
*** **
38049 GGAAAGCTTCTTATGCCCTGCTTTTCACGGTCTGTCTTTGGAATATGCCTTCTTATGACATCATT
1 GGAAAGCTTCTTATGCCCTGCTAGCCAAAGTCTGTCTTTGGAATATGCCTTCTTATGACATCATT
* *
38114 ATAACACCTTAAGTGTACACTG-AAAGTGATACAAAGTCAGTTTAATGCTT
66 ATAACACCTTAAGTGTACACTGAAAACTGATACAAAGTCAGTTTAACGCTT
* *
38164 GGAAAGCTTCTTATGCCCTGCTAGCCAAAGTCTGTCTTTGGAATATGCCTTCTTATGGCATCGTT
1 GGAAAGCTTCTTATGCCCTGCTAGCCAAAGTCTGTCTTTGGAATATGCCTTCTTATGACATCATT
* *
38229 ATAACATCTTAAGTGTACACTGAAAACTGATTCAAAGTCAGTTTAACGCTT
66 ATAACACCTTAAGTGTACACTGAAAACTGATACAAAGTCAGTTTAACGCTT
38280 TTTTAGTACT
Statistics
Matches: 104, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
115 79 0.76
116 25 0.24
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (116 bp):
GGAAAGCTTCTTATGCCCTGCTAGCCAAAGTCTGTCTTTGGAATATGCCTTCTTATGACATCATT
ATAACACCTTAAGTGTACACTGAAAACTGATACAAAGTCAGTTTAACGCTT
Found at i:41768 original size:20 final size:21
Alignment explanation
Indices: 41717--41770 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
41707 TGATCGTTTT
41717 TATTAA-TATATAAATTAAAAA
1 TATTAATTA-ATAAATTAAAAA
41738 TATT--TTCAATAAATT-AAAA
1 TATTAATT-AATAAATTAAAAA
41757 TATTAATTAATAAA
1 TATTAATTAATAAA
41771 AATATTTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
19 8 0.28
20 14 0.48
21 7 0.24
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
TATTAATTAATAAATTAAAAA
Found at i:45778 original size:2 final size:2
Alignment explanation
Indices: 45771--45795 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
45761 CAGAATTACA
45771 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
45796 ATGTCCTGAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:47038 original size:27 final size:27
Alignment explanation
Indices: 47008--47070 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
46998 AAAAAAAAAA
47008 AAACAACAA-AAGAAAGCTGATGACTCC
1 AAAC-ACAAGAAGAAAGCTGATGACTCC
* * *
47035 AAACCCAAGCAGAAAGTTGATGACTCC
1 AAACACAAGAAGAAAGCTGATGACTCC
*
47062 AAACCCAAG
1 AAACACAAG
47071 CGAGATTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
26 3 0.09
27 29 0.91
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.11
Consensus pattern (27 bp):
AAACACAAGAAGAAAGCTGATGACTCC
Found at i:47071 original size:27 final size:27
Alignment explanation
Indices: 47018--47071 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
47008 AAACAACAAA
47018 AGAAAGCTGATGACTCCAAACCCAAGC
1 AGAAAGCTGATGACTCCAAACCCAAGC
*
47045 AGAAAGTTGATGACTCCAAACCCAAGC
1 AGAAAGCTGATGACTCCAAACCCAAGC
47072 GAGATTCAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.41, C:0.28, G:0.19, T:0.13
Consensus pattern (27 bp):
AGAAAGCTGATGACTCCAAACCCAAGC
Found at i:52202 original size:38 final size:38
Alignment explanation
Indices: 52151--52248 Score: 169
Period size: 38 Copynumber: 2.6 Consensus size: 38
52141 CTATCCCTCT
*
52151 GTCTAGCTCTCCAATGCCATCGGGGTATATATCTAGTC
1 GTCTAGCTCTCCAATGCCATCGGGGTATATATCTAGCC
52189 GTCTAGCTCTCCAATGCCATCGGGGTATATATCTAGCC
1 GTCTAGCTCTCCAATGCCATCGGGGTATATATCTAGCC
* *
52227 ATCTAGCTCTCCAACGCCATCG
1 GTCTAGCTCTCCAATGCCATCG
52249 AGGTCTACAT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 57 1.00
ACGTcount: A:0.21, C:0.31, G:0.19, T:0.29
Consensus pattern (38 bp):
GTCTAGCTCTCCAATGCCATCGGGGTATATATCTAGCC
Found at i:52602 original size:48 final size:48
Alignment explanation
Indices: 52531--52660 Score: 197
Period size: 48 Copynumber: 2.7 Consensus size: 48
52521 GTGCTTGAAT
* * *
52531 ATTACATGACTGAATATTTGTTGAACATTGCGTGACTTGTTTATAGAC
1 ATTACATGACTGAATATTTGTTGAGCATTGCGTGACTTGGTTAAAGAC
* * *
52579 ATTACATGATTGAATATTTGTTGAGCGTTGCGTGACTTGGTTAAAGGC
1 ATTACATGACTGAATATTTGTTGAGCATTGCGTGACTTGGTTAAAGAC
*
52627 ATTACGTGACTGAATATTTGTTGAGCATTGCGTG
1 ATTACATGACTGAATATTTGTTGAGCATTGCGTG
52661 GCAATGCATG
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 73 1.00
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (48 bp):
ATTACATGACTGAATATTTGTTGAGCATTGCGTGACTTGGTTAAAGAC
Found at i:59626 original size:24 final size:24
Alignment explanation
Indices: 59597--59644 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
59587 GGCTAAGCAT
* *
59597 GAGGGGCAGCAGCAGAAGTAGGAG
1 GAGGGGCAGCAACAGAAGCAGGAG
*
59621 GAGGGGCAGTAACAGAAGCAGGAG
1 GAGGGGCAGCAACAGAAGCAGGAG
59645 TAGCAGCATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.12, G:0.48, T:0.04
Consensus pattern (24 bp):
GAGGGGCAGCAACAGAAGCAGGAG
Found at i:64506 original size:2 final size:2
Alignment explanation
Indices: 64501--64548 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
64491 TAAGACCATA
64501 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
64543 AT AT AT
1 AT AT AT
64549 TAATCTAATG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:77540 original size:5 final size:5
Alignment explanation
Indices: 77525--77592 Score: 64
Period size: 5 Copynumber: 13.2 Consensus size: 5
77515 AGGTTGGTAG
* * * ** *
77525 AATAA ATTAA AATAA AATAA AATAA TTATTA GGTAAA AATAA AATAA AATAG
1 AATAA AATAA AATAA AATAA AATAA -AATAA AAT-AA AATAA AATAA AATAA
77577 AATAA AATAA AATAA A
1 AATAA AATAA AATAA A
77593 TATTATATAT
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
5 45 0.90
6 5 0.10
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (5 bp):
AATAA
Found at i:77693 original size:11 final size:11
Alignment explanation
Indices: 77679--77703 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
77669 AATAACTTTG
77679 AAATAAAAAAT
1 AAATAAAAAAT
77690 AAATAAAAAAT
1 AAATAAAAAAT
77701 AAA
1 AAA
77704 AAAGATAAAA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAATAAAAAAT
Found at i:77807 original size:20 final size:19
Alignment explanation
Indices: 77770--77808 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
77760 ATTTTTAAAT
77770 ATTAAATAATTTATAATTA
1 ATTAAATAATTTATAATTA
77789 ATTAAA-AATATTAATAATTA
1 ATTAAATAAT-TT-ATAATTA
77809 TAATTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.17
19 8 0.44
20 7 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTAAATAATTTATAATTA
Found at i:77823 original size:26 final size:28
Alignment explanation
Indices: 77765--77823 Score: 86
Period size: 26 Copynumber: 2.2 Consensus size: 28
77755 TTTATATTTT
77765 TAAATATTAAATAATTTATAATTAATTA
1 TAAATATTAAATAATTTATAATTAATTA
* *
77793 AAAATATT-AATAA-TTATAATTTATTA
1 TAAATATTAAATAATTTATAATTAATTA
77819 TAAAT
1 TAAAT
77824 NTTCATTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 16 0.57
27 5 0.18
28 7 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
TAAATATTAAATAATTTATAATTAATTA
Found at i:77948 original size:17 final size:17
Alignment explanation
Indices: 77923--77958 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
77913 TTTAATAAAT
77923 AAAACATTAATAGTTTA
1 AAAACATTAATAGTTTA
* *
77940 AAAATATTAATATTTTA
1 AAAACATTAATAGTTTA
77957 AA
1 AA
77959 TTTTACAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (17 bp):
AAAACATTAATAGTTTA
Found at i:78853 original size:45 final size:45
Alignment explanation
Indices: 78789--78895 Score: 178
Period size: 45 Copynumber: 2.4 Consensus size: 45
78779 AAACATGTCG
78789 TGTCACAGGTTTTTGTACATGACGTGTAACACGCTAACCATAACT
1 TGTCACAGGTTTTTGTACATGACGTGTAACACGCTAACCATAACT
* * *
78834 TGTCACAGGTTTTTGTACATGACGTGTCACACGTTAACCATGACT
1 TGTCACAGGTTTTTGTACATGACGTGTAACACGCTAACCATAACT
*
78879 TGTCACAGATTTTTGTA
1 TGTCACAGGTTTTTGTA
78896 TATAGTGTGT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 58 1.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.35
Consensus pattern (45 bp):
TGTCACAGGTTTTTGTACATGACGTGTAACACGCTAACCATAACT
Found at i:86313 original size:2 final size:2
Alignment explanation
Indices: 86306--86338 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
86296 AGTTCCCTGC
86306 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C- CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
86339 TCACTCCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:101694 original size:13 final size:13
Alignment explanation
Indices: 101676--101702 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
101666 CTAAAATTAT
101676 AACTTATAAAAAA
1 AACTTATAAAAAA
101689 AACTTATAAAAAA
1 AACTTATAAAAAA
101702 A
1 A
101703 TTTACCAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.22
Consensus pattern (13 bp):
AACTTATAAAAAA
Found at i:101904 original size:16 final size:18
Alignment explanation
Indices: 101883--101915 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
101873 AGATAATTTT
101883 TAAATTT-T-TTAAAAAA
1 TAAATTTATCTTAAAAAA
101899 TAAATTTATCTTAAAAA
1 TAAATTTATCTTAAAAA
101916 TATTATTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAATTTATCTTAAAAAA
Found at i:102199 original size:31 final size:31
Alignment explanation
Indices: 102161--102222 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
102151 TGCATATCGT
*
102161 AAACTTCAAACATGACTCAGCAGAAGGCTAC
1 AAACTTCAAACATGACTCAACAGAAGGCTAC
*
102192 AAACTTCAAACATGACTCAACGGAAGGCTAC
1 AAACTTCAAACATGACTCAACAGAAGGCTAC
102223 TGGATGGGCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.42, C:0.26, G:0.16, T:0.16
Consensus pattern (31 bp):
AAACTTCAAACATGACTCAACAGAAGGCTAC
Found at i:103133 original size:23 final size:23
Alignment explanation
Indices: 103103--103148 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
103093 TAGAATAACA
*
103103 ATTCCTAATTTTATTAGGATAAG
1 ATTCCTAATTGTATTAGGATAAG
103126 ATTCCTAATTGTATTAGGATAAG
1 ATTCCTAATTGTATTAGGATAAG
103149 GTTATTGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (23 bp):
ATTCCTAATTGTATTAGGATAAG
Found at i:108288 original size:4 final size:4
Alignment explanation
Indices: 108279--108304 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
108269 TTTATTCAAC
108279 AAAG AAAG AAAG AAAG AAAG AAAG AA
1 AAAG AAAG AAAG AAAG AAAG AAAG AA
108305 GATATATTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:110511 original size:4 final size:4
Alignment explanation
Indices: 110502--110526 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
110492 GTAGAATGTT
110502 GCTG GCTG GCTG GCTG GCTG GCTG G
1 GCTG GCTG GCTG GCTG GCTG GCTG G
110527 TGTTGAAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.52, T:0.24
Consensus pattern (4 bp):
GCTG
Found at i:135350 original size:46 final size:46
Alignment explanation
Indices: 135285--135375 Score: 173
Period size: 46 Copynumber: 2.0 Consensus size: 46
135275 GCCCCAAAAC
*
135285 CCCACCCCCCAACCCAACATTAATAACAAAATAGTGCCTAGGCTAA
1 CCCACCCCCCAACCCAACATTAATAACAAAATAGTACCTAGGCTAA
135331 CCCACCCCCCAACCCAACATTAATAACAAAATAGTACCTAGGCTA
1 CCCACCCCCCAACCCAACATTAATAACAAAATAGTACCTAGGCTA
135376 CTATTACTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.40, C:0.37, G:0.08, T:0.15
Consensus pattern (46 bp):
CCCACCCCCCAACCCAACATTAATAACAAAATAGTACCTAGGCTAA
Found at i:136331 original size:7 final size:7
Alignment explanation
Indices: 136317--136359 Score: 61
Period size: 7 Copynumber: 6.3 Consensus size: 7
136307 GCAGGCGGTT
136317 GATT-GA
1 GATTGGA
*
136323 GATTTGA
1 GATTGGA
*
136330 GATTTGA
1 GATTGGA
136337 GATTGGA
1 GATTGGA
136344 GATTGGA
1 GATTGGA
136351 GATTGGA
1 GATTGGA
136358 GA
1 GA
136360 GTGTGAAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
6 4 0.11
7 31 0.89
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (7 bp):
GATTGGA
Found at i:158174 original size:2 final size:2
Alignment explanation
Indices: 158167--158194 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
158157 GGAAACCTAC
158167 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
158195 GATGATGATG
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:158213 original size:13 final size:13
Alignment explanation
Indices: 158195--158219 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
158185 ATATATATAT
158195 GATGATGATGATA
1 GATGATGATGATA
158208 GATGATGATGAT
1 GATGATGATGAT
158220 GCTNNNNNNN
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (13 bp):
GATGATGATGATA
Found at i:158322 original size:3 final size:3
Alignment explanation
Indices: 158314--158340 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
158304 ATATATATAT
158314 ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG
158341 CTTAATTAAT
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:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:158474 original size:2 final size:2
Alignment explanation
Indices: 158469--158496 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
158459 ACACACACAC
158469 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
158497 CTCATGGGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:161182 original size:25 final size:24
Alignment explanation
Indices: 161138--161192 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
161128 AGCCAACGGG
* *
161138 GAGAAGAAGGAGAAGGAGAAAGAAA
1 GAGAAGAAGAAGAAGAAGAAA-AAA
161163 G-GAAGAAAGAAGAAGAAGAAAAAA
1 GAGAAG-AAGAAGAAGAAGAAAAAA
161187 GAGAAG
1 GAGAAG
161193 GGGGACCCGC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (24 bp):
GAGAAGAAGAAGAAGAAGAAAAAA
Found at i:161235 original size:62 final size:59
Alignment explanation
Indices: 161146--161355 Score: 175
Period size: 61 Copynumber: 3.5 Consensus size: 59
161136 GGGAGAAGAA
*
161146 GGAGAAGGAGAAAGAAAGGAAGAAAGAAGAAGAAGAAAAAAGAGAAGGGGGACCCGCGG
1 GGAGAAAGAGAAAGAAAGGAAGAAAGAAGAAGAAGAAAAAAGAGAAGGGGGACCCGCGG
* * *
161205 GGAGAAAGGAGAGAAAGAGAAGG-AGAAAG-A-AAGAAAGAAAGAAGAAGCCAACGGGAGA--AG
1 GGAG-AA--AGAGAAAGA-AAGGAAGAAAGAAGAAG-AAGAAAAAAG-AG--AA-GGGGGACCCG
**
161265 -AA
57 CGG
* *
161267 GGAGAAAGAGAAAGAAAGGAAGGAAGAAGAAAAAGAAAAAAGAGAAGGGGGACCCGCGG
1 GGAGAAAGAGAAAGAAAGGAAGAAAGAAGAAGAAGAAAAAAGAGAAGGGGGACCCGCGG
161326 GGAGGGAGAAGA-AAAGAAAGAGAA-AAAGAA
1 GGA--GA-AAGAGAAAGAAAG-GAAGAAAGAA
161356 AAAAAGAGAA
Statistics
Matches: 118, Mismatches: 14, Indels: 36
0.70 0.08 0.21
Matches are distributed among these distances:
56 5 0.04
57 2 0.02
58 5 0.04
59 23 0.19
60 15 0.13
61 29 0.25
62 27 0.23
63 5 0.04
64 2 0.02
65 5 0.04
ACGTcount: A:0.56, C:0.05, G:0.39, T:0.00
Consensus pattern (59 bp):
GGAGAAAGAGAAAGAAAGGAAGAAAGAAGAAGAAGAAAAAAGAGAAGGGGGACCCGCGG
Found at i:161280 original size:121 final size:123
Alignment explanation
Indices: 161109--161371 Score: 404
Period size: 121 Copynumber: 2.1 Consensus size: 123
161099 TCGGCAAGGG
*
161109 AGAAAGGAAAGAAAGAAGAAGCCAACGGGGAGAAGAAGGAGAAGGAGAAAGAAAGGAAGAAAGAA
1 AGAAAGGAAAGAAAGAAGAAGCCAACGGGGAGAAGAAGGAGAAAGAGAAAGAAAGGAAGAAAGAA
*
161174 GAAGAAGAAAAAAGAGAAGGGGGACCCGCGGGGAGAAAGGAGAGAAAGAGAAGGAGAA
66 GAAAAAGAAAAAAGAGAAGGGGGACCCGCGGGGAGAAAGGAGAGAAAGAGAAGGAGAA
*
161232 AGAAA-GAAAGAAAGAAGAAGCCAAC-GGGAGAAGAAGGAGAAAGAGAAAGAAAGGAAGGAAGAA
1 AGAAAGGAAAGAAAGAAGAAGCCAACGGGGAGAAGAAGGAGAAAGAGAAAGAAAGGAAGAAAGAA
* * **
161295 GAAAAAGAAAAAAGAGAAGGGGGACCCGCGGGGAGGGAGAAGAAAAGAAAGAGAAAAAGAA
66 GAAAAAGAAAAAAGAGAAGGGGGACCCGCGGGGA--GA-AAGGAGAGAAAGAGAAGGAGAA
*
161356 AAAAAGAGAAAGAAAG
1 AGAAAG-GAAAGAAAG
161372 GAAAGAAAGG
Statistics
Matches: 127, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
121 69 0.54
122 20 0.16
123 7 0.06
124 22 0.17
126 9 0.07
ACGTcount: A:0.57, C:0.05, G:0.37, T:0.00
Consensus pattern (123 bp):
AGAAAGGAAAGAAAGAAGAAGCCAACGGGGAGAAGAAGGAGAAAGAGAAAGAAAGGAAGAAAGAA
GAAAAAGAAAAAAGAGAAGGGGGACCCGCGGGGAGAAAGGAGAGAAAGAGAAGGAGAA
Found at i:161289 original size:21 final size:21
Alignment explanation
Indices: 161264--161304 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
161254 AACGGGAGAA
*
161264 GAAGG-AGAAAGAGAAAGAAAG
1 GAAGGAAG-AAGAAAAAGAAAG
161285 GAAGGAAGAAGAAAAAGAAA
1 GAAGGAAGAAGAAAAAGAAA
161305 AAAGAGAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (21 bp):
GAAGGAAGAAGAAAAAGAAAG
Found at i:161292 original size:25 final size:25
Alignment explanation
Indices: 161259--161314 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
161249 AAGCCAACGG
* *
161259 GAGAA-GAAGGAGAAAGAGAAAGAAA
1 GAGAAGGAAGAAGAAAAAGAAA-AAA
161284 G-GAAGGAAGAAGAAAAAGAAAAAA
1 GAGAAGGAAGAAGAAAAAGAAAAAA
161308 GAGAAGG
1 GAGAAGG
161315 GGGACCCGCG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 7 0.26
25 20 0.74
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (25 bp):
GAGAAGGAAGAAGAAAAAGAAAAAA
Found at i:161313 original size:21 final size:21
Alignment explanation
Indices: 161272--161313 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
161262 AAGAAGGAGA
* *
161272 AAGAGAAAGAAAGGAAGGAAG
1 AAGAAAAAGAAAGAAAGGAAG
161293 AAGAAAAAGAAA-AAAGAGAAG
1 AAGAAAAAGAAAGAAAG-GAAG
161314 GGGGACCCGC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (21 bp):
AAGAAAAAGAAAGAAAGGAAG
Found at i:161363 original size:16 final size:17
Alignment explanation
Indices: 161334--161384 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
161324 GGGGAGGGAG
161334 AAGAAAAGAAAGAGAAA
1 AAGAAAAGAAAGAGAAA
161351 AAGAAAA-AAAGAGAAAGA
1 AAGAAAAGAAAGAG-AA-A
*
161369 AAGGAAAGAAAG-GAAA
1 AAGAAAAGAAAGAGAAA
161385 NNNNNNNNNN
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
16 7 0.23
17 11 0.37
18 8 0.27
19 4 0.13
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (17 bp):
AAGAAAAGAAAGAGAAA
Found at i:164559 original size:2 final size:2
Alignment explanation
Indices: 164554--164602 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
164544 TTATTGACTC
*
164554 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
164596 TA TA TA T
1 TA TA TA T
164603 CAACAAATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:166363 original size:2 final size:2
Alignment explanation
Indices: 166356--166383 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
166346 TGGTTGTTAC
166356 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
166384 TCTCCCTGAT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:179752 original size:98 final size:98
Alignment explanation
Indices: 179583--179776 Score: 334
Period size: 98 Copynumber: 2.0 Consensus size: 98
179573 ACCTGTGCAC
*
179583 AATCACATCTGCAAAGAGGGGAAAGTTGCATACTCAATTTATAGCCTCCTCTTACAACCAAGAAA
1 AATCACATCTGCAAAGAGGGGAAAATTGCATACTCAATTTATAGCCTCCTCTTACAACCAAGAAA
*
179648 TTAGCAAATAAAGGAAAAGCAATAAACAAGTAA
66 TTAGCAAATAAAGGAAAAGCAACAAACAAGTAA
* * *
179681 AATCACATCTGCAAAGAGGGGAAAATTGCATACTCGATTTATAGTCTCCTCTTGCAACCAAGAAA
1 AATCACATCTGCAAAGAGGGGAAAATTGCATACTCAATTTATAGCCTCCTCTTACAACCAAGAAA
*
179746 TTAGCAAATAAAGGAAAAGCAACAGACAAGT
66 TTAGCAAATAAAGGAAAAGCAACAAACAAGT
179777 TTCTATTCAC
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 90 1.00
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.21
Consensus pattern (98 bp):
AATCACATCTGCAAAGAGGGGAAAATTGCATACTCAATTTATAGCCTCCTCTTACAACCAAGAAA
TTAGCAAATAAAGGAAAAGCAACAAACAAGTAA
Found at i:187443 original size:14 final size:14
Alignment explanation
Indices: 187420--187458 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
187410 CAATACTTTA
*
187420 AAATAATTATTTTT
1 AAATTATTATTTTT
*
187434 AAATTTTTA-TTTT
1 AAATTATTATTTTT
187447 AAATTATTATTT
1 AAATTATTATTT
187459 CTTACTATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
AAATTATTATTTTT
Found at i:188305 original size:20 final size:21
Alignment explanation
Indices: 188274--188323 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
188264 AATAAAAATA
188274 TTAAAAACATTTTTATTA-A-TT
1 TTAAAAA-A-TTTTATTAGATTT
188295 TTAAAAAA-TTTATTAGATTT
1 TTAAAAAATTTTATTAGATTT
188315 TTAAAAAAT
1 TTAAAAAAT
188324 ATAAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 7 0.27
19 1 0.04
20 11 0.42
21 7 0.27
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (21 bp):
TTAAAAAATTTTATTAGATTT
Found at i:188308 original size:18 final size:20
Alignment explanation
Indices: 188285--188323 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
188275 TAAAAACATT
188285 TTTATTA-A-TTTTAAAAAA
1 TTTATTAGATTTTTAAAAAA
188303 TTTATTAGATTTTTAAAAAA
1 TTTATTAGATTTTTAAAAAA
188323 T
1 T
188324 ATAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 1 0.05
20 11 0.58
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (20 bp):
TTTATTAGATTTTTAAAAAA
Found at i:188388 original size:23 final size:22
Alignment explanation
Indices: 188361--188445 Score: 73
Period size: 23 Copynumber: 3.5 Consensus size: 22
188351 AGAGTTTTTT
188361 TAATTAATAAAATCATATAATAA
1 TAATT-ATAAAATCATATAATAA
* *
188384 TAATTATAAAAATTAATTAAAGATAA
1 TAATTAT-AAAA-TCA-TATA-ATAA
188410 -AATTNTAATAAAATCATATAATAA
1 TAA-T-T-ATAAAATCATATAATAA
188434 TAATTATAAAAT
1 TAATTATAAAAT
188446 TAATTAAAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 17
0.70 0.06 0.24
Matches are distributed among these distances:
22 9 0.18
23 10 0.20
24 7 0.14
25 10 0.20
26 7 0.14
27 5 0.10
28 2 0.04
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.35
Consensus pattern (22 bp):
TAATTATAAAATCATATAATAA
Found at i:188411 original size:16 final size:16
Alignment explanation
Indices: 188392--188463 Score: 58
Period size: 16 Copynumber: 4.4 Consensus size: 16
188382 AATAATTATA
188392 AAAATTAATTAAAGAT
1 AAAATTAATTAAAGAT
* *
188408 AAAATTNTAATAAAATCAT
1 AAAA-T-TAATTAAA-GAT
* **
188427 ATAA-TAA-TAATTAT
1 AAAATTAATTAAAGAT
188441 AAAATTAATTAAAGAT
1 AAAATTAATTAAAGAT
188457 AAAATTA
1 AAAATTA
188464 TCTTTTTATA
Statistics
Matches: 42, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
14 5 0.12
15 5 0.12
16 19 0.45
17 1 0.02
18 7 0.17
19 5 0.12
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.33
Consensus pattern (16 bp):
AAAATTAATTAAAGAT
Found at i:188419 original size:50 final size:48
Alignment explanation
Indices: 188364--188462 Score: 180
Period size: 50 Copynumber: 2.0 Consensus size: 48
188354 GTTTTTTTAA
188364 TTAATAAAATCATATAATAATAATTATAAAAATTAATTAAAGATAAAAT
1 TTAATAAAATCATATAATAATAATTAT-AAAATTAATTAAAGATAAAAT
188413 TNTAATAAAATCATATAATAATAATTATAAAATTAATTAAAGATAAAAT
1 T-TAATAAAATCATATAATAATAATTATAAAATTAATTAAAGATAAAAT
188462 T
1 T
188463 ATCTTTTTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
49 23 0.47
50 26 0.53
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (48 bp):
TTAATAAAATCATATAATAATAATTATAAAATTAATTAAAGATAAAAT
Found at i:189756 original size:15 final size:15
Alignment explanation
Indices: 189719--189756 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
189709 TAATTTAAAT
189719 ATTAATATTCATCAA
1 ATTAATATTCATCAA
*
189734 ATTTATATTCAT-AA
1 ATTAATATTCATCAA
189748 ACTTAATAT
1 A-TTAATAT
189757 AAAAGTGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 3 0.15
15 17 0.85
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTAATATTCATCAA
Found at i:195235 original size:8 final size:8
Alignment explanation
Indices: 195222--195272 Score: 54
Period size: 8 Copynumber: 6.8 Consensus size: 8
195212 TTATAGAGAC
195222 AAAATTAT
1 AAAATTAT
195230 AAAATT-T
1 AAAATTAT
*
195237 AAAA--AA
1 AAAATTAT
* *
195243 AAAATAAA
1 AAAATTAT
195251 AAAATTAT
1 AAAATTAT
195259 AAAATTAT
1 AAAATTAT
195267 AAAATT
1 AAAATT
195273 TTTAAAGGAG
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
6 4 0.11
7 5 0.14
8 28 0.76
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (8 bp):
AAAATTAT
Found at i:217160 original size:5 final size:5
Alignment explanation
Indices: 217153--217184 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
217143 ATCTTAACCT
*
217153 CCCCT CCCCA CCCCA CCCCA CCCCA CCCCA CC
1 CCCCA CCCCA CCCCA CCCCA CCCCA CCCCA CC
217185 GAAGATGATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.16, C:0.81, G:0.00, T:0.03
Consensus pattern (5 bp):
CCCCA
Found at i:221274 original size:69 final size:69
Alignment explanation
Indices: 221152--221497 Score: 417
Period size: 69 Copynumber: 5.0 Consensus size: 69
221142 CTCCCATAAT
* *
221152 TATAAGCAGGGGTGCTTGGAACAGAATCAGCAAATATAGACGAGCT-TTGCCCCTTGAACATGTT
1 TATAAGCAGGGGTGCTTGGAACAGAATCCGCAAAAATAGACGAGCTCTT-CCCCTTGAACATGTT
221216 ATCTG
65 ATCTG
* * * * * * *
221221 AATAGGCAGGAGTGCTTGGAACAGAATCCGCAAATATGGATGAACTCTTCCCCTTGAACATGTTA
1 TATAAGCAGGGGTGCTTGGAACAGAATCCGCAAAAATAGACGAGCTCTTCCCCTTGAACATGTTA
221286 TCTG
66 TCTG
* * * * *
221290 CATAAGCAGGAGTGCTTGGAACAGAATCTGCAAAAATAGACGAGCTTTTCCCCTTGAACATATTA
1 TATAAGCAGGGGTGCTTGGAACAGAATCCGCAAAAATAGACGAGCTCTTCCCCTTGAACATGTTA
221355 TCTG
66 TCTG
* * * * *
221359 TGTAAGCAGGGGTGCTCGGAACAGAATCCGCAAAAATAGATGAGCTCTTCCCATGGAACATGTTA
1 TATAAGCAGGGGTGCTTGGAACAGAATCCGCAAAAATAGACGAGCTCTTCCCCTTGAACATGTTA
221424 TCTG
66 TCTG
* * * * * * * *
221428 TGTAGGCAGGGGTGCTTGGAACAGAATCTGCAAAAGTAAACGGGC-CTTTCCCTGGGAACATGTT
1 TATAAGCAGGGGTGCTTGGAACAGAATCCGCAAAAATAGACGAGCTCTTCCCCT-TGAACATGTT
221492 ATCTG
65 ATCTG
221497 T
1 T
221498 GTGGGACGAC
Statistics
Matches: 240, Mismatches: 35, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
68 6 0.03
69 232 0.97
70 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (69 bp):
TATAAGCAGGGGTGCTTGGAACAGAATCCGCAAAAATAGACGAGCTCTTCCCCTTGAACATGTTA
TCTG
Found at i:221977 original size:25 final size:25
Alignment explanation
Indices: 221948--221996 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
221938 CAGTAGAAAC
221948 AGAAACAAAAAAAAAAAAAGAAAAA
1 AGAAACAAAAAAAAAAAAAGAAAAA
* * **
221973 AGAAAGAAAGAAAAACTAAGAAAA
1 AGAAACAAAAAAAAAAAAAGAAAA
221997 CCCAAGCTTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.82, C:0.04, G:0.12, T:0.02
Consensus pattern (25 bp):
AGAAACAAAAAAAAAAAAAGAAAAA
Found at i:230224 original size:21 final size:22
Alignment explanation
Indices: 230186--230231 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
230176 TGGTATAATA
*
230186 TTTTAAAATATTCTTAAATTATT
1 TTTTAAAATATTCATAAA-TATT
230209 TTTTAAAA-ATT-ATAAATATT
1 TTTTAAAATATTCATAAATATT
230229 TTT
1 TTT
230232 ATTATTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 7 0.32
21 4 0.18
22 3 0.14
23 8 0.36
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTAAAATATTCATAAATATT
Found at i:238526 original size:12 final size:12
Alignment explanation
Indices: 238511--238545 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
238501 AGAAGTAGAA
238511 GGTGAAGGTGAG
1 GGTGAAGGTGAG
238523 GGTGAAGGTGAG
1 GGTGAAGGTGAG
* *
238535 AGTGACGGTGA
1 GGTGAAGGTGA
238546 AGGAAGAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.26, C:0.03, G:0.54, T:0.17
Consensus pattern (12 bp):
GGTGAAGGTGAG
Found at i:238531 original size:18 final size:18
Alignment explanation
Indices: 238508--238548 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
238498 TGAAGAAGTA
*
238508 GAAGGTGA-AGGTGAGGGT
1 GAAGGTGAGA-GTGACGGT
238526 GAAGGTGAGAGTGACGGT
1 GAAGGTGAGAGTGACGGT
238544 GAAGG
1 GAAGG
238549 AAGAGATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.29, C:0.02, G:0.54, T:0.15
Consensus pattern (18 bp):
GAAGGTGAGAGTGACGGT
Found at i:265393 original size:16 final size:16
Alignment explanation
Indices: 265357--265395 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
265347 TAAAGGAAGG
* *
265357 TTCCTTAATTCCATTA
1 TTCCTTCATTCCATAA
*
265373 CTCCTTCATTCCATAA
1 TTCCTTCATTCCATAA
265389 TTCCTTC
1 TTCCTTC
265396 CCCTTTCTTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.21, C:0.33, G:0.00, T:0.46
Consensus pattern (16 bp):
TTCCTTCATTCCATAA
Found at i:266129 original size:24 final size:24
Alignment explanation
Indices: 266097--266148 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
266087 TTTTTATTCT
266097 ATATCCATGTATCCTGAGAGAGAA
1 ATATCCATGTATCCTGAGAGAGAA
266121 ATATCCATGTATCCTGAGAGAGAA
1 ATATCCATGTATCCTGAGAGAGAA
266145 ATAT
1 ATAT
266149 ATCACAAGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.27
Consensus pattern (24 bp):
ATATCCATGTATCCTGAGAGAGAA
Found at i:283935 original size:29 final size:29
Alignment explanation
Indices: 283880--283936 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
283870 AATTATAATA
*
283880 AAAATTCATAAATAATCAAAATTAACTTC
1 AAAATTCATAAATAATCAAAACTAACTTC
* *
283909 AAAATTCGTAAATAATCGAAACTAACTT
1 AAAATTCATAAATAATCAAAACTAACTT
283937 ATATTGATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.53, C:0.14, G:0.04, T:0.30
Consensus pattern (29 bp):
AAAATTCATAAATAATCAAAACTAACTTC
Found at i:287805 original size:3 final size:3
Alignment explanation
Indices: 287797--287821 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
287787 TTCATTTGAT
287797 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
287822 CACCGGCGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:292849 original size:17 final size:16
Alignment explanation
Indices: 292822--292853 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
292812 CCAAAAACGA
292822 TTTTCTTTTTCTTTTC
1 TTTTCTTTTTCTTTTC
292838 TTTTCTTTTTTCTTTT
1 TTTTC-TTTTTCTTTT
292854 TAAAATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTCTTTTTCTTTTC
Found at i:300736 original size:2 final size:2
Alignment explanation
Indices: 300729--300766 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
300719 GATCATCACC
300729 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
300767 GTGGTCTAGA
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):
AT
Found at i:322207 original size:2 final size:2
Alignment explanation
Indices: 322190--322224 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
322180 TTCTTTAAGG
*
322190 TA TA -A TA TA CA 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
322225 AAGTTTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:323617 original size:16 final size:16
Alignment explanation
Indices: 323593--323633 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
323583 GATCAGAAGC
323593 TATTAGTTAAGATCGT
1 TATTAGTTAAGATCGT
*
323609 TATTCGTTAAGATCGT
1 TATTAGTTAAGATCGT
*
323625 TATTTGTTA
1 TATTAGTTA
323634 TTCGTTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.27, C:0.07, G:0.17, T:0.49
Consensus pattern (16 bp):
TATTAGTTAAGATCGT
Found at i:325424 original size:15 final size:15
Alignment explanation
Indices: 325400--325437 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
325390 TAAAGCTTAT
*
325400 TGGGCCTTTCTTTTC
1 TGGGCCTTTCTTTTA
*
325415 TGGGCTTTTCTTTTA
1 TGGGCCTTTCTTTTA
325430 TGGGCCTT
1 TGGGCCTT
325438 CACTCAGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.03, C:0.21, G:0.24, T:0.53
Consensus pattern (15 bp):
TGGGCCTTTCTTTTA
Found at i:333416 original size:2 final size:2
Alignment explanation
Indices: 333400--333434 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
333390 TCTCCACTAG
* *
333400 CT CT CT GT CT GT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
333435 CATCTTTTCC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.46, G:0.06, T:0.49
Consensus pattern (2 bp):
CT
Found at i:339214 original size:26 final size:26
Alignment explanation
Indices: 339178--339241 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
339168 TAGGTTTCCT
*
339178 TGCAAATTTTTACTGTTTTCTAGTTA
1 TGCAAATTTTTACTGTTTCCTAGTTA
*
339204 TGCAAATTTTTTCTGTTTCCTAGTTA
1 TGCAAATTTTTACTGTTTCCTAGTTA
* *
339230 AGCAAAATTTTA
1 TGCAAATTTTTA
339242 GATATGCCCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.27, C:0.12, G:0.11, T:0.50
Consensus pattern (26 bp):
TGCAAATTTTTACTGTTTCCTAGTTA
Found at i:354556 original size:20 final size:20
Alignment explanation
Indices: 354519--354557 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
354509 TTCCAACAAA
* *
354519 CTCAGCCGATAATAAAATAT
1 CTCAGCAGAGAATAAAATAT
*
354539 CTCAGCAGAGAATCAAATA
1 CTCAGCAGAGAATAAAATA
354558 ATTATGAGAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.21, G:0.13, T:0.21
Consensus pattern (20 bp):
CTCAGCAGAGAATAAAATAT
Found at i:361325 original size:2 final size:2
Alignment explanation
Indices: 361312--361342 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
361302 TAATAATATC
*
361312 AG AG AT AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
361343 AGGAGCAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.45, T:0.03
Consensus pattern (2 bp):
AG
Found at i:362645 original size:17 final size:17
Alignment explanation
Indices: 362625--362710 Score: 57
Period size: 17 Copynumber: 4.9 Consensus size: 17
362615 CTTTTTATGC
362625 ATAAAATATTTTTAAAT
1 ATAAAATATTTTTAAAT
* *
362642 ATAATATTTTTTTATAAT
1 ATAAAATATTTTTA-AAT
* * * *
362660 TTTAACTATTTTTAATT
1 ATAAAATATTTTTAAAT
* *
362677 AAAAAAATTAATTTTAAA-
1 -ATAAAA-TATTTTTAAAT
362695 ATAAAATTATTTTTAA
1 ATAAAA-TATTTTTAA
362711 TGAAATCAAT
Statistics
Matches: 50, Mismatches: 16, Indels: 6
0.69 0.22 0.08
Matches are distributed among these distances:
17 28 0.56
18 14 0.28
19 8 0.16
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (17 bp):
ATAAAATATTTTTAAAT
Found at i:362716 original size:20 final size:19
Alignment explanation
Indices: 362666--362716 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 19
362656 TAATTTTAAC
362666 TATTTTTAATTAAA-AAAAT
1 TATTTTTAA-TAAATAAAAT
*
362685 TAATTTT-A-AAATAAAAT
1 TATTTTTAATAAATAAAAT
362702 TATTTTTAATGAAAT
1 TATTTTTAAT-AAAT
362717 CAATTCATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
16 3 0.12
17 11 0.42
18 2 0.08
19 6 0.23
20 4 0.15
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
TATTTTTAATAAATAAAAT
Found at i:362821 original size:11 final size:10
Alignment explanation
Indices: 362788--362826 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
362778 AAAAAAATTG
*
362788 AAATTATTTT
1 AAATTATTTA
*
362798 AATTTATTTA
1 AAATTATTTA
362808 AAATTATTTAA
1 AAATTATTT-A
362819 AAATTATT
1 AAATTATT
362827 GTTATCAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
AAATTATTTA
Found at i:381940 original size:14 final size:14
Alignment explanation
Indices: 381906--381944 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
381896 TATTTCCAAC
381906 GGAAAATATTCCGTT
1 GGAAAAT-TTCCGTT
*
381921 GG-AAATTTTCGTT
1 GGAAAATTTCCGTT
381934 GGAAAATTTCC
1 GGAAAATTTCC
381945 AATGGATTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 8 0.38
14 11 0.52
15 2 0.10
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.36
Consensus pattern (14 bp):
GGAAAATTTCCGTT
Found at i:387566 original size:6 final size:6
Alignment explanation
Indices: 387557--387638 Score: 119
Period size: 6 Copynumber: 13.7 Consensus size: 6
387547 GGAGAAGATA
* * * *
387557 ATGAAG ATGATG ATGAAG ATGAAG ATGATG ACGAAT ATGAAG ATGAAG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
*
387605 ATGAAG ATGAAT ATGAAG ATGAAG ATGAAG ATGA
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGA
387639 CGATCATGTG
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 66 1.00
ACGTcount: A:0.48, C:0.01, G:0.30, T:0.21
Consensus pattern (6 bp):
ATGAAG
Found at i:389607 original size:12 final size:12
Alignment explanation
Indices: 389590--389615 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
389580 CTTGAATAAG
389590 ATACGTGAAGAA
1 ATACGTGAAGAA
389602 ATACGTGAAGAA
1 ATACGTGAAGAA
389614 AT
1 AT
389616 GAGAAATGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.23, T:0.19
Consensus pattern (12 bp):
ATACGTGAAGAA
Found at i:390121 original size:25 final size:25
Alignment explanation
Indices: 390087--390139 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
390077 TTGGAAATAG
* *
390087 AATTTTCAACAGAAATTCTGTTGGA
1 AATTTCCAACAGAAATTCCGTTGGA
**
390112 AATTTCCAACAGATTTTCCGTTGGA
1 AATTTCCAACAGAAATTCCGTTGGA
390137 AAT
1 AAT
390140 ATACTTTCCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (25 bp):
AATTTCCAACAGAAATTCCGTTGGA
Found at i:390509 original size:2 final size:2
Alignment explanation
Indices: 390502--390537 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
390492 TTAACTTCAA
*
390502 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
390538 TAATCAGGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:395967 original size:55 final size:54
Alignment explanation
Indices: 395879--396047 Score: 178
Period size: 55 Copynumber: 3.1 Consensus size: 54
395869 TTATTTTAAT
* * *
395879 GTGTCACGGCTGTTCCTGGCGTGTTATGAGTTAACT-AGTTTTTTGGGTTGTTAGC
1 GTGTCACGGCTGTTCCTAG-GTGTCATGAGTTAACTGA-TTTTTTGGGTTTTTAGC
** * * * * *
395934 GTGTCACGGCTGTTCCTAAGGTGTGGTGTGTTAACTGAATTTATGGATTTTTGGC
1 GTGTCACGGCTGTTCCT-AGGTGTCATGAGTTAACTGATTTTTTGGGTTTTTAGC
* * *
395989 GTGTCACGACTGTTCCTGACGTGTCATGGGTTAACTGATTTTTTGGGTTTTTAGC
1 GTGTCACGGCTGTTCCT-AGGTGTCATGAGTTAACTGATTTTTTGGGTTTTTAGC
396044 GTGT
1 GTGT
396048 TATGATTGTT
Statistics
Matches: 93, Mismatches: 19, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
55 91 0.98
56 2 0.02
ACGTcount: A:0.14, C:0.14, G:0.30, T:0.41
Consensus pattern (54 bp):
GTGTCACGGCTGTTCCTAGGTGTCATGAGTTAACTGATTTTTTGGGTTTTTAGC
Found at i:396112 original size:23 final size:23
Alignment explanation
Indices: 396086--396165 Score: 106
Period size: 23 Copynumber: 3.5 Consensus size: 23
396076 TTACAATGAT
*
396086 TGGCGTGTCACGACAGTGATGCA
1 TGGCGTGTCACAACAGTGATGCA
396109 TGGCGTGTCACAACAGTGATGCA
1 TGGCGTGTCACAACAGTGATGCA
* * * *
396132 TGGTGTGTAACAATACTGATGCA
1 TGGCGTGTCACAACAGTGATGCA
*
396155 TGACGTGTCAC
1 TGGCGTGTCAC
396166 GATATTTGAC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (23 bp):
TGGCGTGTCACAACAGTGATGCA
Found at i:398683 original size:31 final size:28
Alignment explanation
Indices: 398643--398700 Score: 71
Period size: 31 Copynumber: 2.0 Consensus size: 28
398633 TACAATGAAT
*
398643 TGTATAAAATAAACTGTGTATACAAAAAATG
1 TGTACAAAATAAA-T-TGTATA-AAAAAATG
*
398674 TGTACAAAATGAATTGTATAAAAAAAT
1 TGTACAAAATAAATTGTATAAAAAAAT
398701 TTCTGTATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 7 0.28
29 6 0.24
30 1 0.04
31 11 0.44
ACGTcount: A:0.53, C:0.05, G:0.12, T:0.29
Consensus pattern (28 bp):
TGTACAAAATAAATTGTATAAAAAAATG
Found at i:398696 original size:14 final size:15
Alignment explanation
Indices: 398643--398700 Score: 59
Period size: 14 Copynumber: 3.9 Consensus size: 15
398633 TACAATGAAT
398643 TGTATAAAATAAACTG
1 TGTATAAAATAAA-TG
398659 TGTATACAAA-AAATG
1 TGTATA-AAATAAATG
* *
398674 TGTACAAAATGAAT-
1 TGTATAAAATAAATG
398688 TGTATAAAA-AAAT
1 TGTATAAAATAAAT
398701 TTCTGTATAC
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
13 3 0.08
14 11 0.31
15 10 0.28
16 9 0.25
17 3 0.08
ACGTcount: A:0.53, C:0.05, G:0.12, T:0.29
Consensus pattern (15 bp):
TGTATAAAATAAATG
Found at i:400213 original size:31 final size:31
Alignment explanation
Indices: 400171--400355 Score: 83
Period size: 31 Copynumber: 6.0 Consensus size: 31
400161 CACAAACCAT
* *
400171 AAAC-AGTAAAATATTCTGACACG-CAGTGCA
1 AAACAAGTAAAATATTATCACACGCCA-TGCA
* * *
400201 TACCAAGTAAAATGTTATCACACGCCATGCA
1 AAACAAGTAAAATATTATCACACGCCATGCA
* * *
400232 AAACAAGTAAAAT-GTAGTGACATGCCATGCA
1 AAACAAGTAAAATATTA-TCACACGCCATGCA
* * * * * * *
400263 TAACAAG--ATATACTTGGTGACACGTCAAGGA
1 AAACAAGTAAAATA-TT-ATCACACGCCATGCA
* * * * * *
400294 TAACGAGCAAAATGTTGTGACACGCCATGCA
1 AAACAAGTAAAATATTATCACACGCCATGCA
* * *
400325 AAACAAGTAAAATGTTGTGACACGCCATGCA
1 AAACAAGTAAAATATTATCACACGCCATGCA
400356 TAAAAAGATA
Statistics
Matches: 120, Mismatches: 27, Indels: 15
0.74 0.17 0.09
Matches are distributed among these distances:
29 3 0.03
30 4 0.03
31 106 0.88
32 4 0.03
33 3 0.03
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.21
Consensus pattern (31 bp):
AAACAAGTAAAATATTATCACACGCCATGCA
Found at i:400286 original size:62 final size:62
Alignment explanation
Indices: 400171--400473 Score: 228
Period size: 62 Copynumber: 4.9 Consensus size: 62
400161 CACAAACCAT
* * * * *
400171 AAAC-AGTAAAATATTCTGACACG-CAGTGCATACCAAG-TAAAATGTTATCACACGCCATGCA
1 AAACAAGTAAAATGTTGTGACACGCCA-TGCATAACAAGAT-AAATGTTGTGACACGCCATGCA
* * * * * * *
400232 AAACAAGTAAAATGTAGTGACATGCCATGCATAACAAGATATACT-TGGTGACACGTCAAGGA
1 AAACAAGTAAAATGTTGTGACACGCCATGCATAACAAGATA-AATGTTGTGACACGCCATGCA
* * * *
400294 TAACGAGCAAAATGTTGTGACACGCCATGCAAAACAAG-TAAAATGTTGTGACACGCCATGCA
1 AAACAAGTAAAATGTTGTGACACGCCATGCATAACAAGAT-AAATGTTGTGACACGCCATGCA
* * * *
400356 TAAA-AAGATAAACT-TGGTGACACGCCAAGGATAACAAGCA-AAATGTTGTGACACGCCATGCA
1 -AAACAAG-TAAAATGTTGTGACACGCCATGCATAACAAG-ATAAATGTTGTGACACGCCATGCA
* * * * * * *
400418 TATCAAATCAAATGTTGTGACATGCCATGAATAACAAG-TAAAATATTGTGACACGC
1 AAACAAGTAAAATGTTGTGACACGCCATGCATAACAAGAT-AAATGTTGTGACACGC
400474 TAAGGTTGAC
Statistics
Matches: 187, Mismatches: 41, Indels: 27
0.73 0.16 0.11
Matches are distributed among these distances:
61 12 0.06
62 164 0.88
63 11 0.06
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (62 bp):
AAACAAGTAAAATGTTGTGACACGCCATGCATAACAAGATAAATGTTGTGACACGCCATGCA
Found at i:400327 original size:93 final size:93
Alignment explanation
Indices: 400204--400478 Score: 381
Period size: 93 Copynumber: 3.0 Consensus size: 93
400194 CAGTGCATAC
* * * *
400204 CAAGTAAAATGTTATCACACGCCATGCAAAACAAGTAAAATGTAGTGACATGCCATGCATAACAA
1 CAAGCAAAATGTTGTGACACGCCATGCAAAACAAGTAAAATGTTGTGACATGCCATGCATAACAA
* *
400269 GATATACTTGGTGACACGTCAAGGATAA
66 GATAAACTTGGTGACACGCCAAGGATAA
* * *
400297 CGAGCAAAATGTTGTGACACGCCATGCAAAACAAGTAAAATGTTGTGACACGCCATGCATAAAAA
1 CAAGCAAAATGTTGTGACACGCCATGCAAAACAAGTAAAATGTTGTGACATGCCATGCATAACAA
400362 GATAAACTTGGTGACACGCCAAGGATAA
66 GATAAACTTGGTGACACGCCAAGGATAA
* * * * *
400390 CAAGCAAAATGTTGTGACACGCCATGCATATCAAATCAAATGTTGTGACATGCCATGAATAACAA
1 CAAGCAAAATGTTGTGACACGCCATGCAAAACAAGTAAAATGTTGTGACATGCCATGCATAACAA
* * *
400455 G-TAAAATATTGTGACACGCTAAGG
66 GATAAACT-TGGTGACACGCCAAGG
400479 TTGACATGGC
Statistics
Matches: 161, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
92 5 0.03
93 156 0.97
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.21
Consensus pattern (93 bp):
CAAGCAAAATGTTGTGACACGCCATGCAAAACAAGTAAAATGTTGTGACATGCCATGCATAACAA
GATAAACTTGGTGACACGCCAAGGATAA
Found at i:400376 original size:31 final size:31
Alignment explanation
Indices: 400210--400473 Score: 170
Period size: 31 Copynumber: 8.5 Consensus size: 31
400200 ATACCAAGTA
* *
400210 AAATGTTATCACACGCCATGCA-AAACAAG-T
1 AAATGTTGTGACACGCCATGCATAAA-AAGAT
* * *
400240 AAAATGTAGTGACATGCCATGCATAACAAGAT
1 -AAATGTTGTGACACGCCATGCATAAAAAGAT
* * * * * **
400272 ATACT-TGGTGACACGTCAAGGATAACGAGCA-
1 A-AATGTTGTGACACGCCATGCATAAAAAG-AT
400303 AAATGTTGTGACACGCCATGCA-AAACAAG-T
1 AAATGTTGTGACACGCCATGCATAAA-AAGAT
400333 AAAATGTTGTGACACGCCATGCATAAAAAGAT
1 -AAATGTTGTGACACGCCATGCATAAAAAGAT
* * * *
400365 AAACT-TGGTGACACGCCAAGGATAACAAGCA-
1 AAA-TGTTGTGACACGCCATGCATAAAAAG-AT
**
400396 AAATGTTGTGACACGCCATGCATATCAA-AT
1 AAATGTTGTGACACGCCATGCATAAAAAGAT
* * *
400426 CAAATGTTGTGACATGCCATGAATAACAAG-T
1 -AAATGTTGTGACACGCCATGCATAAAAAGAT
*
400457 AAAATATTGTGACACGC
1 -AAATGTTGTGACACGC
400474 TAAGGTTGAC
Statistics
Matches: 184, Mismatches: 33, Indels: 32
0.74 0.13 0.13
Matches are distributed among these distances:
29 1 0.01
30 5 0.03
31 166 0.90
32 12 0.07
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (31 bp):
AAATGTTGTGACACGCCATGCATAAAAAGAT
Found at i:401125 original size:156 final size:156
Alignment explanation
Indices: 400838--401134 Score: 425
Period size: 156 Copynumber: 1.9 Consensus size: 156
400828 AACTACAATA
400838 ACATATATAACTGTGTTATTCAATAATCATATATGGAATTGTTGAACATTAACCGTTACAACTTT
1 ACATATATAACTGTGTTATTCAATAATCATATATGGAATTGTTGAACATTAACCGTTACAACTTT
* * * * * *
400903 AATATCCTAACCGACGGCTCATTAGCAGTCTACGATGGAGTCGGACCGATTGGTGCTTGAGGACC
66 AATATCCTAACCGACAGCTCATTAGCAGTCTACGATGGAGCCAGACCGATCGATGCTTGAGAACC
400968 TGTCGTCGCTTTCGTAAATTGTAATT
131 TGTCGTCGCTTTCGTAAATTGTAATT
*
400994 ACATATATAACTGTGTTATTCAATAATCATGTATGGAATTGTTGAACATTAACCGTTACAACTTT
1 ACATATATAACTGTGTTATTCAATAATCATATATGGAATTGTTGAACATTAACCGTTACAACTTT
* * ** ** * ** *
401059 AATATCCTTACCGTCAGCTTGTTAGTTGTCTGC-AGTTTAGCCAGATCGATCGATGCTTGAGAAC
66 AATATCCTAACCGACAGCTCATTAGCAGTCTACGA-TGGAGCCAGACCGATCGATGCTTGAGAAC
401123 CTGTCGTCGCTT
130 CTGTCGTCGCTT
401135 CTATAAACTG
Statistics
Matches: 123, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
155 1 0.01
156 122 0.99
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (156 bp):
ACATATATAACTGTGTTATTCAATAATCATATATGGAATTGTTGAACATTAACCGTTACAACTTT
AATATCCTAACCGACAGCTCATTAGCAGTCTACGATGGAGCCAGACCGATCGATGCTTGAGAACC
TGTCGTCGCTTTCGTAAATTGTAATT
Found at i:401150 original size:156 final size:156
Alignment explanation
Indices: 400828--401181 Score: 424
Period size: 156 Copynumber: 2.3 Consensus size: 156
400818 CGACTGGGTT
* *
400828 AACTACAATAACATATATAACTGTGTTATTCAATAATCATATATGGAATTGTTGAACATTAACCG
1 AACTGCAATTACATATATAACTGTGTTATTCAATAATCATATATGGAATTGTTGAACATTAACCG
* * * * *
400893 TTACAACTTTAATATCCTAACCGACGGCTCATTAGCAGTCTACGATGGAGTCGGACCGATTGGTG
66 TTACAACTTTAATATCCTAACCGACAGCTCATTAGCAGTCTACGATGGAGCCAGACCGATCGATG
* *
400958 CTTGAGGACCTGTCGTCGCTTTCGTA
131 CTTGAGAACCTGTCGTCGCTTTCATA
* * *
400984 AATTGTAATTACATATATAACTGTGTTATTCAATAATCATGTATGGAATTGTTGAACATTAACCG
1 AACTGCAATTACATATATAACTGTGTTATTCAATAATCATATATGGAATTGTTGAACATTAACCG
* * ** ** * ** *
401049 TTACAACTTTAATATCCTTACCGTCAGCTTGTTAGTTGTCTGC-AGTTTAGCCAGATCGATCGAT
66 TTACAACTTTAATATCCTAACCGACAGCTCATTAGCAGTCTACGA-TGGAGCCAGACCGATCGAT
401113 GCTTGAGAACCTGTCGTCGC-TTCTATA
130 GCTTGAGAACCTGTCGTCGCTTTC-ATA
* * * * * *
401140 AACTGCAATTACAGAAATTACTGTGTTACTCGATAAACATAT
1 AACTGCAATTACATATATAACTGTGTTATTCAATAATCATAT
401182 GTGGGAATGT
Statistics
Matches: 165, Mismatches: 31, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
155 4 0.02
156 161 0.98
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.34
Consensus pattern (156 bp):
AACTGCAATTACATATATAACTGTGTTATTCAATAATCATATATGGAATTGTTGAACATTAACCG
TTACAACTTTAATATCCTAACCGACAGCTCATTAGCAGTCTACGATGGAGCCAGACCGATCGATG
CTTGAGAACCTGTCGTCGCTTTCATA
Found at i:402938 original size:31 final size:31
Alignment explanation
Indices: 402808--402959 Score: 166
Period size: 31 Copynumber: 4.9 Consensus size: 31
402798 ATAAATATTG
402808 TGACACGCCATGCAT-TGCAA-TCAAAATGTTA
1 TGACACGCCATGCATAT-CAAGT-AAAATGTTA
* * *
402839 TGACACACCATGCATAACAAGTAAAATATTA
1 TGACACGCCATGCATATCAAGTAAAATGTTA
* *
402870 TGACACGCCATGCATAACAAGT-TAATCGTTA
1 TGACACGCCATGCATATCAAGTAAAAT-GTTA
* *
402901 TGACACGCCATGCATATCAAGTAAAATGCTG
1 TGACACGCCATGCATATCAAGTAAAATGTTA
* * *
402932 TCACACGCTATGTATATCAAGTAAAATG
1 TGACACGCCATGCATATCAAGTAAAATG
402960 CTGTCACACG
Statistics
Matches: 104, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
30 3 0.03
31 97 0.93
32 4 0.04
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.25
Consensus pattern (31 bp):
TGACACGCCATGCATATCAAGTAAAATGTTA
Found at i:403496 original size:53 final size:52
Alignment explanation
Indices: 403438--403556 Score: 175
Period size: 53 Copynumber: 2.3 Consensus size: 52
403428 TCTATTTCAA
* * *
403438 ACCATGACGTGTCAGCTGCTCAAGTACTGCCGTGTCACACACTCTAAACCATG
1 ACCATGGCGTGTCAGCTGCTCAAGCAATGCCGTGTCACACACTCTAAA-CATG
** *
403491 ACCATGGCGTGTCAGCTTTTCAAGCAATGTCGTGTCACACACTCTAAACATG
1 ACCATGGCGTGTCAGCTGCTCAAGCAATGCCGTGTCACACACTCTAAACATG
403543 ACCATGGCGTGTCA
1 ACCATGGCGTGTCA
403557 CCAACTATGA
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
52 18 0.30
53 42 0.70
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.24
Consensus pattern (52 bp):
ACCATGGCGTGTCAGCTGCTCAAGCAATGCCGTGTCACACACTCTAAACATG
Found at i:403574 original size:24 final size:23
Alignment explanation
Indices: 403547--403628 Score: 69
Period size: 24 Copynumber: 3.5 Consensus size: 23
403537 AACATGACCA
403547 TGGCGTGTCACCAACTATGAACTC
1 TGGCGTGTCACCAACT-TGAACTC
* * **
403571 TGGCGTGTCA-TAGCTT-CCCTCC
1 TGGCGTGTCACCAACTTGAACT-C
403593 ATGGCGTGTCACCAACTCTGAACTC
1 -TGGCGTGTCACCAACT-TGAACTC
*
403618 TGGTGTGTCAC
1 TGGCGTGTCAC
403629 AGATTCCCTC
Statistics
Matches: 44, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
21 2 0.05
22 2 0.05
23 13 0.30
24 23 0.52
25 2 0.05
26 2 0.05
ACGTcount: A:0.18, C:0.30, G:0.23, T:0.28
Consensus pattern (23 bp):
TGGCGTGTCACCAACTTGAACTC
Found at i:403578 original size:53 final size:53
Alignment explanation
Indices: 403468--403629 Score: 133
Period size: 47 Copynumber: 3.2 Consensus size: 53
403458 CAAGTACTGC
* * * * ** *
403468 CGTGTCACACACTCTAAACCATGACCATGGCGTGTCAGC--TTTTCAAGCAATGT
1 CGTGTCACACACTCTAAA-CATGACCATGGCGTGTCACCAACTATGAA-CTCTGG
403521 CGTGTCACACACTCTAAACATGACCATGGCGTGTCACCAACTATGAACTCTGG
1 CGTGTCACACACTCTAAACATGACCATGGCGTGTCACCAACTATGAACTCTGG
* * * * *
403574 CGTGTCATA-GCT-T--CCCT--CCATGGCGTGTCACCAACTCTGAACTCTGG
1 CGTGTCACACACTCTAAACATGACCATGGCGTGTCACCAACTATGAACTCTGG
*
403621 TGTGTCACA
1 CGTGTCACA
403630 GATTCCCTCC
Statistics
Matches: 93, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
47 36 0.39
49 2 0.02
51 1 0.01
52 21 0.23
53 29 0.31
54 4 0.04
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (53 bp):
CGTGTCACACACTCTAAACATGACCATGGCGTGTCACCAACTATGAACTCTGG
Found at i:403615 original size:47 final size:47
Alignment explanation
Indices: 403544--403941 Score: 449
Period size: 47 Copynumber: 8.5 Consensus size: 47
403534 CTAAACATGA
* * * *
403544 CCATGGCGTGTCACCAACTATGAACTCTGGCGTGTCATAGCTTCCCT
1 CCATGGCGTGTCACCAACTCTGAACTCTAGCGTGTCACAGATTCCCT
* *
403591 CCATGGCGTGTCACCAACTCTGAACTCTGGTGTGTCACAGATTCCCT
1 CCATGGCGTGTCACCAACTCTGAACTCTAGCGTGTCACAGATTCCCT
* * * * *
403638 CCACGGTGTCTCACCAACTCTGAACGCTAGCGTGTCATAGATTCCCT
1 CCATGGCGTGTCACCAACTCTGAACTCTAGCGTGTCACAGATTCCCT
* * * * * *
403685 CCATGGTGTGTCACCAACTCTTAACTCTAGCATTTCATAGATTCCAT
1 CCATGGCGTGTCACCAACTCTGAACTCTAGCGTGTCACAGATTCCCT
* * * * * *
403732 CCATGGCGTCTCACTAACTTTTAACGCTGGCGTGTCACAGATTCCCT
1 CCATGGCGTGTCACCAACTCTGAACTCTAGCGTGTCACAGATTCCCT
* *
403779 CCATGTCGTGTCACCAACTCTTAA-TCTAGCGTGTCACAGATTCCCT
1 CCATGGCGTGTCACCAACTCTGAACTCTAGCGTGTCACAGATTCCCT
* * * *
403825 CCATGACGTCTCACCAACTCTGAACGT-TACCGTGTCACAGATTCCCA
1 CCATGGCGTGTCACCAACTCTGAAC-TCTAGCGTGTCACAGATTCCCT
* * * *
403872 CCATGGCGTGTCACCAACTCTTAACTCTGGTGTCTCACAGATTCCCT
1 CCATGGCGTGTCACCAACTCTGAACTCTAGCGTGTCACAGATTCCCT
** *
403919 CCACAGCGTCTCACCAACTCTGA
1 CCATGGCGTGTCACCAACTCTGA
403942 GCAGTGCTGT
Statistics
Matches: 297, Mismatches: 51, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
46 42 0.14
47 254 0.86
48 1 0.00
ACGTcount: A:0.22, C:0.33, G:0.17, T:0.28
Consensus pattern (47 bp):
CCATGGCGTGTCACCAACTCTGAACTCTAGCGTGTCACAGATTCCCT
Found at i:403916 original size:187 final size:188
Alignment explanation
Indices: 403544--403937 Score: 538
Period size: 187 Copynumber: 2.1 Consensus size: 188
403534 CTAAACATGA
* * * *
403544 CCATGGCGTGTCACCAACTATGAACTCTGGCGTGTCATAGCTTCCCTCCATGGCGTGTCACCAAC
1 CCATGGCGTCTCACCAACTATGAACGCTGGCGTGTCACAGATTCCCTCCATGGCGTGTCACCAAC
* * ** *
403609 TCTGAACTCTGGTGTGTCACAGATTCCCTCCACGGTGTCTCACCAACTCTGAACGCTAGCGTGTC
66 TCTGAACTCTAGCGTGTCACAGATTCCCTCCACGACGTCTCACCAACTCTGAACGCTACCGTGTC
* * * * *
403674 ATAGATTCCCTCCATGGTGTGTCACCAACTCTTAACTCTAGCATTTCATAGATTCCAT
131 ACAGATTCCCACCATGGCGTGTCACCAACTCTTAACTCTAGCATCTCACAGATTCCAT
* * * *
403732 CCATGGCGTCTCACTAACTTTTAACGCTGGCGTGTCACAGATTCCCTCCATGTCGTGTCACCAAC
1 CCATGGCGTCTCACCAACTATGAACGCTGGCGTGTCACAGATTCCCTCCATGGCGTGTCACCAAC
* * *
403797 TCTTAA-TCTAGCGTGTCACAGATTCCCTCCATGACGTCTCACCAACTCTGAACGTTACCGTGTC
66 TCTGAACTCTAGCGTGTCACAGATTCCCTCCACGACGTCTCACCAACTCTGAACGCTACCGTGTC
* ** *
403861 ACAGATTCCCACCATGGCGTGTCACCAACTCTTAACTCTGGTGTCTCACAGATTCCCT
131 ACAGATTCCCACCATGGCGTGTCACCAACTCTTAACTCTAGCATCTCACAGATTCCAT
**
403919 CCACAGCGTCTCACCAACT
1 CCATGGCGTCTCACCAACT
403938 CTGAGCAGTG
Statistics
Matches: 178, Mismatches: 28, Indels: 1
0.86 0.14 0.00
Matches are distributed among these distances:
187 116 0.65
188 62 0.35
ACGTcount: A:0.22, C:0.33, G:0.17, T:0.28
Consensus pattern (188 bp):
CCATGGCGTCTCACCAACTATGAACGCTGGCGTGTCACAGATTCCCTCCATGGCGTGTCACCAAC
TCTGAACTCTAGCGTGTCACAGATTCCCTCCACGACGTCTCACCAACTCTGAACGCTACCGTGTC
ACAGATTCCCACCATGGCGTGTCACCAACTCTTAACTCTAGCATCTCACAGATTCCAT
Found at i:403965 original size:94 final size:94
Alignment explanation
Indices: 403548--403941 Score: 502
Period size: 94 Copynumber: 4.2 Consensus size: 94
403538 ACATGACCAT
* * * * * * *
403548 GGCGTGTCACCAACTATGAACTCTGGCGTGTCATAGCTTCCCTCCATGGCGTGTCACCAACTCTG
1 GGCGTCTCACCAACTCTGAACGCTAGCGTGTCACAGATTCCCTCCATGGCGTGTCACCAACTCTT
* *
403613 AACTCTGGTGTGTCACAGATTCCCTCCAC
66 AACTCTAGCGTGTCACAGATTCCCTCCAC
* * *
403642 GGTGTCTCACCAACTCTGAACGCTAGCGTGTCATAGATTCCCTCCATGGTGTGTCACCAACTCTT
1 GGCGTCTCACCAACTCTGAACGCTAGCGTGTCACAGATTCCCTCCATGGCGTGTCACCAACTCTT
* * * * *
403707 AACTCTAGCATTTCATAGATTCCATCCAT
66 AACTCTAGCGTGTCACAGATTCCCTCCAC
* * * * *
403736 GGCGTCTCACTAACTTTTAACGCTGGCGTGTCACAGATTCCCTCCATGTCGTGTCACCAACTCTT
1 GGCGTCTCACCAACTCTGAACGCTAGCGTGTCACAGATTCCCTCCATGGCGTGTCACCAACTCTT
*
403801 AA-TCTAGCGTGTCACAGATTCCCTCCAT
66 AACTCTAGCGTGTCACAGATTCCCTCCAC
* * * *
403829 GACGTCTCACCAACTCTGAACGTTACCGTGTCACAGATTCCCACCATGGCGTGTCACCAACTCTT
1 GGCGTCTCACCAACTCTGAACGCTAGCGTGTCACAGATTCCCTCCATGGCGTGTCACCAACTCTT
* * *
403894 AACTCTGGTGTCTCACAGATTCCCTCCAC
66 AACTCTAGCGTGTCACAGATTCCCTCCAC
*
403923 AGCGTCTCACCAACTCTGA
1 GGCGTCTCACCAACTCTGA
403942 GCAGTGCTGT
Statistics
Matches: 257, Mismatches: 42, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
93 80 0.31
94 177 0.69
ACGTcount: A:0.22, C:0.33, G:0.18, T:0.28
Consensus pattern (94 bp):
GGCGTCTCACCAACTCTGAACGCTAGCGTGTCACAGATTCCCTCCATGGCGTGTCACCAACTCTT
AACTCTAGCGTGTCACAGATTCCCTCCAC
Found at i:410864 original size:50 final size:50
Alignment explanation
Indices: 410789--410888 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
410779 TGGCTTGTGG
*
410789 ATGGGGAGAGAAACACCAAATTCTTTCATATGAGAATGCAAAAGAAGTGA
1 ATGGGGAGAGAAACACCAAATTCTTTCATATGAGAATGCAAAAAAAGTGA
410839 ATGGGGAGAGAAACACCAAATTCTTTCATATGAGAATGCAAAAAAAGTGA
1 ATGGGGAGAGAAACACCAAATTCTTTCATATGAGAATGCAAAAAAAGTGA
410889 GTTAAAAATC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.45, C:0.12, G:0.23, T:0.20
Consensus pattern (50 bp):
ATGGGGAGAGAAACACCAAATTCTTTCATATGAGAATGCAAAAAAAGTGA
Found at i:420258 original size:12 final size:12
Alignment explanation
Indices: 420243--420287 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
420233 ACTTCTCTTC
420243 TTCTTTTTTTTT
1 TTCTTTTTTTTT
* *
420255 TTCTTTTTTCTC
1 TTCTTTTTTTTT
420267 TTCTTTTTTTTT
1 TTCTTTTTTTTT
*
420279 CTCTTTTTT
1 TTCTTTTTT
420288 CTTAGCCCTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTCTTTTTTTTT
Found at i:420265 original size:27 final size:29
Alignment explanation
Indices: 420215--420278 Score: 89
Period size: 27 Copynumber: 2.2 Consensus size: 29
420205 TTTTTAGTTA
420215 TTTTTTTTTTCTCTTTCTACTTCTCTTCTT
1 TTTTTTTTTTCTCTTTCTA-TTCTCTTCTT
420245 CTTTTTTTTTT-TCTTT-T-TTCTCTTCTT
1 -TTTTTTTTTTCTCTTTCTATTCTCTTCTT
420272 TTTTTTT
1 TTTTTTT
420279 CTCTTTTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
26 7 0.21
27 10 0.30
29 1 0.03
30 5 0.15
31 10 0.30
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.80
Consensus pattern (29 bp):
TTTTTTTTTTCTCTTTCTATTCTCTTCTT
Found at i:420273 original size:22 final size:21
Alignment explanation
Indices: 420245--420290 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 21
420235 TTCTCTTCTT
420245 CTTTTTTTTTTTCT-TTTTTCT
1 CTTTTTTTTTTTCTCTTTTT-T
420266 CTTCTTTTTTTTTCTCTTTTTT
1 CTT-TTTTTTTTTCTCTTTTTT
420288 CTT
1 CTT
420291 AGCCCTCCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (21 bp):
CTTTTTTTTTTTCTCTTTTTT
Found at i:420273 original size:24 final size:24
Alignment explanation
Indices: 420241--420289 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
420231 CTACTTCTCT
*
420241 TCTTCTTTTTTTTTTTCTTTTTTC
1 TCTTCTTTTTTTTTCTCTTTTTTC
420265 TCTTCTTTTTTTTTCTCTTTTTTC
1 TCTTCTTTTTTTTTCTCTTTTTTC
420289 T
1 T
420290 TAGCCCTCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (24 bp):
TCTTCTTTTTTTTTCTCTTTTTTC
Found at i:421716 original size:21 final size:21
Alignment explanation
Indices: 421687--421726 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
421677 TTATAACTAA
*
421687 ATATAATATGAACATGTTATC
1 ATATAATATCAACATGTTATC
*
421708 ATATTATATCAACATGTTA
1 ATATAATATCAACATGTTA
421727 CGTCATAATT
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:0.42, C:0.10, G:0.07, T:0.40
Consensus pattern (21 bp):
ATATAATATCAACATGTTATC
Found at i:422316 original size:22 final size:21
Alignment explanation
Indices: 422275--422317 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
422265 TTTTATAATT
422275 TAATTTATAAGTTAAAATTAA
1 TAATTTATAAGTTAAAATTAA
422296 TAATTTAATAAG-TAAAGATTAA
1 TAATTT-ATAAGTTAAA-ATTAA
422318 ATACATTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (21 bp):
TAATTTATAAGTTAAAATTAA
Found at i:422382 original size:22 final size:24
Alignment explanation
Indices: 422354--422419 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 24
422344 ATATTATTAG
*
422354 TAATTAAATTATTAATT-TTATA-
1 TAATTAAATTATTAATTATTAAAT
*
422376 TAATTAAATATATAAAATTATTAAAT
1 TAATTAAAT-TAT-TAATTATTAAAT
422402 TAATTAAAATTATTAATT
1 TAATT-AAATTATTAATT
422420 GTTTTGATCA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
22 9 0.25
23 3 0.08
24 4 0.11
25 8 0.22
26 8 0.22
27 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TAATTAAATTATTAATTATTAAAT
Found at i:422401 original size:8 final size:8
Alignment explanation
Indices: 422356--422417 Score: 56
Period size: 8 Copynumber: 7.6 Consensus size: 8
422346 ATTATTAGTA
422356 ATTAAATT
1 ATTAAATT
422364 ATT-AATT
1 ATTAAATT
* *
422371 -TTATATA
1 ATTAAATT
422378 ATTAAATAT
1 ATTAAAT-T
*
422387 ATAAAATT
1 ATTAAATT
422395 ATTAAATT
1 ATTAAATT
422403 AATTAAAATT
1 -ATT-AAATT
422413 ATTAA
1 ATTAA
422418 TTGTTTTGAT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
6 2 0.05
7 6 0.14
8 18 0.42
9 12 0.28
10 5 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
ATTAAATT
Found at i:456759 original size:23 final size:23
Alignment explanation
Indices: 456715--456765 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
456705 GTTCGCTATG
456715 CTTTC-GATTTCTCTCTCCTACA
1 CTTTCAGATTTCTCTCTCCTACA
* * **
456737 TTTTCAGATTTCTCTTTTTTACA
1 CTTTCAGATTTCTCTCTCCTACA
456760 CTTTCA
1 CTTTCA
456766 AAACACCAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.16, C:0.27, G:0.04, T:0.53
Consensus pattern (23 bp):
CTTTCAGATTTCTCTCTCCTACA
Found at i:457197 original size:29 final size:28
Alignment explanation
Indices: 457143--457218 Score: 77
Period size: 29 Copynumber: 2.8 Consensus size: 28
457133 ATTAAAGTGT
* *
457143 AACAA-AATATTTTTAAATATATCATGC
1 AACAACAATATTTTTAAACATAACATGC
* *
457170 AACAACAATATTTTTTCAACATAACATGT
1 AACAACAATA-TTTTTAAACATAACATGC
*
457199 AACAAC-AT-TTTTTAACCATA
1 AACAACAATATTTTTAAACATA
457219 GCGTGTAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
26 10 0.24
27 5 0.12
28 6 0.15
29 20 0.49
ACGTcount: A:0.46, C:0.16, G:0.03, T:0.36
Consensus pattern (28 bp):
AACAACAATATTTTTAAACATAACATGC
Found at i:457225 original size:26 final size:25
Alignment explanation
Indices: 457173--457255 Score: 78
Period size: 26 Copynumber: 3.3 Consensus size: 25
457163 ATCATGCAAC
* * *
457173 AACAATATTTTTTCAACATAACATGT
1 AACAACATTTTTT-AACATAGCGTGT
457199 AACAACATTTTTTAACCATAGCGTGT
1 AACAACATTTTTTAA-CATAGCGTGT
* ** *
457225 AA-TATGTTTTTTTACATAGCGTGT
1 AACAACATTTTTTAACATAGCGTGT
457249 AACAACA
1 AACAACA
457256 GTATTTTTNA
Statistics
Matches: 45, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
24 12 0.27
25 11 0.24
26 22 0.49
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (25 bp):
AACAACATTTTTTAACATAGCGTGT
Found at i:457262 original size:26 final size:27
Alignment explanation
Indices: 457196--457263 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 27
457186 CAACATAACA
457196 TGTAACAACA-TTTTTTAACCATAGCG
1 TGTAACAACAGTTTTTTAACCATAGCG
* * *
457222 TGTAA-TA-TGTTTTTTTA-CATAGCG
1 TGTAACAACAGTTTTTTAACCATAGCG
457246 TGTAACAACAGTATTTTT
1 TGTAACAACAGT-TTTTT
457264 NAACAACCTA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
24 12 0.36
25 9 0.27
26 7 0.21
27 5 0.15
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (27 bp):
TGTAACAACAGTTTTTTAACCATAGCG
Found at i:457372 original size:24 final size:24
Alignment explanation
Indices: 457345--457471 Score: 105
Period size: 24 Copynumber: 5.3 Consensus size: 24
457335 ACAACCTAAT
* * *
457345 CATGGCGTGTCATATGTTTTTGCA
1 CATGACGTGTCACATATTTTTGCA
*
457369 CATGACGTGTCACATATTTTTGTA
1 CATGACGTGTCACATATTTTTGCA
* * * *
457393 CATGACATATAACATATTTTTGTA
1 CATGACGTGTCACATATTTTTGCA
** **
457417 CATGACGTGT-A-ACCTTTTTAAA
1 CATGACGTGTCACATATTTTTGCA
* *
457439 CCATGACGTGTAACATATTTTTGTA
1 -CATGACGTGTCACATATTTTTGCA
457464 CATGACGT
1 CATGACGT
457472 ATAATAAATT
Statistics
Matches: 83, Mismatches: 17, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
22 7 0.08
23 11 0.13
24 58 0.70
25 7 0.08
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (24 bp):
CATGACGTGTCACATATTTTTGCA
Found at i:457406 original size:69 final size:69
Alignment explanation
Indices: 457265--457406 Score: 158
Period size: 69 Copynumber: 2.1 Consensus size: 69
457255 AGTATTTTTN
* * * * **
457265 AACAACCTAACCATGACGTGTTATATATTTCTGTACATAACGTGTCACATGTTTCTGTGCATGGT
1 AACAACCTAACCATGACGTGTCATATATTTCTGCACATAACGTGTCACATATTTCTGTACATGAC
* *
457330 GTGT
66 ATAT
* * * * * *
457334 AACAACCTAATCATGGCGTGTCATATGTTTTTGCACATGACGTGTCACATATTTTTGTACATGAC
1 AACAACCTAACCATGACGTGTCATATATTTCTGCACATAACGTGTCACATATTTCTGTACATGAC
457399 ATAT
66 ATAT
457403 AACA
1 AACA
457407 TATTTTTGTA
Statistics
Matches: 59, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
69 59 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (69 bp):
AACAACCTAACCATGACGTGTCATATATTTCTGCACATAACGTGTCACATATTTCTGTACATGAC
ATAT
Found at i:457608 original size:75 final size:75
Alignment explanation
Indices: 457369--457619 Score: 329
Period size: 75 Copynumber: 3.4 Consensus size: 75
457359 TGTTTTTGCA
* *
457369 CATGACGTGTCACATATTTTTGTACATGAC--AT-ATAACA-TATTTTTGT--ACATGACGTGTA
1 CATGACGTGTAACATATTTTTGTACATGACGTATAATAACATTATTTTTTTAAACATGACGTGTA
** *
457428 ACCTTTTTAAAC
66 A-CAATCT-AAC
* *
457440 CATGACGTGTAACATATTTTTGTACATGACGTATAATAA-ATTA-TTTTTTAAATATGACATGTA
1 CATGACGTGTAACATATTTTTGTACATGACGTATAATAACATTATTTTTTTAAACATGACGTGTA
457503 ACAATCTAAC
66 ACAATCTAAC
* *
457513 TATGACGTGTAACATATTTTTGTACATGGCGTATAATAACATTATTTTTTTAAACATGACGTGTA
1 CATGACGTGTAACATATTTTTGTACATGACGTATAATAACATTATTTTTTTAAACATGACGTGTA
457578 ACAATCTAAC
66 ACAATCTAAC
* *
457588 CATGACGTGTCACATGTTTTTGTACATGACGT
1 CATGACGTGTAACATATTTTTGTACATGACGT
457620 GTCACATGTT
Statistics
Matches: 157, Mismatches: 15, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
71 29 0.18
73 48 0.31
74 13 0.08
75 67 0.43
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.39
Consensus pattern (75 bp):
CATGACGTGTAACATATTTTTGTACATGACGTATAATAACATTATTTTTTTAAACATGACGTGTA
ACAATCTAAC
Found at i:457644 original size:23 final size:24
Alignment explanation
Indices: 457588--457706 Score: 95
Period size: 24 Copynumber: 5.1 Consensus size: 24
457578 ACAATCTAAC
*
457588 CATGACGTGTCACATGTTTTTGTA
1 CATGACGTGTCACATGTTTCTGTA
457612 CATGACGTGTCACATGTTTCTGT-
1 CATGACGTGTCACATGTTTCTGTA
** * ** *
457635 CATGGTGTGTAACA---ACCT-AA
1 CATGACGTGTCACATGTTTCTGTA
* *
457655 TCATGGCGTGTTACATGTTTCTGTA
1 -CATGACGTGTCACATGTTTCTGTA
* *
457680 CATGACGTGTCACATTTTTTTGTA
1 CATGACGTGTCACATGTTTCTGTA
457704 CAT
1 CAT
457707 AATGTGTAAC
Statistics
Matches: 73, Mismatches: 16, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
20 2 0.03
21 12 0.16
23 11 0.15
24 47 0.64
25 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.39
Consensus pattern (24 bp):
CATGACGTGTCACATGTTTCTGTA
Found at i:457682 original size:68 final size:69
Alignment explanation
Indices: 457573--457739 Score: 228
Period size: 68 Copynumber: 2.4 Consensus size: 69
457563 TAAACATGAC
* * * *
457573 GTGTAACAATCTAACCATGACGTGTCACATGTTTTTGTACATGACGTGTCACATGTTTCTGT-CA
1 GTGTAACAACCTAATCATGGCGTGTCACATGTTTCTGTACATGACGTGTCACATGTTTCTGTACA
**
457637 TGGT
66 TAAT
* * *
457641 GTGTAACAACCTAATCATGGCGTGTTACATGTTTCTGTACATGACGTGTCACATTTTTTTGTACA
1 GTGTAACAACCTAATCATGGCGTGTCACATGTTTCTGTACATGACGTGTCACATGTTTCTGTACA
457706 TAAT
66 TAAT
* *
457710 GTGTAACAACCTAATAATGGCATGTCACAT
1 GTGTAACAACCTAATCATGGCGTGTCACAT
457740 ATTTTTACAC
Statistics
Matches: 86, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
68 55 0.64
69 31 0.36
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (69 bp):
GTGTAACAACCTAATCATGGCGTGTCACATGTTTCTGTACATGACGTGTCACATGTTTCTGTACA
TAAT
Found at i:457713 original size:24 final size:24
Alignment explanation
Indices: 457661--457713 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
457651 CTAATCATGG
* *
457661 CGTGTTACATGTTTCTGTACATGA
1 CGTGTCACATGTTTCTGTACATAA
* *
457685 CGTGTCACATTTTTTTGTACATAA
1 CGTGTCACATGTTTCTGTACATAA
*
457709 TGTGT
1 CGTGT
457714 AACAACCTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.45
Consensus pattern (24 bp):
CGTGTCACATGTTTCTGTACATAA
Done.