Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 175 of 182
Found at i:52955600 original size:27 final size:26
Alignment explanation
Indices: 52955559--52955631 Score: 110
Period size: 27 Copynumber: 2.8 Consensus size: 26
52955549 CGAAAAAAAA
*
52955559 GTCAACGGTCAAAGTCAACGGTCAGTG
1 GTCAACGGTCAAAGTCAACGGTCA-CG
*
52955586 GTTAACGGTCAAAGTCAACGGTCACG
1 GTCAACGGTCAAAGTCAACGGTCACG
*
52955612 GTCAACAGTCAAAGTCAACG
1 GTCAACGGTCAAAGTCAACG
52955632 CCGGTCAACA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
26 19 0.45
27 23 0.55
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (26 bp):
GTCAACGGTCAAAGTCAACGGTCACG
Found at i:52955648 original size:26 final size:28
Alignment explanation
Indices: 52955563--52955649 Score: 89
Period size: 27 Copynumber: 3.3 Consensus size: 28
52955553 AAAAAAGTCA
* *
52955563 ACGGTCAAAGTCAACGGTCAGTGGT-TA-
1 ACGGTCAAAGTCAACGGTCA-CGGTCAAC
52955590 ACGGTCAAAGTCAACGGTCACGGTCAAC
1 ACGGTCAAAGTCAACGGTCACGGTCAAC
52955618 A--GTCAAAGTCAAC-G-C-CGGTCAAC
1 ACGGTCAAAGTCAACGGTCACGGTCAAC
52955641 ACCGGTCAA
1 A-CGGTCAA
52955650 TGGTTTGACT
Statistics
Matches: 53, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
23 9 0.17
24 1 0.02
25 1 0.02
26 20 0.38
27 21 0.40
28 1 0.02
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.16
Consensus pattern (28 bp):
ACGGTCAAAGTCAACGGTCACGGTCAAC
Found at i:52955694 original size:14 final size:15
Alignment explanation
Indices: 52955675--52955709 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
52955665 TGGGTTGGAC
*
52955675 TTGGTTC-AATTGGT
1 TTGGTTCAAATGGGT
52955689 TTGGTTCAAATGGGT
1 TTGGTTCAAATGGGT
52955704 TTGGTT
1 TTGGTT
52955710 AGGTTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.14, C:0.06, G:0.31, T:0.49
Consensus pattern (15 bp):
TTGGTTCAAATGGGT
Found at i:52955707 original size:20 final size:20
Alignment explanation
Indices: 52955684--52955750 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
52955674 CTTGGTTCAA
*
52955684 TTGGTTTGGTTCAAATGGGT
1 TTGGTTTGGTTTAAATGGGT
*
52955704 TTGGTTAGGTTTAAATGGGT
1 TTGGTTTGGTTTAAATGGGT
52955724 TTGGTTTGGTTTAAATGGGT
1 TTGGTTTGGTTTAAATGGGT
52955744 TTGGTTT
1 TTGGTTT
52955751 AAATGAATGT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.15, C:0.01, G:0.34, T:0.49
Consensus pattern (20 bp):
TTGGTTTGGTTTAAATGGGT
Found at i:52955744 original size:15 final size:15
Alignment explanation
Indices: 52955726--52955755 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
52955716 AAATGGGTTT
52955726 GGTTTGGTTTAAATG
1 GGTTTGGTTTAAATG
52955741 GGTTTGGTTTAAATG
1 GGTTTGGTTTAAATG
52955756 AATGTGGGTT
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:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (15 bp):
GGTTTGGTTTAAATG
Found at i:52962792 original size:13 final size:13
Alignment explanation
Indices: 52962774--52962880 Score: 142
Period size: 13 Copynumber: 8.1 Consensus size: 13
52962764 TTTTCGAAAA
52962774 AAAGTCAACGGTC
1 AAAGTCAACGGTC
*
52962787 AAAGTCAACGATC
1 AAAGTCAACGGTC
52962800 AAAGTCAACGGTC
1 AAAGTCAACGGTC
*
52962813 AAAGTCAATGGTC
1 AAAGTCAACGGTC
**
52962826 AGTGGTCAACGGTC
1 A-AAGTCAACGGTC
52962840 AAAGTCAACGGTC
1 AAAGTCAACGGTC
* *
52962853 AATGGTCAACAGTC
1 AA-AGTCAACGGTC
52962867 AAAGTCAACGGTC
1 AAAGTCAACGGTC
52962880 A
1 A
52962881 GTCAACGATC
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
13 59 0.74
14 21 0.26
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.18
Consensus pattern (13 bp):
AAAGTCAACGGTC
Found at i:52962841 original size:27 final size:27
Alignment explanation
Indices: 52962777--52962882 Score: 151
Period size: 27 Copynumber: 4.0 Consensus size: 27
52962767 TCGAAAAAAA
* **
52962777 GTCAACGGTCAAAGTCAACGATCA-AA
1 GTCAACGGTCAAAGTCAACGGTCAGTG
*
52962803 GTCAACGGTCAAAGTCAATGGTCAGTG
1 GTCAACGGTCAAAGTCAACGGTCAGTG
*
52962830 GTCAACGGTCAAAGTCAACGGTCAATG
1 GTCAACGGTCAAAGTCAACGGTCAGTG
*
52962857 GTCAACAGTCAAAGTCAACGGTCAGT
1 GTCAACGGTCAAAGTCAACGGTCAGT
52962883 CAACGATCGG
Statistics
Matches: 71, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
26 22 0.31
27 49 0.69
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.19
Consensus pattern (27 bp):
GTCAACGGTCAAAGTCAACGGTCAGTG
Found at i:52962880 original size:7 final size:7
Alignment explanation
Indices: 52962777--52962880 Score: 74
Period size: 7 Copynumber: 15.6 Consensus size: 7
52962767 TCGAAAAAAA
52962777 GTCAACG
1 GTCAACG
*
52962784 GTCAA-A
1 GTCAACG
52962790 GTCAACG
1 GTCAACG
* *
52962797 ATCAA-A
1 GTCAACG
52962803 GTCAACG
1 GTCAACG
*
52962810 GTCAA-A
1 GTCAACG
*
52962816 GTCAATG
1 GTCAACG
**
52962823 GTCAGTG
1 GTCAACG
52962830 GTCAACG
1 GTCAACG
*
52962837 GTCAA-A
1 GTCAACG
52962843 GTCAACG
1 GTCAACG
*
52962850 GTCAATG
1 GTCAACG
*
52962857 GTCAACA
1 GTCAACG
*
52962864 GTCAA-A
1 GTCAACG
52962870 GTCAACG
1 GTCAACG
52962877 GTCA
1 GTCA
52962881 GTCAACGATC
Statistics
Matches: 75, Mismatches: 17, Indels: 10
0.74 0.17 0.10
Matches are distributed among these distances:
6 25 0.33
7 50 0.67
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (7 bp):
GTCAACG
Found at i:52962961 original size:14 final size:15
Alignment explanation
Indices: 52962942--52962976 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
52962932 TGGGTTGGAC
*
52962942 TTGGTTC-AATTGGT
1 TTGGTTCAAATGGGT
52962956 TTGGTTCAAATGGGT
1 TTGGTTCAAATGGGT
52962971 TTGGTT
1 TTGGTT
52962977 AAGTTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.14, C:0.06, G:0.31, T:0.49
Consensus pattern (15 bp):
TTGGTTCAAATGGGT
Found at i:52962974 original size:20 final size:20
Alignment explanation
Indices: 52962951--52963017 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
52962941 CTTGGTTCAA
*
52962951 TTGGTTTGGTTCAAATGGGT
1 TTGGTTTGGTTTAAATGGGT
**
52962971 TTGGTTAAGTTTAAATGGGT
1 TTGGTTTGGTTTAAATGGGT
*
52962991 TTTGTTTGGTTTAAATGGGT
1 TTGGTTTGGTTTAAATGGGT
52963011 TTGGTTT
1 TTGGTTT
52963018 AAATGAATGT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.16, C:0.01, G:0.31, T:0.51
Consensus pattern (20 bp):
TTGGTTTGGTTTAAATGGGT
Found at i:52962997 original size:15 final size:15
Alignment explanation
Indices: 52962994--52963022 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
52962984 AATGGGTTTT
52962994 GTTTGGTTTAAATGG
1 GTTTGGTTTAAATGG
52963009 GTTTGGTTTAAATG
1 GTTTGGTTTAAATG
52963023 AATGTGAGTT
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:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (15 bp):
GTTTGGTTTAAATGG
Found at i:52968918 original size:19 final size:20
Alignment explanation
Indices: 52968894--52968938 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
52968884 TTCCTGTGTG
52968894 CTTTATT-TTATTGGTT-GCT
1 CTTTATTGTTA-TGGTTGGCT
52968913 CTTTATTGTTATGGTTGGCT
1 CTTTATTGTTATGGTTGGCT
52968933 -TTTATT
1 CTTTATT
52968939 ACTGGTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.11, C:0.09, G:0.18, T:0.62
Consensus pattern (20 bp):
CTTTATTGTTATGGTTGGCT
Found at i:52981431 original size:42 final size:43
Alignment explanation
Indices: 52981384--52981469 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
52981374 ACTTTAATCC
52981384 TTAA-TTTTTTTTACTCCAATAAATACTTAAAAAAGAGATTTT
1 TTAATTTTTTTTTACTCCAATAAATACTTAAAAAAGAGATTTT
52981426 TTAATTTTTTTTTACTCCAATAAATACTTAAAAAAGAGATTTT
1 TTAATTTTTTTTTACTCCAATAAATACTTAAAAAAGAGATTTT
52981469 T
1 T
52981470 AGATAACCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 4 0.09
43 39 0.91
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.47
Consensus pattern (43 bp):
TTAATTTTTTTTTACTCCAATAAATACTTAAAAAAGAGATTTT
Found at i:52989918 original size:12 final size:12
Alignment explanation
Indices: 52989901--52989943 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
52989891 TCCCCACTCC
52989901 AAAAAAATTGAA
1 AAAAAAATTGAA
*
52989913 AAAAAAATTG-G
1 AAAAAAATTGAA
*
52989924 AAAAAAATTAAA
1 AAAAAAATTGAA
52989936 AAAAAAAT
1 AAAAAAAT
52989944 GGAAGCTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 9 0.33
12 18 0.67
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (12 bp):
AAAAAAATTGAA
Found at i:52989936 original size:22 final size:23
Alignment explanation
Indices: 52989901--52989947 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
52989891 TCCCCACTCC
*
52989901 AAAAAAATTGAAAAAAAAATTGG
1 AAAAAAATTGAAAAAAAAAATGG
52989924 AAAAAAATT-AAAAAAAAAATGG
1 AAAAAAATTGAAAAAAAAAATGG
52989946 AA
1 AA
52989948 GCTTATTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.15
Consensus pattern (23 bp):
AAAAAAATTGAAAAAAAAAATGG
Found at i:52989941 original size:11 final size:11
Alignment explanation
Indices: 52989901--52989941 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
52989891 TCCCCACTCC
52989901 AAAAAAATTGAA
1 AAAAAAATT-AA
**
52989913 AAAAAAATTGG
1 AAAAAAATTAA
52989924 AAAAAAATTAA
1 AAAAAAATTAA
52989935 AAAAAAA
1 AAAAAAA
52989942 ATGGAAGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (11 bp):
AAAAAAATTAA
Found at i:52997061 original size:13 final size:13
Alignment explanation
Indices: 52997025--52997052 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
52997015 AACTTTGAAC
52997025 CTCAAACTCAAAT
1 CTCAAACTCAAAT
52997038 CTCAAACTCAAAT
1 CTCAAACTCAAAT
52997051 CT
1 CT
52997053 TAAATTCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.32, G:0.00, T:0.25
Consensus pattern (13 bp):
CTCAAACTCAAAT
Found at i:52997087 original size:19 final size:19
Alignment explanation
Indices: 52997022--52997080 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
52997012 CCTAACTTTG
*
52997022 AACCTCAAA-CTCAAATCTC
1 AACCTCAAACCTTAAA-CTC
* * *
52997041 AAACTCAAATCTTAAATTC
1 AACCTCAAACCTTAAACTC
52997060 AACCTCAAACCTTAAACTC
1 AACCTCAAACCTTAAACTC
52997079 AA
1 AA
52997081 TTTCAAAGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
19 28 0.85
20 5 0.15
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.24
Consensus pattern (19 bp):
AACCTCAAACCTTAAACTC
Found at i:52997858 original size:4 final size:4
Alignment explanation
Indices: 52997851--52998016 Score: 305
Period size: 4 Copynumber: 41.5 Consensus size: 4
52997841 AGTGGATATA
* * *
52997851 TATG TATG TATG CATG CATG TATG TATG TATG TATG CATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
52997899 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
52997947 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
52997995 TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TA
52998017 AGAAAGAAAA
Statistics
Matches: 158, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 158 1.00
ACGTcount: A:0.25, C:0.02, G:0.25, T:0.48
Consensus pattern (4 bp):
TATG
Found at i:52999471 original size:19 final size:18
Alignment explanation
Indices: 52999443--52999479 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
52999433 GCCAGTTTAC
52999443 TTGCCACGTTGGACAAGTA
1 TTGCCACGTTGGA-AAGTA
*
52999462 TTGCCTCGTTGGAAAGTA
1 TTGCCACGTTGGAAAGTA
52999480 GTAAAAGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (18 bp):
TTGCCACGTTGGAAAGTA
Found at i:53000748 original size:24 final size:24
Alignment explanation
Indices: 53000721--53000772 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
53000711 CAGACAACAT
53000721 TTAGCCCACACGAGCCCAAAATGG
1 TTAGCCCACACGAGCCCAAAATGG
* ** *
53000745 TTAGCTCTTACGAGCCCAGAATGG
1 TTAGCCCACACGAGCCCAAAATGG
53000769 TTAG
1 TTAG
53000773 TTCTTACGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (24 bp):
TTAGCCCACACGAGCCCAAAATGG
Found at i:53000777 original size:24 final size:24
Alignment explanation
Indices: 53000730--53000836 Score: 151
Period size: 24 Copynumber: 4.5 Consensus size: 24
53000720 TTTAGCCCAC
*
53000730 ACGAGCCCAAAATGGTTAGCTCTT
1 ACGAGCCCAGAATGGTTAGCTCTT
*
53000754 ACGAGCCCAGAATGGTTAGTTCTT
1 ACGAGCCCAGAATGGTTAGCTCTT
* *
53000778 ACGAGCCTAGAATGATTAGCTCTT
1 ACGAGCCCAGAATGGTTAGCTCTT
* * *
53000802 ATGAGCTCAGAATGGTTAACTCTT
1 ACGAGCCCAGAATGGTTAGCTCTT
53000826 ACGAGCCCAGA
1 ACGAGCCCAGA
53000837 CAGAGTTTAA
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 71 1.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (24 bp):
ACGAGCCCAGAATGGTTAGCTCTT
Found at i:53003253 original size:3 final size:3
Alignment explanation
Indices: 53003247--53003278 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
53003237 GATGGGTTAT
*
53003247 TTC TTC TTC TTC TTC TTC TTC TTT TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
53003279 TTCCATTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (3 bp):
TTC
Found at i:53003605 original size:24 final size:26
Alignment explanation
Indices: 53003578--53003629 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
53003568 ACTATATTAA
53003578 AAAATTAATAAATA-AAAAAT-ATAT
1 AAAATTAATAAATATAAAAATAATAT
* *
53003602 AAAATTATTAAATATTAAAATAATAT
1 AAAATTAATAAATATAAAAATAATAT
53003628 AA
1 AA
53003630 TATAAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 13 0.54
25 5 0.21
26 6 0.25
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (26 bp):
AAAATTAATAAATATAAAAATAATAT
Found at i:53004891 original size:2 final size:2
Alignment explanation
Indices: 53004884--53004910 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
53004874 TGAACCAAAT
53004884 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 T
53004911 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:53017712 original size:20 final size:19
Alignment explanation
Indices: 53017675--53017714 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
53017665 CCTTCTATTC
53017675 CTTTTATTTTGTTTTCTTT
1 CTTTTATTTTGTTTTCTTT
53017694 CTTTTGATTTT-TTTCTCTTT
1 CTTTT-ATTTTGTTT-TCTTT
53017714 C
1 C
53017715 AATTGTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.05, C:0.15, G:0.05, T:0.75
Consensus pattern (19 bp):
CTTTTATTTTGTTTTCTTT
Found at i:53021398 original size:2 final size:2
Alignment explanation
Indices: 53021391--53021430 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
53021381 TTGTGATTGT
53021391 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
53021431 CTGTGTTATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:53021924 original size:43 final size:43
Alignment explanation
Indices: 53021858--53022127 Score: 371
Period size: 43 Copynumber: 6.3 Consensus size: 43
53021848 ATCTGTTAAT
*
53021858 TTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGACCATATTT
1 TTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGACCATATTC
* ** *
53021901 TTTAGCGGCGTTTATGGTAAAAGCGTCGCTAAAGACCATATTC
1 TTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGACCATATTC
* *
53021944 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGACCATATTC
* * *
53021987 TTTAACGGCGTTTGTGGGGAAAGCGCCACTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGACCATATTC
*** * * *
53022030 TTTAATTGCGTTTAT-AGGTAAGCGCCGCTAAAGACCATATTC
1 TTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGACCATATTC
*
53022072 TTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGACCATATTC
*
53022115 TATAGCGGCGTTT
1 TTTAGCGGCGTTT
53022128 TTCATCATAA
Statistics
Matches: 199, Mismatches: 27, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
42 34 0.17
43 165 0.83
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGACCATATTC
Found at i:53022097 original size:128 final size:128
Alignment explanation
Indices: 53021858--53022127 Score: 425
Period size: 128 Copynumber: 2.1 Consensus size: 128
53021848 ATCTGTTAAT
* * *
53021858 TTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGACCATATTTTTTAGCGGCGTTTATGGTAAAA
1 TTTAGCGGCGTTTGTGGGGAAAGCGCCACTAAAGACCATATTCTTTAACGGCGTTTATGGT-AAA
*
53021923 GCGTCGCTAAAGACCATATTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
65 GCGCCGCTAAAGACCATATTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
* * **
53021987 TTTAACGGCGTTTGTGGGGAAAGCGCCACTAAAGACCATGTTCTTTAATTGCGTTTATAGGT-AA
1 TTTAGCGGCGTTTGTGGGGAAAGCGCCACTAAAGACCATATTCTTTAACGGCGTTTAT-GGTAAA
*
53022051 GCGCCGCTAAAGACCATATTCTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGACCATGTTC
65 GCGCCGCTAAAGACCATATTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
*
53022115 TATAGCGGCGTTT
1 TTTAGCGGCGTTT
53022128 TTCATCATAA
Statistics
Matches: 129, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
128 75 0.58
129 51 0.40
130 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (128 bp):
TTTAGCGGCGTTTGTGGGGAAAGCGCCACTAAAGACCATATTCTTTAACGGCGTTTATGGTAAAG
CGCCGCTAAAGACCATATTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
Found at i:53030092 original size:15 final size:17
Alignment explanation
Indices: 53030074--53030105 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
53030064 TTTTTTCACC
53030074 TTTTTTT-C-TTTTTTT
1 TTTTTTTGCATTTTTTT
53030089 TTTTTTTGCATTTTTTT
1 TTTTTTTGCATTTTTTT
53030106 CTTAGCTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.03, C:0.06, G:0.03, T:0.88
Consensus pattern (17 bp):
TTTTTTTGCATTTTTTT
Found at i:53030364 original size:17 final size:15
Alignment explanation
Indices: 53030324--53030366 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
53030314 TTGAAAATTG
53030324 TTTATATTATTTATAA
1 TTTATA-TATTTATAA
53030340 TTTA-ATATTTAATAA
1 TTTATATATTT-ATAA
53030355 TTTTATATATTT
1 -TTTATATATTT
53030367 TTCACATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 5 0.21
15 5 0.21
16 8 0.33
17 6 0.25
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTATATATTTATAA
Found at i:53031298 original size:15 final size:17
Alignment explanation
Indices: 53031278--53031314 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
53031268 AGAATGGAAA
53031278 GAAAATTGGAA-AGAT-
1 GAAAATTGGAAGAGATG
*
53031293 GAAAATTTGAAGAGATG
1 GAAAATTGGAAGAGATG
53031310 GAAAA
1 GAAAA
53031315 ATAAAAAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 10 0.53
16 4 0.21
17 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.27, T:0.19
Consensus pattern (17 bp):
GAAAATTGGAAGAGATG
Found at i:53035593 original size:3 final size:3
Alignment explanation
Indices: 53035575--53035611 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
53035565 TTTAAACCCT
*
53035575 CAC CAA CAC TCAC CAC CAC CAC CAC CAC CAC CAC CAC
1 CAC CAC CAC -CAC CAC CAC CAC CAC CAC CAC CAC CAC
53035612 TCAAACCTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.35, C:0.62, G:0.00, T:0.03
Consensus pattern (3 bp):
CAC
Found at i:53039615 original size:22 final size:20
Alignment explanation
Indices: 53039562--53039615 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
53039552 TCTATTGTAT
**
53039562 TTTATACTTGTTTGATTTTA
1 TTTATACTTGTTTGATAATA
*
53039582 TGTTATAATTGTTTGTATAAATA
1 T-TTATACTTGTTTG-AT-AATA
53039605 TTTATACTTGT
1 TTTATACTTGT
53039616 AGTATACTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 1 0.04
21 12 0.44
22 11 0.41
23 3 0.11
ACGTcount: A:0.26, C:0.04, G:0.11, T:0.59
Consensus pattern (20 bp):
TTTATACTTGTTTGATAATA
Found at i:53041417 original size:29 final size:29
Alignment explanation
Indices: 53041362--53041431 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
53041352 AATAGTCTAT
* *
53041362 ATTTTTATAATTTTTAAAAGATTAAAT-CA
1 ATTTTTATCA-TTTTAAAAGATAAAATGCA
* *
53041391 ATTTTTATCATTTTAAAGGGATAAAATGTA
1 ATTTTTATCATTTTAAA-AGATAAAATGCA
53041421 A-TTTTATCATT
1 ATTTTTATCATT
53041432 ACTAATTCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 7 0.20
29 26 0.74
30 2 0.06
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (29 bp):
ATTTTTATCATTTTAAAAGATAAAATGCA
Found at i:53045975 original size:18 final size:18
Alignment explanation
Indices: 53045942--53045976 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
53045932 ATAATATTAT
53045942 AATGTAAATATATTTAAA
1 AATGTAAATATATTTAAA
53045960 AATGTTAAATAT-TTTAA
1 AATG-TAAATATATTTAA
53045977 TTAATAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (18 bp):
AATGTAAATATATTTAAA
Found at i:53055710 original size:20 final size:19
Alignment explanation
Indices: 53055668--53055706 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
53055658 TAAATTAAAG
53055668 ATTAAAAAATCAGAAAAAA
1 ATTAAAAAATCAGAAAAAA
*
53055687 ATTAAAAAATTAGAAAAAA
1 ATTAAAAAATCAGAAAAAA
53055706 A
1 A
53055707 ATTACAAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (19 bp):
ATTAAAAAATCAGAAAAAA
Found at i:53058905 original size:2 final size:2
Alignment explanation
Indices: 53058898--53058924 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
53058888 TCAACTCTAG
53058898 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 T
53058925 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:53062951 original size:14 final size:14
Alignment explanation
Indices: 53062934--53062983 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
53062924 GAGCTTTTTA
53062934 ATTTATTTAAATTT
1 ATTTATTTAAATTT
53062948 ATTT-TTTAAAATTTT
1 ATTTATTT-AAA-TTT
53062963 ATTTTATTT--ATTT
1 A-TTTATTTAAATTT
53062976 ATTTATTT
1 ATTTATTT
53062984 TTTCAAATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
12 7 0.22
13 7 0.22
14 8 0.25
15 4 0.12
16 3 0.09
17 3 0.09
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
ATTTATTTAAATTT
Found at i:53062961 original size:20 final size:21
Alignment explanation
Indices: 53062938--53062976 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
53062928 TTTTTAATTT
53062938 ATTTAAATTTATTT-TTTAAA
1 ATTTAAATTTATTTATTTAAA
* *
53062958 ATTTTATTTTATTTATTTA
1 ATTTAAATTTATTTATTTA
53062977 TTTATTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
ATTTAAATTTATTTATTTAAA
Found at i:53067604 original size:81 final size:81
Alignment explanation
Indices: 53067507--53067666 Score: 284
Period size: 81 Copynumber: 2.0 Consensus size: 81
53067497 ATCATCACTA
*
53067507 TTTTGAGAAAATTGATAAATTTAAAAACTAACATAGACTCAAAAAATTAAGGATCAAATTAAAAA
1 TTTTGAGAAAATTGATAAATTTAAAAACTAACATAGACTCAAAAAATTAAAGATCAAATTAAAAA
53067572 TAATTATTAAGTTTTG
66 TAATTATTAAGTTTTG
* *
53067588 TTTTGAGAAAATTGATAAATTTAGAAACTAACATAGACTCGAAAAATTAAAGATCAAATTAAAAA
1 TTTTGAGAAAATTGATAAATTTAAAAACTAACATAGACTCAAAAAATTAAAGATCAAATTAAAAA
*
53067653 TAATTATTAGGTTT
66 TAATTATTAAGTTT
53067667 AAAGATTAAA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 75 1.00
ACGTcount: A:0.50, C:0.06, G:0.11, T:0.33
Consensus pattern (81 bp):
TTTTGAGAAAATTGATAAATTTAAAAACTAACATAGACTCAAAAAATTAAAGATCAAATTAAAAA
TAATTATTAAGTTTTG
Found at i:53068417 original size:17 final size:17
Alignment explanation
Indices: 53068391--53068447 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
53068381 TACTTTATAT
53068391 TTTTTAATATTTATAAA
1 TTTTTAATATTTATAAA
*
53068408 CTTTTT-ATATTTTTAAA
1 -TTTTTAATATTTATAAA
* * *
53068425 TTTTGATTTTTTAT-AA
1 TTTTTAATATTTATAAA
53068441 TTTTTAA
1 TTTTTAA
53068448 ATTATTTATT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
16 11 0.35
17 15 0.48
18 5 0.16
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (17 bp):
TTTTTAATATTTATAAA
Found at i:53068446 original size:9 final size:9
Alignment explanation
Indices: 53068384--53068456 Score: 52
Period size: 8 Copynumber: 8.6 Consensus size: 9
53068374 TCACGTGTAC
53068384 TTTAT-ATT
1 TTTATAATT
*
53068392 TTT-TAATA
1 TTTATAATT
53068400 TTTATAAACTT
1 TTTAT-AA-TT
53068411 TTTAT-ATT
1 TTTATAATT
53068419 TTTA-AATT
1 TTTATAATT
*
53068427 TTGAT--TT
1 TTTATAATT
53068434 TTTATAATT
1 TTTATAATT
53068443 TTTA-AATT
1 TTTATAATT
53068451 ATTTAT
1 -TTTAT
53068457 TGATGTGACA
Statistics
Matches: 51, Mismatches: 4, Indels: 18
0.70 0.05 0.25
Matches are distributed among these distances:
7 7 0.14
8 24 0.47
9 12 0.24
10 2 0.04
11 6 0.12
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (9 bp):
TTTATAATT
Found at i:53070916 original size:26 final size:26
Alignment explanation
Indices: 53070872--53070939 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 26
53070862 ACTTTTTTAA
*
53070872 TTTATTTTCAATTTATTGAAA-AATAT
1 TTTATTTT-AATTTTTTGAAATAATAT
*
53070898 TTTATTTTAATGTTTTTGAAATATTAT
1 TTTATTTTAAT-TTTTTGAAATAATAT
*
53070925 ATT-TTTTAATTTTTT
1 TTTATTTTAATTTTTT
53070940 TTATATAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
25 8 0.22
26 23 0.62
27 6 0.16
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.63
Consensus pattern (26 bp):
TTTATTTTAATTTTTTGAAATAATAT
Found at i:53078237 original size:14 final size:14
Alignment explanation
Indices: 53078214--53078247 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
53078204 GCTATTTTTT
*
53078214 TTATTATTTTATTG
1 TTATTTTTTTATTG
53078228 TTATTTTTTTATTG
1 TTATTTTTTTATTG
53078242 TT-TTTT
1 TTATTTT
53078248 CACTATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (14 bp):
TTATTTTTTTATTG
Found at i:53078245 original size:11 final size:11
Alignment explanation
Indices: 53078209--53078247 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
53078199 AAACTGCTAT
53078209 TTTTTTTATTA
1 TTTTTTTATTA
* *
53078220 TTTTATTGTTA
1 TTTTTTTATTA
*
53078231 TTTTTTTATTG
1 TTTTTTTATTA
53078242 TTTTTT
1 TTTTTT
53078248 CACTATTTTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.13, C:0.00, G:0.05, T:0.82
Consensus pattern (11 bp):
TTTTTTTATTA
Found at i:53078315 original size:17 final size:19
Alignment explanation
Indices: 53078284--53078323 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
53078274 ATTGTTTGGA
53078284 TATTGTATAACTTTGTT-T
1 TATTGTATAACTTTGTTAT
*
53078302 TATTGT-TAATTTTGTTAT
1 TATTGTATAACTTTGTTAT
53078320 TATT
1 TATT
53078324 TTAGAGGCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.23, C:0.03, G:0.10, T:0.65
Consensus pattern (19 bp):
TATTGTATAACTTTGTTAT
Found at i:53080015 original size:104 final size:101
Alignment explanation
Indices: 53079877--53080084 Score: 290
Period size: 104 Copynumber: 2.0 Consensus size: 101
53079867 ATAGGACGTG
* ** *
53079877 TGGCAGTTTTTTTAACTCCTTTGTGGAGTTAAAAAATTGTATTGCTAGTGTACCGAATTCAAACC
1 TGGCAGTTTTTTTAACTCCATTGTGGAGTTAAAAAATTCCATTGCTAGTGTACCAAATTCAAACC
*
53079942 CTATATATATGTGTGCGCATGTATAGTATGAAGCAATT
66 CTATATATATCTGTGCG--TGTATAGTATGAAGCAATT
* **
53079980 TGGCAGTTTTTTTTTACTCCATTGTGGAGTTAAAAAATTCCATTGCTAGTGTACCAAATTTGAAC
1 TGGCAG-TTTTTTTAACTCCATTGTGGAGTTAAAAAATTCCATTGCTAGTGTACCAAATTCAAAC
* * *
53080045 CCTATATGTTTCTGTGTGTGTATAGTATGAAGCAATT
65 CCTATATATATCTGTGCGTGTATAGTATGAAGCAATT
53080082 TGG
1 TGG
53080085 TAACTATATT
Statistics
Matches: 93, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
102 22 0.24
103 6 0.06
104 65 0.70
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.39
Consensus pattern (101 bp):
TGGCAGTTTTTTTAACTCCATTGTGGAGTTAAAAAATTCCATTGCTAGTGTACCAAATTCAAACC
CTATATATATCTGTGCGTGTATAGTATGAAGCAATT
Found at i:53088561 original size:19 final size:18
Alignment explanation
Indices: 53088537--53088590 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
53088527 ATATTTTTCC
53088537 CATAAAAATGATTAAAAAT
1 CATAAAAAT-ATTAAAAAT
53088556 CATAAAAATTATTAAAAAAT
1 CATAAAAA-TATT-AAAAAT
*
53088576 -AAAAAAATATTAAAA
1 CATAAAAATATTAAAA
53088591 TTGATATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 4 0.12
18 4 0.12
19 17 0.53
20 7 0.22
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.26
Consensus pattern (18 bp):
CATAAAAATATTAAAAAT
Found at i:53091802 original size:12 final size:12
Alignment explanation
Indices: 53091783--53091817 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
53091773 AGATCAATCT
53091783 CCGATTCCATCA
1 CCGATTCCATCA
*
53091795 CTGATTCCATCA
1 CCGATTCCATCA
*
53091807 CCGATCCCATC
1 CCGATTCCATC
53091818 GTTTTACCGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.23, C:0.43, G:0.09, T:0.26
Consensus pattern (12 bp):
CCGATTCCATCA
Found at i:53092665 original size:15 final size:16
Alignment explanation
Indices: 53092637--53092669 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
53092627 TTTGAGATAT
*
53092637 ATAATTATTTTTTTTA
1 ATAATTATTATTTTTA
53092653 ATAA-TATTATTTTTA
1 ATAATTATTATTTTTA
53092668 AT
1 AT
53092670 TTTCGAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTATTATTTTTA
Found at i:53093779 original size:21 final size:21
Alignment explanation
Indices: 53093755--53093805 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
53093745 AAAACTTTAA
53093755 AAATATTAATTTTTAAA-CAGT
1 AAATATTAATTTTTAAACCA-T
*
53093776 AAAT-TATATTTTTTAAACCAT
1 AAATAT-TAATTTTTAAACCAT
53093797 AAATATTAA
1 AAATATTAA
53093806 CTCTAAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 1 0.04
21 21 0.84
22 3 0.12
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (21 bp):
AAATATTAATTTTTAAACCAT
Found at i:53096255 original size:29 final size:29
Alignment explanation
Indices: 53096221--53096277 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
53096211 TTTGATTATT
* *
53096221 TTTAATAGTATATGGATCAAATTGATCAA
1 TTTAATAGTAAATGAATCAAATTGATCAA
* *
53096250 TTTAATAGTAAATGAATTAAATTTATCA
1 TTTAATAGTAAATGAATCAAATTGATCA
53096278 TGTTCCTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (29 bp):
TTTAATAGTAAATGAATCAAATTGATCAA
Found at i:53097672 original size:2 final size:2
Alignment explanation
Indices: 53097665--53097690 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
53097655 GAAACTCCTT
53097665 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
53097691 AATTTGTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:53098479 original size:168 final size:168
Alignment explanation
Indices: 53098201--53098512 Score: 468
Period size: 168 Copynumber: 1.9 Consensus size: 168
53098191 ACCATTGAAT
* *
53098201 TTGTTCAACATTTCATATATCATTAGCATTGGATGTTATGTCACGTACGTTGTATATGAATATGT
1 TTGTTCAACATTTCATAGATCATTAGCATTGGATGTTATGTCACGTACATTGTATATGAATATGT
* ** * * *
53098266 GTTATCGGTGTTGGTTTGAGAATTATATTTGATGTATCAACTTGGTTATTGATCTCTGCATTCAT
66 GTCATCGGCATTGGCTTGAGAAATATATTTGATGTATCAACTTGGTTATTAATCTCTGCATTCAT
53098331 ATAACAATTGTTGTTGTTTATACAGTTTTCTGACCGAA
131 ATAACAATTGTTGTTGTTTATACAGTTTTCTGACCGAA
*
53098369 TTGTTCAACATTTCATAGATCATTA-CTATTGGATGTTATGTCACGTATATTGTATAT-AAGTAC
1 TTGTTCAACATTTCATAGATCATTAGC-ATTGGATGTTATGTCACGTACATTGTATATGAA-TA-
* *
53098432 T-TGTCATCGGCATTGGCTTGAGAAATATTTTTGATGTATCAACTTGGTTATTAATCTCTGCTTT
63 TGTGTCATCGGCATTGGCTTGAGAAATATATTTGATGTATCAACTTGGTTATTAATCTCTGCATT
*
53098496 CATATAATAATTGTTGT
128 CATATAACAATTGTTGT
53098513 AGTTATTTAT
Statistics
Matches: 129, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
167 3 0.02
168 125 0.97
169 1 0.01
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.44
Consensus pattern (168 bp):
TTGTTCAACATTTCATAGATCATTAGCATTGGATGTTATGTCACGTACATTGTATATGAATATGT
GTCATCGGCATTGGCTTGAGAAATATATTTGATGTATCAACTTGGTTATTAATCTCTGCATTCAT
ATAACAATTGTTGTTGTTTATACAGTTTTCTGACCGAA
Found at i:53099655 original size:3 final size:3
Alignment explanation
Indices: 53099649--53099692 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
53099639 TCATCATCAT
* * *
53099649 CAC CAC CAC CAC CAC CAT CAC CAC CAC CAT CAC CAT CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
53099693 TAGTGCTGAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.59, G:0.00, T:0.07
Consensus pattern (3 bp):
CAC
Found at i:53099669 original size:18 final size:18
Alignment explanation
Indices: 53099646--53099692 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
53099636 TAATCATCAT
53099646 CATCACCACCACCACCAC
1 CATCACCACCACCACCAC
*
53099664 CATCACCACCACCATCAC
1 CATCACCACCACCACCAC
53099682 CATCACCACCA
1 CATCACCACCA
53099693 TAGTGCTGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.34, C:0.57, G:0.00, T:0.09
Consensus pattern (18 bp):
CATCACCACCACCACCAC
Found at i:53103500 original size:6 final size:6
Alignment explanation
Indices: 53103489--53103518 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
53103479 CTTAAAAAAA
53103489 ACCCGC ACCCGC ACCCGC ACCCGC ACCCGC
1 ACCCGC ACCCGC ACCCGC ACCCGC ACCCGC
53103519 CCACCTGATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.67, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCCGC
Found at i:53113117 original size:16 final size:16
Alignment explanation
Indices: 53113071--53113117 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
53113061 AAAAAAATAT
53113071 TATATTGTTTTATTTTA
1 TATATT-TTTTATTTTA
* *
53113088 -ATATTTAATAATTTTA
1 TATATTT-TTTATTTTA
53113104 TATATTTTTTATTT
1 TATATTTTTTATTT
53113118 ATTGAATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
15 1 0.04
16 17 0.71
17 6 0.25
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (16 bp):
TATATTTTTTATTTTA
Found at i:53113912 original size:24 final size:22
Alignment explanation
Indices: 53113874--53113923 Score: 64
Period size: 24 Copynumber: 2.2 Consensus size: 22
53113864 ACATGCCAAC
*
53113874 AAAAAGTAAAGAAAAAATCACTTA
1 AAAAAGAAAAG-AAAAATCA-TTA
*
53113898 AAAAAGAAAATAAAAATCATTA
1 AAAAAGAAAAGAAAAATCATTA
53113920 AAAA
1 AAAA
53113924 TCCCCAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 7 0.29
23 8 0.33
24 9 0.38
ACGTcount: A:0.72, C:0.06, G:0.06, T:0.16
Consensus pattern (22 bp):
AAAAAGAAAAGAAAAATCATTA
Found at i:53116002 original size:20 final size:20
Alignment explanation
Indices: 53115977--53116014 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
53115967 AGAAATAACT
53115977 AAGTTTTCAAACAACATTAA
1 AAGTTTTCAAACAACATTAA
*
53115997 AAGTTTTCAAACATCATT
1 AAGTTTTCAAACAACATT
53116015 GTTACAGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (20 bp):
AAGTTTTCAAACAACATTAA
Found at i:53119797 original size:22 final size:22
Alignment explanation
Indices: 53119753--53119797 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
53119743 TAAAAAAAAT
*
53119753 TCTCCTCTCTTCTCTTCTCTTC
1 TCTCCTCTCTTCTCTTCTATTC
*
53119775 TCTCCTCTGTT-TCTTCTTATTC
1 TCTCCTCTCTTCTCTTC-TATTC
53119797 T
1 T
53119798 TCTTTTTAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.02, C:0.38, G:0.02, T:0.58
Consensus pattern (22 bp):
TCTCCTCTCTTCTCTTCTATTC
Found at i:53123469 original size:20 final size:20
Alignment explanation
Indices: 53123431--53123470 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
53123421 ATTAGTTTCA
*
53123431 ACACAAAATCATTGCAAAAT
1 ACACAAAATCATTGAAAAAT
53123451 ACACAAAATCGA-TGAAAAAT
1 ACACAAAATC-ATTGAAAAAT
53123471 TTGCTAACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.57, C:0.17, G:0.07, T:0.17
Consensus pattern (20 bp):
ACACAAAATCATTGAAAAAT
Found at i:53126402 original size:25 final size:24
Alignment explanation
Indices: 53126374--53126420 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
53126364 ATTAAAATTA
53126374 AAATT-TGAAATATAATAAAAAAACT
1 AAATTCTGAAA-A-AATAAAAAAACT
*
53126399 AAATTCTTAAAAAATAAAAAAA
1 AAATTCTGAAAAAATAAAAAAA
53126421 AAGTAACTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 10 0.50
25 6 0.30
26 4 0.20
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (24 bp):
AAATTCTGAAAAAATAAAAAAACT
Found at i:53127767 original size:52 final size:56
Alignment explanation
Indices: 53127620--53127768 Score: 155
Period size: 60 Copynumber: 2.6 Consensus size: 56
53127610 ATTTCTAAAG
* * *
53127620 TTCAAACTCCAATATAAAAACAATTATCAAGTTCAAAAACTAACTCGAACAAAAAAATAA
1 TTCAAAC-CCAATATAAAAATAATTAGCAAGTTCAAGAACTAA--C-AACAAAAAAATAA
* *
53127680 TTCAAACCCTAATATGAAAATAATT-GCCGAGTTCAAGAACT-A-AAC-AAAAAA-AA
1 TTCAAACCC-AATATAAAAATAATTAG-CAAGTTCAAGAACTAACAACAAAAAAATAA
*
53127733 TTCAAACCCAATGTAAAAATAATTAGCAAGTTCAAG
1 TTCAAACCCAATATAAAAATAATTAGCAAGTTCAAG
53127769 CCCGAAAAAG
Statistics
Matches: 78, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
52 22 0.28
53 12 0.15
54 6 0.08
55 3 0.04
59 3 0.04
60 32 0.41
ACGTcount: A:0.53, C:0.17, G:0.07, T:0.22
Consensus pattern (56 bp):
TTCAAACCCAATATAAAAATAATTAGCAAGTTCAAGAACTAACAACAAAAAAATAA
Found at i:53131080 original size:88 final size:88
Alignment explanation
Indices: 53130926--53131104 Score: 340
Period size: 88 Copynumber: 2.0 Consensus size: 88
53130916 TCTATGATAC
*
53130926 TTTTACTGCACCTAAACTAATAAACAAGGTGGATTAGGACATTTGTGAAACTATATCATGCATGA
1 TTTTACTGCACCTAAACTAATAAACAAGGTGGATTAGGACATTTGTGAAACTATATCAGGCATGA
53130991 TGAGGGAAATAGAGAACATAGAT
66 TGAGGGAAATAGAGAACATAGAT
*
53131014 TTTTACTGCACCTAAACTAATAAACAAGGTGGATTAGGACATTTGTGAAACTATATCAGGCTTGA
1 TTTTACTGCACCTAAACTAATAAACAAGGTGGATTAGGACATTTGTGAAACTATATCAGGCATGA
53131079 TGAGGGAAATAGAGAACATAGAT
66 TGAGGGAAATAGAGAACATAGAT
53131102 TTT
1 TTT
53131105 CAATGTAGGA
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 89 1.00
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (88 bp):
TTTTACTGCACCTAAACTAATAAACAAGGTGGATTAGGACATTTGTGAAACTATATCAGGCATGA
TGAGGGAAATAGAGAACATAGAT
Found at i:53135043 original size:3 final size:3
Alignment explanation
Indices: 53135035--53135079 Score: 67
Period size: 3 Copynumber: 15.3 Consensus size: 3
53135025 TGCAACTACA
53135035 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC ATT- TTC TT- TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC
53135079 T
1 T
53135080 CTTTTACTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.10
3 33 0.85
4 2 0.05
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:53146200 original size:13 final size:13
Alignment explanation
Indices: 53146184--53146231 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
53146174 ACAATCAATA
53146184 ATTTTTATATAGT
1 ATTTTTATATAGT
53146197 ATTTTTAAATATA-T
1 ATTTTT--ATATAGT
*
53146211 ATTTTGTATATAGA
1 ATTTT-TATATAGT
53146225 ATTTTTA
1 ATTTTTA
53146232 AGTTATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
13 13 0.43
14 11 0.37
15 6 0.20
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (13 bp):
ATTTTTATATAGT
Found at i:53147582 original size:26 final size:25
Alignment explanation
Indices: 53147528--53147585 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
53147518 ACCACATTAG
53147528 TTTTTAACCGTACAAAAGAATGAAA
1 TTTTTAACCGTACAAAAGAATGAAA
53147553 TTTTTAACCGTACAAAAGAATGAAA
1 TTTTTAACCGTACAAAAGAATGAAA
53147578 TTTTTAAC
1 TTTTTAAC
53147586 AGAAATTACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (25 bp):
TTTTTAACCGTACAAAAGAATGAAA
Found at i:53153661 original size:180 final size:183
Alignment explanation
Indices: 53153438--53153774 Score: 495
Period size: 180 Copynumber: 1.8 Consensus size: 183
53153428 TATTGTCATC
* *
53153438 ATCATCAACATCATCATCTTTTTGTTGGATTTCTTTTGGTAGCTTTCGGAAATTAAGTTCTGTTG
1 ATCATCAACATCATCATCTTTTTGCTGGATTTCTTTTGGTAGCTTTCGGAAATTAAGTTCTATTG
* * *
53153503 AAATCTGC-A-T-TGC-T-CTCTGTTAATATTTTGAATACCTTGTATATTAGATCGCAACTCTGT
66 AAATCTGCGATTCTGCATCCTCTGTTAA-A-TTTGAATACCTTGGATATTAGATCGCAAATCTCT
* *
53153563 GGATATGTTTAGTATTTCGATCTGAAGTATCACATATTCACTCGATGTTTTCTTT
129 GGATATATTTAGTATTTAGATCTGAAGTATCACATATTCACTCGATGTTTTCTTT
* *
53153618 ATCATCATCATCATCATCTTTTTGCTGGATTTCTTTTGGTAGCTTTCGGAAATTAAGTTTTATTG
1 ATCATCAACATCATCATCTTTTTGCTGGATTTCTTTTGGTAGCTTTCGGAAATTAAGTTCTATTG
* *
53153683 AAATCTGCGATTCTGCATTGCCTCTGTTAAATTTGAATGCCTTGGATATTGGATCGCAAATCTCT
66 AAATCTGCGATTCTGCA-T-CCTCTGTTAAATTTGAATACCTTGGATATTAGATCGCAAATCTCT
*
53153748 GTATATATTTAGTATTTAGATCTGAAG
129 GGATATATTTAGTATTTAGATCTGAAG
53153775 CATTGCATTT
Statistics
Matches: 138, Mismatches: 12, Indels: 9
0.87 0.08 0.06
Matches are distributed among these distances:
180 69 0.50
181 1 0.01
182 1 0.01
183 3 0.02
185 54 0.39
186 1 0.01
187 9 0.07
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (183 bp):
ATCATCAACATCATCATCTTTTTGCTGGATTTCTTTTGGTAGCTTTCGGAAATTAAGTTCTATTG
AAATCTGCGATTCTGCATCCTCTGTTAAATTTGAATACCTTGGATATTAGATCGCAAATCTCTGG
ATATATTTAGTATTTAGATCTGAAGTATCACATATTCACTCGATGTTTTCTTT
Found at i:53162847 original size:19 final size:19
Alignment explanation
Indices: 53162823--53162881 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
53162813 CAGATGACAC
53162823 AAATTTTTTTAAAATTTAA
1 AAATTTTTTTAAAATTTAA
* *
53162842 AAA--TTTTAAAAATATAA
1 AAATTTTTTTAAAATTTAA
* *
53162859 AAATTATTTTAAAAATTAA
1 AAATTTTTTTAAAATTTAA
53162878 AAAT
1 AAAT
53162882 CATTAAAATC
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
17 15 0.47
19 17 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATTTTTTTAAAATTTAA
Found at i:53162869 original size:20 final size:19
Alignment explanation
Indices: 53162823--53162881 Score: 70
Period size: 20 Copynumber: 3.2 Consensus size: 19
53162813 CAGATGACAC
* *
53162823 AAATT-TTTTTAAAATTTA
1 AAATTATTTTAAAAATTAA
53162841 AAA--ATTTTAAAAATATAA
1 AAATTATTTTAAAAAT-TAA
53162859 AAATTATTTTAAAAATTAA
1 AAATTATTTTAAAAATTAA
53162878 AAAT
1 AAAT
53162882 CATTAAAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
17 9 0.26
18 8 0.23
19 7 0.20
20 11 0.31
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATTATTTTAAAAATTAA
Found at i:53162889 original size:28 final size:28
Alignment explanation
Indices: 53162837--53162899 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
53162827 TTTTTTAAAA
*
53162837 TTTAAAAATTTTAAAAATATAAAAATTAT
1 TTTAAAAA-TTTAAAAATATAAAAATCAT
*
53162866 TTTAAAAA-TTAAAAATCATTAAAATCAT
1 TTTAAAAATTTAAAAAT-ATAAAAATCAT
*
53162894 TATAAA
1 TTTAAA
53162900 CTTATAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 8 0.27
28 14 0.47
29 8 0.27
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (28 bp):
TTTAAAAATTTAAAAATATAAAAATCAT
Found at i:53164951 original size:12 final size:13
Alignment explanation
Indices: 53164923--53164960 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
53164913 TATCGCTTTC
53164923 AATTATTCACTTAA
1 AATTATTCAC-TAA
53164937 AATTATTCA-TAA
1 AATTATTCACTAA
*
53164949 AATAATTCACTA
1 AATTATTCACTA
53164961 TTCACTTCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 11 0.50
13 2 0.09
14 9 0.41
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.39
Consensus pattern (13 bp):
AATTATTCACTAA
Found at i:53167598 original size:2 final size:2
Alignment explanation
Indices: 53167593--53167617 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
53167583 TTTAAAAAAT
53167593 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
53167618 TCCAAAATAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53167660 original size:26 final size:26
Alignment explanation
Indices: 53167631--53167683 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
53167621 AAAATATGTC
53167631 ATAATCTAATCATAATAATAATAAAT
1 ATAATCTAATCATAATAATAATAAAT
53167657 ATAATCTAATCATAATAATAATAAAT
1 ATAATCTAATCATAATAATAATAAAT
53167683 A
1 A
53167684 AAATTTAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (26 bp):
ATAATCTAATCATAATAATAATAAAT
Found at i:53172388 original size:15 final size:15
Alignment explanation
Indices: 53172368--53172399 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
53172358 TCCACTGCAA
53172368 TGCGTAAAAACAAGG
1 TGCGTAAAAACAAGG
*
53172383 TGCGTAAAAACAGGG
1 TGCGTAAAAACAAGG
53172398 TG
1 TG
53172400 AAATTTTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.12, G:0.31, T:0.16
Consensus pattern (15 bp):
TGCGTAAAAACAAGG
Found at i:53173630 original size:114 final size:113
Alignment explanation
Indices: 53173396--53173852 Score: 475
Period size: 114 Copynumber: 4.1 Consensus size: 113
53173386 ACATTAATGA
* *
53173396 TAAAGAAACAATCAATCAAAAACTATCATTGAAACAAACTCCAAAAAGGCAATTCGTTAAAAACC
1 TAAAGAAACTATCAATCAAAATCTATCATTGAAACAAACTCCAAAAAGGCAATTCGTTAAAAACC
**
53173461 GGTATTTAACACTCACACTCGAATCCAAATAATATAGTTAAAGAATCCTC
66 -G-ATTTAACACTCACACTCGAATCCAAATAACGTAGTTAAAGAATCCTC
* * *
53173511 TAAATAAACTATCAATCAGAATGTATCATTGAAACAAACTCCAAAAAGGCAATTCGTTAAAAAAC
1 TAAAGAAACTATCAATCAAAATCTATCATTGAAACAAACTCCAAAAAGGCAATTCGTT-AAAAAC
* * *
53173576 CGATTTAACGCTCACACTCGAATCTAAATAGCGTAGTTAAAGAATCCTC
65 CGATTTAACACTCACACTCGAATCCAAATAACGTAGTTAAAGAATCCTC
* * * * *
53173625 TAAATAAACTATCAATTAAAA-CTTATCATTGACACAAAAC-CCTAAAAGGCAATTTGTTAAAAA
1 TAAAGAAACTATCAATCAAAATC-TATCATTGAAAC-AAACTCCAAAAAGGCAATTCGTT-AAAA
* ** *
53173688 ACC-ATTTTAACGCTCATTCTCGAATCCGAATAACGTAGTT-AAGAATCCTC
63 ACCGA-TTTAACACTCACACTCGAATCCAAATAACGTAGTTAAAGAATCCTC
*
53173738 --------C-A--AA--AAGAA-CTATCATTGAAACAAACCCCAAAAAGGCAATTCGTTAAAAAC
1 TAAAGAAACTATCAATCAA-AATCTATCATTGAAACAAACTCCAAAAAGGCAATTCGTTAAAAAC
* * *
53173789 CGATATTCAACACTCACATTCGAATCCAAATAACG-ATTTTAAGAATCCTC
65 CGAT-TT-AACACTCACACTCGAATCCAAATAACGTAGTTAAAGAATCCTC
*
53173839 CAAAGAAACTATCA
1 TAAAGAAACTATCA
53173853 TTGAAACAAA
Statistics
Matches: 291, Mismatches: 30, Indels: 45
0.80 0.08 0.12
Matches are distributed among these distances:
99 12 0.04
100 35 0.12
101 35 0.12
102 2 0.01
104 1 0.00
105 1 0.00
109 1 0.00
110 1 0.00
112 1 0.00
113 11 0.04
114 126 0.43
115 58 0.20
116 7 0.02
ACGTcount: A:0.45, C:0.21, G:0.09, T:0.24
Consensus pattern (113 bp):
TAAAGAAACTATCAATCAAAATCTATCATTGAAACAAACTCCAAAAAGGCAATTCGTTAAAAACC
GATTTAACACTCACACTCGAATCCAAATAACGTAGTTAAAGAATCCTC
Found at i:53173914 original size:99 final size:99
Alignment explanation
Indices: 53173642--53174041 Score: 342
Period size: 100 Copynumber: 4.1 Consensus size: 99
53173632 ACTATCAATT
* * * *
53173642 AAAACTTATCATTGACACAAAACCCTAAAAGGCAATTTGTTAAAAAACC-AT-TTTAACGCTCAT
1 AAAAC-TATCATTGAAAC-AAACCCCAAAAGGCAATTCGTT-AAAAACCGATATTTAACGCTCAC
* *
53173705 TCTCGAATCCGAATAACGTAGTTAAGAATCCTCCAAA
63 ACTCGAATCCAAATAACGTAGTTAAGAATCCTCCAAA
* *
53173742 AAGAACTATCATTGAAACAAACCCCAAAAAGGCAATTCGTTAAAAACCGATATTCAACACTCACA
1 AA-AACTATCATTGAAACAAACCCC-AAAAGGCAATTCGTTAAAAACCGATATTTAACGCTCACA
* *
53173807 TTCGAATCCAAATAACG-ATTTTAAGAATCCTCCAAA
64 CTCGAATCCAAATAACGTA-GTTAAGAATCCTCCAAA
* * * *
53173843 GAAACTATCATTGAAACAAACCCCCAAAGGCAATTCGTTAAAAACCGGTATTTATCGCTCACA--
1 AAAACTATCATTGAAACAAACCCCAAAAGGCAATTCGTTAAAAACCGATATTTAACGCTCACACT
* * * *
53173906 C---T-CAAAT-CCG-A---ATGAATCCCCCGAA
66 CGAATCCAAATAACGTAGTTAAGAATCCTCCAAA
* * ** * * * *
53173931 CAAACTATCATTTAAACAAAACCTGAAAGAGGCAATTCGTTAAATACTGGTATTTATCGCTCACA
1 AAAACTATCATTGAAAC-AAACCCCAAA-AGGCAATTCGTTAAAAACCGATATTTAACGCTCACA
** *
53173996 CTCGAATCTGAATAACCTAGTTAAAAGAATCCTCCAAA
64 CTCGAATCCAAATAACGTAGTT--AAGAATCCTCCAAA
*
53174034 GAAACTAT
1 AAAACTAT
53174042 AAATCAAAAA
Statistics
Matches: 245, Mismatches: 35, Indels: 37
0.77 0.11 0.12
Matches are distributed among these distances:
88 26 0.11
89 7 0.03
90 34 0.14
92 4 0.02
93 5 0.02
94 1 0.00
95 1 0.00
96 3 0.01
97 2 0.01
98 1 0.00
99 47 0.19
100 52 0.21
101 44 0.18
103 18 0.07
ACGTcount: A:0.42, C:0.23, G:0.11, T:0.24
Consensus pattern (99 bp):
AAAACTATCATTGAAACAAACCCCAAAAGGCAATTCGTTAAAAACCGATATTTAACGCTCACACT
CGAATCCAAATAACGTAGTTAAGAATCCTCCAAA
Found at i:53173987 original size:90 final size:88
Alignment explanation
Indices: 53173745--53174008 Score: 249
Period size: 90 Copynumber: 2.8 Consensus size: 88
53173735 CTCCAAAAAG
* * * *
53173745 AACTATCATTGAAACAAACCCCAAAAAGGCAATTCGTTAAAAACCGATATTCAACACTCACATTC
1 AACTATCATTGAAACAAACCCC-AAAAGGCAATTCGTTAAAAACCGGTATTTATCGCTCACA--C
* * * * *
53173810 GAATCCAAATAACGATTTTAAGAATCCTCCAAAGA
63 ---T-CAAAT-CCGA----ATGAATCCCCCGAACA
*
53173845 AACTATCATTGAAACAAACCCCCAAAGGCAATTCGTTAAAAACCGGTATTTATCGCTCACACTCA
1 AACTATCATTGAAACAAACCCCAAAAGGCAATTCGTTAAAAACCGGTATTTATCGCTCACACTCA
53173910 AATCCGAATGAATCCCCCGAACA
66 AATCCGAATGAATCCCCCGAACA
* ** * *
53173933 AACTATCATTTAAACAAAACCTGAAAGAGGCAATTCGTTAAATACTGGTATTTATCGCTCACACT
1 AACTATCATTGAAAC-AAACCCCAAA-AGGCAATTCGTTAAAAACCGGTATTTATCGCTCACACT
* *
53173998 CGAATCTGAAT
64 CAAATCCGAAT
53174009 AACCTAGTTA
Statistics
Matches: 144, Mismatches: 18, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
88 26 0.18
89 7 0.05
90 45 0.31
92 3 0.02
93 5 0.03
94 1 0.01
97 1 0.01
99 34 0.24
100 22 0.15
ACGTcount: A:0.41, C:0.25, G:0.11, T:0.23
Consensus pattern (88 bp):
AACTATCATTGAAACAAACCCCAAAAGGCAATTCGTTAAAAACCGGTATTTATCGCTCACACTCA
AATCCGAATGAATCCCCCGAACA
Found at i:53194214 original size:24 final size:24
Alignment explanation
Indices: 53194187--53194235 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
53194177 ATAATTACTC
53194187 TCATCATTATTATTGTTTTTAACT
1 TCATCATTATTATTGTTTTTAACT
53194211 TCATCATTATTATTGTTTTTAACT
1 TCATCATTATTATTGTTTTTAACT
53194235 T
1 T
53194236 TTTGAACGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.12, G:0.04, T:0.59
Consensus pattern (24 bp):
TCATCATTATTATTGTTTTTAACT
Found at i:53195971 original size:22 final size:24
Alignment explanation
Indices: 53195937--53195984 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
53195927 TATTTTATAA
* *
53195937 TTTTTCATAATAA-AAAAATTATT
1 TTTTTAATAATAAGAAAAAATATT
53195960 TTTTTAAT-ATAAGAAAAAATATT
1 TTTTTAATAATAAGAAAAAATATT
53195983 TT
1 TT
53195985 CCTTTTTCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (24 bp):
TTTTTAATAATAAGAAAAAATATT
Found at i:53197516 original size:31 final size:31
Alignment explanation
Indices: 53197457--53197518 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
53197447 ACATGTTTTG
*
53197457 ATTGTGTTTTTTGTCCTGTTTCTGTTGGGGTA
1 ATTGTGTTTTTTGTCCTGTTAC-GTTGGGGTA
*
53197489 ATTGTGTTTTTTGTCTTGTTGAC-TTGGGGT
1 ATTGTGTTTTTTGTCCTGTT-ACGTTGGGGT
53197519 TTAGCAGATC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 7 0.26
32 19 0.70
33 1 0.04
ACGTcount: A:0.06, C:0.08, G:0.29, T:0.56
Consensus pattern (31 bp):
ATTGTGTTTTTTGTCCTGTTACGTTGGGGTA
Found at i:53203325 original size:30 final size:30
Alignment explanation
Indices: 53203286--53203343 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
53203276 AAAAAAATCA
53203286 TATTAATATTTTTATAATTAAATTTAAATT
1 TATTAATATTTTTATAATTAAATTTAAATT
* *
53203316 TATTGATATTTTTATAATTAATTTTAAA
1 TATTAATATTTTTATAATTAAATTTAAA
53203344 ATTAGCTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (30 bp):
TATTAATATTTTTATAATTAAATTTAAATT
Found at i:53206326 original size:15 final size:15
Alignment explanation
Indices: 53206308--53206337 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
53206298 AAAACAATAT
53206308 CATCAATCATATTCC
1 CATCAATCATATTCC
*
53206323 CATCAATTATATTCC
1 CATCAATCATATTCC
53206338 AAAAAATCCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.37
Consensus pattern (15 bp):
CATCAATCATATTCC
Found at i:53207053 original size:10 final size:9
Alignment explanation
Indices: 53207038--53207062 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
53207028 GTCATACAAG
53207038 TTTTTTTAT
1 TTTTTTTAT
53207047 TTTTTTTAT
1 TTTTTTTAT
53207056 TTTTTTT
1 TTTTTTT
53207063 GGAAATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:53208320 original size:267 final size:268
Alignment explanation
Indices: 53207818--53208375 Score: 705
Period size: 267 Copynumber: 2.1 Consensus size: 268
53207808 ATGACACGAG
* * *
53207818 TTTAAACCCTAAAAATAAAATACCATTAAAAGATTTCGAGACTTAAATTTTGAGTCAAGTTCGAG
1 TTTAAACCCTAAAGATAAAATACCATTAAAAGATTTCGAGACTTAAATTTTGAATCAAATTCGAG
* ** * *
53207883 ACTACTATTACTCGAGTTTAGCTTGTTTCAATTATACTCCTCTTTTTTAAGGTTTCAATTTTGAA
66 ACTACTATTACTCGAGTTTAACTCATTTCAATTATACTCCTCTTTTTTAAGGTTTCAAGTTCGAA
* *** * * * *
53207948 TATGTTGGAATAAAAATAAAAGAGTAAAAGAACTTTACCTCCATTTAAAAGTTCAACTCTAGATT
131 TAAGACAGAAGAAAAATAAAAAAGTAAAAGAACTTTACCTCCATTTAAAAATTCAACTCTAAATT
* * *
53208013 TAATCGGGATTTAATGTGATTATTCAATACATAAAAAAAACAA-TTTTTTT-CTAAGAGATCATT
196 TAATCGAGATCTAATGTAATTATTCAATACATAAAAAAAACAACTTTTTTTCCTAAGAGATCATT
53208076 ATATATAT
261 ATATATAT
* *
53208084 TTTAAAGCCCTAAAGATAAAATACCATTAAAGGATTTTGAGACTTAAATTTTGAATCAAATTCGA
1 TTTAAA-CCCTAAAGATAAAATACCATTAAAAGATTTCGAGACTTAAATTTTGAATCAAATTCGA
* * *
53208149 GA-TCATTATTATTCGAGTTTAACTCATTTCGATTATACTCCT-TATTTTTAAGGTTTCAAGTTC
65 GACT-ACTATTACTCGAGTTTAACTCATTTCAATTATACTCCTCT-TTTTTAAGGTTTCAAGTTC
** * * ** *
53208212 GAATAAGACAGAAGAAAAATAAAAAAGTTGGAAGAACTTTACTTTCATTTAAAAATTTGACTTTA
128 GAATAAGACAGAAGAAAAATAAAAAAG-TAAAAGAACTTTACCTCCATTTAAAAATTCAACTCTA
* *
53208277 AATTTAATCGAGATCTAATGTAATTA-TCGAATACAT-TAAAAAACAACTTTTTTTTCCTAAGAT
192 AATTTAATCGAGATCTAATGTAATTATTC-AATACATAAAAAAAACAAC-TTTTTTTCCTAAGAG
53208340 ATCATTATATATAT
255 ATCATTATATATAT
*
53208354 TTTAAAACCCTAAAGACAAAAT
1 TTT-AAACCCTAAAGATAAAAT
53208376 GCCACCGAAA
Statistics
Matches: 249, Mismatches: 34, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
266 8 0.03
267 136 0.55
268 58 0.23
269 7 0.03
270 37 0.15
271 3 0.01
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.37
Consensus pattern (268 bp):
TTTAAACCCTAAAGATAAAATACCATTAAAAGATTTCGAGACTTAAATTTTGAATCAAATTCGAG
ACTACTATTACTCGAGTTTAACTCATTTCAATTATACTCCTCTTTTTTAAGGTTTCAAGTTCGAA
TAAGACAGAAGAAAAATAAAAAAGTAAAAGAACTTTACCTCCATTTAAAAATTCAACTCTAAATT
TAATCGAGATCTAATGTAATTATTCAATACATAAAAAAAACAACTTTTTTTCCTAAGAGATCATT
ATATATAT
Found at i:53217480 original size:290 final size:295
Alignment explanation
Indices: 53216831--53217524 Score: 940
Period size: 290 Copynumber: 2.4 Consensus size: 295
53216821 GAGTGTTCAG
* * *
53216831 TTTGAAAGTTAAAAATGGAACGGTTAGGTATTGTTTGGTAAATGATAAGTGATTCTCAATGCGTT
1 TTTGAATGTTAAAAATGGAACGGTTAGGTGTTGTTTGGTAAATGATAAGTAATTCTCAATGCGTT
* *
53216896 TGGTTTCTCATTTTGGAGATTAAGCTTGATTGATTGTTTTCAATAATATATACTACTTATGAGTT
66 TGGTTTCTCATTTTGGAGATTAAGCTTAATTGATTATTTTCAATAATATATACTACTTATGAGTT
* * * *
53216961 AAAGCAATGCTATTCTTTTTCCATCATTTGACCACTTTGAGTTCACTTCCTGTTTGGTTACCGAG
131 AAAGCAATGATATTCTTTTTCCATCATTTGACCACTATGAGTTCACTTCCTGTTTCGTCACCGAG
*
53217026 AAAGTGAAGGAAAATGGAAAGTTGAAACATTGTTTCACTGTGCAAAAGAACCTGGTTTGGTCATC
196 AAAGTGAAGGAAAATGGAAAGTTGAAACATTGTTTCACTGTGCAAAAGAACCTGCTTTGGTCATC
* * *
53217091 TGTGTGTTCAGTAAAGGGTAGTATTTTTGTTTCCATTGTT
261 ---GTG-T-ACTAAAGGGTAGTATTTATGTTTCCATTGGT
* * * *
53217131 TTTGAATGTTAAAAATGGAACGGTTAGGTGTTGTTTGGTGAACGATAAGTAACTCTCAATGCGCT
1 TTTGAATGTTAAAAATGGAACGGTTAGGTGTTGTTTGGTAAATGATAAGTAATTCTCAATGCGTT
*
53217196 TGGTTTCT-ATTTTGGAGATTAAGCTTAATTGATTATTTTCAATAATATATACTACTTAATGCGT
66 TGGTTTCTCATTTTGGAGATTAAGCTTAATTGATTATTTTCAATAATATATACTACTT-ATGAGT
* * * * *
53217260 TACAGCAAT-ATTTTC-TTTT-CATCATTTGACTGA-TATGAGTTCAGTTCTTGTTTCGTCACCG
130 TAAAGCAATGATATTCTTTTTCCATCATTTGAC-CACTATGAGTTCACTTCCTGTTTCGTCACCG
* * * * * *
53217321 AGAAAGTGAAGGAAAATGGAAAGTTGAAATGATTGTTTTACTGTTCATAAGAACCTGCTTTTGTT
194 AGAAAGTGAAGGAAAATGGAAAGTTGAAA-CATTGTTTCACTGTGCAAAAGAACCTGCTTTGGTC
*
53217386 ATC-TG-ACTTAAGGGTAGTATCTTAT-TTT-CATTGGT
258 ATCGTGTACTAAAGGGTAGTAT-TTATGTTTCCATTGGT
*
53217421 TTTGAATGTTAAAAATGGAACGGTTAGGTGTTGTTTGGTAAATGATAAGTAATTCTCAATGCATT
1 TTTGAATGTTAAAAATGGAACGGTTAGGTGTTGTTTGGTAAATGATAAGTAATTCTCAATGCGTT
* *
53217486 TGGTTTCTCA-TTTGGAGATTAAGCTTTATTGGTTATTTT
66 TGGTTTCTCATTTTGGAGATTAAGCTTAATTGATTATTTT
53217525 TGTTTACATA
Statistics
Matches: 352, Mismatches: 37, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
290 101 0.29
291 17 0.05
292 3 0.01
294 2 0.01
297 63 0.18
298 36 0.10
299 51 0.14
300 79 0.22
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (295 bp):
TTTGAATGTTAAAAATGGAACGGTTAGGTGTTGTTTGGTAAATGATAAGTAATTCTCAATGCGTT
TGGTTTCTCATTTTGGAGATTAAGCTTAATTGATTATTTTCAATAATATATACTACTTATGAGTT
AAAGCAATGATATTCTTTTTCCATCATTTGACCACTATGAGTTCACTTCCTGTTTCGTCACCGAG
AAAGTGAAGGAAAATGGAAAGTTGAAACATTGTTTCACTGTGCAAAAGAACCTGCTTTGGTCATC
GTGTACTAAAGGGTAGTATTTATGTTTCCATTGGT
Found at i:53218597 original size:21 final size:21
Alignment explanation
Indices: 53218573--53218614 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
53218563 GTAATTCTCG
53218573 ATGCGCTTGGTTTCTCAATTT
1 ATGCGCTTGGTTTCTCAATTT
53218594 ATGCGCTTGGTTTCTCAATTT
1 ATGCGCTTGGTTTCTCAATTT
53218615 GGAGATCACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.19, G:0.19, T:0.48
Consensus pattern (21 bp):
ATGCGCTTGGTTTCTCAATTT
Found at i:53223644 original size:12 final size:12
Alignment explanation
Indices: 53223627--53223660 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
53223617 TCTCTAAGCA
*
53223627 GTATATATATGT
1 GTATATATATAT
53223639 GTATATATATAT
1 GTATATATATAT
*
53223651 ATATATATAT
1 GTATATATAT
53223661 TATTCTAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (12 bp):
GTATATATATAT
Found at i:53228456 original size:27 final size:25
Alignment explanation
Indices: 53228426--53228557 Score: 88
Period size: 27 Copynumber: 4.9 Consensus size: 25
53228416 TTTAGATATT
53228426 TTAAAAGTTGATAAAAAAATTGAACCC
1 TTAAAAGTT-A-AAAAAAATTGAACCC
**
53228453 TTAAAAGTTAAAAAAAATTAGGGCCC
1 TTAAAAGTTAAAAAAAATT-GAACCC
*** *
53228479 TTAAAAG-TAGATAATATTTTTTG-ACCT
1 TTAAAAGTTA-A-AA-A-AAATTGAACCC
53228506 TTAAAAGTTTAAAAAAAATTGAGACCTC
1 TTAAAAG-TTAAAAAAAATTGA-ACC-C
*
53228534 TTAAAAACTTAAAAAAAATTGAAC
1 TT-AAAAGTTAAAAAAAATTGAAC
53228558 ATCTTTTAGC
Statistics
Matches: 82, Mismatches: 12, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
25 14 0.17
26 14 0.17
27 27 0.33
28 19 0.23
29 8 0.10
ACGTcount: A:0.50, C:0.10, G:0.11, T:0.30
Consensus pattern (25 bp):
TTAAAAGTTAAAAAAAATTGAACCC
Found at i:53228545 original size:28 final size:27
Alignment explanation
Indices: 53228501--53228555 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 27
53228491 AATATTTTTT
**
53228501 GACCTTTAAAAGTTTAAAAAAAATTGA
1 GACCTTTAAAAACTTAAAAAAAATTGA
53228528 GACCTCTTAAAAACTTAAAAAAAATTGA
1 GACCT-TTAAAAACTTAAAAAAAATTGA
53228556 ACATCTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.53, C:0.11, G:0.09, T:0.27
Consensus pattern (27 bp):
GACCTTTAAAAACTTAAAAAAAATTGA
Found at i:53230505 original size:22 final size:21
Alignment explanation
Indices: 53230461--53230505 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
53230451 ATTTTTTATT
* *
53230461 TAAAAATAAAATCTATATCAA
1 TAAAAATAAAATATATATAAA
*
53230482 TAAATATAATAATATATATAAA
1 TAAAAATAA-AATATATATAAA
53230504 TA
1 TA
53230506 TAGGGTTGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAAAATAAAATATATATAAA
Found at i:53239610 original size:233 final size:232
Alignment explanation
Indices: 53239251--53239933 Score: 727
Period size: 233 Copynumber: 2.9 Consensus size: 232
53239241 AAAACAATAT
** * * *
53239251 ATTAACTCCCAGACTCATCCCCTTCTTATACTTACAACGAACATAACAAGCCACGAATTCTGCTT
1 ATTAACTCCCAGACTTGTCCCCTTCTTATACTTATAACGAACATAAAAAGCCACGAATTCTCCTT
* * * *
53239316 TG-CTCATCTTAGAATTACAAACTCAAAGTGCACTCAGAGACAGTCAATTATCGAATATAACCAT
66 CGCCT-ATCTTAGAATGA-AAACTCAAAGTGCACTCAGAGACAGGCAATTATTGAATATAACCAT
* *
53239380 ACAACCTTAACACCTACAAAAGGAGAAGAATAACGGTTCTATATCACGATGCGAATCTTTCAGCC
129 ACAACCTTAACACCTACAAAAGGAGAAAAATAAAGGTTCTATATCACGATGCGAATCTTTCAG-C
*
53239445 AATATATACGATTCTTTCCACATATGACAAGTTGACAACG-
193 AATATATAC-ATTCTTTCCAAATATGACAAGTTGACAACGA
* * ** *
53239485 A-TAACTCCCACACTTGTCTCCTTCTTATACTTATAACGAACATAAAAAGTAACAAATTCTCCTT
1 ATTAACTCCCAGACTTGTCCCCTTCTTATACTTATAACGAACATAAAAAGCCACGAATTCTCCTT
* *
53239549 CGCCTATCTTAAAATGGAAAACTCAAAGTGCACTCAGAGACGGGCAATTATTGAATATAACCATA
66 CGCCTATCTTAGAAT-GAAAACTCAAAGTGCACTCAGAGACAGGCAATTATTGAATATAACCATA
* * * * * * * * * * * *
53239614 CAAACTTAAAACCTACAGAGGGAAAAAAAGGAAAGGCTCTATAACATGATGAGAACCTTT-TG--
130 CAACCTTAACACCTACAAAAGGAGAAAAA-TAAAGGTTCTATATCACGATGCGAATCTTTCAGCA
* * * *
53239676 GT-CA-ACATACTTTCCAAATATGACAAGTTGATAACGAAATAATA
194 ATATATACATTCTTTCCAAATATGACAAGTTGACAACG-------A
* * * *
53239720 CATTAACTCCCAGACTTGTCCCCCTCCTATACTTATAATGAACATAAAAAGCCATGAATTCTCCT
1 -ATTAACTCCCAGACTTGTCCCCTTCTTATACTTATAACGAACATAAAAAGCCACGAATTCTCCT
* * *
53239785 TCGCCCATCTTAGAATTGAAAACTCGAAGTGCACTCAGAGACAGGTAATTATTGAATATAACCAT
65 TCGCCTATCTTAGAA-TGAAAACTCAAAGTGCACTCAGAGACAGGCAATTATTGAATATAACCAT
* * * *
53239850 ACAACCTTAACACCTAC-AGAGGAGAAAAATAATGGTTCTATATCACTATGCGAATCTTTGCATC
129 ACAACCTTAACACCTACAAAAGGAGAAAAATAAAGGTTCTATATCACGATGCGAATCTTT-CAGC
53239914 AATATAATACCATTCTTTCC
193 AATAT-ATA-CATTCTTTCC
53239934 TTGGATGACA
Statistics
Matches: 359, Mismatches: 68, Indels: 35
0.78 0.15 0.08
Matches are distributed among these distances:
227 27 0.08
228 2 0.01
229 1 0.00
230 1 0.00
233 131 0.36
234 27 0.08
235 22 0.06
236 9 0.03
237 126 0.35
238 1 0.00
239 1 0.00
241 1 0.00
242 1 0.00
243 9 0.03
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (232 bp):
ATTAACTCCCAGACTTGTCCCCTTCTTATACTTATAACGAACATAAAAAGCCACGAATTCTCCTT
CGCCTATCTTAGAATGAAAACTCAAAGTGCACTCAGAGACAGGCAATTATTGAATATAACCATAC
AACCTTAACACCTACAAAAGGAGAAAAATAAAGGTTCTATATCACGATGCGAATCTTTCAGCAAT
ATATACATTCTTTCCAAATATGACAAGTTGACAACGA
Found at i:53239789 original size:237 final size:238
Alignment explanation
Indices: 53239118--53239878 Score: 726
Period size: 233 Copynumber: 3.2 Consensus size: 238
53239108 ATCATAAAAC
* * *
53239118 ATAACCATACAACCTTAACACCTACAGAGGTAAAAAAAAGTAAAGGCTCTATATCAGGATGTGAA
1 ATAACCATACAACCTTAACACCTACAGAGG-GAAAAAAAG-AAAGGCTCTATAACACGA--TG--
* * * *
53239183 AATCAAGAACCTTTCAGTCA-ACATATACCAT-TTGTTCCACATATGACAGGTTGACAACAAAAC
60 -----AGAACCTTTCAG-CATAC--ATACGATACT-TTCCACATATGACAAGTTGACAACGAAA-
** * *
53239246 AATATATTAACTCCCAGACTCATCCCCTTCTTATACTTACAACGAACATAACAAGCCACGAATTC
115 AATA-ATTAACTCCCAGACTTGTCCCCTTCTTATACTTATAACGAACATAAAAAGCCACGAATTC
* * * * *
53239311 TGCTTTG-CTCATCTTAGAATTACAAACTCAAAGTGCACTCAGAGACAGTCAATTATCGAAT
179 TCCTTCGCCT-ATCTTAGAATGA-AAACTCAAAGTGCACTCAGAGACAGGCAATTATTGAAT
* * * * * * * * * *
53239372 ATAACCATACAACCTTAACACCTACAAAAGGAGAAGAATAACGGTTCTATATCACGATGCGAATC
1 ATAACCATACAACCTTAACACCTACAGAGGGAAAAAAAGAAAGGCTCTATAACACGATGAGAACC
* *
53239437 TTTCAGCCAATATATACGATTCTTTCCACATATGACAAGTTGACAACG-------A-TAACTCCC
66 TTTCAG-C-ATACATACGATACTTTCCACATATGACAAGTTGACAACGAAAAATAATTAACTCCC
* * ** *
53239494 ACACTTGTCTCCTTCTTATACTTATAACGAACATAAAAAGTAACAAATTCTCCTTCGCCTATCTT
129 AGACTTGTCCCCTTCTTATACTTATAACGAACATAAAAAGCCACGAATTCTCCTTCGCCTATCTT
* *
53239559 AAAATGGAAAACTCAAAGTGCACTCAGAGACGGGCAATTATTGAAT
194 AGAAT-GAAAACTCAAAGTGCACTCAGAGACAGGCAATTATTGAAT
* * *
53239605 ATAACCATACAAACTTAAAACCTACAGAGGGAAAAAAAGGAAAGGCTCTATAACATGATGAGAAC
1 ATAACCATACAACCTTAACACCTACAGAGGGAAAAAAA-GAAAGGCTCTATAACACGATGAGAAC
* * * *
53239670 CTTT-TG-GT-CA-AC-ATACTTTCCAAATATGACAAGTTGATAACGAAATAATACATTAACTCC
65 CTTTCAGCATACATACGATACTTTCCACATATGACAAGTTGACAACGAAA-AATA-ATTAACTCC
* * * * *
53239730 CAGACTTGTCCCCCTCCTATACTTATAATGAACATAAAAAGCCATGAATTCTCCTTCGCCCATCT
128 CAGACTTGTCCCCTTCTTATACTTATAACGAACATAAAAAGCCACGAATTCTCCTTCGCCTATCT
* *
53239795 TAGAATTGAAAACTCGAAGTGCACTCAGAGACAGGTAATTATTGAAT
193 TAGAA-TGAAAACTCAAAGTGCACTCAGAGACAGGCAATTATTGAAT
53239842 ATAACCATACAACCTTAACACCTACAGAGGAGAAAAA
1 ATAACCATACAACCTTAACACCTACAGAGG-GAAAAA
53239879 TAATGGTTCT
Statistics
Matches: 421, Mismatches: 68, Indels: 52
0.78 0.13 0.10
Matches are distributed among these distances:
227 27 0.06
228 2 0.00
229 1 0.00
230 1 0.00
233 131 0.31
234 27 0.06
236 1 0.00
237 131 0.31
238 7 0.02
243 40 0.10
244 2 0.00
245 1 0.00
250 2 0.00
252 15 0.04
253 5 0.01
254 28 0.07
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.25
Consensus pattern (238 bp):
ATAACCATACAACCTTAACACCTACAGAGGGAAAAAAAGAAAGGCTCTATAACACGATGAGAACC
TTTCAGCATACATACGATACTTTCCACATATGACAAGTTGACAACGAAAAATAATTAACTCCCAG
ACTTGTCCCCTTCTTATACTTATAACGAACATAAAAAGCCACGAATTCTCCTTCGCCTATCTTAG
AATGAAAACTCAAAGTGCACTCAGAGACAGGCAATTATTGAAT
Found at i:53243463 original size:15 final size:16
Alignment explanation
Indices: 53243435--53243467 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
53243425 TGACCAACCT
53243435 AAATTTGCAAAAAAAA
1 AAATTTGCAAAAAAAA
53243451 AAATTTG-AAAAAAAA
1 AAATTTGCAAAAAAAA
53243466 AA
1 AA
53243468 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.73, C:0.03, G:0.06, T:0.18
Consensus pattern (16 bp):
AAATTTGCAAAAAAAA
Found at i:53243560 original size:11 final size:11
Alignment explanation
Indices: 53243509--53243560 Score: 59
Period size: 11 Copynumber: 4.7 Consensus size: 11
53243499 TTTATTATTA
*
53243509 TTATTTTTTTG
1 TTATTATTTTG
* *
53243520 TTATCATTTCG
1 TTATTATTTTG
53243531 TTATTATTTTG
1 TTATTATTTTG
*
53243542 TTACTATTTTG
1 TTATTATTTTG
*
53243553 TTGTTATT
1 TTATTATT
53243561 GTTTGGATAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 33 1.00
ACGTcount: A:0.15, C:0.06, G:0.10, T:0.69
Consensus pattern (11 bp):
TTATTATTTTG
Found at i:53245036 original size:62 final size:62
Alignment explanation
Indices: 53244921--53245071 Score: 196
Period size: 62 Copynumber: 2.4 Consensus size: 62
53244911 AATTTGGGGA
* *
53244921 TTTAGGTTTTAAAAATTTAAGGATTTTCAGAATTTTTAGAGTTGTTGGGTTTGGAGAATTTGG
1 TTTAGG-TTTAAAAATTTGAGGATTTTCAGAATTTTTAGAGTTGTTGGATTTGGAGAATTTGG
* * * * *
53244984 TTTAGGTTTAAGAAATTTGAGGATTTTGAG-ATTTTTGGGGTTGTTGGATTTGGCGATTTTGG
1 TTTAGGTTTAA-AAATTTGAGGATTTTCAGAATTTTTAGAGTTGTTGGATTTGGAGAATTTGG
* *
53245046 TTTAAGTTTAAAAATTTGGGGATTTT
1 TTTAGGTTTAAAAATTTGAGGATTTT
53245072 TGGGACTTAG
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
61 14 0.18
62 42 0.54
63 22 0.28
ACGTcount: A:0.25, C:0.01, G:0.27, T:0.47
Consensus pattern (62 bp):
TTTAGGTTTAAAAATTTGAGGATTTTCAGAATTTTTAGAGTTGTTGGATTTGGAGAATTTGG
Found at i:53245958 original size:19 final size:19
Alignment explanation
Indices: 53245919--53245966 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
53245909 GGGAAAATAT
*
53245919 TTTATTGTTTTTAATTTAA
1 TTTATTGTTTTAAATTTAA
53245938 TTTA-TGTTTTAAATTTAAA
1 TTTATTGTTTTAAATTT-AA
*
53245957 TTTTTTGTTT
1 TTTATTGTTT
53245967 ACGTGACATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 11 0.44
19 9 0.36
20 5 0.20
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (19 bp):
TTTATTGTTTTAAATTTAA
Found at i:53252670 original size:7 final size:7
Alignment explanation
Indices: 53252658--53252686 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
53252648 TTAACTTTTT
53252658 AAAAATA
1 AAAAATA
53252665 AAAAATA
1 AAAAATA
53252672 AAAAATA
1 AAAAATA
53252679 AAAAATA
1 AAAAATA
53252686 A
1 A
53252687 TAATTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAATA
Found at i:53255096 original size:16 final size:15
Alignment explanation
Indices: 53255075--53255108 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
53255065 GTAGTTTTAC
53255075 AAATAATATAATATAT
1 AAATAATA-AATATAT
*
53255091 AAATAATAAATTTAT
1 AAATAATAAATATAT
53255106 AAA
1 AAA
53255109 ACAACATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AAATAATAAATATAT
Found at i:53271459 original size:22 final size:22
Alignment explanation
Indices: 53271425--53271467 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
53271415 CGTTAAATCT
* *
53271425 AAACTCAAGTATCAAATTAAAA
1 AAACTAAAATATCAAATTAAAA
53271447 AAACTAAAATATCAAATTAAA
1 AAACTAAAATATCAAATTAAA
53271468 CTTAGAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.63, C:0.12, G:0.02, T:0.23
Consensus pattern (22 bp):
AAACTAAAATATCAAATTAAAA
Found at i:53272204 original size:6 final size:6
Alignment explanation
Indices: 53272184--53272242 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
53272174 TTAACTGGTT
* * *
53272184 TTTAAA TTT-AT TTTAAA TTTAAA TTTACTTA TTTAAA TTT-AC TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA
*
53272232 TTTAAG TTTAA
1 TTTAAA TTTAA
53272243 TCAAATTTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
5 8 0.19
6 29 0.69
8 5 0.12
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:53272219 original size:14 final size:14
Alignment explanation
Indices: 53272200--53272227 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53272190 TTTATTTTAA
53272200 ATTTAAATTTACTT
1 ATTTAAATTTACTT
53272214 ATTTAAATTTACTT
1 ATTTAAATTTACTT
53272228 TAAATTTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTAAATTTACTT
Found at i:53273416 original size:16 final size:15
Alignment explanation
Indices: 53273390--53273422 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
53273380 TAAAGGTTGT
53273390 TTTAAATAAAAAGGA
1 TTTAAATAAAAAGGA
53273405 TTTAAATAAAAAGGA
1 TTTAAATAAAAAGGA
53273420 TTT
1 TTT
53273423 TTTTTTGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (15 bp):
TTTAAATAAAAAGGA
Found at i:53274426 original size:59 final size:55
Alignment explanation
Indices: 53274363--53274527 Score: 206
Period size: 59 Copynumber: 2.8 Consensus size: 55
53274353 CAAAACTTCT
53274363 AAAAATTACCATTTTACCCCTAAACTTTCCTAAATTCCATTTTAACCTTGATTTCACCC
1 AAAAA-TACCATTTTACCCCTAAACTTTCCTAAATTCCATTTTAACC--GATTTCA-CC
*
53274422 AAAAATACCATTTTAACCCTAAACTTT-CTAAAATTCCATTTTTAAATCCGATTTCACC
1 AAAAATACCATTTTACCCCTAAACTTTCCT-AAATTCCA-TTTT-AA-CCGATTTCACC
* *
53274480 AAAAAATACCATTTTACCCCCCAAACTTTCCAAAATTCCATTTTAACC
1 -AAAAATACCATTTTA-CCCCTAAACTTTCCTAAATTCCATTTTAACC
53274528 CCAAAACTTT
Statistics
Matches: 95, Mismatches: 4, Indels: 16
0.83 0.03 0.14
Matches are distributed among these distances:
57 4 0.04
58 33 0.35
59 35 0.37
60 20 0.21
61 3 0.03
ACGTcount: A:0.36, C:0.28, G:0.01, T:0.35
Consensus pattern (55 bp):
AAAAATACCATTTTACCCCTAAACTTTCCTAAATTCCATTTTAACCGATTTCACC
Found at i:53274542 original size:59 final size:55
Alignment explanation
Indices: 53274363--53274645 Score: 242
Period size: 58 Copynumber: 4.9 Consensus size: 55
53274353 CAAAACTTCT
* * **
53274363 AAAAATTACCATTTTACCCCTAAACTTTCCTAAATTCCATTTTAACCTTGATTTC
1 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTAACCCCGATTTC
* * * * **
53274418 ACCCAAAAATACCATTTTAACCCTAAACTTTCTAAAATTCCATTTTTAAATCCGATTTCACC
1 A---AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCA-TTTTAACCCCGATTT---C
* *
53274480 AAAAAATACCATTTTACCCCCCAAACTTTCCAAAATTCCATTTTAACCCCAAAACTTTC
1 AAAAATTACCATTTTA-CCCCCAAACTTTCCAAAATTCCATTTTAACCCC--GA-TTTC
* * * *
53274539 AAAAATTACCATTTTACCCTCGAACTTTCCAAAGTCCCATTTTAAACCCCGATTTC
1 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTT-AACCCCGATTTC
* * * * *
53274595 ACTAAAATTATCATTTTACCCCTCGAACCTTCCAAAATCCCCTTTTAACCC
1 A--AAAATTACCATTTTACCCC-CAAACTTTCCAAAATTCCATTTTAACCC
53274646 TAATTTTTCC
Statistics
Matches: 188, Mismatches: 25, Indels: 27
0.78 0.10 0.11
Matches are distributed among these distances:
55 1 0.01
56 5 0.03
57 1 0.01
58 79 0.42
59 76 0.40
60 20 0.11
61 1 0.01
62 5 0.03
ACGTcount: A:0.35, C:0.30, G:0.02, T:0.33
Consensus pattern (55 bp):
AAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTAACCCCGATTTC
Found at i:53274551 original size:30 final size:30
Alignment explanation
Indices: 53274305--53274554 Score: 132
Period size: 30 Copynumber: 8.5 Consensus size: 30
53274295 AATTATCTAG
* * *
53274305 AAATTA-CATTTTGACCCCAAAAATTTTAGA
1 AAATTACCATTTTAACCCCAAAACTTTCA-A
*
53274335 AAATTA-CATTTTGACCCCCAAAAC-TTCTAA
1 AAATTACCATTTT-AACCCCAAAACTTTC-AA
* **
53274365 AAATTACCATTTT-ACCCCTAAACTTTCCT
1 AAATTACCATTTTAACCCCAAAACTTTCAA
***
53274394 AAATT-CCATTTTAA--CCTTGA-TTTCACCCA
1 AAATTACCATTTTAACCCCAAAACTTTCA---A
* * *
53274423 AAAATACCATTTTAA-CCCTAAACTTTCTA
1 AAATTACCATTTTAACCCCAAAACTTTCAA
** *
53274452 AAATT-CCATTTTTAAATCC--GA-TTTCACCAA
1 AAATTACCA-TTTTAACCCCAAAACTTT---CAA
* * * *
53274482 AAAATACCATTTTACCCCCCAAACTTTCCA
1 AAATTACCATTTTAACCCCAAAACTTTCAA
53274512 AAATT-CCATTTTAACCCCAAAACTTTCAA
1 AAATTACCATTTTAACCCCAAAACTTTCAA
53274541 AAATTACCATTTTA
1 AAATTACCATTTTA
53274555 CCCTCGAACT
Statistics
Matches: 169, Mismatches: 30, Indels: 42
0.70 0.12 0.17
Matches are distributed among these distances:
26 4 0.02
27 7 0.04
28 11 0.07
29 55 0.33
30 62 0.37
31 22 0.13
32 5 0.03
33 3 0.02
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.34
Consensus pattern (30 bp):
AAATTACCATTTTAACCCCAAAACTTTCAA
Found at i:53274551 original size:118 final size:117
Alignment explanation
Indices: 53274363--53274645 Score: 299
Period size: 117 Copynumber: 2.4 Consensus size: 117
53274353 CAAAACTTCT
* * ***
53274363 AAAAATTACCATTTTA-CCCCTAAACTTTCCTAAATTCCATTTTAA--CCTTGATTTCACCCAAA
1 AAAAATTACCATTTTACCCCCCAAACTTTCCAAAATTCCATTTTAACCCCAAAATTTCA--CAAA
* * *
53274425 AATACCATTTTAACCCT-AAACTTTCTAAAATTCCATTTTTAAA-TCCGATTTCACC
64 AATACCATTTT-ACCCTCAAACTTTCCAAAATCCCA-TTTTAAACCCCGATTTCA-C
*
53274480 AAAAAATACCATTTTACCCCCCAAACTTTCCAAAATTCCATTTTAACCCCAAAACTTTCA-AAAA
1 AAAAATTACCATTTTACCCCCCAAACTTTCCAAAATTCCATTTTAACCCCAAAA-TTTCACAAAA
* * *
53274544 TTACCATTTTACCCTCGAACTTTCCAAAGTCCCATTTTAAACCCCGATTTCAC
65 ATACCATTTTACCCTCAAACTTTCCAAAATCCCATTTTAAACCCCGATTTCAC
* * * * * * *
53274597 TAAAATTATCATTTTACCCCTCGAACCTTCCAAAATCCCCTTTTAACCC
1 AAAAATTACCATTTTACCCCCCAAACTTTCCAAAATTCCATTTTAACCC
53274646 TAATTTTTCC
Statistics
Matches: 140, Mismatches: 20, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
117 69 0.49
118 63 0.45
120 3 0.02
121 5 0.04
ACGTcount: A:0.35, C:0.30, G:0.02, T:0.33
Consensus pattern (117 bp):
AAAAATTACCATTTTACCCCCCAAACTTTCCAAAATTCCATTTTAACCCCAAAATTTCACAAAAA
TACCATTTTACCCTCAAACTTTCCAAAATCCCATTTTAAACCCCGATTTCAC
Found at i:53282308 original size:16 final size:16
Alignment explanation
Indices: 53282289--53282319 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53282279 TTTCAAGTTA
53282289 GATTATTTTGAGTTTT
1 GATTATTTTGAGTTTT
*
53282305 GATTATTTTGTGTTT
1 GATTATTTTGAGTTT
53282320 AAGTCAAGTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.19, T:0.65
Consensus pattern (16 bp):
GATTATTTTGAGTTTT
Found at i:53286207 original size:171 final size:170
Alignment explanation
Indices: 53285920--53286261 Score: 515
Period size: 171 Copynumber: 2.0 Consensus size: 170
53285910 TAAAGTCATT
* *
53285920 TACCCTGGGACTTCTACCGGTAGAACTCCTCTTCTACCGATACAACTAAAGTTCTACCGGTACAA
1 TACCCTGAGACTTCTACCGGTAGAACTCCTCTTCTACCGATACAACTAAAGTTCTACCGATACAA
* * * * *
53285985 GTATGCTTTTACCGGAACAACTAAGTTGCAGATTGCTTTTAATAATGGTTTTTATGGCTGCAACG
66 ATATGCTTCTACAGGAACAACTAAGTTGCAGACTGCTTTTAACAATGG-TTTTATGGCTGCAACG
53286050 GCTACATTACTCTCCCAACAACCACAACGGTTAGAATTCAC
130 GCTACATTACTCTCCCAACAACCACAACGGTTAGAATTCAC
* *
53286091 TACCCTGAGACTTCTACCGGTAGAACTCCTCTT-TTCCTGATACAACTATAGTTCTACCGATACA
1 TACCCTGAGACTTCTACCGGTAGAACTCCTCTTCTACC-GATACAACTAAAGTTCTACCGATACA
** *
53286155 AATATGCTTCTACAGGAACAACTAAGTTGCAGACTGCTTTTAACGCTGGTTTTATGGCTGCAATG
65 AATATGCTTCTACAGGAACAACTAAGTTGCAGACTGCTTTTAACAATGGTTTTATGGCTGCAACG
* * * *
53286220 GCTACATTACTTTCCCAACAACCATAATGGTTGGAATTCAC
130 GCTACATTACTCTCCCAACAACCACAACGGTTAGAATTCAC
53286261 T
1 T
53286262 TAGAGGGTAT
Statistics
Matches: 154, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
170 56 0.36
171 98 0.64
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.30
Consensus pattern (170 bp):
TACCCTGAGACTTCTACCGGTAGAACTCCTCTTCTACCGATACAACTAAAGTTCTACCGATACAA
ATATGCTTCTACAGGAACAACTAAGTTGCAGACTGCTTTTAACAATGGTTTTATGGCTGCAACGG
CTACATTACTCTCCCAACAACCACAACGGTTAGAATTCAC
Found at i:53287817 original size:42 final size:42
Alignment explanation
Indices: 53287758--53287841 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
53287748 CCAAGGAGAA
53287758 AGATCCCATTATTTGCTATGAGTGTAAGAAATCGGGACACAT
1 AGATCCCATTATTTGCTATGAGTGTAAGAAATCGGGACACAT
53287800 AGATCCCATTATTTGCTATGAGTGTAAGAAATCGGGACACAT
1 AGATCCCATTATTTGCTATGAGTGTAAGAAATCGGGACACAT
53287842 CAAGTATGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (42 bp):
AGATCCCATTATTTGCTATGAGTGTAAGAAATCGGGACACAT
Found at i:53288744 original size:17 final size:16
Alignment explanation
Indices: 53288721--53288796 Score: 93
Period size: 17 Copynumber: 4.6 Consensus size: 16
53288711 ACCAAACCAT
53288721 TTTAAATTTATTTTAAA
1 TTTAAATTTA-TTTAAA
*
53288738 ATTAAATTTATCTTAAA
1 TTTAAATTTAT-TTAAA
53288755 TTTAAATTTA-TTAAA
1 TTTAAATTTATTTAAA
53288770 TTTAAATTTGGATTT-AA
1 TTTAAATTT--ATTTAAA
53288787 TTTAAATTTA
1 TTTAAATTTA
53288797 AAATTATTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
15 15 0.28
16 1 0.02
17 35 0.66
18 2 0.04
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (16 bp):
TTTAAATTTATTTAAA
Found at i:53288759 original size:6 final size:6
Alignment explanation
Indices: 53288721--53288798 Score: 62
Period size: 6 Copynumber: 14.0 Consensus size: 6
53288711 ACCAAACCAT
* *
53288721 TTTAAA TTT-AT TTTAAA ATTAAA TTT--A TCTTAAA TTTAAA TTT--A
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA
**
53288765 -TTAAA TTTAAA TTTGGA TTT-AA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
53288799 ATTATTATAA
Statistics
Matches: 57, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
3 2 0.04
4 3 0.05
5 11 0.19
6 39 0.68
7 2 0.04
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:53288795 original size:11 final size:11
Alignment explanation
Indices: 53288721--53288797 Score: 59
Period size: 11 Copynumber: 7.0 Consensus size: 11
53288711 ACCAAACCAT
*
53288721 TTTAAATTTAT
1 TTTAAATTTAA
*
53288732 TTTAAAATTAAA
1 TTT-AAATTTAA
** *
53288744 TTTATCTTAAA
1 TTTAAATTTAA
53288755 TTTAAATTT-A
1 TTTAAATTTAA
53288765 -TTAAATTTAAA
1 TTTAAATTT-AA
**
53288776 TTTGGATTTAA
1 TTTAAATTTAA
53288787 TTTAAATTTAA
1 TTTAAATTTAA
53288798 AATTATTATA
Statistics
Matches: 51, Mismatches: 11, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
9 8 0.16
10 1 0.02
11 27 0.53
12 15 0.29
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:53289938 original size:16 final size:17
Alignment explanation
Indices: 53289901--53289939 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
53289891 CTGGGTTTAT
*
53289901 AATGAAACTAAATAAAA
1 AATGAAACCAAATAAAA
*
53289918 AATGAAACCAAA-AAGA
1 AATGAAACCAAATAAAA
53289934 AATGAA
1 AATGAA
53289940 TTGGAAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.69, C:0.08, G:0.10, T:0.13
Consensus pattern (17 bp):
AATGAAACCAAATAAAA
Found at i:53290725 original size:60 final size:60
Alignment explanation
Indices: 53290656--53290958 Score: 371
Period size: 60 Copynumber: 5.1 Consensus size: 60
53290646 ATTATATTTG
* *
53290656 ACCCCTAAACTTTTCTAAAATTATATTTTAACCCCAAAACTTTCTATAAATTACATTTTG
1 ACCCCTAAACTTTTCTAAAATTATATTTTAACCCTAAAACTTTCTATAAATTACATTTTA
* * * * * * *
53290716 ACCCTTAAACTTTT-TCAAAAATATATTTTGACCCCAAAAC-TTATATAAAATATATTTTTA
1 ACCCCTAAACTTTTCT-AAAATTATATTTTAACCCTAAAACTTTCTATAAATTACA-TTTTA
* * * * *
53290776 CCCCCTAAACTTTTCCAAAATTATGTTTTGACCCTAAAACTTTCTATAATTTACATTTTA
1 ACCCCTAAACTTTTCTAAAATTATATTTTAACCCTAAAACTTTCTATAAATTACATTTTA
* * *
53290836 ACCCTTAAACTTTTCCAAAATTATATTATAACCCTAAAACTTTCTATAAATTACATTTTA
1 ACCCCTAAACTTTTCTAAAATTATATTTTAACCCTAAAACTTTCTATAAATTACATTTTA
* * * *
53290896 A-CCCTAAACATTTCTAAAATTATATTTTCACCCTAAAACTCTCTA-AAATTACATTTTT
1 ACCCCTAAACTTTTCTAAAATTATATTTTAACCCTAAAACTTTCTATAAATTACATTTTA
53290954 ACCCC
1 ACCCC
53290959 CAAGTTTTCC
Statistics
Matches: 208, Mismatches: 30, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
58 13 0.06
59 53 0.25
60 132 0.63
61 10 0.05
ACGTcount: A:0.37, C:0.22, G:0.01, T:0.40
Consensus pattern (60 bp):
ACCCCTAAACTTTTCTAAAATTATATTTTAACCCTAAAACTTTCTATAAATTACATTTTA
Found at i:53290923 original size:29 final size:29
Alignment explanation
Indices: 53290643--53290957 Score: 278
Period size: 30 Copynumber: 10.6 Consensus size: 29
53290633 AAACTATCCA
* *
53290643 AAAATTATATTTGACCCCT-AAACTTTTCT
1 AAAATTATATTTTAACCCTAAAAC-TTTCT
*
53290672 AAAATTATATTTTAACCCCAAAACTTTCT
1 AAAATTATATTTTAACCCTAAAACTTTCT
* * * *
53290701 ATAAATTACATTTTGACCCTTAAACTTTTT
1 A-AAATTATATTTTAACCCTAAAACTTTCT
* * * *
53290731 CAAAAATATATTTTGACCCCAAAACTTATAT
1 -AAAATTATATTTTAACCCTAAAACTT-TCT
* *
53290762 AAAA-TATATTTTTACCCCCT-AAACTTTTCC
1 AAAATTATA-TTTTA-ACCCTAAAAC-TTTCT
* *
53290792 AAAATTATGTTTTGACCCTAAAACTTTCT
1 AAAATTATATTTTAACCCTAAAACTTTCT
* * * *
53290821 ATAATTTACATTTTAACCCTTAAACTTTTCC
1 A-AAATTATATTTTAACCCTAAAAC-TTTCT
*
53290852 AAAATTATATTATAACCCTAAAACTTTCT
1 AAAATTATATTTTAACCCTAAAACTTTCT
*
53290881 ATAAATTACATTTTAACCCT-AAACATTTCT
1 A-AAATTATATTTTAACCCTAAAAC-TTTCT
* *
53290911 AAAATTATATTTTCACCCTAAAACTCTCT
1 AAAATTATATTTTAACCCTAAAACTTTCT
* *
53290940 AAAATTACATTTTTACCC
1 AAAATTATATTTTAACCC
53290958 CCAAGTTTTC
Statistics
Matches: 232, Mismatches: 40, Indels: 28
0.77 0.13 0.09
Matches are distributed among these distances:
29 80 0.34
30 136 0.59
31 16 0.07
ACGTcount: A:0.38, C:0.21, G:0.02, T:0.40
Consensus pattern (29 bp):
AAAATTATATTTTAACCCTAAAACTTTCT
Found at i:53291253 original size:27 final size:27
Alignment explanation
Indices: 53291207--53291260 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
53291197 TATCGTGTTC
*
53291207 GCTTTGTTTTTGCCTATCGTTTTATTT
1 GCTTTGTTTTTGCCTATCGTGTTATTT
53291234 GCTTTGTTATTT-CACT-TCGTGTTATTT
1 GCTTTGTT-TTTGC-CTATCGTGTTATTT
53291261 AATATCCGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 19 0.79
28 5 0.21
ACGTcount: A:0.09, C:0.15, G:0.15, T:0.61
Consensus pattern (27 bp):
GCTTTGTTTTTGCCTATCGTGTTATTT
Found at i:53293329 original size:22 final size:23
Alignment explanation
Indices: 53293304--53293346 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
53293294 ATGTATATGT
*
53293304 TTTATTTTTTC-AATATTTTTCA
1 TTTATATTTTCTAATATTTTTCA
*
53293326 TTTATATTTTCTAATTTTTTT
1 TTTATATTTTCTAATATTTTT
53293347 AAATAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (23 bp):
TTTATATTTTCTAATATTTTTCA
Done.