Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008194.1 Hibiscus syriacus cultivar Beakdansim tig00110813_pilon, whole genome shotgun sequence
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: 2426039
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 13
Found at i:1893464 original size:17 final size:18
Alignment explanation
Indices: 1893439--1893472 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1893429 GGTATCGCAA
1893439 AAAAGATTAAAT-TGAAG
1 AAAAGATTAAATATGAAG
*
1893456 AAAATATTAAATATGAA
1 AAAAGATTAAATATGAA
1893473 AGATTAGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.26
Consensus pattern (18 bp):
AAAAGATTAAATATGAAG
Found at i:1894522 original size:3 final size:3
Alignment explanation
Indices: 1894516--1894611 Score: 185
Period size: 3 Copynumber: 32.3 Consensus size: 3
1894506 GCAAAGCATG
1894516 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1894564 TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1894611 T
1 T
1894612 CTGAGATTAA
Statistics
Matches: 92, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 90 0.98
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1894992 original size:18 final size:18
Alignment explanation
Indices: 1894969--1895004 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1894959 GCGACGCCGG
1894969 GCATTGCCAATCCTACAA
1 GCATTGCCAATCCTACAA
1894987 GCATTGCCAATCCTACAA
1 GCATTGCCAATCCTACAA
1895005 CCCTAAATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.11, T:0.22
Consensus pattern (18 bp):
GCATTGCCAATCCTACAA
Found at i:1898277 original size:29 final size:29
Alignment explanation
Indices: 1898235--1898349 Score: 178
Period size: 29 Copynumber: 3.9 Consensus size: 29
1898225 TTGACTTGGG
*
1898235 TAGTTTTGTAAATATTTTTAAAAGAGTGT
1 TAGTTTTGTAAATATTTTTAAAAGGGTGT
1898264 TAGTTTTGTAAATATTTTTAAAACGGGTGT
1 TAGTTTTGTAAATATTTTTAAAA-GGGTGT
*
1898294 TA-TTTTCATAAATATTTTTAAAAGGGTGT
1 TAGTTTT-GTAAATATTTTTAAAAGGGTGT
*
1898323 TAGTTTCGTAAATATTTTTAAAAGGGT
1 TAGTTTTGTAAATATTTTTAAAAGGGT
1898350 AATAATTGTG
Statistics
Matches: 79, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
29 54 0.68
30 25 0.32
ACGTcount: A:0.33, C:0.03, G:0.17, T:0.47
Consensus pattern (29 bp):
TAGTTTTGTAAATATTTTTAAAAGGGTGT
Found at i:1898362 original size:29 final size:29
Alignment explanation
Indices: 1898238--1898363 Score: 155
Period size: 29 Copynumber: 4.3 Consensus size: 29
1898228 ACTTGGGTAG
* *
1898238 TTTTGTAAATATTTTTAAAAGAGTGTTAG
1 TTTTGTAAATATTTTTAAAAGGGTGTTAA
1898267 TTTTGTAAATATTTTTAAAACGGGTGTT-A
1 TTTTGTAAATATTTTTAAAA-GGGTGTTAA
* *
1898296 TTTTCATAAATATTTTTAAAAGGGTGTTAG
1 TTTT-GTAAATATTTTTAAAAGGGTGTTAA
* **
1898326 TTTCGTAAATATTTTTAAAAGGGTAATAA
1 TTTTGTAAATATTTTTAAAAGGGTGTTAA
*
1898355 TTGTGTAAA
1 TTTTGTAAA
1898364 ATGGTTGATC
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
29 59 0.71
30 24 0.29
ACGTcount: A:0.35, C:0.02, G:0.17, T:0.46
Consensus pattern (29 bp):
TTTTGTAAATATTTTTAAAAGGGTGTTAA
Found at i:1905257 original size:16 final size:16
Alignment explanation
Indices: 1905233--1905263 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1905223 GGTCTCGTTA
1905233 AAGTATATATATATAT
1 AAGTATATATATATAT
*
1905249 AAGTGTATATATATA
1 AAGTATATATATATA
1905264 CAAACAGTTA
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:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (16 bp):
AAGTATATATATATAT
Found at i:1911780 original size:28 final size:28
Alignment explanation
Indices: 1911753--1911806 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
1911743 ATTAACTTAG
1911753 GCCC-ATAAGG-TCAATTTAGTAATTTTA
1 GCCCTATAAGGAT-AATTTAGTAATTTTA
*
1911780 GCCCTATAAGGATATTTTAGTAATTTT
1 GCCCTATAAGGATAATTTAGTAATTTT
1911807 CCACACTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
28 19 0.79
29 1 0.04
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (28 bp):
GCCCTATAAGGATAATTTAGTAATTTTA
Found at i:1912795 original size:15 final size:16
Alignment explanation
Indices: 1912755--1912795 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
1912745 AAAAATTATA
1912755 AATATA-TTTAAAAAT
1 AATATATTTTAAAAAT
1912770 AATATGAATTTTAAAAAT
1 AATAT--ATTTTAAAAAT
1912788 -ATATATTT
1 AATATATTT
1912796 GAGAAACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 9 0.39
17 5 0.22
18 9 0.39
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
AATATATTTTAAAAAT
Found at i:1912887 original size:16 final size:17
Alignment explanation
Indices: 1912868--1912901 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1912858 CCAAAAAAAA
1912868 TAAAAATA-AAAATATT
1 TAAAAATATAAAATATT
*
1912884 TAAAAATATCAAATATT
1 TAAAAATATAAAATATT
1912901 T
1 T
1912902 TTAAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAAAATATAAAATATT
Found at i:1915547 original size:14 final size:14
Alignment explanation
Indices: 1915528--1915577 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
1915518 TTAATGTGTA
1915528 TATATGTTATCTAT
1 TATATGTTATCTAT
*
1915542 TATATG---TGTA-
1 TATATGTTATCTAT
1915552 TATATGTATATCTAT
1 TATATGT-TATCTAT
1915567 TATATGTTATC
1 TATATGTTATC
1915578 AATGTTCTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
10 6 0.21
11 3 0.10
14 13 0.45
15 7 0.24
ACGTcount: A:0.30, C:0.06, G:0.10, T:0.54
Consensus pattern (14 bp):
TATATGTTATCTAT
Found at i:1915548 original size:24 final size:25
Alignment explanation
Indices: 1915517--1915573 Score: 100
Period size: 24 Copynumber: 2.4 Consensus size: 25
1915507 AACTTCTGAA
1915517 ATTA-ATGTGTATATATGT-TATCT
1 ATTATATGTGTATATATGTATATCT
1915540 ATTATATGTGTATATATGTATATCT
1 ATTATATGTGTATATATGTATATCT
1915565 ATTATATGT
1 ATTATATGT
1915574 TATCAATGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 4 0.12
24 14 0.44
25 14 0.44
ACGTcount: A:0.32, C:0.04, G:0.12, T:0.53
Consensus pattern (25 bp):
ATTATATGTGTATATATGTATATCT
Found at i:1915713 original size:2 final size:2
Alignment explanation
Indices: 1915706--1915780 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
1915696 GTAGGAAAAT
1915706 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1915748 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1915781 CATTCTATCC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1917644 original size:4 final size:4
Alignment explanation
Indices: 1917635--1917683 Score: 98
Period size: 4 Copynumber: 12.2 Consensus size: 4
1917625 TAATTATTTG
1917635 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
1917683 T
1 T
1917684 AATAATTCAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:1921787 original size:27 final size:27
Alignment explanation
Indices: 1921730--1921788 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
1921720 TCGTCTTTAT
* * **
1921730 AAAAAATTTAAAATTTTAATTTATATT
1 AAAAAACTTAAAATTATAATTTATAAG
*
1921757 AAAAAACTTAAAATTATAATTTTTAAG
1 AAAAAACTTAAAATTATAATTTATAAG
1921784 AAAAA
1 AAAAA
1921789 CCCCAAATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (27 bp):
AAAAAACTTAAAATTATAATTTATAAG
Found at i:1925829 original size:6 final size:6
Alignment explanation
Indices: 1925820--1925845 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1925810 CTTTCTCTGC
1925820 AAAATA AAAATA AAAATA AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AA
1925846 TGGCTAGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:1927977 original size:19 final size:19
Alignment explanation
Indices: 1927948--1928002 Score: 92
Period size: 19 Copynumber: 2.8 Consensus size: 19
1927938 TTTTAATCTC
*
1927948 ATTTAAATATTTGATTTTGA
1 ATTT-AATATTTAATTTTGA
1927968 ATTTAATATTTAATTTTGA
1 ATTTAATATTTAATTTTGA
1927987 ATTTAATATTTAATTT
1 ATTTAATATTTAATTT
1928003 ATACTTAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 30 0.88
20 4 0.12
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAATTTTGA
Found at i:1928694 original size:10 final size:10
Alignment explanation
Indices: 1928679--1928753 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
1928669 CATTTAATAA
1928679 ATAAACGAAC
1 ATAAACGAAC
1928689 ATAAACGAAC
1 ATAAACGAAC
1928699 ----ACGAAC
1 ATAAACGAAC
1928705 ATAAACGAAC
1 ATAAACGAAC
* *
1928715 ATGAAC-ATAA
1 ATAAACGA-AC
1928725 ATGAACACGAAC
1 AT-AA-ACGAAC
1928737 ATAAACGAAC
1 ATAAACGAAC
*
1928747 ATCAACG
1 ATAAACG
1928754 TTGGAGACCC
Statistics
Matches: 52, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 36 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.56, C:0.21, G:0.12, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1928704 original size:16 final size:16
Alignment explanation
Indices: 1928683--1928747 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
1928673 TAATAAATAA
1928683 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1928699 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
* *
1928715 ATGAACATAAATGAAC
1 ACGAACATAAACGAAC
1928731 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1928747 A
1 A
1928748 TCAACGTTGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1929762 original size:24 final size:24
Alignment explanation
Indices: 1929734--1929808 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
1929724 GATTGGGTTA
*
1929734 AACATAAATGAAAGAACATAAACG
1 AACATAAATGAACGAACATAAACG
*
1929758 AACATAATTGAACGAACATAAACG
1 AACATAAATGAACGAACATAAACG
** *
1929782 AACATAACCGAACGAACATAACCG
1 AACATAAATGAACGAACATAAACG
1929806 AAC
1 AAC
1929809 GTTCACGAAC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.56, C:0.20, G:0.12, T:0.12
Consensus pattern (24 bp):
AACATAAATGAACGAACATAAACG
Found at i:1929803 original size:14 final size:14
Alignment explanation
Indices: 1929754--1929809 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
1929744 AAAGAACATA
**
1929754 AACGAACATAATTG
1 AACGAACATAACCG
1929768 AACGAACAT-A---
1 AACGAACATAACCG
1929778 AACGAACATAACCG
1 AACGAACATAACCG
1929792 AACGAACATAACCG
1 AACGAACATAACCG
1929806 AACG
1 AACG
1929810 TTCACGAACG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.52, C:0.23, G:0.14, T:0.11
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:1929808 original size:10 final size:10
Alignment explanation
Indices: 1929747--1929794 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
1929737 ATAAATGAAA
1929747 GAACATAAAC
1 GAACATAAAC
1929757 GAACATAATTGAAC
1 GAACAT-A---AAC
1929771 GAACATAAAC
1 GAACATAAAC
*
1929781 GAACATAACC
1 GAACATAAAC
1929791 GAAC
1 GAAC
1929795 GAACATAACC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.21, G:0.12, T:0.12
Consensus pattern (10 bp):
GAACATAAAC
Found at i:1930803 original size:23 final size:22
Alignment explanation
Indices: 1930767--1930810 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
1930757 TCAAAAATAT
*
1930767 TAAAAAATATTAATATTTTAAA
1 TAAAAAATAATAATATTTTAAA
1930789 TAAAAATATAATAATATTTTAA
1 TAAAAA-ATAATAATATTTTAA
1930811 TTAATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TAAAAAATAATAATATTTTAAA
Found at i:1932896 original size:61 final size:61
Alignment explanation
Indices: 1932811--1932935 Score: 162
Period size: 61 Copynumber: 2.0 Consensus size: 61
1932801 GTGCTCTCCC
* * * ** *
1932811 GGGAACGCGCTTTAACGGGATTTCTGCTGATTGGGATGCCACACGGGTAAGGCGCTTTGGA
1 GGGAACGCGCCTTAACGGGATTTCTGCTGACTGGAATGCCACACGACTAAGGCGCTTTGCA
* *
1932872 GGGAACGCGCCTTACATGGG-TTTCTGCTGACTGGAATGCCACGCGACTAAGGCGCTTTGCA
1 GGGAACGCGCCTTA-ACGGGATTTCTGCTGACTGGAATGCCACACGACTAAGGCGCTTTGCA
1932933 GGG
1 GGG
1932936 GGCGCCTTCG
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
61 51 0.93
62 4 0.07
ACGTcount: A:0.19, C:0.22, G:0.35, T:0.23
Consensus pattern (61 bp):
GGGAACGCGCCTTAACGGGATTTCTGCTGACTGGAATGCCACACGACTAAGGCGCTTTGCA
Found at i:1933208 original size:25 final size:24
Alignment explanation
Indices: 1933180--1933226 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
1933170 TTTAAATTAG
*
1933180 TATATTTTTTTTAAAAAATAGTTGT
1 TATATATTTTTT-AAAAATAGTTGT
*
1933205 TATATATTTTTTATAAATAGTT
1 TATATATTTTTTAAAAATAGTT
1933227 TTTTAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.57
Consensus pattern (24 bp):
TATATATTTTTTAAAAATAGTTGT
Found at i:1933231 original size:39 final size:38
Alignment explanation
Indices: 1933185--1933261 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 38
1933175 ATTAGTATAT
* *
1933185 TTTTTTTAAAAAATAGTTGTTATATATTTT-TTATAAATAG
1 TTTTTTAAAAAAATA-ATGTTATAT-TTTTATTA-AAATAG
1933225 TTTTTTAAAAAAATAATGTTATATTTTTATTAAAATA
1 TTTTTTAAAAAAATAATGTTATATTTTTATTAAAATA
1933262 ATATTTATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 9 0.26
39 11 0.32
40 14 0.41
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (38 bp):
TTTTTTAAAAAAATAATGTTATATTTTTATTAAAATAG
Found at i:1933264 original size:25 final size:22
Alignment explanation
Indices: 1933225--1933271 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 22
1933215 TTATAAATAG
1933225 TTTTTTAAAAAAATAATGTTATAT
1 TTTTTTAAAAAAAT-AT-TTATAT
*
1933249 TTTTATTAAAATAATATTTATAT
1 TTTT-TTAAAAAAATATTTATAT
1933272 AATTATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 6 0.29
24 6 0.29
25 9 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTTTTAAAAAAATATTTATAT
Found at i:1933277 original size:23 final size:22
Alignment explanation
Indices: 1933234--1933279 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
1933224 GTTTTTTAAA
**
1933234 AAAATAATGTTATATTTTTATT
1 AAAATAATGTTATATAATTATT
*
1933256 AAAATAATATTTATATAATTATT
1 AAAATAAT-GTTATATAATTATT
1933279 A
1 A
1933280 TTTATTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
AAAATAATGTTATATAATTATT
Found at i:1934211 original size:12 final size:12
Alignment explanation
Indices: 1934185--1934230 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
1934175 TAATTTTAAA
1934185 ACTGTTCAT--T
1 ACTGTTCATAGT
1934195 ACTGTTCATAGT
1 ACTGTTCATAGT
1934207 ACTGTTCATACGGT
1 ACTGTTCATA--GT
*
1934221 AATGTTCATA
1 ACTGTTCATA
1934231 CCGTATTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
10 9 0.29
12 11 0.35
14 11 0.35
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.41
Consensus pattern (12 bp):
ACTGTTCATAGT
Found at i:1934887 original size:46 final size:46
Alignment explanation
Indices: 1934794--1934887 Score: 102
Period size: 46 Copynumber: 2.0 Consensus size: 46
1934784 TTGTTACAAC
** * ***
1934794 AATGTTTTTAAAATTTAAATTCAAATTCAACATTAAATGTTTGTTA
1 AATGTTTTTAAAATGCAAATCCAAATTCAACATTAAATGTCAATTA
1934840 AATGTTTTTAAAATGCAAATCCAAATTCAAC-TTAATAT-TCCAATTA
1 AATGTTTTTAAAATGCAAATCCAAATTCAACATTAA-ATGT-CAATTA
1934886 AA
1 AA
1934888 ATTTAAAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
45 5 0.12
46 35 0.88
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.40
Consensus pattern (46 bp):
AATGTTTTTAAAATGCAAATCCAAATTCAACATTAAATGTCAATTA
Found at i:1935095 original size:21 final size:21
Alignment explanation
Indices: 1935066--1935106 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1935056 TTTTTAACTT
*
1935066 TAAATAATAATTAATATATTA
1 TAAACAATAATTAATATATTA
*
1935087 TAAACAATATTTAATATATT
1 TAAACAATAATTAATATATT
1935107 CTAATGACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAACAATAATTAATATATTA
Found at i:1935448 original size:137 final size:137
Alignment explanation
Indices: 1935227--1935927 Score: 878
Period size: 137 Copynumber: 5.1 Consensus size: 137
1935217 ACTGGCCTAC
* * **
1935227 CGGGAGACATCACACATAATAGGGCAATTATAAC------T-TGACAAAAAAGGAAAGGTGCATC
1 CGGGGGACATCACACATAATAGGGAAATTATAACATATTTTCTGAC-AAAAAGGAAATATGCATC
* * * *
1935285 CCACAAGAAGCGTTTTCACCATATTGTTGCGTCCCCTTAAACATGATAGGTGTTGATATGAACAG
65 CCACAAGAAGCGCTTTCACCACATTGTTGCGTCCCCTCAAACATGATAGGTGTTGATATGAATAG
*
1935350 TCCTACGT
130 TCCCACGT
* *
1935358 CGGGGGACATCACACATAATAGGGTAATTATAACATATTCTCTGACAAAAAGGAAATATGCATCC
1 CGGGGGACATCACACATAATAGGGAAATTATAACATATTTTCTGACAAAAAGGAAATATGCATCC
* * *
1935423 CACAAGAAGCGCTTTCACCACATTGTTGCGTCCTCTCAAACATGATAAGTGTTGATACGAATAGT
66 CACAAGAAGCGCTTTCACCACATTGTTGCGTCCCCTCAAACATGATAGGTGTTGATATGAATAGT
1935488 CCCACGT
131 CCCACGT
* * * * * *
1935495 CTGGGGACATCACACATAATAGGGCAATTATAACCTATTTTCTAACAAAAAAGAAATATGCGTCC
1 CGGGGGACATCACACATAATAGGGAAATTATAACATATTTTCTGACAAAAAGGAAATATGCATCC
** * * * *
1935560 TTCAAGAAGCACTTTCACCACATTGTTGCATCCCCTCAAACATGATAGATGTTAATATGAATAGT
66 CACAAGAAGCGCTTTCACCACATTGTTGCGTCCCCTCAAACATGATAGGTGTTGATATGAATAGT
1935625 CCCACGT
131 CCCACGT
* * * * * * **
1935632 TGGGGGGCATTACACATAATAGGGAAATTATAACTTATTTTCTGGAAAAAAAAGGAAATGTGTGT
1 CGGGGGACATCACACATAATAGGGAAATTATAACATATTTTCT-G-ACAAAAAGGAAATATGCAT
** *
1935697 TTCACAAGAAGCACTTTCACCACATTGTTGCGTCCCCTCAAACATGATAGGTGTTGATATGAATA
64 CCCACAAGAAGCGCTTTCACCACATTGTTGCGTCCCCTCAAACATGATAGGTGTTGATATGAATA
**
1935762 GTCCCACAC
129 GTCCCACGT
* * *
1935771 CGGGGGACATCACACATAATAGGGAAATTATAACCTATTTTCTGATAAAAAGAAAAGT-TGCATC
1 CGGGGGACATCACACATAATAGGGAAATTATAACATATTTTCTGACAAAAAGGAAA-TATGCATC
* * *
1935835 CAACGAGAAGCGCTTTCACCACATTGTTGCGTCCCCTCAAACATGATAGGTATTGATATGAATAG
65 CCACAAGAAGCGCTTTCACCACATTGTTGCGTCCCCTCAAACATGATAGGTGTTGATATGAATAG
** *
1935900 TCTGACGC
130 TCCCACGT
1935908 CGGGGGACATCACACATAAT
1 CGGGGGACATCACACATAAT
1935928 GTAACACCCC
Statistics
Matches: 495, Mismatches: 65, Indels: 14
0.86 0.11 0.02
Matches are distributed among these distances:
131 32 0.06
137 338 0.68
138 6 0.01
139 119 0.24
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.26
Consensus pattern (137 bp):
CGGGGGACATCACACATAATAGGGAAATTATAACATATTTTCTGACAAAAAGGAAATATGCATCC
CACAAGAAGCGCTTTCACCACATTGTTGCGTCCCCTCAAACATGATAGGTGTTGATATGAATAGT
CCCACGT
Found at i:1935754 original size:276 final size:273
Alignment explanation
Indices: 1935225--1935927 Score: 909
Period size: 276 Copynumber: 2.6 Consensus size: 273
1935215 ATACTGGCCT
* *
1935225 ACCGGGAGACATCACACATAATAGGGCAATTATAA-C-----T-TGACAAAAAAGGAAAGGTGCA
1 ACCGGGGGACATCACACATAATAGGGCAATTATAACCTATTTTCTGACAAAAAA-GAAA-ATGCA
* * * * *
1935283 TCCCACAAGAAGCGTTTTCACCATATTGTTGCGTCCCCTTAAACATGATAGGTGTTGATATGAAC
64 TCCAACAAGAAGCGCTTTCACCACATTGTTGCGTCCCCTCAAACATGATAGGTGTTGATATGAAT
* * *
1935348 AGTCCTACGTCGGGGGACATCACACATAATAGGGTAATTATAACATATTCTCTGACAAAAAGGAA
129 AGTCCCACGTCGGGGGACATCACACATAATAGGGAAATTATAACATATTCTCTGAAAAAAAGGAA
* *
1935413 ATATGCATCCCACAAGAAGCGCTTTCACCACATTGTTGCGTCCTCTCAAACATGATAAGTGTTGA
194 ATATGCATCCCACAAGAAGCACTTTCACCACATTGTTGCGTCCCCTCAAACATGATAAGTGTTGA
1935478 TACGAATAGTCCCAC
259 TACGAATAGTCCCAC
** * * *
1935493 GTCTGGGGACATCACACATAATAGGGCAATTATAACCTATTTTCTAACAAAAAAGAAATATGCGT
1 ACCGGGGGACATCACACATAATAGGGCAATTATAACCTATTTTCTGACAAAAAAGAAA-ATGCAT
** * * * *
1935558 CCTTCAAGAAGCACTTTCACCACATTGTTGCATCCCCTCAAACATGATAGATGTTAATATGAATA
65 CCAACAAGAAGCGCTTTCACCACATTGTTGCGTCCCCTCAAACATGATAGGTGTTGATATGAATA
* * * * *
1935623 GTCCCACGTTGGGGGGCATTACACATAATAGGGAAATTATAACTTATTTTCTGGAAAAAAAAGGA
130 GTCCCACGTCGGGGGACATCACACATAATAGGGAAATTATAACATATTCTCT-G-AAAAAAAGGA
* ** ** *
1935688 AATGTGTGTTTCACAAGAAGCACTTTCACCACATTGTTGCGTCCCCTCAAACATGATAGGTGTTG
193 AATATGCATCCCACAAGAAGCACTTTCACCACATTGTTGCGTCCCCTCAAACATGATAAGTGTTG
*
1935753 ATATGAATAGTCCCAC
258 ATACGAATAGTCCCAC
* *
1935769 ACCGGGGGACATCACACATAATAGGGAAATTATAACCTATTTTCTGA-TAAAAAGAAAAGTTGCA
1 ACCGGGGGACATCACACATAATAGGGCAATTATAACCTATTTTCTGACAAAAAAGAAAA--TGCA
* *
1935833 TCCAACGAGAAGCGCTTTCACCACATTGTTGCGTCCCCTCAAACATGATAGGTATTGATATGAAT
64 TCCAACAAGAAGCGCTTTCACCACATTGTTGCGTCCCCTCAAACATGATAGGTGTTGATATGAAT
** *
1935898 AGTCTGACGCCGGGGGACATCACACATAAT
129 AGTCCCACGTCGGGGGACATCACACATAAT
1935928 GTAACACCCC
Statistics
Matches: 368, Mismatches: 56, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
268 31 0.08
269 1 0.00
274 110 0.30
275 19 0.05
276 207 0.56
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.26
Consensus pattern (273 bp):
ACCGGGGGACATCACACATAATAGGGCAATTATAACCTATTTTCTGACAAAAAAGAAAATGCATC
CAACAAGAAGCGCTTTCACCACATTGTTGCGTCCCCTCAAACATGATAGGTGTTGATATGAATAG
TCCCACGTCGGGGGACATCACACATAATAGGGAAATTATAACATATTCTCTGAAAAAAAGGAAAT
ATGCATCCCACAAGAAGCACTTTCACCACATTGTTGCGTCCCCTCAAACATGATAAGTGTTGATA
CGAATAGTCCCAC
Found at i:1936865 original size:23 final size:23
Alignment explanation
Indices: 1936839--1936902 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
1936829 CAGCTCATAT
1936839 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
1936862 AATTGCACCGGAGTGCCCCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
1936885 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
1936903 TATAATAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.27, C:0.28, G:0.27, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:1937089 original size:103 final size:103
Alignment explanation
Indices: 1936918--1937135 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
1936908 TAATGTCTAT
* *
1936918 AAGGACCACATATCATTCATTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCATTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1936983 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
1937021 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCATTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1937086 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1937124 AAGGACCACATA
1 AAGGACCACATA
1937136 GACCCTCGAC
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCATTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1956775 original size:20 final size:20
Alignment explanation
Indices: 1956738--1956776 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1956728 AGATTGAGTG
* * *
1956738 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
1956758 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
1956777 AGTTTAGGAG
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:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:1957000 original size:20 final size:21
Alignment explanation
Indices: 1956946--1957008 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
1956936 GATTCCCCTG
1956946 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
1956970 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
1956990 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
1957009 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:1963813 original size:21 final size:24
Alignment explanation
Indices: 1963789--1963847 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 24
1963779 GAGGCAACCC
1963789 AATTTTTCT-TTTTC-TT-TTTTT
1 AATTTTTCTATTTTCGTTCTTTTT
1963810 AA-TTTTCTATTTTCGTTCTTTTT
1 AATTTTTCTATTTTCGTTCTTTTT
* *
1963833 ATTTTATTTTATTTT
1 AATTT-TTCTATTTT
1963848 TCCTTGATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
20 6 0.19
21 7 0.23
22 2 0.06
23 6 0.19
24 2 0.06
25 8 0.26
ACGTcount: A:0.14, C:0.08, G:0.02, T:0.76
Consensus pattern (24 bp):
AATTTTTCTATTTTCGTTCTTTTT
Found at i:1965025 original size:14 final size:14
Alignment explanation
Indices: 1965006--1965045 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1964996 TCTTTCAGTG
*
1965006 AAAAAAA-AAACAA
1 AAAAAAAGAAAAAA
*
1965019 AAAAAAAGAAAAAG
1 AAAAAAAGAAAAAA
1965033 AAAAAAAGAAAAA
1 AAAAAAAGAAAAA
1965046 TTGTGCAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 7 0.29
14 17 0.71
ACGTcount: A:0.90, C:0.03, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAAAAA
Found at i:1965030 original size:16 final size:15
Alignment explanation
Indices: 1965006--1965045 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
1964996 TCTTTCAGTG
1965006 AAAAAAAAAACAAAA
1 AAAAAAAAAACAAAA
*
1965021 AAAAAGAAAAAGAAAA
1 AAAAA-AAAAACAAAA
1965037 AAAGAAAAA
1 AAA-AAAAA
1965046 TTGTGCAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 5 0.23
16 15 0.68
17 2 0.09
ACGTcount: A:0.90, C:0.03, G:0.07, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAACAAAA
Found at i:1974199 original size:3 final size:3
Alignment explanation
Indices: 1974191--1974216 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1974181 GTAAAAATGT
1974191 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1974217 TATGTTAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1974547 original size:21 final size:21
Alignment explanation
Indices: 1974523--1974566 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
1974513 TGATAAAATA
*
1974523 TTATTTAAAATATTATTATTT
1 TTATTTAAAATATTAATATTT
1974544 TTATTTAAAATATTAATATTT
1 TTATTTAAAATATTAATATTT
1974565 TT
1 TT
1974567 TAATATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTATTTAAAATATTAATATTT
Found at i:1974973 original size:32 final size:32
Alignment explanation
Indices: 1974928--1974991 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
1974918 TATTTTATAG
* * * *
1974928 TTTTCCCCCTTTTTACAAGTATTTTCTAGTTT
1 TTTTCCCCATTTTTAAAAGTACTTTATAGTTT
*
1974960 TTTTCCTCATTTTTAAAAGTACTTTATAGTTT
1 TTTTCCCCATTTTTAAAAGTACTTTATAGTTT
1974992 AATTTTAACT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.20, C:0.17, G:0.06, T:0.56
Consensus pattern (32 bp):
TTTTCCCCATTTTTAAAAGTACTTTATAGTTT
Found at i:1984327 original size:16 final size:17
Alignment explanation
Indices: 1984294--1984343 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
1984284 AGAATGAGCC
* **
1984294 AAAAATATATTTTTAAT
1 AAAAAGATATTTAAAAT
1984311 AAAAA-ATATTTAAAAT
1 AAAAAGATATTTAAAAT
1984327 ATAAAAGA-ATTTAAAAT
1 A-AAAAGATATTTAAAAT
1984344 TTTCAGGGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 10 0.34
17 18 0.62
18 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
AAAAAGATATTTAAAAT
Found at i:1986122 original size:23 final size:25
Alignment explanation
Indices: 1986092--1986153 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 25
1986082 CTAATTGTCG
1986092 ATTAATTCTCAC-ATTTTTATAC-A
1 ATTAATTCTCACTATTTTTATACAA
*
1986115 ATTAATTCTCACCCTTTTTTTATACAA
1 ATTAATTCTCA--CTATTTTTATACAA
*
1986142 ACTAATTCTCAC
1 ATTAATTCTCAC
1986154 CTTTAAACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 11 0.33
25 2 0.06
26 9 0.27
27 11 0.33
ACGTcount: A:0.32, C:0.23, G:0.00, T:0.45
Consensus pattern (25 bp):
ATTAATTCTCACTATTTTTATACAA
Found at i:1986577 original size:16 final size:16
Alignment explanation
Indices: 1986536--1986578 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
1986526 GATTAAGCGT
*
1986536 TGAATGATTAAAATAC
1 TGAATGATTCAAATAC
1986552 TGAATGATTCAAATAC
1 TGAATGATTCAAATAC
1986568 TGAATGATTCA
1 TGAATGATTCA
1986579 GAGGCTCTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (16 bp):
TGAATGATTCAAATAC
Found at i:1999122 original size:72 final size:72
Alignment explanation
Indices: 1999038--1999178 Score: 180
Period size: 72 Copynumber: 2.0 Consensus size: 72
1999028 TATTAATCGA
* * *
1999038 CTAATTTGGATC-AGTTATTGCATAGGCCCAATATAAAGTGAGCC-ATC-TTACTTAAGGGATTT
1 CTAATTAGGATCAAG-TATTGCATAGACCCAATATAAAGTGA-CCTA-CATTACTTAAGGGATCT
1999100 AGTGTCTCAT
63 AGTGTCTCAT
** *
1999110 CTAATTAGGATCAAGTATTGCATAGACCCAATATGGAGTGACCTACATTCCTTAAGGGATCTAGT
1 CTAATTAGGATCAAGTATTGCATAGACCCAATATAAAGTGACCTACATTACTTAAGGGATCTAGT
1999175 GTCT
66 GTCT
1999179 TATCCCACTA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
71 3 0.05
72 55 0.92
73 2 0.03
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Consensus pattern (72 bp):
CTAATTAGGATCAAGTATTGCATAGACCCAATATAAAGTGACCTACATTACTTAAGGGATCTAGT
GTCTCAT
Found at i:2002020 original size:23 final size:23
Alignment explanation
Indices: 2001969--2002036 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
2001959 TATTGTTTTT
* *
2001969 AAACATATTCGTTTATATGTTCCC
1 AAACATATTCGTTTA-ACGTTCAC
*
2001993 AAACATATTCATTTAACGTTCAC
1 AAACATATTCGTTTAACGTTCAC
* *
2002016 GAACATGTTCGTTTAACGTTC
1 AAACATATTCGTTTAACGTTC
2002037 GTTTATATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
23 24 0.63
24 14 0.37
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (23 bp):
AAACATATTCGTTTAACGTTCAC
Found at i:2003947 original size:23 final size:24
Alignment explanation
Indices: 2003916--2003976 Score: 81
Period size: 23 Copynumber: 2.6 Consensus size: 24
2003906 ATTATTACAA
2003916 AATACCCAAACCAAA-CCAAACCC
1 AATACCCAAACCAAACCCAAACCC
*
2003939 AATATCCAAACCAAACCCAAACCC
1 AATACCCAAACCAAACCCAAACCC
* *
2003963 GA-GCCCAAACCAAA
1 AATACCCAAACCAAA
2003977 GCCCTAACTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 24 0.73
24 9 0.27
ACGTcount: A:0.51, C:0.41, G:0.03, T:0.05
Consensus pattern (24 bp):
AATACCCAAACCAAACCCAAACCC
Found at i:2008958 original size:15 final size:16
Alignment explanation
Indices: 2008940--2008969 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2008930 GTGTGGGCTG
2008940 GTGGGTA-GTGGTTTA
1 GTGGGTATGTGGTTTA
2008955 GTGGGTATGTGGTTT
1 GTGGGTATGTGGTTT
2008970 TTAAGTGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.10, C:0.00, G:0.47, T:0.43
Consensus pattern (16 bp):
GTGGGTATGTGGTTTA
Found at i:2009065 original size:21 final size:22
Alignment explanation
Indices: 2009041--2009092 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
2009031 AAATTACATT
2009041 ATTAATAATATAAT-AAAAATA
1 ATTAATAATATAATAAAAAATA
*
2009062 ATTAA-AA-ATAATAAAAAATT
1 ATTAATAATATAATAAAAAATA
2009082 ATT-ATAATATA
1 ATTAATAATATA
2009093 TATATATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 6 0.22
20 13 0.48
21 8 0.30
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
ATTAATAATATAATAAAAAATA
Found at i:2009093 original size:2 final size:2
Alignment explanation
Indices: 2009084--2009117 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2009074 AAAAAATTAT
2009084 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2009118 TTTTTTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2013492 original size:110 final size:111
Alignment explanation
Indices: 2013291--2013511 Score: 435
Period size: 110 Copynumber: 2.0 Consensus size: 111
2013281 ATAAGAGAAT
2013291 AGAGGATAAAAAGAAATCAATCAAAGAAGAAGTGAGTGAGGTAGGACACTTCACGAAAAGTGGGA
1 AGAGGATAAAAAGAAATCAATCAAAGAAGAAGTGAGTGAGGTAGGACACTTCACGAAAAGTGGGA
2013356 GATATTACCCACCTAAGACGTCCACAGAGGCAGACAATGCGAAAGC
66 GATATTACCCACCTAAGACGTCCACAGAGGCAGACAATGCGAAAGC
2013402 AGAGGAT-AAAAGAAATCAATCAAAGAAGAAGTGAGTGAGGTAGGACACTTCACGAAAAGTGGGA
1 AGAGGATAAAAAGAAATCAATCAAAGAAGAAGTGAGTGAGGTAGGACACTTCACGAAAAGTGGGA
2013466 GATATTACCCACCTAAGACGTCCACAGAGGCAGACAATGCGAAAGC
66 GATATTACCCACCTAAGACGTCCACAGAGGCAGACAATGCGAAAGC
2013512 TAAAGCCAAG
Statistics
Matches: 110, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
110 103 0.94
111 7 0.06
ACGTcount: A:0.43, C:0.17, G:0.26, T:0.14
Consensus pattern (111 bp):
AGAGGATAAAAAGAAATCAATCAAAGAAGAAGTGAGTGAGGTAGGACACTTCACGAAAAGTGGGA
GATATTACCCACCTAAGACGTCCACAGAGGCAGACAATGCGAAAGC
Found at i:2017223 original size:32 final size:34
Alignment explanation
Indices: 2017187--2017256 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
2017177 ACCTTACAAC
* *
2017187 TCCCTAGTTTTT-C-TGGGCTAAACTAGAACTTT
1 TCCCTAGTTTTTACATGGGATAAACTAGAACCTT
*
2017219 TCCCTAGTTTTTACATGGGATAAGCTAGAACCTT
1 TCCCTAGTTTTTACATGGGATAAACTAGAACCTT
2017253 TCCC
1 TCCC
2017257 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 12 0.36
33 1 0.03
34 20 0.61
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.37
Consensus pattern (34 bp):
TCCCTAGTTTTTACATGGGATAAACTAGAACCTT
Found at i:2018145 original size:133 final size:133
Alignment explanation
Indices: 2017974--2018242 Score: 472
Period size: 133 Copynumber: 2.0 Consensus size: 133
2017964 CACTTAAACA
2017974 AAATTGAATTTCAACAAAGAATAAAAAAACATGTTAGTAATACATGAAATTCAATATATCCAAGT
1 AAATTGAATTTCAACAAAG-A-AAAAAAACATGTTAGTAATACATGAAATTCAATATATCCAAGT
2018039 CTAAAATACTTTATGAAATATTAATTATTGAAATTAAGTGCATATGCATAAAGTTTT-CCAAAAA
64 CTAAAATACTTTATGAAATA-TAATTATTG-AATTAA-TGCATATGCATAAAGTTTTCCCAAAAA
2018103 TGTTATGC
126 TGTTATGC
2018111 AAATTGAATTTCAAC-AAG-AAAAAAACATGTTAGTAATACATGAAATTCAATATATCCAAGTCT
1 AAATTGAATTTCAACAAAGAAAAAAAACATGTTAGTAATACATGAAATTCAATATATCCAAGTCT
2018174 AAAATACTTTATGAAATATAATTATTGAATTAATGCATATGCATAAAGTTTTCCCAAAAATGTTA
66 AAAATACTTTATGAAATATAATTATTGAATTAATGCATATGCATAAAGTTTTCCCAAAAATGTTA
2018239 TGC
131 TGC
2018242 A
1 A
2018243 TTTGAAATTT
Statistics
Matches: 131, Mismatches: 0, Indels: 8
0.94 0.00 0.06
Matches are distributed among these distances:
130 19 0.15
131 22 0.17
132 9 0.07
133 63 0.48
136 3 0.02
137 15 0.11
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.33
Consensus pattern (133 bp):
AAATTGAATTTCAACAAAGAAAAAAAACATGTTAGTAATACATGAAATTCAATATATCCAAGTCT
AAAATACTTTATGAAATATAATTATTGAATTAATGCATATGCATAAAGTTTTCCCAAAAATGTTA
TGC
Found at i:2020988 original size:20 final size:19
Alignment explanation
Indices: 2020939--2021012 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
2020929 GCAGCCTTCG
*
2020939 TGCATGGATGCACATCAGGA
1 TGCATCGATGCACAT-AGGA
*
2020959 TGTAATCGATGCACAGTAGGA
1 TG-CATCGATGCACA-TAGGA
*
2020980 TGCATCGATGCACATTAAGA
1 TGCATCGATGCACA-TAGGA
2021000 TGCATCGATGCAC
1 TGCATCGATGCAC
2021013 TAAGTGCATT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
20 30 0.64
21 16 0.34
22 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (19 bp):
TGCATCGATGCACATAGGA
Found at i:2021025 original size:18 final size:19
Alignment explanation
Indices: 2020939--2021021 Score: 80
Period size: 20 Copynumber: 4.3 Consensus size: 19
2020929 GCAGCCTTCG
* *
2020939 TGCATGGATGCACATCAGGA
1 TGCATCGATGCACAT-AAGA
* *
2020959 TGTAATCGATGCACAGTAGGA
1 TG-CATCGATGCACA-TAAGA
2020980 TGCATCGATGCACATTAAGA
1 TGCATCGATGCACA-TAAGA
2021000 TGCATCGATGCAC-TAAG-
1 TGCATCGATGCACATAAGA
2021017 TGCAT
1 TGCAT
2021022 TCGAAATGGA
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
17 5 0.09
18 4 0.07
20 30 0.54
21 16 0.29
22 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.24
Consensus pattern (19 bp):
TGCATCGATGCACATAAGA
Found at i:2021057 original size:20 final size:19
Alignment explanation
Indices: 2021032--2021088 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 19
2021022 TCGAAATGGA
2021032 GTGCATGGATGCACTGCATG
1 GTGCATGGATGCACTGCA-G
*
2021052 GTGCATCGATGCACTAGTGCAG
1 GTGCATGGATGCAC---TGCAG
2021074 GTGCATGGATGCACT
1 GTGCATGGATGCACT
2021089 TTGACACCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
19 1 0.03
20 13 0.41
22 14 0.44
23 4 0.12
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.25
Consensus pattern (19 bp):
GTGCATGGATGCACTGCAG
Found at i:2026983 original size:157 final size:158
Alignment explanation
Indices: 2026691--2027092 Score: 535
Period size: 157 Copynumber: 2.5 Consensus size: 158
2026681 TAAACCAATT
* * *
2026691 AACATTTCCAATGGGAGAGTTTATAGTGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCAAAA
1 AACATTTCCAATGGGAGAGTTCATAATGAGAAGAACTCAT-CAATGAGGGAGAAGAAGTTCATAA
* ** * * *
2026756 TAAGAAGAACTTGTTCAATATTGGCTCATCCATCGCATATGGATTTGGATCTACATCAATATTTT
65 TGAGAAGAACTTGTTCAACCTTGGCCCATCCATCGCATATGGAGTTGGATCTACATCAATACTTT
*
2026821 ATTCGAATCCATCACAGAATGAGGTGGATA
130 ATTCGAATCCATCAC-GAAGGAGGTGGATA
* *
2026851 AACATTTCCAATGGGAGAGTTCATAATGAGAAGAACTCATCAAAT-AAGG-G-AGAAGTTCATAT
1 AACATTTCCAATGGGAGAGTTCATAATGAGAAGAACTCATC-AATGAGGGAGAAGAAGTTCATAA
* * *
2026913 TGAGAAGAACATGTTCAACCTTGGCCCATCTATCGCATATGGAGTTGGATC-AGCAT-TATCACT
65 TGAGAAGAACTTGTTCAACCTTGGCCCATCCATCGCATATGGAGTTGGATCTA-CATCAAT-ACT
* * *
2026976 TTGTTCGATTCCATCACGAAGGAGGTGGATT
128 TTATTCGAATCCATCACGAAGGAGGTGGATA
* *
2027007 GACATTTCCAATGGGAGAGTTCATAATGAGAAGAACTCATTCGATGAGGGAGAAGAAGTTCATAA
1 AACATTTCCAATGGGAGAGTTCATAATGAGAAGAACTCA-TCAATGAGGGAGAAGAAGTTCATAA
2027072 TGAGAAGAACTTGTTCAACCT
65 TGAGAAGAACTTGTTCAACCT
2027093 CGGTTCGATT
Statistics
Matches: 212, Mismatches: 23, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
156 55 0.26
157 79 0.37
158 2 0.01
159 35 0.17
160 41 0.19
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (158 bp):
AACATTTCCAATGGGAGAGTTCATAATGAGAAGAACTCATCAATGAGGGAGAAGAAGTTCATAAT
GAGAAGAACTTGTTCAACCTTGGCCCATCCATCGCATATGGAGTTGGATCTACATCAATACTTTA
TTCGAATCCATCACGAAGGAGGTGGATA
Found at i:2027087 original size:20 final size:19
Alignment explanation
Indices: 2027025--2027088 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 19
2027015 CAATGGGAGA
2027025 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
* **
2027044 CATTCGATGAGGGAGAAGAA--
1 -GTTC-AT-AATGAGAAGAACT
2027064 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAAC-T
2027084 GTTCA
1 GTTCA
2027089 ACCTCGGTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
17 9 0.27
18 2 0.06
19 3 0.09
20 8 0.24
21 2 0.06
22 9 0.27
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.25
Consensus pattern (19 bp):
GTTCATAATGAGAAGAACT
Found at i:2027145 original size:156 final size:155
Alignment explanation
Indices: 2026691--2027168 Score: 459
Period size: 157 Copynumber: 3.0 Consensus size: 155
2026681 TAAACCAATT
* * * *
2026691 AACATTTCCAATGGGAGAGTTTATAGTGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCAAAA
1 AACATTTCCAATGGGAGAGTTCATAATGAGAAGAACTCATTCAATGAGGGAGAAGAAGTTCATAA
* ** * * * * *
2026756 TAAGAAGAACTTGTTCAATATTGGCTCATCCATCGCATATGGATTTGGATCTACATCAATATTTT
66 TGAGAAGAACTTGTTCAACCTTGG-TCATTCATCGCATATGGAGTTGGAACAACATC---ACTTT
* *
2026821 ATTCGAATCCATCACAGAATGAGGTGGATA
127 GTTCG-ATCCATCACAGAAGGAGGTGGATA
*
2026851 AACATTTCCAATGGGAGAGTTCATAATGAGAAGAACTCA-TCAAAT-AAGG-G-AGAAGTTCATA
1 AACATTTCCAATGGGAGAGTTCATAATGAGAAGAACTCATTC-AATGAGGGAGAAGAAGTTCATA
* * * **
2026912 TTGAGAAGAACATGTTCAACCTTGGCCCA-TCTATCGCATATGGAGTTGGATCAGCATTATCACT
65 ATGAGAAGAACTTGTTCAACCTTGG-TCATTC-ATCGCATATGGAGTTGGA--A-CAACATCACT
*
2026976 TTGTTCGATTCCATCAC-GAAGGAGGTGGATT
125 TTGTTCGA-TCCATCACAGAAGGAGGTGGATA
* *
2027007 GACATTTCCAATGGGAGAGTTCATAATGAGAAGAACTCATTCGATGAGGGAGAAGAAGTTCATAA
1 AACATTTCCAATGGGAGAGTTCATAATGAGAAGAACTCATTCAATGAGGGAGAAGAAGTTCATAA
* * * * * *
2027072 TGAGAAGAACTTGTTCAACCTCGGTTCGATTCAT-TCAGAAGGAGTTCGAACAACACCGACTTTG
66 TGAGAAGAACTTGTTCAACCTTGG-TC-ATTCATCGCATATGGAGTTGGAACAACATC-ACTTT-
* * * *
2027136 GCTC-ATCCATCACATAAGGAGTTGGATC
127 GTTCGATCCATCACAGAAGGAGGTGGATA
2027164 AACAT
1 AACAT
2027169 CAGCACTATG
Statistics
Matches: 262, Mismatches: 41, Indels: 33
0.78 0.12 0.10
Matches are distributed among these distances:
156 66 0.25
157 93 0.35
158 5 0.02
159 49 0.19
160 47 0.18
161 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (155 bp):
AACATTTCCAATGGGAGAGTTCATAATGAGAAGAACTCATTCAATGAGGGAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTGGTCATTCATCGCATATGGAGTTGGAACAACATCACTTTGTTC
GATCCATCACAGAAGGAGGTGGATA
Found at i:2027579 original size:24 final size:23
Alignment explanation
Indices: 2027535--2027580 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
2027525 ATTTTTCAAC
2027535 TATTATATATATTATAAAAATAT
1 TATTATATATATTATAAAAATAT
*
2027558 TATT-TATTTATTATTACAAAATA
1 TATTATATATATTA-TA-AAAATA
2027581 CCCAAACCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 8 0.40
23 6 0.30
24 6 0.30
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
TATTATATATATTATAAAAATAT
Found at i:2027622 original size:23 final size:23
Alignment explanation
Indices: 2027587--2027642 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
2027577 AATACCCAAA
2027587 CCAAACCCAATACCCAAACCCGGGC
1 CCAAA-CC-ATACCCAAACCCGGGC
* * *
2027612 CCGAACCATACTCAAACTCGGGC
1 CCAAACCATACCCAAACCCGGGC
2027635 CCAAACCA
1 CCAAACCA
2027643 AAAACCTAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 21 0.78
24 2 0.07
25 4 0.15
ACGTcount: A:0.36, C:0.45, G:0.12, T:0.07
Consensus pattern (23 bp):
CCAAACCATACCCAAACCCGGGC
Found at i:2028657 original size:15 final size:16
Alignment explanation
Indices: 2028639--2028668 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2028629 TGTTTGAATT
2028639 TATTTA-TTTAATTTC
1 TATTTATTTTAATTTC
2028654 TATTTATTTTAATTT
1 TATTTATTTTAATTT
2028669 GGTCCTTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTTATTTTAATTTC
Found at i:2037001 original size:16 final size:16
Alignment explanation
Indices: 2036980--2037012 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2036970 ATCACCGACA
*
2036980 AAAATTTACTATTCAC
1 AAAATTCACTATTCAC
2036996 AAAATTCACTATTCAC
1 AAAATTCACTATTCAC
2037012 A
1 A
2037013 TGAATAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATTCACTATTCAC
Found at i:2037832 original size:14 final size:14
Alignment explanation
Indices: 2037813--2037844 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
2037803 ATGAATTACA
2037813 TTTCTGGAAAACAT
1 TTTCTGGAAAACAT
2037827 TTTCTGGAAAACAT
1 TTTCTGGAAAACAT
2037841 TTTC
1 TTTC
2037845 CAGTGTTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (14 bp):
TTTCTGGAAAACAT
Found at i:2038357 original size:22 final size:20
Alignment explanation
Indices: 2038322--2038370 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
2038312 AGAATATAAC
*
2038322 AAAATTTCTCAAAAACAACAA
1 AAAATGTCTC-AAAACAACAA
* *
2038343 ATAAATGTCTTAAAAGAACAA
1 A-AAATGTCTCAAAACAACAA
2038364 AAAATGT
1 AAAATGT
2038371 ACTAAACATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 6 0.25
21 11 0.46
22 7 0.29
ACGTcount: A:0.59, C:0.12, G:0.06, T:0.22
Consensus pattern (20 bp):
AAAATGTCTCAAAACAACAA
Found at i:2039296 original size:22 final size:22
Alignment explanation
Indices: 2039266--2039307 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
2039256 AAGAACTATC
2039266 ATCTTTCATG-AATAACAAGAT
1 ATCTTTCATGTAATAACAAGAT
*
2039287 ATCTCTTCATGTCATAACAAG
1 ATCT-TTCATGTAATAACAAG
2039308 TTTACCATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 6 0.33
23 8 0.44
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (22 bp):
ATCTTTCATGTAATAACAAGAT
Found at i:2042152 original size:59 final size:60
Alignment explanation
Indices: 2042020--2042171 Score: 143
Period size: 59 Copynumber: 2.5 Consensus size: 60
2042010 AAATCATATG
* * * * * * * *
2042020 TCTCCAAACTATAATCC-TCATTTTAAATT-GATCCTTAAATTTTTTAATATTTTAATTTTA
1 TCTCCAAACTATGA-CCATCATTCTAAGTTAG-TCATTAAAATTTTGAACATTCTAATTTTA
*
2042080 TCTCCAAATTATGACTC-TCATTCTAA-TTAGTCATTAAAATTTTGAACATTCTAATTTTA
1 TCTCCAAACTATGAC-CATCATTCTAAGTTAGTCATTAAAATTTTGAACATTCTAATTTTA
*
2042139 TC-CCTAAACTATGACCATCTTTCTAAGTTAGTC
1 TCTCC-AAACTATGACCATCATTCTAAGTTAGTC
2042172 CCCAAACTTT
Statistics
Matches: 77, Mismatches: 10, Indels: 10
0.79 0.10 0.10
Matches are distributed among these distances:
58 3 0.04
59 46 0.60
60 28 0.36
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.45
Consensus pattern (60 bp):
TCTCCAAACTATGACCATCATTCTAAGTTAGTCATTAAAATTTTGAACATTCTAATTTTA
Found at i:2042517 original size:60 final size:60
Alignment explanation
Indices: 2042327--2042517 Score: 194
Period size: 60 Copynumber: 3.2 Consensus size: 60
2042317 TATACTTATT
* * ** * *
2042327 GTTTG-GGATGAAATTGGAATGTTCAAAAAGTTTAGGAACCAATTTAGAGGTAAG-GTCATA
1 GTTTGAGGATGAAATTGAAATGTT-AAAAAGTTTAGGGACCAATTTA-AAATGAGTATCATA
* *
2042387 GTTTGGGGATGAAATTGAAATGTTAAAAAGTTT-GAGGACTAATTTAAAATGA-TAGTCAT-
1 GTTTGAGGATGAAATTGAAATGTTAAAAAGTTTAG-GGACCAATTTAAAATGAGTA-TCATA
* * *
2042446 GTTTTAGGGATGAAATTGAAATATTTAAAAGTTTAGGGACCAATTTAAAATGAGTATCATA
1 GTTTGA-GGATGAAATTGAAATGTTAAAAAGTTTAGGGACCAATTTAAAATGAGTATCATA
*
2042507 CTTTGAGGATG
1 GTTTGAGGATG
2042518 TGTGATGCAA
Statistics
Matches: 109, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
59 8 0.07
60 77 0.71
61 24 0.22
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (60 bp):
GTTTGAGGATGAAATTGAAATGTTAAAAAGTTTAGGGACCAATTTAAAATGAGTATCATA
Found at i:2043453 original size:22 final size:22
Alignment explanation
Indices: 2043424--2043470 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2043414 ATACATAACC
*
2043424 TAAA-CATAGAATTTAAAAATA
1 TAAATCATAGAATTCAAAAATA
*
2043445 TAAATCATATAATTCAAAAATA
1 TAAATCATAGAATTCAAAAATA
2043467 -AAAT
1 TAAAT
2043471 TTAAACATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (22 bp):
TAAATCATAGAATTCAAAAATA
Found at i:2045459 original size:26 final size:26
Alignment explanation
Indices: 2045430--2045481 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
2045420 TCAAGTCGAA
*
2045430 CGGAAGGAAGC-TTCGGCACTTCCGAT
1 CGGAAGGAAGCATT-GACACTTCCGAT
*
2045456 CGGAAGGAGGCATTGACACTTCCGAT
1 CGGAAGGAAGCATTGACACTTCCGAT
2045482 TCAAGTTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 21 0.91
27 2 0.09
ACGTcount: A:0.25, C:0.25, G:0.31, T:0.19
Consensus pattern (26 bp):
CGGAAGGAAGCATTGACACTTCCGAT
Found at i:2045510 original size:36 final size:37
Alignment explanation
Indices: 2045463--2045568 Score: 144
Period size: 36 Copynumber: 2.9 Consensus size: 37
2045453 GATCGGAAGG
* * *
2045463 AGGCATTGACACTTCCGATTCAAGTTGAACGGTAT-A
1 AGGCATCGACACTTCCGATTCAAGTCGAACGGAATGA
*
2045499 AGGCATCGACACTTCCGATTCAAGTCGAATGGAATGA
1 AGGCATCGACACTTCCGATTCAAGTCGAACGGAATGA
* *
2045536 A-GCATCGGCACTTCCGATTCAAGTCAAACGGAA
1 AGGCATCGACACTTCCGATTCAAGTCGAACGGAA
2045569 GGATGTAGCG
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
36 60 0.97
37 2 0.03
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (37 bp):
AGGCATCGACACTTCCGATTCAAGTCGAACGGAATGA
Found at i:2046597 original size:22 final size:22
Alignment explanation
Indices: 2046557--2046598 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2046547 ACAAGTCCCA
* *
2046557 AATTCAGGAAGACTTGCAATTC
1 AATTCAGGAAAACTAGCAATTC
*
2046579 AATTCAGTAAAACTAGCAAT
1 AATTCAGGAAAACTAGCAAT
2046599 CTTATTAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (22 bp):
AATTCAGGAAAACTAGCAATTC
Found at i:2055124 original size:2 final size:2
Alignment explanation
Indices: 2055119--2055150 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2055109 ATAAAAAATG
2055119 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
2055151 GTGAGAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2055198 original size:15 final size:16
Alignment explanation
Indices: 2055167--2055200 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2055157 ATAAATAAAT
2055167 AAATAATTTTATTTAA
1 AAATAATTTTATTTAA
*
2055183 AAATACTTTT-TTTAA
1 AAATAATTTTATTTAA
2055198 AAA
1 AAA
2055201 GATAAAAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATAATTTTATTTAA
Found at i:2057171 original size:2 final size:2
Alignment explanation
Indices: 2057164--2057228 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
2057154 GGGACAAAAT
2057164 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2057206 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
2057229 GGTAAATTAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2059207 original size:2 final size:2
Alignment explanation
Indices: 2059202--2059227 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2059192 ATTTTTTTTA
2059202 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
2059228 TTAAATTAAG
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):
AT
Found at i:2062988 original size:21 final size:20
Alignment explanation
Indices: 2062962--2063005 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
2062952 GATTTCTGGG
* *
2062962 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCC-TT
2062983 CAAGGGGAACCGATACCCTT
1 CAAGGGGAACCGATACCCTT
2063003 CAA
1 CAA
2063006 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (20 bp):
CAAGGGGAACCGATACCCTT
Found at i:2063379 original size:24 final size:24
Alignment explanation
Indices: 2063335--2063382 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2063325 CCTATGTTTA
*
2063335 ATGCATGAATATGATTATATGTAT
1 ATGCATGAATATAATTATATGTAT
*
2063359 ATGCATGACATA-AATTGTATGTAT
1 ATGCATGA-ATATAATTATATGTAT
2063383 GCATGATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.40
Consensus pattern (24 bp):
ATGCATGAATATAATTATATGTAT
Found at i:2063875 original size:32 final size:32
Alignment explanation
Indices: 2063834--2063929 Score: 117
Period size: 32 Copynumber: 3.0 Consensus size: 32
2063824 GAGTCGAGGG
2063834 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
* *
2063866 TTTACCTATG-TCTTTC-GAGACATATGGATAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
2063897 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
2063929 T
1 T
2063930 ACCGAGGATC
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
31 25 0.47
32 28 0.53
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:2063920 original size:31 final size:30
Alignment explanation
Indices: 2063835--2063932 Score: 108
Period size: 31 Copynumber: 3.2 Consensus size: 30
2063825 AGTCGAGGGT
*
2063835 TTACCTATGTTCTACGGAACATATGGACAG
1 TTACCTATGTTCTAAGGAACATATGGACAG
*** *
2063865 TTTTACCTATG-TCTTTCGAGACATATGGATAG
1 --TTACCTATGTTCTAAGGA-ACATATGGACAG
2063897 TATACCTATGTTCTAAGGAACATATGGACAG
1 T-TACCTATGTTCTAAGGAACATATGGACAG
2063928 TTACC
1 TTACC
2063933 GAGGATCTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
30 5 0.09
31 25 0.45
32 25 0.45
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (30 bp):
TTACCTATGTTCTAAGGAACATATGGACAG
Found at i:2064046 original size:29 final size:30
Alignment explanation
Indices: 2063921--2064043 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
2063911 AAGGAACATA
2063921 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
2063951 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
*
2063981 TGGACAGTTATCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
2064011 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
2064040 TGGA
1 TGGA
2064044 TAGGTCCTTC
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
29 18 0.20
30 70 0.80
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:2064326 original size:2 final size:2
Alignment explanation
Indices: 2064316--2064377 Score: 106
Period size: 2 Copynumber: 31.0 Consensus size: 2
2064306 GTATGTGTGG
*
2064316 AT AT GT 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
*
2064358 AT AT AT AT AT AT AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT
2064378 GAAAGGTGCA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2067926 original size:21 final size:21
Alignment explanation
Indices: 2067900--2067944 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2067890 GATTTCTGGG
* *
2067900 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2067921 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2067942 CAA
1 CAA
2067945 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2068319 original size:24 final size:24
Alignment explanation
Indices: 2068275--2068322 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2068265 CCTATGTTTA
*
2068275 ATGCATGAATATGATTATATGTAT
1 ATGCATGAATATAATTATATGTAT
*
2068299 ATGCATGACATA-AATTGTATGTAT
1 ATGCATGA-ATATAATTATATGTAT
2068323 GCATGATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.40
Consensus pattern (24 bp):
ATGCATGAATATAATTATATGTAT
Found at i:2068816 original size:32 final size:32
Alignment explanation
Indices: 2068775--2068870 Score: 126
Period size: 32 Copynumber: 3.0 Consensus size: 32
2068765 GAGTCGAGGG
2068775 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
2068807 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
2068838 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
2068870 T
1 T
2068871 ACCGAGGATC
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
31 26 0.47
32 29 0.53
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:2068987 original size:29 final size:30
Alignment explanation
Indices: 2068862--2068984 Score: 212
Period size: 30 Copynumber: 4.1 Consensus size: 30
2068852 AAGGAACATA
2068862 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
2068892 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
2068922 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
2068952 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
2068981 TGGA
1 TGGA
2068985 TAGGTCCTTC
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
29 18 0.20
30 72 0.80
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:2072055 original size:138 final size:135
Alignment explanation
Indices: 2071863--2072277 Score: 466
Period size: 137 Copynumber: 3.0 Consensus size: 135
2071853 CCTAAATTAA
* *
2071863 AAGGACTAAATTGAAATCTAA-TCTAA-AGCGGAGGCTCTAATATTAA-CTTAAATTAATTTTAA
1 AAGGACTAAATTGAAAT-TAAGTCTAAGA-TGGA-GCTCTAATATTAATCAT-AATTAATTTTAA
* *
2071925 TCAATATTGCACTTTGAATAATTAAAGTGGAACCTCGAACAAAAGCGAGGACCAAATTAAGAATT
62 TCAATATTG-ACTTTGAATAATTAAATTGGAACCTCGAACAAAAGCGAGGACCAAATTAAAAATT
*
2071990 ATCTTAATTT
126 CTCTTAATTT
2072000 AAGGACTAAATGTGAAATTAAGTCTAAGATGGAGTCTCTAATATTAATCATAATTAATTTTAATC
1 AAGGACTAAAT-TGAAATTAAGTCTAAGATGGAG-CTCTAATATTAATCATAATTAATTTTAATC
* ** * *
2072065 AATTATTGA-TTTGAATAATTAAATTGAAAATTCGAGCAAAAGCGAAGACCAAATTAAAAATTCT
64 AA-TATTGACTTTGAATAATTAAATTGGAACCTCGAACAAAAGCGAGGACCAAATTAAAAATTCT
*
2072129 CCTAATTT
128 CTTAATTT
* * *
2072137 AAGGATTAAATATGAAATT-AGGCATAAGATGGAAGCTCTAATATTAATCCTAATTAATTTTAAT
1 AAGGACTAAAT-TGAAATTAAGTC-TAAGATGG-AGCTCTAATATTAATCATAATTAATTTTAAT
* * * * *
2072201 CAATTATGGACTATCGAATAATT-AATTCAGAACCTC-AAGCATAAGCGAGGACCAAATAAAAAA
63 CAA-TATTGACT-TTGAATAATTAAATT-GGAACCTCGAA-CAAAAGCGAGGACCAAATTAAAAA
*
2072264 TTCTCTTAAATT
124 TTCTCTTAATTT
2072276 AA
1 AA
2072278 AAGTTAAGGG
Statistics
Matches: 239, Mismatches: 27, Indels: 22
0.83 0.09 0.08
Matches are distributed among these distances:
136 3 0.01
137 131 0.55
138 51 0.21
139 54 0.23
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (135 bp):
AAGGACTAAATTGAAATTAAGTCTAAGATGGAGCTCTAATATTAATCATAATTAATTTTAATCAA
TATTGACTTTGAATAATTAAATTGGAACCTCGAACAAAAGCGAGGACCAAATTAAAAATTCTCTT
AATTT
Found at i:2072646 original size:27 final size:28
Alignment explanation
Indices: 2072611--2072665 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
2072601 TAAACAATTA
* *
2072611 AAAATTTTAA-GTAGAAATTAAAATAAT
1 AAAATTTTAACGGAAAAATTAAAATAAT
2072638 AAAATTTTAACGGGAAAAATTAAAATAA
1 AAAATTTTAAC-GGAAAAATTAAAATAA
2072666 CAATAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 10 0.42
29 14 0.58
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.29
Consensus pattern (28 bp):
AAAATTTTAACGGAAAAATTAAAATAAT
Found at i:2088333 original size:36 final size:36
Alignment explanation
Indices: 2088281--2088357 Score: 145
Period size: 36 Copynumber: 2.1 Consensus size: 36
2088271 TGTAGGTCAG
*
2088281 AATGGGAACAATGTTGCTCAGAGCAACACCGAAAAC
1 AATGAGAACAATGTTGCTCAGAGCAACACCGAAAAC
2088317 AATGAGAACAATGTTGCTCAGAGCAACACCGAAAAC
1 AATGAGAACAATGTTGCTCAGAGCAACACCGAAAAC
2088353 AATGA
1 AATGA
2088358 AAGTGCAAGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.14
Consensus pattern (36 bp):
AATGAGAACAATGTTGCTCAGAGCAACACCGAAAAC
Found at i:2088354 original size:90 final size:90
Alignment explanation
Indices: 2088236--2088411 Score: 244
Period size: 90 Copynumber: 2.0 Consensus size: 90
2088226 TGAAAATGTA
* * * * * *
2088236 AATGCTGCTCAGAGCAACACCAAAAACAATGAAACTGTAGGTCAGAATGGGAACAATGTTGCTCA
1 AATGCTGCTCAGAGCAACACCAAAAACAATGAAACTGCAAGTCAGAACGAGAACAATGCTACTCA
2088301 GAGCAACACCGAAAACAATGAGAAC
66 GAGCAACACCGAAAACAATGAGAAC
* * *
2088326 AATGTTGCTCAGAGCAACACCGAAAACAATGAAAGTGCAAGTCAGAACGAGAACAATGCTACTCA
1 AATGCTGCTCAGAGCAACACCAAAAACAATGAAACTGCAAGTCAGAACGAGAACAATGCTACTCA
* * *
2088391 GGGCAACACTGACAACAATGA
66 GAGCAACACCGAAAACAATGA
2088412 AAATGCAACT
Statistics
Matches: 74, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
90 74 1.00
ACGTcount: A:0.43, C:0.22, G:0.21, T:0.14
Consensus pattern (90 bp):
AATGCTGCTCAGAGCAACACCAAAAACAATGAAACTGCAAGTCAGAACGAGAACAATGCTACTCA
GAGCAACACCGAAAACAATGAGAAC
Found at i:2088555 original size:54 final size:54
Alignment explanation
Indices: 2088471--2088627 Score: 260
Period size: 54 Copynumber: 2.9 Consensus size: 54
2088461 GAAAATGCTG
* *
2088471 CTCAGAGCTACACCGAAAACAATGAAAATGCAGGTCAGAACGAGAACAAAGTCA
1 CTCAGAGCAACACCGACAACAATGAAAATGCAGGTCAGAACGAGAACAAAGTCA
* *
2088525 CTCAGAGCAACACCGACAACAATGACAATGCAGGTCAGAACGAGAACAAGGTCA
1 CTCAGAGCAACACCGACAACAATGAAAATGCAGGTCAGAACGAGAACAAAGTCA
* *
2088579 CTCAGAGTAACACCAACAACAATGAAAATGCAGGTCAGAACGAGAACAA
1 CTCAGAGCAACACCGACAACAATGAAAATGCAGGTCAGAACGAGAACAA
2088628 TGCTGCTCAG
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 96 1.00
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.10
Consensus pattern (54 bp):
CTCAGAGCAACACCGACAACAATGAAAATGCAGGTCAGAACGAGAACAAAGTCA
Found at i:2088637 original size:54 final size:54
Alignment explanation
Indices: 2088464--2089026 Score: 361
Period size: 60 Copynumber: 10.0 Consensus size: 54
2088454 TGTAAATGAA
* *
2088464 AATGCTGCTCAGAGCT-ACACCGAA-AACAATGAAAATGCAGGTCAGAACGAGAAC
1 AATGCTGCTCAGAG-TAACACC-AACAACAATGAAAATGCAAGTCAGAATGAGAAC
* * * * * * *
2088518 AAAG-TCACTCAGAGCAACACCGACAACAATGACAATGCAGGTCAGAACGAGAAC
1 AATGCT-GCTCAGAGTAACACCAACAACAATGAAAATGCAAGTCAGAATGAGAAC
* * * *
2088572 AA-GGTCACTCAGAGTAACACCAACAACAATGAAAATGCAGGTCAGAACGAGAAC
1 AATGCT-GCTCAGAGTAACACCAACAACAATGAAAATGCAAGTCAGAATGAGAAC
***** *
2088626 AATGCTGCTCAGAG---CGGTGCCAACAATGAAAATGCAAGTCAGAATGAGAAT
1 AATGCTGCTCAGAGTAACACCAACAACAATGAAAATGCAAGTCAGAATGAGAAC
* * * *
2088677 AATTCTTCTCAGAGCTACAACGACAGCAACAACAATGAAAATGCAAGTCAGAACGAGAAT
1 AATGCTGCTCAGAG-T--AAC-AC--CAACAACAATGAAAATGCAAGTCAGAATGAGAAC
* * * * * *
2088737 AATGCTTCTCAGAGCTACAACGACAGCAACAACAGTGAAAAGGCAAGCCAAAATGAGGAC
1 AATGCTGCTCAGAG-T--AAC-AC--CAACAACAATGAAAATGCAAGTCAGAATGAGAAC
* * * * *
2088797 AATCATGCTGTTCAGAGCAATACCAACACCAATGAAAATGCAAGTCAGAATGAGAAT
1 -A--ATGCTGCTCAGAGTAACACCAACAACAATGAAAATGCAAGTCAGAATGAGAAC
* * *
2088854 AATGCTTCTCAGAGCTACAACGACAACAACAACAACGAAAATGCAAGTCAAAATGAGAAC
1 AATGCTGCTCAGAG-T--AAC-AC--CAACAACAATGAAAATGCAAGTCAGAATGAGAAC
* * *
2088914 AATGATGTCGTTCAGAGCAATACCAACAACAATGAAAACT-CAAGTCAGAATGAGAATAAC
1 AATGCTG-C--TCAGAGTAACACCAACAACAATGAAAA-TGCAAGTCAGAATGAG---AAC
* * * * *
2088974 GATGCTGTTCAGAGCAATACCAACAACAACGAAAACT-CAAGTCAGAATGAGAA
1 AATGCTGCTCAGAGTAACACCAACAACAATGAAAA-TGCAAGTCAGAATGAGAA
2089027 TAACGATGCC
Statistics
Matches: 416, Mismatches: 63, Indels: 60
0.77 0.12 0.11
Matches are distributed among these distances:
51 41 0.10
53 3 0.01
54 115 0.28
55 2 0.00
56 1 0.00
57 99 0.24
58 3 0.01
59 4 0.01
60 129 0.31
61 2 0.00
63 17 0.04
ACGTcount: A:0.45, C:0.21, G:0.19, T:0.15
Consensus pattern (54 bp):
AATGCTGCTCAGAGTAACACCAACAACAATGAAAATGCAAGTCAGAATGAGAAC
Found at i:2088707 original size:108 final size:107
Alignment explanation
Indices: 2088471--2088751 Score: 270
Period size: 108 Copynumber: 2.6 Consensus size: 107
2088461 GAAAATGCTG
* *
2088471 CTCAGAGCTACACCGA-A-AACAATGAAAATGCAGGTCAGAACGAGAACAAAG-TCACTCAGAGC
1 CTCAGAGCTACAACGACACAACAATGAAAATGCAGGTCAGAACGAGAACAATGCT-ACTCAGAG-
* *
2088533 AACACCGACAACAATGACAATGCAGGTCAGAACGAGAACAAGGTCA
64 --CACCGACAACAATGAAAATGCAAGTCAGAACGAGAACAAGGTCA
* *
2088579 CTCAGAG-TA-ACACCA-ACAACAATGAAAATGCAGGTCAGAACGAGAACAATGCTGCTCAGAGC
1 CTCAGAGCTACA-ACGACACAACAATGAAAATGCAGGTCAGAACGAGAACAATGCTACTCAGAGC
*** * * * * *
2088641 GGTGCCAACAATGAAAATGCAAGTCAGAATGAGAATAA-TTCTT
65 ACCGACAACAATGAAAATGCAAGTCAGAACGAGAACAAGGTC-A
* * *
2088684 CTCAGAGCTACAACGACAGCAACAACAATGAAAATGCAAGTCAGAACGAGAATAATGCTTCTCAG
1 CTCAGAGCTACAACG--A-C-ACAACAATGAAAATGCAGGTCAGAACGAGAACAATGCTACTCAG
2088749 AGC
62 AGC
2088752 TACAACGACA
Statistics
Matches: 144, Mismatches: 18, Indels: 19
0.80 0.10 0.10
Matches are distributed among these distances:
104 2 0.01
105 38 0.26
106 5 0.03
107 6 0.04
108 48 0.33
109 1 0.01
111 44 0.31
ACGTcount: A:0.43, C:0.22, G:0.21, T:0.14
Consensus pattern (107 bp):
CTCAGAGCTACAACGACACAACAATGAAAATGCAGGTCAGAACGAGAACAATGCTACTCAGAGCA
CCGACAACAATGAAAATGCAAGTCAGAACGAGAACAAGGTCA
Found at i:2088834 original size:57 final size:57
Alignment explanation
Indices: 2088763--2089102 Score: 323
Period size: 57 Copynumber: 5.9 Consensus size: 57
2088753 ACAACGACAG
* * * * *
2088763 CAACAACAGTGAAAAGGCAAGCCAAAATGAGGACAATC-ATGCTGTTCAGAGCAATAC
1 CAACAACAATGAAAACGCAAGTCAGAATGAGAACAA-CGATGCTGTTCAGAGCAATAC
* * * *
2088820 CAACACCAATGAAAATGCAAGTCAGAATGAGAA-TA--ATGCT-TCTCAGAGCTACAACGAC
1 CAACAACAATGAAAACGCAAGTCAGAATGAGAACAACGATGCTGT-TCAGAG---CAA-TAC
* * * *
2088878 AACAACAACAACGAAAATGCAAGTCAAAATGAGAACAATGATG-TCGTTCAGAGCAATAC
1 --CAACAACAATGAAAACGCAAGTCAGAATGAGAACAACGATGCT-GTTCAGAGCAATAC
* *
2088937 CAACAACAATGAAAACTCAAGTCAGAATGAGAATAACGATGCTGTTCAGAGCAATAC
1 CAACAACAATGAAAACGCAAGTCAGAATGAGAACAACGATGCTGTTCAGAGCAATAC
* * * *
2088994 CAACAACAACGAAAACTCAAGTCAGAATGAGAATAACGATGCCGTTCAGAGCAATAC
1 CAACAACAATGAAAACGCAAGTCAGAATGAGAACAACGATGCTGTTCAGAGCAATAC
** * ** * *
2089051 CAACAGTAATGAAAACTCAAACCAGAATGAGAACAACAATGCCGTTCAGAGC
1 CAACAACAATGAAAACGCAAGTCAGAATGAGAACAACGATGCTGTTCAGAGC
2089103 TTCAACGACA
Statistics
Matches: 242, Mismatches: 28, Indels: 26
0.82 0.09 0.09
Matches are distributed among these distances:
53 1 0.00
54 11 0.05
56 1 0.00
57 179 0.74
58 3 0.01
59 2 0.01
60 33 0.14
61 1 0.00
62 1 0.00
63 9 0.04
64 1 0.00
ACGTcount: A:0.46, C:0.21, G:0.18, T:0.15
Consensus pattern (57 bp):
CAACAACAATGAAAACGCAAGTCAGAATGAGAACAACGATGCTGTTCAGAGCAATAC
Found at i:2088846 original size:117 final size:117
Alignment explanation
Indices: 2088703--2089083 Score: 433
Period size: 117 Copynumber: 3.3 Consensus size: 117
2088693 ACAACGACAG
* *
2088703 CAACAACAATGAAAATGCAAGTCAGAACGAGAATAATGCTTCTCAGAGCTACAACGACAGCAACA
1 CAACAACAATGAAAATGCAAGTCAGAATGAGAATAATGCTTCTCAGAGCTACAACGACAACAACA
** *
2088768 ACAGTGAAAAGGCAAGCCAAAATGAGGACAATCATG-CTGTTCAGAGCAATAC
66 ACAACGAAAAGGCAAGCCAAAATGAGAACAATCATGTC-GTTCAGAGCAATAC
*
2088820 CAACACCAATGAAAATGCAAGTCAGAATGAGAATAATGCTTCTCAGAGCTACAACGACAACAACA
1 CAACAACAATGAAAATGCAAGTCAGAATGAGAATAATGCTTCTCAGAGCTACAACGACAACAACA
* * *
2088885 ACAACGAAAATGCAAGTCAAAATGAGAACAATGATGTCGTTCAGAGCAATAC
66 ACAACGAAAAGGCAAGCCAAAATGAGAACAATCATGTCGTTCAGAGCAATAC
*
2088937 CAACAACAATGAAAACT-CAAGTCAGAATGAGAATAACGATGCTGT-TCAGAG---CAA-TAC--
1 CAACAACAATGAAAA-TGCAAGTCAGAATGAGAAT-A--ATGCT-TCTCAGAGCTACAACGACAA
** * * * *
2088994 CAACAACAACGAAAACTCAAGTCAGAATGAGAATAA-CGATGCCGTTCAGAGCAATAC
61 CAACAACAACGAAAAGGCAAGCCAAAATGAGAACAATC-ATGTCGTTCAGAGCAATAC
** **
2089051 CAACAGTAATGAAAACT-CAAACCAGAATGAGAA
1 CAACAACAATGAAAA-TGCAAGTCAGAATGAGAA
2089084 CAACAATGCC
Statistics
Matches: 236, Mismatches: 21, Indels: 17
0.86 0.08 0.06
Matches are distributed among these distances:
114 79 0.33
116 2 0.01
117 140 0.59
118 3 0.01
120 11 0.05
121 1 0.00
ACGTcount: A:0.46, C:0.21, G:0.18, T:0.15
Consensus pattern (117 bp):
CAACAACAATGAAAATGCAAGTCAGAATGAGAATAATGCTTCTCAGAGCTACAACGACAACAACA
ACAACGAAAAGGCAAGCCAAAATGAGAACAATCATGTCGTTCAGAGCAATAC
Found at i:2093243 original size:161 final size:160
Alignment explanation
Indices: 2092974--2093291 Score: 564
Period size: 161 Copynumber: 2.0 Consensus size: 160
2092964 TATTCCACAG
* * *
2092974 GAAAATCGTTGAGAATGGTGACTATATGATCTATATCTGAAATGGGACTGCCACACGTGGCTAGA
1 GAAAATCGTTGAGAATGGTAACCATATGATCTATATCTGAAATGGGACTGCCACAAGTGGCTAGA
* *
2093039 AGATCACAAATCTCTTTAATATCCATCGTGTAATTCCTCATGGACTAATTGCCTTTTTTCATTGA
66 AGATCAAAAATCTCTTTAACATCCATCGTGTAATTCCTCATGGACTAATTGCCTTTTTTCATTGA
2093104 CCTAAGGTGACAGTGTAGAGCCATGATACA
131 CCTAAGGTGACAGTGTAGAGCCATGATACA
2093134 GAAAGATCGTTGAGAATGGTAACCATATGATCTATATCTGAAATGGGACTGCCACAAGTGGCTAG
1 GAAA-ATCGTTGAGAATGGTAACCATATGATCTATATCTGAAATGGGACTGCCACAAGTGGCTAG
* *
2093199 AAGATGAAAAATCTCTTTAACATCCATCGTGTAATTCCTCATGGACTGATTGCCTTTTTTCATTG
65 AAGATCAAAAATCTCTTTAACATCCATCGTGTAATTCCTCATGGACTAATTGCCTTTTTTCATTG
2093264 ACCTAAGGTGACAGTGTAGAGCCATGAT
130 ACCTAAGGTGACAGTGTAGAGCCATGAT
2093292 CTTTGTTGTG
Statistics
Matches: 150, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
160 4 0.03
161 146 0.97
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (160 bp):
GAAAATCGTTGAGAATGGTAACCATATGATCTATATCTGAAATGGGACTGCCACAAGTGGCTAGA
AGATCAAAAATCTCTTTAACATCCATCGTGTAATTCCTCATGGACTAATTGCCTTTTTTCATTGA
CCTAAGGTGACAGTGTAGAGCCATGATACA
Found at i:2095123 original size:2 final size:2
Alignment explanation
Indices: 2095116--2095159 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2095106 AATTTAAAGA
2095116 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
2095158 AT
1 AT
2095160 TTAAATAACA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2095375 original size:107 final size:106
Alignment explanation
Indices: 2095169--2095375 Score: 247
Period size: 107 Copynumber: 1.9 Consensus size: 106
2095159 TTTAAATAAC
* * * **
2095169 ATATTTATTTATTTAGAAATATCAGAAAAGGGCTTCTAGGTACTTTAAGACAGCTCTTTCTTTTG
1 ATATTTATTTATTTAAAAATATCAGAAAAGGGCTTCTAGGTACTTTAAGACAGCTATTTCCTTCA
**
2095234 ATATTAAAAAATAATAATAATAAATTATTTTAATATAGTAAG
66 ATATTAAAAAATAATAATAATAAA-TATCATAATATAGTAAG
* * ** *
2095276 ATATTTATTTATTTAAAAATATTAGAAAAGGGCTTCTAGTTGTTTTAAGACAGTTATTTCCTTCA
1 ATATTTATTTATTTAAAAATATCAGAAAAGGGCTTCTAGGTACTTTAAGACAGCTATTTCCTTCA
*
2095341 ATATTTAAAAATAAATAAATAACTAAA-A-CATAATA
66 ATATTAAAAAAT-AAT-AATAA-TAAATATCATAATA
2095376 ATAAAATAAA
Statistics
Matches: 84, Mismatches: 13, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
107 71 0.85
108 4 0.05
109 5 0.06
110 4 0.05
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.40
Consensus pattern (106 bp):
ATATTTATTTATTTAAAAATATCAGAAAAGGGCTTCTAGGTACTTTAAGACAGCTATTTCCTTCA
ATATTAAAAAATAATAATAATAAATATCATAATATAGTAAG
Found at i:2096777 original size:16 final size:17
Alignment explanation
Indices: 2096715--2096777 Score: 69
Period size: 16 Copynumber: 3.8 Consensus size: 17
2096705 TGTAATATAT
*
2096715 ATATATATATATTTAATA
1 ATATAT-TATAATTAATA
* *
2096733 ATAAATAATAA-TAATA
1 ATATATTATAATTAATA
2096749 ATATATTAT-ATTAATA
1 ATATATTATAATTAATA
2096765 AT-TATTATAATTA
1 ATATATTATAATTA
2096778 TTATTATGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
15 7 0.18
16 23 0.61
17 3 0.08
18 5 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATATTATAATTAATA
Found at i:2097313 original size:227 final size:224
Alignment explanation
Indices: 2096911--2097391 Score: 840
Period size: 227 Copynumber: 2.1 Consensus size: 224
2096901 AAATGTTTGA
* *
2096911 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTCTTTGAAAACATCAAAAAGCTCCCG
*
2096976 AAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGCCTAAGGCTTTGAAAACATCAAAAAG
66 AAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGCCGAAGGCTTTGAAAACATCAAAAAG
2097041 CTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAA
131 CTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAA
2097106 ACATCAAAAAGCTCCCGAAGGCTTTTTAG
196 ACATCAAAAAGCTCCCGAAGGCTTTTTAG
* *
2097135 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGG-CTTTGAAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTCTTTGAAAACATCAAAAAGCTCCCG
2097199 AAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGC-TTGAAAACATCA
66 AAGGCTTTTTGGAAACATCATGCACTGTAGGACTTAC--A-G--CCGAAGGCTTTGAAAACATCA
2097263 AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTT
126 AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTT
*
2097328 TGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
191 TGAAAACATCAAAAAGCTCCCGAAGGCTTTTTAG
*
2097362 AAACATCATGCACTGTAGGACTTACAGATG
1 AAACATCATGCACTGAAGGACTTACAGATG
2097392 TAGGAAATAG
Statistics
Matches: 245, Mismatches: 7, Indels: 7
0.95 0.03 0.03
Matches are distributed among these distances:
223 61 0.25
224 36 0.15
225 1 0.00
226 1 0.00
227 139 0.57
228 7 0.03
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (224 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTCTTTGAAAACATCAAAAAGCTCCCG
AAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGCCGAAGGCTTTGAAAACATCAAAAAG
CTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAA
ACATCAAAAAGCTCCCGAAGGCTTTTTAG
Found at i:2097337 original size:151 final size:151
Alignment explanation
Indices: 2096906--2097391 Score: 847
Period size: 151 Copynumber: 3.2 Consensus size: 151
2096896 GATGAAAATG
* * * *
2096906 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGG--CTTGAAAACATCAAAAAGC
2096971 TCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTAC--A-G--CCTAAGGCTTTGAAAA
64 TCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAA
2097031 CATCAAAAAGCTCCCGAAGGCTT
129 CATCAAAAAGCTCCCGAAGGCTT
*
2097054 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGC-TTGAAAACATCAAAAAGCT
* *
2097119 CCCGAAGGCTTTTTAGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
65 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
2097184 ATCAAAAAGCTCCCGAAGGCTT
130 ATCAAAAAGCTCCCGAAGGCTT
2097206 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTGAAAACATCAAAAAGCTC
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTGAAAACATCAAAAAGCTC
2097271 CCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACA
66 CCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACA
2097336 TCAAAAAGCTCCCGAAGGCTT
131 TCAAAAAGCTCCCGAAGGCTT
2097357 TTTGGAAACATCATGCACTGTAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATG
2097392 TAGGAAATAG
Statistics
Matches: 322, Mismatches: 10, Indels: 9
0.94 0.03 0.03
Matches are distributed among these distances:
147 58 0.18
148 40 0.12
149 1 0.00
150 1 0.00
151 139 0.43
152 83 0.26
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.23
Consensus pattern (151 bp):
TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTGAAAACATCAAAAAGCTC
CCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACA
TCAAAAAGCTCCCGAAGGCTT
Found at i:2097418 original size:76 final size:76
Alignment explanation
Indices: 2096906--2097391 Score: 849
Period size: 76 Copynumber: 6.5 Consensus size: 76
2096896 GATGAAAATG
* * * * *
2096906 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGG-CTTTGAAAACATCAAAAAGC
2096971 TCCCGAAGGCTT
65 TCCCGAAGGCTT
2096983 TTTGGAAACATCATGCACTGTAGGACTTAC--A-G--CCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
2097043 CCCGAAGGCTT
66 CCCGAAGGCTT
2097054 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
2097119 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
2097130 TTTAGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
2097195 CCCGAAGGCTT
66 CCCGAAGGCTT
*
2097206 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGC-TTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
2097270 CCCGAAGGCTT
66 CCCGAAGGCTT
2097281 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
2097346 CCCGAAGGCTT
66 CCCGAAGGCTT
2097357 TTTGGAAACATCATGCACTGTAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATG
2097392 TAGGAAATAG
Statistics
Matches: 392, Mismatches: 11, Indels: 13
0.94 0.03 0.03
Matches are distributed among these distances:
71 61 0.16
72 6 0.02
73 1 0.00
74 2 0.01
75 75 0.19
76 220 0.56
77 27 0.07
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.23
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:2097641 original size:184 final size:183
Alignment explanation
Indices: 2097332--2097699 Score: 657
Period size: 184 Copynumber: 2.0 Consensus size: 183
2097322 AGGCTTTGAA
* *
2097332 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGTAGGA
1 AACATCAAAAAGCTACCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGTAGGA
2097397 AATAGTTTAATAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCA-TTTTAG
66 AATAGTTTAATAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTAG
2097461 AAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAAC
131 AAAAGATAAAATGAGAAACTATGGAAATCG-TTT-TCATTATTTTTCAAAATAAC
*
2097516 AACATCAAAAAGCTACCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGTGGGA
1 AACATCAAAAAGCTACCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGTAGGA
*
2097581 AATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTAG
66 AATAGTTTAATAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTAG
**
2097646 AAAAGATTGAATGAGAAACTATGGAAATCGTTTTCATTATTTTTCAAAATAAC
131 AAAAGATAAAATGAGAAACTATGGAAATCGTTTTCATTATTTTTCAAAATAAC
2097699 A
1 A
2097700 TGTTGATTGG
Statistics
Matches: 177, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
183 21 0.12
184 122 0.69
185 34 0.19
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.32
Consensus pattern (183 bp):
AACATCAAAAAGCTACCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGTAGGA
AATAGTTTAATAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTAG
AAAAGATAAAATGAGAAACTATGGAAATCGTTTTCATTATTTTTCAAAATAAC
Found at i:2098277 original size:22 final size:22
Alignment explanation
Indices: 2098249--2098303 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
2098239 CATAAAGCTT
2098249 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
2098271 TCATCTTTAAAAAGAGACTCTA
1 TCATCTTTGAAAAGAGAATCTA
2098293 TCATCTTTGAA
1 TCATCTTTGAA
2098304 GAGTATAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:2103076 original size:16 final size:16
Alignment explanation
Indices: 2103055--2103108 Score: 72
Period size: 16 Copynumber: 3.3 Consensus size: 16
2103045 TCAATTTTCC
2103055 TCTTTTTTTTCTTTTT
1 TCTTTTTTTTCTTTTT
**
2103071 TCTTTTTCATCTTTTT
1 TCTTTTTTTTCTTTTT
*
2103087 TCTTTTTTTTTCTTTAT
1 TC-TTTTTTTTCTTTTT
2103104 TCTTT
1 TCTTT
2103109 CTTTGCTGGA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 19 0.59
17 13 0.41
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (16 bp):
TCTTTTTTTTCTTTTT
Found at i:2103077 original size:25 final size:26
Alignment explanation
Indices: 2103049--2103101 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
2103039 CTTGATTCAA
*
2103049 TTTTCCTCTTTTTT-TTCTTTTTTCT
1 TTTTCATCTTTTTTCTTCTTTTTTCT
*
2103074 TTTTCATCTTTTTTCTTTTTTTTTCT
1 TTTTCATCTTTTTTCTTCTTTTTTCT
2103100 TT
1 TT
2103102 ATTCTTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (26 bp):
TTTTCATCTTTTTTCTTCTTTTTTCT
Found at i:2103122 original size:26 final size:26
Alignment explanation
Indices: 2103093--2103145 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
2103083 TTTTTCTTTT
2103093 TTTTTCTTTATTCTTTCTTTGCTGGA
1 TTTTTCTTTATTCTTTCTTTGCTGGA
*
2103119 TTTTTCTTTTTTCTTTCTTTGCTGGA
1 TTTTTCTTTATTCTTTCTTTGCTGGA
2103145 T
1 T
2103146 GAGTATAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.06, C:0.15, G:0.11, T:0.68
Consensus pattern (26 bp):
TTTTTCTTTATTCTTTCTTTGCTGGA
Found at i:2103134 original size:7 final size:7
Alignment explanation
Indices: 2103059--2103112 Score: 56
Period size: 7 Copynumber: 7.4 Consensus size: 7
2103049 TTTTCCTCTT
2103059 TTTTTTC
1 TTTTTTC
2103066 TTTTTTC
1 TTTTTTC
2103073 TTTTTCATC
1 TTTTT--TC
2103082 TTTTTTC
1 TTTTTTC
2103089 TTTTTT-
1 TTTTTTC
*
2103095 TTTCTTTA
1 TTT-TTTC
*
2103103 TTCTTTC
1 TTTTTTC
2103110 TTT
1 TTT
2103113 GCTGGATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
6 3 0.08
7 28 0.70
8 2 0.05
9 7 0.17
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTTC
Found at i:2108885 original size:2 final size:2
Alignment explanation
Indices: 2108878--2108924 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2108868 AATTTAAAGA
2108878 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
2108920 AT AT A
1 AT AT A
2108925 AATAACATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2109215 original size:16 final size:16
Alignment explanation
Indices: 2109196--2109244 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
2109186 ATAATATTGT
2109196 AAATAAATAATGATTA
1 AAATAAATAATGATTA
2109212 AAATAAAATAA--ATTA
1 AAAT-AAATAATGATTA
*
2109227 AAA-ATATAATG-TTA
1 AAATAAATAATGATTA
2109241 AAAT
1 AAAT
2109245 GTAGAATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
13 5 0.18
14 6 0.21
15 7 0.25
16 4 0.14
17 6 0.21
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (16 bp):
AAATAAATAATGATTA
Found at i:2110401 original size:3 final size:3
Alignment explanation
Indices: 2110393--2110443 Score: 57
Period size: 3 Copynumber: 16.3 Consensus size: 3
2110383 TATATATATT
* * *
2110393 TAA TAA TAAA TAA TAA TAA TAA TAA TATA TTA TAT TAA TAA TAA TTA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
2110440 TAA T
1 TAA T
2110444 TATTATTATA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 35 0.88
4 5 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:2110404 original size:22 final size:20
Alignment explanation
Indices: 2110378--2110441 Score: 77
Period size: 19 Copynumber: 3.5 Consensus size: 20
2110368 ATGTAATTTG
2110378 TAATATATATATATTTAATAA
1 TAATATATATATA-TTAATAA
2110399 TAA-ATA-ATA-A-TAATAA
1 TAATATATATATATTAATAA
2110415 TAATATAT-TATATTAATAA
1 TAATATATATATATTAATAA
2110434 TAAT-TATA
1 TAATATATA
2110442 ATTATTATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
16 9 0.24
17 5 0.13
18 5 0.13
19 13 0.34
20 3 0.08
21 3 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TAATATATATATATTAATAA
Found at i:2110413 original size:31 final size:31
Alignment explanation
Indices: 2110378--2110443 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
2110368 ATGTAATTTG
2110378 TAAT-ATATATATATT-TAATAATAAATAATAA
1 TAATAATA-ATATATTATAATAAT-AATAATAA
* *
2110409 TAATAATAATATATTATATTAATAATAATTA
1 TAATAATAATATATTATAATAATAATAATAA
2110440 TAAT
1 TAAT
2110444 TATTATTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 22 0.71
32 9 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
TAATAATAATATATTATAATAATAATAATAA
Found at i:2110445 original size:16 final size:16
Alignment explanation
Indices: 2110396--2110445 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
2110386 ATATATTTAA
*
2110396 TAATAAATAATAATAA-
1 TAAT-AATAATTATAAT
2110412 TAATAATATATTAT-AT
1 TAATAATA-ATTATAAT
2110428 TAATAATAATTATAAT
1 TAATAATAATTATAAT
2110444 TA
1 TA
2110446 TTATTATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
15 10 0.33
16 20 0.67
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAATAATAATTATAAT
Found at i:2110450 original size:22 final size:22
Alignment explanation
Indices: 2110406--2110451 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
2110396 TAATAAATAA
2110406 TAATAATAATAATATATTATAT
1 TAATAATAATAATATATTATAT
*
2110428 TAATAATAATTATA-ATTATTAT
1 TAATAATAATAATATATTA-TAT
2110450 TA
1 TA
2110452 TAAAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TAATAATAATAATATATTATAT
Found at i:2114480 original size:51 final size:51
Alignment explanation
Indices: 2114419--2114525 Score: 187
Period size: 51 Copynumber: 2.1 Consensus size: 51
2114409 AACATATTAA
*
2114419 TTTTTATTTTAATCATTAAATTGATTATTTTAGTAGAAATTTTATTAATTT
1 TTTTTATTTTAATCATTAAATTGATTATTTTAATAGAAATTTTATTAATTT
* *
2114470 TTTTTATTTTAATCATTAACTTGATTGTTTTAATAGAAATTTTATTAATTT
1 TTTTTATTTTAATCATTAAATTGATTATTTTAATAGAAATTTTATTAATTT
2114521 TTTTT
1 TTTTT
2114526 TAAAATTTTG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.61
Consensus pattern (51 bp):
TTTTTATTTTAATCATTAAATTGATTATTTTAATAGAAATTTTATTAATTT
Found at i:2116259 original size:14 final size:14
Alignment explanation
Indices: 2116213--2116259 Score: 76
Period size: 14 Copynumber: 3.4 Consensus size: 14
2116203 TGCTGGGCAT
2116213 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
2116227 CCAAGGCCATCCGA
1 CCGAGGCCATCCGA
2116241 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
2116255 ACGAG
1 CCGAG
2116260 CTATGCGAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.26, C:0.40, G:0.28, T:0.06
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:2116293 original size:33 final size:33
Alignment explanation
Indices: 2116241--2116325 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 33
2116231 GGCCATCCGA
* * * *
2116241 CCGAGGCCATCCGAACGAGCTATGCGAGGGCAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
2116274 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
2116307 CCGAGGG-AAGCCGAGCGAG
1 CCGAGGGCAA-CCGAGCGAG
2116326 GGTAGGTCGC
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
32 2 0.04
33 45 0.96
ACGTcount: A:0.26, C:0.27, G:0.39, T:0.08
Consensus pattern (33 bp):
CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
Found at i:2116375 original size:29 final size:29
Alignment explanation
Indices: 2116329--2116413 Score: 152
Period size: 29 Copynumber: 2.9 Consensus size: 29
2116319 GAGCGAGGGT
* *
2116329 AGGTCGCCCGGAGTGCATGGCGTCCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
2116358 AGGTCGCCCGGAGGGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
2116387 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
2116414 TGTGTTGGGA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.19, C:0.31, G:0.38, T:0.13
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Done.