Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007853.1 Hibiscus syriacus cultivar Beakdansim tig00110213_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: 2309479
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 8
Found at i:1711 original size:14 final size:14
Alignment explanation
Indices: 1692--1748 Score: 69
Period size: 14 Copynumber: 3.8 Consensus size: 14
1682 ATGCGAAATG
1692 AAATCGCAACGACA
1 AAATCGCAACGACA
*
1706 AAATCGCAACGCGAAA
1 AAATCGCAA--CGACA
1722 TGAAATCGCAACGACA
1 --AAATCGCAACGACA
1738 AAATCGCAACG
1 AAATCGCAACG
1749 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.47, C:0.26, G:0.18, T:0.09
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:1720 original size:32 final size:32
Alignment explanation
Indices: 1676--1765 Score: 162
Period size: 32 Copynumber: 2.8 Consensus size: 32
1666 GGAAATGGCT
*
1676 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1708 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1740 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATG-AAATCGCAA
1766 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 47 0.84
33 9 0.16
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:1759 original size:19 final size:19
Alignment explanation
Indices: 1637--1770 Score: 76
Period size: 20 Copynumber: 7.6 Consensus size: 19
1627 TAGTTTACTT
* **
1637 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
1657 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
1677 TCGCAATGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
1695 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
1709 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
1727 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
1741 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1760 TCGCAATGCGA
1 TCGCAACGCGA
1771 TTTGTGTTCG
Statistics
Matches: 91, Mismatches: 10, Indels: 27
0.71 0.08 0.21
Matches are distributed among these distances:
14 20 0.22
16 8 0.09
18 18 0.20
19 20 0.22
20 24 0.26
21 1 0.01
ACGTcount: A:0.43, C:0.24, G:0.21, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1787 original size:18 final size:18
Alignment explanation
Indices: 1766--1825 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
1756 AAAATCGCAA
1766 TGCGATTTGTGTTCGCGT
1 TGCGATTTGTGTTCGCGT
1784 TGCGATTT-TG-T--CGT
1 TGCGATTTGTGTTCGCGT
*
1798 TGCGATTTCAT-TTCGCGT
1 TGCGATTT-GTGTTCGCGT
1816 TGCGATTTGT
1 TGCGATTTGT
1826 CGTTGCGATT
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
14 11 0.31
16 3 0.08
17 3 0.08
18 19 0.53
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTGTGTTCGCGT
Found at i:1828 original size:31 final size:32
Alignment explanation
Indices: 1777--1886 Score: 186
Period size: 31 Copynumber: 3.4 Consensus size: 32
1767 GCGATTTGTG
1777 TTCGCGTTGCGATTTTGTCGTTGCGATTTCAT
1 TTCGCGTTGCGATTTTGTCGTTGCGATTTCAT
1809 TTCGCGTTGCGA-TTTGTCGTTGCGATTTCAT
1 TTCGCGTTGCGATTTTGTCGTTGCGATTTCAT
1840 TTCGCGTTGCGATTTTGTCGTTGCGATTTTTCAT
1 TTCGCGTTGCGATTTTGTCGTTGCGA--TTTCAT
*
1874 TTCGCATTGCGAT
1 TTCGCGTTGCGAT
1887 AGCCATTTCC
Statistics
Matches: 74, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
31 31 0.42
32 25 0.34
34 18 0.24
ACGTcount: A:0.10, C:0.19, G:0.25, T:0.46
Consensus pattern (32 bp):
TTCGCGTTGCGATTTTGTCGTTGCGATTTCAT
Found at i:1829 original size:13 final size:14
Alignment explanation
Indices: 1813--1869 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1803 TTTCATTTCG
1813 CGTTGCGA-TTTGT
1 CGTTGCGATTTTGT
*
1826 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1842 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
1858 CGTTGCGATTTT
1 CGTTGCGATTTT
1870 TCATTTCGCA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
13 8 0.22
14 14 0.38
16 4 0.11
18 11 0.30
ACGTcount: A:0.09, C:0.18, G:0.26, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1841 original size:18 final size:18
Alignment explanation
Indices: 1795--1927 Score: 104
Period size: 20 Copynumber: 7.6 Consensus size: 18
1785 GCGATTTTGT
1795 CGTTGCGATTTCATTTCG
1 CGTTGCGATTTCATTTCG
*
1813 CGTTGCGA-TT--TGT--
1 CGTTGCGATTTCATTTCG
1826 CGTTGCGATTTCATTTCG
1 CGTTGCGATTTCATTTCG
*
1844 CGTTGCGATTT--TGT--
1 CGTTGCGATTTCATTTCG
1858 CGTTGCGATTTTTCATTTCG
1 CGTTGCGA--TTTCATTTCG
* **
1878 CATTGCGATAGCCATTTCCG
1 CGTTGCGAT-TTCATTT-CG
*
1898 CGTTGCGATAGTCATTTCG
1 CGTTGCGAT-TTCATTTCG
1917 CGTTGCGATTT
1 CGTTGCGATTT
1928 TAAGTTTCGT
Statistics
Matches: 92, Mismatches: 10, Indels: 26
0.72 0.08 0.20
Matches are distributed among these distances:
13 8 0.09
14 10 0.11
15 2 0.02
16 7 0.08
17 2 0.02
18 23 0.25
19 16 0.17
20 24 0.26
ACGTcount: A:0.12, C:0.21, G:0.24, T:0.43
Consensus pattern (18 bp):
CGTTGCGATTTCATTTCG
Found at i:3780 original size:14 final size:14
Alignment explanation
Indices: 3763--3798 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3753 GATTGTTTAT
3763 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
3777 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
3791 TGATTTGT
1 TGATTTGT
3799 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3923 original size:13 final size:13
Alignment explanation
Indices: 3905--3956 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
3895 CGAAATGGCT
3905 ATCGCAACGAGAA
1 ATCGCAACGAGAA
3918 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-G-AA
3937 ATCGCAACGAGAA
1 ATCGCAACGAGAA
3950 ATCGCAA
1 ATCGCAA
3957 TGCGATTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 16 0.48
14 1 0.03
15 3 0.09
17 3 0.09
18 1 0.03
19 9 0.27
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12
Consensus pattern (13 bp):
ATCGCAACGAGAA
Found at i:3974 original size:32 final size:32
Alignment explanation
Indices: 3886--3961 Score: 116
Period size: 32 Copynumber: 2.4 Consensus size: 32
3876 CAAACAGACT
* ***
3886 ATCGCAACGCGAAATGGCTATCGCAACGAGAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAA
3918 ATCGCAATGCGAAATGAAAATCGCAACGAGAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAA
3950 ATCGCAATGCGA
1 ATCGCAATGCGA
3962 TTTTCATTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.41, C:0.22, G:0.24, T:0.13
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:4396 original size:14 final size:14
Alignment explanation
Indices: 4377--4412 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
4367 ATTGTTTAAT
4377 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
4391 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
4405 TGATTTGT
1 TGATTTGT
4413 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:5692 original size:24 final size:24
Alignment explanation
Indices: 5636--5694 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
5626 AGTCAGTATT
* *
5636 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACA
* *
5660 CGGACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTGGTCAATACA
*
5684 CGAATTTTGAT
1 CGAAATTTGAT
5695 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACA
Found at i:8227 original size:33 final size:33
Alignment explanation
Indices: 8169--8261 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
8159 GGAAATTACT
8169 ATCGCAATGCGAAATG-AAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
8201 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
8234 ATCGCAATGTGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
8262 CGAATTAATT
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 16 0.28
33 42 0.72
ACGTcount: A:0.43, C:0.18, G:0.25, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:9896 original size:21 final size:21
Alignment explanation
Indices: 9830--9896 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
9820 GTGAATCGGG
*
9830 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
9850 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
9872 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
9893 CTCT
1 CTCT
9897 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:9915 original size:42 final size:41
Alignment explanation
Indices: 9830--9952 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
9820 GTGAATCGGG
* * * * *
9830 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
9872 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
9914 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
9953 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:11995 original size:20 final size:19
Alignment explanation
Indices: 11950--12090 Score: 86
Period size: 19 Copynumber: 7.8 Consensus size: 19
11940 TCTTTTGGTT
11950 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* * *
11969 GATAATGAGAATTGCAACGCG
1 GA-AATGAAAATCGCAACG-A
** *
11990 GAAATGACTATCGCAATGA
1 GAAATGAAAATCGCAACGA
*
12009 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
** *
12023 GAAATGACTATCGCGACGA
1 GAAATGAAAATCGCAACGA
*
12042 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
12056 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
12075 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
12091 TGCGATTTTG
Statistics
Matches: 93, Mismatches: 17, Indels: 24
0.69 0.13 0.18
Matches are distributed among these distances:
14 18 0.19
16 4 0.04
17 4 0.04
19 39 0.42
20 26 0.28
21 2 0.02
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:12032 original size:33 final size:33
Alignment explanation
Indices: 11975--12073 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
11965 ACGAGATAAT
* *
11975 GAGAATTGCAACGCGGAAATGACTATCGCAATGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
12009 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
12042 GAGAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
12074 CGAAATGAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 46 0.78
34 13 0.22
ACGTcount: A:0.39, C:0.21, G:0.26, T:0.13
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:12067 original size:19 final size:19
Alignment explanation
Indices: 12045--12095 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
12035 GCGACGAGAG
12045 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
12064 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
12083 AATCGCAATGCGA
1 AATCGCAACGCGA
12096 TTTTGGTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:12124 original size:19 final size:19
Alignment explanation
Indices: 12091--12157 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
12081 AAAATCGCAA
**
12091 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
12110 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
12129 TGCGATAGTTATTTC-CGATT
1 TGCGATTTTTATTTCGCG--T
12149 TGCGATTTT
1 TGCGATTTT
12158 CATTCTCGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
18 2 0.05
19 30 0.75
20 8 0.20
ACGTcount: A:0.12, C:0.15, G:0.24, T:0.49
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:12748 original size:21 final size:19
Alignment explanation
Indices: 12724--12852 Score: 75
Period size: 20 Copynumber: 6.3 Consensus size: 19
12714 AAGTATCTCG
*
12724 TTGCGATTTTTTATTATCGCA
1 TTGCGATTTTTCA-T-TCGCA
**
12745 TTGCGA-TAGTCAGTATCGCA
1 TTGCGATTTTTCA-T-TCGCA
*
12765 TTGCGATTTTCTCAATTCGCG
1 TTGCGATTTT-TC-ATTCGCA
12786 TTGCGATTTACTT-ATTCGCA
1 TTGCGATTT--TTCATTCGCA
* *
12806 TTGCGAATTTTCCAATTCGCG
1 TTGCG-ATTTTTC-ATTCGCA
12827 TTGCGATTTACTT-ATTCGCA
1 TTGCGATTT--TTCATTCGCA
12847 TTGCGA
1 TTGCGA
12853 ATTGGGAAAA
Statistics
Matches: 86, Mismatches: 12, Indels: 21
0.72 0.10 0.18
Matches are distributed among these distances:
19 1 0.01
20 43 0.50
21 35 0.41
22 5 0.06
23 2 0.02
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.42
Consensus pattern (19 bp):
TTGCGATTTTTCATTCGCA
Found at i:12771 original size:20 final size:20
Alignment explanation
Indices: 12678--12771 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
12668 CGCTAAGTAA
*
12678 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* * *
12698 ATCGCGTTGCAAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
12718 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
12739 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
12759 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
12772 TTTCTCAATT
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 45 0.78
21 13 0.22
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:12790 original size:41 final size:41
Alignment explanation
Indices: 12699--12833 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
12689 AAAGTCAGTA
* * * * * *
12699 TCGCGTTGCAAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCTCAAT
* *
12739 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCTCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCTCAAT
* **
12781 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTTC-CAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCG-ATTTTCTCAAT
12822 TCGCGTTGCGAT
1 TCGCGTTGCGAT
12834 TTACTTATTC
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
40 3 0.04
41 66 0.85
42 9 0.12
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCTCAAT
Found at i:12804 original size:20 final size:20
Alignment explanation
Indices: 12760--12852 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
12750 ATAGTCAGTA
*
12760 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACT-AAT
* *
12781 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
* *
12801 TCGCATTGCGAATTTTCCAAT
1 TCGCATTGCG-ATTTACTAAT
* *
12822 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
12842 TCGCATTGCGA
1 TCGCATTGCGA
12853 ATTGGGAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.47
21 31 0.53
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.41
Consensus pattern (20 bp):
TCGCATTGCGATTTACTAAT
Found at i:12834 original size:41 final size:42
Alignment explanation
Indices: 12760--12855 Score: 178
Period size: 41 Copynumber: 2.3 Consensus size: 42
12750 ATAGTCAGTA
12760 TCGCATTGCG-ATTTTCTCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTTCTCAATTCGCGTTGCGATTTACTTAT
12801 TCGCATTGCGAATTTTC-CAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTTCTCAATTCGCGTTGCGATTTACTTAT
12842 TCGCATTGCGAATT
1 TCGCATTGCGAATT
12856 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
41 48 0.89
42 6 0.11
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.42
Consensus pattern (42 bp):
TCGCATTGCGAATTTTCTCAATTCGCGTTGCGATTTACTTAT
Found at i:15997 original size:19 final size:19
Alignment explanation
Indices: 15973--16012 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
15963 TCACCTGCAA
15973 AAAAATAAAAACAAAAAAC
1 AAAAATAAAAACAAAAAAC
** *
15992 AAAAATCTAAATAAAAAAC
1 AAAAATAAAAACAAAAAAC
16011 AA
1 AA
16013 TTACTTTTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.80, C:0.10, G:0.00, T:0.10
Consensus pattern (19 bp):
AAAAATAAAAACAAAAAAC
Found at i:21135 original size:21 final size:21
Alignment explanation
Indices: 21106--21162 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 21
21096 AATGTGCATA
*
21106 AAAAATAAATATAAAAATACT
1 AAAATTAAATATAAAAATACT
* ** *
21127 AAAATTAAAAATTGAGATACT
1 AAAATTAAATATAAAAATACT
21148 AAAAGTTTAAATATA
1 AAAA--TTAAATATA
21163 TATTAAAAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 20 0.74
23 7 0.26
ACGTcount: A:0.63, C:0.04, G:0.05, T:0.28
Consensus pattern (21 bp):
AAAATTAAATATAAAAATACT
Found at i:22305 original size:134 final size:134
Alignment explanation
Indices: 22016--22326 Score: 356
Period size: 134 Copynumber: 2.3 Consensus size: 134
22006 ATTCGGACTT
* * * * *
22016 AGGAGATCGAGGCGAAGCAACCCATAAAATTTGGGACCGAACAACCACCATATATGGTGACCGAC
1 AGGAGATCGAGACGAAGCGACCAATAAAATCTGAGACCGAACAACCACCATATATGGTGACCGAC
* *
22081 ATTTTGTTTTTCTCACTTTTAATCAGATTTGGAGCTTGTTCCAACAAAATGAAGGTCAGATTCAG
66 ATTTTGTTTTTCTCACTTTTAATCAGATTTCGAGCTTGTTCCAACAAAATGAAGGTCAGATTCAA
*
22146 ACTT
131 ACTC
* * * * * * * *
22150 AGGGGGTCGAGATGAAACGACCAATAAAATCTGAGACCGAATAACCATCATCTATGGTGGCCGAC
1 AGGAGATCGAGACGAAGCGACCAATAAAATCTGAGACCGAACAACCACCATATATGGTGACCGAC
* *** *
22215 ATTTTGTTTTTCTCACTTTTGATC-GAATTTCGAG-TATGTTTTGATAAAATGAAGGTCAGATTC
66 ATTTTGTTTTTCTCACTTTTAATCAG-ATTTCGAGCT-TGTTCCAACAAAATGAAGGTCAGATTC
22278 AAACTC
129 AAACTC
* * * * *
22284 ATGAGATCAAGACGAAGCGACCGATAAAATCTAAGACCAAACA
1 AGGAGATCGAGACGAAGCGACCAATAAAATCTGAGACCGAACA
22327 GTCACCATCT
Statistics
Matches: 144, Mismatches: 31, Indels: 4
0.80 0.17 0.02
Matches are distributed among these distances:
133 2 0.01
134 142 0.99
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (134 bp):
AGGAGATCGAGACGAAGCGACCAATAAAATCTGAGACCGAACAACCACCATATATGGTGACCGAC
ATTTTGTTTTTCTCACTTTTAATCAGATTTCGAGCTTGTTCCAACAAAATGAAGGTCAGATTCAA
ACTC
Found at i:22417 original size:16 final size:17
Alignment explanation
Indices: 22384--22417 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
22374 CATCTGGTTT
*
22384 TTATTTTATATTTTAAA
1 TTATTTTATATATTAAA
22401 TTATTTT-TATATTAAA
1 TTATTTTATATATTAAA
22417 T
1 T
22418 AATAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTTTATATATTAAA
Found at i:25826 original size:82 final size:83
Alignment explanation
Indices: 25706--25863 Score: 230
Period size: 82 Copynumber: 1.9 Consensus size: 83
25696 GCTACGACAA
* *
25706 AGTAGTACTTAGCAGTATTTTTATACAAACACCTCAAT-AGGTTCATCCATAGTAGCG-TTTTTT
1 AGTAGTACTTAGCAGCATTTTTATACAAACACCGCAATAAGGTTCATCCATAGTAGCGTTTTTTT
25769 AAACAAACGTCGTAACAG
66 AAACAAACGTCGTAACAG
* * * *
25787 AGTAGTACTTTAGCAGCGTTTTTATACAAACGCCGCAATAAGGTTCATTCATAGTGGCGTTTTTT
1 AGTAGTAC-TTAGCAGCATTTTTATACAAACACCGCAATAAGGTTCATCCATAGTAGCGTTTTTT
*
25852 TAAATAAACGTC
65 TAAACAAACGTC
25864 ACAGCAAAAT
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 8 0.12
82 26 0.39
83 17 0.25
84 16 0.24
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (83 bp):
AGTAGTACTTAGCAGCATTTTTATACAAACACCGCAATAAGGTTCATCCATAGTAGCGTTTTTTT
AAACAAACGTCGTAACAG
Found at i:25884 original size:84 final size:82
Alignment explanation
Indices: 25702--25884 Score: 233
Period size: 84 Copynumber: 2.2 Consensus size: 82
25692 AAACGCTACG
* *
25702 ACAAAGTAGTAC-TTAGCAGTATTTTTATACAAACACCTCAATAGGTTCATCCATAGTAGCGTTT
1 ACAAAGTAGTACTTTAGCAGCATTTTTATACAAACACCGCAATAGGTTCATCCATAGTAGCGTTT
**
25766 TTTAAACAAACGTCGTA
66 TTTAAACAAACGTCACA
* * * * *
25783 ACAGAGTAGTACTTTAGCAGCGTTTTTATACAAACGCCGCAATAAGGTTCATTCATAGTGGCGTT
1 ACAAAGTAGTACTTTAGCAGCATTTTTATACAAACACCGCAAT-AGGTTCATCCATAGTAGCG-T
*
25848 TTTTTAAATAAACGTCACA
64 TTTTTAAACAAACGTCACA
* *
25867 GCAAAATAGTACTTTAGC
1 ACAAAGTAGTACTTTAGC
25885 GTTGTTTTTA
Statistics
Matches: 86, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
81 11 0.13
82 26 0.30
83 17 0.20
84 32 0.37
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (82 bp):
ACAAAGTAGTACTTTAGCAGCATTTTTATACAAACACCGCAATAGGTTCATCCATAGTAGCGTTT
TTTAAACAAACGTCACA
Found at i:26693 original size:12 final size:12
Alignment explanation
Indices: 26676--26700 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
26666 CTTGATATCG
26676 TTTAAGTAAGAT
1 TTTAAGTAAGAT
26688 TTTAAGTAAGAT
1 TTTAAGTAAGAT
26700 T
1 T
26701 CAAACTCGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (12 bp):
TTTAAGTAAGAT
Found at i:29283 original size:16 final size:16
Alignment explanation
Indices: 29264--29314 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
29254 AGATAAATCT
29264 TGTTCAGATCAGCTCG
1 TGTTCAGATCAGCTCG
* *
29280 TGTTCATGAT-A-TTCT
1 TGTTCA-GATCAGCTCG
29295 TGTTCAGATCAGCTCG
1 TGTTCAGATCAGCTCG
29311 TGTT
1 TGTT
29315 TATGATATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
14 3 0.11
15 9 0.32
16 13 0.46
17 3 0.11
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.41
Consensus pattern (16 bp):
TGTTCAGATCAGCTCG
Found at i:29299 original size:31 final size:31
Alignment explanation
Indices: 29261--29331 Score: 133
Period size: 31 Copynumber: 2.3 Consensus size: 31
29251 GCTAGATAAA
29261 TCTTGTTCAGATCAGCTCGTGTTCATGATAT
1 TCTTGTTCAGATCAGCTCGTGTTCATGATAT
*
29292 TCTTGTTCAGATCAGCTCGTGTTTATGATAT
1 TCTTGTTCAGATCAGCTCGTGTTCATGATAT
29323 TCTTGTTCA
1 TCTTGTTCA
29332 AAACTGCTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.45
Consensus pattern (31 bp):
TCTTGTTCAGATCAGCTCGTGTTCATGATAT
Found at i:29300 original size:15 final size:15
Alignment explanation
Indices: 29280--29331 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
29270 GATCAGCTCG
29280 TGTTCATGATATTCT
1 TGTTCATGATATTCT
* *
29295 TGTTCA-GATCAGCTCG
1 TGTTCATGAT-A-TTCT
*
29311 TGTTTATGATATTCT
1 TGTTCATGATATTCT
29326 TGTTCA
1 TGTTCA
29332 AAACTGCTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
14 3 0.11
15 14 0.50
16 8 0.29
17 3 0.11
ACGTcount: A:0.19, C:0.15, G:0.17, T:0.48
Consensus pattern (15 bp):
TGTTCATGATATTCT
Found at i:30460 original size:20 final size:20
Alignment explanation
Indices: 30432--30476 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
30422 CATATATATA
*
30432 TATACACACACATGTATGCATG
1 TATACACA-A-ATGAATGCATG
*
30454 TATACACAAATGAATGTATG
1 TATACACAAATGAATGCATG
30474 TAT
1 TAT
30477 GTATCTATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 1 0.05
22 8 0.38
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (20 bp):
TATACACAAATGAATGCATG
Found at i:31023 original size:21 final size:22
Alignment explanation
Indices: 31000--31043 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
30990 AGTTTATTTA
*
31000 ATTATTTAAAAAATATTTAAAATT
1 ATTA-TTAAAAAA-ATTCAAAATT
31024 ATTATTAAAAAAATTCAAAA
1 ATTATTAAAAAAATTCAAAA
31044 ACCATTAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 8 0.42
24 4 0.21
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
ATTATTAAAAAAATTCAAAATT
Found at i:31211 original size:27 final size:26
Alignment explanation
Indices: 31175--31227 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
31165 CGAAAGATCC
* *
31175 TTTTTCTGCAATAACGTTCCTTCAATT
1 TTTTTATGCAA-AACGCTCCTTCAATT
*
31202 TTTTTATGCAAAATGCTCCTTCAATT
1 TTTTTATGCAAAACGCTCCTTCAATT
31228 AAATGTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.25, C:0.21, G:0.08, T:0.47
Consensus pattern (26 bp):
TTTTTATGCAAAACGCTCCTTCAATT
Found at i:31993 original size:16 final size:16
Alignment explanation
Indices: 31974--32026 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
31964 AGACAATTCT
*
31974 TGTTCAAATCAGCTCG
1 TGTTCAAATCAGCTCA
* * *
31990 TGTTCATGAT-AGGTCT
1 TGTTCA-AATCAGCTCA
32006 TGTTCAAATCAGCTCA
1 TGTTCAAATCAGCTCA
32022 TGTTC
1 TGTTC
32027 GGAACACTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 2 0.07
16 25 0.86
17 2 0.07
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.38
Consensus pattern (16 bp):
TGTTCAAATCAGCTCA
Found at i:33154 original size:16 final size:16
Alignment explanation
Indices: 33135--33187 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
33125 AGACAATTCT
*
33135 TGTTCAAATCAGCTCG
1 TGTTCAAATCAGCTCA
* * *
33151 TGTTCATGAT-AGGTCT
1 TGTTCA-AATCAGCTCA
33167 TGTTCAAATCAGCTCA
1 TGTTCAAATCAGCTCA
33183 TGTTC
1 TGTTC
33188 GGAACACTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 2 0.07
16 25 0.86
17 2 0.07
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.38
Consensus pattern (16 bp):
TGTTCAAATCAGCTCA
Found at i:33462 original size:581 final size:581
Alignment explanation
Indices: 31937--34261 Score: 4607
Period size: 581 Copynumber: 4.0 Consensus size: 581
31927 CTTGACTGAT
31937 TGCTGCTTTGCTGAAAGTTCTTTTACTAGACAATTCTTGTTCAAATCAGCTCGTGTTCATGATAG
1 TGCTGCTTTGCTGAAAGTTCTTTTACTAGACAATTCTTGTTCAAATCAGCTCGTGTTCATGATAG
32002 GTCTTGTTCAAATCAGCTCATGTTCGGAACACTTTTTGTTTGGAACAGCTTGTGTTTATAACGAT
66 GTCTTGTTCAAATCAGCTCATGTTCGGAACACTTTTTGTTTGGAACAGCTTGTGTTTATAACGAT
32067 GATTTCCCAGAACAGTCTTTGTTAAGAATATCTCCTTCTGAGTAATTCACACAACACTTTCATGT
131 GATTTCCCAGAACAGTCTTTGTTAAGAATATCTCCTTCTGAGTAATTCACACAACACTTTCATGT
* *
32132 AAAAGCTGCTCTCGAAAAAACATCAAGAGAAGATGTGTATTTTATCACCTTCCTCTTTTTACCAA
196 AAAAGCAGCTCTCGAAAAAACATCAAGAGAAGATGTTTATTTTATCACCTTCCTCTTTTTACCAA
32197 ATAATCCTTCATATAGTGCGCTTATTATCCCATTGGTTTTGAATAAGTCTTTTTAAAAAATTCTA
261 ATAATCCTTCATATAGTGCGCTTATTATCCCATTGGTTTTGAATAAGTCTTTTTAAAAAATTCTA
*
32262 GGGAGGAAAAACGAATAAGTATTTGTCCCTATTGTTTGAGTTCTTCGATCCTAATATAAGAGAAC
326 GGGAGGAAAAACGAACAAGTATTTGTCCCTATTGTTTGAGTTCTTCGATCCTAATATAAGAGAAC
32327 ATGTGGTCAACTATCAGGACTATTTGGAAGTTTGATTCTTGGTTGCATTTTAATTAAATACGATG
391 ATGTGGTCAACTATCAGGACTATTTGGAAGTTTGATTCTTGGTTGCATTTTAATTAAATACGATG
32392 ATGCATGGTCAACACCTTCTAGTATAGGAGTATAATTTGGTATTCTATGAGGATGTAGTTCTATT
456 ATGCATGGTCAACACCTTCTAGTATAGGAGTATAATTTGGTATTCTATGAGGATGTAGTTCTATT
32457 CTCTTATGTGGCATATTGATTGTGAAATCTGCAGGTTAATTTATTCGGATTCGGGTGTGAG
521 CTCTTATGTGGCATATTGATTGTGAAATCTGCAGGTTAATTTATTCGGATTCGGGTGTGAG
32518 TGCTGCTTTGCTGAAAGTTCTTTTACTAGACAATTCTTGTTCAAATCAGCTCGTGTTCATGA-AG
1 TGCTGCTTTGCTGAAAGTTCTTTTACTAGACAATTCTTGTTCAAATCAGCTCGTGTTCATGATAG
32582 GTCTTGTTCAAATCAGCTCATGTTCGGAACACTTTTTGTTTGGAACAGCTTGTGTTTATAACGAT
66 GTCTTGTTCAAATCAGCTCATGTTCGGAACACTTTTTGTTTGGAACAGCTTGTGTTTATAACGAT
32647 GATTTCCCAGAACAGTCTTTGTTAAGAATATCTCCTTCTGAGTAATTCACACAACACTTTCATGT
131 GATTTCCCAGAACAGTCTTTGTTAAGAATATCTCCTTCTGAGTAATTCACACAACACTTTCATGT
32712 AAAAGCAGCTCTCGAAAAAACATCAAGAGAAGATGTTTATTTTATCACCTTCCTCTTTTTACCAA
196 AAAAGCAGCTCTCGAAAAAACATCAAGAGAAGATGTTTATTTTATCACCTTCCTCTTTTTACCAA
32777 ATAATCCTTCATATAGTGCGCTTATTATCCCATTGGTTTTGAATAAGTCTTTTTAAAAAATTCTA
261 ATAATCCTTCATATAGTGCGCTTATTATCCCATTGGTTTTGAATAAGTCTTTTTAAAAAATTCTA
32842 GGGAGGAAAAACGAACAAGTATTTGTCCCTATTGTTTGAGTTCTTCGATCCTAATATAAGAGAAC
326 GGGAGGAAAAACGAACAAGTATTTGTCCCTATTGTTTGAGTTCTTCGATCCTAATATAAGAGAAC
32907 ATGTGGTCAACTATCAGGACTATTTGGAAGTTTGATTCTTGGTTGCATTTTAATTAAATACGATG
391 ATGTGGTCAACTATCAGGACTATTTGGAAGTTTGATTCTTGGTTGCATTTTAATTAAATACGATG
32972 ATGCATGGTCAACACCTTCTAGTATAGGAGTATAATTTGGTATTCTATGAGGATGTAGTTCTATT
456 ATGCATGGTCAACACCTTCTAGTATAGGAGTATAATTTGGTATTCTATGAGGATGTAGTTCTATT
33037 CTCTTATGTGGCATATTGATTGTGAAATCTGCAGGTTAATTTATTCGGATTCGGGTGTGAG
521 CTCTTATGTGGCATATTGATTGTGAAATCTGCAGGTTAATTTATTCGGATTCGGGTGTGAG
33098 TGCTGCTTTGCTGAAAGTTCTTTTACTAGACAATTCTTGTTCAAATCAGCTCGTGTTCATGATAG
1 TGCTGCTTTGCTGAAAGTTCTTTTACTAGACAATTCTTGTTCAAATCAGCTCGTGTTCATGATAG
33163 GTCTTGTTCAAATCAGCTCATGTTCGGAACACTTTTTGTTTGGAACAGCTTGTGTTTATAACGAT
66 GTCTTGTTCAAATCAGCTCATGTTCGGAACACTTTTTGTTTGGAACAGCTTGTGTTTATAACGAT
33228 GATTTCCCAGAACAGTCTTTGTTAAGAATATCTCCTTCTGAGTAATTCACACAACACTTTCATGT
131 GATTTCCCAGAACAGTCTTTGTTAAGAATATCTCCTTCTGAGTAATTCACACAACACTTTCATGT
33293 AAAAGCAGCTCTCGAAAAAACATCAAGAGAAGATGTTTATTTTATCACCTTCCTCTTTTTACCAA
196 AAAAGCAGCTCTCGAAAAAACATCAAGAGAAGATGTTTATTTTATCACCTTCCTCTTTTTACCAA
33358 ATAATCCTTCATATAGTGCGCTTATTATCCCATTGGTTTTGAATAAGTCTTTTTAAAAAATTCTA
261 ATAATCCTTCATATAGTGCGCTTATTATCCCATTGGTTTTGAATAAGTCTTTTTAAAAAATTCTA
33423 GGGAGGAAAAACGAACAAGTATTTGTCCCTATTGTTTGAGTTCTTCGATCCTAATATAAGAGAAC
326 GGGAGGAAAAACGAACAAGTATTTGTCCCTATTGTTTGAGTTCTTCGATCCTAATATAAGAGAAC
33488 ATGTGGTCAACTATCAGGACTATTTGGAAGTTTGATTCTTGGTTGCATTTTAATTAAATACGATG
391 ATGTGGTCAACTATCAGGACTATTTGGAAGTTTGATTCTTGGTTGCATTTTAATTAAATACGATG
33553 ATGCATGGTCAACACCTTCTAGTATAGGAGTATAATTTGGTATTCTATGAGGATGTAGTTCTATT
456 ATGCATGGTCAACACCTTCTAGTATAGGAGTATAATTTGGTATTCTATGAGGATGTAGTTCTATT
33618 CTCTTATGTGGCATATTGATTGTGAAATCTGCAGGTTAATTTATTCGGATTCGGGTGTGAG
521 CTCTTATGTGGCATATTGATTGTGAAATCTGCAGGTTAATTTATTCGGATTCGGGTGTGAG
33679 TGCTGCTTTGCTGAAAGTTCTTTTACTAGACAATTCTTGTTCAAATCAGCTCGTGTTCATGATAG
1 TGCTGCTTTGCTGAAAGTTCTTTTACTAGACAATTCTTGTTCAAATCAGCTCGTGTTCATGATAG
33744 GTCTTGTTCAAATCAGCTCATGTTCGGAACACTTTTTGTTTGGAACAGCTTGTGTTTATAACGAT
66 GTCTTGTTCAAATCAGCTCATGTTCGGAACACTTTTTGTTTGGAACAGCTTGTGTTTATAACGAT
33809 GATTTCCCAGAACAGTCTTTGTTAAGAATATCTCCTTCTGAGTAATTCACACAACACTTTCATGT
131 GATTTCCCAGAACAGTCTTTGTTAAGAATATCTCCTTCTGAGTAATTCACACAACACTTTCATGT
33874 AAAAGCAGCTCTCGAAAAAACATCAAGAGAAGATGTTTATTTTATCACCTTCCTCTTTTTACCAA
196 AAAAGCAGCTCTCGAAAAAACATCAAGAGAAGATGTTTATTTTATCACCTTCCTCTTTTTACCAA
33939 ATAATCCTTCATATAGTGCGCTTATTATCCCATTGGTTTTGAATAAGTCTTTTTAAAAAATTCTA
261 ATAATCCTTCATATAGTGCGCTTATTATCCCATTGGTTTTGAATAAGTCTTTTTAAAAAATTCTA
*
34004 GGGAGGAAAAACGAATAAGTATTTGTCCCTATTGTTTGAGTTCTTCGATCCTAATATAAGAGAAC
326 GGGAGGAAAAACGAACAAGTATTTGTCCCTATTGTTTGAGTTCTTCGATCCTAATATAAGAGAAC
34069 ATGTGGTCAACTATCAGGACTATTTGGAAGTTTGATTCTTGGTTGCATTTTAATTAAATACGATG
391 ATGTGGTCAACTATCAGGACTATTTGGAAGTTTGATTCTTGGTTGCATTTTAATTAAATACGATG
34134 ATGCATGGTCAACACCTTCTAGTATAGGAGTATAATTTGGTATTCTATGAGGATGTAGTTCTATT
456 ATGCATGGTCAACACCTTCTAGTATAGGAGTATAATTTGGTATTCTATGAGGATGTAGTTCTATT
34199 CTCTTATGTGGCATATTGATTGTGAAATCTGCAGGTTAATTTATTCGGATTCGGGTGTGAG
521 CTCTTATGTGGCATATTGATTGTGAAATCTGCAGGTTAATTTATTCGGATTCGGGTGTGAG
34260 TG
1 TG
34262 GAAGATTAGA
Statistics
Matches: 1739, Mismatches: 4, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
580 577 0.33
581 1162 0.67
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.37
Consensus pattern (581 bp):
TGCTGCTTTGCTGAAAGTTCTTTTACTAGACAATTCTTGTTCAAATCAGCTCGTGTTCATGATAG
GTCTTGTTCAAATCAGCTCATGTTCGGAACACTTTTTGTTTGGAACAGCTTGTGTTTATAACGAT
GATTTCCCAGAACAGTCTTTGTTAAGAATATCTCCTTCTGAGTAATTCACACAACACTTTCATGT
AAAAGCAGCTCTCGAAAAAACATCAAGAGAAGATGTTTATTTTATCACCTTCCTCTTTTTACCAA
ATAATCCTTCATATAGTGCGCTTATTATCCCATTGGTTTTGAATAAGTCTTTTTAAAAAATTCTA
GGGAGGAAAAACGAACAAGTATTTGTCCCTATTGTTTGAGTTCTTCGATCCTAATATAAGAGAAC
ATGTGGTCAACTATCAGGACTATTTGGAAGTTTGATTCTTGGTTGCATTTTAATTAAATACGATG
ATGCATGGTCAACACCTTCTAGTATAGGAGTATAATTTGGTATTCTATGAGGATGTAGTTCTATT
CTCTTATGTGGCATATTGATTGTGAAATCTGCAGGTTAATTTATTCGGATTCGGGTGTGAG
Found at i:33735 original size:16 final size:16
Alignment explanation
Indices: 33716--33768 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
33706 AGACAATTCT
*
33716 TGTTCAAATCAGCTCG
1 TGTTCAAATCAGCTCA
* * *
33732 TGTTCATGAT-AGGTCT
1 TGTTCA-AATCAGCTCA
33748 TGTTCAAATCAGCTCA
1 TGTTCAAATCAGCTCA
33764 TGTTC
1 TGTTC
33769 GGAACACTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 2 0.07
16 25 0.86
17 2 0.07
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.38
Consensus pattern (16 bp):
TGTTCAAATCAGCTCA
Found at i:40542 original size:35 final size:35
Alignment explanation
Indices: 40496--40587 Score: 121
Period size: 35 Copynumber: 2.6 Consensus size: 35
40486 CAATCATCAT
*
40496 TTACATTCTAAACCCCAAATTTCAAAATACTTCAA
1 TTACATTCTAAACCCCAAATTCCAAAATACTTCAA
** * *
40531 TTACATTCTAAACCTAAAATTCCAAAATATTTTAA
1 TTACATTCTAAACCCCAAATTCCAAAATACTTCAA
* *
40566 TTACATGCTCAACCCCAAATTC
1 TTACATTCTAAACCCCAAATTC
40588 ATAATCCATT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 48 1.00
ACGTcount: A:0.41, C:0.25, G:0.01, T:0.33
Consensus pattern (35 bp):
TTACATTCTAAACCCCAAATTCCAAAATACTTCAA
Found at i:42429 original size:2 final size:2
Alignment explanation
Indices: 42422--42448 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
42412 TTAATATGTG
42422 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
42449 GAGTTGAACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42531 original size:5 final size:5
Alignment explanation
Indices: 42513--42560 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
42503 TTGATTAGTA
* * **
42513 AAATC ACATC AAATT AAATC AAATC AAATC AAAAA AAATTC AAATC AA
1 AAATC AAATC AAATC AAATC AAATC AAATC AAATC AAA-TC AAATC AA
42561 GTTAAACTTT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
5 31 0.91
6 3 0.09
ACGTcount: A:0.62, C:0.17, G:0.00, T:0.21
Consensus pattern (5 bp):
AAATC
Found at i:59490 original size:17 final size:17
Alignment explanation
Indices: 59463--59501 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
59453 TTTTTATAAT
59463 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
59479 TAATTATAAATAATATC
1 TAATTATAAATAATATC
59496 TAATTA
1 TAATTA
59502 ATTTAATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:60585 original size:10 final size:10
Alignment explanation
Indices: 60572--60641 Score: 77
Period size: 10 Copynumber: 7.0 Consensus size: 10
60562 TTTTTTTAAT
60572 GATTAAATTA
1 GATTAAATTA
*
60582 GATTAAAGTA
1 GATTAAATTA
60592 GATTAAATTA
1 GATTAAATTA
* * *
60602 TATTGAAGTA
1 GATTAAATTA
60612 GATTAAATTA
1 GATTAAATTA
* * *
60622 TATTGAAGTA
1 GATTAAATTA
60632 GATTAAATTA
1 GATTAAATTA
60642 CAAGATAGAT
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
10 46 1.00
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39
Consensus pattern (10 bp):
GATTAAATTA
Found at i:60597 original size:20 final size:20
Alignment explanation
Indices: 60572--60641 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
60562 TTTTTTTAAT
* *
60572 GATTAAATTAGATTAAAGTA
1 GATTAAATTATATTGAAGTA
60592 GATTAAATTATATTGAAGTA
1 GATTAAATTATATTGAAGTA
60612 GATTAAATTATATTGAAGTA
1 GATTAAATTATATTGAAGTA
60632 GATTAAATTA
1 GATTAAATTA
60642 CAAGATAGAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39
Consensus pattern (20 bp):
GATTAAATTATATTGAAGTA
Found at i:61001 original size:22 final size:21
Alignment explanation
Indices: 60970--61010 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
60960 AATGTTTCAT
60970 CTCTAAAGTAGAGATAGAGATG
1 CTCTAAAGTAGAGAT-GAGATG
*
60992 CTCTAGAGTAGAGATGAGA
1 CTCTAAAGTAGAGATGAGA
61011 ATTGGAGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.39, C:0.10, G:0.29, T:0.22
Consensus pattern (21 bp):
CTCTAAAGTAGAGATGAGATG
Found at i:63502 original size:42 final size:42
Alignment explanation
Indices: 63443--63533 Score: 173
Period size: 42 Copynumber: 2.2 Consensus size: 42
63433 ACAAGACACG
*
63443 AGAGAGGGGATACTCATCTTTGGACGATCTTCACCGAAAAGA
1 AGAGAGGAGATACTCATCTTTGGACGATCTTCACCGAAAAGA
63485 AGAGAGGAGATACTCATCTTTGGACGATCTTCACCGAAAAGA
1 AGAGAGGAGATACTCATCTTTGGACGATCTTCACCGAAAAGA
63527 AGAGAGG
1 AGAGAGG
63534 TCGTCGAAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (42 bp):
AGAGAGGAGATACTCATCTTTGGACGATCTTCACCGAAAAGA
Found at i:63914 original size:14 final size:14
Alignment explanation
Indices: 63884--63913 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
63874 TATTGATTGG
63884 TTTATTTATTTTAT
1 TTTATTTATTTTAT
63898 TTTATTT-TTTTAT
1 TTTATTTATTTTAT
63911 TTT
1 TTT
63914 TTACTAACGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTATTTATTTTAT
Found at i:67914 original size:105 final size:104
Alignment explanation
Indices: 67580--69062 Score: 2008
Period size: 105 Copynumber: 14.3 Consensus size: 104
67570 CTCGAGAGTA
* ** * * * * *
67580 AATTTCAACTTCTCAATGAAGGATCTT-GAATCCAAGACAACACAAGCTCAACTTCATGACGAAG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCC-AGACAACGCAAGTTCAACTTCACGACGAAG
* * * *
67644 GGGCGGCTGATTGTCAACAAACACTTCCCAATTTCAGAGCC
65 GGACCGCTGGTTGTCAACAAA-ATTTCCCAATTTCAGAGCC
* * * *
67685 AATTTCAACTTCACATCGAAGGATTTTGGACTCCAGACAACGTATA-TTCAACTTCAC-ATGAAG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA-AGTTCAACTTCACGACGAAG
* *
67748 GGACCGCTGGTTGTCAACAAATTTTCCCGATTTCAGAGCC
65 GGACCGCTGGTTGTCAACAAAATTTCCCAATTTCAGAGCC
67788 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* **
67853 GACCGCTGCTTGTCAACAATAATTTCATAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAA-AATTTCCCAATTTCAGAGCC
*
67893 AATTTCAACTTCACAGCGAAGGATATTGGACTCCTGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
67958 GACCGCTGGTTGTCAATAAAAAAATTCCCAATTTCAGAGCC
66 GACCGCTGGTTGTC-A-ACAAAATTTCCCAATTTCAGAGCC
67999 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
68064 GACCGCTAGTTGTCAACAAACATTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAA-ATTTCCCAATTTCAGAGCC
* *
68104 AATTTCAACTTCACAGCGAATGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
68169 GACC-CTGGTTGTCAATAAAAAAATTCCCAATTTCAGAGCC
66 GACCGCTGGTTGTC-A-ACAAAATTTCCCAATTTCAGAGCC
68209 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
68274 GACCGCTGGTTGTCAA-TAAA-----CAACTTC----CC
66 GACCGCTGGTTGTCAACAAAATTTCCCAATTTCAGAGCC
* *
68303 AATTTCAACTTCGCAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * *
68368 GACCGCTGGTTGTCAATAAACAATTTTCCAA-TTCTAGAGTC
66 GACCGCTGGTTGTCAA-CAA-AATTTCCCAATTTC-AGAGCC
* *
68409 AATTTCAACTTCACAGCGAAGGATAGTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * *
68474 GACCACTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAAC-AA-AATTTCCCAATTTCAGAGCC
*
68515 AA-TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
68579 GACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCC
66 GACCGCTGGTTGTCAA-CAA-AATTTCCCAATTTCAGAGCC
* * *
68620 AATTTCAACTTCACATCGAAGGATATTGGACTCCAGACAACGTATGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
68685 GACCGCTGGTTGTCAACAAATTTTCCCGATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAAATTTCCCAATTTCAGAGCC
68724 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * *
68789 GACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCC
66 GACCGCTGGTTGTCAACAA-AATTTCCCAATTTCAGAGCC
* *
68829 AATTTCAAATTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* **
68894 GA-C-CTGCTTGTCAACAAAATTT--C-A-TTCAGAATC
66 GACCGCTGGTTGTCAACAAAATTTCCCAATTTCAGAGCC
* * * * *
68927 AATTTCAACTTCACAACGAAGGATGTTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* ** *
68992 GACGGCTGGTTGTCAACAACCAATTTCCC-GGTTCCGAGCC
66 GACCGCTGGTTGTCAACAA--AATTTCCCAATTTCAGAGCC
69032 AATTTCAACTTCACGAG-G-AGGATATTGGACT
1 AATTTCAACTTCAC-AGCGAAGGATATTGGACT
69063 TGGAACAATG
Statistics
Matches: 1241, Mismatches: 100, Indels: 75
0.88 0.07 0.05
Matches are distributed among these distances:
94 81 0.07
96 1 0.00
97 2 0.00
98 74 0.06
99 1 0.00
100 14 0.01
101 3 0.00
102 13 0.01
103 85 0.07
104 171 0.14
105 506 0.41
106 284 0.23
107 6 0.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (104 bp):
AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
GACCGCTGGTTGTCAACAAAATTTCCCAATTTCAGAGCC
Found at i:68061 original size:211 final size:209
Alignment explanation
Indices: 67580--69062 Score: 2064
Period size: 211 Copynumber: 7.2 Consensus size: 209
67570 CTCGAGAGTA
* ** * * * * *
67580 AATTTCAACTTCTCAATGAAGGATCTT-GAATCCAAGACAACACAAGCTCAACTTCATGACGAAG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCC-AGACAACGCAAGTTCAACTTCACGACGAAG
* * * * *
67644 GGGCGGCTGATTGTCAACAAACACTTCCCAATTTCAGAGCCAATTTCAACTTCACATCGAAGGAT
65 GGACCGCTGGTTGTCAACAAA-A-TTTCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
* * * * *
67709 TTTGGACTCCAGACAACGTATA-TTCAACTTCAC-ATGAAGGGACCGCTGGTTGTCAA-CAA-AT
128 ATTGGACTCCAGACAACGCA-AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA
*
67770 TTTCCCGATTTCAGAGCC
192 TTTCCCAATTTCAGAGCC
67788 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * *
67853 GACCGCTGCTTGTCAACAATAATTTCATAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATA
66 GACCGCTGGTTGTCAACAA-AATTTC-CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATA
* * *
67918 TTGGACTCCTGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAAAAAAT
129 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATT
67983 TCCCAATTTCAGAGCC
194 TCCCAATTTCAGAGCC
67999 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * *
68064 GACCGCTAGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAATGATA
66 GACCGCTGGTTGTCAACAAA-ATTTC-CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATA
* * *
68129 TTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACC-CTGGTTGTCAATAAAAAAAT
129 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATT
68193 TCCCAATTTCAGAGCC
194 TCCCAATTTCAGAGCC
68209 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * *
68274 GACCGCTGGTTGTCAA-TAAA----CAACTTC----CCAATTTCAACTTCGCAACGAAGGATATT
66 GACCGCTGGTTGTCAACAAAATTTCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
*
68330 GGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTT
131 GGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTC
*
68395 CCAA-TTCTAGAGTC
196 CCAATTTC-AGAGCC
* *
68409 AATTTCAACTTCACAGCGAAGGATAGTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
68474 GACCACTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAA-TTCAACTTCACAACGAAGGAT
66 GACCGCTGGTTGTCAAC-AA-AATTTC-CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
*
68538 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAC
128 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAT
68603 TTCCCAATTTCAGAGCC
193 TTCCCAATTTCAGAGCC
* * *
68620 AATTTCAACTTCACATCGAAGGATATTGGACTCCAGACAACGTATGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * *
68685 GACCGCTGGTTGTCAACAAATTTTCCCGATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATAT
66 GACCGCTGGTTGTCAACAAAATTT-CCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
* * *
68750 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA-CAACAACTT
130 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTT
*
68814 CCCAATCTCAGAGCC
195 CCCAATTTCAGAGCC
* *
68829 AATTTCAAATTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* ** *
68894 GA-C-CTGCTTGTCAACAAAATTT-C-A-TTCAGAATCAATTTCAACTTCACAACGAAGGATGTT
66 GACCGCTGGTTGTCAACAAAATTTCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
* * * * * *
68954 GGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACCAATTTC
131 GGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTC
** *
69019 CC-GGTTCCGAGCC
196 CCAATTTCAGAGCC
69032 AATTTCAACTTCACGAG-G-AGGATATTGGACT
1 AATTTCAACTTCAC-AGCGAAGGATATTGGACT
69063 TGGAACAATG
Statistics
Matches: 1162, Mismatches: 86, Indels: 60
0.89 0.07 0.05
Matches are distributed among these distances:
199 70 0.06
200 106 0.09
202 14 0.01
203 110 0.09
204 11 0.01
205 1 0.00
207 21 0.02
208 139 0.12
209 132 0.11
210 198 0.17
211 353 0.30
212 7 0.01
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (209 bp):
AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
GACCGCTGGTTGTCAACAAAATTTCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
GGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTC
CCAATTTCAGAGCC
Found at i:68273 original size:43 final size:43
Alignment explanation
Indices: 68212--68367 Score: 125
Period size: 43 Copynumber: 3.4 Consensus size: 43
68202 CAGAGCCAAT
68212 TTCAACTTCAC-AGCGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACGA-CGAAGGATATTGGACTCCAGACAACGCAAG
*** ** * * * *
68255 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAAT
1 TTCAACTTCACGACGAA-GGA-TATTGG-ACTC--CAGACAA---CGCAAG
* *
68306 TTCAACTTCGCAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACGACGAAGGATATTGGACTCCAGACAACGCAAG
68349 TTCAACTTCACGACGAAGG
1 TTCAACTTCACGACGAAGG
68368 GACCGCTGGT
Statistics
Matches: 82, Mismatches: 22, Indels: 18
0.67 0.18 0.15
Matches are distributed among these distances:
43 36 0.44
44 4 0.05
45 3 0.04
46 7 0.09
48 7 0.09
49 3 0.04
50 3 0.04
51 19 0.23
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (43 bp):
TTCAACTTCACGACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:70155 original size:40 final size:41
Alignment explanation
Indices: 70069--70148 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 41
70059 AACAAGACAC
*
70069 GAGAGAGGGGATACTCATCTTTGGACGATCTTCACCGAAAA
1 GAGAGAGGAGATACTCATCTTTGGACGATCTTCACCGAAAA
70110 GAGAGAGGAGATACTCATC-TTGGACGATCTTCACCGAAA
1 GAGAGAGGAGATACTCATCTTTGGACGATCTTCACCGAAA
70149 GAAGAGATCG
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 20 0.53
41 18 0.47
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.21
Consensus pattern (41 bp):
GAGAGAGGAGATACTCATCTTTGGACGATCTTCACCGAAAA
Found at i:70533 original size:14 final size:14
Alignment explanation
Indices: 70503--70532 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
70493 TATTGATTGG
70503 TTTATTTATTTTAT
1 TTTATTTATTTTAT
70517 TTTATTT-TTTTAT
1 TTTATTTATTTTAT
70530 TTT
1 TTT
70533 TTACTAACGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTATTTATTTTAT
Found at i:73472 original size:58 final size:58
Alignment explanation
Indices: 73395--73507 Score: 158
Period size: 58 Copynumber: 1.9 Consensus size: 58
73385 ATTATGTTGC
* * * *
73395 TTTTAATAGTCGAGGGACTCAACAAAGT-AACT-TCTATAGTTGGGGGACTATTTGTAA
1 TTTTAATAGTCGAGAGACTCAACAAA-TCAACTCTCTATAGTCGAGGGACCATTTGTAA
73452 TTTTAAATAGTCGAGAGACTCAACAAATCAACTCTCTATAGTCGAGGGACCATTTG
1 TTTT-AATAGTCGAGAGACTCAACAAATCAACTCTCTATAGTCGAGGGACCATTTG
73508 AATACTTTAC
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
57 5 0.10
58 25 0.51
59 19 0.39
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (58 bp):
TTTTAATAGTCGAGAGACTCAACAAATCAACTCTCTATAGTCGAGGGACCATTTGTAA
Found at i:80615 original size:25 final size:25
Alignment explanation
Indices: 80568--80615 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
80558 TTAACATTGT
* * **
80568 TTGAACATTTATTTTTTTTAAAAAA
1 TTGAAAATTTATTTATTAAAAAAAA
80593 TTGAAAATTTATTTATTAAAAAA
1 TTGAAAATTTATTTATTAAAAAA
80616 TAAATATAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (25 bp):
TTGAAAATTTATTTATTAAAAAAAA
Found at i:86488 original size:14 final size:14
Alignment explanation
Indices: 86469--86500 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
86459 CAACGGTCAA
*
86469 CGGTCGGGTCAGGC
1 CGGTCGGGTCAGAC
86483 CGGTCGGGTCAGAC
1 CGGTCGGGTCAGAC
86497 CGGT
1 CGGT
86501 TCAAATCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.28, G:0.47, T:0.16
Consensus pattern (14 bp):
CGGTCGGGTCAGAC
Found at i:89508 original size:109 final size:110
Alignment explanation
Indices: 89317--89535 Score: 431
Period size: 109 Copynumber: 2.0 Consensus size: 110
89307 CTTTGTCAAA
89317 GGAGAAGCAATGATCGAGAAGCCCTCAACAAAAGTCGATAATAACCAGCCAAGCCCAAGAAACTG
1 GGAGAAGCAATGATCGAGAAGCCCTCAACAAAAGTCGATAATAACCAGCCAAGCCCAAGAAACTG
89382 CGAATCTCAGAGATATTC-TGGGTCGTTTCCAATTCACAATAGCC
66 CGAATCTCAGAGATATTCTTGGGTCGTTTCCAATTCACAATAGCC
89426 GGAGAAGCAATGATCGAGAAGCCCTCAACAAAAGTCGATAATAACCAGCCAAGCCCAAGAAACTG
1 GGAGAAGCAATGATCGAGAAGCCCTCAACAAAAGTCGATAATAACCAGCCAAGCCCAAGAAACTG
89491 CGAATCTCAGAGATATTCTTGGGTCGTTTCCAATTCACAATAGCC
66 CGAATCTCAGAGATATTCTTGGGTCGTTTCCAATTCACAATAGCC
89536 TCGATCTTGC
Statistics
Matches: 109, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
109 83 0.76
110 26 0.24
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.19
Consensus pattern (110 bp):
GGAGAAGCAATGATCGAGAAGCCCTCAACAAAAGTCGATAATAACCAGCCAAGCCCAAGAAACTG
CGAATCTCAGAGATATTCTTGGGTCGTTTCCAATTCACAATAGCC
Found at i:93805 original size:17 final size:17
Alignment explanation
Indices: 93783--93820 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
93773 AACAGTCAAT
*
93783 GGTCAACGGTCGGGTCG
1 GGTCAACGATCGGGTCG
93800 GGTCAACGATCGGGTCG
1 GGTCAACGATCGGGTCG
93817 GGTC
1 GGTC
93821 GAGTCAGATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.13, C:0.24, G:0.45, T:0.18
Consensus pattern (17 bp):
GGTCAACGATCGGGTCG
Found at i:104049 original size:43 final size:43
Alignment explanation
Indices: 104002--104088 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
103992 TGTATCCACC
104002 AGAGAACCAAAAGTGAT-AATAAGATAAAATGTAGTTTATTCTA
1 AGAGAACCAAAAGTGATAAATAAGAT-AAATGTAGTTTATTCTA
104045 AGAGAACCAAAAGTGATAAATAAGATAAATGTAGTTTATTCTA
1 AGAGAACCAAAAGTGATAAATAAGATAAATGTAGTTTATTCTA
104088 A
1 A
104089 ATCCAAAGCA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
43 35 0.81
44 8 0.19
ACGTcount: A:0.49, C:0.07, G:0.16, T:0.28
Consensus pattern (43 bp):
AGAGAACCAAAAGTGATAAATAAGATAAATGTAGTTTATTCTA
Found at i:105140 original size:118 final size:118
Alignment explanation
Indices: 104995--105214 Score: 358
Period size: 118 Copynumber: 1.9 Consensus size: 118
104985 ACAGGGCTTT
*
104995 CAGGCTGTTATAAAATAAAATAAATCAACATCTTCCAGTTC-AAGATGAGC-ATCTCAATATTTC
1 CAGGCTGTTATAAAATAAAATAAATCAACATCTTCCAGTTCAAAGATGAGCAAGCTCAATATTTC
105058 CAAAGTTCACCGGTAATTAAACACATATAGACCAGTGTCCATTGTCAGGGCTTTTCA
66 C-AAGTTCA-CGGTAATT-AA-ACATATAGACCAGTGTCCATTGTCAGGGCTTTTCA
105115 CAGGCTG-TATAAAAT-AAATAAATCAACATCTTCCAGTTCAAAGATGAGCAAGCTCAATATTTC
1 CAGGCTGTTATAAAATAAAATAAATCAACATCTTCCAGTTCAAAGATGAGCAAGCTCAATATTTC
*
105178 CAAGTTCACGGTAATTAAACATATAGACCATTGTCCA
66 CAAGTTCACGGTAATTAAACATATAGACCAGTGTCCA
105215 CTGGAATTAG
Statistics
Matches: 96, Mismatches: 2, Indels: 8
0.91 0.02 0.08
Matches are distributed among these distances:
116 18 0.19
117 2 0.02
118 32 0.33
119 24 0.25
120 20 0.21
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (118 bp):
CAGGCTGTTATAAAATAAAATAAATCAACATCTTCCAGTTCAAAGATGAGCAAGCTCAATATTTC
CAAGTTCACGGTAATTAAACATATAGACCAGTGTCCATTGTCAGGGCTTTTCA
Found at i:106152 original size:10 final size:10
Alignment explanation
Indices: 106139--106220 Score: 60
Period size: 10 Copynumber: 8.1 Consensus size: 10
106129 ATAATAAATG
106139 TTAATATTTT
1 TTAATATTTT
106149 TTAATATTTTT
1 TTAATA-TTTT
* *
106160 TATAAAATTAT
1 T-TAATATTTT
* *
106171 TTAAAATATTA
1 TTAATAT-TTT
106182 TT--TATTTT
1 TTAATATTTT
* * *
106190 TTAAAAATTA
1 TTAATATTTT
106200 TTAATATTTT
1 TTAATATTTT
106210 TTAATATTTT
1 TTAATATTTT
106220 T
1 T
106221 GGTAAAGTTA
Statistics
Matches: 55, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
8 4 0.07
9 2 0.04
10 33 0.60
11 12 0.22
12 4 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TTAATATTTT
Found at i:106234 original size:31 final size:29
Alignment explanation
Indices: 106139--106238 Score: 96
Period size: 31 Copynumber: 3.3 Consensus size: 29
106129 ATAATAAATG
106139 TTAATATTTTTTAATATTTTTTATAAAATTA
1 TTAATATTTTTTAATA-TTTTT-TAAAATTA
* *
106170 TTTAAAATATTATTT-AT-TTTTTAAAAATTA
1 -TT--AATATTTTTTAATATTTTTTAAAATTA
*
106200 TTAATATTTTTTAATATTTTTGGTAAAGTTA
1 TTAATATTTTTTAATATTTTT--TAAAATTA
106231 TTAATATT
1 TTAATATT
106239 AACATTTTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
27 9 0.16
28 2 0.04
29 7 0.12
30 7 0.12
31 19 0.33
32 2 0.04
33 2 0.04
34 9 0.16
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (29 bp):
TTAATATTTTTTAATATTTTTTAAAATTA
Found at i:106257 original size:61 final size:61
Alignment explanation
Indices: 106139--106257 Score: 134
Period size: 61 Copynumber: 2.0 Consensus size: 61
106129 ATAATAAATG
* ** **
106139 TTAATATTTTTTAATATTTTTTATAAAATTATTTAAAATATTATTTATTTTTTAAAAATTA
1 TTAATATTTTTTAATATTTTTGATAAAATTATTTAAAATAACATTTATTTTAAAAAAATTA
* * *
106200 TTAATATTTTTTAATATTTTTGGTAAAGTTA-TTAATATTAACATTT-TTTATAAAAAAA
1 TTAATATTTTTTAATATTTTTGATAAAATTATTTAA-AATAACATTTATTT-TAAAAAAA
106258 ATAATGTTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
60 7 0.15
61 41 0.85
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (61 bp):
TTAATATTTTTTAATATTTTTGATAAAATTATTTAAAATAACATTTATTTTAAAAAAATTA
Found at i:118738 original size:22 final size:22
Alignment explanation
Indices: 118707--118748 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
118697 ATTAAGTCAT
118707 TCATCTATTATTAT-TTTTTAG
1 TCATCTATTATTATCTTTTTAG
118728 TCATCTAATTATTATCTTTTT
1 TCATCT-ATTATTATCTTTTT
118749 CCAAAATCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.32
22 8 0.42
23 5 0.26
ACGTcount: A:0.24, C:0.12, G:0.02, T:0.62
Consensus pattern (22 bp):
TCATCTATTATTATCTTTTTAG
Found at i:121974 original size:32 final size:32
Alignment explanation
Indices: 121906--121985 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
121896 AAAAATTGGT
* * *
121906 AAATTTAATGATTATTTTATATCAAATTTGAT
1 AAATTTAATGATCATTTTATATCAAATTTAAA
*
121938 AAATTTAATGATCATTTTATAT-TAATTCTAAA
1 AAATTTAATGATCATTTTATATCAAATT-TAAA
*
121970 AAA-TTAATAATCATTT
1 AAATTTAATGATCATTT
121986 ATAAATTTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
31 16 0.38
32 26 0.62
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (32 bp):
AAATTTAATGATCATTTTATATCAAATTTAAA
Found at i:124805 original size:7 final size:7
Alignment explanation
Indices: 124793--124823 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
124783 AAAACTATCA
124793 ATGTAAT
1 ATGTAAT
124800 ATGTAAT
1 ATGTAAT
124807 ATGTAAT
1 ATGTAAT
124814 ATGTAAT
1 ATGTAAT
124821 ATG
1 ATG
124824 CATATTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (7 bp):
ATGTAAT
Found at i:125380 original size:30 final size:30
Alignment explanation
Indices: 125303--125383 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
125293 TAGACAGTAA
** *
125303 AATCAAGTCACTTAATCAATCAATTGTAAC
1 AATCAAGTCACTTAATTTATCAATTGGAAC
*
125333 AATC-AGATCACTCAATTTATCAATTGGAAC
1 AATCAAG-TCACTTAATTTATCAATTGGAAC
*
125363 AATCAAGTCATTTAATTTATC
1 AATCAAGTCACTTAATTTATC
125384 GTTTAAAGCA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.05
30 39 0.91
31 2 0.05
ACGTcount: A:0.41, C:0.19, G:0.07, T:0.33
Consensus pattern (30 bp):
AATCAAGTCACTTAATTTATCAATTGGAAC
Found at i:132889 original size:9 final size:9
Alignment explanation
Indices: 132875--132902 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
132865 CGGTCTTTTA
132875 TCGTTGTTG
1 TCGTTGTTG
132884 TCGTTGTTG
1 TCGTTGTTG
132893 TCGTTGTTG
1 TCGTTGTTG
132902 T
1 T
132903 TTTCTAGTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.11, G:0.32, T:0.57
Consensus pattern (9 bp):
TCGTTGTTG
Found at i:148614 original size:19 final size:19
Alignment explanation
Indices: 148582--148630 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
148572 ATCTGGAGAA
* * *
148582 AAAATATATGAAATTAAAT
1 AAAATAAATAAAATAAAAT
* *
148601 TAAATTAATAAAATAAAAT
1 AAAATAAATAAAATAAAAT
148620 AAAATAAATAA
1 AAAATAAATAA
148631 TATGATATAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAATAAATAAAATAAAAT
Found at i:148640 original size:19 final size:18
Alignment explanation
Indices: 148618--148656 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
148608 ATAAAATAAA
148618 ATAAAATAAATAATATGAT
1 ATAAAATAAATAATAT-AT
* *
148637 ATAAACTATATAATATAT
1 ATAAAATAAATAATATAT
148655 AT
1 AT
148657 TTCAAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (18 bp):
ATAAAATAAATAATATAT
Found at i:148809 original size:36 final size:36
Alignment explanation
Indices: 148639--148940 Score: 190
Period size: 36 Copynumber: 8.5 Consensus size: 36
148629 AATATGATAT
* *
148639 AAACTATATAATATAT-ATTTCAAAAATATGTTTTAGA
1 AAACTATATATTATATAATTTCAAAAA-ATGTTTT-TA
* * **
148676 AAACTATATA-T-TAT-ACTT-AAAAAAAGTTTCCA
1 AAACTATATATTATATAATTTCAAAAAATGTTTTTA
* * *
148708 AAACTATATA-TACATAGTTTTC--AAAACG-TTTT-
1 AAACTATATATTATATA-ATTTCAAAAAATGTTTTTA
148740 AAA--A-ATATTATATAAGTTTTCAAAAAAATGTTTTTA
1 AAACTATATATTATATAA--TTTC-AAAAAATGTTTTTA
148776 AAACTATATATTATATAATTTCAAAAAATGTTTTTA
1 AAACTATATATTATATAATTTCAAAAAATGTTTTTA
** *
148812 AAACTATATACTATATATGTTTTC--AAAATGTTTTAA
1 AAACTATATA-T-TATATAATTTCAAAAAATGTTTTTA
* *
148848 AAACTATATAATATATAAACGTTTTC--AAAATGTTTTCA
1 AAACTATATATTATAT-AA---TTTCAAAAAATGTTTTTA
* **
148886 AAACTATATATTATATATATTTTAAAAATAT-TTTCAA
1 AAACTATATATTATATA-ATTTCAAAAA-ATGTTTTTA
*
148923 AAACTATATAATATATAA
1 AAACTATATATTATATAA
148941 ATTTTCGAAA
Statistics
Matches: 215, Mismatches: 25, Indels: 51
0.74 0.09 0.18
Matches are distributed among these distances:
29 3 0.01
30 6 0.03
31 4 0.02
32 15 0.07
33 9 0.04
34 20 0.09
35 15 0.07
36 50 0.23
37 39 0.18
38 43 0.20
39 11 0.05
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (36 bp):
AAACTATATATTATATAATTTCAAAAAATGTTTTTA
Found at i:148971 original size:75 final size:72
Alignment explanation
Indices: 148763--149006 Score: 221
Period size: 74 Copynumber: 3.3 Consensus size: 72
148753 AAGTTTTCAA
* * * * *
148763 AAAAATGTTTTTAAAACTATATATTATAT-AA--TTTCAAAAAATGTTTTTAAAACTATATACTA
1 AAAAATATTTTAAAAACTATATAATATATAAACTTTTC--AAAATATTTTCAAAACTATATA-TA
*
148825 TATATGTTTT
63 TATATATTTT
* * *
148835 CAAAATGTTTTAAAAACTATATAATATATAAACGTTTTCAAAATGTTTTCAAAACTATATATTAT
1 AAAAATATTTTAAAAACTATATAATATATAAAC-TTTTCAAAATATTTTCAAAACTATATA-TAT
148900 ATATATTTT
64 ATATATTTT
*
148909 AAAAATATTTTCAAAAACTATATAATATATAAA-TTTTCGAAAATCATTTTCTGAAAATTATATA
1 AAAAATATTTT-AAAAACTATATAATATATAAACTTTTC-AAAAT-ATTTTC--AAAACTATATA
148973 T-TATAT-TTTGT
61 TATATATATTT-T
* *
148984 CAAAAACATTTTTACAAACTATA
1 -AAAAATA-TTTTAAAAACTATA
149007 ATAAAAAAAC
Statistics
Matches: 148, Mismatches: 12, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
72 26 0.18
73 7 0.05
74 49 0.33
75 32 0.22
76 20 0.14
77 14 0.09
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (72 bp):
AAAAATATTTTAAAAACTATATAATATATAAACTTTTCAAAATATTTTCAAAACTATATATATAT
ATATTTT
Found at i:150413 original size:65 final size:65
Alignment explanation
Indices: 150309--150444 Score: 263
Period size: 65 Copynumber: 2.1 Consensus size: 65
150299 AATTCTAGAG
*
150309 GCAAACGTGTTCTAGAATTGGTTCACTCTGATGTATGACAAGCACCGGTTACATCCCTAGGCGGA
1 GCAAAAGTGTTCTAGAATTGGTTCACTCTGATGTATGACAAGCACCGGTTACATCCCTAGGCGGA
150374 GCAAAAGTGTTCTAGAATTGGTTCACTCTGATGTATGACAAGCACCGGTTACATCCCTAGGCGGA
1 GCAAAAGTGTTCTAGAATTGGTTCACTCTGATGTATGACAAGCACCGGTTACATCCCTAGGCGGA
150439 GCAAAA
1 GCAAAA
150445 TATTTTGTCT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 70 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (65 bp):
GCAAAAGTGTTCTAGAATTGGTTCACTCTGATGTATGACAAGCACCGGTTACATCCCTAGGCGGA
Found at i:160995 original size:16 final size:18
Alignment explanation
Indices: 160963--160995 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
160953 CATTTGGATT
160963 AATGAAGACACAAACAAC
1 AATGAAGACACAAACAAC
160981 AATGAAG-CA-AAACAA
1 AATGAAGACACAAACAA
160996 AAGTATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.64, C:0.18, G:0.12, T:0.06
Consensus pattern (18 bp):
AATGAAGACACAAACAAC
Found at i:165076 original size:17 final size:18
Alignment explanation
Indices: 165044--165077 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
165034 TAATTAAATA
165044 AAATACTAACAAAATATT
1 AAATACTAACAAAATATT
*
165062 AAATA-TAATAAAATAT
1 AAATACTAACAAAATAT
165078 ACCTTAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATACTAACAAAATATT
Found at i:165753 original size:24 final size:24
Alignment explanation
Indices: 165726--165799 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 24
165716 TTGTTCACGA
165726 ATATGTTCATGAACATGTTTGTTT
1 ATATGTTCATGAACATGTTTGTTT
* *
165750 ATATCTTCAT-AA-ATGTATTCATTT
1 ATATGTTCATGAACATGT-TT-GTTT
* * *
165774 AT-CGTTCATGAACGTGTTCGTTT
1 ATATGTTCATGAACATGTTTGTTT
165797 ATA
1 ATA
165800 CATATTCAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
22 4 0.11
23 14 0.37
24 17 0.45
25 3 0.08
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.47
Consensus pattern (24 bp):
ATATGTTCATGAACATGTTTGTTT
Found at i:165797 original size:23 final size:23
Alignment explanation
Indices: 165730--165798 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 23
165720 TCACGAATAT
* *
165730 GTTCATGAACATGTTTGTTTATATC
1 GTTCATGAACGTGTTCG-TT-TATC
* * * *
165755 -TTCATAAATGTATTCATTTATC
1 GTTCATGAACGTGTTCGTTTATC
165777 GTTCATGAACGTGTTCGTTTAT
1 GTTCATGAACGTGTTCGTTTAT
165799 ACATATTCAA
Statistics
Matches: 33, Mismatches: 10, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
22 4 0.12
23 19 0.58
24 10 0.30
ACGTcount: A:0.25, C:0.13, G:0.14, T:0.48
Consensus pattern (23 bp):
GTTCATGAACGTGTTCGTTTATC
Found at i:169489 original size:17 final size:19
Alignment explanation
Indices: 169453--169491 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
169443 TGCATTAATC
*
169453 AAAATTACTAAAATTGGTA
1 AAAATTACTAAAATTAGTA
169472 AAAATTA-T-AAATTAGTA
1 AAAATTACTAAAATTAGTA
169489 AAA
1 AAA
169492 GTAATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
18 1 0.05
19 7 0.37
ACGTcount: A:0.59, C:0.03, G:0.08, T:0.31
Consensus pattern (19 bp):
AAAATTACTAAAATTAGTA
Found at i:169920 original size:2 final size:2
Alignment explanation
Indices: 169913--169944 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
169903 TTATAAATAA
169913 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
169945 TTCTATTTAT
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:172498 original size:35 final size:34
Alignment explanation
Indices: 172452--172547 Score: 102
Period size: 35 Copynumber: 2.7 Consensus size: 34
172442 CACACAATCA
* *
172452 TCAATTATATTCTTAACCCAAAATTTCAAAATACT
1 TCAATTATATTCTAAACCC-AAATTCCAAAATACT
* *
172487 TCAATTATATTCTAAAGCTCAAATTCCAAAGTACT
1 TCAATTATATTCTAAA-CCCAAATTCCAAAATACT
* * *
172522 TCAATTACATGCTCAACCCCAAATTC
1 TCAATTATATTCT-AAACCCAAATTC
172548 ATAATCTATT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
35 47 0.92
36 4 0.08
ACGTcount: A:0.40, C:0.24, G:0.03, T:0.33
Consensus pattern (34 bp):
TCAATTATATTCTAAACCCAAATTCCAAAATACT
Found at i:185923 original size:50 final size:50
Alignment explanation
Indices: 185838--185936 Score: 144
Period size: 50 Copynumber: 2.0 Consensus size: 50
185828 TTTTGAAAAA
* *
185838 AATGAAAATCTAAGTACCAAAACACGTTTAATACCTAAACCATACTTAAT
1 AATGAAAATCTAAGTACCAAAAAACATTTAATACCTAAACCATACTTAAT
* * * *
185888 AATGAAAGTCTAGGTACCAAAAAACATTTACTACCTAAATCATACTTAA
1 AATGAAAATCTAAGTACCAAAAAACATTTAATACCTAAACCATACTTAA
185937 GTTTTGGATT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.47, C:0.19, G:0.07, T:0.26
Consensus pattern (50 bp):
AATGAAAATCTAAGTACCAAAAAACATTTAATACCTAAACCATACTTAAT
Found at i:188440 original size:15 final size:15
Alignment explanation
Indices: 188420--188450 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
188410 TAGGTATGAT
188420 TAAAAAAATTGAAAA
1 TAAAAAAATTGAAAA
188435 TAAAAAAATTGAAAA
1 TAAAAAAATTGAAAA
188450 T
1 T
188451 TTAAATACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (15 bp):
TAAAAAAATTGAAAA
Found at i:190891 original size:24 final size:24
Alignment explanation
Indices: 190864--190910 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
190854 AAAGTTTTGT
190864 TGTGCAACCCCTGAATTTTTATCC
1 TGTGCAACCCCTGAATTTTTATCC
190888 TGTGCAACCCCTGAATTTTTATC
1 TGTGCAACCCCTGAATTTTTATC
190911 TTGGGTCCGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.21, C:0.28, G:0.13, T:0.38
Consensus pattern (24 bp):
TGTGCAACCCCTGAATTTTTATCC
Found at i:193299 original size:18 final size:17
Alignment explanation
Indices: 193268--193301 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
193258 ATCACCTAAA
193268 ATTTTATAAATTTATAT
1 ATTTTATAAATTTATAT
*
193285 ATTTTTTAAATTT-TAT
1 ATTTTATAAATTTATAT
193301 A
1 A
193302 AGTACACCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTTATAAATTTATAT
Found at i:194940 original size:2 final size:2
Alignment explanation
Indices: 194933--194959 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
194923 ACAATACTCT
194933 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 T
194960 TAAAGAATAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:197870 original size:23 final size:25
Alignment explanation
Indices: 197843--197888 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
197833 TTAATTGTGC
197843 CCAC-TTTCGGTGCA-TTGTTTAAT
1 CCACTTTTCGGTGCATTTGTTTAAT
*
197866 CCACTTTTCGGTGGATTTGTTTA
1 CCACTTTTCGGTGCATTTGTTTA
197889 GTTTTCAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 9 0.45
25 7 0.35
ACGTcount: A:0.15, C:0.20, G:0.20, T:0.46
Consensus pattern (25 bp):
CCACTTTTCGGTGCATTTGTTTAAT
Found at i:202355 original size:20 final size:20
Alignment explanation
Indices: 202330--202368 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
202320 TTTTTCCTTT
*
202330 AGGGGGAATCGATTCCCCCC
1 AGGGGGAATCGATACCCCCC
202350 AGGGGGAATCGATACCCCC
1 AGGGGGAATCGATACCCCC
202369 TGAACATACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.33, G:0.31, T:0.13
Consensus pattern (20 bp):
AGGGGGAATCGATACCCCCC
Found at i:205452 original size:13 final size:13
Alignment explanation
Indices: 205434--205458 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
205424 TCCATTATCA
205434 TTACCATATTTAT
1 TTACCATATTTAT
205447 TTACCATATTTA
1 TTACCATATTTA
205459 GCTCAACTGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (13 bp):
TTACCATATTTAT
Found at i:205569 original size:21 final size:21
Alignment explanation
Indices: 205544--205620 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 21
205534 TAATAGCACC
205544 TTAATTTTTTAAACGAAATCT
1 TTAATTTTTTAAACGAAATCT
* * *
205565 TTAA-TTTTTAATCTATTAATAGCACC
1 TTAATTTTTTAAACGA--AAT----CT
205591 TTAATTTTTTAAACGAAATCT
1 TTAATTTTTTAAACGAAATCT
205612 TTAATTTTT
1 TTAATTTTT
205621 AATCTAGGGT
Statistics
Matches: 43, Mismatches: 6, Indels: 14
0.68 0.10 0.22
Matches are distributed among these distances:
20 9 0.21
21 14 0.33
22 3 0.07
25 3 0.07
26 5 0.12
27 9 0.21
ACGTcount: A:0.35, C:0.10, G:0.04, T:0.51
Consensus pattern (21 bp):
TTAATTTTTTAAACGAAATCT
Found at i:205593 original size:47 final size:47
Alignment explanation
Indices: 205533--205626 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
205523 TTAACATTAT
205533 TTAATAGCACCTTAATTTTTTAAACGAAATCTTTAATTTTTAATCTA
1 TTAATAGCACCTTAATTTTTTAAACGAAATCTTTAATTTTTAATCTA
205580 TTAATAGCACCTTAATTTTTTAAACGAAATCTTTAATTTTTAATCTA
1 TTAATAGCACCTTAATTTTTTAAACGAAATCTTTAATTTTTAATCTA
205627 GGGTACAACC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.36, C:0.13, G:0.04, T:0.47
Consensus pattern (47 bp):
TTAATAGCACCTTAATTTTTTAAACGAAATCTTTAATTTTTAATCTA
Found at i:205681 original size:2 final size:2
Alignment explanation
Indices: 205674--205703 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
205664 TCAATCAAAT
205674 TA TA TA TA TA TA -A 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 T
205704 TCCAATGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:214412 original size:25 final size:25
Alignment explanation
Indices: 214392--214444 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
214382 TAATATTTTT
*
214392 TATTTTTTATATTAATTATATATAA
1 TATTTTATATATTAATTATATATAA
214417 TATTTTATATATTAATTATATATAA
1 TATTTTATATATTAATTATATATAA
214442 TAT
1 TAT
214445 ATAATATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TATTTTATATATTAATTATATATAA
Found at i:214451 original size:25 final size:25
Alignment explanation
Indices: 214399--214471 Score: 91
Period size: 25 Copynumber: 3.0 Consensus size: 25
214389 TTTTATTTTT
* *
214399 TATATTAATTATATATAATATTTTA
1 TATATTAATTATATATAATATATAA
214424 TATATTAATTATATATAATATATAA
1 TATATTAATTATATATAATATATAA
214449 TAT-TT--TTATAT-TAATTATATAA
1 TATATTAATTATATATAA-TATATAA
214471 T
1 T
214472 TCAAACCCTA
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
21 3 0.07
22 14 0.31
24 2 0.04
25 26 0.58
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TATATTAATTATATATAATATATAA
Found at i:214532 original size:16 final size:16
Alignment explanation
Indices: 214511--214543 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
214501 CTAGCTTTTA
214511 TAATTATGTATGTGTT
1 TAATTATGTATGTGTT
214527 TAATTATGTATGTGTT
1 TAATTATGTATGTGTT
214543 T
1 T
214544 TATTTTGGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (16 bp):
TAATTATGTATGTGTT
Found at i:215472 original size:92 final size:93
Alignment explanation
Indices: 215344--215532 Score: 344
Period size: 92 Copynumber: 2.0 Consensus size: 93
215334 ATTTTGTTGG
*
215344 TCAAGTAAGTTTTAATTTTTTTTTTCATTATTAGAGTATTTAAACTGGTGAATGGACGAAGATCT
1 TCAAGTAAGTTTTAATTTTTTTTTTCATTATTAGAGTATTTAAACTGGCGAATGGACGAAGATCT
*
215409 CTCTATGCTAAACGAGTTGTAGAGGACC
66 CTCTACGCTAAACGAGTTGTAGAGGACC
*
215437 TCAAGTAAGTTTT-ATTTTTTTTTTCATTATTAGAGTGTTTAAACTGGCGAATGGACGAAGATCT
1 TCAAGTAAGTTTTAATTTTTTTTTTCATTATTAGAGTATTTAAACTGGCGAATGGACGAAGATCT
215501 CTCTACGCTAAACGAGTTGTAGAGGACC
66 CTCTACGCTAAACGAGTTGTAGAGGACC
215529 TCAA
1 TCAA
215533 AGTTTTTATA
Statistics
Matches: 93, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
92 80 0.86
93 13 0.14
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.38
Consensus pattern (93 bp):
TCAAGTAAGTTTTAATTTTTTTTTTCATTATTAGAGTATTTAAACTGGCGAATGGACGAAGATCT
CTCTACGCTAAACGAGTTGTAGAGGACC
Found at i:216236 original size:29 final size:29
Alignment explanation
Indices: 216199--216256 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
216189 AATGATTCTT
* *
216199 TGAGGTGTAACAACTACAGTATGAGGTAA
1 TGAGATGTAACAACTAAAGTATGAGGTAA
*
216228 TGAGATGTAACACCTAAAGTATGAGGTAA
1 TGAGATGTAACAACTAAAGTATGAGGTAA
216257 GTATCTCAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.40, C:0.10, G:0.26, T:0.24
Consensus pattern (29 bp):
TGAGATGTAACAACTAAAGTATGAGGTAA
Found at i:217208 original size:95 final size:95
Alignment explanation
Indices: 217095--217286 Score: 343
Period size: 95 Copynumber: 2.0 Consensus size: 95
217085 AATTCATTTC
217095 TTTTTATCATAATCAGCTGTCGTTCATATGTATTCGCCAAGTACAAATATAAATTAAATCAAGAT
1 TTTTTATCATAATCAGCTGTCGTTCATATGTATTCGCCAAGTA-AAA-ATAAATTAAATCAAGAT
217160 GTGCATAGTTG-AAGTGATAATGTTAAACATT
64 GTGCATAGTTGAAAGTGATAATGTTAAACATT
217191 TTTTTATC-TAATCAGCTGTCGTTCATATGTATTCGCCAAGTAAAAATAAATTAAATCAAGATGT
1 TTTTTATCATAATCAGCTGTCGTTCATATGTATTCGCCAAGTAAAAATAAATTAAATCAAGATGT
217255 GCATAGTTGATAAGTGATAATGTTAAACATT
66 GCATAGTTGA-AAGTGATAATGTTAAACATT
217286 T
1 T
217287 GTAAAAATAT
Statistics
Matches: 94, Mismatches: 0, Indels: 5
0.95 0.00 0.05
Matches are distributed among these distances:
93 28 0.30
94 3 0.03
95 55 0.59
96 8 0.09
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (95 bp):
TTTTTATCATAATCAGCTGTCGTTCATATGTATTCGCCAAGTAAAAATAAATTAAATCAAGATGT
GCATAGTTGAAAGTGATAATGTTAAACATT
Found at i:218194 original size:15 final size:15
Alignment explanation
Indices: 218174--218240 Score: 73
Period size: 15 Copynumber: 4.5 Consensus size: 15
218164 TTCCGAAAAA
*
218174 TGAATTAATGGAATT
1 TGAATTACTGGAATT
* **
218189 TGAATTACTAGAAAA
1 TGAATTACTGGAATT
218204 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
218219 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
218233 TGAATTAC
1 TGAATTAC
218241 ATTTCTGGAA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
14 12 0.29
15 30 0.71
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.34
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:218240 original size:29 final size:30
Alignment explanation
Indices: 218170--218240 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
218160 GGTTTTCCGA
*
218170 AAAATGAATTAATGGAATTTGAATTACTAG
1 AAAATGAATTACTGGAATTTGAATTACTAG
*
218200 AAAATGAATTACTGGAATTTGAATT-CTGG
1 AAAATGAATTACTGGAATTTGAATTACTAG
218229 AAAATGAATTAC
1 AAAATGAATTAC
218241 ATTTCTGGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 15 0.38
30 24 0.62
ACGTcount: A:0.45, C:0.06, G:0.17, T:0.32
Consensus pattern (30 bp):
AAAATGAATTACTGGAATTTGAATTACTAG
Found at i:218246 original size:20 final size:20
Alignment explanation
Indices: 218223--218292 Score: 140
Period size: 20 Copynumber: 3.5 Consensus size: 20
218213 GGAATTTGAA
218223 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
218243 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
218263 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
218283 TTCTGGAAAA
1 TTCTGGAAAA
218293 CATATGGAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:218694 original size:29 final size:30
Alignment explanation
Indices: 218634--218702 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
218624 TAAATAATAT
218634 TATTCATTATTAAATAATAAAAAAATTATTA
1 TATT-ATTATTAAATAATAAAAAAATTATTA
* * *
218665 TA-TATTATTAAATAA-AAATATATATCTTA
1 TATTATTATTAAATAATAAAAAAAT-TATTA
218694 TATTATTAT
1 TATTATTAT
218703 ATATAATTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 6 0.18
29 18 0.55
30 7 0.21
31 2 0.06
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (30 bp):
TATTATTATTAAATAATAAAAAAATTATTA
Found at i:218708 original size:29 final size:27
Alignment explanation
Indices: 218618--218708 Score: 73
Period size: 29 Copynumber: 3.3 Consensus size: 27
218608 ATATGTTTTA
*
218618 AATATATAAATAA-TATTAT-TCATTATT
1 AATATA-AAAAAATTATTATAT-ATTATT
218645 AAATAATAAAAAAATTATTATATATTATT
1 -AAT-ATAAAAAAATTATTATATATTATT
*
218674 AA-ATAAAAATATATATCT-TATATTATT
1 AATATAAAAAAAT-TAT-TATATATTATT
218701 ATATATAA
1 A-ATATAA
218709 TTGATTATAT
Statistics
Matches: 54, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
26 9 0.17
27 13 0.24
28 12 0.22
29 19 0.35
30 1 0.02
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (27 bp):
AATATAAAAAAATTATTATATATTATT
Found at i:218752 original size:22 final size:23
Alignment explanation
Indices: 218665--218752 Score: 74
Period size: 25 Copynumber: 3.7 Consensus size: 23
218655 AAAATTATTA
218665 TATATTATTAAATAAAAATATATATCT
1 TATATTATT-AATAAAAATATA-A--T
* *
218692 TATATTATT-ATATATAAT-TGAT
1 TATATTATTAATA-AAAATATAAT
218714 TATATTATTAAACTAAAAATATAAT
1 TATATTATT-AA-TAAAAATATAAT
218739 TATATTATT-ATAAA
1 TATATTATTAATAAA
218753 TATTAATAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
22 14 0.27
23 1 0.02
24 6 0.12
25 18 0.35
26 4 0.08
27 9 0.17
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (23 bp):
TATATTATTAATAAAAATATAAT
Found at i:218767 original size:49 final size:48
Alignment explanation
Indices: 218664--218775 Score: 133
Period size: 49 Copynumber: 2.3 Consensus size: 48
218654 AAAAATTATT
*
218664 ATATATTATTAAATAAAAATATATATCTTATATTATTATATATAATTGA
1 ATATATTATTAAATAAAAATATATA-CTTATATTATTATATATAATTAA
*
218713 TTATATTATTAAACTAAAAATATA-A-TTATATTATTATAAATATTAA-TAA
1 ATATATTATTAAA-TAAAAATATATACTTATATTATTAT--ATA-TAATTAA
218762 ATATATT-TTAAATA
1 ATATATTATTAAATA
218776 TTTTAATAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
47 14 0.25
48 5 0.09
49 24 0.43
50 13 0.23
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (48 bp):
ATATATTATTAAATAAAAATATATACTTATATTATTATATATAATTAA
Found at i:218785 original size:76 final size:77
Alignment explanation
Indices: 218607--218792 Score: 172
Period size: 78 Copynumber: 2.4 Consensus size: 77
218597 AAATTACTAG
* * *
218607 TATATGTTTTAAATATATAAATAA-TATTATTCATTATTAAATAATAAAAAAATTATTATATATT
1 TATATATTTTAAATATTTTAATAATTATTATTCATTATTAAATAATAAAAAAATTATTATATATT
218671 ATTAAATAAAAA
66 ATTAAATAAAAA
* * * *
218683 TATATATCTTATATTATTATATATAATTGATTA-T-ATTATTAAACTAA-AAATATAATTA-TAT
1 TATATATTTTA-AATATTTTA-ATAATT-ATTATTCATTATTAAA-TAATAAA-AAAATTATTAT
218744 -TATTA-TAAATATTAATAA
61 ATATTATTAAATA--AA-AA
*
218762 -ATATATTTTAAATATTTTAATAATTAATATT
1 TATATATTTTAAATATTTTAATAATTATTATT
218793 TTGATGAAAA
Statistics
Matches: 89, Mismatches: 11, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
75 3 0.03
76 22 0.25
77 17 0.19
78 30 0.34
79 13 0.15
80 4 0.04
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (77 bp):
TATATATTTTAAATATTTTAATAATTATTATTCATTATTAAATAATAAAAAAATTATTATATATT
ATTAAATAAAAA
Found at i:219021 original size:41 final size:41
Alignment explanation
Indices: 218966--219043 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
218956 ATGAATTACG
* * *
218966 TTCCGAAAAACAAATTACGTAAAATAAACACGAAAAACATT
1 TTCCAAAAAACAAATTACATAAAACAAACACGAAAAACATT
*
219007 TTCCAAAAAACAAATTACATGAAACAAACACGAAAAA
1 TTCCAAAAAACAAATTACATAAAACAAACACGAAAAA
219044 AAACTAATTC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.59, C:0.18, G:0.06, T:0.17
Consensus pattern (41 bp):
TTCCAAAAAACAAATTACATAAAACAAACACGAAAAACATT
Found at i:229090 original size:27 final size:28
Alignment explanation
Indices: 229042--229097 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
229032 AATTTACGAA
* *
229042 TCATATATGTTTTTTTATGGTTGATAAG
1 TCATATACGTTTTTTGATGGTTGATAAG
229070 TCATATACG-TTTTTGATGGTTGATAAG
1 TCATATACGTTTTTTGATGGTTGATAAG
229097 T
1 T
229098 TATGTAGTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 18 0.69
28 8 0.31
ACGTcount: A:0.25, C:0.05, G:0.20, T:0.50
Consensus pattern (28 bp):
TCATATACGTTTTTTGATGGTTGATAAG
Found at i:229786 original size:20 final size:20
Alignment explanation
Indices: 229761--229803 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
229751 GATTTAGACG
229761 ATATTGATTGAAAAGAAAAT
1 ATATTGATTGAAAAGAAAAT
*
229781 ATATTGATTGGAAAGAAAAT
1 ATATTGATTGAAAAGAAAAT
229801 ATA
1 ATA
229804 ATGAGTGGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.30
Consensus pattern (20 bp):
ATATTGATTGAAAAGAAAAT
Found at i:233225 original size:88 final size:89
Alignment explanation
Indices: 233051--233228 Score: 297
Period size: 88 Copynumber: 2.0 Consensus size: 89
233041 ATTCGCCGCA
*
233051 CTCTCTAGTTTGCTGTGATTCTCGTTACTGTGGGTGTTGGCAAGTTGTGTCTAAAACTAATGTCG
1 CTCTCTAGTTTGCTGTGATTCTCGTTACTGAGGGTGTTGGCAAGTTGTGTCTAAAACTAATGTCG
*
233116 TGTACTTTTCAGTGTTTTTGGCTT
66 TGTACTTTGCAGTGTTTTTGGCTT
* *
233140 CTCTCTAGGTTTGCTGTGATTCTCGTTACTGAGGGTGTTGGTAAG-TGTGTCT-AAACTTATGTC
1 CTCTCTA-GTTTGCTGTGATTCTCGTTACTGAGGGTGTTGGCAAGTTGTGTCTAAAACTAATGTC
233203 GTGTACTTTGCAGTGTTTTTGGCTT
65 GTGTACTTTGCAGTGTTTTTGGCTT
233228 C
1 C
233229 GGATTTTAGC
Statistics
Matches: 84, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
88 35 0.42
89 14 0.17
90 35 0.42
ACGTcount: A:0.14, C:0.16, G:0.26, T:0.44
Consensus pattern (89 bp):
CTCTCTAGTTTGCTGTGATTCTCGTTACTGAGGGTGTTGGCAAGTTGTGTCTAAAACTAATGTCG
TGTACTTTGCAGTGTTTTTGGCTT
Found at i:246116 original size:21 final size:21
Alignment explanation
Indices: 246091--246131 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
246081 TGTAGCTTCT
*
246091 TTTTTTCTTTTTTATATATAGA
1 TTTTTT-TTCTTTATATATAGA
*
246113 TTTTTTTTCTTTTTATATA
1 TTTTTTTTCTTTATATATA
246132 AAGAAAGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTTTTTTCTTTATATATAGA
Found at i:248484 original size:31 final size:32
Alignment explanation
Indices: 248448--248514 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 32
248438 GTTTAATTTG
*
248448 TGACATGAGATATGTTATATCATCATTTT-AA
1 TGACATGAGATATGTCATATCATCATTTTGAA
* *
248479 TGACATGATATATGTCATGTCATCATTTTGAA
1 TGACATGAGATATGTCATATCATCATTTTGAA
248511 TGAC
1 TGAC
248515 GTGATGTCAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 26 0.81
32 6 0.19
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (32 bp):
TGACATGAGATATGTCATATCATCATTTTGAA
Found at i:257966 original size:14 final size:15
Alignment explanation
Indices: 257942--257971 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
257932 ATATTAAAAA
257942 ATATGTTAAAATATT
1 ATATGTTAAAATATT
257957 ATAT-TTAAAATATT
1 ATATGTTAAAATATT
257971 A
1 A
257972 AAAATACTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
ATATGTTAAAATATT
Found at i:257996 original size:2 final size:2
Alignment explanation
Indices: 257989--258013 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
257979 TACTTTTTAA
257989 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
258014 AGGAAAACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:258476 original size:20 final size:20
Alignment explanation
Indices: 258451--258492 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
258441 GTTAAAGGCG
*
258451 AAGGTTTTGTTGTGACAGCA
1 AAGGTTTTGTTGTGACAACA
258471 AAGGTTTTGTTGTGACAACA
1 AAGGTTTTGTTGTGACAACA
258491 AA
1 AA
258493 AGGAAATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.10, G:0.26, T:0.33
Consensus pattern (20 bp):
AAGGTTTTGTTGTGACAACA
Found at i:272019 original size:17 final size:17
Alignment explanation
Indices: 271993--272028 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
271983 ATATCATCCC
271993 TTATAAATTTTAAAAAT
1 TTATAAATTTTAAAAAT
* *
272010 TTATATATTTTAAATAT
1 TTATAAATTTTAAAAAT
272027 TT
1 TT
272029 TTATTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATAAATTTTAAAAAT
Found at i:276098 original size:4 final size:4
Alignment explanation
Indices: 276091--276120 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
276081 TATATATATA
276091 TATT TATT TATT TATT TATT TATTT TATT T
1 TATT TATT TATT TATT TATT TA-TT TATT T
276121 TTCTCAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TATT
Found at i:293806 original size:24 final size:23
Alignment explanation
Indices: 293779--293843 Score: 58
Period size: 26 Copynumber: 2.7 Consensus size: 23
293769 CAAATTATTG
293779 AATATTTAAAAATATAAATAAAAT
1 AATATTTAAAAATATAAA-AAAAT
* * **
293803 AATAAATTTAAAATTATTAAAATCT
1 AAT--ATTTAAAAATATAAAAAAAT
293828 ATATATTTAAAAATAT
1 A-ATATTTAAAAATAT
293844 TTATAAACTA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
24 14 0.42
25 4 0.12
26 15 0.45
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
AATATTTAAAAATATAAAAAAAT
Found at i:293844 original size:24 final size:23
Alignment explanation
Indices: 293780--293844 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 23
293770 AAATTATTGA
293780 ATATTTAAAAATATAAATAAAATAAT
1 ATATTTAAAAATAT---TAAAATAAT
* * *
293806 AAATTTAAAATTATTAAAATCTAT
1 ATATTTAAAAATATTAAAAT-AAT
293830 ATATTTAAAAATATT
1 ATATTTAAAAATATT
293845 TATAAACTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
23 6 0.18
24 15 0.45
26 12 0.36
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
ATATTTAAAAATATTAAAATAAT
Done.