Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_235
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: 119779
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:5654 original size:1 final size:1
Alignment explanation
Indices: 5597--5647 Score: 102
Period size: 1 Copynumber: 51.0 Consensus size: 1
5587 CATGAGGACC
5597 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5648 TTAAAAACTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:7838 original size:10 final size:10
Alignment explanation
Indices: 7823--7859 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
7813 AGAAGTGAGC
7823 AAAAAAGAAA
1 AAAAAAGAAA
*
7833 AAAAAAGTAA
1 AAAAAAGAAA
7843 AAAAAAGAACA
1 AAAAAAGAA-A
7854 AAAAAA
1 AAAAAA
7860 AAGTGAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 17 0.71
11 7 0.29
ACGTcount: A:0.86, C:0.03, G:0.08, T:0.03
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:8909 original size:18 final size:17
Alignment explanation
Indices: 8827--8910 Score: 60
Period size: 18 Copynumber: 4.6 Consensus size: 17
8817 GGAACAAGAA
**
8827 ATTGAAAAAGAGAGTGAG
1 ATTGAAAAAGA-AACGAG
8845 ATTGAAGAAAGAAACGAG
1 ATTGAA-AAAGAAACGAG
* *
8863 AGTGTAAAAGAAACGATG
1 ATTGAAAAAGAAACGA-G
* *
8881 TCATGGAAAAAGAAATTGAG
1 --ATTGAAAAAGAAA-CGAG
8901 ATTGAAAAAG
1 ATTGAAAAAG
8911 GATGTGAAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
17 10 0.19
18 24 0.46
19 5 0.10
20 11 0.21
21 2 0.04
ACGTcount: A:0.52, C:0.04, G:0.27, T:0.17
Consensus pattern (17 bp):
ATTGAAAAAGAAACGAG
Found at i:8965 original size:48 final size:47
Alignment explanation
Indices: 8886--8991 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
8876 CGATGTCATG
*
8886 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
8934 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
8982 GAAAAAGAAA
1 GAAAAAGAAA
8992 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:10703 original size:20 final size:20
Alignment explanation
Indices: 10657--10703 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
10647 AGCTCGTTTC
*
10657 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
10677 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
10697 CAGCTCA
1 CAGCTCA
10704 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:12083 original size:10 final size:11
Alignment explanation
Indices: 12068--12096 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
12058 CAACTCAAAT
12068 TTTTTTTTGA-
1 TTTTTTTTGAC
12078 TTTTTTTTGAC
1 TTTTTTTTGAC
12089 TTTTTTTT
1 TTTTTTTT
12097 TACATTACGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTTTTTGAC
Found at i:13533 original size:20 final size:20
Alignment explanation
Indices: 13510--13556 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
13500 GGGTTAAGAT
*
13510 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
13530 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
13550 TGAGCTG
1 TGAGCTG
13557 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:14766 original size:10 final size:10
Alignment explanation
Indices: 14753--14790 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
14743 AGCTCACTCG
*
14753 AGCTCAAGTC
1 AGCTCAATTC
14763 AGCTC-ATTC
1 AGCTCAATTC
14772 AAGCTCAATTC
1 -AGCTCAATTC
14783 AGCTCAAT
1 AGCTCAAT
14791 CTTAACCCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 3 0.12
10 18 0.72
11 4 0.16
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:14767 original size:20 final size:20
Alignment explanation
Indices: 14742--14788 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
14732 AGCTCGTTTC
*
14742 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
14762 CAGCTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
14782 CAGCTCA
1 CAGCTCA
14789 ATCTTAACCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.34, G:0.15, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:17779 original size:11 final size:11
Alignment explanation
Indices: 17729--17795 Score: 55
Period size: 11 Copynumber: 5.7 Consensus size: 11
17719 TTGGAGTAAC
17729 AAAAAAA-TCA
1 AAAAAAATTCA
17739 AAAAAAATTCGAA
1 AAAAAAATTC--A
*
17752 AAAAAATTGATTGA
1 AAAAAA---ATTCA
17766 AAAAAAATTCA
1 AAAAAAATTCA
* *
17777 AAAAAAAGTGA
1 AAAAAAATTCA
17788 AAAAAAAT
1 AAAAAAAT
17796 CGAGCAAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
10 7 0.15
11 22 0.48
13 7 0.15
14 7 0.15
16 3 0.07
ACGTcount: A:0.72, C:0.04, G:0.07, T:0.16
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:17806 original size:27 final size:28
Alignment explanation
Indices: 17776--17849 Score: 73
Period size: 27 Copynumber: 2.7 Consensus size: 28
17766 AAAAAAATTC
17776 AAAAA-AAAGTGAAAAAAA-ATCGAGCAA
1 AAAAAGAAAGTGAAAAAAAGAT-GAGCAA
* *
17803 AAAAAGAAA-AGAAAAAAAGGTGAGCAA
1 AAAAAGAAAGTGAAAAAAAGATGAGCAA
** *
17830 AAAAATCAAGTTAAAAAAAG
1 AAAAAGAAAGTGAAAAAAAG
17850 TGAAAAGTCT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
27 26 0.68
28 12 0.32
ACGTcount: A:0.70, C:0.05, G:0.16, T:0.08
Consensus pattern (28 bp):
AAAAAGAAAGTGAAAAAAAGATGAGCAA
Found at i:17806 original size:37 final size:37
Alignment explanation
Indices: 17729--17807 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 37
17719 TTGGAGTAAC
* *
17729 AAAAAAATCAAAAAAAATTCGAAAAAAAATTGATTG-AA
1 AAAAAAATCAAAAAAAAGTCGAAAAAAAATCGA--GCAA
*
17767 AAAAAATTCAAAAAAAAGT-GAAAAAAAATCGAGCAA
1 AAAAAAATCAAAAAAAAGTCGAAAAAAAATCGAGCAA
17803 AAAAA
1 AAAAA
17808 GAAAAGAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 1 0.03
36 7 0.19
37 12 0.32
38 17 0.46
ACGTcount: A:0.71, C:0.06, G:0.09, T:0.14
Consensus pattern (37 bp):
AAAAAAATCAAAAAAAAGTCGAAAAAAAATCGAGCAA
Found at i:18761 original size:18 final size:17
Alignment explanation
Indices: 18726--18778 Score: 61
Period size: 18 Copynumber: 3.0 Consensus size: 17
18716 AGAAAAGAAA
*
18726 ATTGAAAAAGAGAGTGAG
1 ATTGAAAAAGA-AATGAG
18744 ATTGAAGAAAGAAATGAG
1 ATTGAA-AAAGAAATGAG
* *
18762 AGTGTAAAAGAAATGAG
1 ATTGAAAAAGAAATGAG
18779 TGTCATGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 11 0.35
18 15 0.48
19 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.30, T:0.17
Consensus pattern (17 bp):
ATTGAAAAAGAAATGAG
Found at i:18817 original size:12 final size:12
Alignment explanation
Indices: 18800--18824 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18790 AAGAGAGAGG
18800 GTTTGAAAAAGA
1 GTTTGAAAAAGA
18812 GTTTGAAAAAGA
1 GTTTGAAAAAGA
18824 G
1 G
18825 AAGAGTGAAA
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:0.48, C:0.00, G:0.28, T:0.24
Consensus pattern (12 bp):
GTTTGAAAAAGA
Found at i:20731 original size:15 final size:15
Alignment explanation
Indices: 20711--20758 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 15
20701 AAAAATCAAG
20711 AAAATTTCGAAAAAA
1 AAAATTTCGAAAAAA
*
20726 AAAATTGATTGAAAAAA
1 AAAATT--TCGAAAAAA
20743 AAAA-TTC-AAAAAA
1 AAAATTTCGAAAAAA
20756 AAA
1 AAA
20759 GTGAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
13 9 0.31
14 1 0.03
15 6 0.21
16 1 0.03
17 12 0.41
ACGTcount: A:0.71, C:0.04, G:0.06, T:0.19
Consensus pattern (15 bp):
AAAATTTCGAAAAAA
Found at i:20753 original size:12 final size:12
Alignment explanation
Indices: 20738--20771 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
20728 AATTGATTGA
20738 AAAAAAAAATTC
1 AAAAAAAAATTC
* *
20750 AAAAAAAAAGTG
1 AAAAAAAAATTC
20762 AAAAAAAAAT
1 AAAAAAAAAT
20772 CGAGCAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.79, C:0.03, G:0.06, T:0.12
Consensus pattern (12 bp):
AAAAAAAAATTC
Found at i:20813 original size:32 final size:31
Alignment explanation
Indices: 20750--20822 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
20740 AAAAAAATTC
*
20750 AAAAAAAAAGTG---AAAAAAAAATCGAGCA
1 AAAAAAAAAGTGACCAAAAAAAAATCAAGCA
* *
20778 AAAAAAAAGGTGACCAAAAAAAAATCAAGTTA
1 AAAAAAAAAGTGACCAAAAAAAAATCAAG-CA
20810 AAAAAAAAAGTGA
1 AAAAAAAAAGTGA
20823 AAAGTCTTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 11 0.30
31 13 0.35
32 13 0.35
ACGTcount: A:0.70, C:0.07, G:0.14, T:0.10
Consensus pattern (31 bp):
AAAAAAAAAGTGACCAAAAAAAAATCAAGCA
Found at i:21759 original size:17 final size:17
Alignment explanation
Indices: 21739--21772 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
21729 GTGAGCGAGA
21739 AAATGAAA-AAGAAAAAG
1 AAATGAAAGAA-AAAAAG
21756 AAATGAAAGAAAAAAAG
1 AAATGAAAGAAAAAAAG
21773 GATGAGTGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (17 bp):
AAATGAAAGAAAAAAAG
Found at i:21892 original size:17 final size:18
Alignment explanation
Indices: 21860--21893 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21850 AAAAGAGAGT
*
21860 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
21878 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
21894 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:24729 original size:22 final size:22
Alignment explanation
Indices: 24678--24743 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
24668 GGTATTTGGG
* *
24678 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
24699 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
24721 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
24744 TCAAAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:27835 original size:30 final size:30
Alignment explanation
Indices: 27760--27843 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 30
27750 CTAAAATGAT
* *
27760 CTAAGTTTTAGCTCGTGAGCTAAAGTTAAG
1 CTAAGGTTTAGCTCCTGAGCTAAAGTTAAG
* * * * * * *
27790 CTGAGGCTAAACTCCTAAGCTGAAGTTGAG
1 CTAAGGTTTAGCTCCTGAGCTAAAGTTAAG
27820 CTAAGGTTTAGCTCCTGAGCTAAA
1 CTAAGGTTTAGCTCCTGAGCTAAA
27844 TATGAGCTAG
Statistics
Matches: 39, Mismatches: 15, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.29
Consensus pattern (30 bp):
CTAAGGTTTAGCTCCTGAGCTAAAGTTAAG
Found at i:27850 original size:30 final size:29
Alignment explanation
Indices: 27750--27852 Score: 80
Period size: 30 Copynumber: 3.4 Consensus size: 29
27740 CGAGTTTAAA
* * * *
27750 CTAAAATGATCTAAGTTTTAGCTCGTGAG
1 CTAAATTGAGCTAAGGTTTAGCTCCTGAG
* * * * * *
27779 CTAAAGTTAAGCTGAGGCTAAACTCCTAAG
1 CTAAA-TTGAGCTAAGGTTTAGCTCCTGAG
*
27809 CTGAAGTTGAGCTAAGGTTTAGCTCCTGAG
1 CT-AAATTGAGCTAAGGTTTAGCTCCTGAG
27839 CTAAATATGAGCTA
1 CTAAAT-TGAGCTA
27853 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 18, Indels: 5
0.70 0.24 0.07
Matches are distributed among these distances:
29 8 0.15
30 43 0.81
31 2 0.04
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (29 bp):
CTAAATTGAGCTAAGGTTTAGCTCCTGAG
Found at i:31464 original size:22 final size:22
Alignment explanation
Indices: 31413--31478 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
31403 GGTATTTGGG
* *
31413 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
31434 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
31456 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
31479 TCAAAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:32177 original size:22 final size:22
Alignment explanation
Indices: 32149--32192 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
32139 TTTTGAACCA
32149 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
32171 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
32193 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:42388 original size:17 final size:18
Alignment explanation
Indices: 42366--42399 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42356 ACAACACTCC
*
42366 TTTCTT-CTTCACTCTCG
1 TTTCTTCCTTCAATCTCG
42383 TTTCTTCCTTCAATCTC
1 TTTCTTCCTTCAATCTC
42400 ACTCTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.35, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTCTTCCTTCAATCTCG
Found at i:43475 original size:16 final size:16
Alignment explanation
Indices: 43440--43479 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
43430 TTTAACTTGA
43440 TTTTTTTTTGCTCACCT
1 TTTTTTTTTGCTCA-CT
43457 TTTTTTTTTGCTCGA-T
1 TTTTTTTTTGCTC-ACT
43473 TTTTTTT
1 TTTTTTT
43480 CACTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.36
17 13 0.59
18 1 0.05
ACGTcount: A:0.05, C:0.15, G:0.07, T:0.72
Consensus pattern (16 bp):
TTTTTTTTTGCTCACT
Found at i:43500 original size:14 final size:14
Alignment explanation
Indices: 43483--43545 Score: 67
Period size: 13 Copynumber: 4.5 Consensus size: 14
43473 TTTTTTTCAC
43483 TTTTTTTTTTGAAT
1 TTTTTTTTTTGAAT
* *
43497 TTTTTTTTCAATCAAT
1 TTTTTTTT--TTGAAT
*
43513 TTTTTTTTTCGAA-
1 TTTTTTTTTTGAAT
43526 TTTTTTTTTTG-AT
1 TTTTTTTTTTGAAT
43539 TTTTTTT
1 TTTTTTT
43546 GTTACTCCAA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
12 1 0.03
13 17 0.43
14 10 0.25
16 12 0.30
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.76
Consensus pattern (14 bp):
TTTTTTTTTTGAAT
Found at i:43540 original size:12 final size:12
Alignment explanation
Indices: 43472--43545 Score: 58
Period size: 13 Copynumber: 5.5 Consensus size: 12
43462 TTTTGCTCGA
*
43472 TTTTTTTTCACTT
1 TTTTTTTTGA-TT
43485 TTTTTTTTGAATT
1 TTTTTTTTG-ATT
*
43498 TTTTTTTCAATCAATT
1 TTTTTTT---T-GATT
43514 TTTTTTTTCGAATT
1 TTTTTTTT-G-ATT
43528 TTTTTTTTGATT
1 TTTTTTTTGATT
43540 TTTTTT
1 TTTTTT
43546 GTTACTCCAA
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
12 9 0.17
13 20 0.38
14 12 0.23
16 11 0.21
ACGTcount: A:0.14, C:0.07, G:0.04, T:0.76
Consensus pattern (12 bp):
TTTTTTTTGATT
Found at i:45337 original size:24 final size:25
Alignment explanation
Indices: 45284--45337 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
45274 AACAAATTCT
* *
45284 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
45309 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
45332 TTTTTT
1 TTTTTT
45338 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:46373 original size:30 final size:30
Alignment explanation
Indices: 46339--46435 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
46329 AGCTCACTCC
46339 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
46369 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
46399 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
46429 TAGCTCA
1 TAGCTCA
46436 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:48191 original size:12 final size:13
Alignment explanation
Indices: 48156--48193 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
48146 AAAGGAGAAG
48156 AAATTCAGAAAAAA
1 AAATTC-GAAAAAA
48170 AAATTC-AAAAAA
1 AAATTCGAAAAAA
48182 AAA-TCGAAAAAA
1 AAATTCGAAAAAA
48194 GGAAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 2 0.09
12 15 0.65
14 6 0.26
ACGTcount: A:0.74, C:0.08, G:0.05, T:0.13
Consensus pattern (13 bp):
AAATTCGAAAAAA
Found at i:49185 original size:37 final size:37
Alignment explanation
Indices: 49134--49204 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
49124 CATTCTTGTA
49134 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
49171 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
49205 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:49204 original size:6 final size:6
Alignment explanation
Indices: 49144--49193 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
49134 AAGAGAAAAC
*
49144 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
49193 A
1 A
49194 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:49286 original size:11 final size:12
Alignment explanation
Indices: 49254--49284 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
49244 TTGAGAGAAC
49254 TTGAAAAAGCCT
1 TTGAAAAAGCCT
49266 TTGAAAAAGCCT
1 TTGAAAAAGCCT
49278 TTGAAAA
1 TTGAAAA
49285 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:51499 original size:30 final size:30
Alignment explanation
Indices: 51465--51561 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
51455 AGCTCACTCC
51465 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
51495 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
51525 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
51555 TAGCTCA
1 TAGCTCA
51562 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:54552 original size:13 final size:14
Alignment explanation
Indices: 54518--54552 Score: 56
Period size: 12 Copynumber: 2.6 Consensus size: 14
54508 CCGTATGCAA
54518 TTTTTTTTTGAAAC
1 TTTTTTTTTGAAAC
54532 TTTTTTTTT--AAC
1 TTTTTTTTTGAAAC
54544 TTTTTTTTT
1 TTTTTTTTT
54553 CGAAGCTACG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.57
14 9 0.43
ACGTcount: A:0.14, C:0.06, G:0.03, T:0.77
Consensus pattern (14 bp):
TTTTTTTTTGAAAC
Found at i:58144 original size:33 final size:33
Alignment explanation
Indices: 58106--58168 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
58096 GATTACTCAC
58106 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
58139 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
58169 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:58195 original size:21 final size:21
Alignment explanation
Indices: 58166--58221 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
58156 CAAGCTCTCT
*
58166 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
58187 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
58208 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
58222 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:58208 original size:18 final size:18
Alignment explanation
Indices: 58183--58270 Score: 77
Period size: 18 Copynumber: 4.7 Consensus size: 18
58173 TCTTTTTTCG
58183 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTCAA-TTT
* **
58202 CTTTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCAATTT
* ** *
58222 CTCTCACTTTTTCGATTT
1 CTTTTTCTTTTTCAATTT
*
58240 CTTTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCAATTT
58258 CTTTTTCTTTTTC
1 CTTTTTCTTTTTC
58271 TCGATCAATG
Statistics
Matches: 52, Mismatches: 15, Indels: 5
0.72 0.21 0.07
Matches are distributed among these distances:
18 34 0.65
19 3 0.06
20 7 0.13
21 8 0.15
ACGTcount: A:0.08, C:0.20, G:0.02, T:0.69
Consensus pattern (18 bp):
CTTTTTCTTTTTCAATTT
Found at i:58214 original size:14 final size:14
Alignment explanation
Indices: 58165--58221 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
58155 TCAAGCTCTC
58165 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
58178 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
58192 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
58206 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
58220 TT
1 TT
58222 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:58268 original size:5 final size:6
Alignment explanation
Indices: 58183--58271 Score: 61
Period size: 6 Copynumber: 14.3 Consensus size: 6
58173 TCTTTTTTCG
* * * **
58183 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * **
58234 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CT
58272 CGATCAATGG
Statistics
Matches: 60, Mismatches: 21, Indels: 4
0.71 0.25 0.05
Matches are distributed among these distances:
6 48 0.80
7 9 0.15
8 3 0.05
ACGTcount: A:0.08, C:0.20, G:0.02, T:0.70
Consensus pattern (6 bp):
CTTTTT
Found at i:59336 original size:12 final size:13
Alignment explanation
Indices: 59321--59353 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
59311 TTTTGCTCGA
59321 TTTTTTTTTC-AC
1 TTTTTTTTTCTAC
*
59333 TTTTTTTTTCTTC
1 TTTTTTTTTCTAC
59346 TTTTTTTT
1 TTTTTTTT
59354 AACTCGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTTTTTCTAC
Found at i:59337 original size:41 final size:39
Alignment explanation
Indices: 59256--59393 Score: 141
Period size: 40 Copynumber: 3.3 Consensus size: 39
59246 GACTTTTCAC
*
59256 TTCTTTTTTTTAAACTTGATTTTTTTTTGCTCACCTTTTTTTTCTT
1 TTCTTTTTTTT-AACTCGA--TTTTTTTG-TCA-C-TTTTTTT-TT
** *
59302 TTCTTTTTTTTTTGCTCGATTTTTTTTTCACTTTTTTTTT
1 TTC-TTTTTTTTAACTCGATTTTTTTGTCACTTTTTTTTT
59342 CTTCTTTTTTTTAACTCGATTTTTTTGTCACTTCTTTTTTT
1 -TTCTTTTTTTTAACTCGATTTTTTTGTCACTT-TTTTTTT
*
59383 TTCCTTTTTTT
1 TTCTTTTTTTT
59394 CGATTTTTTT
Statistics
Matches: 81, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
40 38 0.47
41 17 0.21
42 1 0.01
43 3 0.04
44 7 0.09
46 7 0.09
47 8 0.10
ACGTcount: A:0.08, C:0.15, G:0.04, T:0.72
Consensus pattern (39 bp):
TTCTTTTTTTTAACTCGATTTTTTTGTCACTTTTTTTTT
Found at i:59338 original size:14 final size:14
Alignment explanation
Indices: 59275--59393 Score: 52
Period size: 14 Copynumber: 8.5 Consensus size: 14
59265 TTAAACTTGA
*
59275 TTTTTTTTTGCTCACC
1 TTTTTTTTT-TTCA-C
*
59291 TTTTTTTTCTTT-TC
1 TTTTTTTT-TTTCAC
* *
59305 TTTTTTTTTTGCTC
1 TTTTTTTTTTTCAC
**
59319 GATTTTTTTTTCAC
1 TTTTTTTTTTTCAC
59333 --TTTTTTTTT--C
1 TTTTTTTTTTTCAC
* *
59343 TTCTTTTTTTTAAC
1 TTTTTTTTTTTCAC
* *
59357 TCGATTTTTTTGTCAC
1 T--TTTTTTTTTTCAC
59373 TTCTTTTTTTTTC-C
1 TT-TTTTTTTTTCAC
59387 TTTTTTT
1 TTTTTTT
59394 CGATTTTTTT
Statistics
Matches: 80, Mismatches: 14, Indels: 21
0.70 0.12 0.18
Matches are distributed among these distances:
10 1 0.01
12 17 0.21
13 7 0.09
14 26 0.32
15 9 0.11
16 19 0.24
17 1 0.01
ACGTcount: A:0.06, C:0.16, G:0.04, T:0.74
Consensus pattern (14 bp):
TTTTTTTTTTTCAC
Found at i:59340 original size:31 final size:31
Alignment explanation
Indices: 59275--59341 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
59265 TTAAACTTGA
*
59275 TTTTTTTTTGCTCACCTTTTTTTTCTTTTCT
1 TTTTTTTTTGCTCACCTTTTTTTTCCTTTCT
*
59306 TTTTTTTTTGCTCGA-TTTTTTTTTCACTTT-T
1 TTTTTTTTTGCTC-ACCTTTTTTTTC-CTTTCT
59337 TTTTT
1 TTTTT
59342 CTTCTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 28 0.88
32 4 0.12
ACGTcount: A:0.04, C:0.15, G:0.04, T:0.76
Consensus pattern (31 bp):
TTTTTTTTTGCTCACCTTTTTTTTCCTTTCT
Found at i:59412 original size:10 final size:11
Alignment explanation
Indices: 59387--59422 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
59377 TTTTTTTTCC
* *
59387 TTTTTTTCGAT
1 TTTTTTTTGAA
59398 TTTTTTTTGAA
1 TTTTTTTTGAA
59409 TTTTTTTTGAA
1 TTTTTTTTGAA
59420 TTT
1 TTT
59423 CTTCTCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.14, C:0.03, G:0.08, T:0.75
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:61314 original size:11 final size:11
Alignment explanation
Indices: 61298--61331 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
61288 ATCAAATGAG
61298 AGAAAAAGAAA
1 AGAAAAAGAAA
61309 AGAAAAATGAAA
1 AGAAAAA-GAAA
61321 A-AAAAAGAAA
1 AGAAAAAGAAA
61331 A
1 A
61332 TTCAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 5 0.23
11 12 0.55
12 5 0.23
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (11 bp):
AGAAAAAGAAA
Found at i:61326 original size:17 final size:17
Alignment explanation
Indices: 61299--61346 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
61289 TCAAATGAGA
61299 GAAAAAGAAAAGAAAAAT
1 GAAAAA-AAAAGAAAAAT
*
61317 GAAAAAAAAAGAAAATT
1 GAAAAAAAAAGAAAAAT
* *
61334 CAAAAAAAGAGAA
1 GAAAAAAAAAGAA
61347 TGAAAAGAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 21 0.78
18 6 0.22
ACGTcount: A:0.77, C:0.02, G:0.15, T:0.06
Consensus pattern (17 bp):
GAAAAAAAAAGAAAAAT
Found at i:64358 original size:22 final size:22
Alignment explanation
Indices: 64330--64373 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
64320 TTTTGAACCA
64330 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
64352 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
64374 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:64595 original size:20 final size:20
Alignment explanation
Indices: 64572--64625 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
64562 AGTTTTTCCC
*
64572 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
64592 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
64612 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
64626 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:64607 original size:30 final size:30
Alignment explanation
Indices: 64572--64645 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
64562 AGTTTTTCCC
64572 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
64602 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
64632 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
64646 TGGCTTGAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:64635 original size:20 final size:20
Alignment explanation
Indices: 64572--64636 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
64562 AGTTTTTCCC
* * * *
64572 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
64592 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
64611 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
64632 AGCTC
1 AGCTC
64637 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:66276 original size:12 final size:12
Alignment explanation
Indices: 66251--66289 Score: 62
Period size: 11 Copynumber: 3.2 Consensus size: 12
66241 AAAAGAGAAG
66251 AAATTCAGAAAAA
1 AAATTCA-AAAAA
66264 AAATTCAAAAAA
1 AAATTCAAAAAA
66276 AAA-TCAAAAAA
1 AAATTCAAAAAA
66287 AAA
1 AAA
66290 GAAGTGACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 11 0.42
12 8 0.31
13 7 0.27
ACGTcount: A:0.77, C:0.08, G:0.03, T:0.13
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:68200 original size:20 final size:20
Alignment explanation
Indices: 68177--68230 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
68167 AGTTTTTCCC
*
68177 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
68197 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
68217 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
68231 TATTTAGCTC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:70915 original size:15 final size:16
Alignment explanation
Indices: 70889--70920 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
70879 GTGAGCGAGA
70889 AAATGAAAAGAAAAAG
1 AAATGAAAAGAAAAAG
70905 AAATG-AAAGAAAAAG
1 AAATGAAAAGAAAAAG
70920 A
1 A
70921 GGATGAGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (16 bp):
AAATGAAAAGAAAAAG
Found at i:71041 original size:17 final size:18
Alignment explanation
Indices: 71009--71042 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
70999 AAAAGAGAGT
*
71009 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
71027 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
71043 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:72331 original size:20 final size:20
Alignment explanation
Indices: 72308--72361 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
72298 AGTTTTTCCC
*
72308 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
72328 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
72348 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
72362 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:72343 original size:30 final size:30
Alignment explanation
Indices: 72308--72381 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
72298 AGTTTTTCCC
72308 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
72338 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
72368 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
72382 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:72371 original size:20 final size:20
Alignment explanation
Indices: 72308--72372 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
72298 AGTTTTTCCC
* * * *
72308 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
72328 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
72347 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
72368 AGCTC
1 AGCTC
72373 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:75094 original size:20 final size:20
Alignment explanation
Indices: 75071--75118 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
75061 TCCCAACTCG
*
75071 ATTTAGCTCACATGAGCTTA
1 ATTTAGCTCACATGAGCTCA
***
75091 ATTTAGCTCGTTTGAGCTCA
1 ATTTAGCTCACATGAGCTCA
75111 ATTTAGCT
1 ATTTAGCT
75119 TACTTTAGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.40
Consensus pattern (20 bp):
ATTTAGCTCACATGAGCTCA
Found at i:75110 original size:30 final size:30
Alignment explanation
Indices: 75067--75138 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 30
75057 TTTTTCCCAA
75067 CTCGATTT-AGCTCACA-TGAGCTTAATTTAG
1 CTCG-TTTGAGCTCA-ATTGAGCTTAATTTAG
* *
75097 CTCGTTTGAGCTCAATTTAGCTTACTTTAG
1 CTCGTTTGAGCTCAATTGAGCTTAATTTAG
75127 CTCGTTTGAGCT
1 CTCGTTTGAGCT
75139 TGGCTTGAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 4 0.11
30 34 0.89
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.40
Consensus pattern (30 bp):
CTCGTTTGAGCTCAATTGAGCTTAATTTAG
Found at i:77594 original size:10 final size:10
Alignment explanation
Indices: 77579--77616 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
77569 GCTCGTTTCC
*
77579 AGCTCACTCG
1 AGCTCAATCG
77589 AGCTCAAGTC-
1 AGCTCAA-TCG
77599 AGCTCAATCG
1 AGCTCAATCG
77609 AGCTCAAT
1 AGCTCAAT
77617 TTAGCTACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (10 bp):
AGCTCAATCG
Found at i:77622 original size:20 final size:20
Alignment explanation
Indices: 77578--77615 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
77568 AGCTCGTTTC
*
77578 CAGCTCACTCGAGCTCAAGT
1 CAGCTCAATCGAGCTCAAGT
77598 CAGCTCAATCGAGCTCAA
1 CAGCTCAATCGAGCTCAA
77616 TTTAGCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (20 bp):
CAGCTCAATCGAGCTCAAGT
Found at i:77629 original size:11 final size:10
Alignment explanation
Indices: 77589--77639 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
77579 AGCTCACTCG
* *
77589 AGCTCAAGTC
1 AGCTCAATTT
**
77599 AGCTCAATCG
1 AGCTCAATTT
77609 AGCTCAATTT
1 AGCTCAATTT
77619 AGCTACAATTT
1 AGCT-CAATTT
77630 AGCTC-ATTT
1 AGCTCAATTT
77639 A
1 A
77640 TTTTATTGGT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 5 0.14
10 20 0.57
11 10 0.29
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (10 bp):
AGCTCAATTT
Found at i:80588 original size:30 final size:29
Alignment explanation
Indices: 80488--80590 Score: 89
Period size: 30 Copynumber: 3.4 Consensus size: 29
80478 CAAGTTTAAA
* * *
80488 CTAAAGTGAGCTAAGTTTTAGCTCGGGAG
1 CTAAATTGAGCTAAGGTTTAGCTCGTGAG
* * * * * *
80517 CTAAAGTTGAGCTGAGGCTAAACTCCTAAG
1 CTAAA-TTGAGCTAAGGTTTAGCTCGTGAG
*
80547 CTGAAGTTGAGCTAAGGTTTAGCTCGTGAG
1 CT-AAATTGAGCTAAGGTTTAGCTCGTGAG
80577 CTAAATATGAGCTA
1 CTAAAT-TGAGCTA
80591 GGAGTGAGCT
Statistics
Matches: 54, Mismatches: 17, Indels: 5
0.71 0.22 0.07
Matches are distributed among these distances:
29 8 0.15
30 44 0.81
31 2 0.04
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (29 bp):
CTAAATTGAGCTAAGGTTTAGCTCGTGAG
Found at i:82786 original size:12 final size:12
Alignment explanation
Indices: 82771--82801 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
82761 TTCTTTTTGC
82771 TTTTCAAAGGCT
1 TTTTCAAAGGCT
82783 TTTTCAAAGGCT
1 TTTTCAAAGGCT
82795 TTTTCAA
1 TTTTCAA
82802 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:82878 original size:6 final size:6
Alignment explanation
Indices: 82862--82911 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
82852 TTTCTTTTTA
*
82862 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
82911 T
1 T
82912 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:82894 original size:37 final size:37
Alignment explanation
Indices: 82851--82921 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
82841 CTTGCCTCTC
82851 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
82888 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
82922 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:82922 original size:16 final size:16
Alignment explanation
Indices: 82847--82907 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
82837 GCCTCTTGCC
*
82847 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
82863 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
82879 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
82895 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
82908 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:83869 original size:12 final size:13
Alignment explanation
Indices: 83833--83886 Score: 74
Period size: 13 Copynumber: 4.2 Consensus size: 13
83823 TATACTTCGA
83833 TTTTTCAA-TTTT
1 TTTTTCAATTTTT
**
83845 TTTTAAAATTTTT
1 TTTTTCAATTTTT
*
83858 TTTTTCGATTTTT
1 TTTTTCAATTTTT
83871 TTTTTCAATTTTT
1 TTTTTCAATTTTT
83884 TTT
1 TTT
83887 CAAATTTCCA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
12 6 0.17
13 29 0.83
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTTTCAATTTTT
Found at i:83892 original size:12 final size:12
Alignment explanation
Indices: 83833--83893 Score: 54
Period size: 11 Copynumber: 5.0 Consensus size: 12
83823 TATACTTCGA
83833 TTTTTC-AATTT
1 TTTTTCAAATTT
*
83844 TTTTTAAAATTTTT
1 TTTTTCAAA--TTT
**
83858 TTTTTCGATTTTT
1 TTTTTC-AAATTT
83871 TTTTTC-AATTT
1 TTTTTCAAATTT
83882 TTTTTCAAATTT
1 TTTTTCAAATTT
83894 CCACTTCTCT
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
11 14 0.36
12 7 0.18
13 9 0.23
14 8 0.21
15 1 0.03
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.72
Consensus pattern (12 bp):
TTTTTCAAATTT
Found at i:85670 original size:30 final size:29
Alignment explanation
Indices: 85570--85672 Score: 98
Period size: 30 Copynumber: 3.4 Consensus size: 29
85560 CGAGTTTAAA
* *
85570 CTAAAGTGAGCTAAGTTTTAGCTCGTGAG
1 CTAAATTGAGCTAAGGTTTAGCTCGTGAG
* * * * * *
85599 CTAAAGTTGAGCTGAGGCTAAACTCCTAAG
1 CTAAA-TTGAGCTAAGGTTTAGCTCGTGAG
*
85629 CTGAAGTTGAGCTAAGGTTTAGCTCGTGAG
1 CT-AAATTGAGCTAAGGTTTAGCTCGTGAG
85659 CTAAATATGAGCTA
1 CTAAAT-TGAGCTA
85673 GGAGTGAGCT
Statistics
Matches: 55, Mismatches: 16, Indels: 5
0.72 0.21 0.07
Matches are distributed among these distances:
29 8 0.15
30 45 0.82
31 2 0.04
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (29 bp):
CTAAATTGAGCTAAGGTTTAGCTCGTGAG
Found at i:87593 original size:10 final size:10
Alignment explanation
Indices: 87580--87617 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
87570 AGCTCACTCA
*
87580 AGCTCAAGTC
1 AGCTCAATTC
87590 AGCTC-ATTC
1 AGCTCAATTC
87599 GAGCTCAATTC
1 -AGCTCAATTC
87610 AGCTCAAT
1 AGCTCAAT
87618 CTTAACCCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 3 0.12
10 18 0.72
11 4 0.16
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:87594 original size:20 final size:20
Alignment explanation
Indices: 87569--87615 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
87559 AGCTCGTTTC
87569 CAGCTCACTCAAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
87589 CAGCTCATTCGAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
87609 CAGCTCA
1 CAGCTCA
87616 ATCTTAACCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.34, G:0.15, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:92343 original size:20 final size:20
Alignment explanation
Indices: 92320--92373 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
92310 AGTTTTTCCC
*
92320 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
92340 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
92360 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
92374 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:92355 original size:30 final size:30
Alignment explanation
Indices: 92320--92393 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
92310 AGTTTTTCCC
92320 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
92350 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
92380 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
92394 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:92383 original size:20 final size:20
Alignment explanation
Indices: 92320--92384 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
92310 AGTTTTTCCC
* * * *
92320 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
92340 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
92359 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
92380 AGCTC
1 AGCTC
92385 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:94000 original size:13 final size:13
Alignment explanation
Indices: 93984--94061 Score: 52
Period size: 14 Copynumber: 5.6 Consensus size: 13
93974 AAAAAAAATC
93984 AAAAAAAATTCGAA
1 AAAAAAAATTCG-A
*
93998 AAAAAAAATTGATTGAA
1 AAAAAAAA-T--TCG-A
*
94015 AAAAAAAATTCAA
1 AAAAAAAATTCGA
*
94028 AAAAAAAAGT-GA
1 AAAAAAAATTCGA
94040 AAAAAAAA-TCGA
1 AAAAAAAATTCGA
94052 GCAAAAAAAA
1 --AAAAAAAA
94062 AAAGGTGACC
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
11 1 0.02
12 11 0.21
13 10 0.19
14 17 0.32
15 1 0.02
16 1 0.02
17 12 0.23
ACGTcount: A:0.73, C:0.05, G:0.09, T:0.13
Consensus pattern (13 bp):
AAAAAAAATTCGA
Found at i:94001 original size:14 final size:14
Alignment explanation
Indices: 93984--94047 Score: 69
Period size: 13 Copynumber: 4.5 Consensus size: 14
93974 AAAAAAAATC
93984 AAAAAAAATTCGAA
1 AAAAAAAATTCGAA
*
93998 AAAAAAAATTGATTGAA
1 AAAAAAAA-T--TCGAA
94015 AAAAAAAATTC-AA
1 AAAAAAAATTCGAA
*
94028 AAAAAAAAGT-GAA
1 AAAAAAAATTCGAA
94041 AAAAAAA
1 AAAAAAA
94048 TCGAGCAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
13 20 0.47
14 9 0.21
15 1 0.02
16 1 0.02
17 12 0.28
ACGTcount: A:0.75, C:0.03, G:0.08, T:0.14
Consensus pattern (14 bp):
AAAAAAAATTCGAA
Found at i:94076 original size:32 final size:30
Alignment explanation
Indices: 94026--94103 Score: 97
Period size: 32 Copynumber: 2.6 Consensus size: 30
94016 AAAAAAATTC
*
94026 AAAAAAAAAA-GTGAAAAAAAAATCGAGCA
1 AAAAAAAAAAGGTGAAAAAAAAATCAAGCA
**
94055 AAAAAAAAAAGGTGACCAAAAAAAATCAAGTT
1 AAAAAAAAAAGGTGA--AAAAAAAATCAAGCA
94087 AAAAAAAAAA-GTGAAAA
1 AAAAAAAAAAGGTGAAAA
94104 GTCTTGCGAG
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
29 13 0.30
30 4 0.09
31 4 0.09
32 22 0.51
ACGTcount: A:0.72, C:0.06, G:0.13, T:0.09
Consensus pattern (30 bp):
AAAAAAAAAAGGTGAAAAAAAAATCAAGCA
Found at i:95033 original size:15 final size:16
Alignment explanation
Indices: 95013--95044 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
95003 AGAAAATGAA
95013 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
95028 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
95044 A
1 A
95045 GTGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:95159 original size:17 final size:18
Alignment explanation
Indices: 95127--95160 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
95117 AAAAGAGAGT
*
95127 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
95145 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
95161 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:96448 original size:20 final size:20
Alignment explanation
Indices: 96425--96478 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
96415 TAGTTTTCCC
*
96425 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
96445 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
96465 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
96479 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:96459 original size:30 final size:30
Alignment explanation
Indices: 96425--96498 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
96415 TAGTTTTCCC
96425 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
96455 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
96485 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
96499 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:96488 original size:20 final size:20
Alignment explanation
Indices: 96425--96489 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
96415 TAGTTTTCCC
* * * *
96425 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
96445 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
96464 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
96485 AGCTC
1 AGCTC
96490 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:104632 original size:20 final size:19
Alignment explanation
Indices: 104609--104673 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
104599 AAGCTCAAAC
104609 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
104629 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
104649 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
104669 GAGCT
1 GAGCT
104674 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:105036 original size:20 final size:20
Alignment explanation
Indices: 105013--105059 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
105003 GGGTTAAGAT
*
105013 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
105033 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
105053 TGAGCTG
1 TGAGCTG
105060 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:106843 original size:48 final size:48
Alignment explanation
Indices: 106730--106853 Score: 155
Period size: 48 Copynumber: 2.6 Consensus size: 48
106720 TTGTCTTTTC
* *
106730 TTTCTTTTTCAATTT-TCTCTTTTTCCTCACACTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTTTCTTTTT-CTCACACCTTTGTTCAATCTCAA
*
106778 TTTCTTTTTCGATTTCTTTCTCTTTT-TCACATCCTTT-TTCAATCTCAA
1 TTTCTTTTTCAATTTCTTTCT-TTTTCTCACA-CCTTTGTTCAATCTCAA
*
106826 TTTCTTTTTCAATTTCTTGTTTTTTTCT
1 TTTCTTTTTCAATTTCTT-TCTTTTTCT
106854 TTCATTTCTT
Statistics
Matches: 66, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
48 51 0.77
49 11 0.17
50 4 0.06
ACGTcount: A:0.14, C:0.23, G:0.02, T:0.61
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTTTCTTTTTCTCACACCTTTGTTCAATCTCAA
Found at i:106865 original size:15 final size:16
Alignment explanation
Indices: 106777--106868 Score: 52
Period size: 18 Copynumber: 5.8 Consensus size: 16
106767 TTCAATCTCA
106777 ATTTCTTTTTCGATTTC
1 ATTTCTTTTTC-ATTTC
*
106794 TTTCTCTTTTTCA---C
1 ATT-TCTTTTTCATTTC
* *
106808 A-TCCTTTTTCAATCTC
1 ATTTCTTTTTC-ATTTC
106824 AATTTCTTTTTCAATTTC
1 -ATTTCTTTTTC-ATTTC
*
106842 -TTGTTTTTTTC-TTTC
1 ATT-TCTTTTTCATTTC
106857 ATTTCTTTTTCA
1 ATTTCTTTTTCA
106869 ATCTCTTTCT
Statistics
Matches: 58, Mismatches: 7, Indels: 21
0.67 0.08 0.24
Matches are distributed among these distances:
12 7 0.12
13 2 0.03
14 1 0.02
15 11 0.19
16 5 0.09
17 11 0.19
18 21 0.36
ACGTcount: A:0.13, C:0.21, G:0.02, T:0.64
Consensus pattern (16 bp):
ATTTCTTTTTCATTTC
Found at i:107931 original size:12 final size:12
Alignment explanation
Indices: 107915--107986 Score: 74
Period size: 12 Copynumber: 5.8 Consensus size: 12
107905 TTTTTGCTCG
107915 ATTTTTTTTTCA
1 ATTTTTTTTTCA
* *
107927 CTTTTTTTTTGA
1 ATTTTTTTTTCA
107939 ATTTTTTTTTCA
1 ATTTTTTTTTCA
107951 ATCAATTTTTTTTCGA
1 AT---TTTTTTTTC-A
*
107967 ATTTTTTTTT-G
1 ATTTTTTTTTCA
107978 ATTTTTTTT
1 ATTTTTTTT
107987 GTTACTCCAA
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
11 9 0.18
12 22 0.43
13 8 0.16
15 9 0.18
16 3 0.06
ACGTcount: A:0.15, C:0.07, G:0.04, T:0.74
Consensus pattern (12 bp):
ATTTTTTTTTCA
Done.