Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold34
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: 329687
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 1 of 2
Found at i:3921 original size:21 final size:20
Alignment explanation
Indices: 3895--3944 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
3885 AAATTGATTG
*
3895 AAAAAAAAATTC-AAAAAAA
1 AAAAAAAAAATCGAAAAAAA
*
3914 AATGAAAAAAATCGAAAAAAA
1 AA-AAAAAAAATCGAAAAAAA
3935 AAAAAAAAAA
1 AAAAAAAAAA
3945 GTGAAAAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 2 0.08
20 15 0.58
21 9 0.35
ACGTcount: A:0.84, C:0.04, G:0.04, T:0.08
Consensus pattern (20 bp):
AAAAAAAAAATCGAAAAAAA
Found at i:3936 original size:12 final size:12
Alignment explanation
Indices: 3858--3936 Score: 53
Period size: 12 Copynumber: 6.7 Consensus size: 12
3848 TGTATTGAGT
3858 AAAAAAAATC--
1 AAAAAAAATCGA
*
3868 AAAAAAATTCGAA
1 AAAAAAAATCG-A
*
3881 AAAAAAATTGATTGA
1 AAAAAAA---ATCGA
3896 AAAAAAAATTC-A
1 AAAAAAAA-TCGA
3908 AAAAAAAAT-G-
1 AAAAAAAATCGA
3918 -AAAAAAATCGA
1 AAAAAAAATCGA
3929 AAAAAAAA
1 AAAAAAAA
3937 AAAAAAAAGT
Statistics
Matches: 54, Mismatches: 4, Indels: 20
0.69 0.05 0.26
Matches are distributed among these distances:
9 8 0.15
10 10 0.19
11 1 0.02
12 17 0.31
13 8 0.15
15 8 0.15
16 2 0.04
ACGTcount: A:0.75, C:0.05, G:0.06, T:0.14
Consensus pattern (12 bp):
AAAAAAAATCGA
Found at i:3950 original size:20 final size:19
Alignment explanation
Indices: 3895--3952 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
3885 AAATTGATTG
* *
3895 AAAAAAAAATTCAAAAAAA
1 AAAAAAAAAATGAAAAAAA
*
3914 AATGAAAAAAATCGAAAAAAA
1 AA-AAAAAAAAT-GAAAAAAA
3935 AAAAAAAAAAGTGAAAAA
1 AAAAAAAAAA-TGAAAAA
3953 TCATGTTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
19 2 0.06
20 20 0.62
21 10 0.31
ACGTcount: A:0.81, C:0.03, G:0.07, T:0.09
Consensus pattern (19 bp):
AAAAAAAAAATGAAAAAAA
Found at i:3951 original size:12 final size:11
Alignment explanation
Indices: 3893--3952 Score: 56
Period size: 12 Copynumber: 5.6 Consensus size: 11
3883 AAAAATTGAT
3893 TGAAAAAAAAA
1 TGAAAAAAAAA
*
3904 TTCAAAAAAAAA
1 -TGAAAAAAAAA
3916 TG--AAAAAAA
1 TGAAAAAAAAA
3925 TCGAAAAAAAAA
1 T-GAAAAAAAAA
*
3937 --AAAAAAAAG
1 TGAAAAAAAAA
3946 TGAAAAA
1 TGAAAAA
3953 TCATGTTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
9 16 0.40
10 1 0.03
11 6 0.15
12 17 0.43
ACGTcount: A:0.78, C:0.03, G:0.08, T:0.10
Consensus pattern (11 bp):
TGAAAAAAAAA
Found at i:8404 original size:20 final size:21
Alignment explanation
Indices: 8369--8407 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
8359 CAGCTCGTTG
8369 AGCTCAATTCAGCTCATTTCC
1 AGCTCAATTCAGCTCATTTCC
*
8390 AGCTC-ATTGAGCTCATTT
1 AGCTCAATTCAGCTCATTT
8408 GCTTGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.36
Consensus pattern (21 bp):
AGCTCAATTCAGCTCATTTCC
Found at i:8815 original size:13 final size:13
Alignment explanation
Indices: 8797--8822 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8787 TGTGTCCTAA
8797 TATGAATTAAATT
1 TATGAATTAAATT
8810 TATGAATTAAATT
1 TATGAATTAAATT
8823 GCTTTCAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TATGAATTAAATT
Found at i:10940 original size:6 final size:6
Alignment explanation
Indices: 10915--11013 Score: 74
Period size: 6 Copynumber: 16.0 Consensus size: 6
10905 TAATGAATTC
** * *
10915 GAAAAA GAAAGT GAAGAA GAAAAA GAAAACA -AAAAA GAAAAA GAAAAC
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAA-A GAAAAA GAAAAA GAAAAA
** * * *
10963 GAAAAA GTGAGA GAAAAA GAAAAT GAAGAAAA GAAAATT GAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA G-A-AAAA GAAAA-A GAAAAA GAAAAA
11014 TATGAAAATG
Statistics
Matches: 70, Mismatches: 18, Indels: 10
0.71 0.18 0.10
Matches are distributed among these distances:
5 1 0.01
6 57 0.81
7 8 0.11
8 4 0.06
ACGTcount: A:0.73, C:0.02, G:0.20, T:0.05
Consensus pattern (6 bp):
GAAAAA
Found at i:10996 original size:14 final size:13
Alignment explanation
Indices: 10975--11012 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
10965 AAAAGTGAGA
10975 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
10987 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
11002 GAAAAAGAAAA
1 GAAAAAGAAAA
11013 ATATGAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:11056 original size:17 final size:18
Alignment explanation
Indices: 11031--11070 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
11021 ATGAGATTTC
11031 AAAAACAAAA-GAGAGTG
1 AAAAACAAAATGAGAGTG
* *
11048 AAAAGCAAAATGAGATTG
1 AAAAACAAAATGAGAGTG
11066 AAAAA
1 AAAAA
11071 GAAAGAGAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.65, C:0.05, G:0.20, T:0.10
Consensus pattern (18 bp):
AAAAACAAAATGAGAGTG
Found at i:11062 original size:18 final size:17
Alignment explanation
Indices: 11031--11080 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
11021 ATGAGATTTC
11031 AAAAACAAAAGAGAGTG
1 AAAAACAAAAGAGAGTG
* *
11048 AAAAGCAAAATGAGATTG
1 AAAAACAAAA-GAGAGTG
*
11066 AAAAA-GAAAGAGAGT
1 AAAAACAAAAGAGAGT
11081 TTGAAAAGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
16 5 0.19
17 12 0.44
18 10 0.37
ACGTcount: A:0.62, C:0.04, G:0.24, T:0.10
Consensus pattern (17 bp):
AAAAACAAAAGAGAGTG
Found at i:11086 original size:36 final size:34
Alignment explanation
Indices: 11017--11112 Score: 92
Period size: 36 Copynumber: 2.8 Consensus size: 34
11007 AGAAAAATAT
* *
11017 GAAAATGAGATTTCAAAAACAAAAGAGAG-TGAAAA
1 GAAAATGAGA-TTGAAAAA-GAAAGAGAGTTGAAAA
11052 GCAAAATGAGATTGAAAAAGAAAGAGAGTTTGAAAA
1 G-AAAATGAGATTGAAAAAGAAAGAGAG-TTGAAAA
* *
11088 GAAAACGAG--TGAAGAAG-AAGAGAGT
1 GAAAATGAGATTGAAAAAGAAAGAGAGT
11113 GCTCAAACAC
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
31 1 0.02
32 7 0.13
33 7 0.13
34 8 0.15
35 15 0.28
36 16 0.30
ACGTcount: A:0.56, C:0.04, G:0.26, T:0.14
Consensus pattern (34 bp):
GAAAATGAGATTGAAAAAGAAAGAGAGTTGAAAA
Found at i:11089 original size:17 final size:16
Alignment explanation
Indices: 11038--11112 Score: 52
Period size: 16 Copynumber: 4.6 Consensus size: 16
11028 TTCAAAAACA
11038 AAAGAGAG-TGAAAAG
1 AAAGAGAGTTGAAAAG
11053 CAAA-ATGAGATTGAAAAAG
1 -AAAGA-GAG-TTG-AAAAG
11072 AAAGAGAGTTTGAAAAG
1 AAAGAGAG-TTGAAAAG
11089 AAA-ACGAG-TGAAGAAG
1 AAAGA-GAGTTGAA-AAG
11105 -AAGAGAGT
1 AAAGAGAGT
11113 GCTCAAACAC
Statistics
Matches: 49, Mismatches: 1, Indels: 18
0.72 0.01 0.26
Matches are distributed among these distances:
15 10 0.20
16 11 0.22
17 11 0.22
18 11 0.22
19 6 0.12
ACGTcount: A:0.56, C:0.03, G:0.29, T:0.12
Consensus pattern (16 bp):
AAAGAGAGTTGAAAAG
Found at i:14415 original size:13 final size:13
Alignment explanation
Indices: 14397--14422 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
14387 TGTGTCCTAA
14397 TATGAATTAAATT
1 TATGAATTAAATT
14410 TATGAATTAAATT
1 TATGAATTAAATT
14423 GCTTTCAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TATGAATTAAATT
Found at i:19570 original size:11 final size:10
Alignment explanation
Indices: 19556--19595 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 10
19546 AAATTGATTG
19556 AAAAAAAATTC
1 AAAAAAAA-TC
*
19567 AAAAAAAAGTG
1 AAAAAAAA-TC
19578 AAAAAAAATC
1 AAAAAAAATC
19588 AAAAAAAA
1 AAAAAAAA
19596 AAAAGAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.80, C:0.05, G:0.05, T:0.10
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:19570 original size:23 final size:22
Alignment explanation
Indices: 19525--19592 Score: 57
Period size: 23 Copynumber: 3.0 Consensus size: 22
19515 TTTACATTGT
* **
19525 ATTGATTTAAAAAAAAGAGAAAA
1 ATTGATTGAAAAAAAA-TCAAAA
19548 ATTGATTGAAAAAAAATTCAAAA
1 ATTGATTGAAAAAAAA-TCAAAA
** *
19571 A-AAAGTGAAAAAAAATCAAAA
1 ATTGATTGAAAAAAAATCAAAA
19592 A
1 A
19593 AAAAAAAGAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
21 7 0.18
22 11 0.29
23 20 0.53
ACGTcount: A:0.68, C:0.03, G:0.10, T:0.19
Consensus pattern (22 bp):
ATTGATTGAAAAAAAATCAAAA
Found at i:19595 original size:25 final size:25
Alignment explanation
Indices: 19567--19619 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
19557 AAAAAAATTC
**
19567 AAAAAAAAGTGAAAAAAAATCAAAA
1 AAAAAAAAGAAAAAAAAAATCAAAA
*
19592 AAAAAAAAGAAAAAAAAAATGAAAA
1 AAAAAAAAGAAAAAAAAAATCAAAA
19617 AAA
1 AAA
19620 TCAAGTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.85, C:0.02, G:0.08, T:0.06
Consensus pattern (25 bp):
AAAAAAAAGAAAAAAAAAATCAAAA
Found at i:19596 original size:22 final size:22
Alignment explanation
Indices: 19554--19595 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
19544 AAAAATTGAT
19554 TGAAAAAAAATTCAAAAAAAAG
1 TGAAAAAAAATTCAAAAAAAAG
19576 TGAAAAAAAA-TCAAAAAAAA
1 TGAAAAAAAATTCAAAAAAAA
19596 AAAAGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.76, C:0.05, G:0.07, T:0.12
Consensus pattern (22 bp):
TGAAAAAAAATTCAAAAAAAAG
Found at i:19597 original size:12 final size:12
Alignment explanation
Indices: 19556--19642 Score: 63
Period size: 12 Copynumber: 7.2 Consensus size: 12
19546 AAATTGATTG
**
19556 AAAAAAAATTCA
1 AAAAAAAATGAA
*
19568 AAAAAAAGTGAA
1 AAAAAAAATGAA
19580 AAAAAATCAA--AA
1 AAAAAA--AATGAA
19592 AAAAAAAA-GAA
1 AAAAAAAATGAA
19603 AAAAAAAATGAA
1 AAAAAAAATGAA
* *
19615 AAAAATCAAGTTAA
1 AAAAA--AAATGAA
*
19629 AAAAAAAGTGAA
1 AAAAAAAATGAA
19641 AA
1 AA
19643 GTCTTGTGAG
Statistics
Matches: 62, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
10 2 0.03
11 10 0.16
12 39 0.63
14 11 0.18
ACGTcount: A:0.78, C:0.03, G:0.08, T:0.10
Consensus pattern (12 bp):
AAAAAAAATGAA
Found at i:19604 original size:21 final size:22
Alignment explanation
Indices: 19556--19607 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
19546 AAATTGATTG
**
19556 AAAAAAAATTCAAAAAAAAGTG
1 AAAAAAAATTCAAAAAAAAGAA
*
19578 AAAAAAAA-TCAAAAAAAAAAA
1 AAAAAAAATTCAAAAAAAAGAA
19599 AGAAAAAAA
1 A-AAAAAAA
19608 AAATGAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.83, C:0.04, G:0.06, T:0.08
Consensus pattern (22 bp):
AAAAAAAATTCAAAAAAAAGAA
Found at i:34752 original size:20 final size:20
Alignment explanation
Indices: 34706--34752 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
34696 AGCTTGTTTC
*
34706 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
34726 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
34746 CAGCTCA
1 CAGCTCA
34753 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:46865 original size:13 final size:13
Alignment explanation
Indices: 46845--46879 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
46835 ATGGAAACCA
46845 AATTTTTTTTT-G
1 AATTTTTTTTTCG
46857 AATTTTTTTTTCG
1 AATTTTTTTTTCG
*
46870 AGTTTTTTTT
1 AATTTTTTTT
46880 CTAGAAACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.14, C:0.03, G:0.09, T:0.74
Consensus pattern (13 bp):
AATTTTTTTTTCG
Found at i:48601 original size:29 final size:29
Alignment explanation
Indices: 48568--48640 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
48558 ATGTATTAGT
* *
48568 TTAGGACATATTTAAAACACTTGAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
*
48597 TTAGGACATAATTAAAACACCTAAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
48626 TTAGGACATATTTAA
1 TTAGGACATATTTAA
48641 TAATATCTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.30
Consensus pattern (29 bp):
TTAGGACATATTTAAAACACCTAAACTAA
Found at i:50114 original size:21 final size:23
Alignment explanation
Indices: 50069--50115 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
50059 TCACCTACAA
* *
50069 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
50092 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
50113 TAA
1 TAA
50116 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:52873 original size:15 final size:14
Alignment explanation
Indices: 52855--52904 Score: 73
Period size: 16 Copynumber: 3.4 Consensus size: 14
52845 AAAAAATATT
52855 AAAAAAATTCGAAAA
1 AAAAAAATTC-AAAA
52870 AAAAAAATTCAAAAAA
1 AAAAAAATTC--AAAA
52886 AAAAAAATTCAAAA
1 AAAAAAATTCAAAA
52900 AAAAA
1 AAAAA
52905 GTTTGTATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
14 9 0.27
15 10 0.30
16 14 0.42
ACGTcount: A:0.80, C:0.06, G:0.02, T:0.12
Consensus pattern (14 bp):
AAAAAAATTCAAAA
Found at i:52876 original size:16 final size:15
Alignment explanation
Indices: 52855--52904 Score: 82
Period size: 15 Copynumber: 3.3 Consensus size: 15
52845 AAAAAATATT
*
52855 AAAAAAATTCGAAAA
1 AAAAAAATTCAAAAA
52870 AAAAAAATTCAAAAAA
1 AAAAAAATTC-AAAAA
52886 AAAAAAATTCAAAAA
1 AAAAAAATTCAAAAA
52901 AAAA
1 AAAA
52905 GTTTGTATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
15 19 0.58
16 14 0.42
ACGTcount: A:0.80, C:0.06, G:0.02, T:0.12
Consensus pattern (15 bp):
AAAAAAATTCAAAAA
Found at i:52963 original size:13 final size:13
Alignment explanation
Indices: 52945--52970 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52935 ATTTAGTATT
52945 GAAGAAAAAAAAA
1 GAAGAAAAAAAAA
52958 GAAGAAAAAAAAA
1 GAAGAAAAAAAAA
52971 TTCGGAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
GAAGAAAAAAAAA
Found at i:53010 original size:20 final size:20
Alignment explanation
Indices: 52986--53024 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
52976 AATTAAAACA
*
52986 AAAAAAGAAGAAAAAAAAATC
1 AAAATAGAA-AAAAAAAAATC
*
53007 AAAATTGAAAAAAAAAAA
1 AAAATAGAAAAAAAAAAA
53025 AGTGATTGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.82, C:0.03, G:0.08, T:0.08
Consensus pattern (20 bp):
AAAATAGAAAAAAAAAAATC
Found at i:53023 original size:34 final size:35
Alignment explanation
Indices: 52942--53026 Score: 120
Period size: 34 Copynumber: 2.5 Consensus size: 35
52932 TGTATTTAGT
* **
52942 ATTGAAGAAAAAAAAAGAAGAAAAAAAAATTCGGA
1 ATTGAAAAAAAAAAAAGAAGAAAAAAAAATTCAAA
*
52977 ATT-AAAACAAAAAAAGAAGAAAAAAAAA-TCAAA
1 ATTGAAAAAAAAAAAAGAAGAAAAAAAAATTCAAA
53010 ATTGAAAAAAAAAAAAG
1 ATTGAAAAAAAAAAAAG
53027 TGATTGAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
33 6 0.14
34 35 0.80
35 3 0.07
ACGTcount: A:0.74, C:0.04, G:0.12, T:0.11
Consensus pattern (35 bp):
ATTGAAAAAAAAAAAAGAAGAAAAAAAAATTCAAA
Found at i:53941 original size:21 final size:20
Alignment explanation
Indices: 53912--53957 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
53902 AATCTTGAAT
*
53912 GAAATTGAGAGAAGAAAAAAA
1 GAAAATGAGAG-AGAAAAAAA
* *
53933 GAAAATGAGAGTGAGAAAAA
1 GAAAATGAGAGAGAAAAAAA
53953 GAAAA
1 GAAAA
53958 AAGAATTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.65, C:0.00, G:0.26, T:0.09
Consensus pattern (20 bp):
GAAAATGAGAGAGAAAAAAA
Found at i:53984 original size:12 final size:12
Alignment explanation
Indices: 53964--53999 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
53954 AAAAAAGAAT
*
53964 TTGAGATTGAGA
1 TTGATATTGAGA
*
53976 TTGATATTGATA
1 TTGATATTGAGA
53988 TTGATATTGAGA
1 TTGATATTGAGA
54000 AAAAAATTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.42
Consensus pattern (12 bp):
TTGATATTGAGA
Found at i:59843 original size:20 final size:20
Alignment explanation
Indices: 59820--59865 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
59810 CCAGCTCGAA
*
59820 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
59840 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
59860 TTAGCT
1 TTAGCT
59866 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:59847 original size:30 final size:30
Alignment explanation
Indices: 59812--59885 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
59802 AGTTTTTCCC
59812 AGCTCGAATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-ATTGAGCTCA-ATTGAGCTTAATTT
* * *
59842 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTGAGCTCAATTGAGCTTAATTT
*
59872 AGCTCGTTTGAGCT
1 AGCTCGATTGAGCT
59886 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 36 0.92
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGATTGAGCTCAATTGAGCTTAATTT
Found at i:61275 original size:21 final size:21
Alignment explanation
Indices: 61230--61292 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
61220 TTTGAACCAT
* *
61230 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
61252 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
61273 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
61293 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:61651 original size:13 final size:11
Alignment explanation
Indices: 61606--61646 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
61596 AAAAGAGTTC
*
61606 GAAAAAAAA-A
1 GAAAAAAAATT
61616 GAAAAAAAATT
1 GAAAAAAAATT
61627 GAAAAAAAATT
1 GAAAAAAAATT
61638 GAAAAAAAA
1 GAAAAAAAA
61647 AATTGCATAC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
10 9 0.31
11 20 0.69
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (11 bp):
GAAAAAAAATT
Found at i:63321 original size:12 final size:12
Alignment explanation
Indices: 63304--63353 Score: 55
Period size: 12 Copynumber: 4.0 Consensus size: 12
63294 TAGCTCTCTT
63304 TTTTTTTCACAA
1 TTTTTTTCACAA
63316 TTTTTTTTTCACAA
1 --TTTTTTTCACAA
**
63330 TTTTTTTTTCAA
1 TTTTTTTCACAA
*
63342 TTTTTTTTACAA
1 TTTTTTTCACAA
63354 CTTGATATCC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
12 21 0.64
14 12 0.36
ACGTcount: A:0.22, C:0.12, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTTTTTCACAA
Found at i:63321 original size:14 final size:14
Alignment explanation
Indices: 63302--63349 Score: 82
Period size: 14 Copynumber: 3.6 Consensus size: 14
63292 ACTAGCTCTC
63302 TTTTTTTTTCACAA
1 TTTTTTTTTCACAA
63316 TTTTTTTTTCACAA
1 TTTTTTTTTCACAA
63330 TTTTTTTTT--CAA
1 TTTTTTTTTCACAA
63342 TTTTTTTT
1 TTTTTTTT
63350 ACAACTTGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.32
14 23 0.68
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTTTTTTCACAA
Found at i:63409 original size:13 final size:13
Alignment explanation
Indices: 63391--63424 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
63381 TGGAAACTAG
*
63391 TTTTTTTTTTGAA
1 TTTTTTTTTCGAA
*
63404 TTTTTTTTTCGAG
1 TTTTTTTTTCGAA
63417 TTTTTTTT
1 TTTTTTTT
63425 CGAGAAACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.09, C:0.03, G:0.09, T:0.79
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:65196 original size:20 final size:20
Alignment explanation
Indices: 65171--65208 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
65161 AGTAGACTCG
*
65171 TGAAAAAAAATAAAAAAAAT
1 TGAAAAAAAAGAAAAAAAAT
65191 TGAAAAAAAAGAAAAAAA
1 TGAAAAAAAAGAAAAAAA
65209 TTGTATACGG
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:0.82, C:0.00, G:0.08, T:0.11
Consensus pattern (20 bp):
TGAAAAAAAAGAAAAAAAAT
Found at i:65198 original size:19 final size:19
Alignment explanation
Indices: 65171--65211 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
65161 AGTAGACTCG
*
65171 TGAAAAAAAATAAAAAAAAT
1 TGAAAAAAAA-GAAAAAAAT
65191 TGAAAAAAAAGAAAAAAAT
1 TGAAAAAAAAGAAAAAAAT
65210 TG
1 TG
65212 TATACGGTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.15
Consensus pattern (19 bp):
TGAAAAAAAAGAAAAAAAT
Found at i:66534 original size:21 final size:21
Alignment explanation
Indices: 66508--66570 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
66498 TTAGTATTTG
66508 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
66529 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
66550 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
66571 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:70782 original size:22 final size:21
Alignment explanation
Indices: 70751--70801 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
70741 ACCTCTTTGA
70751 ACCATTACCAATTCGTACCAAAT
1 ACCA-TACCAATTCGTACC-AAT
*
70774 ACCATACCATTTCGTACCAAT
1 ACCATACCAATTCGTACCAAT
*
70795 TCCATAC
1 ACCATAC
70802 TATTTTGAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 9 0.35
22 13 0.50
23 4 0.15
ACGTcount: A:0.35, C:0.33, G:0.04, T:0.27
Consensus pattern (21 bp):
ACCATACCAATTCGTACCAAT
Found at i:70801 original size:21 final size:21
Alignment explanation
Indices: 70756--70818 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
70746 TTTGAACCAT
* *
70756 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
70778 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* * *
70799 TACTATTTTGAACCAATTCC
1 TACCATTTCGTACCAATTCC
70819 CAAATACCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 23 0.64
22 13 0.36
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.32
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:73785 original size:6 final size:6
Alignment explanation
Indices: 73753--73860 Score: 67
Period size: 6 Copynumber: 17.7 Consensus size: 6
73743 AAAGAAATTG
* * ** *
73753 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* ** * * *
73800 AAAGAA ATCA-AA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
73851 AAAGAA AAAG
1 AAAGAA AAAG
73861 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 22, Indels: 11
0.69 0.20 0.10
Matches are distributed among these distances:
5 4 0.05
6 59 0.79
7 8 0.11
8 4 0.05
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:73840 original size:14 final size:13
Alignment explanation
Indices: 73821--73858 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
73811 AAAAGTGAGA
73821 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
73833 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
73848 GAAAAAGAAAA
1 GAAAAAGAAAA
73859 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:73872 original size:21 final size:21
Alignment explanation
Indices: 73822--73872 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
73812 AAAGTGAGAG
*
73822 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
73843 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
73864 AAAAAGAAA
1 AAAAAGAAA
73873 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:73912 original size:33 final size:33
Alignment explanation
Indices: 73875--73937 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
73865 AAAAGAAATT
73875 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
73908 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
73938 GTGAGTAATC
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:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:75732 original size:20 final size:20
Alignment explanation
Indices: 75709--75762 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
75699 AGTTTTTCCC
*
75709 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
75729 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
75749 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
75763 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:75744 original size:30 final size:30
Alignment explanation
Indices: 75709--75782 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
75699 AGTTTTTCCC
75709 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
75739 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
75769 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
75783 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:75772 original size:20 final size:20
Alignment explanation
Indices: 75709--75773 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
75699 AGTTTTTCCC
* * * *
75709 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
75729 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
75748 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
75769 AGCTC
1 AGCTC
75774 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:81162 original size:22 final size:22
Alignment explanation
Indices: 81134--81177 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
81124 TTTTGAACCA
81134 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
81156 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
81178 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:81710 original size:12 final size:11
Alignment explanation
Indices: 81691--81748 Score: 107
Period size: 11 Copynumber: 5.2 Consensus size: 11
81681 AATGGAAACC
81691 AATTTTTTTTG
1 AATTTTTTTTG
81702 AATTTTTTTTTG
1 AA-TTTTTTTTG
81714 AATTTTTTTTG
1 AATTTTTTTTG
81725 AATTTTTTTTG
1 AATTTTTTTTG
81736 AATTTTTTTTG
1 AATTTTTTTTG
81747 AA
1 AA
81749 GAAACTGCTA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
11 35 0.76
12 11 0.24
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.71
Consensus pattern (11 bp):
AATTTTTTTTG
Found at i:82777 original size:21 final size:23
Alignment explanation
Indices: 82732--82778 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
82722 TCACCTGCAA
* *
82732 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
82755 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
82776 TAA
1 TAA
82779 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:86221 original size:30 final size:30
Alignment explanation
Indices: 86187--86283 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
86177 TAAACTAAAA
86187 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
86217 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
86247 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
86276 ATGAGCTA
1 -TGAGCTA
86284 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:88522 original size:6 final size:6
Alignment explanation
Indices: 88506--88555 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
88496 TTTCTTTTTA
*
88506 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
88555 T
1 T
88556 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:88538 original size:37 final size:37
Alignment explanation
Indices: 88495--88565 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
88485 CTTGCCTCTC
88495 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
88532 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
88566 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:88566 original size:16 final size:16
Alignment explanation
Indices: 88491--88551 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
88481 GCCTCTTGCC
*
88491 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
88507 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
88523 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
88539 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
88552 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:89524 original size:30 final size:30
Alignment explanation
Indices: 89490--89586 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
89480 AGCTCACTCC
89490 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
89520 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
89550 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
89580 TAGCTCA
1 TAGCTCA
89587 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:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:90513 original size:22 final size:20
Alignment explanation
Indices: 90488--90527 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
90478 TTATGAACTA
90488 TTTTATACATTAGTGTGAACGT
1 TTTTAT-CATT-GTGTGAACGT
*
90510 TTTTATTATTGTGTGAAC
1 TTTTATCATTGTGTGAAC
90528 ACCTAGATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 3 0.18
22 6 0.35
ACGTcount: A:0.25, C:0.07, G:0.17, T:0.50
Consensus pattern (20 bp):
TTTTATCATTGTGTGAACGT
Found at i:91290 original size:11 final size:12
Alignment explanation
Indices: 91276--91322 Score: 55
Period size: 11 Copynumber: 4.2 Consensus size: 12
91266 TTTAACTCGA
91276 TTTTTTTT-AAT
1 TTTTTTTTCAAT
*
91287 TTTTTTTTCGA-
1 TTTTTTTTCAAT
91298 TTTTTTTT-AAT
1 TTTTTTTTCAAT
*
91309 TTTTTTTTGAAT
1 TTTTTTTTCAAT
91321 TT
1 TT
91323 CTTCTCTCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 1 0.03
11 24 0.77
12 6 0.19
ACGTcount: A:0.15, C:0.02, G:0.04, T:0.79
Consensus pattern (12 bp):
TTTTTTTTCAAT
Found at i:91291 original size:12 final size:12
Alignment explanation
Indices: 91276--91322 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
91266 TTTAACTCGA
91276 TTTTTTTTAATT
1 TTTTTTTTAATT
**
91288 TTTTTTTCGA--
1 TTTTTTTTAATT
91298 TTTTTTTTAATT
1 TTTTTTTTAATT
*
91310 TTTTTTTGAATT
1 TTTTTTTTAATT
91322 T
1 T
91323 CTTCTCTCTT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
10 8 0.29
12 20 0.71
ACGTcount: A:0.15, C:0.02, G:0.04, T:0.79
Consensus pattern (12 bp):
TTTTTTTTAATT
Found at i:91322 original size:22 final size:22
Alignment explanation
Indices: 91272--91316 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
91262 TTTTTTTAAC
91272 TCGATTTTTTTTAATTTTTTTT
1 TCGATTTTTTTTAATTTTTTTT
91294 TCGATTTTTTTTAATTTTTTTT
1 TCGATTTTTTTTAATTTTTTTT
91316 T
1 T
91317 GAATTTCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.13, C:0.04, G:0.04, T:0.78
Consensus pattern (22 bp):
TCGATTTTTTTTAATTTTTTTT
Found at i:93067 original size:30 final size:30
Alignment explanation
Indices: 93033--93129 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
93023 TAAACTAAAA
93033 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
93063 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
93093 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
93122 ATGAGCTA
1 -TGAGCTA
93130 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:99176 original size:11 final size:11
Alignment explanation
Indices: 99160--99194 Score: 52
Period size: 11 Copynumber: 3.0 Consensus size: 11
99150 TAGTAGTTTC
99160 TTCAAAAAAAA
1 TTCAAAAAAAA
99171 TTCAAAAAAAAAA
1 TTC--AAAAAAAA
99184 TTCAAAAAAAA
1 TTCAAAAAAAA
99195 ATTGGTTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 11 0.50
13 11 0.50
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:99197 original size:12 final size:13
Alignment explanation
Indices: 99163--99195 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
99153 TAGTTTCTTC
99163 AAAAAAAATTCAA
1 AAAAAAAATTCAA
99176 AAAAAAAATTCAA
1 AAAAAAAATTCAA
99189 AAAAAAA
1 AAAAAAA
99196 TTGGTTTCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.82, C:0.06, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAAAATTCAA
Found at i:99254 original size:15 final size:15
Alignment explanation
Indices: 99234--99290 Score: 105
Period size: 15 Copynumber: 3.7 Consensus size: 15
99224 GATATCAAGT
99234 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
99249 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
99264 TGAAAAAAAAATTTCG
1 TGAAAAAAAAA-TTCG
99280 TGAAAAAAAAA
1 TGAAAAAAAAA
99291 GAAGAAGCTA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
15 26 0.63
16 15 0.37
ACGTcount: A:0.63, C:0.05, G:0.12, T:0.19
Consensus pattern (15 bp):
TGAAAAAAAAATTCG
Found at i:99257 original size:16 final size:16
Alignment explanation
Indices: 99236--99290 Score: 94
Period size: 16 Copynumber: 3.5 Consensus size: 16
99226 TATCAAGTTG
99236 AAAAAAAAATTCGTG-
1 AAAAAAAAATTCGTGA
99251 AAAAAAAAATTCGTGA
1 AAAAAAAAATTCGTGA
*
99267 AAAAAAAATTTCGTGA
1 AAAAAAAAATTCGTGA
99283 AAAAAAAA
1 AAAAAAAA
99291 GAAGAAGCTA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
15 15 0.39
16 23 0.61
ACGTcount: A:0.65, C:0.05, G:0.11, T:0.18
Consensus pattern (16 bp):
AAAAAAAAATTCGTGA
Found at i:101344 original size:11 final size:11
Alignment explanation
Indices: 101328--101372 Score: 81
Period size: 11 Copynumber: 4.0 Consensus size: 11
101318 TAGTAGTTTC
101328 TTCAAAAAAAA
1 TTCAAAAAAAA
101339 TTCAAAAAAAAA
1 TTC-AAAAAAAA
101351 TTCAAAAAAAA
1 TTCAAAAAAAA
101362 TTCAAAAAAAA
1 TTCAAAAAAAA
101373 AATTTGGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 22 0.67
12 11 0.33
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:101348 original size:12 final size:12
Alignment explanation
Indices: 101331--101373 Score: 79
Period size: 12 Copynumber: 3.7 Consensus size: 12
101321 TAGTTTCTTC
101331 AAAAAAAATTCA
1 AAAAAAAATTCA
101343 AAAAAAAATTC-
1 AAAAAAAATTCA
101354 AAAAAAAATTCA
1 AAAAAAAATTCA
101366 AAAAAAAA
1 AAAAAAAA
101374 ATTTGGTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.37
12 19 0.63
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:101358 original size:23 final size:23
Alignment explanation
Indices: 101328--101373 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
101318 TAGTAGTTTC
101328 TTCAAAAAAAATTCAAAAAAAAA
1 TTCAAAAAAAATTCAAAAAAAAA
101351 TTCAAAAAAAATTCAAAAAAAAA
1 TTCAAAAAAAATTCAAAAAAAAA
101374 ATTTGGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (23 bp):
TTCAAAAAAAATTCAAAAAAAAA
Found at i:101451 original size:12 final size:13
Alignment explanation
Indices: 101427--101468 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 13
101417 AAAAACAAAT
101427 TTCGTGAAAAAAA
1 TTCGTGAAAAAAA
101440 TTCGTGAAAAAAAAAA
1 TTCGTG---AAAAAAA
101456 TTCGTGAAAAAAA
1 TTCGTGAAAAAAA
101469 AAGAAGAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 13 0.50
16 13 0.50
ACGTcount: A:0.57, C:0.07, G:0.14, T:0.21
Consensus pattern (13 bp):
TTCGTGAAAAAAA
Found at i:101452 original size:16 final size:16
Alignment explanation
Indices: 101433--101470 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
101423 AAATTTCGTG
101433 AAAAAAATTCGTGAAA
1 AAAAAAATTCGTGAAA
101449 AAAAAAATTCGTGAAA
1 AAAAAAATTCGTGAAA
101465 AAAAAA
1 AAAAAA
101471 GAAGAAGCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.68, C:0.05, G:0.11, T:0.16
Consensus pattern (16 bp):
AAAAAAATTCGTGAAA
Found at i:104985 original size:20 final size:20
Alignment explanation
Indices: 104938--104985 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
104928 AGTAAGCTCG
104938 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
104958 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
104978 GTTGAGCT
1 GTTGAGCT
104986 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:106726 original size:18 final size:18
Alignment explanation
Indices: 106705--106764 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
106695 GACCTCACTC
106705 TCTTTTTTGATTTCTTTT
1 TCTTTTTTGATTTCTTTT
** *
106723 TCTTTTTCAATCTCTTTT
1 TCTTTTTTGATTTCTTTT
106741 TCTTTTCTTTTGATTTCTTTT
1 TC--TT-TTTTGATTTCTTTT
106762 TCT
1 TCT
106765 CGCTCGCACT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
18 17 0.52
19 1 0.03
20 2 0.06
21 13 0.39
ACGTcount: A:0.07, C:0.17, G:0.03, T:0.73
Consensus pattern (18 bp):
TCTTTTTTGATTTCTTTT
Found at i:107570 original size:6 final size:6
Alignment explanation
Indices: 107559--107591 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
107549 AGTTGTAAAG
107559 TTTTAT TTTTATT TTTTAT TTTTAT TTTTAT TT
1 TTTTAT TTTTA-T TTTTAT TTTTAT TTTTAT TT
107592 ATTTATTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:107577 original size:13 final size:12
Alignment explanation
Indices: 107559--107591 Score: 57
Period size: 13 Copynumber: 2.7 Consensus size: 12
107549 AGTTGTAAAG
107559 TTTTATTTTTATT
1 TTTTATTTTTA-T
107572 TTTTATTTTTAT
1 TTTTATTTTTAT
107584 TTTTATTT
1 TTTTATTT
107592 ATTTATTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTATTTTTAT
Found at i:107583 original size:19 final size:20
Alignment explanation
Indices: 107559--107599 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
107549 AGTTGTAAAG
107559 TTTTATTTTTATTT-TTTAT
1 TTTTATTTTTATTTATTTAT
107578 TTTTATTTTTATTTATTTAT
1 TTTTATTTTTATTTATTTAT
107598 TT
1 TT
107600 ACTTAGTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (20 bp):
TTTTATTTTTATTTATTTAT
Found at i:112502 original size:13 final size:12
Alignment explanation
Indices: 112474--112501 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
112464 AAAAAAAAAA
112474 TTTTGAATTTTT
1 TTTTGAATTTTT
112486 TTTTGAATTTTT
1 TTTTGAATTTTT
112498 TTTT
1 TTTT
112502 TCAAATTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (12 bp):
TTTTGAATTTTT
Found at i:120880 original size:32 final size:33
Alignment explanation
Indices: 120844--120909 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 33
120834 GCTGATGATG
*
120844 TTCACACATATTTGACTCTTCAA-AACTAACTT
1 TTCACACATATGTGACTCTTCAACAACTAACTT
* * * *
120876 TTCACACTTGTGTGACTGTTCAACAACTATCTT
1 TTCACACATATGTGACTCTTCAACAACTAACTT
120909 T
1 T
120910 AATGTTCCTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 19 0.68
33 9 0.32
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.39
Consensus pattern (33 bp):
TTCACACATATGTGACTCTTCAACAACTAACTT
Found at i:122532 original size:10 final size:10
Alignment explanation
Indices: 122517--122541 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
122507 GAGGAATTAA
122517 TTCTTGAATT
1 TTCTTGAATT
122527 TTCTTGAATT
1 TTCTTGAATT
122537 TTCTT
1 TTCTT
122542 AGCTTTTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.12, G:0.08, T:0.64
Consensus pattern (10 bp):
TTCTTGAATT
Found at i:123213 original size:14 final size:15
Alignment explanation
Indices: 123189--123219 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
123179 GAGTAAGTAG
123189 ATTTCTGAAAAAAAA
1 ATTTCTGAAAAAAAA
123204 ATTT-TGAAAAAAAA
1 ATTTCTGAAAAAAAA
123218 AT
1 AT
123220 CGAAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.29
Consensus pattern (15 bp):
ATTTCTGAAAAAAAA
Found at i:125538 original size:29 final size:29
Alignment explanation
Indices: 125505--125577 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
125495 ATGTATTAGT
* *
125505 TTAGGACATATTTAAAACACTTGAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
*
125534 TTAGGACATAATTAAAACACCTAAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
125563 TTAGGACATATTTAA
1 TTAGGACATATTTAA
125578 TAATATCTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.30
Consensus pattern (29 bp):
TTAGGACATATTTAAAACACCTAAACTAA
Found at i:132073 original size:15 final size:13
Alignment explanation
Indices: 132036--132061 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
132026 CGTAGCTTCG
132036 AAAAAAAAAAGTT
1 AAAAAAAAAAGTT
132049 AAAAAAAAAAGTT
1 AAAAAAAAAAGTT
132062 TTGAAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (13 bp):
AAAAAAAAAAGTT
Found at i:142596 original size:11 final size:11
Alignment explanation
Indices: 142580--142613 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
142570 TAGTAGTTTC
142580 TTCAAAAAAAA
1 TTCAAAAAAAA
142591 TTCAAAAAAAAA
1 TTC-AAAAAAAA
142603 TTCAAAAAAAA
1 TTCAAAAAAAA
142614 ATTTGGTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.18
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:142600 original size:12 final size:12
Alignment explanation
Indices: 142583--142616 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
142573 TAGTTTCTTC
142583 AAAAAAAATTCA
1 AAAAAAAATTCA
142595 AAAAAAAATTCA
1 AAAAAAAATTCA
142607 AAAAAAAATT
1 AAAAAAAATT
142617 TGGTTTCCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:142677 original size:15 final size:15
Alignment explanation
Indices: 142657--142694 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
142647 ATCAAGTTGA
142657 AAAAAAAAATTCGTG
1 AAAAAAAAATTCGTG
142672 AAAAAAAAATTCGTG
1 AAAAAAAAATTCGTG
142687 AAAAAAAA
1 AAAAAAAA
142695 GAAGAAGCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.68, C:0.05, G:0.11, T:0.16
Consensus pattern (15 bp):
AAAAAAAAATTCGTG
Found at i:158641 original size:13 final size:13
Alignment explanation
Indices: 158597--158665 Score: 70
Period size: 13 Copynumber: 5.2 Consensus size: 13
158587 AATCGTAGCT
158597 TTGAAAAAAAAAA
1 TTGAAAAAAAAAA
**
158610 GTT-AAAAAAAAGTT
1 -TTGAAAAAAAA-AA
158624 TTG-AAAAAAAAA
1 TTGAAAAAAAAAA
158636 TCTGAAAAAAAAAA
1 T-TGAAAAAAAAAA
*
158650 TTGCAAAAAAAAA
1 TTGAAAAAAAAAA
158663 TTG
1 TTG
158666 CATACGGTCT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
12 1 0.02
13 33 0.72
14 12 0.26
ACGTcount: A:0.67, C:0.03, G:0.10, T:0.20
Consensus pattern (13 bp):
TTGAAAAAAAAAA
Found at i:158643 original size:27 final size:27
Alignment explanation
Indices: 158596--158647 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
158586 AAATCGTAGC
* *
158596 TTTGAAAAAAAAAAGTTAAAAAAAAGT
1 TTTGAAAAAAAAAACTGAAAAAAAAGT
*
158623 TTTGAAAAAAAAATCTGAAAAAAAA
1 TTTGAAAAAAAAAACTGAAAAAAAA
158648 AATTGCAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.67, C:0.02, G:0.10, T:0.21
Consensus pattern (27 bp):
TTTGAAAAAAAAAACTGAAAAAAAAGT
Found at i:160946 original size:24 final size:25
Alignment explanation
Indices: 160919--160972 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
160909 ATGAGTGATA
*
160919 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
160943 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
160967 AAAAAA
1 AAAAAA
160973 AGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:166983 original size:33 final size:33
Alignment explanation
Indices: 166945--167007 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
166935 GATTACTCAC
166945 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
166978 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
167008 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:167034 original size:21 final size:21
Alignment explanation
Indices: 167005--167060 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
166995 CAAGCTCTCT
*
167005 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
167026 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
167047 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
167061 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:167053 original size:14 final size:14
Alignment explanation
Indices: 167004--167060 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
166994 TCAAGCTCTC
167004 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
167017 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
167031 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
167045 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
167059 TT
1 TT
167061 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:167468 original size:15 final size:16
Alignment explanation
Indices: 167447--167488 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
167437 ACTAGCTTCT
167447 TTTTTTTTCACGAAAA
1 TTTTTTTTCACGAAAA
*
167463 TTTTTTTTTCACG-AAT
1 -TTTTTTTTCACGAAAA
167479 TTTTTTTTCA
1 TTTTTTTTCA
167489 ACTTGATATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 10 0.42
16 2 0.08
17 12 0.50
ACGTcount: A:0.21, C:0.12, G:0.05, T:0.62
Consensus pattern (16 bp):
TTTTTTTTCACGAAAA
Found at i:167468 original size:17 final size:15
Alignment explanation
Indices: 167446--167488 Score: 68
Period size: 15 Copynumber: 2.7 Consensus size: 15
167436 AACTAGCTTC
167446 TTTTTTTTTCACGAAAA
1 TTTTTTTTTCACG--AA
167463 TTTTTTTTTCACGAA
1 TTTTTTTTTCACGAA
167478 TTTTTTTTTCA
1 TTTTTTTTTCA
167489 ACTTGATATC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 13 0.50
17 13 0.50
ACGTcount: A:0.21, C:0.12, G:0.05, T:0.63
Consensus pattern (15 bp):
TTTTTTTTTCACGAA
Found at i:167545 original size:13 final size:13
Alignment explanation
Indices: 167527--167559 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
167517 TGGAAACCAA
167527 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
167540 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
167553 TTTTTTT
1 TTTTTTT
167560 GAAGAAACGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (13 bp):
TTTTTTTTTGAAT
Found at i:167930 original size:46 final size:46
Alignment explanation
Indices: 167877--167970 Score: 163
Period size: 46 Copynumber: 2.0 Consensus size: 46
167867 CAAAGAAAAG
*
167877 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAAGAACCTTGGTATATGATGA
167923 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
167969 AC
1 AC
167971 GCCACACTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 45 0.98
47 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
Found at i:170496 original size:23 final size:21
Alignment explanation
Indices: 170470--170515 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
170460 AAGAAAAAGG
170470 AGAAGAGAAAAAAAAAGTGAAAA
1 AGAAGA-AAAAAAAAA-TGAAAA
**
170493 AGAAGAAAATGAAAATGAAAA
1 AGAAGAAAAAAAAAATGAAAA
170514 AG
1 AG
170516 GCGAAAAGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 7 0.33
23 6 0.29
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.07
Consensus pattern (21 bp):
AGAAGAAAAAAAAAATGAAAA
Found at i:170499 original size:21 final size:21
Alignment explanation
Indices: 170475--170515 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
170465 AAAGGAGAAG
170475 AGAAAA-AAAAAGTGAAAAAGA
1 AGAAAATAAAAA-TGAAAAAGA
*
170496 AGAAAATGAAAATGAAAAAG
1 AGAAAATAAAAATGAAAAAG
170516 GCGAAAAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (21 bp):
AGAAAATAAAAATGAAAAAGA
Found at i:170521 original size:21 final size:22
Alignment explanation
Indices: 170482--170527 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
170472 AAGAGAAAAA
*
170482 AAAAGTGAAAAAGAAGAAAATG
1 AAAAGTGAAAAAGAAGAAAAGG
**
170504 AAAA-TGAAAAAGGCGAAAAGG
1 AAAAGTGAAAAAGAAGAAAAGG
170525 AAA
1 AAA
170528 GCGAGAGAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.67, C:0.02, G:0.24, T:0.07
Consensus pattern (22 bp):
AAAAGTGAAAAAGAAGAAAAGG
Found at i:173776 original size:21 final size:23
Alignment explanation
Indices: 173731--173777 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
173721 TCACCTGCAA
* *
173731 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
173754 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
173775 TAA
1 TAA
173778 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:186523 original size:23 final size:23
Alignment explanation
Indices: 186492--186542 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
186482 ACCTACTTTC
*
186492 TTACTGTAGTAATTTTCAGGG-TA
1 TTACAGTAGTAATTTTC-GGGATA
186515 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
186538 TTACA
1 TTACA
186543 TCTTCAGCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 3 0.12
23 23 0.88
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:194115 original size:34 final size:35
Alignment explanation
Indices: 194071--194137 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
194061 CAGTAAAACA
*
194071 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
194105 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
194138 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:199351 original size:10 final size:10
Alignment explanation
Indices: 199335--199392 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
199325 CAACTCCGAC
199335 CAGCTCAATT
1 CAGCTCAATT
* *
199345 GAGCTCATTT
1 CAGCTCAATT
199355 CAGCTCAA-T
1 CAGCTCAATT
199364 CGAGCTCAATT
1 C-AGCTCAATT
*
199375 TAGCTACAATT
1 CAGCT-CAATT
199386 CAGCTCA
1 CAGCTCA
199393 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:199358 original size:20 final size:20
Alignment explanation
Indices: 199335--199395 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
199325 CAACTCCGAC
199335 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
199355 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
199376 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
199396 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:200740 original size:10 final size:11
Alignment explanation
Indices: 200725--200767 Score: 61
Period size: 13 Copynumber: 3.8 Consensus size: 11
200715 ATTGGAGTAA
200725 CAAAAAAAA-T
1 CAAAAAAAATT
200735 CAAAAAAAATT
1 CAAAAAAAATT
200746 CAAAAAAAAAATT
1 C--AAAAAAAATT
200759 CAAAAAAAA
1 CAAAAAAAA
200768 AGTGAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
10 9 0.30
11 10 0.33
13 11 0.37
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.12
Consensus pattern (11 bp):
CAAAAAAAATT
Found at i:200752 original size:13 final size:13
Alignment explanation
Indices: 200736--200768 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
200726 AAAAAAAATC
200736 AAAAAAAATTCAA
1 AAAAAAAATTCAA
200749 AAAAAAAATTCAA
1 AAAAAAAATTCAA
200762 AAAAAAA
1 AAAAAAA
200769 GTGAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.82, C:0.06, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAAAATTCAA
Found at i:200776 original size:13 final size:12
Alignment explanation
Indices: 200726--200779 Score: 65
Period size: 12 Copynumber: 4.5 Consensus size: 12
200716 TTGGAGTAAC
200726 AAAAAAAATC-A
1 AAAAAAAATCAA
*
200737 AAAAAAATTCAA
1 AAAAAAAATCAA
200749 AAAAAAAATTCAA
1 AAAAAAAA-TCAA
* *
200762 AAAAAAAGTGAA
1 AAAAAAAATCAA
200774 AAAAAA
1 AAAAAA
200780 TCGAGCAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
11 9 0.24
12 17 0.46
13 11 0.30
ACGTcount: A:0.80, C:0.06, G:0.04, T:0.11
Consensus pattern (12 bp):
AAAAAAAATCAA
Found at i:200821 original size:16 final size:16
Alignment explanation
Indices: 200782--200826 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
200772 AAAAAAAATC
200782 GAGCAAAAAAAAAGAA
1 GAGCAAAAAAAAAGAA
* * **
200798 AAGAAAAAAAAAAGGT
1 GAGCAAAAAAAAAGAA
200814 GAGCAAAAAAAAA
1 GAGCAAAAAAAAA
200827 TCAAGTTTAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.02
Consensus pattern (16 bp):
GAGCAAAAAAAAAGAA
Found at i:201896 original size:6 final size:6
Alignment explanation
Indices: 201862--201917 Score: 58
Period size: 6 Copynumber: 9.2 Consensus size: 6
201852 AAAGAAATTG
* * ** *
201862 AAAGAA AACAAAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AA-AGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
201911 AAAGAA A
1 AAAGAA A
201918 TCAAAATAGT
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
6 34 0.87
7 5 0.13
ACGTcount: A:0.77, C:0.05, G:0.14, T:0.04
Consensus pattern (6 bp):
AAAGAA
Found at i:201977 original size:18 final size:18
Alignment explanation
Indices: 201956--201990 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
201946 AGAAAAGAAA
201956 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
201974 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
201991 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:204082 original size:20 final size:20
Alignment explanation
Indices: 204058--204109 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 20
204048 CAACTCCGAC
204058 CAGCTCATTTCAGCT-CAA-T
1 CAGCTCATTT-AGCTACAATT
204077 CGAGCTCAATTTAGCTACAATT
1 C-AGCTC-ATTTAGCTACAATT
204099 CAGCTCATTTA
1 CAGCTCATTTA
204110 TTTTATTGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
19 1 0.03
20 14 0.48
21 12 0.41
22 2 0.07
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.33
Consensus pattern (20 bp):
CAGCTCATTTAGCTACAATT
Found at i:204103 original size:11 final size:10
Alignment explanation
Indices: 204058--204105 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
204048 CAACTCCGAC
*
204058 CAGCTCATTT
1 CAGCTCAATT
204068 CAGCTCAA-T
1 CAGCTCAATT
204077 CGAGCTCAATT
1 C-AGCTCAATT
*
204088 TAGCTACAATT
1 CAGCT-CAATT
204099 CAGCTCA
1 CAGCTCA
204106 TTTATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
9 2 0.06
10 20 0.62
11 10 0.31
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:209686 original size:9 final size:9
Alignment explanation
Indices: 209671--209705 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
209661 TGGATTTCAT
209671 CTTTTTTGA
1 CTTTTTTGA
*
209680 TTTTTTTGA
1 CTTTTTTGA
209689 CTTTTTTGA
1 CTTTTTTGA
209698 CTTCTTTT
1 CTT-TTTT
209706 TTGCGGGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 19 0.83
10 4 0.17
ACGTcount: A:0.09, C:0.11, G:0.09, T:0.71
Consensus pattern (9 bp):
CTTTTTTGA
Found at i:212507 original size:22 final size:23
Alignment explanation
Indices: 212476--212518 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
212466 GTCCTTTTGA
212476 ACCATTACCAATTCGTACCAAAT
1 ACCATTACCAATTCGTACCAAAT
*
212499 ACCA-TACCATTTCGTACCAA
1 ACCATTACCAATTCGTACCAA
212519 TTCCATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.37, C:0.33, G:0.05, T:0.26
Consensus pattern (23 bp):
ACCATTACCAATTCGTACCAAAT
Found at i:212531 original size:21 final size:21
Alignment explanation
Indices: 212487--212543 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
212477 CCATTACCAA
* *
212487 TTCGTACCAAATACCATACCAT
1 TTCGTACC-AATTCCATAACAT
*
212509 TTCGTACCAATTCCATAATAT
1 TTCGTACCAATTCCATAACAT
*
212530 TTCGAACCAATTCC
1 TTCGTACCAATTCC
212544 CAAATACCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 23 0.74
22 8 0.26
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.32
Consensus pattern (21 bp):
TTCGTACCAATTCCATAACAT
Found at i:214760 original size:147 final size:146
Alignment explanation
Indices: 214477--214766 Score: 437
Period size: 147 Copynumber: 2.0 Consensus size: 146
214467 TGATACGGGG
214477 TTGCGCGCGGACCAAGATCGAGTTGCCAAGTCACGGGAAACTCCTACGAAAACCCTAAACAATCA
1 TTGCGCGCGGACCAAGATCGAGTTGCCAAGTCACGGGAAACTCCTACGAAAACCCTAAACAATCA
*
214542 GATCCGAAACGAAATAGAAAAATTAAAAGATTAGAACTTTGAATTTCCAGATCTGAAATAAAATC
66 GATCCGAAACGAAACAGAAAAATTAAAAGATTAGAACTTTGAATTTCCAGATC-GAAATAAAATC
214607 CCCAAATCAGCAAGAAA
130 CCCAAATCAGCAAGAAA
*
214624 TTGCGCGCGGACCAAGATCGAGTTGCCAAGTCAC-GGAAACTCCTACGAAAACCCTAAACAATTA
1 TTGCGCGCGGACCAAGATCGAGTTGCCAAGTCACGGGAAACTCCTACGAAAACCCTAAACAATCA
* **
214688 GATCTGAAACGAAACAG-AAAATTAAAAGATTA-ATTTTTGAAAGATTT-CAGATC-AAATCTGA
66 GATCCGAAACGAAACAGAAAAATTAAAAGATTAGAACTTTG--A-ATTTCCAGATCGAAA--T-A
214749 AAATCCCCAAATCAGCAA
125 AAATCCCCAAATCAGCAA
214767 AGAATCAAAT
Statistics
Matches: 132, Mismatches: 5, Indels: 12
0.89 0.03 0.08
Matches are distributed among these distances:
144 8 0.06
145 15 0.11
146 52 0.39
147 57 0.43
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.20
Consensus pattern (146 bp):
TTGCGCGCGGACCAAGATCGAGTTGCCAAGTCACGGGAAACTCCTACGAAAACCCTAAACAATCA
GATCCGAAACGAAACAGAAAAATTAAAAGATTAGAACTTTGAATTTCCAGATCGAAATAAAATCC
CCAAATCAGCAAGAAA
Found at i:216861 original size:23 final size:22
Alignment explanation
Indices: 216809--216861 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
216799 TCCACGTCTT
*
216809 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
216831 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
216854 TTTCTTTT
1 TTTCTTTT
216862 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:219528 original size:17 final size:17
Alignment explanation
Indices: 219483--219536 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
219473 AGAAAAGAGT
* *
219483 GAAAATACAAAAGAAAA
1 GAAAATTCAAAAAAAAA
* *
219500 GAAAAATGAAAAAAAAA
1 GAAAATTCAAAAAAAAA
*
219517 GAAAATTCAAAAAAAGA
1 GAAAATTCAAAAAAAAA
219534 GAA
1 GAA
219537 TGAAAAGAGA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.76, C:0.04, G:0.13, T:0.07
Consensus pattern (17 bp):
GAAAATTCAAAAAAAAA
Found at i:222684 original size:21 final size:21
Alignment explanation
Indices: 222639--222701 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
222629 TTTGAACCAT
* *
222639 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
222661 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
222682 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
222702 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:225385 original size:21 final size:23
Alignment explanation
Indices: 225340--225386 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
225330 TCACCTGCAA
* *
225340 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
225363 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
225384 TAA
1 TAA
225387 TCATAAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:230752 original size:16 final size:16
Alignment explanation
Indices: 230731--230784 Score: 101
Period size: 16 Copynumber: 3.4 Consensus size: 16
230721 TAGCTTCTTC
230731 TTTTTTTTCACGAATT
1 TTTTTTTTCACGAATT
230747 TTTTTTTTCACGAATT
1 TTTTTTTTCACGAATT
230763 TTTTTTTTCACG-ATT
1 TTTTTTTTCACGAATT
230778 TTTTTTT
1 TTTTTTT
230785 CAACTTGATA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 10 0.26
16 28 0.74
ACGTcount: A:0.15, C:0.11, G:0.06, T:0.69
Consensus pattern (16 bp):
TTTTTTTTCACGAATT
Done.