Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_49
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: 341629
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 1 of 2
Found at i:7237 original size:21 final size:21
Alignment explanation
Indices: 7211--7273 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
7201 TTGGTATTTG
7211 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
7232 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
7253 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
7274 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:14952 original size:15 final size:15
Alignment explanation
Indices: 14932--14970 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
14922 CTTCTTCTTC
14932 TTTTTTTCACGAATT
1 TTTTTTTCACGAATT
14947 TTTTTTTCACGAATT
1 TTTTTTTCACGAATT
14962 TTTTTTTCA
1 TTTTTTTCA
14971 ACTTGATATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.18, C:0.13, G:0.05, T:0.64
Consensus pattern (15 bp):
TTTTTTTCACGAATT
Found at i:15044 original size:11 final size:12
Alignment explanation
Indices: 15010--15041 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
15000 GGAAACCAAT
15010 TTTTTTTTTGAA
1 TTTTTTTTTGAA
15022 TTTTTTTTTGAA
1 TTTTTTTTTGAA
15034 TTTTTTTT
1 TTTTTTTT
15042 GAAGAAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.81
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:17514 original size:20 final size:20
Alignment explanation
Indices: 17468--17514 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
17458 AGCTCGTTTC
*
17468 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
17488 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
17508 CAGCTCA
1 CAGCTCA
17515 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:18055 original size:30 final size:30
Alignment explanation
Indices: 18021--18117 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
18011 AGCTCACTCC
18021 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
18051 TAGCTCAACTTCAGCTTAGGAGTTTACCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
18081 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
18111 TAGCTCA
1 TAGCTCA
18118 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:0.28, G:0.14, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:19047 original size:22 final size:20
Alignment explanation
Indices: 19015--19063 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
19005 GCCGAATTTA
19015 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
19038 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
19058 TGAACA
1 TGAACA
19064 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:23756 original size:20 final size:20
Alignment explanation
Indices: 23710--23756 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
23700 AGCTCGTTTC
*
23710 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
23730 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
23750 CAGCTCA
1 CAGCTCA
23757 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:26607 original size:22 final size:22
Alignment explanation
Indices: 26582--26625 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
26572 TTTTGAATCA
26582 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
26604 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
26626 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:27965 original size:21 final size:21
Alignment explanation
Indices: 27939--27978 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
27929 CAAATACCAT
27939 ACCATTTCATACCAATTCCAA
1 ACCATTTCATACCAATTCCAA
*
27960 ACCATTTCGTACCAATTCC
1 ACCATTTCATACCAATTCC
27979 CAAATACCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.30
Consensus pattern (21 bp):
ACCATTTCATACCAATTCCAA
Found at i:28299 original size:10 final size:8
Alignment explanation
Indices: 28277--28310 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
28267 AGTAAGTGAT
28277 TAAAAAAA
1 TAAAAAAA
28285 TAAAAAAA
1 TAAAAAAA
28293 TCGAAAAAAA
1 T--AAAAAAA
28303 TAAAAAAA
1 TAAAAAAA
28311 AAAGTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 16 0.67
10 8 0.33
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (8 bp):
TAAAAAAA
Found at i:29466 original size:13 final size:13
Alignment explanation
Indices: 29448--29472 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29438 TGGTCATCAT
29448 GGTGTGAACACAA
1 GGTGTGAACACAA
29461 GGTGTGAACACA
1 GGTGTGAACACA
29473 TGATCAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:30960 original size:6 final size:6
Alignment explanation
Indices: 30935--31033 Score: 74
Period size: 6 Copynumber: 16.0 Consensus size: 6
30925 TAATGAATTC
** * *
30935 GAAAAA GAAAGT GAAGAA GAAAAA GAAAACA -AAAAA GAAAAA GAAAAC
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAA-A GAAAAA GAAAAA GAAAAA
** * * *
30983 GAAAAA GTGAGA GAAAAA GAAAAT GAAGAAAA GAAAATT GAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA G-A-AAAA GAAAA-A GAAAAA GAAAAA
31034 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:31016 original size:14 final size:13
Alignment explanation
Indices: 30995--31032 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
30985 AAAAGTGAGA
30995 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
31007 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
31022 GAAAAAGAAAA
1 GAAAAAGAAAA
31033 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:31076 original size:17 final size:18
Alignment explanation
Indices: 31051--31090 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
31041 ATGAGATTTC
31051 AAAAACAAAA-GAGAGTG
1 AAAAACAAAATGAGAGTG
* *
31068 AAAAGCAAAATGAGATTG
1 AAAAACAAAATGAGAGTG
31086 AAAAA
1 AAAAA
31091 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:31082 original size:18 final size:17
Alignment explanation
Indices: 31051--31100 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
31041 ATGAGATTTC
31051 AAAAACAAAAGAGAGTG
1 AAAAACAAAAGAGAGTG
* *
31068 AAAAGCAAAATGAGATTG
1 AAAAACAAAA-GAGAGTG
*
31086 AAAAA-GAAAGAGAGT
1 AAAAACAAAAGAGAGT
31101 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:31106 original size:36 final size:34
Alignment explanation
Indices: 31037--31132 Score: 92
Period size: 36 Copynumber: 2.8 Consensus size: 34
31027 AGAAAAATAT
* *
31037 GAAAATGAGATTTCAAAAACAAAAGAGAG-TGAAAA
1 GAAAATGAGA-TTGAAAAA-GAAAGAGAGTTGAAAA
31072 GCAAAATGAGATTGAAAAAGAAAGAGAGTTTGAAAA
1 G-AAAATGAGATTGAAAAAGAAAGAGAG-TTGAAAA
* *
31108 GAAAACGAG--TGAAGAAG-AAGAGAGT
1 GAAAATGAGATTGAAAAAGAAAGAGAGT
31133 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:31109 original size:17 final size:16
Alignment explanation
Indices: 31058--31132 Score: 52
Period size: 16 Copynumber: 4.6 Consensus size: 16
31048 TTCAAAAACA
31058 AAAGAGAG-TGAAAAG
1 AAAGAGAGTTGAAAAG
31073 CAAA-ATGAGATTGAAAAAG
1 -AAAGA-GAG-TTG-AAAAG
31092 AAAGAGAGTTTGAAAAG
1 AAAGAGAG-TTGAAAAG
31109 AAA-ACGAG-TGAAGAAG
1 AAAGA-GAGTTGAA-AAG
31125 -AAGAGAGT
1 AAAGAGAGT
31133 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:32401 original size:20 final size:21
Alignment explanation
Indices: 32366--32404 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
32356 CAGCTCGTTG
32366 AGCTCAATTCAGCTCATTTCC
1 AGCTCAATTCAGCTCATTTCC
*
32387 AGCTC-ATTGAGCTCATTT
1 AGCTCAATTCAGCTCATTT
32405 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:32812 original size:13 final size:13
Alignment explanation
Indices: 32794--32819 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
32784 TGTGTCCTAA
32794 TATGAATTAAATT
1 TATGAATTAAATT
32807 TATGAATTAAATT
1 TATGAATTAAATT
32820 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:39816 original size:12 final size:12
Alignment explanation
Indices: 39795--39960 Score: 54
Period size: 12 Copynumber: 13.7 Consensus size: 12
39785 AGAAAAGGAG
*
39795 AAAGAGATTGAA
1 AAAGAAATTGAA
39807 AAAGAAATTG--
1 AAAGAAATTGAA
**
39817 AAAGAAA-ACAA
1 AAAGAAATTGAA
**
39828 AAAGAAAACGAA
1 AAAGAAATTGAA
**
39840 AAAGAAAAAGAA
1 AAAGAAATTGAA
** *
39852 ATTGCAAA-AGAA
1 AAAG-AAATTGAA
*
39864 AAAGAAATCGAA
1 AAAGAAATTGAA
** **
39876 AAAGTGAGAGAA
1 AAAGAAATTGAA
*
39888 AAAGAAAATGAAGA
1 AAAGAAATTG-A-A
39902 AAAGAAAATTGAA
1 AAAG-AAATTGAA
*
39915 AAAGAAAAAGTGAAA
1 AAAG--AAATTG-AA
39930 AAAGAAATTGAA
1 AAAGAAATTGAA
* **
39942 AGAGAGCTTG-A
1 AAAGAAATTGAA
39953 AAAGAAAT
1 AAAGAAAT
39961 CAAGTGAAAA
Statistics
Matches: 116, Mismatches: 28, Indels: 21
0.70 0.17 0.13
Matches are distributed among these distances:
10 7 0.06
11 16 0.14
12 56 0.48
13 14 0.12
14 12 0.10
15 11 0.09
ACGTcount: A:0.67, C:0.03, G:0.20, T:0.10
Consensus pattern (12 bp):
AAAGAAATTGAA
Found at i:39847 original size:18 final size:18
Alignment explanation
Indices: 39821--39924 Score: 82
Period size: 18 Copynumber: 5.6 Consensus size: 18
39811 AAATTGAAAG
*
39821 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
39839 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
*
39857 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAAACGA
** * *
39875 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAACGA
* *
39893 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-CGA
39914 AAAAGAAAAAG
1 AAAAGAAAAAG
39925 TGAAAAAAGA
Statistics
Matches: 66, Mismatches: 17, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
18 47 0.71
19 5 0.08
20 8 0.12
21 6 0.09
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:39849 original size:6 final size:6
Alignment explanation
Indices: 39817--39924 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
39807 AAAGAAATTG
* * ** *
39817 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
39864 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
39915 AAAGAA AAAG
1 AAAGAA AAAG
39925 TGAAAAAAGA
Statistics
Matches: 75, Mismatches: 24, Indels: 7
0.71 0.23 0.07
Matches are distributed among these distances:
5 3 0.04
6 61 0.81
7 7 0.09
8 4 0.05
ACGTcount: A:0.71, C:0.04, G:0.19, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:39915 original size:27 final size:27
Alignment explanation
Indices: 39885--39942 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 27
39875 AAAAGTGAGA
39885 GAAAAAG-AAAA-TGAAGAAAAGAAAATT
1 GAAAAAGAAAAAGTGAA-AAAAG-AAATT
39912 GAAAAAGAAAAAGTGAAAAAAGAAATT
1 GAAAAAGAAAAAGTGAAAAAAGAAATT
39939 GAAA
1 GAAA
39943 GAGAGCTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
27 16 0.55
28 9 0.31
29 4 0.14
ACGTcount: A:0.71, C:0.00, G:0.19, T:0.10
Consensus pattern (27 bp):
GAAAAAGAAAAAGTGAAAAAAGAAATT
Found at i:39931 original size:15 final size:13
Alignment explanation
Indices: 39886--39942 Score: 62
Period size: 14 Copynumber: 4.2 Consensus size: 13
39876 AAAGTGAGAG
39886 AAAAAGAAAATGA
1 AAAAAGAAAATGA
39899 AGAAAAGAAAATTG-
1 A-AAAAGAAAA-TGA
39913 AAAAAGAAAAAGTGA
1 AAAAAG-AAAA-TGA
*
39928 AAAAAGAAATTGA
1 AAAAAGAAAATGA
39941 AA
1 AA
39943 GAGAGCTTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
13 11 0.29
14 19 0.50
15 8 0.21
ACGTcount: A:0.72, C:0.00, G:0.18, T:0.11
Consensus pattern (13 bp):
AAAAAGAAAATGA
Found at i:39976 original size:33 final size:33
Alignment explanation
Indices: 39939--40001 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
39929 AAAAGAAATT
39939 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
39972 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
40002 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:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:47097 original size:20 final size:20
Alignment explanation
Indices: 47074--47120 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
47064 GGGTTAAGAT
*
47074 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
47094 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
47114 TGAGCTG
1 TGAGCTG
47121 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:48848 original size:12 final size:12
Alignment explanation
Indices: 48791--48917 Score: 55
Period size: 12 Copynumber: 10.6 Consensus size: 12
48781 TTGTCTTTTC
48791 TTTCTTTTTCAA
1 TTTCTTTTTCAA
*
48803 TTTTCTTTTCTTCAT
1 -TTTC-TTT-TTCAA
**
48818 TTTCTTTTTCTC
1 TTTCTTTTTCAA
**
48830 TCACTTTTTCAA
1 TTTCTTTTTCAA
*
48842 TTTCTTTTTC-T
1 TTTCTTTTTCAA
** **
48853 TTTGCAATTTCTT
1 TTT-CTTTTTCAA
**
48866 TTTCTTTTTCGT
1 TTTCTTTTTCAA
*
48878 TTTCTTTTT--G
1 TTTCTTTTTCAA
*
48888 TTT-TCTTTCAA
1 TTTCTTTTTCAA
48899 TTTCTTTTTCAA
1 TTTCTTTTTCAA
*
48911 TCTCTTT
1 TTTCTTT
48918 CTCCTTTTCT
Statistics
Matches: 87, Mismatches: 20, Indels: 15
0.71 0.16 0.12
Matches are distributed among these distances:
9 4 0.05
10 3 0.03
11 6 0.07
12 52 0.60
13 11 0.13
14 7 0.08
15 4 0.05
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTCTTTTTCAA
Found at i:48886 original size:18 final size:18
Alignment explanation
Indices: 48791--48891 Score: 85
Period size: 18 Copynumber: 5.4 Consensus size: 18
48781 TTGTCTTTTC
48791 TTTCTTTTTCAATTTTCTTT
1 TTTCTTTTTC-ATTTTC-TT
* * *
48811 TCTTCATTTTCTTTTTCTC
1 T-TTCTTTTTCATTTTCTT
** *
48830 TCACTTTTTCAATTTCTT
1 TTTCTTTTTCATTTTCTT
* *
48848 TTTCTTTTGCAATTTCTT
1 TTTCTTTTTCATTTTCTT
*
48866 TTTCTTTTTCGTTTTCTT
1 TTTCTTTTTCATTTTCTT
*
48884 TTTGTTTT
1 TTTCTTTT
48892 CTTTCAATTT
Statistics
Matches: 64, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
18 48 0.75
19 2 0.03
20 6 0.09
21 8 0.12
ACGTcount: A:0.08, C:0.18, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTCTTTTTCATTTTCTT
Found at i:48908 original size:6 final size:6
Alignment explanation
Indices: 48791--48895 Score: 68
Period size: 6 Copynumber: 17.2 Consensus size: 6
48781 TTGTCTTTTC
* * * ** **
48791 TTTCTT TTTCAAT TTTCTTT TCTTCAT TTTCTT TTTCTC TCACTT TTTCAA
1 TTTCTT TTTC-TT TTTC-TT T-TTCTT TTTCTT TTTCTT TTTCTT TTTCTT
* ** * *
48842 TTTCTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCGT TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
48889 TTTCTT T
1 TTTCTT T
48896 CAATTTCTTT
Statistics
Matches: 71, Mismatches: 25, Indels: 6
0.70 0.25 0.06
Matches are distributed among these distances:
5 4 0.06
6 55 0.77
7 9 0.13
8 3 0.04
ACGTcount: A:0.08, C:0.18, G:0.03, T:0.71
Consensus pattern (6 bp):
TTTCTT
Found at i:49472 original size:12 final size:12
Alignment explanation
Indices: 49441--49499 Score: 57
Period size: 12 Copynumber: 4.6 Consensus size: 12
49431 TTGGAGTAAC
49441 AAAAAAAA-TCA
1 AAAAAAAATTCA
49452 AAAAAAAATTCGA
1 AAAAAAAATTC-A
*
49465 AAAAAAATTTGATTGA
1 AAAAAAA----ATTCA
49481 AAAAAAAATTCA
1 AAAAAAAATTCA
49493 AAAAAAA
1 AAAAAAA
49500 GTGAAAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
11 8 0.20
12 13 0.32
13 8 0.20
16 8 0.20
17 3 0.08
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.17
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:55754 original size:17 final size:18
Alignment explanation
Indices: 55734--55774 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
55724 TCGTTTCTTT
55734 TCTTTTGAATCACTC-TC
1 TCTTTTGAATCACTCATC
**
55751 TCTTTTTTATCACTCATC
1 TCTTTTGAATCACTCATC
55769 T-TTTTG
1 TCTTTTG
55775 TTTTTCTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.15, C:0.24, G:0.05, T:0.56
Consensus pattern (18 bp):
TCTTTTGAATCACTCATC
Found at i:58025 original size:17 final size:16
Alignment explanation
Indices: 58003--58050 Score: 69
Period size: 17 Copynumber: 2.9 Consensus size: 16
57993 CTAGACCGTA
58003 TGCAATTTTTTTTTTCT
1 TGCAATTTTTTTTTT-T
58020 TGCAATTTTTTTTTTT
1 TGCAATTTTTTTTTTT
*
58036 TGAAACTTTTTTTTT
1 TGCAA-TTTTTTTTT
58051 AACTTTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 5 0.17
17 24 0.83
ACGTcount: A:0.15, C:0.08, G:0.06, T:0.71
Consensus pattern (16 bp):
TGCAATTTTTTTTTTT
Found at i:58030 original size:16 final size:17
Alignment explanation
Indices: 58003--58050 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 17
57993 CTAGACCGTA
*
58003 TGCAATTTTTTTTTTCT
1 TGCAACTTTTTTTTTCT
*
58020 TGCAA-TTTTTTTTTTT
1 TGCAACTTTTTTTTTCT
*
58036 TGAAACTTTTTTTTT
1 TGCAACTTTTTTTTT
58051 AACTTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 14 0.50
17 14 0.50
ACGTcount: A:0.15, C:0.08, G:0.06, T:0.71
Consensus pattern (17 bp):
TGCAACTTTTTTTTTCT
Found at i:58070 original size:13 final size:13
Alignment explanation
Indices: 58028--58073 Score: 60
Period size: 12 Copynumber: 3.6 Consensus size: 13
58018 CTTGCAATTT
58028 TTTTTTTTTGAAAC
1 TTTTTTTTTG-AAC
58042 TTTTTTTTT-AAC
1 TTTTTTTTTGAAC
*
58054 TTTTTTTTTGGA-
1 TTTTTTTTTGAAC
58066 TTTTTTTT
1 TTTTTTTT
58074 CGAAGCTACG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 20 0.67
13 1 0.03
14 9 0.30
ACGTcount: A:0.13, C:0.04, G:0.07, T:0.76
Consensus pattern (13 bp):
TTTTTTTTTGAAC
Found at i:60701 original size:20 final size:20
Alignment explanation
Indices: 60655--60701 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
60645 AGCTCGTTTC
*
60655 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
60675 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
60695 CAGCTCA
1 CAGCTCA
60702 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:62228 original size:11 final size:11
Alignment explanation
Indices: 62212--62243 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
62202 GGAAATTTGA
62212 AAAAAAAATTC
1 AAAAAAAATTC
62223 AAAAAAAATTC
1 AAAAAAAATTC
62234 AAAAAAAATT
1 AAAAAAAATT
62244 GAAGTATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:63342 original size:18 final size:18
Alignment explanation
Indices: 63316--63418 Score: 66
Period size: 18 Copynumber: 5.6 Consensus size: 18
63306 AAATTGAAAG
*
63316 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
* *
63334 AAAAGAAAAAGAAATTC-C
1 AAAAGAAAAAGAAA-ACGA
*
63352 AAAAGAAAAAGAAATC-A
1 AAAAGAAAAAGAAAACGA
** * *
63369 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAACGA
* *
63387 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-CGA
63408 AAAAGAAAAAG
1 AAAAGAAAAAG
63419 CGAAAAAAGA
Statistics
Matches: 65, Mismatches: 15, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
17 13 0.20
18 32 0.49
19 6 0.09
20 8 0.12
21 6 0.09
ACGTcount: A:0.72, C:0.05, G:0.17, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:63344 original size:6 final size:6
Alignment explanation
Indices: 63312--63418 Score: 56
Period size: 6 Copynumber: 17.7 Consensus size: 6
63302 AGAGAAATTG
* * ****
63312 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTCCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
63359 AAAG-A AATCAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
63409 AAAGAA AAAG
1 AAAGAA AAAG
63419 CGAAAAAAGA
Statistics
Matches: 71, Mismatches: 26, Indels: 9
0.67 0.25 0.08
Matches are distributed among these distances:
5 6 0.08
6 54 0.76
7 7 0.10
8 4 0.06
ACGTcount: A:0.72, C:0.05, G:0.17, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:63400 original size:14 final size:13
Alignment explanation
Indices: 63379--63416 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
63369 AAAAGTGAGA
63379 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
63391 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
63406 GAAAAAGAAAA
1 GAAAAAGAAAA
63417 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:63453 original size:12 final size:12
Alignment explanation
Indices: 63422--63453 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
63412 GAAAAAGCGA
*
63422 AAAAAGAATTTG
1 AAAAAGAGTTTG
63434 AAAAAGAGTTTG
1 AAAAAGAGTTTG
63446 AAAAAGAG
1 AAAAAGAG
63454 AAGAGTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (12 bp):
AAAAAGAGTTTG
Found at i:65748 original size:4 final size:4
Alignment explanation
Indices: 65739--65771 Score: 57
Period size: 4 Copynumber: 8.0 Consensus size: 4
65729 AAGTTTTATT
65739 TTTA TTTA TTTA TTTA TTTA TTTA TTTA GTTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA
65772 AATTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:72213 original size:4 final size:4
Alignment explanation
Indices: 72204--72237 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
72194 AAGTTTTATT
72204 TTTA TTTA TTTA TTTA TTTA TTTTA TTTA GTTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA
72238 AATTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:72245 original size:22 final size:22
Alignment explanation
Indices: 72187--72246 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
72177 AAGTGGCCCA
*
72187 AGTTGTAAAGTTTTATTTTTATTT
1 AGTT-TAAATTTTTA-TTTTATTT
*
72211 A-TTT-ATTTATTTATTTTATTT
1 AGTTTAAATT-TTTATTTTATTT
72232 AGTTTAAATTTTTAT
1 AGTTTAAATTTTTAT
72247 ATTCAGTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 11 0.37
22 13 0.43
23 5 0.17
24 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (22 bp):
AGTTTAAATTTTTATTTTATTT
Found at i:74275 original size:33 final size:33
Alignment explanation
Indices: 74237--74299 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
74227 GATTACTCAC
74237 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
74270 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
74300 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:74326 original size:21 final size:21
Alignment explanation
Indices: 74297--74352 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
74287 CAAGCTCTCT
*
74297 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
74318 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
74339 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
74353 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:74345 original size:14 final size:14
Alignment explanation
Indices: 74296--74352 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
74286 TCAAGCTCTC
74296 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
74309 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
74323 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
74337 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
74351 TT
1 TT
74353 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:74412 original size:18 final size:18
Alignment explanation
Indices: 74314--74417 Score: 84
Period size: 18 Copynumber: 5.6 Consensus size: 18
74304 TCTTTTTTCG
74314 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTC-ATTTT
* *
74333 CTTTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCATTTT
* **
74353 CTCTCACTTTTTCGA-TTT
1 CTTTTTCTTTTTC-ATTTT
* *
74371 CTTTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCATTTT
*
74389 CTTTTTCTTTTTCGTTTT
1 CTTTTTCTTTTTCATTTT
*
74407 CTTTTTGTTTT
1 CTTTTTCTTTT
74418 CTTTCAATTT
Statistics
Matches: 66, Mismatches: 15, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
17 1 0.02
18 46 0.70
19 3 0.05
20 8 0.12
21 8 0.12
ACGTcount: A:0.07, C:0.18, G:0.04, T:0.71
Consensus pattern (18 bp):
CTTTTTCTTTTTCATTTT
Found at i:74440 original size:6 final size:6
Alignment explanation
Indices: 74314--74421 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
74304 TCTTTTTTCG
* * * **
74314 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
74365 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
74413 -GTTTT CTTT
1 CTTTTT CTTT
74422 CAATTTCAAT
Statistics
Matches: 74, Mismatches: 25, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
5 4 0.05
6 58 0.78
7 9 0.12
8 3 0.04
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:75487 original size:29 final size:26
Alignment explanation
Indices: 75440--75517 Score: 77
Period size: 29 Copynumber: 2.8 Consensus size: 26
75430 GACTTTTCAC
*
75440 TTTTTTTTAACTTGATTTTTTTGCTC-A
1 TTTTTTTTCACTT--TTTTTTTGCTCGA
*
75467 CCTTTTTTTTCTTTCTTTTTTTTTGCTCGA
1 --TTTTTTTTC--ACTTTTTTTTTGCTCGA
75497 TTTTTTTTCACTTTTTTTTTG
1 TTTTTTTTCACTTTTTTTTTG
75518 AATTTTTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
26 11 0.26
28 9 0.21
29 19 0.44
30 1 0.02
31 3 0.07
ACGTcount: A:0.08, C:0.14, G:0.06, T:0.72
Consensus pattern (26 bp):
TTTTTTTTCACTTTTTTTTTGCTCGA
Found at i:75512 original size:12 final size:12
Alignment explanation
Indices: 75497--75553 Score: 62
Period size: 12 Copynumber: 4.6 Consensus size: 12
75487 TTTTGCTCGA
*
75497 TTTTTTTTCACT
1 TTTTTTTTCAAT
*
75509 TTTTTTTTGAA-
1 TTTTTTTTCAAT
75520 TTTTTTTTCAAT
1 TTTTTTTTCAAT
75532 CAATTTTTTTTCAAT
1 ---TTTTTTTTCAAT
75547 TTTTTTT
1 TTTTTTT
75554 GATTTTTTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
11 10 0.26
12 16 0.42
15 12 0.32
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.74
Consensus pattern (12 bp):
TTTTTTTTCAAT
Found at i:75553 original size:15 final size:15
Alignment explanation
Indices: 75518--75546 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
75508 TTTTTTTTTG
75518 AATTTTTTTTCAATC
1 AATTTTTTTTCAATC
75533 AATTTTTTTTCAAT
1 AATTTTTTTTCAAT
75547 TTTTTTTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (15 bp):
AATTTTTTTTCAATC
Found at i:77591 original size:4 final size:4
Alignment explanation
Indices: 77582--77609 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
77572 AAGTTTTATT
77582 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
77610 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:90946 original size:18 final size:18
Alignment explanation
Indices: 90925--90959 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
90915 TTTTTCTTTT
90925 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
90943 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
90960 TTTCTTTTCT
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:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:91945 original size:15 final size:14
Alignment explanation
Indices: 91872--91947 Score: 61
Period size: 13 Copynumber: 5.3 Consensus size: 14
91862 TTGGTCACCT
91872 TTTTTTTTTGCTCG-A
1 TTTTTTTTT--TCGAA
*
91887 TTTTTTTTTTC-AC
1 TTTTTTTTTTCGAA
91900 TTTTTTTTTT-GAA
1 TTTTTTTTTTCGAA
91913 TTTTTTTTTCAATC-AA
1 TTTTTTTTT---TCGAA
91929 TTTTTTTTTTCGAAA
1 TTTTTTTTTTCG-AA
91944 TTTT
1 TTTT
91948 CTTATTTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
13 24 0.47
15 15 0.29
16 12 0.24
ACGTcount: A:0.14, C:0.09, G:0.05, T:0.71
Consensus pattern (14 bp):
TTTTTTTTTTCGAA
Found at i:95532 original size:24 final size:25
Alignment explanation
Indices: 95479--95532 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
95469 AACAAATTCT
* *
95479 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
95504 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
95527 TTTTTT
1 TTTTTT
95533 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:97843 original size:14 final size:13
Alignment explanation
Indices: 97783--97847 Score: 62
Period size: 14 Copynumber: 4.9 Consensus size: 13
97773 AGACCGTATG
97783 CAATTTTTTTTTT
1 CAATTTTTTTTTT
97796 GCAATTTTTTTTTT
1 -CAATTTTTTTTTT
**
97810 CGAA-ACTTTTTTT
1 C-AATTTTTTTTTT
*
97823 -AACTTTTTTTTT
1 CAATTTTTTTTTT
97835 CAGATTTTTTTTT
1 CA-ATTTTTTTTT
97848 CGAAGCTACG
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
11 2 0.05
12 7 0.17
13 9 0.21
14 24 0.57
ACGTcount: A:0.17, C:0.09, G:0.05, T:0.69
Consensus pattern (13 bp):
CAATTTTTTTTTT
Found at i:104978 original size:33 final size:33
Alignment explanation
Indices: 104940--105002 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
104930 GATTACTCAC
104940 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
104973 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
105003 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:105029 original size:21 final size:21
Alignment explanation
Indices: 105000--105055 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
104990 CAAGCTCTCT
*
105000 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
105021 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
105042 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
105056 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:105048 original size:14 final size:14
Alignment explanation
Indices: 104999--105055 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
104989 TCAAGCTCTC
104999 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
105012 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
105026 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
105040 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
105054 TT
1 TT
105056 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:105115 original size:18 final size:18
Alignment explanation
Indices: 105017--105120 Score: 84
Period size: 18 Copynumber: 5.6 Consensus size: 18
105007 TCTTTTTTCG
105017 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTC-ATTTT
* *
105036 CTTTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCATTTT
* **
105056 CTCTCACTTTTTCGA-TTT
1 CTTTTTCTTTTTC-ATTTT
* *
105074 CTTTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCATTTT
*
105092 CTTTTTCTTTTTCGTTTT
1 CTTTTTCTTTTTCATTTT
*
105110 CTTTTTGTTTT
1 CTTTTTCTTTT
105121 CTTTCAATTT
Statistics
Matches: 66, Mismatches: 15, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
17 1 0.02
18 46 0.70
19 3 0.05
20 8 0.12
21 8 0.12
ACGTcount: A:0.07, C:0.18, G:0.04, T:0.71
Consensus pattern (18 bp):
CTTTTTCTTTTTCATTTT
Found at i:105143 original size:6 final size:6
Alignment explanation
Indices: 105017--105124 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
105007 TCTTTTTTCG
* * * **
105017 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
105068 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
105116 -GTTTT CTTT
1 CTTTTT CTTT
105125 CAATTTCAAT
Statistics
Matches: 74, Mismatches: 25, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
5 4 0.05
6 58 0.78
7 9 0.12
8 3 0.04
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:106223 original size:12 final size:12
Alignment explanation
Indices: 106208--106279 Score: 54
Period size: 12 Copynumber: 5.6 Consensus size: 12
106198 TTTTGCTCGA
*
106208 TTTTTTTTCACT
1 TTTTTTTTCAAT
*
106220 TTTTTTTTGAAT
1 TTTTTTTTCAAT
*
106232 TTTTTTTCAATCAAA
1 TTTTTTT---TCAAT
106247 TTTTTTTTCAAAAT
1 TTTTTTTTC--AAT
**
106261 TTTTTTTTTGAT
1 TTTTTTTTCAAT
106273 TTTTTTT
1 TTTTTTT
106280 GTTACTCCAA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
12 28 0.58
14 10 0.21
15 10 0.21
ACGTcount: A:0.18, C:0.07, G:0.03, T:0.72
Consensus pattern (12 bp):
TTTTTTTTCAAT
Found at i:110678 original size:27 final size:27
Alignment explanation
Indices: 110646--110701 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
110636 TAAAACAAGT
110646 GAGGAAAAAGAAAAAGAGAATGAAAAA
1 GAGGAAAAAGAAAAAGAGAATGAAAAA
* ** *
110673 GAGGAAAAAGAGATTGAGAGTGAAAAA
1 GAGGAAAAAGAAAAAGAGAATGAAAAA
110700 GA
1 GA
110702 AATTGAAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.30, T:0.07
Consensus pattern (27 bp):
GAGGAAAAAGAAAAAGAGAATGAAAAA
Found at i:110699 original size:18 final size:17
Alignment explanation
Indices: 110672--110707 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
110662 AGAATGAAAA
*
110672 AGAGGAAAAAGAGATTG
1 AGAGGAAAAAGAAATTG
110689 AGAGTGAAAAAGAAATTG
1 AGAG-GAAAAAGAAATTG
110707 A
1 A
110708 AGAAAGAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.56, C:0.00, G:0.31, T:0.14
Consensus pattern (17 bp):
AGAGGAAAAAGAAATTG
Found at i:113507 original size:20 final size:20
Alignment explanation
Indices: 113461--113507 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
113451 AGCTTGTTTC
*
113461 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
113481 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
113501 CAGCTCA
1 CAGCTCA
113508 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:124479 original size:24 final size:23
Alignment explanation
Indices: 124428--124482 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
124418 AATCGAAAAA
124428 GAAAAAGAAAAAGAAAAAAAGTT
1 GAAAAAGAAAAAGAAAAAAAGTT
* ** *
124451 AAAAAAGAAATTGAGAAAGAAGTT
1 GAAAAAGAAAAAGA-AAAAAAGTT
124475 GAAAAAGA
1 GAAAAAGA
124483 GATAGAATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.69, C:0.00, G:0.20, T:0.11
Consensus pattern (23 bp):
GAAAAAGAAAAAGAAAAAAAGTT
Found at i:124484 original size:18 final size:18
Alignment explanation
Indices: 124463--124500 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
124453 AAAAGAAATT
124463 GAGAAAGAAGTTGAAAAA
1 GAGAAAGAAGTTGAAAAA
* *
124481 GAGATAGAATTTGAAAAA
1 GAGAAAGAAGTTGAAAAA
124499 GA
1 GA
124501 ACATAAGAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.26, T:0.16
Consensus pattern (18 bp):
GAGAAAGAAGTTGAAAAA
Found at i:126395 original size:12 final size:11
Alignment explanation
Indices: 126378--126419 Score: 59
Period size: 13 Copynumber: 3.7 Consensus size: 11
126368 AGTTTCTTCA
126378 AAAAAAAATTC
1 AAAAAAAATTC
126389 GAAAAAAAAATTC
1 --AAAAAAAATTC
126402 -AAAAAAATTC
1 AAAAAAAATTC
126412 AAAAAAAA
1 AAAAAAAA
126420 ATTGGTTTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.36
11 7 0.25
13 11 0.39
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.14
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:126409 original size:23 final size:22
Alignment explanation
Indices: 126379--126422 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
126369 GTTTCTTCAA
126379 AAAAAAATTCGAAAAAAAAATTC
1 AAAAAAATTC-AAAAAAAAATTC
126402 AAAAAAATTCAAAAAAAAATT
1 AAAAAAATTCAAAAAAAAATT
126423 GGTTTCCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.73, C:0.07, G:0.02, T:0.18
Consensus pattern (22 bp):
AAAAAAATTCAAAAAAAAATTC
Found at i:126418 original size:10 final size:10
Alignment explanation
Indices: 126392--126418 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
126382 AAAATTCGAA
126392 AAAAAAATTC
1 AAAAAAATTC
126402 AAAAAAATTC
1 AAAAAAATTC
126412 AAAAAAA
1 AAAAAAA
126419 AATTGGTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:126420 original size:12 final size:12
Alignment explanation
Indices: 126374--126422 Score: 75
Period size: 12 Copynumber: 4.2 Consensus size: 12
126364 TAGTAGTTTC
126374 TTCAAAAAAAAA
1 TTCAAAAAAAAA
126386 TTCGAAAAAAAAA
1 TTC-AAAAAAAAA
126399 TTC--AAAAAAA
1 TTCAAAAAAAAA
126409 TTCAAAAAAAAA
1 TTCAAAAAAAAA
126421 TT
1 TT
126423 GGTTTCCTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
10 10 0.29
12 12 0.35
13 12 0.35
ACGTcount: A:0.69, C:0.08, G:0.02, T:0.20
Consensus pattern (12 bp):
TTCAAAAAAAAA
Found at i:134686 original size:22 final size:22
Alignment explanation
Indices: 134627--134692 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
134617 GGTATTTGGG
* *
134627 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
*
134648 AATTGGTATGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
134670 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
134693 TCAAAGAGGT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
21 18 0.49
22 14 0.38
23 5 0.14
ACGTcount: A:0.30, C:0.03, G:0.30, T:0.36
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:143532 original size:21 final size:23
Alignment explanation
Indices: 143487--143533 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
143477 TCACCTGCAA
* *
143487 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
143510 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
143531 TAA
1 TAA
143534 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:144357 original size:20 final size:20
Alignment explanation
Indices: 144311--144357 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
144301 AGCTTGTTTC
*
144311 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
144331 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
144351 CAGCTCA
1 CAGCTCA
144358 ATCTTAACCT
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:145923 original size:16 final size:16
Alignment explanation
Indices: 145869--145924 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
145859 GAAATTCAAA
** *
145869 AAAAAAAGAAGTGAGC
1 AAAAAAAGAAAAGAAC
145885 AAAAAAAGAAAA-AA-
1 AAAAAAAGAAAAGAAC
145899 AAAGTAAAAGAAAAGAAC
1 AAA--AAAAGAAAAGAAC
145917 AAAAAAAG
1 AAAAAAAG
145925 TGAAAAGTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
14 3 0.09
15 1 0.03
16 24 0.73
17 2 0.06
18 3 0.09
ACGTcount: A:0.77, C:0.04, G:0.16, T:0.04
Consensus pattern (16 bp):
AAAAAAAGAAAAGAAC
Found at i:145930 original size:10 final size:10
Alignment explanation
Indices: 145885--145924 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 10
145875 AGAAGTGAGC
145885 AAAAAAAGAA
1 AAAAAAAGAA
145895 AAAAAAAGTAA
1 AAAAAAAG-AA
*
145906 AAGAAAAGAA
1 AAAAAAAGAA
145916 CAAAAAAAG
1 -AAAAAAAG
145925 TGAAAAGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.82, C:0.03, G:0.12, T:0.03
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:145930 original size:23 final size:22
Alignment explanation
Indices: 145869--145931 Score: 76
Period size: 22 Copynumber: 2.8 Consensus size: 22
145859 GAAATTCAAA
145869 AAAAAAAGAAGTGAGCAAA-AAAAG
1 AAAAAAA-AAGTGA--AAAGAAAAG
145893 AAAAAAAAAGT-AAAAGAAAAG
1 AAAAAAAAAGTGAAAAGAAAAG
145914 AACAAAAAAAGTGAAAAG
1 AA-AAAAAAAGTGAAAAG
145932 TATTGCGAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
20 3 0.08
21 7 0.19
22 10 0.28
23 9 0.25
24 7 0.19
ACGTcount: A:0.75, C:0.03, G:0.17, T:0.05
Consensus pattern (22 bp):
AAAAAAAAAGTGAAAAGAAAAG
Found at i:147028 original size:48 final size:46
Alignment explanation
Indices: 146949--147053 Score: 133
Period size: 48 Copynumber: 2.2 Consensus size: 46
146939 GAGTGTCATG
*
146949 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AG--AGAAATC
*
146997 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAGAAATC
147044 GAAAAAGAAA
1 GAAAAAGAAA
147054 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
47 16 0.31
48 26 0.50
49 6 0.12
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (46 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAGAAATC
Found at i:148770 original size:20 final size:20
Alignment explanation
Indices: 148724--148770 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
148714 AGCTTGTTTC
*
148724 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
148744 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
148764 CAGCTCA
1 CAGCTCA
148771 ATCTTAACCT
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:150315 original size:23 final size:23
Alignment explanation
Indices: 150280--150344 Score: 73
Period size: 23 Copynumber: 2.8 Consensus size: 23
150270 CGAAATTCAA
150280 AAAAAAAAGAAGTGAGCAAA-AAAAG
1 AAAAAAAA-AAGTGA--AAAGAAAAG
150305 -AAAAAAAAAGT-AAAAGAAAAG
1 AAAAAAAAAAGTGAAAAGAAAAG
150326 AACAAAAAAAAGTGAAAAG
1 AA-AAAAAAAAGTGAAAAG
150345 TATTGCGAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
20 3 0.08
21 5 0.14
22 2 0.06
23 14 0.39
24 12 0.33
ACGTcount: A:0.75, C:0.03, G:0.17, T:0.05
Consensus pattern (23 bp):
AAAAAAAAAAGTGAAAAGAAAAG
Found at i:150335 original size:16 final size:16
Alignment explanation
Indices: 150281--150335 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
150271 GAAATTCAAA
** *
150281 AAAAAAAGAAGTGAGC
1 AAAAAAAGAAAAGAAC
150297 AAAAAAAGAAAA-AA-
1 AAAAAAAGAAAAGAAC
150311 AAAGTAAAAGAAAAGAAC
1 AAA--AAAAGAAAAGAAC
150329 AAAAAAA
1 AAAAAAA
150336 AGTGAAAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 3 0.09
15 1 0.03
16 23 0.72
17 2 0.06
18 3 0.09
ACGTcount: A:0.78, C:0.04, G:0.15, T:0.04
Consensus pattern (16 bp):
AAAAAAAGAAAAGAAC
Found at i:154485 original size:17 final size:16
Alignment explanation
Indices: 154465--154507 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
154455 AAAAAAATCG
154465 AAAAAAAAAATTAATT-A
1 AAAAAAAAAATT--TTGA
*
154482 AAAAAAAATATTTTGA
1 AAAAAAAAAATTTTGA
154498 AAAAAAAAAA
1 AAAAAAAAAA
154508 ATTGCATACG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 2 0.09
16 10 0.43
17 11 0.48
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (16 bp):
AAAAAAAAAATTTTGA
Found at i:159407 original size:48 final size:47
Alignment explanation
Indices: 159328--159433 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
159318 GAGTGTCATG
*
159328 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
159376 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
159424 GAAAAAGAAA
1 GAAAAAGAAA
159434 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:161150 original size:20 final size:20
Alignment explanation
Indices: 161104--161150 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
161094 AGCTTGTTTC
*
161104 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
161124 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
161144 CAGCTCA
1 CAGCTCA
161151 ATCTTAACCT
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:167175 original size:15 final size:16
Alignment explanation
Indices: 167155--167194 Score: 73
Period size: 15 Copynumber: 2.6 Consensus size: 16
167145 TAGCTTCTTC
167155 TTTTTTTCACGAAATT
1 TTTTTTTCACGAAATT
167171 TTTTTTTCACG-AATT
1 TTTTTTTCACGAAATT
167186 TTTTTTTCA
1 TTTTTTTCA
167195 ACTTGATATC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.20, C:0.12, G:0.05, T:0.62
Consensus pattern (16 bp):
TTTTTTTCACGAAATT
Found at i:167268 original size:11 final size:12
Alignment explanation
Indices: 167232--167265 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
167222 ATGGAAACCA
167232 AATTTTTTTTTG
1 AATTTTTTTTTG
167244 AATTTTTTTTTG
1 AATTTTTTTTTG
167256 AATTTTTTTT
1 AATTTTTTTT
167266 GAAGAAACTA
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:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:169868 original size:21 final size:23
Alignment explanation
Indices: 169823--169869 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
169813 TCACCTGCAA
* *
169823 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
169846 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
169867 TAA
1 TAA
169870 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:170403 original size:12 final size:11
Alignment explanation
Indices: 170386--170437 Score: 79
Period size: 11 Copynumber: 4.7 Consensus size: 11
170376 TAGTTTCTCG
*
170386 AAAAAAAACTC
1 AAAAAAAATTC
170397 -AAAAAAATTC
1 AAAAAAAATTC
170407 AAAAAAAAATTC
1 -AAAAAAAATTC
170419 AAAAAAAATTC
1 AAAAAAAATTC
170430 AAAAAAAA
1 AAAAAAAA
170438 AATTGGTTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
10 9 0.24
11 19 0.50
12 10 0.26
ACGTcount: A:0.77, C:0.10, G:0.00, T:0.13
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:170423 original size:23 final size:22
Alignment explanation
Indices: 170386--170438 Score: 88
Period size: 23 Copynumber: 2.4 Consensus size: 22
170376 TAGTTTCTCG
170386 AAAAAAAACTCAAAAAAATTCA
1 AAAAAAAACTCAAAAAAATTCA
*
170408 AAAAAAAATTCAAAAAAAATTCA
1 AAAAAAAACTC-AAAAAAATTCA
170431 AAAAAAAA
1 AAAAAAAA
170439 ATTGGTTTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 10 0.34
23 19 0.66
ACGTcount: A:0.77, C:0.09, G:0.00, T:0.13
Consensus pattern (22 bp):
AAAAAAAACTCAAAAAAATTCA
Found at i:170438 original size:12 final size:12
Alignment explanation
Indices: 170397--170438 Score: 77
Period size: 12 Copynumber: 3.6 Consensus size: 12
170387 AAAAAAACTC
170397 AAAAAAATTCAA
1 AAAAAAATTCAA
170409 AAAAAAATTC-A
1 AAAAAAATTCAA
170420 AAAAAAATTCAA
1 AAAAAAATTCAA
170432 AAAAAAA
1 AAAAAAA
170439 ATTGGTTTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.38
12 18 0.62
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:170498 original size:12 final size:14
Alignment explanation
Indices: 170478--170531 Score: 67
Period size: 15 Copynumber: 3.8 Consensus size: 14
170468 GATATCAAGT
170478 TGAAAAAAAAATTC-
1 TGAAAAAAAAA-TCG
170492 T-AAAAAAAAATCG
1 TGAAAAAAAAATCG
170505 TGAAAAAAAAAATTCG
1 TG-AAAAAAAAA-TCG
170521 TGAAAAAAAAA
1 TGAAAAAAAAA
170532 GAAGAAGCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
12 2 0.06
13 10 0.28
14 1 0.03
15 18 0.50
16 5 0.14
ACGTcount: A:0.69, C:0.06, G:0.09, T:0.17
Consensus pattern (14 bp):
TGAAAAAAAAATCG
Found at i:170500 original size:15 final size:15
Alignment explanation
Indices: 170480--170531 Score: 65
Period size: 16 Copynumber: 3.5 Consensus size: 15
170470 TATCAAGTTG
170480 AAAAAAAAATTC-T-
1 AAAAAAAAATTCGTA
170493 AAAAAAAAA-TCGTGA
1 AAAAAAAAATTCGT-A
170508 AAAAAAAAATTCGTGA
1 AAAAAAAAATTCGT-A
170524 AAAAAAAA
1 AAAAAAAA
170532 GAAGAAGCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
12 2 0.06
13 10 0.29
15 9 0.26
16 14 0.40
ACGTcount: A:0.71, C:0.06, G:0.08, T:0.15
Consensus pattern (15 bp):
AAAAAAAAATTCGTA
Found at i:170512 original size:16 final size:16
Alignment explanation
Indices: 170493--170531 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
170483 AAAAAATTCT
170493 AAAAAAAAATCGTGAA
1 AAAAAAAAATCGTGAA
*
170509 AAAAAAAATTCGTGAA
1 AAAAAAAAATCGTGAA
170525 AAAAAAA
1 AAAAAAA
170532 GAAGAAGCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.72, C:0.05, G:0.10, T:0.13
Consensus pattern (16 bp):
AAAAAAAAATCGTGAA
Found at i:171479 original size:18 final size:17
Alignment explanation
Indices: 171458--171502 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
171448 GAGTGACGAG
171458 AGAAAAAGAAACTGAAAA
1 AGAAAAA-AAACTGAAAA
*
171476 AGAAACAAAAATTGAAAA
1 AGAAA-AAAAACTGAAAA
171494 AGAGAAAAA
1 AGA-AAAAA
171503 GATTGGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.73, C:0.04, G:0.16, T:0.07
Consensus pattern (17 bp):
AGAAAAAAAACTGAAAA
Found at i:171507 original size:18 final size:18
Alignment explanation
Indices: 171456--171507 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
171446 AAGAGTGACG
*
171456 AGAGAAAAAGAAACTGAAAA
1 AGAGAAAAAG--ATTGAAAA
*
171476 AGA-AACAAAAATTGAAAA
1 AGAGAA-AAAGATTGAAAA
171494 AGAGAAAAAGATTG
1 AGAGAAAAAGATTG
171508 GAGAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 17 0.63
19 4 0.15
20 6 0.22
ACGTcount: A:0.67, C:0.04, G:0.19, T:0.10
Consensus pattern (18 bp):
AGAGAAAAAGATTGAAAA
Found at i:178285 original size:22 final size:22
Alignment explanation
Indices: 178257--178300 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
178247 TTTTGAACCA
178257 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
178279 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
178301 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:182530 original size:12 final size:12
Alignment explanation
Indices: 182513--182538 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
182503 AAAAGAGAAG
182513 AAATTCAAAAAA
1 AAATTCAAAAAA
182525 AAATTCAAAAAA
1 AAATTCAAAAAA
182537 AA
1 AA
182539 TCGAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:183645 original size:18 final size:18
Alignment explanation
Indices: 183619--183668 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
183609 AAATTGAAAG
*
183619 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
183637 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
183655 AAAAGAAAAAGAAA
1 AAAAGAAAAAGAAA
183669 TCAAAATAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.76, C:0.06, G:0.14, T:0.04
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:183647 original size:6 final size:6
Alignment explanation
Indices: 183615--183668 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
183605 AAAGAAATTG
* * ** *
183615 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
183662 AAAGAA A
1 AAAGAA A
183669 TCAAAATAGT
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
5 3 0.08
6 35 0.92
ACGTcount: A:0.76, C:0.06, G:0.15, T:0.04
Consensus pattern (6 bp):
AAAGAA
Found at i:183728 original size:18 final size:18
Alignment explanation
Indices: 183707--183741 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
183697 AGAAAAGAAA
183707 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
183725 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
183742 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:191881 original size:22 final size:22
Alignment explanation
Indices: 191851--191894 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
191841 TTTGGTATTT
191851 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
191873 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
191895 TGGTTCAAAA
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:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:193224 original size:20 final size:20
Alignment explanation
Indices: 193183--193236 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
193173 TCATTTTCCC
*
193183 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* **
193203 AGCTTAATTTAGCTCATTTG
1 AGCTCAATTTAGCTCACATG
*
193223 AGCTCAATCTAGCT
1 AGCTCAATTTAGCT
193237 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:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:193227 original size:30 final size:30
Alignment explanation
Indices: 193183--193256 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
193173 TCATTTTCCC
193183 AGCTCGATTT-AGCTCACAT-GAGCTTAATTT
1 AGCTC-ATTTGAGCTCA-ATCGAGCTTAATTT
* *
193213 AGCTCATTTGAGCTCAATCTAGCTTACTTT
1 AGCTCATTTGAGCTCAATCGAGCTTAATTT
*
193243 AGCTCGTTTGAGCT
1 AGCTCATTTGAGCT
193257 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 6 0.15
30 33 0.85
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.38
Consensus pattern (30 bp):
AGCTCATTTGAGCTCAATCGAGCTTAATTT
Found at i:194886 original size:9 final size:10
Alignment explanation
Indices: 194855--194886 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
194845 AAAAGAGAAG
194855 AAATTCAAAA
1 AAATTCAAAA
194865 AAATTCAAAA
1 AAATTCAAAA
194875 AAA-TCAAAA
1 AAATTCAAAA
194884 AAA
1 AAA
194887 AAGAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.75, C:0.09, G:0.00, T:0.16
Consensus pattern (10 bp):
AAATTCAAAA
Found at i:194893 original size:19 final size:19
Alignment explanation
Indices: 194841--194896 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
194831 TATTGGATTT
* *
194841 AAAAAAAAGAGAAGAAATTC
1 AAAAAAAA-AGAAAAAAATC
***
194861 AAAAAAATTCAAAAAAATC
1 AAAAAAAAAGAAAAAAATC
194880 AAAAAAAAAGAAAAAAA
1 AAAAAAAAAGAAAAAAA
194897 AGAAGAAAAA
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
19 21 0.75
20 7 0.25
ACGTcount: A:0.79, C:0.05, G:0.07, T:0.09
Consensus pattern (19 bp):
AAAAAAAAAGAAAAAAATC
Found at i:194910 original size:12 final size:12
Alignment explanation
Indices: 194880--194910 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
194870 CAAAAAAATC
194880 AAAAAAA-AAGA
1 AAAAAAAGAAGA
194891 AAAAAAAGAAGA
1 AAAAAAAGAAGA
194903 AAAAAAAG
1 AAAAAAAG
194911 TGAAAAGTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.37
12 12 0.63
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAGA
Found at i:195959 original size:18 final size:18
Alignment explanation
Indices: 195933--195991 Score: 82
Period size: 18 Copynumber: 3.3 Consensus size: 18
195923 AAATTGAAAG
* *
195933 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAATCGA
* *
195951 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAATCGA
195969 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAATCGA
195987 AAAAG
1 AAAAG
195992 TGAGAGAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.73, C:0.07, G:0.15, T:0.05
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCGA
Found at i:195961 original size:6 final size:6
Alignment explanation
Indices: 195929--196036 Score: 67
Period size: 6 Copynumber: 17.7 Consensus size: 6
195919 AAAGAAATTG
* * ** *
195929 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * *
195976 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTA-AA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA--AGAA
196027 AAAGAA AAAG
1 AAAGAA AAAG
196037 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 60 0.80
7 6 0.08
8 5 0.07
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:196018 original size:14 final size:13
Alignment explanation
Indices: 195998--196054 Score: 60
Period size: 14 Copynumber: 4.2 Consensus size: 13
195988 AAAGTGAGAG
195998 AAAAAGAAAATGA
1 AAAAAGAAAATGA
*
196011 AGAAAAGAAAATTA
1 A-AAAAGAAAATGA
*
196025 AAAAAGAAAAAGCGA
1 AAAAAG-AAAA-TGA
*
196040 AAAAAGAAATTGA
1 AAAAAGAAAATGA
196053 AA
1 AA
196055 GAGAGCTTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
13 10 0.28
14 19 0.53
15 7 0.19
ACGTcount: A:0.74, C:0.02, G:0.16, T:0.09
Consensus pattern (13 bp):
AAAAAGAAAATGA
Found at i:196088 original size:33 final size:33
Alignment explanation
Indices: 196051--196113 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
196041 AAAAGAAATT
196051 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
196084 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
196114 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:197925 original size:30 final size:29
Alignment explanation
Indices: 197890--197959 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 29
197880 AGTTTTTCCC
197890 AGCTCGATTTAGCTCACAT-GAGCTTAATTT
1 AGCTCG-TTTAGCTCA-ATCGAGCTTAATTT
* *
197920 AGCTCGTTTGAGCTCAATCTAGCTTACTTT
1 AGCTCGTTT-AGCTCAATCGAGCTTAATTT
197950 AGCTCGTTTA
1 AGCTCGTTTA
197960 AGCTTGGCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
29 6 0.17
30 30 0.83
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (29 bp):
AGCTCGTTTAGCTCAATCGAGCTTAATTT
Found at i:199482 original size:25 final size:25
Alignment explanation
Indices: 199400--199482 Score: 62
Period size: 27 Copynumber: 3.2 Consensus size: 25
199390 TCACATCATC
*
199400 TTTAATATGTCTATA-TTAAGTCACAAA
1 TTTAATATGT-T-TAGTTAA-TGACAAA
* *
199427 TTAAATATGTTTAGTTAATTACAAA
1 TTTAATATGTTTAGTTAATGACAAA
*
199452 GTTTTAATGTGTTTAGATTAA-GACAAA
1 --TTTAATATGTTTAG-TTAATGACAAA
199479 TTTA
1 TTTA
199483 TTAGTGGCTG
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
25 12 0.26
26 5 0.11
27 26 0.55
28 4 0.09
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (25 bp):
TTTAATATGTTTAGTTAATGACAAA
Found at i:204723 original size:13 final size:13
Alignment explanation
Indices: 204705--204730 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
204695 GGATATCAAG
204705 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
204718 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
204731 ATAGAGCTAG
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:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (13 bp):
TTGTGAAAAAAAA
Found at i:207042 original size:18 final size:17
Alignment explanation
Indices: 207021--207065 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
207011 GAGTGACGAG
207021 AGAAAAAGAAATCGAAAA
1 AGAAAAA-AAATCGAAAA
*
207039 AGAAACAAAAATTGAAAA
1 AGAAA-AAAAATCGAAAA
207057 AGAGAAAAA
1 AGA-AAAAA
207066 GATTGGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.73, C:0.04, G:0.16, T:0.07
Consensus pattern (17 bp):
AGAAAAAAAATCGAAAA
Found at i:207070 original size:18 final size:18
Alignment explanation
Indices: 207019--207070 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
207009 AAGAGTGACG
*
207019 AGAGAAAAAGAAATCGAAAA
1 AGAGAAAAAG--ATTGAAAA
*
207039 AGA-AACAAAAATTGAAAA
1 AGAGAA-AAAGATTGAAAA
207057 AGAGAAAAAGATTG
1 AGAGAAAAAGATTG
207071 GAGAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 17 0.63
19 4 0.15
20 6 0.22
ACGTcount: A:0.67, C:0.04, G:0.19, T:0.10
Consensus pattern (18 bp):
AGAGAAAAAGATTGAAAA
Found at i:220674 original size:15 final size:16
Alignment explanation
Indices: 220654--220685 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
220644 AGAAAATGAA
220654 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
220669 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
220685 A
1 A
220686 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:220800 original size:17 final size:18
Alignment explanation
Indices: 220768--220801 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
220758 AAAAGAGAGT
*
220768 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
220786 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
220802 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:237633 original size:11 final size:12
Alignment explanation
Indices: 237617--237699 Score: 55
Period size: 11 Copynumber: 6.6 Consensus size: 12
237607 TTGGAGTAAC
237617 AAAAAAATC-AA
1 AAAAAAATCGAA
*
237628 AAAAAATTCGAA
1 AAAAAAATCGAA
*
237640 AAAAAAATTGATTGA
1 AAAAAAATCGA---A
*
237655 AAAAAAATTCAAA
1 AAAAAAA-TCGAA
237668 AAAAAAAGT-G-A
1 AAAAAAA-TCGAA
237679 AAAAAAATCGAGCA
1 AAAAAAATCGA--A
237693 AAAAAAA
1 AAAAAAA
237700 AGGTGAGCAA
Statistics
Matches: 56, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
10 1 0.02
11 17 0.30
12 11 0.20
13 9 0.16
14 8 0.14
15 8 0.14
16 2 0.04
ACGTcount: A:0.72, C:0.06, G:0.08, T:0.13
Consensus pattern (12 bp):
AAAAAAATCGAA
Found at i:237642 original size:13 final size:12
Alignment explanation
Indices: 237626--237685 Score: 57
Period size: 13 Copynumber: 4.6 Consensus size: 12
237616 CAAAAAAATC
237626 AAAAAAAATTCGA
1 AAAAAAAATT-GA
237639 AAAAAAAATTGA
1 AAAAAAAATTGA
*
237651 TTGAAAAAAAATTCAA
1 ---AAAAAAAATT-GA
*
237667 AAAAAAAAGTGA
1 AAAAAAAATTGA
237679 AAAAAAA
1 AAAAAAA
237686 TCGAGCAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
12 10 0.25
13 19 0.47
15 10 0.25
16 1 0.03
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.15
Consensus pattern (12 bp):
AAAAAAAATTGA
Found at i:237685 original size:28 final size:28
Alignment explanation
Indices: 237626--237685 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
237616 CAAAAAAATC
* * ***
237626 AAAAAAAATTCGAAAAAAAAATTGATTG
1 AAAAAAAATTCAAAAAAAAAAGTGAAAA
237654 AAAAAAAATTCAAAAAAAAAAGTGAAAA
1 AAAAAAAATTCAAAAAAAAAAGTGAAAA
237682 AAAA
1 AAAA
237686 TCGAGCAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.15
Consensus pattern (28 bp):
AAAAAAAATTCAAAAAAAAAAGTGAAAA
Done.