Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2119
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: 282876
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4808 original size:12 final size:12
Alignment explanation
Indices: 4763--4810 Score: 69
Period size: 12 Copynumber: 3.8 Consensus size: 12
4753 TAGTTTCTCG
*
4763 AAAAAAAACTCGA
1 AAAAAAAATTC-A
4776 AAAAGAAAATTCA
1 AAAA-AAAATTCA
4789 AAAAAAAATTCA
1 AAAAAAAATTCA
4801 AAAAAAAATT
1 AAAAAAAATT
4811 TTTTTGGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
12 18 0.55
13 9 0.27
14 6 0.18
ACGTcount: A:0.73, C:0.08, G:0.04, T:0.15
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:4875 original size:11 final size:12
Alignment explanation
Indices: 4859--4888 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
4849 AGTTGTGAAA
4859 AAAAAAATT-TG
1 AAAAAAATTGTG
4870 AAAAAAATTGTG
1 AAAAAAATTGTG
4882 AAAAAAA
1 AAAAAAA
4889 GAAGAGCTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (12 bp):
AAAAAAATTGTG
Found at i:8020 original size:23 final size:20
Alignment explanation
Indices: 7962--8041 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 20
7952 ATTGTAATTG
*
7962 AAAAAAAATC-AAAAAAAAA
1 AAAAAAAATCGAAAAAAAAT
7981 AAGAAGAGGAAATTCGAAAAAAAATTT
1 AA-AA-A--AAA-TCGAAAAAAAA--T
8008 AAAAAAAAATCGAAAAAAAAT
1 -AAAAAAAATCGAAAAAAAAT
8029 AAAAAAAATCGAA
1 AAAAAAAATCGAA
8042 GTATATAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 17
0.74 0.01 0.25
Matches are distributed among these distances:
19 2 0.04
20 15 0.29
21 2 0.04
23 14 0.27
24 5 0.10
25 8 0.16
26 1 0.02
27 2 0.04
28 2 0.04
ACGTcount: A:0.75, C:0.05, G:0.09, T:0.11
Consensus pattern (20 bp):
AAAAAAAATCGAAAAAAAAT
Found at i:8052 original size:20 final size:19
Alignment explanation
Indices: 8007--8055 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
7997 AAAAAAAATT
8007 TAAAAAAAAATCGAAAAAA
1 TAAAAAAAAATCGAAAAAA
* * *
8026 AATAAAAAAAATCGAAGTATA
1 TA-AAAAAAAATCGAA-AAAA
8047 TAAAAAAAA
1 TAAAAAAAA
8056 GGAGTGAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 1 0.04
20 20 0.83
21 3 0.12
ACGTcount: A:0.76, C:0.04, G:0.06, T:0.14
Consensus pattern (19 bp):
TAAAAAAAAATCGAAAAAA
Found at i:8939 original size:37 final size:37
Alignment explanation
Indices: 8888--8958 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
8878 CATTCTTGTA
8888 AAGAGAAAATAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAATAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
8925 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AATAAAGAAAATGAAAGAAAAAGAAAA
8959 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.01, G:0.18, T:0.04
Consensus pattern (37 bp):
AAGAGAAAATAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:8958 original size:6 final size:6
Alignment explanation
Indices: 8898--8947 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
8888 AAGAGAAAAT
*
8898 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
8947 A
1 A
8948 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:9041 original size:11 final size:12
Alignment explanation
Indices: 9009--9039 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
8999 TTGAGAGAAC
9009 TTGAAAAAGCCT
1 TTGAAAAAGCCT
9021 TTGAAAAAGCCT
1 TTGAAAAAGCCT
9033 TTGAAAA
1 TTGAAAA
9040 GCAAAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:11204 original size:19 final size:19
Alignment explanation
Indices: 11182--11267 Score: 61
Period size: 19 Copynumber: 4.4 Consensus size: 19
11172 TAGCTCATAT
11182 TTAGCTCACGAGCTAAAGC
1 TTAGCTCACGAGCTAAAGC
* * *
11201 TTAGCTCAACTTCAGCTTAGGAGT
1 TTAGCTC-AC--GAGC-TA-AAGC
* *
11225 TTAGC-CTC-AGCTCAA-C
1 TTAGCTCACGAGCTAAAGC
11241 TTAGCTCACGAGCTAAAGC
1 TTAGCTCACGAGCTAAAGC
11260 TTAGCTCA
1 TTAGCTCA
11268 TTTTAGTTTT
Statistics
Matches: 50, Mismatches: 9, Indels: 16
0.67 0.12 0.21
Matches are distributed among these distances:
16 5 0.10
17 3 0.06
18 7 0.14
19 19 0.38
20 2 0.04
22 4 0.08
23 3 0.06
24 7 0.14
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.27
Consensus pattern (19 bp):
TTAGCTCACGAGCTAAAGC
Found at i:11206 original size:30 final size:29
Alignment explanation
Indices: 11172--11273 Score: 98
Period size: 30 Copynumber: 3.4 Consensus size: 29
11162 AGCTCACTCC
11172 TAGCTCATATTTAGCTCACGAGCTAAAGCT
1 TAGCTCA-ATTTAGCTCACGAGCTAAAGCT
* * * **
11202 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAA-TTTAGCTCACGAGCTAAAG-CT
* *
11232 CAGCTCAACTTAGCTCACGAGCTAAAGCT
1 TAGCTCAATTTAGCTCACGAGCTAAAGCT
*
11261 TAGCTCATTTTAG
1 TAGCTCAATTTAG
11274 TTTTAACTCG
Statistics
Matches: 54, Mismatches: 15, Indels: 7
0.71 0.20 0.09
Matches are distributed among these distances:
29 25 0.46
30 29 0.54
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (29 bp):
TAGCTCAATTTAGCTCACGAGCTAAAGCT
Found at i:12195 original size:22 final size:20
Alignment explanation
Indices: 12163--12211 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
12153 TGCCGAATTA
12163 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
12186 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
12206 TGAACA
1 TGAACA
12212 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:19092 original size:14 final size:14
Alignment explanation
Indices: 19075--19120 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
19065 TCAATTTCAA
19075 TTTTTTTCTTCTTC
1 TTTTTTTCTTCTTC
** **
19089 TTTTTTAATTCTGA
1 TTTTTTTCTTCTTC
19103 TTTTTTTCTTCTTC
1 TTTTTTTCTTCTTC
19117 TTTT
1 TTTT
19121 CTTCAATACT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.07, C:0.15, G:0.02, T:0.76
Consensus pattern (14 bp):
TTTTTTTCTTCTTC
Found at i:19181 original size:11 final size:11
Alignment explanation
Indices: 19165--19200 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
19155 GAATACAAAC
19165 TTTTTTTGAAT
1 TTTTTTTGAAT
19176 TTTTTTTGAA-
1 TTTTTTTGAAT
19186 -TTTTTTGAAT
1 TTTTTTTGAAT
19196 TTTTT
1 TTTTT
19201 ATTTTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 9 0.39
11 14 0.61
ACGTcount: A:0.17, C:0.00, G:0.08, T:0.75
Consensus pattern (11 bp):
TTTTTTTGAAT
Found at i:19189 original size:8 final size:9
Alignment explanation
Indices: 19166--19200 Score: 52
Period size: 9 Copynumber: 3.7 Consensus size: 9
19156 AATACAAACT
19166 TTTTTTGAA
1 TTTTTTGAA
19175 TTTTTTTTGAA
1 --TTTTTTGAA
19186 TTTTTTGAA
1 TTTTTTGAA
19195 TTTTTT
1 TTTTTT
19201 ATTTTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 15 0.62
11 9 0.38
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (9 bp):
TTTTTTGAA
Found at i:22787 original size:22 final size:22
Alignment explanation
Indices: 22757--22800 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
22747 TTTGGTATTT
22757 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
22779 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
22801 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:33294 original size:24 final size:23
Alignment explanation
Indices: 33239--33295 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
33229 TGGTTTAAGT
**
33239 CGAAATGGTATTTGGTTTTGGTA
1 CGAAATGGTATTTGGAATTGGTA
***
33262 CGTTTTGGTATTTGGGAATTGGTA
1 CGAAATGGTATTT-GGAATTGGTA
33286 CGAAATGGTA
1 CGAAATGGTA
33296 ATGGTTCAAA
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
23 10 0.40
24 15 0.60
ACGTcount: A:0.23, C:0.05, G:0.32, T:0.40
Consensus pattern (23 bp):
CGAAATGGTATTTGGAATTGGTA
Found at i:40621 original size:11 final size:11
Alignment explanation
Indices: 40605--40635 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
40595 AATATATCTC
40605 TTTTTTTCAAT
1 TTTTTTTCAAT
40616 TTTTTTT-AAT
1 TTTTTTTCAAT
40626 TTTTTTTCAA
1 TTTTTTTCAA
40636 AATTTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTTTTCAAT
Found at i:40631 original size:21 final size:21
Alignment explanation
Indices: 40605--40644 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
40595 AATATATCTC
**
40605 TTTTTTTCAATTTTTTTTAAT
1 TTTTTTTCAAAATTTTTTAAT
40626 TTTTTTTCAAAATTTTTTA
1 TTTTTTTCAAAATTTTTTA
40645 TGAACCTACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTTTTCAAAATTTTTTAAT
Found at i:51674 original size:9 final size:9
Alignment explanation
Indices: 51660--51695 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
51650 TTGTAGATTC
51660 AAAAAAAAT
1 AAAAAAAAT
51669 AAAAAAAAT
1 AAAAAAAAT
*
51678 CAAAAAAATT
1 -AAAAAAAAT
51688 AAAAAAAA
1 AAAAAAAA
51696 CAAACTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.86, C:0.03, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:51682 original size:19 final size:19
Alignment explanation
Indices: 51658--51699 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
51648 AATTGTAGAT
51658 TCAAAAAAAATAAAAAAAA
1 TCAAAAAAAATAAAAAAAA
*
51677 TCAAAAAAATTAAAAAAAA
1 TCAAAAAAAATAAAAAAAA
51696 -CAAA
1 TCAAA
51700 CTTTTTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.81, C:0.07, G:0.00, T:0.12
Consensus pattern (19 bp):
TCAAAAAAAATAAAAAAAA
Found at i:54662 original size:10 final size:10
Alignment explanation
Indices: 54647--54688 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
54637 TTGTAGATTC
54647 AAAAAAATCAA
1 AAAAAAATC-A
*
54658 AAAAAAATCG
1 AAAAAAATCA
*
54668 AAAAAAATTA
1 AAAAAAATCA
54678 AAAAAAA-CA
1 AAAAAAATCA
54687 AA
1 AA
54689 TTTTTTGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 3 0.11
10 15 0.56
11 9 0.33
ACGTcount: A:0.81, C:0.07, G:0.02, T:0.10
Consensus pattern (10 bp):
AAAAAAATCA
Found at i:54663 original size:11 final size:11
Alignment explanation
Indices: 54647--54684 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
54637 TTGTAGATTC
54647 AAAAAAATCAA
1 AAAAAAATCAA
*
54658 AAAAAAATC-G
1 AAAAAAATCAA
*
54668 AAAAAAATTAA
1 AAAAAAATCAA
54679 AAAAAA
1 AAAAAA
54685 CAAATTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.82, C:0.05, G:0.03, T:0.11
Consensus pattern (11 bp):
AAAAAAATCAA
Found at i:59896 original size:6 final size:6
Alignment explanation
Indices: 59887--59936 Score: 66
Period size: 6 Copynumber: 8.5 Consensus size: 6
59877 AAACAGCATG
* * *
59887 AGAAAA AGAAAA AGAAAA AGAAAG TG-AAA AGAAAT AGAAAA AGAAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
59934 AGA
1 AGA
59937 GTGCGAGCGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
5 3 0.08
6 34 0.92
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (6 bp):
AGAAAA
Found at i:60326 original size:22 final size:22
Alignment explanation
Indices: 60296--60338 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
60286 TTTGGTATTT
60296 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
60318 GGGATTTGGTACGAAATGGTA
1 GGGAATTGGTACGAAATGGTA
60339 TGGTTCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.05, G:0.37, T:0.26
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:64523 original size:17 final size:17
Alignment explanation
Indices: 64498--64538 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
64488 TCTCTTTTCA
*
64498 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
**
64515 TTCTTTTTTTTTTCATT
1 TTCTTTTTTTTTGAATT
64532 TTCTTTT
1 TTCTTTT
64539 CTTTGTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.07, C:0.12, G:0.02, T:0.78
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:66741 original size:12 final size:12
Alignment explanation
Indices: 66724--66768 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 12
66714 ACCGTATGCA
66724 ATTTTTTTTTTC
1 ATTTTTTTTTTC
66736 A--TTTTTTTTC
1 ATTTTTTTTTTC
*
66746 AATTTTTTTTTC
1 ATTTTTTTTTTC
66758 AATTTTTTTTT
1 -ATTTTTTTTT
66769 GAACTCCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 10 0.34
12 10 0.34
13 9 0.31
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (12 bp):
ATTTTTTTTTTC
Found at i:66742 original size:11 final size:12
Alignment explanation
Indices: 66726--66768 Score: 72
Period size: 12 Copynumber: 3.8 Consensus size: 12
66716 CGTATGCAAT
66726 TTTTTTTTTC-A
1 TTTTTTTTTCAA
66737 -TTTTTTTTCAA
1 TTTTTTTTTCAA
66748 TTTTTTTTTCAA
1 TTTTTTTTTCAA
66760 TTTTTTTTT
1 TTTTTTTTT
66769 GAACTCCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 9 0.30
11 1 0.03
12 20 0.67
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:81047 original size:6 final size:6
Alignment explanation
Indices: 81038--81088 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
81028 AAACAGCATG
* * *
81038 AGAAAA AGAAAA AGAAAA AGAAAG TGAAAA AGAAAT AGAAAA AGAAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
81086 AGA
1 AGA
81089 GTGCGAGCGA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (6 bp):
AGAAAA
Found at i:81079 original size:24 final size:24
Alignment explanation
Indices: 81039--81084 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
81029 AACAGCATGA
81039 GAAAAAGAAAAAGAAAAAGAAAGT
1 GAAAAAGAAAAAGAAAAAGAAAGT
*
81063 GAAAAAGAAATAGAAAAAGAAA
1 GAAAAAGAAAAAGAAAAAGAAA
81085 AAGAGTGCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (24 bp):
GAAAAAGAAAAAGAAAAAGAAAGT
Found at i:81489 original size:22 final size:22
Alignment explanation
Indices: 81459--81502 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
81449 TTTGGTATTT
81459 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
81481 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
81503 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:85714 original size:17 final size:17
Alignment explanation
Indices: 85689--85742 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
85679 TCTCTTTTCA
*
85689 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
* *
85706 TTCTTTTTTTTTCATTT
1 TTCTTTTTTTTTGAATT
* *
85723 TTCTTTTCTTTTGTATT
1 TTCTTTTTTTTTGAATT
85740 TTC
1 TTC
85743 GCTCTTTTCT
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:0.07, C:0.13, G:0.04, T:0.76
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:87966 original size:11 final size:11
Alignment explanation
Indices: 87950--87991 Score: 75
Period size: 11 Copynumber: 3.7 Consensus size: 11
87940 GTATGCAATT
87950 TTTTTTTTCAA
1 TTTTTTTTCAA
87961 TTTTTTTTCAA
1 TTTTTTTTCAA
87972 TTTTTTTTTCAA
1 -TTTTTTTTCAA
87984 TTTTTTTT
1 TTTTTTTT
87992 TGAACTCCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 19 0.63
12 11 0.37
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:87966 original size:12 final size:12
Alignment explanation
Indices: 87949--87992 Score: 81
Period size: 12 Copynumber: 3.8 Consensus size: 12
87939 CGTATGCAAT
87949 TTTTTTTTTCAA
1 TTTTTTTTTCAA
87961 -TTTTTTTTCAA
1 TTTTTTTTTCAA
87972 TTTTTTTTTCAA
1 TTTTTTTTTCAA
87984 TTTTTTTTT
1 TTTTTTTTT
87993 GAACTCCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.35
12 20 0.65
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:88334 original size:22 final size:22
Alignment explanation
Indices: 88304--88347 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
88294 TTTGGTATTT
88304 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
88326 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
88348 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:92913 original size:21 final size:23
Alignment explanation
Indices: 92868--92914 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
92858 TCACCTGCAA
* *
92868 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
92891 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
92912 TAA
1 TAA
92915 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:98749 original size:19 final size:18
Alignment explanation
Indices: 98713--98752 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
98703 TTTCCACTCG
*
98713 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
98731 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
98750 TTT
1 TTT
98753 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:103852 original size:45 final size:45
Alignment explanation
Indices: 103803--103990 Score: 286
Period size: 45 Copynumber: 4.2 Consensus size: 45
103793 TCGGCCATGG
* * * *
103803 TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
* *
103848 TGCTTCCTTAAATTCTTCCATGAATTATGCATGACGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
103893 TGTTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
* * *
103938 TGCTTCCTCAAATTATCCCATGAATTATGCATGATTTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
103983 TGCTTCCT
1 TGCTTCCT
103991 TAATTTCATG
Statistics
Matches: 130, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 130 1.00
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:105221 original size:30 final size:30
Alignment explanation
Indices: 105187--105259 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
105177 AGCTCACTCC
*
105187 TAGCTCATATTTAGCTCACGAGCTAAACCT
1 TAGCTCATATTTAGCTCACGAGCTAAAACT
105217 TAGCTCA-ACTTTAGCTCACGAGCTAAAACT
1 TAGCTCATA-TTTAGCTCACGAGCTAAAACT
105247 TAGCTCAT-TTTAG
1 TAGCTCATATTTAG
105260 TTTAAACTCG
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
29 6 0.15
30 34 0.85
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.32
Consensus pattern (30 bp):
TAGCTCATATTTAGCTCACGAGCTAAAACT
Found at i:115882 original size:17 final size:16
Alignment explanation
Indices: 115860--115904 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
115850 TTTCAATCAC
115860 TTTTTTTTAATTTCGAA
1 TTTTTTTTAATTTC-AA
**
115877 TTTTTTTTGAATTTCTC
1 TTTTTTTT-AATTTCAA
115894 TTTTTTTTAAT
1 TTTTTTTTAAT
115905 ACCGAATACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 3 0.12
17 16 0.64
18 6 0.24
ACGTcount: A:0.18, C:0.07, G:0.04, T:0.71
Consensus pattern (16 bp):
TTTTTTTTAATTTCAA
Found at i:116735 original size:45 final size:45
Alignment explanation
Indices: 116684--116871 Score: 295
Period size: 45 Copynumber: 4.2 Consensus size: 45
116674 TCGACCATGG
* * * *
116684 TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
116729 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
116774 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
* * * *
116819 TGCTTCCTCAAATTATCCCACGAATTATGCATGATTTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
116864 TGCTTCCT
1 TGCTTCCT
116872 TAATTTCATG
Statistics
Matches: 133, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 133 1.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:123412 original size:21 final size:21
Alignment explanation
Indices: 123359--123416 Score: 70
Period size: 19 Copynumber: 2.9 Consensus size: 21
123349 AAGGCAAAGG
123359 AACAAAAAG-AAAAGATG-GAA
1 AACAAAAAGAAAAAG-TGAGAA
*
123379 AA-AGAAA-AAAAAGTGAGAA
1 AACAAAAAGAAAAAGTGAGAA
123398 AACAAAAAGAAAAAGTGAG
1 AACAAAAAGAAAAAGTGAG
123417 TTGAAATTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
18 2 0.06
19 14 0.44
20 6 0.19
21 10 0.31
ACGTcount: A:0.71, C:0.03, G:0.21, T:0.05
Consensus pattern (21 bp):
AACAAAAAGAAAAAGTGAGAA
Found at i:125380 original size:21 final size:21
Alignment explanation
Indices: 125354--125397 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
125344 AAAAGTTTTG
125354 AAAAAAAAATCGAAAAAAAAA
1 AAAAAAAAATCGAAAAAAAAA
* *
125375 AAAAAAAAATTGCAAAAAAAA
1 AAAAAAAAATCGAAAAAAAAA
125396 AA
1 AA
125398 TTGCATACGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.84, C:0.05, G:0.05, T:0.07
Consensus pattern (21 bp):
AAAAAAAAATCGAAAAAAAAA
Found at i:125391 original size:14 final size:14
Alignment explanation
Indices: 125374--125402 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
125364 CGAAAAAAAA
125374 AAAAAAAAAATTGC
1 AAAAAAAAAATTGC
125388 AAAAAAAAAATTGC
1 AAAAAAAAAATTGC
125402 A
1 A
125403 TACGGTCTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.72, C:0.07, G:0.07, T:0.14
Consensus pattern (14 bp):
AAAAAAAAAATTGC
Found at i:127681 original size:24 final size:25
Alignment explanation
Indices: 127654--127707 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
127644 ATGAGTGATA
*
127654 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
127678 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
127702 AAAAAA
1 AAAAAA
127708 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:141430 original size:13 final size:13
Alignment explanation
Indices: 141408--141459 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 13
141398 ATAGTAGTTT
141408 CTCG-AAAAAAAA
1 CTCGAAAAAAAAA
141420 CTCGAAAAAAAAA
1 CTCGAAAAAAAAA
*
141433 TTC-AAAAAAAAA
1 CTCGAAAAAAAAA
* *
141445 ATTGAAAAAAAAA
1 CTCGAAAAAAAAA
141458 CT
1 CT
141460 AGTTTCCATT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
12 14 0.41
13 20 0.59
ACGTcount: A:0.69, C:0.12, G:0.06, T:0.13
Consensus pattern (13 bp):
CTCGAAAAAAAAA
Found at i:141457 original size:12 final size:12
Alignment explanation
Indices: 141411--141457 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
141401 GTAGTTTCTC
* *
141411 GAAAAAAAACTC
1 GAAAAAAAAATT
141423 GAAAAAAAAATT
1 GAAAAAAAAATT
*
141435 CAAAAAAAAAATT
1 -GAAAAAAAAATT
141448 GAAAAAAAAA
1 GAAAAAAAAA
141458 CTAGTTTCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
12 19 0.63
13 11 0.37
ACGTcount: A:0.77, C:0.06, G:0.06, T:0.11
Consensus pattern (12 bp):
GAAAAAAAAATT
Found at i:141513 original size:13 final size:13
Alignment explanation
Indices: 141495--141533 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
141485 GGATATCAAG
141495 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
141508 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
141521 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
141534 GAGAGCTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (13 bp):
TTGTGAAAAAAAA
Found at i:148467 original size:19 final size:18
Alignment explanation
Indices: 148431--148470 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
148421 TTTCCACTCG
*
148431 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
148449 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
148468 TTT
1 TTT
148471 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:149551 original size:12 final size:12
Alignment explanation
Indices: 149522--149550 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
149512 CTTCTTTTTC
149522 TTTTTTCACAAT
1 TTTTTTCACAAT
149534 TTTTTTCA-AAT
1 TTTTTTCACAAT
149545 TTTTTT
1 TTTTTT
149551 TTCAACTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTTTCACAAT
Found at i:149611 original size:13 final size:13
Alignment explanation
Indices: 149593--149627 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
149583 TGGAAACTAG
*
149593 TTTTTTTTTCGAA
1 TTTTTTTTTCAAA
149606 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
149619 TTTTTTTTT
1 TTTTTTTTT
149628 GTTTTTTTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.14, C:0.06, G:0.03, T:0.77
Consensus pattern (13 bp):
TTTTTTTTTCAAA
Found at i:163054 original size:20 final size:20
Alignment explanation
Indices: 163008--163054 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
162998 AGCTTGTTTC
*
163008 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
163028 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
163048 CAGCTCA
1 CAGCTCA
163055 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:167412 original size:11 final size:11
Alignment explanation
Indices: 167396--167426 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
167386 AGGAAATTTG
167396 AAAAAAAATCA
1 AAAAAAAATCA
*
167407 AAAAAAATTCA
1 AAAAAAAATCA
167418 AAAAAAAAT
1 AAAAAAAAT
167427 TGAAGTATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.13
Consensus pattern (11 bp):
AAAAAAAATCA
Found at i:171754 original size:10 final size:10
Alignment explanation
Indices: 171739--171803 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 10
171729 AGTTTTTCCC
171739 AGCTCAATTT
1 AGCTCAATTT
*
171749 AGCTCACA-TG
1 AGCTCA-ATTT
*
171759 AGCTTAATTT
1 AGCTCAATTT
*
171769 AGCTC-GTTT
1 AGCTCAATTT
171778 GAGCTCAATTT
1 -AGCTCAATTT
* *
171789 AGCTTACTTT
1 AGCTCAATTT
171799 AGCTC
1 AGCTC
171804 GTTTGAGCTT
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
9 4 0.10
10 34 0.81
11 4 0.10
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (10 bp):
AGCTCAATTT
Found at i:171762 original size:20 final size:20
Alignment explanation
Indices: 171739--171792 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
171729 AGTTTTTCCC
171739 AGCTCAATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
171759 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
171779 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
171793 TACTTTAGCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:171773 original size:30 final size:30
Alignment explanation
Indices: 171739--171812 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
171729 AGTTTTTCCC
171739 AGCTCAATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTC-ATTTGAGCTCA-ATTGAGCTTAATTT
* * *
171769 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCATTTGAGCTCAATTGAGCTTAATTT
*
171799 AGCTCGTTTGAGCT
1 AGCTCATTTGAGCT
171813 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 4 0.10
30 35 0.90
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (30 bp):
AGCTCATTTGAGCTCAATTGAGCTTAATTT
Found at i:171802 original size:20 final size:20
Alignment explanation
Indices: 171739--171803 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
171729 AGTTTTTCCC
* * *
171739 AGCTCAATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
171759 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
171778 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
171799 AGCTC
1 AGCTC
171804 GTTTGAGCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 29 0.81
21 4 0.11
22 1 0.03
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:182568 original size:12 final size:12
Alignment explanation
Indices: 182553--182615 Score: 51
Period size: 12 Copynumber: 5.2 Consensus size: 12
182543 TCTAGCTCTC
182553 TTTCAATTTCTT
1 TTTCAATTTCTT
*
182565 TTTCCACTCTTTCTT
1 TTT-CA--ATTTCTT
*
182580 TTTC---TTCTC
1 TTTCAATTTCTT
182589 TTTCAATTTCTT
1 TTTCAATTTCTT
*
182601 TTTCAATCTCTT
1 TTTCAATTTCTT
182613 TTT
1 TTT
182616 GCTTTTCACT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
9 8 0.20
12 21 0.51
13 2 0.05
14 1 0.02
15 9 0.22
ACGTcount: A:0.11, C:0.24, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTCAATTTCTT
Found at i:182576 original size:21 final size:20
Alignment explanation
Indices: 182550--182605 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 20
182540 TTTTCTAGCT
182550 CTCTTTCAATTTCTTTTTCCA
1 CTCTTTCAATTTCTTTTT-CA
*
182571 CTCTTTC--TTT-TTCTT--
1 CTCTTTCAATTTCTTTTTCA
182586 CTCTTTCAATTTCTTTTTCA
1 CTCTTTCAATTTCTTTTTCA
182606 ATCTCTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 11
0.68 0.05 0.27
Matches are distributed among these distances:
15 7 0.25
17 3 0.11
18 8 0.29
19 3 0.11
21 7 0.25
ACGTcount: A:0.11, C:0.27, G:0.00, T:0.62
Consensus pattern (20 bp):
CTCTTTCAATTTCTTTTTCA
Found at i:182676 original size:15 final size:16
Alignment explanation
Indices: 182645--182691 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 16
182635 TTTTGAAATC
**
182645 TCATTTTCACATT-TT
1 TCATTTTCATTTTCTT
*
182660 TCTTTTTCA-TTTCTT
1 TCATTTTCATTTTCTT
182675 TCATTTTCATTTTCTT
1 TCATTTTCATTTTCTT
182691 T
1 T
182692 ATTCTTTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 2 0.07
15 18 0.67
16 7 0.26
ACGTcount: A:0.13, C:0.19, G:0.00, T:0.68
Consensus pattern (16 bp):
TCATTTTCATTTTCTT
Found at i:182685 original size:28 final size:29
Alignment explanation
Indices: 182645--182701 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
182635 TTTTGAAATC
182645 TCATTTTCACATTTTTCTTT-TTCATTTCTT
1 TCATTTT-ACA-TTTTCTTTATTCATTTCTT
*
182675 TCATTTT-CATTTTCTTTATTCTTTTCT
1 TCATTTTACATTTTCTTTATTCATTTCT
182702 CGCTCAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 8 0.32
28 10 0.40
30 7 0.28
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.68
Consensus pattern (29 bp):
TCATTTTACATTTTCTTTATTCATTTCTT
Found at i:183759 original size:24 final size:23
Alignment explanation
Indices: 183727--183810 Score: 75
Period size: 24 Copynumber: 3.7 Consensus size: 23
183717 CTCGCAAGAC
183727 TTTTCACTTTTTTTTCTTCTTTTT
1 TTTTCACTTTTTTTTCTT-TTTTT
*
183751 TTTTTACTTTTTTTTC--TTTTT
1 TTTTCACTTTTTTTTCTTTTTTT
** *
183772 TGCTCACTTCTTTTTT-TTCTTTT
1 TTTTCACTT-TTTTTTCTTTTTTT
*
183795 TTTTCGAATTTTTTTT
1 TTTTC-ACTTTTTTTT
183811 TGAATTTCGA
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
21 11 0.23
22 6 0.12
23 13 0.27
24 18 0.38
ACGTcount: A:0.06, C:0.14, G:0.02, T:0.77
Consensus pattern (23 bp):
TTTTCACTTTTTTTTCTTTTTTT
Found at i:185856 original size:30 final size:30
Alignment explanation
Indices: 185822--185918 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
185812 TAAACTAAAA
185822 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
185852 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
185882 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
185911 ATGAGCTA
1 -TGAGCTA
185919 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:188101 original size:12 final size:12
Alignment explanation
Indices: 188086--188116 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
188076 TTCTTTTTGC
188086 TTTTCAAAGGCT
1 TTTTCAAAGGCT
188098 TTTTCAAAGGCT
1 TTTTCAAAGGCT
188110 TTTTCAA
1 TTTTCAA
188117 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:188199 original size:27 final size:27
Alignment explanation
Indices: 188177--188230 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
188167 TTTCTTTTTA
188177 TTTCATTTTCTTTTTCTTCTCTTGCTT
1 TTTCATTTTCTTTTTCTTCTCTTGCTT
* *
188204 TTTCTTTTTCTTTTTTTTCT-TTG-TT
1 TTTCATTTTCTTTTTCTTCTCTTGCTT
188229 TT
1 TT
188231 CTCTTTACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.16
26 3 0.12
27 18 0.72
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.78
Consensus pattern (27 bp):
TTTCATTTTCTTTTTCTTCTCTTGCTT
Found at i:188220 original size:15 final size:15
Alignment explanation
Indices: 188166--188232 Score: 55
Period size: 15 Copynumber: 4.4 Consensus size: 15
188156 CTTGCCTCTC
* *
188166 TTTTCTTTTTATTTCA
1 TTTTCTTTTTCTTT-T
*
188182 TTTTCTTTTTCTTCT
1 TTTTCTTTTTCTTTT
* *
188197 CTTGCTTTTTCTTTT
1 TTTTCTTTTTCTTTT
*
188212 TCTTT-TTTTTCTTTG
1 T-TTTCTTTTTCTTTT
188227 TTTTCT
1 TTTTCT
188233 CTTTACAAGA
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
14 3 0.08
15 23 0.57
16 14 0.35
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.78
Consensus pattern (15 bp):
TTTTCTTTTTCTTTT
Found at i:188222 original size:36 final size:37
Alignment explanation
Indices: 188166--188235 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 37
188156 CTTGCCTCTC
188166 TTTTCTTTTTATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTATTTCATTTTCTTTGTT-TTCTCTTGCT
* *
188203 TTTTCTTTTTCTTT-TTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTATTTCATTTTCTTTGTTTTCTCTT
188236 TACAAGAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
36 15 0.50
37 15 0.50
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.77
Consensus pattern (37 bp):
TTTTCTTTTTATTTCATTTTCTTTGTTTTCTCTTGCT
Found at i:189164 original size:12 final size:12
Alignment explanation
Indices: 189149--189203 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
189139 TTTGCTCACC
189149 TTTTTTTTTGAA
1 TTTTTTTTTGAA
*
189161 TTTTTTTTTCAA
1 TTTTTTTTTGAA
189173 TCTTTTTTTTGAA
1 T-TTTTTTTTGAA
189186 --TTTTTTTG-A
1 TTTTTTTTTGAA
189195 TTTTTTTTT
1 TTTTTTTTT
189204 TATCCAATAC
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
9 1 0.03
10 8 0.21
11 7 0.18
12 12 0.32
13 10 0.26
ACGTcount: A:0.13, C:0.04, G:0.05, T:0.78
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:189166 original size:10 final size:11
Alignment explanation
Indices: 189150--189202 Score: 56
Period size: 10 Copynumber: 4.7 Consensus size: 11
189140 TTGCTCACCT
189150 TTTTTTTTGAA
1 TTTTTTTTGAA
*
189161 TTTTTTTTTCAA
1 -TTTTTTTTGAA
189173 TCTTTTTTTTGAA
1 --TTTTTTTTGAA
189186 -TTTTTTTG-A
1 TTTTTTTTGAA
189195 TTTTTTTT
1 TTTTTTTT
189203 TTATCCAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
9 1 0.03
10 15 0.42
12 10 0.28
13 10 0.28
ACGTcount: A:0.13, C:0.04, G:0.06, T:0.77
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:189203 original size:25 final size:24
Alignment explanation
Indices: 189149--189204 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
189139 TTTGCTCACC
189149 TTTTTTTTTGAATTTTTTTTTCAAT
1 TTTTTTTTTGAATTTTTTTTT-AAT
* *
189174 CTTTTTTTTGAA--TTTTTTTGAT
1 TTTTTTTTTGAATTTTTTTTTAAT
189196 TTTTTTTTT
1 TTTTTTTTT
189205 ATCCAATACA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.36
23 7 0.25
25 11 0.39
ACGTcount: A:0.12, C:0.04, G:0.05, T:0.79
Consensus pattern (24 bp):
TTTTTTTTTGAATTTTTTTTTAAT
Found at i:190911 original size:30 final size:30
Alignment explanation
Indices: 190877--190973 Score: 83
Period size: 30 Copynumber: 3.2 Consensus size: 30
190867 TAAACTAAAA
190877 TGAGCTAAGCTTTAGCCCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCCCGTGAGCTAAAGT
* * * * *
190907 TGAGCTGAGGC-TAAACTCC-TAAGCTGAAGT
1 TGAGCT-AAGCTTTAGC-CCGTGAGCTAAAGT
* *
190937 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCCCGTGAGCTAAAGT
190966 ATGAGCTA
1 -TGAGCTA
190974 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
29 4 0.08
30 41 0.82
31 5 0.10
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCCCGTGAGCTAAAGT
Found at i:192856 original size:13 final size:12
Alignment explanation
Indices: 192840--192883 Score: 70
Period size: 12 Copynumber: 3.6 Consensus size: 12
192830 AAAAAAATAT
192840 AAAAAAATTCAA
1 AAAAAAATTCAA
*
192852 AAAAAAATTTGAA
1 AAAAAAA-TTCAA
192865 AAAAAAATTCAA
1 AAAAAAATTCAA
192877 AAAAAAA
1 AAAAAAA
192884 GTTTGTATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 18 0.62
13 11 0.38
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:192868 original size:25 final size:26
Alignment explanation
Indices: 192840--192888 Score: 91
Period size: 25 Copynumber: 1.9 Consensus size: 26
192830 AAAAAAATAT
192840 AAAAAAATTCAAAAAAAAA-TTTGAA
1 AAAAAAATTCAAAAAAAAAGTTTGAA
192865 AAAAAAATTCAAAAAAAAAGTTTG
1 AAAAAAATTCAAAAAAAAAGTTTG
192889 TATTCAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.20
Consensus pattern (26 bp):
AAAAAAATTCAAAAAAAAAGTTTGAA
Found at i:192940 original size:12 final size:12
Alignment explanation
Indices: 192923--192974 Score: 50
Period size: 12 Copynumber: 3.9 Consensus size: 12
192913 ATTTAGTATT
192923 GAAGAAAAAAAA
1 GAAGAAAAAAAA
192935 GAAGAAAAAAAA
1 GAAGAAAAAAAA
*
192947 TTGGAATTAAAAAAAAA
1 ---GAA--GAAAAAAAA
192964 GAAGAAAAAAA
1 GAAGAAAAAAA
192975 TCAAAATTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
12 19 0.58
14 3 0.09
15 3 0.09
17 8 0.24
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (12 bp):
GAAGAAAAAAAA
Found at i:192971 original size:28 final size:30
Alignment explanation
Indices: 192927--192994 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
192917 AGTATTGAAG
***
192927 AAAAAAAAGAAGAAAAAAAATTGGAATT-A
1 AAAAAAAAGAAGAAAAAAAATCAAAATTGA
192956 AAAAAAAAGAAG-AAAAAAATCAAAATTGA
1 AAAAAAAAGAAGAAAAAAAATCAAAATTGA
192985 AAAAAAAAGA
1 AAAAAAAAGA
192995 GTGATTGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
28 12 0.34
29 23 0.66
ACGTcount: A:0.76, C:0.01, G:0.12, T:0.10
Consensus pattern (30 bp):
AAAAAAAAGAAGAAAAAAAATCAAAATTGA
Found at i:193829 original size:21 final size:20
Alignment explanation
Indices: 193800--193845 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
193790 AATCTTGAAT
*
193800 GAAATTGAGAGAAGAAAAAAA
1 GAAAATGAGAG-AGAAAAAAA
* *
193821 GAAAATGAGAGTGAGAAAAA
1 GAAAATGAGAGAGAAAAAAA
193841 GAAAA
1 GAAAA
193846 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:193861 original size:6 final size:6
Alignment explanation
Indices: 193852--193893 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
193842 AAAAAAGAAT
* * *
193852 TTGAGA TTGAGA TTGAGA TTGATA TTGATA TTGATA TTGAGA
1 TTGAGA TTGAGA TTGAGA TTGAGA TTGAGA TTGAGA TTGAGA
193894 AAAAAATTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.40
Consensus pattern (6 bp):
TTGAGA
Found at i:193869 original size:12 final size:12
Alignment explanation
Indices: 193852--193893 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
193842 AAAAAAGAAT
*
193852 TTGAGATTGAGA
1 TTGAGATTGATA
193864 TTGAGATTGATA
1 TTGAGATTGATA
*
193876 TTGATATTGATA
1 TTGAGATTGATA
193888 TTGAGA
1 TTGAGA
193894 AAAAAATTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.40
Consensus pattern (12 bp):
TTGAGATTGATA
Found at i:195385 original size:20 final size:20
Alignment explanation
Indices: 195339--195385 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
195329 AGCTCGTTTC
*
195339 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
195359 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
195379 CAGCTCA
1 CAGCTCA
195386 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:202010 original size:10 final size:10
Alignment explanation
Indices: 201995--202036 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
201985 TTTGCAAGTT
201995 TTGAGCTAAA
1 TTGAGCTAAA
* *
202005 TTGAGCTGAT
1 TTGAGCTAAA
*
202015 TTGAGCT-CA
1 TTGAGCTAAA
202024 TTGAGCTAAA
1 TTGAGCTAAA
202034 TTG
1 TTG
202037 GAAGTTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (10 bp):
TTGAGCTAAA
Found at i:205084 original size:19 final size:20
Alignment explanation
Indices: 205060--205104 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
205050 CTTTTCATTC
*
205060 TCTTTTTTTGAATTTTC-TT
1 TCTTTTTTTCAATTTTCTTT
*
205079 TCTTTTTTTCATTTTTCTTT
1 TCTTTTTTTCAATTTTCTTT
205099 TCTTTT
1 TCTTTT
205105 GTATTTTCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.07, C:0.13, G:0.02, T:0.78
Consensus pattern (20 bp):
TCTTTTTTTCAATTTTCTTT
Found at i:206967 original size:21 final size:21
Alignment explanation
Indices: 206941--207004 Score: 94
Period size: 21 Copynumber: 3.0 Consensus size: 21
206931 TTTTGGTAAT
206941 TGGAATTGGTACGAAATGGTA
1 TGGAATTGGTACGAAATGGTA
206962 TGGAATTGGTACGAAATGGTA
1 TGGAATTGGTACGAAATGGTA
*
206983 TGGTATTTGGTAC-AAATTGGTA
1 TGG-AATTGGTACGAAA-TGGTA
207005 ATGGTTCAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
21 27 0.68
22 13 0.32
ACGTcount: A:0.31, C:0.05, G:0.31, T:0.33
Consensus pattern (21 bp):
TGGAATTGGTACGAAATGGTA
Found at i:208929 original size:10 final size:10
Alignment explanation
Indices: 208900--208989 Score: 58
Period size: 10 Copynumber: 8.9 Consensus size: 10
208890 CCAATAAAAT
208900 AAATGAGCTG
1 AAATGAGCTG
208910 AAATGTAGCTG
1 AAATG-AGCTG
208921 AAATGAGCT-
1 AAATGAGCTG
*
208930 CAATAGAGCTG
1 AAAT-GAGCTG
**** *
208941 GTCGGAGCTA
1 AAATGAGCTG
*
208951 AAACGAGCT-
1 AAATGAGCTG
* *
208960 AGAGGAGCTG
1 AAATGAGCTG
208970 AAATGGAGCTG
1 AAAT-GAGCTG
208981 AAATGAGCT
1 AAATGAGCT
208990 TGCACAAGAA
Statistics
Matches: 61, Mismatches: 14, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
9 10 0.16
10 31 0.51
11 20 0.33
ACGTcount: A:0.37, C:0.13, G:0.31, T:0.19
Consensus pattern (10 bp):
AAATGAGCTG
Found at i:214189 original size:22 final size:21
Alignment explanation
Indices: 214158--214208 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
214148 ACCTCTTTGA
214158 ACCATTACCAATTCGTACCAAAT
1 ACCA-TACCAATTCGTACC-AAT
* *
214181 ACCATACCATTTTGTACCAAT
1 ACCATACCAATTCGTACCAAT
*
214202 TCCATAC
1 ACCATAC
214209 TTTTTCGAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 9 0.36
22 12 0.48
23 4 0.16
ACGTcount: A:0.35, C:0.31, G:0.04, T:0.29
Consensus pattern (21 bp):
ACCATACCAATTCGTACCAAT
Found at i:214208 original size:21 final size:21
Alignment explanation
Indices: 214163--214225 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
214153 TTTGAACCAT
* * *
214163 TACCAATTCGTACCAAATACCA
1 TACCATTTTGTACC-AATTCCA
214185 TACCATTTTGTACCAATTCCA
1 TACCATTTTGTACCAATTCCA
* *
214206 TA-CTTTTTCGAACCAATTCC
1 TACCATTTT-GTACCAATTCC
214226 CAAATACCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 5 0.14
21 18 0.51
22 12 0.34
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.33
Consensus pattern (21 bp):
TACCATTTTGTACCAATTCCA
Found at i:214571 original size:14 final size:14
Alignment explanation
Indices: 214554--214588 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
214544 CAAAATCAAA
*
214554 AAAAAATTGAAAGG
1 AAAAAATTGAAAAG
214568 AAAAAATTGAAAAG
1 AAAAAATTGAAAAG
214582 AAAAAAT
1 AAAAAAT
214589 ATTGCATACG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AAAAAATTGAAAAG
Found at i:214571 original size:15 final size:15
Alignment explanation
Indices: 214553--214592 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
214543 TCAAAATCAA
214553 AAAAAAATTG-AAAG
1 AAAAAAATTGAAAAG
*
214567 GAAAAAATTGAAAAG
1 AAAAAAATTGAAAAG
214582 AAAAAATATTG
1 AAAAAA-ATTG
214593 CATACGGTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 9 0.41
15 9 0.41
16 4 0.18
ACGTcount: A:0.68, C:0.00, G:0.15, T:0.17
Consensus pattern (15 bp):
AAAAAAATTGAAAAG
Found at i:218147 original size:19 final size:18
Alignment explanation
Indices: 218111--218150 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
218101 TTTCCACTCG
*
218111 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
218129 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
218148 TTT
1 TTT
218151 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:219958 original size:45 final size:45
Alignment explanation
Indices: 219898--219989 Score: 143
Period size: 45 Copynumber: 2.0 Consensus size: 45
219888 CAAAGAAAAG
*
219898 ACCTCGACCACTATCAA-GAATGATAGGAACCTTGGTATAT-ATGA
1 ACCTCGACCACTATCAATG-ATGATAAGAACCTTGGTATATGATGA
219942 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
1 ACCTCGA-CCACTATCAATGATGATAAGAACCTTGGTATATGATGA
219988 AC
1 AC
219990 GCCACACTAT
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
44 7 0.16
45 30 0.68
46 7 0.16
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (45 bp):
ACCTCGACCACTATCAATGATGATAAGAACCTTGGTATATGATGA
Found at i:220632 original size:118 final size:116
Alignment explanation
Indices: 220424--220657 Score: 400
Period size: 118 Copynumber: 2.0 Consensus size: 116
220414 TGGAAGTGGA
* *
220424 AGAGTTGCTGCTGAATTTTAACGGGCATAAAATGCTCTTTAAAAACTCCTTTAATGATTTTAAGC
1 AGAGTTGCTGCTGAATTTTAAAGGGCATAAAATGCTATTTAAAAACTCCTTTAATGATTTTAAGC
220489 TCCCTTATAAACAGCCCCTTTAATTGTAACTCAAAAGAACTTGAACAGCCACT
66 TCCCTTATAAACAGCCCCTTTAATTGTAACTC-AAA-AACTTGAACAGCCACT
220542 AGAGTTGCTGCTGAATTTTAAAGGGCATAAAATGCTATTT-AAAACTCCTTTAATGAATTTTTAA
1 AGAGTTGCTGCTGAATTTTAAAGGGCATAAAATGCTATTTAAAAACTCCTTTAATG-A-TTTTAA
220606 GCTCCCTTAT-AACAGCCCCTTTAATTGTAACTCAAAAACTTGAACAGCCACT
64 GCTCCCTTATAAACAGCCCCTTTAATTGTAACTCAAAAACTTGAACAGCCACT
220658 TAATTAATGT
Statistics
Matches: 112, Mismatches: 2, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
116 16 0.14
117 18 0.16
118 62 0.55
119 16 0.14
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (116 bp):
AGAGTTGCTGCTGAATTTTAAAGGGCATAAAATGCTATTTAAAAACTCCTTTAATGATTTTAAGC
TCCCTTATAAACAGCCCCTTTAATTGTAACTCAAAAACTTGAACAGCCACT
Found at i:224593 original size:46 final size:46
Alignment explanation
Indices: 224540--224633 Score: 163
Period size: 46 Copynumber: 2.0 Consensus size: 46
224530 CAAAGAAAAG
*
224540 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAAGAACCTTGGTATATGATGA
224586 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
224632 AC
1 AC
224634 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:227427 original size:19 final size:18
Alignment explanation
Indices: 227391--227430 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
227381 TTTCCACTCG
*
227391 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
227409 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
227428 TTT
1 TTT
227431 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:228510 original size:15 final size:15
Alignment explanation
Indices: 228490--228544 Score: 82
Period size: 14 Copynumber: 3.9 Consensus size: 15
228480 ACTAGCTCTC
228490 TTTTTTTTT--CAAT
1 TTTTTTTTTCACAAT
228503 TTTTTTTTTCACAA-
1 TTTTTTTTTCACAAT
228517 TTTTTTTTTCACAA-
1 TTTTTTTTTCACAAT
228531 TTTTTTTTTCACAA
1 TTTTTTTTTCACAA
228545 CTTGATATCC
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
13 9 0.22
14 28 0.70
15 3 0.08
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTTTTTTCACAAT
Found at i:228534 original size:28 final size:27
Alignment explanation
Indices: 228490--228544 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 27
228480 ACTAGCTCTC
*
228490 TTTTTTTTTCAATTTTTTTTTTCACAA
1 TTTTTTTTTCAAATTTTTTTTTCACAA
228517 TTTTTTTTTCACAATTTTTTTTTCACAA
1 TTTTTTTTTCA-AATTTTTTTTTCACAA
228545 CTTGATATCC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 11 0.42
28 15 0.58
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTTTTTTTCAAATTTTTTTTTCACAA
Found at i:228629 original size:12 final size:12
Alignment explanation
Indices: 228582--228628 Score: 67
Period size: 12 Copynumber: 3.8 Consensus size: 12
228572 TGGAAACTAG
228582 TTTTTTTTGAAT
1 TTTTTTTTGAAT
*
228594 TTTTTTTTCAAAT
1 TTTTTTTT-GAAT
*
228607 TTTTTTTTGAGT
1 TTTTTTTTGAAT
228619 TTTTTTTTGA
1 TTTTTTTTGA
228629 GAAACTACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
12 20 0.65
13 11 0.35
ACGTcount: A:0.15, C:0.02, G:0.09, T:0.74
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:228996 original size:46 final size:46
Alignment explanation
Indices: 228943--229032 Score: 155
Period size: 46 Copynumber: 2.0 Consensus size: 46
228933 CAAAGAAAAG
*
228943 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGTATATGATAA
1 ACCTCGACCCACTATCAATG-ATGATAAGAACCTTGGTATATGATAA
228989 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGAT
1 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGAT
229033 GAACGCCACA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
46 41 0.98
47 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.26
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATAA
Found at i:231242 original size:21 final size:21
Alignment explanation
Indices: 231197--231259 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
231187 TTTGAACCAT
* *
231197 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
231219 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
231240 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
231260 CAAATACAAA
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:241947 original size:30 final size:30
Alignment explanation
Indices: 241913--242009 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
241903 TAAACTAAAA
241913 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
241943 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
241973 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
242002 ATGAGCTA
1 -TGAGCTA
242010 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:244225 original size:14 final size:14
Alignment explanation
Indices: 244196--244232 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
244186 TTCAACATCT
244196 TTTTC-TTTTTCAA
1 TTTTCTTTTTTCAA
244209 TTTTCTTTTCTTC-A
1 TTTTCTTTT-TTCAA
244223 TTTTCTTTTT
1 TTTTCTTTTT
244233 CTCTCACTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.27
14 13 0.59
15 3 0.14
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTCTTTTTTCAA
Found at i:248189 original size:17 final size:18
Alignment explanation
Indices: 248162--248197 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
248152 AGGCAGCAAT
248162 AGAAGAAAAACATGGAGA
1 AGAAGAAAAACATGGAGA
*
248180 AGAA-AAAAACATTGAGA
1 AGAAGAAAAACATGGAGA
248197 A
1 A
248198 AATGAGTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.64, C:0.06, G:0.22, T:0.08
Consensus pattern (18 bp):
AGAAGAAAAACATGGAGA
Found at i:257453 original size:21 final size:21
Alignment explanation
Indices: 257427--257489 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
257417 TTGGTATTTG
257427 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
257448 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
257469 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
257490 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:258584 original size:10 final size:10
Alignment explanation
Indices: 258569--258610 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
258559 TTTGCAAGTT
258569 TTGAGCTAAA
1 TTGAGCTAAA
* *
258579 TTGAGCTGAT
1 TTGAGCTAAA
*
258589 TTGAGCT-CA
1 TTGAGCTAAA
258598 TTGAGCTAAA
1 TTGAGCTAAA
258608 TTG
1 TTG
258611 GAAGTTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (10 bp):
TTGAGCTAAA
Found at i:263812 original size:39 final size:39
Alignment explanation
Indices: 263753--263961 Score: 219
Period size: 39 Copynumber: 5.3 Consensus size: 39
263743 CATTTGAATG
* *
263753 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATT
1 ATAT-CGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
263793 TTATCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * *
263832 ATACCCGGG-TTAGACCCGAAGGCAATTGTGCTAGTGATT
1 ATA-TCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* *
263871 TTATCCGGGCTAAGA-CCGAAGGCATTTGTGCGAGTTGA-T
1 ATAT-CGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* *
263910 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTT
1 ATAT-CGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
*
263950 ATATCCGGCTAA
1 ATATCGGGCTAA
263962 ATTTCGAAGA
Statistics
Matches: 140, Mismatches: 21, Indels: 17
0.79 0.12 0.10
Matches are distributed among these distances:
38 2 0.01
39 100 0.71
40 38 0.27
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (39 bp):
ATATCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
Found at i:263890 original size:78 final size:80
Alignment explanation
Indices: 263757--263961 Score: 310
Period size: 78 Copynumber: 2.6 Consensus size: 80
263747 TGAATGATAT
*
263757 CCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATTTTAT-CGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
*
263821 TGCGAGTTGCTATAC
66 TGCGAGTTGATATAC
*
263836 CCGGG-TTAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGA-CCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
*
263899 TGCGAGTTGATATAT
66 TGCGAGTTGATATAC
* * * *
263914 CCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTTATATCC-GGCTAA
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAA
263962 ATTTCGAAGA
Statistics
Matches: 115, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
78 69 0.60
79 46 0.40
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.27
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
TGCGAGTTGATATAC
Found at i:280689 original size:14 final size:14
Alignment explanation
Indices: 280670--280703 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
280660 TATGTAATTT
*
280670 TTTTTTCTTTTCAA
1 TTTTTTCCTTTCAA
280684 TTTTTTCCTTTCAA
1 TTTTTTCCTTTCAA
280698 TTTTTT
1 TTTTTT
280704 TTTCGATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTTCCTTTCAA
Found at i:281058 original size:21 final size:20
Alignment explanation
Indices: 281033--281075 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
281023 TTGGTATTTG
*
281033 GGAATTGGTTCGAAATAGTAT
1 GGAATTGG-TAGAAATAGTAT
*
281054 GGAATTGGTAGAAATGGTAT
1 GGAATTGGTAGAAATAGTAT
281074 GG
1 GG
281076 TATTTGGTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.33, C:0.02, G:0.35, T:0.30
Consensus pattern (20 bp):
GGAATTGGTAGAAATAGTAT
Found at i:281073 original size:20 final size:20
Alignment explanation
Indices: 281033--281094 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
281023 TTGGTATTTG
* *
281033 GGAATTGGTTCGAAATAGTAT
1 GGAATTGG-TAGAAATGGTAT
281054 GGAATTGGTAGAAATGGTAT
1 GGAATTGGTAGAAATGGTAT
* *
281074 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTA-GAAATGGTA
281095 ATGGTTCAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 12 0.34
21 15 0.43
22 8 0.23
ACGTcount: A:0.31, C:0.03, G:0.32, T:0.34
Consensus pattern (20 bp):
GGAATTGGTAGAAATGGTAT
Done.