Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 96 of 187
Found at i:28671129 original size:29 final size:28
Alignment explanation
Indices: 28671042--28671129 Score: 76
Period size: 28 Copynumber: 3.1 Consensus size: 28
28671032 TTTATTATTA
28671042 TTTTTTC-T-TTCTCTTTTTCTTTGTTCTT-
1 TTTTTTCTTCTTC-CTTTTTC-TT-TTCTTC
* *
28671070 TTTTTT-TTCTTTCTTTTTCCTTTTTTCTC
1 TTTTTTCTTCTTCCTTTTT-CTTTTCT-TC
28671099 TTTTTTCTTCTTCCTTTTTCTTCTTCTTC
1 TTTTTTCTTCTTCCTTTTTCTT-TTCTTC
28671128 TT
1 TT
28671130 CGGGCCGAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
27 3 0.06
28 16 0.33
29 16 0.33
30 14 0.29
ACGTcount: A:0.00, C:0.22, G:0.01, T:0.77
Consensus pattern (28 bp):
TTTTTTCTTCTTCCTTTTTCTTTTCTTC
Found at i:28672164 original size:21 final size:21
Alignment explanation
Indices: 28672138--28672180 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
28672128 TGAAACAGAG
28672138 ATAGAGCAAAGACTTAAAAGC
1 ATAGAGCAAAGACTTAAAAGC
28672159 ATAGAGCAAAGACTTAAAAGC
1 ATAGAGCAAAGACTTAAAAGC
28672180 A
1 A
28672181 CTGAATTGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.53, C:0.14, G:0.19, T:0.14
Consensus pattern (21 bp):
ATAGAGCAAAGACTTAAAAGC
Found at i:28672420 original size:81 final size:78
Alignment explanation
Indices: 28672258--28672713 Score: 462
Period size: 79 Copynumber: 5.8 Consensus size: 78
28672248 TCAGCATGAT
* * *** *
28672258 CCGAGTCTCAACTCACCTCTCGCATTATGAGTTGATTTTGGAGAAATG--GAAATTTAAAAGAAA
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAGAAATTT-AAA-AAA
*
28672321 TACCTCGATATGTGAC
64 TACCTCG-GATGTGAC
* *
28672337 CCGAGGTTCAACTCACCTCTGGCAATATGAGTTGATTTTTTTGAAAAGCAGAAATTTAAAAGAAA
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAGAAATTT-AAA-AAA
*
28672402 TACATCGGTATGTGAC
64 TACCTCGG-ATGTGAC
* * * ** *
28672418 CCGAGACTCAACTCACCTCTCGCAATATGAGTCGATTTTTTTCAAAAATAGAAA-TTGAAAAATA
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAGAAATTTAAAAAATA
*
28672482 CCTCAGGATATGAC
66 CCTC-GGATGTGAC
** * * * *
28672496 TTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGTGAAAACCA-AAAATTGAAAAATA
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAGAAATTTAAAAAATA
* *
28672560 CCTC-GACGTGAT
66 CCTCGGATGTGAC
* * *
28672572 TCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAACGCGGAAA-TTGAAAA
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTGAAAA-GCAGAAATTTAAAAA
28672636 ATACCTCAGGA--TGAC
63 ATACCTC-GGATGTGAC
* *
28672651 CCGAGGCTCAACTCACCTCTAGCATTATGAGTTGA-TTTTTTGAAAAAAGCAGAAATTTAAAAA
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG--AAAAGCAGAAATTTAAAAA
28672714 TATAATTCTT
Statistics
Matches: 322, Mismatches: 41, Indels: 29
0.82 0.10 0.07
Matches are distributed among these distances:
76 46 0.14
77 9 0.03
78 91 0.28
79 94 0.29
80 5 0.02
81 77 0.24
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (78 bp):
CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAGAAATTTAAAAAATA
CCTCGGATGTGAC
Found at i:28679647 original size:20 final size:20
Alignment explanation
Indices: 28679622--28679663 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
28679612 CAACCTTTTC
* *
28679622 TTTTTTGAAAA-ACACGAAT
1 TTTTTTTAAAATACAAGAAT
28679641 TTTTTTTAAAATACAAGAAT
1 TTTTTTTAAAATACAAGAAT
28679661 TTT
1 TTT
28679664 AGAAACACGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (20 bp):
TTTTTTTAAAATACAAGAAT
Found at i:28679777 original size:20 final size:18
Alignment explanation
Indices: 28679729--28679939 Score: 128
Period size: 17 Copynumber: 11.3 Consensus size: 18
28679719 GAGGATTTTT
*
28679729 TTTTTG-AAACACAAAAA
1 TTTTTGAAAACACGAAAA
* *
28679746 TTTATG-AAACACGATCAAT
1 TTTTTGAAAACACGA--AAA
28679765 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* **
28679783 TTTTTG-AAAGACGAATTT
1 TTTTTGAAAACACGAA-AA
* *
28679801 TTTTTGAAAATACGGAAA
1 TTTTTGAAAACACGAAAA
*
28679819 TTTATG-AAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
28679836 TTTTTTTTGAAAACAAGAAAA
1 ---TTTTTGAAAACACGAAAA
* *
28679857 TTTTTG-AAATACGAGAA
1 TTTTTGAAAACACGAAAA
* *
28679874 TTTTTAAAAATACGAAAACA
1 TTTTTGAAAACACG-AAA-A
28679894 TGAAAATTTTGAAAACACGAAAA
1 T-----TTTTGAAAACACGAAAA
28679917 TTTTTG-AAACACGAGAAA
1 TTTTTGAAAACACGA-AAA
28679935 TTTTT
1 TTTTT
28679940 TTTTGAAAAC
Statistics
Matches: 152, Mismatches: 24, Indels: 35
0.72 0.11 0.17
Matches are distributed among these distances:
17 50 0.33
18 45 0.30
19 16 0.11
20 15 0.10
21 10 0.07
23 2 0.01
24 3 0.02
25 11 0.07
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.33
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:28679804 original size:36 final size:36
Alignment explanation
Indices: 28679726--28679870 Score: 159
Period size: 36 Copynumber: 4.0 Consensus size: 36
28679716 CACGAGGATT
*
28679726 TTTTTTTTG-AAACACAAAAATTTATGAAACACG-A
1 TTTTTTTTGAAAACACGAAAATTTATGAAACACGAA
* * *
28679760 TCAATTTTTTGAAAACACGAAAATTTTTGAAAGACGAA
1 T--TTTTTTTGAAAACACGAAAATTTATGAAACACGAA
* *
28679798 TTTTTTTTGAAAATACGGAAATTTATGAAACACGAAAA
1 TTTTTTTTGAAAACACGAAAATTTATGAAACACG--AA
* * *
28679836 TTTTTTTTGAAAACAAGAAAATTTTTGAAATACGA
1 TTTTTTTTGAAAACACGAAAATTTATGAAACACGA
28679871 GAATTTTTAA
Statistics
Matches: 91, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
34 1 0.01
36 36 0.40
37 21 0.23
38 33 0.36
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (36 bp):
TTTTTTTTGAAAACACGAAAATTTATGAAACACGAA
Found at i:28679847 original size:38 final size:37
Alignment explanation
Indices: 28679726--28679878 Score: 170
Period size: 38 Copynumber: 4.1 Consensus size: 37
28679716 CACGAGGATT
*
28679726 TTTTTTTTG-AAACACAAAAATTTATGAAACACGATCAA
1 TTTTTTTTGAAAACACGAAAATTTATGAAACACGA--AA
* *
28679764 --TTTTTTGAAAACACGAAAATTTTTGAAAGACG-AA
1 TTTTTTTTGAAAACACGAAAATTTATGAAACACGAAA
* *
28679798 TTTTTTTTGAAAATACGGAAATTTATGAAACACGAAAA
1 TTTTTTTTGAAAACACGAAAATTTATGAAACACG-AAA
* * *
28679836 TTTTTTTTGAAAACAAGAAAATTTTTGAAATACGAGAA
1 TTTTTTTTGAAAACACGAAAATTTATGAAACACGA-AA
28679874 TTTTT
1 TTTTT
28679879 AAAAATACGA
Statistics
Matches: 97, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
34 2 0.02
36 35 0.36
37 22 0.23
38 38 0.39
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.37
Consensus pattern (37 bp):
TTTTTTTTGAAAACACGAAAATTTATGAAACACGAAA
Found at i:28679878 original size:73 final size:72
Alignment explanation
Indices: 28679743--28679887 Score: 195
Period size: 74 Copynumber: 2.0 Consensus size: 72
28679733 TGAAACACAA
* * * *
28679743 AAATTTATGAAACACGATCAATTTTTTGAAAACACGAAAATTTTTGAAAGACGAATTTTTTTTGA
1 AAATTTATGAAACACGATAAATTTTTTGAAAACAAGAAAATTTTTGAAAGACGAA-TATTTTTAA
28679808 AAATACGG
65 AAATACGG
*
28679816 AAATTTATGAAACACGA-AAATTTTTTTTGAAAACAAGAAAATTTTTGAAATACGAGA-ATTTTT
1 AAATTTATGAAACACGATAAA--TTTTTTGAAAACAAGAAAATTTTTGAAAGACGA-ATATTTTT
28679879 AAAAATACG
63 AAAAATACG
28679888 AAAACATGAA
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
72 2 0.03
73 30 0.47
74 31 0.48
75 1 0.02
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.34
Consensus pattern (72 bp):
AAATTTATGAAACACGATAAATTTTTTGAAAACAAGAAAATTTTTGAAAGACGAATATTTTTAAA
AATACGG
Found at i:28679966 original size:108 final size:106
Alignment explanation
Indices: 28679852--28680152 Score: 252
Period size: 98 Copynumber: 2.9 Consensus size: 106
28679842 TTGAAAACAA
* * * * ***
28679852 GAAAATTTTTGAAATAC-GAGAA-TTTTTAAAAATACGAAAACATGAAAATTTTGAAAACACGA-
1 GAAAATTTTTCAAACACAG-GAATTTTTTAAAAACACGAAAACATCAAAAAAAT--AAACACGAG
28679914 AAATTTTTGAAACACGAGAAATTTTTTTTTGAAAACACGAAAATGT
63 AAATTTTTGAAACACGAG-AA-TTTTTTTTGAAAACACGAAAATGT
* * ** **
28679960 GAAAATTTTTCAAACACAGGAATTTTTTGAAAACACGATAACATCAAAAAAATATTCACGAGAGT
1 GAAAATTTTTCAAACACAGGAATTTTTTAAAAACACGAAAACATCAAAAAAATAAACACGAGAAA
*
28680025 TTTTTGAAACACGAGAATTTTTTTTGAAGACAC--------
66 TTTTTGAAACACGAGAATTTTTTTTGAAAACACGAAAATGT
* * * * ** *
28680058 GAAAATTTTTCAAACAC-GGAAATTTTTGAAAACACGATAACGTCAAAAAAAATATTCACGAGAG
1 GAAAATTTTTCAAACACAGGAATTTTTTAAAAACACGAAAACATC-AAAAAAATAAACACGAGAA
*
28680122 TTTTTTGAAACACGAGAA--TTTTTTGAAAACA
65 ATTTTTGAAACACGAGAATTTTTTTTGAAAACA
28680153 TTTTTCAAAC
Statistics
Matches: 172, Mismatches: 17, Indels: 20
0.82 0.08 0.10
Matches are distributed among these distances:
96 12 0.07
97 25 0.15
98 54 0.31
106 15 0.09
107 8 0.05
108 34 0.20
109 24 0.14
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (106 bp):
GAAAATTTTTCAAACACAGGAATTTTTTAAAAACACGAAAACATCAAAAAAATAAACACGAGAAA
TTTTTGAAACACGAGAATTTTTTTTGAAAACACGAAAATGT
Found at i:28680049 original size:20 final size:21
Alignment explanation
Indices: 28680024--28680067 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
28680014 TTCACGAGAG
*
28680024 TTTTTTGAA-ACACGAGAATT
1 TTTTTTGAAGACACGAAAATT
28680044 TTTTTTGAAGACACGAAAATT
1 TTTTTTGAAGACACGAAAATT
28680065 TTT
1 TTT
28680068 CAAACACGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (21 bp):
TTTTTTGAAGACACGAAAATT
Found at i:28680066 original size:18 final size:17
Alignment explanation
Indices: 28680025--28680094 Score: 68
Period size: 18 Copynumber: 3.8 Consensus size: 17
28680015 TCACGAGAGT
*
28680025 TTTTTGAAACACGAGAATTT
1 TTTTTGAAACACGA-AA--A
28680045 TTTTTGAAGACACGAAAA
1 TTTTTGAA-ACACGAAAA
* *
28680063 TTTTTCAAACACGGAAA
1 TTTTTGAAACACGAAAA
28680080 TTTTTGAAAACACGA
1 TTTTTG-AAACACGA
28680095 TAACGTCAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
17 13 0.30
18 14 0.33
20 10 0.23
21 6 0.14
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:28680070 original size:98 final size:93
Alignment explanation
Indices: 28679960--28680184 Score: 334
Period size: 98 Copynumber: 2.4 Consensus size: 93
28679950 ACGAAAATGT
28679960 GAAAATTTTTCAAACACAGGAATTTTTTGAAAACACGATAACATC-AAAAAAATATTCACGAGAG
1 GAAAATTTTTCAAACAC-GGAA-TTTTTGAAAACACGATAACATCAAAAAAAATATTCACGAGAG
28680024 TTTTTTGAAACACGAGAATTTTTTTTGAAGACAC
64 TTTTTTGAAACACGAGAA--TTTTTTGAA-A-AC
*
28680058 GAAAATTTTTCAAACACGGAAATTTTTGAAAACACGATAACGTCAAAAAAAATATTCACGAGAGT
1 GAAAATTTTTCAAACACGG-AATTTTTGAAAACACGATAACATCAAAAAAAATATTCACGAGAGT
28680123 TTTTTGAAACACGAGAATTTTTTGAAAAC
65 TTTTTGAAACACGAGAATTTTTTGAAAAC
28680152 ----ATTTTTCAAACACGGGAATTTTTGAAAACACGA
1 GAAAATTTTTCAAACAC-GGAATTTTTGAAAACACGA
28680185 AAATTTTTTA
Statistics
Matches: 123, Mismatches: 1, Indels: 14
0.89 0.01 0.10
Matches are distributed among these distances:
90 30 0.24
91 2 0.02
94 2 0.02
95 1 0.01
96 9 0.07
97 23 0.19
98 56 0.46
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (93 bp):
GAAAATTTTTCAAACACGGAATTTTTGAAAACACGATAACATCAAAAAAAATATTCACGAGAGTT
TTTTGAAACACGAGAATTTTTTGAAAAC
Found at i:28680074 original size:17 final size:18
Alignment explanation
Indices: 28680045--28680094 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
28680035 ACGAGAATTT
*
28680045 TTTTTGAAGACACGAAAA
1 TTTTTGAAAACACGAAAA
* *
28680063 TTTTT-CAAACACGGAAA
1 TTTTTGAAAACACGAAAA
28680080 TTTTTGAAAACACGA
1 TTTTTGAAAACACGA
28680095 TAACGTCAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:28680137 original size:18 final size:18
Alignment explanation
Indices: 28680114--28680227 Score: 86
Period size: 18 Copynumber: 6.8 Consensus size: 18
28680104 AAAAAATATT
*
28680114 CACGAGAGTTTTTTGAAA
1 CACGAGAATTTTTTGAAA
28680132 CACGAGAATTTTTTGAAA
1 CACGAGAATTTTTTGAAA
*
28680150 -AC----A-TTTTTCAAA
1 CACGAGAATTTTTTGAAA
*
28680162 CACGGGAA-TTTTTGAAAA
1 CACGAGAATTTTTTG-AAA
* **
28680180 CACGAAAATTTTTT-ATT
1 CACGAGAATTTTTTGAAA
28680197 CACGAGAA-TTTTTGAAA
1 CACGAGAATTTTTTGAAA
28680214 CACGA-AATATTTTT
1 CACGAGAAT-TTTTT
28680228 TAAAAAAAAG
Statistics
Matches: 76, Mismatches: 10, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
12 8 0.11
13 3 0.04
16 7 0.09
17 22 0.29
18 31 0.41
19 5 0.07
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (18 bp):
CACGAGAATTTTTTGAAA
Found at i:28680174 original size:17 final size:17
Alignment explanation
Indices: 28680152--28680232 Score: 63
Period size: 17 Copynumber: 4.6 Consensus size: 17
28680142 TTTTGAAAAC
* *
28680152 ATTTTTCAAACACGGGA
1 ATTTTTAAAACACGAGA
*
28680169 ATTTTTGAAAACACGAAA
1 ATTTTT-AAAACACGAGA
* **
28680187 ATTTTTTATTCACGAGA
1 ATTTTTAAAACACGAGA
* *
28680204 ATTTTTGAAACACGAAA
1 ATTTTTAAAACACGAGA
28680221 TATTTTTTAAAA
1 -A-TTTTTAAAA
28680233 AAAAGGAAAC
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
17 26 0.53
18 15 0.31
19 8 0.16
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (17 bp):
ATTTTTAAAACACGAGA
Found at i:28680174 original size:29 final size:30
Alignment explanation
Indices: 28680123--28680181 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
28680113 TCACGAGAGT
*
28680123 TTTTTGAAACACGAGAATTTTTTGAAAACA
1 TTTTTCAAACACGAGAATTTTTTGAAAACA
*
28680153 TTTTTCAAACACGGGAA-TTTTTGAAAACA
1 TTTTTCAAACACGAGAATTTTTTGAAAACA
28680182 CGAAAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 12 0.44
30 15 0.56
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.36
Consensus pattern (30 bp):
TTTTTCAAACACGAGAATTTTTTGAAAACA
Found at i:28680206 original size:35 final size:35
Alignment explanation
Indices: 28680162--28680229 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 35
28680152 ATTTTTCAAA
*
28680162 CACGGGAATTTTTGAAAACACGAAA-ATTTTTTATT
1 CACGAGAATTTTTG-AAACACGAAATATTTTTTATT
28680197 CACGAGAATTTTTGAAACACGAAATATTTTTTA
1 CACGAGAATTTTTGAAACACGAAATATTTTTTA
28680230 AAAAAAAGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 10 0.32
35 21 0.68
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (35 bp):
CACGAGAATTTTTGAAACACGAAATATTTTTTATT
Found at i:28680306 original size:17 final size:16
Alignment explanation
Indices: 28680284--28680332 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
28680274 TATTATTATT
28680284 ATTTTGAAACACGAGAA
1 ATTTTGAAACACGA-AA
*
28680301 ATTTTGAAAACATGAAA
1 ATTTTG-AAACACGAAA
28680318 ATTTTTGAAACACGA
1 A-TTTTGAAACACGA
28680333 TTTTTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 16 0.57
18 12 0.43
ACGTcount: A:0.47, C:0.10, G:0.14, T:0.29
Consensus pattern (16 bp):
ATTTTGAAACACGAAA
Found at i:28681107 original size:7 final size:6
Alignment explanation
Indices: 28681080--28681162 Score: 78
Period size: 6 Copynumber: 13.3 Consensus size: 6
28681070 ATTATTATTT
* * *
28681080 TTTTTC TTTCTC TTTTTC TTTGTTC TTTTTT TTCTTTC TTTTTC CTTTT-
1 TTTTTC TTTTTC TTTTTC TTT-TTC TTTTTC TT-TTTC TTTTTC TTTTTC
* *
28681129 TTTCTC TTTTTTC TTCTTTC TTTTTC TTCTTC TT
1 TTTTTC -TTTTTC TT-TTTC TTTTTC TTTTTC TT
28681163 CTTCGGGCCG
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
5 3 0.05
6 38 0.60
7 22 0.35
ACGTcount: A:0.00, C:0.20, G:0.01, T:0.78
Consensus pattern (6 bp):
TTTTTC
Found at i:28681117 original size:28 final size:28
Alignment explanation
Indices: 28681077--28681156 Score: 99
Period size: 28 Copynumber: 2.8 Consensus size: 28
28681067 TTTATTATTA
28681077 TTTTTTTTCTTTCTCTTTTTCTTTGTTC
1 TTTTTTTTCTTTCTCTTTTTCTTTGTTC
* *
28681105 TTTTTTTTCTTTCT-TTTTCCTTTTTTTC
1 TTTTTTTTCTTTCTCTTTTTC-TTTGTTC
* *
28681133 TCTTTTTTCTTCTTTCTTTTTCTT
1 TTTTTTTTCTT-TCTCTTTTTCTT
28681157 CTTCTTCTTC
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
27 5 0.11
28 30 0.68
29 4 0.09
30 5 0.11
ACGTcount: A:0.00, C:0.19, G:0.01, T:0.80
Consensus pattern (28 bp):
TTTTTTTTCTTTCTCTTTTTCTTTGTTC
Found at i:28681119 original size:20 final size:19
Alignment explanation
Indices: 28681080--28681165 Score: 79
Period size: 20 Copynumber: 4.4 Consensus size: 19
28681070 ATTATTATTT
* *
28681080 TTTTTCTTTCTCTT-TTTC
1 TTTTTCTTTTTTTTCTTTC
28681098 TTTGTTCTTTTTTTTCTTTC
1 TTT-TTCTTTTTTTTCTTTC
28681118 TTTTTCCTTTTTTTCTCTTT-
1 TTTTT-CTTTTTTT-TCTTTC
28681138 TTTCTTCTTTCTTTTTC-TTC
1 TTT-TTCTTT-TTTTTCTTTC
*
28681158 TTCTTCTT
1 TTTTTCTT
28681166 CGGGCCGAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
18 3 0.05
19 18 0.31
20 26 0.45
21 11 0.19
ACGTcount: A:0.00, C:0.21, G:0.01, T:0.78
Consensus pattern (19 bp):
TTTTTCTTTTTTTTCTTTC
Found at i:28681140 original size:31 final size:28
Alignment explanation
Indices: 28681096--28681155 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 28
28681086 TTTCTCTTTT
28681096 TCTTTGTTCTTTTTTTTCTTTCTTTTTCC
1 TCTTTGTTCTTTTTTTTCTTTCTTTTT-C
* *
28681125 TTTTTTTCTCTTTTTTCTTCTTTCTTTTTC
1 TCTTTGT-TCTTTTTT-TTCTTTCTTTTTC
28681155 T
1 T
28681156 TCTTCTTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 5 0.19
30 10 0.37
31 12 0.44
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (28 bp):
TCTTTGTTCTTTTTTTTCTTTCTTTTTC
Found at i:28681158 original size:16 final size:16
Alignment explanation
Indices: 28681082--28681162 Score: 71
Period size: 16 Copynumber: 5.1 Consensus size: 16
28681072 TATTATTTTT
* *
28681082 TTTCTTTCTCTTTTTC
1 TTTCTTTTTCTTCTTC
* *
28681098 TTTGTTCTTT-TTTTTC
1 TTTCTT-TTTCTTCTTC
28681114 TTTCTTTTTCCTT-TT-
1 TTTCTTTTT-CTTCTTC
28681129 TTTCTCTTTT-TTCTTC
1 TTTCT-TTTTCTTCTTC
28681145 TTTCTTTTTCTTCTTC
1 TTTCTTTTTCTTCTTC
28681161 TT
1 TT
28681163 CTTCGGGCCG
Statistics
Matches: 55, Mismatches: 3, Indels: 14
0.76 0.04 0.19
Matches are distributed among these distances:
14 2 0.04
15 14 0.25
16 35 0.64
17 4 0.07
ACGTcount: A:0.00, C:0.21, G:0.01, T:0.78
Consensus pattern (16 bp):
TTTCTTTTTCTTCTTC
Found at i:28681161 original size:28 final size:27
Alignment explanation
Indices: 28681079--28681161 Score: 82
Period size: 26 Copynumber: 3.0 Consensus size: 27
28681069 TATTATTATT
*
28681079 TTTTTTCTT-TCTCTTTTTCTTTGT-TC
1 TTTTTTCTTCTTTCTTTTTCTTT-TCTC
28681105 TTTTTT-TTCTTTCTTTTTCCTTTTTTTCTC
1 TTTTTTCTTCTTTCTTTTT-C---TTTTCTC
28681135 TTTTTTCTTCTTTCTTTTTCTTCTTCT
1 TTTTTTCTTCTTTCTTTTTCTT-TTCT
28681162 TCTTCGGGCC
Statistics
Matches: 48, Mismatches: 1, Indels: 14
0.76 0.02 0.22
Matches are distributed among these distances:
25 2 0.04
26 14 0.29
27 3 0.06
28 4 0.08
29 1 0.02
30 12 0.25
31 12 0.25
ACGTcount: A:0.00, C:0.20, G:0.01, T:0.78
Consensus pattern (27 bp):
TTTTTTCTTCTTTCTTTTTCTTTTCTC
Found at i:28684957 original size:36 final size:35
Alignment explanation
Indices: 28684839--28684984 Score: 154
Period size: 36 Copynumber: 4.1 Consensus size: 35
28684829 ATTCAATAAA
*
28684839 AAAAACAAAAACA-AAAACAAAATCAAAATCAAAATC
1 AAAAACAAAAA-AGAAGA-AAAATCAAAATCAAAATC
* * *
28684875 AAAATCAAAATCA-AAGTCAAAATCAAAATCAAAATC
1 AAAAACAAAA-AAGAAG-AAAAATCAAAATCAAAATC
*
28684911 AAAAACAAAAAGAGAAGAAAAATCAAAATCAAAGTC
1 AAAAACAAAAA-AGAAGAAAAATCAAAATCAAAATC
* * *
28684947 AAAAGCAAAAAAGAA-AAAAATCAAAATAAAAATG
1 AAAAACAAAAAAGAAGAAAAATCAAAATCAAAATC
28684981 AAAA
1 AAAA
28684985 TAAAAAGGAG
Statistics
Matches: 94, Mismatches: 12, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
34 20 0.21
35 4 0.04
36 67 0.71
37 3 0.03
ACGTcount: A:0.72, C:0.12, G:0.05, T:0.10
Consensus pattern (35 bp):
AAAAACAAAAAAGAAGAAAAATCAAAATCAAAATC
Found at i:28684990 original size:6 final size:6
Alignment explanation
Indices: 28684839--28684989 Score: 130
Period size: 6 Copynumber: 25.7 Consensus size: 6
28684829 ATTCAATAAA
* * *
28684839 AAAAAC AAAAAC AAAAAC AAAATC AAAATC AAAATC AAAATC AAAATC
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
* * ** * **
28684887 AAAGTC AAAATC AAAATC AAAATC AAAAAC AAAAAG AGAAGA AAAATC
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
* * * * *
28684935 AAAATC AAAGTC AAAAGC AAAA-- AAGAA-A AAAATC AAAATA AAAATG
1 AAAATC AAAATC AAAATC AAAATC AA-AATC AAAATC AAAATC AAAATC
28684981 AAAAT- AAAA
1 AAAATC AAAA
28684990 AGGAGAAAAA
Statistics
Matches: 125, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
4 2 0.02
5 8 0.06
6 115 0.92
ACGTcount: A:0.72, C:0.12, G:0.05, T:0.11
Consensus pattern (6 bp):
AAAATC
Found at i:28686511 original size:15 final size:14
Alignment explanation
Indices: 28686477--28686512 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
28686467 TATTTGTTAG
28686477 AAAAA-AAATGAAA
1 AAAAATAAATGAAA
28686490 AAAAATAAATGAAA
1 AAAAATAAATGAAA
28686504 AAATAATAA
1 AAA-AATAA
28686513 TTACATTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 5 0.24
14 11 0.52
15 5 0.24
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.14
Consensus pattern (14 bp):
AAAAATAAATGAAA
Found at i:28688376 original size:45 final size:45
Alignment explanation
Indices: 28688314--28688435 Score: 135
Period size: 45 Copynumber: 2.8 Consensus size: 45
28688304 ACCAGATGCG
* *
28688314 ATCTGCT-CT-CTGCAACTTTAGAGAGATAAGATCT-GTAATTTTA
1 ATCTGCTCCTACTGCAACTTCAGAGAGATAAGAT-TAGTAACTTTA
* * * **
28688357 ATCTGCTCCTACTGCAACTTCAGGGAGATAGGATTATTGGCTTTA
1 ATCTGCTCCTACTGCAACTTCAGAGAGATAAGATTAGTAACTTTA
*
28688402 ATCTACTCC-ACTGCAACTTCAGAGAGATAAGATT
1 ATCTGCTCCTACTGCAACTTCAGAGAGATAAGATT
28688436 CTCAATCTTC
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
43 7 0.11
44 26 0.39
45 33 0.50
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Consensus pattern (45 bp):
ATCTGCTCCTACTGCAACTTCAGAGAGATAAGATTAGTAACTTTA
Found at i:28688488 original size:44 final size:43
Alignment explanation
Indices: 28688425--28688695 Score: 192
Period size: 44 Copynumber: 6.2 Consensus size: 43
28688415 CAACTTCAGA
* * *
28688425 GAGATAAGATTC-TCAATCTTCAACCTATTCCCCTGCTGACCAGG
1 GAGATAGGATTCAT-AATCTTCAACCTATTCCACTACTG-CCAGG
*
28688469 GAGATAGGATTCATAATCTTCAACCTATTCCACTGCTGACCAGG
1 GAGATAGGATTCATAATCTTCAACCTATTCCACTACTG-CCAGG
* * * * ** *
28688513 GAGATAAGG-CT-ATGGA-CTTCGATCTGCTCCACTACTGCTTAGG
1 GAGAT-AGGATTCAT-AATCTTCAACCTATTCCACTACTGC-CAGG
* * * * *
28688556 GAGAGAAGA-TCTATAATTTTCAACCTACTCTACTACTGCTCAGG
1 GAGATAGGATTC-ATAATCTTCAACCTATTCCACTACTGC-CAGG
* * * * * *
28688600 GAGACATGATTCACAATCTTTAACCTATTCCACTGCTGATCAGG
1 GAGATAGGATTCATAATCTTCAACCTATTCCACTACTG-CCAGG
* * *
28688644 GAGATAGAATTCACAATCTTCAGCCTATTCCACTACTGCCTAGG
1 GAGATAGGATTCATAATCTTCAACCTATTCCACTACTGCC-AGG
28688688 GAGATAGG
1 GAGATAGG
28688696 GCTGGGTCAT
Statistics
Matches: 180, Mismatches: 36, Indels: 22
0.76 0.15 0.09
Matches are distributed among these distances:
42 4 0.02
43 27 0.15
44 143 0.79
45 6 0.03
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.28
Consensus pattern (43 bp):
GAGATAGGATTCATAATCTTCAACCTATTCCACTACTGCCAGG
Found at i:28689037 original size:88 final size:88
Alignment explanation
Indices: 28688883--28689102 Score: 395
Period size: 88 Copynumber: 2.5 Consensus size: 88
28688873 NNNNNNNTGG
* * *
28688883 TGTCTTCGATCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAACCTGCTCTGCT
1 TGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAAACTGCTCCGCT
*
28688948 GCAACCCAGGGAGGCAAGGTTGC
66 GCAACCCAGGGAGGCAAGGCTGC
28688971 TGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAAACTGCTCCGCT
1 TGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAAACTGCTCCGCT
*
28689036 GCAACCCAGGGAGGCAAGGCTGG
66 GCAACCCAGGGAGGCAAGGCTGC
28689059 TGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTG
1 TGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTG
28689103 TTATCTTCAC
Statistics
Matches: 127, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
88 127 1.00
ACGTcount: A:0.19, C:0.25, G:0.29, T:0.28
Consensus pattern (88 bp):
TGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAAACTGCTCCGCT
GCAACCCAGGGAGGCAAGGCTGC
Found at i:28689095 original size:44 final size:45
Alignment explanation
Indices: 28688883--28689098 Score: 154
Period size: 44 Copynumber: 4.9 Consensus size: 45
28688873 NNNNNNNTGG
* *
28688883 TGTCTTCGATCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCTGC
1 TGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGAGCTGC
* * ** * **** * *
28688928 TATTTTTAACCTGC-TCTGCTG-CAACCCAGGGAGGCAAG-GTTGC
1 TGTCTTCGATCTGCTTC-GCTGTCGGTGCAGGAAGGCAAGAGCTGC
*
28688971 TGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGC
1 TGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGAGCTGC
* * ** * * **** * *
28689016 TATTTTTAAACTGCTCCGCTG-CAACCCAGGGAGGCAAG-GCTGG
1 TGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGAGCTGC
28689059 TGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGA
1 TGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGA
28689099 TCTGTTATCT
Statistics
Matches: 116, Mismatches: 49, Indels: 12
0.66 0.28 0.07
Matches are distributed among these distances:
43 34 0.29
44 51 0.44
45 31 0.27
ACGTcount: A:0.19, C:0.25, G:0.29, T:0.27
Consensus pattern (45 bp):
TGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGAGCTGC
Found at i:28690742 original size:17 final size:17
Alignment explanation
Indices: 28690699--28690742 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
28690689 CCCGGTAGAG
*
28690699 TTTTTTTTTACGCCATC
1 TTTTTTTTTGCGCCATC
28690716 TTTTTTTTTGCGCCATC
1 TTTTTTTTTGCGCCATC
28690733 TTTTTTTTTG
1 TTTTTTTTTG
28690743 GGCAATATGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.07, C:0.18, G:0.09, T:0.66
Consensus pattern (17 bp):
TTTTTTTTTGCGCCATC
Found at i:28699956 original size:128 final size:128
Alignment explanation
Indices: 28699785--28700578 Score: 1198
Period size: 128 Copynumber: 6.2 Consensus size: 128
28699775 AAGATACTAG
* * *
28699785 CCTATCTCCCTGGTCAGCAGTGGAATGGGTTATAAATTACAGATCTTGTCTCCTTAAGCAGTAGC
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGC
* * *
28699850 GGAGCAGATCGAAGACAGCAAATCTTATTTTCAAGAGTAAGGAAGTAGATTTAAGCCACAAGT
66 GGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGT
*
28699913 CCTATCTCCCTGGTCAGCAGTGGAATAGGTCAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGC
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGC
** * *
28699978 GGAGCAGATCGAAGACGGTGAATCTTATCTTCAAGAGTAAGGAAGTAGATTTAAGCCATAAGT
66 GGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGT
* * * * ** *
28700041 CCTATCTCCCTAGTCAGCAGTGGAATAGGTTGGAAATTATAGATCTTGCCTCCCTTTGTAGTAGC
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGC
**
28700106 GGAGCAGATCGAAGACGGTGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAG-CACAAGT
66 GGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGT
* *
28700168 CCTATCTCCCTGGTCAGCAGTGGAATAGG-TCGAAAATTACAGTTCTTGTCTCCCTAAGCAGTAG
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAG-AAATTACAGATCTTGTCTCCCTAAGCAGTAG
* * * * *
28700232 TGGAGCAGATCAAAGATGACGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGT
65 CGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGT
* * * * * * * * *
28700296 CCAATCTCCCTTGTCAGTAGTGGAATGGGTTGGAAATTGCAGAACTTGTCTCTCTAGGCAGTAGC
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGC
* *
28700361 GGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGTAGATTTAAGGCACAAGT
66 GGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGT
28700424 CC-ATCTCCCTGGTCAGCAGTGGAATAGGTTAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGC
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGC
*
28700488 GGAGCAGATCGAAGATGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGT
66 GGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGT
*
28700551 TCTATCTCCCTGGTCAGCAGTGGAATAG
1 CCTATCTCCCTGGTCAGCAGTGGAATAG
28700579 ATTGAAGATT
Statistics
Matches: 601, Mismatches: 61, Indels: 8
0.90 0.09 0.01
Matches are distributed among these distances:
126 2 0.00
127 225 0.37
128 372 0.62
129 2 0.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (128 bp):
CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGC
GGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGT
Found at i:28700262 original size:255 final size:255
Alignment explanation
Indices: 28699785--28700578 Score: 1236
Period size: 255 Copynumber: 3.1 Consensus size: 255
28699775 AAGATACTAG
* **
28699785 CCTATCTCCCTGGTCAGCAGTGGAATGGGTTATAAATTACAGATCTTGTCT-CCTTAAGCAGTAG
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTT-AGCAGTAG
* *
28699849 CGGAGCAGATCGAAGACAGCAAATCTTATTTTCAAGAGTAAGGAAGTAGATTTAAGCCACAAGTC
65 CGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGTAGATTTAAG-CACAAGTC
28699914 CTATCTCCCTGGTCAGCAGTGGAATAGGTCAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCG
129 CTATCTCCCTGGTCAGCAGTGGAATAGGTCAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCG
* * * *
28699979 GAGCAGATCGAAGACGGTGAATCTTATCTTCAAGAGTAAGGAAGTAGATTTAAGCCATAAGT
194 GAGCAGATCGAAGATGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGT
* * * * *
28700041 CCTATCTCCCTAGTCAGCAGTGGAATAGGTTGGAAATTATAGATCTTGCCTCCCTTTGTAGTAGC
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTTAGCAGTAGC
** *
28700106 GGAGCAGATCGAAGACGGTGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCACAAGTCCT
66 GGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGTAGATTTAAGCACAAGTCCT
* *
28700171 ATCTCCCTGGTCAGCAGTGGAATAGGTC-GAAAATTACAGTTCTTGTCTCCCTAAGCAGTAGTGG
131 ATCTCCCTGGTCAGCAGTGGAATAGGTCAG-AAATTACAGATCTTGTCTCCCTAAGCAGTAGCGG
* *
28700235 AGCAGATCAAAGATGACGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGT
195 AGCAGATCGAAGATGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGT
* * * * * * *
28700296 CCAATCTCCCTTGTCAGTAGTGGAATGGGTTGGAAATTGCAGAACTTGTCTCTC-TAGGCAGTAG
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTTA-GCAGTAG
28700360 CGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGTAGATTTAAGGCACAAGTC
65 CGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGTAGATTTAA-GCACAAGTC
*
28700425 C-ATCTCCCTGGTCAGCAGTGGAATAGGTTAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCG
129 CTATCTCCCTGGTCAGCAGTGGAATAGGTCAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCG
*
28700489 GAGCAGATCGAAGATGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGT
194 GAGCAGATCGAAGATGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGT
*
28700551 TCTATCTCCCTGGTCAGCAGTGGAATAG
1 CCTATCTCCCTGGTCAGCAGTGGAATAG
28700579 ATTGAAGATT
Statistics
Matches: 487, Mismatches: 46, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
254 2 0.00
255 368 0.76
256 113 0.23
257 4 0.01
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (255 bp):
CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTTAGCAGTAGC
GGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGTAGATTTAAGCACAAGTCCT
ATCTCCCTGGTCAGCAGTGGAATAGGTCAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGA
GCAGATCGAAGATGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGT
Found at i:28700605 original size:383 final size:383
Alignment explanation
Indices: 28699785--28700584 Score: 1228
Period size: 383 Copynumber: 2.1 Consensus size: 383
28699775 AAGATACTAG
* *
28699785 CCTATCTCCCTGGTCAGCAGTGGAATGGGTT-ATAAATTACAGATCTTGTCTCCTTAAGCAGTAG
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGA-AAATTACAGATCTTGTCTCCCTAAGCAGTAG
* * *
28699849 CGGAGCAGATCGAAGACAGCAAATCTTATTTTCAAGAGTAAGGAAGTAGATTTAAGCCACAAGTC
65 CGGAGCAGATCAAAGACAGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTC
* *
28699914 CTATCTCCCTGGTCAGCAGTGGAATAGGTCAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCG
130 CAATCTCCCTGGTCAGCAGTGGAATAGGTCAGAAATTACAGAACTTGTCTCCCTAAGCAGTAGCG
** *
28699979 GAGCAGATCGAAGACGGTGAATCTTATCTTCAAGAGTAAGGAAGTAGATTTAAGCCATAAGTCCT
195 GAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGTAGATTTAAGCCACAAGTCCT
* * ** *
28700044 ATCTCCCTAGTCAGCAGTGGAATAGGTTGGAAATTATAGATCTTGCCTCCCTTTGTAGTAGCGGA
260 ATCTCCCTAGTCAGCAGTGGAATAGGTTAGAAATTACAGATCTTGCCTCCCTAAGCAGTAGCGGA
**
28700109 GCAGATCGAAGACGGTGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCACAAGT
325 GCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCACAAGT
* * *
28700168 CCTATCTCCCTGGTCAGCAGTGGAATAGGTCGAAAATTACAGTTCTTGTCTCCCTAAGCAGTAGT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAAATTACAGATCTTGTCTCCCTAAGCAGTAGC
* *
28700233 GGAGCAGATCAAAGA-TGACGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTC
66 GGAGCAGATCAAAGACAG-CAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTC
* * * ** * * *
28700297 CAATCTCCCTTGTCAGTAGTGGAATGGGTTGGAAATTGCAGAACTTGTCTCTCTAGGCAGTAGCG
130 CAATCTCCCTGGTCAGCAGTGGAATAGGTCAGAAATTACAGAACTTGTCTCCCTAAGCAGTAGCG
*
28700362 GAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGTAGATTTAAGGCACAAGTCC-
195 GAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGTAGATTTAAGCCACAAGTCCT
* *
28700426 ATCTCCCTGGTCAGCAGTGGAATAGGTTAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGA
260 ATCTCCCTAGTCAGCAGTGGAATAGGTTAGAAATTACAGATCTTGCCTCCCTAAGCAGTAGCGGA
*
28700491 GCAGATCGAAGATGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGT
325 GCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAG-CACAAGT
* *
28700551 TCTATCTCCCTGGTCAGCAGTGGAATAGATTGAA
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAA
28700585 GATTGCGAAT
Statistics
Matches: 377, Mismatches: 37, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
382 108 0.29
383 268 0.71
384 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (383 bp):
CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAAATTACAGATCTTGTCTCCCTAAGCAGTAGC
GGAGCAGATCAAAGACAGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCC
AATCTCCCTGGTCAGCAGTGGAATAGGTCAGAAATTACAGAACTTGTCTCCCTAAGCAGTAGCGG
AGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGTAGATTTAAGCCACAAGTCCTA
TCTCCCTAGTCAGCAGTGGAATAGGTTAGAAATTACAGATCTTGCCTCCCTAAGCAGTAGCGGAG
CAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCACAAGT
Found at i:28700816 original size:44 final size:45
Alignment explanation
Indices: 28700766--28700884 Score: 125
Period size: 44 Copynumber: 2.7 Consensus size: 45
28700756 TCGCATCAGG
* * *
28700766 TCTTATCTCCCTGAGGTTGCAGCGGAGCAGACCGAAGA-AGCAGA
1 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGACCAAAGATAGCAAA
* * ** * * * *
28700810 TCTTATCTCTCT-AAGCAGTAGTGGAGTAGATCAAAGATGGCAAA
1 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGACCAAAGATAGCAAA
28700854 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGA
1 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGA
28700885 TTGAAGCCGA
Statistics
Matches: 56, Mismatches: 17, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
43 17 0.30
44 26 0.46
45 13 0.23
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (45 bp):
TCTTATCTCCCTGAGGTTGCAGTGGAGCAGACCAAAGATAGCAAA
Found at i:28700945 original size:44 final size:44
Alignment explanation
Indices: 28700852--28700964 Score: 138
Period size: 44 Copynumber: 2.6 Consensus size: 44
28700842 AAAGATGGCA
* * *
28700852 AATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* * *
28700896 AATCTTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAG-TAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* *
28700939 AGATCTTATCTCTCGGAAGTTGCAGT
1 A-ATCTTATCTCCCTGAAGTTGCAGT
28700965 AGAGTGGATC
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
43 3 0.05
44 56 0.95
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.31
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
Found at i:28701977 original size:15 final size:16
Alignment explanation
Indices: 28701946--28701983 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
28701936 CGATTTTCCC
*
28701946 TTTTTTCTTCTTTATT
1 TTTTTTCTTCTTAATT
28701962 TTTTTTCTT-TTAATT
1 TTTTTTCTTCTTAATT
*
28701977 TGTTTTC
1 TTTTTTC
28701984 ATAAACTGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.08, C:0.11, G:0.03, T:0.79
Consensus pattern (16 bp):
TTTTTTCTTCTTAATT
Found at i:28702612 original size:3 final size:3
Alignment explanation
Indices: 28702604--28702628 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
28702594 TAATATTTCC
28702604 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
28702629 GTTTTTTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:28702695 original size:23 final size:23
Alignment explanation
Indices: 28702659--28702713 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
28702649 ATATAGATCC
28702659 TTTTATTTTATTATATACTATTA
1 TTTTATTTTATTATATACTATTA
* *
28702682 TTTTATGTTT-TTATGTATTATTA
1 TTTTAT-TTTATTATATACTATTA
*
28702705 -CTTATTTTA
1 TTTTATTTTA
28702714 CAAATATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 3 0.11
22 4 0.15
23 17 0.63
24 3 0.11
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (23 bp):
TTTTATTTTATTATATACTATTA
Found at i:28712512 original size:18 final size:17
Alignment explanation
Indices: 28712479--28712517 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
28712469 TTTTATTAAT
28712479 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
28712497 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
28712514 TGTG
1 TGTG
28712518 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:28712769 original size:23 final size:23
Alignment explanation
Indices: 28712743--28712841 Score: 171
Period size: 23 Copynumber: 4.3 Consensus size: 23
28712733 AGTGTTATTG
*
28712743 ATCAGTGGTAGCTTCGACTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
28712766 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
28712789 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
28712812 AACAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
28712835 ATCAGTG
1 ATCAGTG
28712842 TGTCACTTAT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 71 1.00
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:28719066 original size:23 final size:23
Alignment explanation
Indices: 28719040--28719138 Score: 171
Period size: 23 Copynumber: 4.3 Consensus size: 23
28719030 AGTGTTATTG
28719040 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
28719063 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
28719086 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
28719109 AACAATGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
28719132 ATCAGTG
1 ATCAGTG
28719139 TGGCAATTAT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:28722756 original size:14 final size:14
Alignment explanation
Indices: 28722737--28722800 Score: 55
Period size: 14 Copynumber: 4.9 Consensus size: 14
28722727 TAGAAGTGTA
28722737 CGGAGATTGGTTAT
1 CGGAGATTGGTTAT
*
28722751 CGGAGATTGGTTCT
1 CGGAGATTGGTTAT
*
28722765 -GGA-ATTGATT-T
1 CGGAGATTGGTTAT
** *
28722776 -GTTGATTTGTTAT
1 CGGAGATTGGTTAT
28722789 CGGAGATTGGTT
1 CGGAGATTGGTT
28722801 CTGGAATTGA
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
11 2 0.05
12 11 0.29
13 4 0.11
14 21 0.55
ACGTcount: A:0.19, C:0.06, G:0.33, T:0.42
Consensus pattern (14 bp):
CGGAGATTGGTTAT
Found at i:28722822 original size:38 final size:38
Alignment explanation
Indices: 28722740--28722822 Score: 114
Period size: 38 Copynumber: 2.2 Consensus size: 38
28722730 AAGTGTACGG
* * *
28722740 AGATTGGTTATCGGAGATTGGTTCTGGAATTGATTTGT
1 AGATTTGTTATCGGAGATTGGTTCTGGAATTGATTCGA
*
28722778 TGATTTGTTATCGGAGATTGGTTCTGGAATTGA-TCGA
1 AGATTTGTTATCGGAGATTGGTTCTGGAATTGATTCGA
28722815 AGAATTTG
1 AG-ATTTG
28722823 ACAACATTAC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
37 3 0.08
38 36 0.92
ACGTcount: A:0.23, C:0.06, G:0.30, T:0.41
Consensus pattern (38 bp):
AGATTTGTTATCGGAGATTGGTTCTGGAATTGATTCGA
Found at i:28725050 original size:217 final size:217
Alignment explanation
Indices: 28724675--28725181 Score: 818
Period size: 217 Copynumber: 2.3 Consensus size: 217
28724665 GGTGGCCAAT
* * **
28724675 AATCTTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGCCGATAATCCTATCTCTTTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTG
*
28724740 CAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCCGAAGTTGCAGACAGCAGATCGCATCTAG
66 CAGTGGAGCGAATTAAAACCTTGGATCTTATCTCTCCGAAGTTGCAGACAGCAGATCGCATCTAG
* * * *
28724805 TCTTATCTCCCTAAAGTTACAGTGGAGCAGACTAAGTAAACAAGTCTTATCCTTCTGAAGTTTCA
131 TCTTATCTCCCTAAAGTGACAGTGGAGCAAACTAAGTAAACAAGTCTTATCCTCCTGAAGTTGCA
*
28724870 ATCAGGCAAACTGAAGATGGCA
196 ATCAGGCAAACTGAAGATGGAA
28724892 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTG
* * * *
28724957 CAGTGGAGCGAATTAAAACCTTGGATCTTATCTCTCTGAAGTTGTAGAGAGTAGATCGCATCTAG
66 CAGTGGAGCGAATTAAAACCTTGGATCTTATCTCTCCGAAGTTGCAGACAGCAGATCGCATCTAG
*
28725022 TCTTATCTCCCTAAAGTGGCAGTGGAGCAAACTAAGTAAACAAGTCTTATCCTCCTGAAGTTGCA
131 TCTTATCTCCCTAAAGTGACAGTGGAGCAAACTAAGTAAACAAGTCTTATCCTCCTGAAGTTGCA
* * *
28725087 GTGAGGCAGACTGAAGATGGAA
196 ATCAGGCAAACTGAAGATGGAA
*
28725109 AATCTTATCTCCCTG-AGATTGCAGTGGAGCAGATGAAAGCCGATAATCCTATCTCCCTGAAGTT
1 AATCTTATCTCCCTGAAG-TTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTT
*
28725173 GCAGAGGAG
65 GCAGTGGAG
28725182 TAGATTGAAG
Statistics
Matches: 269, Mismatches: 20, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
216 2 0.01
217 267 0.99
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (217 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTG
CAGTGGAGCGAATTAAAACCTTGGATCTTATCTCTCCGAAGTTGCAGACAGCAGATCGCATCTAG
TCTTATCTCCCTAAAGTGACAGTGGAGCAAACTAAGTAAACAAGTCTTATCCTCCTGAAGTTGCA
ATCAGGCAAACTGAAGATGGAA
Found at i:28725175 original size:44 final size:44
Alignment explanation
Indices: 28724673--28725186 Score: 182
Period size: 44 Copynumber: 11.8 Consensus size: 44
28724663 TCGGTGGCCA
* * *
28724673 ATAATCTTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGCCG
1 ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAAAGCCG
* ** * * *
28724717 ATAATCCTATCTCTTTGAAGTTGCAGTGGAGCGGATTAAAACC-
1 ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAAAGCCG
* * ** * *
28724760 TTGGATCTTATCTCTCC-GAAGTTGCAG-ACAGCAGATCG-CA-TC-
1 AT-AATCTTATCTC-CCTGAAGTTGCAGTGGAGCAGAT-GAAAGCCG
* * * ***
28724802 -TAGTCTTATCTCCCTAAAGTTACAGTGGAGCAGACT--AAGTAA
1 ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TGAAAGCCG
* * * * * * *
28724844 ACAAGTCTTATC-CTTCTGAAGTTTCAAT-CAGGCAAACTGAAGATGGC-
1 ATAA-TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TGAA-A-GCCG
*
28724891 A-AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCG
1 ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAAAGCCG
* * *
28724934 ATAATCCTATCTCCCTGAAGTTGCAGTGGAGC-GAATTAAAACC-
1 ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAG-ATGAAAGCCG
* * * * * * * *
28724977 TTGGATCTTATCTCTCTGAAGTTGTAG-AGAGTAGATCG-CA-TC-
1 AT-AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT-GAAAGCCG
* * * * ***
28725019 -TAGTCTTATCTCCCTAAAGTGGCAGTGGAGCAAACT--AAGTAA
1 ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TGAAAGCCG
*
28725061 ACAAGTCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATG--G
1 ATAA-TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TGAA-A-GCCG
*
28725107 AAAATCTTATCTCCCTG-AGATTGCAGTGGAGCAGATGAAAGCCG
1 ATAATCTTATCTCCCTGAAG-TTGCAGTGGAGCAGATGAAAGCCG
* * *
28725151 ATAATCCTATCTCCCTGAAGTTGCAGAGGAGTAGAT
1 ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
28725187 TGAAGCACTA
Statistics
Matches: 353, Mismatches: 75, Indels: 84
0.69 0.15 0.16
Matches are distributed among these distances:
39 2 0.01
40 37 0.10
41 15 0.04
42 7 0.02
43 26 0.07
44 202 0.57
45 47 0.13
46 12 0.03
47 3 0.01
48 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (44 bp):
ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAAAGCCG
Found at i:28726641 original size:23 final size:22
Alignment explanation
Indices: 28726614--28726657 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
28726604 ACTTCCATAA
*
28726614 TGTAATTATTTTTATTTTTTATC
1 TGTAATTATTTTT-TTATTTATC
28726637 TGTAATTATTTTTTTATTTAT
1 TGTAATTATTTTTTTATTTAT
28726658 ATATATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (22 bp):
TGTAATTATTTTTTTATTTATC
Found at i:28726681 original size:19 final size:18
Alignment explanation
Indices: 28726649--28726700 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
28726639 TAATTATTTT
*
28726649 TTTATTTATATATATATA
1 TTTATTTTTATATATATA
* *
28726667 TGTTGTTTTTATATACATA
1 T-TTATTTTTATATATATA
*
28726686 TTTATTTTTTTATAT
1 TTTATTTTTATATAT
28726701 TCATATATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
18 12 0.44
19 15 0.56
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (18 bp):
TTTATTTTTATATATATA
Found at i:28732377 original size:15 final size:15
Alignment explanation
Indices: 28732357--28732421 Score: 69
Period size: 15 Copynumber: 4.1 Consensus size: 15
28732347 ATCCAAACAA
*
28732357 AATAAAATGATAAAT
1 AATAAAATAATAAAT
28732372 AATAAAATAATAAAT
1 AATAAAATAATAAAT
*
28732387 AATACAATAAAATAAAAT
1 AATA-AA-ATAAT-AAAT
28732405 AATAAAATTAA-AAAT
1 AATAAAA-TAATAAAT
28732420 AA
1 AA
28732422 AAATAAAGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
15 24 0.56
16 3 0.07
17 8 0.19
18 8 0.19
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (15 bp):
AATAAAATAATAAAT
Found at i:28732420 original size:25 final size:26
Alignment explanation
Indices: 28732372--28732428 Score: 75
Period size: 25 Copynumber: 2.2 Consensus size: 26
28732362 AATGATAAAT
28732372 AATAAAATAATAAATAATACAAT-AA
1 AATAAAATAATAAATAATACAATAAA
28732397 AATAAAATAATAAAATTAA-A-AATAAA
1 AATAAAATAAT-AAA-TAATACAATAAA
28732423 AATAAA
1 AATAAA
28732429 GAAAAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
25 14 0.48
26 12 0.41
27 3 0.10
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (26 bp):
AATAAAATAATAAATAATACAATAAA
Found at i:28736902 original size:30 final size:30
Alignment explanation
Indices: 28736861--28736921 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
28736851 AAAAAGGGAA
*
28736861 AGCACGTAATTTGATTTGATCCTCAGTTAC
1 AGCACGCAATTTGATTTGATCCTCAGTTAC
*
28736891 AGCACGCAATTTGATTTGATCTTCAGTTAC
1 AGCACGCAATTTGATTTGATCCTCAGTTAC
28736921 A
1 A
28736922 CCCTGAGGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (30 bp):
AGCACGCAATTTGATTTGATCCTCAGTTAC
Found at i:28743962 original size:17 final size:17
Alignment explanation
Indices: 28743924--28743967 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
28743914 GGGTGAGAAG
28743924 TAAAAGTTTTGGGAAAAA
1 TAAAAGTTTTGGG-AAAA
*
28743942 TAAAAAGTTTTGGG-GAA
1 T-AAAAGTTTTGGGAAAA
28743959 TAAAAGTTT
1 TAAAAGTTT
28743968 GAGAGAAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 8 0.33
17 3 0.12
18 1 0.04
19 12 0.50
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (17 bp):
TAAAAGTTTTGGGAAAA
Found at i:28744350 original size:9 final size:9
Alignment explanation
Indices: 28744333--28744369 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
28744323 TATAATTTGA
*
28744333 TATTAGAAT
1 TATTCGAAT
28744342 TATTCGAAT
1 TATTCGAAT
*
28744351 TATTCGAGT
1 TATTCGAAT
28744360 TATTCGAAT
1 TATTCGAAT
28744369 T
1 T
28744370 TGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:28744961 original size:42 final size:42
Alignment explanation
Indices: 28744883--28745066 Score: 277
Period size: 42 Copynumber: 4.5 Consensus size: 42
28744873 AATATATTTA
* *
28744883 TTTTTTT-AATTTTAAAATATTTTTTACATAC-TTTTTTAAT
1 TTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTAAT
*
28744923 TTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTAAA
1 TTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTAAT
*
28744965 ATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTAA-
1 TTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTAAT
*
28745006 TTTTTTT-AATTTAAAAATATTTTTAAAATACTTTTTTTAAT
1 TTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTAAT
**
28745047 TTTTTAAAAATTTTAAAATA
1 TTTTTTTAAATTTTAAAATA
28745067 AAAATGGGCC
Statistics
Matches: 131, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
40 39 0.30
41 33 0.25
42 59 0.45
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (42 bp):
TTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTAAT
Found at i:28744971 original size:13 final size:14
Alignment explanation
Indices: 28744943--28745045 Score: 67
Period size: 14 Copynumber: 7.5 Consensus size: 14
28744933 TTTTAAAATA
28744943 TTTTTAAAATACTT
1 TTTTTAAAATACTT
**
28744957 TTTTTAAAATTTTT
1 TTTTTAAAATACTT
28744971 TAAATTTTAAAATA---
1 T---TTTTAAAATACTT
28744985 TTTTTAAAATACTT
1 TTTTTAAAATACTT
**
28744999 TTTTT--AATTTTT
1 TTTTTAAAATACTT
*
28745011 TTAATTTAAAA-A-TA
1 TT--TTTAAAATACTT
28745025 TTTTTAAAATACTT
1 TTTTTAAAATACTT
28745039 TTTTTAA
1 TTTTTAA
28745046 TTTTTTAAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 24
0.68 0.08 0.24
Matches are distributed among these distances:
11 10 0.14
12 14 0.20
13 1 0.01
14 33 0.48
16 2 0.03
17 9 0.13
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTTTAAAATACTT
Found at i:28744980 original size:17 final size:18
Alignment explanation
Indices: 28744958--28744992 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
28744948 AAAATACTTT
28744958 TTTTAAAAT-TTTTTAAA
1 TTTTAAAATATTTTTAAA
28744975 TTTTAAAATATTTTTAAA
1 TTTTAAAATATTTTTAAA
28744993 ATACTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTAAAATATTTTTAAA
Found at i:28745001 original size:31 final size:30
Alignment explanation
Indices: 28744944--28745009 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 30
28744934 TTTAAAATAT
*
28744944 TTTTAAAATACTTTTTTTAAAATTTTTTAAA
1 TTTTAAAATAC-TTTTTAAAAATTTTTTAAA
*
28744975 TTTTAAAATA-TTTTTAAAATACTTTTTTTAA
1 TTTTAAAATACTTTTTAAAA-A-TTTTTTAAA
28745006 TTTT
1 TTTT
28745010 TTTAATTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 8 0.26
30 1 0.03
31 22 0.71
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (30 bp):
TTTTAAAATACTTTTTAAAAATTTTTTAAA
Found at i:28745023 original size:82 final size:81
Alignment explanation
Indices: 28744882--28745066 Score: 275
Period size: 82 Copynumber: 2.2 Consensus size: 81
28744872 AAATATATTT
* * * *
28744882 ATTTTTTTAATTTTAAAATATTTTTTACATACTTTTTTAATTTTTTTTAAATTTTAAAATATTTT
1 ATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTAATTTTTTTTAAATTTAAAAATATTTT
28744947 TAAAATACTTTTTTTAAA
66 TAAAATACTTTTTTT--A
28744965 ATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTAA-TTTTTTT-AATTTAAAAATATTT
1 ATTTTTTAAATTTTAAAATATTTTTAAAATAC-TTTTTTAATTTTTTTTAAATTTAAAAATATTT
28745028 TTAAAATACTTTTTTTA
65 TTAAAATACTTTTTTTA
28745045 ATTTTTTAAAAATTTTAAAATA
1 ATTTTTT--AAATTTTAAAATA
28745067 AAAATGGGCC
Statistics
Matches: 95, Mismatches: 4, Indels: 7
0.90 0.04 0.07
Matches are distributed among these distances:
80 8 0.08
82 43 0.45
83 36 0.38
84 8 0.08
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (81 bp):
ATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTAATTTTTTTTAAATTTAAAAATATTTT
TAAAATACTTTTTTTA
Found at i:28745060 original size:32 final size:30
Alignment explanation
Indices: 28745006--28745066 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
28744996 CTTTTTTTAA
28745006 TTTTTTTAATTTAAAAATATTTTTAAAATAC
1 TTTTTTTAATTTAAAAATA-TTTTAAAATAC
*
28745037 TTTTTTTAATTTTTTAAAA-ATTTTAAAATA
1 TTTTTTTAA--TTTAAAAATATTTTAAAATA
28745067 AAAATGGGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 19 0.70
32 1 0.04
33 7 0.26
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (30 bp):
TTTTTTTAATTTAAAAATATTTTAAAATAC
Found at i:28751584 original size:68 final size:68
Alignment explanation
Indices: 28751506--28751639 Score: 173
Period size: 68 Copynumber: 2.0 Consensus size: 68
28751496 TTTTAATAAT
* * ** *
28751506 TTAATATTAAATTTAATTTAA-ATCTTATCTTAAT-AGTATTTTATTAATTTAATATTAAAGTGA
1 TTAATATTAAA-TTAATCTAATAT-TTATCTTAATAAATATTAGATGAATTTAATATTAAAGTGA
28751569 TTATC
64 TTATC
* *
28751574 TTAATGTTAAATTAATCTAATATTTATCTTGATAAATATTAGATGAATTTAATATTAAAGTGATT
1 TTAATATTAAATTAATCTAATATTTATCTTAATAAATATTAGATGAATTTAATATTAAAGTGATT
28751639 A
66 A
28751640 AGTTTAATTA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
67 17 0.30
68 40 0.70
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.49
Consensus pattern (68 bp):
TTAATATTAAATTAATCTAATATTTATCTTAATAAATATTAGATGAATTTAATATTAAAGTGATT
ATC
Found at i:28752576 original size:16 final size:16
Alignment explanation
Indices: 28752555--28752605 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
28752545 TATAATTGTT
28752555 TATAATATTTATATTA
1 TATAATATTTATATTA
*
28752571 TATAATA-TTATAATTG
1 TATAATATTTAT-ATTA
*
28752587 TGAT-ATATATATATTA
1 T-ATAATATTTATATTA
28752603 TAT
1 TAT
28752606 GATCCATAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
15 6 0.21
16 18 0.62
17 5 0.17
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (16 bp):
TATAATATTTATATTA
Found at i:28756992 original size:20 final size:18
Alignment explanation
Indices: 28756945--28756993 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
28756935 CAAGATAAAC
28756945 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
28756962 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
28756982 ATTAAATTAATA
1 ATTAAATTAATA
28756994 AAATATTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:28761349 original size:17 final size:17
Alignment explanation
Indices: 28761320--28761352 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28761310 AGATTTTGAA
28761320 TTTTTGAATTAGATTTC
1 TTTTTGAATTAGATTTC
28761337 TTTTT-AATCTAGATTT
1 TTTTTGAAT-TAGATTT
28761353 GAGTTAGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.24, C:0.06, G:0.09, T:0.61
Consensus pattern (17 bp):
TTTTTGAATTAGATTTC
Found at i:28765960 original size:21 final size:21
Alignment explanation
Indices: 28765895--28765970 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
28765885 ACTATCACAA
28765895 TTTTAAATTC--AAAATAT-T
1 TTTTAAATTCAGAAAATATAT
* * * *
28765913 TTTTAAAATAAGTAAAAAATTAA
1 TTTTAAATTCAG-AAAATA-TAT
28765936 TTTTAAATTCAGAAAATATAT
1 TTTTAAATTCAGAAAATATAT
*
28765957 TTTTAAATTTAGAA
1 TTTTAAATTCAGAA
28765971 TTTAAAAATA
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
18 8 0.18
21 20 0.45
22 6 0.14
23 10 0.23
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (21 bp):
TTTTAAATTCAGAAAATATAT
Found at i:28767628 original size:21 final size:21
Alignment explanation
Indices: 28767579--28767628 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
28767569 CACGTATCTC
28767579 TTTAAAAATTTAATTAATAAAT
1 TTTAAAAATTTAATTAAT-AAT
*
28767601 TTT-AAAATTTACTTAAT-AT
1 TTTAAAAATTTAATTAATAAT
28767620 TTCTAAAAA
1 TT-TAAAAA
28767629 ATATTTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 4 0.16
20 1 0.04
21 17 0.68
22 3 0.12
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (21 bp):
TTTAAAAATTTAATTAATAAT
Found at i:28772410 original size:20 final size:20
Alignment explanation
Indices: 28772385--28772425 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
28772375 AGGAGCGATT
28772385 TGTAAGCTGAACTCAACTTC
1 TGTAAGCTGAACTCAACTTC
28772405 TGTAAGCTGAACTCAACTTC
1 TGTAAGCTGAACTCAACTTC
28772425 T
1 T
28772426 CAATTTAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (20 bp):
TGTAAGCTGAACTCAACTTC
Found at i:28776908 original size:16 final size:17
Alignment explanation
Indices: 28776884--28776916 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
28776874 TGTTACAAAT
28776884 TATAATATA-TATAAAC
1 TATAATATATTATAAAC
*
28776900 TATATTATATTATAAAC
1 TATAATATATTATAAAC
28776917 ATAGAAATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (17 bp):
TATAATATATTATAAAC
Found at i:28777802 original size:2 final size:2
Alignment explanation
Indices: 28777790--28777833 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
28777780 TTTATAGGTC
28777790 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28777831 AT A
1 AT A
28777834 ACTTTAAACT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28778452 original size:28 final size:28
Alignment explanation
Indices: 28778412--28778468 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
28778402 AATTAGTTAG
28778412 TATTTTGAAGAATGTTACTTTTCTTTAA
1 TATTTTGAAGAATGTTACTTTTCTTTAA
*
28778440 TATTTTGAAGAATGTTATTTTTCTTTAA
1 TATTTTGAAGAATGTTACTTTTCTTTAA
28778468 T
1 T
28778469 TACCTAAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.28, C:0.05, G:0.11, T:0.56
Consensus pattern (28 bp):
TATTTTGAAGAATGTTACTTTTCTTTAA
Found at i:28778981 original size:21 final size:22
Alignment explanation
Indices: 28778944--28778984 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
28778934 GACAATGTGA
28778944 GATTAAAATTAATTTTTTAAGG
1 GATTAAAATTAATTTTTTAAGG
28778966 GATTAAAATT-ATTTTTTAA
1 GATTAAAATTAATTTTTTAA
28778985 TTAAACCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (22 bp):
GATTAAAATTAATTTTTTAAGG
Found at i:28779182 original size:22 final size:22
Alignment explanation
Indices: 28779103--28779174 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
28779093 ATTGTTCAAA
* **
28779103 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
28779125 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
28779147 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
28779169 CATGAG
1 CATGAG
28779175 TCTCTAGTCC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:28779510 original size:69 final size:69
Alignment explanation
Indices: 28779399--28779572 Score: 226
Period size: 69 Copynumber: 2.5 Consensus size: 69
28779389 CTTTTTAAGG
* * * * ** * **
28779399 GATTAAAATTAA-TTTTTAATGAAAATATTGATCGAAGTGAGCTATGTGAGTATTCTCTAGTGAA
1 GATTAAAATTAACTTTTTAATAAAAATAGTGA-AGAAGCGAGCTATAAGAATATTCTCTAGCCAA
*
28779463 TGTGA
65 TATGA
28779468 GATTAAAATTAACTTTGTT-ATAAAAATAGTGAAGAAGCGAGCTATAAGAATATTCTCTAGCCAA
1 GATTAAAATTAACTTT-TTAATAAAAATAGTGAAGAAGCGAGCTATAAGAATATTCTCTAGCCAA
28779532 TATGA
65 TATGA
28779537 GATTAAAATTAACTTTTTAATAAAAATAGTGAAGAA
1 GATTAAAATTAACTTTTTAATAAAAATAGTGAAGAA
28779573 ATTAACACTT
Statistics
Matches: 92, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
68 2 0.02
69 74 0.80
70 14 0.15
71 2 0.02
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.34
Consensus pattern (69 bp):
GATTAAAATTAACTTTTTAATAAAAATAGTGAAGAAGCGAGCTATAAGAATATTCTCTAGCCAAT
ATGA
Found at i:28781943 original size:69 final size:69
Alignment explanation
Indices: 28781819--28781987 Score: 225
Period size: 69 Copynumber: 2.5 Consensus size: 69
28781809 TTTTTAAAAG
* * * * * *
28781819 ATTAAAATTAA-TGTTTAATGAAAATAGTGAAGAAGTGAGTTATAGGAGTCTTCTCTAGTCAATG
1 ATTAAAATTAACTTTTTAATGAAAATAGTGAAGAACTAAGCTATAGAAGTATTCTCTAGTCAATG
28781883 TGGA
66 TGGA
*
28781887 ATTAAATTTAACTTTTTAATGAAAATAGTGAAGAACTAAGCTAT-GAAAGTATTCTCTAGTCAAT
1 ATTAAAATTAACTTTTTAATGAAAATAGTGAAGAACTAAGCTATAG-AAGTATTCTCTAGTCAAT
*
28781951 GTGGG
65 GTGGA
* *
28781956 ATTAAAATAAACTTTTTAATAAAAATAGTGAA
1 ATTAAAATTAACTTTTTAATGAAAATAGTGAA
28781988 AAATTGTCAC
Statistics
Matches: 88, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
68 11 0.12
69 77 0.88
ACGTcount: A:0.42, C:0.07, G:0.17, T:0.34
Consensus pattern (69 bp):
ATTAAAATTAACTTTTTAATGAAAATAGTGAAGAACTAAGCTATAGAAGTATTCTCTAGTCAATG
TGGA
Found at i:28782067 original size:161 final size:165
Alignment explanation
Indices: 28781864--28782233 Score: 445
Period size: 165 Copynumber: 2.3 Consensus size: 165
28781854 TGAGTTATAG
*
28781864 GAGTCTTCTCTAGTCAATGTGGAATTA-AATTTAACTTTTTAATGAAAA-TAGTGAAGAAC-TAA
1 GAGTGTTCTCTAGTCAATGT-GAATTAGAA-TTAACTTTTTAATGAAAATTA-TGAAG-ACGTAA
*
28781926 GCTATGA-AAGTATTCTCTAGTC-A-A-TGTGGGATTAAAATAAACTTTTTAATAAAAATAGTGA
62 GCTATGAGAA-TATTCTCTAGTCAATATTGTGGGATTAAAATAAACATTTTAATAAAAATAGTGA
* *
28781987 A-AAATTGTCACTTATTTATAAGAAAAATGTGAGATATTA
126 AGAAATTGTCACTTATTTATAAGAAAAATGTGAAATATGA
* * **
28782026 GAGTGTTCTCTAGTCAATAT-AGATTAGAATTAACTTTTTAATGAAAATTATGAAGACGTGATTT
1 GAGTGTTCTCTAGTCAATGTGA-ATTAGAATTAACTTTTTAATGAAAATTATGAAGACGTAAGCT
* * * *
28782090 ATGAGAATATTCTCTAGTCAATATTGTGGGATTAAAATTATCATTTTCATGAAAATAGTGAAGAA
65 ATGAGAATATTCTCTAGTCAATATTGTGGGATTAAAATAAACATTTTAATAAAAATAGTGAAGAA
** *
28782155 ATTGTCACTTATTTATAAGTTAAATGTTAAATATGA
130 ATTGTCACTTATTTATAAGAAAAATGTGAAATATGA
* *
28782191 GAGTGTTCTGTAATCAATGTGTAATT-GAAATTAACTTTTTAAT
1 GAGTGTTCTCTAGTCAATGTG-AATTAG-AATTAACTTTTTAAT
28782234 TTCTTAAATT
Statistics
Matches: 178, Mismatches: 18, Indels: 20
0.82 0.08 0.09
Matches are distributed among these distances:
160 3 0.02
161 46 0.26
162 25 0.14
163 1 0.01
164 33 0.19
165 51 0.29
166 18 0.10
167 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.38
Consensus pattern (165 bp):
GAGTGTTCTCTAGTCAATGTGAATTAGAATTAACTTTTTAATGAAAATTATGAAGACGTAAGCTA
TGAGAATATTCTCTAGTCAATATTGTGGGATTAAAATAAACATTTTAATAAAAATAGTGAAGAAA
TTGTCACTTATTTATAAGAAAAATGTGAAATATGA
Found at i:28783838 original size:12 final size:12
Alignment explanation
Indices: 28783821--28783879 Score: 55
Period size: 12 Copynumber: 4.9 Consensus size: 12
28783811 TGGTGCTGGT
28783821 GGTGGAGTTGGA
1 GGTGGAGTTGGA
*
28783833 GGTGGAGTCGGA
1 GGTGGAGTTGGA
** *
28783845 GGTGCTGTTGGC
1 GGTGGAGTTGGA
* *
28783857 GGTGGAGCTGGT
1 GGTGGAGTTGGA
*
28783869 GGTGGTGTTGG
1 GGTGGAGTTGG
28783880 CACTGGTGTC
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.08, C:0.07, G:0.58, T:0.27
Consensus pattern (12 bp):
GGTGGAGTTGGA
Found at i:28783872 original size:24 final size:24
Alignment explanation
Indices: 28783806--28783880 Score: 80
Period size: 24 Copynumber: 3.1 Consensus size: 24
28783796 CTTGGGTGGC
* * *
28783806 GGCGCTGGTGCTGGTGGTGGAGTT
1 GGCGGTGGAGCTGGTGGTGGTGTT
* * *
28783830 GGAGGTGGAG-TCGGAGGTGCTGTT
1 GGCGGTGGAGCT-GGTGGTGGTGTT
28783854 GGCGGTGGAGCTGGTGGTGGTGTT
1 GGCGGTGGAGCTGGTGGTGGTGTT
28783878 GGC
1 GGC
28783881 ACTGGTGTCC
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
23 1 0.03
24 38 0.95
25 1 0.03
ACGTcount: A:0.07, C:0.11, G:0.56, T:0.27
Consensus pattern (24 bp):
GGCGGTGGAGCTGGTGGTGGTGTT
Found at i:28784585 original size:3 final size:3
Alignment explanation
Indices: 28784577--28784621 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
28784567 AGCAAATAAC
28784577 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28784622 ATACGTGCAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:28790980 original size:22 final size:22
Alignment explanation
Indices: 28790937--28790980 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
28790927 GGCAACACAC
*
28790937 TTATGACAATGTCATTGAACGA
1 TTATGACAATGTCATCGAACGA
*
28790959 TTATGACAATGTCATCGGACGA
1 TTATGACAATGTCATCGAACGA
28790981 GCACTGATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (22 bp):
TTATGACAATGTCATCGAACGA
Found at i:28806427 original size:22 final size:25
Alignment explanation
Indices: 28806399--28806444 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
28806389 TAACCAAATA
28806399 AATCATTT-CAT-A-AATAAATCAC
1 AATCATTTCCATGATAATAAATCAC
28806421 AATCATTTCCATGATAATAAATCA
1 AATCATTTCCATGATAATAAATCA
28806445 TAAGTGGACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.38
23 3 0.14
24 1 0.05
25 9 0.43
ACGTcount: A:0.48, C:0.17, G:0.02, T:0.33
Consensus pattern (25 bp):
AATCATTTCCATGATAATAAATCAC
Found at i:28809853 original size:16 final size:16
Alignment explanation
Indices: 28809832--28809864 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
28809822 TTCTTGAATA
28809832 TTCTATGACGACCCAC
1 TTCTATGACGACCCAC
28809848 TTCTATGACGACCCAC
1 TTCTATGACGACCCAC
28809864 T
1 T
28809865 CCTACATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.36, G:0.12, T:0.27
Consensus pattern (16 bp):
TTCTATGACGACCCAC
Found at i:28821249 original size:12 final size:12
Alignment explanation
Indices: 28821240--28821283 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
28821230 GATTAAATTA
28821240 AAAATAAAATAT
1 AAAATAAAATAT
**
28821252 AAAATAAAGGACT
1 AAAATAAAATA-T
28821265 AAAATAAAA-AT
1 AAAATAAAATAT
28821276 AAAATAAA
1 AAAATAAA
28821284 TTCAAGTGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
11 9 0.32
12 10 0.36
13 9 0.32
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (12 bp):
AAAATAAAATAT
Found at i:28821262 original size:31 final size:31
Alignment explanation
Indices: 28821220--28821281 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
28821210 TGAAGAATCC
* * *
28821220 TAAAATGAAGGATTAAATTAAAAATAAAATA
1 TAAAATAAAGGACTAAAATAAAAATAAAATA
28821251 TAAAATAAAGGACTAAAATAAAAATAAAATA
1 TAAAATAAAGGACTAAAATAAAAATAAAATA
28821282 AATTCAAGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.23
Consensus pattern (31 bp):
TAAAATAAAGGACTAAAATAAAAATAAAATA
Found at i:28822586 original size:44 final size:44
Alignment explanation
Indices: 28822520--28822868 Score: 281
Period size: 44 Copynumber: 7.9 Consensus size: 44
28822510 GAAGTGTTAT
** ** *
28822520 TTCAATCTACTCCACCACAACTTCAGAAAGATAAGAATTGTAGC
1 TTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
* *
28822564 TTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGT-GAC
1 TTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAG-C
* * * * * * * *
28822608 TTGTAGT-T-TTACCACTGTAACTTCAAGGAAATAAGATTCGCTATC
1 TT-CAATCTACT-CCACTGCAACTTCAGGGAGATAAGATTTG-TAGC
* * *
28822653 TTCAATCTACTCCACTGCAACTTCAGGAAGATAAGATTCGTTATC
1 TTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGC
* ** *
28822698 TTCAATCTGCTATACTGCAACTTCAGGGAGATAAGATTTGTGGC
1 TTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
* * * ** * *
28822742 TTTAATTTACTCCACTGAAACTTCAATGAGATGAGATTTGTAAC
1 TTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
* * * * * * *
28822786 TTTAATTTGCTCCACTGCAACTTTAGTGAGATGAGATTTATAGC
1 TTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
* * *
28822830 TTTAATCTACTCTACTGCAACTTCAGAGAGATAAGATTT
1 TTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTT
28822869 ATACCTTTAA
Statistics
Matches: 246, Mismatches: 52, Indels: 14
0.79 0.17 0.04
Matches are distributed among these distances:
43 2 0.01
44 172 0.70
45 71 0.29
46 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.33
Consensus pattern (44 bp):
TTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
Found at i:28830978 original size:19 final size:20
Alignment explanation
Indices: 28830943--28830992 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
28830933 TCTTTTTGTG
*
28830943 AAATTTAATGCATATG-ATC
1 AAATGTAATGCATATGAATC
*
28830962 AAATGTAATGC-TGATGAATG
1 AAATGTAATGCAT-ATGAATC
28830982 AAATG-AATGCA
1 AAATGTAATGCA
28830993 AAAAGAGGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 1 0.04
19 18 0.69
20 7 0.27
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.30
Consensus pattern (20 bp):
AAATGTAATGCATATGAATC
Found at i:28834758 original size:12 final size:12
Alignment explanation
Indices: 28834735--28834771 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
28834725 ACGAAATAGT
*
28834735 AAAACTAAAATA
1 AAAAATAAAATA
*
28834747 AAAAATATAATA
1 AAAAATAAAATA
28834759 AAAAATAAAATA
1 AAAAATAAAATA
28834771 A
1 A
28834772 TTATAACAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (12 bp):
AAAAATAAAATA
Found at i:28836225 original size:23 final size:25
Alignment explanation
Indices: 28836198--28836248 Score: 63
Period size: 23 Copynumber: 2.1 Consensus size: 25
28836188 TTTGCTACTA
28836198 TTTCTG-CTGCTATTCTTT-T-CTTT
1 TTTCTGTCTGCT-TTCTTTGTCCTTT
*
28836221 TTTCTGTCTTCTTTCTTTGTCCTTT
1 TTTCTGTCTGCTTTCTTTGTCCTTT
28836246 TTT
1 TTT
28836249 GCAAGCATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 12 0.50
24 5 0.21
25 7 0.29
ACGTcount: A:0.02, C:0.22, G:0.08, T:0.69
Consensus pattern (25 bp):
TTTCTGTCTGCTTTCTTTGTCCTTT
Found at i:28839569 original size:17 final size:17
Alignment explanation
Indices: 28839543--28839575 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
28839533 TATTTTTAAT
28839543 AAAAATTAT-AATTTTA
1 AAAAATTATAAATTTTA
28839559 AAAAATATATAAATTTT
1 AAAAAT-TATAAATTTT
28839576 TCTTATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 3 0.20
18 6 0.40
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAAAATTATAAATTTTA
Found at i:28849246 original size:25 final size:25
Alignment explanation
Indices: 28849212--28849264 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
28849202 TTGAACCGAG
*
28849212 TTGGGTGATCGATGGGTTTTGGGTC
1 TTGGGTGATCGACGGGTTTTGGGTC
28849237 TTGGGTGATCGACGGGTTTTGGGTC
1 TTGGGTGATCGACGGGTTTTGGGTC
28849262 TTG
1 TTG
28849265 AGTTGGTGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.08, C:0.09, G:0.43, T:0.40
Consensus pattern (25 bp):
TTGGGTGATCGACGGGTTTTGGGTC
Found at i:28850243 original size:18 final size:18
Alignment explanation
Indices: 28850216--28850250 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28850206 CTTTCCTCTT
* *
28850216 CTTTCCTTTTCTTTTTTA
1 CTTTCATTTTATTTTTTA
28850234 CTTTCATTTTATTTTTT
1 CTTTCATTTTATTTTTT
28850251 TTTCTCAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (18 bp):
CTTTCATTTTATTTTTTA
Found at i:28850985 original size:63 final size:63
Alignment explanation
Indices: 28850904--28851022 Score: 166
Period size: 63 Copynumber: 1.9 Consensus size: 63
28850894 TTAGATGTAG
* *
28850904 GAGTCACACGGGTGAGACACACAAGCGTGTGTCCAGGCCGTGTAACTCACTAAGTTCGTATTA
1 GAGTCACACGAGTAAGACACACAAGCGTGTGTCCAGGCCGTGTAACTCACTAAGTTCGTATTA
* * ** * *
28850967 GAGTCACACGAGTAAGACATACAGGCGTGTGTCCAGGTTGTGTGACTCACTTAGTT
1 GAGTCACACGAGTAAGACACACAAGCGTGTGTCCAGGCCGTGTAACTCACTAAGTT
28851023 TATATGAGCT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 48 1.00
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (63 bp):
GAGTCACACGAGTAAGACACACAAGCGTGTGTCCAGGCCGTGTAACTCACTAAGTTCGTATTA
Found at i:28855301 original size:19 final size:19
Alignment explanation
Indices: 28855277--28855313 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
28855267 CATAATAATA
28855277 AAAATTTT-ATATATAAATG
1 AAAATTTTAATAT-TAAATG
28855296 AAAATTTTAATATTAAAT
1 AAAATTTTAATATTAAAT
28855314 ATTATTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (19 bp):
AAAATTTTAATATTAAATG
Found at i:28859626 original size:31 final size:31
Alignment explanation
Indices: 28859591--28859649 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
28859581 TATGTGAGTT
28859591 AATTAAGTTATTCGGATTAACTCGAATAAAA
1 AATTAAGTTATTCGGATTAACTCGAATAAAA
* * *
28859622 AATTAAGTTTTTGGGTTTAACTCGAATA
1 AATTAAGTTATTCGGATTAACTCGAATA
28859650 TGAATTACAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.37
Consensus pattern (31 bp):
AATTAAGTTATTCGGATTAACTCGAATAAAA
Found at i:28877959 original size:50 final size:51
Alignment explanation
Indices: 28877905--28878059 Score: 140
Period size: 50 Copynumber: 3.1 Consensus size: 51
28877895 TGAATCTTAC
*
28877905 TCCCCTGGCAGTGTAATGGAAAAGA-TGAAGCTACGACGGCGAATCGTGTT
1 TCCCCTGGCAGTGTAATGGAAAAGATTGAAGCTACGACGGCGAATCTTGTT
** * ** **
28877955 TCCCC-AACATTGTAATTTAAAAGATTGAAGC--CGTAACGGCGAATCTTACT
1 TCCCCTGGCAGTGTAATGGAAAAGATTGAAGCTACG--ACGGCGAATCTTGTT
* * ** *
28878005 T-CCCTGGCAGTGCAGTGGATCAGATTGAAGCTACGACGACGAATCTTGTT
1 TCCCCTGGCAGTGTAATGGAAAAGATTGAAGCTACGACGGCGAATCTTGTT
28878055 TCCCC
1 TCCCC
28878060 GACATTGCAG
Statistics
Matches: 78, Mismatches: 20, Indels: 13
0.70 0.18 0.12
Matches are distributed among these distances:
48 2 0.03
49 17 0.22
50 54 0.69
51 3 0.04
52 2 0.03
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (51 bp):
TCCCCTGGCAGTGTAATGGAAAAGATTGAAGCTACGACGGCGAATCTTGTT
Found at i:28878069 original size:50 final size:50
Alignment explanation
Indices: 28877930--28878084 Score: 145
Period size: 50 Copynumber: 3.1 Consensus size: 50
28877920 ATGGAAAAGA
* * * *
28877930 TGAAGCTACGACGGCGAATCGTGTTTCCCCAACATTGTAATTTAAA-AGAT
1 TGAAGCTACGACGGCGAATCTTGTTTCCCCGACATTG-CAGTTAAACAGAT
** * * * ** *
28877980 TGAAGC--CGTAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGATCAGAT
1 TGAAGCTACG--ACGGCGAATCTTGTTTCCCCGACATTGCAGTTAAACAGAT
*
28878030 TGAAGCTACGACGACGAATCTTGTTTCCCCGACATTGCAGTTAAACAGAT
1 TGAAGCTACGACGGCGAATCTTGTTTCCCCGACATTGCAGTTAAACAGAT
28878080 TGAAG
1 TGAAG
28878085 ATGGCAAATC
Statistics
Matches: 79, Mismatches: 21, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
48 2 0.03
49 3 0.04
50 72 0.91
52 2 0.03
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (50 bp):
TGAAGCTACGACGGCGAATCTTGTTTCCCCGACATTGCAGTTAAACAGAT
Found at i:28878080 original size:100 final size:100
Alignment explanation
Indices: 28877876--28878084 Score: 278
Period size: 99 Copynumber: 2.1 Consensus size: 100
28877866 TACGGTGTAG
* * *
28877876 CAGATTAAAGCCGCAACGGTGAATCTTACTCCCCTGGCAGTGTAATGGAAAAGATGAAGCTACGA
1 CAGATTGAAGCCGCAACGGCGAATCTTACTCCCCTGGCAGTGCAATGGAAAAGATGAAGCTACGA
* *
28877941 CGGCGAATCGTGTTTCCCCAACATTGTAATTTAAA
66 CGACGAATCGTGTTTCCCCAACATTGTAAGTTAAA
* * * **
28877976 -AGATTGAAGCCGTAACGGCGAATCTTACTTCCCTGGCAGTGCAGTGGATCAGATTGAAGCTACG
1 CAGATTGAAGCCGCAACGGCGAATCTTACTCCCCTGGCAGTGCAATGGAAAAGA-TGAAGCTACG
* * *
28878040 ACGACGAATCTTGTTTCCCCGACATTG-CAGTTAAA
65 ACGACGAATCGTGTTTCCCCAACATTGTAAGTTAAA
28878075 CAGATTGAAG
1 CAGATTGAAG
28878085 ATGGCAAATC
Statistics
Matches: 94, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
99 51 0.54
100 43 0.46
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.24
Consensus pattern (100 bp):
CAGATTGAAGCCGCAACGGCGAATCTTACTCCCCTGGCAGTGCAATGGAAAAGATGAAGCTACGA
CGACGAATCGTGTTTCCCCAACATTGTAAGTTAAA
Found at i:28878188 original size:44 final size:44
Alignment explanation
Indices: 28878092--28878346 Score: 179
Period size: 44 Copynumber: 5.9 Consensus size: 44
28878082 AAGATGGCAA
* * ** *
28878092 ATCTTATCTCCCTGAAGTTGCAGAGCAGCAGATTAAAGCCTATA-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATC-ACAG
28878136 AT-TCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAG
1 ATCT-TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAG
* * * * * * *
28878180 ATCTTATCTCTCTGAAGTTCCAG-AGAGGAGA-TCATATC-TAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAG
* * * *
28878221 -TCGTATCTCCCTGAAGTTGCAGTGGAACAGACTAAGTAAGCA-AG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AATCACAG
* * * * **
28878265 -TCTTATC-CTCCTGAAGTTACAGTGGGGCAAACTAAAGATGGC-G
1 ATCTTATCTC-CCTGAAGTTGCAGTGGAGCAGATTAAA-ATCACAG
28878308 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAA
1 -ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAA
28878347 CCTATACTTG
Statistics
Matches: 164, Mismatches: 33, Indels: 28
0.73 0.15 0.12
Matches are distributed among these distances:
40 19 0.12
41 7 0.04
42 8 0.05
43 12 0.07
44 86 0.52
45 31 0.19
46 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAG
Found at i:28880058 original size:21 final size:22
Alignment explanation
Indices: 28880034--28880075 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
28880024 AATTTATATA
28880034 TATGT-ATATTTATTGTTTTCT
1 TATGTAATATTTATTGTTTTCT
28880055 TATGTACATATTTATTGTTTT
1 TATGTA-ATATTTATTGTTTT
28880076 TTCAACTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 5 0.26
23 14 0.74
ACGTcount: A:0.21, C:0.05, G:0.10, T:0.64
Consensus pattern (22 bp):
TATGTAATATTTATTGTTTTCT
Found at i:28882982 original size:21 final size:18
Alignment explanation
Indices: 28882931--28882987 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 18
28882921 CTCGATTTTT
28882931 CAAAGGGTATTGATACTTC
1 CAAA-GGTATTGATACTTC
**
28882950 CAAAAATATTGATACTTGGC
1 CAAAGGTATTGATACTT--C
28882970 CAAATGGTATTGATACTT
1 CAAA-GGTATTGATACTT
28882988 TTTGGCTTGG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
18 11 0.35
19 4 0.13
20 5 0.16
21 11 0.35
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (18 bp):
CAAAGGTATTGATACTTC
Found at i:28883053 original size:20 final size:20
Alignment explanation
Indices: 28883022--28883079 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
28883012 GTTTGATGTG
28883022 TTAAAATGATTTTAACTTGA
1 TTAAAATGATTTTAACTTGA
* * * *
28883042 TTGAAATCATTTTGACTTGG
1 TTAAAATGATTTTAACTTGA
*
28883062 TTAAAATGATTTTCACTT
1 TTAAAATGATTTTAACTT
28883080 AATTTTCAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.47
Consensus pattern (20 bp):
TTAAAATGATTTTAACTTGA
Found at i:28887940 original size:17 final size:17
Alignment explanation
Indices: 28887918--28887981 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
28887908 AATCTTAGAG
28887918 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
* *
28887935 TTCTAATTGTGT-CTTAGAG
1 TTCTAATTGTATAC--AG-C
*
28887954 TTCTAATTGTATACAAC
1 TTCTAATTGTATACAGC
*
28887971 TTTTAATTGTA
1 TTCTAATTGTA
28887982 GCCCTTGATG
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
16 1 0.03
17 21 0.57
18 3 0.08
19 11 0.30
20 1 0.03
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (17 bp):
TTCTAATTGTATACAGC
Found at i:28887957 original size:36 final size:36
Alignment explanation
Indices: 28887910--28887980 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
28887900 GATTATAAAA
*
28887910 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
1 TCTTAGAGTTCTAATTGTATACAACTTCTAATTGTG
*
28887946 TCTTAGAGTTCTAATTGTATACAACTTTTAATTGT
1 TCTTAGAGTTCTAATTGTATACAACTTCTAATTGT
28887981 AGCCCTTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.46
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAACTTCTAATTGTG
Found at i:28887959 original size:19 final size:19
Alignment explanation
Indices: 28887909--28887965 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
28887899 TGATTATAAA
28887909 ATCTTAGAGTTCTAATTGT
1 ATCTTAGAGTTCTAATTGT
*
28887928 ATAC--AG-CTTCTAATTGT
1 AT-CTTAGAGTTCTAATTGT
*
28887945 GTCTTAGAGTTCTAATTGT
1 ATCTTAGAGTTCTAATTGT
28887964 AT
1 AT
28887966 ACAACTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
16 1 0.03
17 11 0.37
18 4 0.13
19 13 0.43
20 1 0.03
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.46
Consensus pattern (19 bp):
ATCTTAGAGTTCTAATTGT
Found at i:28905220 original size:8 final size:8
Alignment explanation
Indices: 28905207--28905232 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
28905197 CGACGTTACC
28905207 TTTCTTCT
1 TTTCTTCT
28905215 TTTCTTCT
1 TTTCTTCT
28905223 TTTCTTCT
1 TTTCTTCT
28905231 TT
1 TT
28905233 CTTTTCTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTCTTCT
Found at i:28905242 original size:16 final size:15
Alignment explanation
Indices: 28905206--28905244 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
28905196 CCGACGTTAC
28905206 CTTTCTTCTTTTCTT
1 CTTTCTTCTTTTCTT
*
28905221 CTTTTCTTCTTTCTTTT
1 C-TTTCTTCTTT-TCTT
28905238 CTTTCTT
1 CTTTCTT
28905245 TCTATTTGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 16 0.76
17 4 0.19
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (15 bp):
CTTTCTTCTTTTCTT
Found at i:28905282 original size:3 final size:3
Alignment explanation
Indices: 28905262--28905314 Score: 88
Period size: 3 Copynumber: 17.7 Consensus size: 3
28905252 GCATGCAATA
* *
28905262 TAT TAT AAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28905310 TAT TA
1 TAT TA
28905315 CATGCAATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:28916151 original size:29 final size:29
Alignment explanation
Indices: 28916113--28916181 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 29
28916103 GTTCTGTAGC
* * *
28916113 CAGTCAAAATTGTTGAGAGTTCGCAGCCA
1 CAGTCGAAATTGCTAAGAGTTCGCAGCCA
* *
28916142 TAGTCGAAATTGCTAAGAGTTCGTAGCCA
1 CAGTCGAAATTGCTAAGAGTTCGCAGCCA
28916171 CAGTCGAAATT
1 CAGTCGAAATT
28916182 AACTTCCACT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (29 bp):
CAGTCGAAATTGCTAAGAGTTCGCAGCCA
Found at i:28926179 original size:132 final size:131
Alignment explanation
Indices: 28926017--28927296 Score: 1738
Period size: 132 Copynumber: 9.7 Consensus size: 131
28926007 CCATACTATC
* * * * * * * *
28926017 TTGGGAAGATAAGATGCACCATCTTTGATCTGTTCAACTACTGCTTAGGGAGACAAAATTTGCAA
1 TTGGGAAGATAAGATTCA-CAACTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
* * * * * * *
28926082 TCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGGCTAATGGTTTATATCTGCTTCTCCACTA
65 TCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
28926147 TA
130 TA
* * * * *
28926149 TTGGGAATATAAGATTTACAACATTCGATCTGCTGCACTACTACTTAGGGGGACAGAATCTGCAA
1 TTGGGAAGATAAGATTCACAAC-TTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
* **
28926214 TCTTCAACCTACTCCACCACTGCTTAGGGTGATAAAACTAATGGCTTAAATCTGCTTCTCCACTG
65 TCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
28926279 TA
130 TA
* * *
28926281 TTGGGAAGATAAGATTCACCATCTTCGATTTGCTCCACTACTGTTTAGGGTGACAGAATCTGCAA
1 TTGGGAAGATAAGATTCA-CAACTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
28926346 TCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
65 TCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
28926411 TA
130 TA
* * *
28926413 TTGGGAAGATAAGATTCACCACCTTCGATCTG-TATCACTACTGGTTAGGGTGACAGAATCTGCA
1 TTGGGAAGATAAGATTCA-CAACTTCGATCTGCT-CCACTACTGCTTAGGGTGACAGAATCTGCA
*
28926477 ATCTTCAACCGACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACT
64 ATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACT
28926542 GTA
129 GTA
* * *
28926545 TTGGGAAGATAAGATTCATCATA-TTCGATCTACTCCACTACTGTTTAGGGTGACAAAATCTGCA
1 TTGGGAAGATAAGATTCA-CA-ACTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
* * * *
28926609 ATC-TCTAACCTACTCCACTACGGCTTAGGGAGATAGGACTAATAGCTTAAATCTACTTCTCCAC
64 ATCTTC-AACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCAC
28926673 TGTA
128 TGTA
* ** * *
28926677 TTGGGAAGATAAGATTCACAATCTTCTATCTATTCCACTACTGCTTAGGGTGACAGAATCTCCAT
1 TTGGGAAGATAAGATTCACAA-CTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
* ** * * * *
28926742 TCTTCAACCTACTCCACTACTGCTCAAAGAGATTGGACTAATGGCTTAAATATGCTTCTCCACTA
65 TCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
*
28926807 TC
130 TA
* * ** * **
28926809 TTGAGAAAATAAGATTCACCATTTTCGTTCCACTCCACTACTGCTTAGGGTGACAGAATCTGCAA
1 TTGGGAAGATAAGATTCA-CAACTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
* * * * *
28926874 TCTTCGACCTACTCCACTTCTACTTAGGGTGATAGAACTAAAGGCTTAAATCTGCTTCTCCACTG
65 TCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
28926939 TA
130 TA
* * *
28926941 TTTGGAAGATAAGATTCACAATCTTTGATCTGCTCCACTACTACTTAGGGTGACAGAATCTGCAA
1 TTGGGAAGATAAGATTCACAA-CTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
*
28927006 TCTTCAACCTACTCCACCACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
65 TCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
28927071 TA
130 TA
* * *
28927073 TTGGGAAGATAAGATTCACAGTCTTCGATCTGCTCCACTACTGCATAGGGTGACAGAATCTGTAA
1 TTGGGAAGATAAGATTCACA-ACTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
*
28927138 TCTTCAACCTACTCCACTACTGCTTAGGGTGATATGACTAATGGCTTAAATCTGCTTCTCCACTG
65 TCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
28927203 TA
130 TA
* ** *
28927205 TTGAGAAGATAAGATTCACCATTTTCGTTCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
1 TTGGGAAGATAAGATTCA-CAACTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
* *
28927270 TCTTCGACCTATTCCACTACTGCTTAG
65 TCTTCAACCTACTCCACTACTGCTTAG
28927297 NNNNNNNNNN
Statistics
Matches: 1016, Mismatches: 119, Indels: 26
0.88 0.10 0.02
Matches are distributed among these distances:
130 1 0.00
131 10 0.01
132 995 0.98
133 10 0.01
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.31
Consensus pattern (131 bp):
TTGGGAAGATAAGATTCACAACTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAAT
CTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGT
A
Found at i:28927634 original size:132 final size:132
Alignment explanation
Indices: 28927397--28928903 Score: 2153
Period size: 132 Copynumber: 11.4 Consensus size: 132
28927387 NNNNNNNNNN
* *
28927397 CTGCTTCTCTACTGTATCT-GGAAGATAAGATTCACAATCTTCGATCTGCTCCACTACTGCTTAG
1 CTGCTTCTCCACTGTAT-TGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAG
* *
28927461 GGTGACAGAATCTACAATCTTCAAACC-ACTCCACCACTGCTTAGGGTGATAGGACTAATGGCTT
65 GGTGACAGAATCTGCAATCTTC-AACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTT
28927525 AAAT
129 AAAT
* ** * *
28927529 CTGCTTCTCCACTGTAATGGGAAGATAAGATTCATAATCTTCGATCTGCTCCACTACAGCATAGG
1 CTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGG
* * * *
28927594 GTGACAGAATCTGCAATCTTCAACCTACTCCGCAACTGCTTAGGGTGATAGGACTACTAGCTTAA
66 GTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAA
28927659 AT
131 AT
* * *
28927661 CTTCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTG-TATCACTACTGGTTAG
1 CTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCT-CCACTACTGCTTAG
* * * *
28927725 GATGACAGAATCTGCAATCTTCAACCGACTCCACTACTGCTTAGGATGATAGGACTAATGACTTA
65 GGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTA
28927790 AAT
130 AAT
** * *
28927793 CTGCTTCTCCACTGTATTGGGAAGATAAGATTCATAATCTTCGATCTGCTGCACTACTGCATAGG
1 CTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGG
* *
28927858 GTGACAGAATCTGCAATCTTCAACCTACTCCACAACTGCTTAGGGTGATAGGGCTAATGGCTTAA
66 GTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAA
28927923 AT
131 AT
* *
28927925 TTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACGACTGCTTAGG
1 CTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGG
* *
28927990 GTGACAGAATCTGCAATCTTCAACCTACTCCAGTACTGCTTAGGGTGATAGGACTAATGGCTGAA
66 GTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAA
28928055 AT
131 AT
* * * * * * **
28928057 TTGGTTCTCCATTGTATTGGGAAGATAAGATTCATCATATTCGATCTGCTCCACTACTGTTTAAT
1 CTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGG
* * * *
28928122 GTGACAGAATCTGTAATC-TCAACCTACTCCACTACTGCTTAGAGAGATAGGTCTAATGGCTTAA
66 GTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAA
28928186 AT
131 AT
* * * * * * *
28928188 CTGCTTCTCTACTGTACTAGGAAGATAGGATTCACCACCTTCGATCTACTCCACTACTGCTTATG
1 CTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGG
* * * ** * * * *
28928253 GTGACAGAATCTACAATCTTCAACATAATCCACTACTGCTTAGGAAGATTGGATTAAAGGCTTAC
66 GTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAA
28928318 AT
131 AT
* * ** * * * * * *
28928320 CTG-TTCTCCACTATCTTAAGAAGATATGATTCACCGTATTTGATCCGCTGCACTACTGCTTAGG
1 CTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGG
*
28928384 GTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGACTTAA
66 GTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAA
28928449 AT
131 AT
* * *
28928451 CTGCTTCTCCACTGTATTGGGAATATAAGATTCACCATCTTCGATCTGCTCCTCTGCTGCTTAGG
1 CTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGG
* * * *
28928516 GTGACAGAATCTCCAATCTTCAACCTACTCCACTACAGCTTAGGGAGATTGGACTAATGGCTTAA
66 GTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAA
28928581 AT
131 AT
* * *
28928583 CTGCTTCTCTACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTACAT-CACTACTGGTTAG
1 CTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGC-TCCACTACTGCTTAG
* * * *
28928647 GGTGACAGTATCGGCAATCTACAACCGACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTA
65 GGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTA
28928712 AAT
130 AAT
*
28928715 TTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGG
1 CTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGG
*
28928780 GTGACAGAATCTGCAATCTTCAACCTACTCCACCACTGCTTAGGGTGATAGGACTAATGGCTTAA
66 GTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAA
28928845 AT
131 AT
* *
28928847 CTACTTCTCCACTGTATTGGGAAGATAAGATTCACAATCTTCGATCTGCTCCACTAC
1 CTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTAC
28928904 NNNNNNNNNN
Statistics
Matches: 1212, Mismatches: 155, Indels: 16
0.88 0.11 0.01
Matches are distributed among these distances:
131 224 0.18
132 986 0.81
133 2 0.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.30
Consensus pattern (132 bp):
CTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGG
GTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAA
AT
Found at i:28929245 original size:132 final size:131
Alignment explanation
Indices: 28929004--28929346 Score: 483
Period size: 132 Copynumber: 2.6 Consensus size: 131
28928994 NNNNNNNNNN
* * *
28929004 GAATCTGTAATCTTCAACCTACTCCACTATTGCTTAGGGTGATATGACTAATGGCTTAAATCTGC
1 GAATCTGCAATCTTAAACCTACTCCACTACTGCTTAGGGTGATA-GACTAATGGCTTAAATCTGC
* * *
28929069 TTCTCCACTGTATTGAGAAGATAAGATTCACCATTTTCGTTCTGCTCCACTACTGCTTAGGGTGA
65 TTCTCCACTGTATTGAGAAGATAAGATTCACAATCTTCGATCTGCTCCACTACTGCTTAGGGTGA
28929134 CA
130 CA
** * * *
28929136 GAATCTGCAATCTTTGACCTATTCCACTACTGTTTAGAGTGATAGAACTAATGGCTTAAATCTGC
1 GAATCTGCAATCTTAAACCTACTCCACTACTGCTTAGGGTGATAG-ACTAATGGCTTAAATCTGC
*
28929201 TTCTCTACTGTATTTG-GAAGATAAGATTCACAATCTTCGATCTGCTCCACTACTGCTTAGGGTG
65 TTCTCCACTGTA-TTGAGAAGATAAGATTCACAATCTTCGATCTGCTCCACTACTGCTTAGGGTG
28929265 ACA
129 ACA
* *
28929268 GAATCTACAATCTTCAAACC-ACTCCACCACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTG
1 GAATCTGCAATCTT-AAACCTACTCCACTACTGCTTAGGGTGATA-GACTAATGGCTTAAATCTG
* *
28929332 CTCCTCCAGTGTATT
64 CTTCTCCACTGTATT
28929347 NNNNNNNNNN
Statistics
Matches: 186, Mismatches: 21, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
131 3 0.02
132 176 0.95
133 7 0.04
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (131 bp):
GAATCTGCAATCTTAAACCTACTCCACTACTGCTTAGGGTGATAGACTAATGGCTTAAATCTGCT
TCTCCACTGTATTGAGAAGATAAGATTCACAATCTTCGATCTGCTCCACTACTGCTTAGGGTGAC
A
Found at i:28929933 original size:132 final size:132
Alignment explanation
Indices: 28929681--28935577 Score: 2719
Period size: 132 Copynumber: 44.5 Consensus size: 132
28929671 NNNNNNNNNN
* * *
28929681 CCTACTCCACAACTGCTTAGGGTGATAGGGCTAATGGCTTAAATTTGCTTCTCCACTGTATTGGG
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
*
28929746 AAGATAAGATTCACCATCTTCGATCTGCTCCACGACTGCTTAGGGTGACAGAATCTGCAATCTTC
66 AAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
28929811 AA
131 AA
* * * * * *
28929813 CCTATTCCAGTACTGCTTAGGGTGATAGGACTAATGGCTGAAATTTGGTTCTCCATTGTATTGGG
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
* * * * * * *
28929878 AAGATAAGATTCATCATGTTCGATCTACTCCACTACTGTTTAGGGTGACAAAATCTGTAATCTTT
66 AAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
28929943 AA
131 AA
* * *
28929945 CCTACTCCAATACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGG
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
* ** *
28930010 AAGATAAGATTCACAATCTTCGATCTATTCCACTACTGCTTAGGGTGACAGAATCTCCAATCTTC
66 AAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
28930075 AA
131 AA
* ** * * * * * *
28930077 CCTACTCCACTACTGCTCAAAGAGATTGGACTAATGGCTTAAATATGCTTCTCCACTATCTTGAG
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
* * **
28930142 AAGATAAGATTCACCATTTTCGTTCCACTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
66 AAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
*
28930207 GA
131 AA
* * * * * * *
28930209 CTTACTCCACTTCTACTTAGGGTGATAGAACTAAAGGCTTAAATCTGCTTCTCCACTATATTTGG
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
* * * *
28930274 AAGATAATATTCACAATCTTTGATCTGCTCCACTACTACTTAGGGTGACAGAATCTGCAATCTTC
66 AAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
28930339 AA
131 AA
*
28930341 CCTACTCCACCACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
* * * *
28930406 AAGATAAGATTCA-CAGTCTTCTATCTGCTCCACTACTGCATAGGGTGACACAATCTGTAATCTT
66 AAGATAAGATTCACCA-TCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTT
28930470 CAA
130 CAA
* * ** *
28930473 CCTACTCCACTACTGCTTAGGGAGATAAGACTAATGGCTTATTTCTGCTTCTCCACTGTTATTGA
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG-TATTGG
* * *
28930538 GAAGATAAGATTCACCATATTTCGTTCTGCTCCACTATCTGCTTAGGGTGCCAGAAATCTGCAAT
65 GAAGATAAGATTCACCAT-CTTCGATCTGCTCCACTA-CTGCTTAGGGTGACAG-AATCTGCAAT
**
28930603 CATTTGA
127 C-TTCAA
* * ** * * *
28930610 CCTATTCCACTACTGCTTAGAGTGATACCTACTAATGGCTTATATCTGCTTCTCTACTGTATTTG
1 CCTACTCCACTACTGCTTAGGGTGATA-GGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGG
* *
28930675 GAAGATAAGATTCACAATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTACAATCTT
65 GAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTT
28930740 CAAA
130 C-AA
* * *
28930744 CC-ACTCCACCACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTCCTCCAGTGTATTGGG
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
** * *
28930808 AAGATAAGATTCATAATCTTCGATCTGCTCCACTACAGCATAGGGTGACAGAATCTGCAATCTTC
66 AAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
28930873 AA
131 AA
* * * *
28930875 CCTACTCCGCAACTGCTTAGGGTGATAGGAATACTGGCTTAAATCTGCTTCTCCACTGTATTGGG
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
* * * * *
28930940 AAGATAAGATTCACCATCTTCGATCTG-TATCACAACTGGTTAGGATGACAGAATCTGCAATCGT
66 AAGATAAGATTCACCATCTTCGATCTGCT-CCACTACTGCTTAGGGTGACAGAATCTGCAATCTT
28931004 CAA
130 CAA
* ************************************************************
28931007 CCGACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
*************************************************
28931072 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGAATCTGCAATCTTC
66 AAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
28931137 AA
131 AA
* * *
28931139 CCTACTCCACAACTGCTTAGGGTGATAGGGCTAATGGCTTAAATTTGCTTCTCCACTGTATTGGG
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
* *
28931204 AAGATAAGATTCACCATCTTCGATCTGTTCCACGACTGCTTAGGGTGACAGAATCTGCAATCTTC
66 AAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
28931269 AA
131 AA
* * * * *
28931271 CCTACTCCAGTACTGCTTAGGGTGATAGGACTAATGGCTGAAATTTGGTTCTCCATTGTATTGGG
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
* * * ** *
28931336 AAGATAAGATTCATCATATTCGATCTGCTCCACTACTGTTTAATGTGACAGAATCTGTAATC-TC
66 AAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
28931400 AA
131 AA
* * * *
28931402 CCTACTCCACTACTGCTTAGGGAGATAGGTCTAATGGCTTAAATCTGCTTCTCTACTGTACTGGG
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
* * * *
28931467 AAGATAGGATTCACCACCTTCGATCTGCTCCACTACTGCTTATGGTGACAGAATCTACAATCTTC
66 AAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
28931532 AA
131 AA
* ** * * * * * * **
28931534 CCTAATCCACTACTGCTTAGGAAGATTGGATTAAAGGCTTACATCTG-TTCTCCACTATCTTAAG
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
* * * * *
28931598 AAGATATGATTCACCATATTTGATCCGCTGCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
66 AAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
28931663 AA
131 AA
*
28931665 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGACTTAAATCTGCTTCTCCACTGTATTGGG
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
* * * *
28931730 AATATAAGATTCACCATCTTCGATCTGCTCCTCTGCTGCTTAGGGTGACAGAATCTCCAATCTTC
66 AAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
28931795 AA
131 AA
* * * *
28931797 CCTACTCCACTACAGCTTAGGGAGATTGGACTAATGGCTTAAATCTGCTTCTCTACTGTATTGGG
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
* *
28931862 AAGATAAGATTCACCATCCTCGATCCGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
66 AAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
28931927 AA
131 AA
* *
28931929 CCTACTCCACCACTGCTTAGGGTGATAGGACTAATGGCTTTAAATTTGCTTCTTCCACTGTATTG
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGC-TTAAATCTGCTTC-TCCACTGTATTG
28931994 GGAAGATAAGATTCACCATCTTCGATCTGCTCTCACTACTGCTTAGGGTGACAGAATCTGCAATC
64 GGAAGATAAGATTCACCATCTTCGATCTGCTC-CACTACTGCTTAGGGTGACAGAATCTGCAATC
28932059 TTCAA
128 TTCAA
* **
28932064 CCTACTCCACCACTGCTTAGGGTGATAAAACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
* **************************
28932129 AAGATAAGATTCACCATCTTCGATTTGCTCCACTACTGCNNNNNNNNNNNNNNNNNNNNNNNNNN
66 AAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
**
28932194 NN
131 AA
*****************************************************************
28932196 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
******* * ** * * * * * * * *
28932261 NNNNNNNGACT-A--ATGGCTTAAATCTGCTTCTCCACTGTATTGAGAAGAT-A-AGATTC-ACC
66 AAGATAAGATTCACCAT--CTTCGATCTGCTCCACTACTG-CTT-AG--GGTGACAGAATCTGCA
*
28932320 ATCCTTCGA
125 AT-CTTCAA
* * * * ** * * *
28932329 TCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAAT--CTTCGACCT-ATTC-CACTACTG-C
1 CCTACTCCACTACTGCTTAGGGTGATAGGA-CT--AATGGCTTAAATCTGCTTCTC-C-ACTGTA
* * * ** * * * *
28932389 TT-AGAGTGAT-AGA---ACTAATGGCTTAAATCTGCTTCTCTACTGTATTGAGAAGAT-A-AGA
61 TTGGGA-AGATAAGATTCAC-CAT--CTTCGATCTGCTCCACTACTG-CTT-AG--GGTGACAGA
* * *
28932447 TTC-ACAATCTTCGA
118 ATCTGCAATCTTCAA
* * * * ** * * *
28932461 TCTGCTCCACTACTGCTTAGGGTGACAGAATCTACAAT--CTTCAAA-CCACTCCACCACT-TCT
1 CCTACTCCACTACTGCTTAGGGTGATAGGA-CT--AATGGCTT-AAATCTGCTTCTCCACTGTAT
* * * ** * * * ** * *
28932522 TAGGG-TGATAGGACT-A--ATGGCTTAAATCTGCTTCTCTACTG-TATCTGGAAGATAAGATTC
62 T-GGGAAGATAAGATTCACCAT--CTTCGATCTGCTCCACTACTGCT-T-AGGGTGA-CAGAATC
* *
28932582 -ACAATCTTCGA
121 TGCAATCTTCAA
* * * * ** * *
28932593 TCTGCTCCACTACTGCTTAGGGTGACAGAATCTACAAT--CTTCAAA-CCACTCCACCACTGCT-
1 CCTACTCCACTACTGCTTAGGGTGATAGGA-CT--AATGGCTT-AAATCTGCTTCTCCACTG-TA
* * * * ** * * * * * * *
28932654 TAGGG-TGATAGGACT-A--ATGGCTTAAATCTGCTCCTCCAGTG-TATTGGGAAGATAAGATTC
61 TTGGGAAGATAAGATTCACCAT--CTTCGATCTGCTCCACTACTGCT-TAGGG-TGA-CAGAATC
*
28932714 ATG--ATCTTCGA
121 -TGCAATCTTCAA
* * * * * * * * * * * *
28932725 TCTGCTCCACTACAGCATAGGGTGACAGAATCTGCAAT--CTTCAACCTACTCCGCAACTGCT-T
1 CCTACTCCACTACTGCTTAGGGTGATAGGA-CT--AATGGCTTAAATCTGCTTCTCCACTG-TAT
* * * * *** * * * * * * * * *
28932787 AGGG-TGATAGGACT-ACTGGCTT-AACTCTGCTTCTCCACTG-TATTGGGAAGATAAGATTC-A
62 TGGGAAGATAAGATTCACCATCTTCGA-TCTGCTCCACTACTGCT-TAGGG-TGA-CAGAATCTG
* *
28932847 CCATCTTCGAT
123 CAATCTTC-AA
* * * * * * * * * * *
28932858 CTGTA-T-CACTACTGGTTAGGATGACAGAATCTGCAAT--CTTCAA-CCGACTCCACTACTG-C
1 C-CTACTCCACTACTGCTTAGGGTGATAGGA-CT--AATGGCTTAAATCTG-CTTCTCCACTGTA
* * * * * ** ** * * * * * * * *
28932917 TTAGGATGATAGGACTAATGA-CTTAAATCTACTTCTCCACTG-TATTGGGAAGATAAGATTCAT
61 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCT-TAGGG-TGA-CAGAATC-T
*
28932980 --AATCTTCGA
122 GCAATCTTCAA
* * * * * * * * ** * ** * *
28932989 TCTGCTGCACTACTGCATAGGGTGACA-GTCTAAATTGCCTAGCGTCGGAGT-T-GATTTGNNNN
1 CCTACTCCACTACTGCTTAGGGTGATAGGACT-AATGGCTTA-AATCTGCTTCTCCA-CTG----
*******************************************************
28933051 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
59 ----------TATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGA
*******************
28933116 NNNNNNNNNNNNNNNNNNN
114 CAGAATCTGCAATCTTCAA
************ * * *
28933135 NNNNNNNNNNNNCTGCTTAGGGAGATAGGACTAATGGCTTAAATCTACTTCTCCGCTGTATTGGG
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
* * * * *
28933200 AAGATAAGATTCACAATCTTCGATCTGCTCTAGTACTACTTAGGGTGACAGAATCTGCAATCTTT
66 AAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
28933265 AA
131 AA
* * * * *
28933267 CCGACTCCACTACTTCTTAGGGTGATAGGACTAATAGCTTAAATCTACTTCTCCACTCTATTGGG
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
** * *
28933332 AAGATAAGAAACACCATCTTCGATCTACTCCACTACTGCTTAGGGTGACAGAATCTGCAATTTTC
66 AAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
28933397 AA
131 AA
* * * *
28933399 CCTACTCTACCACTGCCTAGGATGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
* * * * * * * *
28933464 AAAAGAAGATTCATCATATTTGATCTGCTTCACTACTGTTTAGTGTGACAGAATCTGCAATCTTC
66 AAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
28933529 AA
131 AA
* * * * *
28933531 CCAACTTCACTA-TGGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTTTATTAG
1 CCTACTCCACTACT-GCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGG
* *
28933595 GAAGATAAGATTCACCATCATCGATTTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTT
65 GAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTT
* *
28933660 TAG
130 CAA
* *
28933663 CCTACTCCACTATTGCTGAGGGTGA-ATGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGG
1 CCTACTCCACTACTGCTTAGGGTGATA-GGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGG
* * * *
28933727 GAAGATAAGAATCACCATCTTCGATCTCCTCCACTATTGCTTAGGGTGACAGAATCTGGAATCTT
65 GAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTT
28933792 CAA
130 CAA
* * *
28933795 CCTACTGCACTACTTCTTAGGGTGATTGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
* * * * * *
28933860 AAGATAAGATTCATCATATTCGATCTGCTCAACTA-TAGTTTAGGGTGACAAAATTTGCAATCTT
66 AAGATAAGATTCACCATCTTCGATCTGCTCCACTACT-GCTTAGGGTGACAGAATCTGCAATCTT
*
28933924 TAA
130 CAA
* * * *
28933927 CCTACTCCACTACTGCTAAGGGAGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTCGG
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
* * * *
28933992 AAGATAAGATTCACCATATTCGATCTACTCCGCTACTGCTTAGGGTGACAAAATCTGCAATCTTC
66 AAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
28934057 AA
131 AA
* ** * *
28934059 CCTACTCCACTACAGCTTTTGGAGATTGGACTAATGGCTTAAATCTGCTTCTCCAC--TATCTGT
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTAT-TG-
* * *
28934122 AGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTATGGTGACAGAATCTACAATCT
64 GGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCT
28934187 TCAA
129 TCAA
* ** * * * * * * **
28934191 CCTAATCCACTACTGCTTAGGAAGATTGGATTAAAGGCTTACATCTG-TTCTCCACTATCTTAAG
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
* * * * *
28934255 AAGATATGATTCACCATATTTGATCCGCTGCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
66 AAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
28934320 AA
131 AA
* * *****************************************
28934322 CCTACTCCACTGCTGCTCAGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
1 CCTACTCCACTACTGCTTAGG---GTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATT
******************************************************** *
28934387 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCTCCAATC
63 GGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATC
28934452 TTCAA
128 TTCAA
* * * * * * * *
28934457 CCTACTCCACTACTGCTCAAAGGAGATTGGACTAATGGCTTAAATATGCTTCTCCACTATCTTGA
1 CCTACTCCACTACTGCT-TAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGG
* * **
28934522 GAAGATAAGATTCACCATTTTCGTTCCACTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTT
65 GAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTT
*
28934587 CGA
130 CAA
* * * * * *
28934590 CTTACTCCACTTCTACTTAGGGTGATAGAACTAAAGGCTTAAATCTGCTTCTCCACTGTATTTGG
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
* * * *
28934655 AAGATAATATTCACAATCTTTGATCTGCTCCACTACTACTTAGGGTGACAGAATCTGCAATCTTC
66 AAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
28934720 AA
131 AA
* *
28934722 CCTACTCCACCACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGAG
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
* *
28934787 AAGATAAGATTCA-CAGTCTTCGATCTGCTCCACTACTGCATAGGGTGACAGAATCTGTAATCTT
66 AAGATAAGATTCACCA-TCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTT
28934851 CAA
130 CAA
* *
28934854 CCTACTCCACTACTGCTTAGGGTGATATGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGAG
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
* * * *
28934919 AAGATAAGATTCACCATTTTGGTTCCGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
66 AAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
*
28934984 GA
131 AA
* * * * * * *
28934986 CCTATTCCACTACTGTTTAGAGTGATAGAACTAATGGCTTAAATCTGCTTCTCTACTGAATTTGG
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
* *
28935051 AAGATAAGATTCACAATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTACAATCTTC
66 AAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
28935116 AAA
131 -AA
* * *
28935119 CC-ACTCCACCACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTCCTCCAGTGTATTGGG
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
** * *
28935183 AAGATAAGATTCATAATCTTCGATCTGCTCCACTACAGCATAGGGTGACAGAATCTGCAATCTTC
66 AAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
28935248 AA
131 AA
* * * * *
28935250 CCTACTCCGCAACTGCTTAGGGTGATAGGACTACTAGCTTAAATCTTCTTCTCCACTGTATTGGG
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
* * * *
28935315 AAGATAAGATTCACCATCTTCGATCTG-TATCACTACTGGTTAGGATGACAGAATCTGCAATCGT
66 AAGATAAGATTCACCATCTTCGATCTGCT-CCACTACTGCTTAGGGTGACAGAATCTGCAATCTT
28935379 CAA
130 CAA
* * *
28935382 CCGACTCCACTACTGCTTAGGATGATAGGACTAATGACTTAAATCTGCTTCTCCACTGTATTGGG
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
* ** * *
28935447 AAGAGAAGATTCATAATCTTCGATCTGCTACACTACTGCATAGGGTGACAGAATCTGCAATCTTC
66 AAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
28935512 AA
131 AA
* * *
28935514 CCTACTCCACAACTGCTTAGGGTGATAGGGCTAATGGCTTAAATTTGCTTCTCCACTGTATTGG
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGG
28935578 NNNNNNNNNN
Statistics
Matches: 4286, Mismatches: 1363, Indels: 232
0.73 0.23 0.04
Matches are distributed among these distances:
129 7 0.00
130 10 0.00
131 360 0.08
132 3366 0.79
133 194 0.05
134 87 0.02
135 131 0.03
136 28 0.01
137 48 0.01
138 27 0.01
145 3 0.00
146 22 0.01
147 3 0.00
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.29
Consensus pattern (132 bp):
CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
AAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTC
AA
Found at i:28930349 original size:44 final size:44
Alignment explanation
Indices: 28930168--28930365 Score: 120
Period size: 44 Copynumber: 4.5 Consensus size: 44
28930158 TTTTCGTTCC
* * *
28930168 ACTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCGACTT
1 ACTCCACTACTACTTAGGGTGACAGAATCTGCAATCTTCAACCT
* * * * *
28930212 ACTCCACTTCTACTTAGGGTGATAGAA-CT-AAAGGCTTAAATCTGCT
1 ACTCCACTACTACTTAGGGTGACAGAATCTGCAA-TCTTCAA-C--CT
* * ** * * ** *
28930258 TCTCCACTA-TA-TTTGGAAGATA-ATAT-TCACAATCTTTGATCT
1 ACTCCACTACTACTTAGGGTGACAGA-ATCT-GCAATCTTCAACCT
*
28930300 GCTCCACTACTACTTAGGGTGACAGAATCTGCAATCTTCAACCT
1 ACTCCACTACTACTTAGGGTGACAGAATCTGCAATCTTCAACCT
* *
28930344 ACTCCACCACTGCTTAGGGTGA
1 ACTCCACTACTACTTAGGGTGA
28930366 TAGGACTAAT
Statistics
Matches: 112, Mismatches: 30, Indels: 24
0.67 0.18 0.14
Matches are distributed among these distances:
42 12 0.11
43 9 0.08
44 73 0.65
45 8 0.07
46 10 0.09
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (44 bp):
ACTCCACTACTACTTAGGGTGACAGAATCTGCAATCTTCAACCT
Found at i:28931667 original size:263 final size:263
Alignment explanation
Indices: 28931121--28932167 Score: 1529
Period size: 263 Copynumber: 4.0 Consensus size: 263
28931111 NNNNNNNNNN
* * *
28931121 AGAATCTGCAATCTTCAACCTACTCCACAACTGCTTAGGGTGATAGGGCTAATGGCTTAAATTTG
1 AGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTG
* *
28931186 CTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGTTCCACGACTGCTTAGGGTG
66 CTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTG
* * * * *
28931251 ACAGAATCTGCAATCTTCAACCTACTCCAGTACTGCTTAGGGTGATAGGACTAATGGCTGAAATT
131 ACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATTGGACTAATGGCTTAAATC
* * * * **
28931316 TGGTTCTCCATTGTATTGGGAAGATAAGATTCATCATATTCGATCTGCTCCACTACTGTTTAATG
196 T-GTTCTCCACTGTATTGGGAAGATAAGATTCACCATATTCGATCCGCTCCACTACTGCTTAGGG
28931381 TGAC
260 TGAC
* * *
28931385 AGAATCTGTAATC-TCAACCTACTCCACTACTGCTTAGGGAGATAGGTCTAATGGCTTAAATCTG
1 AGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTG
* * * * *
28931449 CTTCTCTACTGTACTGGGAAGATAGGATTCACCACCTTCGATCTGCTCCACTACTGCTTATGGTG
66 CTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTG
* * * * * *
28931514 ACAGAATCTACAATCTTCAACCTAATCCACTACTGCTTAGGAAGATTGGATTAAAGGCTTACATC
131 ACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATTGGACTAATGGCTTAAATC
* * ** * * *
28931579 TGTTCTCCACTATCTTAAGAAGATATGATTCACCATATTTGATCCGCTGCACTACTGCTTAGGGT
196 TGTTCTCCACTGTATTGGGAAGATAAGATTCACCATATTCGATCCGCTCCACTACTGCTTAGGGT
28931644 GAC
261 GAC
*
28931647 AGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGACTTAAATCTG
1 AGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTG
* * *
28931712 CTTCTCCACTGTATTGGGAATATAAGATTCACCATCTTCGATCTGCTCCTCTGCTGCTTAGGGTG
66 CTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTG
* *
28931777 ACAGAATCTCCAATCTTCAACCTACTCCACTACAGCTTAGGGAGATTGGACTAATGGCTTAAATC
131 ACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATTGGACTAATGGCTTAAATC
* **
28931842 TGCTTCTCTACTGTATTGGGAAGATAAGATTCACCATCCTCGATCCGCTCCACTACTGCTTAGGG
196 TG-TTCTCCACTGTATTGGGAAGATAAGATTCACCATATTCGATCCGCTCCACTACTGCTTAGGG
28931907 TGAC
260 TGAC
* *
28931911 AGAATCTGCAATCTTCAACCTACTCCACCACTGCTTAGGGTGATAGGACTAATGGCTTTAAATTT
1 AGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGC-TTAAATCT
28931976 GCTTCTTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCTCACTACTGCTTAGG
65 GCTTC-TCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTC-CACTACTGCTTAGG
* * ***
28932041 GTGACAGAATCTGCAATCTTCAACCTACTCCACCACTGCTTAGGGTGATAAAACTAATGGCTTAA
128 GTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATTGGACTAATGGCTTAA
* **
28932106 ATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATTTGCTCCACTACTGC
193 ATCTG-TTCTCCACTGTATTGGGAAGATAAGATTCACCATATTCGATCCGCTCCACTACTGC
28932168 NNNNNNNNNN
Statistics
Matches: 696, Mismatches: 82, Indels: 7
0.89 0.10 0.01
Matches are distributed among these distances:
262 66 0.09
263 325 0.47
264 122 0.18
265 12 0.02
266 43 0.06
267 128 0.18
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (263 bp):
AGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTG
CTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTG
ACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATTGGACTAATGGCTTAAATC
TGTTCTCCACTGTATTGGGAAGATAAGATTCACCATATTCGATCCGCTCCACTACTGCTTAGGGT
GAC
Found at i:28932513 original size:44 final size:44
Alignment explanation
Indices: 28932465--28932661 Score: 136
Period size: 44 Copynumber: 4.5 Consensus size: 44
28932455 CTTCGATCTG
28932465 CTCCACTACTGCTTAGGGTGACAGAATCTACAATCTTCAAACCA
1 CTCCACTACTGCTTAGGGTGACAGAATCTACAATCTTCAAACCA
* * * * **
28932509 CTCCACCACTTCTTAGGGTGATAGGA-CT--AATGGCTT-AAATCTG
1 CTCCACTACTGCTTAGGGTGACAGAATCTACAAT--CTTCAAA-CCA
* * * ** * * * * **
28932552 CTTCTCTACTG-TATCTGGAAGATAAGATTC-ACAATCTTCGATCTG
1 CTCCACTACTGCT-T-AGGGTGA-CAGAATCTACAATCTTCAAACCA
28932597 CTCCACTACTGCTTAGGGTGACAGAATCTACAATCTTCAAACCA
1 CTCCACTACTGCTTAGGGTGACAGAATCTACAATCTTCAAACCA
*
28932641 CTCCACCACTGCTTAGGGTGA
1 CTCCACTACTGCTTAGGGTGA
28932662 TAGGACTAAT
Statistics
Matches: 111, Mismatches: 30, Indels: 24
0.67 0.18 0.15
Matches are distributed among these distances:
41 3 0.03
42 4 0.04
43 19 0.17
44 61 0.55
45 18 0.16
46 3 0.03
47 3 0.03
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (44 bp):
CTCCACTACTGCTTAGGGTGACAGAATCTACAATCTTCAAACCA
Found at i:28935960 original size:131 final size:132
Alignment explanation
Indices: 28935702--28936133 Score: 489
Period size: 131 Copynumber: 3.3 Consensus size: 132
28935692 GGTTCTTCAT
* * * *
28935702 TGTATTGGGAAGATAAGATTCATCATATTCGATCTGCTCCACTACTGTTTAAT-GTGACAGAATT
1 TGTACTGGGAAGATAAGATTCACCATATTCGATCTGCTCCACTACTGCTT-ATGGTGACAGAATC
* *
28935766 TGTAATC-TCAACCTACTCCACTACTGCTTA-GAGAGATAGG-TCTAATGGCTTAAATTTGCTTC
65 TGCAATCTTCAACCTACTCCACTACTGCTTAGGA-AGATAGGAT-TAATGGCTTAAATCTGCTTC
*
28935828 TCTAC
128 TCCAC
** * *
28935833 TGTACTGGGAAGATAAGATTCACCACCTTCGATCTACTCCACTACTGCTTATGGTGACAAAATCT
1 TGTACTGGGAAGATAAGATTCACCATATTCGATCTGCTCCACTACTGCTTATGGTGACAGAATCT
* * * * * *
28935898 ACAATCTTCAACATAATCCACTACTGCTTAGGAAGATTGGATTAAAGGCTTACATCTG-TTCTCC
66 GCAATCTTCAACCTACTCCACTACTGCTTAGGAAGATAGGATTAATGGCTTAAATCTGCTTCTCC
28935962 AC
131 AC
* ** * * * * * *
28935964 TAT-CTTAAGAAGATATGATTCACCGTATTTGATCCGCTGCACTACTGCTTAGGGTGACAGAATC
1 TGTAC-TGGGAAGATAAGATTCACCATATTCGATCTGCTCCACTACTGCTTATGGTGACAGAATC
** * *
28936028 TGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGACTTAAATCTGCTTCTC
65 TGCAATCTTCAACCTACTCCACTACTGCTTAGGAAGATAGGATTAATGGCTTAAATCTGCTTCTC
28936093 CAC
130 CAC
* * *
28936096 TGTATTGGGAATATAAGATTCACCATCTTCGATCTGCT
1 TGTACTGGGAAGATAAGATTCACCATATTCGATCTGCT
28936134 NNNNNNNNNN
Statistics
Matches: 244, Mismatches: 50, Indels: 13
0.79 0.16 0.04
Matches are distributed among these distances:
130 3 0.01
131 163 0.67
132 75 0.31
133 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.32
Consensus pattern (132 bp):
TGTACTGGGAAGATAAGATTCACCATATTCGATCTGCTCCACTACTGCTTATGGTGACAGAATCT
GCAATCTTCAACCTACTCCACTACTGCTTAGGAAGATAGGATTAATGGCTTAAATCTGCTTCTCC
AC
Found at i:28949838 original size:132 final size:132
Alignment explanation
Indices: 28949589--28951315 Score: 2229
Period size: 132 Copynumber: 13.1 Consensus size: 132
28949579 NNNNNNNNNG
* * * * *
28949589 TCCACTATATTAGGAAAATAAGATTCATCAT-ATTCGATCTGCTTCACTACTGTTTAGGGTGACA
1 TCCACTGTATTGGGAAAATAAGATTCACCATCA-TCGATCTGCTCCACTACTGCTTAGGGTGACA
* * * * *
28949653 GAATCTGTAATCTTCAACCAATTCCACTA-TGGCTTAGGGAGATAGGACAAATGGCTTAAATCTG
65 GAATCTGCAATCTTCAACCTACTCCACTACT-GCTTAGGGTGATAGGACTAATGGCTTAAATCTG
28949717 CTTC
129 CTTC
* * *
28949721 TCCATTGTATTGGGAAAATAAGATTCACCATCATCGATCTACTCCAATACTGCTTAGGGTGACAG
1 TCCACTGTATTGGGAAAATAAGATTCACCATCATCGATCTGCTCCACTACTGCTTAGGGTGACAG
* * *
28949786 AATCTGCAATCTTCAACCGACTCCACTACTGCTTAGGGAGATTGGACTAATGGCTTAAATCTGCT
66 AATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCT
28949851 TC
131 TC
* *
28949853 TCCACTGTATT--GAAAGATAAGATTCACCATCTTCGATCTACTCCACTACTGCTTAGGG-GACA
1 TCCACTGTATTGGGAAA-ATAAGATTCACCATCATCGATCTGCTCCACTACTGCTTAGGGTGACA
* * * * *
28949915 GAATCTGCAATCTTCAGCCTACTCCACTACTACTTCAGGGTGATAGGACTAATCGCTGAAATCAG
65 GAATCTGCAATCTTCAACCTACTCCACTACTGCTT-AGGGTGATAGGACTAATGGCTTAAATCTG
*
28949980 ATTC
129 CTTC
* * * * *
28949984 TCCACTGTATTGCGAAAGTAAGATTCATCAT-ATTCGATCTCCTTCAGC-ACTGCTTAGGGTGAC
1 TCCACTGTATTGGGAAAATAAGATTCACCATCA-TCGATCTGCTCCA-CTACTGCTTAGGGTGAC
* * * * * *
28950047 TGAATCTACAATCTTCAACCAATTCCACTA-TGGCTTAGGGAGATAGGACAAATGGCTTAAATCT
64 AGAATCTGCAATCTTCAACCTACTCCACTACT-GCTTAGGGTGATAGGACTAATGGCTTAAATCT
28950111 GCTTC
128 GCTTC
* * * * *
28950116 TCCACAGTATTGGGAAGATAAGATTCATCATCTTCGATCTGCTCCACTACAGCTTAGGGTGACAG
1 TCCACTGTATTGGGAAAATAAGATTCACCATCATCGATCTGCTCCACTACTGCTTAGGGTGACAG
* * * *
28950181 AATCTGGAATCTTCAACCGACTCCACTTCTGCTTAGGGTGATAGGACTAATAGCTTAAATCTGCT
66 AATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCT
28950246 TC
131 TC
* * * *
28950248 TCTACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGAGTGACAG
1 TCCACTGTATTGGGAAAATAAGATTCACCATCATCGATCTGCTCCACTACTGCTTAGGGTGACAG
** * * * * *
28950313 AATCTAAAATCTTCAACATACTTCAGTACTACTTAGGGTGATAGGACTAATGGCTTAAATCTCCT
66 AATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCT
28950378 TC
131 TC
* * *
28950380 TCCACTGTATTGGGAAGATAAGATTGACCAT-ATTCGATCTGCTCCACTACTACTTAGGGTGACA
1 TCCACTGTATTGGGAAAATAAGATTCACCATCA-TCGATCTGCTCCACTACTGCTTAGGGTGACA
* * * *
28950444 GAATCTGCAATCTTCAACCGACTCCACTGCTGCTTAGGGTGATAGGACGAATAGCTTAAATCTGC
65 GAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGC
28950509 TTC
130 TTC
* * * * *
28950512 TCTACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTTCTTAGAGTGACAG
1 TCCACTGTATTGGGAAAATAAGATTCACCATCATCGATCTGCTCCACTACTGCTTAGGGTGACAG
** * * * *
28950577 AATCTAAAATCTTCAACATACTTCAGTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTCCT
66 AATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCT
28950642 TC
131 TC
* * * *
28950644 TCCACTGTATTGGGAAGATAAGATTGACCAT-ATTCGTTCTGCTCCACTACTACTTAGGGTGACA
1 TCCACTGTATTGGGAAAATAAGATTCACCATCA-TCGATCTGCTCCACTACTGCTTAGGGTGACA
* *
28950708 GAATCTGCAATCTTCAACCTACTCCACTTCTGCTTAGGGTGATTGGACTAATGGCTTAAATCTGC
65 GAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGC
28950773 TTC
130 TTC
* * *
28950776 TCCACTGTATTGGGAAAATAAGATTCACTATCTTCGATCTACTCCACTACTGCTTAGGGTGACAG
1 TCCACTGTATTGGGAAAATAAGATTCACCATCATCGATCTGCTCCACTACTGCTTAGGGTGACAG
* * *
28950841 AATCTGCAATCTTTAACCTACACCACTACTGCTTAGGGTGATATGACTAATGGCTTAAATCTGCT
66 AATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCT
28950906 TC
131 TC
* ** * * *
28950908 TCCAGTGTATTGGGAAAATAAGATTCATTAT-ATTCGATCTGCTTCACTACTGTTTTGGGTGACA
1 TCCACTGTATTGGGAAAATAAGATTCACCATCA-TCGATCTGCTCCACTACTGCTTAGGGTGACA
* * * * *
28950972 GAATCTGTAATCTTCAACCAATTCCACTA-TGGCTTAGGGAGATAGGACAAATGGCTTAAATCTG
65 GAATCTGCAATCTTCAACCTACTCCACTACT-GCTTAGGGTGATAGGACTAATGGCTTAAATCTG
28951036 CTTC
129 CTTC
* ** * *
28951040 TCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTATTCCAATACTGCCTAGGGTGACAG
1 TCCACTGTATTGGGAAAATAAGATTCACCATCATCGATCTGCTCCACTACTGCTTAGGGTGACAG
* * * * * * *
28951105 TATCTGCACTCTTCAACCTACTCCACTACTGCGTAGAGAGATTGGACTAATGGCTTAAATCTGTT
66 AATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCT
28951170 TC
131 TC
* * *
28951172 TCCACTGTATTGGGAGGAA-AGGATTCACCATCGTCGATCTGCTCCACTACTGCTTAGGGTGACA
1 TCCACTGTATTGGGA-AAATAAGATTCACCATCATCGATCTGCTCCACTACTGCTTAGGGTGACA
* * *
28951236 GAATCTGCAATCTTTAACCTACTCCACTACAGCTTCGGGTGATAGGACTAATGGCTTAAATCTGC
65 GAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGC
28951301 TTC
130 TTC
28951304 TCCACTGTATTG
1 TCCACTGTATTG
28951316 CTTAATCTCC
Statistics
Matches: 1389, Mismatches: 184, Indels: 44
0.86 0.11 0.03
Matches are distributed among these distances:
130 40 0.03
131 80 0.06
132 1227 0.88
133 42 0.03
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (132 bp):
TCCACTGTATTGGGAAAATAAGATTCACCATCATCGATCTGCTCCACTACTGCTTAGGGTGACAG
AATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCT
TC
Found at i:28952541 original size:132 final size:131
Alignment explanation
Indices: 28952294--28952881 Score: 833
Period size: 132 Copynumber: 4.5 Consensus size: 131
28952284 NNNNNCTGCA
* *
28952294 TCTCCACTATATTGGGAAGATAAGATTCATCATCTTCGATCTGCTCCACTACTGGTTAGGGTGAC
1 TCTCCACTGTATTGGGAAGATAAGATTCATCATCTTCGATCTGCTCCACTACTGCTTA-GGTGAC
* ** * *
28952359 AGAATCTGGAATCTTCAA-CTGACTCCACTACTGCTTAGAATGATACGACTAATGGATTAAATCT
65 AGAATCTGTAATCTTCAACCT-ACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCT
*
28952423 ACT
129 CCT
* *
28952426 TCTCTACTGTATTGGGAAGATAAGATTCAGCATCTTCGATCTGCTCCACTACTGCTTAGAGTGAC
1 TCTCCACTGTATTGGGAAGATAAGATTCATCATCTTCGATCTGCTCCACTACTGCTTAG-GTGAC
*
28952491 AGAATCTGTAATCTTCAACCTACTCCAGTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTC
65 AGAATCTGTAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTC
28952556 CT
130 CT
* * * *
28952558 TCTCCACTGTATTGGGAAGACAAGATTGACCATATTCGATCTGCTCCACTACTGCTTACGGTGAC
1 TCTCCACTGTATTGGGAAGATAAGATTCATCATCTTCGATCTGCTCCACTACTGCTTA-GGTGAC
* *
28952623 AGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATTGGACTAATGGCTTAAATCTC
65 AGAATCTGTAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTC
28952688 CT
130 CT
28952690 TCTCCACTGTATTGGGAAGATAAGATTCA-CTATCTTCGATCTGCTCCACTACTGCTTACGGTGA
1 TCTCCACTGTATTGGGAAGATAAGATTCATC-ATCTTCGATCTGCTCCACTACTGCTTA-GGTGA
* * * * *
28952754 CAGAATTTGTAATCTTTAACCTACACCACTACTGCTTTGGGTGATAGGACTAATAGCTTAAATC-
64 CAGAATCTGTAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCT
28952818 CGCT
129 C-CT
* * * * *
28952822 TCTCCACTGTATTGGGAAAATAAGATTCATCATTCTT-TATCTCCTACACTACTGGTTAGG
1 TCTCCACTGTATTGGGAAGATAAGATTCATCA-TCTTCGATCTGCTCCACTACTGCTTAGG
28952882 GTGATAGGAC
Statistics
Matches: 415, Mismatches: 34, Indels: 15
0.89 0.07 0.03
Matches are distributed among these distances:
131 5 0.01
132 402 0.97
133 8 0.02
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (131 bp):
TCTCCACTGTATTGGGAAGATAAGATTCATCATCTTCGATCTGCTCCACTACTGCTTAGGTGACA
GAATCTGTAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTCC
T
Found at i:28952665 original size:44 final size:44
Alignment explanation
Indices: 28952469--28952665 Score: 127
Period size: 44 Copynumber: 4.5 Consensus size: 44
28952459 CTTCGATCTG
* *
28952469 CTCCACTACTGCTTAGAGTGACAGAATCTGTAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTA
* * * * * *
28952513 CTCCAGTACTGCTTAGGGTGATAGGA-CT--AATGGCTTAAATCTC
1 CTCCACTACTGCTTAGGGTGACAGAATCTGCAAT--CTTCAACCTA
* * * * * * * * * *
28952556 CTTCTCCACTG-TATTGGGAAGACA-AGAT-TGACCATATTCGATCTG
1 CTCCACTACTGCT-TAGGG-TGACAGA-ATCTG-CAATCTTCAACCTA
*
28952601 CTCCACTACTGCTTACGGTGACAGAATCTGCAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTA
28952645 CTCCACTACTGCTTAGGGTGA
1 CTCCACTACTGCTTAGGGTGA
28952666 TTGGACTAAT
Statistics
Matches: 109, Mismatches: 32, Indels: 24
0.66 0.19 0.15
Matches are distributed among these distances:
41 3 0.03
42 1 0.01
43 20 0.18
44 62 0.57
45 20 0.18
46 1 0.01
47 2 0.02
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.29
Consensus pattern (44 bp):
CTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTA
Found at i:28952926 original size:220 final size:220
Alignment explanation
Indices: 28952648--28953070 Score: 657
Period size: 220 Copynumber: 1.9 Consensus size: 220
28952638 CAACCTACTC
*
28952648 CACTACTGCTTAGGGTGATTGGACTAATGGCTTAAATCTCCTTCTCCACTGTATTGGGAAGATAA
1 CACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTCCTTCTCCACTGTATTGGGAAGATAA
* * * * * *
28952713 GATTCACTATCTTCGATCTGCTCCACTACTGCTTACGGTGACAGAATTTGTAATCTTTAACCTAC
66 GATTCACCATCTTCGATCTGCTCCACTACTGCTTACAGTGACAGAATCTGCAATCATCAACCTAC
**
28952778 ACCACTACTGCTTTGGGTGATAGGACTAATAGCTTAAATCCGCTTCTCCACTGTATTGGGAAAAT
131 ACCACTACTGCTTACGGTGATAGGACTAATAGCTTAAATCCGCTTCTCCACTGTATTGGGAAAAT
28952843 AAGATTCATCATTCTTTATCTCCTA
196 AAGATTCATCATTCTTTATCTCCTA
* * *
28952868 CACTACTGGTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCTACTGTATTGGGAAGATAA
1 CACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTCCTTCTCCACTGTATTGGGAAGATAA
* *
28952933 GATTCACCATCTTCGATCTGCTCCACTACTGCTTATAGTGACAGAATCTGCAATCATCAACCTAT
66 GATTCACCATCTTCGATCTGCTCCACTACTGCTTACAGTGACAGAATCTGCAATCATCAACCTAC
* * * ** *
28952998 TCCAGTACTGCTTACGGTGATAGGACTAATGGCTTAAATGTGCTTCTCCACTGTATTGGGAAGAT
131 ACCACTACTGCTTACGGTGATAGGACTAATAGCTTAAATCCGCTTCTCCACTGTATTGGGAAAAT
*
28953063 AGGATTCA
196 AAGATTCA
28953071 CCATCGTCGA
Statistics
Matches: 182, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
220 182 1.00
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.33
Consensus pattern (220 bp):
CACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTCCTTCTCCACTGTATTGGGAAGATAA
GATTCACCATCTTCGATCTGCTCCACTACTGCTTACAGTGACAGAATCTGCAATCATCAACCTAC
ACCACTACTGCTTACGGTGATAGGACTAATAGCTTAAATCCGCTTCTCCACTGTATTGGGAAAAT
AAGATTCATCATTCTTTATCTCCTA
Found at i:28952960 original size:88 final size:88
Alignment explanation
Indices: 28952779--28952967 Score: 272
Period size: 88 Copynumber: 2.1 Consensus size: 88
28952769 TTAACCTACA
*
28952779 CCACTACTGCTTTGGGTGATAGGACTAATAGCTTAAATCCGCTTCTCCACTGTATTGGGAAAATA
1 CCACTACTGCTTAGGGTGATAGGACTAATAGCTTAAATCCGCTTCTCCACTGTATTGGGAAAATA
* *
28952844 AGATTCATCATTCTTTATCTCCT
66 AGATTCACCATTCTTGATCTCCT
* * * * * *
28952867 ACACTACTGGTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCTACTGTATTGGGAAGATA
1 CCACTACTGCTTAGGGTGATAGGACTAATAGCTTAAATCCGCTTCTCCACTGTATTGGGAAAATA
*
28952932 AGATTCACCA-TCTTCGATCTGCT
66 AGATTCACCATTCTT-GATCTCCT
28952955 CCACTACTGCTTA
1 CCACTACTGCTTA
28952968 TAGTGACAGA
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
87 4 0.05
88 84 0.95
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (88 bp):
CCACTACTGCTTAGGGTGATAGGACTAATAGCTTAAATCCGCTTCTCCACTGTATTGGGAAAATA
AGATTCACCATTCTTGATCTCCT
Done.