Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 22 of 168
Found at i:5700207 original size:29 final size:29
Alignment explanation
Indices: 5700044--5700209 Score: 120
Period size: 29 Copynumber: 5.6 Consensus size: 29
5700034 CAAAACTTTT
* *
5700044 GGGTCCAAAGTGTAATTTTGAGAAAATTTTA-
1 GGGT-CAAAATGTAATTTT-A-AAAAGTTTAG
* * * *
5700075 GGGTCAAAATGTAATTTCGAGATAGTTCAG
1 GGGTCAAAATGTAATTT-TAAAAAGTTTAG
* * * *
5700105 GGGTTAAAATGTAATTTCAAAAGGTTTAA
1 GGGTCAAAATGTAATTTTAAAAAGTTTAG
* *
5700134 AGGTCATAATGTAATTTTAAAAAGTTTAG
1 GGGTCAAAATGTAATTTTAAAAAGTTTAG
* * *
5700163 TGGTTAAAATGCAATTTTAAAAA-TTTCAG
1 GGGTCAAAATGTAATTTTAAAAAGTTT-AG
* *
5700192 GGGTCAGAATTTAATTTT
1 GGGTCAAAATGTAATTTT
5700210 TATTTTTTGT
Statistics
Matches: 104, Mismatches: 28, Indels: 8
0.74 0.20 0.06
Matches are distributed among these distances:
28 3 0.03
29 68 0.65
30 29 0.28
31 4 0.04
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.36
Consensus pattern (29 bp):
GGGTCAAAATGTAATTTTAAAAAGTTTAG
Found at i:5700580 original size:78 final size:78
Alignment explanation
Indices: 5700407--5701072 Score: 839
Period size: 78 Copynumber: 8.7 Consensus size: 78
5700397 GTGTGGCCCA
* ** * *
5700407 AGGCTTAACTCACCTCTCGCAATATGAGTTGATTTAAAAAAAAAACAGAAA-TT--GA-AAATTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTT--TTAAAAAACAGAAATTTAAAAGAAATAC
*
5700468 CTCAGC-GTGACCCG
64 CTCGGCAGTGACCCG
* *
5700482 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATATAAAAGAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAATTTAAAAGAAATACCT
5700547 CGGCATGTGA-CCG
66 CGGCA-GTGACCCG
* * *
5700560 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTTAAAAGAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAATTTAAAAGAAATACCT
5700625 CGGCA-TGACCCG
66 CGGCAGTGACCCG
* * * ** * * *
5700637 AGGCTCAGCTCACCTCTCGTATTATGAGTTGATTTAAAAAAAATAGAAA-TT--GA-AAATTCCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAATTTAAAAGAAATACCT
* *
5700698 CAGC-GTAACCCG
66 CGGCAGTGACCCG
* *
5700710 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATATAAAAGAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAATTTAAAAGAAATACCT
5700775 CGGCATGTGA-CCG
66 CGGCA-GTGACCCG
* * * *
5700788 AGGCTCAACTCACTTCTCACAATATGAGTTGATTTTTGAAAAACTGAAATTTAAAAGAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAATTTAAAAGAAATACCT
5700853 CGGCA-TGACCCG
66 CGGCAGTGACCCG
* * * *
5700865 AGGCTCAACTCACCTTTCGCATTATGAGTTGA-TTTAAAAAAATAGAAATTTAAAAGAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAATTTAAAAGAAATACCT
5700929 CGGCA-TGACCCG
66 CGGCAGTGACCCG
* *
5700941 AGGCTCAACTCACCTCTCGCATTATGAGTTGA--TTTAAAAAATAGAAATTTAAAAGAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAATTTAAAAGAAATACCT
5701004 CGGCATGTGA-CCG
66 CGGCA-GTGACCCG
* *
5701017 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAAAAACAGAAATTGAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAATTTAAAA
5701073 ATATTTCTTG
Statistics
Matches: 520, Mismatches: 52, Indels: 35
0.86 0.09 0.06
Matches are distributed among these distances:
73 69 0.13
74 3 0.01
75 69 0.13
76 115 0.22
77 99 0.19
78 158 0.30
79 7 0.01
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.26
Consensus pattern (78 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAATTTAAAAGAAATACCT
CGGCAGTGACCCG
Found at i:5700763 original size:228 final size:228
Alignment explanation
Indices: 5700407--5701072 Score: 1052
Period size: 228 Copynumber: 2.9 Consensus size: 228
5700397 GTGTGGCCCA
* * *
5700407 AGGCTTAACTCACCTCTCGCAATATGAGTTGATTTAAAAAAAAAACAGAAATTGAAAATTCCTCA
1 AGGCTCAACTCACCTCTCGCATTATGAGTTGATTT--AAAAAAAATAGAAATTGAAAATTCCTCA
5700472 GCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATATAAA
64 GCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATATAAA
5700537 AGAAATACCTCGGCATGTGACCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAA
129 AGAAATACCTCGGCATGTGACCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAA
5700602 ATAGAAATTTAAAAGAAATACCTCGGCATGACCCG
194 ATAGAAATTTAAAAGAAATACCTCGGCATGACCCG
* *
5700637 AGGCTCAGCTCACCTCTCGTATTATGAGTTGATTTAAAAAAAATAGAAATTGAAAATTCCTCAGC
1 AGGCTCAACTCACCTCTCGCATTATGAGTTGATTTAAAAAAAATAGAAATTGAAAATTCCTCAGC
*
5700702 GTAACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATATAAAAG
66 GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATATAAAAG
*
5700767 AAATACCTCGGCATGTGACCGAGGCTCAACTCACTTCTCACAATATGAGTTGATTTTTGAAAAAC
131 AAATACCTCGGCATGTGACCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAA-
5700832 T-GAAATTTAAAAGAAATACCTCGGCATGACCCG
195 TAGAAATTTAAAAGAAATACCTCGGCATGACCCG
* * *
5700865 AGGCTCAACTCACCTTTCGCATTATGAGTTGATTT-AAAAAAATAGAAATTTAAAAGAAATACCT
1 AGGCTCAACTCACCTCTCGCATTATGAGTTGATTTAAAAAAAATAGAAA-TT--GA-AAATTCCT
* * * * * *
5700929 CGGCATGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA--TTTAAAAAATAGAAATTTA
62 CAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATATA
* **
5700992 AAAGAAATACCTCGGCATGTGACCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAA
127 AAAGAAATACCTCGGCATGTGACCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAA
* *
5701057 AAACAGAAATTGAAAA
192 AAATAGAAATTTAAAA
5701073 ATATTTCTTG
Statistics
Matches: 405, Mismatches: 25, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
227 13 0.03
228 222 0.55
229 91 0.22
230 32 0.08
231 47 0.12
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.26
Consensus pattern (228 bp):
AGGCTCAACTCACCTCTCGCATTATGAGTTGATTTAAAAAAAATAGAAATTGAAAATTCCTCAGC
GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATATAAAAG
AAATACCTCGGCATGTGACCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAAT
AGAAATTTAAAAGAAATACCTCGGCATGACCCG
Found at i:5702237 original size:14 final size:14
Alignment explanation
Indices: 5702218--5702252 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
5702208 TGACAAATTG
5702218 CCTTCAAGCGTTTC
1 CCTTCAAGCGTTTC
5702232 CCTTCAAGCGTTTC
1 CCTTCAAGCGTTTC
*
5702246 CATTCAA
1 CCTTCAA
5702253 TAAGGTTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.20, C:0.34, G:0.11, T:0.34
Consensus pattern (14 bp):
CCTTCAAGCGTTTC
Found at i:5712936 original size:27 final size:25
Alignment explanation
Indices: 5712863--5712936 Score: 78
Period size: 25 Copynumber: 2.9 Consensus size: 25
5712853 GATCCGATTG
* *
5712863 AAACACAAGAAATTTTTTAAAAAAA
1 AAACACGAGAATTTTTTTAAAAAAA
* *
5712888 AAACACGAGAATTTGTTGAAAATACAA
1 AAACACGAGAATTTTTTTAAAA-A-AA
*
5712915 AAACACGA-AATTTTTTTTAAAA
1 AAACACGAGAATTTTTTTAAAAA
5712937 CGCGAAAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
25 19 0.47
26 11 0.28
27 10 0.25
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.27
Consensus pattern (25 bp):
AAACACGAGAATTTTTTTAAAAAAA
Found at i:5713382 original size:11 final size:10
Alignment explanation
Indices: 5713361--5713415 Score: 51
Period size: 11 Copynumber: 5.4 Consensus size: 10
5713351 ATTTTTCCTA
5713361 TTTTC-TTCT
1 TTTTCTTTCT
5713370 TTTCTCTTTCT
1 TTT-TCTTTCT
*
5713381 TTTT-TCTCT
1 TTTTCTTTCT
5713390 TTTTCTTCTCT
1 TTTTCTT-TCT
*
5713401 TTTCTTTTTCT
1 TTT-TCTTTCT
5713412 TTTT
1 TTTT
5713416 TTTTTCTGCT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
9 11 0.29
10 5 0.13
11 19 0.50
12 3 0.08
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTCTTTCT
Found at i:5713393 original size:29 final size:31
Alignment explanation
Indices: 5713352--5713416 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
5713342 TTTTTTCCTA
5713352 TTTTTCCTATTTTC-T-TCTTTTCTCTTTCT
1 TTTTTCCTATTTTCTTCTCTTTTCTCTTTCT
*
5713381 TTTTTCTCT-TTTTCTTCTCTTTTCTTTTTCT
1 TTTTTC-CTATTTTCTTCTCTTTTCTCTTTCT
5713412 TTTTT
1 TTTTT
5713417 TTTTCTGCTG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 11 0.34
30 3 0.09
31 18 0.56
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.77
Consensus pattern (31 bp):
TTTTTCCTATTTTCTTCTCTTTTCTCTTTCT
Found at i:5713408 original size:24 final size:24
Alignment explanation
Indices: 5713371--5713422 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
5713361 TTTTCTTCTT
5713371 TTCTCTTTCTTTTTTCTCTTTTTC
1 TTCTCTTTCTTTTTTCTCTTTTTC
* *
5713395 TTCTCTTT-TCTTTTTCTTTTTTTT
1 TTCTCTTTCT-TTTTTCTCTTTTTC
5713419 TTCT
1 TTCT
5713423 GCTGGGCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (24 bp):
TTCTCTTTCTTTTTTCTCTTTTTC
Found at i:5713419 original size:11 final size:11
Alignment explanation
Indices: 5713369--5713422 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
5713359 TATTTTCTTC
*
5713369 TTTTCTCTTTCT
1 TTTTTTCTTT-T
5713381 TTTTTCTCTTTT
1 TTTTT-TCTTTT
* *
5713393 TCTTCTCTTTT
1 TTTTTTCTTTT
*
5713404 CTTTTTCTTTT
1 TTTTTTCTTTT
5713415 TTTTTTCT
1 TTTTTTCT
5713423 GCTGGGCTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
11 21 0.62
12 8 0.24
13 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:5713596 original size:6 final size:6
Alignment explanation
Indices: 5713580--5713624 Score: 54
Period size: 6 Copynumber: 7.0 Consensus size: 6
5713570 TTTTATGCTT
*
5713580 TTTTTC TTTTTTC TTTTTC TTTTTC TTCTTC TTCCTTTC TTTTTC
1 TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC TT--TTTC TTTTTC
5713625 AAAACCCTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
6 23 0.68
7 6 0.18
8 5 0.15
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTTC
Found at i:5713728 original size:20 final size:20
Alignment explanation
Indices: 5713705--5713754 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
5713695 CTCCTCTACT
*
5713705 TCTC-TTTTCTTCTCTCTTTC
1 TCTCTTTTTCCTCT-TCTTTC
*
5713725 TCTCCTTTTTCCTCTTCTTTT
1 TCT-CTTTTTCCTCTTCTTTC
5713746 TCTCTTTTT
1 TCTCTTTTT
5713755 TGCAAGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 9 0.35
21 9 0.35
22 8 0.31
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (20 bp):
TCTCTTTTTCCTCTTCTTTC
Found at i:5713743 original size:21 final size:22
Alignment explanation
Indices: 5713709--5713755 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
5713699 TCTACTTCTC
*
5713709 TTTTCTTCTCTCTTTCTCTCCT
1 TTTTCCTCTCTCTTTCTCTCCT
* *
5713731 TTTTCCTCT-TCTTTTTCTCTT
1 TTTTCCTCTCTCTTTCTCTCCT
5713752 TTTT
1 TTTT
5713756 GCAAGTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTCCTCTCTCTTTCTCTCCT
Found at i:5714128 original size:58 final size:59
Alignment explanation
Indices: 5714006--5714140 Score: 155
Period size: 58 Copynumber: 2.3 Consensus size: 59
5713996 AGAAAATTTT
* * *
5714006 GGGTCAAAATGTAATTTTGAGATAGTTCAGCGGTCAAAATGAAATTTCAAAAGGTTTAA
1 GGGTCAAAATGTAATTTTGAAAAAGTTCAGCGGTCAAAATGAAATTTCAAAAAGTTTAA
* * * * * * * *
5714065 AGGTCATAATGTAATTTT-AAAAAGTTTAGTGGTTAAAATGCAATTTTAAAAAGTTTAG
1 GGGTCAAAATGTAATTTTGAAAAAGTTCAGCGGTCAAAATGAAATTTCAAAAAGTTTAA
*
5714123 GGGTCAAAATATAATTTT
1 GGGTCAAAATGTAATTTT
5714141 TTATTTTTTG
Statistics
Matches: 62, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
58 46 0.74
59 16 0.26
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.35
Consensus pattern (59 bp):
GGGTCAAAATGTAATTTTGAAAAAGTTCAGCGGTCAAAATGAAATTTCAAAAAGTTTAA
Found at i:5714138 original size:29 final size:29
Alignment explanation
Indices: 5714006--5714140 Score: 135
Period size: 29 Copynumber: 4.6 Consensus size: 29
5713996 AGAAAATTTT
* * *
5714006 GGGTCAAAATGTAATTTTGAGATAGTTCAG
1 GGGTCAAAATGTAATTTT-AAAAAGTTTAG
* * * * *
5714036 CGGTCAAAATGAAATTTCAAAAGGTTTAA
1 GGGTCAAAATGTAATTTTAAAAAGTTTAG
* *
5714065 AGGTCATAATGTAATTTTAAAAAGTTTAG
1 GGGTCAAAATGTAATTTTAAAAAGTTTAG
* * *
5714094 TGGTTAAAATGCAATTTTAAAAAGTTTAG
1 GGGTCAAAATGTAATTTTAAAAAGTTTAG
*
5714123 GGGTCAAAATATAATTTT
1 GGGTCAAAATGTAATTTT
5714141 TTATTTTTTG
Statistics
Matches: 83, Mismatches: 22, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
29 68 0.82
30 15 0.18
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.35
Consensus pattern (29 bp):
GGGTCAAAATGTAATTTTAAAAAGTTTAG
Found at i:5714154 original size:9 final size:8
Alignment explanation
Indices: 5714137--5714170 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
5714127 CAAAATATAA
5714137 TTTTTTAT
1 TTTTTTAT
5714145 TTTTTGTAT
1 TTTTT-TAT
*
5714154 TTTTTGAT
1 TTTTTTAT
5714162 TTTTTTAT
1 TTTTTTAT
5714170 T
1 T
5714171 AAAAAAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (8 bp):
TTTTTTAT
Found at i:5715605 original size:29 final size:30
Alignment explanation
Indices: 5715563--5715621 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
5715553 GAATTGAATC
*
5715563 AAATTAAAATTTTAAGTATA-AATTTACATA
1 AAATCAAAATTTTAAGTATACAA-TTACATA
*
5715593 AAATCAAAA-TTTATGTATACAATTACATA
1 AAATCAAAATTTTAAGTATACAATTACATA
5715622 TTAAACCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (30 bp):
AAATCAAAATTTTAAGTATACAATTACATA
Found at i:5716245 original size:14 final size:14
Alignment explanation
Indices: 5716228--5716263 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
5716218 CACTCTCAAC
*
5716228 TCTCAATTTATTTT
1 TCTCAATTTATTAT
*
5716242 TCTCAATTTCTTAT
1 TCTCAATTTATTAT
5716256 TCTCAATT
1 TCTCAATT
5716264 GCCAAATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.22, C:0.19, G:0.00, T:0.58
Consensus pattern (14 bp):
TCTCAATTTATTAT
Found at i:5719121 original size:34 final size:34
Alignment explanation
Indices: 5719069--5719137 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
5719059 GCCAAGTAAC
* *
5719069 CTTCAAGAACCTGCTTCAAAAGTCGTATAGAAAG
1 CTTCAACAACATGCTTCAAAAGTCGTATAGAAAG
* * *
5719103 CTTCAACAACATGTTTCAAAAGTTGTATGGAAAG
1 CTTCAACAACATGCTTCAAAAGTCGTATAGAAAG
5719137 C
1 C
5719138 CAAATGCTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (34 bp):
CTTCAACAACATGCTTCAAAAGTCGTATAGAAAG
Found at i:5727042 original size:27 final size:27
Alignment explanation
Indices: 5726995--5727051 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
5726985 TTTAATAAAG
5726995 AATGTAATTTTATGCTATTTTGCATTA
1 AATGTAATTTTATGCTATTTTGCATTA
*
5727022 AATGTAATTTTATGCTATTTTGTATTA
1 AATGTAATTTTATGCTATTTTGCATTA
5727049 AAT
1 AAT
5727052 TTGTGTAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.53
Consensus pattern (27 bp):
AATGTAATTTTATGCTATTTTGCATTA
Found at i:5742327 original size:89 final size:89
Alignment explanation
Indices: 5742077--5742717 Score: 1007
Period size: 89 Copynumber: 7.2 Consensus size: 89
5742067 TTTCACGCCA
* * * * *
5742077 ATGAAAACAAGGTCTG-TTCTCTTCGATCTACTCTC-CCACCAGTATGGGGAGACAAGATCTGTT
1 ATGAAGACAAGATCTGCTT-TCTTCGATCT-GTTTCGCCACCAGTATGGGAAGACAAGATCTGTT
* * *
5742140 GTCTTTGATATACTTCACGCCAATAC
64 ATCTTTGATCTACTTCACGCCAGTAC
* * ** * * *
5742166 ATGAAGACAATATCTGTTTTTTCCTTCGATCTACTTCACCACCAGTCTGGGAAGACAAGATCTAT
1 ATGAAGACAAGATCTG--CTTT-CTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTGT
*
5742231 TATCTTTGATCTACTTCATGCCAGTAC
63 TATCTTTGATCTACTTCACGCCAGTAC
* *
5742258 ATGAAGACAAGATATGCTTTCTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTGTTAC
1 ATGAAGACAAGATCTGCTTTCTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTGTTAT
5742323 CTTTGATCTACTTCACGCCAGTAC
66 CTTTGATCTACTTCACGCCAGTAC
* *
5742347 ATGAAGACAAGATCTGCTTTCTTCGATCTGTTTCACCACCAGTATGAGAAGACAAGATCTGTTAT
1 ATGAAGACAAGATCTGCTTTCTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTGTTAT
*
5742412 CTTTGATCTACTTCACGCTAGTAC
66 CTTTGATCTACTTCACGCCAGTAC
* *
5742436 ATGAAGACAAGATCTGCTTTCTTTGATCTGTTTCGCCACCAGTATGGGAAAACAAGATCTGTTAT
1 ATGAAGACAAGATCTGCTTTCTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTGTTAT
5742501 CTTTGATCTACTTCACGCCAGTAC
66 CTTTGATCTACTTCACGCCAGTAC
5742525 ATGAAGACAAGATCTGCTTTCTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTGTTAT
1 ATGAAGACAAGATCTGCTTTCTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTGTTAT
5742590 CTTTGATCTACTTCACGCCAGTAC
66 CTTTGATCTACTTCACGCCAGTAC
*
5742614 ATGAAGACAAGATCTGCTTTCTTCGATCTATTTCGCCACCAGTATGGGAAGACAAGATCTGTTAT
1 ATGAAGACAAGATCTGCTTTCTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTGTTAT
5742679 CTTTGATCTACTTCACGCCAGTAC
66 CTTTGATCTACTTCACGCCAGTAC
5742703 ATGAAGACAAGATCT
1 ATGAAGACAAGATCT
5742718 ACNNNNNNNN
Statistics
Matches: 511, Mismatches: 36, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
89 433 0.85
90 3 0.01
91 3 0.01
92 72 0.14
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (89 bp):
ATGAAGACAAGATCTGCTTTCTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTGTTAT
CTTTGATCTACTTCACGCCAGTAC
Found at i:5742891 original size:44 final size:44
Alignment explanation
Indices: 5742839--5743171 Score: 303
Period size: 44 Copynumber: 7.5 Consensus size: 44
5742829 ACCAGTATGG
5742839 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACAT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACAT
* ** * * ***
5742883 GAAGACAAGATCTGCTT-TCTTCGATCTGTTTCGCCACCAGTATGG
1 GAAGACAAGATCTG-TTATCTTTGATCTACTTC-ACGCCAGTACAT
* *
5742928 GAAGACAAGATCTGTTATCTTTGATTTACTTTACGCCAGTACAT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACAT
* * * * ***
5742972 GAAGACAAGATATGCTT-TCTTTGATCTGCTTCGCCACCAGTATGG
1 GAAGACAAGATCTG-TTATCTTTGATCTACTTC-ACGCCAGTACAT
* * *
5743017 GAAGGCAAGATCTATTATCTTTGATCTACTCCACGCCAGTACAT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACAT
* * * * ***
5743061 GAAGACAAGATCTACTT-TCTTTGATCTGCTTCGCCACCAGTATGG
1 GAAGACAAGATCT-GTTATCTTTGATCTACTTC-ACGCCAGTACAT
* * * *
5743106 GAAGGCAAGATCTGGTATCTCTGATCTACTTCACGTCAGTACAT
1 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACAT
*
5743150 GAAGACAAGATCAGTTATCTTT
1 GAAGACAAGATCTGTTATCTTT
5743172 CAACCTGCTC
Statistics
Matches: 219, Mismatches: 61, Indels: 18
0.73 0.20 0.06
Matches are distributed among these distances:
44 119 0.54
45 100 0.46
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (44 bp):
GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACAT
Found at i:5742971 original size:89 final size:89
Alignment explanation
Indices: 5742823--5743161 Score: 561
Period size: 89 Copynumber: 3.8 Consensus size: 89
5742813 NNNNNNNTGT
5742823 TTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGA
1 TTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGA
* *
5742888 CAAGATCTGCTTTCTTCGATCTGT
66 CAAGATCTGCTTTCTTTGATCTGC
* *
5742912 TTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATTTACTTTACGCCAGTACATGAAGA
1 TTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGA
*
5742977 CAAGATATGCTTTCTTTGATCTGC
66 CAAGATCTGCTTTCTTTGATCTGC
* * *
5743001 TTCGCCACCAGTATGGGAAGGCAAGATCTATTATCTTTGATCTACTCCACGCCAGTACATGAAGA
1 TTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGA
*
5743066 CAAGATCTACTTTCTTTGATCTGC
66 CAAGATCTGCTTTCTTTGATCTGC
* * * *
5743090 TTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTCACGTCAGTACATGAAGA
1 TTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGA
5743155 CAAGATC
66 CAAGATC
5743162 AGTTATCTTT
Statistics
Matches: 233, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
89 233 1.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.30
Consensus pattern (89 bp):
TTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGA
CAAGATCTGCTTTCTTTGATCTGC
Found at i:5744055 original size:13 final size:13
Alignment explanation
Indices: 5744037--5744061 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5744027 AAATTGTCGA
5744037 GGATAACAAAGAT
1 GGATAACAAAGAT
5744050 GGATAACAAAGA
1 GGATAACAAAGA
5744062 AATTGATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.24, T:0.12
Consensus pattern (13 bp):
GGATAACAAAGAT
Found at i:5745418 original size:17 final size:18
Alignment explanation
Indices: 5745396--5745436 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
5745386 AAAAAATCCA
*
5745396 AAAGAAT-GTAAAGAATG
1 AAAGAATCGTAAAAAATG
5745413 AAAGAATCGTAAAAAATG
1 AAAGAATCGTAAAAAATG
*
5745431 ACAGAA
1 AAAGAA
5745437 CATTTGCTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.61, C:0.05, G:0.20, T:0.15
Consensus pattern (18 bp):
AAAGAATCGTAAAAAATG
Found at i:5747320 original size:19 final size:19
Alignment explanation
Indices: 5747280--5747321 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
5747270 ATAATCTTTG
* *
5747280 ATGCATATGATGTAATGTA
1 ATGCAAATGATGAAATGTA
5747299 ATGCAAATGCATGAAATG-A
1 ATGCAAATG-ATGAAATGTA
5747318 ATGC
1 ATGC
5747322 GAAAAGAGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (19 bp):
ATGCAAATGATGAAATGTA
Found at i:5747369 original size:13 final size:13
Alignment explanation
Indices: 5747351--5747376 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5747341 TGTTCAATTT
5747351 TTTACTAGAAAAC
1 TTTACTAGAAAAC
5747364 TTTACTAGAAAAC
1 TTTACTAGAAAAC
5747377 AAATCTCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
TTTACTAGAAAAC
Found at i:5752487 original size:45 final size:45
Alignment explanation
Indices: 5751808--5752493 Score: 483
Period size: 45 Copynumber: 15.3 Consensus size: 45
5751798 AGGTCTGTTC
* * * * * * * *
5751808 TCTTCGATCTACTCCCCCACTAGTATGGGGAGACAAGATTTGTTG
1 TCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTA
* * * *** * *
5751853 TCTTTGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGTTTTT
1 TCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTG--CTA
* * * **
5751899 TCCTTCGATCTACTTCGTCACCAGTCTGGGAAGACAAGATCTATTA
1 T-CTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTA
* * *** *
5751945 TCTTTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGCTT
1 TCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTA
* ** * * *
5751989 TCTTCGATCTGTTTTGCCACCAGTATGGGAAAACAAGATCTGTTA
1 TCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTA
* * * *** *
5752034 TCTTTGATCTACATC-ACGCCAGTACATGAAGACAAGATCTACT-
1 TCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTA
* ** * *
5752077 TTTTTCGATCTGTTTCGCCACCAGTATGGGAAGACAGGATCTGTTA
1 TCTTT-GATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTA
* * * ***
5752123 TCTTTGATATACTTC-ACGCCAGTACATGAAGACAAGATCTGCCT-
1 TCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTG-CTA
* ** *
5752167 TCTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTGTTA
1 TCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTA
* * *** *
5752212 TCTTTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGCTT
1 TCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTA
* ** *
5752256 TCTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTGTTA
1 TCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTA
* * *** *
5752301 TCTTTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGCTT
1 TCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTA
* * *
5752345 TCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTA
1 TCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTA
* *** * *
5752390 TCTTTGATCTAC-TC-CACGCCAGTACATGAAGACAAGATCTACTT
1 TCTTTGATCTACTTCGC-CACCAGTATGGGAAGACAAGATCTGCTA
* ** *
5752434 TCTTTGATCTGCTTCGCCACCAGTATGGGAAGGTAAGATCTGGTA
1 TCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTA
*
5752479 TCTCTGATCTACTTC
1 TCTTTGATCTACTTC
5752494 ACGTCAGTAC
Statistics
Matches: 475, Mismatches: 150, Indels: 32
0.72 0.23 0.05
Matches are distributed among these distances:
43 5 0.01
44 210 0.44
45 218 0.46
46 11 0.02
47 13 0.03
48 18 0.04
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.32
Consensus pattern (45 bp):
TCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTA
Found at i:5752527 original size:89 final size:89
Alignment explanation
Indices: 5751789--5752519 Score: 1086
Period size: 89 Copynumber: 8.2 Consensus size: 89
5751779 TTTCACGCCA
* * * * * * * * *
5751789 ATGAAAACAAGGTCTG-TTCTCTTCGATCTACTCCCCCACTAGTATGGGGAGACAAGATTTGTTG
1 ATGAAGACAAGATCTGCTT-TCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTTA
*
5751853 TCTTTGATCTACTTCACGCCAATAC
65 TCTTTGATCTACTTCACGCCAGTAC
* * * * *
5751878 ATGAAGACAAGATCTGTTTTTTCCTTCGATCTACTTCGTCACCAGTCTGGGAAGACAAGATCTAT
1 ATGAAGACAAGATCTG--CTTT-CTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGT
5751943 TATCTTTGATCTACTTCACGCCAGTAC
63 TATCTTTGATCTACTTCACGCCAGTAC
* * *
5751970 ATGAAGACAAGATCTGCTTTCTTCGATCTGTTTTGCCACCAGTATGGGAAAACAAGATCTGTTAT
1 ATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTTAT
*
5752035 CTTTGATCTACATCACGCCAGTAC
66 CTTTGATCTACTTCACGCCAGTAC
* * * *
5752059 ATGAAGACAAGATCTACTTTTTTCGATCTGTTTCGCCACCAGTATGGGAAGACAGGATCTGTTAT
1 ATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTTAT
*
5752124 CTTTGATATACTTCACGCCAGTAC
66 CTTTGATCTACTTCACGCCAGTAC
* *
5752148 ATGAAGACAAGATCTGCCTTCTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTGTTAT
1 ATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTTAT
5752213 CTTTGATCTACTTCACGCCAGTAC
66 CTTTGATCTACTTCACGCCAGTAC
*
5752237 ATGAAGACAAGATCTGCTTTCTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTGTTAT
1 ATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTTAT
5752302 CTTTGATCTACTTCACGCCAGTAC
66 CTTTGATCTACTTCACGCCAGTAC
* *
5752326 ATGAAGACAAGATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTAT
1 ATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTTAT
*
5752391 CTTTGATCTACTCCACGCCAGTAC
66 CTTTGATCTACTTCACGCCAGTAC
* * ** *
5752415 ATGAAGACAAGATCTACTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGTAAGATCTGGTAT
1 ATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTTAT
* *
5752480 CTCTGATCTACTTCACGTCAGTAC
66 CTTTGATCTACTTCACGCCAGTAC
5752504 ATGAAGACAAGATCTG
1 ATGAAGACAAGATCTG
5752520 TTATCTTTCA
Statistics
Matches: 593, Mismatches: 45, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
89 512 0.86
90 3 0.01
91 1 0.00
92 77 0.13
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (89 bp):
ATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTTAT
CTTTGATCTACTTCACGCCAGTAC
Found at i:5757684 original size:20 final size:20
Alignment explanation
Indices: 5757637--5757688 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 20
5757627 TTTTAAATAA
* *
5757637 ATATAAATATTTTTTTGTAT
1 ATATAATTATTTATTTGTAT
*
5757657 -TA-AATTATTTATTTGTTT
1 ATATAATTATTTATTTGTAT
5757675 ATATAATTATTTAT
1 ATATAATTATTTAT
5757689 ATTTATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 13 0.48
19 4 0.15
20 10 0.37
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (20 bp):
ATATAATTATTTATTTGTAT
Found at i:5762190 original size:18 final size:18
Alignment explanation
Indices: 5762150--5762318 Score: 134
Period size: 18 Copynumber: 9.4 Consensus size: 18
5762140 ACACGCTAAT
*
5762150 AATTTTTTAAAACACGA-
1 AATTTTTTGAAACACGAG
5762167 AA-TTTTTGAAACACGAG
1 AATTTTTTGAAACACGAG
* *
5762184 AACTTTTTGAGAACATGA-
1 AATTTTTTGA-AACACGAG
* ** *
5762202 AATTTTTTTTAAACGTGAA
1 AA-TTTTTTGAAACACGAG
*
5762221 AATTTTTTGAAACACGAA
1 AATTTTTTGAAACACGAG
* *
5762239 AATTTTTTCAAA-ACGCG
1 AATTTTTTGAAACACGAG
* *
5762256 AATTTTTTTATACACGAG
1 AATTTTTTGAAACACGAG
5762274 AATTTTTTTTGAAAACACGAG
1 AA--TTTTTTG-AAACACGAG
*
5762295 AA-TTTTTAAAACACGA-
1 AATTTTTTGAAACACGAG
5762311 AATTTTTT
1 AATTTTTT
5762319 TTGAAAACGC
Statistics
Matches: 125, Mismatches: 17, Indels: 20
0.77 0.10 0.12
Matches are distributed among these distances:
16 15 0.12
17 30 0.24
18 50 0.40
19 14 0.11
20 6 0.05
21 10 0.08
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (18 bp):
AATTTTTTGAAACACGAG
Found at i:5762210 original size:37 final size:36
Alignment explanation
Indices: 5762150--5762324 Score: 160
Period size: 37 Copynumber: 4.8 Consensus size: 36
5762140 ACACGCTAAT
*
5762150 AATTTTTTAAAACACGAAA--TTTTTGAAACACGAG
1 AATTTTTTGAAACACGAAATTTTTTTGAAACACGAG
* * * ** *
5762184 AACTTTTTGAGAACATGAAATTTTTTTTAAACGTGAA
1 AATTTTTTGA-AACACGAAATTTTTTTGAAACACGAG
* * *
5762221 AATTTTTTGAAACACGAAAATTTTTTCAAA-ACGCG
1 AATTTTTTGAAACACGAAATTTTTTTGAAACACGAG
* *
5762256 AATTTTTTTATACACGAGAATTTTTTTTGAAAACACGAG
1 AATTTTTTGAAACACGA-AA-TTTTTTTG-AAACACGAG
*
5762295 AA-TTTTTAAAACACGAAATTTTTTTTGAAA
1 AATTTTTTGAAACACGAAA-TTTTTTTGAAA
5762325 ACGCAAAAAT
Statistics
Matches: 112, Mismatches: 22, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
34 8 0.07
35 24 0.21
36 22 0.20
37 37 0.33
38 15 0.13
39 6 0.05
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.38
Consensus pattern (36 bp):
AATTTTTTGAAACACGAAATTTTTTTGAAACACGAG
Found at i:5762235 original size:55 final size:53
Alignment explanation
Indices: 5762169--5762337 Score: 171
Period size: 55 Copynumber: 3.1 Consensus size: 53
5762159 AAACACGAAA
* * *
5762169 TTTTTGAAACACGAGAACTTTTTGAGAACATGAAATTTTTTTTAAACGTGAAAAT
1 TTTTTGAAACACGAGAA-TTTTT-AAAACACGAAATTTTTTTTAAACGAGAAAAT
* * * **
5762224 TTTTTGAAACACGAAAATTTTTTCAAAACGCG-AATTTTTTTATACACGAGAATTT
1 TTTTTGAAACACGAGAA-TTTTT-AAAACACGAAATTTTTTT-TAAACGAGAAAAT
5762279 TTTTTGAAAACACGAGAATTTTTAAAACACGAAATTTTTTTTGAAAACGCA-AAAAT
1 TTTTTG-AAACACGAGAATTTTTAAAACACGAAATTTTTTTT--AAACG-AGAAAAT
5762335 TTT
1 TTT
5762338 GAAAAGAAGT
Statistics
Matches: 93, Mismatches: 15, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
54 17 0.18
55 55 0.59
56 20 0.22
57 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (53 bp):
TTTTTGAAACACGAGAATTTTTAAAACACGAAATTTTTTTTAAACGAGAAAAT
Found at i:5762291 original size:21 final size:21
Alignment explanation
Indices: 5762267--5762326 Score: 85
Period size: 17 Copynumber: 3.1 Consensus size: 21
5762257 ATTTTTTTAT
5762267 ACACGAGAATTTTTTTTGAAA
1 ACACGAGAATTTTTTTTGAAA
5762288 ACACGAGAA---TTTTT-AAA
1 ACACGAGAATTTTTTTTGAAA
5762305 ACACGA-AATTTTTTTTGAAA
1 ACACGAGAATTTTTTTTGAAA
5762325 AC
1 AC
5762327 GCAAAAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
16 2 0.06
17 9 0.26
18 5 0.14
19 5 0.14
20 5 0.14
21 9 0.26
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (21 bp):
ACACGAGAATTTTTTTTGAAA
Found at i:5763011 original size:17 final size:17
Alignment explanation
Indices: 5762988--5763035 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
5762978 TTGGACAGGC
5762988 CTGCTATTTTTTTGCTG
1 CTGCTATTTTTTTGCTG
* * *
5763005 TTGCTATTTTCTTACTG
1 CTGCTATTTTTTTGCTG
*
5763022 CTGCTGTTTTTTTG
1 CTGCTATTTTTTTG
5763036 GGCTGATCTG
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.06, C:0.17, G:0.17, T:0.60
Consensus pattern (17 bp):
CTGCTATTTTTTTGCTG
Found at i:5763145 original size:7 final size:7
Alignment explanation
Indices: 5763117--5763191 Score: 52
Period size: 7 Copynumber: 11.1 Consensus size: 7
5763107 TTTTTATTTT
5763117 TTTC-TC
1 TTTCTTC
*
5763123 TTTTTTC
1 TTTCTTC
*
5763130 TTTC-CC
1 TTTCTTC
5763136 TTTCTTC
1 TTTCTTC
*
5763143 TTTCTTT
1 TTTCTTC
5763150 TTTCTTC
1 TTTCTTC
*
5763157 TATCTTTC
1 TTTC-TTC
5763165 TTCTCTT-
1 TT-TCTTC
*
5763172 TTTCTCC
1 TTTCTTC
5763179 TTT-TTC
1 TTTCTTC
5763185 -TTCTTC
1 TTTCTTC
5763191 T
1 T
5763192 CCTTCGACAG
Statistics
Matches: 52, Mismatches: 10, Indels: 13
0.69 0.13 0.17
Matches are distributed among these distances:
5 2 0.04
6 16 0.31
7 26 0.50
8 6 0.12
9 2 0.04
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTCTTC
Found at i:5763175 original size:11 final size:11
Alignment explanation
Indices: 5763113--5763188 Score: 61
Period size: 11 Copynumber: 6.9 Consensus size: 11
5763103 AAAATTTTTA
5763113 TTTTT-TTCTC
1 TTTTTCTTCTC
*
5763123 TTTTTTCTTTCCC
1 -TTTTTC-TTCTC
5763136 TTTCTTCTT-TC
1 TTT-TTCTTCTC
*
5763147 TTTTTTCTTCTA
1 -TTTTTCTTCTC
*
5763159 TCTTTCTTCTC
1 TTTTTCTTCTC
5763170 TTTTTC-TC-C
1 TTTTTCTTCTC
5763179 TTTTTCTTCT
1 TTTTTCTTCT
5763189 TCTCCTTCGA
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
9 7 0.13
10 4 0.08
11 25 0.48
12 9 0.17
13 7 0.13
ACGTcount: A:0.01, C:0.26, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTTTCTTCTC
Found at i:5763839 original size:30 final size:29
Alignment explanation
Indices: 5763710--5763844 Score: 73
Period size: 30 Copynumber: 4.6 Consensus size: 29
5763700 TAAGAAATAT
*
5763710 GGGGCAAAAATGTAATTTTTAGAAAGTTTA
1 GGGGC-AAAATGTAATTTTTACAAAGTTTA
** * *
5763740 GGGGCCCAATTTAA--TTTACAAATTATTA
1 GGGGCAAAATGTAATTTTTACAAAGT-TTA
* * ** *
5763768 GGGG-ATAAGATGTAA-ATTTAGAAAAAATAA
1 GGGGCA-AA-ATGTAATTTTTA-CAAAGTTTA
*
5763798 GGGTCAAAATGTAATTTTTGA-AAAGTTTA
1 GGGGCAAAATGTAATTTTT-ACAAAGTTTA
5763827 GGGGCTAAAATGTAATTT
1 GGGGC-AAAATGTAATTT
5763845 GTATTTTTTC
Statistics
Matches: 78, Mismatches: 18, Indels: 18
0.68 0.16 0.16
Matches are distributed among these distances:
27 8 0.10
28 8 0.10
29 26 0.33
30 31 0.40
31 5 0.06
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.33
Consensus pattern (29 bp):
GGGGCAAAATGTAATTTTTACAAAGTTTA
Found at i:5764258 original size:76 final size:74
Alignment explanation
Indices: 5764155--5765207 Score: 1236
Period size: 76 Copynumber: 13.7 Consensus size: 74
5764145 AATCCGAAGT
* **
5764155 TCAACTCACTTCTCAG-ATTATGAGTTGA-CCTTTGAAAAATAGAAATTGAAAAATACCTCGACG
1 TCAACTCACCTCTC-GCATTATGAGTTGATTTTTTGAAAAATAGAAATT-AAAAATACCTC-A-G
*
5764218 TGTGACCCGAGGC
62 CGTGACCCGAGGC
* * ** * * *
5764231 TCAACTCACCTCTCGCATTATGTGTTGATTTTTTTTGAAGAGCATAAATTGAAAATACCTCAGCA
1 TCAACTCACCTCTCGCATTATGAGTTGA--TTTTTTGAAAAATAGAAATTAAAAATACCTCAGCG
*
5764296 TGACCCGAGAC
64 TGACCCGAGGC
5764307 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTTTTTGAAAAATAGAAATTAAAAATACCTCAG
1 TCAACTCACCTCTCGCATTATGAGTTGA----TTTTTTGAAAAATAGAAATTAAAAATACCTCAG
*
5764372 CGTGACCTGAGGC
62 CGTGACCCGAGGC
5764385 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTTTGAAAAATAGAAATTAAAAATACCTTC-GC
1 TCAACTCACCTCTCGCATTATGAGTTGA--TTTTTTGAAAAATAGAAATTAAAAATACC-TCAGC
5764449 GTGACCCGAGGC
63 GTGACCCGAGGC
* * *
5764461 TCAACTCACCTCTCGTATTATGAGTTGATTTTTTTTGAAAAATAGAAGTTAAAAATACCTTAGCG
1 TCAACTCACCTCTCGCATTATGAGTTGA--TTTTTTGAAAAATAGAAATTAAAAATACCTCAGCG
5764526 TGACCCGAGGC
64 TGACCCGAGGC
* ** *
5764537 TCAACTCACCTCTCGCATTATAAGTTGATTTTTAAAAAAAATAGAAATTAAAAATACCTCAGTGT
1 TCAACTCACCTCTCGCATTATGAGTTGATTTTT-TGAAAAATAGAAATTAAAAATACCTCAGCGT
5764602 GACCCGAGGC
65 GACCCGAGGC
*
5764612 TCAAATCACCTCTCGCATTATGAGTTGATATTTTTTTGAAAAATAGAAATTAAAAATACCTCAGC
1 TCAACTCACCTCTCGCATTATGAGTTG--A-TTTTTTGAAAAATAGAAATTAAAAATACCTCAGC
* *
5764677 ATGACCCGAGGT
63 GTGACCCGAGGC
* ** * * *
5764689 TCAACTCACCTCTCGCATTGTGAGCCGATTTTTTTTTGAAAAATAAAAAATAAAAATATCTCAGC
1 TCAACTCACCTCTCGCATTATGAGTTGA---TTTTTTGAAAAATAGAAATTAAAAATACCTCAGC
5764754 GTGACCCGAGGC
63 GTGACCCGAGGC
* * *
5764766 TCAACTCACCTCTCGCATTATGAGTTAATTTTTTTTGAAAAATAGAAATAAAAAATACCTCAGTG
1 TCAACTCACCTCTCGCATTATGAGTTGA--TTTTTTGAAAAATAGAAATTAAAAATACCTCAGCG
5764831 TGACCCGAGGC
64 TGACCCGAGGC
*
5764842 TCAACTCACCTCTCGCATTATGAGTTGTTTTTTTTTGAAAAATAGAAATTAAAAATACCTCAGCG
1 TCAACTCACCTCTCGCATTATGAGTTG--ATTTTTTGAAAAATAGAAATTAAAAATACCTCAGCG
5764907 TGACCCGAGGC
64 TGACCCGAGGC
* *
5764918 TCAACTCACCTCTCGCATTATGAGTTGTTTTTTTTTTAAAAAATAGAAATTAAAAATACCTCAGC
1 TCAACTCACCTCTCGCATTATGAGTTG---ATTTTTTGAAAAATAGAAATTAAAAATACCTCAGC
5764983 GTGACCCGAGGC
63 GTGACCCGAGGC
* * *
5764995 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTTTGAAAAACATAAATTGAAAATACCTCAGCG
1 TCAACTCACCTCTCGCATTATGAGTTGA--TTTTTTGAAAAATAGAAATTAAAAATACCTCAGCG
*
5765060 TGACCCAAGGC
64 TGACCCGAGGC
** * * * *
5765071 TCAACTCAGTTCTCGCCA-TCTGAGATGA-TTTTTGAAAAAAACATAAATTTAAAAAAATACCTC
1 TCAACTCACCTCTCG-CATTATGAGTTGATTTTTTG--AAAAATAGAAA-TT--AAAAATACCTC
**
5765134 GATATGTGACCCGAGGC
60 -A-GCGTGACCCGAGGC
* * *
5765151 TCAACTTACCTCTCGCAATATTAGTTGA-TTTTTGAAAAAAATAGAAATTGAAAAATA
1 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTG--AAAAATAGAAATT-AAAAATA
5765208 TTTCTTGAAA
Statistics
Matches: 864, Mismatches: 85, Indels: 54
0.86 0.08 0.05
Matches are distributed among these distances:
73 6 0.01
74 5 0.01
75 75 0.09
76 407 0.47
77 206 0.24
78 100 0.12
79 18 0.02
80 47 0.05
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (74 bp):
TCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAATAGAAATTAAAAATACCTCAGCGTG
ACCCGAGGC
Found at i:5764784 original size:229 final size:228
Alignment explanation
Indices: 5764185--5765207 Score: 1381
Period size: 229 Copynumber: 4.4 Consensus size: 228
5764175 TGAGTTGACC
*
5764185 TTTGAAAAATAGAAATTGAAAAATACCTCGACGTGTGACCCGAGGCTCAACTCACCTCTCGCATT
1 TTTGAAAAATAGAAATT-AAAAATACCTC-A-GCGTGACCCGAGGCTCAACTCACCTCTCGCATT
* * ** * * * *
5764250 ATGTGTTGATTTTTTTTGAAGAGCATAAATTGAAAATACCTCAGCATGACCCGAGACTCAACTCA
63 ATGAGTTGATTTTTTTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCA
*
5764315 CCTCTCGCATTATGAGTTGATTTTTTTTTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCT
128 CCTCTCGCATTATGAGTTGA--TTTTTTTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCC
5764380 GAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTT
191 GAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTT
*
5764418 TTTGAAAAATAGAAATTAAAAATACCTTC-GCGTGACCCGAGGCTCAACTCACCTCTCGTATTAT
1 TTTGAAAAATAGAAATTAAAAATACC-TCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTAT
* *
5764482 GAGTTGATTTTTTTTGAAAAATAGAAGTTAAAAATACCTTAGCGTGACCCGAGGCTCAACTCACC
65 GAGTTGATTTTTTTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACC
* *** *
5764547 TCTCGCATTATAAGTTGA-TTTTTAAAAAAAATAGAAATTAAAAATACCTCAGTGTGACCCGAGG
130 TCTCGCATTATGAGTTGATTTTTTTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGG
*
5764611 CTCAAATCACCTCTCGCATTATGAGTTGATATTTT
195 CTCAACTCACCTCTCGCATTATGAGTTGAT-TTTT
* * *
5764646 TTTGAAAAATAGAAATTAAAAATACCTCAGCATGACCCGAGGTTCAACTCACCTCTCGCATTGTG
1 TTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATG
** * * *
5764711 AGCCGATTTTTTTTTGAAAAATAAAAAATAAAAATATCTCAGCGTGACCCGAGGCTCAACTCACC
66 AGTTGA-TTTTTTTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACC
* * *
5764776 TCTCGCATTATGAGTTAATTTTTTTTGAAAAATAGAAATAAAAAATACCTCAGTGTGACCCGAGG
130 TCTCGCATTATGAGTTGATTTTTTTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGG
*
5764841 CTCAACTCACCTCTCGCATTATGAGTTGTTTTTT
195 CTCAACTCACCTCTCGCATTATGAGTTGATTTTT
5764875 TTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATG
1 TTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATG
* *
5764940 AGTTGTTTTTTTTTTAAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACC
66 AGTTG-ATTTTTTTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACC
* * * *
5765005 TCTCGCATTATGAGTTGATTTTTTTTGAAAAACATAAATTGAAAATACCTCAGCGTGACCCAAGG
130 TCTCGCATTATGAGTTGATTTTTTTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGG
** * *
5765070 CTCAACTCAGTTCTCGCCA-TCTGAGATGATTTTT
195 CTCAACTCACCTCTCG-CATTATGAGTTGATTTTT
**** * ** *
5765104 GAAAAAAACATA-AATTTAAAAAAATACCTCGATATGTGACCCGAGGCTCAACTTACCTCTCGCA
1 TTTGAAAA-ATAGAAATT--AAAAATACCTC-A-GCGTGACCCGAGGCTCAACTCACCTCTCGCA
* * ***
5765168 ATATTAGTTGA-TTTTTGAAAAAAATAGAAATTGAAAAATA
61 TTATGAGTTGATTTTTTTTGAAAAATAGAAATT-AAAAATA
5765208 TTTCTTGAAA
Statistics
Matches: 704, Mismatches: 73, Indels: 27
0.88 0.09 0.03
Matches are distributed among these distances:
227 72 0.10
228 66 0.09
229 284 0.40
230 180 0.26
231 30 0.04
232 17 0.02
233 55 0.08
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (228 bp):
TTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATG
AGTTGATTTTTTTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCT
CTCGCATTATGAGTTGATTTTTTTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGC
TCAACTCACCTCTCGCATTATGAGTTGATTTTT
Found at i:5764864 original size:381 final size:382
Alignment explanation
Indices: 5764189--5765078 Score: 1435
Period size: 381 Copynumber: 2.3 Consensus size: 382
5764179 TTGACCTTTG
*
5764189 AAAAATAGAAATTGAAAAATACCTCGACGTGTGACCCGAGGCTCAACTCACCTCTCGCATTATGT
1 AAAAATAGAAATT-AAAAATACCTC-A-GTGTGACCCGAGGCTCAACTCACCTCTCGCATTATGA
* * *
5764254 GTTGATTTTTTTTGAAGAGCATAAATTGAAAATACCTCAGCATGACCCGAGACTCAACTCACCTC
63 GTTGATTTTTTTTGAAAAACATAAATTGAAAATACCTCAGCATGACCCGAGGCTCAACTCACCTC
** * * *
5764319 TCGCATTATGAGTTGATTTTTTTTTTGAAAAATAGAAATTAAAAATACCTCAGCGTGACCTGAGG
128 TCGCATTATGAGCCGATTTTTTTTTTGAAAAATAAAAAATAAAAATACCTCAGCGTGACCCGAGG
* *
5764384 CTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTTGAAAAATAGAAATTAAAAATACCTTCGC
193 CTCAACTCACCTCTCGCATTATGAGTTAATTTTTTTTGAAAAATAGAAATAAAAAATACCTTCGC
* *
5764449 GTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTTTTGAAAAATAGAAGTTAAA
258 GTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTTGAAAAATAGAAATTAAA
*
5764514 AATACCTTAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATAAGTTG-ATTTTTAAA
323 AATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATAAGTTGTATTTTTAAA
*
5764573 AAAAATAGAAATTAAAAATACCTCAGTGTGACCCGAGGCTCAAATCACCTCTCGCATTATGAGTT
1 AAAAATAGAAATTAAAAATACCTCAGTGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTT
* * * *
5764638 GATATTTTTTTGAAAAATAGAAATTAAAAATACCTCAGCATGACCCGAGGTTCAACTCACCTCTC
66 GAT-TTTTTTTGAAAAACATAAATTGAAAATACCTCAGCATGACCCGAGGCTCAACTCACCTCTC
* *
5764703 GCATTGTGAGCCGA-TTTTTTTTTGAAAAATAAAAAATAAAAATATCTCAGCGTGACCCGAGGCT
130 GCATTATGAGCCGATTTTTTTTTTGAAAAATAAAAAATAAAAATACCTCAGCGTGACCCGAGGCT
*
5764767 CAACTCACCTCTCGCATTATGAGTTAATTTTTTTTGAAAAATAGAAATAAAAAATACC-TCAGTG
195 CAACTCACCTCTCGCATTATGAGTTAATTTTTTTTGAAAAATAGAAATAAAAAATACCTTC-GCG
*
5764831 TGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGTTTTTTTTTGAAAAATAGAAATTAAAA
259 TGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTTGAAAAATAGAAATTAAAA
* * **
5764896 ATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGTTTTTTTTTTA
324 ATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATAAGTTG-TATTTTTAAA
*
5764956 AAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTT
1 AAAAATAGAAATTAAAAATACCTCAGTGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTT
* *
5765021 GATTTTTTTTGAAAAACATAAATTGAAAATACCTCAGCGTGACCCAAGGCTCAACTCA
66 GATTTTTTTTGAAAAACATAAATTGAAAATACCTCAGCATGACCCGAGGCTCAACTCA
5765079 GTTCTCGCCA
Statistics
Matches: 467, Mismatches: 35, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
380 2 0.00
381 254 0.54
382 115 0.25
383 83 0.18
384 13 0.03
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (382 bp):
AAAAATAGAAATTAAAAATACCTCAGTGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTT
GATTTTTTTTGAAAAACATAAATTGAAAATACCTCAGCATGACCCGAGGCTCAACTCACCTCTCG
CATTATGAGCCGATTTTTTTTTTGAAAAATAAAAAATAAAAATACCTCAGCGTGACCCGAGGCTC
AACTCACCTCTCGCATTATGAGTTAATTTTTTTTGAAAAATAGAAATAAAAAATACCTTCGCGTG
ACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTTGAAAAATAGAAATTAAAAAT
ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATAAGTTGTATTTTTAAA
Found at i:5766063 original size:1 final size:1
Alignment explanation
Indices: 5766057--5766106 Score: 55
Period size: 1 Copynumber: 50.0 Consensus size: 1
5766047 TTCATCTTGG
* * * * *
5766057 TTTTTTTCTTTTTTTTGTTTTTGTTTTTTGTTTTTTTTTTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5766107 AGGCATAATA
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.00, C:0.02, G:0.08, T:0.90
Consensus pattern (1 bp):
T
Found at i:5766070 original size:7 final size:7
Alignment explanation
Indices: 5766067--5766106 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
5766057 TTTTTTTCTT
5766067 TTTTTTG
1 TTTTTTG
5766074 -TTTTTG
1 TTTTTTG
5766080 TTTTTTG
1 TTTTTTG
*
5766087 TTTTTTT
1 TTTTTTG
5766094 TTTTTTG
1 TTTTTTG
5766101 TTTTTT
1 TTTTTT
5766107 AGGCATAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 6 0.20
7 24 0.80
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (7 bp):
TTTTTTG
Found at i:5766083 original size:21 final size:21
Alignment explanation
Indices: 5766066--5766106 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
5766056 GTTTTTTTCT
5766066 TTTTTTTGTTTTTGTTTTTTG
1 TTTTTTTGTTTTTGTTTTTTG
*
5766087 TTTTTTTTTTTTTGTTTTTT
1 TTTTTTTGTTTTTGTTTTTT
5766107 AGGCATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (21 bp):
TTTTTTTGTTTTTGTTTTTTG
Found at i:5771273 original size:4 final size:4
Alignment explanation
Indices: 5771259--5771295 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
5771249 ATGTACATGC
*
5771259 AATG CATG AATG AATG AATG AATG AATG AATG AATG A
1 AATG AATG AATG AATG AATG AATG AATG AATG AATG A
5771296 CAAGTGAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.24, T:0.24
Consensus pattern (4 bp):
AATG
Found at i:5773447 original size:16 final size:17
Alignment explanation
Indices: 5773402--5773616 Score: 113
Period size: 18 Copynumber: 12.1 Consensus size: 17
5773392 CGTGATTCGA
*
5773402 TTGAAACACGAGATTTTTT
1 TTGAAACACGAGA--ATTT
*
5773421 TTAAAAACACGAGAA-TT
1 TT-GAAACACGAGAATTT
* *
5773438 TTGTAACACGGTAATAATTT
1 TTGAAACAC-G--AGAATTT
5773458 TTGAAAACACGA-AATTT
1 TTG-AAACACGAGAATTT
5773475 TTGAAACACGAGAATTTT
1 TTGAAACACGAGAA-TTT
5773493 TTGAAA-AC-ATGAATTTT
1 TTGAAACACGA-GAA-TTT
* * * *
5773510 TTTAAACTCAAAAAATTT
1 TTGAAACAC-GAGAATTT
5773528 TTGAAACACGA-AATTTTT
1 TTGAAACACGAGAA--TTT
* *
5773546 TTGAAAACGCGAAAATTT
1 TTG-AAACACGAGAATTT
5773564 TT-AAACACGAGAATTTTT
1 TTGAAACACGAGAA--TTT
*
5773582 TTGAAAACACGAGAATTC
1 TTG-AAACACGAGAATTT
*
5773600 TTAAAACAC-A-AATTT
1 TTGAAACACGAGAATTT
5773615 TT
1 TT
5773617 TTTTGAAAAC
Statistics
Matches: 158, Mismatches: 18, Indels: 44
0.72 0.08 0.20
Matches are distributed among these distances:
15 6 0.04
16 26 0.16
17 36 0.23
18 41 0.26
19 14 0.09
20 30 0.19
21 5 0.03
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (17 bp):
TTGAAACACGAGAATTT
Found at i:5773501 original size:35 final size:35
Alignment explanation
Indices: 5773402--5773616 Score: 142
Period size: 35 Copynumber: 6.1 Consensus size: 35
5773392 CGTGATTCGA
* *
5773402 TTGAAACACGAGATTTTTTTTAAAAACACGAGAA-TT
1 TTGAAACACGAGA-ATTTTTTGAAAACACGA-AATTT
*
5773438 TTGTAACACG-GTAATAATTTTTGAAAACACGAAATTT
1 TTGAAACACGAG-AAT--TTTTTGAAAACACGAAATTT
* *
5773475 TTGAAACACGAGAATTTTTTGAAAACATGAATTTT
1 TTGAAACACGAGAATTTTTTGAAAACACGAAATTT
* * * * *
5773510 TTTAAACTCAAAAAATTTTTG-AAACACGAAATTTTT
1 TTGAAACACGAGAATTTTTTGAAAACACGAAA--TTT
* *
5773546 TTGAAA-ACGCGAAAATTTTT--AAACACGAGAATTTTT
1 TTGAAACACGAG-AATTTTTTGAAAACACGA-AA--TTT
*
5773582 TTGAAAACACGAGAA-TTCTT-AAAACAC-AAATTT
1 TTG-AAACACGAGAATTTTTTGAAAACACGAAATTT
5773615 TT
1 TT
5773617 TTTTGAAAAC
Statistics
Matches: 147, Mismatches: 20, Indels: 27
0.76 0.10 0.14
Matches are distributed among these distances:
33 5 0.03
34 8 0.05
35 47 0.32
36 43 0.29
37 39 0.27
38 5 0.03
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (35 bp):
TTGAAACACGAGAATTTTTTGAAAACACGAAATTT
Found at i:5773512 original size:53 final size:52
Alignment explanation
Indices: 5773455--5773641 Score: 148
Period size: 53 Copynumber: 3.5 Consensus size: 52
5773445 ACGGTAATAA
* * *
5773455 TTTTTGAAAACACGAAATTTTTGAAACACGAGAATTTTTTGAAAACATGAAT
1 TTTTTTAAAACACAAAATTTTTGAAACACGAGAATTTTTTGAAAACACGAAT
* * * *
5773507 TTTTTTAAACTCAAAAAATTTTTGAAACACGA-AATTTTTTTGAAAACGCGAAA
1 TTTTTTAAA-ACACAAAATTTTTGAAACACGAGAA-TTTTTTGAAAACACGAAT
* * * *
5773560 ATTTTT-AAACACGAGAATTTTTTTGAAAACACGAGAA-TTCTT-AAAACACAAATTT
1 TTTTTTAAAACAC-A-AA-ATTTTTG-AAACACGAGAATTTTTTGAAAACACGAA--T
* *
5773615 TTTTTTGAAAACGCAAAAATTTTGAAA
1 TTTTTT-AAAACACAAAATTTTTGAAA
5773642 AGAAGTATCT
Statistics
Matches: 105, Mismatches: 19, Indels: 21
0.72 0.13 0.14
Matches are distributed among these distances:
51 2 0.02
52 13 0.12
53 52 0.50
54 15 0.14
55 15 0.14
56 3 0.03
57 5 0.05
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (52 bp):
TTTTTTAAAACACAAAATTTTTGAAACACGAGAATTTTTTGAAAACACGAAT
Found at i:5773561 original size:36 final size:36
Alignment explanation
Indices: 5773453--5773641 Score: 162
Period size: 36 Copynumber: 5.3 Consensus size: 36
5773443 ACACGGTAAT
5773453 AATTTTTGAAAACACGAAA--TTTTTG-AAACACGAGA
1 AATTTTTG-AAACACGAAATTTTTTTGAAAACACGA-A
* * * *
5773488 ATTTTTTGAAAACATG-AATTTTTTT--AAACTCAAAA
1 AATTTTTG-AAACACGAAATTTTTTTGAAAACAC-GAA
*
5773523 AATTTTTGAAACACGAAATTTTTTTGAAAACGCGAA
1 AATTTTTGAAACACGAAATTTTTTTGAAAACACGAA
*
5773559 AATTTTT-AAACACGAGAATTTTTTTGAAAACACGAG
1 AATTTTTGAAACACGA-AATTTTTTTGAAAACACGAA
* * *
5773595 AATTCTTAAAACAC-AAATTTTTTTTTGAAAACGC-AA
1 AATTTTTGAAACACGAAA--TTTTTTTGAAAACACGAA
*
5773631 AAATTTTGAAA
1 AATTTTTGAAA
5773642 AGAAGTATCT
Statistics
Matches: 128, Mismatches: 16, Indels: 19
0.79 0.10 0.12
Matches are distributed among these distances:
34 8 0.06
35 46 0.36
36 49 0.38
37 25 0.20
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.35
Consensus pattern (36 bp):
AATTTTTGAAACACGAAATTTTTTTGAAAACACGAA
Found at i:5773618 original size:37 final size:36
Alignment explanation
Indices: 5773521--5773642 Score: 124
Period size: 37 Copynumber: 3.3 Consensus size: 36
5773511 TTAAACTCAA
* *
5773521 AAAATTTTTGAAACACGA-AATTTTTTTGAAAACGCG
1 AAAA-TTTTAAAACACGAGAATTTTTTTGAAAACACG
*
5773557 AAAATTTTTAAACACGAGAATTTTTTTGAAAACACG
1 AAAATTTTAAAACACGAGAATTTTTTTGAAAACACG
* * *
5773593 AGAATTCTTAAAACAC-A-AATTTTTTTTTGAAAACGCA
1 AAAATT-TTAAAACACGAGAA--TTTTTTTGAAAACACG
5773630 AAAATTTTGAAAA
1 AAAATTTT-AAAA
5773643 GAAGTATCTT
Statistics
Matches: 74, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
35 14 0.19
36 29 0.39
37 31 0.42
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.34
Consensus pattern (36 bp):
AAAATTTTAAAACACGAGAATTTTTTTGAAAACACG
Found at i:5774334 original size:15 final size:15
Alignment explanation
Indices: 5774314--5774361 Score: 51
Period size: 17 Copynumber: 3.0 Consensus size: 15
5774304 TTGGACAGGC
5774314 CTGCTATTTTTTTTG
1 CTGCTATTTTTTTTG
*
5774329 CTGCTAATGTTTTTTTA
1 CTGCT-AT-TTTTTTTG
*
5774346 CTGTTACTTTTTTTTG
1 CTGCTA-TTTTTTTTG
5774362 GGGCTGATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 5 0.19
16 10 0.37
17 12 0.44
ACGTcount: A:0.10, C:0.12, G:0.12, T:0.65
Consensus pattern (15 bp):
CTGCTATTTTTTTTG
Found at i:5774457 original size:7 final size:7
Alignment explanation
Indices: 5774442--5774502 Score: 50
Period size: 7 Copynumber: 8.1 Consensus size: 7
5774432 ATTTTTATTG
*
5774442 TTTTCTC
1 TTTTTTC
5774449 TTTTTTC
1 TTTTTTC
5774456 TTTCCCTTTC
1 TTT---TTTC
*
5774466 TTCTTTC
1 TTTTTTC
5774473 TTTTTTC
1 TTTTTTC
*
5774480 TTCTTTC
1 TTTTTTC
*
5774487 TTTCTTC
1 TTTTTTC
5774494 TATTTTTC
1 T-TTTTTC
5774502 T
1 T
5774503 CCTTTTTCGT
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
7 31 0.72
8 6 0.14
10 6 0.14
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTTTC
Found at i:5774480 original size:11 final size:11
Alignment explanation
Indices: 5774447--5774502 Score: 53
Period size: 11 Copynumber: 4.9 Consensus size: 11
5774437 TATTGTTTTC
5774447 TCTTTTTTCTT
1 TCTTTTTTCTT
*
5774458 TCCCTTTCTTCTT
1 T--CTTTTTTCTT
5774471 TCTTTTTTC-T
1 TCTTTTTTCTT
5774481 TCTTTCTTTC-T
1 TCTTT-TTTCTT
5774492 TCTATTTTTCT
1 TCT-TTTTTCT
5774503 CCTTTTTCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
10 6 0.16
11 20 0.53
12 2 0.05
13 10 0.26
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (11 bp):
TCTTTTTTCTT
Found at i:5774481 original size:14 final size:14
Alignment explanation
Indices: 5774462--5774494 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
5774452 TTTCTTTCCC
5774462 TTTCTTCTTTCTTT
1 TTTCTTCTTTCTTT
5774476 TTTCTTCTTTCTTT
1 TTTCTTCTTTCTTT
*
5774490 CTTCT
1 TTTCT
5774495 ATTTTTCTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTCTTCTTTCTTT
Found at i:5774642 original size:13 final size:13
Alignment explanation
Indices: 5774617--5774652 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
5774607 TTTTCTCTTC
5774617 TTTCTTCTTTACTG
1 TTTCTT-TTTACTG
*
5774631 TTTCTTTTTACTT
1 TTTCTTTTTACTG
5774644 TTTCTTTTT
1 TTTCTTTTT
5774653 CTTGCTGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.06, C:0.17, G:0.03, T:0.75
Consensus pattern (13 bp):
TTTCTTTTTACTG
Found at i:5781225 original size:72 final size:72
Alignment explanation
Indices: 5781144--5781291 Score: 269
Period size: 72 Copynumber: 2.1 Consensus size: 72
5781134 ATGGGGTGGA
* *
5781144 ACCATTTATTTTATTTTTGTAAAGAGAGAACGATTCCAGTCTGGATAAATTACCCAAAGAGGAAG
1 ACCATTTATTTTATTTTTGTAAAGAAAGAACGATTCCAGGCTGGATAAATTACCCAAAGAGGAAG
5781209 GGATGGG
66 GGATGGG
*
5781216 ACCATTTATTTTATTTTTGTAAAGAAAGAACGATTCCAGGCTGGATAAATTACCCGAAGAGGAAG
1 ACCATTTATTTTATTTTTGTAAAGAAAGAACGATTCCAGGCTGGATAAATTACCCAAAGAGGAAG
5781281 GGATGGG
66 GGATGGG
5781288 ACCA
1 ACCA
5781292 ACAAGCATAT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.28
Consensus pattern (72 bp):
ACCATTTATTTTATTTTTGTAAAGAAAGAACGATTCCAGGCTGGATAAATTACCCAAAGAGGAAG
GGATGGG
Found at i:5781477 original size:144 final size:144
Alignment explanation
Indices: 5781280--5781587 Score: 564
Period size: 144 Copynumber: 2.1 Consensus size: 144
5781270 CGAAGAGGAA
* *
5781280 GGGATGGGACCAACAAGCATATTAGACGATAGAGTCAGTGTAATCAAATTCGTTAGCCTCCCAAT
1 GGGATTGGACCAACAAGCATATTAGACCATAGAGTCAGTGTAATCAAATTCGTTAGCCTCCCAAT
*
5781345 TTCCTGTGGAATGGATCCATTAAGCTGGTTGTCCTGAAGGAGCAACGACTCTAGATTGGTTACAT
66 TTCCTGTGGAATGGATCCATTAAGCTGGTTGTCCTGAAGAAGCAACGACTCTAGATTGGTTACAT
5781410 TGCTGATAGAAGAT
131 TGCTGATAGAAGAT
5781424 GGGATTGGACCAACAAGCATATTAGACCATAGA-TACAGTGTAATCAAATTCGTTAGCCTCCCAA
1 GGGATTGGACCAACAAGCATATTAGACCATAGAGT-CAGTGTAATCAAATTCGTTAGCCTCCCAA
*
5781488 TTTCCTGTGGAATGGATCCATTAAGTTGGTTGTCCTGAAGAAGCAACGACTCTAGATTGGTTACA
65 TTTCCTGTGGAATGGATCCATTAAGCTGGTTGTCCTGAAGAAGCAACGACTCTAGATTGGTTACA
5781553 TTGCTGATAGAAGAT
130 TTGCTGATAGAAGAT
5781568 GGGATTGGACCAACAAGCAT
1 GGGATTGGACCAACAAGCAT
5781588 GTTGTTCGAG
Statistics
Matches: 159, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
143 1 0.01
144 158 0.99
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (144 bp):
GGGATTGGACCAACAAGCATATTAGACCATAGAGTCAGTGTAATCAAATTCGTTAGCCTCCCAAT
TTCCTGTGGAATGGATCCATTAAGCTGGTTGTCCTGAAGAAGCAACGACTCTAGATTGGTTACAT
TGCTGATAGAAGAT
Found at i:5786926 original size:32 final size:32
Alignment explanation
Indices: 5786888--5786954 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
5786878 ATATTCAACA
5786888 ATCTTCATAACAACCAATATACATATATGCCT
1 ATCTTCATAACAACCAATATACATATATGCCT
5786920 ATCTTCATAACAACCAATATACATATATGCCT
1 ATCTTCATAACAACCAATATACATATATGCCT
5786952 ATC
1 ATC
5786955 CACTAAACAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.40, C:0.25, G:0.03, T:0.31
Consensus pattern (32 bp):
ATCTTCATAACAACCAATATACATATATGCCT
Found at i:5787158 original size:41 final size:41
Alignment explanation
Indices: 5787096--5787205 Score: 175
Period size: 41 Copynumber: 2.7 Consensus size: 41
5787086 ATTTAACATC
* *
5787096 TTCAGATCACCAGCACTTAGCCTGCTAGGTTTATAACCTGA
1 TTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGA
* * *
5787137 TTCATATCACCGGCACTTAGCCTACTAGGCTTATAGCCTGA
1 TTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGA
5787178 TTCAGATCACCGGCACTTAGCCTGCTAG
1 TTCAGATCACCGGCACTTAGCCTGCTAG
5787206 ACGTAAAGTC
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (41 bp):
TTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGA
Found at i:5787229 original size:41 final size:41
Alignment explanation
Indices: 5787098--5787260 Score: 132
Period size: 41 Copynumber: 4.0 Consensus size: 41
5787088 TTAACATCTT
* *** * **
5787098 CAGATCACCAGCACTTAGCCTGCTAGGTTTATAA-CCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGACGTA-AAGTCTGAAA
* * * * * * **
5787139 CATATCACCGGCACTTAGCCTACTAGGCTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGACGTAAAGTCTGAAA
5787180 CAGATCACCGGCACTTAGCCTGCTAGACGTAAAGTCTGAAA
1 CAGATCACCGGCACTTAGCCTGCTAGACGTAAAGTCTGAAA
** *
5787221 CATTTCACCGGCA-TCAAGCCTGCTAGACGTAAAGTCTGAA
1 CAGATCACCGGCACT-TAGCCTGCTAGACGTAAAGTCTGAA
5787261 TTATCTCATT
Statistics
Matches: 104, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
40 2 0.02
41 102 0.98
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGACGTAAAGTCTGAAA
Found at i:5787241 original size:82 final size:82
Alignment explanation
Indices: 5787096--5787246 Score: 180
Period size: 82 Copynumber: 1.8 Consensus size: 82
5787086 ATTTAACATC
*** ** *
5787096 TTCAGATCACCAGCACTTAGCCTGCTAGGTTTATAACCTGATTCATATCACCGGCACTTAGCCTA
1 TTCAGATCACCAGCACTTAGCCTGCTAGACGTATAACCTGAAACATATCACCGGCACTAAGCCTA
5787161 CTAGGCTTATAGCCTGA
66 CTAGGCTTATAGCCTGA
* * *
5787178 TTCAGATCACCGGCACTTAGCCTGCTAGACGTA-AAGTCTGAAACATTTCACCGGCA-TCAAGCC
1 TTCAGATCACCAGCACTTAGCCTGCTAGACGTATAA-CCTGAAACATATCACCGGCACT-AAGCC
*
5787241 TGCTAG
64 TACTAG
5787247 ACGTAAAGTC
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
81 3 0.05
82 54 0.95
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.26
Consensus pattern (82 bp):
TTCAGATCACCAGCACTTAGCCTGCTAGACGTATAACCTGAAACATATCACCGGCACTAAGCCTA
CTAGGCTTATAGCCTGA
Found at i:5792393 original size:19 final size:20
Alignment explanation
Indices: 5792366--5792413 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
5792356 TAAATTTACG
*
5792366 ATCATTTTGTTTC-A-TTTC
1 ATCATTTTGTTGCGATTTTC
5792384 ATCGATTTTGTTGCGATTTTC
1 ATC-ATTTTGTTGCGATTTTC
5792405 ATCATTTTG
1 ATCATTTTG
5792414 CTTTATAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 3 0.12
19 9 0.35
20 7 0.27
21 7 0.27
ACGTcount: A:0.17, C:0.15, G:0.12, T:0.56
Consensus pattern (20 bp):
ATCATTTTGTTGCGATTTTC
Found at i:5793229 original size:15 final size:15
Alignment explanation
Indices: 5793209--5793237 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5793199 ACATAAGGAT
5793209 ATGAGGAAAGGATCA
1 ATGAGGAAAGGATCA
5793224 ATGAGGAAAGGATC
1 ATGAGGAAAGGATC
5793238 GATGTCTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.07, G:0.34, T:0.14
Consensus pattern (15 bp):
ATGAGGAAAGGATCA
Found at i:5797205 original size:42 final size:42
Alignment explanation
Indices: 5797158--5797325 Score: 237
Period size: 42 Copynumber: 4.0 Consensus size: 42
5797148 CAAACAAAAA
* *
5797158 CGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTTTTTACAAG
1 CGCCGCTAAAGAACATGTTCTTTAGTGGCGTTTTTTTACAAG
*
5797200 CGCCGCTAAAGAACATGTTCTTTAGTGGCGTTTTTCTACAAG
1 CGCCGCTAAAGAACATGTTCTTTAGTGGCGTTTTTTTACAAG
* * *
5797242 CGCCGCTAAAGAACATGTTCTTTAGTGTCATTTTTTTTACAAA
1 CGCCGCTAAAGAACATGTTCTTTAGTGGC-GTTTTTTTACAAG
* * * *
5797285 CGCCGCGAAAGAATATGTTCTTTAGTGGCGCTTTTATACAA
1 CGCCGCTAAAGAACATGTTCTTTAGTGGCGTTTTTTTACAA
5797326 AAACGCCACT
Statistics
Matches: 112, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
42 76 0.68
43 36 0.32
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.35
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGTTCTTTAGTGGCGTTTTTTTACAAG
Found at i:5797306 original size:85 final size:84
Alignment explanation
Indices: 5797158--5797325 Score: 246
Period size: 85 Copynumber: 2.0 Consensus size: 84
5797148 CAAACAAAAA
* * *
5797158 CGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTTTTTACAAGCGCCGCTAAAGAACATGTTCTTT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTACAAACGCCGCGAAAGAACATGTTCTTT
* *
5797223 AGTGGCGTTTTTCTACAAG
66 AGTGGCGCTTTTATACAAG
* * * *
5797242 CGCCGCTAAAGAACATGTTCTTTAGTGTCATTTTTTTTACAAACGCCGCGAAAGAATATGTTCTT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGC-GTTTTTTTACAAACGCCGCGAAAGAACATGTTCTT
5797307 TAGTGGCGCTTTTATACAA
65 TAGTGGCGCTTTTATACAA
5797326 AAACGCCACT
Statistics
Matches: 74, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
84 26 0.35
85 48 0.65
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.35
Consensus pattern (84 bp):
CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTACAAACGCCGCGAAAGAACATGTTCTTT
AGTGGCGCTTTTATACAAG
Found at i:5797409 original size:14 final size:14
Alignment explanation
Indices: 5797386--5797419 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
5797376 GCCCTCCTGT
*
5797386 AGCAAAAATTCAAA
1 AGCAACAATTCAAA
5797400 AGCAACAATTCAAA
1 AGCAACAATTCAAA
5797414 AGCAAC
1 AGCAAC
5797420 CAATAGTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.59, C:0.21, G:0.09, T:0.12
Consensus pattern (14 bp):
AGCAACAATTCAAA
Found at i:5797711 original size:21 final size:21
Alignment explanation
Indices: 5797643--5797713 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 21
5797633 TTTTGCTCTG
* *
5797643 CTCTACTTCTCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
*
5797664 CTCCGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * *
5797685 CGCTGCTTCCCTCGCTTCCGC
1 CTCTGCTTCCCTCGCTGCAGC
5797706 CTCTGCTT
1 CTCTGCTT
5797714 TAAGTTGTAG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.04, C:0.48, G:0.17, T:0.31
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:5803312 original size:51 final size:50
Alignment explanation
Indices: 5803229--5803801 Score: 779
Period size: 51 Copynumber: 11.1 Consensus size: 50
5803219 CAATGGTAAG
5803229 TTATGTAAGTTATGTAAGTTAAATGTATTATGTAAGTTGTAAGTTAAATGTA
1 TTATGTAAG-T-TGTAAGTTAAATGTATTATGTAAGTTGTAAGTTAAATGTA
*
5803281 TTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTAAATGTA
1 TTATGTAAGTTGTAAGTTA-AATGTATTATGTAAGTTGTAAGTTAAATGTA
* * * * *
5803332 TTATGTAGGTTATGTTA-TTATTATGTATTATGGAAGTTCTAAGTTAAATGTA
1 TTATGTAAG-T-TGTAAGTTA-AATGTATTATGTAAGTTGTAAGTTAAATGTA
* *
5803384 TTGTGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTAAATGTA
1 TTATGTAAGTTGTAAGTTA-AATGTATTATGTAAGTTGTAAGTTAAATGTA
* *
5803435 TTGTGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTAAATGTA
1 TTATGTAAGTTGTAAGTTA-AATGTATTATGTAAGTTGTAAGTTAAATGTA
* * *
5803486 TTGTGTAAGTTGTAAGTTAAATGTATTGTGTAAGTTGTAAGTTATTATGTA
1 TTATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTA-AATGTA
* * *
5803537 TTATGTAAGTTGTAAGTTAAATGTATTGTGTAAGTCGTAAGTTATTATGTA
1 TTATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTA-AATGTA
* * * *
5803588 TTATGTAAGTTGTAATTTAAATGTATTGTGTAAGTCGTAAGTTATTATGTA
1 TTATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTA-AATGTA
* *
5803639 TTATGTAAGTTGTAAGTTAAATGTATTATGTAAGTCGTAAGTTATTATGTA
1 TTATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTA-AATGTA
*
5803690 TTATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTA
1 TTATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTA-AATGTA
5803741 TTATGTAAGTTATGTAAGTTAAATGTATTATGTAAGTTATGTAAGTTAAATGTA
1 TTATGTAAG-T-TGTAAGTTAAATGTATTATGTAAG-T-TGTAAGTTAAATGTA
5803795 TTATGTA
1 TTATGTA
5803802 GGTTATGTAG
Statistics
Matches: 492, Mismatches: 20, Indels: 16
0.93 0.04 0.03
Matches are distributed among these distances:
50 36 0.07
51 355 0.72
52 51 0.10
53 28 0.06
54 13 0.03
55 9 0.02
ACGTcount: A:0.33, C:0.01, G:0.20, T:0.46
Consensus pattern (50 bp):
TTATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTAAATGTA
Found at i:5803755 original size:9 final size:9
Alignment explanation
Indices: 5803690--5803816 Score: 78
Period size: 9 Copynumber: 14.4 Consensus size: 9
5803680 TTATTATGTA
5803690 TTATGTAAG
1 TTATGTAAG
5803699 -T-TGTAAG
1 TTATGTAAG
5803706 TTAAATGT-A-
1 TT--ATGTAAG
5803715 TTATGTAAG
1 TTATGTAAG
5803724 -T-TGTAAG
1 TTATGTAAG
*
5803731 TTAT-TATG
1 TTATGTAAG
5803739 TATTATGTAAG
1 --TTATGTAAG
5803750 TTATGTAAG
1 TTATGTAAG
5803759 TTAAATGT-A-
1 TT--ATGTAAG
5803768 TTATGTAAG
1 TTATGTAAG
5803777 TTATGTAAG
1 TTATGTAAG
5803786 TTAAATGT-A-
1 TT--ATGTAAG
*
5803795 TTATGTAGG
1 TTATGTAAG
*
5803804 TTATGTAGG
1 TTATGTAAG
5803813 TTAT
1 TTAT
5803817 TGTTATTAAA
Statistics
Matches: 96, Mismatches: 3, Indels: 38
0.70 0.02 0.28
Matches are distributed among these distances:
7 24 0.25
8 9 0.09
9 42 0.44
10 7 0.07
11 14 0.15
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:5803823 original size:27 final size:26
Alignment explanation
Indices: 5803229--5803824 Score: 492
Period size: 25 Copynumber: 23.1 Consensus size: 26
5803219 CAATGGTAAG
5803229 TTATGTAAGTTATGTAAGTTAAATGTA
1 TTATGTAAGTTATGTAAGTT-AATGTA
5803256 TTATGTAAG-T-TGTAAGTTAAATGTA
1 TTATGTAAGTTATGTAAGTT-AATGTA
5803281 TTATGTAAG-T-TGTAAGTTATTATGTA
1 TTATGTAAGTTATGTAAGTTA--ATGTA
5803307 TTATGTAAG-T-TGTAAGTTAAATGTA
1 TTATGTAAGTTATGTAAGTT-AATGTA
* *
5803332 TTATGTAGGTTATGTTA-TTATTATGTA
1 TTATGTAAGTTATGTAAGTTA--ATGTA
* *
5803359 TTATGGAAG-T-TCTAAGTTAAATGTA
1 TTATGTAAGTTATGTAAGTT-AATGTA
*
5803384 TTGTGTAAG-T-TGTAAGTTATTATGTA
1 TTATGTAAGTTATGTAAGTTA--ATGTA
5803410 TTATGTAAG-T-TGTAAGTTAAATGTA
1 TTATGTAAGTTATGTAAGTT-AATGTA
*
5803435 TTGTGTAAG-T-TGTAAGTTATTATGTA
1 TTATGTAAGTTATGTAAGTTA--ATGTA
5803461 TTATGTAAG-T-TGTAAGTTAAATGTA
1 TTATGTAAGTTATGTAAGTT-AATGTA
*
5803486 TTGTGTAAG-T-TGTAAGTTAAATGTA
1 TTATGTAAGTTATGTAAGTT-AATGTA
*
5803511 TTGTGTAAG-T-TGTAAGTTATTATGTA
1 TTATGTAAGTTATGTAAGTTA--ATGTA
5803537 TTATGTAAG-T-TGTAAGTTAAATGTA
1 TTATGTAAGTTATGTAAGTT-AATGTA
* *
5803562 TTGTGTAAG-T-CGTAAGTTATTATGTA
1 TTATGTAAGTTATGTAAGTTA--ATGTA
*
5803588 TTATGTAAG-T-TGTAATTTAAATGTA
1 TTATGTAAGTTATGTAAGTT-AATGTA
* *
5803613 TTGTGTAAG-T-CGTAAGTTATTATGTA
1 TTATGTAAGTTATGTAAGTTA--ATGTA
5803639 TTATGTAAG-T-TGTAAGTTAAATGTA
1 TTATGTAAGTTATGTAAGTT-AATGTA
*
5803664 TTATGTAAG-T-CGTAAGTTATTATGTA
1 TTATGTAAGTTATGTAAGTTA--ATGTA
5803690 TTATGTAAG-T-TGTAAGTTAAATGTA
1 TTATGTAAGTTATGTAAGTT-AATGTA
5803715 TTATGTAAG-T-TGTAAGTTATTATGTA
1 TTATGTAAGTTATGTAAGTTA--ATGTA
5803741 TTATGTAAGTTATGTAAGTTAAATGTA
1 TTATGTAAGTTATGTAAGTT-AATGTA
5803768 TTATGTAAGTTATGTAAGTTAAATGTA
1 TTATGTAAGTTATGTAAGTT-AATGTA
* * *
5803795 TTATGTAGGTTATGTAGGTTATTGTTA
1 TTATGTAAGTTATGTAAGTTAATG-TA
5803822 TTA
1 TTA
5803825 AATTTTAATA
Statistics
Matches: 507, Mismatches: 29, Indels: 66
0.84 0.05 0.11
Matches are distributed among these distances:
24 8 0.02
25 225 0.44
26 176 0.35
27 89 0.18
28 8 0.02
29 1 0.00
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.47
Consensus pattern (26 bp):
TTATGTAAGTTATGTAAGTTAATGTA
Found at i:5804015 original size:34 final size:34
Alignment explanation
Indices: 5803977--5804089 Score: 97
Period size: 34 Copynumber: 3.2 Consensus size: 34
5803967 ATTAATAATA
5803977 TTTAATAAAATAACATTTTATTTTAATAGTCAAT
1 TTTAATAAAATAACATTTTATTTTAATAGTCAAT
* * * *
5804011 TTTAAT--ATTCCACATATTT-TTTATAATTATTAATAAT
1 TTTAATAAAAT-AACAT-TTTATTT-TAA-TAGT--CAAT
*
5804048 ATTTAATAAAATAACATTTTATTTTAGTAGTCAAT
1 -TTTAATAAAATAACATTTTATTTTAATAGTCAAT
5804083 TTTAATA
1 TTTAATA
5804090 TTCCACATAT
Statistics
Matches: 60, Mismatches: 9, Indels: 20
0.67 0.10 0.22
Matches are distributed among these distances:
32 2 0.03
33 7 0.12
34 19 0.32
35 6 0.10
37 6 0.10
38 11 0.18
39 7 0.12
40 2 0.03
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.50
Consensus pattern (34 bp):
TTTAATAAAATAACATTTTATTTTAATAGTCAAT
Found at i:5804044 original size:72 final size:72
Alignment explanation
Indices: 5803960--5804104 Score: 281
Period size: 72 Copynumber: 2.0 Consensus size: 72
5803950 ACATTACTAA
5803960 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
1 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
5804025 TATTTTT
66 TATTTTT
*
5804032 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAGTAGTCAATTTTAATATTCCACA
1 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
5804097 TATTTTT
66 TATTTTT
5804104 T
1 T
5804105 TATATTTTAT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (72 bp):
TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
TATTTTT
Found at i:5804810 original size:31 final size:32
Alignment explanation
Indices: 5804763--5804829 Score: 109
Period size: 31 Copynumber: 2.1 Consensus size: 32
5804753 AGCAGAAATT
5804763 AATAGAAGCGGTACCATCTTAGCAGCAAAAACC
1 AATAGAA-CGGTACCATCTTAGCAGCAAAAACC
*
5804796 AATAGAA-GGTACCATCTTAGCTGCAAAAACC
1 AATAGAACGGTACCATCTTAGCAGCAAAAACC
5804827 AAT
1 AAT
5804830 TAAAATTCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
31 26 0.79
33 7 0.21
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.18
Consensus pattern (32 bp):
AATAGAACGGTACCATCTTAGCAGCAAAAACC
Found at i:5805452 original size:17 final size:17
Alignment explanation
Indices: 5805430--5805467 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
5805420 GAATCCGAAT
5805430 GTCTGCCCACCTTCTCC
1 GTCTGCCCACCTTCTCC
5805447 GTCTGCCCACCTTCTCC
1 GTCTGCCCACCTTCTCC
5805464 GTCT
1 GTCT
5805468 TCTCTGTCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.05, C:0.50, G:0.13, T:0.32
Consensus pattern (17 bp):
GTCTGCCCACCTTCTCC
Found at i:5806822 original size:32 final size:31
Alignment explanation
Indices: 5806761--5806822 Score: 72
Period size: 32 Copynumber: 1.9 Consensus size: 31
5806751 ATTCCTAACC
* *
5806761 CATAAGCCCTAAATCCCCCTTAACTCTTAAAG
1 CATAAACCCTAAA-CCCCCTAAACTCTTAAAG
5806793 CATAAACCCTAAA-CCCCTAAATCTCCTTAA
1 CATAAACCCTAAACCCCCTAAA-CT-CTTAA
5806823 CCCCTAAAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
30 7 0.27
31 2 0.08
32 17 0.65
ACGTcount: A:0.37, C:0.35, G:0.03, T:0.24
Consensus pattern (31 bp):
CATAAACCCTAAACCCCCTAAACTCTTAAAG
Found at i:5806832 original size:39 final size:40
Alignment explanation
Indices: 5806767--5806844 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 40
5806757 AACCCATAAG
* *
5806767 CCCTAAATCCCCCTTAACTCTTAAAGCATAAACCCTAAAC
1 CCCTAAATCCCCCTTAACCCCTAAAGCATAAACCCTAAAC
* *
5806807 CCCTAAAT-CTCCTTAACCCCTAAAGCATAACCCCTAAA
1 CCCTAAATCCCCCTTAACCCCTAAAGCATAAACCCTAAA
5806845 AAAATTTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 26 0.76
40 8 0.24
ACGTcount: A:0.37, C:0.38, G:0.03, T:0.22
Consensus pattern (40 bp):
CCCTAAATCCCCCTTAACCCCTAAAGCATAAACCCTAAAC
Found at i:5808189 original size:114 final size:114
Alignment explanation
Indices: 5807988--5808539 Score: 570
Period size: 114 Copynumber: 4.9 Consensus size: 114
5807978 ATTTTAAATC
* * * * * * *
5807988 CCTGAGCATTAGCGGCGCTTT-TTTAAAAACGCCGCTAAAACCC-CAACAGTTCAGAAAACGACG
1 CCTGAGCATTAGCGGCGCTTTCTATAAAAGCGCCGCTAAATCCCTGAA-AGCTCGGGAAACGACG
* * * *
5808051 TCGTTGGGCTTAGGTTTTTAGCGGCGCTTTCACAAAAACGCCGCTAAAAA
65 TCGTTGCGCTTAGGTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGA
* * * * * * *
5808101 CATGAGCATTAGCGGCGCTTTCTATAAAAGCGCCACTAAAGCCCTGAAAGGTGGGGAGACGACAT
1 CCTGAGCATTAGCGGCGCTTTCTATAAAAGCGCCGCTAAATCCCTGAAAGCTCGGGAAACGACGT
5808166 CGTTGCGC-TAGGTTTTTTTGCGGCGC-TTCCCTAAAAACGCCGCTAAAGA
66 CGTTGCGCTTAGG-TTTTTTGCGGCGCTTTCCC-AAAAACGCCGCTAAAGA
** ** * *
5808215 CCTGAGTTTTAGCGGCGAATTCTAT-AAAGCGCCGCTAAATCCCTAAAAAGCTCGGGAAACGTCG
1 CCTGAGCATTAGCGGCGCTTTCTATAAAAGCGCCGCTAAATCCCT-GAAAGCTCGGGAAACGACG
* *
5808279 TCGTTGCGCTTAGTTTTTTTGCGGCGCTTTCCCACAAACGCCGCTAAAGA
65 TCGTTGCGCTTAGGTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGA
* * * * *
5808329 CCTGAGCATTAGCGGCGC-TT-TACTAAAA-CACCGCTAAATTCAC-GAAAGCTCAGAAAACGGC
1 CCTGAGCATTAGCGGCGCTTTCTA-TAAAAGCGCCGCTAAA-TCCCTGAAAGCTCGGGAAACGAC
* * * *
5808390 GTTGTTGGGCTTATGTTTTTTGCGGCGCTTTCCTAAAAACGCCGCTAAAG-
64 GTCGTTGCGCTTAGGTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGA
** ** * * * *
5808440 CCTTGAGCATTAGCGGCGCTTAAT-TAAAAATGCTGCTAAATCCCCGAATGCTCGGGAAACGGCG
1 CC-TGAGCATTAGCGGCGCTTTCTATAAAAGCGCCGCTAAATCCCTGAAAGCTCGGGAAACGACG
5808504 TCGTTGCGC-TAGGTTTTTTGCGGCGCTTTCCCAAAA
65 TCGTTGCGCTTAGGTTTTTTGCGGCGCTTTCCCAAAA
5808540 TCGCTGGTAA
Statistics
Matches: 366, Mismatches: 58, Indels: 31
0.80 0.13 0.07
Matches are distributed among these distances:
111 2 0.01
112 109 0.30
113 88 0.24
114 157 0.43
115 10 0.03
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.25
Consensus pattern (114 bp):
CCTGAGCATTAGCGGCGCTTTCTATAAAAGCGCCGCTAAATCCCTGAAAGCTCGGGAAACGACGT
CGTTGCGCTTAGGTTTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAAGA
Found at i:5809001 original size:4 final size:4
Alignment explanation
Indices: 5808992--5809026 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
5808982 ATATTCCTTT
5808992 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTA
5809027 TTATATTACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (4 bp):
TTAA
Found at i:5810420 original size:20 final size:20
Alignment explanation
Indices: 5810368--5810416 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
5810358 ATGCGATGAC
* * * *
5810368 TATATCAAACAAATAAAATT
1 TATATAAAATAAACAAAATG
5810388 TATATAAAATAAACAAAATG
1 TATATAAAATAAACAAAATG
5810408 TATA-AAAAT
1 TATATAAAAT
5810417 TAAAATTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (20 bp):
TATATAAAATAAACAAAATG
Found at i:5810796 original size:8 final size:8
Alignment explanation
Indices: 5810783--5810821 Score: 69
Period size: 8 Copynumber: 4.9 Consensus size: 8
5810773 ACCACTACAT
5810783 AAGAATCC
1 AAGAATCC
5810791 AAGAATCC
1 AAGAATCC
5810799 AAGAATCC
1 AAGAATCC
5810807 AAGAATCC
1 AAGAATCC
*
5810815 AACAATC
1 AAGAATC
5810822 ATTCTTATTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.51, C:0.26, G:0.10, T:0.13
Consensus pattern (8 bp):
AAGAATCC
Found at i:5818526 original size:324 final size:324
Alignment explanation
Indices: 5817906--5818536 Score: 987
Period size: 324 Copynumber: 1.9 Consensus size: 324
5817896 GGCTAAGATC
* * * *
5817906 AATGTTTTGGGAATTGAGTTGAGAAGGTATATCTCCGCTAATGATGTTATGTCTTAGATCAAGCT
1 AATGTTTTGGGAATTGAGTTGAGAAGGAATATCTCCACTAATGATGTTATGGCTTAGATCAAGCA
* *
5817971 GGTATAGAGATAAGCCACCAATTTGCAGGGGAATCCTTCCACTCAAGTTATTTTTTGCCAAAATT
66 GGTATAGAGATAAGCCACCAATTTGCAGGGGAATCCTTCCACTCAAGTTATTGTTTGCCAAAACT
* * * * * *
5818036 AAGTACATTAAATTTGACAAATTACCAATTTGAGTTGGAATGGGTCCACTCAATTTGTTTTCTGA
131 AAGCACATTAAATTTGACAAATTACCAATCTGAGATGGAATGGGGCCACTAAATTTGTTGTCTGA
* * *
5818101 AAGATCTAAGTGTTCCAGGGCTTTCAGATTCTCAATTTCATGGGGTATGGGACCTTCCAAAAGAT
196 AAGATCTAAGTGATCCAGGGCTTTCAAACTCTCAATTTCATGGGGTATGGGACCTTCCAAAAGAT
* *
5818166 TCGAAGCAATGAATAGATACCGCAAATTGTGTAAATGAAATAGAGATGAAGACATGGAATTGGA
261 TCGAAGCAATGAATAGATACCACAAATTGGGTAAATGAAATAGAGATGAAGACATGGAATTGGA
5818230 AATGTTTTGGGAATTGAGTTGAGAAGGAATATCTCCACTAATGATGTTATGGCTTAGATCAAGCA
1 AATGTTTTGGGAATTGAGTTGAGAAGGAATATCTCCACTAATGATGTTATGGCTTAGATCAAGCA
*
5818295 GGTATAGAGATAAGCCACCAATTTGCTGGGGAATCCTTCCACTCAAGTTATTGTTTGCCAAAACT
66 GGTATAGAGATAAGCCACCAATTTGCAGGGGAATCCTTCCACTCAAGTTATTGTTTGCCAAAACT
**
5818360 AAGCATGTTAAATTTGACAAATTACCAATCTGAGATGGAATGGGGCCACTAAATTTGTTGTCTGA
131 AAGCACATTAAATTTGACAAATTACCAATCTGAGATGGAATGGGGCCACTAAATTTGTTGTCTGA
*
5818425 GAGATCTAAGT-ATCGCAGGG-TATTCAAACTCTCAATTTCATGGGGTATGGGACCTTCCAAAAG
196 AAGATCTAAGTGATC-CAGGGCT-TTCAAACTCTCAATTTCATGGGGTATGGGACCTTCCAAAAG
* * * * * *
5818488 ATTTGAAGCCATGGATAGATGCCATAAATTGGGTAAATGAAGTAGAGAT
259 ATTCGAAGCAATGAATAGATACCACAAATTGGGTAAATGAAATAGAGAT
5818537 AAAGGGATTG
Statistics
Matches: 278, Mismatches: 27, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
323 3 0.01
324 275 0.99
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.30
Consensus pattern (324 bp):
AATGTTTTGGGAATTGAGTTGAGAAGGAATATCTCCACTAATGATGTTATGGCTTAGATCAAGCA
GGTATAGAGATAAGCCACCAATTTGCAGGGGAATCCTTCCACTCAAGTTATTGTTTGCCAAAACT
AAGCACATTAAATTTGACAAATTACCAATCTGAGATGGAATGGGGCCACTAAATTTGTTGTCTGA
AAGATCTAAGTGATCCAGGGCTTTCAAACTCTCAATTTCATGGGGTATGGGACCTTCCAAAAGAT
TCGAAGCAATGAATAGATACCACAAATTGGGTAAATGAAATAGAGATGAAGACATGGAATTGGA
Found at i:5839963 original size:5 final size:5
Alignment explanation
Indices: 5839919--5839947 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
5839909 TTATTTATTA
5839919 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
5839948 TTATATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:5847288 original size:18 final size:18
Alignment explanation
Indices: 5847253--5847312 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 18
5847243 TCATACTGTT
* * *
5847253 TTTATTTTTAAAAATTTA
1 TTTAATTTTAATATTTTA
*
5847271 TTTAATTTTGATATTTTA
1 TTTAATTTTAATATTTTA
5847289 TTT--TTTTAATATTTT-
1 TTTAATTTTAATATTTTA
*
5847304 TATAATTTT
1 TTTAATTTT
5847313 TAAAATATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
15 2 0.06
16 11 0.32
17 4 0.12
18 17 0.50
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTAATTTTAATATTTTA
Found at i:5850632 original size:25 final size:26
Alignment explanation
Indices: 5850576--5850638 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
5850566 AGAAACATGA
*
5850576 AAAATATATTATATAAAAAATGACAT
1 AAAATATAATATATAAAAAATGACAT
* *
5850602 ATAATAGTAATATAT-AAAAATGA-TT
1 AAAATA-TAATATATAAAAAATGACAT
5850627 AAAATAATAATA
1 AAAAT-ATAATA
5850639 CCCAGTAGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
25 10 0.32
26 14 0.45
27 7 0.23
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.32
Consensus pattern (26 bp):
AAAATATAATATATAAAAAATGACAT
Found at i:5850709 original size:4 final size:4
Alignment explanation
Indices: 5850700--5850731 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
5850690 TAATAGAACT
5850700 AGTA AGTA AGTA AGTA AGTA AGTA AGTA AGTA
1 AGTA AGTA AGTA AGTA AGTA AGTA AGTA AGTA
5850732 GTACTAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
AGTA
Found at i:5850742 original size:3 final size:3
Alignment explanation
Indices: 5850736--5850838 Score: 172
Period size: 3 Copynumber: 34.7 Consensus size: 3
5850726 TAAGTAGTAC
5850736 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
5850784 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA GAC TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
5850831 TAA AAA TA
1 TAA TAA TA
5850839 TTGATAAACT
Statistics
Matches: 94, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
2 2 0.02
3 92 0.98
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:5851327 original size:19 final size:20
Alignment explanation
Indices: 5851298--5851338 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
5851288 TTCATTTTTC
5851298 AAAACGAAAAGAAAAAAAAT
1 AAAACGAAAAGAAAAAAAAT
*
5851318 AAAA-GAAAAGAAAAATAAT
1 AAAACGAAAAGAAAAAAAAT
5851337 AA
1 AA
5851339 TAAAAACAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.80, C:0.02, G:0.10, T:0.07
Consensus pattern (20 bp):
AAAACGAAAAGAAAAAAAAT
Found at i:5857003 original size:111 final size:110
Alignment explanation
Indices: 5856838--5857213 Score: 556
Period size: 111 Copynumber: 3.4 Consensus size: 110
5856828 GAAATTCAAG
* * * * *
5856838 AGGATATTTGGCTATTCGGTTAAATGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
1 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
* *
5856903 GAATTTCCCAAATGCAAAACATTGCCTTATTTCTAAAATTTTTTAA
66 GAATTTCCCAAACGCAAAACATTGCCTTATTT-TAAAATTTTTAAA
* * *
5856949 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACATCCATCACCTTAGGGCACGTTCTCTC
1 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
* * *
5857014 AAATTTCCCAAACGCAAAACATTGCCTTATTTGAAAAGTTTTAAA
66 GAATTTCCCAAACGCAAAACATTGCCTTATTTTAAAATTTTTAAA
* * * *
5857059 AGGATATTAAGCCATTTGGTTGAATGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTCCTC
1 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
* *
5857124 GAATTT-CCAAACGTAAAACATTGCCTTATTTTAAAATTTTTGAA
66 GAATTTCCCAAACGCAAAACATTGCCTTATTTTAAAATTTTTAAA
*
5857168 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGACACCCAGCA
1 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCA
5857214 NNNNNNNNNN
Statistics
Matches: 237, Mismatches: 28, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
109 77 0.32
110 73 0.31
111 87 0.37
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.30
Consensus pattern (110 bp):
AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
GAATTTCCCAAACGCAAAACATTGCCTTATTTTAAAATTTTTAAA
Found at i:5857843 original size:3 final size:3
Alignment explanation
Indices: 5857778--5857824 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
5857768 AAATGGAAAT
* *
5857778 ATA ATG ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
5857825 GGTAACATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5858794 original size:21 final size:23
Alignment explanation
Indices: 5858750--5858795 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
5858740 TATAGCCGAA
*
5858750 TGCTACTGCTTTTGTTGTCTTGTT
1 TGCTACTGC-TTTCTTGTCTTGTT
5858774 TGCTACTG-TTTCTTG-CTTGTT
1 TGCTACTGCTTTCTTGTCTTGTT
5858795 T
1 T
5858796 CTTTCTTTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 6 0.29
24 8 0.38
ACGTcount: A:0.04, C:0.17, G:0.20, T:0.59
Consensus pattern (23 bp):
TGCTACTGCTTTCTTGTCTTGTT
Found at i:5859657 original size:129 final size:129
Alignment explanation
Indices: 5859427--5860794 Score: 2043
Period size: 129 Copynumber: 10.6 Consensus size: 129
5859417 TTGTGGTAGA
* * ** *
5859427 TTTAATCCGAC-CTACTGCAACTTCAGAG-GTATAGGATTCATTAT-TTTAATCCGCTCCACTGC
1 TTTAATCCG-CTCCACTGCAACTTCAGAGAG-ATAGGATTGATT-TCTTTCGTCTGCTCCACTGC
* * * *
5859489 AACTTCAGGGAGATAGGATTGGATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGGG
63 AACTTCAGGGAGATAAGACTGGATGTGACCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTG
5859554 GT
128 GT
* * *
5859556 TTTAATCCGCTCCTCTGTAACTTCAGAGAGATAGGATTGATTTCTTTCGTCTTCTCCACTGCAAC
1 TTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGATTGATTTCTTTCGTCTGCTCCACTGCAAC
* *
5859621 TTCAGGGAGATAAGACTGTATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGT
66 TTCAGGGAGATAAGACTGGATGTGACCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGT
* * * * * *
5859685 TTTTATCCGTTCCACTACAACTTCAGGGAGATAGGATTGATTTCTTTTGTCTGCTCCATTGCAAC
1 TTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGATTGATTTCTTTCGTCTGCTCCACTGCAAC
*
5859750 TTCAGGGAGATAAGGCTGGATGTGACCTGCTCTACTGCAACTTCAGAGAGATAAGATCTAG-GGT
66 TTCAGGGAGATAAGACTGGATGTGACCTGCTCTACTGCAACTTCAGAGAGATAAGATCT-GTGGT
* * * *
5859814 TTTAATCCGCTCCTCTGCAACTTCAGTGGGATAAGATTGATTTCTTTCGTCTGCTCCACTGCAAC
1 TTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGATTGATTTCTTTCGTCTGCTCCACTGCAAC
*
5859879 TTCAGGGAGATAAGACTGGATGTGACCTGCTCTACTGCAACTTCAGAGAGATAAGATATGTGGT
66 TTCAGGGAGATAAGACTGGATGTGACCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGT
* *
5859943 TTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTGATTTCTTTCGTCTGCTCCACTGCAAC
1 TTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGATTGATTTCTTTCGTCTGCTCCACTGCAAC
* * * * *
5860008 TTCAGGGAGATAATACTGTATGTGATCTGCTCTACAGCAACTTCAGAGAGATAAGATCTATGGT
66 TTCAGGGAGATAAGACTGGATGTGACCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGT
* * *
5860072 TTTAATCCGCTCCACTACAACTTCA-AGGAGATGGGATTGATTTCTTTTGTCTGCTCCACTGCAA
1 TTTAATCCGCTCCACTGCAACTTCAGA-GAGATAGGATTGATTTCTTTCGTCTGCTCCACTGCAA
*
5860136 CTTCAGGGAGATAAGACTGGATGTGACCTGCTCTACTGCAACTTCAGAGGGATAAGATCTGTGGT
65 CTTCAGGGAGATAAGACTGGATGTGACCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGT
* * * *
5860201 TTTAATCCGCTCTACTGCAACTTCAGGGATATAGGATTGATTTCTTTCGTCTGCTCCACTGTAAC
1 TTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGATTGATTTCTTTCGTCTGCTCCACTGCAAC
* * * *
5860266 TTTAGGGAGATAAGCCTGTATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGT
66 TTCAGGGAGATAAGACTGGATGTGACCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGT
* * *
5860330 TTTAATCCGCTCCACTACAACTTCA-AGGAGATGGGATTGATTTCTTTTGTCTGCTCCACTGCAA
1 TTTAATCCGCTCCACTGCAACTTCAGA-GAGATAGGATTGATTTCTTTCGTCTGCTCCACTGCAA
*
5860394 CTTCAGGGAGATAAGACTGGATGTGACCTGCTCTACTGCAACTTCAGAGGGATAAGATCTGTGGT
65 CTTCAGGGAGATAAGACTGGATGTGACCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGT
5860459 TTTAATCCGCTCCACTGCAACTTCAG-GAAGATAGGATTGATTTCTTTCGTCTGCTCCACTGCAA
1 TTTAATCCGCTCCACTGCAACTTCAGAG-AGATAGGATTGATTTCTTTCGTCTGCTCCACTGCAA
* * ** *
5860523 CTTTAGGGAGATAAGCCTTTATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGT
65 CTTCAGGGAGATAAGACTGGATGTGACCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGT
* * * *
5860588 TTTAATCCGCTCCACTACAACTTCA-AGGAGATGGGATTGATTTCTTTTGTTTGCTCCACTGCAA
1 TTTAATCCGCTCCACTGCAACTTCAGA-GAGATAGGATTGATTTCTTTCGTCTGCTCCACTGCAA
* *
5860652 CTTCAGAGAGATAAGACTGGATGTGACCTACTCTA-TGCAACTTCAGAGAGATAAGATCTGTGGT
65 CTTCAGGGAGATAAGACTGGATGTGACCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGT
* *
5860716 TTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTTCGTCTGCTCCACTGCAAC
1 TTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGATTGATTTCTTTCGTCTGCTCCACTGCAAC
5860781 TTCAGGGAGATAAG
66 TTCAGGGAGATAAG
5860795 GTTTGAAATT
Statistics
Matches: 1118, Mismatches: 108, Indels: 27
0.89 0.09 0.02
Matches are distributed among these distances:
128 104 0.09
129 1011 0.90
130 3 0.00
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (129 bp):
TTTAATCCGCTCCACTGCAACTTCAGAGAGATAGGATTGATTTCTTTCGTCTGCTCCACTGCAAC
TTCAGGGAGATAAGACTGGATGTGACCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGT
Found at i:5860819 original size:46 final size:44
Alignment explanation
Indices: 5859480--5860836 Score: 261
Period size: 44 Copynumber: 31.5 Consensus size: 44
5859470 TTTTAATCCG
* * *
5859480 CTCCACTGCAACTTCAGGGAGATAGGATTGGA---TGT-GATCTG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCG-TCTA
* * * *** ** **
5859521 CTCTACTGCAACTTCAGAGAGATAAGATCTGGGGT-TTTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAGGAT-TGAATTCTTTCGTCTA
* * * * *
5859565 CTCCTCTGTAACTTCAGAGAGATAGGATTGATTTCTTTCGTCTT
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCGTCTA
* * * * *
5859609 CTCCACTGCAACTTCAGGGAGATAAGACTG---TATGT-GATCTG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCG-TCTA
* * * ** * **
5859650 CTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTT-TTT-ATCCG
1 CTCCACTGCAACTTCAGGGAGATAGGAT-TG-AATTCTTTCGTCTA
* * * * *
5859694 TTCCACTACAACTTCAGGGAGATAGGATTGATTTCTTTTGTCTG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCGTCTA
* * * * ** *
5859738 CTCCATTGCAACTTCAGGGAGATAAGG-CTGGA-TGTGAC--CTG
1 CTCCACTGCAACTTCAGGGAGAT-AGGATTGAATTCTTTCGTCTA
* * * ** ** **
5859779 CTCTACTGCAACTTCAGAGAGATAAGATCT-AGGGT-TTTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAGGAT-TGA-ATTCTTTCGTCTA
* * * *
5859823 CTCCTCTGCAACTTCAGTGG-GATAAGATTGATTTCTTTCGTCTG
1 CTCCACTGCAACTTCAG-GGAGATAGGATTGAATTCTTTCGTCTA
* * * * ** *
5859867 CTCCACTGCAACTTCAGGGAGATAAGACTGGA-TGTGAC--CTG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCGTCTA
* * * *** ** **
5859908 CTCTACTGCAACTTCAGAGAGATAAGATATGTGGT-TTTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAGGAT-TGAATTCTTTCGTCTA
* * *
5859952 CTCCACTGTAACTTCAGGGAGATAGGATTGATTTCTTTCGTCTG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCGTCTA
* * * *
5859996 CTCCACTGCAACTTCAGGGAGATA--A-T-ACTGTATGT-GATCTG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAAT-TCTTTCG-TCTA
* * * * ** **
5860037 CTCTACAGCAACTTCAGAGAGATAAGATCT--ATGGT-TTTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAGGAT-TGAAT--TCTTTCGTCTA
* * * * * *
5860081 CTCCACTACAACTTCAAGGAGATGGGATTGATTTCTTTTGTCTG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCGTCTA
* * * * ** *
5860125 CTCCACTGCAACTTCAGGGAGATAAGACTGGA-TGTGAC--CTG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCGTCTA
* * *** ** **
5860166 CTCTACTGCAACTTCAGAGG-GATAAGATCTGTGGT-TTTAATCCG
1 CTCCACTGCAACTTCAG-GGAGATAGGAT-TGAATTCTTTCGTCTA
* * * *
5860210 CTCTACTGCAACTTCAGGGATATAGGATTGATTTCTTTCGTCTG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCGTCTA
* * * ** * * *
5860254 CTCCACTGTAACTTTAGGGAGATAAGCCTG---TATGT-GATCTG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCG-TCTA
* * * *** ** **
5860295 CTCTACTGCAACTTCAGAGAGATAAGATCTGTGGT-TTTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAGGAT-TGAATTCTTTCGTCTA
* * * * * *
5860339 CTCCACTACAACTTCAAGGAGATGGGATTGATTTCTTTTGTCTG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCGTCTA
* * * * ** *
5860383 CTCCACTGCAACTTCAGGGAGATAAGACTGGA-TGTGAC--CTG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCGTCTA
* * *** ** **
5860424 CTCTACTGCAACTTCAGAGG-GATAAGATCTGTGGT-TTTAATCCG
1 CTCCACTGCAACTTCAG-GGAGATAGGAT-TGAATTCTTTCGTCTA
* * *
5860468 CTCCACTGCAACTTCAGGAAGATAGGATTGATTTCTTTCGTCTG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCGTCTA
* * ** * * *
5860512 CTCCACTGCAACTTTAGGGAGATAAGCCT---TTATGT-GATCTG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCG-TCTA
* * * *** ** **
5860553 CTCTACTGCAACTTCAGAGAGATAAGATCTGTGGT-TTTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAGGAT-TGAATTCTTTCGTCTA
* * * * * * *
5860597 CTCCACTACAACTTCAAGGAGATGGGATTGATTTCTTTTGTTTG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCGTCTA
* * * * * **
5860641 CTCCACTGCAACTTCAGAGAGATAAGACTGGA-TGTGAC--CTA
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCGTCTA
* * * *** ** *
5860682 CTCTA-TGCAACTTCAGAGAGATAAGATCTGTGGT-TTTAATCCA
1 CTCCACTGCAACTTCAGGGAGATAGGAT-TGAATTCTTTCGTCTA
* *
5860725 CTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTTCGTCTG
1 CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCGTCTA
*
5860769 CTCCACTGCAACTTCAGGGAGATAAGGTTTGAAATTC-TTCGGTCTA
1 CTCCACTGCAACTTCAGGGAGAT-AGGATTG-AATTCTTTC-GTCTA
* *
5860815 CTCCACTGTAACCTCAGGGAGA
1 CTCCACTGCAACTTCAGGGAGA
5860837 ATAGACCTGA
Statistics
Matches: 970, Mismatches: 269, Indels: 149
0.70 0.19 0.11
Matches are distributed among these distances:
40 29 0.03
41 256 0.26
42 27 0.03
43 57 0.06
44 551 0.57
45 21 0.02
46 29 0.03
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.31
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAGGATTGAATTCTTTCGTCTA
Found at i:5860916 original size:85 final size:82
Alignment explanation
Indices: 5860814--5861097 Score: 275
Period size: 85 Copynumber: 3.3 Consensus size: 82
5860804 TCTTCGGTCT
5860814 ACTCCACTGTAACCTCAGGGAGAATAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGAT
1 ACTCCACTGTAACCTCAGGGAG-ATAGACCT-AT-CGATCTACTCTGCTGTAACTTCAGAGAGAT
5860879 AAGATCCTTGATTTTAATCC
63 AAGATCCTTGATTTTAATCC
* * * ** *
5860899 ACTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTTGATCTGCTCCACTGTAA-TCTCAGGG
1 ACTCCACTGTAACCTCAGGGAGATA-GA--CCTATC---GATCTACTCTGCTGTAACT-TCAGAG
** * *
5860963 AGATAAGAT-CTCTGGCTTCAATCT
59 AGATAAGATCCT-TGATTTTAATCC
* *
5860987 GCTCCACTGTAACCTCAGGGAGATAAGACCTAATATGATCTACTCTGCTGTAACTTCAGAGAGAT
1 ACTCCACTGTAACCTCAGGGAGAT-AGACCT-AT-CGATCTACTCTGCTGTAACTTCAGAGAGAT
*
5861052 AAGATCCTTTATTTTAATCC
63 AAGATCCTTGATTTTAATCC
* * * *
5861072 GCTCTACTGTGACTTCAGGGAGATAG
1 ACTCCACTGTAACCTCAGGGAGATAG
5861098 GATAGTGTCT
Statistics
Matches: 160, Mismatches: 26, Indels: 27
0.75 0.12 0.13
Matches are distributed among these distances:
84 5 0.03
85 80 0.50
86 7 0.04
87 7 0.04
88 60 0.38
89 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (82 bp):
ACTCCACTGTAACCTCAGGGAGATAGACCTATCGATCTACTCTGCTGTAACTTCAGAGAGATAAG
ATCCTTGATTTTAATCC
Found at i:5860948 original size:44 final size:44
Alignment explanation
Indices: 5860900--5861189 Score: 204
Period size: 44 Copynumber: 6.7 Consensus size: 44
5860890 TTTTAATCCA
* * **
5860900 CTCCACTGTAATCTCAGGGAGATAGGAT-TACTATCTTTGATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCT-CTAGCTTCAATCTG
*
5860944 CTCCACTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCTCTAGCTTCAATCTG
* * * *
5860988 CTCCACTGTAACCTCAGGGAGATAAGA-C-CTA-ATAT-GATCTA
1 CTCCACTGTAATCTCAGGGAGATAAGATCTCTAGCT-TCAATCTG
** * * * * *
5861029 CTCTGCTGTAA-CTTCAGAGAGATAAGATCCTTTA-TTTTAATCCG
1 CTCCACTGTAATC-TCAGGGAGATAAGAT-CTCTAGCTTCAATCTG
* * * ** *
5861073 CTCTACTGTGA-CTTCAGGGAGATAGGAT-AGT-GTCTTCGATCTG
1 CTCCACTGTAATC-TCAGGGAGATAAGATCTCTAG-CTTCAATCTG
* * * *
5861116 CTCCGCTGTAATCTCAGGGAAATAAGATCTCTGGCTTCAATTTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCTCTAGCTTCAATCTG
* *
5861160 CTCCACTGTGACCTCAGGGAGATAAGATCT
1 CTCCACTGTAATCTCAGGGAGATAAGATCT
5861190 GAAATATTCA
Statistics
Matches: 193, Mismatches: 41, Indels: 24
0.75 0.16 0.09
Matches are distributed among these distances:
40 1 0.01
41 27 0.14
42 4 0.02
43 30 0.16
44 129 0.67
45 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (44 bp):
CTCCACTGTAATCTCAGGGAGATAAGATCTCTAGCTTCAATCTG
Found at i:5861059 original size:173 final size:172
Alignment explanation
Indices: 5860639--5861191 Score: 658
Period size: 173 Copynumber: 3.2 Consensus size: 172
5860629 TTCTTTTGTT
* * * * * *
5860639 TGCTCCACTGCAACTTCAGAGAGATAAGA-CTGGATGTGACCTACTCT-ATGCAACTTCAGAGAG
1 TGCTCCACTGTAACCTCAGGGAGATAAGACCT-GATGTGATCTACTCTGCTGTAACTTCAGAGAG
* * *
5860702 ATAAGAT-CTGTGGTTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTTCG-
65 ATAAGATCCT-TGATTTTAATCCACTCCACTGTAACTTCAGGGAGATAGGATT-ATATCTTT-GA
* * * **
5860765 TCTGCTCCACTGCAA-CTTCAGGGAGATAAGGT-T-TGAAATTCTTCGGTC
127 TCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTCTG----GCTTCAATC
* *
5860813 TACTCCACTGTAACCTCAGGGAGA-ATAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAG
1 TGCTCCACTGTAACCTCAGGGAGATA-AGACCTGATGTGATCTACTCTGCTGTAACTTCAGAGAG
5860877 ATAAGATCCTTGATTTTAATCCACTCCACTGTAA-TCTCAGGGAGATAGGATTACTATCTTTGAT
65 ATAAGATCCTTGATTTTAATCCACTCCACTGTAACT-TCAGGGAGATAGGATTA-TATCTTTGAT
5860941 CTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATC
128 CTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATC
* *
5860986 TGCTCCACTGTAACCTCAGGGAGATAAGACCTAATATGATCTACTCTGCTGTAACTTCAGAGAGA
1 TGCTCCACTGTAACCTCAGGGAGATAAGACCTGATGTGATCTACTCTGCTGTAACTTCAGAGAGA
* * * * * *
5861051 TAAGATCCTTTATTTTAATCCGCTCTACTGTGACTTCAGGGAGATAGGA-TAGTGTCTTCGATCT
66 TAAGATCCTTGATTTTAATCCACTCCACTGTAACTTCAGGGAGATAGGATTA-TATCTTTGATCT
* * *
5861115 GCTCCGCTGTAATCTCAGGGAAATAAGATCTCTGGCTTCAATT
130 GCTCCACTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATC
* *
5861158 TGCTCCACTGTGACCTCAGGGAGATAAGATCTGA
1 TGCTCCACTGTAACCTCAGGGAGATAAGACCTGA
5861192 AATATTCATT
Statistics
Matches: 334, Mismatches: 33, Indels: 26
0.85 0.08 0.07
Matches are distributed among these distances:
172 83 0.25
173 109 0.33
174 41 0.12
175 95 0.28
176 4 0.01
177 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (172 bp):
TGCTCCACTGTAACCTCAGGGAGATAAGACCTGATGTGATCTACTCTGCTGTAACTTCAGAGAGA
TAAGATCCTTGATTTTAATCCACTCCACTGTAACTTCAGGGAGATAGGATTATATCTTTGATCTG
CTCCACTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATC
Found at i:5862577 original size:21 final size:21
Alignment explanation
Indices: 5862553--5862598 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
5862543 TTCTTTCTTC
*
5862553 TTTTTGTTTTTTTTATTTTAA
1 TTTTTGATTTTTTTATTTTAA
*
5862574 TTTTTGATTTTTTTATTTTCA
1 TTTTTGATTTTTTTATTTTAA
5862595 TTTT
1 TTTT
5862599 GACTTTGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.13, C:0.02, G:0.04, T:0.80
Consensus pattern (21 bp):
TTTTTGATTTTTTTATTTTAA
Found at i:5866211 original size:110 final size:109
Alignment explanation
Indices: 5865981--5866377 Score: 614
Period size: 109 Copynumber: 3.6 Consensus size: 109
5865971 TCCGCTAAAT
*
5865981 GAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCCAAATGCAAAACATTGC
1 GAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTT-CCAAACGCAAAACATTGC
5866046 CTTATTTCAAAAAATTTTTAAAAGGATATTTAGCCATTTGGTTGAAC
65 CTTATTT--AAAAATTTTTAAAAGGATATTTAGCCATTTGGTTGAAC
* *
5866093 GAGAAAAATCGACACCCAGCACCTCAGGGCACGTTCTCTCGAATTTCCCAAACGCAAAACATTGC
1 GAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTT-CCAAACGCAAAACATTGC
* * * *
5866158 CTTATTTGAAAAGTTTTAAAAGGATATTAAGCCATTTGGTTGAAT
65 CTTATTTAAAAATTTTTAAAAGGATATTTAGCCATTTGGTTGAAC
* * *
5866203 GAGAAAAATCGACACTCAGCACCTTAGGGCATGTTTCCTCGAATTTCCAAACGCAAAACATTGCC
1 GAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAACATTGCC
* * *
5866268 TTATTTTAAAATTTTTGAAAGGATATTTAGCTATTTGGTTGAAC
66 TTATTTAAAAATTTTTAAAAGGATATTTAGCCATTTGGTTGAAC
* * *
5866312 GAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTTCAAACGCTAAATATTGCC
1 GAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAACATTGCC
5866377 T
66 T
5866378 CAATTAGAAA
Statistics
Matches: 261, Mismatches: 24, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
109 117 0.45
110 75 0.29
112 69 0.26
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (109 bp):
GAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAACATTGCC
TTATTTAAAAATTTTTAAAAGGATATTTAGCCATTTGGTTGAAC
Found at i:5866343 original size:219 final size:220
Alignment explanation
Indices: 5865978--5866377 Score: 660
Period size: 219 Copynumber: 1.8 Consensus size: 220
5865968 TATTCCGCTA
* *
5865978 AATGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCCAAATGCAAAACAT
1 AATGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTCCTCGAATTTCCCAAACGCAAAACAT
5866043 TGCCTTATTTCAAAAAATTTTTAAAAGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACAC
66 TGCCTTATTT-AAAAAATTTTTAAAAGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACAC
5866108 CCAGCACCTCAGGGCACGTTCTCTCGAATTTCCCAAACGCAAAACATTGCCTTATTTGAAAAGTT
130 CCAGCACCTCAGGGCACGTTCTCTCGAATTT-CCAAACGCAAAACATTGCCTTATTTGAAAAGTT
5866173 TTAAAAGGATATTAAGCCATTTGGTTG
194 TTAAAAGGATATTAAGCCATTTGGTTG
* *
5866200 AATGAGAAAAATCGACACTCAGCACCTTAGGGCATGTTTCCTCGAATTT-CCAAACGCAAAACAT
1 AATGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTCCTCGAATTTCCCAAACGCAAAACAT
* * *
5866264 TGCCTTATTT-TAAAATTTTTGAAAGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGACACC
66 TGCCTTATTTAAAAAATTTTTAAAAGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACC
* * * * *
5866328 CAGCACCTTAGGGCACGTTTTCTCGAATTTTCAAACGCTAAATATTGCCT
131 CAGCACCTCAGGGCACGTTCTCTCGAATTTCCAAACGCAAAACATTGCCT
5866378 CAATTAGAAA
Statistics
Matches: 166, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
218 17 0.10
219 79 0.48
221 24 0.14
222 46 0.28
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (220 bp):
AATGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTCCTCGAATTTCCCAAACGCAAAACAT
TGCCTTATTTAAAAAATTTTTAAAAGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACC
CAGCACCTCAGGGCACGTTCTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTGAAAAGTTTT
AAAAGGATATTAAGCCATTTGGTTG
Found at i:5866949 original size:3 final size:3
Alignment explanation
Indices: 5866869--5866930 Score: 106
Period size: 3 Copynumber: 20.7 Consensus size: 3
5866859 AAATGGAAAT
* *
5866869 ATA ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5866917 ATA ATA ATA ATA AT
1 ATA ATA ATA ATA AT
5866931 GGTAACATTA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5867897 original size:21 final size:23
Alignment explanation
Indices: 5867853--5867898 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
5867843 TATAGCCGAA
*
5867853 TGCTACTGCTTTTGTTGTCTTGTT
1 TGCTACTGC-TTTCTTGTCTTGTT
5867877 TGCTACTG-TTTCTTG-CTTGTT
1 TGCTACTGCTTTCTTGTCTTGTT
5867898 T
1 T
5867899 CTTTCTTTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 6 0.29
24 8 0.38
ACGTcount: A:0.04, C:0.17, G:0.20, T:0.59
Consensus pattern (23 bp):
TGCTACTGCTTTCTTGTCTTGTT
Found at i:5871562 original size:2 final size:2
Alignment explanation
Indices: 5871551--5871580 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5871541 TATACTTTTC
5871551 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5871581 CTCGTTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5874978 original size:87 final size:86
Alignment explanation
Indices: 5874797--5875068 Score: 235
Period size: 86 Copynumber: 3.2 Consensus size: 86
5874787 AAGGTGTTGG
* * ** * * * * * *
5874797 TCTTTAGCGGCGC-TTCTAGCACAAACGCCGCTGAAGAATAAGACCTTTAGCGGCGCTTTAG-TA
1 TCTTTAGCGGCGCTTTC-AGGACAAACGCCGCTAAAGACCAGGATCTTTAGTGGCGCCTTCGACA
* * *
5874860 GAAGCGCCGCTAAAGACCCTGA
65 CAAACGCCGCTAAAGACCCTAA
* ** * * * *
5874882 TCTTTAGCGGCGTTTTTGGGATAAGCGCCGCTAAAGATCAGGGGTCTTTAGTGGCGCC-TCGACA
1 TCTTTAGCGGCGCTTTCAGGACAAACGCCGCTAAAGACCA-GGATCTTTAGTGGCGCCTTCGACA
* *
5874946 GCAAACGCCACTAAAGAACCTAA
65 -CAAACGCCGCTAAAGACCCTAA
** * ***
5874969 TCTTTAGCGGCGCTTTCATTACAAACGCCGCTAAAGACCATGATCTTTAGTGGCGCCTTTTCCAC
1 TCTTTAGCGGCGCTTTCAGGACAAACGCCGCTAAAGACCAGGATCTTTAGTGGCGCCTTCGACAC
*
5875034 AAACGCCGCAAAAGACCCTAA
66 AAACGCCGCTAAAGACCCTAA
5875055 TCTTTAGCGGCGCT
1 TCTTTAGCGGCGCT
5875069 NNNNNNNNNN
Statistics
Matches: 145, Mismatches: 37, Indels: 9
0.76 0.19 0.05
Matches are distributed among these distances:
85 30 0.21
86 63 0.43
87 52 0.36
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (86 bp):
TCTTTAGCGGCGCTTTCAGGACAAACGCCGCTAAAGACCAGGATCTTTAGTGGCGCCTTCGACAC
AAACGCCGCTAAAGACCCTAA
Found at i:5874981 original size:43 final size:41
Alignment explanation
Indices: 5874926--5875067 Score: 126
Period size: 43 Copynumber: 3.3 Consensus size: 41
5874916 AGATCAGGGG
* *
5874926 TCTTTAGTGGCGCCTCGACAGCAAACGCCACTAAAGAACCTAA
1 TCTTTAGCGGCGCCTC-ACA-CAAACGCCGCTAAAGAACCTAA
* * *
5874969 TCTTTAGCGGCGCTTTCATTACAAACGCCGCTAAAG-ACCATGA
1 TCTTTAGCGGCGC-CTCA-CACAAACGCCGCTAAAGAACC-TAA
* * *
5875012 TCTTTAGTGGCGCCTTTTC-CACAAACGCCGCAAAAGACCCTAA
1 TCTTTAGCGGCGCC---TCACACAAACGCCGCTAAAGAACCTAA
5875055 TCTTTAGCGGCGC
1 TCTTTAGCGGCGC
5875068 TNNNNNNNNN
Statistics
Matches: 80, Mismatches: 12, Indels: 14
0.75 0.11 0.13
Matches are distributed among these distances:
42 3 0.04
43 70 0.88
44 5 0.06
45 2 0.03
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.23
Consensus pattern (41 bp):
TCTTTAGCGGCGCCTCACACAAACGCCGCTAAAGAACCTAA
Found at i:5875054 original size:86 final size:87
Alignment explanation
Indices: 5874864--5875068 Score: 234
Period size: 87 Copynumber: 2.4 Consensus size: 87
5874854 TTAGTAGAAG
* * ** * * * *
5874864 CGCCGCTAAAGACCCTGATCTTTAGCGGCGTTTTTGGGATAAGCGCCGCTAAAGATCAGGGGTCT
1 CGCCGCTAAAGACCCTAATCTTTAGCGGCGCTTTCAGGACAAACGCCGCTAAAGACCAGGGATCT
5874929 TTAGTGGCGCCTCGACAGCAAA
66 TTAGTGGCGCCTCGACAGCAAA
* * ** *
5874951 CGCCACTAAAGAACCTAATCTTTAGCGGCGCTTTCATTACAAACGCCGCTAAAGACCA-TGATCT
1 CGCCGCTAAAGACCCTAATCTTTAGCGGCGCTTTCAGGACAAACGCCGCTAAAGACCAGGGATCT
***
5875015 TTAGTGGCGCCTTTTCCA-CAAA
66 TTAGTGGCGCC-TCGACAGCAAA
*
5875037 CGCCGCAAAAGACCCTAATCTTTAGCGGCGCT
1 CGCCGCTAAAGACCCTAATCTTTAGCGGCGCT
5875069 NNNNNNNNNN
Statistics
Matches: 98, Mismatches: 19, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
86 48 0.49
87 50 0.51
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.23
Consensus pattern (87 bp):
CGCCGCTAAAGACCCTAATCTTTAGCGGCGCTTTCAGGACAAACGCCGCTAAAGACCAGGGATCT
TTAGTGGCGCCTCGACAGCAAA
Found at i:5875207 original size:21 final size:21
Alignment explanation
Indices: 5875178--5875265 Score: 106
Period size: 21 Copynumber: 4.2 Consensus size: 21
5875168 NTTGACGCTG
*
5875178 CTCTGCTTCCCTCGCTGCAGC
1 CTCTACTTCCCTCGCTGCAGC
**
5875199 CTCTACTTCCCTCGCTTTAGC
1 CTCTACTTCCCTCGCTGCAGC
*
5875220 CTCTGCTTCCCTCGCTGCAGC
1 CTCTACTTCCCTCGCTGCAGC
* *
5875241 CTATACTTCTCTCGCTGTC-GC
1 CTCTACTTCCCTCGCTG-CAGC
5875262 CTCT
1 CTCT
5875266 GCTTTTCTTG
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
21 55 0.98
22 1 0.02
ACGTcount: A:0.07, C:0.44, G:0.15, T:0.34
Consensus pattern (21 bp):
CTCTACTTCCCTCGCTGCAGC
Found at i:5875237 original size:42 final size:42
Alignment explanation
Indices: 5875178--5875269 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
5875168 NTTGACGCTG
* *
5875178 CTCTGCTTCCCTCGCTGCAGCCTCTACTTCCCTCGCTTTAGC
1 CTCTGCTTCCCTCGCTGCAGCCTATACTTCCCTCGCTGTAGC
* *
5875220 CTCTGCTTCCCTCGCTGCAGCCTATACTTCTCTCGCTGTCGC
1 CTCTGCTTCCCTCGCTGCAGCCTATACTTCCCTCGCTGTAGC
5875262 CTCTGCTT
1 CTCTGCTT
5875270 TTCTTGCCGC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.07, C:0.43, G:0.15, T:0.35
Consensus pattern (42 bp):
CTCTGCTTCCCTCGCTGCAGCCTATACTTCCCTCGCTGTAGC
Found at i:5875372 original size:66 final size:66
Alignment explanation
Indices: 5875281--5875430 Score: 221
Period size: 66 Copynumber: 2.3 Consensus size: 66
5875271 TCTTGCCGCC
* * * *
5875281 GCATCTGCTCTAAGCTGTTGCTGGAGTTCTTCATA-CTTTCGTTGAACCTCAGCTTCTCTCGCTG
1 GCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTT-GTTGAACCTCAGCTTCTCTCGATG
5875345 CT
65 CT
* *
5875347 GCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGAACCTCAGCTTCTCTCGATGT
1 GCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTGTTGAACCTCAGCTTCTCTCGATGC
5875412 T
66 T
*
5875413 GCCTCTGCTTTAAGTTGT
1 GCATCTGCTTTAAGTTGT
5875431 GTAATTTGCT
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
66 72 0.95
67 4 0.05
ACGTcount: A:0.15, C:0.25, G:0.19, T:0.41
Consensus pattern (66 bp):
GCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTGTTGAACCTCAGCTTCTCTCGATGC
T
Found at i:5880845 original size:9 final size:9
Alignment explanation
Indices: 5880809--5881163 Score: 151
Period size: 9 Copynumber: 42.6 Consensus size: 9
5880799 AATTGCACGG
5880809 GTAAGTTAT
1 GTAAGTTAT
*
5880818 GT-A-TTGT
1 GTAAGTTAT
*
5880825 GTAAGCTAT
1 GTAAGTTAT
*
5880834 GTAAGTTGT
1 GTAAGTTAT
5880843 GT-A-TTAT
1 GTAAGTTAT
5880850 GTAAGTTAT
1 GTAAGTTAT
5880859 -T-A-TTAT
1 GTAAGTTAT
5880865 GCTTTAAGTTAT
1 G---TAAGTTAT
5880877 GTAAG---T
1 GTAAGTTAT
*
5880883 GTAAATTAT
1 GTAAGTTAT
* *
5880892 GTAAGATGT
1 GTAAGTTAT
*
5880901 GT-A-TAAT
1 GTAAGTTAT
* *
5880908 GTTAGTTAC
1 GTAAGTTAT
**
5880917 CAAAGTTAT
1 GTAAGTTAT
5880926 GT-A-TTAT
1 GTAAGTTAT
5880933 GTAAGTTAT
1 GTAAGTTAT
*
5880942 TTAAGTTAT
1 GTAAGTTAT
*
5880951 GTAA--CAT
1 GTAAGTTAT
*
5880958 GTAAATTAT
1 GTAAGTTAT
*
5880967 GTAAGTTGT
1 GTAAGTTAT
* *
5880976 GTAGGCTAT
1 GTAAGTTAT
* *
5880985 GTATGTTAA
1 GTAAGTTAT
5880994 GTAAGTTAT
1 GTAAGTTAT
5881003 GT-A-TTAT
1 GTAAGTTAT
*
5881010 GTAAGTTGT
1 GTAAGTTAT
*
5881019 GT-A-TAAT
1 GTAAGTTAT
*
5881026 GTTAGTTAT
1 GTAAGTTAT
**
5881035 CAAAGTTAT
1 GTAAGTTAT
5881044 GT-A-TTAT
1 GTAAGTTAT
5881051 GTAAGTTAT
1 GTAAGTTAT
* *
5881060 TTAAGTTAA
1 GTAAGTTAT
*
5881069 GT--GGT-T
1 GTAAGTTAT
*
5881075 GTAAATTAT
1 GTAAGTTAT
* *
5881084 GTAAGATGT
1 GTAAGTTAT
5881093 GT-A-TTAT
1 GTAAGTTAT
5881100 GTAAGTTAT
1 GTAAGTTAT
**
5881109 CAAAGTTAT
1 GTAAGTTAT
5881118 GT-A-TTAT
1 GTAAGTTAT
5881125 GTAAGTTAT
1 GTAAGTTAT
*
5881134 TTAAGTTAT
1 GTAAGTTAT
*
5881143 GTAA--CAT
1 GTAAGTTAT
*
5881150 GTAAATTAT
1 GTAAGTTAT
5881159 GTAAG
1 GTAAG
5881164 ATGTGTATAA
Statistics
Matches: 247, Mismatches: 65, Indels: 68
0.65 0.17 0.18
Matches are distributed among these distances:
6 11 0.04
7 60 0.24
8 20 0.08
9 149 0.60
10 1 0.00
11 1 0.00
12 5 0.02
ACGTcount: A:0.33, C:0.03, G:0.20, T:0.45
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:5880850 original size:16 final size:15
Alignment explanation
Indices: 5880831--5880865 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
5880821 TTGTGTAAGC
*
5880831 TATGTAAGTTGTGTAT
1 TATGTAAGTTAT-TAT
5880847 TATGTAAGTTATTAT
1 TATGTAAGTTATTAT
5880862 TATG
1 TATG
5880866 CTTTAAGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (15 bp):
TATGTAAGTTATTAT
Found at i:5880940 original size:16 final size:16
Alignment explanation
Indices: 5880938--5881034 Score: 59
Period size: 16 Copynumber: 5.8 Consensus size: 16
5880928 ATTATGTAAG
*
5880938 TTATTTAAGTTATGTA
1 TTATGTAAGTTATGTA
** *
5880954 ACATGTAAATTATGTAA
1 TTATGTAAGTTATGT-A
* * *
5880971 GTTGTGTAGGCTATGTA
1 -TTATGTAAGTTATGTA
*
5880988 TGTTAAGTAAGTTATGTA
1 --TTATGTAAGTTATGTA
*
5881006 TTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTA
* *
5881022 TAATGTTAGTTAT
1 TTATGTAAGTTAT
5881035 CAAAGTTATG
Statistics
Matches: 59, Mismatches: 19, Indels: 6
0.70 0.23 0.07
Matches are distributed among these distances:
16 35 0.59
17 2 0.03
18 22 0.37
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.46
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:5880947 original size:25 final size:25
Alignment explanation
Indices: 5880869--5881021 Score: 112
Period size: 25 Copynumber: 6.1 Consensus size: 25
5880859 TATTATGCTT
*
5880869 TAAGTTATGTA--AGTGTAAATTATG
1 TAAGTTATGTATTA-TGTAAGTTATG
* * * * **
5880893 TAAGATGTGTATAATGTTAGTTACC
1 TAAGTTATGTATTATGTAAGTTATG
* *
5880918 AAAGTTATGTATTATGTAAGTTATT
1 TAAGTTATGTATTATGTAAGTTATG
** *
5880943 TAAGTTATGTAACATGTAAATTATG
1 TAAGTTATGTATTATGTAAGTTATG
* * * *
5880968 TAAGTTGTGTAGGCTATGTATGTTAAG
1 TAAGTTATGTA--TTATGTAAGTTATG
*
5880995 TAAGTTATGTATTATGTAAGTTGTG
1 TAAGTTATGTATTATGTAAGTTATG
5881020 TA
1 TA
5881022 TAATGTTAGT
Statistics
Matches: 96, Mismatches: 29, Indels: 7
0.73 0.22 0.05
Matches are distributed among these distances:
24 9 0.09
25 67 0.70
26 1 0.01
27 19 0.20
ACGTcount: A:0.33, C:0.03, G:0.21, T:0.43
Consensus pattern (25 bp):
TAAGTTATGTATTATGTAAGTTATG
Found at i:5881030 original size:118 final size:115
Alignment explanation
Indices: 5880887--5881131 Score: 355
Period size: 118 Copynumber: 2.1 Consensus size: 115
5880877 GTAAGTGTAA
* *
5880887 ATTATGTAAGATGTGTATAATGTTAGTTACCAAAGTTATGTATTATGTAAGTTATTTAAGTTATG
1 ATTATGTAAGTTGTGTATAATGTTAGTTACCAAAGTTATGTATTATGTAAGTTATTTAAGTTAAG
* * **
5880952 TAACATGTAAATTATGTAAGTTGTGTAGGCTATGTATGTTAAGTAAGTTATGT
66 T-ACATGTAAATTATGTAAGATGTGTA--CTATGTAAGTTAACAAAGTTATGT
*
5881005 ATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTATTATGTAAGTTATTTAAGTTAAG
1 ATTATGTAAGTTGTGTATAATGTTAGTTACCAAAGTTATGTATTATGTAAGTTATTTAAGTTAAG
*** * *
5881070 TGGTTGTAAATTATGTAAGATGTGTATTATGTAAGTTATCAAAGTTATGT
66 TACATGTAAATTATGTAAGATGTGTACTATGTAAGTTAACAAAGTTATGT
5881120 ATTATGTAAGTT
1 ATTATGTAAGTT
5881132 ATTTAAGTTA
Statistics
Matches: 115, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
115 31 0.27
117 21 0.18
118 63 0.55
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.44
Consensus pattern (115 bp):
ATTATGTAAGTTGTGTATAATGTTAGTTACCAAAGTTATGTATTATGTAAGTTATTTAAGTTAAG
TACATGTAAATTATGTAAGATGTGTACTATGTAAGTTAACAAAGTTATGT
Found at i:5881034 original size:25 final size:25
Alignment explanation
Indices: 5881006--5881207 Score: 133
Period size: 25 Copynumber: 8.1 Consensus size: 25
5880996 AAGTTATGTA
*
5881006 TTATGTAAGTTGTGTATAATGTTAG
1 TTATGTAAGTTGTGTATAATGTAAG
** * *
5881031 TTATCAAAGTTATGTATTATGTAAG
1 TTATGTAAGTTGTGTATAATGTAAG
* * *
5881056 TTATTTAAGTTAAGTG-GT--TGTAAA
1 TTATGTAAGTT--GTGTATAATGTAAG
* *
5881080 TTATGTAAGATGTGTATTATGTAAG
1 TTATGTAAGTTGTGTATAATGTAAG
** * *
5881105 TTATCAAAGTTATGTATTATGTAAG
1 TTATGTAAGTTGTGTATAATGTAAG
* * *
5881130 TTATTTAAGTTATGTA-ACATGTAAA
1 TTATGTAAGTTGTGTATA-ATGTAAG
* *
5881155 TTATGTAAGATGTGTATAATGTTAG
1 TTATGTAAGTTGTGTATAATGTAAG
*** * *
5881180 TTACCAAAGTTATGTATTATGTAAG
1 TTATGTAAGTTGTGTATAATGTAAG
5881205 TTA
1 TTA
5881208 NNNNNNNNNN
Statistics
Matches: 136, Mismatches: 34, Indels: 14
0.74 0.18 0.08
Matches are distributed among these distances:
22 3 0.02
23 1 0.01
24 14 0.10
25 114 0.84
26 2 0.01
27 2 0.01
ACGTcount: A:0.34, C:0.02, G:0.19, T:0.45
Consensus pattern (25 bp):
TTATGTAAGTTGTGTATAATGTAAG
Found at i:5881094 original size:74 final size:75
Alignment explanation
Indices: 5881005--5881207 Score: 327
Period size: 74 Copynumber: 2.7 Consensus size: 75
5880995 TAAGTTATGT
*
5881005 ATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTATTATGTAAGTTATTTAAGTTAAG
1 ATTATGTAAGATGTGTATAATGTTAGTTATCAAAGTTATGTATTATGTAAGTTATTTAAGTTAAG
***
5881070 T-GGTTGTAA
66 TAACATGTAA
* * *
5881079 ATTATGTAAGATGTGTATTATGTAAGTTATCAAAGTTATGTATTATGTAAGTTATTTAAGTTATG
1 ATTATGTAAGATGTGTATAATGTTAGTTATCAAAGTTATGTATTATGTAAGTTATTTAAGTTAAG
5881144 TAACATGTAA
66 TAACATGTAA
*
5881154 ATTATGTAAGATGTGTATAATGTTAGTTACCAAAGTTATGTATTATGTAAGTTA
1 ATTATGTAAGATGTGTATAATGTTAGTTATCAAAGTTATGTATTATGTAAGTTA
5881208 NNNNNNNNNN
Statistics
Matches: 118, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
74 62 0.53
75 56 0.47
ACGTcount: A:0.34, C:0.02, G:0.19, T:0.44
Consensus pattern (75 bp):
ATTATGTAAGATGTGTATAATGTTAGTTATCAAAGTTATGTATTATGTAAGTTATTTAAGTTAAG
TAACATGTAA
Found at i:5881402 original size:16 final size:16
Alignment explanation
Indices: 5881378--5881420 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
5881368 TCTATTTAAG
* *
5881378 TTATATAAGTTGTGTA
1 TTATGTAAGTTGTATA
5881394 TTATGTAAGTTGTATA
1 TTATGTAAGTTGTATA
5881410 TTATGTAAGTT
1 TTATGTAAGTT
5881421 ATTAAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (16 bp):
TTATGTAAGTTGTATA
Found at i:5881517 original size:27 final size:27
Alignment explanation
Indices: 5881479--5881763 Score: 225
Period size: 27 Copynumber: 11.1 Consensus size: 27
5881469 TATATTAAAA
5881479 ATATAGGTTTTAATATTTAAAAATAAC
1 ATATAGGTTTTAATATTTAAAAATAAC
5881506 ATATAGGTTTTAATATTTAAAAATAAC
1 ATATAGGTTTTAATATTTAAAAATAAC
*
5881533 AAATAGGTTTTAATATTTAAAAATAAC
1 ATATAGGTTTTAATATTTAAAAATAAC
5881560 ATATAGGTTTTAATATTTAAAAATAAC
1 ATATAGGTTTTAATATTTAAAAATAAC
* ** * *
5881587 ATTTA-CATTT-ATTTTTAAAATTATAAA
1 ATATAGGTTTTAATATTTAAAA--ATAAC
*
5881614 AT-TCA--TTTCT-A-A--TAAAATTGAA-
1 ATAT-AGGTTT-TAATATTTAAAAAT-AAC
* * *** *
5881636 ATGTAGG-----ATATATATCCATACC
1 ATATAGGTTTTAATATTTAAAAATAAC
**
5881658 ATATATGG-GGTAATATATT---AA-AA-
1 ATATA-GGTTTTAATAT-TTAAAAATAAC
5881681 ATATAGGTTTTAATATTTAAAAATAAC
1 ATATAGGTTTTAATATTTAAAAATAAC
5881708 ATATAGGTTTTAATATTTAAAAATAAC
1 ATATAGGTTTTAATATTTAAAAATAAC
5881735 ATATAGGTTTTAATATTTAAAAATAAC
1 ATATAGGTTTTAATATTTAAAAATAAC
5881762 AT
1 AT
5881764 TTACATTTAT
Statistics
Matches: 213, Mismatches: 21, Indels: 48
0.76 0.07 0.17
Matches are distributed among these distances:
19 1 0.00
20 1 0.00
21 1 0.00
22 15 0.07
23 16 0.08
24 6 0.03
25 12 0.06
26 8 0.04
27 152 0.71
28 1 0.00
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (27 bp):
ATATAGGTTTTAATATTTAAAAATAAC
Found at i:5881758 original size:175 final size:175
Alignment explanation
Indices: 5881506--5881911 Score: 794
Period size: 175 Copynumber: 2.3 Consensus size: 175
5881496 TAAAAATAAC
*
5881506 ATATAGGTTTTAATATTTAAAAATAACAAATAGGTTTTAATATTTAAAAATAACATATAGGTTTT
1 ATATAGGTTTTAATATTTAAAAATAACATATAGGTTTTAATATTTAAAAATAACATATAGGTTTT
5881571 AATATTTAAAAATAACATTTACATTTATTTTTAAAATTATAAAATTCATTTCTAATAAAATTGAA
66 AATATTTAAAAATAACATTTACATTTATTTTTAAAATTATAAAATTCATTTCTAATAAAATTGAA
5881636 ATGTAGGATATATATCCATACCATATATGGGGTAATATATTAAAA
131 ATGTAGGATATATATCCATACCATATATGGGGTAATATATTAAAA
5881681 ATATAGGTTTTAATATTTAAAAATAACATATAGGTTTTAATATTTAAAAATAACATATAGGTTTT
1 ATATAGGTTTTAATATTTAAAAATAACATATAGGTTTTAATATTTAAAAATAACATATAGGTTTT
5881746 AATATTTAAAAATAACATTTACATTTATTTTTAAAATTATAAAATTCATTTCTAATAAAATTGAA
66 AATATTTAAAAATAACATTTACATTTATTTTTAAAATTATAAAATTCATTTCTAATAAAATTGAA
*
5881811 ATGTAGGATATATATCCATACCATATATGGGGTGATATATTAAAA
131 ATGTAGGATATATATCCATACCATATATGGGGTAATATATTAAAA
5881856 ATATAGGTTTTAATATTTAAAAATAACATATAGGTTTTAATATTTAAAAATAACAT
1 ATATAGGTTTTAATATTTAAAAATAACATATAGGTTTTAATATTTAAAAATAACAT
5881912 TTACATTTAT
Statistics
Matches: 229, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
175 229 1.00
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.40
Consensus pattern (175 bp):
ATATAGGTTTTAATATTTAAAAATAACATATAGGTTTTAATATTTAAAAATAACATATAGGTTTT
AATATTTAAAAATAACATTTACATTTATTTTTAAAATTATAAAATTCATTTCTAATAAAATTGAA
ATGTAGGATATATATCCATACCATATATGGGGTAATATATTAAAA
Found at i:5881822 original size:148 final size:147
Alignment explanation
Indices: 5881708--5882032 Score: 551
Period size: 148 Copynumber: 2.2 Consensus size: 147
5881698 TAAAAATAAC
5881708 ATATAGGTTTTAATATTTAAAAATAACATATAGGTTTTAATATTTAAAAATAACATTTACATTTA
1 ATATAGGTTTTAATATTTAAAAATAACATATAGGTTTTAATATTTAAAAATAACATTTACATTTA
* **
5881773 TTTTTAAAATTATAAAATTCATTTCTAATAAAATTGAAATGTAGGATATATATCCATACCATATA
66 TTTTTAAAATTATAAAATTCATTTCTAATAAAATTGAAATATAGGATATATAT-CATAAAATATA
*
5881838 TGGGGTGATATATTAAAA
130 TGGGGTAATATATTAAAA
5881856 ATATAGGTTTTAATATTTAAAAATAACATATAGGTTTTAATATTTAAAAATAACATTTACATTTA
1 ATATAGGTTTTAATATTTAAAAATAACATATAGGTTTTAATATTTAAAAATAACATTTACATTTA
* **
5881921 TTTTTAAAATTATAAAATTCATTTCTAATAAAATTGAAATATAGGTTATATATCCATACCATATA
66 TTTTTAAAATTATAAAATTCATTTCTAATAAAATTGAAATATAGGATATATAT-CATAAAATATA
* *
5881986 TGGGCTGATATATTAAAA
130 TGGGGTAATATATTAAAA
5882004 ATATAGGTTTTAATATTTAAAAATAACAT
1 ATATAGGTTTTAATATTTAAAAATAACAT
5882033 TTACAATTAT
Statistics
Matches: 174, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
148 174 1.00
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (147 bp):
ATATAGGTTTTAATATTTAAAAATAACATATAGGTTTTAATATTTAAAAATAACATTTACATTTA
TTTTTAAAATTATAAAATTCATTTCTAATAAAATTGAAATATAGGATATATATCATAAAATATAT
GGGGTAATATATTAAAA
Found at i:5881850 original size:202 final size:202
Alignment explanation
Indices: 5881425--5881807 Score: 596
Period size: 202 Copynumber: 1.9 Consensus size: 202
5881415 TAAGTTATTA
* *
5881425 AAAATTGAAATGTAGGATATATATCCATACCATATATGGGGTGATATATTAAAAATATAGGTTTT
1 AAAATTGAAATGGAGGATATATATCCATACCATATATGGGGTAATATATTAAAAATATAGGTTTT
5881490 AATATTTAAAAATAACATATAGGTTTTAATATTTAAAAATAACAAATAGGTTTTAATATTTAAAA
66 AATATTTAAAAATAACATATAGGTTTTAATATTTAAAAATAACAAATAGGTTTTAATATTTAAAA
** * * **
5881555 ATAACATATAGGTTTTAATATTTAAAAATAACATTTACATTTATTTTTAAAATTATAAAATTCAT
131 ATAACATATAGCATTTAATATTTAAAAATAACAATTACATTTACTAATAAAATTATAAAATTCAT
*
5881620 TTCTAAT
196 ATCTAAT
*
5881627 AAAATTGAAATGTAGGATATATATCCATACCATATATGGGGTAATATATTAAAAATATAGGTTTT
1 AAAATTGAAATGGAGGATATATATCCATACCATATATGGGGTAATATATTAAAAATATAGGTTTT
*
5881692 AATATTTAAAAATAACATATAGGTTTTAATATTTAAAAATAACATATAGGTTTTAATATTTAAAA
66 AATATTTAAAAATAACATATAGGTTTTAATATTTAAAAATAACAAATAGGTTTTAATATTTAAAA
* *
5881757 ATAACATTTA-CATTT-ATTTTTAAAATTATAA-AATT-CATTT-CTAATAAAATT
131 ATAACATATAGCATTTAATATTTAAAA--ATAACAATTACATTTACTAATAAAATT
5881808 GAAATGTAGG
Statistics
Matches: 169, Mismatches: 10, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
199 8 0.05
200 14 0.08
201 6 0.04
202 141 0.83
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.40
Consensus pattern (202 bp):
AAAATTGAAATGGAGGATATATATCCATACCATATATGGGGTAATATATTAAAAATATAGGTTTT
AATATTTAAAAATAACATATAGGTTTTAATATTTAAAAATAACAAATAGGTTTTAATATTTAAAA
ATAACATATAGCATTTAATATTTAAAAATAACAATTACATTTACTAATAAAATTATAAAATTCAT
ATCTAAT
Found at i:5881894 original size:27 final size:27
Alignment explanation
Indices: 5881856--5881911 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
5881846 TATATTAAAA
5881856 ATATAGGTTTTAATATTTAAAAATAAC
1 ATATAGGTTTTAATATTTAAAAATAAC
5881883 ATATAGGTTTTAATATTTAAAAATAAC
1 ATATAGGTTTTAATATTTAAAAATAAC
5881910 AT
1 AT
5881912 TTACATTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (27 bp):
ATATAGGTTTTAATATTTAAAAATAAC
Found at i:5882097 original size:121 final size:121
Alignment explanation
Indices: 5881883--5882106 Score: 369
Period size: 121 Copynumber: 1.9 Consensus size: 121
5881873 TAAAAATAAC
* *** *
5881883 ATATAGGTTTTAATATTTAAAAATAACATTTACATTTATTTTTAAAATTATAAAATTCATTTCTA
1 ATATAGGTTTTAATATTTAAAAATAACATTTACAATTATTGGCAAAATTATAAAATTCATTACTA
5881948 ATAAAATTGAAATATAGGTTATATATCCATACCATATATGGGCTGATATATTAAAA
66 ATAAAATTGAAATATAGGTTATATATCCATACCATATATGGGCTGATATATTAAAA
*
5882004 ATATAGGTTTTAATATTTAAAAATAACATTTACAATTATTGGCAAAATTATAAAATTTATTGAC-
1 ATATAGGTTTTAATATTTAAAAATAACATTTACAATTATTGGCAAAATTATAAAATTCATT-ACT
*
5882068 AATAAAATTGGAATATAGGTTATATATCCATACCATATA
65 AATAAAATTGAAATATAGGTTATATATCCATACCATATA
5882107 GCTAAATTTT
Statistics
Matches: 95, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
121 94 0.99
122 1 0.01
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.40
Consensus pattern (121 bp):
ATATAGGTTTTAATATTTAAAAATAACATTTACAATTATTGGCAAAATTATAAAATTCATTACTA
ATAAAATTGAAATATAGGTTATATATCCATACCATATATGGGCTGATATATTAAAA
Done.