Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 7 of 136
Found at i:1898125 original size:27 final size:26
Alignment explanation
Indices: 1898078--1898181 Score: 94
Period size: 24 Copynumber: 4.1 Consensus size: 26
1898068 GATGATATTA
1898078 ATAATAATAATA-ACG--ATAATAATG
1 ATAATAATAATAGA-GTAATAATAATG
*
1898102 ATAATAATAATAGTAGTAAAAATAA--
1 ATAATAATAATAG-AGTAATAATAATG
**
1898127 A-AATAATAATACGAGTAATAATAAAA
1 ATAATAATAATA-GAGTAATAATAATG
*
1898153 ATAATAGTAATAGGAGTAATAATAATG
1 ATAATAATAATA-GAGTAATAATAATG
1898180 AT
1 AT
1898182 TAAAATTAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
24 32 0.48
25 3 0.05
26 2 0.03
27 29 0.44
ACGTcount: A:0.60, C:0.02, G:0.11, T:0.28
Consensus pattern (26 bp):
ATAATAATAATAGAGTAATAATAATG
Found at i:1907350 original size:88 final size:87
Alignment explanation
Indices: 1907199--1907533 Score: 447
Period size: 88 Copynumber: 3.8 Consensus size: 87
1907189 AATAGTTTGA
*
1907199 AGAAGACAGCGAGTCTTCTTTTCTTTGGCATTGTAGCGGAGCAGATTAAAGCTGAAGGCAGCGAA
1 AGAAGACAGCGAGTCTTCTTTTCTCTGGCATTGTAGCGGAGCAGATTAAAGCTGAAGGCAGCGAA
*
1907264 TTTTATCTCCTTAGCGTTAAGAC
66 TCTTATCTCCTT-GCGTTAAGAC
* ** * *
1907287 AGAAGACAGCGAGTCTTCTTTTCTCTGGCGTTGTAATGGAGCAGATTAAAGCTAAAGGTAGCGAA
1 AGAAGACAGCGAGTCTTCTTTTCTCTGGCATTGTAGCGGAGCAGATTAAAGCTGAAGGCAGCGAA
* * *
1907352 TCTTATCTCCCTGACCTTAAGAA
66 TCTTATCTCCTTG-CGTTAAGAC
* * *
1907375 AGAAGACAGCGAGTCTTCTTTTCCCTGGCGTTGTAGCGGAGCAAATTAAAGCTGAAGGCAGCGAA
1 AGAAGACAGCGAGTCTTCTTTTCTCTGGCATTGTAGCGGAGCAGATTAAAGCTGAAGGCAGCGAA
*
1907440 TCTTCTCTCCTTGGCGTTAAGAC
66 TCTTATCTCCTT-GCGTTAAGAC
* * * * *
1907463 TGAAGATAGCGAGTCTTATTTT-TCTTGGCATTGTAGCGGAGTAGATTAAAGCTGAAGGCAGCAA
1 AGAAGACAGCGAGTCTTCTTTTCTC-TGGCATTGTAGCGGAGCAGATTAAAGCTGAAGGCAGCGA
*
1907527 ATTTTAT
65 ATCTTAT
1907534 ATCGCTAGCG
Statistics
Matches: 214, Mismatches: 30, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
87 2 0.01
88 211 0.99
89 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (87 bp):
AGAAGACAGCGAGTCTTCTTTTCTCTGGCATTGTAGCGGAGCAGATTAAAGCTGAAGGCAGCGAA
TCTTATCTCCTTGCGTTAAGAC
Found at i:1907511 original size:176 final size:176
Alignment explanation
Indices: 1907198--1907520 Score: 495
Period size: 176 Copynumber: 1.8 Consensus size: 176
1907188 GAATAGTTTG
** *
1907198 AAGAAGACAGCGAGTCTTCTTTTCTTTGGCATTGTAGCGGAGCAGATTAAAGCTGAAGGCAGCGA
1 AAGAAGACAGCGAGTCTTCTTTTCCCTGGCATTGTAGCGGAGCAAATTAAAGCTGAAGGCAGCGA
* * *
1907263 ATTTTATCTCCTTAGCGTTAAGACAGAAGACAGCGAGTCTTCTTTTCTCTGGCGTTGTAATGGAG
66 ATCTTATCTCCTTAGCGTTAAGACAGAAGACAGCGAGTCTTCTTTTCTCTGGCATTGTAACGGAG
1907328 CAGATTAAAGCTAAAGGTAGCGAATCTTATCTCCCTGACCTTAAGA
131 CAGATTAAAGCTAAAGGTAGCGAATCTTATCTCCCTGACCTTAAGA
*
1907374 AAGAAGACAGCGAGTCTTCTTTTCCCTGGCGTTGTAGCGGAGCAAATTAAAGCTGAAGGCAGCGA
1 AAGAAGACAGCGAGTCTTCTTTTCCCTGGCATTGTAGCGGAGCAAATTAAAGCTGAAGGCAGCGA
* * * * * *
1907439 ATCTTCTCTCCTTGGCGTTAAGACTGAAGATAGCGAGTCTTATTTT-TCTTGGCATTGTAGCGGA
66 ATCTTATCTCCTTAGCGTTAAGACAGAAGACAGCGAGTCTTCTTTTCTC-TGGCATTGTAACGGA
* *
1907503 GTAGATTAAAGCTGAAGG
130 GCAGATTAAAGCTAAAGG
1907521 CAGCAAATTT
Statistics
Matches: 131, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
175 2 0.02
176 129 0.98
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (176 bp):
AAGAAGACAGCGAGTCTTCTTTTCCCTGGCATTGTAGCGGAGCAAATTAAAGCTGAAGGCAGCGA
ATCTTATCTCCTTAGCGTTAAGACAGAAGACAGCGAGTCTTCTTTTCTCTGGCATTGTAACGGAG
CAGATTAAAGCTAAAGGTAGCGAATCTTATCTCCCTGACCTTAAGA
Found at i:1909577 original size:21 final size:20
Alignment explanation
Indices: 1909553--1909591 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1909543 CTTTTACACA
*
1909553 TACATATATTTTTCTTATATG
1 TACATATATATTT-TTATATG
1909574 TACATATATATTTTTATA
1 TACATATATATTTTTATA
1909592 GTTTATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (20 bp):
TACATATATATTTTTATATG
Found at i:1911706 original size:22 final size:22
Alignment explanation
Indices: 1911660--1911706 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1911650 TTCTTTCATG
****
1911660 TTTCCCCCCCCCCCCCCTTTTT
1 TTTCCCCCCCCCCCCCCCCCAT
1911682 TTTCCCCCCCCCCCCCCCCCAT
1 TTTCCCCCCCCCCCCCCCCCAT
1911704 TTT
1 TTT
1911707 TAGCAGTATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.02, C:0.66, G:0.00, T:0.32
Consensus pattern (22 bp):
TTTCCCCCCCCCCCCCCCCCAT
Found at i:1914893 original size:16 final size:16
Alignment explanation
Indices: 1914856--1914895 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
1914846 TTGATAAAAT
* *
1914856 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
1914872 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
1914888 TAAAATTA
1 TAAAATTA
1914896 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:1915215 original size:12 final size:13
Alignment explanation
Indices: 1915198--1915226 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1915188 TAAACATAAA
1915198 AAAACTAAAAC-T
1 AAAACTAAAACAT
1915210 AAAACTAAAACAT
1 AAAACTAAAACAT
1915223 AAAA
1 AAAA
1915227 TATATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.72, C:0.14, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAACTAAAACAT
Found at i:1919208 original size:13 final size:14
Alignment explanation
Indices: 1919170--1919207 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1919160 TTTTTCAATA
*
1919170 AAATTATTTTTCAG
1 AAATCATTTTTCAG
1919184 AAATCATTTTTC-G
1 AAATCATTTTTCAG
1919197 AAAGTCATTTT
1 AAA-TCATTTT
1919208 CAGTGAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.47
Consensus pattern (14 bp):
AAATCATTTTTCAG
Found at i:1922400 original size:34 final size:34
Alignment explanation
Indices: 1922350--1922507 Score: 172
Period size: 34 Copynumber: 4.6 Consensus size: 34
1922340 ACATATACGA
* * * * *
1922350 ATATCATATCAGAATGTCACATTACTAGAAACAT
1 ATATCAAATCAAAATGTCATATTTCCAGAAACAT
1922384 ATATCAAATCAAAATGTCATATTTCCAGAAACAT
1 ATATCAAATCAAAATGTCATATTTCCAGAAACAT
* *
1922418 ATACCAGATCAAAATGTCATATTTCCAGAAACAT
1 ATATCAAATCAAAATGTCATATTTCCAGAAACAT
* * * * * *
1922452 ATACCAGATCATAATTTCATATTTTCATAAACAT
1 ATATCAAATCAAAATGTCATATTTCCAGAAACAT
* * *
1922486 ATATCATATCAGAACGTCATAT
1 ATATCAAATCAAAATGTCATAT
1922508 CATATTAGAA
Statistics
Matches: 108, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 108 1.00
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.31
Consensus pattern (34 bp):
ATATCAAATCAAAATGTCATATTTCCAGAAACAT
Found at i:1923923 original size:2 final size:2
Alignment explanation
Indices: 1923916--1923940 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1923906 TAATTAAGTA
1923916 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1923941 GTGTGAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1924168 original size:34 final size:35
Alignment explanation
Indices: 1924124--1924193 Score: 124
Period size: 34 Copynumber: 2.0 Consensus size: 35
1924114 ATACAAGTGA
*
1924124 AATACATAGAAATTTGGTGTGGAAAATGAGATAGT
1 AATACATAGAAATTTGATGTGGAAAATGAGATAGT
1924159 AATA-ATAGAAATTTGATGTGGAAAATGAGATAGT
1 AATACATAGAAATTTGATGTGGAAAATGAGATAGT
1924193 A
1 A
1924194 TAGTTAATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 30 0.88
35 4 0.12
ACGTcount: A:0.46, C:0.01, G:0.24, T:0.29
Consensus pattern (35 bp):
AATACATAGAAATTTGATGTGGAAAATGAGATAGT
Found at i:1924913 original size:22 final size:22
Alignment explanation
Indices: 1924867--1924952 Score: 82
Period size: 22 Copynumber: 3.8 Consensus size: 22
1924857 TATTATCACG
*
1924867 TTAGTACTCTCCGATTAGTAGCACA
1 TTAGTGCTCTCCG-TT--TAGCACA
1924892 TTAGTGCTCTCCGTTTAGCACA
1 TTAGTGCTCTCCGTTTAGCACA
* ** * *
1924914 TTTGTGCTCTCTATATAGCACT
1 TTAGTGCTCTCCGTTTAGCACA
*
1924936 TTAGTGCTCTCTGTTTA
1 TTAGTGCTCTCCGTTTA
1924953 ATAGTGCATA
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
22 38 0.73
24 2 0.04
25 12 0.23
ACGTcount: A:0.20, C:0.23, G:0.16, T:0.41
Consensus pattern (22 bp):
TTAGTGCTCTCCGTTTAGCACA
Found at i:1927455 original size:22 final size:20
Alignment explanation
Indices: 1927407--1927447 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
1927397 GATAAGAAAA
1927407 ATTTAT-TTTG-TTAGTATT
1 ATTTATGTTTGTTTAGTATT
*
1927425 ATATA-GTTTGTTTAGTATT
1 ATTTATGTTTGTTTAGTATT
1927444 ATTT
1 ATTT
1927448 TTATGTTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.63
Consensus pattern (20 bp):
ATTTATGTTTGTTTAGTATT
Found at i:1930507 original size:62 final size:62
Alignment explanation
Indices: 1930431--1930660 Score: 370
Period size: 62 Copynumber: 3.7 Consensus size: 62
1930421 CAATGTACCT
* *
1930431 AATTTATATTACAAAGTTTGCTCCAAGTTTTAATGTTATAATGTATTTAATTTATATAACAA
1 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTTATATAACAA
* * *
1930493 AATTTATATTACAAAGTTTGTTCTAATTTTTAATGTTGTAATGTATTTAATTTATATAAAAA
1 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTTATATAACAA
* * * *
1930555 AATTTATATTACAAATTTTGTTCCAATTTTTAATATTGTAATGTATTTAATTTATATTACAA
1 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTTATATAACAA
*
1930617 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATCTTGTAATGT
1 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGT
1930661 TATAATGTTG
Statistics
Matches: 155, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 155 1.00
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.49
Consensus pattern (62 bp):
AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTTATATAACAA
Found at i:1930622 original size:14 final size:14
Alignment explanation
Indices: 1930603--1930631 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1930593 TAATGTATTT
1930603 AATTTATATTACAA
1 AATTTATATTACAA
1930617 AATTTATATTACAA
1 AATTTATATTACAA
1930631 A
1 A
1930632 GTTTGTTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
AATTTATATTACAA
Found at i:1931890 original size:14 final size:14
Alignment explanation
Indices: 1931871--1931905 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1931861 TAAATTACAT
*
1931871 GTTAGAATAGTATC
1 GTTAGAATAATATC
1931885 GTTAGAATAATATC
1 GTTAGAATAATATC
*
1931899 ATTAGAA
1 GTTAGAA
1931906 AAAAATGTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.34
Consensus pattern (14 bp):
GTTAGAATAATATC
Found at i:1933797 original size:31 final size:31
Alignment explanation
Indices: 1933762--1933827 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
1933752 ATAAAATCCG
1933762 AATTAAATCAACAATAA-TAACAACAAAAATA
1 AATTAAATCAACAATAATTAACAACAAAAA-A
* * * *
1933793 AATTAAATTAACATTAATTTATAACAAAAAA
1 AATTAAATCAACAATAATTAACAACAAAAAA
1933824 AATT
1 AATT
1933828 GTCTTTTCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 20 0.67
32 10 0.33
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (31 bp):
AATTAAATCAACAATAATTAACAACAAAAAA
Found at i:1934969 original size:11 final size:11
Alignment explanation
Indices: 1934955--1935005 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
1934945 AGATCTAAAC
*
1934955 AATAATAATAA
1 AATAATAGTAA
* *
1934966 AATAGTAGGAA
1 AATAATAGTAA
*
1934977 CATAATAGTAA
1 AATAATAGTAA
*
1934988 AATAGTAGTAA
1 AATAATAGTAA
1934999 AATAATA
1 AATAATA
1935006 AAAAATAGCA
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.61, C:0.02, G:0.12, T:0.25
Consensus pattern (11 bp):
AATAATAGTAA
Found at i:1934982 original size:22 final size:22
Alignment explanation
Indices: 1934955--1935013 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
1934945 AGATCTAAAC
1934955 AATAATAATAAAATAGTAGGAA
1 AATAATAATAAAATAGTAGGAA
* * *
1934977 CATAATAGTAAAATAGTAGTAA
1 AATAATAATAAAATAGTAGGAA
1934999 AATAATAA-AAAATAG
1 AATAATAATAAAATAG
1935014 CAAAAAAAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 7 0.22
22 25 0.78
ACGTcount: A:0.63, C:0.02, G:0.12, T:0.24
Consensus pattern (22 bp):
AATAATAATAAAATAGTAGGAA
Found at i:1936498 original size:20 final size:20
Alignment explanation
Indices: 1936462--1936499 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1936452 AGTGGAAGCA
*
1936462 GTTCCGGTGTAAAAAAAGTT
1 GTTCCGATGTAAAAAAAGTT
1936482 GTTCCGATG-AAAGAAAAG
1 GTTCCGATGTAAA-AAAAG
1936500 GCATCAATGG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.24
Consensus pattern (20 bp):
GTTCCGATGTAAAAAAAGTT
Found at i:1943545 original size:195 final size:195
Alignment explanation
Indices: 1943213--1943608 Score: 756
Period size: 195 Copynumber: 2.0 Consensus size: 195
1943203 AACAGTAAAA
*
1943213 ATAGATGGAATTTTTAATAAAAAGGAACGGTTTACTCTTTCATGTAATGTTCAAAGACTAATTTA
1 ATAGATGGAATTTTTAATAAAAAGGAACGGTTTACTCTTTCATCTAATGTTCAAAGACTAATTTA
1943278 CTCATTTTTTGAATAAATGGTTCAATATGCAATCTAAATCATAATTCATGGGCCTCCATGGTACT
66 CTCATTTTTTGAATAAATGGTTCAATATGCAATCTAAATCATAATTCATGGGCCTCCATGGTACT
1943343 ATTACCAATAACTAACCTATGTTATTTAGTTATGGGATGAGTATCGGGTACAAATACATCCCCAC
131 ATTACCAATAACTAACCTATGTTATTTAGTTATGGGATGAGTATCGGGTACAAATACATCCCCAC
*
1943408 ATAGATGGAATTTTTAATAAAAAGGAACGGTTTACTCTTTGATCTAATGTTCAAAGACTAATTTA
1 ATAGATGGAATTTTTAATAAAAAGGAACGGTTTACTCTTTCATCTAATGTTCAAAGACTAATTTA
1943473 CTCATTTTTTGAATAAATGGTTCAATATGCAATCTAAATCATAATTCATGGGCCTCCATGGTACT
66 CTCATTTTTTGAATAAATGGTTCAATATGCAATCTAAATCATAATTCATGGGCCTCCATGGTACT
* *
1943538 ATTACCAATAACTAACCTATGTTATTTGGTTATGGGATGAGTATCGGGTACAAATACATCCCCAT
131 ATTACCAATAACTAACCTATGTTATTTAGTTATGGGATGAGTATCGGGTACAAATACATCCCCAC
1943603 ATAGAT
1 ATAGAT
1943609 ACTTAAATTT
Statistics
Matches: 197, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
195 197 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Consensus pattern (195 bp):
ATAGATGGAATTTTTAATAAAAAGGAACGGTTTACTCTTTCATCTAATGTTCAAAGACTAATTTA
CTCATTTTTTGAATAAATGGTTCAATATGCAATCTAAATCATAATTCATGGGCCTCCATGGTACT
ATTACCAATAACTAACCTATGTTATTTAGTTATGGGATGAGTATCGGGTACAAATACATCCCCAC
Found at i:1946496 original size:103 final size:103
Alignment explanation
Indices: 1946315--1946507 Score: 273
Period size: 103 Copynumber: 1.9 Consensus size: 103
1946305 GGTAATTGAA
* * *
1946315 TTTCAAGCTTTAAACTTGAATCGTGTCTTCTCCATTTGCTTATATAAGCCTCAAAGTTCAAATTT
1 TTTCAAGCTTCAAACTTGAATCGGGTCTTCTCCATTTGCTTATATAAGCCTCAAAGTTCAAATAT
*
1946380 TTTGTTGTGTTTATGCCAAAATAATTCTCTGTTTCTGG
66 TTTGTCGTGTTTATGCCAAAATAATTCTCTGTTTCTGG
* * *
1946418 TTTCAAGCTTCAAACTTGAAAT-GGGTCTTTTCTATTTTCTTATATAAGCCTCAAAGTTCAAACT
1 TTTCAAGCTTCAAACTTG-AATCGGGTCTTCTCCATTTGCTTATATAAGCCTCAAAGTTCAAA-T
* *
1946482 ATTTT-TCGTTTTTATGCCAAATTAAT
64 ATTTTGTCGTGTTTATGCCAAAATAAT
1946508 ATACTTTCTT
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
103 71 0.90
104 8 0.10
ACGTcount: A:0.26, C:0.17, G:0.12, T:0.45
Consensus pattern (103 bp):
TTTCAAGCTTCAAACTTGAATCGGGTCTTCTCCATTTGCTTATATAAGCCTCAAAGTTCAAATAT
TTTGTCGTGTTTATGCCAAAATAATTCTCTGTTTCTGG
Found at i:1949364 original size:15 final size:15
Alignment explanation
Indices: 1949327--1949365 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
1949317 ATAGTAAAAA
1949327 TATAATTTATCATTT
1 TATAATTTATCATTT
1949342 TAATAATTTAT-ATCTT
1 T-ATAATTTATCAT-TT
1949358 TATAATTT
1 TATAATTT
1949366 TTAAAGGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (15 bp):
TATAATTTATCATTT
Found at i:1949450 original size:22 final size:22
Alignment explanation
Indices: 1949411--1949452 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1949401 GCAAAAATGT
*
1949411 AATTTTATTATTATTAATTTAA
1 AATTTTATAATTATTAATTTAA
1949433 AATTTTATAATTCA-TAATTT
1 AATTTTATAATT-ATTAATTT
1949453 CTCAAGACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
AATTTTATAATTATTAATTTAA
Found at i:1951175 original size:76 final size:76
Alignment explanation
Indices: 1951048--1951197 Score: 192
Period size: 76 Copynumber: 2.0 Consensus size: 76
1951038 AATAGTTATT
* * * *
1951048 AACTTTCAGACAGACTGTGATGAAGCTTCTCGACTGTCAGTTGCTCAAGTATCCAAATCATTGTC
1 AACTTTCAGACAGACTGAGATAAAGCTTCTCGACTGCCAGTTGCTCAAGTATCCAAATCATTATC
1951113 GAGTTTCTTCC
66 GAGTTTCTTCC
* * * ** ** *
1951124 AACTTTCAGACAGTCTGAGATAAAGCTTCTTGACTGCCGGTTGCTTGAGTATCGGAATCATTATT
1 AACTTTCAGACAGACTGAGATAAAGCTTCTCGACTGCCAGTTGCTCAAGTATCCAAATCATTATC
1951189 GAGTTTCTT
66 GAGTTTCTT
1951198 GAAGACTAGC
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
76 62 1.00
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.35
Consensus pattern (76 bp):
AACTTTCAGACAGACTGAGATAAAGCTTCTCGACTGCCAGTTGCTCAAGTATCCAAATCATTATC
GAGTTTCTTCC
Found at i:1952527 original size:20 final size:20
Alignment explanation
Indices: 1952502--1952542 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1952492 CAGTTAGTTG
1952502 ACTACCTCTCAAGGACAATA
1 ACTACCTCTCAAGGACAATA
1952522 ACTACCTCTCAAGGACAATA
1 ACTACCTCTCAAGGACAATA
1952542 A
1 A
1952543 ATGGCAACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.29, G:0.10, T:0.20
Consensus pattern (20 bp):
ACTACCTCTCAAGGACAATA
Found at i:1957036 original size:124 final size:124
Alignment explanation
Indices: 1956693--1957070 Score: 548
Period size: 126 Copynumber: 3.0 Consensus size: 124
1956683 TAAGGGTTTT
* ** **
1956693 TAGGTCCTGGAAGAAATAATTTTGAGTTGACGTTTCTGATAAAATAGTATAAAATCGCTTCTAGC
1 TAGGTCATGGAAGAAATAATTTT-TTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
1956758 AGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCC-C-TCATGGACGCGCTTTTGCTACAG
65 AGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCTCGTCA--GACGCGCTTTTGCTACAG
* * *
1956818 TAGATCACGGAAGAAATAATTATTTTTTTGACGATTCTGAGCAAATAGTATAAAATCGCTTCTAG
1 TAGGTCATGGAAGAAATAA-T-TTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAG
* *
1956883 CAGGATGCTATTTGAGAAGAATTTTTGAAATCGCAGCCTCGTCAG-TGCGCTTTTGCTACAG
64 CAGGATGCTATTTGAGAAGAATTTGTGAAATCGC-GCCTCGTCAGACGCGCTTTTGCTACAG
* *
1956944 TAGGTCATGTAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCA
1 TAGGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCA
*
1957009 GGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGT-GGACGCGCTTTTGCTACAG
66 GGATGCTATTTGAGAAGAATTTGTGAAATCGCG-CCTCGTCAGACGCGCTTTTGCTACAG
1957068 TAG
1 TAG
1957071 CATGATTGGG
Statistics
Matches: 228, Mismatches: 18, Indels: 15
0.87 0.07 0.06
Matches are distributed among these distances:
123 2 0.01
124 98 0.43
125 17 0.07
126 100 0.44
127 7 0.03
128 1 0.00
129 3 0.01
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (124 bp):
TAGGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCA
GGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCTCGTCAGACGCGCTTTTGCTACAG
Found at i:1957969 original size:21 final size:21
Alignment explanation
Indices: 1957944--1957987 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
1957934 ACATTACGTT
*
1957944 AAGG-TTAGGGTTTTTAAGTTA
1 AAGGTTTAGAGTTTTTAA-TTA
1957965 AAGGTTTAGAGTTTTTAATTA
1 AAGGTTTAGAGTTTTTAATTA
1957986 AA
1 AA
1957988 TTAGGTTAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.43
Consensus pattern (21 bp):
AAGGTTTAGAGTTTTTAATTA
Found at i:1958007 original size:29 final size:29
Alignment explanation
Indices: 1957970--1958220 Score: 271
Period size: 29 Copynumber: 8.6 Consensus size: 29
1957960 AGTTAAAGGT
*
1957970 TTAGAGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGG
1957999 TTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGG
* * *
1958028 TTAGGGTCTTTAATTAATTTAGATTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGG
* *
1958057 TTAGGGTCTTTAATTAAATTTGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGG
*
1958086 TTAGGGTCTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGG
* *
1958115 TTAGGGTTTTTAATTAATGGTTTTTAAGTTAAGGG
1 TTAGGGTTTTTAATTAA-----ATTAGGTT-AGGG
* * *
1958150 TTTAGGGCTTTGAATTAAATTA----A--A
1 -TTAGGGTTTTTAATTAAATTAGGTTAGGG
*
1958174 TTAGGGTTTTTAATTAAATTAGGTTAAGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGG
1958203 TTAGGGTTTTTAAGTTAA
1 TTAGGGTTTTTAA-TTAA
1958221 GGGTTTATGG
Statistics
Matches: 190, Mismatches: 18, Indels: 27
0.81 0.08 0.11
Matches are distributed among these distances:
23 19 0.10
26 1 0.01
27 1 0.01
29 137 0.72
30 4 0.02
31 3 0.02
34 6 0.03
35 4 0.02
36 15 0.08
ACGTcount: A:0.29, C:0.02, G:0.25, T:0.45
Consensus pattern (29 bp):
TTAGGGTTTTTAATTAAATTAGGTTAGGG
Found at i:1958138 original size:14 final size:15
Alignment explanation
Indices: 1958117--1958152 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
1958107 GGTTAGGGTT
1958117 AGGGTTTTTAA-TTA
1 AGGGTTTTTAAGTTA
*
1958131 ATGGTTTTTAAGTTA
1 AGGGTTTTTAAGTTA
1958146 AGGGTTT
1 AGGGTTT
1958153 AGGGCTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (15 bp):
AGGGTTTTTAAGTTA
Found at i:1958188 original size:23 final size:23
Alignment explanation
Indices: 1958151--1958194 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1958141 AGTTAAGGGT
1958151 TTAGGGCTTTGAATTAAATTAAA
1 TTAGGGCTTTGAATTAAATTAAA
* *
1958174 TTAGGGTTTTTAATTAAATTA
1 TTAGGGCTTTGAATTAAATTA
1958195 GGTTAAGGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.02, G:0.16, T:0.45
Consensus pattern (23 bp):
TTAGGGCTTTGAATTAAATTAAA
Found at i:1958235 original size:22 final size:22
Alignment explanation
Indices: 1958207--1958249 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1958197 TTAAGGTTAG
1958207 GGTTTTTAAGTTAAGGGTTTAT
1 GGTTTTTAAGTTAAGGGTTTAT
1958229 GGTTTTTAAGTTAAGGGTTTA
1 GGTTTTTAAGTTAAGGGTTTA
1958250 GGGCTTTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (22 bp):
GGTTTTTAAGTTAAGGGTTTAT
Found at i:1958254 original size:96 final size:96
Alignment explanation
Indices: 1958131--1958337 Score: 371
Period size: 96 Copynumber: 2.2 Consensus size: 96
1958121 TTTTTAATTA
1958131 ATGGTTTTTAAGTTAAGGGTTTAGGGCTTTGAATTAAATTAAATTAGGGTTTTTAATTAAATTAG
1 ATGGTTTTTAAGTTAAGGGTTTAGGGCTTTGAATTAAATTAAATTAGGGTTTTTAATTAAATTAG
1958196 GTTAAGGTTAGGGTTTTTAAGTTAAGGGTTT
66 GTTAAGGTTAGGGTTTTTAAGTTAAGGGTTT
* * *
1958227 ATGGTTTTTAAGTTAAGGGTTTAGGGCTTTGAATTAAATTAAATTATGTTTTTTAATTAAATTTG
1 ATGGTTTTTAAGTTAAGGGTTTAGGGCTTTGAATTAAATTAAATTAGGGTTTTTAATTAAATTAG
1958292 GTTAAGGTTAGGGTTTTTAAGTTAAGGGTTT
66 GTTAAGGTTAGGGTTTTTAAGTTAAGGGTTT
*
1958323 AGGGTTTTTAA-TTAA
1 ATGGTTTTTAAGTTAA
1958338 ATTAGGTTAG
Statistics
Matches: 107, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
95 4 0.04
96 103 0.96
ACGTcount: A:0.29, C:0.01, G:0.24, T:0.46
Consensus pattern (96 bp):
ATGGTTTTTAAGTTAAGGGTTTAGGGCTTTGAATTAAATTAAATTAGGGTTTTTAATTAAATTAG
GTTAAGGTTAGGGTTTTTAAGTTAAGGGTTT
Found at i:1958327 original size:22 final size:20
Alignment explanation
Indices: 1958292--1958414 Score: 77
Period size: 22 Copynumber: 5.3 Consensus size: 20
1958282 ATTAAATTTG
1958292 GTTAAGGTTAGGGTTTTTAA
1 GTTAAGGTTAGGGTTTTTAA
1958312 GTTAAGGGTTTAGGGTTTTTAA
1 GTTAA-GG-TTAGGGTTTTTAA
1958334 -TTAAATTAGGTTAGGGTTTTTAATTAAATTA
1 GTT--A--AGGTTAGGG--TTT--TT--A--A
1958365 GGTTAAGGTTAGGGTTTTTAA
1 -GTTAAGGTTAGGGTTTTTAA
*
1958386 GTTAAGGGTTTATGGTTTTTAA
1 GTTAA-GG-TTAGGGTTTTTAA
1958408 GTTAAGG
1 GTTAAGG
1958415 GTTTAGGGCT
Statistics
Matches: 84, Mismatches: 1, Indels: 35
0.70 0.01 0.29
Matches are distributed among these distances:
20 10 0.12
21 9 0.11
22 30 0.36
23 8 0.10
24 2 0.02
25 6 0.07
27 5 0.06
29 10 0.12
31 2 0.02
33 2 0.02
ACGTcount: A:0.27, C:0.00, G:0.28, T:0.46
Consensus pattern (20 bp):
GTTAAGGTTAGGGTTTTTAA
Found at i:1958347 original size:23 final size:23
Alignment explanation
Indices: 1958296--1958470 Score: 105
Period size: 23 Copynumber: 7.5 Consensus size: 23
1958286 AATTTGGTTA
1958296 AGGTTAGGGTTTTTAAGTT-AA--
1 AGGTTAGGGTTTTTAA-TTAAATT
*
1958317 GGGTTTAGGGTTTTTAATTAAATT
1 AGG-TTAGGGTTTTTAATTAAATT
1958341 AGGTTAGGGTTTTTAATTAAATT
1 AGGTTAGGGTTTTTAATTAAATT
* *
1958364 AGGTTAAGGTTAGGGTTT--TTAAGTT
1 AGGTTAGGGTT----TTTAATTAAATT
*
1958389 AAGGGTTTATGGTTTTTAAGTT-AA--
1 -A-GG-TTAGGGTTTTTAA-TTAAATT
* * *
1958413 GGGTTTAGGGCTTTGAATTAAATT
1 AGG-TTAGGGTTTTTAATTAAATT
**
1958437 AAATTAGGGTTTTTAATTAAATT
1 AGGTTAGGGTTTTTAATTAAATT
*
1958460 AGGTTAAGGTT
1 AGGTTAGGGTT
1958471 AGGGTTTTTN
Statistics
Matches: 119, Mismatches: 18, Indels: 32
0.70 0.11 0.19
Matches are distributed among these distances:
21 6 0.05
22 30 0.25
23 56 0.47
24 5 0.04
25 6 0.05
26 2 0.02
27 7 0.06
28 7 0.06
ACGTcount: A:0.29, C:0.01, G:0.26, T:0.45
Consensus pattern (23 bp):
AGGTTAGGGTTTTTAATTAAATT
Found at i:1958350 original size:170 final size:170
Alignment explanation
Indices: 1958133--1958479 Score: 631
Period size: 170 Copynumber: 2.0 Consensus size: 170
1958123 TTTAATTAAT
1958133 GGTTTTTAAGTTAAGGGTTTAGGGCTTTGAATTAAATTAAATTAGGGTTTTTAATTAAATTAGGT
1 GGTTTTTAAGTTAAGGGTTTAGGGCTTTGAATTAAATTAAATTAGGGTTTTTAATTAAATTAGGT
1958198 TAAGGTTAGGGTTTTTAAGTTAAGGGTTTATGGTTTTTAAGTTAAGGGTTTAGGGCTTTGAATTA
66 TAAGGTTAGGGTTTTTAAGTTAAGGGTTTATGGTTTTTAAGTTAAGGGTTTAGGGCTTTGAATTA
* * *
1958263 AATTAAATTATGTTTTTTAATTAAATTTGGTTAAGGTTAG
131 AATTAAATTAGGGTTTTTAATTAAATTAGGTTAAGGTTAG
* * **
1958303 GGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGT
1 GGTTTTTAAGTTAAGGGTTTAGGGCTTTGAATTAAATTAAATTAGGGTTTTTAATTAAATTAGGT
1958368 TAAGGTTAGGGTTTTTAAGTTAAGGGTTTATGGTTTTTAAGTTAAGGGTTTAGGGCTTTGAATTA
66 TAAGGTTAGGGTTTTTAAGTTAAGGGTTTATGGTTTTTAAGTTAAGGGTTTAGGGCTTTGAATTA
1958433 AATTAAATTAGGGTTTTTAATTAAATTAGGTTAAGGTTAG
131 AATTAAATTAGGGTTTTTAATTAAATTAGGTTAAGGTTAG
1958473 GGTTTTT
1 GGTTTTT
1958480 NNNNNNNNNN
Statistics
Matches: 170, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
170 170 1.00
ACGTcount: A:0.29, C:0.01, G:0.24, T:0.46
Consensus pattern (170 bp):
GGTTTTTAAGTTAAGGGTTTAGGGCTTTGAATTAAATTAAATTAGGGTTTTTAATTAAATTAGGT
TAAGGTTAGGGTTTTTAAGTTAAGGGTTTATGGTTTTTAAGTTAAGGGTTTAGGGCTTTGAATTA
AATTAAATTAGGGTTTTTAATTAAATTAGGTTAAGGTTAG
Found at i:1958403 original size:74 final size:74
Alignment explanation
Indices: 1958229--1958412 Score: 287
Period size: 74 Copynumber: 2.5 Consensus size: 74
1958219 AAGGGTTTAT
* * * * *
1958229 GGTTTTTAAGTTAAGGGTTTAGGGCTTTGAATTAAATTAAATTATGTTTTTTAATTAAATTTGGT
1 GGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAAATTAGGGTTTTTAATTAAATTAGGT
1958294 TAAGGTTAG
66 TAAGGTTAG
**
1958303 GGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGT
1 GGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAAATTAGGGTTTTTAATTAAATTAGGT
1958368 TAAGGTTAG
66 TAAGGTTAG
*
1958377 GGTTTTTAAGTTAAGGGTTTATGGTTTTTAAGTTAA
1 GGTTTTTAAGTTAAGGGTTTAGGGTTTTTAA-TTAA
1958413 GGGTTTAGGG
Statistics
Matches: 101, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
74 97 0.96
75 4 0.04
ACGTcount: A:0.28, C:0.01, G:0.24, T:0.47
Consensus pattern (74 bp):
GGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAAATTAGGGTTTTTAATTAAATTAGGT
TAAGGTTAG
Found at i:1958403 original size:96 final size:96
Alignment explanation
Indices: 1958303--1958479 Score: 318
Period size: 96 Copynumber: 1.8 Consensus size: 96
1958293 TTAAGGTTAG
* * **
1958303 GGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGT
1 GGTTTTTAAGTTAAGGGTTTAGGGCTTTGAATTAAATTAAATTAGGGTTTTTAATTAAATTAGGT
1958368 TAAGGTTAGGGTTTTTAAGTTAAGGGTTTAT
66 TAAGGTTAGGGTTTTTAAGTTAAGGGTTTAT
1958399 GGTTTTTAAGTTAAGGGTTTAGGGCTTTGAATTAAATTAAATTAGGGTTTTTAATTAAATTAGGT
1 GGTTTTTAAGTTAAGGGTTTAGGGCTTTGAATTAAATTAAATTAGGGTTTTTAATTAAATTAGGT
1958464 TAAGGTTAGGGTTTTT
66 TAAGGTTAGGGTTTTT
1958480 NNNNNNNNNN
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
96 77 1.00
ACGTcount: A:0.28, C:0.01, G:0.25, T:0.46
Consensus pattern (96 bp):
GGTTTTTAAGTTAAGGGTTTAGGGCTTTGAATTAAATTAAATTAGGGTTTTTAATTAAATTAGGT
TAAGGTTAGGGTTTTTAAGTTAAGGGTTTAT
Found at i:1958415 original size:22 final size:22
Alignment explanation
Indices: 1958377--1958419 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1958367 TTAAGGTTAG
1958377 GGTTTTTAAGTTAAGGGTTTAT
1 GGTTTTTAAGTTAAGGGTTTAT
1958399 GGTTTTTAAGTTAAGGGTTTA
1 GGTTTTTAAGTTAAGGGTTTA
1958420 GGGCTTTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (22 bp):
GGTTTTTAAGTTAAGGGTTTAT
Found at i:1958564 original size:7 final size:7
Alignment explanation
Indices: 1958539--1958597 Score: 75
Period size: 7 Copynumber: 8.3 Consensus size: 7
1958529 TTAAATTAGG
1958539 TTAGGG-
1 TTAGGGT
*
1958545 TTAGAGCT
1 TTAG-GGT
1958553 TTAGGGT
1 TTAGGGT
1958560 TTAGGGT
1 TTAGGGT
1958567 TTAGGGGT
1 TTA-GGGT
*
1958575 TTAAGGT
1 TTAGGGT
1958582 TTAGGGT
1 TTAGGGT
1958589 TTAGGGT
1 TTAGGGT
1958596 TT
1 TT
1958598 TTAATTAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
6 4 0.09
7 31 0.67
8 11 0.24
ACGTcount: A:0.17, C:0.02, G:0.39, T:0.42
Consensus pattern (7 bp):
TTAGGGT
Found at i:1958577 original size:22 final size:22
Alignment explanation
Indices: 1958539--1958594 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
1958529 TTAAATTAGG
* *
1958539 TTAGGG-TTAGAGCTTTAGGGT
1 TTAGGGTTTAGGGCTTTAAGGT
*
1958560 TTAGGGTTTAGGGGTTTAAGGT
1 TTAGGGTTTAGGGCTTTAAGGT
1958582 TTAGGGTTTAGGG
1 TTAGGGTTTAGGG
1958595 TTTTTAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
21 6 0.19
22 25 0.81
ACGTcount: A:0.18, C:0.02, G:0.41, T:0.39
Consensus pattern (22 bp):
TTAGGGTTTAGGGCTTTAAGGT
Found at i:1958621 original size:29 final size:29
Alignment explanation
Indices: 1958589--1958816 Score: 159
Period size: 29 Copynumber: 8.3 Consensus size: 29
1958579 GGTTTAGGGT
1958589 TTAGGGTTTTTAATTAAATTAGGTTAAGG
1 TTAGGGTTTTTAATTAAATTAGGTTAAGG
1958618 TTAGGGTTTTTAATTAAATTAGGTTAAGG
1 TTAGGGTTTTTAATTAAATTAGGTTAAGG
* *
1958647 TTAGGGTTTTTAAGTT-AA--GGGTTTAGG
1 TTAGGGTTTTTAA-TTAAATTAGGTTAAGG
* * * *
1958674 ATT--TGTAATTAAATT--A-G--GTTAAGG
1 -TTAGGGT-TTTTAATTAAATTAGGTTAAGG
1958698 TTAGGGTTTTTAAGTT-AA-T-GG-T---G
1 TTAGGGTTTTTAA-TTAAATTAGGTTAAGG
*
1958721 -TAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAAGG
* * * *
1958749 TTAAGGTTTGTAATTAATTTAGGTTAGGGG
1 TTAGGGTTTTTAATTAAATTAGGTTA-AGG
* *
1958779 TTAGGGTTTTTAATTAATTTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAAGG
1958808 TTTAGGGTT
1 -TTAGGGTT
1958817 AAATTAAGTT
Statistics
Matches: 165, Mismatches: 15, Indels: 37
0.76 0.07 0.17
Matches are distributed among these distances:
21 2 0.01
22 14 0.08
23 4 0.02
24 12 0.07
25 6 0.04
26 6 0.04
27 12 0.07
28 3 0.02
29 69 0.42
30 37 0.22
ACGTcount: A:0.27, C:0.00, G:0.28, T:0.45
Consensus pattern (29 bp):
TTAGGGTTTTTAATTAAATTAGGTTAAGG
Found at i:1958673 original size:51 final size:52
Alignment explanation
Indices: 1958611--1958833 Score: 222
Period size: 51 Copynumber: 4.2 Consensus size: 52
1958601 ATTAAATTAG
1958611 GTTAA-GG-TTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTT-TTTAA
1 GTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTATTTAA
* *
1958660 GTTAAGGGTTTAGGATTTGTAATTAAATTAGGTTAAGGTTAGGGTT-TTTAA
1 GTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTATTTAA
* * * * *
1958711 GTTAATGGTGTAGGGTTTTTAATTAAATTAGGTTAGGGTTAAGGTTTGTAATTAA
1 GTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAAGGTT-AGG-GT-TATTTAA
* * * * *
1958766 TTTAGGTTAGGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTTAGGGTTAAATTAA
1 GTTA----AGGGTTTAGGGTTTTTAATTAAATTAGGTTAAGG-TTAGGGTT-ATTTAA
1958824 GTT-AGGGTTT
1 GTTAAGGGTTT
1958834 TTATTACATC
Statistics
Matches: 145, Mismatches: 17, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
49 5 0.03
50 2 0.01
51 75 0.52
52 3 0.02
53 7 0.05
54 1 0.01
55 7 0.05
57 1 0.01
58 9 0.06
59 33 0.23
60 2 0.01
ACGTcount: A:0.27, C:0.00, G:0.28, T:0.44
Consensus pattern (52 bp):
GTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTATTTAA
Found at i:1958683 original size:80 final size:80
Alignment explanation
Indices: 1958560--1958833 Score: 292
Period size: 80 Copynumber: 3.4 Consensus size: 80
1958550 GCTTTAGGGT
* *
1958560 TTAGGGTTTAGGGGT--TTAAGGTTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGG
1 TTAGGGTTTAGGGTTAATTAA-G-TTAGGGTTTA-GGTTTGTAATTAAATTAGGTTAAGGTTAGG
1958623 GTTTTTAATTAAATTAGG
63 GTTTTTAATTAAATTAGG
* *
1958641 TTAAGG-TTAGGGTT-TTTAAGTTAAGGGTTTAGGATTTGTAATTAAATTAGGTTAAGGTTAGGG
1 TTAGGGTTTAGGGTTAATTAAGTT-AGGGTTTAGG-TTTGTAATTAAATTAGGTTAAGGTTAGGG
1958704 TTTTTAAGTT-AA-T-GG
64 TTTTTAA-TTAAATTAGG
**** * * * *
1958719 TGTAGGGTTTTTAATTAAATTAGGTTAGGGTTAAGGTTTGTAATTAATTTAGGTTAGGGGTTAGG
1 T-TAGGGTTTAGGGTT-AATTAAGTTAGGGTTTAGGTTTGTAATTAAATTAGGTTA-AGGTTAGG
*
1958784 GTTTTTAATTAATTTAGG
63 GTTTTTAATTAAATTAGG
1958802 TTAGGGTTTAGGGTTAAATTAAGTTAGGGTTT
1 TTAGGGTTTAGGGTT-AATTAAGTTAGGGTTT
1958834 TTATTACATC
Statistics
Matches: 161, Mismatches: 20, Indels: 23
0.79 0.10 0.11
Matches are distributed among these distances:
78 3 0.02
79 9 0.06
80 78 0.48
81 36 0.22
82 32 0.20
83 3 0.02
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.45
Consensus pattern (80 bp):
TTAGGGTTTAGGGTTAATTAAGTTAGGGTTTAGGTTTGTAATTAAATTAGGTTAAGGTTAGGGTT
TTTAATTAAATTAGG
Found at i:1958736 original size:21 final size:20
Alignment explanation
Indices: 1958691--1958736 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 20
1958681 ATTAAATTAG
1958691 GTTAAGGTTAGGGTTTTTAA
1 GTTAAGGTTAGGGTTTTTAA
1958711 GTTAATGGTGTAGGGTTTTTAA
1 GTTAA-GGT-TAGGGTTTTTAA
1958733 -TTAA
1 GTTAA
1958737 ATTAGGTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 5 0.21
21 7 0.29
22 12 0.50
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.46
Consensus pattern (20 bp):
GTTAAGGTTAGGGTTTTTAA
Found at i:1958747 original size:23 final size:23
Alignment explanation
Indices: 1958695--1958836 Score: 74
Period size: 23 Copynumber: 5.7 Consensus size: 23
1958685 AATTAGGTTA
1958695 AGGTTAGGGTTTTTAAGTT-AA-T
1 AGGTTAGGGTTTTTAA-TTAAATT
1958717 -GGTGTAGGGTTTTTAATTAAATT
1 AGGT-TAGGGTTTTTAATTAAATT
1958740 AGGTTAGGGTTAAGGTTTGTAATTAATTTAGGTT
1 AGGTTAGGG-T----TTT-TAATTAA---A--TT
*
1958774 AGGGGTTAGGGTTTTTAATTAATTT
1 A--GGTTAGGGTTTTTAATTAAATT
****
1958799 AGGTTAGGGTTTAGGGTTAAATT
1 AGGTTAGGGTTTTTAATTAAATT
*
1958822 AAGTTAGGGTTTTTA
1 AGGTTAGGGTTTTTA
1958837 TTACATCAAA
Statistics
Matches: 93, Mismatches: 10, Indels: 33
0.68 0.07 0.24
Matches are distributed among these distances:
21 5 0.05
22 14 0.15
23 34 0.37
24 4 0.04
25 3 0.03
28 3 0.03
29 7 0.08
30 7 0.08
31 3 0.03
32 1 0.01
34 3 0.03
35 1 0.01
36 8 0.09
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.45
Consensus pattern (23 bp):
AGGTTAGGGTTTTTAATTAAATT
Found at i:1958781 original size:30 final size:30
Alignment explanation
Indices: 1958721--1958816 Score: 149
Period size: 30 Copynumber: 3.2 Consensus size: 30
1958711 GTTAATGGTG
*
1958721 TAGGGTTTTTAATTAAATTAGGTTA-GGGT
1 TAGGGTTTTTAATTAATTTAGGTTAGGGGT
* *
1958750 TAAGGTTTGTAATTAATTTAGGTTAGGGGT
1 TAGGGTTTTTAATTAATTTAGGTTAGGGGT
*
1958780 TAGGGTTTTTAATTAATTTAGGTTAGGGTT
1 TAGGGTTTTTAATTAATTTAGGTTAGGGGT
1958810 TAGGGTT
1 TAGGGTT
1958817 AAATTAAGTT
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
29 22 0.37
30 38 0.63
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.46
Consensus pattern (30 bp):
TAGGGTTTTTAATTAATTTAGGTTAGGGGT
Found at i:1958832 original size:29 final size:28
Alignment explanation
Indices: 1958728--1958829 Score: 123
Period size: 30 Copynumber: 3.5 Consensus size: 28
1958718 GTGTAGGGTT
* * *
1958728 TTTAATTAAATTAGGTTAGGGTTAAGGT
1 TTTAATTAATTTAGGTTAGGGTTTAGGG
*
1958756 TTGTAATTAATTTAGGTTAGGGGTTAGGG
1 TT-TAATTAATTTAGGTTAGGGTTTAGGG
1958785 TTTTTAATTAATTTAGGTTAGGGTTTAGGG
1 --TTTAATTAATTTAGGTTAGGGTTTAGGG
* *
1958815 TTAAATTAAGTTAGG
1 TTTAATTAATTTAGG
1958830 GTTTTTATTA
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
28 15 0.23
29 22 0.34
30 25 0.39
31 2 0.03
ACGTcount: A:0.28, C:0.00, G:0.27, T:0.44
Consensus pattern (28 bp):
TTTAATTAATTTAGGTTAGGGTTTAGGG
Found at i:1958954 original size:63 final size:64
Alignment explanation
Indices: 1958846--1958979 Score: 234
Period size: 63 Copynumber: 2.1 Consensus size: 64
1958836 ATTACATCAA
*
1958846 ATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAATTTCTATTCTTTTAC
1 ATAAAATTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAATTTCTATTCTTTTAC
* *
1958910 ATAAAATT-TATTTTATTACATTAAATAATATCAAAATAACTCAAAAAATTTCTATTTTTTTAC
1 ATAAAATTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAATTTCTATTCTTTTAC
1958973 ATAAAAT
1 ATAAAAT
1958980 AATATCAAAA
Statistics
Matches: 67, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
63 60 0.90
64 7 0.10
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (64 bp):
ATAAAATTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAATTTCTATTCTTTTAC
Found at i:1959437 original size:18 final size:18
Alignment explanation
Indices: 1959414--1959448 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1959404 TGGAAAACAA
*
1959414 TACATATAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
1959432 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
1959449 AAACGCACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:1960094 original size:7 final size:7
Alignment explanation
Indices: 1960084--1960108 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1960074 TTATATACAT
1960084 AATACTA
1 AATACTA
1960091 AATACTA
1 AATACTA
1960098 AATACTA
1 AATACTA
1960105 AATA
1 AATA
1960109 TTAATCGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:1961148 original size:29 final size:29
Alignment explanation
Indices: 1961116--1961199 Score: 67
Period size: 29 Copynumber: 3.1 Consensus size: 29
1961106 AATTGAAATT
1961116 AAATATGGATTTGAGAGAATTTTTGAAGG
1 AAATATGGATTTGAGAGAATTTTTGAAGG
* **
1961145 AAAT-T-GA---GAG-GAA--ATTGAAATT
1 AAATATGGATTTGAGAGAATTTTTG-AAGG
*
1961167 AAATATGGATTTGAGAGAATTTTGGAAGG
1 AAATATGGATTTGAGAGAATTTTTGAAGG
1961196 AAAT
1 AAAT
1961200 TAAGAGAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 18
0.61 0.11 0.28
Matches are distributed among these distances:
21 3 0.08
22 6 0.15
23 4 0.10
24 5 0.13
27 5 0.13
28 4 0.10
29 10 0.26
30 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.26, T:0.31
Consensus pattern (29 bp):
AAATATGGATTTGAGAGAATTTTTGAAGG
Found at i:1961169 original size:51 final size:51
Alignment explanation
Indices: 1961093--1961205 Score: 208
Period size: 51 Copynumber: 2.2 Consensus size: 51
1961083 NNNNNNNNNN
*
1961093 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTTGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
1961144 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
*
1961195 GAAATTAAGAG
1 GAAATTGAGAG
1961206 AATTTTGGAA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.44, C:0.00, G:0.27, T:0.29
Consensus pattern (51 bp):
GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
Found at i:1961205 original size:22 final size:22
Alignment explanation
Indices: 1961180--1961232 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
1961170 TATGGATTTG
1961180 AGAGAATTTTGGAAGGAAATTA
1 AGAGAATTTTGGAAGGAAATTA
*
1961202 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTGGAAGGAAATTA
1961224 AGAGGAATT
1 AGA-GAATT
1961233 GAGAGGAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 24 0.83
23 5 0.17
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.26
Consensus pattern (22 bp):
AGAGAATTTTGGAAGGAAATTA
Found at i:1966077 original size:21 final size:21
Alignment explanation
Indices: 1966051--1966096 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1966041 TCACGAAAAG
*
1966051 TTTTTAAATGATTTTAAAAT-A
1 TTTTTAAA-GATTTCAAAATGA
*
1966072 TTTTTAAAGCTTTCAAAATGA
1 TTTTTAAAGATTTCAAAATGA
1966093 TTTT
1 TTTT
1966097 ATCTTATTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (21 bp):
TTTTTAAAGATTTCAAAATGA
Found at i:1974511 original size:14 final size:14
Alignment explanation
Indices: 1974492--1974521 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1974482 TATTATATAT
1974492 ATCCGGTCATGCAA
1 ATCCGGTCATGCAA
1974506 ATCCGGTCATGCAA
1 ATCCGGTCATGCAA
1974520 AT
1 AT
1974522 TAACTTCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (14 bp):
ATCCGGTCATGCAA
Found at i:1976333 original size:43 final size:42
Alignment explanation
Indices: 1976184--1976348 Score: 140
Period size: 43 Copynumber: 3.9 Consensus size: 42
1976174 ATATCGAACA
* * * *
1976184 ATGCCAACGTCCCAGACATGGTCTTACATGCTATCTC-ATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACG-AAACACAATA-CG
* * * *
1976227 ATGCC-ACTTTCCCTGACAGGGTCTTACACGAATCA-AATACG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGAAACACAATACG
* *
1976268 ATGCCAATGTCCTAGACATGGTCTTACACGTAAACACAAGT-CG
1 ATGCCAACGTCCCAGACATGGTCTTACACG-AAACACAA-TACG
* *
1976311 ATGCCGACGTCCCAGACGTGGTCTTACACGAAAACACA
1 ATGCCAACGTCCCAGACATGGTCTTACACG-AAACACA
1976349 TATCAGAGTA
Statistics
Matches: 99, Mismatches: 17, Indels: 12
0.77 0.13 0.09
Matches are distributed among these distances:
41 25 0.25
42 13 0.13
43 60 0.61
44 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGAAACACAATACG
Found at i:1979336 original size:29 final size:29
Alignment explanation
Indices: 1979294--1979351 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
1979284 TAGGTACATG
1979294 CCATTTATTGAAACAACAGAAATTCATAC
1 CCATTTATTGAAACAACAGAAATTCATAC
1979323 CCATTTATTGAAACAACAGAAATTCATAC
1 CCATTTATTGAAACAACAGAAATTCATAC
1979352 TTTACCCCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.45, C:0.21, G:0.07, T:0.28
Consensus pattern (29 bp):
CCATTTATTGAAACAACAGAAATTCATAC
Found at i:1979734 original size:11 final size:12
Alignment explanation
Indices: 1979701--1979738 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 12
1979691 TATGTGTTAA
1979701 AAATATATTATT
1 AAATATATTATT
1979713 AAATTAGTATTATT
1 AAA-TA-TATTATT
1979727 AAAT-TATTATT
1 AAATATATTATT
1979738 A
1 A
1979739 TTATTATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 8 0.33
12 3 0.12
13 3 0.12
14 10 0.42
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (12 bp):
AAATATATTATT
Found at i:1979748 original size:14 final size:14
Alignment explanation
Indices: 1979706--1979741 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1979696 GTTAAAAATA
1979706 TATTATTAAATTAG
1 TATTATTAAATTAG
*
1979720 TATTATTAAATTAT
1 TATTATTAAATTAG
1979734 TATTATTA
1 TATTATTA
1979742 TTATATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (14 bp):
TATTATTAAATTAG
Found at i:1979876 original size:3 final size:3
Alignment explanation
Indices: 1979870--1979901 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1979860 TATAATAATA
1979870 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1979902 ACTAATGCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1982152 original size:25 final size:25
Alignment explanation
Indices: 1982116--1982177 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
1982106 ACAAATGTGC
*
1982116 TAATCA-ATGAGCACTGACATACTAA
1 TAATCAGA-GAGCACTAACATACTAA
* *
1982141 TAATCAGAGAGCACTAACGTTCTAA
1 TAATCAGAGAGCACTAACATACTAA
*
1982166 TAACCAGAGAGC
1 TAATCAGAGAGC
1982178 GCGCTAGGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 31 0.97
26 1 0.03
ACGTcount: A:0.42, C:0.21, G:0.16, T:0.21
Consensus pattern (25 bp):
TAATCAGAGAGCACTAACATACTAA
Found at i:1985099 original size:6 final size:5
Alignment explanation
Indices: 1985074--1985109 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
1985064 AAACAAACAA
1985074 AAAAT AAAAT AAAAT AAAAT AGAAAT -AAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT A-AAAT AAAAT AAAAT A
1985110 GCAATGTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.14
5 21 0.72
6 4 0.14
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:1986344 original size:28 final size:28
Alignment explanation
Indices: 1986308--1986364 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
1986298 TTTAATCGTT
*
1986308 TCTCCAAATAAATTTATATTAATATTTA
1 TCTCCAAATAAATTCATATTAATATTTA
*
1986336 TCTCTAAATAAATTCATATTAATATTTA
1 TCTCCAAATAAATTCATATTAATATTTA
1986364 T
1 T
1986365 ACTTTTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (28 bp):
TCTCCAAATAAATTCATATTAATATTTA
Found at i:1986668 original size:67 final size:66
Alignment explanation
Indices: 1986608--1986735 Score: 168
Period size: 67 Copynumber: 1.9 Consensus size: 66
1986598 TGATTTTTGT
* *
1986608 AGATATGCCTCACCTCAAT-AGAGAGTTGTTGAATGGTTCATGGAAGAGCCCAAATGTTGATGGT
1 AGATATGCCTCACCT--ATCAGAGAGCTGTTGAATGGTTCATGAAAGAGCCCAAATGTTGATGGT
1986672 TGG
64 TGG
** * *
1986675 AGATATGCCTTGCCTATGCAGAGAGCTGTTGAATGGTTCATGAAAGGGCCTAAATGTTGAT
1 AGATATGCCTCACCTAT-CAGAGAGCTGTTGAATGGTTCATGAAAGAGCCCAAATGTTGAT
1986736 CAAAAGCCAA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
65 2 0.04
67 51 0.96
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (66 bp):
AGATATGCCTCACCTATCAGAGAGCTGTTGAATGGTTCATGAAAGAGCCCAAATGTTGATGGTTG
G
Found at i:1994031 original size:29 final size:30
Alignment explanation
Indices: 1993999--1994061 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
1993989 GAGAGAGAAG
*
1993999 TAAAAGAGAATGAAAAAT-AAAGAAAAAAA
1 TAAAAGAGAAAGAAAAATAAAAGAAAAAAA
** * *
1994028 TAAAAGTTAAAGAAACATAAAAGAAAAAAT
1 TAAAAGAGAAAGAAAAATAAAAGAAAAAAA
1994058 TAAA
1 TAAA
1994062 TTGCTCAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 14 0.50
30 14 0.50
ACGTcount: A:0.73, C:0.02, G:0.11, T:0.14
Consensus pattern (30 bp):
TAAAAGAGAAAGAAAAATAAAAGAAAAAAA
Found at i:1997406 original size:147 final size:147
Alignment explanation
Indices: 1997151--1997577 Score: 767
Period size: 147 Copynumber: 2.9 Consensus size: 147
1997141 AGAGAATAAA
*
1997151 AATAAAAATAAAAATGGTGAGCTTTTGTTGAAAAGGCAAGGGATTCAACCAAAAGTGAAGAAAGC
1 AATAAAAATAAAAATGGTGAGCTTTTGTTGAAAAGGCAAGGGATTCAACCAAAAGTGAAGAAAAC
*
1997216 TGTAAGCTTTACTGAAAATGGGAATGTTTATAGGATTATTAGCAATGGAGATGAGGTTAGTTCAA
66 TGTAAGCTTTGCTGAAAATGGGAATGTTTATAGGATTATTAGCAATGGAGATGAGGTTAGTTCAA
1997281 GTGGAGATGAAGCAGAG
131 GTGGAGATGAAGCAGAG
1997298 AATAAAAATAAAAATGGTGAGCTTTTGTTGAAAAGGCAAGGGATTCAACCAAAAGTGAAGAAAAC
1 AATAAAAATAAAAATGGTGAGCTTTTGTTGAAAAGGCAAGGGATTCAACCAAAAGTGAAGAAAAC
*
1997363 TGTAAGCTTTGCTGAAAATGGGAATGTTTATAGGATTATTAGCAATGGAGATGAGGTTACTTCAA
66 TGTAAGCTTTGCTGAAAATGGGAATGTTTATAGGATTATTAGCAATGGAGATGAGGTTAGTTCAA
1997428 GTGGAGATGAAGCAGAG
131 GTGGAGATGAAGCAGAG
*
1997445 ------AACAAAAATGGTGAGCTTTTGTTGAAAAGGCAAGGGATTCAACCAAAAGTGAAGAAAAC
1 AATAAAAATAAAAATGGTGAGCTTTTGTTGAAAAGGCAAGGGATTCAACCAAAAGTGAAGAAAAC
*
1997504 TGTAAGCTTTGCTGAAAATGGGAATGTTTACAGGATTATTAGCAATGGAGATGAGGTTAGTTCAA
66 TGTAAGCTTTGCTGAAAATGGGAATGTTTATAGGATTATTAGCAATGGAGATGAGGTTAGTTCAA
1997569 GTGGAGATG
131 GTGGAGATG
1997578 GTAGTTTAAC
Statistics
Matches: 274, Mismatches: 6, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
141 130 0.47
147 144 0.53
ACGTcount: A:0.39, C:0.08, G:0.27, T:0.25
Consensus pattern (147 bp):
AATAAAAATAAAAATGGTGAGCTTTTGTTGAAAAGGCAAGGGATTCAACCAAAAGTGAAGAAAAC
TGTAAGCTTTGCTGAAAATGGGAATGTTTATAGGATTATTAGCAATGGAGATGAGGTTAGTTCAA
GTGGAGATGAAGCAGAG
Found at i:2005919 original size:50 final size:51
Alignment explanation
Indices: 2005842--2005943 Score: 188
Period size: 50 Copynumber: 2.0 Consensus size: 51
2005832 AACAGTGGTT
2005842 TCGGGACCATAAATCCGACGAAAAAAAAATGTAATGGCCTGAATTTTCAGAG
1 TCGGGACCAT-AATCCGACGAAAAAAAAATGTAATGGCCTGAATTTTCAGAG
2005894 TCGGGACCAT-ATCCGACGAAAAAAAAATGTAATGGCCTGAATTTTCAGAG
1 TCGGGACCATAATCCGACGAAAAAAAAATGTAATGGCCTGAATTTTCAGAG
2005944 GTGTCGGAAC
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
50 40 0.80
52 10 0.20
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.22
Consensus pattern (51 bp):
TCGGGACCATAATCCGACGAAAAAAAAATGTAATGGCCTGAATTTTCAGAG
Found at i:2007805 original size:36 final size:36
Alignment explanation
Indices: 2007759--2007877 Score: 220
Period size: 36 Copynumber: 3.3 Consensus size: 36
2007749 GGTAGCTTTA
2007759 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
*
2007795 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
*
2007831 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
2007867 GCTACACTTAT
1 GCTACACTTAT
2007878 TTGGTCAGGG
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 81 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.30
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:2007815 original size:21 final size:20
Alignment explanation
Indices: 2007787--2007852 Score: 52
Period size: 21 Copynumber: 3.5 Consensus size: 20
2007777 AGTGAAAAAG
2007787 TGATAAGTGCTATACTTATC
1 TGATAAGTGCTATACTTATC
* **
2007807 TGATCAAGTG--A-A--AAAG
1 TGAT-AAGTGCTATACTTATC
2007823 TGATAAGTGCTATACTTATC
1 TGATAAGTGCTATACTTATC
2007843 TGATCAAGTG
1 TGAT-AAGTG
2007853 AAAAAGTGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 13
0.63 0.12 0.25
Matches are distributed among these distances:
15 5 0.15
16 5 0.15
17 1 0.03
18 2 0.06
19 1 0.03
20 9 0.27
21 10 0.30
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (20 bp):
TGATAAGTGCTATACTTATC
Found at i:2009914 original size:20 final size:21
Alignment explanation
Indices: 2009889--2009928 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
2009879 CCTAGGGTTT
2009889 TCTTTTTTCTTTTT-CTGTTA
1 TCTTTTTTCTTTTTGCTGTTA
*
2009909 TCTTTTTTTTTTTTGCTGTT
1 TCTTTTTTCTTTTTGCTGTT
2009929 GGTTTTGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.03, C:0.12, G:0.07, T:0.78
Consensus pattern (21 bp):
TCTTTTTTCTTTTTGCTGTTA
Found at i:2010009 original size:21 final size:21
Alignment explanation
Indices: 2009963--2010009 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
2009953 GTTTGGTTAT
2009963 ATTTTGGGCTGTTGGGTTTAG
1 ATTTTGGGCTGTTGGGTTTAG
* *
2009984 TTTTTGGGCTGTTGGGTTTGG
1 ATTTTGGGCTGTTGGGTTTAG
2010005 ATTTT
1 ATTTT
2010010 TATTTTGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.06, C:0.04, G:0.36, T:0.53
Consensus pattern (21 bp):
ATTTTGGGCTGTTGGGTTTAG
Found at i:2012644 original size:103 final size:105
Alignment explanation
Indices: 2012514--2013201 Score: 624
Period size: 114 Copynumber: 6.4 Consensus size: 105
2012504 CCAGGTATTG
* *
2012514 GTCTGTCAATGGTC-GGCACCAGAATACGAAAAAAGT-AAAAAAAA-TTGGTAGTGGCCTGCCAA
1 GTCTGTCAATGG-CAGGCACCAGTATACGAAAAAAGTAAAAAAAAATTTGGTGGTGGCCTGCCAA
2012576 TGGCCGGCACCAC-CTTAAAAACAATTTTTTTTTTACTTTT
65 TGGCCGGCACCACTCTTAAAAACAATTTTTTTTTTACTTTT
*
2012616 TTCGTGTCAATGGCAGGCACCAGTATACGAAAAAAGTAAAAAAAAATTT-GTGGTGGCCTGCCAA
1 GTC-TGTCAATGGCAGGCACCAGTATACGAAAAAAGTAAAAAAAAATTTGGTGGTGGCCTGCCAA
* * *
2012680 TGGCCAGCAACAC-CTTAAAAAGTAATTTTTTTATTT--TTTT
65 TGGCCGGCACCACTCTTAAAAA-CAATTTTTTT-TTTACTTTT
* *
2012720 G--TGTCAATAGCAGACACCAGTATACGAAAAAAGTAAAAAAAAAATTTGGTGGTGGCCTGCCAA
1 GTCTGTCAATGGCAGGCACCAGTATACGAAAAAAGT-AAAAAAAAATTTGGTGGTGGCCTGCCAA
* * **
2012783 TGGCCGGCACCATCTTTATTGAAAAAAAATATTTTTATTTTTTTTTT
65 TGGCCGGCACCA-C--TCTT-AAAAACAAT-TTTTT-TTTTACTTTT
* * * * *
2012830 TTGTGTCAATAGTAGGCACCAGTATACGAAAAAAGTAAAAAAAATAATTTTTGGTGGTGGCTTGC
1 GTCTGTCAATGGCAGGCACCAGTATACGAAAAAAGT-AAAAAAA-AA--TTTGGTGGTGGCCTGC
* *****
2012895 CAATGGCCGGCACCACTTTTTTTCCCCAATTTTTTTTTTACTTTT
62 CAATGGCCGGCACCAC-TCTTAAAAACAATTTTTTTTTTACTTTT
* * *
2012940 GGTCTATCAATGGCCGGCACCAGTATACGAAAAAAGTAAAAATAAAATAAAATTTTGGTGGTAGC
1 -GTCTGTCAATGGCAGGCACCAGTATACGAAAAAAGT----A-AAAA-AAAA-TTTGGTGGTGGC
* *****
2013005 CTACCAATGGCCGGCACCACCTCTTTTCCCCTAA-TTTTTTTTTACTTTT
58 CTGCCAATGGCCGGCACCA-CTCTTAAAAAC-AATTTTTTTTTTACTTTT
* * * * *
2013054 GGTCTATCAATGACCGGCACCAGTATACGAAAAAAGTAAAAAAAAAATTGGTGGTGGCTTGCCAA
1 -GTCTGTCAATGGCAGGCACCAGTATACGAAAAAAGTAAAAAAAAATTTGGTGGTGGCCTGCCAA
* * ***** *
2013119 TGGCCGGCATCACTTTTTTTCCCAATTTTTTTTTTACTTTCG
65 TGGCCGGCACCACTCTTAAAAACAATTTTTTTTTTACTTT-T
* *
2013161 GTCTGTCAATGGCGGGCACCAGTATACGAAAAAAGTTAAAA
1 GTCTGTCAATGGCAGGCACCAGTATACGAAAAAAGTAAAAA
2013202 TTTTCTTTTT
Statistics
Matches: 505, Mismatches: 49, Indels: 60
0.82 0.08 0.10
Matches are distributed among these distances:
101 31 0.06
102 15 0.03
103 55 0.11
104 46 0.09
105 13 0.03
106 63 0.12
107 31 0.06
108 17 0.03
109 5 0.01
110 13 0.03
111 35 0.07
112 42 0.08
113 6 0.01
114 92 0.18
115 39 0.08
116 2 0.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Consensus pattern (105 bp):
GTCTGTCAATGGCAGGCACCAGTATACGAAAAAAGTAAAAAAAAATTTGGTGGTGGCCTGCCAAT
GGCCGGCACCACTCTTAAAAACAATTTTTTTTTTACTTTT
Found at i:2012850 original size:112 final size:114
Alignment explanation
Indices: 2012530--2013024 Score: 417
Period size: 112 Copynumber: 4.6 Consensus size: 114
2012520 CAATGGTCGG
* *
2012530 CACCAGAATACGAAAAAAGT--AAAAAA-AA--TTGGTAGTGGCCTGCCAATGGCCGGCACCAC-
1 CACCAGTATACGAAAAAAGTAAAAAAAATAATTTTGGTGGTGGCCTGCCAATGGCCGGCACCACT
* * * * *
2012589 --CTT--AAAAACA-ATTTTT-TTTTTACTTTTTTCGTGTCAATGGCAGG
66 TTATTGAAAAAAAATATTTTTATTTTTA-TTTTTTTGTGTCAATAGCAGA
* *
2012633 CACCAGTATACGAAAAAAGT-AAAAAAA-AA-TTT-GTGGTGGCCTGCCAATGGCCAGCAACAC-
1 CACCAGTATACGAAAAAAGTAAAAAAAATAATTTTGGTGGTGGCCTGCCAATGGCCGGCACCACT
* * *
2012693 --CTT---AAAAAGTA--ATT-TTTTTATTTTTTTGTGTCAATAGCAGA
66 TTATTGAAAAAAAATATTTTTATTTTTATTTTTTTGTGTCAATAGCAGA
2012734 CACCAGTATACGAAAAAAGTAAAAAAAA-AA-TTTGGTGGTGGCCTGCCAATGGCCGGCACCATC
1 CACCAGTATACGAAAAAAGTAAAAAAAATAATTTTGGTGGTGGCCTGCCAATGGCCGGCACCA-C
* *
2012797 TTTATTGAAAAAAAATATTTTTATTTTT-TTTTTTTGTGTCAATAGTAGG
65 TTTATTGAAAAAAAATATTTTTATTTTTATTTTTTTGTGTCAATAGCAGA
*
2012846 CACCAGTATACGAAAAAAGTAAAAAAAATAATTTTTGGTGGTGGCTTGCCAATGGCCGGCACCAC
1 CACCAGTATACGAAAAAAGTAAAAAAAATAA-TTTTGGTGGTGGCCTGCCAATGGCCGGCACCAC
****** ** * * * * *
2012911 TTT-TT--TTCCCCA-ATTTTT-TTTTTACTTTTGGTCTATCAATGGCCGG
65 TTTATTGAAAAAAAATATTTTTATTTTTA-TTTTTTTGTGTCAATAGCAGA
* *
2012957 CACCAGTATACGAAAAAAGTAAAAATAAAATAAAATTTTGGTGGTAGCCTACCAATGGCCGGCAC
1 CACCAGTATACGAAAAAAGT-AAAA-AAAAT--AATTTTGGTGGTGGCCTGCCAATGGCCGGCAC
2013022 CAC
62 CAC
2013025 CTCTTTTCCC
Statistics
Matches: 334, Mismatches: 34, Indels: 37
0.82 0.08 0.09
Matches are distributed among these distances:
101 38 0.11
102 20 0.06
103 48 0.14
104 38 0.11
105 2 0.01
107 2 0.01
109 5 0.01
110 13 0.04
111 35 0.10
112 53 0.16
113 14 0.04
114 34 0.10
115 32 0.10
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30
Consensus pattern (114 bp):
CACCAGTATACGAAAAAAGTAAAAAAAATAATTTTGGTGGTGGCCTGCCAATGGCCGGCACCACT
TTATTGAAAAAAAATATTTTTATTTTTATTTTTTTGTGTCAATAGCAGA
Found at i:2014950 original size:212 final size:211
Alignment explanation
Indices: 2014545--2015129 Score: 683
Period size: 209 Copynumber: 2.7 Consensus size: 211
2014535 TTGATAAATT
* ***
2014545 TGGTGCCGGCCATTGGCCGGCCACCACCAAAATTTTTTAAAACTTTTTTCGTATACTGGTGCCGG
1 TGGTGCCGGCCATTGGCAGGCCACCACCAAAATTTTTTTTTACTTTTTTCGTATACTGGTGCCGG
* ** * ** *
2014610 CCTTTGACAGACCAAAAGTAAAAAAAAATAAAAATTTCCCCATAAAGGTGGCACCGACCATAGGC
66 CCATTGACAGACCAAAAGT--AAAAAAA-AAAAA-TT--GGAAAAAGGTGGTGCCGACCATTGGC
* * *
2014675 AAGCCACCACCAAATTTTTTTTTAACTTTTTTCGTATACTGGTGCCGGCTATTGACAGACCAAAA
125 AAGCCACCACCAAATTTTTTTTTAACTTTTTTCGTATACTGATGCCGGCAATTAACAGACCAAAA
*
2014740 GTAAAAAAAAATTGGAAAAAGG
190 ATAAAAAAAAATTGGAAAAAGG
* *
2014762 TGGTACCGGCCATTGGCAGGCCACCACCAAAATTATTTTTTTACTTTTTTCGTATACTGGTGTCG
1 TGGTGCCGGCCATTGGCAGGCCACCACCAAAATT-TTTTTTTACTTTTTTCGTATACTGGTGCCG
* * *
2014827 ACCATTGAGAGACGAAAAGTAAAAAAAAAAAATTGGAAAAAAGGTGGTGCCGACCATTGGCAAGC
65 GCCATTGACAGACCAAAAGTAAAAAAAAAAAATTGG-AAAAAGGTGGTGCCGACCATTGGCAAGC
* *
2014892 CACCACAAAATTTTTTTTT-ACTTTTTTCGTATACTGATGCCGGCAATTAACAGACCAAAAATAT
129 CACCACCAAATTTTTTTTTAACTTTTTTCGTATACTGATGCCGGCAATTAACAGACCAAAAATAA
******* *
2014956 TTTTTTTTTGGAAATAGG
194 AAAAAAATTGGAAAAAGG
* * * * *
2014974 TGATGCCTGCCATTGGCAGACCACTACC--AATTTTTTTTTACTTTTTTCTTATACTGGTGCCGG
1 TGGTGCCGGCCATTGGCAGGCCACCACCAAAATTTTTTTTTACTTTTTTCGTATACTGGTGCCGG
* * * * *
2015037 CTATTGACAGACCAAAAGTAAAAACAAAAAAATTGGAAATAGGTGGTG-CTAGCAATTGGCAGGC
66 CCATTGACAGACCAAAAGTAAAAA-AAAAAAATTGGAAAAAGGTGGTGCCGA-CCATTGGCAAGC
*
2015101 CACCACCAATTTTTTTTTTAACTTTTTTC
129 CACCACCAAATTTTTTTTTAACTTTTTTC
2015130 ATGTCAATGA
Statistics
Matches: 316, Mismatches: 47, Indels: 17
0.83 0.12 0.04
Matches are distributed among these distances:
208 2 0.01
209 87 0.28
210 24 0.08
212 73 0.23
213 42 0.13
214 2 0.01
215 5 0.02
216 7 0.02
217 32 0.10
218 42 0.13
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (211 bp):
TGGTGCCGGCCATTGGCAGGCCACCACCAAAATTTTTTTTTACTTTTTTCGTATACTGGTGCCGG
CCATTGACAGACCAAAAGTAAAAAAAAAAAATTGGAAAAAGGTGGTGCCGACCATTGGCAAGCCA
CCACCAAATTTTTTTTTAACTTTTTTCGTATACTGATGCCGGCAATTAACAGACCAAAAATAAAA
AAAAATTGGAAAAAGG
Found at i:2017080 original size:115 final size:109
Alignment explanation
Indices: 2016935--2017349 Score: 404
Period size: 104 Copynumber: 3.8 Consensus size: 109
2016925 AGGTCTAGTA
* *
2016935 CCGGCCACTGGCAAGCCACCACAAAATTTTTTTTTTACTTTTTTCGTATACTGGTGCAGGCTATT
1 CCGGCCATTGGCAAGCCACCAC--AA-TTTTTTTTTACTTTTTTCGTATACTGGTGCCGGCTATT
*
2017000 GACAAACCAAAAGTAAAAAAAAAAAGAATTTTTTTTGGAAAAAGGTGGTG
63 GACAGACCAAAAGT--AAAAAAAAAGAATTTTTTTTGGAAAAA-GTGGTG
* * * * *
2017050 CCGGCCATTGGCAGGCCACCCCCAATTTTTTTTTTTACTTTTTTAC-TATACTAGTGCTGGCCAT
1 CCGGCCATTGGCAAGCCA-CCACAA--TTTTTTTTTACTTTTTT-CGTATACTGGTGCCGGCTAT
* *
2017114 TGACAGACCAAAAGTAAAAAAAAA-AA-----TTAGGAAAATGTGGTG
62 TGACAGACCAAAAGTAAAAAAAAAGAATTTTTTTTGGAAAAAGTGGTG
* * * * * *
2017156 TCGGCCATTGGCAAGTCATCACAATTTTTTTTTACTTTTTTCGTATACTGGTGCCGACAATTGAT
1 CCGGCCATTGGCAAGCCACCACAATTTTTTTTTACTTTTTTCGTATACTGGTGCCGGCTATTGAC
*** ** *
2017221 AGACCAAAAGT---AAACTTG--TTTTTTTTTTAAATAGTGGTG
66 AGACCAAAAGTAAAAAAAAAGAATTTTTTTTGGAAAAAGTGGTG
* * * * *
2017260 CCGGCCATTGGTAGGTCACTACAATTTTTTTTTACTTTTTTCGTATACTGGTGCCGGCTATTTAC
1 CCGGCCATTGGCAAGCCACCACAATTTTTTTTTACTTTTTTCGTATACTGGTGCCGGCTATTGAC
*
2017325 AGACCAAAAGTAAAAAAAAAAAATT
66 AGACCAAAAGTAAAAAAAAAGAATT
2017350 GGGAAATAGG
Statistics
Matches: 245, Mismatches: 40, Indels: 36
0.76 0.12 0.11
Matches are distributed among these distances:
100 3 0.01
102 1 0.00
103 45 0.18
104 78 0.32
105 4 0.02
106 21 0.09
107 11 0.04
109 2 0.01
112 2 0.01
113 9 0.04
114 2 0.01
115 63 0.26
116 4 0.02
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (109 bp):
CCGGCCATTGGCAAGCCACCACAATTTTTTTTTACTTTTTTCGTATACTGGTGCCGGCTATTGAC
AGACCAAAAGTAAAAAAAAAGAATTTTTTTTGGAAAAAGTGGTG
Found at i:2017314 original size:53 final size:52
Alignment explanation
Indices: 2017151--2017317 Score: 133
Period size: 53 Copynumber: 3.2 Consensus size: 52
2017141 TAGGAAAATG
* * *
2017151 TGGTGTCGGCCATTGGCAAGTCATCACAATTTTTTTTTACTTTTTTCGTATAC
1 TGGTGCCGGCCATTGGTAGGTCAT-ACAATTTTTTTTTACTTTTTTCGTATAC
* * * ** * * ** * ** *
2017204 TGGTGCCGACAATTGATAGACCAAAAGTAAACTTGTTTT--TTTTTT-AAATAG
1 TGGTGCCGGCCATTGGTAGGTC-ATA-CAATTTTTTTTTACTTTTTTCGTATAC
2017255 TGGTGCCGGCCATTGGTAGGTCACTACAATTTTTTTTTACTTTTTTCGTATAC
1 TGGTGCCGGCCATTGGTAGGTCA-TACAATTTTTTTTTACTTTTTTCGTATAC
2017308 TGGTGCCGGC
1 TGGTGCCGGC
2017318 TATTTACAGA
Statistics
Matches: 79, Mismatches: 29, Indels: 12
0.66 0.24 0.10
Matches are distributed among these distances:
50 9 0.11
51 21 0.27
52 12 0.15
53 28 0.35
54 9 0.11
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (52 bp):
TGGTGCCGGCCATTGGTAGGTCATACAATTTTTTTTTACTTTTTTCGTATAC
Found at i:2023355 original size:6 final size:6
Alignment explanation
Indices: 2023340--2023396 Score: 53
Period size: 6 Copynumber: 9.5 Consensus size: 6
2023330 TGGAGAATCC
* * * * *
2023340 GAAGAG GAAGAA GAAGCA GAAGCA GAAGCA GAAGCA GAAGAA GAA-AA
1 GAAGAA GAAGAA GAAGAA GAAGAA GAAGAA GAAGAA GAAGAA GAAGAA
2023387 GGAAGAA GAA
1 -GAAGAA GAA
2023397 AAACTTAAGC
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
5 2 0.04
6 42 0.91
7 2 0.04
ACGTcount: A:0.58, C:0.07, G:0.35, T:0.00
Consensus pattern (6 bp):
GAAGAA
Found at i:2023391 original size:18 final size:18
Alignment explanation
Indices: 2023340--2023384 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
2023330 TGGAGAATCC
*
2023340 GAAGAGGAAGAAGAAGCA
1 GAAGAAGAAGAAGAAGCA
* *
2023358 GAAGCAGAAGCAGAAGCA
1 GAAGAAGAAGAAGAAGCA
2023376 GAAGAAGAA
1 GAAGAAGAA
2023385 AAGGAAGAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.56, C:0.09, G:0.36, T:0.00
Consensus pattern (18 bp):
GAAGAAGAAGAAGAAGCA
Found at i:2025853 original size:70 final size:70
Alignment explanation
Indices: 2025766--2025896 Score: 253
Period size: 70 Copynumber: 1.9 Consensus size: 70
2025756 CTTGTAAAAG
*
2025766 GATGTAATCTTCTTTATAACTTGGGAAAGCCTATATCAGTTTGATGAAGCATTATACATTATATC
1 GATGTAATCTTCTTTATAACTTGCGAAAGCCTATATCAGTTTGATGAAGCATTATACATTATATC
2025831 AGTTT
66 AGTTT
2025836 GATGTAATCTTCTTTATAACTTGCGAAAGCCTATATCAGTTTGATGAAGCATTATACATTA
1 GATGTAATCTTCTTTATAACTTGCGAAAGCCTATATCAGTTTGATGAAGCATTATACATTA
2025897 GTTATTTTAT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
70 60 1.00
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (70 bp):
GATGTAATCTTCTTTATAACTTGCGAAAGCCTATATCAGTTTGATGAAGCATTATACATTATATC
AGTTT
Found at i:2028346 original size:16 final size:16
Alignment explanation
Indices: 2028325--2028358 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
2028315 TTTTGCTCCC
2028325 TCTACTAAATAGTT-CT
1 TCTACTAAA-AGTTACT
2028341 TCTACTAAAAGTTACT
1 TCTACTAAAAGTTACT
2028357 TC
1 TC
2028359 CATTTTTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.41
Consensus pattern (16 bp):
TCTACTAAAAGTTACT
Found at i:2038344 original size:23 final size:22
Alignment explanation
Indices: 2038291--2038349 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
2038281 TAAATATTAG
*
2038291 TTTATTAATATTTTAATTTGAT
1 TTTATTAATATATTAATTTGAT
* *
2038313 TTTTTTAATGATATT-ATTTTAT
1 TTTATTAAT-ATATTAATTTGAT
*
2038335 TGTTATTAATTTATT
1 T-TTATTAATATATT
2038350 TAGTATATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
22 19 0.63
23 11 0.37
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (22 bp):
TTTATTAATATATTAATTTGAT
Found at i:2043653 original size:77 final size:78
Alignment explanation
Indices: 2043555--2043711 Score: 307
Period size: 77 Copynumber: 2.0 Consensus size: 78
2043545 TACTTTTGGA
2043555 AAAGCTCAATTATTTCGGGTTTTATTAAAAGAGATCATGTCCCGTAAGTTAGAACACAATCTTTC
1 AAAGCTCAATTATTTCGGGTTTTATTAAAAGAGATCATGTCCCGTAAGTTAGAACACAATCTTTC
2043620 ATAAATCCCCGAT
66 ATAAATCCCCGAT
2043633 AAAGCTCAA-TATTTCGGGTTTTATTAAAAGAGATCATGTCCCGTAAGTTAGAACACAATCTTTC
1 AAAGCTCAATTATTTCGGGTTTTATTAAAAGAGATCATGTCCCGTAAGTTAGAACACAATCTTTC
2043697 ATAAATCCCCGAT
66 ATAAATCCCCGAT
2043710 AA
1 AA
2043712 TATTTAAAAG
Statistics
Matches: 79, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
77 70 0.89
78 9 0.11
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (78 bp):
AAAGCTCAATTATTTCGGGTTTTATTAAAAGAGATCATGTCCCGTAAGTTAGAACACAATCTTTC
ATAAATCCCCGAT
Found at i:2060247 original size:15 final size:15
Alignment explanation
Indices: 2060224--2060260 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
2060214 TTGGGCTGAA
2060224 GGGTATTGGGCTATTC
1 GGGT-TTGGGCTATTC
2060240 GGGTTTGGGCTATTC
1 GGGTTTGGGCTATTC
2060255 GGGTTT
1 GGGTTT
2060261 TGCTAGTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.08, C:0.11, G:0.41, T:0.41
Consensus pattern (15 bp):
GGGTTTGGGCTATTC
Found at i:2062017 original size:42 final size:43
Alignment explanation
Indices: 2061935--2062077 Score: 139
Period size: 43 Copynumber: 3.3 Consensus size: 43
2061925 TCCCATGCGT
* *
2061935 GGTCTTACATGTAATCAAATATCGATGCCACTATCCCAGACAG
1 GGTCTTACACGAAATCAAATATCGATGCCACTATCCCAGACAG
* * *
2061978 GGTCTTACACGAAATCATATAT-GATGCCGA-TGTCCCAGACAT
1 GGTCTTACACGAAATCAAATATCGATGCC-ACTATCCCAGACAG
* ** * *
2062020 GGTCTTACACGTAAATCTCAA-ATCGATGCCACCGTCCCAGATAT
1 GGTCTTACACG-AAATC-AAATATCGATGCCACTATCCCAGACAG
*
2062064 GGTCTTACATGAAA
1 GGTCTTACACGAAA
2062078 ACATATCTCG
Statistics
Matches: 85, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
42 27 0.32
43 31 0.36
44 27 0.32
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.26
Consensus pattern (43 bp):
GGTCTTACACGAAATCAAATATCGATGCCACTATCCCAGACAG
Found at i:2063391 original size:25 final size:25
Alignment explanation
Indices: 2063329--2063383 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
2063319 AAGTGCTATA
2063329 CAGAGAGCACTAATATGCTAATAAT
1 CAGAGAGCACTAATATGCTAATAAT
* * *
2063354 CGGAGAGCACTAATGTGCTAATGAT
1 CAGAGAGCACTAATATGCTAATAAT
2063379 CAGAG
1 CAGAG
2063384 CGCGCTAAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (25 bp):
CAGAGAGCACTAATATGCTAATAAT
Found at i:2067716 original size:20 final size:19
Alignment explanation
Indices: 2067674--2067716 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
2067664 CTTTAAAATA
* *
2067674 AATTTAACTCCCTATTTTC
1 AATTAAACTCCCAATTTTC
*
2067693 AATTAAACTCCTCAATTTTG
1 AATTAAACTCC-CAATTTTC
2067713 AATT
1 AATT
2067717 TTTCACAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.33, C:0.21, G:0.02, T:0.44
Consensus pattern (19 bp):
AATTAAACTCCCAATTTTC
Found at i:2069453 original size:12 final size:11
Alignment explanation
Indices: 2069434--2069466 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
2069424 AACAAAAACA
2069434 ATAATAAAAAT
1 ATAATAAAAAT
2069445 ATAATTAAAAAT
1 ATAA-TAAAAAT
2069457 ATAA-AAAAAT
1 ATAATAAAAAT
2069467 TGAAAATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.29
11 4 0.19
12 11 0.52
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
ATAATAAAAAT
Found at i:2072995 original size:29 final size:29
Alignment explanation
Indices: 2072943--2072998 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
2072933 TATACAGACA
*
2072943 GATCAAATTAGTCCCTCAATTATTAAATC
1 GATCAAATTAGTCCCTCAACTATTAAATC
*
2072972 GATCAATTTAGTCCCT-ATACTATTAAA
1 GATCAAATTAGTCCCTCA-ACTATTAAA
2072999 AAGAGTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.04
29 23 0.96
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.36
Consensus pattern (29 bp):
GATCAAATTAGTCCCTCAACTATTAAATC
Found at i:2106337 original size:23 final size:22
Alignment explanation
Indices: 2106303--2106345 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
2106293 TAGGCTCTCG
2106303 AGTATTTAATGAGTTTGTTTTCA
1 AGTATTTAATGAGTTT-TTTTCA
2106326 AGTAGTTT-ATGAGTTTTTTT
1 AGTA-TTTAATGAGTTTTTTT
2106346 ATTTTTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 4 0.21
23 12 0.63
24 3 0.16
ACGTcount: A:0.23, C:0.02, G:0.19, T:0.56
Consensus pattern (22 bp):
AGTATTTAATGAGTTTTTTTCA
Found at i:2107449 original size:26 final size:26
Alignment explanation
Indices: 2107387--2107449 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
2107377 AAAAATGCAC
*
2107387 AAAACTTTTAAAAATATATAAAAAGTT
1 AAAA-TTTTATAAATATATAAAAAGTT
*
2107414 AGAAA-ATTATAAATATATAAAAA-TT
1 A-AAATTTTATAAATATATAAAAAGTT
2107439 AAAAGTTTTAT
1 AAAA-TTTTAT
2107450 TAAAAATTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
24 3 0.10
25 3 0.10
26 20 0.67
27 1 0.03
28 3 0.10
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.35
Consensus pattern (26 bp):
AAAATTTTATAAATATATAAAAAGTT
Found at i:2108216 original size:21 final size:21
Alignment explanation
Indices: 2108192--2108264 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
2108182 TTTGTTTTGA
2108192 AATTTTTATATATGTTTTTTT
1 AATTTTTATATATGTTTTTTT
* * *
2108213 AATTTTTATATATTGGATTTATA
1 AATTTTTATATA-T-GTTTTTTT
* *
2108236 AATTTTTATTTATGTTTTTAT
1 AATTTTTATATATGTTTTTTT
*
2108257 ATTTTTTA
1 AATTTTTA
2108265 AAATTTTTAT
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
21 23 0.56
22 2 0.05
23 16 0.39
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.67
Consensus pattern (21 bp):
AATTTTTATATATGTTTTTTT
Found at i:2111388 original size:77 final size:82
Alignment explanation
Indices: 2111302--2111502 Score: 241
Period size: 85 Copynumber: 2.5 Consensus size: 82
2111292 CCCAAACTCA
*
2111302 GATTACAAATGCAGCTCATACAAAGTCTAAC-TTCA-C-CA-TAACAT-AAATCTATGATTCAAG
1 GATTACAAATGCAGCTCATACAAAGTCTAACATTCAGCACACTAACATAAAATCTATAATTCAAG
*
2111362 AGCTAATCCAAAAATCG
66 AGCTAAACCAAAAATCG
* * *
2111379 GATTGCAAATGCAGCTCACACAAAGTCTAACTTTCAGCAACACCGTAACATAAAATCTATAATTC
1 GATTACAAATGCAGCTCATACAAAGTCTAACATTCAGC-ACA-C-TAACATAAAATCTATAATTC
** *
2111444 AAGAGCTAAACCTGAACTCG
63 AAGAGCTAAACCAAAAATCG
* * *
2111464 GATTACAAATACAACTCATAAAAAGTCTAACATTCAGCA
1 GATTACAAATGCAGCTCATACAAAGTCTAACATTCAGCA
2111503 AAACCATATA
Statistics
Matches: 103, Mismatches: 13, Indels: 9
0.82 0.10 0.07
Matches are distributed among these distances:
77 29 0.28
78 4 0.04
79 1 0.01
81 2 0.02
84 7 0.07
85 60 0.58
ACGTcount: A:0.43, C:0.23, G:0.11, T:0.23
Consensus pattern (82 bp):
GATTACAAATGCAGCTCATACAAAGTCTAACATTCAGCACACTAACATAAAATCTATAATTCAAG
AGCTAAACCAAAAATCG
Found at i:2111565 original size:83 final size:84
Alignment explanation
Indices: 2111336--2111656 Score: 240
Period size: 85 Copynumber: 3.8 Consensus size: 84
2111326 GTCTAACTTC
* * * ** * * *
2111336 ACCATAACAT-AAATCTATGATTCAAGAGCTAATCCAAAAATCGGATTGCAAATGCAGCTCACAC
1 ACCATAACATAAAATCTATAAAT-AAGAGCTAAACCCGAACTCGGATTACAAATGCAGCTCATAC
*
2111400 AAAGTCTAACTTTCAGCAAC
65 AAAGTCTAACTTTCAGCAAA
* * * * * *
2111420 ACCGTAACATAAAATCTATAATTCAAGAGCTAAACCTGAACTCGGATTACAAATACAACTCATAA
1 ACCATAACATAAAATCTATAAAT-AAGAGCTAAACCCGAACTCGGATTACAAATGCAGCTCATAC
*
2111485 AAAGTCTAACATTCAGCAAA
65 AAAGTCTAACTTTCAGCAAA
* * *
2111505 ACCAT-ATAT-AAATCTATTACAAT-AGAGCTAAGCCCGAACTCAGG-TTATAAATGCAGCTCAT
1 ACCATAACATAAAATCTA-TA-AATAAGAGCTAAACCCGAACTC-GGATTACAAATGCAGCTCAT
* * ** *
2111566 GCAAAGTTTAACTTTCAGTGAC
63 ACAAAGTCTAACTTTCAGCAAA
* ** * * * * * * *
2111588 ACAATAACAT-AAATCTATCAAACGAGGGCTAAACCTGAATTTGGGTTATAAATGCAGCTCATGC
1 ACCATAACATAAAATCTAT-AAATAAGAGCTAAACCCGAACTCGGATTACAAATGCAGCTCATAC
2111652 AAAGT
65 AAAGT
2111657 TCACAACATA
Statistics
Matches: 193, Mismatches: 36, Indels: 16
0.79 0.15 0.07
Matches are distributed among these distances:
83 61 0.32
84 64 0.33
85 68 0.35
ACGTcount: A:0.42, C:0.21, G:0.13, T:0.24
Consensus pattern (84 bp):
ACCATAACATAAAATCTATAAATAAGAGCTAAACCCGAACTCGGATTACAAATGCAGCTCATACA
AAGTCTAACTTTCAGCAAA
Found at i:2111702 original size:68 final size:68
Alignment explanation
Indices: 2111593--2111724 Score: 264
Period size: 68 Copynumber: 1.9 Consensus size: 68
2111583 GTGACACAAT
2111593 AACATAAATCTATCAAACGAGGGCTAAACCTGAATTTGGGTTATAAATGCAGCTCATGCAAAGTT
1 AACATAAATCTATCAAACGAGGGCTAAACCTGAATTTGGGTTATAAATGCAGCTCATGCAAAGTT
2111658 CAC
66 CAC
2111661 AACATAAATCTATCAAACGAGGGCTAAACCTGAATTTGGGTTATAAATGCAGCTCATGCAAAGT
1 AACATAAATCTATCAAACGAGGGCTAAACCTGAATTTGGGTTATAAATGCAGCTCATGCAAAGT
2111725 CTAACTTTCA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (68 bp):
AACATAAATCTATCAAACGAGGGCTAAACCTGAATTTGGGTTATAAATGCAGCTCATGCAAAGTT
CAC
Found at i:2111807 original size:84 final size:84
Alignment explanation
Indices: 2111661--2112358 Score: 801
Period size: 84 Copynumber: 8.3 Consensus size: 84
2111651 CAAAGTTCAC
* * * * * * * * * * *
2111661 AACATAAATCTATCAAACGAGGGCTAAACCTGAATTTGGGTTATAAATGCAGCTCATGCAAAGTC
1 AACATAAATCTATTATATGAGAGCTAAACCCGAACTCGGATTACAAATGCAGCTTATACAAAGTC
* *
2111726 TAACTTTCAGCGACACAAT
66 TAACTTTCAGTGACACCAT
* * * * * * *
2111745 AACATAAATCTATCAAACGAGGGCTAAACCTGAACTTGGATTACAAATGCAACTTATACAAAGTC
1 AACATAAATCTATTATATGAGAGCTAAACCCGAACTCGGATTACAAATGCAGCTTATACAAAGTC
*
2111810 TAACTTTCAGTGACACCAC
66 TAACTTTCAGTGACACCAT
* * * *
2111829 AACATAAATATATTATATGAGAGCTGAACCCGAACTCGGATTACAAATGCAGCTTGTGCAAAGTC
1 AACATAAATCTATTATATGAGAGCTAAACCCGAACTCGGATTACAAATGCAGCTTATACAAAGTC
*
2111894 TAACTTTCAGTGACATCAT
66 TAACTTTCAGTGACACCAT
* * * * *
2111913 AACATAAATCTA-T-TATGAGAGCTGAACCCGAACTTGGGTTACAAATACAACTTATACAAAGTC
1 AACATAAATCTATTATATGAGAGCTAAACCCGAACTCGGATTACAAATGCAGCTTATACAAAGTC
2111976 TAACTTTCAGTGACACCAT
66 TAACTTTCAGTGACACCAT
* * * * *
2111995 AACATAAATATATTATATGAGAGCCAAACCCGAACTCAGATTACAAATGCAGCTTCTACAATGTC
1 AACATAAATCTATTATATGAGAGCTAAACCCGAACTCGGATTACAAATGCAGCTTATACAAAGTC
* * *
2112060 TAACTTTCAGCGATACAAT
66 TAACTTTCAGTGACACCAT
* * * * * * * *
2112079 AACATAAATCTATCAAACGAGGGCTAAACCAGAACTCGGATCACAAATACAGCTTAAACAAAGTC
1 AACATAAATCTATTATATGAGAGCTAAACCCGAACTCGGATTACAAATGCAGCTTATACAAAGTC
*
2112144 TTAACTTTCAATGACACCAT
66 -TAACTTTCAGTGACACCAT
* * ** *
2112164 AACATAAATCTATTATATAAGAGCTGAACTTGAACTCGGATTACAAATACAGCTTATACAAAGTC
1 AACATAAATCTATTATATGAGAGCTAAACCCGAACTCGGATTACAAATGCAGCTTATACAAAGTC
2112229 TAACTTTCAGTGACACCAT
66 TAACTTTCAGTGACACCAT
* *
2112248 AAC--AAATCTATTATATGAGAGCTGAACCCGAACTCGGATTAACAAATGCAGCTTATACAAAGC
1 AACATAAATCTATTATATGAGAGCTAAACCCGAACTCGGATT-ACAAATGCAGCTTATACAAAGT
*
2112311 CTAACTTTCAGTGACAACAT
65 CTAACTTTCAGTGACACCAT
* ** * *
2112331 GACATAAATGGATGATAGGAGAGCTAAA
1 AACATAAATCTATTATATGAGAGCTAAA
2112359 ACCGGACTAT
Statistics
Matches: 525, Mismatches: 83, Indels: 11
0.85 0.13 0.02
Matches are distributed among these distances:
82 107 0.20
83 43 0.08
84 287 0.55
85 88 0.17
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.25
Consensus pattern (84 bp):
AACATAAATCTATTATATGAGAGCTAAACCCGAACTCGGATTACAAATGCAGCTTATACAAAGTC
TAACTTTCAGTGACACCAT
Found at i:2112001 original size:166 final size:167
Alignment explanation
Indices: 2111705--2112339 Score: 810
Period size: 166 Copynumber: 3.8 Consensus size: 167
2111695 TTTGGGTTAT
* * *
2111705 AAATGCAGCTCATGCAAAGTCTAACTTTCAGCGACACAATAACATAAATCTATCAAACGAGGGCT
1 AAATGCAGCTTATACAAAGTCTAACTTTCAGCGACACAATAACATAAATCTAT-AAACGAGAGCT
* * * *
2111770 AAACCTGAACTTGGATTACAAATGCAACTTATACAAAGTCTAACTTTCAGTGACACCACAACATA
65 AAACCCGAACTCGGATTACAAATACAACTTATACAAAGTCTAACTTTCAGTGACACCATAACATA
2111835 AATATATTATATGAGAGCTGAACCCGAACTCGGATTAC
130 AATATATTATATGAGAGCTGAACCCGAACTCGGATTAC
* * * * *
2111873 AAATGCAGCTTGTGCAAAGTCTAACTTTCAGTGACATC-ATAACATAAATCTAT-TATGAGAGCT
1 AAATGCAGCTTATACAAAGTCTAACTTTCAGCGACA-CAATAACATAAATCTATAAACGAGAGCT
* * *
2111936 GAACCCGAACTTGGGTTACAAATACAACTTATACAAAGTCTAACTTTCAGTGACACCATAACATA
65 AAACCCGAACTCGGATTACAAATACAACTTATACAAAGTCTAACTTTCAGTGACACCATAACATA
** *
2112001 AATATATTATATGAGAGCCAAACCCGAACTCAGATTAC
130 AATATATTATATGAGAGCTGAACCCGAACTCGGATTAC
* * * *
2112039 AAATGCAGCTTCTACAATGTCTAACTTTCAGCGATACAATAACATAAATCTATCAAACGAGGGCT
1 AAATGCAGCTTATACAAAGTCTAACTTTCAGCGACACAATAACATAAATCTAT-AAACGAGAGCT
* * * * *
2112104 AAACCAGAACTCGGATCACAAATACAGCTTAAACAAAGTCTTAACTTTCAATGACACCATAACAT
65 AAACCCGAACTCGGATTACAAATACAACTTATACAAAGTC-TAACTTTCAGTGACACCATAACAT
* * **
2112169 AAATCTATTATATAAGAGCTGAACTTGAACTCGGATTAC
129 AAATATATTATATGAGAGCTGAACCCGAACTCGGATTAC
* * * * *
2112208 AAATACAGCTTATACAAAGTCTAACTTTCAGTGACACCATAAC--AAATCTATTATATGAGAGCT
1 AAATGCAGCTTATACAAAGTCTAACTTTCAGCGACACAATAACATAAATCTA-TAAACGAGAGCT
* * * * * *
2112271 GAACCCGAACTCGGATTAACAAATGCAGCTTATACAAAGCCTAACTTTCAGTGACAACATGACAT
65 AAACCCGAACTCGGATT-ACAAATACAACTTATACAAAGTCTAACTTTCAGTGACACCATAACAT
2112336 AAAT
129 AAAT
2112340 GGATGATAGG
Statistics
Matches: 405, Mismatches: 55, Indels: 15
0.85 0.12 0.03
Matches are distributed among these distances:
165 1 0.00
166 148 0.37
167 54 0.13
168 109 0.27
169 93 0.23
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.25
Consensus pattern (167 bp):
AAATGCAGCTTATACAAAGTCTAACTTTCAGCGACACAATAACATAAATCTATAAACGAGAGCTA
AACCCGAACTCGGATTACAAATACAACTTATACAAAGTCTAACTTTCAGTGACACCATAACATAA
ATATATTATATGAGAGCTGAACCCGAACTCGGATTAC
Found at i:2112143 original size:250 final size:253
Alignment explanation
Indices: 2111687--2112326 Score: 822
Period size: 250 Copynumber: 2.5 Consensus size: 253
2111677 ACGAGGGCTA
* * * * * * *
2111687 AACCTGAATTTGGGTTATAAATGCAGCTCATGCAAAGTCTAACTTTCAGCGACACAATAACATAA
1 AACCTGAACTTGGGTTACAAATACAGCTTATACAAAGTCTAACTTTCAGTGACACCATAACATAA
* * * * * * *
2111752 ATCTATCAAACGAGGGCTAAACCTGAACTTGGATTACAAATGCAACTTATACAAAGTCTAACTTT
66 ATCTATTATATGAGAGCTAAACCCGAACTCGGATTACAAATGCAGCTTATACAAAGTCTAACTTT
* * * * * * * * *
2111817 CAGTGACACCACAACATAAATATATTATATGAGAGCTGAACCCGAACTCGGATTACAAATGCAGC
131 CAGCGACACAACAACATAAATATATCAAACGAGAGCTAAACCAGAACTCGGATCACAAATACAGC
*** * * *
2111882 TTGTGCAAAGTC-TAACTTTCAGTGACATCATAACATAAATCTA-T-TATGAGAGCTG
196 TTAAACAAAGTCTTAACTTTCAATGACACCATAACATAAATCTATTATATAAGAGCTG
* *
2111937 AACCCGAACTTGGGTTACAAATACAACTTATACAAAGTCTAACTTTCAGTGACACCATAACATAA
1 AACCTGAACTTGGGTTACAAATACAGCTTATACAAAGTCTAACTTTCAGTGACACCATAACATAA
* * * * *
2112002 ATATATTATATGAGAGCCAAACCCGAACTCAGATTACAAATGCAGCTTCTACAATGTCTAACTTT
66 ATCTATTATATGAGAGCTAAACCCGAACTCGGATTACAAATGCAGCTTATACAAAGTCTAACTTT
* * * *
2112067 CAGCGATACAATAACATAAATCTATCAAACGAGGGCTAAACCAGAACTCGGATCACAAATACAGC
131 CAGCGACACAACAACATAAATATATCAAACGAGAGCTAAACCAGAACTCGGATCACAAATACAGC
2112132 TTAAACAAAGTCTTAACTTTCAATGACACCATAACATAAATCTATTATATAAGAGCTG
196 TTAAACAAAGTCTTAACTTTCAATGACACCATAACATAAATCTATTATATAAGAGCTG
* * *
2112190 AACTTGAACTCGGATTACAAATACAGCTTATACAAAGTCTAACTTTCAGTGACACCATAAC--AA
1 AACCTGAACTTGGGTTACAAATACAGCTTATACAAAGTCTAACTTTCAGTGACACCATAACATAA
* *
2112253 ATCTATTATATGAGAGCTGAACCCGAACTCGGATTAACAAATGCAGCTTATACAAAGCCTAACTT
66 ATCTATTATATGAGAGCTAAACCCGAACTCGGATT-ACAAATGCAGCTTATACAAAGTCTAACTT
*
2112318 TCAGTGACA
130 TCAGCGACA
2112327 ACATGACATA
Statistics
Matches: 332, Mismatches: 54, Indels: 6
0.85 0.14 0.02
Matches are distributed among these distances:
250 170 0.51
251 62 0.19
252 34 0.10
253 66 0.20
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.26
Consensus pattern (253 bp):
AACCTGAACTTGGGTTACAAATACAGCTTATACAAAGTCTAACTTTCAGTGACACCATAACATAA
ATCTATTATATGAGAGCTAAACCCGAACTCGGATTACAAATGCAGCTTATACAAAGTCTAACTTT
CAGCGACACAACAACATAAATATATCAAACGAGAGCTAAACCAGAACTCGGATCACAAATACAGC
TTAAACAAAGTCTTAACTTTCAATGACACCATAACATAAATCTATTATATAAGAGCTG
Found at i:2119761 original size:34 final size:35
Alignment explanation
Indices: 2119717--2119783 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
2119707 CAGTAAAATA
2119717 TTTTCCGTAAAATGATTT-CTGGAAAATATTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
2119751 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
2119784 CTGGTGTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 17 0.55
35 14 0.45
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:2119957 original size:21 final size:21
Alignment explanation
Indices: 2119928--2119969 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2119918 TACGGAATTG
*
2119928 AAAAGGTAAGACATTTTCCCT
1 AAAAGGTAACACATTTTCCCT
* *
2119949 AAAATGTAACCCATTTTCCCT
1 AAAAGGTAACACATTTTCCCT
2119970 TGTTTTGGAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.31
Consensus pattern (21 bp):
AAAAGGTAACACATTTTCCCT
Found at i:2121283 original size:26 final size:26
Alignment explanation
Indices: 2121254--2121310 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
2121244 GGTAGTTTTC
*
2121254 TATAATTTCTAATTATATTTTTATTT
1 TATAATTTATAATTATATTTTTATTT
*
2121280 TATAATTTATATTTATATTTTTATTT
1 TATAATTTATAATTATATTTTTATTT
2121306 T-TAAT
1 TATAAT
2121311 ACATATTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 4 0.14
26 25 0.86
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (26 bp):
TATAATTTATAATTATATTTTTATTT
Found at i:2121553 original size:140 final size:141
Alignment explanation
Indices: 2121300--2121580 Score: 555
Period size: 140 Copynumber: 2.0 Consensus size: 141
2121290 ATTTATATTT
2121300 TTATTTTTAATACATATTGAAGTGTCACATGGCACATACTTTTTTTTTTTAACCACAGTGGCTGA
1 TTATTTTTAATACATATTGAAGTGTCACATGGCACATACTTTTTTTTTTTAACCACAGTGGCTGA
2121365 ATCGACTAAAAAAAAGTAACTTTAGATACCAAAATGAAAAAATAAGCTTTAAGCCAAAAAGAAAC
66 ATCGACTAAAAAAAAGTAACTTTAGATACCAAAATGAAAAAATAAGCTTTAAGCCAAAAAGAAAC
2121430 AAAATCGAATA
131 AAAATCGAATA
2121441 TTATTTTTAA-ACATATTGAAGTGTCACATGGCACATACTTTTTTTTTTTAACCACAGTGGCTGA
1 TTATTTTTAATACATATTGAAGTGTCACATGGCACATACTTTTTTTTTTTAACCACAGTGGCTGA
2121505 ATCGACTAAAAAAAAGTAACTTTAGATACCAAAATGAAAAAATAAGCTTTAAGCCAAAAAGAAAC
66 ATCGACTAAAAAAAAGTAACTTTAGATACCAAAATGAAAAAATAAGCTTTAAGCCAAAAAGAAAC
2121570 AAAATCGAATA
131 AAAATCGAATA
2121581 ATTGGATAAC
Statistics
Matches: 140, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
140 130 0.93
141 10 0.07
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (141 bp):
TTATTTTTAATACATATTGAAGTGTCACATGGCACATACTTTTTTTTTTTAACCACAGTGGCTGA
ATCGACTAAAAAAAAGTAACTTTAGATACCAAAATGAAAAAATAAGCTTTAAGCCAAAAAGAAAC
AAAATCGAATA
Found at i:2130674 original size:28 final size:28
Alignment explanation
Indices: 2130632--2130687 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
2130622 AGCCGGTAAG
* *
2130632 CATTTAGAAGGTACTATGTGTCAGTGAT
1 CATTTAGAAGCTACTATGTATCAGTGAT
*
2130660 CATTTAGCAGCTACTATGTATCAGTGAT
1 CATTTAGAAGCTACTATGTATCAGTGAT
2130688 ATAGACCGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (28 bp):
CATTTAGAAGCTACTATGTATCAGTGAT
Found at i:2153250 original size:116 final size:116
Alignment explanation
Indices: 2153040--2153254 Score: 333
Period size: 116 Copynumber: 1.9 Consensus size: 116
2153030 AAGTTGAAGA
*
2153040 TTGTTGGATCTGGTGCCCTAAATATAGTATATTCGTTTGTACACTTATAATTTTTTCAAACAGAC
1 TTGTTGGATCTGGTGCCCTAAATATAGTATATTCATTTGTACACTTATAATTTTTTCAAACAGAC
* *
2153105 TAGTTAGTAAAATTATTCATGAATTACATTAATACCTTTTGTATGTTGTCC
66 TAGTTAATAAAATTATTCATGAATAACATTAATACCTTTTGTATGTTGTCC
* * *
2153156 TTGTTGGATCTGG-GACCCTAAGTGTAGTATATTCATTTGTACACTTATAATTTTTTCGAACAGA
1 TTGTTGGATCTGGTG-CCCTAAATATAGTATATTCATTTGTACACTTATAATTTTTTCAAACAGA
* * *
2153220 TTGGTTAATAAAATTATTCATGGATAACATTAATA
65 CTAGTTAATAAAATTATTCATGAATAACATTAATA
2153255 TACTTTGTAT
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
115 1 0.01
116 88 0.99
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.42
Consensus pattern (116 bp):
TTGTTGGATCTGGTGCCCTAAATATAGTATATTCATTTGTACACTTATAATTTTTTCAAACAGAC
TAGTTAATAAAATTATTCATGAATAACATTAATACCTTTTGTATGTTGTCC
Found at i:2155451 original size:25 final size:24
Alignment explanation
Indices: 2155423--2155498 Score: 84
Period size: 25 Copynumber: 3.1 Consensus size: 24
2155413 AAGCTCCTTC
*
2155423 GAGCTGAATATTGGTAAGCTCATAT
1 GAGCTGAA-ATCGGTAAGCTCATAT
*
2155448 GAGCTGTGAAA-CGGTAAGCTC-TCAC
1 GAGC--TGAAATCGGTAAGCTCAT-AT
2155473 GAGCTGAAATCGGTAAGCTCATAT
1 GAGCTGAAATCGGTAAGCTCATAT
2155497 GA
1 GA
2155499 ACTGTGGTGT
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
23 5 0.12
24 14 0.33
25 19 0.44
26 1 0.02
27 4 0.09
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (24 bp):
GAGCTGAAATCGGTAAGCTCATAT
Found at i:2155491 original size:24 final size:24
Alignment explanation
Indices: 2155412--2155495 Score: 82
Period size: 25 Copynumber: 3.4 Consensus size: 24
2155402 GCGATAAACA
* * *
2155412 TAAGCTCCTTCGAGCTGAATATTGG
1 TAAGCTCATACGAGCTGAA-ATCGG
*
2155437 TAAGCTCATATGAGCTGTGAAA-CGG
1 TAAGCTCATACGAGC--TGAAATCGG
2155462 TAAGCTC-TCACGAGCTGAAATCGG
1 TAAGCTCAT-ACGAGCTGAAATCGG
2155486 TAAGCTCATA
1 TAAGCTCATA
2155496 TGAACTGTGG
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
23 5 0.10
24 12 0.24
25 27 0.55
26 1 0.02
27 4 0.08
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (24 bp):
TAAGCTCATACGAGCTGAAATCGG
Found at i:2163987 original size:43 final size:44
Alignment explanation
Indices: 2163935--2164021 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
2163925 TAAATTGCCA
*
2163935 ATTCAGTCTTCCTTCTCTT-GGAACCAATATCCCAAAATTTTAT
1 ATTCAGTCTTCCTTCTCTTCGCAACCAATATCCCAAAATTTTAT
2163978 ATTCAGTCTTCCTTCTCTTCGCAACCAATATCCCAAAATTTTAT
1 ATTCAGTCTTCCTTCTCTTCGCAACCAATATCCCAAAATTTTAT
2164022 GCAAATGTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
43 19 0.45
44 23 0.55
ACGTcount: A:0.28, C:0.28, G:0.06, T:0.39
Consensus pattern (44 bp):
ATTCAGTCTTCCTTCTCTTCGCAACCAATATCCCAAAATTTTAT
Found at i:2169377 original size:9 final size:9
Alignment explanation
Indices: 2169359--2169425 Score: 57
Period size: 10 Copynumber: 7.3 Consensus size: 9
2169349 TTTTTTTATT
2169359 AAAAAT-TA
1 AAAAATATA
2169367 AAAAATATA
1 AAAAATATA
*
2169376 AAAAATCGTA
1 AAAAAT-ATA
*
2169386 AAAAATTGTA
1 AAAAA-TATA
2169396 AAAAAT-TA
1 AAAAATATA
*
2169404 TAAAATATA
1 AAAAATATA
*
2169413 TAGAAATATA
1 -AAAAATATA
2169423 AAA
1 AAA
2169426 TTTTATAAAG
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
8 13 0.27
9 13 0.27
10 22 0.45
11 1 0.02
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.25
Consensus pattern (9 bp):
AAAAATATA
Found at i:2169447 original size:46 final size:45
Alignment explanation
Indices: 2169393--2169481 Score: 117
Period size: 48 Copynumber: 1.9 Consensus size: 45
2169383 GTAAAAAATT
* *
2169393 GTAAAAAATTAT-AAAATATATAGAAATATAAAATTTTATAAAGTC
1 GTAAAAAATTATAAAAATATAAAGAAATAT-AAATTTCATAAAGTC
*
2169438 GTAAGAAAATTATACAAAATGTAAAGAAATATAAATTTCATAAA
1 GTAA-AAAATTATA-AAAATATAAAGAAATATAAATTTCATAAA
2169482 AAAAATTATA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
45 4 0.11
46 8 0.21
47 11 0.29
48 15 0.39
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.30
Consensus pattern (45 bp):
GTAAAAAATTATAAAAATATAAAGAAATATAAATTTCATAAAGTC
Found at i:2169759 original size:29 final size:30
Alignment explanation
Indices: 2169699--2169771 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
2169689 AATTTCTAAT
2169699 TTTTAAT-AATTTTTAAATTTTTATTGAAA
1 TTTTAATAAATTTTTAAATTTTTATTGAAA
*
2169728 -TTTAATAAATTTTCTAAA-TTTTATT-ATTA
1 TTTTAATAAATTTT-TAAATTTTTATTGA-AA
*
2169757 TTTTTATAAATTTTT
1 TTTTAATAAATTTTT
2169772 TTCTAATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
28 7 0.18
29 15 0.39
30 16 0.42
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (30 bp):
TTTTAATAAATTTTTAAATTTTTATTGAAA
Found at i:2169780 original size:21 final size:21
Alignment explanation
Indices: 2169732--2169783 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
2169722 TTGAAATTTA
* *
2169732 ATAAATTTTCTAAATTTTATT
1 ATAATTTTTATAAATTTTATT
* *
2169753 ATTATTTTTATAAATTTTTTT
1 ATAATTTTTATAAATTTTATT
*
2169774 CTAATTTTTA
1 ATAATTTTTA
2169784 ATAAGAGCAG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (21 bp):
ATAATTTTTATAAATTTTATT
Found at i:2174456 original size:34 final size:34
Alignment explanation
Indices: 2174417--2174515 Score: 112
Period size: 34 Copynumber: 2.9 Consensus size: 34
2174407 AGTGCAATAT
*
2174417 GACATGCTTATAATAGATCAATACGGTAGCAAG-
1 GACATGCTTATAACAGATCAATACGGTAGCAAGA
* * * *
2174450 GAACATGCTTATGACAGATCAATACGATATCAATA
1 G-ACATGCTTATAACAGATCAATACGGTAGCAAGA
* *
2174485 GATATG-TTATAACAGATCAATATGGTAGCAA
1 GACATGCTTATAACAGATCAATACGGTAGCAA
2174516 TTTATCGAGT
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
33 22 0.41
34 31 0.57
35 1 0.02
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.26
Consensus pattern (34 bp):
GACATGCTTATAACAGATCAATACGGTAGCAAGA
Found at i:2181638 original size:16 final size:16
Alignment explanation
Indices: 2181612--2181671 Score: 68
Period size: 16 Copynumber: 3.6 Consensus size: 16
2181602 TGTATGTGTA
2181612 ATAAA-TACATAATAT
1 ATAAATTACATAATAT
2181627 ATAAATTACATAATAT
1 ATAAATTACATAATAT
*
2181643 ATAAAAATAACATAATAT
1 AT--AAATTACATAATAT
*
2181661 AAAATATTACA
1 ATAA-ATTACA
2181672 AACATAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
15 5 0.13
16 14 0.37
17 5 0.13
18 14 0.37
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.32
Consensus pattern (16 bp):
ATAAATTACATAATAT
Found at i:2181650 original size:18 final size:18
Alignment explanation
Indices: 2181617--2181671 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
2181607 GTGTAATAAA
2181617 TACATAATATAT--AAAT
1 TACATAATATATAAAAAT
2181633 TACATAATATATAAAAAT
1 TACATAATATATAAAAAT
* *
2181651 AACATAATATA-AAATAT
1 TACATAATATATAAAAAT
2181668 TACA
1 TACA
2181672 AACATAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
16 12 0.35
17 8 0.24
18 14 0.41
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (18 bp):
TACATAATATATAAAAAT
Found at i:2182024 original size:50 final size:50
Alignment explanation
Indices: 2181943--2182040 Score: 126
Period size: 50 Copynumber: 2.0 Consensus size: 50
2181933 AACTTATTCT
* * *
2181943 AATCAATGTCAAATAGAAAGAGAGAAGTTCTATACGGATTCTACTTGTAC
1 AATCAATATCAAATAGAAAGAGAGAACTTCTATACGGATTCCACTTGTAC
* * *
2181993 AATCAATATCAAATAG-AAGAAGTGTACTTCTATACGTATTCCACTTGT
1 AATCAATATCAAATAGAAAG-AGAGAACTTCTATACGGATTCCACTTGT
2182041 GCAGCTTGTA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
49 3 0.07
50 38 0.93
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (50 bp):
AATCAATATCAAATAGAAAGAGAGAACTTCTATACGGATTCCACTTGTAC
Found at i:2192179 original size:35 final size:35
Alignment explanation
Indices: 2192133--2192255 Score: 129
Period size: 35 Copynumber: 3.5 Consensus size: 35
2192123 CACATGTTTT
* * *
2192133 TCGGTTCTACCGACCAGCGCAGGGTGCATTTATTA
1 TCGGTTATACCGACCAGCGCAGGGCGCATTTATTG
* * * **
2192168 TCGGTTATACCGACCAGTGCTGGGCACACATATTTG
1 TCGGTTATACCGACCAGCGCAGGGCGCATTTA-TTG
* *
2192204 TCGGTTCTACCGACCAACGCAGGGCGCATTTATTG
1 TCGGTTATACCGACCAGCGCAGGGCGCATTTATTG
* *
2192239 TCAGTTATACTGACCAG
1 TCGGTTATACCGACCAG
2192256 TGCTAGGCAC
Statistics
Matches: 68, Mismatches: 19, Indels: 2
0.76 0.21 0.02
Matches are distributed among these distances:
35 41 0.60
36 27 0.40
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (35 bp):
TCGGTTATACCGACCAGCGCAGGGCGCATTTATTG
Found at i:2192215 original size:36 final size:36
Alignment explanation
Indices: 2192121--2192228 Score: 110
Period size: 35 Copynumber: 3.0 Consensus size: 36
2192111 GAAATGATTT
* *
2192121 CACACATGTTTTTCGGTTCTACCGACCAGCGCAGGG
1 CACACATATTTATCGGTTCTACCGACCAGCGCAGGG
** ** * * *
2192157 TGCATTTA-TTATCGGTTATACCGACCAGTGCTGGG
1 CACACATATTTATCGGTTCTACCGACCAGCGCAGGG
* *
2192192 CACACATATTTGTCGGTTCTACCGACCAACGCAGGG
1 CACACATATTTATCGGTTCTACCGACCAGCGCAGGG
2192228 C
1 C
2192229 GCATTTATTG
Statistics
Matches: 53, Mismatches: 18, Indels: 2
0.73 0.25 0.03
Matches are distributed among these distances:
35 27 0.51
36 26 0.49
ACGTcount: A:0.21, C:0.28, G:0.24, T:0.27
Consensus pattern (36 bp):
CACACATATTTATCGGTTCTACCGACCAGCGCAGGG
Found at i:2192237 original size:71 final size:71
Alignment explanation
Indices: 2192121--2192267 Score: 222
Period size: 71 Copynumber: 2.1 Consensus size: 71
2192111 GAAATGATTT
* * * * *
2192121 CACACATGTTTTTCGGTTCTACCGACCAGCGCAGGGTGCATTTATTATCGGTTATACCGACCAGT
1 CACACATATTTGTCGGTTCTACCGACCAACGCAGGGCGCATTTATTATCAGTTATACCGACCAGT
*
2192186 GCTGGG
66 GCTAGG
* *
2192192 CACACATATTTGTCGGTTCTACCGACCAACGCAGGGCGCATTTATTGTCAGTTATACTGACCAGT
1 CACACATATTTGTCGGTTCTACCGACCAACGCAGGGCGCATTTATTATCAGTTATACCGACCAGT
2192257 GCTAGG
66 GCTAGG
2192263 CACAC
1 CACAC
2192268 TCATTGTCAA
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.28
Consensus pattern (71 bp):
CACACATATTTGTCGGTTCTACCGACCAACGCAGGGCGCATTTATTATCAGTTATACCGACCAGT
GCTAGG
Found at i:2196129 original size:22 final size:22
Alignment explanation
Indices: 2196101--2196144 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2196091 TTTGTTCCAA
2196101 AAGATTGTCAATACAAAAAATG
1 AAGATTGTCAATACAAAAAATG
2196123 AAGATTGTCAATACAAAAAATG
1 AAGATTGTCAATACAAAAAATG
2196145 GCAAGTTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.55, C:0.09, G:0.14, T:0.23
Consensus pattern (22 bp):
AAGATTGTCAATACAAAAAATG
Found at i:2196749 original size:19 final size:19
Alignment explanation
Indices: 2196725--2196763 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2196715 CTACATCTAT
*
2196725 TTTCTTTTTATATTTTTCA
1 TTTCTTTTTATACTTTTCA
2196744 TTTCTTTTTATACTTTTCA
1 TTTCTTTTTATACTTTTCA
2196763 T
1 T
2196764 GTCCGTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTCTTTTTATACTTTTCA
Done.