Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 93 of 292
Found at i:28644222 original size:23 final size:22
Alignment explanation
Indices: 28644193--28644235 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
28644183 ATATATATAT
28644193 AAAAGAA-ACAAAAGAAAGAAACA
1 AAAAGAAGA-AAAAG-AAGAAACA
28644216 AAAAGAAGAAAAAGAAGAAA
1 AAAAGAAGAAAAAGAAGAAA
28644236 AGAAACAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.32
23 12 0.63
24 1 0.05
ACGTcount: A:0.79, C:0.05, G:0.16, T:0.00
Consensus pattern (22 bp):
AAAAGAAGAAAAAGAAGAAACA
Found at i:28644245 original size:14 final size:14
Alignment explanation
Indices: 28644193--28644245 Score: 58
Period size: 13 Copynumber: 3.9 Consensus size: 14
28644183 ATATATATAT
*
28644193 AAAAGAAACAAAAG
1 AAAAGAAACAGAAG
28644207 -AAAGAAACA-AA-
1 AAAAGAAACAGAAG
*
28644218 AAGAAGAAAAAGAAG
1 AA-AAGAAACAGAAG
28644233 AAAAGAAACAGAA
1 AAAAGAAACAGAA
28644246 TAGCAGGGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
12 3 0.09
13 16 0.48
14 12 0.36
15 2 0.06
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAGAAACAGAAG
Found at i:28644824 original size:51 final size:51
Alignment explanation
Indices: 28644714--28644815 Score: 125
Period size: 51 Copynumber: 2.0 Consensus size: 51
28644704 AGAACTAAAT
* * * * *
28644714 TATCTGGATGAAATATGAAGCTCTTGTTGAAACTAGAGCAATAAAGTAATA
1 TATCCGGATGAAATATGAAGCTCTTGATGAAACCAGAACAAAAAAGTAATA
* *
28644765 TATCCGGATGAAATAT-AGAGTTCTTGATGAAGCCAGAACAAAAAAGTAATA
1 TATCCGGATGAAATATGA-AGCTCTTGATGAAACCAGAACAAAAAAGTAATA
28644816 ATTTCGGATA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
50 1 0.02
51 42 0.98
ACGTcount: A:0.43, C:0.11, G:0.20, T:0.26
Consensus pattern (51 bp):
TATCCGGATGAAATATGAAGCTCTTGATGAAACCAGAACAAAAAAGTAATA
Found at i:28645169 original size:15 final size:15
Alignment explanation
Indices: 28645151--28645200 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
28645141 TTTATTGAGT
28645151 TTATATTGATTGAAA
1 TTATATTGATTGAAA
* *
28645166 TTAT-TCTAATTGAAT
1 TTATAT-TGATTGAAA
28645181 TTATATTGATTG-AA
1 TTATATTGATTGAAA
28645195 TTATAT
1 TTATAT
28645201 AATATATATG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
14 8 0.28
15 20 0.69
16 1 0.03
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.52
Consensus pattern (15 bp):
TTATATTGATTGAAA
Found at i:28645360 original size:17 final size:18
Alignment explanation
Indices: 28645335--28645383 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
28645325 TTGAAAAGTG
28645335 AATTGAATTATATTGAAT
1 AATTGAATTATATTGAAT
*
28645353 TA-TGAATTA-ATGTGAAT
1 AATTGAATTATAT-TGAAT
*
28645370 AATTGAAATATATT
1 AATTGAATTATATT
28645384 TGTTGAATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
16 2 0.08
17 13 0.52
18 8 0.32
19 2 0.08
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.43
Consensus pattern (18 bp):
AATTGAATTATATTGAAT
Found at i:28645605 original size:23 final size:22
Alignment explanation
Indices: 28645575--28645640 Score: 80
Period size: 23 Copynumber: 3.0 Consensus size: 22
28645565 GCTTTACCGA
28645575 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGT-TT
* * *
28645598 TCAGGCACCTTGTGTGTCCTTT
1 TCAGGCACTTTATGTGTCGTTT
*
28645620 T-AGGCAGTTTATGTGTCGTTT
1 TCAGGCACTTTATGTGTCGTTT
28645641 ACTGATCAGG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
21 16 0.44
22 3 0.08
23 17 0.47
ACGTcount: A:0.14, C:0.18, G:0.24, T:0.44
Consensus pattern (22 bp):
TCAGGCACTTTATGTGTCGTTT
Found at i:28649552 original size:27 final size:26
Alignment explanation
Indices: 28649513--28649607 Score: 127
Period size: 27 Copynumber: 3.5 Consensus size: 26
28649503 TATGCCACAA
* *
28649513 ATTATCTGATCTGGTGGCTTTGCCAC
1 ATTATCTGTTCTGGTGGCTCTGCCAC
28649539 ATATATCTGTTCTGGTGGCTCTGCCAC
1 AT-TATCTGTTCTGGTGGCTCTGCCAC
* *
28649566 GATTATCTGTATCTGGTGACTCTGTCAC
1 -ATTATCTGT-TCTGGTGGCTCTGCCAC
28649594 ATTATCTGTTCTGG
1 ATTATCTGTTCTGG
28649608 CAGCCATGCT
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
26 7 0.11
27 38 0.61
28 17 0.27
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.40
Consensus pattern (26 bp):
ATTATCTGTTCTGGTGGCTCTGCCAC
Found at i:28653435 original size:38 final size:38
Alignment explanation
Indices: 28653393--28653465 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
28653383 CCGCCTAGGT
* *
28653393 CAGTGCCAGAAATACGGAGTTTTCTAGGATTGGCAGGA
1 CAGTGCCAGAAATACAGAGTTTTCTAAGATTGGCAGGA
* *
28653431 CAGTGTCGGAAATACAGAGTTTTCTAAGATTGGCA
1 CAGTGCCAGAAATACAGAGTTTTCTAAGATTGGCA
28653466 AGTTACTACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.26
Consensus pattern (38 bp):
CAGTGCCAGAAATACAGAGTTTTCTAAGATTGGCAGGA
Found at i:28657433 original size:27 final size:26
Alignment explanation
Indices: 28657375--28657487 Score: 127
Period size: 27 Copynumber: 4.2 Consensus size: 26
28657365 AGGAAGCGTC
* * *
28657375 CTGGTGGTTATGCCACAAATTATCTGAT
1 CTGGTGGCTCTGCCAC--ATTATCTGTT
28657403 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGTT
28657430 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTGT-T
* **
28657458 CTGGTGACTCTGTTACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGTT
28657484 CTGG
1 CTGG
28657488 CAGCCATGCT
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
26 7 0.09
27 39 0.51
28 30 0.39
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGTT
Found at i:28657460 original size:55 final size:54
Alignment explanation
Indices: 28657375--28657487 Score: 147
Period size: 55 Copynumber: 2.1 Consensus size: 54
28657365 AGGAAGCGTC
* *
28657375 CTGGTGGTTATGCCACAAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAAATTATCTGATCTGGTGACTCTGCCACAT-TATCTGTT
* * **
28657430 CTGGTGGCTCTGCCAC-GATTATCTGTATCTGGTGACTCTGTTACATTATCTGTT
1 CTGGTGGCTATGCCACAAATTATCTG-ATCTGGTGACTCTGCCACATTATCTGTT
28657484 CTGG
1 CTGG
28657488 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
54 20 0.39
55 31 0.61
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAAATTATCTGATCTGGTGACTCTGCCACATTATCTGTT
Found at i:28659194 original size:29 final size:29
Alignment explanation
Indices: 28659162--28659297 Score: 157
Period size: 29 Copynumber: 4.7 Consensus size: 29
28659152 ATACCCTTCG
** * *
28659162 AGCTCGCACACCCAGTGCCGTATTTTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
* * * *
28659191 AGCTTGCACACATAGTGTCATATTTTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
*
28659220 AGCAT-GCACACTTAGTGCCTTATATTTCC
1 AGC-TCGCACACTTAGTGCCATATATTTCC
*
28659249 AGCACGCACACTTAGTGCCATATATTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
*
28659278 AGCACGCACACTTAGTGCCA
1 AGCTCGCACACTTAGTGCCA
28659298 ATCTCGTCAC
Statistics
Matches: 94, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
29 93 0.99
30 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.15, T:0.29
Consensus pattern (29 bp):
AGCTCGCACACTTAGTGCCATATATTTCC
Found at i:28660131 original size:143 final size:141
Alignment explanation
Indices: 28659941--28660232 Score: 557
Period size: 143 Copynumber: 2.1 Consensus size: 141
28659931 AAATTCTATA
28659941 GCATGGCCGAATACTCATGCACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTT
1 GCATGGCCGAATACTCATGCACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTT
28660006 TGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAG
66 TGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAG
*
28660071 GAAGACAACAT
131 GAAAACAACAT
28660082 GCATGGCCGAATACTCATGCACACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTT
1 GCATGGCCGAATACTCATG--CACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTT
28660147 TTTGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCA
64 TTTGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCA
28660212 AGGAAAACAACAT
129 AGGAAAACAACAT
28660225 GCATGGCC
1 GCATGGCC
28660233 AAAATTTAAC
Statistics
Matches: 148, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
141 19 0.13
143 129 0.87
ACGTcount: A:0.39, C:0.29, G:0.10, T:0.22
Consensus pattern (141 bp):
GCATGGCCGAATACTCATGCACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTT
TGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAG
GAAAACAACAT
Found at i:28662984 original size:20 final size:20
Alignment explanation
Indices: 28662918--28662984 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
28662908 ATTTTGATAA
*
28662918 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
28662938 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
28662958 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
28662978 ACGTGAT
1 ACATGAT
28662985 GTACATAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:28663134 original size:24 final size:23
Alignment explanation
Indices: 28663033--28663171 Score: 226
Period size: 23 Copynumber: 6.0 Consensus size: 23
28663023 AGGAAGTGAA
28663033 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
28663056 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
28663079 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
28663102 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
28663125 AAAAGGGCTTTTGCCCCAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
*
28663149 AAAGAGGC-TAGGCCTCCAGTTAT
1 AAAG-GGCTTATGCC-CCAGTTAT
28663172 ATGATAAAGC
Statistics
Matches: 110, Mismatches: 3, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
23 77 0.70
24 33 0.30
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:28663413 original size:31 final size:29
Alignment explanation
Indices: 28663361--28663422 Score: 88
Period size: 31 Copynumber: 2.1 Consensus size: 29
28663351 CGTTTACAGT
28663361 AAAGGCTTCCCCAGTAATATGAAATATGA
1 AAAGGCTTCCCCAGTAATATGAAATATGA
**
28663390 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTC--CCCAGTAATATGAAATATGA
28663421 AA
1 AA
28663423 TATGAAAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 9 0.31
31 20 0.69
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (29 bp):
AAAGGCTTCCCCAGTAATATGAAATATGA
Found at i:28671072 original size:20 final size:20
Alignment explanation
Indices: 28671006--28671072 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
28670996 ATTTTGATAA
*
28671006 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
28671026 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
28671046 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
28671066 ACGTGAT
1 ACATGAT
28671073 GTAATCATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:28671242 original size:24 final size:23
Alignment explanation
Indices: 28671122--28671240 Score: 202
Period size: 23 Copynumber: 5.1 Consensus size: 23
28671112 AGGAAGTGAA
28671122 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
28671145 AAAGGGCTTGTGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
28671168 AAAGGGCTTATGGCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
28671191 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
28671214 AAAAGGGCTTTTGCCCCAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
28671238 AAA
1 AAA
28671241 AGAGGCTAGG
Statistics
Matches: 90, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
23 68 0.76
24 22 0.24
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:28671491 original size:30 final size:31
Alignment explanation
Indices: 28671455--28671517 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
28671445 CGTTTACAGT
28671455 AAAGGC-TTCGCCCAGTAATATGAAATATGA
1 AAAGGCTTTCGCCCAGTAATATGAAATATGA
* **
28671485 AAAGGCTTTGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTTCGCCCAGTAATATGAAATATGA
28671516 AA
1 AA
28671518 TATGAAAAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 6 0.21
31 23 0.79
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.25
Consensus pattern (31 bp):
AAAGGCTTTCGCCCAGTAATATGAAATATGA
Found at i:28675501 original size:13 final size:14
Alignment explanation
Indices: 28675480--28675508 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
28675470 TGAAAAATGG
28675480 ATTAGAAAATATTT
1 ATTAGAAAATATTT
28675494 ATTA-AAAATATTT
1 ATTAGAAAATATTT
28675507 AT
1 AT
28675509 GAAGTTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (14 bp):
ATTAGAAAATATTT
Found at i:28676043 original size:21 final size:21
Alignment explanation
Indices: 28676018--28676060 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
28676008 ATCTTTACTT
*
28676018 ATTATATAATTATAT-TATTAA
1 ATTAT-TAAATATATATATTAA
28676039 ATTATTAAATATATATATTAA
1 ATTATTAAATATATATATTAA
28676060 A
1 A
28676061 GAAAAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTATTAAATATATATATTAA
Found at i:28676187 original size:13 final size:13
Alignment explanation
Indices: 28676169--28676193 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28676159 TATATATATA
28676169 AAAGAAACAAAAG
1 AAAGAAACAAAAG
28676182 AAAGAAACAAAA
1 AAAGAAACAAAA
28676194 AGAATAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.08, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAGAAACAAAAG
Found at i:28676197 original size:23 final size:23
Alignment explanation
Indices: 28676168--28676222 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
28676158 ATATATATAT
28676168 AAAAGAA-ACAAAAGAAAGAAACA
1 AAAAGAATA-AAAAGAAAGAAACA
* *
28676191 AAAAGAATAAAAAGAAGGAAAGA
1 AAAAGAATAAAAAGAAAGAAACA
*
28676214 AATAGAATA
1 AAAAGAATA
28676223 GCAGGGGACG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 27 0.96
24 1 0.04
ACGTcount: A:0.75, C:0.04, G:0.16, T:0.05
Consensus pattern (23 bp):
AAAAGAATAAAAAGAAAGAAACA
Found at i:28676786 original size:51 final size:51
Alignment explanation
Indices: 28676689--28676799 Score: 127
Period size: 51 Copynumber: 2.2 Consensus size: 51
28676679 AGAACTAAGT
* * * *
28676689 TATCCGGATGAAATATGAAGCTCTTGTTGAAACTAGAGCACTAAAGTAATA
1 TATCCGGATGAAATATAAAGCTCTTGATGAAACCAGAACACTAAAGTAATA
* * *
28676740 TATCCGGATGAAATATAAAGTTCTTGATGAAGCCATAACAAC-AAAGTAATA
1 TATCCGGATGAAATATAAAGCTCTTGATGAAACCAGAAC-ACTAAAGTAATA
28676791 -ATTCCGGAT
1 TA-TCCGGAT
28676800 AAAGTATGAA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
50 1 0.02
51 48 0.94
52 2 0.04
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (51 bp):
TATCCGGATGAAATATAAAGCTCTTGATGAAACCAGAACACTAAAGTAATA
Found at i:28677141 original size:15 final size:15
Alignment explanation
Indices: 28677123--28677172 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
28677113 TTTATTGAGT
28677123 TTATATTGATTGAAA
1 TTATATTGATTGAAA
* *
28677138 TTAT-TCAGATTGAAT
1 TTATAT-TGATTGAAA
*
28677153 TTAAATTGATTG-AA
1 TTATATTGATTGAAA
28677167 TTATAT
1 TTATAT
28677173 AATATATATG
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
14 7 0.26
15 19 0.70
16 1 0.04
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (15 bp):
TTATATTGATTGAAA
Found at i:28677577 original size:23 final size:23
Alignment explanation
Indices: 28677547--28677629 Score: 84
Period size: 21 Copynumber: 3.8 Consensus size: 23
28677537 GCTATACCGA
* *
28677547 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
28677570 TCAGGCACCTCATGTGTTGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
28677591 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* *
28677613 T-AGGCACTTTATGTGTC
1 TCAGGCACCTCATGTGTC
28677630 ATATCTGATC
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
21 31 0.62
22 1 0.02
23 18 0.36
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.39
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:28677596 original size:44 final size:42
Alignment explanation
Indices: 28677546--28677628 Score: 103
Period size: 44 Copynumber: 1.9 Consensus size: 42
28677536 AGCTATACCG
* *
28677546 ATCAGGCACTTTATGTGTCGTATTTCAGGCACCTCATGTGTTGT
1 ATCAGGCACCTCATGTGTCGT-TTT-AGGCACCTCATGTGTTGT
* * *
28677590 ATCAGGCACCTCGTGTGTCGTTTTAGGCACTTTATGTGT
1 ATCAGGCACCTCATGTGTCGTTTTAGGCACCTCATGTGT
28677629 CATATCTGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 13 0.38
43 3 0.09
44 18 0.53
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (42 bp):
ATCAGGCACCTCATGTGTCGTTTTAGGCACCTCATGTGTTGT
Found at i:28681635 original size:39 final size:39
Alignment explanation
Indices: 28681543--28681752 Score: 303
Period size: 39 Copynumber: 5.4 Consensus size: 39
28681533 CCTTTGGACA
* ** * ** *
28681543 TAGCCCGGTTATGGTAACCCGCACAAAAGCCTTAGGGACT
1 TAGCCCGGATATCATAACTCGCACAATTGCCTTCGGG-CT
* * * *
28681583 TAACCCGGATATCACAATTTGCACAATTGCCTTCGGGCT
1 TAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCT
*
28681622 TAGCCCGGATATCATAACTCGCCCAATTGCCTTCGGGCT
1 TAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCT
28681661 TAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCT
1 TAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCT
28681700 TAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCT
1 TAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCT
28681739 TAGCCCGGATATCA
1 TAGCCCGGATATCA
28681753 CTCGAACATT
Statistics
Matches: 153, Mismatches: 17, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 127 0.83
40 26 0.17
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.25
Consensus pattern (39 bp):
TAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCT
Found at i:28689576 original size:77 final size:78
Alignment explanation
Indices: 28689423--28689644 Score: 320
Period size: 77 Copynumber: 2.8 Consensus size: 78
28689413 TCGTTCAAAC
* * ** * ** *
28689423 GCCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATC
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGG-CTTAGCCCGGATATC
* *
28689488 ACAATTTGCACAATT
64 ACAACTCGCACAATT
*
28689503 GCCTTCGGGCTTAGCCCGGATATCATAACTCGC-CAATTGCCTTCGGGCTTAGCCCGGATATCAT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
28689567 AACTCGCACAATT
66 AACTCGCACAATT
28689580 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
28689645 TCGAACATTC
Statistics
Matches: 129, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
77 59 0.46
78 42 0.33
79 19 0.15
80 9 0.07
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24
Consensus pattern (78 bp):
GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
AACTCGCACAATT
Found at i:28689590 original size:39 final size:39
Alignment explanation
Indices: 28689423--28689643 Score: 318
Period size: 39 Copynumber: 5.6 Consensus size: 39
28689413 TCGTTCAAAC
* * ** * **
28689423 GCCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAAG
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
* * * *
28689463 GCCTTCGGGACTTAACCCGGATATCACAATTTGCACAATT
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
28689503 GCCTTCGGGCTTAGCCCGGATATCATAACTCGC-CAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
28689541 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
28689580 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
28689619 GCCTTCGGGCTTAGCCCGGATATCA
1 GCCTTCGGGCTTAGCCCGGATATCA
28689644 CTCGAACATT
Statistics
Matches: 165, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
38 38 0.23
39 89 0.54
40 38 0.23
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.24
Consensus pattern (39 bp):
GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
Found at i:28689623 original size:116 final size:118
Alignment explanation
Indices: 28689423--28689643 Score: 329
Period size: 116 Copynumber: 1.9 Consensus size: 118
28689413 TCGTTCAAAC
* **
28689423 GCCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATC
1 GCCTTCGGGACATAGCCCGGATATCATAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATC
* *
28689488 ACAATTTGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAACTCGCCAATT
66 ACAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAACTCGCCAATT
* * ** *
28689541 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGG-CTTAGCCCGGATATC
1 GCCTTCGGGACATAGCCCGGATATCATAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATC
*
28689604 ATAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCA
66 ACAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCA
28689644 CTCGAACATT
Statistics
Matches: 92, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
116 51 0.55
117 32 0.35
118 9 0.10
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.24
Consensus pattern (118 bp):
GCCTTCGGGACATAGCCCGGATATCATAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATC
ACAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAACTCGCCAATT
Found at i:28692508 original size:40 final size:40
Alignment explanation
Indices: 28692451--28692656 Score: 265
Period size: 40 Copynumber: 5.2 Consensus size: 40
28692441 GAATGATACT
* *
28692451 CGGGCTAAG-CCCGAAGGCATTTATGCTAG-TGATTATATC
1 CGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATATC
*
28692490 CGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATC
1 CGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATATC
* *
28692530 CGAGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATATC
1 CGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATATC
* * *
28692570 CGGGCTAAGACCCAAAGGCATTTGTGCGAGTTGCTATACC
1 CGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATATC
* * ** *
28692610 CGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATATC
1 CGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATATC
28692650 C-GGCTAA
1 CGGGCTAA
28692657 ATTCCGAAGA
Statistics
Matches: 145, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
39 14 0.10
40 129 0.89
41 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
CGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATATC
Found at i:28692593 original size:80 final size:80
Alignment explanation
Indices: 28692456--28692656 Score: 300
Period size: 80 Copynumber: 2.5 Consensus size: 80
28692446 ATACTCGGGC
* *
28692456 TAAG-CCCGAAGGCATTTATGCTAG-TGATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA
1 TAAGACCCGAAGGCATTTGTGCTAGTTG-TTATATCCGGGCTAAGACCCAAAGGCATTTGTGCGA
*
28692519 GTTGCTATATCCGAGT
65 GTTGCTATACCCGAGT
*
28692535 TAAGACCCGAAGGCATTTGTGCGAGTTGTTATATCCGGGCTAAGACCCAAAGGCATTTGTGCGAG
1 TAAGACCCGAAGGCATTTGTGCTAGTTGTTATATCCGGGCTAAGACCCAAAGGCATTTGTGCGAG
*
28692600 TTGCTATACCCGGGT
66 TTGCTATACCCGAGT
* * *
28692615 TAAGACCCGAAGGCAATTGTGCTTGTGGTTATATCC-GGCTAA
1 TAAGACCCGAAGGCATTTGTGCTAGTTGTTATATCCGGGCTAA
28692657 ATTCCGAAGA
Statistics
Matches: 111, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
79 10 0.09
80 99 0.89
81 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (80 bp):
TAAGACCCGAAGGCATTTGTGCTAGTTGTTATATCCGGGCTAAGACCCAAAGGCATTTGTGCGAG
TTGCTATACCCGAGT
Found at i:28696355 original size:28 final size:28
Alignment explanation
Indices: 28696294--28696391 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 28
28696284 TCACAAATTG
** * *
28696294 GCACTAAGTGTGCGGGTTCAAATTATACA
1 GCACTAAGTGTGCAAGTTC-GATTATATA
*
28696323 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCAAGTTCGATTATATA
* *
28696351 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCAAGTTCGATTATAT-A
28696379 GCACTAAGTGTGC
1 GCACTAAGTGTGC
28696392 GGGCTTATGG
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.02
28 43 0.72
29 16 0.27
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCAAGTTCGATTATATA
Found at i:28699539 original size:29 final size:29
Alignment explanation
Indices: 28699507--28699638 Score: 237
Period size: 29 Copynumber: 4.5 Consensus size: 29
28699497 ATAGTGAATC
28699507 CGCACACTTAGTGCTATATATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAGCT
28699536 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATAT-ATTTTCAGCT
*
28699566 CGCACACTTAGTGCTATATATTTTCAGTT
1 CGCACACTTAGTGCTATATATTTTCAGCT
*
28699595 CGCACACTTAGTGCTATATATTTTCAGTT
1 CGCACACTTAGTGCTATATATTTTCAGCT
28699624 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28699639 GTACAATTTT
Statistics
Matches: 101, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
29 72 0.71
30 29 0.29
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.38
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATATTTTCAGCT
Found at i:28699648 original size:59 final size:59
Alignment explanation
Indices: 28699507--28699638 Score: 239
Period size: 59 Copynumber: 2.3 Consensus size: 59
28699497 ATAGTGAATC
28699507 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
* *
28699566 CGCACACTTAGTGCTATATATTTTCAGTTCGCACACTTAGTGCTATAT-ATTTTCAGTT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
28699624 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28699639 GTACAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
58 24 0.34
59 47 0.66
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.38
Consensus pattern (59 bp):
CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
Found at i:28704810 original size:29 final size:29
Alignment explanation
Indices: 28704786--28704879 Score: 179
Period size: 29 Copynumber: 3.2 Consensus size: 29
28704776 TCGCACACCC
*
28704786 AGTGCCGTATATTTCCAGCATGCACACTT
1 AGTGCCATATATTTCCAGCATGCACACTT
28704815 AGTGCCATATATTTCCAGCATGCACACTT
1 AGTGCCATATATTTCCAGCATGCACACTT
28704844 AGTGCCATATATTTCCAGCATGCACACTT
1 AGTGCCATATATTTCCAGCATGCACACTT
28704873 AGTGCCA
1 AGTGCCA
28704880 ATCTCGTCAC
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 64 1.00
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.30
Consensus pattern (29 bp):
AGTGCCATATATTTCCAGCATGCACACTT
Found at i:28704818 original size:58 final size:58
Alignment explanation
Indices: 28704751--28704879 Score: 170
Period size: 58 Copynumber: 2.2 Consensus size: 58
28704741 TTAAGCCCGA
* * * *
28704751 ACACATAGTGCCATACCCTTCGAGC-TCGCACACCCAGTGCCGTATATTTCCAGCATGC
1 ACACTTAGTGCCATACACTTCCAGCAT-GCACACCCAGTGCCATATATTTCCAGCATGC
* * **
28704809 ACACTTAGTGCCATATATTTCCAGCATGCACACTTAGTGCCATATATTTCCAGCATGC
1 ACACTTAGTGCCATACACTTCCAGCATGCACACCCAGTGCCATATATTTCCAGCATGC
28704867 ACACTTAGTGCCA
1 ACACTTAGTGCCA
28704880 ATCTCGTCAC
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
58 61 0.98
59 1 0.02
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (58 bp):
ACACTTAGTGCCATACACTTCCAGCATGCACACCCAGTGCCATATATTTCCAGCATGC
Found at i:28712772 original size:29 final size:29
Alignment explanation
Indices: 28712682--28712865 Score: 228
Period size: 29 Copynumber: 6.3 Consensus size: 29
28712672 ACTCGATTTC
* * **
28712682 GCACACTTAGTGCCATGTGATTT-AAGCCC
1 GCACACTTAGTGCCATAT-ATTTCCAGCAT
* *** *
28712711 GCACACATAGTGCCATACCCTTCGAGC-T
1 GCACACTTAGTGCCATATATTTCCAGCAT
** *
28712739 CGCACACCCAGTGCCGTATATTTCCAGCAT
1 -GCACACTTAGTGCCATATATTTCCAGCAT
28712769 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
28712798 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
28712827 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
28712856 GCACACTTAG
1 GCACACTTAG
28712866 CCAATGTCGT
Statistics
Matches: 135, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
28 2 0.01
29 132 0.98
30 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.27
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:28715075 original size:29 final size:29
Alignment explanation
Indices: 28714985--28715144 Score: 180
Period size: 29 Copynumber: 5.5 Consensus size: 29
28714975 ACTCGATTTC
* * **
28714985 GCACACTTAGTGCCATGTGATTT-AAGCCC
1 GCACACTTAGTGCCATAT-ATTTCCAGCAT
* *** *
28715014 GCACACATAGTGCCATACCCTTCGAGC-T
1 GCACACTTAGTGCCATATATTTCCAGCAT
** *
28715042 CGCACACCCAGTGCCGTATATTTCCAGCAT
1 -GCACACTTAGTGCCATATATTTCCAGCAT
28715072 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
28715101 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
28715130 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
28715145 ATCTCGTCAC
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.02
29 108 0.97
30 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:28720724 original size:40 final size:39
Alignment explanation
Indices: 28720680--28720827 Score: 163
Period size: 40 Copynumber: 3.7 Consensus size: 39
28720670 TAATCCACAA
* * *** *
28720680 GCACAATTGCCTTCGGGTCTTAACCCGGATTTGGTAACTT
1 GCACAA-TGCCTTCGGGTCTTAGCCCGGATATAACAACTC
28720720 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAACAACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATATAACAACTC
*
28720760 GCACGAATGCCTTCGGGTCTTAGCCCGGATATAATC-ACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATATAA-CAACTC
* *
28720800 GCATAAATGCCTTCGGGACTTAGCCCGG
1 GCA-CAATGCCTTCGGGTCTTAGCCCGG
28720828 GTATCATTCA
Statistics
Matches: 95, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
40 92 0.97
41 3 0.03
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.26
Consensus pattern (39 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATATAACAACTC
Found at i:28728776 original size:40 final size:40
Alignment explanation
Indices: 28728731--28728879 Score: 190
Period size: 40 Copynumber: 3.7 Consensus size: 40
28728721 ATAATCCACA
* * * *
28728731 AGCACAATTGCCTTCGGGTCTTAACCCGGATTTGGTAACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATATGATAACT
* * *
28728771 TGCACAAATGCCTTCGGGTCTTAGCCCGGATATAACAACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATATGATAACT
* * *
28728811 CGCACGAATGCCTTCGGGTCTTAGCCCGGATATGATCACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATATGATAACT
* *
28728851 AGCATAAATGCCTTCGGGACTTAGCCCGG
1 AGCACAAATGCCTTCGGGTCTTAGCCCGG
28728880 GTATCATTCA
Statistics
Matches: 93, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 93 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (40 bp):
AGCACAAATGCCTTCGGGTCTTAGCCCGGATATGATAACT
Found at i:28731287 original size:46 final size:46
Alignment explanation
Indices: 28731186--28731310 Score: 150
Period size: 46 Copynumber: 2.7 Consensus size: 46
28731176 CATTTTGAGA
*
28731186 GCTAGTGTAAGACCATGTCTGGGACATGGAATCGACACTGAGACGAGT
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGACACTGAGACGAGT
* *
28731234 GCTAGTGTAAGACATATCTGGGACATGCTTCGAC-CTTGAGACGTAAG-
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGACAC-TGAGACG--AGT
28731281 GC-AGTGTAAGA-ATGTCTGGGACATGCATCG
1 GCTAGTGTAAGACATGTCTGGGACATGCATCG
28731311 GCTACGAGAT
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
45 18 0.26
46 22 0.32
47 15 0.22
48 14 0.20
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.23
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGACACTGAGACGAGT
Found at i:28733982 original size:8 final size:8
Alignment explanation
Indices: 28733969--28734016 Score: 51
Period size: 8 Copynumber: 6.0 Consensus size: 8
28733959 TCAGTTTTTT
28733969 GGCATTTC
1 GGCATTTC
28733977 GGCATTTC
1 GGCATTTC
* *
28733985 AGCTTTTC
1 GGCATTTC
*
28733993 GGCATTTT
1 GGCATTTC
* *
28734001 AGCTTTTC
1 GGCATTTC
28734009 GGCATTTC
1 GGCATTTC
28734017 TGCTTTTGCC
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (8 bp):
GGCATTTC
Found at i:28733992 original size:16 final size:16
Alignment explanation
Indices: 28733973--28734023 Score: 84
Period size: 16 Copynumber: 3.2 Consensus size: 16
28733963 TTTTTTGGCA
28733973 TTTCGGCATTTCAGCT
1 TTTCGGCATTTCAGCT
*
28733989 TTTCGGCATTTTAGCT
1 TTTCGGCATTTCAGCT
*
28734005 TTTCGGCATTTCTGCT
1 TTTCGGCATTTCAGCT
28734021 TTT
1 TTT
28734024 GCCGATACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.10, C:0.22, G:0.18, T:0.51
Consensus pattern (16 bp):
TTTCGGCATTTCAGCT
Found at i:28734008 original size:24 final size:24
Alignment explanation
Indices: 28733957--28734008 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
28733947 GTAGCCAAAC
* * *
28733957 TTTCAGTTTTTTGGCATTTCGGCA
1 TTTCAGCTTTTCGGCATTTCAGCA
* *
28733981 TTTCAGCTTTTCGGCATTTTAGCT
1 TTTCAGCTTTTCGGCATTTCAGCA
28734005 TTTC
1 TTTC
28734009 GGCATTTCTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.19, G:0.17, T:0.52
Consensus pattern (24 bp):
TTTCAGCTTTTCGGCATTTCAGCA
Found at i:28736513 original size:40 final size:40
Alignment explanation
Indices: 28736447--28736613 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
28736437 AAATTGAATG
* * *
28736447 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
28736486 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
28736526 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
28736566 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
28736606 ATATCCGG
1 ATATCCGG
28736614 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:28744511 original size:40 final size:40
Alignment explanation
Indices: 28744445--28744611 Score: 160
Period size: 40 Copynumber: 4.2 Consensus size: 40
28744435 AAATTGAATG
* * * *
28744445 ATATCCGGGCTAA-TCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
28744484 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
28744524 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
28744564 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
28744604 ATATCCGG
1 ATATCCGG
28744612 TTATATTCCG
Statistics
Matches: 104, Mismatches: 19, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
39 15 0.14
40 87 0.84
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:28746491 original size:29 final size:29
Alignment explanation
Indices: 28746458--28746544 Score: 133
Period size: 29 Copynumber: 3.1 Consensus size: 29
28746448 TTATATTCAC
*
28746458 ATGGCTCATTAGGCCCACATCACATTTAT
1 ATGGCTCATTAGGCCCAAATCACATTTAT
* *
28746487 ATGGCTCTTTAGGCCTAAATCACATTTAT
1 ATGGCTCATTAGGCCCAAATCACATTTAT
28746516 ATGGC-CATTAGGCCCAAATCACA-TTAT
1 ATGGCTCATTAGGCCCAAATCACATTTAT
28746543 AT
1 AT
28746545 TCATGCTCAC
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
27 6 0.11
28 16 0.30
29 31 0.58
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (29 bp):
ATGGCTCATTAGGCCCAAATCACATTTAT
Found at i:28747613 original size:539 final size:539
Alignment explanation
Indices: 28746596--28747673 Score: 2030
Period size: 539 Copynumber: 2.0 Consensus size: 539
28746586 CAATTTTTGG
*
28746596 CCTATTATGGGCCCAACAGCCCATCGGGCCCATTAAGCCTATTCTGACCCAGTTGGCCAATTCAT
1 CCTATTATGGGCCCAACAGCCCATCAGGCCCATTAAGCCTATTCTGACCCAGTTGGCCAATTCAT
**
28746661 AGCCCAAGTCCATGGAGTCGCCCATGGGCTGCAGATAACCTACCAGTTTTCTCCTCACGAGTGTT
66 AGCCCAAGTCCATGGAGTCGCCCATGGGCCACAGATAACCTACCAGTTTTCTCCTCACGAGTGTT
*
28746726 TACGCACGTGAAAGACTATCATAGCCAAACTTTCGGCTTTTCGGCATTTCGGCTTTTGCCAATCT
131 TACGCACGTGAAAGACTATCATAGCCAAACTTTCAGCTTTTCGGCATTTCGGCTTTTGCCAATCT
*
28746791 ATTTGTATGTGCAGTGTATGTACACACCTAGTAAGCAAGTGTGCTATGATTCCCTTAGTCACCAA
196 ACTTGTATGTGCAGTGTATGTACACACCTAGTAAGCAAGTGTGCTATGATTCCCTTAGTCACCAA
28746856 CCTACAAAAGATATCACCCTTCAATTAATCGTATGCTTAATATATATTTTAGCCAAAAACCGAAA
261 CCTACAAAAGATATCACCCTTCAATTAATCGTATGCTTAATATATATTTTAGCCAAAAACCGAAA
*
28746921 CCTCACCTTAACCTTATCTTGAGTACCAATCCCTAATAGCTTTTCCTAGATCACGTACTCCCTAG
326 CCTCACCTTAACCTTATCTTGAGCACCAATCCCTAATAGCTTTTCCTAGATCACGTACTCCCTAG
28746986 ATCTGCATTAATCTTACCCATTAAAACCAAATACTAGGGGACTAGCATCCAACATAATTCACCCC
391 ATCTGCATTAATCTTACCCATTAAAACCAAATACTAGGGGACTAGCATCCAACATAATTCACCCC
28747051 CTTATCTCACTTAAGACCATTCGGCCAACCTTAGCCAATAAGAGAGAAATACTTACCAAAACTGC
456 CTTATCTCACTTAAGACCATTCGGCCAACCTTAGCCAATAAGAGAGAAATACTTACCAAAACTGC
28747116 AAAACACCTAAGGAACAAT
521 AAAACACCTAAGGAACAAT
*
28747135 CCTATTATGGGCCCAACAGCCCATCAGGCCCATTAAGCCTATTCTGGCCCAGTTGGCCAATTCAT
1 CCTATTATGGGCCCAACAGCCCATCAGGCCCATTAAGCCTATTCTGACCCAGTTGGCCAATTCAT
28747200 AGCCCAAGTCCATGGAGTCGCCCATGGGCCACAGATAACCTACCAGTTTTCTCCTCACGAGTGTT
66 AGCCCAAGTCCATGGAGTCGCCCATGGGCCACAGATAACCTACCAGTTTTCTCCTCACGAGTGTT
*
28747265 TACGCACGTGCAAGACTATCATAGCCAAACTTTCAGCTTTTCGGCATTTCGGCTTTTGCCAATCT
131 TACGCACGTGAAAGACTATCATAGCCAAACTTTCAGCTTTTCGGCATTTCGGCTTTTGCCAATCT
*
28747330 ACTTGTGTGTGCAGTGTATGTACACACCTAGTAAGCAAGTGTGCTATGATTCCCTTAGTCACCAA
196 ACTTGTATGTGCAGTGTATGTACACACCTAGTAAGCAAGTGTGCTATGATTCCCTTAGTCACCAA
*
28747395 CCTACAAAAGATATCACCCTTCAATTAATCGTATGCTTAATATATATTTTAGCCAAAAACTGAAA
261 CCTACAAAAGATATCACCCTTCAATTAATCGTATGCTTAATATATATTTTAGCCAAAAACCGAAA
*
28747460 CCTCACCTTAACTTTATCTTGAGCACCAATCCCTAATAGCTTTTCCTAGATCACGTACTCCCTAG
326 CCTCACCTTAACCTTATCTTGAGCACCAATCCCTAATAGCTTTTCCTAGATCACGTACTCCCTAG
28747525 ATCTGCATTAATCTTACCCATTAAAACCAAATACTAGGGGACTAGCATCCAACATAATTCACCCC
391 ATCTGCATTAATCTTACCCATTAAAACCAAATACTAGGGGACTAGCATCCAACATAATTCACCCC
*
28747590 CTTATCTCACTTGAGACCATTCGGCCAACCTTAGCCAATAAGAGAGAAATACTTACCAAAACTGC
456 CTTATCTCACTTAAGACCATTCGGCCAACCTTAGCCAATAAGAGAGAAATACTTACCAAAACTGC
* *
28747655 AAAACACTTAAGGAGCAAT
521 AAAACACCTAAGGAACAAT
28747674 TTCGGCAGAG
Statistics
Matches: 525, Mismatches: 14, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
539 525 1.00
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (539 bp):
CCTATTATGGGCCCAACAGCCCATCAGGCCCATTAAGCCTATTCTGACCCAGTTGGCCAATTCAT
AGCCCAAGTCCATGGAGTCGCCCATGGGCCACAGATAACCTACCAGTTTTCTCCTCACGAGTGTT
TACGCACGTGAAAGACTATCATAGCCAAACTTTCAGCTTTTCGGCATTTCGGCTTTTGCCAATCT
ACTTGTATGTGCAGTGTATGTACACACCTAGTAAGCAAGTGTGCTATGATTCCCTTAGTCACCAA
CCTACAAAAGATATCACCCTTCAATTAATCGTATGCTTAATATATATTTTAGCCAAAAACCGAAA
CCTCACCTTAACCTTATCTTGAGCACCAATCCCTAATAGCTTTTCCTAGATCACGTACTCCCTAG
ATCTGCATTAATCTTACCCATTAAAACCAAATACTAGGGGACTAGCATCCAACATAATTCACCCC
CTTATCTCACTTAAGACCATTCGGCCAACCTTAGCCAATAAGAGAGAAATACTTACCAAAACTGC
AAAACACCTAAGGAACAAT
Found at i:28749937 original size:46 final size:46
Alignment explanation
Indices: 28749817--28749939 Score: 210
Period size: 46 Copynumber: 2.7 Consensus size: 46
28749807 AACCCGCCCC
* *
28749817 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCA
28749863 TAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCA
**
28749909 TAAGTGAACTCATACTCAACTCAACGAGTTC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC
28749940 GAATGCTCAA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 73 1.00
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCA
Found at i:28749961 original size:46 final size:46
Alignment explanation
Indices: 28749817--28749953 Score: 170
Period size: 46 Copynumber: 3.0 Consensus size: 46
28749807 AACCCGCCCC
* * * * *
28749817 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCA
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCAGACATGCGCAACCA
* * *
28749863 TAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCA
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCAGACATGCGCAACCA
* *
28749909 TAAGTGAACTCATACTCAACTCAACGAGTTC-GA-ATGCTCAACCA
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCAGACATGCGCAACCA
28749953 T
1 T
28749954 CCTAGTGACA
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
44 9 0.11
45 2 0.02
46 73 0.87
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCAGACTCAACTCAACGAGTTCAGACATGCGCAACCA
Found at i:28752448 original size:20 final size:21
Alignment explanation
Indices: 28752410--28752448 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28752400 GAATTAATTT
28752410 CACACGGGCATGCTGCCCTTC
1 CACACGGGCATGCTGCCCTTC
*
28752431 CACACGGGCGTG-TGCCCT
1 CACACGGGCATGCTGCCCT
28752449 GTTTCAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.13, C:0.41, G:0.28, T:0.18
Consensus pattern (21 bp):
CACACGGGCATGCTGCCCTTC
Found at i:28755877 original size:26 final size:26
Alignment explanation
Indices: 28755848--28755925 Score: 66
Period size: 26 Copynumber: 2.9 Consensus size: 26
28755838 AACCTTAACC
*
28755848 CTAGAGGTATATCAGTAATTTTACTT
1 CTAGAGGTATATCAGTAATTTTACCT
* * *
28755874 CTAGGGGTAAATCTGTAAATTTTCCACCT
1 CTAGAGGTATATCAGT-AATTTT--ACCT
* * *
28755903 ATAAAGGTATTTCAGTAATTTTA
1 CTAGAGGTATATCAGTAATTTTA
28755926 TTAGTTTTAA
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
26 14 0.36
27 6 0.15
28 6 0.15
29 13 0.33
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (26 bp):
CTAGAGGTATATCAGTAATTTTACCT
Found at i:28758272 original size:45 final size:44
Alignment explanation
Indices: 28758162--28758277 Score: 137
Period size: 45 Copynumber: 2.6 Consensus size: 44
28758152 TGTGTGAACT
*
28758162 AGTGTAAGA-CATGTCTGGGACATGCATCGGCCACATTTTGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGCATCGGCCACA---TGAGAGCC
* * *
28758208 AGTGTAAGACTATGTCTGGGACATGCATCGGCTACGA-GATGTGCC
1 AGTGTAAGACCATGTCTGGGACATGCATCGGCCAC-ATGA-GAGCC
28758253 AGTGTAAGACCATGTCTGGGACATG
1 AGTGTAAGACCATGTCTGGGACATG
28758278 GCAATGACAC
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
44 2 0.03
45 27 0.44
46 9 0.15
47 23 0.37
48 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (44 bp):
AGTGTAAGACCATGTCTGGGACATGCATCGGCCACATGAGAGCC
Found at i:28765313 original size:47 final size:47
Alignment explanation
Indices: 28765248--28765378 Score: 163
Period size: 47 Copynumber: 2.8 Consensus size: 47
28765238 GGTGTGAATA
* * * * *
28765248 ATACCTTAATTTGGCTACGGGCCATGATATAAGTATTTTGAGAGGAG
1 ATACCTTGATTTGGCTACGGGCCATGGTATAAGTACTCTGAGAGAAG
* * * * *
28765295 TTACCTTGATTTGACTACGGGCCATGGTATAGGTACTCTGGGATAAG
1 ATACCTTGATTTGGCTACGGGCCATGGTATAAGTACTCTGAGAGAAG
*
28765342 ATACCTTGATTTGGCTATGGGCCATGGTATAAGTACT
1 ATACCTTGATTTGGCTACGGGCCATGGTATAAGTACT
28765379 TACCAATTTT
Statistics
Matches: 70, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
47 70 1.00
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (47 bp):
ATACCTTGATTTGGCTACGGGCCATGGTATAAGTACTCTGAGAGAAG
Found at i:28767405 original size:7 final size:7
Alignment explanation
Indices: 28767393--28767423 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
28767383 GTTGTTAAAT
28767393 GATGAAA
1 GATGAAA
28767400 GATGAAA
1 GATGAAA
28767407 GATGAAA
1 GATGAAA
*
28767414 AATGAAA
1 GATGAAA
28767421 GAT
1 GAT
28767424 ATGTGATAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.26, T:0.16
Consensus pattern (7 bp):
GATGAAA
Found at i:28768994 original size:31 final size:30
Alignment explanation
Indices: 28768950--28769028 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 30
28768940 TTTAACGGTT
28768950 ACTGGGCGTAAGCCTTTTCATAAATCATATC
1 ACTGGGCG-AAGCCTTTTCATAAATCATATC
*
28768981 ACTGGGCTGAAGCCTTTTCATAAATCATTTC
1 ACTGGGC-GAAGCCTTTTCATAAATCATATC
28769012 ACTGGGCCGAAGCCTTT
1 ACTGGG-CGAAGCCTTT
28769029 ACTATAAACG
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
31 43 0.96
32 2 0.04
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (30 bp):
ACTGGGCGAAGCCTTTTCATAAATCATATC
Found at i:28769110 original size:43 final size:43
Alignment explanation
Indices: 28769062--28769144 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
28769052 GCTCATTTAA
* ** * *
28769062 ATATCACATGTAATGTCAATGGATGTATGCAAGCCCATTTCAT
1 ATATCACATGAAATACCAATGAATGTAGGCAAGCCCATTTCAT
* *
28769105 ATATCATATGAAATACCAATGAATGTAGGCAGGCCCATTT
1 ATATCACATGAAATACCAATGAATGTAGGCAAGCCCATTT
28769145 GGGGAGACTA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (43 bp):
ATATCACATGAAATACCAATGAATGTAGGCAAGCCCATTTCAT
Found at i:28769361 original size:26 final size:26
Alignment explanation
Indices: 28769277--28769438 Score: 251
Period size: 26 Copynumber: 6.3 Consensus size: 26
28769267 CTAGAGGCCT
28769277 AGCCTCTTTT-AAT-AACTGGGGCA-A
1 AGCC-CTTTTCAATAAACTGGGGCATA
**
28769301 AGCCCTTTTCGGTAAACTGGGGCA-A
1 AGCCCTTTTCAATAAACTGGGGCATA
28769326 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
*
28769352 AGCCCTTTTCGATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
28769378 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
*
28769404 AGCCCTTTTCAATAAACTAGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
28769430 AGCCCTTTT
1 AGCCCTTTT
28769439 GCACTTCCTC
Statistics
Matches: 128, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
23 5 0.04
24 5 0.04
25 33 0.26
26 85 0.66
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.28
Consensus pattern (26 bp):
AGCCCTTTTCAATAAACTGGGGCATA
Found at i:28769513 original size:20 final size:20
Alignment explanation
Indices: 28769488--28769574 Score: 131
Period size: 20 Copynumber: 4.3 Consensus size: 20
28769478 TTATGAATAC
28769488 ATCATGTGCATTTCATACAT
1 ATCATGTGCATTTCATACAT
28769508 ATCATGTGCATTTCATACAT
1 ATCATGTGCATTTCATACAT
* *
28769528 ATCATGTGAATTTTATACAT
1 ATCATGTGCATTTCATACAT
*
28769548 ATCATGTGCATATCATATCA-
1 ATCATGTGCATTTCATA-CAT
28769568 ATCATGT
1 ATCATGT
28769575 ATATCATATC
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
20 59 0.97
21 2 0.03
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.40
Consensus pattern (20 bp):
ATCATGTGCATTTCATACAT
Found at i:28770320 original size:27 final size:27
Alignment explanation
Indices: 28770259--28770322 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
28770249 GGCGTATTCA
28770259 TCATTTTACCATACAAGGGTATTACGG
1 TCATTTTACCATACAAGGGTATTACGG
* * *
28770286 TCACTTTACCCTACAGGGGCT-TTACGG
1 TCATTTTACCATACAAGGG-TATTACGG
*
28770313 TCTTTTTACC
1 TCATTTTACC
28770323 TATTAGGGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (27 bp):
TCATTTTACCATACAAGGGTATTACGG
Found at i:28770488 original size:27 final size:27
Alignment explanation
Indices: 28770361--28770630 Score: 129
Period size: 27 Copynumber: 10.0 Consensus size: 27
28770351 TACAATGGTG
* * *
28770361 TTTTGGTAAATCTACAAATCAAGGGTA
1 TTTTGGTAATTTTACAAATCAGGGGTA
** **
28770388 TTTT-GTAATTTTGTAAATCAATGGTA
1 TTTTGGTAATTTTACAAATCAGGGGTA
*** * *
28770414 TTTCCATAATTTTTAGAAAGTCAAGGGTA
1 TTTTGGTAA-TTTTACAAA-TCAGGGGTA
* **
28770443 TTTCT-GTAACTTTGTAAATCAGGGGTA
1 TTT-TGGTAATTTTACAAATCAGGGGTA
* * *
28770470 CTTTGGTAATTTTACAAATTAAGGGTA
1 TTTTGGTAATTTTACAAATCAGGGGTA
** * * *
28770497 TTTCAGTAATTTCACAAACCAGTGGTA
1 TTTTGGTAATTTTACAAATCAGGGGTA
*
28770524 TTTTGGTAATTTTACAAA-CTAGGGGTG
1 TTTTGGTAATTTTACAAATC-AGGGGTA
* **
28770551 TTTTGGTAATTCTACCCTAT-AGGGGTA
1 TTTTGGTAATTTTA-CAAATCAGGGGTA
** *
28770578 TTTCAGTAATTTCAC-AATC-GAGGGTA
1 TTTTGGTAATTTTACAAATCAG-GGGTA
*** * *
28770604 AAATGGTAATTTTATAAATCAAGGGTA
1 TTTTGGTAATTTTACAAATCAGGGGTA
28770631 AAATAGTAAT
Statistics
Matches: 179, Mismatches: 52, Indels: 24
0.70 0.20 0.09
Matches are distributed among these distances:
25 3 0.02
26 36 0.20
27 111 0.62
28 15 0.08
29 14 0.08
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (27 bp):
TTTTGGTAATTTTACAAATCAGGGGTA
Found at i:28770529 original size:54 final size:54
Alignment explanation
Indices: 28770329--28770541 Score: 162
Period size: 54 Copynumber: 3.9 Consensus size: 54
28770319 TACCTATTAG
* ** * * *
28770329 GGGTATTTCAGTCATTTCATCCTA-CAATGGTGTTTTGGTAAATCTACAAATCAA
1 GGGTATTTCAGTAATTTCA-CAAATCAATGGTATTTTGGTAATTTTACAAATCAA
* *** *** *
28770383 GGGTATTT-TGTAATTTTGTAAATCAATGGTATTTCCATAATTTTTAGAAAGTCAA
1 GGGTATTTCAGTAATTTCACAAATCAATGGTATTTTGGTAA-TTTTACAAA-TCAA
* ** ** * *
28770438 GGGTATTTCTGTAACTTT-GTAAATCAGGGGTACTTTGGTAATTTTACAAATTAA
1 GGGTATTTCAGTAA-TTTCACAAATCAATGGTATTTTGGTAATTTTACAAATCAA
* *
28770492 GGGTATTTCAGTAATTTCACAAACCAGTGGTATTTTGGTAATTTTACAAA
1 GGGTATTTCAGTAATTTCACAAATCAATGGTATTTTGGTAATTTTACAAA
28770542 CTAGGGGTGT
Statistics
Matches: 125, Mismatches: 28, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
52 1 0.01
53 22 0.18
54 57 0.46
55 20 0.16
56 22 0.18
57 3 0.02
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (54 bp):
GGGTATTTCAGTAATTTCACAAATCAATGGTATTTTGGTAATTTTACAAATCAA
Found at i:28770631 original size:27 final size:27
Alignment explanation
Indices: 28770593--28770793 Score: 145
Period size: 27 Copynumber: 7.4 Consensus size: 27
28770583 GTAATTTCAC
*
28770593 AATCGAGGGTAAAATGGTAATTTTATA
1 AATCGAGGGTAAAATAGTAATTTTATA
* * *
28770620 AATCAAGGGTAAAATAGTAATTCTGTA
1 AATCGAGGGTAAAATAGTAATTTTATA
* * *
28770647 AATCGAGGGTAAAACAGTAGTATTATA
1 AATCGAGGGTAAAATAGTAATTTTATA
*** *
28770674 AATCGAGGGTACTTTGGTAATTTT-TA
1 AATCGAGGGTAAAATAGTAATTTTATA
*** *
28770700 CAAGTCGAGGGTATTTTAGTAATTTTACA
1 -AA-TCGAGGGTAAAATAGTAATTTTATA
* *** *
28770729 AA-CCAGCGGTATTTTAGTAATTTTGTA
1 AATCGAG-GGTAAAATAGTAATTTTATA
* * *
28770756 AATCGGGGGTAAAACAGTAATTATATA
1 AATCGAGGGTAAAATAGTAATTTTATA
*
28770783 AATTGAGGGTA
1 AATCGAGGGTA
28770794 CTTTGGTAAT
Statistics
Matches: 136, Mismatches: 33, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
26 5 0.04
27 106 0.78
28 24 0.18
29 1 0.01
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.33
Consensus pattern (27 bp):
AATCGAGGGTAAAATAGTAATTTTATA
Found at i:28770694 original size:54 final size:53
Alignment explanation
Indices: 28770593--28770811 Score: 188
Period size: 54 Copynumber: 4.0 Consensus size: 53
28770583 GTAATTTCAC
** * ***
28770593 AATCGAGGGTAAAATGGTAATTTTATAAATCAAGGGTAAAATAGTAATTCTGTA
1 AATCGAGGGTAAAACAGTAATTTTATAAATCGAGGGTACTTTAGTAATT-TGTA
* * * *
28770647 AATCGAGGGTAAAACAGTAGTATTATAAATCGAGGGTACTTTGGTAATTTTTA
1 AATCGAGGGTAAAACAGTAATTTTATAAATCGAGGGTACTTTAGTAATTTGTA
**** * * *
28770700 CAAGTCGAGGGTATTTTAGTAATTTTACAAA-CCAGCGGTATTTTAGTAATTTTGTA
1 -AA-TCGAGGGTAAAACAGTAATTTTATAAATCGAG-GGTACTTTAGTAA-TTTGTA
* * * *
28770756 AATCGGGGGTAAAACAGTAATTATATAAATTGAGGGTACTTTGGTAATTTGGTA
1 AATCGAGGGTAAAACAGTAATTTTATAAATCGAGGGTACTTTAGTAATTT-GTA
28770810 AA
1 AA
28770812 CTAAAGTATT
Statistics
Matches: 127, Mismatches: 32, Indels: 12
0.74 0.19 0.07
Matches are distributed among these distances:
53 6 0.05
54 81 0.64
55 35 0.28
56 5 0.04
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (53 bp):
AATCGAGGGTAAAACAGTAATTTTATAAATCGAGGGTACTTTAGTAATTTGTA
Found at i:28775550 original size:15 final size:15
Alignment explanation
Indices: 28775511--28775567 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
28775501 CATATATATT
28775511 ATATAA-TTCAATCA
1 ATATAATTTCAATCA
* *
28775525 ATTTAAATTCAATCA
1 ATATAATTTCAATCA
28775540 GA-ATAATTTCAATCA
1 -ATATAATTTCAATCA
*
28775555 ATATAATCTCAAT
1 ATATAATTTCAAT
28775568 AAATTCATCG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
14 6 0.17
15 29 0.81
16 1 0.03
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.37
Consensus pattern (15 bp):
ATATAATTTCAATCA
Found at i:28776492 original size:23 final size:24
Alignment explanation
Indices: 28776455--28776509 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
28776445 CGTCCCCTGC
*
28776455 TATTCTGTTTCTTTCCTTCTTTT-
1 TATTCTTTTTCTTTCCTTCTTTTG
* *
28776478 TATTCTTTTTGTTTCTTTCTTTTG
1 TATTCTTTTTCTTTCCTTCTTTTG
28776502 T-TTCTTTT
1 TATTCTTTT
28776510 ATATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 27 0.96
24 1 0.04
ACGTcount: A:0.04, C:0.16, G:0.05, T:0.75
Consensus pattern (24 bp):
TATTCTTTTTCTTTCCTTCTTTTG
Found at i:28776502 original size:13 final size:13
Alignment explanation
Indices: 28776484--28776508 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28776474 TTTTTATTCT
28776484 TTTTGTTTCTTTC
1 TTTTGTTTCTTTC
28776497 TTTTGTTTCTTT
1 TTTTGTTTCTTT
28776509 TATATATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.08, T:0.80
Consensus pattern (13 bp):
TTTTGTTTCTTTC
Found at i:28776641 original size:21 final size:21
Alignment explanation
Indices: 28776617--28776659 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
28776607 TTTTCTTTCC
*
28776617 TTTAATATATATATTTA-ATAA
1 TTTAATA-ATATAATTATATAA
28776638 TTTAATAATATAATTATATAA
1 TTTAATAATATAATTATATAA
28776659 T
1 T
28776660 AAGTAAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTAATAATATAATTATATAA
Found at i:28777193 original size:13 final size:14
Alignment explanation
Indices: 28777175--28777203 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
28777165 TATTAACTTC
28777175 ATAAATATTTT-TA
1 ATAAATATTTTCTA
28777188 ATAAATATTTTCTA
1 ATAAATATTTTCTA
28777202 AT
1 AT
28777204 CCATTTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAAATATTTTCTA
Found at i:28781493 original size:40 final size:40
Alignment explanation
Indices: 28781448--28781634 Score: 232
Period size: 40 Copynumber: 4.7 Consensus size: 40
28781438 ATAACCACAA
* * *
28781448 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTT
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
* * *
28781488 GCACAAATGCCTTCGAGTCTTAGCCCGGATATAACAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
* *
28781528 GCACAAATGCCTTTGGGTCTTAACCCAGATATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
* * *
28781568 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAT-AGCAACTC
* * *
28781608 GCATAAATGCCTTCGGGGCTTAGCCCG
1 GCACAAATGCCTTCGGGTCTTAACCCG
28781635 AGTATCATTC
Statistics
Matches: 128, Mismatches: 18, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
40 126 0.98
41 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
Found at i:28781566 original size:80 final size:79
Alignment explanation
Indices: 28781433--28781629 Score: 277
Period size: 80 Copynumber: 2.5 Consensus size: 79
28781423 GGAATTTAGT
* * * * *
28781433 CGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTTGCACAAATGC
1 CGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAACCCAGATATAGCAACTCGCACAAATGC
28781498 CTTCGAGTCTTAGCC
65 CTTCGAGTCTTAGCC
* *
28781513 CGGATATAACAACTCGCACAAATGCCTTTGGGTCTTAACCCAGATATAGCAACTCGCACAAATGC
1 CGGATATAAC-ACTAGCACAAATGCCTTCGGGTCTTAACCCAGATATAGCAACTCGCACAAATGC
*
28781578 CTTCGGGTCTTAGCC
65 CTTCGAGTCTTAGCC
* *
28781593 CGGATATAATCACTAGCATAAATGCCTTCGGGGCTTA
1 CGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTA
28781630 GCCCGAGTAT
Statistics
Matches: 103, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
79 1 0.01
80 101 0.98
81 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.24
Consensus pattern (79 bp):
CGGATATAACACTAGCACAAATGCCTTCGGGTCTTAACCCAGATATAGCAACTCGCACAAATGCC
TTCGAGTCTTAGCC
Found at i:28786800 original size:29 final size:29
Alignment explanation
Indices: 28786767--28786955 Score: 238
Period size: 29 Copynumber: 6.5 Consensus size: 29
28786757 GTGACGAGAT
28786767 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
28786796 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
28786825 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
28786854 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* ** * ***
28786883 CGGCACTGGGTGTGCGA-GCTCGAAGGGTA
1 TGGCACTAAGTGTGC-ATGCTGGAAATATA
* ** * *
28786912 TGGCACTATGTGTGCGGGCT-TAAATCACA
1 TGGCACTAAGTGTGCATGCTGGAAAT-ATA
28786941 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
28786956 GAAATCGAGT
Statistics
Matches: 140, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
28 2 0.01
29 137 0.98
30 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:28794790 original size:29 final size:29
Alignment explanation
Indices: 28794757--28794843 Score: 174
Period size: 29 Copynumber: 3.0 Consensus size: 29
28794747 GTGACGAGAT
28794757 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
28794786 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
28794815 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
28794844 CGGGTGTGCG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:28797299 original size:40 final size:40
Alignment explanation
Indices: 28797212--28797378 Score: 194
Period size: 40 Copynumber: 4.2 Consensus size: 40
28797202 TTGAATGATC
* * *
28797212 CCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGTTATAT
* *
28797251 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGTTATAT
* *** *
28797291 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGTTATAT
* * * *
28797331 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGTTATAT
28797371 CC-GGCTAA
1 CCGGGCTAA
28797379 ATTCCGAAGA
Statistics
Matches: 106, Mismatches: 21, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
39 32 0.30
40 74 0.70
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGTTATAT
Found at i:28805297 original size:40 final size:40
Alignment explanation
Indices: 28805242--28805382 Score: 176
Period size: 40 Copynumber: 3.5 Consensus size: 40
28805232 TGAATGATAC
* * *
28805242 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATCATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTGATCATAT
* * *
28805282 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAG-TGATCATAT
* * *
28805322 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTGATCATAT
*
28805362 CCGGGTTAAGACCCGAAGGCA
1 CCGGGCTAAGACCCGAAGGCA
28805383 AATGTGCTTG
Statistics
Matches: 87, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 1 0.01
40 84 0.97
41 2 0.02
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.22
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTGATCATAT
Found at i:28805409 original size:80 final size:80
Alignment explanation
Indices: 28805242--28805410 Score: 207
Period size: 80 Copynumber: 2.1 Consensus size: 80
28805232 TGAATGATAC
* * * * *
28805242 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATCATATCCGGGCTAAGACCCGAAGGCATTCG
1 CCGGGCTAAGACCCGAAGGCATTTATGCAAGTGACCAAATCCGGGCTAAGACCCGAAGGCAATCG
*
28805307 TGCGAGTTGTTATAT
66 TGCGAGTGGTTATAT
* * *
28805322 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAATCCGGGTTAAGACCCGAAGGCAAAT-
1 CCGGGCTAAGACCCGAAGGCATTTATGCAAGTGACCAAATCCGGGCTAAGACCCGAAGGC-AATC
**
28805386 GTGCTTGTGGATTATAT
65 GTGCGAGTGG-TTATAT
28805403 CC-GGCTAA
1 CCGGGCTAA
28805411 ATTCTGAAGA
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
80 66 0.87
81 10 0.13
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.24
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCATTTATGCAAGTGACCAAATCCGGGCTAAGACCCGAAGGCAATCG
TGCGAGTGGTTATAT
Found at i:28808380 original size:32 final size:32
Alignment explanation
Indices: 28808339--28808403 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
28808329 ATAGGTTTTG
28808339 TACGTACCTATGCCACCTCGTACTAATCTCTT
1 TACGTACCTATGCCACCTCGTACTAATCTCTT
28808371 TACGTACCTATGCCACCTCGTACTAATCTCTT
1 TACGTACCTATGCCACCTCGTACTAATCTCTT
28808403 T
1 T
28808404 CTCAAACAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.22, C:0.34, G:0.09, T:0.35
Consensus pattern (32 bp):
TACGTACCTATGCCACCTCGTACTAATCTCTT
Found at i:28809327 original size:12 final size:12
Alignment explanation
Indices: 28809310--28809338 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
28809300 GTACTCAAAG
28809310 AAACGATCACAA
1 AAACGATCACAA
28809322 AAACGATCACAA
1 AAACGATCACAA
28809334 AAACG
1 AAACG
28809339 TAGAAATCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.59, C:0.24, G:0.10, T:0.07
Consensus pattern (12 bp):
AAACGATCACAA
Found at i:28819760 original size:21 final size:22
Alignment explanation
Indices: 28819727--28819770 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
28819717 ATAAGATAAT
*
28819727 AAACATATTTAA-TAATACATGA
1 AAACATATGTAATTAATA-ATGA
28819749 AAACATA-GTAATTAATAATGA
1 AAACATATGTAATTAATAATGA
28819770 A
1 A
28819771 TTTTGAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (22 bp):
AAACATATGTAATTAATAATGA
Found at i:28819942 original size:16 final size:15
Alignment explanation
Indices: 28819906--28819960 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
28819896 AATAATGTGA
28819906 ATAATAATATACATG
1 ATAATAATATACATG
*
28819921 AAAATATATATA-ATAG
1 ATAATA-ATATACAT-G
*
28819937 ATAATAATA-ATATG
1 ATAATAATATACATG
28819951 A-AATAATATA
1 ATAATAATATA
28819961 TTGTTAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
13 7 0.21
14 4 0.12
15 12 0.35
16 11 0.32
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (15 bp):
ATAATAATATACATG
Found at i:28820113 original size:25 final size:25
Alignment explanation
Indices: 28820073--28820151 Score: 85
Period size: 25 Copynumber: 3.2 Consensus size: 25
28820063 TGATAATAGA
28820073 AAAATATGAAGT-AATATAATATAAT
1 AAAATAT-AAGTAAATATAATATAAT
28820098 AAAATATAAGTAAATAATAATAT-AT
1 AAAATATAAGTAAAT-ATAATATAAT
* * *
28820123 AATATATAA-TACATAT-ATATATT
1 AAAATATAAGTAAATATAATATAAT
28820146 AAAATA
1 AAAATA
28820152 AAATAATATA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
22 4 0.09
23 8 0.17
24 8 0.17
25 20 0.43
26 7 0.15
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (25 bp):
AAAATATAAGTAAATATAATATAAT
Found at i:28820116 original size:18 final size:17
Alignment explanation
Indices: 28820085--28820156 Score: 60
Period size: 18 Copynumber: 4.2 Consensus size: 17
28820075 AATATGAAGT
28820085 AATATAAT--ATAATAA
1 AATATAATAAATAATAA
28820100 AATATAAGTAAATAATAA
1 AATATAA-TAAATAATAA
* *
28820118 TATATAATATATAATACA
1 AATATAATAAATAATA-A
* *
28820136 TATATATATTAA-AATAA
1 AATATA-ATAAATAATAA
28820153 AATA
1 AATA
28820157 ATATATATAC
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
15 7 0.15
16 1 0.02
17 12 0.26
18 24 0.51
19 3 0.06
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (17 bp):
AATATAATAAATAATAA
Found at i:28820157 original size:26 final size:26
Alignment explanation
Indices: 28820128--28820179 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
28820118 TATATAATAT
*
28820128 ATAATACATATA-TATATTAAAATAAA
1 ATAATACATATACAAT-TTAAAATAAA
*
28820154 ATAATATATATACAATTTAAAATAAA
1 ATAATACATATACAATTTAAAATAAA
28820180 TAAGTTATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 21 0.91
27 2 0.09
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (26 bp):
ATAATACATATACAATTTAAAATAAA
Found at i:28820195 original size:25 final size:27
Alignment explanation
Indices: 28820144--28820201 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
28820134 CATATATATA
*
28820144 TTAAAATAAAATAATATATATACAA-T
1 TTAAAATAAAATAATATATAAACAATT
*
28820170 TTAAAAT-AAATAAGT-TATAAATAATT
1 TTAAAATAAAATAA-TATATAAACAATT
28820196 TTAAAA
1 TTAAAA
28820202 GGGATAAACG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 13 0.46
26 15 0.54
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (27 bp):
TTAAAATAAAATAATATATAAACAATT
Found at i:28822175 original size:206 final size:206
Alignment explanation
Indices: 28821804--28822388 Score: 902
Period size: 206 Copynumber: 2.8 Consensus size: 206
28821794 AAGTCTGCTT
* * * * * *
28821804 CTTCAATTTATTCTCTAACAATACAGAGATGCCAAATCATCTTCGATTTGCTTCAGCATAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAGCGTAAGCAC
* * * * * * *
28821869 GCGAAAACCAAATCAGCTATG-TCTTCGATTTGCTCCTTGTAAGCACAAGGATACCAAACCATCT
66 GTGAAAGCTAAATCAGCTATGAT-TTCGATTTGTTCCTTGTAAACACAAGGATGCCAAATCATCT
* * * *
28821933 TGGATCTGCTTTAGTCTAATCATCTGAAGGTTAGATCTGCTATGTGTCTGCCCTCCATCGAATAT
130 TGGATCTGCTTCAGTATAATCATCTGAAGGTTAGATCTGCTATGTGCCTGCCCTCCATCAAATAT
*
28821998 GGAGACGTCAAA
195 GGAGACGCCAAA
28822010 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAGCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAGCGTAAGCAC
*
28822075 GTGAAAGCTAAATCAGCTATGATTTTGATTTGTTCCTTGTAAACACAAGGATGCCAAATCATCTT
66 GTGAAAGCTAAATCAGCTATGATTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAATCATCTT
* * *
28822140 GGATCTACTTCAGTATAATCATCTGAAGGTTAGATCTGCTATGTGCCTGCCCTCCGTTAAATATG
131 GGATCTGCTTCAGTATAATCATCTGAAGGTTAGATCTGCTATGTGCCTGCCCTCCATCAAATATG
28822205 GAGACGCCAAA
196 GAGACGCCAAA
*
28822216 CTTCGATTTGTTCTCTGACGATACAGAGATGCCAAATCATCTTAGACTTGCTTCAGCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAGCGTAAGCAC
* *
28822281 GTGAAAGCTAAATTAGCTATGATTTCGATTTGTTCCTTATAAACACAAGGATGCCAAATCATCTT
66 GTGAAAGCTAAATCAGCTATGATTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAATCATCTT
* **
28822346 GGATCTGCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATG
131 GGATCTGCTTCAGTATAATCATCTGAAGGTTAGATCTGCTATG
28822389 CTGCGGTCAT
Statistics
Matches: 348, Mismatches: 30, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
206 347 1.00
207 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (206 bp):
CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAGCGTAAGCAC
GTGAAAGCTAAATCAGCTATGATTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAATCATCTT
GGATCTGCTTCAGTATAATCATCTGAAGGTTAGATCTGCTATGTGCCTGCCCTCCATCAAATATG
GAGACGCCAAA
Found at i:28823274 original size:7 final size:7
Alignment explanation
Indices: 28823264--28823311 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
28823254 CTTCTCTCTT
28823264 TTTTTTG
1 TTTTTTG
28823271 TTTTTTG
1 TTTTTTG
*
28823278 TTTTTTC
1 TTTTTTG
*
28823285 TTTTCTG
1 TTTTTTG
28823292 TTTGTTT-
1 TTT-TTTG
*
28823299 TTTTTTC
1 TTTTTTG
28823306 TTTTTT
1 TTTTTT
28823312 TGATTTTCGA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
6 3 0.09
7 30 0.86
8 2 0.06
ACGTcount: A:0.00, C:0.06, G:0.08, T:0.85
Consensus pattern (7 bp):
TTTTTTG
Found at i:28823288 original size:21 final size:21
Alignment explanation
Indices: 28823264--28823311 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
28823254 CTTCTCTCTT
28823264 TTTTTTGTTT-TTTGTTTTTTC
1 TTTTTTGTTTGTTT-TTTTTTC
*
28823285 TTTTCTGTTTGTTTTTTTTTC
1 TTTTTTGTTTGTTTTTTTTTC
28823306 TTTTTT
1 TTTTTT
28823312 TGATTTTCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.00, C:0.06, G:0.08, T:0.85
Consensus pattern (21 bp):
TTTTTTGTTTGTTTTTTTTTC
Found at i:28831154 original size:27 final size:27
Alignment explanation
Indices: 28831124--28831254 Score: 156
Period size: 27 Copynumber: 4.9 Consensus size: 27
28831114 ATTACCAAAG
*
28831124 TACCCTTGATTTATAGAATTACTGTTT
1 TACCCTTGATTTACAGAATTACTGTTT
* *
28831151 TACCCTCGATTTACAAAATTA-TCGTTT
1 TACCCTTGATTTACAGAATTACT-GTTT
** *
28831178 TACCCTTGATTTGTAGAATTACTATTT
1 TACCCTTGATTTACAGAATTACTGTTT
*
28831205 TACCCTTGATTTACACAATTACTGTTT
1 TACCCTTGATTTACAGAATTACTGTTT
** *
28831232 TACCCTCAATTTACAAAATTACT
1 TACCCTTGATTTACAGAATTACT
28831255 AAAATACCCT
Statistics
Matches: 87, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
26 1 0.01
27 85 0.98
28 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.08, T:0.44
Consensus pattern (27 bp):
TACCCTTGATTTACAGAATTACTGTTT
Found at i:28831155 original size:54 final size:54
Alignment explanation
Indices: 28831097--28831210 Score: 129
Period size: 54 Copynumber: 2.1 Consensus size: 54
28831087 ATTACTGAAA
** *
28831097 TACCCTCAAATTGTAAAATTACCAAAGTACCCTTGATTTATAGAATTACTGTTT
1 TACCCTCAAATTACAAAATTACCAAAGTACCCTTGATTTATAGAATTACTATTT
* * * **** *
28831151 TACCCTCGATTTACAAAATTATCGTTTTACCCTTGATTTGTAGAATTACTATTT
1 TACCCTCAAATTACAAAATTACCAAAGTACCCTTGATTTATAGAATTACTATTT
28831205 TACCCT
1 TACCCT
28831211 TGATTTACAC
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (54 bp):
TACCCTCAAATTACAAAATTACCAAAGTACCCTTGATTTATAGAATTACTATTT
Found at i:28831216 original size:54 final size:54
Alignment explanation
Indices: 28831124--28831280 Score: 190
Period size: 54 Copynumber: 2.9 Consensus size: 54
28831114 ATTACCAAAG
*
28831124 TACCCTTGATTTATAGAATTACTGTTTTACCCTCGATTTACAAAATTA-TCGTTT
1 TACCCTTGATTTATAGAATTACTATTTTACCCTCGATTTACAAAATTACT-GTTT
* * *
28831178 TACCCTTGATTTGTAGAATTACTATTTTACCCTTGATTTACACAATTACTGTTT
1 TACCCTTGATTTATAGAATTACTATTTTACCCTCGATTTACAAAATTACTGTTT
** * * *** *
28831232 TACCCTCAATTTACAAAATTACTAAAATACCCTCGGTTTACAAAATTAC
1 TACCCTTGATTTATAGAATTACTATTTTACCCTCGATTTACAAAATTAC
28831281 CAAAATACCC
Statistics
Matches: 87, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
54 86 0.99
55 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.41
Consensus pattern (54 bp):
TACCCTTGATTTATAGAATTACTATTTTACCCTCGATTTACAAAATTACTGTTT
Found at i:28831263 original size:81 final size:80
Alignment explanation
Indices: 28831079--28831295 Score: 211
Period size: 81 Copynumber: 2.7 Consensus size: 80
28831069 AATACTTTAG
* * *
28831079 TTTACCAAATTACTGAAATACCCTCAAATTGTAAAATTACCAAAGTACCCTTGATTTATAGAATT
1 TTTACAAAATTACT-AAATACCCTCAAATTGTAAAATTACCAAAGTACCCTTGATTTACACAATT
*
28831144 ACTGTTTTACCCTCGA
65 ACTGTTTTACCCTCAA
** ** * * * ***
28831160 TTTACAAAATTATCGT-TTTACCCTTGATTTGTAGAATTACTATTTTACCCTTGATTTACACAAT
1 TTTACAAAATTA-C-TAAATACCCTCAAATTGTAAAATTACCAAAGTACCCTTGATTTACACAAT
28831224 TACTGTTTTACCCTCAA
64 TACTGTTTTACCCTCAA
*** ** *
28831241 TTTACAAAATTACTAAAATACCCTCGGTTTACAAAATTACCAAAATACCCTTGAT
1 TTTACAAAATTACT-AAATACCCTCAAATTGTAAAATTACCAAAGTACCCTTGAT
28831296 CAGTAAAATT
Statistics
Matches: 107, Mismatches: 25, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
79 1 0.01
80 1 0.01
81 103 0.96
82 1 0.01
83 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.07, T:0.37
Consensus pattern (80 bp):
TTTACAAAATTACTAAATACCCTCAAATTGTAAAATTACCAAAGTACCCTTGATTTACACAATTA
CTGTTTTACCCTCAA
Found at i:28831290 original size:54 final size:54
Alignment explanation
Indices: 28831232--28831506 Score: 263
Period size: 54 Copynumber: 5.1 Consensus size: 54
28831222 ATTACTGTTT
** * * *
28831232 TACCCTCAATTTACAAAATTACTAAAATACCCTCGGTTTACAAAATTACCAAAA
1 TACCCTCAATTTGTAAAATTACCAAAATACCCTCGATTTATAAAATTACCAAAA
** ** * * * *
28831286 TACCCTTGATCAGTAAAATTACCAAAATACCCTAG-TCTATAAAATTGCTAAAA
1 TACCCTCAATTTGTAAAATTACCAAAATACCCTCGATTTATAAAATTACCAAAA
*** * *
28831339 TACCCTTGGTTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTCAATTTGTAAAATTACCAAAATACCCTCGATTTATAAAATTACCAAAA
* * * *
28831393 TACCC-CTAGTTTGTAAAATTACCAAAATACCACT-GATTTGTGAAATTACCGAAA
1 TACCCTC-AATTTGTAAAATTACCAAAATACC-CTCGATTTATAAAATTACCAAAA
* *
28831447 TACCCTCAATTTGTAAAATTACCAAAATACCC-CTGATTTACAAAGTTA-CAGAAA
1 TACCCTCAATTTGTAAAATTACCAAAATACCCTC-GATTTATAAAATTACCA-AAA
28831501 TACCCT
1 TACCCT
28831507 TGACTTTCTA
Statistics
Matches: 182, Mismatches: 32, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
53 46 0.25
54 133 0.73
55 3 0.02
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.29
Consensus pattern (54 bp):
TACCCTCAATTTGTAAAATTACCAAAATACCCTCGATTTATAAAATTACCAAAA
Found at i:28831448 original size:81 final size:81
Alignment explanation
Indices: 28831246--28831519 Score: 304
Period size: 81 Copynumber: 3.4 Consensus size: 81
28831236 CTCAATTTAC
* * * ** ** **
28831246 AAAATTACTAAAATACCCTCGGTTTACAAAATTACCAAAATACCCTTGATCAGTAAAATTACCAA
1 AAAATTACCAAAATACCCTTGATTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATTACCAA
28831311 AATA-CCCTAGTCTAT
66 AATACCCCTAGTCTAT
* * *
28831326 AAAATTGCTAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATTACCAA
1 AAAATTACCAAAATACCCTTGATTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATTACCAA
* *
28831391 AATACCCCTAGTTTGT
66 AATACCCCTAGTCTAT
* *
28831407 AAAATTACCAAAATACCAC-TGATTTGTGAAATTACCGAAATACCCTCAATTTGTAAAATTACCA
1 AAAATTACCAAAATACC-CTTGATTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATTACCA
* *
28831471 AAATACCCCT-GATTTAC
65 AAATACCCCTAG-TCTAT
* *
28831488 AAAGTTA-CAGAAATACCCTTGACTTTCTAAAA
1 AAAATTACCA-AAATACCCTTGA-TTTGTAAAA
28831520 ATTATGGAAA
Statistics
Matches: 168, Mismatches: 20, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
80 65 0.39
81 95 0.57
82 8 0.05
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (81 bp):
AAAATTACCAAAATACCCTTGATTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATTACCAA
AATACCCCTAGTCTAT
Found at i:28831485 original size:27 final size:27
Alignment explanation
Indices: 28831246--28831485 Score: 231
Period size: 27 Copynumber: 8.9 Consensus size: 27
28831236 CTCAATTTAC
* * **
28831246 AAAATTACTAAAATA-CCCTCGGTTTAC
1 AAAATTACCAAAATACCCCT-GATTTGT
* **
28831273 AAAATTACCAAAATACCCTTGATCAGT
1 AAAATTACCAAAATACCCCTGATTTGT
* *
28831300 AAAATTACCAAAATA-CCCT-AGTCTAT
1 AAAATTACCAAAATACCCCTGA-TTTGT
* * * *
28831326 AAAATTGCTAAAATACCCTTGGTTTGT
1 AAAATTACCAAAATACCCCTGATTTGT
*
28831353 AAAATTACCAAAATA-CCCTCAATTTGT
1 AAAATTACCAAAATACCCCT-GATTTGT
28831380 AAAATTACCAAAATACCCCT-AGTTTGT
1 AAAATTACCAAAATACCCCTGA-TTTGT
*
28831407 AAAATTACCAAAATACCACTGATTTGT
1 AAAATTACCAAAATACCCCTGATTTGT
* * *
28831434 GAAATTACCGAAATA-CCCTCAATTTGT
1 AAAATTACCAAAATACCCCT-GATTTGT
28831461 AAAATTACCAAAATACCCCTGATTT
1 AAAATTACCAAAATACCCCTGATTT
28831486 ACAAAGTTAC
Statistics
Matches: 174, Mismatches: 29, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
25 1 0.01
26 26 0.15
27 135 0.78
28 12 0.07
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.30
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCTGATTTGT
Found at i:28831495 original size:27 final size:27
Alignment explanation
Indices: 28831240--28831519 Score: 207
Period size: 27 Copynumber: 10.4 Consensus size: 27
28831230 TTTACCCTCA
* *
28831240 ATTTACAAAATTACTAAAATA-CCCTCG
1 ATTTATAAAATTACCAAAATACCCCT-G
* * *
28831267 GTTTACAAAATTACCAAAATACCCTTG
1 ATTTATAAAATTACCAAAATACCCCTG
*
28831294 A-TCAGTAAAATTACCAAAATA-CCCT-
1 ATTTA-TAAAATTACCAAAATACCCCTG
* * * *
28831319 AGTCTATAAAATTGCTAAAATACCCTTG
1 A-TTTATAAAATTACCAAAATACCCCTG
* * *
28831347 GTTTGTAAAATTACCAAAATA-CCCTCA
1 ATTTATAAAATTACCAAAATACCCCT-G
*
28831374 ATTTGTAAAATTACCAAAATACCCCT-
1 ATTTATAAAATTACCAAAATACCCCTG
* *
28831400 AGTTTGTAAAATTACCAAAATACCACTG
1 A-TTTATAAAATTACCAAAATACCCCTG
* * * *
28831428 ATTTGTGAAATTACCGAAATA-CCCTCA
1 ATTTATAAAATTACCAAAATACCCCT-G
*
28831455 ATTTGTAAAATTACCAAAATACCCCTG
1 ATTTATAAAATTACCAAAATACCCCTG
* * *
28831482 ATTTACAAAGTTA-CAGAAATACCCTTG
1 ATTTATAAAATTACCA-AAATACCCCTG
*
28831509 ACTTTCTAAAA
1 A-TTTATAAAA
28831520 ATTATGGAAA
Statistics
Matches: 204, Mismatches: 35, Indels: 27
0.77 0.13 0.10
Matches are distributed among these distances:
25 1 0.00
26 28 0.14
27 157 0.77
28 18 0.09
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.30
Consensus pattern (27 bp):
ATTTATAAAATTACCAAAATACCCCTG
Found at i:28831556 original size:27 final size:27
Alignment explanation
Indices: 28831517--28831568 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
28831507 TGACTTTCTA
*
28831517 AAAATTATGGAAATACCATTGGTTTAC
1 AAAATTATGGAAATACCATTAGTTTAC
28831544 AAAATTACT-GAAATACCATTAGTTT
1 AAAATTA-TGGAAATACCATTAGTTT
28831569 GTAGATTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (27 bp):
AAAATTATGGAAATACCATTAGTTTAC
Found at i:28831682 original size:27 final size:27
Alignment explanation
Indices: 28831622--28831708 Score: 113
Period size: 27 Copynumber: 3.2 Consensus size: 27
28831612 ACCCCTATTA
* *
28831622 GGTAAAAAGACTGTAAAGCCCCTATAG
1 GGTAAAGAGACTGTAAAGCCCCTGTAG
*
28831649 GGTAAAGAGACCGTAAAGCCCCTGTAG
1 GGTAAAGAGACTGTAAAGCCCCTGTAG
* *
28831676 GGTAAAGTGACTGTAATA-CCCCTGTAT
1 GGTAAAGAGACTGTAA-AGCCCCTGTAG
28831703 GGTAAA
1 GGTAAA
28831709 ATGACGAATA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
27 52 0.98
28 1 0.02
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (27 bp):
GGTAAAGAGACTGTAAAGCCCCTGTAG
Found at i:28831713 original size:27 final size:27
Alignment explanation
Indices: 28831613--28831713 Score: 100
Period size: 27 Copynumber: 3.7 Consensus size: 27
28831603 GACTAAAATA
*
28831613 CCCCTATTA-GGTAAAAAGACTGTAAAG
1 CCCCTA-TAGGGTAAAATGACTGTAAAG
*
28831640 CCCCTATAGGGTAAAGA-GACCGTAAAG
1 CCCCTATAGGGTAAA-ATGACTGTAAAG
* *
28831667 CCCCTGTAGGGTAAAGTGACTGTAATA-
1 CCCCTATAGGGTAAAATGACTGTAA-AG
* *
28831694 CCCCTGTATGGTAAAATGAC
1 CCCCTATAGGGTAAAATGAC
28831714 GAATATGCCC
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
26 2 0.03
27 60 0.94
28 2 0.03
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.22
Consensus pattern (27 bp):
CCCCTATAGGGTAAAATGACTGTAAAG
Found at i:28832545 original size:26 final size:26
Alignment explanation
Indices: 28832515--28832664 Score: 230
Period size: 26 Copynumber: 5.8 Consensus size: 26
28832505 GAGGAAGTGC
*
28832515 AAAAGGGCTTATGCCCCAGTTTACCA
1 AAAAGGGCTTATGCCCCAGTTTACCG
**
28832541 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
28832567 AAAATGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
* **
28832593 AAAAGGGCTTATGCCCTAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
28832619 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
28832645 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
28832665 ATTAAAGAGG
Statistics
Matches: 111, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
25 10 0.09
26 101 0.91
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:28832598 original size:52 final size:52
Alignment explanation
Indices: 28832515--28832664 Score: 266
Period size: 52 Copynumber: 2.9 Consensus size: 52
28832505 GAGGAAGTGC
*
28832515 AAAAGGGCTTATGCCCCAGTTTACCAAAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
* *
28832567 AAAATGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCTAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
28832619 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTT
28832665 ATTAAAGAGG
Statistics
Matches: 93, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
51 9 0.10
52 84 0.90
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.27
Consensus pattern (52 bp):
AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
Found at i:28832868 original size:42 final size:42
Alignment explanation
Indices: 28832809--28832900 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
28832799 TAGTCTCCCC
* ** *
28832809 AAATGGGCTTGCATACATTCATCGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATCGACATTACATGTGATATTG
*
28832851 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATCGACATTACATGTGATATTG
28832893 AAATGGGC
1 AAATGGGC
28832901 CTATGGGCCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATCGACATTACATGTGATATTG
Found at i:28832959 original size:31 final size:31
Alignment explanation
Indices: 28832924--28833002 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
28832914 TGTTTACAGT
28832924 AAAGGCTTCGGCCCAGTGAAATGATTCATGA
1 AAAGGCTTCGGCCCAGTGAAATGATTCATGA
* * *
28832955 AAAGGCTTTGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGAAATGATTCATGA
28832986 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
28833003 AATCGTTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGAAATGATTCATGA
Found at i:28837465 original size:29 final size:29
Alignment explanation
Indices: 28837431--28837562 Score: 140
Period size: 29 Copynumber: 4.6 Consensus size: 29
28837421 TACTCGATTT
** * *
28837431 CGCACACTTAGTGCCATGCGATTT-AAGCC
1 CGCACACTTAGTGCCAT-ATATTTCCAGCA
* **** * *
28837460 CGCACACATAGTGCCATGCCCTTCGAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
28837489 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
28837518 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
28837547 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
28837563 ATCTCGTCAC
Statistics
Matches: 86, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
28 2 0.02
29 84 0.98
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:28845195 original size:29 final size:29
Alignment explanation
Indices: 28845161--28845292 Score: 140
Period size: 29 Copynumber: 4.6 Consensus size: 29
28845151 TACTCGATTT
** * *
28845161 CGCACACTTAGTGCCATGCGATTT-AAGCC
1 CGCACACTTAGTGCCAT-ATATTTCCAGCA
* **** * *
28845190 CGCACACATAGTGCCATGCCCTTCGAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
28845219 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
28845248 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
28845277 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
28845293 ATCTCGTCAC
Statistics
Matches: 86, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
28 2 0.02
29 84 0.98
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:28849220 original size:5 final size:5
Alignment explanation
Indices: 28849210--28849289 Score: 53
Period size: 5 Copynumber: 16.4 Consensus size: 5
28849200 AAATATGAAG
* *
28849210 TAATA TAATA TAATA AAATA TAAGTA -AATAA TAATA TAAAA T-ATA TAATA
1 TAATA TAATA TAATA TAATA TAA-TA TAAT-A TAATA TAATA TAATA TAATA
* * *
28849260 CATATA TATTA CAATA -AA-A TAATA T-ATA TA
1 TA-ATA TAATA TAATA TAATA TAATA TAATA TA
28849290 CAATTTAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
3 1 0.02
4 12 0.21
5 36 0.62
6 9 0.16
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (5 bp):
TAATA
Found at i:28849241 original size:28 final size:26
Alignment explanation
Indices: 28849212--28849280 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 26
28849202 ATATGAAGTA
28849212 ATATAATATAATAAAATATAAGTAAAT
1 ATATAATATAATAAAATATAA-TAAAT
* *
28849239 A-ATAATATAA-AATATATAATACAT
1 ATATAATATAATAAAATATAATAAAT
* *
28849263 ATATATTACAATAAAATA
1 ATATAATATAATAAAATA
28849281 ATATATATAC
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
24 5 0.14
25 15 0.43
26 14 0.40
27 1 0.03
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.33
Consensus pattern (26 bp):
ATATAATATAATAAAATATAATAAAT
Found at i:28849284 original size:20 final size:20
Alignment explanation
Indices: 28849234--28849298 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
28849224 AAAATATAAG
*
28849234 TAAATAATA-ATATAAAATA
1 TAAATAATATATATACAATA
28849253 TATAATACATATATATTACAATA
1 TA-AATA-ATATATA-TACAATA
*
28849276 -AAATAATATATATACAATT
1 TAAATAATATATATACAATA
28849295 TAAA
1 TAAA
28849299 ATAAATAAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
19 8 0.21
20 14 0.36
21 7 0.18
22 4 0.10
23 6 0.15
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
TAAATAATATATATACAATA
Found at i:28854336 original size:45 final size:45
Alignment explanation
Indices: 28854241--28854401 Score: 204
Period size: 45 Copynumber: 3.7 Consensus size: 45
28854231 AAAGCCACTA
* * * * *
28854241 TCCCAGACAGGGTCTTACACG-AATCA-A-ATA-CGATGTCGATG
1 TCCCAGACATGGTCTTACACGAAAACACATATATCGATGCCAACG
* * *
28854282 TCCCAGACATGGTCTTACACGTAACCACATATATTGATGCCAACG
1 TCCCAGACATGGTCTTACACGAAAACACATATATCGATGCCAACG
28854327 TCCCAGACATGGTCTTACACGAAAACACATATATCGATGCCAACG
1 TCCCAGACATGGTCTTACACGAAAACACATATATCGATGCCAACG
**
28854372 TCCCAGATGTGGTCTTACACGAAAACACAT
1 TCCCAGACATGGTCTTACACGAAAACACAT
28854402 CAGAATCCTA
Statistics
Matches: 105, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
41 20 0.19
42 4 0.04
43 1 0.01
44 3 0.03
45 77 0.73
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.22
Consensus pattern (45 bp):
TCCCAGACATGGTCTTACACGAAAACACATATATCGATGCCAACG
Found at i:28854975 original size:15 final size:15
Alignment explanation
Indices: 28854952--28854982 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28854942 TCAAAAATTC
28854952 CAATACAAAACATAT
1 CAATACAAAACATAT
*
28854967 CAATCCAAAACATAT
1 CAATACAAAACATAT
28854982 C
1 C
28854983 TTTCGTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.19
Consensus pattern (15 bp):
CAATACAAAACATAT
Found at i:28859171 original size:20 final size:20
Alignment explanation
Indices: 28859146--28859216 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
28859136 ATTTTGATAA
*
28859146 ACATGATATGTATGACATGC
1 ACATGATATGTATGATATGC
*
28859166 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
28859186 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
28859206 ACATGAGATGT
1 ACATGATATGT
28859217 TCATAAATGC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:28859293 original size:23 final size:23
Alignment explanation
Indices: 28859263--28859405 Score: 241
Period size: 23 Copynumber: 6.1 Consensus size: 23
28859253 AGGAAGTGCA
28859263 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
28859286 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
28859309 AAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
28859333 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
28859356 AAAGGGCTTATGCCCCAATTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
28859379 AAAAGGGCTTTTGCCCCAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
28859403 AAA
1 AAA
28859406 AGAGGCTAGG
Statistics
Matches: 113, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
23 70 0.62
24 43 0.38
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:28859341 original size:24 final size:23
Alignment explanation
Indices: 28859262--28859425 Score: 222
Period size: 23 Copynumber: 7.0 Consensus size: 23
28859252 GAGGAAGTGC
28859262 AAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
28859285 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
28859308 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
28859331 CAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
* *
28859355 TAAAGGGCTTATGCCCCAATTATT
1 AAAAGGGCTTATGCCCCAGTTA-T
*
28859379 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTA-T
*
28859403 AAAAGAGGC-TAGGCCTCCAGTTA
1 AAAAG-GGCTTATGCC-CCAGTTA
28859426 CATGATAAAG
Statistics
Matches: 128, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
23 65 0.51
24 53 0.41
25 10 0.08
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (23 bp):
AAAAGGGCTTATGCCCCAGTTAT
Found at i:28859354 original size:47 final size:46
Alignment explanation
Indices: 28859263--28859405 Score: 241
Period size: 47 Copynumber: 3.1 Consensus size: 46
28859253 AGGAAGTGCA
*
28859263 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
28859309 AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATT
* *
28859356 AAAGGGCTTATGCCCCAATTATTAAAAGGGCTTTTGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTA-TAAAAGGGCTTATGCCCCAGTTATT
28859403 AAA
1 AAA
28859406 AGAGGCTAGG
Statistics
Matches: 92, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
46 22 0.24
47 69 0.75
48 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (46 bp):
AAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
Found at i:28865219 original size:44 final size:43
Alignment explanation
Indices: 28865171--28865278 Score: 135
Period size: 44 Copynumber: 2.4 Consensus size: 43
28865161 GATGGCAATG
* * *
28865171 TCCCAGAAATGGTCTTACACTTAAATCTCAAATCGATGCCAACA
1 TCCCA-AAGTGGTCTTACACTTAAATCTCAAAACAATGCCAACA
* *
28865215 TCCCAAATGTGGTCTTACACTTACATCTCAAAACAATGCCAACG
1 TCCCAAA-GTGGTCTTACACTTAAATCTCAAAACAATGCCAACA
*
28865259 TCCCACATGTGGTCTTACAC
1 TCCCA-AAGTGGTCTTACAC
28865279 GATAACATAT
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
43 2 0.04
44 53 0.95
45 1 0.02
ACGTcount: A:0.32, C:0.30, G:0.12, T:0.26
Consensus pattern (43 bp):
TCCCAAAGTGGTCTTACACTTAAATCTCAAAACAATGCCAACA
Found at i:28876857 original size:19 final size:19
Alignment explanation
Indices: 28876821--28876859 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
28876811 TTTTCATCAT
* *
28876821 AGTAAAATAAAATAATAAA
1 AGTAAAACAAAACAATAAA
*
28876840 AGTAAAACAAAACCATAAA
1 AGTAAAACAAAACAATAAA
28876859 A
1 A
28876860 ATAATTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (19 bp):
AGTAAAACAAAACAATAAA
Found at i:28877363 original size:55 final size:56
Alignment explanation
Indices: 28877298--28877412 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 56
28877288 AGCATGGCTG
* * *
28877298 CCAGATACAGA-AAATGTGACAGAGTCACCAGATACAGATATTTTGTGGCAGT-GCCA
1 CCAGATACAGATAAACGTGACAGAGCCACCAGA-ACAGATAATTTGTGGCA-TAGCCA
* * *
28877354 CCAGA-ACAGATATACGTGGCAGGGCCACCAGAACAGATAATTTGTGGCATAGCCA
1 CCAGATACAGATAAACGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
28877409 CCAG
1 CCAG
28877413 GACGCTTCCT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
54 1 0.02
55 29 0.57
56 21 0.41
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (56 bp):
CCAGATACAGATAAACGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
Found at i:28877409 original size:28 final size:27
Alignment explanation
Indices: 28877323--28877412 Score: 101
Period size: 27 Copynumber: 3.2 Consensus size: 27
28877313 GTGACAGAGT
*
28877323 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATAATTTGTGGCA-TGC
** *
28877352 CACCAGAACAGAT-ATACGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCA-TGC
28877379 CACCAGAACAGATAATTTGTGGCATAGC
1 CACCAGAACAGATAATTTGTGGCAT-GC
28877407 CACCAG
1 CACCAG
28877413 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 23 0.44
28 22 0.42
29 7 0.13
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.19
Consensus pattern (27 bp):
CACCAGAACAGATAATTTGTGGCATGC
Found at i:28877565 original size:28 final size:28
Alignment explanation
Indices: 28877518--28877581 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
28877508 AAATTAACCC
*
28877518 TAGGGGTATAGAGGTCATTTTGCATACA
1 TAGGGGTATAGAGGTAATTTTGCATACA
28877546 TAGGGGTATA-ATGGTAATTTTGCATACA
1 TAGGGGTATAGA-GGTAATTTTGCATACA
28877574 TAGGGGTA
1 TAGGGGTA
28877582 CTCTAGTACA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 1 0.03
28 33 0.97
ACGTcount: A:0.30, C:0.08, G:0.30, T:0.33
Consensus pattern (28 bp):
TAGGGGTATAGAGGTAATTTTGCATACA
Found at i:28884729 original size:19 final size:19
Alignment explanation
Indices: 28884693--28884731 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
28884683 TTTTCATCAT
* *
28884693 AGTAAAATAAAATAATAAA
1 AGTAAAACAAAACAATAAA
*
28884712 AGTAAAACAAAACCATAAA
1 AGTAAAACAAAACAATAAA
28884731 A
1 A
28884732 ATAATTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (19 bp):
AGTAAAACAAAACAATAAA
Done.