Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold371
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: 1142270
ACGTcount: A:0.15, C:0.08, G:0.08, T:0.15
Warning! 606714 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:176631 original size:79 final size:78
Alignment explanation
Indices: 176520--176737 Score: 276
Period size: 79 Copynumber: 2.8 Consensus size: 78
176510 GAGATAATAA
* * * * * *
176520 CGGGGTTGGAGTGTTCCGTTGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA
1 CGGGGTTGGAGTATTCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAAT-A
176585 -TTAGAAAAAAAAAT
65 TTTAG-AAAAAAAAT
* * *
176599 CGGGATTGGAGTATTCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATTCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATA-
*
176664 TTTAGAAAAAAAGT
65 TTTAGAAAAAAAAT
* * *
176678 CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATTCCCGATTGTGAAGAAAT
1 CGGGGTTGGAGTATTCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTG-AGAAAT
176738 TGGTGTTTTT
Statistics
Matches: 120, Mismatches: 16, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
78 1 0.01
79 109 0.91
80 10 0.08
ACGTcount: A:0.32, C:0.14, G:0.29, T:0.25
Consensus pattern (78 bp):
CGGGGTTGGAGTATTCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATAT
TTAGAAAAAAAAT
Found at i:176779 original size:54 final size:51
Alignment explanation
Indices: 176710--176840 Score: 147
Period size: 51 Copynumber: 2.5 Consensus size: 51
176700 AAATAACGGG
* * * *
176710 GTTGGAGTATTCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTG-AGAAATTAGTG--TATTGAAAATAAAATCGGA
*
176764 GTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTATTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAG-AAATTAGTGTATTGAAAATAAAATCGGA
* *
176815 GTTGAAATATCCCCGATTGTGGAGAA
1 GTTGGAGTATCCCCGATTGT-GAGAA
176841 TTGAGAAACT
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
51 34 0.52
52 4 0.06
53 10 0.15
54 18 0.27
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAGAAATTAGTGTATTGAAAATAAAATCGGA
Found at i:179211 original size:13 final size:13
Alignment explanation
Indices: 179193--179218 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
179183 ACAAAGATCC
179193 ATGTATCGATACA
1 ATGTATCGATACA
179206 ATGTATCGATACA
1 ATGTATCGATACA
179219 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:179214 original size:33 final size:33
Alignment explanation
Indices: 179172--179238 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
179162 AAAATTTCCA
***
179172 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
179205 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
179238 A
1 A
179239 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:179282 original size:19 final size:18
Alignment explanation
Indices: 179258--179357 Score: 85
Period size: 19 Copynumber: 5.9 Consensus size: 18
179248 CAGTAGCTAA
179258 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
*
179277 TTATGTAACGATAC--A-
1 TTATGTATCGATACAAAC
179292 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
179309 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
*
179324 -T-TGTATCGATAGAAAAC
1 TTATGTATCGATA-CAAAC
179341 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
179358 TTGTTGAATT
Statistics
Matches: 65, Mismatches: 4, Indels: 25
0.69 0.04 0.27
Matches are distributed among these distances:
13 20 0.31
14 2 0.03
16 4 0.06
18 5 0.08
19 34 0.52
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:179302 original size:32 final size:32
Alignment explanation
Indices: 179261--179355 Score: 163
Period size: 32 Copynumber: 3.0 Consensus size: 32
179251 TAGCTAATTA
* *
179261 TGTATCGATACAATACTTATGTAACGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
179293 TGTATCGATACAAAACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
*
179325 TGTATCGATAGAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
179356 AATTGTTGAA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 60 1.00
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.34
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:179437 original size:21 final size:21
Alignment explanation
Indices: 179413--179469 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
179403 CATTTGTAGG
179413 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
* *
179434 ATGTATTGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
179455 ATGTATCGATACATT
1 ATGTATCGATACATT
179470 TGGATAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.35
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:179497 original size:15 final size:15
Alignment explanation
Indices: 179477--179512 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
179467 ATTTGGATAA
179477 TTTTTTTTTAATTAT
1 TTTTTTTTTAATTAT
179492 TTTTTTTTTAATTAT
1 TTTTTTTTTAATTAT
179507 TTTTTT
1 TTTTTT
179513 CAAACACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTTTTTAATTAT
Found at i:180310 original size:55 final size:55
Alignment explanation
Indices: 180226--181091 Score: 990
Period size: 55 Copynumber: 15.3 Consensus size: 55
180216 ATAAAGTGTA
* * * * * *
180226 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
**
180281 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTG
* * *
180342 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTCGGGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* **
180396 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTG
** * *
180457 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
180512 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* **
180567 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTG
* ** * *
180628 TCCTACTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * *
180683 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
180738 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* **
180793 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTG
* ** * *
180854 TCCTGCTCTTTGAGGACTAAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
180909 TCCTGCTCTTTGAGGATTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* * * *
180964 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGGGTAGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
181019 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTCGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
181074 TCCCGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
181092 AAAAAGCGGA
Statistics
Matches: 708, Mismatches: 69, Indels: 68
0.84 0.08 0.08
Matches are distributed among these distances:
54 35 0.05
55 451 0.64
56 30 0.04
59 4 0.01
60 37 0.05
61 151 0.21
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:180585 original size:171 final size:165
Alignment explanation
Indices: 180226--181091 Score: 1076
Period size: 171 Copynumber: 5.1 Consensus size: 165
180216 ATAAAGTGTA
* * * * *
180226 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAG-GCGTCCTGCTCT
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGAGCGTCCTGCTCT
** **
180290 TTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGA
66 TTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTT-AAAAG-----GTGTCCTGCTCTTTGA
** * *
180355 GGACTGAAGGTGCCACCAACTCGGGTGGGCTTTAAAAGGTG
125 GGACTGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
* *
180396 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAG----AGCGTCCT
*
180461 GCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAG
61 GCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAG
*
180526 GACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
126 GACT-GAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
* *
180567 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAG----AGCGTCCT
* *
180632 ACTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAG
61 GCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAG
*
180697 GACTGGAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
126 GACT-GAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
* *
180738 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAG-GTGTCCTGCTC
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGAGCGTCCTGCTC
* ** **
180801 TTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTG
65 TTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTT-AAAAG-----GTGTCCTGCTCTTTG
* *
180866 AGGACTAAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
124 AGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
* *
180909 TCCTGCTCTTTGAGGATTGAAAGGTGCCACCAACTTGTGTGGGCTTT--AAGAGGTGTCCTGCTC
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGA-GCGTCCTGCTC
* * * *
180972 TTTGAGGACTGGAAAATGCCACCAACTTGGGTAGGCTTTAAAAGGTGTCCTGCTCTTTGGGGACT
65 TTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACT
* * *
181037 GAAAGGTGCCACCAACTCGTGTGGGCTTTAAGAGGTG
130 GAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
*
181074 TCCCGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
181092 AAAAAGCGGA
Statistics
Matches: 627, Mismatches: 51, Indels: 41
0.87 0.07 0.06
Matches are distributed among these distances:
164 3 0.00
165 105 0.17
166 5 0.01
169 3 0.00
170 74 0.12
171 382 0.61
172 4 0.01
175 5 0.01
176 46 0.07
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (165 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGAGCGTCCTGCTCT
TTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTG
AAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
Found at i:180617 original size:29 final size:29
Alignment explanation
Indices: 180536--180617 Score: 84
Period size: 26 Copynumber: 2.9 Consensus size: 29
180526 GACTGGAAAA
180536 TGCCACCAACTTGTGTGGGCTTTGAAAGG
1 TGCCACCAACTTGTGTGGGCTTTGAAAGG
** *
180565 TGTCCTGC-TCTT-TG-GGGAC--TGAAAGG
1 TG-CCACCAACTTGTGTGGG-CTTTGAAAGG
180591 TGCCACCAACTTGTGTGGGCTTTGAAA
1 TGCCACCAACTTGTGTGGGCTTTGAAA
180618 AGAAAAAGCA
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
25 3 0.08
26 12 0.30
27 6 0.15
28 6 0.15
29 10 0.25
30 3 0.08
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (29 bp):
TGCCACCAACTTGTGTGGGCTTTGAAAGG
Found at i:180678 original size:27 final size:27
Alignment explanation
Indices: 180648--180733 Score: 64
Period size: 27 Copynumber: 3.1 Consensus size: 27
180638 TGAGGACTGA
180648 AAAATGCCACCAACCTGTGTGGGCTTT
1 AAAATGCCACCAACCTGTGTGGGCTTT
* *** ** * * * **
180675 AAAAGGTGTCCTGCTCTTTGAGGACTGG
1 AAAATGCCACCAAC-CTGTGTGGGCTTT
180703 AAAATGCCACCAACCTGTGTGGGCTTT
1 AAAATGCCACCAACCTGTGTGGGCTTT
180730 AAAA
1 AAAA
180734 GGTGTCCTGC
Statistics
Matches: 36, Mismatches: 22, Indels: 2
0.60 0.37 0.03
Matches are distributed among these distances:
27 20 0.56
28 16 0.44
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (27 bp):
AAAATGCCACCAACCTGTGTGGGCTTT
Found at i:180721 original size:226 final size:226
Alignment explanation
Indices: 180226--181065 Score: 1205
Period size: 226 Copynumber: 3.7 Consensus size: 226
180216 ATAAAGTGTA
* * * *
180226 TCCTGCTCATTGAGGAGT-AAAAAGTGCCACCAA-CTCGTGTGGGCTTTGAAAGGCGTCCTGCTC
1 TCCTGCTCTTTGAGGACTGAAAAA-TGCCACCAACCT-GTGTGGGCTTTAAAAGGTGTCCTGCTC
* **
180289 TTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTT
64 TTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTGTCCTGCTCTTT
* * ** *
180353 GAGGACTG-AAGGTGCCACCAACTCGGGTGGGCTTT-AAAAG-----GTGTCCTGCTCTTTGGGG
122 GGGGACTGAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGG
** * **
180411 ACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
187 ACTGAAAAATGCCACCAACCTGTGTGGGCTTT-AAAAG-----GTG
180457 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTT
180522 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACTGA
66 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACTGA
* *
180587 AAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTACTCTTTGAGGACTGAAAAA
131 AAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAAAA
180652 TGCCACCAACCTGTGTGGGCTTTAAAAGGTG
196 TGCCACCAACCTGTGTGGGCTTTAAAAGGTG
*
180683 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTT
180748 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACTGA
66 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACTGA
* *
180813 AAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTAAAAAA
131 AAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAAAA
180878 TGCCACCAACCTGTGTGGGCTTTAAAAGGTG
196 TGCCACCAACCTGTGTGGGCTTTAAAAGGTG
* ** * *
180909 TCCTGCTCTTTGAGGATTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTT
* * *
180974 TGAGGACTGGAAAATGCCACCAACTTGGGTAGGCTTTAAAAGGTGTCCTGCTCTTTGGGGACTGA
66 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACTGA
181039 AAGGTGCCACCAACTCGTGTGGGCTTT
131 AAGGTGCCACCAACTCGTGTGGGCTTT
181066 AAGAGGTGTC
Statistics
Matches: 567, Mismatches: 32, Indels: 25
0.91 0.05 0.04
Matches are distributed among these distances:
225 19 0.03
226 396 0.70
227 5 0.01
230 4 0.01
231 89 0.16
232 54 0.10
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (226 bp):
TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTT
TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACTGA
AAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAAAA
TGCCACCAACCTGTGTGGGCTTTAAAAGGTG
Found at i:180843 original size:29 final size:29
Alignment explanation
Indices: 180762--180843 Score: 84
Period size: 26 Copynumber: 2.9 Consensus size: 29
180752 GACTGGAAAA
180762 TGCCACCAACTTGTGTGGGCTTTGAAAGG
1 TGCCACCAACTTGTGTGGGCTTTGAAAGG
** *
180791 TGTCCTGC-TCTT-TG-GGGAC--TGAAAGG
1 TG-CCACCAACTTGTGTGGG-CTTTGAAAGG
180817 TGCCACCAACTTGTGTGGGCTTTGAAA
1 TGCCACCAACTTGTGTGGGCTTTGAAA
180844 AGAAAAAGCA
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
25 3 0.08
26 12 0.30
27 6 0.15
28 6 0.15
29 10 0.25
30 3 0.08
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (29 bp):
TGCCACCAACTTGTGTGGGCTTTGAAAGG
Found at i:189580 original size:51 final size:51
Alignment explanation
Indices: 189518--189688 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
189508 TTATTTCTGA
* *
189518 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCAATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
189569 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
189622 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
**
189674 AAGGATACTCCAACC
1 GGGGATACTCCAACC
189689 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 37 0.38
52 17 0.18
53 32 0.33
54 11 0.11
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:189645 original size:53 final size:51
Alignment explanation
Indices: 189342--189688 Score: 184
Period size: 51 Copynumber: 6.6 Consensus size: 51
189332 TTGAGTTGCT
* * * * * * *
189342 CAATTCTCCACAATCGAGGATATTCCAACTCCGATTTTACTTTCAAAACAT
1 CAATTTTCCATAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACAC
* * * *
189393 TAATTTTCTATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAAACAC
1 CAATTTTCCATAATCGGGGATACTCCAACCCCGATTTTATTTTC---AAAACAC
* * * ** *
189447 CAATTTCTTCACAATCGGGGACACTCCAACCCCG-TTAATCATCGGGGATACTCCAAAC-C
1 CAATTT-TCCATAATCGGGGATACTCCAACCCCGATT--T--T-----ATTTTCAAAACAC
* * * * * *
189506 C-GTTATTTC-TGA--GGGGATACTCCAACCCCGACTTTATTTTCAAAATAT
1 CAATT-TTCCATAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACAC
* * *
189554 CAATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTTCACAACAC
1 CAATTTTCCATAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACAC
* ** * *
189605 CAATTTCTCCTTTAATCGGGGATACTCCAATTCCGATTTTATTTCCAAAAATAC
1 CAATTT-TCC-ATAATCGGGGATACTCCAACCCCGATTTTATTTTC-AAAACAC
* * **
189659 CAATTTTTCACAATCAAGGATACTCCAACC
1 CAATTTTCCATAATCGGGGATACTCCAACC
189689 TCGTTATTTC
Statistics
Matches: 222, Mismatches: 51, Indels: 45
0.70 0.16 0.14
Matches are distributed among these distances:
47 7 0.03
48 5 0.02
49 4 0.02
51 73 0.33
52 18 0.08
53 32 0.14
54 25 0.11
55 39 0.18
56 2 0.01
57 1 0.00
58 6 0.03
59 3 0.01
60 4 0.02
63 3 0.01
ACGTcount: A:0.31, C:0.27, G:0.11, T:0.31
Consensus pattern (51 bp):
CAATTTTCCATAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACAC
Found at i:189707 original size:28 final size:28
Alignment explanation
Indices: 189671--189752 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
189661 ATTTTTCACA
*
189671 ATCAAGGATACTCCAACCTCGTTATTTC
1 ATCAGGGATACTCCAACCTCGTTATTTC
* *
189699 ATCAGGGATACTCCAACCCCGTTACTTC
1 ATCAGGGATACTCCAACCTCGTTATTTC
*
189727 --CGAGGGAACACTCCAACCTCGTTATT
1 ATC-AGGG-ATACTCCAACCTCGTTATT
189753 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 1 0.02
27 4 0.09
28 41 0.89
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.27
Consensus pattern (28 bp):
ATCAGGGATACTCCAACCTCGTTATTTC
Found at i:198395 original size:79 final size:79
Alignment explanation
Indices: 198304--198501 Score: 265
Period size: 79 Copynumber: 2.5 Consensus size: 79
198294 GTGTTCTCTT
* *
198304 GAAAATAACGGGGCTGGAGTATCCCCAGTTGTGAGAAATCGATGA-TTAGAAAAAAAAATCGGGA
1 GAAAATAACGGGGTTGGAGTATCCCCAGTTGTGAGAAATCAAT-ATTTAGAAAAAAAAATCGGGA
198368 TTGGAGTATCCCCTC
65 TTGGAGTATCCCCTC
* * * * * * *
198383 GAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAATAAAGTCGGGGT
1 GAAAATAACGGGGTTGGAGTATCCCCAGTTGTGAGAAATCAATATTTAGAAAAAAAAATCGGGAT
198448 TGGAGTATCCCCTC
66 TGGAGTATCCCCTC
*
198462 GGAAATAACGGGGTTGGAGTATCCCC-GATTGTGAAGAAAT
1 GAAAATAACGGGGTTGGAGTATCCCCAG-TTGTG-AGAAAT
198502 TGGTGTTTTT
Statistics
Matches: 104, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
78 1 0.01
79 97 0.93
80 6 0.06
ACGTcount: A:0.34, C:0.15, G:0.27, T:0.24
Consensus pattern (79 bp):
GAAAATAACGGGGTTGGAGTATCCCCAGTTGTGAGAAATCAATATTTAGAAAAAAAAATCGGGAT
TGGAGTATCCCCTC
Found at i:198541 original size:54 final size:51
Alignment explanation
Indices: 198474--198604 Score: 174
Period size: 51 Copynumber: 2.5 Consensus size: 51
198464 AAATAACGGG
* *
198474 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTG-AGAAATTAGTG--TTTTGAAAATAAAATCGGA
*
198528 GTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAG-AAATTAGTGTTTTGAAAATAAAATCGGA
*
198579 GTTGGAATATCCCCGATTGTGGAGAA
1 GTTGGAGTATCCCCGATTGT-GAGAA
198605 TTGAGAAACT
Statistics
Matches: 69, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
51 36 0.52
52 4 0.06
53 10 0.14
54 19 0.28
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAGAAATTAGTGTTTTGAAAATAAAATCGGA
Found at i:200964 original size:20 final size:20
Alignment explanation
Indices: 200937--200991 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
200927 TAAAATTTCC
*
200937 AAATGTATCGATACAAAGAT
1 AAATGTATCGATACAAAGAA
** *
200957 CCATGTATCGATACACAGAA
1 AAATGTATCGATACAAAGAA
200977 AAATGTATCGATACA
1 AAATGTATCGATACA
200992 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (20 bp):
AAATGTATCGATACAAAGAA
Found at i:201035 original size:19 final size:18
Alignment explanation
Indices: 201011--201078 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
201001 CAGTAGCTAA
201011 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
201030 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
201045 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
201062 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
201079 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:201051 original size:13 final size:13
Alignment explanation
Indices: 201033--201057 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
201023 ACAATACTTA
201033 TGTATCGATACAT
1 TGTATCGATACAT
201046 TGTATCGATACA
1 TGTATCGATACA
201058 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:201055 original size:32 final size:32
Alignment explanation
Indices: 201014--201076 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
201004 TAGCTAATTA
*
201014 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
201046 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
201077 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:201158 original size:21 final size:21
Alignment explanation
Indices: 201134--201190 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
201124 CATTTGTAGG
201134 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
201155 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
201176 ATGTATCGATACATT
1 ATGTATCGATACATT
201191 TGGATAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:201216 original size:12 final size:12
Alignment explanation
Indices: 201195--201232 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
201185 TACATTTGGA
*
201195 TAATTTTTTTTT
1 TAATTATTTTTT
201207 TAATTATTTTTTT
1 TAATTA-TTTTTT
201220 TAATTATTTTTT
1 TAATTATTTTTT
201232 T
1 T
201233 TCAAACACTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 12 0.50
13 12 0.50
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
TAATTATTTTTT
Found at i:201218 original size:13 final size:13
Alignment explanation
Indices: 201195--201233 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
201185 TACATTTGGA
201195 TAATT-TTTTTTT
1 TAATTATTTTTTT
201207 TAATTATTTTTTT
1 TAATTATTTTTTT
201220 TAATTATTTTTTT
1 TAATTATTTTTTT
201233 T
1 T
201234 CAAACACTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 5 0.19
13 21 0.81
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TAATTATTTTTTT
Found at i:203405 original size:15 final size:15
Alignment explanation
Indices: 203385--203415 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
203375 TAAAAATGTC
*
203385 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
203400 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
203415 C
1 C
203416 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:205516 original size:13 final size:13
Alignment explanation
Indices: 205498--205535 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
205488 CATTTTTCTT
205498 TGTATCGATACAA
1 TGTATCGATACAA
*
205511 TGTATCGATACAC
1 TGTATCGATACAA
205524 TGTATCGATACA
1 TGTATCGATACA
205536 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:205690 original size:20 final size:20
Alignment explanation
Indices: 205647--205692 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
205637 AAATCTTTTG
205647 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
205668 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
205688 CAAAA
1 CAAAA
205693 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:208104 original size:13 final size:13
Alignment explanation
Indices: 208086--208111 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
208076 TACACCAAGT
208086 ATGTATCGATACA
1 ATGTATCGATACA
208099 ATGTATCGATACA
1 ATGTATCGATACA
208112 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:209268 original size:23 final size:23
Alignment explanation
Indices: 209238--209305 Score: 88
Period size: 23 Copynumber: 3.1 Consensus size: 23
209228 TACATTGAAC
*
209238 AATGTATCGATACATCTGGGTAG
1 AATGTATCGATACATCTGGGTAA
*
209261 AATGTATCGATACAT-T--GAAA
1 AATGTATCGATACATCTGGGTAA
*
209281 AATGTTTCGATACATCTGGGTAA
1 AATGTATCGATACATCTGGGTAA
209304 AA
1 AA
209306 AGATAAAATG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
20 16 0.42
21 1 0.03
22 1 0.03
23 20 0.53
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.31
Consensus pattern (23 bp):
AATGTATCGATACATCTGGGTAA
Found at i:209270 original size:43 final size:44
Alignment explanation
Indices: 209222--209361 Score: 183
Period size: 51 Copynumber: 3.0 Consensus size: 44
209212 TAACTAGATC
*
209222 TATCGATACATTGAACAATGTATCGATACATCTGGGTAG-AATG
1 TATCGATACATTGAAAAATGTATCGATACATCTGGGTAGAAATG
*
209265 TATCGATACATTGAAAAATGTTTCGATACATCTGGGTAAAAAGATAAAATG
1 TATCGATACATTGAAAAATGTATCGATACATCTGGGT----AG---AAATG
*
209316 TATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAATG
1 TATCGATACATTGAAAAATGTATCGATACATCTGGGTAGAAATG
209360 TA
1 TA
209362 ACTTTTTCAT
Statistics
Matches: 85, Mismatches: 4, Indels: 15
0.82 0.04 0.14
Matches are distributed among these distances:
43 35 0.41
44 7 0.08
47 3 0.04
51 40 0.47
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (44 bp):
TATCGATACATTGAAAAATGTATCGATACATCTGGGTAGAAATG
Found at i:209342 original size:51 final size:51
Alignment explanation
Indices: 209261--209357 Score: 185
Period size: 51 Copynumber: 1.9 Consensus size: 51
209251 ATCTGGGTAG
*
209261 AATGTATCGATACATTGAAAAATGTTTCGATACATCTGGGTAAAAAGATAA
1 AATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGATAA
209312 AATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAA
1 AATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAA
209358 TGTAACTTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.43, C:0.10, G:0.18, T:0.29
Consensus pattern (51 bp):
AATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGATAA
Found at i:209361 original size:24 final size:20
Alignment explanation
Indices: 209222--209346 Score: 88
Period size: 20 Copynumber: 5.5 Consensus size: 20
209212 TAACTAGATC
*
209222 TATCGATACATTGAACAATG
1 TATCGATACATTGAAAAATG
* *
209242 TATCGATACATCTGGGTAGAATG
1 TATCGATACAT-T--GAAAAATG
209265 TATCGATACATTGAAAAATG
1 TATCGATACATTGAAAAATG
*
209285 TTTCGATACATCTGGGTAAAAAGATAAAATG
1 TATCGATACA--T---T-----GA-AAAATG
209316 TATCGATACATTGAAAAATG
1 TATCGATACATTGAAAAATG
209336 TATCGATACAT
1 TATCGATACAT
209347 CTGGGTAAAA
Statistics
Matches: 85, Mismatches: 6, Indels: 28
0.71 0.05 0.24
Matches are distributed among these distances:
20 43 0.51
21 3 0.04
22 2 0.02
23 17 0.20
25 1 0.01
26 1 0.01
29 1 0.01
30 2 0.02
31 15 0.18
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (20 bp):
TATCGATACATTGAAAAATG
Found at i:210260 original size:53 final size:51
Alignment explanation
Indices: 210202--210338 Score: 175
Period size: 53 Copynumber: 2.6 Consensus size: 51
210192 TGCCCGCATG
* * *
210202 TATCGATGCATTGAAGAATGTATCGATACATTTGGGTCAAAATCCCAGAATC
1 TATCGATACAATGAAAAATGTATCGATACATTTGGGTCAAAA-CCCAGAATC
* * * *
210254 TAATCGATACAATGAAAAATGTAGCAATACATTTGGGTCAAAACCCATAATG
1 T-ATCGATACAATGAAAAATGTATCGATACATTTGGGTCAAAACCCAGAATC
* *
210306 TATTGATACAATGAAAAATGTATTGATACATTT
1 TATCGATACAATGAAAAATGTATCGATACATTT
210339 TCATTCCAAA
Statistics
Matches: 73, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
51 28 0.38
52 9 0.12
53 36 0.49
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (51 bp):
TATCGATACAATGAAAAATGTATCGATACATTTGGGTCAAAACCCAGAATC
Found at i:215473 original size:20 final size:20
Alignment explanation
Indices: 215448--215501 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
215438 CATTTGAGAC
* *
215448 ATGTATCTATGCATTCACCT
1 ATGTATCAATACATTCACCT
215468 ATGTATCAATACATTCA-CT
1 ATGTATCAATACATTCACCT
215487 AATTGTATCAATACA
1 -A-TGTATCAATACA
215502 AATTGTAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 16 0.53
21 12 0.40
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.37
Consensus pattern (20 bp):
ATGTATCAATACATTCACCT
Found at i:218278 original size:167 final size:163
Alignment explanation
Indices: 217994--218376 Score: 482
Period size: 167 Copynumber: 2.3 Consensus size: 163
217984 CAAAAAATTC
* * * * * *
217994 AAAATTCATGAAATAAATTGAATTTTGAAAAATTGATTTAATGTGAATTTACTGACAATATTAGA
1 AAAACTCATGAAA-AAAATGAATTTTGCAAAATTGATTTAGTGGGAA-TTAATGACAATATTAGA
* * * *
218059 TGAATTTTAAAACTTTTAAATTGAGAAAAATCTCCCCAAAAATATTTATGGAATAGAAAACTCGA
64 TGAATTTTAAAACTTTTAAATCGAGAAAAATCCCCCCAAAAACATTTATGGAATAGAAAACTCAA
* *
218124 TTTTTTGGAAACA-GAGAAATTTTAAGCGAAAAAAAAAGA
129 TTTTTCGAAAACAGGA-AAATTTTAAG-G---AAAAAAGA
* *
218163 AAAACTCATGAAAACAAATGAATTTTTCAAAATTGATTTAGTGGGAATTAATGACAATATTATAT
1 AAAACTCATGAAAA-AAATGAATTTTGCAAAATTGATTTAGTGGGAATTAATGACAATATTAGAT
*
218228 GAATTTTAAAA-TTTTAAATCGAGAAAAATCCCCCCGAAAACATTTATGGAATAGAAAACTCAAT
65 GAATTTTAAAACTTTTAAATCGAGAAAAATCCCCCCAAAAACATTTATGGAATAGAAAACTCAAT
* *
218292 TTTTCGAAAATAGGAAAATTTTAAGGAAAAATGA
130 TTTTCGAAAACAGGAAAATTTTAAGGAAAAAAGA
* * * *
218326 AAAACTCATGAAAATAAGTGAATTTTGCAAAACTGATTTAGTAGCAATTAA
1 AAAACTCATGAAAA-AAATGAATTTTGCAAAATTGATTTAGTGGGAATTAA
218377 ATAATAATAT
Statistics
Matches: 189, Mismatches: 23, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
163 52 0.28
166 1 0.01
167 67 0.35
168 30 0.16
169 39 0.21
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (163 bp):
AAAACTCATGAAAAAAATGAATTTTGCAAAATTGATTTAGTGGGAATTAATGACAATATTAGATG
AATTTTAAAACTTTTAAATCGAGAAAAATCCCCCCAAAAACATTTATGGAATAGAAAACTCAATT
TTTCGAAAACAGGAAAATTTTAAGGAAAAAAGA
Found at i:220816 original size:13 final size:13
Alignment explanation
Indices: 220798--220822 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
220788 AATTGAGTGC
220798 GTATCGATACAAT
1 GTATCGATACAAT
220811 GTATCGATACAA
1 GTATCGATACAA
220823 AGCATAATTT
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:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (13 bp):
GTATCGATACAAT
Found at i:225821 original size:52 final size:52
Alignment explanation
Indices: 225743--225891 Score: 237
Period size: 52 Copynumber: 2.9 Consensus size: 52
225733 CGAAATATGA
*
225743 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGAATAATGTATCGATACATCTGGGC
**
225795 AAATTTGCCTGCATGTATCGATACATTTCATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGAATAATGTATCGATACATCTGGGC
**
225847 AAATTTGCCTGCATGTATCGATACAAAG-ATCAATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAAT-AATGTATCGATACA
225892 ATGTATCGAT
Statistics
Matches: 90, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
51 2 0.02
52 88 0.98
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTGAATAATGTATCGATACATCTGGGC
Found at i:225895 original size:13 final size:13
Alignment explanation
Indices: 225877--225904 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
225867 ATACAAAGAT
225877 CAATGTATCGATA
1 CAATGTATCGATA
225890 CAATGTATCGATA
1 CAATGTATCGATA
225903 CA
1 CA
225905 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:225982 original size:33 final size:33
Alignment explanation
Indices: 225945--226011 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
225935 AGTAGCTTAA
225945 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
225978 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
226011 A
1 A
226012 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:225985 original size:13 final size:13
Alignment explanation
Indices: 225967--225991 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
225957 CAAAAAAATA
225967 TGTATCGATACAT
1 TGTATCGATACAT
225980 TGTATCGATACA
1 TGTATCGATACA
225992 ACACTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:226927 original size:43 final size:45
Alignment explanation
Indices: 226864--227003 Score: 167
Period size: 43 Copynumber: 3.0 Consensus size: 45
226854 TGTTAAAGAT
226864 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTT-G
1 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAG
* *
226908 G-AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
1 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTT--AG
* *
226954 GTACCAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAG
1 G-----AAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAG
227004 AAGAAGACGC
Statistics
Matches: 81, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
43 39 0.48
44 1 0.01
46 2 0.02
50 2 0.02
52 37 0.46
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.24
Consensus pattern (45 bp):
GAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAG
Found at i:227082 original size:28 final size:28
Alignment explanation
Indices: 227050--227206 Score: 188
Period size: 28 Copynumber: 5.4 Consensus size: 28
227040 GATTGCATCA
*
227050 ACTTGTGTGCTTTTGAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
* *
227078 ACTTGTGGGCTTTTAAAGATTGCCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
*
227106 ACTTGTGGGCTTTTAAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTG
* *
227134 ACTTGTGGGCTTTTGAAAAGAGATGCCACTA
1 ACTTGTGGGCTTTTG--AAG-GTTGCCACTG
* * *
227165 ACTTATGGGCTTTTGAAAAGGGTGCCACTA
1 ACTTGTGGGCTTTTG--AAGGTTGCCACTG
227195 ACTTGTGGGCTT
1 ACTTGTGGGCTT
227207 AAAAGGAAAA
Statistics
Matches: 116, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
28 66 0.57
30 23 0.20
31 27 0.23
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.34
Consensus pattern (28 bp):
ACTTGTGGGCTTTTGAAGGTTGCCACTG
Found at i:227125 original size:56 final size:57
Alignment explanation
Indices: 227024--227206 Score: 228
Period size: 56 Copynumber: 3.2 Consensus size: 57
227014 CACCAACTTG
* *
227024 TGTGGGCTTTTAAAAGGATTG-CA-TCAACTTGTGTGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTAAAA-GATTGCCACT-AACTTGTGGGCTTTTAAAGGTTGCCACTGACT
*
227081 TGTGGGCTTTT-AAAGATTGCCACTGACTTGTGGGCTTTTAAAGGTTGCCACTGACT
1 TGTGGGCTTTTAAAAGATTGCCACTAACTTGTGGGCTTTTAAAGGTTGCCACTGACT
* * * *
227137 TGTGGGCTTTTGAAAAGAGATGCCACTAACTTATGGGCTTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTT-AAAAGA-TTGCCACTAACTTGTGGGCTTTT--AAAGGTTGCCACTGACT
227198 TGTGGGCTT
1 TGTGGGCTT
227207 AAAAGGAAAA
Statistics
Matches: 111, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
55 5 0.05
56 45 0.41
57 12 0.11
58 5 0.05
59 20 0.18
61 24 0.22
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.34
Consensus pattern (57 bp):
TGTGGGCTTTTAAAAGATTGCCACTAACTTGTGGGCTTTTAAAGGTTGCCACTGACT
Found at i:227193 original size:30 final size:30
Alignment explanation
Indices: 227050--227515 Score: 312
Period size: 30 Copynumber: 15.6 Consensus size: 30
227040 GATTGCATCA
* *
227050 ACTTGTGTGCTTTTG--AAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
**
227078 ACTTGTGGGCTTTT--AAAGATTGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
*
227106 ACTTGTGGGCTTTT--AAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
* *
227134 ACTTGTGGGCTTTTGAAAAGAGATGCCACTA
1 ACTTGTGGGCTTTTGAAAAG-GGTGCCACTG
* *
227165 ACTTATGGGCTTTTGAAAAGGGTGCCACTA
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
** * *
227195 ACTTGTGGGCTTAAAAGGAAAAAGAGTGCTA-TAG
1 ACTTGTGGGCTT---TTG-AAAAGGGTGCCACT-G
* * ** * *
227229 AGTTGTGAGCTTACAAAAGAAAAAGAGTGCCACGG
1 ACTTGTGGGCTT----TTG-AAAAGGGTGCCACTG
* * * * *
227264 AGTTGTGGACTTTGGAAAA-GATGCCACCG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
* * *
227293 ACTTATGGGC-TTCGAAAAAAGGTGCCACTG
1 ACTTGTGGGCTTTTG-AAAAGGGTGCCACTG
* * * *
227323 ATTTGTGGGC-TTTGAAAAAGATGCCACCG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
***
227352 ACTTGTGGGCTTCAAAAAAGGGTGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
* * * *
227382 ATTTATGGGC-TTTG--AAGGTTGCCACCG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
* *
227409 ATTTGTGGGCTTTTGAAAAGGGTGCCACTA
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
* * *
227439 ACTTGTGGGCTTTTGAAAAAAGATGCCATTG
1 ACTTGTGGGCTTTTG-AAAAGGGTGCCACTG
* *
227470 ACTTGTGGGC-TTTGAAAAAGATGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
227499 ACTTGTGGGCTTTTGAA
1 ACTTGTGGGCTTTTGAA
227516 GGGTGAGGAA
Statistics
Matches: 358, Mismatches: 61, Indels: 36
0.79 0.13 0.08
Matches are distributed among these distances:
27 20 0.06
28 73 0.20
29 65 0.18
30 102 0.28
31 49 0.14
33 2 0.01
34 20 0.06
35 27 0.08
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (30 bp):
ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
Found at i:227267 original size:35 final size:34
Alignment explanation
Indices: 227180--227270 Score: 94
Period size: 35 Copynumber: 2.6 Consensus size: 34
227170 TGGGCTTTTG
* * * *
227180 AAAAGGGTGCCACTA-ACTTGTGGGCTTAAAAGGA
1 AAAAGAGTGCCAC-AGAGTTGTGAGCTTAAAAAGA
* *
227214 AAAAGAGTGCTATAGAGTTGTGAGCTTACAAAAGA
1 AAAAGAGTGCCACAGAGTTGTGAGCTTA-AAAAGA
*
227249 AAAAGAGTGCCACGGAGTTGTG
1 AAAAGAGTGCCACAGAGTTGTG
227271 GACTTTGGAA
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
33 1 0.02
34 21 0.46
35 24 0.52
ACGTcount: A:0.37, C:0.12, G:0.30, T:0.21
Consensus pattern (34 bp):
AAAAGAGTGCCACAGAGTTGTGAGCTTAAAAAGA
Found at i:227342 original size:59 final size:58
Alignment explanation
Indices: 227065--227511 Score: 339
Period size: 59 Copynumber: 7.4 Consensus size: 58
227055 TGTGCTTTTG
* * **
227065 AAGGTTGCCACTGACTTGTGGGCTTT--TAAAGATTGCCACTGACTTGTGGGCTT--TTA
1 AAGG-TGCCACTGACTTGTGGGCTTTGAAAAAGA-TGCCACCGACTTGTGGGCTTCGAAA
** * *
227121 AAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGAGATGCCACTAACTTATGGGCTTTTGAAA
1 AAGG-TGCCACTGACTTGTGGGC-TTTGAAAA-AGATGCCACCGACTTGTGGGC-TTCGAAA
* * * * ** * *
227183 AGGGTGCCACTAACTTGTGGGCTTAAAAGGAAAAAGAGTGCTATAGAGTTGTGAGCTTACAAAAG
1 AAGGTGCCACTGACTTGTGGGCTT----TGAAAAAGA-TGCCACCGACTTGTGGGCTT-C----G
227248 AAA
56 AAA
* * * * *
227251 AAGAGTGCCACGGAGTTGTGGACTTTGGAAAAGATGCCACCGACTTATGGGCTTCGAAAA
1 AAG-GTGCCACTGACTTGTGGGCTTTGAAAAAGATGCCACCGACTTGTGGGCTTCG-AAA
* *
227311 AAGGTGCCACTGATTTGTGGGCTTTGAAAAAGATGCCACCGACTTGTGGGCTTCAAAA
1 AAGGTGCCACTGACTTGTGGGCTTTGAAAAAGATGCCACCGACTTGTGGGCTTCGAAA
* * * * * *
227369 AAGGGTGCCACTGATTTATGGGCTTTG--AAGGTTGCCACCGATTTGTGGGCTTTTGAAA
1 AA-GGTGCCACTGACTTGTGGGCTTTGAAAAAGATGCCACCGACTTGTGGGC-TTCGAAA
* * ** *
227427 AGGGTGCCACTAACTTGTGGGCTTTTGAAAAAAGATGCCATTGACTTGTGGGCTTTGAAA
1 AAGGTGCCACTGACTTGTGGGC-TTTG-AAAAAGATGCCACCGACTTGTGGGCTTCGAAA
*
227487 AAGATGCCACTGACTTGTGGGCTTT
1 AAGGTGCCACTGACTTGTGGGCTTT
227512 TGAAGGGTGA
Statistics
Matches: 313, Mismatches: 53, Indels: 47
0.76 0.13 0.11
Matches are distributed among these distances:
56 23 0.07
57 40 0.13
58 15 0.05
59 91 0.29
60 39 0.12
61 35 0.11
62 4 0.01
63 6 0.02
64 30 0.10
65 7 0.02
68 6 0.02
69 17 0.05
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.28
Consensus pattern (58 bp):
AAGGTGCCACTGACTTGTGGGCTTTGAAAAAGATGCCACCGACTTGTGGGCTTCGAAA
Found at i:227411 original size:27 final size:27
Alignment explanation
Indices: 227369--227436 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 27
227359 GGCTTCAAAA
*
227369 AAGGGTGCCACTGATTTATGGGCTTTG
1 AAGGGTGCCACCGATTTATGGGCTTTG
* *
227396 AAGGTTGCCACCGATTTGTGGGCTTTTG
1 AAGGGTGCCACCGATTTATGGGC-TTTG
227424 AAAAGGGTGCCAC
1 --AAGGGTGCCAC
227437 TAACTTGTGG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 20 0.59
28 4 0.12
30 10 0.29
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (27 bp):
AAGGGTGCCACCGATTTATGGGCTTTG
Found at i:228958 original size:1 final size:1
Alignment explanation
Indices: 228952--229023 Score: 72
Period size: 1 Copynumber: 72.0 Consensus size: 1
228942 TCCGGACCCC
* * * * * * * *
228952 TTTTTTTGTTTTTGTTTTTTTGTTTTGTTTTTTTTTGTTTTTTTTGTTTTTTTTGTTTTGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
229017 TTTTTTT
1 TTTTTTT
229024 GTGGAGGACG
Statistics
Matches: 55, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (1 bp):
T
Found at i:228971 original size:14 final size:13
Alignment explanation
Indices: 228952--229025 Score: 98
Period size: 14 Copynumber: 5.7 Consensus size: 13
228942 TCCGGACCCC
228952 TTTTTTTGTTTTT
1 TTTTTTTGTTTTT
228965 GTTTTTTTG-TTTT
1 -TTTTTTTGTTTTT
* *
228978 GTTTTTT-TTTGT
1 TTTTTTTGTTTTT
228990 TTTTTTTGTTTTT
1 TTTTTTTGTTTTT
229003 TTTGTTTTGTTTTT
1 TTT-TTTTGTTTTT
229017 TTTTTTTGT
1 TTTTTTTGT
229026 GGAGGACGCC
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
12 15 0.28
13 17 0.32
14 21 0.40
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (13 bp):
TTTTTTTGTTTTT
Found at i:228990 original size:23 final size:23
Alignment explanation
Indices: 228955--229025 Score: 99
Period size: 23 Copynumber: 3.0 Consensus size: 23
228945 GGACCCCTTT
228955 TTTTGTTTTTGTTTTTTTGTTTTG
1 TTTT-TTTTTGTTTTTTTGTTTTG
228979 TTTTTTTTTGTTTTTTTTGTTTT-
1 TTTTTTTTTG-TTTTTTTGTTTTG
* *
229002 TTTTGTTTTGTTTTTTTTTTTTG
1 TTTTTTTTTGTTTTTTTGTTTTG
229025 T
1 T
229026 GGAGGACGCC
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
22 11 0.26
23 16 0.37
24 16 0.37
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (23 bp):
TTTTTTTTTGTTTTTTTGTTTTG
Found at i:228994 original size:38 final size:37
Alignment explanation
Indices: 228952--229023 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 37
228942 TCCGGACCCC
228952 TTTTTTTGTTTTTGTTT-TTTTGTTTTGTTTTTTTTTGT
1 TTTTTTTGTTTTT-TTTGTTTTGTTTT-TTTTTTTTTGT
228990 TTTTTTTGTTTTTTTTGTTTTGTTTTTTTTTTTT
1 TTTTTTTGTTTTTTTTGTTTTGTTTTTTTTTTTT
229024 GTGGAGGACG
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
37 11 0.33
38 22 0.67
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (37 bp):
TTTTTTTGTTTTTTTTGTTTTGTTTTTTTTTTTTTGT
Found at i:229008 original size:33 final size:31
Alignment explanation
Indices: 228952--229022 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 31
228942 TCCGGACCCC
228952 TTTTTTTGTTTTTGTTTTTTTGTTTTGTTTT
1 TTTTTTTGTTTTTGTTTTTTTGTTTTGTTTT
*
228983 TTTTTGTTTTTTTTGTTTTTTTTGTTTTGTTTT
1 TTTTT-TTGTTTTTG-TTTTTTTGTTTTGTTTT
229016 TTTTTTT
1 TTTTTTT
229023 TGTGGAGGAC
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
31 5 0.14
32 10 0.27
33 22 0.59
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (31 bp):
TTTTTTTGTTTTTGTTTTTTTGTTTTGTTTT
Found at i:229021 original size:19 final size:19
Alignment explanation
Indices: 228955--229023 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
228945 GGACCCCTTT
*
228955 TTTTGTTTTTGTTTTTTTG
1 TTTTGTTTTTTTTTTTTTG
228974 TTTTGTTTTTTTTTGTTTT-
1 TTTTGTTTTTTTTT-TTTTG
*
228993 TTTTGTTTTTTTTGTTTTG
1 TTTTGTTTTTTTTTTTTTG
229012 TTTT-TTTTTTTT
1 TTTTGTTTTTTTT
229024 GTGGAGGACG
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
18 12 0.26
19 30 0.65
20 4 0.09
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (19 bp):
TTTTGTTTTTTTTTTTTTG
Found at i:236878 original size:28 final size:28
Alignment explanation
Indices: 236846--236901 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
236836 GATTCGTCTT
236846 GACAAGCCTGGAGGGATTGCTCTAACTC
1 GACAAGCCTGGAGGGATTGCTCTAACTC
236874 GACAAGCCTGGAGGGATTGCTCTAACTC
1 GACAAGCCTGGAGGGATTGCTCTAACTC
236902 TTGGATTCTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.25, G:0.29, T:0.21
Consensus pattern (28 bp):
GACAAGCCTGGAGGGATTGCTCTAACTC
Found at i:238875 original size:21 final size:21
Alignment explanation
Indices: 238846--238890 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
238836 AAGTTTTCAT
*
238846 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
238866 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
238888 TTT
1 TTT
238891 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:244672 original size:8 final size:8
Alignment explanation
Indices: 244659--244684 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
244649 ATTTGATTAA
244659 ATTTTGTG
1 ATTTTGTG
244667 ATTTTGTG
1 ATTTTGTG
244675 ATTTTGTG
1 ATTTTGTG
244683 AT
1 AT
244685 GGATGATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:244905 original size:13 final size:13
Alignment explanation
Indices: 244887--244911 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
244877 CAACATTCTC
244887 TGTATCGATACAT
1 TGTATCGATACAT
244900 TGTATCGATACA
1 TGTATCGATACA
244912 AAGGGTTTAT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:245078 original size:20 final size:20
Alignment explanation
Indices: 245043--245084 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
245033 CAAATTTCTT
245043 ATTTTTCACTTCAAAATACATC
1 ATTTTTCAC-TCAAAAT-CATC
245065 ATTTTTCA-TCAAAATCATC
1 ATTTTTCACTCAAAATCATC
245084 A
1 A
245085 ACAAAAACAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 7 0.35
22 8 0.40
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTTTTCACTCAAAATCATC
Found at i:247239 original size:23 final size:20
Alignment explanation
Indices: 247209--247250 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 20
247199 GATAAGTATA
247209 AATGTTTTCAAAGCTTAAAATG
1 AATGTTTTC-AAG-TTAAAATG
247231 AATGATTTTCAAGTTAAAAT
1 AATG-TTTTCAAGTTAAAAT
247251 ATATCAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 7 0.37
23 5 0.26
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (20 bp):
AATGTTTTCAAGTTAAAATG
Found at i:247388 original size:13 final size:13
Alignment explanation
Indices: 247370--247394 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
247360 AGATTGCATA
247370 GTATCGATACATT
1 GTATCGATACATT
247383 GTATCGATACAT
1 GTATCGATACAT
247395 GATCAAATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:247407 original size:33 final size:32
Alignment explanation
Indices: 247349--247416 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 32
247339 CACCTTCAAA
*
247349 TGTATCGATACAGATTGCATAGTATCGATACAT
1 TGTATCGATACAGATTGCAAAGTATCGATAC-T
247382 TGTATCGATACATGA-T-CAAATGTATCGATACT
1 TGTATCGATACA-GATTGCAAA-GTATCGATACT
247414 TGT
1 TGT
247417 TAAGAATATA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
32 7 0.22
33 23 0.72
34 2 0.06
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAGATTGCAAAGTATCGATACT
Found at i:247512 original size:13 final size:13
Alignment explanation
Indices: 247494--247519 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
247484 TACACACAAG
247494 ATGTATCGATACA
1 ATGTATCGATACA
247507 ATGTATCGATACA
1 ATGTATCGATACA
247520 TACCAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:247536 original size:33 final size:32
Alignment explanation
Indices: 247476--247539 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
247466 CTTAACTGTT
*
247476 TGTATCGATACACACAAGATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
*
247508 TGTATCGATACATACCAAAATGTATCGATACA
1 TGTATCGATACACA-CAAAATGTATCGATACA
247540 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.27
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:253808 original size:13 final size:13
Alignment explanation
Indices: 253790--253814 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
253780 ACAGCAAGTT
253790 TGTATCGATACAA
1 TGTATCGATACAA
253803 TGTATCGATACA
1 TGTATCGATACA
253815 CAAAAAATTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:256946 original size:13 final size:13
Alignment explanation
Indices: 256928--256980 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
256918 CGATACATGG
256928 TACATTGTATCGA
1 TACATTGTATCGA
256941 TACATTGTATCGA
1 TACATTGTATCGA
256954 TACA-TG-AT-GA
1 TACATTGTATCGA
256964 -A-A-TGTATCGA
1 TACATTGTATCGA
256974 TACATTG
1 TACATTG
256981 CTTGTAACGG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
8 3 0.09
9 3 0.09
10 4 0.11
11 3 0.09
12 3 0.09
13 19 0.54
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:256954 original size:33 final size:33
Alignment explanation
Indices: 256912--256980 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
256902 CTATAACTAT
* *
256912 TTGTATCGATACATGGT-ACATTGTATCGATACA
1 TTGTATCGATACATGATGA-AATGTATCGATACA
256945 TTGTATCGATACATGATGAAATGTATCGATACA
1 TTGTATCGATACATGATGAAATGTATCGATACA
256978 TTG
1 TTG
256981 CTTGTAACGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATGATGAAATGTATCGATACA
Found at i:265694 original size:20 final size:20
Alignment explanation
Indices: 265652--265704 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
265642 CGCACCCAGA
265652 TGTATCGATACAT-GATCAT
1 TGTATCGATACATGGATCAT
265671 TGTATCGATACATGGA-CAAT
1 TGTATCGATACATGGATC-AT
265691 TGTATCGATACATG
1 TGTATCGATACATG
265705 AAACTGGCAG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 14 0.44
20 18 0.56
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (20 bp):
TGTATCGATACATGGATCAT
Found at i:265770 original size:13 final size:13
Alignment explanation
Indices: 265749--265778 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
265739 CGATACATGG
*
265749 TACATTGTATCGA
1 TACAATGTATCGA
265762 TACAATGTATCGA
1 TACAATGTATCGA
265775 TACA
1 TACA
265779 TGATGAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
TACAATGTATCGA
Found at i:268126 original size:47 final size:47
Alignment explanation
Indices: 268047--268137 Score: 128
Period size: 47 Copynumber: 1.9 Consensus size: 47
268037 AATACCGTGC
*
268047 ATGTACCAATACATTAATAAGTATATCAATACATTCTGGAAACCTAG
1 ATGTACCAATACATTAATAACTATATCAATACATTCTGGAAACCTAG
* * * * *
268094 ATGTATCAATACATTATTCACTGTATCGATACATTCTGGAAACC
1 ATGTACCAATACATTAATAACTATATCAATACATTCTGGAAACC
268138 CAAAAGTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 38 1.00
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (47 bp):
ATGTACCAATACATTAATAACTATATCAATACATTCTGGAAACCTAG
Found at i:268154 original size:27 final size:27
Alignment explanation
Indices: 268116--268181 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
268106 ATTATTCACT
* *
268116 GTATCGATACATTCTGGAAACCCAAAA
1 GTATCGATACATTCTAGAAAACCAAAA
* * *
268143 GTATTGATACATTCTAGAAAACCTAGA
1 GTATCGATACATTCTAGAAAACCAAAA
268170 GTATCGATACAT
1 GTATCGATACAT
268182 CATTCAAAGT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.27
Consensus pattern (27 bp):
GTATCGATACATTCTAGAAAACCAAAA
Found at i:272272 original size:19 final size:20
Alignment explanation
Indices: 272248--272300 Score: 81
Period size: 19 Copynumber: 2.7 Consensus size: 20
272238 ATAATTTGGC
*
272248 CATGTATCGATACAATG-AA
1 CATGTATCGATACAAAGCAA
*
272267 CATGTATCGATACAAAGCAG
1 CATGTATCGATACAAAGCAA
272287 CATGTATCGATACA
1 CATGTATCGATACA
272301 TCTGGGTGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.25
Consensus pattern (20 bp):
CATGTATCGATACAAAGCAA
Found at i:272874 original size:36 final size:36
Alignment explanation
Indices: 272825--272899 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
272815 TCATCATTTT
* *
272825 TCTCCCCTTAAAAAAATTCTCCCCC-TTAAACGATTA
1 TCTCCCC-TAAAAAAAATCTCCCCCTTTAAACGACTA
*
272861 TCTCCTCTAAAAAAAATCTCCCCCTTTAAACGACTA
1 TCTCCCCTAAAAAAAATCTCCCCCTTTAAACGACTA
272897 TCT
1 TCT
272900 TCTCCCCCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
35 16 0.46
36 19 0.54
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.31
Consensus pattern (36 bp):
TCTCCCCTAAAAAAAATCTCCCCCTTTAAACGACTA
Found at i:274777 original size:13 final size:13
Alignment explanation
Indices: 274759--274786 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
274749 AATAGTACCT
274759 AATGTATCGATAC
1 AATGTATCGATAC
274772 AATGTATCGATAC
1 AATGTATCGATAC
274785 AA
1 AA
274787 GGAATGTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:281068 original size:13 final size:13
Alignment explanation
Indices: 281050--281076 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
281040 TACAATGAAC
281050 ATGTATCGATACA
1 ATGTATCGATACA
281063 ATGTATCGATACA
1 ATGTATCGATACA
281076 A
1 A
281077 AGCAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:281091 original size:33 final size:32
Alignment explanation
Indices: 281031--281095 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
281021 CAATTTGGCC
* *
281031 ATGTATCTATACAATGAACATGTATCGATACA
1 ATGTATCGATACAAAGAACATGTATCGATACA
*
281063 ATGTATCGATACAAAGCAGCATGTATCGATACA
1 ATGTATCGATACAAAG-AACATGTATCGATACA
281096 TCTGGGTGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (32 bp):
ATGTATCGATACAAAGAACATGTATCGATACA
Found at i:284173 original size:20 final size:20
Alignment explanation
Indices: 284125--284166 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
284115 AGTTGTAGCT
*
284125 TAGA-GTATCGATACATATT
1 TAGATGTATCGATACATATG
284144 TAGATGTATCGATACATTATG
1 TAGATGTATCGATACA-TATG
284165 TA
1 TA
284167 TTGTATCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 11 0.55
21 5 0.25
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.38
Consensus pattern (20 bp):
TAGATGTATCGATACATATG
Found at i:284285 original size:20 final size:20
Alignment explanation
Indices: 284259--284312 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
284249 CATTTATGTA
*
284259 ATGTATCGATACATTGT-AT
1 ATGTATCGATACATTCTGAT
284278 ATTGTATCGATACATTCTGAT
1 A-TGTATCGATACATTCTGAT
*
284299 ATGTATCTATACAT
1 ATGTATCGATACAT
284313 ATAGAGTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 1 0.03
20 27 0.87
21 3 0.10
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTCTGAT
Found at i:284374 original size:111 final size:112
Alignment explanation
Indices: 284146--284384 Score: 282
Period size: 111 Copynumber: 2.1 Consensus size: 112
284136 TACATATTTA
* * * * *
284146 GATGTATCGATACATTATGTATTGTATCAATATATTTTTATATATATCAATACAAATGAGGGTTT
1 GATGTATCGATACATTATATATTGTATCAATACATTCTGATATATATCAATACAAATGAGAGTTT
* * * * ** *
284211 CAAGATTTCTTTAGCTATTGCCAACAGATGTGTTGATGCATTTATGT
66 CAAGATTTCCTTAGCTACTACCAACAGATGTATCAATGCATTCATGT
* * * * * *
284258 AATGTATCGATACATTGTATATTGTATCGATACATTCTGATATGTATCTATACATAT-AGAGTTT
1 GATGTATCGATACATTATATATTGTATCAATACATTCTGATATATATCAATACAAATGAGAGTTT
* **
284322 TAAGATTTCCTTAGCTACTACCAGTAGATGTATCAATGCATTCATGT
66 CAAGATTTCCTTAGCTACTACCAACAGATGTATCAATGCATTCATGT
284369 GATGTATCGATACATT
1 GATGTATCGATACATT
284385 TAATCATAAA
Statistics
Matches: 105, Mismatches: 22, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
111 58 0.55
112 47 0.45
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (112 bp):
GATGTATCGATACATTATATATTGTATCAATACATTCTGATATATATCAATACAAATGAGAGTTT
CAAGATTTCCTTAGCTACTACCAACAGATGTATCAATGCATTCATGT
Found at i:286893 original size:19 final size:20
Alignment explanation
Indices: 286850--286900 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
286840 TACAAGCCAA
**
286850 TGTATCGATACATTTTATGG
1 TGTATCGATACATACTATGG
286870 TGTATCGATACATACTAT-G
1 TGTATCGATACATACTATGG
286889 TGTATCGATACA
1 TGTATCGATACA
286901 AGTTTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATACTATGG
Found at i:288065 original size:20 final size:19
Alignment explanation
Indices: 288040--288094 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
288030 TTGCCAGTTT
*
288040 TATGTATTGATACAATTGA
1 TATGTATCGATACAATTGA
*
288059 GTATGTATCCATACAA-TGA
1 -TATGTATCGATACAATTGA
288078 TCATGTATCGATACAAT
1 T-ATGTATCGATACAAT
288095 GTATCAAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 1 0.03
19 16 0.53
20 13 0.43
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (19 bp):
TATGTATCGATACAATTGA
Found at i:288085 original size:19 final size:20
Alignment explanation
Indices: 288061--288100 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
288051 ACAATTGAGT
288061 ATGTATCCATACAATG-ATC
1 ATGTATCCATACAATGTATC
*
288080 ATGTATCGATACAATGTATC
1 ATGTATCCATACAATGTATC
288100 A
1 A
288101 AAACAAAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGTATCCATACAATGTATC
Found at i:296857 original size:20 final size:19
Alignment explanation
Indices: 296832--296887 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
296822 TTGGGCATAT
*
296832 TGTATCGATACATTTCTTCA
1 TGTATCGATACATTTC-CCA
*
296852 TGTATCGATACAATGTCCCA
1 TGTATCGATAC-ATTTCCCA
296872 TGTATCGATACATTTC
1 TGTATCGATACATTTC
296888 ACTTAGGGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.12
20 24 0.75
21 4 0.12
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.39
Consensus pattern (19 bp):
TGTATCGATACATTTCCCA
Found at i:296957 original size:19 final size:19
Alignment explanation
Indices: 296911--296972 Score: 81
Period size: 19 Copynumber: 3.2 Consensus size: 19
296901 ACTGCCAGTT
296911 TCATGTATCGATACAATTGA
1 TCATGTATCGATACAA-TGA
*
296931 GT-ATGTATCCATACAATGA
1 -TCATGTATCGATACAATGA
296950 TCATGTATCGATACAATGTA
1 TCATGTATCGATACAATG-A
296970 TCA
1 TCA
296973 ATACAAAGCA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
18 1 0.03
19 18 0.49
20 17 0.46
21 1 0.03
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (19 bp):
TCATGTATCGATACAATGA
Found at i:296994 original size:33 final size:32
Alignment explanation
Indices: 296933--296997 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
296923 ACAATTGAGT
* * *
296933 ATGTATCCATACAATGATCATGTATCGATACA
1 ATGTATCAATACAAAGATAATGTATCGATACA
296965 ATGTATCAATACAAAGCATAATGTATCGATACA
1 ATGTATCAATACAAAG-ATAATGTATCGATACA
296998 TCAGGGTGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (32 bp):
ATGTATCAATACAAAGATAATGTATCGATACA
Found at i:301470 original size:46 final size:46
Alignment explanation
Indices: 301418--301565 Score: 142
Period size: 46 Copynumber: 3.2 Consensus size: 46
301408 AACAGATTTC
301418 TTCCCCTTTTTGTTATCTCCCAAATTTTACAAAACTACCACAAAAT
1 TTCCCCTTTTTGTTATCTCCCAAATTTTACAAAACTACCACAAAAT
* * * ** * ** *
301464 TTCCCC-TTTT-ATA-AT-ACAAATTTTGTTAAACTCTAAAACAAATT
1 TTCCCCTTTTTGTTATCTCCCAAATTTT-ACAAA-ACTACCACAAAAT
301508 TCTCACCCTTTTTGTTATCTCCCAAATTTTACAAAACTACCACAAAAT
1 T-TC-CCCTTTTTGTTATCTCCCAAATTTTACAAAACTACCACAAAAT
*
301556 CTCCCCTTTT
1 TTCCCCTTTT
301566 ATAAAACAAA
Statistics
Matches: 75, Mismatches: 19, Indels: 16
0.68 0.17 0.15
Matches are distributed among these distances:
42 8 0.11
43 4 0.05
44 12 0.16
45 6 0.08
46 16 0.21
47 6 0.08
48 11 0.15
49 4 0.05
50 8 0.11
ACGTcount: A:0.32, C:0.27, G:0.02, T:0.39
Consensus pattern (46 bp):
TTCCCCTTTTTGTTATCTCCCAAATTTTACAAAACTACCACAAAAT
Found at i:301484 original size:42 final size:42
Alignment explanation
Indices: 301438--301578 Score: 111
Period size: 42 Copynumber: 3.2 Consensus size: 42
301428 TGTTATCTCC
301438 CAAATTTTACAAAACTACCACAAAATTTCCCCTTTTATAATA
1 CAAATTTTACAAAACTACCACAAAATTTCCCCTTTTATAATA
** * ** * * * *
301480 CAAATTTTGTTAAACTCTAAAACAAATTTCTCACCCTTTTTGTTATCTCC
1 CAAATTTT-ACAAA-ACTACCACAAAATT-TC-CCC-TTTT-ATA-AT-A
* *
301530 CAAATTTTACAAAACTACCACAAAATCTCCCCTTTTATAAAA
1 CAAATTTTACAAAACTACCACAAAATTTCCCCTTTTATAATA
301572 CAAATTT
1 CAAATTT
301579 ATTTGAAAAT
Statistics
Matches: 71, Mismatches: 20, Indels: 16
0.66 0.19 0.15
Matches are distributed among these distances:
42 15 0.21
43 3 0.04
44 12 0.17
45 6 0.08
46 6 0.08
47 6 0.08
48 11 0.15
49 4 0.06
50 8 0.11
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.35
Consensus pattern (42 bp):
CAAATTTTACAAAACTACCACAAAATTTCCCCTTTTATAATA
Found at i:301549 original size:92 final size:92
Alignment explanation
Indices: 301392--301578 Score: 331
Period size: 92 Copynumber: 2.0 Consensus size: 92
301382 TAATGCTTTC
*
301392 TTTTGTTAAACTCTAAAACAGATTTCTTCCCCTTTTTGTTATCTCCCAAATTTTACAAAACTACC
1 TTTTGTTAAACTCTAAAACAAATTTCTTCCCCTTTTTGTTATCTCCCAAATTTTACAAAACTACC
* *
301457 ACAAAATTTCCCCTTTTATAATACAAA
66 ACAAAATCTCCCCTTTTATAAAACAAA
301484 TTTTGTTAAACTCTAAAACAAATTTC-TCACCCTTTTTGTTATCTCCCAAATTTTACAAAACTAC
1 TTTTGTTAAACTCTAAAACAAATTTCTTC-CCCTTTTTGTTATCTCCCAAATTTTACAAAACTAC
301548 CACAAAATCTCCCCTTTTATAAAACAAA
65 CACAAAATCTCCCCTTTTATAAAACAAA
301576 TTT
1 TTT
301579 ATTTGAAAAT
Statistics
Matches: 91, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
91 2 0.02
92 89 0.98
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.39
Consensus pattern (92 bp):
TTTTGTTAAACTCTAAAACAAATTTCTTCCCCTTTTTGTTATCTCCCAAATTTTACAAAACTACC
ACAAAATCTCCCCTTTTATAAAACAAA
Found at i:305545 original size:15 final size:15
Alignment explanation
Indices: 305527--305555 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
305517 CAAGTCAACT
305527 TCTTCATCATCATCA
1 TCTTCATCATCATCA
305542 TCTTCATCATCATC
1 TCTTCATCATCATC
305556 GATGGTTGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.34, G:0.00, T:0.41
Consensus pattern (15 bp):
TCTTCATCATCATCA
Found at i:307155 original size:13 final size:13
Alignment explanation
Indices: 307137--307162 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
307127 TTAGGCTCAA
307137 TGTATCGATACAT
1 TGTATCGATACAT
307150 TGTATCGATACAT
1 TGTATCGATACAT
307163 GATGAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:309009 original size:23 final size:22
Alignment explanation
Indices: 308983--309033 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
308973 TTTTGTTGGT
*
308983 TTTAATTGGACTTTTAGTTCAGA
1 TTTAA-TGGACTTTTAGTTCAAA
*
309006 TTTAGATGGACTTTTAGTTTAAA
1 TTTA-ATGGACTTTTAGTTCAAA
309029 TTTAA
1 TTTAA
309034 ATAGGTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 1 0.04
23 23 0.92
24 1 0.04
ACGTcount: A:0.29, C:0.06, G:0.16, T:0.49
Consensus pattern (22 bp):
TTTAATGGACTTTTAGTTCAAA
Found at i:309999 original size:2 final size:2
Alignment explanation
Indices: 309992--310033 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
309982 CACTAAGAAA
* *
309992 AT AT AT AT AT AT AG AT AT AT AT AT AT AT AT AT AC AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
310033 A
1 A
310034 AGTCACCATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:315761 original size:12 final size:11
Alignment explanation
Indices: 315739--315814 Score: 61
Period size: 12 Copynumber: 6.9 Consensus size: 11
315729 AGAGAAAGAA
*
315739 GAGAGAGGAGG
1 GAGATAGGAGG
315750 GATGATAGGAGG
1 GA-GATAGGAGG
*
315762 AGAGACAGGA--
1 -GAGATAGGAGG
*
315772 GAGATAGTA--
1 GAGATAGGAGG
315781 GAGATAGGAGG
1 GAGATAGGAGG
315792 GATGATAGGAGG
1 GA-GATAGGAGG
315804 AGAGATAGGAG
1 -GAGATAGGAG
315815 AGATAATAGA
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.07
12 31 0.57
13 4 0.07
ACGTcount: A:0.39, C:0.01, G:0.49, T:0.11
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:315771 original size:24 final size:24
Alignment explanation
Indices: 315738--315823 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
315728 AAGAGAAAGA
*
315738 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGATAGGAGGGATGATAGGAGG
* *
315762 AGAGACAGGA--GA-GAT---AGT
1 AGAGATAGGAGGGATGATAGGAGG
315780 AGAGATAGGAGGGATGATAGGAGG
1 AGAGATAGGAGGGATGATAGGAGG
* *
315804 AGAGATAGGAGAGATAATAG
1 AGAGATAGGAGGGATGATAG
315824 AGAGAGGAGG
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 29 0.58
ACGTcount: A:0.42, C:0.01, G:0.45, T:0.12
Consensus pattern (24 bp):
AGAGATAGGAGGGATGATAGGAGG
Found at i:315773 original size:9 final size:9
Alignment explanation
Indices: 315759--315819 Score: 56
Period size: 9 Copynumber: 7.1 Consensus size: 9
315749 GGATGATAGG
*
315759 AGGAGAGAC
1 AGGAGAGAT
315768 AGGAGAGAT
1 AGGAGAGAT
*
315777 AGTAGAGAT
1 AGGAGAGAT
*
315786 AGGAGGGAT
1 AGGAGAGAT
* *
315795 --GATAG-G
1 AGGAGAGAT
315801 AGGAGAGAT
1 AGGAGAGAT
315810 AGGAGAGAT
1 AGGAGAGAT
315819 A
1 A
315820 ATAGAGAGAG
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
7 3 0.08
8 4 0.10
9 33 0.82
ACGTcount: A:0.43, C:0.02, G:0.44, T:0.11
Consensus pattern (9 bp):
AGGAGAGAT
Found at i:315790 original size:42 final size:42
Alignment explanation
Indices: 315729--315847 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
315719 TAGCCCTCAA
* *
315729 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
315771 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGATAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
315813 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
315848 GAGAGAAGAA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.43, C:0.02, G:0.46, T:0.09
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:315823 original size:12 final size:12
Alignment explanation
Indices: 315783--315828 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
315773 AGATAGTAGA
*
315783 GATAGGAGGGAT
1 GATAGGAGAGAT
315795 GATAGGAGGAGA-
1 GATAGGA-GAGAT
315807 GATAGGAGAGAT
1 GATAGGAGAGAT
*
315819 AATA-GAGAGA
1 GATAGGAGAGA
315829 GGAGGGATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
11 10 0.33
12 17 0.57
13 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.43, T:0.13
Consensus pattern (12 bp):
GATAGGAGAGAT
Found at i:324092 original size:6 final size:6
Alignment explanation
Indices: 324083--324136 Score: 51
Period size: 6 Copynumber: 9.2 Consensus size: 6
324073 TTGAAAACCA
*
324083 AAAAAG AAAAAGG AGAAAG -AAAA- AAAAAG AAAAAG AAAAA- AAAAGAG
1 AAAAAG AAAAA-G AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA-AG
*
324130 TAAAAG A
1 AAAAAG A
324137 GAGCTTTTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
5 11 0.28
6 20 0.51
7 8 0.21
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:324117 original size:16 final size:16
Alignment explanation
Indices: 324084--324128 Score: 63
Period size: 16 Copynumber: 2.7 Consensus size: 16
324074 TGAAAACCAA
*
324084 AAAAGAAAAAGGAGAAAG
1 AAAA-AAAAA-GAAAAAG
324102 AAAAAAAAAGAAAAAG
1 AAAAAAAAAGAAAAAG
324118 AAAAAAAAAGA
1 AAAAAAAAAGA
324129 GTAAAAGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 17 0.65
17 5 0.19
18 4 0.15
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAGAAAAAG
Found at i:324868 original size:59 final size:59
Alignment explanation
Indices: 324778--324944 Score: 162
Period size: 59 Copynumber: 2.8 Consensus size: 59
324768 ATTTTTATGT
* * *
324778 ATTTT-AGAGTCATCTAAGTTATTTTATATAGTATAGGGACCTTTTAGCAAGTTCCATAC
1 ATTTTAAG-GTCATTTAAGTTAATTTATATAGTATAGGGACCATTTAGCAAGTTCCATAC
* * * * * * * *
324837 ATTTT-AGGATTATTT-AGTTTAATTTACATAGTCTAGAGACCATTTAGTAATTTTCATGC
1 ATTTTAAGG-TCATTTAAG-TTAATTTATATAGTATAGGGACCATTTAGCAAGTTCCATAC
* *
324896 ATTTTAAGGTCATTTAAGTTATTTTATATA-TTTAGGGACCATTTAGCAA
1 ATTTTAAGGTCATTTAAGTTAATTTATATAGTATAGGGACCATTTAGCAA
324945 CTTTTTCAAG
Statistics
Matches: 87, Mismatches: 17, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
58 19 0.22
59 63 0.72
60 5 0.06
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (59 bp):
ATTTTAAGGTCATTTAAGTTAATTTATATAGTATAGGGACCATTTAGCAAGTTCCATAC
Found at i:325028 original size:48 final size:48
Alignment explanation
Indices: 324957--325141 Score: 158
Period size: 48 Copynumber: 3.8 Consensus size: 48
324947 TTTTCAAGTC
* * * * *
324957 TCTTTTACGATTATTTTTGTACTTCTACCAAAACTAACCAAAATTAAG
1 TCTTTTAAGGTTAGTTTTGTACTTCTATCAAAACCAACCAAAATTAAG
* * * * *
325005 TCTTTTAAGGTTAGTTTTATACTTTCCATTAAAACCAGCCAAAATCAAG
1 TCTTTTAAGGTTAGTTTTGTAC-TTCTATCAAAACCAACCAAAATTAAG
* * * * *
325054 TC-TTTGAGAGTTAGTTTTGTACTTTTGTCAAAATCGATCC-AAATTAAG
1 TCTTTTAAG-GTTAGTTTTGTACTTCTATCAAAA-CCAACCAAAATTAAG
* * *
325102 TTTTTTAGGGTTAGCTTTGTACTTACTATCAAAACCAACC
1 TCTTTTAAGGTTAGTTTTGTACTT-CTATCAAAACCAACC
325142 GAAACTGAAC
Statistics
Matches: 105, Mismatches: 27, Indels: 10
0.74 0.19 0.07
Matches are distributed among these distances:
48 56 0.53
49 49 0.47
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.39
Consensus pattern (48 bp):
TCTTTTAAGGTTAGTTTTGTACTTCTATCAAAACCAACCAAAATTAAG
Found at i:935592 original size:28 final size:29
Alignment explanation
Indices: 935552--935613 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 29
935542 ATAAGGTAAT
935552 TTACACACATATCAAAAA-TTATTTGCAC
1 TTACACACATATCAAAAATTTATTTGCAC
935580 TTACACACATATCAAAAATTTATTTGCAC
1 TTACACACATATCAAAAATTTATTTGCAC
*
935609 ATACA
1 TTACA
935614 TACTATCTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 18 0.56
29 14 0.44
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.32
Consensus pattern (29 bp):
TTACACACATATCAAAAATTTATTTGCAC
Found at i:937407 original size:13 final size:13
Alignment explanation
Indices: 937389--937413 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
937379 ATAATCCCCC
937389 TGTATCGATACAG
1 TGTATCGATACAG
937402 TGTATCGATACA
1 TGTATCGATACA
937414 AAGAAAAATG
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:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:943582 original size:20 final size:21
Alignment explanation
Indices: 943557--943609 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
943547 TACAAGCCAA
* *
943557 TGTATCGATACAAT-TTTTTG
1 TGTATCGATACAATACTTTGG
943577 TGTATCGATAC-ATACTTTGG
1 TGTATCGATACAATACTTTGG
943597 TGTATCGATACAA
1 TGTATCGATACAA
943610 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 26 0.90
21 1 0.03
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (21 bp):
TGTATCGATACAATACTTTGG
Found at i:943614 original size:19 final size:19
Alignment explanation
Indices: 943557--943615 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 19
943547 TACAAGCCAA
* *
943557 TGTATCGATACAATTTTTTG
1 TGTATCGATACAA-CTTTGG
943577 TGTATCGATACATACTTTGG
1 TGTATCGATACA-ACTTTGG
*
943597 TGTATCGATACAAGTTTGG
1 TGTATCGATACAACTTTGG
943616 CTACTGCCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
19 6 0.17
20 28 0.80
21 1 0.03
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.42
Consensus pattern (19 bp):
TGTATCGATACAACTTTGG
Found at i:950478 original size:19 final size:19
Alignment explanation
Indices: 950435--950490 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
950425 CTGCCAGTTT
*
950435 CATGTATCGATACAATTGTA
1 CATGTATCGATACAA-TGAA
*
950455 CATGTATTGATACAATGAA
1 CATGTATCGATACAATGAA
950474 CATGTATCGATACAATG
1 CATGTATCGATACAATG
950491 TATCGATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:950493 original size:13 final size:13
Alignment explanation
Indices: 950475--950501 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
950465 TACAATGAAC
950475 ATGTATCGATACA
1 ATGTATCGATACA
950488 ATGTATCGATACA
1 ATGTATCGATACA
950501 A
1 A
950502 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:951087 original size:13 final size:13
Alignment explanation
Indices: 951069--951095 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
951059 ACATTATGCT
951069 TTGTATCGATACA
1 TTGTATCGATACA
951082 TTGTATCGATACA
1 TTGTATCGATACA
951095 T
1 T
951096 GATCACTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:951127 original size:20 final size:19
Alignment explanation
Indices: 951080--951136 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
951070 TGTATCGATA
*
951080 CATTGTATCGATACATGAT
1 CATTGTATCGATACATGAC
* *
951099 CACTGTATCGATACATGGC
1 CATTGTATCGATACATGAC
951118 CAATTGTATCGATACATGA
1 C-ATTGTATCGATACATGA
951137 AACTGGCAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (19 bp):
CATTGTATCGATACATGAC
Found at i:951189 original size:20 final size:20
Alignment explanation
Indices: 951164--951202 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
951154 CTACCACTAT
*
951164 TTGTATCGATACATGGTATA
1 TTGTATCGACACATGGTATA
*
951184 TTGTATCGACACATTGTAT
1 TTGTATCGACACATGGTAT
951203 CGAAACATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (20 bp):
TTGTATCGACACATGGTATA
Found at i:951199 original size:13 final size:13
Alignment explanation
Indices: 951183--951245 Score: 57
Period size: 13 Copynumber: 5.3 Consensus size: 13
951173 TACATGGTAT
951183 ATTGTATCGACAC
1 ATTGTATCGACAC
*
951196 ATTGTATCGAAAC
1 ATTGTATCGACAC
*
951209 A-TG----G-TAC
1 ATTGTATCGACAC
951216 ATTGTATCGACAC
1 ATTGTATCGACAC
*
951229 ATTGTATCGATAC
1 ATTGTATCGACAC
951242 ATTG
1 ATTG
951246 CTTATAACGG
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
7 3 0.08
8 3 0.08
12 3 0.08
13 31 0.77
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Consensus pattern (13 bp):
ATTGTATCGACAC
Found at i:951211 original size:33 final size:33
Alignment explanation
Indices: 951164--951243 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
951154 CTACCACTAT
*
951164 TTGTATCGATACATGGTATATTGTATCGACACA
1 TTGTATCGATACATGGTACATTGTATCGACACA
*
951197 TTGTATCGAAACATGGTACATTGTATCGACACA
1 TTGTATCGATACATGGTACATTGTATCGACACA
951230 TTGTATCGATACAT
1 TTGTATCGATACAT
951244 TGCTTATAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35
Consensus pattern (33 bp):
TTGTATCGATACATGGTACATTGTATCGACACA
Found at i:959977 original size:13 final size:13
Alignment explanation
Indices: 959959--959985 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
959949 ACATTATGCT
959959 TTGTATCGATACA
1 TTGTATCGATACA
959972 TTGTATCGATACA
1 TTGTATCGATACA
959985 T
1 T
959986 GATCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:959982 original size:33 final size:32
Alignment explanation
Indices: 959940--960004 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
959930 CACACCCAGA
* *
959940 TGTATCGATACATTATGCTTTGTATCGATACAT
1 TGTATCGATACATGAT-CATTGTATCGATACAT
959973 TGTATCGATACATGATCATTGTATCGATACAT
1 TGTATCGATACATGATCATTGTATCGATACAT
960005 AGACAATTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATGATCATTGTATCGATACAT
Found at i:960015 original size:20 final size:19
Alignment explanation
Indices: 959970--960147 Score: 112
Period size: 20 Copynumber: 8.8 Consensus size: 19
959960 TGTATCGATA
959970 CATTGTATCGATACATGAT
1 CATTGTATCGATACATGAT
959989 CATTGTATCGATACATAGA-
1 CATTGTATCGATACAT-GAT
960008 CAATTGTATCGATACATGA-
1 C-ATTGTATCGATACATGAT
* * * * * * * *
960027 AACTGGCAATAGCTACCTTAC
1 CA-TTG-TATCGATACATGAT
960048 CACTGCTTGTATCGATACATGGTAT
1 CA----TTGTATCGATACAT-G-AT
960073 -ATTGTATCGATACATGAT
1 CATTGTATCGATACATGAT
*
960091 GAATTGTATCGATACATGGTAT
1 -CATTGTATCGATACAT-G-AT
960113 -ATTGTATCGATACATGAT
1 CATTGTATCGATACATGAT
*
960131 GAATTGTATCGATACAT
1 -CATTGTATCGATACAT
960148 TACTTGTAAC
Statistics
Matches: 128, Mismatches: 15, Indels: 31
0.74 0.09 0.18
Matches are distributed among these distances:
18 5 0.04
19 23 0.18
20 84 0.66
21 2 0.02
22 2 0.02
23 7 0.05
24 4 0.03
25 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (19 bp):
CATTGTATCGATACATGAT
Found at i:960108 original size:40 final size:40
Alignment explanation
Indices: 960054--960147 Score: 188
Period size: 40 Copynumber: 2.4 Consensus size: 40
960044 TTACCACTGC
960054 TTGTATCGATACATGGTATATTGTATCGATACATGATGAA
1 TTGTATCGATACATGGTATATTGTATCGATACATGATGAA
960094 TTGTATCGATACATGGTATATTGTATCGATACATGATGAA
1 TTGTATCGATACATGGTATATTGTATCGATACATGATGAA
960134 TTGTATCGATACAT
1 TTGTATCGATACAT
960148 TACTTGTAAC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (40 bp):
TTGTATCGATACATGGTATATTGTATCGATACATGATGAA
Found at i:965370 original size:93 final size:93
Alignment explanation
Indices: 965211--965397 Score: 356
Period size: 93 Copynumber: 2.0 Consensus size: 93
965201 AGGTCAAAAG
965211 CAGTTTCCCCAGCTAAAATGCCAGGATATGTTGCATACACGAAATCCTTAATCAAGTTGATAATT
1 CAGTTTCCCCAGCTAAAATGCCAGGATATGTTGCATACACGAAATCCTTAATCAAGTTGATAATT
965276 GACTTACCAAGACTAAACATGGCCATTC
66 GACTTACCAAGACTAAACATGGCCATTC
965304 CAGTTTCCCCAGCTAAAATGCCAGGATATGTTGCATACACGAAATCCTTAATCAAGTTGATAATT
1 CAGTTTCCCCAGCTAAAATGCCAGGATATGTTGCATACACGAAATCCTTAATCAAGTTGATAATT
* *
965369 GACTTACCAATACTAAGCATGGCCATTC
66 GACTTACCAAGACTAAACATGGCCATTC
965397 C
1 C
965398 GGAACCTGCC
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (93 bp):
CAGTTTCCCCAGCTAAAATGCCAGGATATGTTGCATACACGAAATCCTTAATCAAGTTGATAATT
GACTTACCAAGACTAAACATGGCCATTC
Found at i:970578 original size:22 final size:22
Alignment explanation
Indices: 970553--970602 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
970543 TTCGAGCTAT
*
970553 TACATTTAGTTATAG-GATTATA
1 TACATTTAGTTATAGTCA-TATA
970575 TACATTTAGTTATAGTCATATA
1 TACATTTAGTTATAGTCATATA
970597 TACATT
1 TACATT
970603 CAATTATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 25 0.96
23 1 0.04
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (22 bp):
TACATTTAGTTATAGTCATATA
Found at i:970979 original size:2 final size:2
Alignment explanation
Indices: 970972--970999 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
970962 AGTTCTAATG
970972 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
971000 TTAGGTTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.