Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1355
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: 343905
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:284614 original size:27 final size:27
Alignment explanation
Indices: 284573--285659 Score: 261
Period size: 27 Copynumber: 35.0 Consensus size: 27
284563 CTTTAAAATG
*
284573 AAAAAGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
284600 AAAAGGGTGCTACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
284627 AAAAGGAAAAAAAAGTGCCACGGAGTTGTGGGCTTT
1 AAAAGG--------GTGCCACGGAGTTGTGGAC-TT
*
284663 AAAAAGAAAAAGGTGCCACGGAGTTGTAGACTT
1 -AAAAG-----GGTGCCACGGAGTTGTGGACTT
*
284696 AAAAGGGTGCCACAGAGTTGTGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
* *
284724 GAAAAGAAAAAGGTGCCACAGAGTCGTGGACTTT
1 -AAAAG-----GGTGCCACGGAGTTGTGGAC-TT
* *
284758 AAGCAAAAGATGCCACGGAGTTGTGGACTT
1 -A--AAAGGGTGCCACGGAGTTGTGGACTT
* ** *
284788 AAAAGGGTGCCACGAAGTAATGAACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
** *
284815 AAAAGGAAAAAGATGCCACGGAGTCATGGGCTTT
1 AAAAGG-----G-TGCCACGGAGTTGTGGAC-TT
*
284849 AAAAAGAAAAAGGTGTCACGGAGTTGTGGACTT
1 -AAAAG-----GGTGCCACGGAGTTGTGGACTT
284882 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
284909 AAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTT
1 AAAA-G-----G-GTGCCACGGAGTTGTGGAC-TT
284944 AAAAAGAAAAAGGTGCCACGGAGTTGTGGACTT
1 -AAAAG-----GGTGCCACGGAGTTGTGGACTT
**
284977 AAAAGGGTGCCACAAAGTTGTGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
** *
285005 GAAAAGAAAAAGGTGCCACAAAGTCGTGGACTTT
1 -AAAAG-----GGTGCCACGGAGTTGTGGAC-TT
* * *
285039 AAGAAAAAGATGCCACGAAGTTGTGGACTT
1 ---AAAAGGGTGCCACGGAGTTGTGGACTT
**
285069 AAAAGGGTGCCACGGAGTAATGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* * ** *
285096 AAGAGGAAAAAGATGCCATGGAGTCATGGGCTTT
1 AAAAGG-----G-TGCCACGGAGTTGTGGAC-TT
*
285130 AAAAAGAAAAAGGTGTCACGGAGTTGTGGACTT
1 -AAAAG-----GGTGCCACGGAGTTGTGGACTT
*
285163 AAAAGGGTGCCACGGAGTTATGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
**
285190 AAAAGGAAAAGGAGTGCCACGGTCTTGTGG-CTTT
1 ------AAAAGG-GTGCCACGGAGTTGTGGAC-TT
* **
285224 AAAAAGAAAAATGTGCCACAAAGTTGTGGACTT
1 -AAAAG-----GGTGCCACGGAGTTGTGGACTT
* **
285257 AAAAAGGTGCCATAGAGTTGTGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
*
285285 GAAAAGAAAAAGGTGCCACAGAGTTGTGGACTTT
1 -AAAAG-----GGTGCCACGGAGTTGTGGAC-TT
* * *
285319 AAGAAAAAGATGCCACAGAGTTGTGGACTT
1 ---AAAAGGGTGCCACGGAGTTGTGGACTT
* * *
285349 AAAAGGGTGCCACTGAGTTATAGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
285376 AAAAGGAAAAAGATGCCACGGAGTTGTAGG-CTTT
1 AAAAGG-----G-TGCCACGGAGTTGT-GGAC-TT
* *
285410 AAAAAAAAAAAGGTGTCACGGAGTTGTGGACTT
1 ------AAAAGGGTGCCACGGAGTTGTGGACTT
* *
285443 AAAAGGAAAAAGAGTGCCACGAAGTTGTGGGCTTT
1 AAAA-G-----G-GTGCCACGGAGTTGTGGAC-TT
285478 AAAAAGAAAAAGGTGCCACGGAGTTGTGGACTT
1 -AAAAG-----GGTGCCACGGAGTTGTGGACTT
* *
285511 AAAAAGGTGCCACAGAGTTGTGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
* ** *
285539 GAAAAGAAAAAGGTGCCACAGAGTCATGGATTTT
1 -AAAAG-----GGTGCCACGGAGTTGTGGA-CTT
* * *
285573 GAGAAAAAGATGCCATGGAGTTGTGGACTT
1 ---AAAAGGGTGCCACGGAGTTGTGGACTT
*
285603 AAAAGGGTGCCACAGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
285630 AAAAAAGAGATGCCACTGAGTTGTGGACTT
1 --AAAAG-GGTGCCACGGAGTTGTGGACTT
285660 TGAAGAAAAG
Statistics
Matches: 823, Mismatches: 109, Indels: 253
0.69 0.09 0.21
Matches are distributed among these distances:
27 256 0.31
28 9 0.01
29 29 0.04
30 28 0.03
31 67 0.08
32 31 0.04
33 80 0.10
34 235 0.29
35 47 0.06
36 28 0.03
37 5 0.01
40 7 0.01
42 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.30, T:0.21
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTTGTGGACTT
Found at i:284875 original size:186 final size:185
Alignment explanation
Indices: 284113--285720 Score: 1235
Period size: 186 Copynumber: 8.5 Consensus size: 185
284103 CTTAAAAGGG
* * * * * * *
284113 AAAAAGGTGCCAC-GAAGTCGTGGACTTAAAA-AGAAAAGGCGCTACAGAGTTGAGGACTTAAAA
1 AAAAGGGTGCCACAG-AGTTGTGGACTTAAAAGA-AAAAGGTGCCACAGAGTCGTGGACTTTAAA
* * * * * * *
284176 GGAACAAGGTACCACGGAGTTGTGCACTTAAAAGGAAAAAGATACCACGAAGGTGTGGGCTTAAA
64 -GAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG-----G-TGCCACGAAGTTATGGACTTAAA
* * * *
284241 AGGGAAAAGGGTGCCACGGAGTCGTGGAC-TTAAAAAG-AAAAGGTGCCACGGAGTTGTGGGCTT
122 A-GGAAAAAGATGCCACGGAGTCGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGAC-T
284304 T
185 T
* * * *
284305 AAAAAGAAAAATGTGCCACGGAGTTGTGGACTTAAAAGGGAAAAGGGATGCCACGGAGGT-GTGG
1 -AAAAG-----GGTGCCACAGAGTTGTGGACTTAAAA--GAAAAAGG-TGCCACAGA-GTCGTGG
* * * * *
284369 ACTTAAAAGGAAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTG
56 ACTTTAAA-G-AAAAAGGTGCCACGGAGTTGTGGAC-TT-AAAAG-----GGTGCCACGAAGTTA
* * ** * * **
284434 TGGACTTAAAAGG-----G-TGCTACAGAGTTATGGACTTTGAAAAGAAAAAGGTGCCACAAAGT
112 TGGACTTAAAAGGAAAAAGATGCCACGGAGTCGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
*
284493 CGTGGACTTT
177 TGTGGAC-TT
* * * * *
284503 GGAAAAAAGATGCCA-TGAAGTTGTGGACTTAAAAGGAAAAAGATGCCACAGAGTCGTGGGCTTT
1 ---AAAAGGGTGCCACAG-AGTTGTGGACTTAAAA-GAAAAAGGTGCCACAGAGTCGTGGACTTT
* * *
284567 AAAATGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCTACGGAGTTGTGGACTTAAAAG
61 -AAA-GAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGAAGTTATGGACTTAAAAG
* * *
284632 GAAAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTAGACTT
124 G-AAAAAGA-TGCCACGGAGTCGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTT
284696 AAAAGGGTGCCACAGAGTTGTGGACTTTGAAAAGAAAAAGGTGCCACAGAGTCGTGGACTTT-AA
1 AAAAGGGTGCCACAGAGTTGTGGAC-TT-AAAAGAAAAAGGTGCCACAGAGTCGTGGACTTTAAA
* * * *
284760 GCAAAAGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGAAGTAATGAACTTAAAAGGAAAA
64 GAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGAAGTTATGGACTTAAAAGGAAAA
* *
284825 AGATGCCACGGAGTCATGGGCTTTAAAAAGAAAAAGGTGTCACGGAGTTGTGGACTT
129 AGATGCCACGGAGTCGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTT
* * *
284882 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAA
1 AAAAGGGTGCCACAGAGTTGTGGACTTAAAA-GAAAAAG-GTGCCACAGAGTCGTGGACTTT--A
* *
284947 AAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAAAGTTGTGGACTTTGAAAA-G
62 AAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGAAGTTATGGAC-TT-AAAAGG
* ** * * *
285011 AAAAAGGTGCCACAAAGTCGTGGACTTT---AAGAAAAAGATGCCACGAAGTTGTGGACTT
125 AAAAAGATGCCACGGAGTCGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTT
* ** * * ** * *
285069 AAAAGGGTGCCACGGAGTAATGGACTTAAGAGGAAAAAGATGCCATGGAGTCATGGGCTTTAAAA
1 AAAAGGGTGCCACAGAGTTGTGGACTTAA-AAGAAAAAGGTGCCACAGAGTCGTGGACTTT--AA
* *
285134 AGAAAAAGGTGTCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTATGGACTTAAAAGGAAA
63 AGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGAAGTTATGGACTTAAAAGGAAA
* * * **
285199 AGGAGTGCCAC-G-GTCTTGTGGCTTTAAAAAGAAAAATGTGCCACAAAGTTGTGGACTT
128 AAGA-TGCCACGGAGTCGTG-GGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTT
* * *
285257 AAAAAGGTGCCATAGAGTTGTGGACTTTGAAAAGAAAAAGGTGCCACAGAGTTGTGGACTTT-AA
1 AAAAGGGTGCCACAGAGTTGTGGAC-TT-AAAAGAAAAAGGTGCCACAGAGTCGTGGACTTTAAA
* * *
285321 GAAAAAGATGCCACAGAGTTGTGGACTTAAAAGGGTGCCACTG-AGTTATAGACTTAAAAGGAAA
64 GAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCAC-GAAGTTATGGACTTAAAAGGAAA
* * * *
285385 AAGATGCCACGGAGTTGTAGGCTTTAAAAAAAAAAAGGTGTCACGGAGTTGTGGACTT
128 AAGATGCCACGGAGTCGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTT
* * *
285443 AAAAGGAAAAAGAGTGCCAC-GAAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGG
1 AAAA-G-----G-GTGCCACAG-AGTTGTGGAC-TT-AAAAGAAAAAGGTGCCACAGAGTCGTGG
* *
285507 AC-TT----AAAAAGGTGCCACAGAGTTGTGGACTTTGAAAAGAAAAAGGTGCCAC-AGAGTCAT
56 ACTTTAAAGAAAAAGGTGCCACGGAGTTGTGGAC-TT-AAAAG-----GGTGCCACGA-AGTTAT
*** * * * *
285566 GGA-TTTTGA-GAAAAAGATGCCATGGAGTTGTGGAC-TT-AAAAG-----GGTGCCACAGAGTT
113 GGACTTAAAAGGAAAAAGATGCCACGGAGTCGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTT
285622 GTGGACTT
178 GTGGACTT
* * ** * *
285630 AAAAAAGAGATGCCACTGAGTTGTGGACTTTGAAG-AAAAGATGCCACTGAGTCGTGGACTTT--
1 --AAAAG-GGTGCCACAGAGTTGTGGACTTAAAAGAAAAAGGTGCCACAGAGTCGTGGACTTTAA
* * * *
285692 AGAACAAGATGCCACTGAGTCGTGGACTT
63 AGAAAAAGGTGCCACGGAGTTGTGGACTT
285721 TGAAGAAAAA
Statistics
Matches: 1180, Mismatches: 156, Indels: 169
0.78 0.10 0.11
Matches are distributed among these distances:
180 21 0.02
181 5 0.00
182 4 0.00
183 36 0.03
184 16 0.01
185 28 0.02
186 300 0.25
187 91 0.08
188 103 0.09
189 105 0.09
190 50 0.04
191 44 0.04
192 16 0.01
193 93 0.08
194 78 0.07
195 24 0.02
196 29 0.02
197 8 0.01
198 45 0.04
199 1 0.00
200 10 0.01
201 20 0.02
202 24 0.02
203 22 0.02
204 6 0.01
209 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.30, T:0.21
Consensus pattern (185 bp):
AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAAAAAGGTGCCACAGAGTCGTGGACTTTAAAGA
AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGAAGTTATGGACTTAAAAGGAAAAAG
ATGCCACGGAGTCGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTT
Found at i:285033 original size:281 final size:281
Alignment explanation
Indices: 284235--285516 Score: 1577
Period size: 281 Copynumber: 4.5 Consensus size: 281
284225 AAGGTGTGGG
* * * *
284235 CTTAAAAGGGAAAAGGGTGCCACGGAGTCGTGGAC-TTAAAAAG-AAAAGGTGCCACGGAGTTGT
1 CTTAAAA-GGAAAAAGATGCCACGGAGTCGTGGGCTTTAAAAAGAAAAAGGTGTCACGGAGTTGT
* * * *
284298 GGGCTTTAAAAAGAAAAATGTGCCACGGAGTTGTGGACTTAAAAGGGAAAAGGGATGCCACGGAG
65 GGAC-TT-AAAAG-----GGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAG-TGCCACGGAG
* * * * *
284363 GTGTGGAC-TTAAAAGGAAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCAC
122 TTGTGGGCTTTAAAAAG-AAAAAGGTGCCACGGAGTTGTGGAC-TT-AAAAG-----GGTGCCAC
* * ** *
284427 GGAGTTGTGGAC-TT-AAAAG-----GGTGCTACAGAGTTATGGACTTTGAAAAGAAAAAGGTGC
179 AGAGTTGTGGACTTTGAAAAGAAAAAGGTGCCACAGAGTCGTGGACTTT---AAGAAAAAGATGC
* * * * ** *
284485 CACAAAGTCGTGGACTTTGGAAAAAAGATGCCATGAAGTTGTGGA
241 CACAAAGTTGTGGAC-TT---AAAAGGGTGCCACGAAGTAATGAA
* * *
284530 CTTAAAAGGAAAAAGATGCCACAGAGTCGTGGGCTTTAAAATGAAAAAGGTGCCACGGAGTTGTG
1 CTTAAAAGGAAAAAGATGCCACGGAGTCGTGGGCTTTAAAAAGAAAAAGGTGTCACGGAGTTGTG
* *
284595 GACTTAAAAGGGTGCTACGGAGTTGTGGACTTAAAAGGAAAAAAAAGTGCCACGGAGTTGTGGGC
66 GACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGG-AAAAAGAGTGCCACGGAGTTGTGGGC
*
284660 TTTAAAAAGAAAAAGGTGCCACGGAGTTGTAGACTTAAAAGGGTGCCACAGAGTTGTGGACTTTG
130 TTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTTG
* **
284725 AAAAGAAAAAGGTGCCACAGAGTCGTGGACTTTAAGCAAAAGATGCCACGGAGTTGTGGACTTAA
195 AAAAGAAAAAGGTGCCACAGAGTCGTGGACTTTAAGAAAAAGATGCCACAAAGTTGTGGACTTAA
284790 AAGGGTGCCACGAAGTAATGAA
260 AAGGGTGCCACGAAGTAATGAA
*
284812 CTTAAAAGGAAAAAGATGCCACGGAGTCATGGGCTTTAAAAAGAAAAAGGTGTCACGGAGTTGTG
1 CTTAAAAGGAAAAAGATGCCACGGAGTCGTGGGCTTTAAAAAGAAAAAGGTGTCACGGAGTTGTG
*
284877 GACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCT
66 GACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCT
*
284942 TTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAAAGTTGTGGACTTTGA
131 TTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTTGA
* *
285007 AAAGAAAAAGGTGCCACAAAGTCGTGGACTTTAAGAAAAAGATGCCACGAAGTTGTGGACTTAAA
196 AAAGAAAAAGGTGCCACAGAGTCGTGGACTTTAAGAAAAAGATGCCACAAAGTTGTGGACTTAAA
* *
285072 AGGGTGCCACGGAGTAATGGA
261 AGGGTGCCACGAAGTAATGAA
* * *
285093 CTTAAGAGGAAAAAGATGCCATGGAGTCATGGGCTTTAAAAAGAAAAAGGTGTCACGGAGTTGTG
1 CTTAAAAGGAAAAAGATGCCACGGAGTCGTGGGCTTTAAAAAGAAAAAGGTGTCACGGAGTTGTG
* * **
285158 GACTTAAAAGGGTGCCACGGAGTTATGGACTTAAAAGGAAAAGGAGTGCCACGGTCTTGT-GGCT
66 GACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCT
* ** * *
285222 TTAAAAAGAAAAATGTGCCACAAAGTTGTGGACTTAAAAAGGTGCCATAGAGTTGTGGACTTTGA
131 TTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTTGA
* *
285287 AAAGAAAAAGGTGCCACAGAGTTGTGGACTTTAAGAAAAAGATGCCACAGAGTTGTGGACTTAAA
196 AAAGAAAAAGGTGCCACAGAGTCGTGGACTTTAAGAAAAAGATGCCACAAAGTTGTGGACTTAAA
*
285352 AGGGTGCCACTG-AGTTAT-AGA
261 AGGGTGCCAC-GAAGTAATGA-A
* * *
285373 CTTAAAAGGAAAAAGATGCCACGGAGTTGTAGGCTTTAAAAAAAAAAAGGTGTCACGGAGTTGTG
1 CTTAAAAGGAAAAAGATGCCACGGAGTCGTGGGCTTTAAAAAGAAAAAGGTGTCACGGAGTTGTG
* * *
285438 GACTTAAAAGGAAAAAGAGTGCCACGAAGTTGTGGGCTTTAAAAAGAAAAAG-GTGCCACGGAGT
66 GACTTAAAA-G-----G-GTGCCACGGAGTTGTGGAC-TTAAAAGGAAAAAGAGTGCCACGGAGT
*
285502 TGTGGAC-TTAAAAAG
123 TGTGGGCTTTAAAAAG
285517 GTGCCACAGA
Statistics
Matches: 886, Mismatches: 79, Indels: 52
0.87 0.08 0.05
Matches are distributed among these distances:
280 208 0.23
281 289 0.33
282 135 0.15
283 2 0.00
284 5 0.01
285 2 0.00
286 24 0.03
287 42 0.05
288 16 0.02
289 84 0.09
290 12 0.01
294 28 0.03
295 16 0.02
296 23 0.03
ACGTcount: A:0.37, C:0.13, G:0.30, T:0.21
Consensus pattern (281 bp):
CTTAAAAGGAAAAAGATGCCACGGAGTCGTGGGCTTTAAAAAGAAAAAGGTGTCACGGAGTTGTG
GACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCT
TTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTTGA
AAAGAAAAAGGTGCCACAGAGTCGTGGACTTTAAGAAAAAGATGCCACAAAGTTGTGGACTTAAA
AGGGTGCCACGAAGTAATGAA
Found at i:285702 original size:61 final size:62
Alignment explanation
Indices: 284252--285896 Score: 564
Period size: 61 Copynumber: 26.2 Consensus size: 62
284242 GGGAAAAGGG
* * ** * * *
284252 TGCCACGGAGTCGTGGACTTAAAAAGAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAT
1 TGCCACTGAGTTGTGGACTT-TGAAGAAAAGGTGCCACTGAGTTGTGGACTTT---GAGAAAAA-
284317 G-
61 GA
* ** * * **
284318 TGCCACGGAGTTGTGGACTTAAAAGGGAAAAGGGATGCCACGGAGGTGTGGACTTAAAAGGAAAA
1 TGCCACTGAGTTGTGGACTTTGAA--GAAAA-GG-TGCCACTGAGTTGTGGACTT-TGA-GAAAA
*
284383 AAA
60 AGA
* * * * *
284386 GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGAC-TT---AAAAGG
1 -TGCCACTGAGTTGTGGACTTT--GAAG-AAAAGGTGCCACTGAGTTGTGGACTTTGAGAAAAAG
*
284447 G
62 A
* * * ** *
284448 TGCTACAGAGTTATGGACTTTGAAAAGAAAAAGGTGCCACAAAGTCGTGGACTTTG-GAAAAAAG
1 TGCCACTGAGTTGTGGACTTTG--AAG-AAAAGGTGCCACTGAGTTGTGGACTTTGAG-AAAAAG
284512 A
62 A
** * * * * *
284513 TGCCA-TGAAGTTGTGGACTTAAAAGGAAAAAGATGCCACAGAGTCGTGGGCTTTAAAATGAAAA
1 TGCCACTG-AGTTGTGGACTTTGAA-G-AAAAGGTGCCACTGAGTTGTGGACTTT--GA-GAAAA
*
284577 AGG
60 AGA
* * * * ** *
284580 TGCCACGGAGTTGTGGAC-TT--A-AAAGGGTGCTACGGAGTTGTGGACTTAAAAGGAAAAAAAA
1 TGCCACTGAGTTGTGGACTTTGAAGAAAAGGTGCCACTGAGTTGTGGACTT-TGA-G-AAAAAGA
* * * * * *
284641 GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTAGAC-TT---AAAAGG
1 -TGCCACTGAGTTGTGGACTTT--GAAG-AAAAGGTGCCACTGAGTTGTGGACTTTGAGAAAAAG
*
284702 G
62 A
* * * * *
284703 TGCCACAGAGTTGTGGACTTTGAAAAGAAAAAGGTGCCACAGAGTCGTGGACTTTAAGCAAAAGA
1 TGCCACTGAGTTGTGGACTTTG--AAG-AAAAGGTGCCACTGAGTTGTGGACTTTGAGAAAAAGA
* * ** * **
284768 TGCCACGGAGTTGTGGAC-TT--A-AAAGGGTGCCAC-GAAGTAATGAACTTAAAAGGAAAAAGA
1 TGCCACTGAGTTGTGGACTTTGAAGAAAAGGTGCCACTG-AGTTGTGGACTT-TGA-GAAAAAGA
* ** * * * * * *
284828 TGCCACGGAGTCATGGGCTTTAAAAAGAAAAAGGTGTCACGGAGTTGTGGAC-TT---AAAAGGG
1 TGCCACTGAGTTGTGGACTTT--GAAG-AAAAGGTGCCACTGAGTTGTGGACTTTGAGAAAAAGA
* ** * * *
284889 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAA
1 TGCCACTGAGTTGTGGACTTTGAA-G-AAAAG-GTGCCACTGAGTTGTGGACTTT---GAGAAAA
*
284954 AGG
60 AGA
* * ** *
284957 TGCCACGGAGTTGTGGAC-TT--A-AAAGGGTGCCACAAAGTTGTGGACTTTGAAAAGAAAAAGG
1 TGCCACTGAGTTGTGGACTTTGAAGAAAAGGTGCCACTGAGTTGTGGACTTTG---AGAAAAAGA
** * * * *
285018 TGCCACAAAGTCGTGGACTTT-AAGAAAAAGATGCCAC-GAAGTTGTGGAC-TT---AAAAGGG
1 TGCCACTGAGTTGTGGACTTTGAAG-AAAAGGTGCCACTG-AGTTGTGGACTTTGAGAAAAAGA
* ** * * * ** * *
285076 TGCCACGGAGTAATGGACTTAAGAGGAAAAAGATGCCA-TGGAGTCATGGGCTTTAAAAAGAAAA
1 TGCCACTGAGTTGTGGACTT-TGAAG-AAAAGGTGCCACT-GAGTTGTGGACTTT---GAGAAAA
*
285140 AGG
60 AGA
* * * * * ** *
285143 TGTCACGGAGTTGTGGAC-TT--A-AAAGGGTGCCACGGAGTTATGGACTTAAAAGGAAAAGGA
1 TGCCACTGAGTTGTGGACTTTGAAGAAAAGGTGCCACTGAGTTGTGGACTT-TGA-GAAAAAGA
* ** * * **
285203 GTGCCACGGTCTTGTGG-CTTTAAAAAGAAAAATGTGCCACAAAGTTGTGGAC-TT---AAAAAG
1 -TGCCACTGAGTTGTGGACTTT--GAAG-AAAAGGTGCCACTGAGTTGTGGACTTTGAGAAAAAG
*
285263 G
62 A
* *
285264 TGCCA-TAGAGTTGTGGACTTTGAAAAGAAAAAGGTGCCACAGAGTTGTGGACTTTAAGAAAAAG
1 TGCCACT-GAGTTGTGGACTTTG--AAG-AAAAGGTGCCACTGAGTTGTGGACTTTGAGAAAAAG
285328 A
62 A
* * * * **
285329 TGCCACAGAGTTGTGGAC-TT--A-AAAGGGTGCCACTGAGTTATAGACTTAAAAGGAAAAAGA
1 TGCCACTGAGTTGTGGACTTTGAAGAAAAGGTGCCACTGAGTTGTGGACTT-TGA-GAAAAAGA
* * * * * **
285389 TGCCACGGAGTTGTAGG-CTTTAAAAAAAAAAAGGTGTCACGGAGTTGTGGACTTAAAAGGAAAA
1 TGCCACTGAGTTGT-GGACTTT---GAAGAAAAGGTGCCACTGAGTTGTGGACTT-TGA-GAAAA
285453 AGA
60 AGA
* * *
285456 GTGCCAC-GAAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGAC-TT---AAAAA
1 -TGCCACTG-AGTTGTGGACTTT--GAAG-AAAAGGTGCCACTGAGTTGTGGACTTTGAGAAAAA
*
285516 GG
61 GA
* * ** *
285518 TGCCACAGAGTTGTGGACTTTGAAAAGAAAAAGGTGCCACAGAGTCATGGATTTTGAGAAAAAGA
1 TGCCACTGAGTTGTGGACTTTG--AAG-AAAAGGTGCCACTGAGTTGTGGACTTTGAGAAAAAGA
* * *
285583 TGCCA-TGGAGTTGTGGAC-TT--A-AAAGGGTGCCACAGAGTTGTGGAC-TT-AAAAAAGAGA
1 TGCCACT-GAGTTGTGGACTTTGAAGAAAAGGTGCCACTGAGTTGTGGACTTTGAGAAAA-AGA
* * *
285640 TGCCACTGAGTTGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTT-AGAACAAGA
1 TGCCACTGAGTTGTGGACTTTGAAGAAAAGGTGCCACTGAGTTGTGGACTTTGAGAAAAAGA
* * *
285701 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGATGCCACTGAGTCGTGGACTTTGA-AGAAAAGA
1 TGCCACTGAGTTGTGGACTTTGAAG--AAAAGGTGCCACTGAGTTGTGGACTTTGAGA-AAAAGA
** * * * *
285765 TGCCACTGAGTCATGGACTTTG-GGAAAAGATGCCACTGAGTAGTGGACTTTGAG-AAGAGA
1 TGCCACTGAGTTGTGGACTTTGAAGAAAAGGTGCCACTGAGTTGTGGACTTTGAGAAAAAGA
** * * * *
285825 TTGCCACTGAGTCATGGACTTTG-AGAAAAGATGCCACTGAGTCGTGGACTTTG-GGAAGAGA
1 -TGCCACTGAGTTGTGGACTTTGAAGAAAAGGTGCCACTGAGTTGTGGACTTTGAGAAAAAGA
285886 TGCCACTGAGT
1 TGCCACTGAGT
285897 CGTTGGCGCC
Statistics
Matches: 1261, Mismatches: 183, Indels: 276
0.73 0.11 0.16
Matches are distributed among these distances:
56 5 0.00
57 22 0.02
58 87 0.07
59 9 0.01
60 115 0.09
61 445 0.35
62 54 0.04
63 34 0.03
64 63 0.05
65 112 0.09
66 24 0.02
67 131 0.10
68 92 0.07
69 61 0.05
70 4 0.00
71 3 0.00
ACGTcount: A:0.36, C:0.13, G:0.30, T:0.21
Consensus pattern (62 bp):
TGCCACTGAGTTGTGGACTTTGAAGAAAAGGTGCCACTGAGTTGTGGACTTTGAGAAAAAGA
Found at i:285794 original size:30 final size:30
Alignment explanation
Indices: 285485--285899 Score: 416
Period size: 30 Copynumber: 13.7 Consensus size: 30
285475 TTTAAAAAGA
* * *
285485 AAAAGGTGCCACGGAGTTGTGGAC-TT-A-
1 AAAAGATGCCACTGAGTCGTGGACTTTGAG
* * *
285512 AAAAGGTGCCACAGAGTTGTGGACTTTGAAAAG
1 AAAAGATGCCACTGAGTCGTGGACTTTG---AG
* * * *
285545 AAAAAGGTGCCACAGAGTCATGGATTTTGAG
1 -AAAAGATGCCACTGAGTCGTGGACTTTGAG
*
285576 AAAAAGATGCCA-TGGAGTTGTGGAC-TT-A-
1 -AAAAGATGCCACT-GAGTCGTGGACTTTGAG
* * * * * *
285604 AAAGGGTGCCACAGAGTTGTGGAC-TTAAA
1 AAAAGATGCCACTGAGTCGTGGACTTTGAG
*
285633 AAAGAGATGCCACTGAGTTGTGGACTTTGAAG
1 AAA-AGATGCCACTGAGTCGTGGACTTTG-AG
285665 AAAAGATGCCACTGAGTCGTGGACTTT-AG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAG
285694 AACAAGATGCCACTGAGTCGTGGACTTTGAAG
1 AA-AAGATGCCACTGAGTCGTGGACTTTG-AG
285726 AAAAAAGATGCCACTGAGTCGTGGACTTTGAAG
1 --AAAAGATGCCACTGAGTCGTGGACTTTG-AG
* *
285759 AAAAGATGCCACTGAGTCATGGACTTTGGG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAG
*
285789 AAAAGATGCCACTGAGTAGTGGACTTTGAG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAG
* *
285819 AAGAGATTGCCACTGAGTCATGGACTTTGAG
1 AAAAGA-TGCCACTGAGTCGTGGACTTTGAG
*
285850 AAAAGATGCCACTGAGTCGTGGACTTTGGG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAG
*
285880 AAGAGATGCCACTGAGTCGT
1 AAAAGATGCCACTGAGTCGT
285900 TGGCGCCGTT
Statistics
Matches: 338, Mismatches: 30, Indels: 37
0.83 0.07 0.09
Matches are distributed among these distances:
27 45 0.13
28 3 0.01
29 8 0.02
30 119 0.35
31 100 0.30
32 7 0.02
33 29 0.09
34 27 0.08
ACGTcount: A:0.32, C:0.15, G:0.30, T:0.23
Consensus pattern (30 bp):
AAAAGATGCCACTGAGTCGTGGACTTTGAG
Found at i:286731 original size:112 final size:110
Alignment explanation
Indices: 286533--286971 Score: 515
Period size: 112 Copynumber: 3.9 Consensus size: 110
286523 ACTTGAAAGA
***
286533 ACATCAAATTTGTCTAATTTTTAAAGAAATTTGCGTTTTATACAACCTAATCCATGTT-TGCCTA
1 ACATCAAATTTGTCTAATTTTTAAAGAAATTCATGTTTTATACAACCTAATCCAT-TTGTGCCTA
* * * *
286597 GGAAAATAGGGCATATATCCTATTACTTTTGAAATTTATAAGCCAAC
65 GGAAAATGGGGCATGTATCCTATCACTTTTGAAATTT-TAATCCAAC
* * *
286644 AGCATCAAATTTATCT-ATCTTTTAAAGAAATTCATGTTTTATACAACCTGATCCATTTGTACCT
1 A-CATCAAATTTGTCTAAT-TTTTAAAGAAATTCATGTTTTATACAACCTAATCCATTTGTGCCT
*
286708 AGGAAAATGGGGCATGTATCCTATCAAC-TTTGAAACTTTTAATCGAAC
64 AGGAAAATGGGGCATGTATCCTATC-ACTTTTGAAA-TTTTAATCCAAC
* * * *
286756 AACATCAAATTTGTCTGATTTCTAAAGAAATTCATGTTTTATACAACTTGATCCATTTGTGCCTA
1 -ACATCAAATTTGTCTAATTTTTAAAGAAATTCATGTTTTATACAACCTAATCCATTTGTGCCTA
* * * * *
286821 GGAAAATGAGGCATGTATCCTAACAATTTTTAAATTTTTGATCCAAC
65 GGAAAATGGGGCATGTATCCTATCACTTTTGAAA-TTTTAATCCAAC
* * * * * *
286868 TACATCAATTTTGTCTAATTTTCAAGGAAATTCATGATTTATACAATCTAATCCATTCGTGCCTA
1 -ACATCAAATTTGTCTAATTTTTAAAGAAATTCATGTTTTATACAACCTAATCCATTTGTGCCTA
* * *
286933 GAAAAATGGAGCATGTATCCTATCAGTTTTGAAATTTTA
65 GGAAAATGGGGCATGTATCCTATCACTTTTGAAATTTTA
286972 CCAAAGTTTT
Statistics
Matches: 280, Mismatches: 40, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
111 10 0.04
112 262 0.94
113 8 0.03
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.37
Consensus pattern (110 bp):
ACATCAAATTTGTCTAATTTTTAAAGAAATTCATGTTTTATACAACCTAATCCATTTGTGCCTAG
GAAAATGGGGCATGTATCCTATCACTTTTGAAATTTTAATCCAAC
Found at i:287554 original size:44 final size:43
Alignment explanation
Indices: 287506--287644 Score: 129
Period size: 44 Copynumber: 3.2 Consensus size: 43
287496 ATGCTTACAG
* *
287506 TTGCATTGTTTTATGCACATTTGCATTTTAGATGACATTGGCAT
1 TTGCATCGTTTCATGCACATTTGCATTTTAGATGACATT-GCAT
* ** * * *
287550 TTGCATCATTTCATGTTCATTTACATCTTTA-TTGA-AGCTTGCAC
1 TTGCATCGTTTCATGCACATTTGCAT-TTTAGATGACA--TTGCAT
* *
287594 TTACATCGTTTCATGCACATTTGCACTTTAGATGACATTAGCAT
1 TTGCATCGTTTCATGCACATTTGCATTTTAGATGACATT-GCAT
287638 TTGCATC
1 TTGCATC
287645 ATCCCACATG
Statistics
Matches: 72, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
43 7 0.10
44 58 0.81
45 7 0.10
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (43 bp):
TTGCATCGTTTCATGCACATTTGCATTTTAGATGACATTGCAT
Found at i:287659 original size:88 final size:87
Alignment explanation
Indices: 287443--287695 Score: 283
Period size: 88 Copynumber: 2.9 Consensus size: 87
287433 GTATCTATAC
* * * * *
287443 CTTTATATCACATTGGCATTTGTATCATTTCATATGCATTTGCCA-CTTTATTGATGCTTACAGT
1 CTTTAGATGACATTGGCATTTGCATCATTTCATATGCATTT-ACATCTTTATTGATGCTTGCA-T
* * *
287507 TGCATTGTTTTATGCACATTTGCA
64 TACATCGTTTCATGCACATTTGCA
* * * *
287531 TTTTAGATGACATTGGCATTTGCATCATTTCATGTTCATTTACATCTTTATTGAAGCTTGCACTT
1 CTTTAGATGACATTGGCATTTGCATCATTTCATATGCATTTACATCTTTATTGATGCTTGCA-TT
287596 ACATCGTTTCATGCACATTTGCA
65 ACATCGTTTCATGCACATTTGCA
* ** * * * * *
287619 CTTTAGATGACATTAGCATTTGCATCATCCCACATGCATTTACCTCATTGTGGATGCTTGCATTA
1 CTTTAGATGACATTGGCATTTGCATCATTTCATATGCATTTACATCTTTATTGATGCTTGCATTA
287684 GCATCGTTTCAT
66 -CATCGTTTCAT
287696 TAACATTTAC
Statistics
Matches: 138, Mismatches: 25, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
87 5 0.04
88 133 0.96
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.42
Consensus pattern (87 bp):
CTTTAGATGACATTGGCATTTGCATCATTTCATATGCATTTACATCTTTATTGATGCTTGCATTA
CATCGTTTCATGCACATTTGCA
Found at i:288070 original size:59 final size:59
Alignment explanation
Indices: 288005--288396 Score: 324
Period size: 59 Copynumber: 6.6 Consensus size: 59
287995 CATATATAGC
* * *
288005 CATTGTTAGGTTTCTAGTTTTATCCAGGCTATTTCT-TTAAATCTTGGTTTTACCCAAGT
1 CATTGTTAGGTTTCTAGTTTTATCCAGGCCATTT-TGTTAAGTCTTGGTTTTGCCCAAGT
* * ** * *
288064 CATTGTTTAAGTTTAT-GTTTTATCCAGGCCATTTCCTTAAGTATTGGTTTTACCCAAGT
1 CATTG-TTAGGTTTCTAGTTTTATCCAGGCCATTTTGTTAAGTCTTGGTTTTGCCCAAGT
* * * * *
288123 CATTGTTTAGGATTCTAGTTTTGTCCAAGCCATTTTGTTGAG-CTTGGTTTTGCCTAAGT
1 CATTG-TTAGGTTTCTAGTTTTATCCAGGCCATTTTGTTAAGTCTTGGTTTTGCCCAAGT
* * * ** ** * *
288182 TATTGTTTAGGTTTTTGGTTCCATCCAAACTATTTTGTTAAGTCTTGGTTTTGCCTAAGT
1 CATTG-TTAGGTTTCTAGTTTTATCCAGGCCATTTTGTTAAGTCTTGGTTTTGCCCAAGT
* * ** * * *
288242 CATTATTCAGGTTTTTAG-TTTAGTTTAGGCCATTTTATTGAGTTTTGGTTTTGCCACAAGT
1 CATTGTT-AGGTTTCTAGTTTTA-TCCAGGCCATTTTGTTAAGTCTTGGTTTTGCC-CAAGT
* ** * * * * *
288303 CATAGTTAGGTTTCTAGTTTTATCCAGGCCATTTCATTGAGTTTTGGTTATGCCTAAAT
1 CATTGTTAGGTTTCTAGTTTTATCCAGGCCATTTTGTTAAGTCTTGGTTTTGCCCAAGT
* * *
288362 CATTGTTAAGTTTCTGGTTTTATCTAGGCCATTTT
1 CATTGTTAGGTTTCTAGTTTTATCCAGGCCATTTT
288397 TTTGTGTCTT
Statistics
Matches: 270, Mismatches: 55, Indels: 16
0.79 0.16 0.05
Matches are distributed among these distances:
59 139 0.51
60 118 0.44
61 13 0.05
ACGTcount: A:0.20, C:0.15, G:0.18, T:0.47
Consensus pattern (59 bp):
CATTGTTAGGTTTCTAGTTTTATCCAGGCCATTTTGTTAAGTCTTGGTTTTGCCCAAGT
Found at i:288083 original size:29 final size:29
Alignment explanation
Indices: 288048--288131 Score: 91
Period size: 30 Copynumber: 2.9 Consensus size: 29
288038 TCTTTAAATC
288048 TTGGTTTTACCCAAGTCATTGTTTAAGT-
1 TTGGTTTTACCCAAGTCATTGTTTAAGTA
* * * *
288076 TTATGTTTTATCCAGGCCATT-TCCTTAAGTA
1 TT-GGTTTTACCCAAGTCATTGT--TTAAGTA
288107 TTGGTTTTACCCAAGTCATTGTTTA
1 TTGGTTTTACCCAAGTCATTGTTTA
288132 GGATTCTAGT
Statistics
Matches: 43, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
28 3 0.07
29 17 0.40
30 20 0.47
31 3 0.07
ACGTcount: A:0.21, C:0.17, G:0.15, T:0.46
Consensus pattern (29 bp):
TTGGTTTTACCCAAGTCATTGTTTAAGTA
Found at i:288114 original size:30 final size:28
Alignment explanation
Indices: 288021--288115 Score: 75
Period size: 30 Copynumber: 3.2 Consensus size: 28
288011 TAGGTTTCTA
* *
288021 GTTTTATCCAGGCTATTTCTTTAAATCTTG
1 GTTTTATCCAGGCCATTTC-TTAAGT-TTG
* * * *
288051 GTTTTACCCAAGTCATTGT-TTAAGTTTAT
1 GTTTTATCCAGGCCATT-TCTTAAGTTT-G
288080 GTTTTATCCAGGCCATTTCCTTAAGTATTG
1 GTTTTATCCAGGCCATTT-CTTAAGT-TTG
288110 GTTTTA
1 GTTTTA
288116 CCCAAGTCAT
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
28 3 0.06
29 19 0.38
30 25 0.50
31 3 0.06
ACGTcount: A:0.21, C:0.16, G:0.15, T:0.48
Consensus pattern (28 bp):
GTTTTATCCAGGCCATTTCTTAAGTTTG
Found at i:288277 original size:60 final size:60
Alignment explanation
Indices: 288010--288336 Score: 229
Period size: 60 Copynumber: 5.5 Consensus size: 60
288000 ATAGCCATTG
* * * * *
288010 TTAGGTTTCTAGTTTTA-TCCAGGCTATTTCT-TTAAATCTTGGTTTTACCCAAGTCATTGT
1 TTAGGTTTCTAG-TTTAGTCCAAGCCATTT-TGTTAAGTCTTGGTTTTGCCCAAGTCATTAT
* * * ** * * *
288070 TTAAGTTTAT-GTTTTA-TCCAGGCCATTTCCTTAAGTATTGGTTTTACCCAAGTCATTGT
1 TTAGGTTTCTAG-TTTAGTCCAAGCCATTTTGTTAAGTCTTGGTTTTGCCCAAGTCATTAT
* * * * * *
288129 TTAGGATTCTAGTTTTGTCCAAGCCATTTTGTTGAG-CTTGGTTTTGCCTAAGTTATTGT
1 TTAGGTTTCTAGTTTAGTCCAAGCCATTTTGTTAAGTCTTGGTTTTGCCCAAGTCATTAT
* * * * * *
288188 TTAGGTTTTTGGTTCCA-TCCAAACTATTTTGTTAAGTCTTGGTTTTGCCTAAGTCATTAT
1 TTAGGTTTCTAGTT-TAGTCCAAGCCATTTTGTTAAGTCTTGGTTTTGCCCAAGTCATTAT
* * ** * * * * *
288248 TCAGGTTTTTAGTTTAGTTTAGGCCATTTTATTGAGTTTTGGTTTTGCCACAAGTCA-TAG
1 TTAGGTTTCTAGTTTAGTCCAAGCCATTTTGTTAAGTCTTGGTTTTGCC-CAAGTCATTAT
*
288308 TTAGGTTTCTAGTTTTA-TCCAGGCCATTT
1 TTAGGTTTCTAG-TTTAGTCCAAGCCATTT
288337 CATTGAGTTT
Statistics
Matches: 214, Mismatches: 45, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
59 101 0.47
60 103 0.48
61 10 0.05
ACGTcount: A:0.20, C:0.15, G:0.18, T:0.47
Consensus pattern (60 bp):
TTAGGTTTCTAGTTTAGTCCAAGCCATTTTGTTAAGTCTTGGTTTTGCCCAAGTCATTAT
Found at i:288593 original size:70 final size:70
Alignment explanation
Indices: 288512--288729 Score: 197
Period size: 70 Copynumber: 3.0 Consensus size: 70
288502 ATATCCCCCC
* * * *
288512 TATCATGTTCTTCTTCTTCAGCTCATTGTCAATTTGTTTAGTTGTTAATGGAAATTTTAGAAACC
1 TATCATATTCTTCTTCTTTAGCTCATTATCAGTTTGTTTAGTTGTTAATGGAAATTTTAGAAACC
288577 ACATA
66 ACATA
* * * * * * * *
288582 TATCATATTCTTTTTCTTTAGCTCGTTATTAGTTTATTTCAGCTATTAGTGGAGAATTTTGGAAA
1 TATCATATTCTTCTTCTTTAGCTCATTATCAGTTTGTTT-AGTTGTTAATGGA-AATTTTAGAAA
*
288647 CCATATA
64 CCACATA
* * *
288654 T-TCACTATCATGTTCTTCTAATTAGCTTATTATCAGTTTGTTTTAGTTGTTAATAGGAAATTAT
1 TATCA-TAT--TCTTCTTCT--TTAGCTCATTATCAGTTTG-TTTAGTTGTTAAT-GGAAATTTT
288718 AG-AACCACATA
59 AGAAACCACATA
288729 T
1 T
288730 TCCCCATCAT
Statistics
Matches: 114, Mismatches: 25, Indels: 13
0.75 0.16 0.09
Matches are distributed among these distances:
70 31 0.27
71 13 0.11
72 20 0.18
74 7 0.06
75 9 0.08
76 28 0.25
77 6 0.05
ACGTcount: A:0.28, C:0.14, G:0.13, T:0.45
Consensus pattern (70 bp):
TATCATATTCTTCTTCTTTAGCTCATTATCAGTTTGTTTAGTTGTTAATGGAAATTTTAGAAACC
ACATA
Found at i:289340 original size:40 final size:39
Alignment explanation
Indices: 289239--289340 Score: 109
Period size: 40 Copynumber: 2.6 Consensus size: 39
289229 CAAATGTCAC
* *
289239 TCAACCCTTCTCATCTATTGACTTGTCAGTTTTTCTCAA
1 TCAACCCTTCTCATATTTTGACTTGTCAGTTTTTCTCAA
* * *
289278 TAAACCCTT-TCTTATTTGTTGACTTG-CAAGTTTTGTCTCGA
1 TCAACCCTTCTCATA-TT-TTGACTTGTC-AGTTTT-TCTCAA
289319 TCAACCCTTCTCATATTTTGAC
1 TCAACCCTTCTCATATTTTGAC
289341 GTATCGGTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
38 3 0.06
39 10 0.20
40 19 0.37
41 15 0.29
42 4 0.08
ACGTcount: A:0.21, C:0.25, G:0.10, T:0.44
Consensus pattern (39 bp):
TCAACCCTTCTCATATTTTGACTTGTCAGTTTTTCTCAA
Found at i:289373 original size:80 final size:80
Alignment explanation
Indices: 289239--289409 Score: 175
Period size: 80 Copynumber: 2.1 Consensus size: 80
289229 CAAATGTCAC
* * * ** *
289239 TCAACCCTTCTCATCTATTGACTTGTCAGTTTTTCTCAATAAACCCTTTCTTATTTGTTGACTTG
1 TCAACCCTTCTCATATATTGACGTATCAGTTTTTCTCAATAAACCCTTTCTTATTCATTGACTTA
289304 CAAGTTTTGTCTCGA-
66 CAAGTTTTGTC-CGAG
* * * * * *
289319 TCAACCCTTCTCATATTTTGACGTATCGGTTTTGTCTTAGTTAA-CCTTTTTTATTCATTGACTT
1 TCAACCCTTCTCATATATTGACGTATCAGTTTT-TCTCAATAAACCCTTTCTTATTCATTGACTT
* * *
289383 ATAGGTTTTGTCCTAG
65 ACAAGTTTTGTCCGAG
289399 TCAACCCTTCT
1 TCAACCCTTCT
289410 TATCTGTTGA
Statistics
Matches: 74, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
79 2 0.03
80 65 0.88
81 7 0.09
ACGTcount: A:0.19, C:0.23, G:0.12, T:0.46
Consensus pattern (80 bp):
TCAACCCTTCTCATATATTGACGTATCAGTTTTTCTCAATAAACCCTTTCTTATTCATTGACTTA
CAAGTTTTGTCCGAG
Found at i:289420 original size:40 final size:40
Alignment explanation
Indices: 289280--289849 Score: 137
Period size: 40 Copynumber: 14.1 Consensus size: 40
289270 TTTCTCAATA
* ** * *
289280 AACCCTTTCTTATTTGTTGACTTGCAAGTTTTGT-CTCGATC
1 AACCC-TTCTTATCTGTTGACTTATAGGTTTTGTCCTAG-TC
* * * * * * *
289321 AACCCTTCTCATATTTTGACGTATCGGTTTTGTCTTAGTT
1 AACCCTTCTTATCTGTTGACTTATAGGTTTTGTCCTAGTC
* * *
289361 AACCTTTTTTAT-TCATTGACTTATAGGTTTTGTCCTAGTC
1 AACCCTTCTTATCT-GTTGACTTATAGGTTTTGTCCTAGTC
* *
289401 AACCCTTCTTATCTGTTGACTTGTCA-GTTTTGTCCCT-GTT
1 AACCCTTCTTATCTGTTGACTTAT-AGGTTTTGT-CCTAGTC
* * * * *** * *
289441 AACTTCTTTTTAT-TCGTTAACTTAAAGGTGGGGTCCCAATC
1 AAC-CCTTCTTATCT-GTTGACTTATAGGTTTTGTCCTAGTC
* * *
289482 AACCCCTTTTTAAT-TGTTGACTTGTAGATTTTGTCCTAGTC
1 AA-CCCTTCTT-ATCTGTTGACTTATAGGTTTTGTCCTAGTC
* * * *
289523 AACCTTTTTTATCTGTTGACTTATCA-ATTTTGTCC-CGATC
1 AACCCTTCTTATCTGTTGACTTAT-AGGTTTTGTCCTAG-TC
* * * * ** * *
289563 AACACCTTCTTATTTGTTGAGTTCTAAGTTTTGTATTGGTT
1 AAC-CCTTCTTATCTGTTGACTTATAGGTTTTGTCCTAGTC
** * * *
289604 AACCCTTC-GCTCTTAATTGACTTGTACGTTTTGTCCT-GATC
1 AACCCTTCTTATC-T-GTTGACTTATAGGTTTTGTCCTAG-TC
** * * * *
289645 AACTATTCTCATCTGTTGACTTGTTA-G--TTGT-CTCGATT
1 AACCCTTCTTATCTGTTGACTT-ATAGGTTTTGTCCTAG-TC
* * * * *
289683 AACCTTTCTCATCTATTGACTTATGGGTTTTGTCCCAGTC
1 AACCCTTCTTATCTGTTGACTTATAGGTTTTGTCCTAGTC
* ** * ** * *
289723 AACCTTTC-GCTCTTAGTTGAATTATATATTTTATCCTTGTC
1 AACCCTTCTTATC-T-GTTGACTTATAGGTTTTGTCCTAGTC
* * * * *
289764 AACCTTTCTCATCTGTTAACTTGTTGGTTTTGTCCTTA-TC
1 AACCCTTCTTATCTGTTGACTTATAGGTTTTGTCC-TAGTC
* * * * ** * *
289804 AACCCCTTATTATTTGTTAACTTGTAGAATCTATCCTAGTC
1 AA-CCCTTCTTATCTGTTGACTTATAGGTTTTGTCCTAGTC
289845 AACCC
1 AACCC
289850 CTTAAACTTA
Statistics
Matches: 384, Mismatches: 112, Indels: 67
0.68 0.20 0.12
Matches are distributed among these distances:
37 3 0.01
38 27 0.07
39 7 0.02
40 169 0.44
41 169 0.44
42 9 0.02
ACGTcount: A:0.19, C:0.21, G:0.14, T:0.46
Consensus pattern (40 bp):
AACCCTTCTTATCTGTTGACTTATAGGTTTTGTCCTAGTC
Found at i:289533 original size:81 final size:80
Alignment explanation
Indices: 289318--289534 Score: 206
Period size: 81 Copynumber: 2.7 Consensus size: 80
289308 TTTTGTCTCG
* * * * * * * *
289318 ATCAACCCTTCTCATATTTTGACGTATCGGTTTTGTCTTAGTTAACCTTTTTTATTCATTGACTT
1 ATCAACCCTTCTTATCTGTTGACTTGTCAGTTTTGTCCTAGTTAACCTTTTTTATTCATTAACTT
* *** *
289383 ATAGGTTTTGTCCTA
66 AAAGGTGGGGTCCCA
* * *
289398 GTCAACCCTTCTTATCTGTTGACTTGTCAGTTTTGTCCCT-GTTAACTTCTTTTTATTCGTTAAC
1 ATCAACCCTTCTTATCTGTTGACTTGTCAGTTTTGT-CCTAGTTAACCT-TTTTTATTCATTAAC
289462 TTAAAGGTGGGGTCCCA
64 TTAAAGGTGGGGTCCCA
* *
289479 ATCAACCCCTTTTTAAT-TGTTGACTTGT-AGATTTTGTCCTAGTCAACCTTTTTTAT
1 ATCAA-CCCTTCTT-ATCTGTTGACTTGTCAG-TTTTGTCCTAGTTAACCTTTTTTAT
289535 CTGTTGACTT
Statistics
Matches: 111, Mismatches: 20, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
80 36 0.32
81 43 0.39
82 30 0.27
83 2 0.02
ACGTcount: A:0.19, C:0.20, G:0.14, T:0.47
Consensus pattern (80 bp):
ATCAACCCTTCTTATCTGTTGACTTGTCAGTTTTGTCCTAGTTAACCTTTTTTATTCATTAACTT
AAAGGTGGGGTCCCA
Found at i:289582 original size:41 final size:40
Alignment explanation
Indices: 289275--289582 Score: 140
Period size: 40 Copynumber: 7.6 Consensus size: 40
289265 CAGTTTTTCT
* *
289275 CAATAAACCCTTTCTTATTTGTTGACTTGCA-AG-TTTTGTCT
1 CAATCAACCCTTT-TTATTTGTTGACTT--ATAGATTTTGTCC
* * * * * * *
289316 CGATCAACCCTTCTCATATT-TTGACGTATCGGTTTTGTCT
1 CAATCAACCCTTTTTAT-TTGTTGACTTATAGATTTTGTCC
* * * * ** *
289356 TAGTTAACCTTTTTTATTCATTGACTTATAGGTTTTGTCC
1 CAATCAACCCTTTTTATTTGTTGACTTATAGATTTTGTCC
* * * * *
289396 TAGTCAACCCTTCTTATCTGTTGACTTGTCAG-TTTTGTCC
1 CAATCAACCCTTTTTATTTGTTGACTTAT-AGATTTTGTCC
** * * * * * * ***
289436 CTGTTAACTTCTTTTTATTCGTTAACTTAAAGGTGGGGTCC
1 CAATCAAC-CCTTTTTATTTGTTGACTTATAGATTTTGTCC
* *
289477 CAATCAACCCCTTTTTAATTGTTGACTTGTAGATTTTGTCC
1 CAATCAA-CCCTTTTTATTTGTTGACTTATAGATTTTGTCC
* * * *
289518 TAGTCAACCTTTTTTATCTGTTGACTTATCA-ATTTTGTCC
1 CAATCAACCCTTTTTATTTGTTGACTTAT-AGATTTTGTCC
* *
289558 CGATCAACACCTTCTTATTTGTTGA
1 CAATCAAC-CCTTTTTATTTGTTGA
289583 GTTCTAAGTT
Statistics
Matches: 195, Mismatches: 62, Indels: 20
0.70 0.22 0.07
Matches are distributed among these distances:
38 1 0.01
39 2 0.01
40 113 0.58
41 78 0.40
42 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.14, T:0.46
Consensus pattern (40 bp):
CAATCAACCCTTTTTATTTGTTGACTTATAGATTTTGTCC
Found at i:290281 original size:74 final size:74
Alignment explanation
Indices: 290101--290389 Score: 264
Period size: 74 Copynumber: 3.9 Consensus size: 74
290091 TATCCTAATC
** * * * **
290101 ACCCTTAGTTGACTGATTTGGTTTTGCCC-TAGTGAACTCTTTTTGACTTAGGTCTCATCCTAGT
1 ACCCTTAGTTGACT-ATTTTATTTTGCCCTTGGTCAACCCTTTTCAACTTAGGTCTCATCCTAGT
290165 CA-CTTTTTT
65 CACCTTTTTT
* * * * * *
290174 ACCTTTAGTTGATTATTGTAGTTT-CCCTTTGGTCAACCCTTTTCAACTTAAGTCTCATCCTAAT
1 ACCCTTAGTTGACTATTTTATTTTGCCC-TTGGTCAACCCTTTTCAACTTAGGTCTCATCCTAGT
*
290238 CACCCTTTTT
65 CACCTTTTTT
* * * *
290248 ACCCTTAGTTGACTATTCTTATTTTGTCC-TGGTCAACCTTTTTCAATTTAGGTGTCATCCTAGT
1 ACCCTTAGTTGACTATT-TTATTTTGCCCTTGGTCAACCCTTTTCAACTTAGGTCTCATCCTAGT
*
290312 CACATTTTTT
65 CACCTTTTTT
* * * * * * * *
290322 ACCCTTTGTTGGCTATTCTAGTTTTG-CCTTGGTCAACCCTTTCCGATTTAGGTTTCATTCTAGT
1 ACCCTTAGTTGACTATTTTA-TTTTGCCCTTGGTCAACCCTTTTCAACTTAGGTCTCATCCTAGT
290386 CACC
65 CACC
290390 CTTAGTTAAC
Statistics
Matches: 174, Mismatches: 35, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
71 3 0.02
72 6 0.03
73 46 0.26
74 112 0.64
75 5 0.03
76 2 0.01
ACGTcount: A:0.18, C:0.24, G:0.13, T:0.45
Consensus pattern (74 bp):
ACCCTTAGTTGACTATTTTATTTTGCCCTTGGTCAACCCTTTTCAACTTAGGTCTCATCCTAGTC
ACCTTTTTT
Found at i:294059 original size:15 final size:15
Alignment explanation
Indices: 294039--294077 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
294029 TTCTCGCTAT
*
294039 TTTCTTCTCTTTTTC
1 TTTCTTCTCTTTCTC
*
294054 TTTCTTTTCTTTCTC
1 TTTCTTCTCTTTCTC
294069 TTT-TTCTCT
1 TTTCTTCTCT
294078 CCTCTTTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTCTTCTCTTTCTC
Found at i:294087 original size:21 final size:21
Alignment explanation
Indices: 294043--294087 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
294033 CGCTATTTTC
* *
294043 TTCTCTTTTTCTTTCTTTTCT
1 TTCTCTTTTTCTTCCTCTTCT
294064 TTCTCTTTTTCTCTCCTCTT-T
1 TTCTCTTTTTCT-TCCTCTTCT
294085 TTC
1 TTC
294088 AGCTGAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (21 bp):
TTCTCTTTTTCTTCCTCTTCT
Found at i:294921 original size:167 final size:166
Alignment explanation
Indices: 294584--295133 Score: 518
Period size: 167 Copynumber: 3.4 Consensus size: 166
294574 TGACATAATT
** * * * * * * **
294584 TGAATTTTGCAAAATTGATTTAATGTGAA-TATAATGATAATATTAGATAAATTTTAAAAATTTT
1 TGAATTTTTAAAAAATGATTTAATATGAATTA-AATAATAATATTTGATGAATTTCAAAAATTAA
* * * * * * * ** *
294648 AAATCGAGAAAAATC-TCCCTGAAAATATTTATGGGATAGAAAACTCGATTTTTTTAAAATAGGT
65 AAACCAAGAAAAATCATCCC-GAAAACATTTACGGAACAGAAAACTCCATTTTTCAAAAATAGGA
* * *
294712 AAATTTCAAAGAAAAAATAAAAAACT-CATGAAAATAAA
129 AAATTTCAAGGAAAAAATGAAAAA-TGAATGAAAATAAA
** * *
294750 TGAATTTTT-TGACATAGATTTAATATGAATTAAATAATAATATTTTATGAATTTCAAAAATTAA
1 TGAATTTTTAAAAAAT-GATTTAATATGAATTAAATAATAATATTTGATGAATTTCAAAAATTAA
* * *
294814 AAACCAAGAAAAATCATCTCGAAAAACATTTACGGAACAGAAAACTCCATTGTTTGGAAACA-A-
65 AAACCAAGAAAAATCATCCCG-AAAACATTTACGGAACAGAAAACTCCATT-TTT-CAAAAATAG
* *
294877 GAGAATTTCAAGGAAAAAATGAAAAATGAATGAAAATGAA
127 GAAAATTTCAAGGAAAAAATGAAAAATGAATGAAAATAAA
** * *
294917 TGAATTTTTAAAAAATGATTTGCTATGATTTAAATAATAATATTTGATGAATTTTAAAAATTAAA
1 TGAATTTTTAAAAAATGATTTAATATGAATTAAATAATAATATTTGATGAATTTCAAAAATTAAA
* * * * * *
294982 AAGCAAGAAAACTCTTCCCGAAAACATTTATGGAGCAGAAAACTCCGTTTTTCAAAAATAGGAAA
66 AACCAAGAAAAATCATCCCGAAAACATTTACGGAACAGAAAACTCCATTTTTCAAAAATAGGAAA
*
295047 ATTTCAAGG----AA--AAAAATG-A--AAAATGAA
131 ATTTCAAGGAAAAAATGAAAAATGAATGAAAATAAA
* * *
295074 TGAATTTTTAAAAATTGATTTAATATGAATTAAATAATAATATTTGGTGAATTTTAAAAA
1 TGAATTTTTAAAAAATGATTTAATATGAATTAAATAATAATATTTGATGAATTTCAAAAA
295134 AATTTGGATC
Statistics
Matches: 321, Mismatches: 53, Indels: 29
0.80 0.13 0.07
Matches are distributed among these distances:
157 63 0.20
159 1 0.00
160 7 0.02
162 2 0.01
164 4 0.01
165 6 0.02
166 98 0.31
167 130 0.40
168 7 0.02
169 3 0.01
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.32
Consensus pattern (166 bp):
TGAATTTTTAAAAAATGATTTAATATGAATTAAATAATAATATTTGATGAATTTCAAAAATTAAA
AACCAAGAAAAATCATCCCGAAAACATTTACGGAACAGAAAACTCCATTTTTCAAAAATAGGAAA
ATTTCAAGGAAAAAATGAAAAATGAATGAAAATAAA
Found at i:299682 original size:22 final size:22
Alignment explanation
Indices: 299637--299683 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
299627 TATTGCTATT
* *
299637 TTTTTCTATTTTTCTTTCTTTA
1 TTTTTCTAGTTTTCTTTCTCTA
299659 TTTTTCTAGTTTTCTTGT-TCTA
1 TTTTTCTAGTTTTCTT-TCTCTA
299681 TTT
1 TTT
299684 CCATTGCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.09, C:0.13, G:0.04, T:0.74
Consensus pattern (22 bp):
TTTTTCTAGTTTTCTTTCTCTA
Found at i:300000 original size:30 final size:30
Alignment explanation
Indices: 299938--300004 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
299928 TTCCTTGCTG
* *
299938 CTTGATTCATTTTTGTCTTCATTGTAGCAT
1 CTTGATTCATTTTTGTCTTCATTGCAACAT
* *
299968 CTTGATTCGTTTTTGTCTTCATTGCAATAT
1 CTTGATTCATTTTTGTCTTCATTGCAACAT
299998 CTTGATT
1 CTTGATT
300005 ACTTTAATTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.16, C:0.16, G:0.13, T:0.54
Consensus pattern (30 bp):
CTTGATTCATTTTTGTCTTCATTGCAACAT
Found at i:300091 original size:12 final size:12
Alignment explanation
Indices: 300076--300117 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
300066 ACTTTGCCGT
300076 TTGCTTTCTTCA
1 TTGCTTTCTTCA
300088 TTGCATTTGCTTCA
1 TTGC-TTT-CTTCA
*
300102 TTGTTTTCTTCA
1 TTGCTTTCTTCA
300114 TTGC
1 TTGC
300118 ACCTTAGCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 12 0.46
13 6 0.23
14 8 0.31
ACGTcount: A:0.10, C:0.21, G:0.12, T:0.57
Consensus pattern (12 bp):
TTGCTTTCTTCA
Found at i:301839 original size:34 final size:34
Alignment explanation
Indices: 301797--301868 Score: 135
Period size: 34 Copynumber: 2.1 Consensus size: 34
301787 GGCTTGCTAA
*
301797 AAAATTTTCAAGATTTTCTCCCCCTTATTGTTAT
1 AAAATTTTCAAGATTTTCTCCCACTTATTGTTAT
301831 AAAATTTTCAAGATTTTCTCCCACTTATTGTTAT
1 AAAATTTTCAAGATTTTCTCCCACTTATTGTTAT
301865 AAAA
1 AAAA
301869 AATCTTTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (34 bp):
AAAATTTTCAAGATTTTCTCCCACTTATTGTTAT
Found at i:307679 original size:13 final size:13
Alignment explanation
Indices: 307661--307687 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
307651 ACATGCTACT
307661 TTGTATCGATACA
1 TTGTATCGATACA
307674 TTGTATCGATACA
1 TTGTATCGATACA
307687 T
1 T
307688 GTTCAATGTA
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:307699 original size:19 final size:21
Alignment explanation
Indices: 307675--307728 Score: 76
Period size: 19 Copynumber: 2.7 Consensus size: 21
307665 ATCGATACAT
**
307675 TGTATCGATACATGTTC-AA-
1 TGTATCGATACATGGACAAAC
307694 TGTATCGATACATGGACAAAC
1 TGTATCGATACATGGACAAAC
307715 TGTATCGATACATG
1 TGTATCGATACATG
307729 AAATTGGCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 15 0.48
20 2 0.06
21 14 0.45
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (21 bp):
TGTATCGATACATGGACAAAC
Found at i:313959 original size:13 final size:13
Alignment explanation
Indices: 313941--313968 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
313931 ACAACATTCC
313941 TTGTATCGATACA
1 TTGTATCGATACA
313954 TTGTATCGATACA
1 TTGTATCGATACA
313967 TT
1 TT
313969 AGGTACTATT
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:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:315809 original size:19 final size:18
Alignment explanation
Indices: 315787--315826 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
315777 TAAATTTTTT
315787 ATATAAAAAGGGGGAGAAG
1 ATATAAAAA-GGGGAGAAG
315806 ATATAAAAAGGGGAGAAG
1 ATATAAAAAGGGGAGAAG
315824 ATA
1 ATA
315827 ATCGTTTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.55, C:0.00, G:0.33, T:0.12
Consensus pattern (18 bp):
ATATAAAAAGGGGAGAAG
Found at i:315872 original size:37 final size:37
Alignment explanation
Indices: 315822--315898 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
315812 AAAGGGGAGA
*
315822 AGATAATCGTTTAAGGGGGAGAATTTTTTTTAAGAGG
1 AGATAATCGTTTAAGGGGGAGAATATTTTTTAAGAGG
*
315859 AGATAATCGTTTAAGGGGGAGAATATTTTTTAAGGGG
1 AGATAATCGTTTAAGGGGGAGAATATTTTTTAAGAGG
315896 AGA
1 AGA
315899 AAAACGAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.34, C:0.03, G:0.31, T:0.32
Consensus pattern (37 bp):
AGATAATCGTTTAAGGGGGAGAATATTTTTTAAGAGG
Found at i:315897 original size:18 final size:19
Alignment explanation
Indices: 315831--315899 Score: 72
Period size: 18 Copynumber: 3.7 Consensus size: 19
315821 AAGATAATCG
*
315831 TTTAAGGGGGAGAATTTTT
1 TTTAAGGGGGAGAATATTT
* **
315850 TTTAA-GAGGAG-ATAATCG
1 TTTAAGGGGGAGAAT-ATTT
315868 TTTAAGGGGGAGAATATTT
1 TTTAAGGGGGAGAATATTT
315887 TTTAA-GGGGAGAA
1 TTTAAGGGGGAGAA
315900 AAACGAAAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
17 2 0.05
18 19 0.47
19 17 0.43
20 2 0.05
ACGTcount: A:0.33, C:0.01, G:0.32, T:0.33
Consensus pattern (19 bp):
TTTAAGGGGGAGAATATTT
Found at i:316457 original size:13 final size:13
Alignment explanation
Indices: 316439--316465 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
316429 ACATGCTACT
316439 TTGTATCGATACA
1 TTGTATCGATACA
316452 TTGTATCGATACA
1 TTGTATCGATACA
316465 T
1 T
316466 GTTCAATGTA
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:316477 original size:19 final size:21
Alignment explanation
Indices: 316451--316506 Score: 80
Period size: 19 Copynumber: 2.8 Consensus size: 21
316441 GTATCGATAC
**
316451 ATTGTATCGATACATGTTC-A
1 ATTGTATCGATACATGGACAA
316471 A-TGTATCGATACATGGACAA
1 ATTGTATCGATACATGGACAA
316491 ATTGTATCGATACATG
1 ATTGTATCGATACATG
316507 AAATTGGCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 15 0.47
20 3 0.09
21 14 0.44
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (21 bp):
ATTGTATCGATACATGGACAA
Found at i:316572 original size:13 final size:13
Alignment explanation
Indices: 316551--316581 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
316541 CGATACATGG
*
316551 TACAATGTATCGA
1 TACATTGTATCGA
316564 TACATTGTATCGA
1 TACATTGTATCGA
316577 TACAT
1 TACAT
316582 GAAGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:316577 original size:33 final size:32
Alignment explanation
Indices: 316535--316601 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 32
316525 CTATCACTAT
316535 TTGTATCGATACATG-GTACAATGTATCGATACA
1 TTGTATCGATACATGAG-A-AATGTATCGATACA
316568 TTGTATCGATACATGAAGAAATGTATCGATACA
1 TTGTATCGATACATG-AGAAATGTATCGATACA
316601 T
1 T
316602 AGCTTGTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (32 bp):
TTGTATCGATACATGAGAAATGTATCGATACA
Found at i:319898 original size:20 final size:20
Alignment explanation
Indices: 319873--319920 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
319863 TGGGACAATA
*
319873 TATCGATACAAT-TCTTCATG
1 TATCGATACAATGT-GTCATG
319893 TATCGATACAATGTGTCATG
1 TATCGATACAATGTGTCATG
319913 TATCGATA
1 TATCGATA
319921 TAAACAGTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.38
Consensus pattern (20 bp):
TATCGATACAATGTGTCATG
Found at i:320254 original size:21 final size:20
Alignment explanation
Indices: 320230--320269 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
320220 TTTAAACGAA
320230 CAAAACTTGTTTACGATTTTT
1 CAAAA-TTGTTTACGATTTTT
* *
320251 CAAAATTTTTTTCGATTTT
1 CAAAATTGTTTACGATTTT
320270 ATTCACATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.28, C:0.12, G:0.07, T:0.53
Consensus pattern (20 bp):
CAAAATTGTTTACGATTTTT
Found at i:322676 original size:42 final size:42
Alignment explanation
Indices: 320887--322676 Score: 1185
Period size: 42 Copynumber: 42.8 Consensus size: 42
320877 AATAGGTGAA
* * *
320887 AAAGTCTCTAAGGTCAAAGCCAACAGGCAGACTGAGGGTAAG
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGTAAG
* * * *
320929 AAAGTCTCCAAGGTCAAAGCCGATAGGCAAACTTAAGGTGAG
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGTAAG
** *
320971 GCAGTCTCCAAGGTCAAAGCCGACAGGTAGACT-AAGGGTAAG
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAA-GGTAAG
* *
321013 AAAGTCTCCAAGGTCAAAGCCAACAGGTAGACTTG-AGGTAAG
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGAC-TGAAGGTAAG
** * * *
321055 GTAGCCTCTAAGGTCAAAGCCGACAGGCAGACTGAAGGTAAA
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGTAAG
* * * *
321097 AAAGTCTCCAAGGTCAAAGCCAACAGGCAGACTTAATGTGAG
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGTAAG
* * * * *
321139 ATAGTCTCTAATGTCAAAGCCGACAAGCAGACTTG-AGGTGAG
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGAC-TGAAGGTAAG
** * * *
321181 GCAGTCTCCAGGGTCAAAGTCG-CAGGCAGACTGAGGGTAAG
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGTAAG
*
321222 AAAGTCTCCACCA-GTCAAAGCCAACAGGCAGACTTG-AGG--AG
1 AAAGTCTCCA--AGGTCAAAGCCGACAGGCAGAC-TGAAGGTAAG
** * * * * *
321263 ATGCGGTTTCTAGGGTCAAAGCCGATAGGCAGACTGAGGGTAAG
1 A--AAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGTAAG
* *
321307 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTTG-GGGTGAG
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGAC-TGAAGGTAAG
** * ** * * *
321349 GTAGTCTCCAAGGTTAAAGTTGATAGGTAGAC-AAAGGGTAAG
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAA-GGTAAG
*
321391 AAAGTCTCCAGGGGTCAAAGCCGACAGGCAGACTTG-AGGTGAAG
1 AAAGTCTCCA-AGGTCAAAGCCGACAGGCAGAC-TGAAGGT-AAG
* * * * * *
321435 TAA-TCTCC-AGAGTCAAAACTGACAGGCAAACTTAGGGTAAG
1 AAAGTCTCCAAG-GTCAAAGCCGACAGGCAGACTGAAGGTAAG
* * * * * * * *
321476 AAAATCTCCAAGGTTAAAACTGACAAGCAAACTTAAGGTGAG
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGTAAG
** *
321518 GCAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGTAGG
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGTAAG
* * * * **
321560 AAAGTCTCCAAGGTCAAAGCCAATAAGCAGACTTG-ATGTGGG
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGAC-TGAAGGTAAG
** * *
321602 GTAGTCTCCAAGGTCAAAGCTG-CAGGCAGACTGAGGGTAAG
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGTAAG
* * *
321643 AAAGTCTCCAGGGTCAAAGCCGACAGGTAAACTTG-AGGTAAG
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGAC-TGAAGGTAAG
** * * * * * *
321685 GCAGTCTCTAGGGT-AAAGTCGATAGGCAGACTGAGGGCAAG
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGTAAG
* * * * * * *
321726 AAAATCT-CTAGAGTTAAAACTGACAGGCAGACTTAGGGTGAA-
1 AAAGTCTCCAAG-GTCAAAGCCGACAGGCAGACTGAAGGT-AAG
* * * *
321768 ACAGTCTCCAAAGTCAAAGCCAACAGGCAGACT-AAGAGTAAA
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAG-GTAAG
* * * * * *
321810 AAAGTCTCTAGGGTCAAAGTCGATAGGCAGACTTGGA-GTGAG
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGAC-TGAAGGTAAG
** * * * * * *
321852 GTAGTTTCCAGGGTCAAAGTCG-CAGGTAGACTAAAAGTAGAG
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGTA-AG
* * * * *
321894 AAAGTCTCTAGGGTCAAAGCCGATAGGTAAACTTG-AGGTAAG
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGAC-TGAAGGTAAG
** * * *
321936 GTAGTCTCTAGGGTCAAAGCC-ACAGGCAGACTGAGGGTAAG
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGTAAG
* * * *
321977 AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTAGGGTGAGG
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGT-AAG
* * * * *
322020 CAA-TCTCTAAAGTCAAAGCCGACAGGCAGACTGAGGGGAAG
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGTAAG
** * * * * *
322061 AAAGTCT-CAAGGGTCAAAATCAACAAGCAGACTTAGGGTGAG
1 AAAGTCTCCAA-GGTCAAAGCCGACAGGCAGACTGAAGGTAAG
** *
322103 GTAGTCTCCAAGGTCAAAGCCGACAAGCAGACTGAAGGT-AG
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGTAAG
* * * *
322144 AGAGTCTCCAAGGTCAAAACCGATAAGCAGACTTG-AGGTGAAG
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGAC-TGAAGGT-AAG
* *
322187 -TAGTCTCC-AGAGTCAAAGCCG-CAGGCAGACTGAGGGTAAG
1 AAAGTCTCCAAG-GTCAAAGCCGACAGGCAGACTGAAGGTAAG
* * *
322227 AAAGTCTCCAGGGTCAAA-CCGACAGGCAGACTTG-AGATGAG
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGAC-TGAAGGTAAG
** * * *
322268 GTAGTCT-GAGGGTCAAAGCTGACAGGCAGACTG-AGGATAAG
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGG-TAAG
* * * * *
322309 AAAGTCTCCATGGTCAAAGCCGACAGGCAAACTTAGGGTGAG
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGTAAG
* * * * *
322351 ACAGTCTCCAGGGTCAAAGCCGACTGGCAGTCTGAGGGTAAG
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGTAAG
* * * * *
322393 AAAGTCTCCTAGATCAAAGCTGACAGGTAGATTTG-AGGTAAG
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGA-CTGAAGGTAAG
** * * * *
322435 GTAGTCTCCAGGGTCAAAGCTGACAAGCAGACTGAGGGTAAG
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGTAAG
** * * *
322477 AAAGTCT-CTTGGATCAAAACTGACAAGCAGACTTG-AGGTAAG
1 AAAGTCTCCAAGG-TCAAAGCCGACAGGCAGAC-TGAAGGTAAG
* * * * *
322519 GAAGTCTCTAAGGTCAAAGCTGATAGGCAGACTGAAGGTAAA
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGTAAG
** * * * * *
322561 AAAGTCTGTAAGTTTAAAGCCGACAAGCAGATTTG-AGGTGAG
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGA-CTGAAGGTAAG
* ** * *
322603 -TAGTCTCCAAGGTCAAAGCTAATAGGCAGACTGAAGGTAAA
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGTAAG
* * *
322644 AAAATCTCCAAGGTCAAAGCCGATAAGCAGACT
1 AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACT
322677 TGAGAAAGTT
Statistics
Matches: 1352, Mismatches: 324, Indels: 144
0.74 0.18 0.08
Matches are distributed among these distances:
40 34 0.03
41 269 0.20
42 950 0.70
43 86 0.06
44 13 0.01
ACGTcount: A:0.35, C:0.19, G:0.29, T:0.17
Consensus pattern (42 bp):
AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGTAAG
Found at i:322856 original size:44 final size:44
Alignment explanation
Indices: 322806--322906 Score: 116
Period size: 44 Copynumber: 2.3 Consensus size: 44
322796 TTTGACTAGG
* * *
322806 GTGGTAACCATATG-TAAAAAAGAA-AGGAAAGAGATTTAACCAGA
1 GTGGTAACCATACGTTAAAAAAGAATA-AAAAGA-ATCTAACCAGA
* * *
322850 GTGGTAACCATACGTTAAATAAGAATAAAAAGAATCTAACTAGG
1 GTGGTAACCATACGTTAAAAAAGAATAAAAAGAATCTAACCAGA
322894 GTGGTAACCATAC
1 GTGGTAACCATAC
322907 ATCAGACCAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
44 34 0.69
45 14 0.29
46 1 0.02
ACGTcount: A:0.47, C:0.12, G:0.21, T:0.21
Consensus pattern (44 bp):
GTGGTAACCATACGTTAAAAAAGAATAAAAAGAATCTAACCAGA
Found at i:323399 original size:89 final size:89
Alignment explanation
Indices: 323306--323500 Score: 255
Period size: 89 Copynumber: 2.2 Consensus size: 89
323296 GGTGGTTAGA
* *
323306 TAAAGGGGATATGATTAAGAATCTGTGGGCTGCACCTTGCCCTAAGGAAATCAAACTCTGTGATG
1 TAAAGGGGATATGATTAAGAATCTGTAGGCTGCACCTTGCCCTAAGGAAATCAAACTCTGCGATG
* * * **
323371 GATCAATACCATCTAATGGTTGGG
66 CATCAATACCATCTAAAGGCTAAG
* ** * * * *
323395 TAAAGGGAATATGATTGGGAATGTGTAGGCTGCACCTTGCCCTTAGGAAATCAAGCTTTGCGATG
1 TAAAGGGGATATGATTAAGAATCTGTAGGCTGCACCTTGCCCTAAGGAAATCAAACTCTGCGATG
323460 CATCAATACCATCTAAAGGCTAAG
66 CATCAATACCATCTAAAGGCTAAG
*
323484 TGAAGGGGATATGATTA
1 TAAAGGGGATATGATTA
323501 GGAAATGTGT
Statistics
Matches: 89, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (89 bp):
TAAAGGGGATATGATTAAGAATCTGTAGGCTGCACCTTGCCCTAAGGAAATCAAACTCTGCGATG
CATCAATACCATCTAAAGGCTAAG
Found at i:323920 original size:88 final size:87
Alignment explanation
Indices: 323765--323928 Score: 202
Period size: 88 Copynumber: 1.9 Consensus size: 87
323755 GCAGATATGC
* * * * * * *
323765 GTGAAACGATGCAAATGCAAGTATTAATAAAATGGCAAATGCCTATGCAATGACGCTAATGCCAA
1 GTGAAACAATGCAAATGCAAGGATCAATAAAATAGCAAATGCATATGCAATAACGCAAATGCCAA
323830 TGTCATCTAAAATGCAAATGTAG
66 TGTCATC-AAAATGCAAATGTAG
* * * **
323853 GTGAAACAATGCAAATGTAGGGATCAATAAAATAGCAAATGCATATGCAATAATGCAAATGTGAA
1 GTGAAACAATGCAAATGCAAGGATCAATAAAATAGCAAATGCATATGCAATAACGCAAATGCCAA
*
323918 TGTTATCAAAA
66 TGTCATCAAAA
323929 CTATGAATGT
Statistics
Matches: 63, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
87 4 0.06
88 59 0.94
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.24
Consensus pattern (87 bp):
GTGAAACAATGCAAATGCAAGGATCAATAAAATAGCAAATGCATATGCAATAACGCAAATGCCAA
TGTCATCAAAATGCAAATGTAG
Found at i:324247 original size:88 final size:89
Alignment explanation
Indices: 324008--324240 Score: 224
Period size: 88 Copynumber: 2.7 Consensus size: 89
323998 TGAAACAATG
* ** * **
324008 CAAATACAAGCATCAGTAAAGTGGCAAATGCATATGAAAATGATGCAAATGCTAATGTTATCT-A
1 CAAATGCAAGCATCAACAAAATGGCAAATGCATATGAAAATGATGCAAATGCTAATGCCATCTAA
*
324072 AATGCAAATGCATGCAGAATGATA
66 AATGCAAATGCATGCAGAATAATA
* * * * * * * *
324096 CAAATGCAAGCATCAACAAAAGGGCAAACGAATATG-CAATGATACAAATACCACTGCCATCTAA
1 CAAATGCAAGCATCAACAAAATGGCAAATGCATATGAAAATGATGCAAATGCTAATGCCATCTAA
* *
324160 AATGCAAATGTCGGTG-AG-GTAATA
66 AATGCAAATG-C-ATGCAGAATAATA
* * * *
324184 CAAATGCAATCATTAATAGAATGGCAAATGCATATGAAAAT-ATGCAAATGCTAATGC
1 CAAATGCAAGCATCAACAAAATGGCAAATGCATATGAAAATGATGCAAATGCTAATGC
324241 AGTCTAATCC
Statistics
Matches: 112, Mismatches: 29, Indels: 8
0.75 0.19 0.05
Matches are distributed among these distances:
87 19 0.17
88 85 0.76
89 6 0.05
90 2 0.02
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.22
Consensus pattern (89 bp):
CAAATGCAAGCATCAACAAAATGGCAAATGCATATGAAAATGATGCAAATGCTAATGCCATCTAA
AATGCAAATGCATGCAGAATAATA
Found at i:325276 original size:18 final size:18
Alignment explanation
Indices: 325255--325295 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
325245 CTATCCACAC
325255 TTTTTCCATTTCTTACTT
1 TTTTTCCATTTCTTACTT
** *
325273 TTTTTCTTTTTCTTTCTT
1 TTTTTCCATTTCTTACTT
325291 TTTTT
1 TTTTT
325296 TTATTTAGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTCCATTTCTTACTT
Found at i:331292 original size:20 final size:21
Alignment explanation
Indices: 331260--331307 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
331250 AGGAAAACAA
*
331260 AGTTTTCTAAATTTTAAAATT
1 AGTTTTCTAAATTTCAAAATT
331281 AGTTTT-TAAATTTCAAAAATT
1 AGTTTTCTAAATTTC-AAAATT
331302 ATGTTT
1 A-GTTT
331308 CATACCCAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 7 0.29
21 13 0.54
22 4 0.17
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (21 bp):
AGTTTTCTAAATTTCAAAATT
Found at i:332336 original size:10 final size:10
Alignment explanation
Indices: 332303--332336 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
332293 GTATTATGGC
*
332303 TGCTGGTGCT
1 TGCTGTTGCT
*
332313 TGCCGTTGCT
1 TGCTGTTGCT
332323 TGCTGTTGCT
1 TGCTGTTGCT
332333 TGCT
1 TGCT
332337 ATTTTTTGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.32, T:0.44
Consensus pattern (10 bp):
TGCTGTTGCT
Found at i:332515 original size:19 final size:18
Alignment explanation
Indices: 332491--332539 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
332481 TTTGTTTCTG
**
332491 TTGTTTTTTTCTTCTTTTT
1 TTGTTTTTTTC-AATTTTT
332510 TTGTTTTATTTCAATTTTT
1 TTGTTTT-TTTCAATTTTT
*
332529 TTCTTTTTTTC
1 TTGTTTTTTTC
332540 GATTGCTACT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 4 0.15
19 18 0.69
20 4 0.15
ACGTcount: A:0.06, C:0.10, G:0.04, T:0.80
Consensus pattern (18 bp):
TTGTTTTTTTCAATTTTT
Found at i:332952 original size:30 final size:30
Alignment explanation
Indices: 332917--332983 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
332907 TTCTTTGCTG
* *
332917 CTTGATTCGTTTTTGTCTTCATTACAGCAT
1 CTTGATTCATTTTTGTCTTCATTACAACAT
*
332947 CTTGATTCATTTTTGTCTTCATTGCAACAT
1 CTTGATTCATTTTTGTCTTCATTACAACAT
332977 CTTGATT
1 CTTGATT
332984 GCTTTAATTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.18, C:0.19, G:0.12, T:0.51
Consensus pattern (30 bp):
CTTGATTCATTTTTGTCTTCATTACAACAT
Found at i:333077 original size:25 final size:25
Alignment explanation
Indices: 333047--333096 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
333037 TCATGCTGAC
333047 TTTGCTGT-TTGCTTTTTTCATTGCA
1 TTTGCTGTATTG-TTTTTTCATTGCA
*
333072 TTTGCTTTATTGTTTTTTCATTGCA
1 TTTGCTGTATTGTTTTTTCATTGCA
333097 CCTCAGTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 20 0.87
26 3 0.13
ACGTcount: A:0.10, C:0.14, G:0.14, T:0.62
Consensus pattern (25 bp):
TTTGCTGTATTGTTTTTTCATTGCA
Found at i:333429 original size:10 final size:10
Alignment explanation
Indices: 333414--333459 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
333404 TAATTATCAC
333414 TATTTTTATA
1 TATTTTTATA
333424 TATTTTT-TA
1 TATTTTTATA
333433 -ATTATTT-TA
1 TATT-TTTATA
333442 TATTTTTATA
1 TATTTTTATA
*
333452 TTTTTTTA
1 TATTTTTA
333460 ATGTCAAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
8 3 0.09
9 10 0.31
10 19 0.59
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
TATTTTTATA
Found at i:333437 original size:27 final size:26
Alignment explanation
Indices: 333403--333461 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 26
333393 CTTTTTTTAA
333403 TTAATTA-TCACTATTTTTATATATTTT
1 TTAATTATTCA-TATTTTTATAT-TTTT
*
333430 TTAATTATTTTATATTTTTATATTTTT
1 TTAATTA-TTCATATTTTTATATTTTT
333457 TTAAT
1 TTAAT
333462 GTCAAAGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 16 0.55
28 11 0.38
29 2 0.07
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (26 bp):
TTAATTATTCATATTTTTATATTTTT
Found at i:335727 original size:155 final size:155
Alignment explanation
Indices: 335420--335820 Score: 391
Period size: 155 Copynumber: 2.6 Consensus size: 155
335410 TAGTCACTAG
* * ** **
335420 GTCACTTTTATGCCAAAGATAT-TCGTTTAGGATAGGTTCATCCTTTTATTATCTTTTTGTGTAT
1 GTCACTTTTATGCCAAAGGTATAT-GTTTAGGATAGGTTCATCCTTTTATAATCTTTTCATGTCC
* * * * *
335484 TTTAAGGTTACCGAGATACTTTCACGTCGAAGGTAAACCCCCAAGGCATTTAGGTAATTTTTTCT
65 TTTAAAGTTACAGAGATACTTTCACGTCAAAAGTAAACCCCCAAGGCATTTAGATAATTTTTTCT
*
335549 AGAATCGAATCCTAAGTAATCATCGA
130 AGAATCAAATCCTAAGTAATCATCGA
** * * *
335575 GTCGTTTTTATGCCAGAGGTATATGTTTAGGATAGGTTCATTCTTTTATGATCTTTTCATGTCCT
1 GTCACTTTTATGCCAAAGGTATATGTTTAGGATAGGTTCATCCTTTTATAATCTTTTCATGTCCT
* * ** * *
335640 TTAAAGTTACGGAGATACTTTCACGTCAAAAGT-ATCCCTTAGGGTTATTTAGATAATTTTTTCT
66 TTAAAGTTACAGAGATACTTTCACGTCAAAAGTAAACCCCCAAGG-CATTTAGATAATTTTTTCT
* * * * *
335704 ATAA-CAAAGTTCTAGGTAGTCATCGG
130 AGAATCAAA-TCCTAAGTAATCATCGA
* * * ** * *
335730 GTCACTTTTATACCAAATGTATATATTTAGGATAAACTT-GTCCTTTTATAATCCTTTCATGTCC
1 GTCACTTTTATGCCAAAGGTATATGTTTAGGAT-AGGTTCATCCTTTTATAATCTTTTCATGTCC
335794 TTT-AAGATTATCAGA-ATACTTTCACGT
65 TTTAAAG-TTA-CAGAGATACTTTCACGT
335821 TGAATATATA
Statistics
Matches: 201, Mismatches: 39, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
154 13 0.06
155 181 0.90
156 7 0.03
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.40
Consensus pattern (155 bp):
GTCACTTTTATGCCAAAGGTATATGTTTAGGATAGGTTCATCCTTTTATAATCTTTTCATGTCCT
TTAAAGTTACAGAGATACTTTCACGTCAAAAGTAAACCCCCAAGGCATTTAGATAATTTTTTCTA
GAATCAAATCCTAAGTAATCATCGA
Found at i:337652 original size:15 final size:15
Alignment explanation
Indices: 337613--337653 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
337603 TTGATATTCT
**
337613 TAATTATTGGAAAGA
1 TAATTATTGTCAAGA
337628 TAATTATTGTCAAGA
1 TAATTATTGTCAAGA
337643 TAATTATTGTC
1 TAATTATTGTC
337654 GATATCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.39, C:0.05, G:0.15, T:0.41
Consensus pattern (15 bp):
TAATTATTGTCAAGA
Found at i:339466 original size:16 final size:17
Alignment explanation
Indices: 339445--339476 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
339435 ATTTAAGTTC
339445 AATCATTTT-GAATTCG
1 AATCATTTTCGAATTCG
339461 AATCATTTTCGAATTC
1 AATCATTTTCGAATTC
339477 ATATTTGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.44
Consensus pattern (17 bp):
AATCATTTTCGAATTCG
Found at i:339554 original size:27 final size:26
Alignment explanation
Indices: 339512--339566 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 26
339502 TTTTTTTATC
339512 AATTAAATTAAATTTAAATTCAAATT
1 AATTAAATTAAATTTAAATTCAAATT
339538 AATT-AATTAAATTTTTAAATTCAAATT
1 AATTAAATTAAA--TTTAAATTCAAATT
339565 AA
1 AA
339567 AATTAACAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 7 0.26
26 4 0.15
27 16 0.59
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (26 bp):
AATTAAATTAAATTTAAATTCAAATT
Found at i:343126 original size:13 final size:13
Alignment explanation
Indices: 343108--343133 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
343098 ACAGCAAAGT
343108 ATGTATCGATACA
1 ATGTATCGATACA
343121 ATGTATCGATACA
1 ATGTATCGATACA
343134 CAAAAATTGT
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:343131 original size:33 final size:32
Alignment explanation
Indices: 343089--343152 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
343079 GTGCCAAACT
*
343089 TGTATCGATACAGC-AAAGTATGTATCGATACAA
1 TGTATCGATACA-CAAAAAT-TGTATCGATACAA
343122 TGTATCGATACACAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAATTGTATCGATACA
343153 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACAAAAATTGTATCGATACAA
Found at i:343150 original size:32 final size:33
Alignment explanation
Indices: 343089--343152 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
343079 GTGCCAAACT
*
343089 TGTATCGATACAGCAAAGTATGTATCGATACAA
1 TGTATCGATACAGCAAAATATGTATCGATACAA
343122 TGTATCGATACA-CAAAA-ATTGTATCGATACA
1 TGTATCGATACAGCAAAATA-TGTATCGATACA
343153 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 1 0.03
32 16 0.55
33 12 0.41
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (33 bp):
TGTATCGATACAGCAAAATATGTATCGATACAA
Done.