Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 160 of 320
Found at i:52775540 original size:250 final size:248
Alignment explanation
Indices: 52775083--52775941 Score: 774
Period size: 250 Copynumber: 3.4 Consensus size: 248
52775073 GAAAAAATTG
*
52775083 AAAAA-CAGAAATTGAAAATACCTCAGCGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGT
1 AAAAAGCAGAAATTGAAAATACCTCAGCGTGCCTTGAAGCTCAACTCACCTCTCGCAATATGAGT
* *
52775147 TGATTTTTGAAAAACAGAAATTAAAAGCAGAAATTGAAAAACAGAAATTAAAAATACCTCGGCGT
66 TGATTTTTGAAAAACAGAAATTAAAAACAGAAATTGAAAAACAGAAATTAAAAAGACCTCGGCGT
* * * *
52775212 GCCCCGAGGCTCAGCTCACCTCTCGCAATATGAGTTGATTTTTAAAAAGCATAAATTGAAATTAC
131 GCCCCGAGACTCAACTCACCTCTCGCAATACGAGTTGATTTTTAAAAAGCAGAAATTGAAATTAC
52775277 CTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-T-TTTT
196 CTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTTT
* * *
52775328 AAAAAGCATAAATTGAAATTACCTCAGCGTGTCC-TGAATCTCAACTCACCTCTCGCAATATGAG
1 AAAAAGCAGAAATTGAAAATACCTCAGCGTG-CCTTGAAGCTCAACTCACCTCTCGCAATATGAG
* * *
52775392 TTGATTTTTTGAAAAGCATAAATTGAAAAAACAGAAATTG-AAAACA-AAATTTGAAAAGACCTC
65 TTGA-TTTTTGAAAAACAGAAATT--AAAAACAGAAATTGAAAAACAGAAA-TTAAAAAGACCTC
* * * *
52775455 GGCGTATGGCTCGAGACTCAACTCACCTCTCGCAATACGAGTTGATTTTTTGACAA-CAGAAATT
126 GGCG--TGCCCCGAGACTCAACTCACCTCTCGCAATACGAGTTGA-TTTTTAAAAAGCAGAAATT
52775519 GAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTTTGAAA
188 GAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTC-TTT----
52775584 AGT
248 --T
* *
52775587 AGAAATTGAAAAGCAGAAATTGAAAATACCTCAACACGTGAGCC--GAGGCTCAACTCACCTCTC
1 ----A---AAAAGCAGAAATTGAAAATACCTC-A-GCGT--GCCTTGAAGCTCAACTCACCTCTC
* * * *
52775650 GCAATATAAGTTGGATTTTTG----A-A-AAA-T--------AAATTGACAAACGGAAATTGAAA
55 GCAATATGAGTT-GATTTTTGAAAAACAGAAATTAAAAACAGAAATTGAAAAACAGAAATTAAAA
* * ** * *
52775700 ATACCTCAGCGT--CTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGATTTTTT
119 AGACCTCGGCGTGCCCCGAGACTCAACTCACCTCTCGCAATACGAGTTGA--TTTTT-A------
* * *
52775763 TTGAAAGACAGAAATTG-AATATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATG
175 --AAAAG-CAGAAATTGAAAT-TACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
*
52775827 AGTTGATTTTTTT
236 AGTTGATTCTTTT
*
52775840 GAAAAA-CAGAAATT-AAAATTACCTCAGCGTGTCC-TGAGGCTCAACTCACCTCTCGCAATATG
1 -AAAAAGCAGAAATTGAAAA-TACCTCAGCGTG-CCTTGAAGCTCAACTCACCTCTCGCAATATG
* *
52775902 AGTTGATTCTTT-AAAAACAGACATT-AAAATAGAAATTGAA
63 AGTTGATT-TTTGAAAAACAGAAATTAAAAACAGAAATTGAA
52775942 CATAGCTCAG
Statistics
Matches: 509, Mismatches: 42, Indels: 114
0.77 0.06 0.17
Matches are distributed among these distances:
242 1 0.00
243 6 0.01
244 36 0.07
245 10 0.02
246 69 0.14
247 27 0.05
248 55 0.11
249 21 0.04
250 98 0.19
251 15 0.03
252 19 0.04
253 7 0.01
257 7 0.01
258 2 0.00
259 7 0.01
260 58 0.11
261 1 0.00
262 3 0.01
263 2 0.00
266 22 0.04
267 1 0.00
268 37 0.07
269 4 0.01
270 1 0.00
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.28
Consensus pattern (248 bp):
AAAAAGCAGAAATTGAAAATACCTCAGCGTGCCTTGAAGCTCAACTCACCTCTCGCAATATGAGT
TGATTTTTGAAAAACAGAAATTAAAAACAGAAATTGAAAAACAGAAATTAAAAAGACCTCGGCGT
GCCCCGAGACTCAACTCACCTCTCGCAATACGAGTTGATTTTTAAAAAGCAGAAATTGAAATTAC
CTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTTT
Found at i:52775597 original size:14 final size:14
Alignment explanation
Indices: 52775578--52775612 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
52775568 GTTGATTCTT
*
52775578 TTGAAAAGTAGAAA
1 TTGAAAAGCAGAAA
52775592 TTGAAAAGCAGAAA
1 TTGAAAAGCAGAAA
52775606 TTGAAAA
1 TTGAAAA
52775613 TACCTCAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.57, C:0.03, G:0.20, T:0.20
Consensus pattern (14 bp):
TTGAAAAGCAGAAA
Found at i:52775606 original size:177 final size:177
Alignment explanation
Indices: 52775294--52775612 Score: 525
Period size: 177 Copynumber: 1.8 Consensus size: 177
52775284 TGTCCTGAGG
* *
52775294 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAGCATAAATTGAAATTACCTCAGCGTG
1 CTCAACTCACCTCTCGCAATACGAGTTGATTTTTAAAAAGCAGAAATTGAAATTACCTCAGCGTG
* *
52775359 TCCTGAATCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAGCATAAATTGAAAAAAC
66 TCCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAGCAGAAATTGAAAAAAC
52775424 AGAAATTGAAAACAAAATTTGAAAAGACCTCGGCGTATGGCTCGAGA
131 AGAAATTGAAAACAAAATTTGAAAAGACCTCGGCGTATGGCTCGAGA
* *
52775471 CTCAACTCACCTCTCGCAATACGAGTTGATTTTTTGACAA-CAGAAATTGAAATTACCTCAGCGT
1 CTCAACTCACCTCTCGCAATACGAGTTGA-TTTTTAAAAAGCAGAAATTGAAATTACCTCAGCGT
* *
52775535 GTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTTTGAAAAGTAGAAATTG-AAAA
65 GTCCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATT-TTTTGAAAAGCAGAAATTGAAAAA
*
52775599 GCAGAAATTGAAAA
129 ACAGAAATTGAAAA
52775613 TACCTCAACA
Statistics
Matches: 131, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
177 106 0.81
178 25 0.19
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (177 bp):
CTCAACTCACCTCTCGCAATACGAGTTGATTTTTAAAAAGCAGAAATTGAAATTACCTCAGCGTG
TCCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAGCAGAAATTGAAAAAAC
AGAAATTGAAAACAAAATTTGAAAAGACCTCGGCGTATGGCTCGAGA
Found at i:52775818 original size:85 final size:83
Alignment explanation
Indices: 52775503--52776165 Score: 526
Period size: 85 Copynumber: 8.0 Consensus size: 83
52775493 GAGTTGATTT
* * *
52775503 TTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTTGAAAACAGAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
*
52775568 GTTGATTCTTTTGAAAAGTAGAA
66 GTTGATTTTTTTG--AA-T--AA
* *
52775591 ATTGAAAAGCAGAAATTGAAAATACCTCAACACGTGAGCC-GAGGCTCAACTCACCTCTCGCAAT
1 TTTGAAAA-CAGAAATTGAAAATACCTC-A-ACGTG-TCCTGAGGCTCAACTCACCTCTCGCAAT
* ***
52775655 ATAAGTTGGATTTTTGAAAAATAA
62 ATGAGTT-GATTTTT-TTGAATAA
* * * *
52775679 ATTGACAAACGGAAATTGAAAATACCTC-A-GCGTCTTGAGGCTCAACTCACCTCTCGCAATATG
1 TTTGA-AAACAGAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
* **
52775742 AGTTGATTTTTTTGATTTTT
65 AGTTGATTTTTTTGA-ATAA
* *
52775762 TTTGAAAGACAGAAATTGAATATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATG
1 TTTGAAA-ACAGAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
52775827 AGTTGATTTTTTTG----A
65 AGTTGATTTTTTTGAATAA
*
52775842 ----AAAACAGAAATT-AAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTTGAAAACAGAAATTGAAAA-TACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
*** *
52775902 AGTTGATTCTTTAAAAACAGA
65 AGTTGATT-TTTTTGAATA-A
* * * * * * * *
52775923 CATT-AAAATAGAAATTGAACATAGCTCAGCACGTGAGCC-AAGGCTCAACTCACTTCTCGTAAT
1 -TTTGAAAACAGAAATTGAAAATACCTCA--ACGTG-TCCTGAGGCTCAACTCACCTCTCGCAAT
*
52775986 ATGAATTGATTTTTTT-AA-AA
62 ATGAGTTGATTTTTTTGAATAA
* * *
52776006 ---G---ACAGAAATTGAGAATACCTCAACTTGTCTTGAGGCTCAACTCACCTCCTCGCAATATG
1 TTTGAAAACAGAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCT-CTCGCAATATG
*** *
52776065 AGTTGATTTTTGAAAACAGAA
65 AGTTGATTTTT-TTGA-ATAA
** * **
52776086 TTTGAAAAACAGATTTTGAAAATACCTCAGCGTG-CCCAAGGCTCAACTCACCTCTCGCAATATG
1 TTTG-AAAACAGAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
*
52776150 AGTAGATTTTTTTGAA
65 AGTTGATTTTTTTGAA
52776166 AACAGAAATA
Statistics
Matches: 466, Mismatches: 68, Indels: 87
0.75 0.11 0.14
Matches are distributed among these distances:
74 4 0.01
75 76 0.16
76 26 0.06
77 17 0.04
78 1 0.00
79 1 0.00
80 2 0.00
81 1 0.00
82 3 0.01
83 34 0.07
84 35 0.08
85 88 0.19
86 22 0.05
87 56 0.12
88 33 0.07
89 21 0.05
90 2 0.00
91 36 0.08
92 8 0.02
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (83 bp):
TTTGAAAACAGAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTTTTTGAATAA
Found at i:52775878 original size:75 final size:76
Alignment explanation
Indices: 52775753--52776179 Score: 277
Period size: 75 Copynumber: 5.4 Consensus size: 76
52775743 GTTGATTTTT
* * *
52775753 TTGATTTTTTTTGAAAGACAGAAATT-GAATATACCTCAACGTGTCTTGAGGCTCAACTCACCTC
1 TTGA-TTTTTTTGAAAAACAGAAATTAAAATATACCTCAACGTGTCCTGAGGCTCAACTCACCTC
52775817 TCGCAATATGAG
65 TCGCAATATGAG
*
52775829 TTGATTTTTTTGAAAAACAGAAATTAAAAT-TACCTCAGCGTGTCCTGAGGCTCAACTCACCTCT
1 TTGATTTTTTTGAAAAACAGAAATTAAAATATACCTCAACGTGTCCTGAGGCTCAACTCACCTCT
52775893 CGCAATATGAG
66 CGCAATATGAG
* * * ** * *
52775904 TTGA-TTCTTT-AAAAACAGACATTAAAATAGAAATTGAACATAGCTCAGCACGTGA-GC-CAAG
1 TTGATTTTTTTGAAAAACAGAAATTAAAATA-TACCTCAACGT-G-T---C-C-TGAGGCTCAA-
* *
52775965 GCTCAACTCACTTCTCGTAATATGAA
57 -CTC-A--C-C-TCTCGCAATATGAG
* * * *
52775991 TTGATTTTTTT-AAAAGACAGAAATTGAGA-ATACCTCAACTTGTCTTGAGGCTCAACTCACCTC
1 TTGATTTTTTTGAAAA-ACAGAAATTAAAATATACCTCAACGTGTCCTGAGGCTCAACTCACCT-
52776054 CTCGCAATATGAG
64 CTCGCAATATGAG
* * **
52776067 TTGA--TTTTTG-AAAACAGAATTTGAAAAACAGATTTTGAAAATACCTCAGCGTG-CCCAAGGC
1 TTGATTTTTTTGAAAAACAGAAATT----AA-A-A---T----ATACCTCAACGTGTCCTGAGGC
52776128 TCAACTCACCTCTCGCAATATGAG
53 TCAACTCACCTCTCGCAATATGAG
* *
52776152 TAGATTTTTTTG-AAAACAGAAATAAAAA
1 TTGATTTTTTTGAAAAACAGAAATTAAAA
52776180 CATCAAAATA
Statistics
Matches: 275, Mismatches: 37, Indels: 73
0.71 0.10 0.19
Matches are distributed among these distances:
73 25 0.09
74 13 0.05
75 73 0.27
76 24 0.09
77 3 0.01
79 2 0.01
80 10 0.04
81 6 0.02
82 11 0.04
83 3 0.01
85 18 0.07
86 18 0.07
87 49 0.18
88 10 0.04
89 10 0.04
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (76 bp):
TTGATTTTTTTGAAAAACAGAAATTAAAATATACCTCAACGTGTCCTGAGGCTCAACTCACCTCT
CGCAATATGAG
Found at i:52776027 original size:162 final size:159
Alignment explanation
Indices: 52775685--52776179 Score: 513
Period size: 162 Copynumber: 3.1 Consensus size: 159
52775675 ATAAATTGAC
* * *
52775685 AAACGGAAATTGAAAA-TACCTC-A-GCGTCTTGAGGCTCAACTCACCT-CTCGCAATATGAGTT
1 AAACAGAAATT-AAAATTACCTCAACGTGTCCTGAGGCTCAACTCACCTCCTCGCAATATGAGTT
*** ***** * * * ***
52775746 GATTTTT-TTGATTTTTTTTGAAAGACAGAAATTGAATATACCTCAACGTGTCTTGAGGCTCAAC
65 GATTTTTAAAAACAGAATTT-AAAAACAGAAATTGAAAATACCTCAGCGTG-CCCAAGGCTCAAC
52775810 TCACCTCTCGCAATATGAGTTGATTTTTTTGAA
128 TCACCTCTCGCAATATGAGTTGATTTTTTT-AA
*
52775843 AAACAGAAATTAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCT-CTCGCAATATGAGTTG
1 AAACAGAAATTAAAATTACCTCAACGTGTCCTGAGGCTCAACTCACCTCCTCGCAATATGAGTTG
* * * *
52775907 ATTCTTTAAAAACAGACA-TT-AAAATAGAAATTGAACATAGCTCAGCACGTGAGCCAAGGCTCA
66 ATT-TTTAAAAACAGA-ATTTAAAAACAGAAATTGAAAATACCTCAG--CGTG-CCCAAGGCTCA
* * *
52775970 ACTCACTTCTCGTAATATGAATTGATTTTTTTAA
126 ACTCACCTCTCGCAATATGAGTTGATTTTTTTAA
* * *
52776004 AAGACAGAAATTGAGAA-TACCTCAACTTGTCTTGAGGCTCAACTCACCTCCTCGCAATATGAGT
1 AA-ACAGAAATT-AAAATTACCTCAACGTGTCCTGAGGCTCAACTCACCTCCTCGCAATATGAGT
* **
52776068 TGATTTTTGAAAACAGAATTTGAAAAACAGATTTTGAAAATACCTCAGCGTGCCCAAGGCTCAAC
64 TGATTTTTAAAAACAGAATTT-AAAAACAGAAATTGAAAATACCTCAGCGTGCCCAAGGCTCAAC
* *
52776133 TCACCTCTCGCAATATGAGTAGATTTTTTTGA
128 TCACCTCTCGCAATATGAGTTGATTTTTTTAA
*
52776165 AAACAGAAATAAAAA
1 AAACAGAAATTAAAA
52776180 CATCAAAATA
Statistics
Matches: 280, Mismatches: 43, Indels: 27
0.80 0.12 0.08
Matches are distributed among these distances:
157 4 0.01
158 16 0.06
159 3 0.01
160 68 0.24
161 49 0.17
162 98 0.35
163 22 0.08
164 20 0.07
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.30
Consensus pattern (159 bp):
AAACAGAAATTAAAATTACCTCAACGTGTCCTGAGGCTCAACTCACCTCCTCGCAATATGAGTTG
ATTTTTAAAAACAGAATTTAAAAACAGAAATTGAAAATACCTCAGCGTGCCCAAGGCTCAACTCA
CCTCTCGCAATATGAGTTGATTTTTTTAA
Found at i:52776096 original size:14 final size:14
Alignment explanation
Indices: 52776073--52776107 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
52776063 TGAGTTGATT
52776073 TTTG-AAAACAGAA
1 TTTGAAAAACAGAA
*
52776086 TTTGAAAAACAGAT
1 TTTGAAAAACAGAA
52776100 TTTGAAAA
1 TTTGAAAA
52776108 TACCTCAGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.29
Consensus pattern (14 bp):
TTTGAAAAACAGAA
Found at i:52783667 original size:18 final size:18
Alignment explanation
Indices: 52783644--52783697 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
52783634 ACAAGTGGTG
52783644 GTGGAGCAAGTGTGGCTA
1 GTGGAGCAAGTGTGGCTA
*
52783662 GT-G-G--AGT-AGG-TA
1 GTGGAGCAAGTGTGGCTA
52783674 GTGGAGCAAGTGTGGCTA
1 GTGGAGCAAGTGTGGCTA
52783692 GTGGAG
1 GTGGAG
52783698 TTGGTGGTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
12 4 0.14
13 3 0.11
14 4 0.14
16 4 0.14
17 3 0.11
18 10 0.36
ACGTcount: A:0.22, C:0.07, G:0.48, T:0.22
Consensus pattern (18 bp):
GTGGAGCAAGTGTGGCTA
Found at i:52783680 original size:30 final size:30
Alignment explanation
Indices: 52783639--52783737 Score: 162
Period size: 30 Copynumber: 3.3 Consensus size: 30
52783629 TAGGTACAAG
52783639 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
* *
52783669 AGGTAGTGGAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
* *
52783699 TGGTGGTGGAGCAATTGTAGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
52783729 TGGTGGTGG
1 TGGTGGTGG
52783738 CAAAGGCTAG
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 63 1.00
ACGTcount: A:0.18, C:0.06, G:0.48, T:0.27
Consensus pattern (30 bp):
TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
Found at i:52786110 original size:20 final size:20
Alignment explanation
Indices: 52786085--52786124 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
52786075 AAATTGCATT
52786085 AAAAAAT-GAATAGAAATAAA
1 AAAAAATCGAATA-AAATAAA
*
52786105 AAAAAATCGCATAAAATAAA
1 AAAAAATCGAATAAAATAAA
52786125 GTTTTTAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.72, C:0.05, G:0.07, T:0.15
Consensus pattern (20 bp):
AAAAAATCGAATAAAATAAA
Found at i:52787660 original size:10 final size:11
Alignment explanation
Indices: 52787618--52787657 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
52787608 AGTTCAATCG
*
52787618 ATTCGATTAGAA
1 ATTC-ATTAAAA
*
52787630 ATTTATTAAAA
1 ATTCATTAAAA
52787641 ATTCATTAAAA
1 ATTCATTAAAA
52787652 ATTCAT
1 ATTCAT
52787658 AAAGTATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
11 22 0.88
12 3 0.12
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.40
Consensus pattern (11 bp):
ATTCATTAAAA
Found at i:52794658 original size:19 final size:20
Alignment explanation
Indices: 52794620--52794663 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
52794610 ACATAATTAT
*
52794620 AATAATATAATTAGAATAAA
1 AATAATATAATCAGAATAAA
*
52794640 AATAATTTAATCA-AATAAA
1 AATAATATAATCAGAATAAA
52794659 AATAA
1 AATAA
52794664 ATTATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (20 bp):
AATAATATAATCAGAATAAA
Found at i:52799441 original size:40 final size:41
Alignment explanation
Indices: 52799385--52799586 Score: 176
Period size: 43 Copynumber: 4.9 Consensus size: 41
52799375 TTTTATCAAA
* * *
52799385 TCACCGGCATTTAGCCTGCTAGGTTTTAAACCCGAATTCA-
1 TCACCGGCATTAAGCCTGCTAGGCTTTAAGCCCGAATTCAT
* * * * * *
52799425 TCACCGGCATGAAGCCTGTTAGACTTTAAGTCTGAACTCAT
1 TCACCGGCATTAAGCCTGCTAGGCTTTAAGCCCGAATTCAT
** *
52799466 TCACCGGCATTTCGCCTGCTAGGCTTGAAGCCC-AATATCATT
1 TCACCGGCATTAAGCCTGCTAGGCTTTAAGCCCGAAT-TCA-T
***
52799508 TCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGATATT-AT
1 TCACCGGCATTA-AGCCTGCTAGGCTTTAAGCCCGA-ATTCAT
* *
52799550 CTCACCGGCATTATAGCCTGCTAGGCCTGAAGCCCGA
1 -TCACCGGCATTA-AGCCTGCTAGGCTTTAAGCCCGA
52799587 TAATATTATT
Statistics
Matches: 132, Mismatches: 23, Indels: 11
0.80 0.14 0.07
Matches are distributed among these distances:
40 33 0.25
41 28 0.21
42 13 0.10
43 54 0.41
44 2 0.02
45 2 0.02
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (41 bp):
TCACCGGCATTAAGCCTGCTAGGCTTTAAGCCCGAATTCAT
Found at i:52799483 original size:41 final size:40
Alignment explanation
Indices: 52799384--52799530 Score: 116
Period size: 40 Copynumber: 3.6 Consensus size: 40
52799374 CTTTTATCAA
** *
52799384 ATCACCGGCATTTAGCCTGCTAGGTTTTAAACCCGAATTC
1 ATCACCGGCATTTAGCCTGCTAGACTTTAAACCCGAACTC
** * ** *
52799424 ATCACCGGCATGAAGCCTGTTAGACTTTAAGTCTGAACTC
1 ATCACCGGCATTTAGCCTGCTAGACTTTAAACCCGAACTC
* * * * *
52799464 ATTCACCGGCATTTCGCCTGCTAGGCTTGAAGCCC-AATATC
1 A-TCACCGGCATTTAGCCTGCTAGACTTTAAACCCGAA-CTC
52799505 ATTTCACCGGCATTATAGCCTGCTAG
1 A--TCACCGGCATT-TAGCCTGCTAG
52799531 GCCCGAAGCC
Statistics
Matches: 84, Mismatches: 19, Indels: 5
0.78 0.18 0.05
Matches are distributed among these distances:
40 34 0.40
41 28 0.33
42 12 0.14
43 10 0.12
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (40 bp):
ATCACCGGCATTTAGCCTGCTAGACTTTAAACCCGAACTC
Found at i:52799539 original size:43 final size:43
Alignment explanation
Indices: 52799465--52799635 Score: 170
Period size: 43 Copynumber: 4.0 Consensus size: 43
52799455 TCTGAACTCA
* **
52799465 TTCACCGGCATT-TCGCCTGCTAGGCTTGAAGCCCAATATCAT
1 TTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCAATATCAT
* *
52799507 TTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGATATTAT
1 TTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCAATATCAT
* * *
52799550 CTCACCGGCATTATAGCCTGCTAGGCCTGAAGCCCGATAAT-ATT
1 TTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCAAT-ATCA-T
* * * *
52799594 ATTCACCAGC-TTAAAGCTTGCTAGG-CCGAGGCCCGAATATCA
1 -TTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCC-AATATCA
52799636 CATTTTGATA
Statistics
Matches: 109, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
42 12 0.11
43 71 0.65
44 19 0.17
45 7 0.06
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (43 bp):
TTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCAATATCAT
Found at i:52799628 original size:86 final size:85
Alignment explanation
Indices: 52799466--52799629 Score: 208
Period size: 86 Copynumber: 1.9 Consensus size: 85
52799456 CTGAACTCAT
* * * *
52799466 TCACCGGCATTTCGCCTGCTAGGCTTGAAGCCCAATATCATTTCACCGGCATTATAGCCTGCTAG
1 TCACCGGCATTTAGCCTGCTAGGCCTGAAGCCCAATATCATTTCACCAGCATTAAAGCCTGCTAG
52799531 GCCCGAAGCCCGATATTATC
66 GCCCGAAGCCCGATATTATC
* *
52799551 TCACCGGCATTATAGCCTGCTAGGCCTGAAGCCCGATAAT-ATTATTCACCAGC-TTAAAGCTTG
1 TCACCGGCATT-TAGCCTGCTAGGCCTGAAGCCCAAT-ATCA-T-TTCACCAGCATTAAAGCCTG
*
52799614 CTAGG-CCGAGGCCCGA
62 CTAGGCCCGAAGCCCGA
52799630 ATATCACATT
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
85 11 0.16
86 33 0.49
87 16 0.24
88 8 0.12
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.24
Consensus pattern (85 bp):
TCACCGGCATTTAGCCTGCTAGGCCTGAAGCCCAATATCATTTCACCAGCATTAAAGCCTGCTAG
GCCCGAAGCCCGATATTATC
Found at i:52801452 original size:14 final size:15
Alignment explanation
Indices: 52801423--52801452 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
52801413 CAAAATTTAG
52801423 ACATGATACTTTCAC
1 ACATGATACTTTCAC
52801438 ACATGATAC-TTCAC
1 ACATGATACTTTCAC
52801452 A
1 A
52801453 TATAATAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.30
Consensus pattern (15 bp):
ACATGATACTTTCAC
Found at i:52803830 original size:6 final size:6
Alignment explanation
Indices: 52803801--52803862 Score: 61
Period size: 6 Copynumber: 10.2 Consensus size: 6
52803791 AAAGAAAGTG
* * * * * *
52803801 AGAAAA ATAAAA ATGAAAT TGAAAA AGAAAG TGAAAA AGAAAA AGAGAA
1 AGAAAA AGAAAA A-GAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
52803850 AGAAAA AGAAAA A
1 AGAAAA AGAAAA A
52803863 AAGGTCGAGA
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
6 40 0.93
7 3 0.07
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (6 bp):
AGAAAA
Found at i:52803830 original size:12 final size:12
Alignment explanation
Indices: 52803789--52803842 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
52803779 GAAACAAAGC
52803789 AAAAAGAAAGTG
1 AAAAAGAAAGTG
*
52803801 -AGAA-AAA-T-
1 AAAAAGAAAGTG
*
52803809 AAAAATGAAATTG
1 AAAAA-GAAAGTG
52803822 AAAAAGAAAGTG
1 AAAAAGAAAGTG
52803834 AAAAAGAAA
1 AAAAAGAAA
52803843 AAGAGAAAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
9 4 0.12
10 3 0.09
11 6 0.18
12 16 0.47
13 5 0.15
ACGTcount: A:0.70, C:0.00, G:0.19, T:0.11
Consensus pattern (12 bp):
AAAAAGAAAGTG
Found at i:52804230 original size:36 final size:36
Alignment explanation
Indices: 52804181--52804255 Score: 114
Period size: 36 Copynumber: 2.1 Consensus size: 36
52804171 CCAAAAGGTA
* * * *
52804181 AGCAATGTCTGAGTTTTGAAGTTTTTAAAACATATC
1 AGCAAGGTATGAGTTTTAAAGTTTTTAAAACACATC
52804217 AGCAAGGTATGAGTTTTAAAGTTTTTAAAACACATC
1 AGCAAGGTATGAGTTTTAAAGTTTTTAAAACACATC
52804253 AGC
1 AGC
52804256 CTCATTCGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (36 bp):
AGCAAGGTATGAGTTTTAAAGTTTTTAAAACACATC
Found at i:52807710 original size:104 final size:105
Alignment explanation
Indices: 52807529--52807720 Score: 332
Period size: 104 Copynumber: 1.8 Consensus size: 105
52807519 TTGGACAGTC
*
52807529 ACACGCCCGTGTCCTCAGCCCGTGTAACTCTTTGTTTATGACATCAGCAAACATTTAGGGTCACA
1 ACACGCCCGTGTCCTCAGCCCGTGTAACTCTCTGTTTATGACATCAGCAAACATTTAGGGTCACA
52807594 CGACCAAGTCACACGCCCGTGTGGTAGGCCAGGTGGTCTT
66 CGACCAAGTCACACGCCCGTGTGGTAGGCCAGGTGGTCTT
* *
52807634 ACACGCCCGTGTCCTCAGCCCGTGTAACTCTCTG-TTATGACGTCAGTAAACATTTAGGGTCACA
1 ACACGCCCGTGTCCTCAGCCCGTGTAACTCTCTGTTTATGACATCAGCAAACATTTAGGGTCACA
* *
52807698 CGACTAAGTCACACGCCTGTGTG
66 CGACCAAGTCACACGCCCGTGTG
52807721 CTTGGCCCTG
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
104 49 0.60
105 33 0.40
ACGTcount: A:0.22, C:0.30, G:0.23, T:0.25
Consensus pattern (105 bp):
ACACGCCCGTGTCCTCAGCCCGTGTAACTCTCTGTTTATGACATCAGCAAACATTTAGGGTCACA
CGACCAAGTCACACGCCCGTGTGGTAGGCCAGGTGGTCTT
Found at i:52810418 original size:69 final size:68
Alignment explanation
Indices: 52810238--52810428 Score: 238
Period size: 69 Copynumber: 2.8 Consensus size: 68
52810228 ATTTTTGGAA
* * * *
52810238 AGCACATTAAGCATTTAAAATGGATGTAAATGAACACATTTTCAAGACAACAAATTAGCCCTTTA
1 AGCACATTAAGCATTT-AAATGAATGTAAATGAACACATTTTTAAGATAACAAATTAGCACTTTA
*
52810303 CAGC
65 CAAC
* * * *
52810307 AGCACATTAAGCATCTAAAATTAATGTGAGTGAACACATTTTTAAGATAACAAATTAGCACTTTA
1 AGCACATTAAGCAT-TTAAATGAATGTAAATGAACACATTTTTAAGATAACAAATTAGCACTTTA
52810372 CAAC
65 CAAC
* * * *
52810376 ATCACATTAAGCATTTAAATCGAACGTAAATGAAGACATTTTTAATATAACAA
1 AGCACATTAAGCATTTAAAT-GAATGTAAATGAACACATTTTTAAGATAACAA
52810429 CTCATCAATT
Statistics
Matches: 103, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
68 5 0.05
69 97 0.94
70 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (68 bp):
AGCACATTAAGCATTTAAATGAATGTAAATGAACACATTTTTAAGATAACAAATTAGCACTTTAC
AAC
Found at i:52810781 original size:68 final size:68
Alignment explanation
Indices: 52810625--52810774 Score: 196
Period size: 68 Copynumber: 2.2 Consensus size: 68
52810615 TTAACTGTGA
* * * *
52810625 AATC-AACAGATTCGGACAGCTACATTTACTAAATAAAACAACATATATGGTAGTGCATCGAACA
1 AATCTAACACATTCGGACAGCTACATTTACCAAATAAAACAACATAAATGATAGTGCATCGAACA
52810689 ATG
66 ATG
* ** * *
52810692 AATTTAACACATTCGGACAGCTACATTTACCAAATAAAACAGTATAAATGAT-GATGCTTTGAAC
1 AATCTAACACATTCGGACAGCTACATTTACCAAATAAAACAACATAAATGATAG-TGCATCGAAC
52810756 AATG
65 AATG
52810760 AATCTAACACATTCG
1 AATCTAACACATTCG
52810775 AGCAGCTTAA
Statistics
Matches: 71, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
67 4 0.06
68 67 0.94
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (68 bp):
AATCTAACACATTCGGACAGCTACATTTACCAAATAAAACAACATAAATGATAGTGCATCGAACA
ATG
Found at i:52825180 original size:43 final size:42
Alignment explanation
Indices: 52825112--52825229 Score: 146
Period size: 43 Copynumber: 2.8 Consensus size: 42
52825102 TCACATGTAT
* * *
52825112 CACATCCATTATGAACTCGGGCCACTCAACGAGCTCGGATGC
1 CACATCCATAATGAACTCAGACCACTCAACGAGCTCGGATGC
*
52825154 TCGCATCCATAATGAACTCAGACCACTCAACGAGCTCGGATGC
1 -CACATCCATAATGAACTCAGACCACTCAACGAGCTCGGATGC
** * * *
52825197 CACATATATCACGAACCCAGACCACTCAACGAG
1 CACATCCATAATGAACTCAGACCACTCAACGAG
52825230 TTCAGGCTTT
Statistics
Matches: 65, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
42 27 0.42
43 38 0.58
ACGTcount: A:0.31, C:0.34, G:0.18, T:0.17
Consensus pattern (42 bp):
CACATCCATAATGAACTCAGACCACTCAACGAGCTCGGATGC
Found at i:52832885 original size:21 final size:21
Alignment explanation
Indices: 52832843--52832886 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
52832833 GTAAAGTTTG
**
52832843 TAATTTTACATAATTAGGTGT
1 TAATTTTACATAATTACATGT
* *
52832864 TAATTTTACATCATTTCATGT
1 TAATTTTACATAATTACATGT
52832885 TA
1 TA
52832887 TTATGCTACA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (21 bp):
TAATTTTACATAATTACATGT
Found at i:52838250 original size:47 final size:47
Alignment explanation
Indices: 52838181--52838304 Score: 221
Period size: 47 Copynumber: 2.6 Consensus size: 47
52838171 TATAATGCCA
52838181 ATGCCATGTCCCAAACATGGTCTTACACTGGCTCATCCATTAAGTCG
1 ATGCCATGTCCCAAACATGGTCTTACACTGGCTCATCCATTAAGTCG
* *
52838228 ATGCCATGTACCAAACATGGTCTTACACTGGCTTATCCATTAAGTCG
1 ATGCCATGTCCCAAACATGGTCTTACACTGGCTCATCCATTAAGTCG
*
52838275 ATGCCATGTCCCAGACATGGTCTTACACTG
1 ATGCCATGTCCCAAACATGGTCTTACACTG
52838305 ACTATCGAAA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 73 1.00
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (47 bp):
ATGCCATGTCCCAAACATGGTCTTACACTGGCTCATCCATTAAGTCG
Found at i:52841349 original size:27 final size:26
Alignment explanation
Indices: 52841318--52841495 Score: 169
Period size: 27 Copynumber: 6.6 Consensus size: 26
52841308 TAAATTGTAC
52841318 AGCACTAAGTGTGCGATTCGACTATGT
1 AGCACTAAGTGTGCGATT-GACTATGT
* * *
52841345 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTGACTATGT
* *
52841371 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCG-ATTGACTATGT
*
52841399 GGCACTAAGTGTGCGAGTCTGACTATGT
1 AGCACTAAGTGTGCGA-T-TGACTATGT
* *
52841427 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* * *
52841454 GGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-TTGACTATGT
*
52841481 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
52841496 GGCTCAATAT
Statistics
Matches: 126, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
26 1 0.01
27 100 0.79
28 25 0.20
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTGACTATGT
Found at i:52841434 original size:82 final size:81
Alignment explanation
Indices: 52841319--52841474 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
52841309 AAATTGTACA
* * *
52841319 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
52841383 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
52841400 GCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAGTC-GACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
52841465 TGCGAGTTGA
65 TGCGAATTGA
52841475 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 18 0.27
82 48 0.73
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:52841486 original size:82 final size:81
Alignment explanation
Indices: 52841315--52841495 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
52841305 GATTAAATTG
* * *
52841315 TACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
52841380 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
52841396 TGCGGCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGAGTC-GACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
52841460 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
52841478 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
52841496 GGCTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 20 0.24
82 63 0.76
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:52847853 original size:37 final size:37
Alignment explanation
Indices: 52847803--52847882 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
52847793 CTTATTACGA
* *
52847803 AGTCTTACCCGGACATAA-TCTCCACACGAAGTTATCG
1 AGTCTTACCCGGACAAAATTC-CCACACGAAGTCATCG
*
52847840 AGTCTTACCCGGACAAAATTCCCACACGCAGTCATCG
1 AGTCTTACCCGGACAAAATTCCCACACGAAGTCATCG
*
52847877 GGTCTT
1 AGTCTT
52847883 TAGAGCCCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (37 bp):
AGTCTTACCCGGACAAAATTCCCACACGAAGTCATCG
Found at i:52848072 original size:47 final size:47
Alignment explanation
Indices: 52848013--52848437 Score: 647
Period size: 47 Copynumber: 9.1 Consensus size: 47
52848003 TATCACATTT
* * * *
52848013 ATACAC-T-TTCACATTCATCACATCGGCCATTAGGCCTTATCTCAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
* * *
52848058 ATACACATGCTCACATTCATCACATTGGCCACTCGGCCTTATCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
*
52848105 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
* *
52848152 ATATACATGTTCACTTTCATCACATTGGCCATTCGGCTTTATCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
* *
52848199 ATATACATGTTCACTTTCATCACATTGGCCATTCGGTCTTATCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
*
52848246 ATACACACGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
*
52848293 ATATACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
* * * *
52848340 ATACACCTATTCACATTCATCACATTGGCCATTCGGCCTTATCACGC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
* *
52848387 ATATACATGTTCACTTTCATCACATTGGCCATTCGGCCCTATTCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTA-TCACAC
52848435 ATA
1 ATA
52848438 TACACTTTCA
Statistics
Matches: 349, Mismatches: 28, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
45 6 0.02
46 1 0.00
47 334 0.96
48 8 0.02
ACGTcount: A:0.26, C:0.32, G:0.10, T:0.32
Consensus pattern (47 bp):
ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
Found at i:52848174 original size:25 final size:25
Alignment explanation
Indices: 52848145--52848222 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
52848135 ATTCGGCCTT
52848145 ATCACACATATACATGTTCACTTTC
1 ATCACACATATACATGTTCACTTTC
* *** *
52848170 ATCACA-TTGGCCA--TTCGGCTTT-
1 ATCACACATATACATGTTC-ACTTTC
52848192 ATCACACATATACATGTTCACTTTC
1 ATCACACATATACATGTTCACTTTC
52848217 ATCACA
1 ATCACA
52848223 TTGGCCATTC
Statistics
Matches: 38, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 9 0.24
23 7 0.18
24 7 0.18
25 15 0.39
ACGTcount: A:0.29, C:0.28, G:0.08, T:0.35
Consensus pattern (25 bp):
ATCACACATATACATGTTCACTTTC
Found at i:52848338 original size:22 final size:22
Alignment explanation
Indices: 52848311--52848384 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
52848301 GTTCACTTTC
52848311 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
*** * *
52848333 ATCACACATACACCTATTC-ACATT
1 AT--CACATTGGCC-ATTCGGCCTT
52848357 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
52848380 ATCAC
1 ATCAC
52848385 GCATATACAT
Statistics
Matches: 37, Mismatches: 10, Indels: 10
0.65 0.18 0.18
Matches are distributed among these distances:
22 11 0.30
23 10 0.27
24 10 0.27
25 6 0.16
ACGTcount: A:0.26, C:0.34, G:0.11, T:0.30
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:52854182 original size:27 final size:26
Alignment explanation
Indices: 52854151--52854328 Score: 169
Period size: 27 Copynumber: 6.6 Consensus size: 26
52854141 TAAATTGTAC
52854151 AGCACTAAGTGTGCGATTCGACTATGT
1 AGCACTAAGTGTGCGATT-GACTATGT
* * *
52854178 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTGACTATGT
* *
52854204 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCG-ATTGACTATGT
*
52854232 GGCACTAAGTGTGCGAGTCTGACTATGT
1 AGCACTAAGTGTGCGA-T-TGACTATGT
* *
52854260 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* * *
52854287 GGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-TTGACTATGT
*
52854314 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
52854329 GGCTCAATAT
Statistics
Matches: 126, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
26 1 0.01
27 100 0.79
28 25 0.20
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTGACTATGT
Found at i:52854267 original size:82 final size:81
Alignment explanation
Indices: 52854152--52854307 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
52854142 AAATTGTACA
* * *
52854152 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
52854216 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
52854233 GCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAGTC-GACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
52854298 TGCGAGTTGA
65 TGCGAATTGA
52854308 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 18 0.27
82 48 0.73
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:52854319 original size:82 final size:81
Alignment explanation
Indices: 52854148--52854328 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
52854138 GATTAAATTG
* * *
52854148 TACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
52854213 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
52854229 TGCGGCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGAGTC-GACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
52854293 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
52854311 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
52854329 GGCTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 20 0.24
82 63 0.76
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:52857472 original size:15 final size:15
Alignment explanation
Indices: 52857437--52857466 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52857427 AGTGTTAATG
*
52857437 GAATCTATTGGTTGT
1 GAATCTACTGGTTGT
52857452 GAATCTACTGGTTGT
1 GAATCTACTGGTTGT
52857467 ATATCTTACG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.10, G:0.27, T:0.43
Consensus pattern (15 bp):
GAATCTACTGGTTGT
Found at i:52865282 original size:16 final size:17
Alignment explanation
Indices: 52865248--52865283 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
52865238 ATAATAGCGA
52865248 AAACATAAATAGATAAG
1 AAACATAAATAGATAAG
52865265 AAACATAAATAG-TAAG
1 AAACATAAATAGATAAG
52865281 AAA
1 AAA
52865284 ATATATATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.67, C:0.06, G:0.11, T:0.17
Consensus pattern (17 bp):
AAACATAAATAGATAAG
Found at i:52865293 original size:17 final size:16
Alignment explanation
Indices: 52865255--52865311 Score: 64
Period size: 16 Copynumber: 3.5 Consensus size: 16
52865245 CGAAAACATA
52865255 AATAGATAAGAAACATA-
1 AATAG-TAAGAAA-ATAT
52865272 AATAGTAAGAAAATAT
1 AATAGTAAGAAAATAT
*
52865288 ATATAG-ATGAAAATAT
1 A-ATAGTAAGAAAATAT
52865304 AATAGTAA
1 AATAGTAA
52865312 TAATAATACG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
15 7 0.20
16 19 0.54
17 9 0.26
ACGTcount: A:0.61, C:0.02, G:0.12, T:0.25
Consensus pattern (16 bp):
AATAGTAAGAAAATAT
Found at i:52865395 original size:3 final size:3
Alignment explanation
Indices: 52865387--52865767 Score: 172
Period size: 3 Copynumber: 125.7 Consensus size: 3
52865377 TGATAGTGAC
* * * * * * *
52865387 AAT AAT AAT AAT AAT AAT -AT TAT TAT TAT TAT TAT ATT GAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
* * * * * * *
52865435 AA- AAGG AAT AAA AAT AAT AGT AAT AAA AAT ATT AAC AAT AGT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
52865480 AAT AAC GAT AAT -AT AAAT ACT AAT ATAT ACAT GAAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT -AAT AAT AAT A-AT A-AT -AAT AAT AAT AAT AAT
* * * *
52865528 AGT AAT AAT AAT AAT AAC AAT AAT AAT AAC AAT ACATT AAT ATAT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-A-T AAT A-AT AAT
* * * * * *
52865576 AAT -AT CAAT AAT ATT AGT AAGT AA- AAA AAGGG AAT AAT AAT AGT AGT
1 AAT AAT -AAT AAT AAT AAT AA-T AAT AAT AA--T AAT AAT AAT AAT AAT
* * * * *
52865623 AAT AAT AAT AAC AAT AGT AAG AAT AAT AAT GAT AAT -AT AAC AA- ACAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
* * * **
52865670 AGT AAT -AT AAT CAAT AA- AAT -AT AAT AGT AAT AAA AAT AAT GCT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* ** * *
52865713 AAC GGT AAT AAT AAT AAT AAT GAT AGT AAT -AT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
52865760 AAT AAT AA
1 AAT AAT AA
52865768 GTAAAATGAT
Statistics
Matches: 284, Mismatches: 69, Indels: 50
0.70 0.17 0.12
Matches are distributed among these distances:
2 21 0.07
3 231 0.81
4 27 0.10
5 5 0.02
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:52896928 original size:53 final size:55
Alignment explanation
Indices: 52896832--52896950 Score: 206
Period size: 53 Copynumber: 2.2 Consensus size: 55
52896822 TCACAAAAAG
52896832 GGGGGATTTTGATGTTTTTTTTTTGGAGATTTCAAAGGGGATCGATAGTA-TTTAA
1 GGGGGATTTTGATG-TTTTTTTTTGGAGATTTCAAAGGGGATCGATAGTATTTTAA
*
52896887 GGGGGATTTTGATG-TTTTTTTTGGAGATTTCAAAGGGGATCGATAGTATTTTAG
1 GGGGGATTTTGATGTTTTTTTTTGGAGATTTCAAAGGGGATCGATAGTATTTTAA
52896941 GGGGGATTTT
1 GGGGGATTTT
52896951 TTGATATTTC
Statistics
Matches: 62, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
53 34 0.55
54 14 0.23
55 14 0.23
ACGTcount: A:0.22, C:0.03, G:0.32, T:0.43
Consensus pattern (55 bp):
GGGGGATTTTGATGTTTTTTTTTGGAGATTTCAAAGGGGATCGATAGTATTTTAA
Found at i:52897829 original size:14 final size:15
Alignment explanation
Indices: 52897796--52897847 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
52897786 AATTATTTTC
*
52897796 CTATTATTTATTATA
1 CTATTATTTATTACA
*
52897811 CTATT-TTTTTTACA
1 CTATTATTTATTACA
*
52897825 CTATTATTTATTATA
1 CTATTATTTATTACA
52897840 CTTATTAT
1 C-TATTAT
52897848 ATCATTTTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
14 12 0.39
15 13 0.42
16 6 0.19
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.62
Consensus pattern (15 bp):
CTATTATTTATTACA
Found at i:52900079 original size:62 final size:62
Alignment explanation
Indices: 52899895--52900079 Score: 298
Period size: 62 Copynumber: 3.0 Consensus size: 62
52899885 CACGTATCTC
* *
52899895 TTCATTCATTAACATTACATTTCATTACATACAATAAATTTCCTAAAATCCAAAAATACGCG
1 TTCATGCATTAACATTACATTTCATTACATACAATAAATTTCCTAAAATCCAAAAATACGTG
* **
52899957 TTCATGCATTAACATTACATTTTATTACATACAATAAATTTCCTAAAATTTAAAAATACGTG
1 TTCATGCATTAACATTACATTTCATTACATACAATAAATTTCCTAAAATCCAAAAATACGTG
* * *
52900019 TTCATGCATCAACATTACATTTCATTGCATACAATAAATTTCCTAAAATCCAAAAGTACGT
1 TTCATGCATTAACATTACATTTCATTACATACAATAAATTTCCTAAAATCCAAAAATACGT
52900080 CGAGTTTAGA
Statistics
Matches: 112, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 112 1.00
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.35
Consensus pattern (62 bp):
TTCATGCATTAACATTACATTTCATTACATACAATAAATTTCCTAAAATCCAAAAATACGTG
Found at i:52901335 original size:23 final size:24
Alignment explanation
Indices: 52901308--52901366 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
52901298 TTAGTGGAGG
*
52901308 CCAAAAAAAAGAAC-AAA-TAAAAA
1 CCAAAAAAAA-AACAAAAGCAAAAA
*
52901331 CCAAATAAAAAACAAAAGCAAAAA
1 CCAAAAAAAAAACAAAAGCAAAAA
*
52901355 CAAAAAAAAAAA
1 CCAAAAAAAAAA
52901367 ACTCTACCAG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 3 0.10
23 12 0.40
24 15 0.50
ACGTcount: A:0.80, C:0.14, G:0.03, T:0.03
Consensus pattern (24 bp):
CCAAAAAAAAAACAAAAGCAAAAA
Found at i:52901337 original size:11 final size:11
Alignment explanation
Indices: 52901309--52901364 Score: 53
Period size: 12 Copynumber: 5.0 Consensus size: 11
52901299 TAGTGGAGGC
*
52901309 CAAAAAAAAGAA
1 CAAATAAAA-AA
*
52901321 CAAATAAAAAC
1 CAAATAAAAAA
52901332 CAAATAAAAAA
1 CAAATAAAAAA
52901343 CAAA-AGCAAAAA
1 CAAATA--AAAAA
52901355 CAAA-AAAAAA
1 CAAATAAAAAA
52901365 AAACTCTACC
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
10 6 0.15
11 15 0.38
12 18 0.46
ACGTcount: A:0.80, C:0.12, G:0.04, T:0.04
Consensus pattern (11 bp):
CAAATAAAAAA
Found at i:52901365 original size:11 final size:11
Alignment explanation
Indices: 52901309--52901365 Score: 60
Period size: 11 Copynumber: 5.0 Consensus size: 11
52901299 TAGTGGAGGC
52901309 CAAAAAAAAGAA
1 CAAAAAAAA-AA
* *
52901321 CAAATAAAAAC
1 CAAAAAAAAAA
*
52901332 CAAATAAAAAA
1 CAAAAAAAAAA
*
52901343 CAAAAGCAAAAA
1 CAAAA-AAAAAA
52901355 CAAAAAAAAAA
1 CAAAAAAAAAA
52901366 AACTCTACCA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
11 20 0.53
12 18 0.47
ACGTcount: A:0.81, C:0.12, G:0.04, T:0.04
Consensus pattern (11 bp):
CAAAAAAAAAA
Found at i:52902874 original size:44 final size:44
Alignment explanation
Indices: 52902807--52903211 Score: 361
Period size: 44 Copynumber: 9.2 Consensus size: 44
52902797 AAGTCACGAA
* * * * *
52902807 AGCAGATCTTCTCTTCATGTATTGGCATGAAGTAGATCGAGGAT
1 AGCAGATCTTGTCTTCCTATATTGGCAGGAAGTAGATCGAAGAT
* * * *
52902851 AGCAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGCAGGAAGTAGATCGAAGAT
* ** *
52902895 -GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCCTATATTGGCAG-GAAGTAGATCGAAGAT
* * *
52902939 AGCAGATCTTGTCTTCATGTATTGGC-GTGAAGTAGATCGAAGGT
1 AGCAGATCTTGTCTTCCTATATTGGCAG-GAAGTAGATCGAAGAT
* * * * *
52902983 AGCAGATCCTATCTTCCTATATT-GTAGGAAGTGGATCAAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGCAGGAAGTAGATCGAAGAT
* ** *
52903026 -GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCCTATATTGGCAG-GAAGTAGATCGAAGAT
* * *
52903070 AGCAGATCTTGTCTTCATGTATTGGC-GTGAAGTAGATCGAAGGT
1 AGCAGATCTTGTCTTCCTATATTGGCAG-GAAGTAGATCGAAGAT
* * * *
52903114 AGCAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGAT
1 AGCAGATCTTGTCTTCCTATATTGGCAGGAAGTAGATCGAAGAT
* * * * * *
52903158 TGCAGATCTTGCCTTCTTGTATTTGGCAGCGAAGCAGATCAAAAGAT
1 AGCAGATCTTGTCTTCCTATA-TTGGCAG-GAAGTAGATC-GAAGAT
*
52903205 GGCAGAT
1 AGCAGAT
52903212 TTTACCTCCC
Statistics
Matches: 290, Mismatches: 61, Indels: 17
0.79 0.17 0.05
Matches are distributed among these distances:
42 19 0.07
43 40 0.14
44 163 0.56
45 49 0.17
46 8 0.03
47 11 0.04
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (44 bp):
AGCAGATCTTGTCTTCCTATATTGGCAGGAAGTAGATCGAAGAT
Found at i:52903072 original size:131 final size:132
Alignment explanation
Indices: 52902804--52903173 Score: 672
Period size: 131 Copynumber: 2.8 Consensus size: 132
52902794 TTGAAGTCAC
* *
52902804 GAAAGCAGATCTTCTCTTCATGTATTGGCATGAAGTAGATCG-AGGATAGCAGATCCTATCTTCC
1 GAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGG-TAGCAGATCCTATCTTCC
52902868 TATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATC
65 TATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATC
52902933 GAA
130 GAA
52902936 GAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCT
1 GAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCT
*
52903001 ATATT-GTAGGAAGTGGATCAAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG
66 ATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG
52903065 AA
131 AA
52903067 GAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCT
1 GAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCT
*
52903132 ATATTGGTAGGAAGTGGATCGAAGATTGCAGATCTTGCCTTC
66 ATATTGGTAGGAAGTGGATCGAAGA-TGCAGATCTTGTCTTC
52903174 TTGTATTTGG
Statistics
Matches: 230, Mismatches: 5, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
131 130 0.57
132 82 0.36
133 18 0.08
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (132 bp):
GAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCT
ATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG
AA
Found at i:52903321 original size:46 final size:46
Alignment explanation
Indices: 52903259--52904854 Score: 317
Period size: 46 Copynumber: 35.2 Consensus size: 46
52903249 ATAACTCTAT
**
52903259 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTACAGATCTTGC
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATGGCAGATCTTGC
* * * ** * *
52903305 CTTCCTGTATTTGGCAG-CGAAGCAGATCAAAAGATGGCAGATTTTAC
1 CTCCCTGTATTTGGCAGTGGAA-TAGAT-TGAAGATGGCAGATCTTGC
* * * * * ** **
52903352 CTCCATGTGA-CT-ACAGTGGAGTACATTGAAGCCGATA-ACTCTAT--
1 CTCCCTGT-ATTTGGCAGTGGAATAGATTGAAGATGGCAGA-TCT-TGC
* *
52903396 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATATTGC
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATGGCAGATCTTGC
* * * ** * *
52903442 CTTCCTGTATTTGGCAG-CGAAGCAGATCAAAAGATGGCAGATTTTAC
1 CTCCCTGTATTTGGCAGTGGAA-TAGAT-TGAAGATGGCAGATCTTGC
*** * * ** **
52903489 CTCCCTG-A--CCACAGTGGAGTACATTGAAGCCGATA-ACTCTAT--
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATGGCAGA-TCT-TGC
*
52903531 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGC
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATGGCAGATCTTGC
* ** * ** * *
52903577 CTTCCTGTATTTGGCAG-CAAAGCAGATCAAAGATGGCAGATTTTAC
1 CTCCCTGTATTTGGCAGTGGAA-TAGATTGAAGATGGCAGATCTTGC
* * * * ** **
52903623 CTCCCTG-A-CT-ACAGTGGAGTACATTGAAGCCGATA-ATTCTAT--
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATGGCAGA-TCT-TGC
*
52903665 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGC
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATGGCAGATCTTGC
* * * ** * *
52903711 CTTCCTGTATTTGGCAG-CGAAGCAGATCAAAGATGGCAGATTTTAC
1 CTCCCTGTATTTGGCAGTGGAA-TAGATTGAAGATGGCAGATCTTGC
* * * * ** **
52903757 CTCCCTG-A-CT-ACAGTGGAGTACATTGAAGCCGATA-ATTCTAT--
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATGGCAGA-TCT-TGC
*
52903799 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGC
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATGGCAGATCTTGC
* * * * ** * *
52903845 CTTCCTGTATTTGGCAGCGAAACAGATCAAAGATGGCAGATTTTAC
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATGGCAGATCTTGC
* * * * ** **
52903891 CTCCCTG-A-CT-ACAGTGGAGTACATTGAAGCCGATA-ATTCTAT--
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATGGCAGA-TCT-TGC
* *
52903933 CTCCCTGTATTTGGCAGTGGAATAGATTAAAGATTGCAGATCTTGC
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATGGCAGATCTTGC
* * * ** * * *
52903979 CTTCCTGTATTTGGCAG-CGAAGCAGATCAAAGATAGCAGATTTTAC
1 CTCCCTGTATTTGGCAGTGGAA-TAGATTGAAGATGGCAGATCTTGC
* * * * * ** **
52904025 CTCCTTG-A-CT-ACAGTGGAGTACATTGAAGCCGATA-ACTCTAT--
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATGGCAGA-TCT-TGC
* * *
52904067 CTCCCTGCATTTGGCAGTGGAATAGATTGAAGATCAAAGATGGCAGATTTTAC
1 CTCCCTGTATTTGGCAGTGGAATAGATT---G----AAGATGGCAGATCTTGC
* * * * ** **
52904120 CTCCCTG-A-CT-ACAGTGGAGTACATTGAAGCCGATA-ACTCTAT--
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATGGCAGA-TCT-TGC
* * *
52904162 CTCCCTGCATTTGGCAGTGGAATAGATTGAAGATCAAAGATGGCAGATTTTAC
1 CTCCCTGTATTTGGCAGTGGAATAGATT---G----AAGATGGCAGATCTTGC
* * * * ** **
52904215 CTCCCTG-A-CT-ACAGTGGAGTACATTGAAGCCGATA-ACTCTAT--
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATGGCAGA-TCT-TGC
* * *
52904257 CTCCCTGCATTTGGCAGTGGAATAGATTGAAGATCAAAGATGGCAGATTTTAC
1 CTCCCTGTATTTGGCAGTGGAATAGATT---G----AAGATGGCAGATCTTGC
* * * * ** **
52904310 CTCCCTG-A-CT-ACAGTGGAGTACATTGAAGCCGATA-ATTCTAT--
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATGGCAGA-TCT-TGC
*
52904352 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGC
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATGGCAGATCTTGC
* * * ** * * *
52904398 CTTCCTGTATTTGGCAG-CGAAGCAGATCAAATATGGCAGATTTTAC
1 CTCCCTGTATTTGGCAGTGGAA-TAGATTGAAGATGGCAGATCTTGC
* * * * ** ** **
52904444 CTCCCCG-A-CT-ACAGTGGAGTACCTTGAAGCCGATA-ATTCTAT--
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATGGCAGA-TCT-TGC
*
52904486 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGC
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATGGCAGATCTTGC
* * * ** * *
52904532 CTTCTTGTATTTGGCAGT-GAAGCAGATCAAAGATGGCAGATTTTAC
1 CTCCCTGTATTTGGCAGTGGAA-TAGATTGAAGATGGCAGATCTTGC
* * * * ** **
52904578 CTCCCTG-A-CT-ACAGTGGAGTACATTGAAGCCGATA-ACTCTAT--
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATGGCAGA-TCT-TGC
*
52904620 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGC
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATGGCAGATCTTGC
* * * * ** * *
52904666 CTTCTTGTATTTGGCAG-CGAAGCAGATCAAAGATGGCAGATTTTAC
1 CTCCCTGTATTTGGCAGTGGAA-TAGATTGAAGATGGCAGATCTTGC
* * * * * ** **
52904712 CTCCATGTGA-CT-ACAGTGGAGTACATTGAAGCCGATA-ACTCTAT--
1 CTCCCTGT-ATTTGGCAGTGGAATAGATTGAAGATGGCAGA-TCT-TGC
* *
52904756 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATCGAAGATCTTGC
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATGGCAGATCTTGC
* * * ** * *
52904802 CTTCCTGTATTTGGCAG-CGAAGCAGATCAAAGATGGCAGATTTTAC
1 CTCCCTGTATTTGGCAGTGGAA-TAGATTGAAGATGGCAGATCTTGC
52904848 CTCCCTG
1 CTCCCTG
52904855 ACTACAGTGG
Statistics
Matches: 1049, Mismatches: 365, Indels: 272
0.62 0.22 0.16
Matches are distributed among these distances:
42 78 0.07
43 118 0.11
44 67 0.06
45 267 0.25
46 379 0.36
47 46 0.04
48 4 0.00
50 36 0.03
51 6 0.01
52 24 0.02
53 24 0.02
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (46 bp):
CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATGGCAGATCTTGC
Found at i:52903685 original size:45 final size:45
Alignment explanation
Indices: 52903634--52903830 Score: 118
Period size: 45 Copynumber: 4.4 Consensus size: 45
52903624 TCCCTGACTA
*
52903634 CAGTGGAGTACATTGAAGCCGATAATTCTATCTCCCTGTATTTGG
1 CAGTGGAGTAGATTGAAGCCGATAATTCTATCTCCCTGTATTTGG
* ** * *
52903679 CAGTGGAATAGATTGAAGATTGCA-GA-TCT-TGCCTTCCTGTATTTGG
1 CAGTGGAGTAGATTGAAG-CCG-ATAATTCTAT--CTCCCTGTATTTGG
* * * ** ** ** * * * *
52903725 CAGCGAAGCAGATCAAAGATGGCAGATTTTACCTCCCTG-A-CT-A
1 CAGTGGAGTAGATTGAAGCCGATA-ATTCTATCTCCCTGTATTTGG
*
52903768 CAGTGGAGTACATTGAAGCCGATAATTCTATCTCCCTGTATTTGG
1 CAGTGGAGTAGATTGAAGCCGATAATTCTATCTCCCTGTATTTGG
*
52903813 CAGTGGAATAGATTGAAG
1 CAGTGGAGTAGATTGAAG
52903831 ATTGCAGATC
Statistics
Matches: 105, Mismatches: 36, Indels: 22
0.64 0.22 0.13
Matches are distributed among these distances:
42 12 0.11
43 15 0.14
44 3 0.03
45 38 0.36
46 34 0.32
47 3 0.03
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (45 bp):
CAGTGGAGTAGATTGAAGCCGATAATTCTATCTCCCTGTATTTGG
Found at i:52903698 original size:88 final size:91
Alignment explanation
Indices: 52903600--52903988 Score: 219
Period size: 88 Copynumber: 4.4 Consensus size: 91
52903590 GCAGCAAAGC
*
52903600 AGATCAAAGATGGCAGATTTTACCTCCCTG-A-CT-ACAGTGGAGTACATTGAAGCCGATAATTC
1 AGATTAAAGATGGCAGATTTTACCTCCCTGTATCTGACAGTGGAGTACATTGAAGCCGATAATTC
52903662 TATCTCCCTGTATTTGGCAGTGGAAT
66 TATCTCCCTGTATTTGGCAGTGGAAT
* * * * * * * * * * * ** ** **
52903688 AGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATT
1 AGATTAAAGATGGCAGATTTTACCTCCCTGTATCTGACAGTGGAGTACATTGAAGCCGATA-ATT
* * * * *
52903753 TTACCTCCCTG-A-CT-ACAGTGGAGT
65 CTATCTCCCTGTATTTGGCAGTGGAAT
* * ** ** * * * * * * ** *
52903777 ACATTGAAGCCGATA-ATTCTATCTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCA-GA-
1 AGATTAAAGATGGCAGATTTTACCTCCCTGTATCTGACAGTGGAGTACATTGAAG-CCG-ATAAT
* * * *
52903839 TCT-TGCCTTCCTGTATTTGGCAGCGAAAC
64 TCTAT--CTCCCTGTATTTGGCAGTGGAAT
*
52903868 AGATCAAAGATGGCAGATTTTACCTCCCTG-A-CT-ACAGTGGAGTACATTGAAGCCGATAATTC
1 AGATTAAAGATGGCAGATTTTACCTCCCTGTATCTGACAGTGGAGTACATTGAAGCCGATAATTC
52903930 TATCTCCCTGTATTTGGCAGTGGAAT
66 TATCTCCCTGTATTTGGCAGTGGAAT
* * * *
52903956 AGATTAAAGATTGCAGATCTTGCCTTCCTGTAT
1 AGATTAAAGATGGCAGATTTTACCTCCCTGTAT
52903989 TTGGCAGCGA
Statistics
Matches: 207, Mismatches: 77, Indels: 32
0.66 0.24 0.10
Matches are distributed among these distances:
87 3 0.01
88 105 0.51
89 41 0.20
90 5 0.02
91 29 0.14
92 24 0.12
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (91 bp):
AGATTAAAGATGGCAGATTTTACCTCCCTGTATCTGACAGTGGAGTACATTGAAGCCGATAATTC
TATCTCCCTGTATTTGGCAGTGGAAT
Found at i:52904113 original size:95 final size:95
Alignment explanation
Indices: 52904002--52904385 Score: 732
Period size: 95 Copynumber: 4.0 Consensus size: 95
52903992 GCAGCGAAGC
* *
52904002 AGATCAAAGATAGCAGATTTTACCTCCTTGACTACAGTGGAGTACATTGAAGCCGATAACTCTAT
1 AGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTAT
52904067 CTCCCTGCATTTGGCAGTGGAATAGATTGA
66 CTCCCTGCATTTGGCAGTGGAATAGATTGA
52904097 AGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTAT
1 AGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTAT
52904162 CTCCCTGCATTTGGCAGTGGAATAGATTGA
66 CTCCCTGCATTTGGCAGTGGAATAGATTGA
52904192 AGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTAT
1 AGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTAT
52904257 CTCCCTGCATTTGGCAGTGGAATAGATTGA
66 CTCCCTGCATTTGGCAGTGGAATAGATTGA
*
52904287 AGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAATTCTAT
1 AGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTAT
*
52904352 CTCCCTGTATTTGGCAGTGGAATAGATTGA
66 CTCCCTGCATTTGGCAGTGGAATAGATTGA
52904382 AGAT
1 AGAT
52904386 TGCAGATCTT
Statistics
Matches: 285, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 285 1.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (95 bp):
AGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTAT
CTCCCTGCATTTGGCAGTGGAATAGATTGA
Found at i:52904146 original size:50 final size:50
Alignment explanation
Indices: 52904081--52904338 Score: 188
Period size: 50 Copynumber: 5.4 Consensus size: 50
52904071 CTGCATTTGG
*
52904081 CAGTGGAATAGATTGAAGATCAAAGATGGCAGATTTTACCTCCCTGACTA
1 CAGTGGAATACATTGAAGATCAAAGATGGCAGATTTTACCTCCCTGACTA
* * * * * * *
52904131 CAGTGGAGTACATTGAAG--C--CGAT---A-ACTCTATCTCCCTGCATTTGG
1 CAGTGGAATACATTGAAGATCAAAGATGGCAGATTTTACCTCCCTG-A-CT-A
*
52904176 CAGTGGAATAGATTGAAGATCAAAGATGGCAGATTTTACCTCCCTGACTA
1 CAGTGGAATACATTGAAGATCAAAGATGGCAGATTTTACCTCCCTGACTA
* * * * * * *
52904226 CAGTGGAGTACATTGAAG--C--CGAT---A-ACTCTATCTCCCTGCATTTGG
1 CAGTGGAATACATTGAAGATCAAAGATGGCAGATTTTACCTCCCTG-A-CT-A
*
52904271 CAGTGGAATAGATTGAAGATCAAAGATGGCAGATTTTACCTCCCTGACTA
1 CAGTGGAATACATTGAAGATCAAAGATGGCAGATTTTACCTCCCTGACTA
*
52904321 CAGTGGAGTACATTGAAG
1 CAGTGGAATACATTGAAG
52904339 CCGATAATTC
Statistics
Matches: 152, Mismatches: 34, Indels: 44
0.66 0.15 0.19
Matches are distributed among these distances:
42 22 0.14
43 4 0.03
44 2 0.01
45 32 0.21
46 6 0.04
47 2 0.01
48 2 0.01
49 6 0.04
50 48 0.32
51 2 0.01
52 4 0.03
53 22 0.14
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.27
Consensus pattern (50 bp):
CAGTGGAATACATTGAAGATCAAAGATGGCAGATTTTACCTCCCTGACTA
Found at i:52904182 original size:45 final size:44
Alignment explanation
Indices: 52904131--52904383 Score: 145
Period size: 45 Copynumber: 5.4 Consensus size: 44
52904121 TCCCTGACTA
* *
52904131 CAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGCATTTGG
1 CAGTGGAATACATTGAAGCCGATAATTCTATCTCCCTG-ATTTGG
* * * * * *
52904176 CAGTGGAATAGATTGAAGATCAAAGATGGCAGATTTTACCTCCCTGA-CT-A
1 CAGTGGAATACATTGAAG--C--CGAT---A-ATTCTATCTCCCTGATTTGG
* *
52904226 CAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGCATTTGG
1 CAGTGGAATACATTGAAGCCGATAATTCTATCTCCCTG-ATTTGG
* * * * * *
52904271 CAGTGGAATAGATTGAAGATCAAAGATGGCAGATTTTACCTCCCTGA-CT-A
1 CAGTGGAATACATTGAAG--C--CGAT---A-ATTCTATCTCCCTGATTTGG
*
52904321 CAGTGGAGTACATTGAAGCCGATAATTCTATCTCCCTGTATTTGG
1 CAGTGGAATACATTGAAGCCGATAATTCTATCTCCCTG-ATTTGG
*
52904366 CAGTGGAATAGATTGAAG
1 CAGTGGAATACATTGAAG
52904384 ATTGCAGATC
Statistics
Matches: 153, Mismatches: 33, Indels: 44
0.67 0.14 0.19
Matches are distributed among these distances:
42 23 0.15
43 4 0.03
44 2 0.01
45 48 0.31
46 6 0.04
47 2 0.01
48 2 0.01
49 6 0.04
50 32 0.21
51 2 0.01
52 4 0.03
53 22 0.14
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (44 bp):
CAGTGGAATACATTGAAGCCGATAATTCTATCTCCCTGATTTGG
Found at i:52904499 original size:687 final size:678
Alignment explanation
Indices: 52903152--52904922 Score: 2519
Period size: 687 Copynumber: 2.6 Consensus size: 678
52903142 GAAGTGGATC
52903152 GAAGATTGCAGATCTTGCCTTCTTGTATTTGGCAGCGAAGCAGATCAAAAGATGGCAGATTTTAC
1 GAAGATTGCAGATCTTGCCTTCTTGTATTTGGCAGCGAAGCAGATC-AAAGATGGCAGATTTTAC
52903217 CTCCCTGA-TCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAA
65 CTCCCTGACT-ACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAA
*
52903281 TAGATTGAAGATTACAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAAGATGGCAGA
129 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATC-AAAGATGGCAGA
52903346 TTTTACCTCCATGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGC
193 TTTTACCTCCATGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGC
* * * * *
52903411 AGTGGAATAGATTGAAGAT-----TGCAGATATTGCCTTCCTGTATTTGGCAGCGAAGCAGATCA
258 AGTGGAATAGATTGAAGATCAAGATGCAGATATTACCTCCCTGTATCTGACAGCGAAGCACATCA
* * * * * * *
52903471 AAAGATGGCAGATTTTACCTCCCTGACCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCC
323 AAAGACGACAGACTCTACCTCCCTGACCACAGTGGAATACATTGAAGCAGATAACTCTACCTCCC
* * * ** * * * * * *
52903536 TGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCAAAGCA
388 TGTATCTGACAGTGGAATACATTGAAGACCGCAGAACTTACCTCCCTGCATTTGGCAGAAAAGAA
52903601 GATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAATTCTATC
453 GATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAATTCTATC
52903666 TCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGA
518 TCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGA
*
52903731 AGCAGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAATTC
583 AGCAGATCAAAGATGGCAGATTTTACCTCCCCGACTACAGTGGAGTACATTGAAGCCGATAATTC
52903796 TATCTCCCTGTATTTGGCAGTGGAATAGATT
648 TATCTCCCTGTATTTGGCAGTGGAATAGATT
* *
52903827 GAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAACAGATCAAAGATGGCAGATTTTACC
1 GAAGATTGCAGATCTTGCCTTCTTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACC
*
52903892 TCCCTGACTACAGTGGAGTACATTGAAGCCGATAATTCTATCTCCCTGTATTTGGCAGTGGAATA
66 TCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATA
* *
52903957 GATTAAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATAGCAGATTT
131 GATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTT
*
52904022 TACCTCC-T-TGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGCATTTGGCAGT
196 TACCTCCATGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGT
* * * * **
52904085 GGAATAGATTGAAGATCAAAGATGGCAGATTTTACCTCCCTG-A-CT-ACAGTGGAGTACAT-TG
261 GGAATAGATTGAAGATC-AAGAT-GCAGATATTACCTCCCTGTATCTGACAGCGAAGCACATCAA
* * * *** * *
52904146 AAGCCGATA-ACTCTATCTCCCTGCATTTGGCAGTGGAATAGATTGAAGATCAAAGATGGCAGAT
324 AAGACGACAGACTCTACCTCCCTG-A--CCACAGTGGAATACATTGAAG--C--AGAT---A-AC
* * * *
52904210 TTTACCTCCCTG-A-CT-ACAGTGGAGTACATTGAAG-CCG-ATAACTCTATCTCCCTGCATTTG
378 TCTACCTCCCTGTATCTGACAGTGGAATACATTGAAGACCGCAGAACT-TACCTCCCTGCATTTG
52904270 GCAGTGGAATAGATTGAAGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATT
442 GCA---GAA-A-A--GAAGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATT
52904335 GAAGCCGATAATTCTATCTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGCCT
500 GAAGCCGATAATTCTATCTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGCCT
*
52904400 TCCTGTATTTGGCAGCGAAGCAGATCAAATATGGCAGATTTTACCTCCCCGACTACAGTGGAGTA
565 TCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACCTCCCCGACTACAGTGGAGTA
*
52904465 CCTTGAAGCCGATAATTCTATCTCCCTGTATTTGGCAGTGGAATAGATT
630 CATTGAAGCCGATAATTCTATCTCCCTGTATTTGGCAGTGGAATAGATT
*
52904514 GAAGATTGCAGATCTTGCCTTCTTGTATTTGGCAGTGAAGCAGATCAAAGATGGCAGATTTTACC
1 GAAGATTGCAGATCTTGCCTTCTTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACC
52904579 TCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATA
66 TCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATA
*
52904644 GATTGAAGATTGCAGATCTTGCCTTCTTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTT
131 GATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTT
52904709 TACCTCCATGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGT
196 TACCTCCATGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGT
* * * * * *
52904774 GGAATAGATTGAAGATC--GA---AGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATC-AAA
261 GGAATAGATTGAAGATCAAGATGCAGATATTACCTCCCTGTATCTGACAGCGAAGCACATCAAAA
* * * * * * * * *
52904833 GATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTAAAGCCGATAACTCTATCTCCCTGT
326 GACGACAGACTCTACCTCCCTGACCACAGTGGAATACATTGAAGCAGATAACTCTACCTCCCTGT
* * *
52904898 ATTTGGCAGTGGAATAGATTGAAGA
391 ATCTGACAGTGGAATACATTGAAGA
52904923 TCGAAGATGG
Statistics
Matches: 968, Mismatches: 90, Indels: 72
0.86 0.08 0.06
Matches are distributed among these distances:
671 70 0.07
672 1 0.00
673 32 0.03
674 135 0.14
675 65 0.07
676 19 0.02
677 3 0.00
678 32 0.03
679 7 0.01
680 19 0.02
681 17 0.02
682 14 0.01
683 20 0.02
684 13 0.01
685 16 0.02
686 13 0.01
687 420 0.43
688 1 0.00
689 71 0.07
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (678 bp):
GAAGATTGCAGATCTTGCCTTCTTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACC
TCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATA
GATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTT
TACCTCCATGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGT
GGAATAGATTGAAGATCAAGATGCAGATATTACCTCCCTGTATCTGACAGCGAAGCACATCAAAA
GACGACAGACTCTACCTCCCTGACCACAGTGGAATACATTGAAGCAGATAACTCTACCTCCCTGT
ATCTGACAGTGGAATACATTGAAGACCGCAGAACTTACCTCCCTGCATTTGGCAGAAAAGAAGAT
CAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAATTCTATCTCC
CTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGC
AGATCAAAGATGGCAGATTTTACCTCCCCGACTACAGTGGAGTACATTGAAGCCGATAATTCTAT
CTCCCTGTATTTGGCAGTGGAATAGATT
Found at i:52904910 original size:45 final size:46
Alignment explanation
Indices: 52904725--52904910 Score: 109
Period size: 46 Copynumber: 4.2 Consensus size: 46
52904715 CATGTGACTA
*
52904725 CAGTGGAGTACATTGAAGCCGATA-ACTCTATCTCCCTGTATTTGG
1 CAGTGGAGTACATTAAAGCCGATAGACTCTATCTCCCTGTATTTGG
* * * * *
52904770 CAGTGGAATAGATTGAAGATCGA-AGA-TCT-TGCCTTCCTGTATTTGG
1 CAGTGGAGTACATTAAAG-CCGATAGACTCTAT--CTCCCTGTATTTGG
* * * * * ** ** * * * * *
52904816 CAGCGAAGCAGATCAAAGATGGCAGATTTTACCTCCCTG-A-CT-A
1 CAGTGGAGTACATTAAAGCCGATAGACTCTATCTCCCTGTATTTGG
52904859 CAGTGGAGTACATTAAAGCCGATA-ACTCTATCTCCCTGTATTTGG
1 CAGTGGAGTACATTAAAGCCGATAGACTCTATCTCCCTGTATTTGG
52904904 CAGTGGA
1 CAGTGGA
52904911 ATAGATTGAA
Statistics
Matches: 99, Mismatches: 32, Indels: 20
0.66 0.21 0.13
Matches are distributed among these distances:
42 11 0.11
43 16 0.16
44 3 0.03
45 29 0.29
46 38 0.38
47 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.28
Consensus pattern (46 bp):
CAGTGGAGTACATTAAAGCCGATAGACTCTATCTCCCTGTATTTGG
Found at i:52904930 original size:134 final size:134
Alignment explanation
Indices: 52903152--52904923 Score: 2574
Period size: 134 Copynumber: 13.0 Consensus size: 134
52903142 GAAGTGGATC
*
52903152 GAAGATTGCAGATCTTGCCTTCTTGTATTTGGCAGCGAAGCAGATCAAAAGATGGCAGATTTTAC
1 GAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATC-AAAGATGGCAGATTTTAC
52903217 CTCCCTGA-TCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAA
65 CTCCCTGACT-ACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAA
52903281 TAGATT
129 TAGATT
*
52903287 GAAGATTACAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAAGATGGCAGATTTTAC
1 GAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATC-AAAGATGGCAGATTTTAC
*
52903352 CTCCATGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGA
65 CTCC--CTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGA
52903417 ATAGATT
128 ATAGATT
*
52903424 GAAGATTGCAGATATTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAAGATGGCAGATTTTAC
1 GAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATC-AAAGATGGCAGATTTTAC
*
52903489 CTCCCTGACCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAAT
65 CTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAAT
52903554 AGATT
130 AGATT
*
52903559 GAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCAAAGCAGATCAAAGATGGCAGATTTTACC
1 GAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACC
*
52903624 TCCCTGACTACAGTGGAGTACATTGAAGCCGATAATTCTATCTCCCTGTATTTGGCAGTGGAATA
66 TCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATA
52903689 GATT
131 GATT
52903693 GAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACC
1 GAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACC
*
52903758 TCCCTGACTACAGTGGAGTACATTGAAGCCGATAATTCTATCTCCCTGTATTTGGCAGTGGAATA
66 TCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATA
52903823 GATT
131 GATT
*
52903827 GAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAACAGATCAAAGATGGCAGATTTTACC
1 GAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACC
*
52903892 TCCCTGACTACAGTGGAGTACATTGAAGCCGATAATTCTATCTCCCTGTATTTGGCAGTGGAATA
66 TCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATA
52903957 GATT
131 GATT
* *
52903961 AAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATAGCAGATTTTACC
1 GAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACC
* *
52904026 TCCTTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGCATTTGGCAGTGGAATA
66 TCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATA
52904091 GATT
131 GATT
* * * * * * * * * ** ** **
52904095 GAAGATCAAAGATGGCAGATTTTACCTCCCTG-A-CT-ACAGTGGAGTACATTGAAGCCGATA-A
1 GAAGAT------T-GCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGA
* * * * * * * * * * *
52904156 CTCTATCTCCCTGCATTTGGCAGTGGAATAGATTGAAGATCAAAGATGGCAGATTTTACCTCCCT
59 TTTTACCTCCCTG-A-CT-ACAGTGGAGTACATTGAAG--C--CGAT---A-ACTCTATCTCCCT
* * * *
52904221 G-A-CT-ACAGTGGAGTACATT
113 GTATTTGGCAGTGGAATAGATT
** * * ** * * * *
52904240 GAAG-CCG-ATAACTCTATCTCCCTGCATTTGGCAGTGGAATAGATTGAAGATCAAAGATGGCAG
1 GAAGATTGCAGATCT-TGCCTTCCTGTATTTGGCAG-CG---A-A--GCAGATCAAAGATGGCAG
*
52904303 ATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAATTCTATCTCCCTGTATTTGGCA
58 ATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCA
52904368 GTGGAATAGATT
123 GTGGAATAGATT
*
52904380 GAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAATATGGCAGATTTTACC
1 GAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACC
* * *
52904445 TCCCCGACTACAGTGGAGTACCTTGAAGCCGATAATTCTATCTCCCTGTATTTGGCAGTGGAATA
66 TCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATA
52904510 GATT
131 GATT
* *
52904514 GAAGATTGCAGATCTTGCCTTCTTGTATTTGGCAGTGAAGCAGATCAAAGATGGCAGATTTTACC
1 GAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACC
52904579 TCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATA
66 TCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATA
52904644 GATT
131 GATT
*
52904648 GAAGATTGCAGATCTTGCCTTCTTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACC
1 GAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACC
*
52904713 TCCATGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAA
66 TCC--CTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAA
52904778 TAGATT
129 TAGATT
* *
52904784 GAAGATCGAAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACC
1 GAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACC
*
52904849 TCCCTGACTACAGTGGAGTACATTAAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATA
66 TCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATA
52904914 GATT
131 GATT
52904918 GAAGAT
1 GAAGAT
52904924 CGAAGATGGC
Statistics
Matches: 1487, Mismatches: 110, Indels: 81
0.89 0.07 0.05
Matches are distributed among these distances:
134 841 0.57
135 175 0.12
136 134 0.09
137 163 0.11
138 18 0.01
139 4 0.00
140 38 0.03
141 36 0.02
142 5 0.00
143 1 0.00
144 3 0.00
145 33 0.02
146 2 0.00
147 12 0.01
148 22 0.01
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (134 bp):
GAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTACC
TCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAATA
GATT
Found at i:52904943 original size:95 final size:95
Alignment explanation
Indices: 52904825--52905018 Score: 343
Period size: 95 Copynumber: 2.0 Consensus size: 95
52904815 GCAGCGAAGC
*
52904825 AGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTAAAGCCGATAACTCTAT
1 AGATCAAAGATGGCAGAGTTTACCTCCCTGACTACAGTGGAGTACATTAAAGCCGATAACTCTAT
52904890 CTCCCTGTATTTGGCAGTGGAATAGATTGA
66 CTCCCTGTATTTGGCAGTGGAATAGATTGA
* * * *
52904920 AGATCGAAGATGGCAGAGTTTACCTCCCTGACTACAGTGGAGTATATTGAAGCTGATAACTCTAT
1 AGATCAAAGATGGCAGAGTTTACCTCCCTGACTACAGTGGAGTACATTAAAGCCGATAACTCTAT
52904985 CTCCCTGTATTTGGCAGTGGAATAGATTGA
66 CTCCCTGTATTTGGCAGTGGAATAGATTGA
52905015 AGAT
1 AGAT
52905019 TACAGATCTT
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
95 94 1.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.29
Consensus pattern (95 bp):
AGATCAAAGATGGCAGAGTTTACCTCCCTGACTACAGTGGAGTACATTAAAGCCGATAACTCTAT
CTCCCTGTATTTGGCAGTGGAATAGATTGA
Found at i:52905061 original size:44 final size:44
Alignment explanation
Indices: 52904999--52905191 Score: 120
Period size: 44 Copynumber: 4.4 Consensus size: 44
52904989 CTGTATTTGG
** * *
52904999 CAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAA
1 CAGTGGAGCAGATCGAAGATGACAGATCTTATCTCCCTAAGCAA
* * * * * * * * **
52905043 TAGTGGAGCAGGTCGAAGACGGCGGATTTTACCTCCCTGA-TTA
1 CAGTGGAGCAGATCGAAGATGACAGATCTTATCTCCCTAAGCAA
* * * * ** * **
52905086 CAGTGGAGTACATTGAAGCTGGTAGTTC-TATCTCCCTGGGCAA
1 CAGTGGAGCAGATCGAAGATGACAGATCTTATCTCCCTAAGCAA
** *
52905129 CAGTGGAATAGATCGAAGATTACAGATCTTATCTCCCTAAGCAA
1 CAGTGGAGCAGATCGAAGATGACAGATCTTATCTCCCTAAGCAA
* *
52905173 TAGTGGAGCAGGTCGAAGA
1 CAGTGGAGCAGATCGAAGA
52905192 CGGCGGATTT
Statistics
Matches: 104, Mismatches: 43, Indels: 4
0.69 0.28 0.03
Matches are distributed among these distances:
42 9 0.09
43 39 0.38
44 56 0.54
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.25
Consensus pattern (44 bp):
CAGTGGAGCAGATCGAAGATGACAGATCTTATCTCCCTAAGCAA
Found at i:52905132 original size:43 final size:43
Alignment explanation
Indices: 52905085--52905276 Score: 120
Period size: 43 Copynumber: 4.4 Consensus size: 43
52905075 CTCCCTGATT
* * *
52905085 ACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTCCCTGGGCA
1 ACAGTGGAGTACATCGAAGCTGGCAGTTCTATCTCCCTGGACA
* * * ** * *
52905128 ACAGTGGAATAGATCGAAGATTACAGATCTTATCTCCCT-AAGCA
1 ACAGTGGAGTACATCGAAGCTGGCAGTTC-TATCTCCCTGGA-CA
* * ** * * * **
52905172 ATAGTGGAGCAGGTCGAAGAC-GGCGGATTTTACCTCCCT-GATT
1 ACAGTGGAGTACATCGAAG-CTGGCAG-TTCTATCTCCCTGGACA
* *
52905215 ACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTCCCTGGACA
1 ACAGTGGAGTACATCGAAGCTGGCAGTTCTATCTCCCTGGACA
* *
52905258 ACAGTGGAATAGATCGAAG
1 ACAGTGGAGTACATCGAAG
52905277 AAAACAACAT
Statistics
Matches: 105, Mismatches: 38, Indels: 12
0.68 0.25 0.08
Matches are distributed among these distances:
42 11 0.10
43 56 0.53
44 37 0.35
45 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.26
Consensus pattern (43 bp):
ACAGTGGAGTACATCGAAGCTGGCAGTTCTATCTCCCTGGACA
Found at i:52905183 original size:130 final size:130
Alignment explanation
Indices: 52904923--52905277 Score: 566
Period size: 130 Copynumber: 2.7 Consensus size: 130
52904913 AGATTGAAGA
* * * * * * **
52904923 TCGAAGATGGCAGAGTTTACCTCCCTGACTACAGTGGAGTATATTGAAGCTGATAACTCTATCTC
1 TCGAAGACGGCGGATTTTACCTCCCTGATTACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTC
* *** *
52904988 CCTGTATTTGGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCA
66 CCTGGA--CAACAGTGGAATAGATCGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCA
52905053 GG
129 GG
52905055 TCGAAGACGGCGGATTTTACCTCCCTGATTACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTC
1 TCGAAGACGGCGGATTTTACCTCCCTGATTACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTC
*
52905120 CCTGGGCAACAGTGGAATAGATCGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGG
66 CCTGGACAACAGTGGAATAGATCGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGG
52905185 TCGAAGACGGCGGATTTTACCTCCCTGATTACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTC
1 TCGAAGACGGCGGATTTTACCTCCCTGATTACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTC
52905250 CCTGGACAACAGTGGAATAGATCGAAGA
66 CCTGGACAACAGTGGAATAGATCGAAGA
52905278 AAACAACATT
Statistics
Matches: 208, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
130 147 0.71
132 61 0.29
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (130 bp):
TCGAAGACGGCGGATTTTACCTCCCTGATTACAGTGGAGTACATTGAAGCTGGTAGTTCTATCTC
CCTGGACAACAGTGGAATAGATCGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGG
Found at i:52905209 original size:44 final size:44
Alignment explanation
Indices: 52905031--52905210 Score: 114
Period size: 44 Copynumber: 4.1 Consensus size: 44
52905021 CAGATCTTAT
* *
52905031 CTCCCTAAGCAATAGTGGAGCAGGTCGAAGACGGCGGATTTTAC
1 CTCCCTAAGCAACAGTGGAGCAGATCGAAGACGGCGGATTTTAC
* ** * * * * * * *
52905075 CTCCCTGA-TTACAGTGGAGTACATTGAAG-CTG-GTAGTTCTAT
1 CTCCCTAAGCAACAGTGGAGCAGATCGAAGACGGCGGA-TTTTAC
** ** *** * * *
52905117 CTCCCTGGGCAACAGTGGAATAGATCGAAGATTACAGATCTTAT
1 CTCCCTAAGCAACAGTGGAGCAGATCGAAGACGGCGGATTTTAC
* *
52905161 CTCCCTAAGCAATAGTGGAGCAGGTCGAAGACGGCGGATTTTAC
1 CTCCCTAAGCAACAGTGGAGCAGATCGAAGACGGCGGATTTTAC
52905205 CTCCCT
1 CTCCCT
52905211 GATTACAGTG
Statistics
Matches: 96, Mismatches: 36, Indels: 8
0.69 0.26 0.06
Matches are distributed among these distances:
41 2 0.02
42 13 0.14
43 30 0.31
44 50 0.52
45 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.25
Consensus pattern (44 bp):
CTCCCTAAGCAACAGTGGAGCAGATCGAAGACGGCGGATTTTAC
Found at i:52906044 original size:55 final size:56
Alignment explanation
Indices: 52905959--52906080 Score: 228
Period size: 55 Copynumber: 2.2 Consensus size: 56
52905949 TCACAAAAAG
52905959 GGGGGGATTTTGATGTTTTTTTTTTGGAGATTTCAAAGGGGATCGATAGTATTTAA
1 GGGGGGATTTTGATGTTTTTTTTTTGGAGATTTCAAAGGGGATCGATAGTATTTAA
*
52906015 GGGGGGATTTTGATG-TTTTTTTTTGGAGATTTCAAAGGGGATCGATAGTATTTTA
1 GGGGGGATTTTGATGTTTTTTTTTTGGAGATTTCAAAGGGGATCGATAGTATTTAA
52906070 GGGGGGATTTT
1 GGGGGGATTTT
52906081 TTGATATTTC
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
55 50 0.77
56 15 0.23
ACGTcount: A:0.21, C:0.03, G:0.33, T:0.43
Consensus pattern (56 bp):
GGGGGGATTTTGATGTTTTTTTTTTGGAGATTTCAAAGGGGATCGATAGTATTTAA
Found at i:52906963 original size:14 final size:15
Alignment explanation
Indices: 52906930--52906981 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
52906920 AATTATTTTC
*
52906930 CTATTATTTATTATA
1 CTATTATTTATTACA
*
52906945 CTATT-TTTTTTACA
1 CTATTATTTATTACA
*
52906959 CTATTATTTATTATA
1 CTATTATTTATTACA
52906974 CTTATTAT
1 C-TATTAT
52906982 ATCATTTTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
14 12 0.39
15 13 0.42
16 6 0.19
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.62
Consensus pattern (15 bp):
CTATTATTTATTACA
Found at i:52908529 original size:42 final size:43
Alignment explanation
Indices: 52908425--52908542 Score: 132
Period size: 42 Copynumber: 2.8 Consensus size: 43
52908415 GTACGTATCA
* * * *
52908425 ATGCCATACCCCAGATATGGTCTTACATGAAAT-ATCATATCG
1 ATGCCATATCCCAGATATGGTCTTATACGAAATCATCATACCG
* * * * *
52908467 ACGCTATGTCCCTGACATGGTCTTATACGAAATCA-CATACCG
1 ATGCCATATCCCAGATATGGTCTTATACGAAATCATCATACCG
*
52908509 ATGCCATATCCCAGATATGGTCTTATACGGAATC
1 ATGCCATATCCCAGATATGGTCTTATACGAAATC
52908543 TCGGTAGTAC
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
42 59 0.98
43 1 0.02
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (43 bp):
ATGCCATATCCCAGATATGGTCTTATACGAAATCATCATACCG
Found at i:52909456 original size:501 final size:501
Alignment explanation
Indices: 52908514--52909497 Score: 1950
Period size: 501 Copynumber: 2.0 Consensus size: 501
52908504 TACCGATGCC
52908514 ATATCCCAGATATGGTCTTATACGGAATCTCGGTAGTACTAATATCATGACATTTGTATTCTACC
1 ATATCCCAGATATGGTCTTATACGGAATCTCGGTAGTACTAATATCATGACATTTGTATTCTACC
52908579 TTTGAGGTTATATTGGGATTTCTCATTTCTTGAAACTTCGTTAAAATCGTCATTAATCAATTTCA
66 TTTGAGGTTATATTGGGATTTCTCATTTCTTGAAACTTCGTTAAAATCGTCATTAATCAATTTCA
52908644 TAAAAACAAATGTATACAATTCATGCAATATGAAAATAGTAAATACACAACATAAGGTTGCATTA
131 TAAAAACAAATGTATACAATTCATGCAATATGAAAATAGTAAATACACAACATAAGGTTGCATTA
52908709 TTTACGCATGAACTTACCTCAATACCAAAATGGAAAAAAGGGACCTAACTATCAAATTTCACATT
196 TTTACGCATGAACTTACCTCAATACCAAAATGGAAAAAAGGGACCTAACTATCAAATTTCACATT
52908774 TTCCCCCGTTCTAGGCCTGAATCTTGTTTTATTTGATCTATAATATCATATTCGGCCTATTTATT
261 TTCCCCCGTTCTAGGCCTGAATCTTGTTTTATTTGATCTATAATATCATATTCGGCCTATTTATT
52908839 AGTCATATTATTCAAAATGGTCCAAAAATCATATTATGGAAAAATTACATTTTTGCCCCTAAAGT
326 AGTCATATTATTCAAAATGGTCCAAAAATCATATTATGGAAAAATTACATTTTTGCCCCTAAAGT
52908904 TTGACACATTTATAATTTTGCCCCTAGGCTTGTAAAATGAAATGTGTTCAATTTATTTACTATCC
391 TTGACACATTTATAATTTTGCCCCTAGGCTTGTAAAATGAAATGTGTTCAATTTATTTACTATCC
52908969 ATGCATATTAAAATCATTTTCATGCCTAAAATGAAAATAGTATACA
456 ATGCATATTAAAATCATTTTCATGCCTAAAATGAAAATAGTATACA
52909015 ATATCCCAGATATGGTCTTATACGGAATCTCGGTAGTACTAATATCATGACATTTGTATTCTACC
1 ATATCCCAGATATGGTCTTATACGGAATCTCGGTAGTACTAATATCATGACATTTGTATTCTACC
52909080 TTTGAGGTTATATTGGGATTTCTCATTTCTTGAAACTTCGTTAAAATCGTCATTAATCAATTTCA
66 TTTGAGGTTATATTGGGATTTCTCATTTCTTGAAACTTCGTTAAAATCGTCATTAATCAATTTCA
52909145 TAAAAACAAATGTATACAATTCATGCAATATGAAAATAGTAAATACACAACATAAGGTTGCATTA
131 TAAAAACAAATGTATACAATTCATGCAATATGAAAATAGTAAATACACAACATAAGGTTGCATTA
*
52909210 TTTACGCATGAACTTACCTCAATACCAAAATGGAAAAAAGGGACCTAACTGTCAAATTTCACATT
196 TTTACGCATGAACTTACCTCAATACCAAAATGGAAAAAAGGGACCTAACTATCAAATTTCACATT
52909275 TTCCCCCGTTCTAGGCCTGAATCTTGTTTTATTTGATCTATAATATCATATTCGGCCTATTTATT
261 TTCCCCCGTTCTAGGCCTGAATCTTGTTTTATTTGATCTATAATATCATATTCGGCCTATTTATT
52909340 AGTCATATTATTCAAAATGGTCCAAAAATCATATTATGGAAAAATTACATTTTTGCCCCTAAAGT
326 AGTCATATTATTCAAAATGGTCCAAAAATCATATTATGGAAAAATTACATTTTTGCCCCTAAAGT
52909405 TTGACACATTTATAATTTTGCCCCTAGGCTTGTAAAATGAAATGTGTTCAATTTATTTACTATCC
391 TTGACACATTTATAATTTTGCCCCTAGGCTTGTAAAATGAAATGTGTTCAATTTATTTACTATCC
*
52909470 ATGCATATTCAAATCATTTTCATGCCTA
456 ATGCATATTAAAATCATTTTCATGCCTA
52909498 TAGCAGCTCA
Statistics
Matches: 481, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
501 481 1.00
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.36
Consensus pattern (501 bp):
ATATCCCAGATATGGTCTTATACGGAATCTCGGTAGTACTAATATCATGACATTTGTATTCTACC
TTTGAGGTTATATTGGGATTTCTCATTTCTTGAAACTTCGTTAAAATCGTCATTAATCAATTTCA
TAAAAACAAATGTATACAATTCATGCAATATGAAAATAGTAAATACACAACATAAGGTTGCATTA
TTTACGCATGAACTTACCTCAATACCAAAATGGAAAAAAGGGACCTAACTATCAAATTTCACATT
TTCCCCCGTTCTAGGCCTGAATCTTGTTTTATTTGATCTATAATATCATATTCGGCCTATTTATT
AGTCATATTATTCAAAATGGTCCAAAAATCATATTATGGAAAAATTACATTTTTGCCCCTAAAGT
TTGACACATTTATAATTTTGCCCCTAGGCTTGTAAAATGAAATGTGTTCAATTTATTTACTATCC
ATGCATATTAAAATCATTTTCATGCCTAAAATGAAAATAGTATACA
Found at i:52913396 original size:68 final size:69
Alignment explanation
Indices: 52913319--52913466 Score: 162
Period size: 67 Copynumber: 2.2 Consensus size: 69
52913309 CATCATGTGT
* * * *
52913319 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTACAAGACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
52913381 ATGTAG
64 ATGTAG
* ** * *
52913387 ACAAGAGAGCT--ATGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCAT
1 ACAAGAGAGCTACAAGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCAT
52913450 GTAG
66 GTAG
52913454 ACAAGAGAGCTAC
1 ACAAGAGAGCTAC
52913467 GAGATAAACT
Statistics
Matches: 66, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
64 20 0.30
65 7 0.11
66 5 0.08
67 23 0.35
68 11 0.17
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.22
Consensus pattern (69 bp):
ACAAGAGAGCTACAAGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCAT
GTAG
Found at i:52915864 original size:20 final size:20
Alignment explanation
Indices: 52915831--52915871 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
52915821 AGCTCAATAC
52915831 ATAAGCTAGATGAATGGACA
1 ATAAGCTAGATGAATGGACA
* *
52915851 ATAAGTTAGCTGAATGGACA
1 ATAAGCTAGATGAATGGACA
52915871 A
1 A
52915872 CTTGTGTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.10, G:0.24, T:0.22
Consensus pattern (20 bp):
ATAAGCTAGATGAATGGACA
Found at i:52916418 original size:40 final size:39
Alignment explanation
Indices: 52916363--52916440 Score: 129
Period size: 40 Copynumber: 2.0 Consensus size: 39
52916353 TTAACTCAAC
* *
52916363 CAGCTAATTAAGTTGTAATGAGCTAAGACATACTTAAATT
1 CAGCTAATTAAGTTGTAATAAGCTAAGACA-AATTAAATT
52916403 CAGCTAATTAAGTTGTAATAAGCTAAGACAAATTAAAT
1 CAGCTAATTAAGTTGTAATAAGCTAAGACAAATTAAAT
52916441 AGCTGTACTA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 7 0.19
40 29 0.81
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.31
Consensus pattern (39 bp):
CAGCTAATTAAGTTGTAATAAGCTAAGACAAATTAAATT
Found at i:52916507 original size:47 final size:47
Alignment explanation
Indices: 52916426--52916582 Score: 224
Period size: 47 Copynumber: 3.3 Consensus size: 47
52916416 TGTAATAAGC
* * * *
52916426 TAAGACAAATTAAATAGCTGTACTAACTAAAACATATTAAATTAACT
1 TAAGACAAATTAAATAGCTGAACTAATTAGAACATATTAAATAAACT
* *
52916473 TAGGACATATTAAATAGCTGAACTAATTAGAACATATTAAATAAACT
1 TAAGACAAATTAAATAGCTGAACTAATTAGAACATATTAAATAAACT
* * *
52916520 TAAGACAAATTAAATTGCTGAACTAATCAGAACACATTAAATAAACT
1 TAAGACAAATTAAATAGCTGAACTAATTAGAACATATTAAATAAACT
*
52916567 TAAGACAAATCAAATA
1 TAAGACAAATTAAATA
52916583 CTTAAGCTAA
Statistics
Matches: 97, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 97 1.00
ACGTcount: A:0.52, C:0.13, G:0.08, T:0.27
Consensus pattern (47 bp):
TAAGACAAATTAAATAGCTGAACTAATTAGAACATATTAAATAAACT
Found at i:52919612 original size:49 final size:49
Alignment explanation
Indices: 52919540--52919670 Score: 172
Period size: 49 Copynumber: 2.7 Consensus size: 49
52919530 TGTTGTTTGT
* * *
52919540 TAGTGTAAGACTTGTCTGGGACATGGCATCGACATCGATAGATGAGAGC
1 TAGTGTAAGACCTGTCTGAGACATGGCATCGACATCGATAGATGAAAGC
* * * * *
52919589 TAGTGTAAGACCTGCCTGTGACATGGCATCGACCTCGATATATGAAAGT
1 TAGTGTAAGACCTGTCTGAGACATGGCATCGACATCGATAGATGAAAGC
* *
52919638 TAGTGTAAGACCTGTCTGAGACTTTGCATCGAC
1 TAGTGTAAGACCTGTCTGAGACATGGCATCGAC
52919671 TTTAATGTGC
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 71 1.00
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (49 bp):
TAGTGTAAGACCTGTCTGAGACATGGCATCGACATCGATAGATGAAAGC
Found at i:52929671 original size:43 final size:43
Alignment explanation
Indices: 52929590--52929675 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
52929580 AAATCATATA
**
52929590 ATGCCAATGTCCCAGATGTGGTCTTACATGTAGCCACATATCG
1 ATGCCAATGTCCCAGATGTGGTCTTACATGTAAACACATATCG
*
52929633 ATGCCACTGTCCCAGATAG-GGTCTTAC-TCGTAAACACATATCG
1 ATGCCAATGTCCCAGAT-GTGGTCTTACAT-GTAAACACATATCG
52929676 GAATCACAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 1 0.03
43 36 0.95
44 1 0.03
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (43 bp):
ATGCCAATGTCCCAGATGTGGTCTTACATGTAAACACATATCG
Found at i:52937955 original size:10 final size:10
Alignment explanation
Indices: 52937942--52937987 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
52937932 AGCTCACTTG
52937942 AGCTCGTTTT
1 AGCTCGTTTT
*
52937952 AGCTCGTTTG
1 AGCTCGTTTT
*
52937962 AGCTCGAATTT
1 AGCTCG-TTTT
*
52937973 AGCTCGTTTC
1 AGCTCGTTTT
52937983 AGCTC
1 AGCTC
52937988 ATTCCTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 22 0.73
11 8 0.27
ACGTcount: A:0.15, C:0.24, G:0.22, T:0.39
Consensus pattern (10 bp):
AGCTCGTTTT
Found at i:52937975 original size:21 final size:20
Alignment explanation
Indices: 52937939--52937987 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
52937929 ATCAGCTCAC
*
52937939 TTGAGCTCGTTTTAGCTCGT
1 TTGAGCTCGATTTAGCTCGT
52937959 TTGAGCTCGAATTTAGCTCGT
1 TTGAGCTCG-ATTTAGCTCGT
*
52937980 TTCAGCTC
1 TTGAGCTC
52937988 ATTCCTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.41
Consensus pattern (20 bp):
TTGAGCTCGATTTAGCTCGT
Found at i:52938230 original size:13 final size:13
Alignment explanation
Indices: 52938212--52938240 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
52938202 AATAGTTGTG
52938212 TGTTATTTAATTA
1 TGTTATTTAATTA
52938225 TGTTATTTAATTA
1 TGTTATTTAATTA
52938238 TGT
1 TGT
52938241 AGGTTAGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:52942623 original size:10 final size:10
Alignment explanation
Indices: 52942610--52942655 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
52942600 AGCTCACTTG
52942610 AGCTCGTTTT
1 AGCTCGTTTT
*
52942620 AGCTCGTTTG
1 AGCTCGTTTT
*
52942630 AGCTCGAATTT
1 AGCTCG-TTTT
*
52942641 AGCTCGTTTC
1 AGCTCGTTTT
52942651 AGCTC
1 AGCTC
52942656 ATTCCTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 22 0.73
11 8 0.27
ACGTcount: A:0.15, C:0.24, G:0.22, T:0.39
Consensus pattern (10 bp):
AGCTCGTTTT
Found at i:52942643 original size:21 final size:20
Alignment explanation
Indices: 52942607--52942655 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
52942597 ATCAGCTCAC
*
52942607 TTGAGCTCGTTTTAGCTCGT
1 TTGAGCTCGATTTAGCTCGT
52942627 TTGAGCTCGAATTTAGCTCGT
1 TTGAGCTCG-ATTTAGCTCGT
*
52942648 TTCAGCTC
1 TTGAGCTC
52942656 ATTCCTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.41
Consensus pattern (20 bp):
TTGAGCTCGATTTAGCTCGT
Found at i:52942898 original size:13 final size:13
Alignment explanation
Indices: 52942880--52942908 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
52942870 AATAGTTGCG
52942880 TGTTATTTAATTA
1 TGTTATTTAATTA
52942893 TGTTATTTAATTA
1 TGTTATTTAATTA
52942906 TGT
1 TGT
52942909 AGGTTAGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:52945326 original size:93 final size:93
Alignment explanation
Indices: 52945167--52945338 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
52945157 GGATGGTTGA
* * *
52945167 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
52945232 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
52945260 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
52945325 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
52945339 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:52945343 original size:46 final size:46
Alignment explanation
Indices: 52945171--52945345 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 46
52945161 GGTTGAGCAT
* * *
52945171 CCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* * * *
52945217 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---GC
*
52945262 ATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* *
52945310 CCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
52945346 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
45 3 0.03
46 63 0.58
47 27 0.25
48 4 0.04
50 3 0.03
51 3 0.03
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:52954154 original size:40 final size:39
Alignment explanation
Indices: 52954065--52954162 Score: 115
Period size: 40 Copynumber: 2.5 Consensus size: 39
52954055 CTAAGTCGGT
* *
52954065 ACCGCACACTTAGTGCCCTCTATAGCCGAAGCTATGCCA
1 ACCGCACACTTAGTGCCATCTATAGCCGAAGCTATGCAA
* * * **
52954104 ACTCGTACACTTAGTGCCATTTGTAGCCGAAGCTATATTAA
1 AC-CGCACACTTAGTGCCATCTATAGCCGAAGCTAT-GCAA
52954145 ACCGCACACTTAGTGCCA
1 ACCGCACACTTAGTGCCA
52954163 ATCATAGTCG
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
39 2 0.04
40 44 0.90
41 3 0.06
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (39 bp):
ACCGCACACTTAGTGCCATCTATAGCCGAAGCTATGCAA
Found at i:52956082 original size:46 final size:46
Alignment explanation
Indices: 52956013--52956141 Score: 163
Period size: 46 Copynumber: 2.8 Consensus size: 46
52956003 GGTGGTAGGT
*
52956013 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACAT-CATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCA-ATACACGA
* * * *
52956059 GTGCTAGTGTAAGACATGTCTGGGATATGCATCGG-CATTGAGACGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAAT-ACACGA
* *
52956105 GAGCTAGTGTCATACATGTCTGGGACATGCATCGGCC
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCC
52956142 TCGGGATATA
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
44 1 0.01
45 2 0.03
46 67 0.94
47 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (46 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAATACACGA
Found at i:52956933 original size:21 final size:21
Alignment explanation
Indices: 52956886--52956926 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
52956876 GGCTAATATT
**
52956886 AAAATTTTTTTTATGAATGCA
1 AAAATTTTTTCCATGAATGCA
52956907 AGAAATTTTTTCCATGAATG
1 A-AAATTTTTTCCATGAATG
52956927 TGAAAATGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 1 0.06
22 16 0.94
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (21 bp):
AAAATTTTTTCCATGAATGCA
Found at i:52957557 original size:21 final size:20
Alignment explanation
Indices: 52957527--52957566 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
52957517 GTCATGATGG
52957527 CCACACGGGCGTGTTGCCCTT
1 CCACACGGGCGTGTT-CCCTT
*
52957548 CCACATGGGCGTGTTCCCT
1 CCACACGGGCGTGTTCCCT
52957567 GCTTCAAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.10, C:0.38, G:0.28, T:0.25
Consensus pattern (20 bp):
CCACACGGGCGTGTTCCCTT
Found at i:52959118 original size:21 final size:22
Alignment explanation
Indices: 52959092--52959149 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
52959082 CAGCTTGTCT
52959092 GAGCTTACTATT-AACTCGATA-
1 GAGCTTACTATTCAACTCG-TAC
*
52959113 GAGCTTACCATTTCAACTCGTAC
1 GAGCTTACTA-TTCAACTCGTAC
*
52959136 GAACTTACTATTCA
1 GAGCTTACTATTCA
52959150 TCAACTCAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 9 0.29
22 8 0.26
23 14 0.45
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (22 bp):
GAGCTTACTATTCAACTCGTAC
Found at i:52964781 original size:27 final size:27
Alignment explanation
Indices: 52964751--52964803 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
52964741 TATTCTACCA
*
52964751 TACAGGGGTATTACGGTCATTTTACAC
1 TACAAGGGTATTACGGTCATTTTACAC
* *
52964778 TACAAGGGTATTTCGGTTATTTTACA
1 TACAAGGGTATTACGGTCATTTTACA
52964804 AATCGAGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (27 bp):
TACAAGGGTATTACGGTCATTTTACAC
Found at i:52968360 original size:5 final size:5
Alignment explanation
Indices: 52968350--52968375 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
52968340 GCCTTTTTGA
52968350 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
52968376 TAAAAAACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:52973528 original size:27 final size:27
Alignment explanation
Indices: 52973498--52973558 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
52973488 GGGCATAATC
52973498 ATCATTCTACCA-TACAAGGGTATTGCG
1 ATCATT-TACCACTACAAGGGTATTGCG
** *
52973525 ATCATTTTTCACTACAAGGGTATTTCG
1 ATCATTTACCACTACAAGGGTATTGCG
*
52973552 ATGATTT
1 ATCATTT
52973559 TACAAACCGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 3 0.10
27 26 0.90
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (27 bp):
ATCATTTACCACTACAAGGGTATTGCG
Found at i:52979943 original size:24 final size:24
Alignment explanation
Indices: 52979916--52979973 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
52979906 AGCTCCCGTT
*
52979916 ATATGGCTCTTTGTGAGCTTCCTG
1 ATATGGCTCTTTGTGAACTTCCTG
*
52979940 ATATGGTTCTTTGTGAACTTCCTG
1 ATATGGCTCTTTGTGAACTTCCTG
52979964 ACTATGGCTC
1 A-TATGGCTC
52979974 GTATGAGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 23 0.77
25 7 0.23
ACGTcount: A:0.16, C:0.21, G:0.22, T:0.41
Consensus pattern (24 bp):
ATATGGCTCTTTGTGAACTTCCTG
Found at i:52982194 original size:44 final size:42
Alignment explanation
Indices: 52982137--52982235 Score: 110
Period size: 44 Copynumber: 2.3 Consensus size: 42
52982127 TTCGATATGC
* * *
52982137 AATTTCATGTAAGACCACATCTAGGACGTTGGCATCG-ATTT
1 AATTTCGTGTAAGACCACATCTAGGACATCGGCATCGTATTT
** *
52982178 GAGATTTACGTGTAAGACCATGTCTGGGACATCGGCATCGTATTT
1 -A-ATTT-CGTGTAAGACCACATCTAGGACATCGGCATCGTATTT
52982223 AATTTCGTGTAAG
1 AATTTCGTGTAAG
52982236 GCCTTGTCTG
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
42 9 0.19
43 8 0.17
44 27 0.56
45 4 0.08
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (42 bp):
AATTTCGTGTAAGACCACATCTAGGACATCGGCATCGTATTT
Found at i:52982244 original size:42 final size:44
Alignment explanation
Indices: 52982144--52982291 Score: 117
Period size: 42 Copynumber: 3.4 Consensus size: 44
52982134 TGCAATTTCA
** * * *
52982144 TGTAAGACCACATCTAGGACGTTGGCATCGATTTGAGATTTACG
1 TGTAAGACCATGTCTGGGACATCGGCATCGATTTGAGATTTACG
52982188 TGTAAGACCATGTCTGGGACATCGGCATCGTATTT-A-ATTT-CG
1 TGTAAGACCATGTCTGGGACATCGGCATCG-ATTTGAGATTTACG
* * * * * * *
52982230 TGTAAGGCCTTGTCTGGGATAGT-GGCATTGATATGTGA-TTACA
1 TGTAAGACCATGTCTGGGACA-TCGGCATCGATTTGAGATTTACG
**
52982273 TGTAAGACCACATCTGGGA
1 TGTAAGACCATGTCTGGGA
52982292 TGTTGGCATT
Statistics
Matches: 83, Mismatches: 16, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
41 3 0.04
42 28 0.34
43 22 0.27
44 26 0.31
45 4 0.05
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (44 bp):
TGTAAGACCATGTCTGGGACATCGGCATCGATTTGAGATTTACG
Found at i:52989804 original size:44 final size:44
Alignment explanation
Indices: 52989754--52989908 Score: 169
Period size: 43 Copynumber: 3.6 Consensus size: 44
52989744 TGAAATTTCA
52989754 TGTAAGACCACGTCTGGGACATTGGCATC-AATTTGAGATTTACG
1 TGTAAGACCACGTCTGGGACATTGGCATCGAATTT-AGATTTACG
* * *
52989798 TGTAAGACCATGTCTGGGACATCGGCATCGTATTTA-ATTT-CG
1 TGTAAGACCACGTCTGGGACATTGGCATCGAATTTAGATTTACG
* *
52989840 TGTAAGACC-CTGTCTGGGACAGTGGCATCGATATTT-GA-TTACA
1 TGTAAGACCAC-GTCTGGGACATTGGCATCGA-ATTTAGATTTACG
* * *
52989883 TGTAAGACCAGGTCTAGGACGTTGGC
1 TGTAAGACCACGTCTGGGACATTGGC
52989909 GTTGTATGAG
Statistics
Matches: 93, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
42 30 0.32
43 31 0.33
44 28 0.30
45 4 0.04
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (44 bp):
TGTAAGACCACGTCTGGGACATTGGCATCGAATTTAGATTTACG
Found at i:52989855 original size:42 final size:41
Alignment explanation
Indices: 52989747--52989891 Score: 150
Period size: 42 Copynumber: 3.4 Consensus size: 41
52989737 TCCGATATGA
*
52989747 AATTTCATGTAAGACCAC-GTCTGGGACATTGGCATC-AATTT
1 AATTTCATGTAAGACC-CTGTCTGGGACA-TGGCATCGTATTT
* *
52989788 GAGATTTACGTGTAAGACCATGTCTGGGACATCGGCATCGTATTT
1 -A-ATTT-CATGTAAGACCCTGTCTGGGACAT-GGCATCGTATTT
*
52989833 AATTTCGTGTAAGACCCTGTCTGGGACAGTGGCATCGATATTT
1 AATTTCATGTAAGACCCTGTCTGGGACA-TGGCATCG-TATTT
* *
52989876 GATTACATGTAAGACC
1 AATTTCATGTAAGACC
52989892 AGGTCTAGGA
Statistics
Matches: 89, Mismatches: 7, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
42 30 0.34
43 28 0.31
44 27 0.30
45 4 0.04
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (41 bp):
AATTTCATGTAAGACCCTGTCTGGGACATGGCATCGTATTT
Found at i:52991777 original size:46 final size:46
Alignment explanation
Indices: 52991642--52991815 Score: 158
Period size: 46 Copynumber: 3.7 Consensus size: 46
52991632 GTTATTGTGA
* * ** *
52991642 GCTAGTGTAAGACATGTCTAGGACATGCATCGGCCAC-ATTATAAGA
1 GCTAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGA-GACGAGT
* * * * *
52991688 GCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCATTGAGACGAGT
1 GCTAGTGTAAGA-CATGTCTAGGACAT-GCATCGGCCTCGAGACGAGT
*
52991736 GCTAGTGTAAGACATGT-TTGGAACATGCATCGGCCTCGAGACGTAAGT
1 GCTAGTGTAAGACATGTCTAGG-ACATGCATCGGCCTCGAGACG--AGT
*
52991784 -C-AGTGTAAGATATGTCTAGGACATGCATCGGC
1 GCTAGTGTAAGACATGTCTAGGACATGCATCGGC
52991816 TATGAGATGT
Statistics
Matches: 104, Mismatches: 17, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
46 53 0.51
47 26 0.25
48 24 0.23
49 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.24
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGACGAGT
Found at i:52991858 original size:46 final size:45
Alignment explanation
Indices: 52991645--52991860 Score: 120
Period size: 46 Copynumber: 4.7 Consensus size: 45
52991635 ATTGTGAGCT
* * * * *
52991645 AGTGTAAGACATGTCTAGGACATGCATCGGCCACATTATAAG-AGC-C
1 AGTGTAAGACATGTCTGGGACAGGCATCGG-C-TATGAGAAGTA-CTC
* *
52991691 AGTGTAAGACCATGTCTGGGACATGGCATCAGC-ATTGAGACGAGTGCT-
1 AGTGTAAGA-CATGTCTGGGACA-GGCATCGGCTA-TGAGA--AGTACTC
* * * * * *
52991739 AGTGTAAGACATGTTTGGAACATGCATCGGCCT-CGAGACGTAAGTC
1 AGTGTAAGACATGTCTGGGACAGGCATCGG-CTATGAGAAGT-ACTC
* * * *
52991785 AGTGTAAGATATGTCTAGGACATGCATCGGCTATGAGATGT-CTC
1 AGTGTAAGACATGTCTGGGACAGGCATCGGCTATGAGAAGTACTC
*
52991829 AGTGTAAGACCATGTTTGGGACACGGCATCGG
1 AGTGTAAGA-CATGTCTGGGACA-GGCATCGG
52991861 AACAGATATG
Statistics
Matches: 131, Mismatches: 25, Indels: 28
0.71 0.14 0.15
Matches are distributed among these distances:
44 13 0.10
45 14 0.11
46 61 0.47
47 25 0.19
48 18 0.14
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACAGGCATCGGCTATGAGAAGTACTC
Found at i:52994835 original size:27 final size:27
Alignment explanation
Indices: 52994804--52994980 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
52994794 ATATCGAGTC
* * *
52994804 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAAAT
*
52994831 TGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
*
52994858 CGCACACTTAGTGCTACAT-GTCAAACT
1 CGCACACTTAGTGCTACATAATCAAA-T
** ** *
52994885 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAAAT
* **
52994912 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAAAT
* *
52994939 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
52994966 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
52994981 GTACAATTTA
Statistics
Matches: 129, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
26 5 0.04
27 118 0.91
28 6 0.05
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAAAT
Found at i:53009154 original size:18 final size:20
Alignment explanation
Indices: 53009115--53009156 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
53009105 TATTATGGGA
*
53009115 AATTACGAGTTTTAGGCTTT
1 AATTACGAGTTTAAGGCTTT
53009135 AATT-CGAGTTTAAGGC-TT
1 AATTACGAGTTTAAGGCTTT
53009153 AATT
1 AATT
53009157 TTGTTTATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
19 11 0.52
20 4 0.19
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.43
Consensus pattern (20 bp):
AATTACGAGTTTAAGGCTTT
Found at i:53010573 original size:19 final size:19
Alignment explanation
Indices: 53010549--53010595 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
53010539 GTCAAATTTG
*
53010549 TTTTATAATTTTATAATAT
1 TTTTATAATTTTAAAATAT
*
53010568 TTTTATAGTTTTAAAATAT
1 TTTTATAATTTTAAAATAT
53010587 TTTTATAAT
1 TTTTATAAT
53010596 ATGTTATGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTATAATTTTAAAATAT
Found at i:53010633 original size:19 final size:19
Alignment explanation
Indices: 53010549--53010697 Score: 72
Period size: 19 Copynumber: 7.6 Consensus size: 19
53010539 GTCAAATTTG
*
53010549 TTTTATAA-TTTTATAATAT
1 TTTTATAATTTTTAT-ATAA
* * * *
53010568 TTTTATAGTTTTAAAATAT
1 TTTTATAATTTTTATATAA
* * **
53010587 TTTTATAATATGT-TATGC
1 TTTTATAATTTTTATATAA
*
53010605 TTTCATAATTTTTATATAA
1 TTTTATAATTTTTATATAA
*
53010624 TTTTATAATTTTCTAT-TAG
1 TTTTATAATTTT-TATATAA
*
53010643 TTTTAATAAGTTTTT-TAAGGAA
1 TTTT-ATAA-TTTTTAT-A-TAA
*
53010665 TTTTAATAAGTTTTTTTATAA
1 TTTT-ATAA-TTTTTATATAA
*
53010686 TTTTGTAATTTT
1 TTTTATAATTTT
53010698 ATAATTTTTA
Statistics
Matches: 100, Mismatches: 21, Indels: 18
0.72 0.15 0.13
Matches are distributed among these distances:
18 12 0.12
19 45 0.45
20 15 0.15
21 10 0.10
22 17 0.17
23 1 0.01
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (19 bp):
TTTTATAATTTTTATATAA
Found at i:53010713 original size:16 final size:17
Alignment explanation
Indices: 53010676--53010713 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
53010666 TTTAATAAGT
53010676 TTTTTTATAATTTTGTA
1 TTTTTTATAATTTTGTA
*
53010693 -ATTTTATAATTTT-TA
1 TTTTTTATAATTTTGTA
53010708 TTTTTT
1 TTTTTT
53010714 GAATATCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 3
0.78 0.09 0.13
Matches are distributed among these distances:
15 2 0.11
16 16 0.89
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTTTTATAATTTTGTA
Found at i:53010935 original size:18 final size:18
Alignment explanation
Indices: 53010914--53010955 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
53010904 TTACAGGGAC
53010914 TTTTTATTATATTA-AGAA
1 TTTTTATTA-ATTATAGAA
*
53010932 TTTTTA-TAATTATATAA
1 TTTTTATTAATTATAGAA
53010949 TTTTTAT
1 TTTTTAT
53010956 AACATTTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 4 0.19
17 11 0.52
18 6 0.29
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTTTATTAATTATAGAA
Found at i:53014013 original size:73 final size:74
Alignment explanation
Indices: 53013921--53014064 Score: 211
Period size: 74 Copynumber: 2.0 Consensus size: 74
53013911 GAAAACCAAA
* * * * *
53013921 ATTATTCCCTTCTTAATAGATAAG-CAAATGGAAAGTTAG-AAAATGAAATATATTCTTTTCGAA
1 ATTATTCCCTTATTAATAGAGAAGACAAATGGAAAATTAGAAAAATGAAATATA-TCTTTCCAAA
53013984 AGAATATAGG
65 AGAATATAGG
*
53013994 ATTATTCCCTTATTAATAGAGAAGACAAATGGAAAATTAGAAAAATGAATTATATCTTTCCAAAA
1 ATTATTCCCTTATTAATAGAGAAGACAAATGGAAAATTAGAAAAATGAAATATATCTTTCCAAAA
53014059 GAATAT
66 GAATAT
53014065 TAATTCCATA
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
73 22 0.35
74 29 0.46
75 12 0.19
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (74 bp):
ATTATTCCCTTATTAATAGAGAAGACAAATGGAAAATTAGAAAAATGAAATATATCTTTCCAAAA
GAATATAGG
Found at i:53014297 original size:22 final size:23
Alignment explanation
Indices: 53014238--53014298 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
53014228 AATGTTCACA
* *
53014238 AACATGTTCATTTAAC-TTAATCG
1 AACATGTTCA-TGAACATTAAACG
* *
53014261 AACATGTTTACGAACATTAAAC-
1 AACATGTTCATGAACATTAAACG
53014283 AACATGTTCATGAACA
1 AACATGTTCATGAACA
53014299 AATATTGAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
22 17 0.55
23 14 0.45
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (23 bp):
AACATGTTCATGAACATTAAACG
Found at i:53014336 original size:4 final size:4
Alignment explanation
Indices: 53014327--53014364 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
53014317 GAACAATGTT
*
53014327 AATA AATA AATA AATA AA-A TAATA AATA AATA CATA AA
1 AATA AATA AATA AATA AATA -AATA AATA AATA AATA AA
53014365 AACACATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 1 0.03
4 28 0.93
5 1 0.03
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:53014351 original size:20 final size:20
Alignment explanation
Indices: 53014326--53014365 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
53014316 CGAACAATGT
53014326 TAATAAATAAATAAATAAAA
1 TAATAAATAAATAAATAAAA
*
53014346 TAATAAATAAATACATAAAA
1 TAATAAATAAATAAATAAAA
53014366 ACACATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (20 bp):
TAATAAATAAATAAATAAAA
Found at i:53014523 original size:12 final size:12
Alignment explanation
Indices: 53014497--53014543 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
53014487 TCATTAATAA
53014497 ATAAACGAG-TT
1 ATAAACGAGCTT
53014508 ATAAACGAGCTT
1 ATAAACGAGCTT
* **
53014520 ATAAATGAGCCA
1 ATAAACGAGCTT
*
53014532 ATAAATGAGCTT
1 ATAAACGAGCTT
53014544 TTTAATGAGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 9 0.30
12 21 0.70
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.26
Consensus pattern (12 bp):
ATAAACGAGCTT
Found at i:53014541 original size:24 final size:24
Alignment explanation
Indices: 53014508--53014553 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
53014498 TAAACGAGTT
53014508 ATAAACGAGCTTATAAATGAGCCA
1 ATAAACGAGCTTATAAATGAGCCA
* * *
53014532 ATAAATGAGCTTTTTAATGAGC
1 ATAAACGAGCTTATAAATGAGC
53014554 TATTCATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.28
Consensus pattern (24 bp):
ATAAACGAGCTTATAAATGAGCCA
Found at i:53016357 original size:13 final size:13
Alignment explanation
Indices: 53016339--53016387 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 13
53016329 TTTACTAGTA
53016339 TATTATATATCAT
1 TATTATATATCAT
53016352 TATTAT-TAT-AT
1 TATTATATATCAT
53016363 T-TT-TATATGCAT
1 TATTATATAT-CAT
53016375 TATTTATATATCA
1 TA-TTATATATCA
53016388 ACTAATAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 11
0.73 0.00 0.27
Matches are distributed among these distances:
9 1 0.03
10 5 0.17
11 3 0.10
12 6 0.20
13 6 0.20
14 4 0.13
15 5 0.17
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (13 bp):
TATTATATATCAT
Found at i:53020636 original size:21 final size:22
Alignment explanation
Indices: 53020606--53020646 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
53020596 TGAGTCAAAA
53020606 AAAAGATGAAAAAATGAAAATT
1 AAAAGATGAAAAAATGAAAATT
53020628 AAAA-ATGAAAAAATGAAAA
1 AAAAGATGAAAAAATGAAAA
53020647 AGTTAAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.15
Consensus pattern (22 bp):
AAAAGATGAAAAAATGAAAATT
Found at i:53022086 original size:44 final size:44
Alignment explanation
Indices: 53022020--53022284 Score: 223
Period size: 44 Copynumber: 5.8 Consensus size: 44
53022010 GGAAATGGTG
53022020 AATCTTATCTCCCTGATG-TTACAGTGGAGCAGATTGAAGCCAGA
1 AATCTTATCTCCCTGA-GATTACAGTGGAGCAGATTGAAGCCAGA
** * *
53022064 AATCTTATCTCCCTGAGATTACAACGGAGCAGATTGAAGCTAGT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGA
* * * *
53022108 AATCCTATCTCCATGAGATTACAGTGGAGCAGATT-AAACTA-A
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGA
* *
53022150 AGGATCTTATCTCTCT-AAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGA
1 A--ATCTTATCTCCCTGAGA-TTACAGT---G--GA--G---CAGATTGAAGCCAGA
* * *
53022206 AATCTTATCTCCCTGAGATTACAGCGGAGCTGATTGAAGCCAGT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGA
* * * *
53022250 AATCCTATTTCCCTAAGATTACAGTGGAGCGGATT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATT
53022285 AAAATAAAGG
Statistics
Matches: 178, Mismatches: 26, Indels: 34
0.75 0.11 0.14
Matches are distributed among these distances:
42 1 0.01
43 8 0.04
44 129 0.72
47 2 0.01
49 4 0.02
51 2 0.01
54 24 0.13
55 6 0.03
56 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.28
Consensus pattern (44 bp):
AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGA
Found at i:53022225 original size:142 final size:141
Alignment explanation
Indices: 53022049--53022334 Score: 482
Period size: 142 Copynumber: 2.0 Consensus size: 141
53022039 TACAGTGGAG
*
53022049 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAACGGAGCAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAACGGAGCAGATTGAAGCCAGTAATCCT
* *
53022114 ATCTCCATGAGATTACAGTGGAGCAGATTAAACTAAAGGATCTTATCTCTCTAAAGTTACAGTAG
66 ATCTCCATAAGATTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAG
53022179 AGTAGATCGCAT
131 A-TAGATCGCAT
* *
53022191 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCTGATTGAAGCCAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAACGGAGCAGATTGAAGCCAGTAATCCT
* * * *
53022256 ATTTCCCTAAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTATAGTAG
66 ATCTCCATAAGATTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAG
53022321 ATAGATCGCAT
131 ATAGATCGCAT
53022332 CAG
1 CAG
53022335 TTCTTATCTC
Statistics
Matches: 135, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
141 13 0.10
142 122 0.90
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (141 bp):
CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAACGGAGCAGATTGAAGCCAGTAATCCT
ATCTCCATAAGATTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAG
ATAGATCGCAT
Found at i:53022503 original size:49 final size:49
Alignment explanation
Indices: 53022411--53022584 Score: 145
Period size: 49 Copynumber: 3.6 Consensus size: 49
53022401 GCAGTGGAAC
* * * ** *
53022411 AGATTAAAGCCACAACGGTGAATCTTGCCTCCTTAACATTGCAGTTAAAA
1 AGATTAAAGCCACAACAGCGAATCTTACCTCC-CGACAGTGCAGTTAAAA
* * * ** *
53022461 AGATT-AAGCTACAACAGCGAATCTTACCTCCCAGGCGGTGCAGTGGAAC
1 AGATTAAAGCCACAACAGCGAATCTTACCTCCC-GACAGTGCAGTTAAAA
*** * * * *
53022510 AGATTAAAGCCACATTGGTG-ATCTTGCTTCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACAGCGAATCTTACCTCCCGACAGTGCAGTTAAAA
53022558 AGATTAAAGCCACAACAGCGAATCTTA
1 AGATTAAAGCCACAACAGCGAATCTTA
53022585 ATTCCTGGCG
Statistics
Matches: 91, Mismatches: 30, Indels: 7
0.71 0.23 0.05
Matches are distributed among these distances:
48 26 0.29
49 51 0.56
50 14 0.15
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (49 bp):
AGATTAAAGCCACAACAGCGAATCTTACCTCCCGACAGTGCAGTTAAAA
Found at i:53022660 original size:98 final size:99
Alignment explanation
Indices: 53022390--53022663 Score: 356
Period size: 98 Copynumber: 2.8 Consensus size: 99
53022380 GATCTTAGTT
* * *
53022390 TCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCCTCCTTAACATTGCAG
1 TCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACAATGGTGAATCTTGCTTCC-CAACATTGCAG
* *
53022455 TTAAAAAGATT-AAGCTACAACAGCGAATCTTACC
65 TTAAAAAGATTAAAGCCACAACAGCGAATCTTACA
* * *
53022489 TCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACATTGGTG-ATCTTGCTTCCCGACATTGCAGT
1 TCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACAATGGTGAATCTTGCTTCCCAACATTGCAGT
53022553 TAAAAAGATTAAAGCCACAACAGCGAATCTTA-A
66 TAAAAAGATTAAAGCCACAACAGCGAATCTTACA
* * * * * * **
53022586 TTCCTGGCGATGCAGTGGAACGGATTAAATCTACAATGGTGAATCTTGTTTCCCAACATCACAGT
1 TCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACAATGGTGAATCTTGCTTCCCAACATTGCAGT
**
53022651 TAAGTAGATTAAA
66 TAAAAAGATTAAA
53022664 ATTGCGAGTT
Statistics
Matches: 152, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
97 54 0.36
98 60 0.39
99 38 0.25
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (99 bp):
TCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACAATGGTGAATCTTGCTTCCCAACATTGCAGT
TAAAAAGATTAAAGCCACAACAGCGAATCTTACA
Found at i:53041145 original size:14 final size:14
Alignment explanation
Indices: 53041126--53041161 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
53041116 AAAACGTTTG
53041126 AATTTTGGTTCATA
1 AATTTTGGTTCATA
53041140 AATTTTGGTTCATA
1 AATTTTGGTTCATA
53041154 AATTTTGG
1 AATTTTGG
53041162 CATTCAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.28, C:0.06, G:0.17, T:0.50
Consensus pattern (14 bp):
AATTTTGGTTCATA
Found at i:53044091 original size:15 final size:15
Alignment explanation
Indices: 53044068--53044100 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
53044058 AAAAAATATG
*
53044068 TTTCTTTCTTTTTTC
1 TTTCCTTCTTTTTTC
53044083 TTTCCTTCTTTTTTC
1 TTTCCTTCTTTTTTC
53044098 TTT
1 TTT
53044101 ATTTATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTCCTTCTTTTTTC
Found at i:53053797 original size:14 final size:14
Alignment explanation
Indices: 53053778--53053813 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
53053768 GCTTTGAATG
53053778 CCAAAATTTATGAA
1 CCAAAATTTATGAA
53053792 CCAAAATTTATGAA
1 CCAAAATTTATGAA
53053806 CCAAAATT
1 CCAAAATT
53053814 CAAACGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.50, C:0.17, G:0.06, T:0.28
Consensus pattern (14 bp):
CCAAAATTTATGAA
Found at i:53060905 original size:46 final size:46
Alignment explanation
Indices: 53060855--53061027 Score: 174
Period size: 46 Copynumber: 3.7 Consensus size: 46
53060845 TGGTTGAGCA
*
53060855 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * * *
53060901 TCCGAGCTCGTTGAATTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* * *
53060948 TCCGAACTCGTTAAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
*
53060994 -CTCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TC-CGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
53061028 GGGGCGGGTT
Statistics
Matches: 101, Mismatches: 18, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
43 6 0.06
45 4 0.04
46 57 0.56
47 26 0.26
48 3 0.03
50 5 0.05
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:53061013 original size:93 final size:93
Alignment explanation
Indices: 53060852--53061022 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
53060842 GGATGGTTGA
* *
53060852 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAGCTCGTTGAAT
1 GCATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAGCTCGTTGAAT
53060917 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
53060945 GCATCCGAACTCGTTAAGTTGAGTCCGAGTTCATTTATGGATGCGAACG-CTCGAGCTCGTTGAG
1 GCATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTC-CGAGCTCGTTGAA
53061009 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
53061023 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 1 0.01
93 71 0.99
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAGCTCGTTGAAT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:53061580 original size:27 final size:27
Alignment explanation
Indices: 53061542--53061596 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
53061532 TGTGTAAATA
53061542 ATTTTATGATATGACCATGTTTGGTTG
1 ATTTTATGATATGACCATGTTTGGTTG
53061569 ATTTTATGATATGACCATGTTTGGTTG
1 ATTTTATGATATGACCATGTTTGGTTG
53061596 A
1 A
53061597 GAAAATGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.24, C:0.07, G:0.22, T:0.47
Consensus pattern (27 bp):
ATTTTATGATATGACCATGTTTGGTTG
Found at i:53066648 original size:40 final size:40
Alignment explanation
Indices: 53066550--53066812 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
53066540 TCCTCGTTCA
* * * * *
53066550 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
53066589 AATGCCTTCGGGACATAACCCGAATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
53066629 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
53066669 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
53066709 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
53066749 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
53066789 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
53066813 CAGCATTCAA
Statistics
Matches: 198, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
39 36 0.18
40 154 0.78
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Done.