Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold148
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: 1464219
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.32
Warning! 85296 characters in sequence are not A, C, G, or T
File 3 of 9
Found at i:318560 original size:13 final size:13
Alignment explanation
Indices: 318542--318566 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
318532 TTTTCCAGAT
318542 TGTATCGATACAA
1 TGTATCGATACAA
318555 TGTATCGATACA
1 TGTATCGATACA
318567 TTGCTTCAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:320132 original size:13 final size:13
Alignment explanation
Indices: 320114--320138 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
320104 ACACAAAGTA
320114 TGTATCGATACAT
1 TGTATCGATACAT
320127 TGTATCGATACA
1 TGTATCGATACA
320139 CCATAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:320135 original size:32 final size:33
Alignment explanation
Indices: 320094--320161 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
320084 GTAGCCAAAC
*
320094 TTGTATCGATACA-CA-AAGTATGTATCGATACA
1 TTGTATCGATACACCATAA-AATGTATCGATACA
320126 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCATAAAATGTATCGATACA
320159 TTG
1 TTG
320162 GCTTGTAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 13 0.39
33 18 0.55
34 2 0.06
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACACCATAAAATGTATCGATACA
Found at i:320660 original size:34 final size:35
Alignment explanation
Indices: 320597--320663 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
320587 CTAAGTGATT
320597 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
320633 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
320664 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:324037 original size:30 final size:29
Alignment explanation
Indices: 323967--324990 Score: 799
Period size: 28 Copynumber: 34.4 Consensus size: 29
323957 TATGCTAGTA
* *
323967 ACTTGGTGGGCTTTGAAAAAAGTTGCCACCG
1 ACTT-GTGGGCTTTGAAAAGAG-TGCCACTG
* *
323998 ACTCGTGTGGGCTTTGAAAAGAATTACCACTG
1 ACT--TGTGGGCTTTGAAAAG-AGTGCCACTG
* *
324030 GCTTGTGGGCTTTGAAAAGAATGCCACTG
1 ACTTGTGGGCTTTGAAAAGAGTGCCACTG
* *
324059 ACTTGTGGGTTTTG-AAAGGGTGCCACTG
1 ACTTGTGGGCTTTGAAAAGAGTGCCACTG
*
324087 ACTTGTGGGCTTTGAAAAGA-TGCCACTA
1 ACTTGTGGGCTTTGAAAAGAGTGCCACTG
* *
324115 ACTTGTGGGCTTTGAAAAGAGTGTCATTG
1 ACTTGTGGGCTTTGAAAAGAGTGCCACTG
* *
324144 ACTTGTGGGCTTTG-AAAGGGTGCCACTA
1 ACTTGTGGGCTTTGAAAAGAGTGCCACTG
*
324172 ACTTGTGGGCTTTGAAAAGAGTGCTACTG
1 ACTTGTGGGCTTTGAAAAGAGTGCCACTG
* *
324201 ACTTGCGTGGGCTTTG-AAAGGGTGCCACTA
1 ACTT--GTGGGCTTTGAAAAGAGTGCCACTG
*
324231 ACTTGCGTGGGCTTTG-AAAGGGTGCCACTG
1 ACTT--GTGGGCTTTGAAAAGAGTGCCACTG
324261 ACTTGTGGGCTTTG-AAAGAGTGCCACTG
1 ACTTGTGGGCTTTGAAAAGAGTGCCACTG
* *
324289 ACTTGTGGGCTTTG-AAAGGGTGCCACTA
1 ACTTGTGGGCTTTGAAAAGAGTGCCACTG
* *
324317 ACTGGTGAGCTTTG-AAAGAGTGCCACTG
1 ACTTGTGGGCTTTGAAAAGAGTGCCACTG
** * *
324345 ACTCATGGGCTTTGAAAGGA-TGCCACTA
1 ACTTGTGGGCTTTGAAAAGAGTGCCACTG
*
324373 ACTTGTGGGCTTTGAAAAGAGTTGCCACAG
1 ACTTGTGGGCTTTGAAAAGAG-TGCCACTG
* *
324403 ACTCGTAGGCTTTGAAAAGA-TGCCACTG
1 ACTTGTGGGCTTTGAAAAGAGTGCCACTG
*
324431 ACTTG-GGGCTTTGAAAAGAGTTGCCACCG
1 ACTTGTGGGCTTTGAAAAGAG-TGCCACTG
* *
324460 ACTCGTGGGCTTTGAAAGGA-TGCCACTG
1 ACTTGTGGGCTTTGAAAAGAGTGCCACTG
* *
324488 ACTTGTGGCCTTTGAAAAGAGTTGCCACCG
1 ACTTGTGGGCTTTGAAAAGAG-TGCCACTG
324518 ACTGATGTGGGCTTTGAAAAGA-TGCCACTG
1 ACT--TGTGGGCTTTGAAAAGAGTGCCACTG
* * **
324548 ACTTATGGGCTTTGGAATAG-GTTGCCACCA
1 ACTTGTGGGCTTT-GAAAAGAG-TGCCACTG
* * *
324578 ACTTGTGTGGGCTTTCAAATGAGTTGCCACCG
1 AC-T-TGTGGGCTTTGAAAAGAG-TGCCACTG
* **
324610 ATTTGTGTGGGCTTTGAAGTGA-TGCCACTG
1 A-CT-TGTGGGCTTTGAAAAGAGTGCCACTG
* * **
324640 ACTTTTGTGGGCTTTGAAATGGGTTGCCACCA
1 AC--TTGTGGGCTTTGAAAAGAG-TGCCACTG
* * * *
324672 ACTTGTATAGGCTTTCAAATGAGTTGCCACCG
1 ACTTG--TGGGCTTTGAAAAGAG-TGCCACTG
* *
324704 ATTTGTGTGGGCTTTGAAATGA-TGCCACTG
1 A-CT-TGTGGGCTTTGAAAAGAGTGCCACTG
*
324734 ACTTGTGGGCTTTGAAATGA-TGCCACTG
1 ACTTGTGGGCTTTGAAAAGAGTGCCACTG
* * * * **
324762 TCTTGTGGGCTTTGAAATGGGTTACCACCA
1 ACTTGTGGGCTTTGAAAAGAG-TGCCACTG
* * * *
324792 ACTTGTTTAGGCTTTGAAATGGGTTGCCACCG
1 ACTTG--TGGGCTTTGAAAAGAG-TGCCACTG
* * * *
324824 ACTTGTGTGGGCTTTCAAATGAGTTTCCACCG
1 AC-T-TGTGGGCTTTGAAAAGAG-TGCCACTG
* * **
324856 ACTTGTGTGGGCTTTGAAATGGGTTGCCACCA
1 AC-T-TGTGGGCTTTGAAAAGAG-TGCCACTG
* * * * *
324888 ACTTGTGTGGGCTTTCAAATGAGTTACTACCG
1 AC-T-TGTGGGCTTTGAAAAGAG-TGCCACTG
*
324920 ACTTGTGTGGGCTTTGAAATGA-TGCCACTG
1 AC-T-TGTGGGCTTTGAAAAGAGTGCCACTG
* *
324950 ACTTGTGGGCTTTGAAATGA-TGCCACTA
1 ACTTGTGGGCTTTGAAAAGAGTGCCACTG
324978 ACTTGTGGGCTTT
1 ACTTGTGGGCTTT
324991 AGAAGGGTGC
Statistics
Matches: 840, Mismatches: 114, Indels: 81
0.81 0.11 0.08
Matches are distributed among these distances:
27 13 0.02
28 308 0.37
29 80 0.10
30 175 0.21
31 18 0.02
32 238 0.28
33 4 0.00
34 4 0.00
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.30
Consensus pattern (29 bp):
ACTTGTGGGCTTTGAAAAGAGTGCCACTG
Found at i:324085 original size:28 final size:28
Alignment explanation
Indices: 324024--325280 Score: 727
Period size: 28 Copynumber: 43.1 Consensus size: 28
324014 AAAAGAATTA
* **
324024 CCACTGGCTTGTGGGCTTTGAAAAGAATG
1 CCACTGACTTGTGGGCTTTG-AAAGGGTG
*
324053 CCACTGACTTGTGGGTTTTGAAAGGGTG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* *
324081 CCACTGACTTGTGGGCTTTGAAAAGATG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* *
324109 CCACTAACTTGTGGGCTTTGAAAAGAGTG
1 CCACTGACTTGTGGGCTTTG-AAAGGGTG
* *
324138 TCATTGACTTGTGGGCTTTGAAAGGGTG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* *
324166 CCACTAACTTGTGGGCTTTGAAAAGAGTG
1 CCACTGACTTGTGGGCTTTG-AAAGGGTG
*
324195 CTACTGACTTGCGTGGGCTTTGAAAGGGTG
1 CCACTGACTT--GTGGGCTTTGAAAGGGTG
*
324225 CCACTAACTTGCGTGGGCTTTGAAAGGGTG
1 CCACTGACTT--GTGGGCTTTGAAAGGGTG
*
324255 CCACTGACTTGTGGGCTTTGAAAGAGTG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
324283 CCACTGACTTGTGGGCTTTGAAAGGGTG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* * * *
324311 CCACTAACTGGTGAGCTTTGAAAGAGTG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
** *
324339 CCACTGACTCATGGGCTTTGAAAGGATG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* *
324367 CCACTAACTTGTGGGCTTTGAAAAGAGTTG
1 CCACTGACTTGTGGGCTTTG-AAAG-GGTG
* * * * *
324397 CCACAGACTCGTAGGCTTTGAAAAGATG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
*
324425 CCACTGACTTG-GGGCTTTGAAAAGAGTTG
1 CCACTGACTTGTGGGCTTTG-AAAG-GGTG
* * *
324454 CCACCGACTCGTGGGCTTTGAAAGGATG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* *
324482 CCACTGACTTGTGGCCTTTGAAAAGAGTTG
1 CCACTGACTTGTGGGCTTTG-AAAG-GGTG
* * *
324512 CCACCGACTGATGTGGGCTTTGAAAAGATG
1 CCACTGACT--TGTGGGCTTTGAAAGGGTG
* *
324542 CCACTGACTTATGGGCTTTGGAATAGGTTG
1 CCACTGACTTGTGGGCTTT-GAA-AGGGTG
** * *
324572 CCACCAACTTGTGTGGGCTTTCAAATGAGTTG
1 CCACTGAC-T-TGTGGGCTTTGAAA-G-GGTG
* * *
324604 CCACCGATTTGTGTGGGCTTTG-AAGTGATG
1 CCACTGA-CT-TGTGGGCTTTGAAAG-GGTG
324634 CCACTGACTTTTGTGGGCTTTGAAATGGGTTG
1 CCACTGAC--TTGTGGGCTTTGAAA-GGG-TG
** * * *
324666 CCACCAACTTGTATAGGCTTTCAAATGAGTTG
1 CCACTGACTTG--TGGGCTTTGAAA-G-GGTG
* * * *
324698 CCACCGATTTGTGTGGGCTTTGAAATGATG
1 CCACTGA-CT-TGTGGGCTTTGAAAGGGTG
* *
324728 CCACTGACTTGTGGGCTTTGAAATGATG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* *
324756 CCACTGTCTTGTGGGCTTTGAAATGGGTTA
1 CCACTGACTTGTGGGCTTTGAAA-GGG-TG
** *
324786 CCACCAACTTGTTTAGGCTTTGAAATGGGTTG
1 CCACTGACTTG--TGGGCTTTGAAA-GGG-TG
* * * *
324818 CCACCGACTTGTGTGGGCTTTCAAATGAGTTT
1 CCACTGAC-T-TGTGGGCTTTGAAA-G-GGTG
*
324850 CCACCGACTTGTGTGGGCTTTGAAATGGGTTG
1 CCACTGAC-T-TGTGGGCTTTGAAA-GGG-TG
** * * *
324882 CCACCAACTTGTGTGGGCTTTCAAATGAGTTA
1 CCACTGAC-T-TGTGGGCTTTGAAA-G-GGTG
* * * *
324914 CTACCGACTTGTGTGGGCTTTGAAATGATG
1 CCACTGAC-T-TGTGGGCTTTGAAAGGGTG
* *
324944 CCACTGACTTGTGGGCTTTGAAATGATG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* *
324972 CCACTAACTTGTGGGCTTTAGAAGGGTGCTG
1 CCACTGACTTGTGGGCTTT-GAAAGG-G-TG
* * * * *
325003 CCACGGAGTTGTGGAC-TTAAAAGGATG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* * * * *
325030 CCACAGAGTTGTGGAC-TTAAAAGGATG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* * * * * *
325057 CCACGGAGTTGTGGAC-TTAAAAGGATA
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* * * * *
325084 CCACAGAGTTGTGGAC-TTAAAAGTGT-
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* * * * * *
325110 CCACGGAGTGGTGGACTTTAAAAGAGTG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* * * *
325138 CCA-TGAAGTTGTGGACTTTAAAAGGATG
1 CCACTG-ACTTGTGGGCTTTGAAAGGGTG
* **
325166 CCAC-GAAGTTGTGAACTTT-AATAGGGTG
1 CCACTG-ACTTGTGGGCTTTGAA-AGGGTG
* * * * *
325194 CCACGGAGTTGTGGACTTTAAAAGGATG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* * * * *
325222 CCACAGAGTTGTGGAC-TTAAAAGGATG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
* * * * *
325249 CCACGGAGTGGTGGACTTTAAAAGGGTG
1 CCACTGACTTGTGGGCTTTGAAAGGGTG
325277 CCAC
1 CCAC
325281 GAAGTTATGG
Statistics
Matches: 1025, Mismatches: 153, Indels: 101
0.80 0.12 0.08
Matches are distributed among these distances:
26 14 0.01
27 120 0.12
28 397 0.39
29 99 0.10
30 156 0.15
31 38 0.04
32 192 0.19
33 5 0.00
34 4 0.00
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.29
Consensus pattern (28 bp):
CCACTGACTTGTGGGCTTTGAAAGGGTG
Found at i:324095 original size:57 final size:57
Alignment explanation
Indices: 323967--324990 Score: 743
Period size: 57 Copynumber: 17.2 Consensus size: 57
323957 TATGCTAGTA
* * ** *
323967 ACTTGGTGGGCTTTGAAAAAAGTTGCCACCGACTCGTGTGGGCTTTGAAAAGAATTACCACTG
1 ACTT-GTGGGCTTTGAAAAGA-TTGCCACTGACT--TGTGGGCTTTG-AAAG-GGTGCCACTG
* * *
324030 GCTTGTGGGCTTTGAAAAGAATGCCACTGACTTGTGGGTTTTGAAAGGGTGCCACTG
1 ACTTGTGGGCTTTGAAAAGATTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTG
* * * *
324087 ACTTGTGGGCTTTGAAAAGA-TGCCACTAACTTGTGGGCTTTGAAAAGAGTGTCATTG
1 ACTTGTGGGCTTTGAAAAGATTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTG
** * * *
324144 ACTTGTGGGCTTTG-AAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCTACTG
1 ACTTGTGGGCTTTGAAAAGATTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTG
** *
324201 ACTTGCGTGGGCTTTG-AAAGGGTGCCACTAACTTGCGTGGGCTTTGAAAGGGTGCCACTG
1 ACTT--GTGGGCTTTGAAAAGATTGCCACTGACTT--GTGGGCTTTGAAAGGGTGCCACTG
* *
324261 ACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTA
1 ACTTGTGGGCTTTGAAAAGATTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTG
* * * ** * *
324317 ACTGGTGAGCTTTG-AAAGAGTGCCACTGACTCATGGGCTTTGAAAGGATGCCACTA
1 ACTTGTGGGCTTTGAAAAGATTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTG
* * * * *
324373 ACTTGTGGGCTTTGAAAAGAGTTGCCACAGACTCGTAGGCTTTGAAAAGATGCCACTG
1 ACTTGTGGGCTTTGAAAAGA-TTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTG
* * *
324431 ACTTG-GGGCTTTGAAAAGAGTTGCCACCGACTCGTGGGCTTTGAAAGGATGCCACTG
1 ACTTGTGGGCTTTGAAAAGA-TTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTG
* * * *
324488 ACTTGTGGCCTTTGAAAAGAGTTGCCACCGACTGATGTGGGCTTTGAAAAGATGCCACTG
1 ACTTGTGGGCTTTGAAAAGA-TTGCCACTGACT--TGTGGGCTTTGAAAGGGTGCCACTG
* * * ** * * *
324548 ACTTATGGGCTTTGGAATAGGTTGCCACCAACTTGTGTGGGCTTTCAAATGAGTTGCCACCG
1 ACTTGTGGGCTTT-GAAAAGATTGCCACTGAC-T-TGTGGGCTTTGAAA-G-GGTGCCACTG
* ** **
324610 ATTTGTGTGGGCTTTGAAGTGA-TGCCACTGACTTTTGTGGGCTTTGAAATGGGTTGCCACCA
1 A-CT-TGTGGGCTTTGAAAAGATTGCCACTGAC--TTGTGGGCTTTGAAA-GGG-TGCCACTG
* * * * * * *
324672 ACTTGTATAGGCTTTCAAATGAGTTGCCACCGATTTGTGTGGGCTTTGAAATGATGCCACTG
1 ACTTG--TGGGCTTTGAAAAGA-TTGCCACTGA-CT-TGTGGGCTTTGAAAGGGTGCCACTG
* * * **
324734 ACTTGTGGGCTTTGAAATGA-TGCCACTGTCTTGTGGGCTTTGAAATGGGTTACCACCA
1 ACTTGTGGGCTTTGAAAAGATTGCCACTGACTTGTGGGCTTTGAAA-GGG-TGCCACTG
* * * * * * * *
324792 ACTTGTTTAGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTCAAATGAGTTTCCACCG
1 ACTTG--TGGGCTTTGAAA-AGATTGCCACTGAC-T-TGTGGGCTTTGAAA-G-GGTGCCACTG
* * ** * * * * *
324856 ACTTGTGTGGGCTTTGAAATGGGTTGCCACCAACTTGTGTGGGCTTTCAAATGAGTTACTACCG
1 AC-T-TGTGGGCTTTGAAA-AGATTGCCACTGAC-T-TGTGGGCTTTGAAA-G-GGTGCCACTG
* * * *
324920 ACTTGTGTGGGCTTTGAAATGA-TGCCACTGACTTGTGGGCTTTGAAATGATGCCACTA
1 AC-T-TGTGGGCTTTGAAAAGATTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTG
324978 ACTTGTGGGCTTT
1 ACTTGTGGGCTTT
324991 AGAAGGGTGC
Statistics
Matches: 819, Mismatches: 106, Indels: 79
0.82 0.11 0.08
Matches are distributed among these distances:
56 134 0.16
57 151 0.18
58 116 0.14
59 38 0.05
60 112 0.14
61 30 0.04
62 94 0.11
63 14 0.02
64 126 0.15
65 2 0.00
66 2 0.00
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.30
Consensus pattern (57 bp):
ACTTGTGGGCTTTGAAAAGATTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTG
Found at i:324648 original size:64 final size:63
Alignment explanation
Indices: 324570--324969 Score: 389
Period size: 64 Copynumber: 6.5 Consensus size: 63
324560 TGGAATAGGT
* * *
324570 TGCCACCAAC-TTGTGTGGGCTTTCAAATGAGTTGCCACCGATTTGTGTGGGCTTTGAAGTGA
1 TGCCACCGACTTTGTGTGGGCTTTCAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGA
* * * * * * *
324632 TGCCACTGACTTT-TGTGGGCTTTGAAATGGGTTGCCACCAACTTGTATAGGCTTTCAAATGA
1 TGCCACCGACTTTGTGTGGGCTTTCAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGA
* *
324694 GTTGCCACCGA-TTTGTGTGGGCTTTGAAATGA--TGCCACTGAC-T-TGTGGGCTTTGAAATGA
1 --TGCCACCGACTTTGTGTGGGCTTTCAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGA
* * * * * * * * *
324754 TGCCACTG--TCT-TGTGGGCTTTGAAATGGGTTACCACCAACTTGTTTAGGCTTTGAAATGGGT
1 TGCCACCGACTTTGTGTGGGCTTTCAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAAT--GA
* *
324816 TGCCACCGAC-TTGTGTGGGCTTTCAAATGAGTTTCCACCGACTTGTGTGGGCTTTGAAATGGGT
1 TGCCACCGACTTTGTGTGGGCTTTCAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAAT--GA
* * *
324880 TGCCACCAAC-TTGTGTGGGCTTTCAAATGAGTTACTACCGACTTGTGTGGGCTTTGAAATGA
1 TGCCACCGACTTTGTGTGGGCTTTCAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGA
* *
324942 TGCCACTGAC--T-TGTGGGCTTTGAAATGA
1 TGCCACCGACTTTGTGTGGGCTTTCAAATGA
324970 TGCCACTAAC
Statistics
Matches: 284, Mismatches: 41, Indels: 28
0.80 0.12 0.08
Matches are distributed among these distances:
56 16 0.06
57 2 0.01
58 14 0.05
59 1 0.00
60 43 0.15
61 2 0.01
62 74 0.26
63 6 0.02
64 126 0.44
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (63 bp):
TGCCACCGACTTTGTGTGGGCTTTCAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGA
Found at i:324941 original size:216 final size:206
Alignment explanation
Indices: 323966--324998 Score: 983
Period size: 216 Copynumber: 5.0 Consensus size: 206
323956 ATATGCTAGT
* * * * * *
323966 AACTTGGTGGGCTTTGAAAAAAGTTGCCACCGACTCGTGTGGGCTTTGAAAAGAATTACCACTGG
1 AACTT-GTGGGCTTTGAAAAGAGTTGCCACCGACTTGCGTGGGCTTTG-AAAG-AGTGCCACTGA
* ** ** * * * *
324031 C-T-TGTGGGCTTTGAAA-AGAATGCCACTGACTTGTGGGTTTTGAAAG-GGTGCCACTGACTTG
63 CTTGTGTGGGCTTTGAAATGGGTTGCCACCAACTTGTGGGCTTTCAAAGAGTTGCCACCGACTTG
* * *
324092 TGGGCTTTGAAAAGATGCCACTAACTTGTGGGCTTTGAAAAGAGTGTCATTGACTTGTGGGCTTT
128 TGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGA-TGCCACTGACTTGTGGGCTTT
*
324157 GAAAGGG-TGCCACT
192 GAAAGGGTTGCCACC
* * * *
324171 AACTTGTGGGCTTTGAAAAGAG-TGCTACTGACTTGCGTGGGCTTTGAAAGGGTGCCACTAACTT
1 AACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTTGCGTGGGCTTTGAAAGAGTGCCACTGACTT
* ** * *
324235 GCGTGGGCTTTGAAA-GGG-TGCCACTGACTTGTGGGCTTTGAAAGAG-TGCCACTGACTTGTGG
66 GTGTGGGCTTTGAAATGGGTTGCCACCAACTTGTGGGCTTTCAAAGAGTTGCCACCGACTTGTGG
* * * * * **
324297 GCTTTGAAAGGGTGCCACTAACTGGTGAGCTTTG-AAAGAGTGCCACTGACTCATGGGCTTTGAA
131 GCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGA-TGCCACTGACTTGTGGGCTTTGAA
* *
324361 A-GGATGCCACT
195 AGGGTTGCCACC
* *
324372 AACTTGTGGGCTTTGAAAAGAGTTGCCACAGAC-T-CGTAGGCTTTGAAA-AGATGCCACTGAC-
1 AACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTTGCGTGGGCTTTGAAAGAG-TGCCACTGACT
* * * * * * *
324433 T-TG-GGGCTTTGAAAAGAGTTGCCACCGACTCGTGGGCTTTGAAAG-GATGCCACTGACTTGTG
65 TGTGTGGGCTTTGAAATGGGTTGCCACCAACTTGTGGGCTTTCAAAGAGTTGCCACCGACTTGTG
* * *
324495 GCCTTTGAAAAGAGTTGCCACCGACTGATGTGGGCTTTGAAAAGATGCCACTGACTTATGGGCTT
130 GGCTTTGAAAAGA--TGCCACTGACT--TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTT
324560 TGGAATA-GGTTGCCACC
191 T-GAA-AGGGTTGCCACC
* * * * *
324577 AACTTGTGTGGGCTTTCAAATGAGTTGCCACCGATTTGTGTGGGCTTTG-AAGTGATGCCACTGA
1 AAC-T-TGTGGGCTTTGAAAAGAGTTGCCACCGACTTGCGTGGGCTTTGAAAGAG-TGCCACTGA
* *
324641 CTTTTGTGGGCTTTGAAATGGGTTGCCACCAACTTGTATAGGCTTTCAAATGAGTTGCCACCGAT
63 CTTGTGTGGGCTTTGAAATGGGTTGCCACCAACTTG--TGGGCTTTCAAA-GAGTTGCCACCGA-
* * * *
324706 TTGTGTGGGCTTTGAAATGATGCCACTGACTTGTGGGCTTTGAAATGATGCCACTGTCTTGTGGG
124 CT-TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGG
*
324771 CTTTGAAATGGGTTACCACC
188 CTTTGAAA-GGGTTGCCACC
* * * * * * *
324791 AACTTGTTTAGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTCAAATGAGTTTCCACCG
1 AACTTG--TGGGCTTTGAAAAGAGTTGCCACCGACTTGCGTGGGCTTTGAAA-GAG-TGCCACTG
* *
324856 ACTTGTGTGGGCTTTGAAATGGGTTGCCACCAACTTGTGTGGGCTTTCAAATGAGTTACTACCGA
62 ACTTGTGTGGGCTTTGAAATGGGTTGCCACCAAC-T-TGTGGGCTTTCAAA-GAGTTGCCACCGA
* * *
324921 CTTGTGTGGGCTTTGAAATGATGCCACTGACTTGTGGGCTTTGAAATGATGCCACTAACTTGTGG
124 C-T-TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGG
324986 GCTTT-AGAAGGGT
187 GCTTTGA-AAGGGT
324999 GCTGCCACGG
Statistics
Matches: 708, Mismatches: 80, Indels: 70
0.83 0.09 0.08
Matches are distributed among these distances:
197 11 0.02
198 4 0.01
199 51 0.07
200 24 0.03
201 73 0.10
202 84 0.12
203 64 0.09
204 24 0.03
205 17 0.02
206 1 0.00
207 25 0.04
208 3 0.00
209 21 0.03
210 1 0.00
211 2 0.00
212 28 0.04
213 4 0.01
214 93 0.13
215 8 0.01
216 151 0.21
217 2 0.00
218 17 0.02
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.30
Consensus pattern (206 bp):
AACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTTGCGTGGGCTTTGAAAGAGTGCCACTGACTT
GTGTGGGCTTTGAAATGGGTTGCCACCAACTTGTGGGCTTTCAAAGAGTTGCCACCGACTTGTGG
GCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAA
GGGTTGCCACC
Found at i:325039 original size:27 final size:27
Alignment explanation
Indices: 325001--325678 Score: 763
Period size: 27 Copynumber: 24.7 Consensus size: 27
324991 AGAAGGGTGC
325001 TGCCACGGAGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGA
*
325028 TGCCACAGAGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGA
325055 TGCCACGGAGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGA
* *
325082 TACCACAGAGTTGTGGACTTAAAA-G-
1 TGCCACGGAGTTGTGGACTTAAAAGGA
*
325107 TGTCCACGGAGTGGTGGACTTTAAAA-GA
1 TG-CCACGGAGTTGTGGAC-TTAAAAGGA
* *
325135 GTGCCATGAAGTTGTGGACTTTAAAAGGA
1 -TGCCACGGAGTTGTGGAC-TTAAAAGGA
* * * *
325164 TGCCACGAAGTTGTGAACTTTAATAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGA
325192 TGCCACGGAGTTGTGGACTTTAAAAGGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGA
*
325220 TGCCACAGAGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGA
* *
325247 TGCCACGGAGTGGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGA
* * * * *
325275 TGCCACGAAGTTATGGATTTTAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGA
* *
325302 TGCCACGGAGTTATAGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGA
* * *
325329 TTCCACGGAGTTATGGACATAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGA
* * * *
325356 TGTCACGAAGTTGTGGATTTTAAAAGGG
1 TGCCACGGAGTTGTGGA-CTTAAAAGGA
325384 TGCCACAGG-GTTGTGGACTTTAAAAGGA
1 TGCCAC-GGAGTTGTGGAC-TTAAAAGGA
*
325412 TGCCACGGAGTTGTGGACTTAAAATGA
1 TGCCACGGAGTTGTGGACTTAAAAGGA
* ** * *
325439 TGACACAAAGTGGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGA
* *
325467 TGCCACAGAGTTGTGGACCTT-AAAGGG
1 TGCCACGGAGTTGTGGA-CTTAAAAGGA
*
325494 TGCCACGAAGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGA
* * *
325521 TGCCATGGAGTTATGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGA
325549 TGCCACGGAGTTGTGGACTTTAAAAGGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGA
* *
325577 TGCCATGGAGTTGTGAACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGA
* * *
325604 TGCCATGAAGTTGTGGACTTTGAAAGGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGA
* *
325632 TGCCATGGAGTTGTGAACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGA
*
325659 TGCCACGAAGTTGTGGACTT
1 TGCCACGGAGTTGTGGACTT
325679 TGAAATGAAA
Statistics
Matches: 559, Mismatches: 77, Indels: 30
0.84 0.12 0.05
Matches are distributed among these distances:
25 1 0.00
26 18 0.03
27 288 0.52
28 246 0.44
29 6 0.01
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.25
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGACTTAAAAGGA
Found at i:325326 original size:165 final size:165
Alignment explanation
Indices: 325001--325678 Score: 857
Period size: 165 Copynumber: 4.1 Consensus size: 165
324991 AGAAGGGTGC
* * *
325001 TGCCACGGAGTTGTGGACTTAAAAGGATGCCACAGAGTTGTGGAC-TTAAAAGGATGCCACGGAG
1 TGCCACGAAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACAGAG
* * *
325065 TTGTGGAC-TTAAAAGGATACCACAGAGTTGTGGACTTAAAA-G-TGTCCACGGAGTGGTGGACT
66 TTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGATG-CCACGAAGTGGTGGACT
* * *
325127 TTAAAAGAGTGCCATGAAGTTGTGGACTTTAAAAGGA
130 TTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGA
* * *
325164 TGCCACGAAGTTGTGAACTTTAATAGGGTGCCACGGAGTTGTGGACTTTAAAAGGATGCCACAGA
1 TGCCACGAAGTTGTGGAC-TTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACAGA
* * **
325229 GTTGTGGAC-TTAAAAGGATGCCACGGAGTGGTGGACTTTAAAAGGGTGCCACGAAGTTATGGA-
65 GTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGATGCCACGAAGTGGTGGAC
* * *
325292 TTTTAAAGGGTGCCACGGAGTTATAGACTTAAAAGGA
129 TTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGA
* * * * * * * * *
325329 TTCCACGGAGTTATGGACATAAAAGGATGTCACGAAGTTGTGGATTTTAAAAGGGTGCCACAGGG
1 TGCCACGAAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACAGAG
* * *
325394 TTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTAAAATGATGACACAAAGTGGTGGACTT
66 TTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGATGCCACGAAGTGGTGGACTT
* *
325459 TAAAAGGGTGCCACAGAGTTGTGGACCTT-AAAGGG
131 TAAAAGGGTGCCACGGAGTTGTGGA-CTTAAAAGGA
* * * *
325494 TGCCACGAAGTTGTGGACTTAAAAGGATGCCATGGAGTTATGGACTTTAAAAGGGTGCCACGGAG
1 TGCCACGAAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACAGAG
* * * *
325559 TTGTGGACTTTAAAAGGATGCCATGGAGTTGTGAACTTAAAAGGATGCCATGAAGTTGTGGACTT
66 TTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGATGCCACGAAGTGGTGGACTT
* * * *
325624 TGAAAGGATGCCATGGAGTTGTGAACTTAAAAGGA
131 TAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGA
325659 TGCCACGAAGTTGTGGACTT
1 TGCCACGAAGTTGTGGACTT
325679 TGAAATGAAA
Statistics
Matches: 440, Mismatches: 66, Indels: 16
0.84 0.13 0.03
Matches are distributed among these distances:
163 16 0.04
164 94 0.21
165 284 0.65
166 31 0.07
167 13 0.03
168 2 0.00
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.25
Consensus pattern (165 bp):
TGCCACGAAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACAGAG
TTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGATGCCACGAAGTGGTGGACTT
TAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGA
Found at i:325354 original size:192 final size:191
Alignment explanation
Indices: 324959--325679 Score: 880
Period size: 192 Copynumber: 3.7 Consensus size: 191
324949 GACTTGTGGG
* * * * * *
324959 CTTTGAAATGATGCCACTAACTTGTGGGCTTTAGAAGGGTGCTGCCACGGAGTTGTGGACTTAAA
1 CTTTAAAAGGATGCCACGAAGTTGTGGACTTTA-AAAGG-G-TGCCACGGAGTTGTGGACTTAAA
* *
325024 AGGATGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGATACCACA
63 AGGATGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTGGTGGACTTAAAAGGATGCCACA
* * * * *
325089 GAGTTGTGGACTTAAAAGTGT-CCACGGAGTGGTGGACTTTAAAA-GAGTGCCATGAAGTTGTGG
128 GAGTTGTGGACTTTAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGA-TGCCATGGAGTTATGG
325152 A
191 A
* *
325153 CTTTAAAAGGATGCCACGAAGTTGTGAACTTTAATAGGGTGCCACGGAGTTGTGGACTTTAAAAG
1 CTTTAAAAGGATGCCACGAAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAG
*
325218 GATGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTGGTGGACTTTAAAAGGGTGCCAC-G
65 GATGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTGGTGGAC-TTAAAAGGATGCCACAG
* * * * * *
325282 AAGTTATGGATTTTAAAGGGTGCCACGGAGTTATAGACTTAAAAGGATTCCACGGAGTTATGGA
129 -AGTTGTGGACTTTAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCATGGAGTTATGGA
* * *
325346 C-ATAAAAGGATGTCACGAAGTTGTGGATTTTAAAAGGGTGCCACAGG-GTTGTGGACTTTAAAA
1 CTTTAAAAGGATGCCACGAAGTTGTGGACTTTAAAAGGGTGCCAC-GGAGTTGTGGAC-TTAAAA
* * * ** *
325409 GGATGCCACGGAGTTGTGGACTTAAAATGATGACACAAAGTGGTGGACTTTAAAAGGGTGCCACA
64 GGATGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTGGTGGAC-TTAAAAGGATGCCACA
* *
325474 GAGTTGTGGACCTTAAAGGGTGCCACGAAGTTGTGGACTTAAAAGGATGCCATGGAGTTATGGA
128 GAGTTGTGGACTTTAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCATGGAGTTATGGA
* * * * *
325538 CTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGATGCCATGGAGTTGTGAACTTAAAAGG
1 CTTTAAAAGGATGCCACGAAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGG
* * * * *
325603 ATGCCA-TGAAGTTGTGGACTTTGAAAGGATGCCATGGAGTTGTGAACTTAAAAGGATGCCAC-G
66 ATGCCACAG-AGTTGTGGAC-TTAAAAGGATGCCACGGAGTGGTGGACTTAAAAGGATGCCACAG
325666 AAGTTGTGGACTTT
129 -AGTTGTGGACTTT
325680 GAAATGAAAT
Statistics
Matches: 456, Mismatches: 59, Indels: 26
0.84 0.11 0.05
Matches are distributed among these distances:
191 20 0.04
192 276 0.61
193 118 0.26
194 42 0.09
ACGTcount: A:0.30, C:0.14, G:0.31, T:0.26
Consensus pattern (191 bp):
CTTTAAAAGGATGCCACGAAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGG
ATGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTGGTGGACTTAAAAGGATGCCACAGAG
TTGTGGACTTTAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCATGGAGTTATGGA
Found at i:334107 original size:20 final size:20
Alignment explanation
Indices: 334082--334158 Score: 95
Period size: 20 Copynumber: 3.9 Consensus size: 20
334072 GTAAAAAGAC
*
334082 AGAATGTATCGATATATTGA
1 AGAATGTATCGATACATTGA
*
334102 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
*
334122 TACG--TGTATTGATACATTGA
1 -A-GAATGTATCGATACATTGA
334142 AGAATGTATCGATACAT
1 AGAATGTATCGATACAT
334159 CTGGGTATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
18 1 0.02
19 1 0.02
20 44 0.92
21 1 0.02
22 1 0.02
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:335375 original size:42 final size:41
Alignment explanation
Indices: 335319--336133 Score: 316
Period size: 42 Copynumber: 19.4 Consensus size: 41
335309 GCTTGTCAGT
* *
335319 TTTGACTCTGGAGACTGCCTCATCTAAAGTGTGCCTGTCAGC
1 TTTGACCCTGGAGACTGCCTCATCTAAAGTCTGCCTGTC-GC
* * *
335361 TTTGACTCTAGAGACTGCCTCATCTAAAGTCTGCTTGTCGAC
1 TTTGACCCTGGAGACTGCCTCATCTAAAGTCTGCCTGTCG-C
* ** *
335403 TTTGACCC-GGAGACTTTCCTC-TCTTCAGTTTGCCTGTCGGC
1 TTTGACCCTGGAGAC-TGCCTCATCTAAAGTCTGCCTGTC-GC
* * * * ** * *
335444 TTTGACCCTAGAGATTTTCCT-ACCCTTCAGTCTACCTGTTGGC
1 TTTGACCCTGGAGA-CTGCCTCA-TCTAAAGTCTGCCTG-TCGC
* * *
335487 TTTGACCTTGGAGATTGCCTCATCTAAAGTTTGCCTGTCGAC
1 TTTGACCCTGGAGACTGCCTCATCTAAAGTCTGCCTGTCG-C
* * ** * *
335529 TTTGACCCTGGAGACTTTCCT-TTCTTTAGTTTGTCTGTCGAC
1 TTTGACCCTGGAGAC-TGCCTCATCTAAAGTCTGCCTGTCG-C
* *
335571 TTTGACCCTAGAGACTGTCTCATCTAAAGTCTGCCTGTCGGC
1 TTTGACCCTGGAGACTGCCTCATCTAAAGTCTGCCTGTC-GC
* * ** * * * *
335613 TTTGACCTTGGAGACTTTCCT-ATCTTTCAGTCTACCTATTAGT
1 TTTGACCCTGGAGAC-TGCCTCATC-TAAAGTCTGCCT-GTCGC
* * * * ** *
335656 TTTGACCCTAGAGACTTTCTTTAT-TTCAGTCTACCTGTCAGC
1 TTTGACCCTGGAGAC-TGCCTCATCTAAAGTCTGCCTGTC-GC
* * **
335698 TTTGACCCTGGAAACT--TTCATTCCTTTAGTCTGCCTGTCAGC
1 TTTGACCCTGGAGACTGCCTCA-T-CTAAAGTCTGCCTGTC-GC
* * * ** *
335740 TTTGACCTTGGAAACTTTCCT--TCCTTCAGTCTGCCTGTCAAC
1 TTTGACCCTGGAGAC-TGCCTCAT-CTAAAGTCTGCCTGTC-GC
* * *
335782 TTTAACCCTGGAGACTGCCTCATCTAAAGTCTACTTGTCGGC
1 TTTGACCCTGGAGACTGCCTCATCTAAAGTCTGCCTGTC-GC
* * * ** * *
335824 TTTAACCTTGGAGACTTTCCT--TCCTTTAGTTTGCCTGTTGAC
1 TTTGACCCTGGAGAC-TGCCTCAT-CTAAAGTCTGCCTGTCG-C
** ** * *
335866 TTTGACCCTGGAGACT-TTTCTATCCTTCAGTTTGCCTATCGGC
1 TTTGACCCTGGAGACTGCCTC-AT-CTAAAGTCTGCCTGTC-GC
* * *
335909 TTTGACCTTGGAGATTGCCTCATCTAAAGTCTGTCTGTCGAC
1 TTTGACCCTGGAGACTGCCTCATCTAAAGTCTGCCTGTCG-C
* * * * * *
335951 TTTGACCCTAGAGACTTTCCATAAT-T-CAGTCTGCTTATCGAC
1 TTTGACCCTGGAGAC-TGCC-TCATCTAAAGTCTGCCTGTCG-C
** * *
335993 TTTGACCCTAAAGACTGCCTCA-CTAAAGTCTGCCTATCGGT
1 TTTGACCCTGGAGACTGCCTCATCTAAAGTCTGCCTGTC-GC
* * * ** *
336034 TTTGACCCTAGAGACTTTCCATCAT-T-CAGTCTATCTATCAGC
1 TTTGACCCTGGAGAC-TGCC-TCATCTAAAGTCTGCCTGTC-GC
* * * * *
336076 TTTGACCTTGGAGATTGTCTCATCTAAAGTTTGCTTGTCGGC
1 TTTGACCCTGGAGACTGCCTCATCTAAAGTCTGCCTGTC-GC
*
336118 TTTGACCATGGAGACT
1 TTTGACCCTGGAGACT
336134 TTCTTATCTT
Statistics
Matches: 593, Mismatches: 135, Indels: 90
0.72 0.17 0.11
Matches are distributed among these distances:
39 3 0.01
40 9 0.02
41 74 0.12
42 387 0.65
43 109 0.18
44 10 0.02
45 1 0.00
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.37
Consensus pattern (41 bp):
TTTGACCCTGGAGACTGCCTCATCTAAAGTCTGCCTGTCGC
Found at i:335602 original size:126 final size:125
Alignment explanation
Indices: 335319--335628 Score: 390
Period size: 126 Copynumber: 2.5 Consensus size: 125
335309 GCTTGTCAGT
* * * * * *
335319 TTTGACTCTGGAGACTGCCTCATCTAAAGTGTGCCTGTCAGCTTTGA-CTCTAGAGACTGCCTCA
1 TTTGACCCTAGAGACTGTCTCATCTAAAGTCTGCCTGTCGGCTTTGACCT-TGGAGACTGCCTCA
* *
335383 TCTAAAGTCTGCTTGTCGACTTTGACCCGGAGACTTTCCTCTCTTCAGTTTGCCTGTCGGC
65 TCTAAAGTCTGCCTGTCGACTTTGACCCGGAGACTTTCCTCTCTTCAGTTTGCCTGTCGAC
* * * ** * * *
335444 TTTGACCCTAGAGATTTTC-CTACCCTTCAGTCTACCTGTTGGCTTTGACCTTGGAGATTGCCTC
1 TTTGACCCTAGAGACTGTCTC-A-TCTAAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTC
* * * *
335508 ATCTAAAGTTTGCCTGTCGACTTTGACCCTGGAGACTTTCCTTTCTTTAGTTTGTCTGTCGAC
64 ATCTAAAGTCTGCCTGTCGACTTTGACCC-GGAGACTTTCCTCTCTTCAGTTTGCCTGTCGAC
335571 TTTGACCCTAGAGACTGTCTCATCTAAAGTCTGCCTGTCGGCTTTGACCTTGGAGACT
1 TTTGACCCTAGAGACTGTCTCATCTAAAGTCTGCCTGTCGGCTTTGACCTTGGAGACT
335629 TTCCTATCTT
Statistics
Matches: 152, Mismatches: 28, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
124 1 0.01
125 15 0.10
126 86 0.57
127 49 0.32
128 1 0.01
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.36
Consensus pattern (125 bp):
TTTGACCCTAGAGACTGTCTCATCTAAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCAT
CTAAAGTCTGCCTGTCGACTTTGACCCGGAGACTTTCCTCTCTTCAGTTTGCCTGTCGAC
Found at i:335610 original size:84 final size:84
Alignment explanation
Indices: 335319--336176 Score: 495
Period size: 84 Copynumber: 10.2 Consensus size: 84
335309 GCTTGTCAGT
* * * * * *
335319 TTTGACTCTGGAGACTGCCTCATCTAAAGTGTGCCTGTC-AGCTTTGACTCTAGAGAC-TGCCTC
1 TTTGACCCTGGAGACTGTCTCATCTAAAGTCTGCCTGTCGA-CTTTGACCCTGGAGACTTTCCT-
* ** *
335382 ATCTAAAGTCTGCTTGTCGAC
64 TTCTTCAGTCTGCCTGTCGAC
* ** * * * *
335403 TTTGACCC-GGAGACTTTCCTC-TCTTCAGTTTGCCTGTCGGCTTTGACCCTAGAGATTTTCCTA
1 TTTGACCCTGGAGACTGT-CTCATCTAAAGTCTGCCTGTCGACTTTGACCCTGGAGACTTTCCT-
** * * *
335466 CCCTTCAGTCTACCTGTTGGC
64 TTCTTCAGTCTGCCTGTCGAC
* * * *
335487 TTTGACCTTGGAGATTGCCTCATCTAAAGTTTGCCTGTCGACTTTGACCCTGGAGACTTTCCTTT
1 TTTGACCCTGGAGACTGTCTCATCTAAAGTCTGCCTGTCGACTTTGACCCTGGAGACTTTCCTTT
* * *
335552 CTTTAGTTTGTCTGTCGAC
66 CTTCAGTCTGCCTGTCGAC
* * * *
335571 TTTGACCCTAGAGACTGTCTCATCTAAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCCTAT
1 TTTGACCCTGGAGACTGTCTCATCTAAAGTCTGCCTGTCGACTTTGACCCTGGAGACTTTCCTTT
* * * *
335636 CTTTCAGTCTACCTAT-TAGT
66 C-TTCAGTCTGCCTGTCGA-C
* * * ** * * *
335656 TTTGACCCTAGAGACTTTCTTTAT-TTCAGTCTACCTGTC-AGCTTTGACCCTGGAAACTTTCAT
1 TTTGACCCTGGAGACTGTC-TCATCTAAAGTCTGCCTGTCGA-CTTTGACCCTGGAGACTTTCCT
* *
335719 TCCTTTAGTCTGCCTGTC-AGC
64 TTCTTCAGTCTGCCTGTCGA-C
* * * * ** * * *
335740 TTTGACCTTGGAAACTTTC-CTTCCTTCAGTCTGCCTGTCAACTTTAACCCTGGAGAC-TGCCTC
1 TTTGACCCTGGAGACTGTCTCAT-CTAAAGTCTGCCTGTCGACTTTGACCCTGGAGACTTTCCT-
* ** * * *
335803 ATCTAAAGTCTACTTGTCGGC
64 TTCTTCAGTCTGCCTGTCGAC
* * * * ** * * *
335824 TTTAACCTTGGAGACTTTC-CTTCCTTTAGTTTGCCTGTTGACTTTGACCCTGGAGACTTTTCTA
1 TTTGACCCTGGAGACTGTCTCAT-CTAAAGTCTGCCTGTCGACTTTGACCCTGGAGACTTTCCT-
* * * *
335888 TCCTTCAGTTTGCCTATCGGC
64 TTCTTCAGTCTGCCTGTCGAC
* * * * * * *
335909 TTTGACCTTGGAGATTGCCTCATCTAAAGTCTGTCTGTCGACTTTGACCCTAGAGACTTTCCATA
1 TTTGACCCTGGAGACTGTCTCATCTAAAGTCTGCCTGTCGACTTTGACCCTGGAGACTTTCCTTT
* * *
335974 ATTCAGTCTGCTTATCGAC
66 CTTCAGTCTGCCTGTCGAC
** * * ** * *
335993 TTTGACCCTAAAGACTGCCTCA-CTAAAGTCTGCCTATCGGTTTTGACCCTAGAGACTTTCC-AT
1 TTTGACCCTGGAGACTGTCTCATCTAAAGTCTGCCTGTCGACTTTGACCCTGGAGACTTTCCTTT
** *
336056 CATTCAGTCTATCTATC-AGC
66 C-TTCAGTCTGCCTGTCGA-C
* * * * * *
336076 TTTGACCTTGGAGATTGTCTCATCTAAAGTTTGCTTGTCGGCTTTGACCATGGAGACTTT-CTTA
1 TTTGACCCTGGAGACTGTCTCATCTAAAGTCTGCCTGTCGACTTTGACCCTGGAGACTTTCCTT-
* * * *
336140 TCTTTCAATCTACCTGCCGGC
65 TC-TTCAGTCTGCCTGTCGAC
*
336161 TTTGACCCTAGAGACT
1 TTTGACCCTGGAGACT
336177 TTCCTTCCTT
Statistics
Matches: 597, Mismatches: 154, Indels: 45
0.75 0.19 0.06
Matches are distributed among these distances:
82 2 0.00
83 104 0.17
84 294 0.49
85 192 0.32
86 5 0.01
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.37
Consensus pattern (84 bp):
TTTGACCCTGGAGACTGTCTCATCTAAAGTCTGCCTGTCGACTTTGACCCTGGAGACTTTCCTTT
CTTCAGTCTGCCTGTCGAC
Found at i:335660 original size:127 final size:126
Alignment explanation
Indices: 335319--336252 Score: 542
Period size: 127 Copynumber: 7.4 Consensus size: 126
335309 GCTTGTCAGT
* * * * * * *
335319 TTTGACTCTGGAGACTGCCTCATCTAAAGTGTGCCTGTCAGCTTTGA-CTCTAGAGAC-TGCCTC
1 TTTGACCCTGGAGACTGTCTCATCTTAAGTCTGCCTGTCGGCTTTGACCT-TGGAGACTTTCCT-
** * * * * * * *
335382 ATCTAAAGTCTGCTTGTCGACTTTGACCC-GGAGACTTTCCTCTCTTCAGTTTGCCTGTCGGC
64 ATCTTCAGTCTGCCTATCGGCTTTGACCCTGGAGACTTTCCTATCTTCAGTCTGTCTGTCGAC
* * * * * * * *
335444 TTTGACCCTAGAGATTTTC-CTACCCTTCAGTCTACCTGTTGGCTTTGACCTTGGAGA-TTGCCT
1 TTTGACCCTGGAGACTGTCTC-A-TCTTAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCCT
** * * * * * *
335507 CATCTAAAGTTTGCCTGTCGACTTTGACCCTGGAGACTTTCCTTTCTTTAGTTTGTCTGTCGAC
64 -ATCTTCAGTCTGCCTATCGGCTTTGACCCTGGAGACTTTCCTATCTTCAGTCTGTCTGTCGAC
* *
335571 TTTGACCCTAGAGACTGTCTCATCTAAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCCTAT
1 TTTGACCCTGGAGACTGTCTCATCTTAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCCTAT
* ** * * * **
335636 CTTTCAGTCTACCTATTAGTTTTGACCCTAGAGACTTTCTTTAT-TTCAGTCTACCTGTC-AGC
66 C-TTCAGTCTGCCTATCGGCTTTGACCCTGGAGACTTTC-CTATCTTCAGTCTGTCTGTCGA-C
* * * *
335698 TTTGACCCTGGAAACT-T-TCATTCCTTTAGTCTGCCTGTCAGCTTTGACCTTGGAAACTTTCCT
1 TTTGACCCTGGAGACTGTCTCA-T-CTTAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCCT
* ** * * ** * *
335761 -TCCTTCAGTCTGCCTGTCAACTTTAACCCTGGAGAC-TGCCTCATCTAAAGTCT-ACTTGTCGG
64 AT-CTTCAGTCTGCCTATCGGCTTTGACCCTGGAGACTTTCCT-ATCTTCAGTCTGTC-TGTCGA
335823 C
126 C
* * * * * * * * * *
335824 TTTAACCTTGGAGACTTTC-CTTCCTTTAGTTTGCCTGTTGACTTTGACCCTGGAGACTTTTCTA
1 TTTGACCCTGGAGACTGTCTCAT-CTTAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCCTA
* * * **
335888 TCCTTCAGTTTGCCTATCGGCTTTGACCTTGGAGA-TTGCCTCATCTAAAGTCTGTCTGTCGAC
65 T-CTTCAGTCTGCCTATCGGCTTTGACCCTGGAGACTTTCCT-ATCTTCAGTCTGTCTGTCGAC
* * * * * * * * ** *
335951 TTTGACCCTAGAGACTTTC-CATAATTCAGTCTGCTTATCGACTTTGACCCTAAAGAC-TGCCTC
1 TTTGACCCTGGAGACTGTCTCAT-CTTAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCCT-
** * * * *
336014 A-CTAAAGTCTGCCTATCGGTTTTGACCCTAGAGACTTTCC-ATCATTCAGTCTATCTATC-AGC
64 ATCTTCAGTCTGCCTATCGGCTTTGACCCTGGAGACTTTCCTATC-TTCAGTCTGTCTGTCGA-C
* * * * * * *
336076 TTTGACCTTGGAGATTGTCTCATCTAAAGTTTGCTTGTCGGCTTTGACCATGGAGACTTTCTTAT
1 TTTGACCCTGGAGACTGTCTCATCTTAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCCTAT
* * ** * * * * *
336141 CTTTCAATCTACCTGCCGGCTTTGACCCTAGAGACTTTCCT-TCCTTCAATCTGTCTATTGGC
66 C-TTCAGTCTGCCTATCGGCTTTGACCCTGGAGACTTTCCTAT-CTTCAGTCTGTCTGTCGAC
* * * * *
336203 TTTAACCCTGGAGACTGCCTTATCTAAAGT-TCGCTTGTCGGCTTTGACCT
1 TTTGACCCTGGAGACTGTCTCATCTTAAGTCT-GCCTGTCGGCTTTGACCT
336253 AGGGATCTTT
Statistics
Matches: 636, Mismatches: 139, Indels: 66
0.76 0.17 0.08
Matches are distributed among these distances:
124 6 0.01
125 103 0.16
126 192 0.30
127 330 0.52
128 5 0.01
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.37
Consensus pattern (126 bp):
TTTGACCCTGGAGACTGTCTCATCTTAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCCTAT
CTTCAGTCTGCCTATCGGCTTTGACCCTGGAGACTTTCCTATCTTCAGTCTGTCTGTCGAC
Found at i:337567 original size:31 final size:30
Alignment explanation
Indices: 337518--337576 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
337508 GGCTGCCAGC
* *
337518 AAAAAAACAACATACAACATGAAAAAAAGA
1 AAAAAAACAACAAACAACAAGAAAAAAAGA
* *
337548 AAAAAAACAGCAAATCAACAAGCAAAAAA
1 AAAAAAACAACAAA-CAACAAGAAAAAAA
337577 TGGCTATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 12 0.50
31 12 0.50
ACGTcount: A:0.73, C:0.15, G:0.07, T:0.05
Consensus pattern (30 bp):
AAAAAAACAACAAACAACAAGAAAAAAAGA
Found at i:337736 original size:40 final size:40
Alignment explanation
Indices: 337690--337837 Score: 147
Period size: 40 Copynumber: 3.7 Consensus size: 40
337680 AGGAGCATAA
*
337690 AAAACCAACCCCAGCAGTAGCTTCTAGTCCACAAGCACCC
1 AAAACCAACACCAGCAGTAGCTTCTAGTCCACAAGCACCC
* * * * *
337730 AAAACCAACACC-GACAGCAGCTTTTAG-CAGCAGAAGCATCT
1 AAAACCAACACCAG-CAGTAGCTTCTAGTC--CACAAGCACCC
* * * *
337771 GAAACTAACACCAGCAGTAGCTTCCAGTCCACGAGCACCC
1 AAAACCAACACCAGCAGTAGCTTCTAGTCCACAAGCACCC
**
337811 AAAACCAACACCAATAGTAGCTTCTAG
1 AAAACCAACACCAGCAGTAGCTTCTAG
337838 CAGTAGGAGC
Statistics
Matches: 83, Mismatches: 20, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
39 2 0.02
40 51 0.61
41 28 0.34
42 2 0.02
ACGTcount: A:0.37, C:0.34, G:0.15, T:0.14
Consensus pattern (40 bp):
AAAACCAACACCAGCAGTAGCTTCTAGTCCACAAGCACCC
Found at i:337800 original size:81 final size:80
Alignment explanation
Indices: 337691--337854 Score: 229
Period size: 81 Copynumber: 2.0 Consensus size: 80
337681 GGAGCATAAA
* * * *
337691 AAACCAACCCCAGCAGTAGCTTCTAGTCCACAAGCACCCAAAACCAACACCGACAGCAGCTTTTA
1 AAACCAACACCAGCAGTAGCTTCCAGTCCACAAGCACCCAAAACCAACACCAACAGCAGCTTCTA
337756 GCAGCAGAAGCATCTG
66 GCAGCAGAAGCATC-G
* * * *
337772 AAACTAACACCAGCAGTAGCTTCCAGTCCACGAGCACCCAAAACCAACACCAATAGTAGCTTCTA
1 AAACCAACACCAGCAGTAGCTTCCAGTCCACAAGCACCCAAAACCAACACCAACAGCAGCTTCTA
* *
337837 GCAGTAGGAGCATCG
66 GCAGCAGAAGCATCG
337852 AAA
1 AAA
337855 AAACCAATAC
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
80 4 0.05
81 69 0.95
ACGTcount: A:0.37, C:0.32, G:0.16, T:0.14
Consensus pattern (80 bp):
AAACCAACACCAGCAGTAGCTTCCAGTCCACAAGCACCCAAAACCAACACCAACAGCAGCTTCTA
GCAGCAGAAGCATCG
Found at i:338081 original size:13 final size:13
Alignment explanation
Indices: 338063--338098 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
338053 AAAACCAACA
338063 CCGACAGTAGCTT
1 CCGACAGTAGCTT
338076 CCGACAGTAGCTT
1 CCGACAGTAGCTT
*
338089 CCAACAGTAG
1 CCGACAGTAG
338099 AAGCATCCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.28, C:0.31, G:0.22, T:0.19
Consensus pattern (13 bp):
CCGACAGTAGCTT
Found at i:338264 original size:22 final size:22
Alignment explanation
Indices: 338239--338315 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
338229 CTTCTAGCAG
338239 CTCCAGCAGCTTCCACGGTAGC
1 CTCCAGCAGCTTCCACGGTAGC
338261 CTCCAGCAGCTTCCACGGTAGC
1 CTCCAGCAGCTTCCACGGTAGC
*
338283 CTCCAGCAGCTTCCAAGGTAGC
1 CTCCAGCAGCTTCCACGGTAGC
*
338305 CTCTAGCAGCT
1 CTCCAGCAGCT
338316 CCAGCAACTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.19, C:0.39, G:0.22, T:0.19
Consensus pattern (22 bp):
CTCCAGCAGCTTCCACGGTAGC
Found at i:338268 original size:71 final size:73
Alignment explanation
Indices: 338137--338328 Score: 208
Period size: 71 Copynumber: 2.6 Consensus size: 73
338127 TTTCCAGCAG
* * * * * *
338137 CTCCAGCAGTTTCCACAGCAACTTCCAGCAGCTCGAACAATTTCCATGGTAGCCTCCAGCAGCTC
1 CTCCAGCAGCTT-C-CAGCAACTTCTAGCAGCTCCAGCAACTTCCACGGTAGCCTCCAGCAGCTC
338202 CCACGACAGC
64 CCACGACAGC
* * *
338212 CTCTAGCAG-TT-CAGCAACTTCTAGCAGCTCCAGCAGCTTCCACGGTAGCCTCCAGCAGCTTCC
1 CTCCAGCAGCTTCCAGCAACTTCTAGCAGCTCCAGCAACTTCCACGGTAGCCTCCAGCAGCTCCC
**
338275 ACGGTAGC
66 ACGACAGC
* * *
338283 CTCCAGCAGCTTCCAAGGTAGCCTCTAGCAGCTCCAGCAACTTCCA
1 CTCCAGCAGCTTCC-A-GCAACTTCTAGCAGCTCCAGCAACTTCCA
338329 GCAACTCTAG
Statistics
Matches: 98, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
71 59 0.60
72 2 0.02
73 1 0.01
74 3 0.03
75 33 0.34
ACGTcount: A:0.23, C:0.38, G:0.19, T:0.20
Consensus pattern (73 bp):
CTCCAGCAGCTTCCAGCAACTTCTAGCAGCTCCAGCAACTTCCACGGTAGCCTCCAGCAGCTCCC
ACGACAGC
Found at i:338306 original size:93 final size:94
Alignment explanation
Indices: 338178--338348 Score: 254
Period size: 93 Copynumber: 1.8 Consensus size: 94
338168 CTCGAACAAT
* * * * *
338178 TTCCATGGTAGCCTCCAGCAGCTCCCACGACAGCCTCTAGCAG-TTCAGCAACTTCTAGCAGCTC
1 TTCCACGGTAGCCTCCAGCAGCTCCCAAGACAGCCTCTAGCAGCTCCAGCAACTTCCAGCAACTC
338242 CAGCAGCTTCCACGGTAGCCTCCAGCAGC
66 CAGCAGCTTCCACGGTAGCCTCCAGCAGC
* **
338271 TTCCACGGTAGCCTCCAGCAGCTTCCAAGGTAGCCTCTAGCAGCTCCAGCAACTTCCAGCAACTC
1 TTCCACGGTAGCCTCCAGCAGCTCCCAAGACAGCCTCTAGCAGCTCCAGCAACTTCCAGCAACTC
*
338336 TAGCAGCTTCCAC
66 CAGCAGCTTCCAC
338349 TGCAACCTCC
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
93 38 0.56
94 30 0.44
ACGTcount: A:0.22, C:0.39, G:0.19, T:0.20
Consensus pattern (94 bp):
TTCCACGGTAGCCTCCAGCAGCTCCCAAGACAGCCTCTAGCAGCTCCAGCAACTTCCAGCAACTC
CAGCAGCTTCCACGGTAGCCTCCAGCAGC
Found at i:338368 original size:94 final size:93
Alignment explanation
Indices: 338178--338369 Score: 251
Period size: 94 Copynumber: 2.1 Consensus size: 93
338168 CTCGAACAAT
* * * * *
338178 TTCCATGGTAGCCTCCAGCAGCTCCCACGACAGCCTCTAGCAGTTCAGCAACTTCTAGCAGCTCC
1 TTCCACGGTAGCCTCCAGCAGCTCCCAAGACAGCCTCTAGCAGTCCAGCAACTTCCAGCAACTCC
* *
338243 AGCAGCTTCCACGGTAGCCTCCAGCAGC
66 AGCAGCTTCCACGGCAACCTCCAGCAGC
* **
338271 TTCCACGGTAGCCTCCAGCAGCTTCCAAGGTAGCCTCTAGCAGCTCCAGCAACTTCCAGCAACTC
1 TTCCACGGTAGCCTCCAGCAGCTCCCAAGACAGCCTCTAGCAG-TCCAGCAACTTCCAGCAACTC
* *
338336 TAGCAGCTTCCACTGCAACCTCCAGCCA-C
65 CAGCAGCTTCCACGGCAACCTCCAG-CAGC
338365 TTCCA
1 TTCCA
338370 GCAGCTCCAT
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
93 38 0.45
94 45 0.53
95 2 0.02
ACGTcount: A:0.22, C:0.40, G:0.18, T:0.20
Consensus pattern (93 bp):
TTCCACGGTAGCCTCCAGCAGCTCCCAAGACAGCCTCTAGCAGTCCAGCAACTTCCAGCAACTCC
AGCAGCTTCCACGGCAACCTCCAGCAGC
Found at i:338377 original size:19 final size:19
Alignment explanation
Indices: 338309--338378 Score: 61
Period size: 19 Copynumber: 3.5 Consensus size: 19
338299 GGTAGCCTCT
*
338309 AGCAGCTCCAGCAACTTCC
1 AGCAGCTCCAGCCACTTCC
* *
338328 AGCAACTCTAG-CAGCTTCC
1 AGCAGCTCCAGCCA-CTTCC
*
338347 ACTGCAACCTCCAGCCACTTCC
1 A--GC-AGCTCCAGCCACTTCC
338369 AGCAGCTCCA
1 AGCAGCTCCA
338379 TAGCAGCCAA
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
18 1 0.03
19 21 0.52
20 2 0.05
21 2 0.05
22 12 0.30
23 2 0.05
ACGTcount: A:0.26, C:0.43, G:0.14, T:0.17
Consensus pattern (19 bp):
AGCAGCTCCAGCCACTTCC
Found at i:343487 original size:16 final size:16
Alignment explanation
Indices: 343466--343498 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
343456 TGAATTCGAT
343466 AATAACTAGAACCTAA
1 AATAACTAGAACCTAA
*
343482 AATAACTTGAACCTAA
1 AATAACTAGAACCTAA
343498 A
1 A
343499 TTGACTCGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.18, G:0.06, T:0.21
Consensus pattern (16 bp):
AATAACTAGAACCTAA
Found at i:345376 original size:28 final size:28
Alignment explanation
Indices: 345344--345651 Score: 300
Period size: 28 Copynumber: 11.0 Consensus size: 28
345334 CAAATTTTTT
345344 ACAAGTCAGTGGCATCCTTTCAAAGCCC
1 ACAAGTCAGTGGCATCCTTTCAAAGCCC
* * *
345372 ACAAGTCAGAGGCATCCTTTCAAAACTC
1 ACAAGTCAGTGGCATCCTTTCAAAGCCC
* * * *
345400 ACATGTTAGCGGCATCCTTTCAAAGACC
1 ACAAGTCAGTGGCATCCTTTCAAAGCCC
** *
345428 ACAAGTCAACGGCATCATTTCAAAGCCC
1 ACAAGTCAGTGGCATCCTTTCAAAGCCC
* *
345456 ACATGTCAGTGGCATCCTTTCAAAGCCT
1 ACAAGTCAGTGGCATCCTTTCAAAGCCC
** * *
345484 ACATTTTAGTGGCATCCTTTCAAGGCCC
1 ACAAGTCAGTGGCATCCTTTCAAAGCCC
* *
345512 ACAAG-CTTGTGGCACCCTTTCAAAGCCC
1 ACAAGTC-AGTGGCATCCTTTCAAAGCCC
*
345540 ACAAGTCAGTGACA-CTCTTTCAAAGCCC
1 ACAAGTCAGTGGCATC-CTTTCAAAGCCC
* * * *
345568 ACAAGTTAGTGGCACCCTCTCGAAGCCC
1 ACAAGTCAGTGGCATCCTTTCAAAGCCC
* * *
345596 ATAA-TCAGTGGCATCCTTTTAAAGTCC
1 ACAAGTCAGTGGCATCCTTTCAAAGCCC
** *
345623 ACAAGTTGGTGGCAACCTTTCTAAA-CCC
1 ACAAGTCAGTGGCATCCTTTC-AAAGCCC
345651 A
1 A
345652 ATGTCGTTGG
Statistics
Matches: 226, Mismatches: 48, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
27 21 0.09
28 200 0.88
29 5 0.02
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (28 bp):
ACAAGTCAGTGGCATCCTTTCAAAGCCC
Found at i:346608 original size:31 final size:31
Alignment explanation
Indices: 346573--346631 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
346563 AAATGTCATA
**
346573 TTTTTACGTAGATGTATCAATACATTTTGTC
1 TTTTTACCCAGATGTATCAATACATTTTGTC
*
346604 TTTTTACCCAGATGTATCGATACATTTT
1 TTTTTACCCAGATGTATCAATACATTTT
346632 TCAATGTATC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.47
Consensus pattern (31 bp):
TTTTTACCCAGATGTATCAATACATTTTGTC
Found at i:347068 original size:40 final size:40
Alignment explanation
Indices: 347012--347087 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
347002 ATGCAATCCT
*
347012 AGCAAAGGATCTCCTTTTCAACCACATATTCTAGCCCCAC
1 AGCAAAGGATCCCCTTTTCAACCACATATTCTAGCCCCAC
*
347052 AGCAAAGGATCCCCTTTTCAACCACATTTTCTAGCC
1 AGCAAAGGATCCCCTTTTCAACCACATATTCTAGCC
347088 TTATTACCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.29, C:0.34, G:0.11, T:0.26
Consensus pattern (40 bp):
AGCAAAGGATCCCCTTTTCAACCACATATTCTAGCCCCAC
Found at i:354626 original size:15 final size:15
Alignment explanation
Indices: 354606--354649 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
354596 ATTCCGCCAA
354606 ATCCACCACAAAATT
1 ATCCACCACAAAATT
**
354621 ATCCACCACCTAATT
1 ATCCACCACAAAATT
*
354636 ATCCATCACAAAAT
1 ATCCACCACAAAAT
354650 CATCGATACA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.43, C:0.34, G:0.00, T:0.23
Consensus pattern (15 bp):
ATCCACCACAAAATT
Found at i:359635 original size:13 final size:13
Alignment explanation
Indices: 359617--359642 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
359607 CAATTTGGGA
359617 TGTATCGATACAT
1 TGTATCGATACAT
359630 TGTATCGATACAT
1 TGTATCGATACAT
359643 CTTGTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:359639 original size:33 final size:32
Alignment explanation
Indices: 359597--359660 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
359587 CCTGTGTTAA
359597 TGTATCGATACAAT-TTGGGATGTATCGATACAT
1 TGTATCGATAC-ATCTTGGG-TGTATCGATACAT
*
359630 TGTATCGATACATCTTGTGTGTATCGATACA
1 TGTATCGATACATCTTGGGTGTATCGATACA
359661 AACAGTTAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATCTTGGGTGTATCGATACAT
Found at i:359749 original size:20 final size:21
Alignment explanation
Indices: 359702--359754 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
359692 GCCAATCACC
*
359702 TGTATCGATACATTCTTTGCA
1 TGTATCGATACATTCTGTGCA
*
359723 AGTATCGATACATT-TG-GTCA
1 TGTATCGATACATTCTGTG-CA
359743 TGTATCGATACA
1 TGTATCGATACA
359755 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.04
20 14 0.50
21 13 0.46
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTGCA
Found at i:360384 original size:16 final size:16
Alignment explanation
Indices: 360360--360391 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
360350 CCTTAATAAA
*
360360 GCAATTTAACAATTTC
1 GCAAATTAACAATTTC
360376 GCAAATTAACAATTTC
1 GCAAATTAACAATTTC
360392 TTTTAATCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.34
Consensus pattern (16 bp):
GCAAATTAACAATTTC
Found at i:362273 original size:13 final size:13
Alignment explanation
Indices: 362255--362279 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
362245 ATAAACCCTT
362255 TGTATCGATACAA
1 TGTATCGATACAA
362268 TGTATCGATACA
1 TGTATCGATACA
362280 GAGAATGTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:368584 original size:20 final size:21
Alignment explanation
Indices: 368537--368589 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
368527 GCCAATCACC
*
368537 TGTATCGATACATTCTTTGCA
1 TGTATCGATACATTCTGTGCA
*
368558 AGTATCGATACATT-TG-GTCA
1 TGTATCGATACATTCTGTG-CA
368578 TGTATCGATACA
1 TGTATCGATACA
368590 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.04
20 14 0.50
21 13 0.46
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTGCA
Found at i:368595 original size:13 final size:13
Alignment explanation
Indices: 368577--368601 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
368567 ACATTTGGTC
368577 ATGTATCGATACA
1 ATGTATCGATACA
368590 ATGTATCGATAC
1 ATGTATCGATAC
368602 TGTGCAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:457089 original size:13 final size:12
Alignment explanation
Indices: 457056--457120 Score: 51
Period size: 13 Copynumber: 5.1 Consensus size: 12
457046 AAGAAATGGT
*
457056 TGTCAAGAAATTA
1 TGTCAAG-AATTC
457069 TCGTCAAGAACTTC
1 T-GTCAAGAA-TTC
*
457083 TGTCAAGAATGC
1 TGTCAAGAATTC
*
457095 TTGTCAAAGACTT-
1 -TGTC-AAGAATTC
457108 TGTCAAGAATTC
1 TGTCAAGAATTC
457120 T
1 T
457121 TCGTCAATAC
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
11 6 0.14
12 7 0.17
13 15 0.36
14 14 0.33
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (12 bp):
TGTCAAGAATTC
Found at i:457117 original size:25 final size:27
Alignment explanation
Indices: 457069--457127 Score: 79
Period size: 25 Copynumber: 2.3 Consensus size: 27
457059 CAAGAAATTA
457069 TCGTC-AAGAACTTCTGTCAAGAATGCT
1 TCGTCAAAG-ACTTCTGTCAAGAATGCT
*
457096 T-GTCAAAGACTT-TGTCAAGAATTCT
1 TCGTCAAAGACTTCTGTCAAGAATGCT
457121 TCGTCAA
1 TCGTCAA
457128 TACGACCCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 13 0.45
26 12 0.41
27 4 0.14
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (27 bp):
TCGTCAAAGACTTCTGTCAAGAATGCT
Found at i:457552 original size:28 final size:28
Alignment explanation
Indices: 457137--457544 Score: 505
Period size: 28 Copynumber: 14.6 Consensus size: 28
457127 ATACGACCCT
*
457137 TTTCAAAG-CCACAAGTCAGTGGCATTC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
457164 TTTCAAAGCTCACAAGTTAGTAGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
457192 TTTCAAAGCCCACAAGTCAATAGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
457220 TTTCAAAGCTCACAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
457248 TTTCAAAGCCCACATGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
457276 TTTCAAAGCCCACATGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
457304 TTTTAAAGCCCACAAGTCAGTGGCTTCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
457332 TTTCAAAGCCTACAAGTTAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
457360 TTTCAAAGCCCACATGTCAATGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
457388 TTTCGAAGCCCACATGTCAGCGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
457416 TTTCGAAGCCCACAAGTCAATGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
457444 TTTCGAAA-CCCACAAGTCAATGGCACCC
1 TTTC-AAAGCCCACAAGTCAGTGGCATCC
** * *
457472 TTTTGAAGCCCACAAGTTAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * * *
457500 TTTCGAAGCCCATAAATCATTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
457528 TTTTAAAGCCCACAAGT
1 TTTCAAAGCCCACAAGT
457545 TGGTGGCAAA
Statistics
Matches: 333, Mismatches: 45, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
27 10 0.03
28 321 0.96
29 2 0.01
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCC
Found at i:458560 original size:20 final size:20
Alignment explanation
Indices: 458535--458582 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
458525 TACCCAAATG
458535 TATCGATATATTTTTTAATA
1 TATCGATATATTTTTTAATA
*
458555 TATCGATATATTTTTTAATG
1 TATCGATATATTTTTTAATA
458575 TATCGATA
1 TATCGATA
458583 CATGTATGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.52
Consensus pattern (20 bp):
TATCGATATATTTTTTAATA
Found at i:460270 original size:34 final size:35
Alignment explanation
Indices: 460232--460298 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
460222 CCTTACAACA
460232 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
460266 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
460299 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:460783 original size:13 final size:13
Alignment explanation
Indices: 460765--460793 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
460755 GATACTATTC
460765 ACACTGTATCGAT
1 ACACTGTATCGAT
460778 ACACTGTATCGAT
1 ACACTGTATCGAT
460791 ACA
1 ACA
460794 TGAATAGTGA
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:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (13 bp):
ACACTGTATCGAT
Found at i:460862 original size:24 final size:24
Alignment explanation
Indices: 460826--460903 Score: 79
Period size: 24 Copynumber: 3.3 Consensus size: 24
460816 TTATCGATAC
* * *
460826 ATGAATAGTGATACGTGAACAGTG
1 ATGAACAGCGATACATGAACAGTG
*
460850 ATGAACAGCGATATATGAACAGTG
1 ATGAACAGCGATACATGAACAGTG
* * *
460874 ATG--TATCGATACATGAATAGTG
1 ATGAACAGCGATACATGAACAGTG
460896 ATGAACAG
1 ATGAACAG
460904 TGAAAAAAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
22 18 0.43
24 24 0.57
ACGTcount: A:0.40, C:0.10, G:0.26, T:0.24
Consensus pattern (24 bp):
ATGAACAGCGATACATGAACAGTG
Found at i:460955 original size:13 final size:13
Alignment explanation
Indices: 460937--460961 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
460927 TGCCAATGCT
460937 ATGTATCGATACA
1 ATGTATCGATACA
460950 ATGTATCGATAC
1 ATGTATCGATAC
460962 TTAGCAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:469703 original size:52 final size:51
Alignment explanation
Indices: 469618--469741 Score: 205
Period size: 52 Copynumber: 2.4 Consensus size: 51
469608 ATATGAAAAG
* *
469618 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAA
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
469669 TTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGCAAA
1 -TTGCCTGCATGTATCGATACA-TTTAATAATGTATCGATACATCTGGGCAAA
469721 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
469742 AAGATTAGTG
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
51 21 0.30
52 43 0.62
53 5 0.07
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
Found at i:469768 original size:13 final size:13
Alignment explanation
Indices: 469750--469774 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
469740 CAAAGATTAG
469750 TGTATCGATACAA
1 TGTATCGATACAA
469763 TGTATCGATACA
1 TGTATCGATACA
469775 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:469852 original size:33 final size:33
Alignment explanation
Indices: 469815--469881 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
469805 AGTAGCTTAA
469815 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
469848 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
469881 A
1 A
469882 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:469855 original size:13 final size:13
Alignment explanation
Indices: 469837--469861 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
469827 CAAAAAAATA
469837 TGTATCGATACAT
1 TGTATCGATACAT
469850 TGTATCGATACA
1 TGTATCGATACA
469862 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:472733 original size:17 final size:18
Alignment explanation
Indices: 472700--472736 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
472690 TAGCCAAACT
472700 TGTATCGATACACAATGTA
1 TGTATCGATA-ACAATGTA
472719 TGTATCGAT-ACAATGTA
1 TGTATCGATAACAATGTA
472736 T
1 T
472737 CGATACACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
19 9 0.50
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (18 bp):
TGTATCGATAACAATGTA
Found at i:472736 original size:13 final size:13
Alignment explanation
Indices: 472718--472743 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
472708 TACACAATGT
472718 ATGTATCGATACA
1 ATGTATCGATACA
472731 ATGTATCGATACA
1 ATGTATCGATACA
472744 CAAAAATATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:472741 original size:32 final size:33
Alignment explanation
Indices: 472700--472763 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
472690 TAGCCAAACT
**
472700 TGTATCGATACAC-AATGTATGTATCGATACAA
1 TGTATCGATACACAAAAATATGTATCGATACAA
472732 TGTATCGATACACAAAAATATGTATCGATACA
1 TGTATCGATACACAAAAATATGTATCGATACA
472764 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCGATACAA
Found at i:475637 original size:52 final size:51
Alignment explanation
Indices: 475552--475675 Score: 205
Period size: 52 Copynumber: 2.4 Consensus size: 51
475542 ATATGAAAAG
* *
475552 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAA
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
475603 TTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGCAAA
1 -TTGCCTGCATGTATCGATACA-TTTAATAATGTATCGATACATCTGGGCAAA
475655 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
475676 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
51 21 0.30
52 43 0.62
53 5 0.07
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
Found at i:475688 original size:51 final size:50
Alignment explanation
Indices: 475552--475695 Score: 177
Period size: 52 Copynumber: 2.8 Consensus size: 50
475542 ATATGAAAAG
* *
475552 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA--AAATAGTGTATCGATACATCTGGGCAAAT
475604 TTGCCTGCATGTATCGATACATTTTAAA-A-TGTATCGATACATCTGGGCAAA-
1 TTGCCTGCATGTATCGATACA----AAATAGTGTATCGATACATCTGGGCAAAT
475655 TTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACAAA-AT-AGTGTATCGATACA
475696 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 2, Indels: 13
0.85 0.02 0.13
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
50 1 0.01
51 33 0.39
52 42 0.50
53 1 0.01
54 4 0.05
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (50 bp):
TTGCCTGCATGTATCGATACAAAATAGTGTATCGATACATCTGGGCAAAT
Found at i:475702 original size:13 final size:13
Alignment explanation
Indices: 475684--475708 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
475674 CAAAGATCAG
475684 TGTATCGATACAA
1 TGTATCGATACAA
475697 TGTATCGATACA
1 TGTATCGATACA
475709 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:475786 original size:33 final size:33
Alignment explanation
Indices: 475749--475815 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
475739 AGTAGCTTAA
475749 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
475782 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
475815 A
1 A
475816 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:475789 original size:13 final size:13
Alignment explanation
Indices: 475771--475795 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
475761 CAAAAAAATA
475771 TGTATCGATACAT
1 TGTATCGATACAT
475784 TGTATCGATACA
1 TGTATCGATACA
475796 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:476731 original size:67 final size:68
Alignment explanation
Indices: 476605--476731 Score: 166
Period size: 67 Copynumber: 1.9 Consensus size: 68
476595 ATTGGGTTTT
* * * *
476605 AAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATG
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATGGGACTTAAAGATGAAGATG
476670 AGA
66 AGA
* * * * *
476673 AAAG-TGATAAAGATGCCAATATGTTGATTCACGGCCAACGATATGGGGCTTAATGATGA
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATGGGACTTAAAGATGA
476732 GAAAAAGGAT
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
67 46 0.92
68 4 0.08
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.24
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATGGGACTTAAAGATGAAGATG
AGA
Found at i:477198 original size:92 final size:93
Alignment explanation
Indices: 476734--477205 Score: 642
Period size: 92 Copynumber: 5.0 Consensus size: 93
476724 AATGATGAGA
* * * *
476734 AAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACGTAAAGATGGAAAATGTGCCAA
1 AAAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAA
476799 TATGCTGATTCAAGGCCAGCTATATTGGACTT
62 TATGCTGATTCAAGGCCAGCTATATTGGACTT
* * *
476831 -AAAGGTGCCAATGTGCTGATTCAAGGACAGCTACATTGGACTTAAAGATGAAGATGCCAATGTG
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATG
* *
476895 CTGAGTCAAGGCCAGCTACATTGGACTT
66 CTGATTCAAGGCCAGCTATATTGGACTT
476923 AAAGATGAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAA
1 -AA-A--AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAA
* * *
476988 TGTGCTGAGTCAAGGCCAGCTACATTGGACTT
62 TATGCTGATTCAAGGCCAGCTATATTGGACTT
* * *
477020 AAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGATGATGCCA
1 --A-A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCA
*
477085 ATATGCTGATTCAAGGCCAGCGATATTGGACTT
61 ATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
477118 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTACCAATATG
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATG
*
477182 CTGATTCAAGGCCAGCGATATTGG
66 CTGATTCAAGGCCAGCTATATTGG
477206 GGTTAGAAGG
Statistics
Matches: 344, Mismatches: 23, Indels: 21
0.89 0.06 0.05
Matches are distributed among these distances:
92 119 0.35
94 3 0.01
95 41 0.12
96 5 0.01
97 88 0.26
98 85 0.25
99 1 0.00
100 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (93 bp):
AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATG
CTGATTCAAGGCCAGCTATATTGGACTT
Found at i:477205 original size:49 final size:49
Alignment explanation
Indices: 476744--477197 Score: 628
Period size: 49 Copynumber: 9.5 Consensus size: 49
476734 AAAAGGATGT
* * *
476744 CAATGTGCTGATTCAAGGCCAGCTACATTGAACGTAAAGATGGAAAATGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* *
476796 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
476839 CAATGTGCTGATTCAAGGACAGCTACATTGGACTTAAAGATGAAGATGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
476888 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
476936 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
476985 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
477034 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGATGATGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
477083 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
477126 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTAC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
477175 CAATATGCTGATTCAAGGCCAGC
1 CAATGTGCTGATTCAAGGCCAGC
477198 GATATTGGGG
Statistics
Matches: 363, Mismatches: 26, Indels: 29
0.87 0.06 0.07
Matches are distributed among these distances:
43 76 0.21
45 1 0.00
47 2 0.01
48 47 0.13
49 206 0.57
52 31 0.09
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:477252 original size:33 final size:33
Alignment explanation
Indices: 477210--477313 Score: 167
Period size: 32 Copynumber: 3.2 Consensus size: 33
477200 TATTGGGGTT
477210 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
477243 AGAATGGTTGCCACCGACTTGTGTGGGC-TTCG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
477275 AGAAGGGTTGCCACCAACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
477308 -GAAGGG
1 AGAAGGG
477314 AGAAAGATGC
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
32 35 0.54
33 30 0.46
ACGTcount: A:0.19, C:0.18, G:0.37, T:0.26
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:477354 original size:34 final size:33
Alignment explanation
Indices: 477316--477657 Score: 263
Period size: 34 Copynumber: 10.6 Consensus size: 33
477306 AGGAAGGGAG
*
477316 AAAGATGCCACGGAGTTGTGGACTTAAAAGGGAA
1 AAAGATGCCACGGAGTTGTGGGCTTAAAA-GGAA
*
477350 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAA
1 AAAGA-TGCCACGGAGTTGTGGGC-TTAAAAG--GAA
* * * *
477387 AAAGGTGCCACAGAGTTGTGGACTTAAAGATGAA
1 AAAGATGCCACGGAGTTGTGGGCTTAAA-AGGAA
*
477421 AAA-AGTGCCACGGAGTTATGGGCTTAAAAGG--
1 AAAGA-TGCCACGGAGTTGTGGGCTTAAAAGGAA
*
477452 ---G-TGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
* **
477481 AAAGAGTGCCACAGAGTTGTGGGCTTAGGAGGAA
1 AAAGA-TGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
477515 AAAGAGTGCCACGGAGTTATGGGCTT-TAA--AA
1 AAAGA-TGCCACGGAGTTGTGGGCTTAAAAGGAA
* * *
477546 AGAG-TGCCACGGAGTCGTGGGCTTTGAAAGG--
1 AAAGATGCCACGGAGTTGTGGGC-TTAAAAGGAA
*
477577 ---G-TGCCACGGAGTTGTGGACTTAAAAGGAA
1 AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
* * *
477606 CAAGGTGCCACGGAGTTGTGGGCTTTAAA-GAA
1 AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
477638 AAA-ATGCCACTGAGTCGTGG
1 AAAGATGCCACGGAGTTGTGG
477658 ACTTTGAGAC
Statistics
Matches: 251, Mismatches: 33, Indels: 51
0.75 0.10 0.15
Matches are distributed among these distances:
27 31 0.12
28 17 0.07
29 16 0.06
30 2 0.01
31 21 0.08
32 7 0.03
33 25 0.10
34 80 0.32
35 23 0.09
36 23 0.09
37 6 0.02
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (33 bp):
AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
Found at i:477464 original size:61 final size:60
Alignment explanation
Indices: 477385--477635 Score: 226
Period size: 61 Copynumber: 4.1 Consensus size: 60
477375 TTAAAAGAAA
* * *
477385 AAAAAGGTGCCACAGAGTTGTGGACTTAAAGATGAAAAA-AGTGCCACGGAGTTATGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT-AA-ATGAAAAAGAGTGCCACGGAGTTGTGGGCTT
* * *
477446 AAAAGGGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTA-AATGAAAAAGAGTGCCACGGAGTTGTGGGCTT
* * * *
477507 AGGAGGAAAAAGAGTGCCACGGAGTTATGGGCTT---T-AAAAAGAGTGCCACGGAGTCGTGGGC
1 -------AAAAGGGTGCCACGGAGTTGTGGACTTAAATGAAAAAGAGTGCCACGGAGTTGTGGGC
477568 TTT
59 -TT
* * *
477571 GAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAACAAG-GTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT-AAATGAAAAAGAGTGCCACGGAGTTGTGGGCTT
*
477631 TAAAG
1 AAAAG
477636 AAAAAATGCC
Statistics
Matches: 156, Mismatches: 19, Indels: 31
0.76 0.09 0.15
Matches are distributed among these distances:
57 23 0.15
60 14 0.09
61 63 0.40
62 5 0.03
63 24 0.15
64 2 0.01
68 25 0.16
ACGTcount: A:0.31, C:0.14, G:0.35, T:0.20
Consensus pattern (60 bp):
AAAAGGGTGCCACGGAGTTGTGGACTTAAATGAAAAAGAGTGCCACGGAGTTGTGGGCTT
Found at i:477467 original size:97 final size:95
Alignment explanation
Indices: 477349--477636 Score: 335
Period size: 97 Copynumber: 3.1 Consensus size: 95
477339 TTAAAAGGGA
477349 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAAAGGTGCCACAGAGTTGTGGACTTAA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAG-AAAAAAAGGTGCCACAGAGTTGTGGACTTAA
*
477414 AGATGAAAAAAGTGCCACGGAGTTATGGGCTT
64 AGAGGAAAAAAGTGCCACGGAGTTATGGGCTT
* * *
477446 AAAAGGGTGCCACGGAGTTGTGGGC-TTAGAAG-GAAAAAGAGTGCCACAGAGTTGTGGGCTT-A
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTA-AAGAAAAAAAG-GTGCCACAGAGTTGTGGACTTAA
*
477508 GGAGGAAAAAGAGTGCCACGGAGTTATGGGCTTT
64 AGAGGAAAAA-AGTGCCACGGAGTTATGGGC-TT
* * *
477542 AAAAAGAGTGCCACGGAGTCGTGGGCTTT---G---AAAGGGTGCCACGGAGTTGTGGACTTAAA
1 -AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAGAAAAAAAGGTGCCACAGAGTTGTGGACTTAAA
* * *
477601 -AGGAACAAGGTGCCACGGAGTTGTGGGCTT
65 GAGGAAAAAAGTGCCACGGAGTTATGGGCTT
*
477631 TAAAGA
1 AAAAGA
477637 AAAAATGCCA
Statistics
Matches: 169, Mismatches: 15, Indels: 23
0.82 0.07 0.11
Matches are distributed among these distances:
88 5 0.03
89 2 0.01
90 18 0.11
91 26 0.15
92 5 0.03
94 16 0.09
95 41 0.24
96 7 0.04
97 47 0.28
98 2 0.01
ACGTcount: A:0.32, C:0.13, G:0.34, T:0.20
Consensus pattern (95 bp):
AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAGAAAAAAAGGTGCCACAGAGTTGTGGACTTAAAG
AGGAAAAAAGTGCCACGGAGTTATGGGCTT
Found at i:477673 original size:30 final size:31
Alignment explanation
Indices: 477578--477695 Score: 121
Period size: 30 Copynumber: 3.8 Consensus size: 31
477568 TTTGAAAGGG
* * * **
477578 TGCCACGGAGTTGTGGACTTAAAAGGAACAAGG
1 TGCCACTGAGTCGTGGACTTTAAA-GAA-AAAA
* * *
477611 TGCCACGGAGTTGTGGGCTTTAAAGAAAAAA
1 TGCCACTGAGTCGTGGACTTTAAAGAAAAAA
* *
477642 TGCCACTGAGTCGTGGACTTT-GAGACAAAA
1 TGCCACTGAGTCGTGGACTTTAAAGAAAAAA
477672 TGCCACTGAGTCGTGGACTTTAAA
1 TGCCACTGAGTCGTGGACTTTAAA
477696 AAGGTATTTG
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
30 28 0.38
31 21 0.28
32 3 0.04
33 22 0.30
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (31 bp):
TGCCACTGAGTCGTGGACTTTAAAGAAAAAA
Found at i:485993 original size:52 final size:51
Alignment explanation
Indices: 485908--486031 Score: 205
Period size: 52 Copynumber: 2.4 Consensus size: 51
485898 ATATGAAAAG
* *
485908 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAA
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
485959 TTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGCAAA
1 -TTGCCTGCATGTATCGATACA-TTTAATAATGTATCGATACATCTGGGCAAA
486011 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
486032 AAGATTAGTG
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
51 21 0.30
52 43 0.62
53 5 0.07
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
Found at i:486058 original size:13 final size:13
Alignment explanation
Indices: 486040--486064 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
486030 CAAAGATTAG
486040 TGTATCGATACAA
1 TGTATCGATACAA
486053 TGTATCGATACA
1 TGTATCGATACA
486065 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:486142 original size:33 final size:33
Alignment explanation
Indices: 486105--486171 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
486095 AGTAGCTTAA
486105 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
486138 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
486171 A
1 A
486172 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:486145 original size:13 final size:13
Alignment explanation
Indices: 486127--486151 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
486117 CAAAAAAATA
486127 TGTATCGATACAT
1 TGTATCGATACAT
486140 TGTATCGATACA
1 TGTATCGATACA
486152 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:489023 original size:17 final size:18
Alignment explanation
Indices: 488990--489026 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
488980 TAGCCAAACT
488990 TGTATCGATACACAATGTA
1 TGTATCGATA-ACAATGTA
489009 TGTATCGAT-ACAATGTA
1 TGTATCGATAACAATGTA
489026 T
1 T
489027 CGATACACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
19 9 0.50
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (18 bp):
TGTATCGATAACAATGTA
Found at i:489026 original size:13 final size:13
Alignment explanation
Indices: 489008--489033 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
488998 TACACAATGT
489008 ATGTATCGATACA
1 ATGTATCGATACA
489021 ATGTATCGATACA
1 ATGTATCGATACA
489034 CAAAAATATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:489031 original size:32 final size:33
Alignment explanation
Indices: 488990--489053 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
488980 TAGCCAAACT
**
488990 TGTATCGATACAC-AATGTATGTATCGATACAA
1 TGTATCGATACACAAAAATATGTATCGATACAA
489022 TGTATCGATACACAAAAATATGTATCGATACA
1 TGTATCGATACACAAAAATATGTATCGATACA
489054 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCGATACAA
Found at i:498460 original size:1 final size:1
Alignment explanation
Indices: 498456--498480 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
498446 TTTTTTTTGT
498456 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
498481 AATAAGTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:498666 original size:20 final size:20
Alignment explanation
Indices: 498643--498684 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
498633 AGAGATGGGT
*
498643 TTTTAAAGGGAGGGGAGAGG
1 TTTTAAAGGGAAGGGAGAGG
**
498663 TTTTGCAGGGAAGGGAGAGG
1 TTTTAAAGGGAAGGGAGAGG
498683 TT
1 TT
498685 CGAGAGGGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.02, G:0.48, T:0.24
Consensus pattern (20 bp):
TTTTAAAGGGAAGGGAGAGG
Found at i:498775 original size:20 final size:19
Alignment explanation
Indices: 498741--498780 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
498731 TATTTCTAAA
498741 AAAAATATTAATAAATTATT
1 AAAAATATTAATAAA-TATT
**
498761 AAAAATATTTTTAAATATT
1 AAAAATATTAATAAATATT
498780 A
1 A
498781 TTTCTAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAAATATTAATAAATATT
Found at i:498993 original size:46 final size:46
Alignment explanation
Indices: 498943--499053 Score: 168
Period size: 46 Copynumber: 2.4 Consensus size: 46
498933 TAATATATTT
* * * *
498943 TTTAAATATTATATTCTTATTCATAAATAAAATTTTAGAAATAATA
1 TTTAATTATTATATTATTAGTCATAAATAAAATTTTAAAAATAATA
*
498989 TTTAATTATTATATTATTAGTCATAAATAAAATTTTAAAAATAGTA
1 TTTAATTATTATATTATTAGTCATAAATAAAATTTTAAAAATAATA
*
499035 TTTAATTATTATATCATTA
1 TTTAATTATTATATTATTA
499054 TTTAATATTT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 59 1.00
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.48
Consensus pattern (46 bp):
TTTAATTATTATATTATTAGTCATAAATAAAATTTTAAAAATAATA
Found at i:499127 original size:33 final size:31
Alignment explanation
Indices: 499086--499159 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
499076 ATTGTCAAAG
499086 ATAA-ATATTA-TATATTTAATAATATATAATAT
1 ATAATATATTATTA-ATTTAA-AATATATAA-AT
* * *
499118 TTAATATATTCTTAATTTAAAATATTTAAAT
1 ATAATATATTATTAATTTAAAATATATAAAT
499149 ATAATATATTA
1 ATAATATATTA
499160 AAATTTTATT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
31 11 0.31
32 11 0.31
33 11 0.31
34 2 0.06
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (31 bp):
ATAATATATTATTAATTTAAAATATATAAAT
Found at i:499135 original size:16 final size:15
Alignment explanation
Indices: 499099--499165 Score: 62
Period size: 15 Copynumber: 4.3 Consensus size: 15
499089 AATATTATAT
*
499099 ATTTAATAATATATAA
1 ATTTAAT-ATATTTAA
*
499115 TATTTAATATATTCTTA
1 -ATTTAATATATT-TAA
*
499132 ATTTAAAATATTTAA
1 ATTTAATATATTTAA
* *
499147 ATATAATATATTAAA
1 ATTTAATATATTTAA
499162 ATTT
1 ATTT
499166 TATTTAAAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
15 17 0.41
16 15 0.37
17 9 0.22
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTTAATATATTTAA
Found at i:501304 original size:2 final size:2
Alignment explanation
Indices: 501297--501321 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
501287 AACATTGGGG
501297 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
501322 TTGTTTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:501333 original size:62 final size:62
Alignment explanation
Indices: 501240--501358 Score: 238
Period size: 62 Copynumber: 1.9 Consensus size: 62
501230 CTATTTATTC
501240 ATATATATATATATATATATTTGTTTTTCTGATATAAATGAGAGCGAAACATTGGGGTATAT
1 ATATATATATATATATATATTTGTTTTTCTGATATAAATGAGAGCGAAACATTGGGGTATAT
501302 ATATATATATATATATATATTTGTTTTTCTGATATAAATGAGAGCGAAACATTGGGG
1 ATATATATATATATATATATTTGTTTTTCTGATATAAATGAGAGCGAAACATTGGGG
501359 GGCTTGCGCT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.37, C:0.05, G:0.17, T:0.41
Consensus pattern (62 bp):
ATATATATATATATATATATTTGTTTTTCTGATATAAATGAGAGCGAAACATTGGGGTATAT
Found at i:506044 original size:24 final size:23
Alignment explanation
Indices: 505997--506044 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
505987 GATCTTAAAT
* *
505997 AAATTTTTTTTACATAAAATTTA
1 AAATTTTTATTACATAAAACTTA
*
506020 AAATTTTATATTACATAATACTTA
1 AAATTTT-TATTACATAAAACTTA
506044 A
1 A
506045 GTTATTTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (23 bp):
AAATTTTTATTACATAAAACTTA
Found at i:506119 original size:14 final size:15
Alignment explanation
Indices: 506102--506160 Score: 52
Period size: 15 Copynumber: 3.9 Consensus size: 15
506092 TTTTATTTAC
506102 TATAATTTAAAA-AT
1 TATAATTTAAAATAT
506116 TATAAATATTAAAATAT
1 TAT-AAT-TTAAAATAT
506133 TA-AATTTAATAATA-
1 TATAATTTAA-AATAT
* *
506147 TAAAAATTAAAATA
1 TATAATTTAAAATA
506161 CTTTATTTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 13 0.33
15 16 0.41
16 6 0.15
17 4 0.10
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TATAATTTAAAATAT
Found at i:506130 original size:8 final size:8
Alignment explanation
Indices: 506108--506160 Score: 53
Period size: 8 Copynumber: 7.0 Consensus size: 8
506098 TTACTATAAT
506108 TTAAAA-A
1 TTAAAATA
506115 TTATAAATA
1 TTA-AAATA
506124 TTAAAATA
1 TTAAAATA
506132 TT-AAAT-
1 TTAAAATA
506138 TTAATAATA
1 TTAA-AATA
506147 -TAAAA-A
1 TTAAAATA
506153 TTAAAATA
1 TTAAAATA
506161 CTTTATTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
6 3 0.08
7 15 0.38
8 17 0.44
9 4 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
TTAAAATA
Found at i:506136 original size:15 final size:14
Alignment explanation
Indices: 506111--506160 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 14
506101 CTATAATTTA
506111 AAAATTATAAATATT
1 AAAA-TATAAATATT
506126 AAAATATTAAAT-TT
1 AAAATA-TAAATATT
*
506140 AATAATATAAAAATT
1 AA-AATATAAATATT
506155 AAAATA
1 AAAATA
506161 CTTTATTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 14 0.45
15 17 0.55
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AAAATATAAATATT
Found at i:506155 original size:29 final size:29
Alignment explanation
Indices: 506099--506182 Score: 89
Period size: 29 Copynumber: 2.8 Consensus size: 29
506089 ATTTTTTATT
* *
506099 TACTATAATTTAAAAATTATAAATATTAAAA
1 TACT-TAATTTAATAA-TATAAAAATTAAAA
506130 TA-TTAAATTTAATAATATAAAAATTAAAA
1 TACTT-AATTTAATAATATAAAAATTAAAA
*
506159 TACTTTATTTATTATAATATAAAA
1 TACTTAATTTA--ATAATATAAAA
506183 TTTTTAATAA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
29 21 0.46
30 12 0.26
31 13 0.28
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (29 bp):
TACTTAATTTAATAATATAAAAATTAAAA
Found at i:506769 original size:15 final size:14
Alignment explanation
Indices: 506720--506774 Score: 58
Period size: 15 Copynumber: 3.9 Consensus size: 14
506710 ATTAATACAT
*
506720 ATAAT-TAAATATA
1 ATAATATAAATATG
*
506733 ATAATATTATATATG
1 ATAATA-TAAATATG
*
506748 ATTATATAAATATG
1 ATAATATAAATATG
506762 ATACATATAAATA
1 ATA-ATATAAATA
506775 ATATAACATA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
13 5 0.15
14 9 0.26
15 20 0.59
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40
Consensus pattern (14 bp):
ATAATATAAATATG
Found at i:506793 original size:16 final size:18
Alignment explanation
Indices: 506753--506797 Score: 60
Period size: 16 Copynumber: 2.6 Consensus size: 18
506743 ATATGATTAT
506753 ATAAATATGATACATATAA
1 ATAAATAT-ATACATATAA
506772 AT-AATATA-ACATA-AA
1 ATAAATATATACATATAA
506787 ATAAATATATA
1 ATAAATATATA
506798 TTTCAAAACG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 4 0.17
16 11 0.46
17 2 0.08
18 5 0.21
19 2 0.08
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (18 bp):
ATAAATATATACATATAA
Found at i:507236 original size:11 final size:11
Alignment explanation
Indices: 507222--507267 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
507212 TTATATATTT
507222 ATTATATTATA
1 ATTATATTATA
507233 ATTATATT-TAA
1 ATTATATTAT-A
*
507244 ATTATTTTATA
1 ATTATATTATA
*
507255 TTTATATTA-A
1 ATTATATTATA
507265 ATT
1 ATT
507268 TAATATATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
10 4 0.14
11 24 0.83
12 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
ATTATATTATA
Found at i:507237 original size:22 final size:22
Alignment explanation
Indices: 507212--507289 Score: 61
Period size: 22 Copynumber: 3.4 Consensus size: 22
507202 TTATATTTTT
507212 TTATATATTTATTATATTATAA
1 TTATATATTTATTATATTATAA
* * *
507234 TTATAT-TTAAATTATTTTATAT
1 TTATATATT-TATTATATTATAA
*
507256 TTATATTAAATTTAATATATTAATAA
1 TTATA-T--ATTTATTATATT-ATAA
507282 TT-TATATT
1 TTATATATT
507290 ATAAAATTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
21 2 0.05
22 24 0.56
23 1 0.02
24 1 0.02
25 8 0.19
26 7 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTATATATTTATTATATTATAA
Found at i:507252 original size:38 final size:36
Alignment explanation
Indices: 507193--507276 Score: 98
Period size: 38 Copynumber: 2.3 Consensus size: 36
507183 ATTATAATAA
* * * *
507193 TTAACATATTTATATTTTTTTATATATT-TATTATAT
1 TTAATATATTTAAATTATTTTATAT-TTATATTAAAT
507229 TATAATTATATTTAAATTATTTTATATTTATATTAAAT
1 T-TAA-TATATTTAAATTATTTTATATTTATATTAAAT
507267 TTAATATATT
1 TTAATATATT
507277 AATAATTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
36 7 0.17
37 8 0.20
38 26 0.63
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (36 bp):
TTAATATATTTAAATTATTTTATATTTATATTAAAT
Found at i:507263 original size:27 final size:26
Alignment explanation
Indices: 507198--507292 Score: 79
Period size: 27 Copynumber: 3.5 Consensus size: 26
507188 AATAATTAAC
* *
507198 ATATTTATATT-TTTTTATATA-TTT
1 ATATTTATATTATATTTAAATATTTT
507222 ATTATATTATAATTATATTTAAATTATTTT
1 A-TAT-TTAT-ATTATATTTAAA-TATTTT
* *
507252 ATATTTATATTAAATTT-AATATATTA
1 ATATTTATATTATATTTAAATAT-TTT
507278 ATAATTTATATTATA
1 AT-ATTTATATTATA
507293 AAATTTTAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
24 1 0.02
25 6 0.10
26 10 0.17
27 22 0.38
28 10 0.17
29 5 0.09
30 4 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
ATATTTATATTATATTTAAATATTTT
Found at i:507469 original size:6 final size:6
Alignment explanation
Indices: 507458--507484 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
507448 TGATTACCCT
507458 TTTTGC TTTTGC TTTTGC TTTTGC TTT
1 TTTTGC TTTTGC TTTTGC TTTTGC TTT
507485 AGCTCTCCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.15, T:0.70
Consensus pattern (6 bp):
TTTTGC
Found at i:507581 original size:14 final size:16
Alignment explanation
Indices: 507551--507582 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
507541 CTGATTAATT
507551 TATATAATTATTATAA
1 TATATAATTATTATAA
507567 TATATAA-TATT-TAA
1 TATATAATTATTATAA
507581 TA
1 TA
507583 AATTTATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 4 0.25
16 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TATATAATTATTATAA
Found at i:507590 original size:18 final size:19
Alignment explanation
Indices: 507546--507592 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
507536 TCAATCTGAT
*
507546 TAATTTAT-ATAATTATTA
1 TAATTTATAATAATTAATA
* *
507564 TAATATATAATATTTAATA
1 TAATTTATAATAATTAATA
507583 -AATTTATAAT
1 TAATTTATAAT
507593 TTAAATTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATTTATAATAATTAATA
Found at i:508705 original size:31 final size:30
Alignment explanation
Indices: 508652--508715 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
508642 AAGATTATTT
*
508652 TATTTAATTTTTTACCTTTT-AAATATTAAA
1 TATTTAATTTTATACCTTTTAAAATA-TAAA
508682 TATTTATATTTTATA-CTTATTAAAATATAAA
1 TATTTA-ATTTTATACCTT-TTAAAATATAAA
508713 TAT
1 TAT
508716 AAATTTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 9 0.30
31 16 0.53
32 5 0.17
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (30 bp):
TATTTAATTTTATACCTTTTAAAATATAAA
Found at i:508741 original size:17 final size:18
Alignment explanation
Indices: 508701--508742 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 18
508691 TTTATACTTA
508701 TTAAAATATAAATATAAAT
1 TTAAAATAT-AATATAAAT
508720 TTAAAATAT-ATA-AAATT
1 TTAAAATATAATATAAA-T
508737 TTAAAA
1 TTAAAA
508743 AATTAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 3 0.14
17 10 0.45
19 9 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TTAAAATATAATATAAAT
Found at i:511425 original size:19 final size:19
Alignment explanation
Indices: 511401--511437 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
511391 TATTTTTTTC
511401 AAGAATACAAAAAAAAAGA
1 AAGAATACAAAAAAAAAGA
*
511420 AAGAATACAAAAAGAAAG
1 AAGAATACAAAAAAAAAG
511438 GAAAAAAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.76, C:0.05, G:0.14, T:0.05
Consensus pattern (19 bp):
AAGAATACAAAAAAAAAGA
Found at i:512226 original size:9 final size:9
Alignment explanation
Indices: 512212--512243 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
512202 GGATGATAGA
512212 AGGAGAGAT
1 AGGAGAGAT
512221 AGGAGAGAT
1 AGGAGAGAT
*
512230 AGTAGAGAT
1 AGGAGAGAT
512239 AGGAG
1 AGGAG
512244 GGATGATAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.44, T:0.12
Consensus pattern (9 bp):
AGGAGAGAT
Found at i:512238 original size:18 final size:18
Alignment explanation
Indices: 512215--512285 Score: 61
Period size: 18 Copynumber: 3.6 Consensus size: 18
512205 TGATAGAAGG
512215 AGAGATAGGAGAGATAGT
1 AGAGATAGGAGAGATAGT
512233 AGAGATAGGAGGGATGATAGGAT
1 AGAGATAGGA--GA-GATA-G-T
* *
512256 GAGAGATATGAGAGATAAT
1 -AGAGATAGGAGAGATAGT
*
512275 AGAGAGAGGAG
1 AGAGATAGGAG
512286 GGATGACAGG
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
18 19 0.44
19 1 0.02
20 2 0.05
21 8 0.19
22 3 0.07
23 1 0.02
24 9 0.21
ACGTcount: A:0.44, C:0.00, G:0.41, T:0.15
Consensus pattern (18 bp):
AGAGATAGGAGAGATAGT
Found at i:512245 original size:42 final size:42
Alignment explanation
Indices: 512199--512300 Score: 150
Period size: 42 Copynumber: 2.4 Consensus size: 42
512189 GAAGAGAAAT
* * *
512199 GAGGGATGATAGAAGGAGAGATAGGAGAGATAGTAGAGATAG
1 GAGGGATGATAGGAGGAGAGATAGGAGAGATAATAGAGAGAG
* *
512241 GAGGGATGATAGGATGAGAGATATGAGAGATAATAGAGAGAG
1 GAGGGATGATAGGAGGAGAGATAGGAGAGATAATAGAGAGAG
*
512283 GAGGGATGACAGGAGGAG
1 GAGGGATGATAGGAGGAG
512301 GAGAGAAGAA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.41, C:0.01, G:0.44, T:0.14
Consensus pattern (42 bp):
GAGGGATGATAGGAGGAGAGATAGGAGAGATAATAGAGAGAG
Found at i:518932 original size:31 final size:31
Alignment explanation
Indices: 518863--518949 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
518853 TATGTTTATC
* *
518863 AAAATTTTTAAAAAATTAAAAATGATCAATA
1 AAAATTTTTAAAAAATAAAAAATTATCAATA
** **
518894 ATTATTTTTAAAAAATAAAAAATTATCTTTA
1 AAAATTTTTAAAAAATAAAAAATTATCAATA
*
518925 AAAA-TTTT-AAAGATGAAAAAATTAT
1 AAAATTTTTAAAAAAT-AAAAAATTAT
518950 TATTAACAGT
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
29 5 0.11
30 14 0.30
31 27 0.59
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.37
Consensus pattern (31 bp):
AAAATTTTTAAAAAATAAAAAATTATCAATA
Found at i:521665 original size:13 final size:13
Alignment explanation
Indices: 521632--521665 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
521622 AGATTATCTC
521632 AAAAAT-ATTTTA
1 AAAAATAATTTTA
521644 AAAATATAATTTTA
1 AAAA-ATAATTTTA
521658 AAAAATAA
1 AAAAATAA
521666 CTATTAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.20
13 6 0.30
14 10 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AAAAATAATTTTA
Found at i:522159 original size:2 final size:2
Alignment explanation
Indices: 522152--522190 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
522142 AATGATTCAC
522152 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
522191 CCATCATCCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:523336 original size:15 final size:15
Alignment explanation
Indices: 523318--523348 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
523308 TAATAAATTA
*
523318 AGTTTAAATAATTTG
1 AGTTCAAATAATTTG
523333 AGTTCAAATAATTTG
1 AGTTCAAATAATTTG
523348 A
1 A
523349 ATGTAAAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.03, G:0.13, T:0.42
Consensus pattern (15 bp):
AGTTCAAATAATTTG
Found at i:523495 original size:16 final size:16
Alignment explanation
Indices: 523474--523525 Score: 77
Period size: 16 Copynumber: 3.1 Consensus size: 16
523464 ATGATACAAA
523474 TTAAATTTAAAATAAT
1 TTAAATTTAAAATAAT
523490 TTAAATTTAAAAATAAAT
1 TTAAATTT-AAAAT-AAT
*
523508 TTAAATTTAAATTAAT
1 TTAAATTTAAAATAAT
523524 TT
1 TT
523526 GACTCAAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
16 13 0.39
17 9 0.27
18 11 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TTAAATTTAAAATAAT
Found at i:523496 original size:6 final size:6
Alignment explanation
Indices: 523474--523520 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
523464 ATGATACAAA
* * *
523474 TTAAAT TTAAA- AT-AAT TTAAAT TTAAAA ATAAAT TTAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
523520 T
1 T
523521 AATTTGACTC
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
4 2 0.06
5 2 0.06
6 29 0.88
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
TTAAAT
Found at i:523510 original size:18 final size:17
Alignment explanation
Indices: 523474--523518 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 17
523464 ATGATACAAA
523474 TTAAATTT-AAAATAAT
1 TTAAATTTAAAAATAAT
523490 TTAAATTTAAAAATAAAT
1 TTAAATTTAAAAAT-AAT
523508 TTAAATTTAAA
1 TTAAATTTAAA
523519 TTAATTTGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 8 0.30
17 5 0.19
18 14 0.52
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAAATTTAAAAATAAT
Found at i:523818 original size:3 final size:3
Alignment explanation
Indices: 523810--523843 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
523800 AGCATTACTC
523810 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
523844 AAGATAACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:524876 original size:23 final size:23
Alignment explanation
Indices: 524806--524880 Score: 66
Period size: 23 Copynumber: 3.1 Consensus size: 23
524796 ATATTATTTA
*
524806 ATTAATA-AAAAATAATTTTATTAAA
1 ATTAATATAAAAATAA-TTTA--AAT
524831 ATTTAATTATAAAAAT--TTATAAAT
1 A-TTAA-TATAAAAATAATT-TAAAT
524855 ATTAATATAAAAATAATTTAAAT
1 ATTAATATAAAAATAATTTAAAT
524878 ATT
1 ATT
524881 TTTAAGTAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 14
0.74 0.02 0.24
Matches are distributed among these distances:
22 9 0.21
23 12 0.28
24 5 0.12
25 3 0.07
26 6 0.14
27 2 0.05
28 6 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
ATTAATATAAAAATAATTTAAAT
Found at i:524898 original size:33 final size:34
Alignment explanation
Indices: 524834--524899 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 34
524824 TATTAAAATT
* *
524834 TAATTATAAAAATTTATAAATATTAATATAAAAA
1 TAATTATAAAAATTTATAAATAATAAAATAAAAA
* * *
524868 TAATT-TAAATATTTTTAAGTAATAAAATAAAA
1 TAATTATAAAAATTTATAAATAATAAAATAAAA
524900 TTTTTGAATC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 22 0.81
34 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (34 bp):
TAATTATAAAAATTTATAAATAATAAAATAAAAA
Found at i:528343 original size:14 final size:16
Alignment explanation
Indices: 528315--528346 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
528305 ATATAAAGAA
528315 TATATATGTATAATAT
1 TATATATGTATAATAT
528331 TATA-ATGTA-AATAT
1 TATATATGTATAATAT
528345 TA
1 TA
528347 AAAAATATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 5 0.31
16 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (16 bp):
TATATATGTATAATAT
Found at i:528424 original size:15 final size:16
Alignment explanation
Indices: 528385--528426 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
528375 AAATTTAATA
528385 AAAAATATTAAATTATT
1 AAAAA-ATTAAATTATT
*
528402 -AAAGATTAAATT-TT
1 AAAAAATTAAATTATT
528416 AAAAAATTAAA
1 AAAAAATTAAA
528427 AAAAACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 2 0.09
15 17 0.77
16 3 0.14
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (16 bp):
AAAAAATTAAATTATT
Found at i:528497 original size:17 final size:17
Alignment explanation
Indices: 528475--528512 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
528465 AATAAATTAA
528475 AAATTATGATTGAGATT
1 AAATTATGATTGAGATT
528492 AAATTATGATTGAGATT
1 AAATTATGATTGAGATT
528509 AAAT
1 AAAT
528513 AAGCTTAGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.16, T:0.39
Consensus pattern (17 bp):
AAATTATGATTGAGATT
Found at i:531396 original size:2 final size:2
Alignment explanation
Indices: 531389--531428 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
531379 ACAATACAAA
* *
531389 CT CT CT CT CT CT CT CT GT CT CT CT GT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
531429 GATGTAAGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.45, G:0.05, T:0.50
Consensus pattern (2 bp):
CT
Found at i:531615 original size:2 final size:2
Alignment explanation
Indices: 531598--531635 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
531588 TCAATGCAAA
* *
531598 AT AT AA AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
531636 GCACACATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:539236 original size:25 final size:23
Alignment explanation
Indices: 539201--539271 Score: 72
Period size: 25 Copynumber: 3.0 Consensus size: 23
539191 ATATATTTTT
539201 TAAAA-TATTTAAAATTTTAAAA
1 TAAAAGTATTTAAAATTTTAAAA
* *
539223 TAAATTGTTATTTAAATATTTGACAAA
1 TAAA-AG-TATTTAAA-ATTTTA-AAA
*
539250 TAAAAGTAATTAAAATTTTAAA
1 TAAAAGTATTTAAAATTTTAAA
539272 TAATAATAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
22 4 0.10
23 2 0.05
24 5 0.13
25 15 0.38
26 6 0.15
27 7 0.18
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (23 bp):
TAAAAGTATTTAAAATTTTAAAA
Found at i:541382 original size:10 final size:10
Alignment explanation
Indices: 541351--541388 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
541341 ATAAAAATAT
541351 TTTTAATTTTA
1 TTTTAA-TTTA
541362 TTTT-A-TTA
1 TTTTAATTTA
541370 TTTTAATTTA
1 TTTTAATTTA
541380 TTTTAATTT
1 TTTTAATTT
541389 TATAACAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
8 7 0.28
9 1 0.04
10 13 0.52
11 4 0.16
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTAATTTA
Found at i:542306 original size:30 final size:32
Alignment explanation
Indices: 542264--542329 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 32
542254 AGAAATACAA
542264 TTCT-CTCTTTATCTCTATTTT-CTCT-TCTTT
1 TTCTACTCTTTATCT-TATTTTACTCTATCTTT
* *
542294 TTCTACTC-TTATCTTTTTTTACTTTATCTTT
1 TTCTACTCTTTATCTTATTTTACTCTATCTTT
542325 TTCTA
1 TTCTA
542330 TTCTATCACT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 5 0.16
30 13 0.42
31 13 0.42
ACGTcount: A:0.11, C:0.23, G:0.00, T:0.67
Consensus pattern (32 bp):
TTCTACTCTTTATCTTATTTTACTCTATCTTT
Found at i:542320 original size:15 final size:16
Alignment explanation
Indices: 542289--542329 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
542279 TATTTTCTCT
542289 TCTTTTTCTACTCTTA
1 TCTTTTTCTACTCTTA
*
542305 TCTTTTTTTACT-TTA
1 TCTTTTTCTACTCTTA
542320 TCTTTTTCTA
1 TCTTTTTCTA
542330 TTCTATCACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.12, C:0.20, G:0.00, T:0.68
Consensus pattern (16 bp):
TCTTTTTCTACTCTTA
Done.